1
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Bonanata J. The role of the active site lysine residue on FAD reduction by NADPH in glutathione reductase. Comput Biol Chem 2024; 110:108075. [PMID: 38678729 DOI: 10.1016/j.compbiolchem.2024.108075] [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: 11/22/2023] [Revised: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
Glutathione reductase (GR) is a two dinucleotide binding domain flavoprotein (tDBDF) that catalyzes the reduction of glutathione disulfide to glutathione coupled to the oxidation of NADPH to NADP+. An interesting feature of GR and other tDBDFs is the presence of a lysine residue (Lys-66 in human GR) at the active site, which interacts with the flavin group, but has an unknown function. To better understand the role of this residue, the dynamics of GR was studied using molecular dynamics simulations, and the reaction mechanism of FAD reduction by NADPH was studied using QM/MM molecular modeling. The two possible protonation states of Lys-66 were considered: neutral and protonated. Molecular dynamics results suggest that the active site is more structured for neutral Lys-66 than for protonated Lys-66. QM/MM modeling results suggest that Lys-66 should be in its neutral state for a thermodynamically favorable reduction of FAD by NADPH. Since the reaction is unfavorable with protonated Lys-66, the reverse reaction (the reduction of NADP+ by FADH-) is expected to take place. A phylogenetic analysis of various tDBDFs was performed, finding that an active site lysine is present in different the tDBDFs enzymes, suggesting that it has a conserved biological role. Overall, these results suggest that the protonation state of the active site lysine determines the energetics of the reaction, controlling its reversibility.
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Affiliation(s)
- Jenner Bonanata
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Uruguay; Centro de Investigaciones Biomédicas, Universidad de la República, Uruguay.
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2
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Brosey CA, Link TM, Shen R, Moiani D, Burnett K, Hura GL, Jones DE, Tainer JA. Chemical screening by time-resolved X-ray scattering to discover allosteric probes. Nat Chem Biol 2024:10.1038/s41589-024-01609-1. [PMID: 38671223 DOI: 10.1038/s41589-024-01609-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 03/20/2024] [Indexed: 04/28/2024]
Abstract
Drug discovery relies on efficient identification of small-molecule leads and their interactions with macromolecular targets. However, understanding how chemotypes impact mechanistically important conformational states often remains secondary among high-throughput discovery methods. Here, we present a conformational discovery pipeline integrating time-resolved, high-throughput small-angle X-ray scattering (TR-HT-SAXS) and classic fragment screening applied to allosteric states of the mitochondrial import oxidoreductase apoptosis-inducing factor (AIF). By monitoring oxidized and X-ray-reduced AIF states, TR-HT-SAXS leverages structure and kinetics to generate a multidimensional screening dataset that identifies fragment chemotypes allosterically stimulating AIF dimerization. Fragment-induced dimerization rates, quantified with time-resolved SAXS similarity analysis (kVR), capture structure-activity relationships (SAR) across the top-ranked 4-aminoquinoline chemotype. Crystallized AIF-aminoquinoline complexes validate TR-SAXS-guided SAR, supporting this conformational chemotype for optimization. AIF-aminoquinoline structures and mutational analysis reveal active site F482 as an underappreciated allosteric stabilizer of AIF dimerization. This conformational discovery pipeline illustrates TR-HT-SAXS as an effective technology for targeting chemical leads to important macromolecular states.
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Affiliation(s)
- Chris A Brosey
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Todd M Link
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Runze Shen
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Davide Moiani
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathryn Burnett
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Greg L Hura
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Darin E Jones
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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3
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Pijuan J, Sevrioukova IF, García-Campos Ó, Hernaez M, Gort L, Gómez-Chiari M, Jou C, Candela-Cantó S, Rumiá J, Artuch R, Palau F, Hoenicka J, Ortigoza-Escobar JD. A Novel AIFM1-Related Disorder Phenotype Treated with Deep Brain Stimulation. Mov Disord 2024; 39:215-217. [PMID: 37787095 DOI: 10.1002/mds.29616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/09/2023] [Accepted: 09/11/2023] [Indexed: 10/04/2023] Open
Affiliation(s)
- Jordi Pijuan
- Laboratory of Neurogenetics and Molecular Medicine-IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Óscar García-Campos
- Department of Pediatric Neurology, Hospital General Universitario de Toledo, Toledo, Spain
| | - Mar Hernaez
- Laboratory of Neurogenetics and Molecular Medicine-IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Laura Gort
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, CDB, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Marta Gómez-Chiari
- Department of Radiology, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Cristina Jou
- Pathology Department, Institut de Recerca Sant Joan de Déu, CIBERER, Barcelona, Spain
| | | | - Jordi Rumiá
- Department of Neurosurgery, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- Department of Neurosurgery, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Rafael Artuch
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Francesc Palau
- Laboratory of Neurogenetics and Molecular Medicine-IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Department of Genetic and Molecular Medicine, IPER, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
- Division of Pediatrics, University of Barcelona School of Medicine and Health Sciences, Barcelona, Spain
- European Reference Network for Rare Malformation Syndromes, Intellectual and Other Neurodevelopmental Disorders, (ERN-ITHACA), Barcelona, Spain
| | - Janet Hoenicka
- Laboratory of Neurogenetics and Molecular Medicine-IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Dario Ortigoza-Escobar
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Movement Disorders Unit, Pediatric Neurology Department, Institut de Recerca, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
- European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
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4
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Qiu Y, Wang H, Pan H, Ding X, Guan J, Zhuang Q, Wu K, Lei Z, Cai H, Dong Y, Zhou H, Lin A, Wang Q, Yan Q. NADH improves AIF dimerization and inhibits apoptosis in iPSCs-derived neurons from patients with auditory neuropathy spectrum disorder. Hear Res 2024; 441:108919. [PMID: 38043402 DOI: 10.1016/j.heares.2023.108919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
Auditory neuropathy spectrum disorder (ANSD) is a hearing impairment involving disruptions to inner hair cells (IHCs), ribbon synapses, spiral ganglion neurons (SGNs), and/or the auditory nerve itself. The outcomes of cochlear implants (CI) for ANSD are variable and dependent on the location of lesion sites. Discovering a potential therapeutic agent for ANSD remains an urgent requirement. Here, 293T stable transfection cell lines and patient induced pluripotent stem cells (iPSCs)-derived auditory neurons carrying the apoptosis inducing factor (AIF) p.R422Q variant were used to pursue a therapeutic regent for ANSD. Nicotinamide adenine dinucleotide (NADH) is a main electron donor in the electron transport chain (ETC). In 293T stable transfection cells with the p.R422Q variant, NADH treatment improved AIF dimerization, rescued mitochondrial dysfunctions, and decreased cell apoptosis. The effects of NADH were further confirmed in patient iPSCs-derived neurons. The relative level of AIF dimers was increased to 150.7 % (P = 0.026) from 59.2 % in patient-neurons upon NADH treatment. Such increased AIF dimerization promoted the mitochondrial import of coiled-coil-helix-coiled-coil-helix domain-containing protein 4 (CHCHD4), which further restored mitochondrial functions. Similarly, the content of mitochondrial calcium (mCa2+) was downregulated from 136.7 % to 102.3 % (P = 0.0024) in patient-neurons upon NADH treatment. Such decreased mCa2+ levels inhibited calpain activity, ultimately reducing the percentage of apoptotic cells from 30.5 % to 21.1 % (P = 0.021). We also compared the therapeutic effects of gene correction and NADH treatment on hereditary ANSD. NADH treatment had comparable restorative effects on functions of ANSD patient-specific cells to that of gene correction. Our findings offer evidence of the molecular mechanisms of ANSD and introduce NADH as a potential therapeutic agent for ANSD therapy.
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Affiliation(s)
- Yue Qiu
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China; Institute of Brain Science, Wannan Medical College, Wuhu, Anhui 241000, China
| | - Hongyang Wang
- Department of Audiology and Vestibular Medicine, Senior Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, the Sixth Medicine Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing 100853, China
| | - Huaye Pan
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xue Ding
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jing Guan
- Department of Audiology and Vestibular Medicine, Senior Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, the Sixth Medicine Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing 100853, China
| | - Qianqian Zhuang
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Kaiwen Wu
- Department of Audiology and Vestibular Medicine, Senior Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, the Sixth Medicine Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing 100853, China
| | - Zhaoying Lei
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huajian Cai
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yufei Dong
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Zhou
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Aifu Lin
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qiuju Wang
- Department of Audiology and Vestibular Medicine, Senior Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, the Sixth Medicine Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing 100853, China
| | - Qingfeng Yan
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China; Department of Pediatrics, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, Zhejiang 310058, China.
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5
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Zambon AA, Ghezzi D, Baldoli C, Cutillo G, Fontana K, Sofia V, Patricelli MG, Nasca A, Vinci S, Spiga I, Lamantea E, Fanelli GF, Sora MGN, Rovelli R, Poloniato A, Carrera P, Filippi M, Barera G. Expanding the spectrum of neonatal-onset AIFM1-associated disorders. Ann Clin Transl Neurol 2023; 10:1844-1853. [PMID: 37644805 PMCID: PMC10578896 DOI: 10.1002/acn3.51876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/14/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023] Open
Abstract
OBJECTIVES Pathogenic variants in AIFM1 have been associated with a wide spectrum of disorders, spanning from CMT4X to mitochondrial encephalopathy. Here we present a novel phenotype and review the existing literature on AIFM1-related disorders. METHODS We performed EEG recordings, brain MRI and MR Spectroscopy, metabolic screening, echocardiogram, clinical exome sequencing (CES) and family study. Effects of the variant were established on cultured fibroblasts from skin punch biopsy. RESULTS The patient presented with drug-resistant, electro-clinical, multifocal seizures 6 h after birth. Brain MRI revealed prominent brain swelling of both hemispheres and widespread signal alteration in large part of the cortex and of the thalami, with sparing of the basal nuclei. CES analysis revealed the likely pathogenic variant c.5T>C; p.(Phe2Ser) in the AIFM1 gene. The affected amino acid residue is located in the mitochondrial targeting sequence. Functional studies on cultured fibroblast showed a clear reduction in AIFM1 protein amount and defective activities of respiratory chain complexes I, III and IV. No evidence of protein mislocalization or accumulation of precursor protein was observed. Riboflavin, Coenzyme Q10 and thiamine supplementation was therefore given. At 6 months of age, the patient exhibited microcephaly but did not experience any further deterioration. He is still fed orally and there is no evidence of muscle weakness or atrophy. INTERPRETATION This is the first AIFM1 case associated with neonatal seizures and diffuse white matter involvement with relative sparing of basal ganglia, in the absence of clinical signs suggestive of myopathy or motor neuron disease.
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Affiliation(s)
- Alberto A. Zambon
- Unit of NeurologySan Raffaele Scientific InstituteMilanItaly
- Neuromuscular Repair Unit, Institute of Experimental Neurology (InSpe), Division of NeuroscienceIRCCS Ospedale San RaffaeleMilanItaly
| | - Daniele Ghezzi
- Medical Genetics and Neurogenetics UnitFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
- Department of Pathophysiology and TransplantationUniversity of MilanMilanItaly
| | - Cristina Baldoli
- Department of NeuroradiologySan Raffaele Scientific InstituteMilanItaly
| | - Gianni Cutillo
- Unit of NeurologySan Raffaele Scientific InstituteMilanItaly
- Neurophysiology ServiceSan Raffaele Scientific InstituteMilanItaly
| | - Katia Fontana
- Department of NeonatologySan Raffaele Scientific InstituteMilanItaly
| | - Valentina Sofia
- Department of NeonatologySan Raffaele Scientific InstituteMilanItaly
| | | | - Alessia Nasca
- Medical Genetics and Neurogenetics UnitFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Stefano Vinci
- Medical Genetics and Neurogenetics UnitFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Ivana Spiga
- Laboratory of Genomics and Clinical GeneticsSan Raffaele Scientific InstituteMilanItaly
| | - Eleonora Lamantea
- Medical Genetics and Neurogenetics UnitFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | | | | | - Rosanna Rovelli
- Medical Genetics and Neurogenetics UnitFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Antonella Poloniato
- Medical Genetics and Neurogenetics UnitFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Paola Carrera
- Laboratory of Genomics and Clinical GeneticsSan Raffaele Scientific InstituteMilanItaly
- Unit of Genomics for Human Disease DiagnosisSan Raffaele Scientific InstituteMilanItaly
| | - Massimo Filippi
- Unit of NeurologySan Raffaele Scientific InstituteMilanItaly
- Neurophysiology ServiceSan Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Graziano Barera
- Medical Genetics and Neurogenetics UnitFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
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6
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Qiu Y, Wang H, Fan M, Pan H, Guan J, Jiang Y, Jia Z, Wu K, Zhou H, Zhuang Q, Lei Z, Ding X, Cai H, Dong Y, Yan L, Lin A, Fu Y, Zhang D, Yan Q, Wang Q. Impaired AIF-CHCHD4 interaction and mitochondrial calcium overload contribute to auditory neuropathy spectrum disorder in patient-iPSC-derived neurons with AIFM1 variant. Cell Death Dis 2023; 14:375. [PMID: 37365177 DOI: 10.1038/s41419-023-05899-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023]
Abstract
Auditory neuropathy spectrum disorder (ANSD) is a hearing impairment caused by dysfunction of inner hair cells, ribbon synapses, spiral ganglion neurons and/or the auditory nerve itself. Approximately 1/7000 newborns have abnormal auditory nerve function, accounting for 10%-14% of cases of permanent hearing loss in children. Although we previously identified the AIFM1 c.1265 G > A variant to be associated with ANSD, the mechanism by which ANSD is associated with AIFM1 is poorly understood. We generated induced pluripotent stem cells (iPSCs) from peripheral blood mononuclear cells (PBMCs) via nucleofection with episomal plasmids. The patient-specific iPSCs were edited via CRISPR/Cas9 technology to generate gene-corrected isogenic iPSCs. These iPSCs were further differentiated into neurons via neural stem cells (NSCs). The pathogenic mechanism was explored in these neurons. In patient cells (PBMCs, iPSCs, and neurons), the AIFM1 c.1265 G > A variant caused a novel splicing variant (c.1267-1305del), resulting in AIF p.R422Q and p.423-435del proteins, which impaired AIF dimerization. Such impaired AIF dimerization then weakened the interaction between AIF and coiled-coil-helix-coiled-coil-helix domain-containing protein 4 (CHCHD4). On the one hand, the mitochondrial import of ETC complex subunits was inhibited, subsequently leading to an increased ADP/ATP ratio and elevated ROS levels. On the other hand, MICU1-MICU2 heterodimerization was impaired, leading to mCa2+ overload. Calpain was activated by mCa2+ and subsequently cleaved AIF for its translocation into the nucleus, ultimately resulting in caspase-independent apoptosis. Interestingly, correction of the AIFM1 variant significantly restored the structure and function of AIF, further improving the physiological state of patient-specific iPSC-derived neurons. This study demonstrates that the AIFM1 variant is one of the molecular bases of ANSD. Mitochondrial dysfunction, especially mCa2+ overload, plays a prominent role in ANSD associated with AIFM1. Our findings help elucidate the mechanism of ANSD and may lead to the provision of novel therapies.
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Affiliation(s)
- Yue Qiu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Hongyang Wang
- Senior Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Mingjie Fan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Department of Pediatrics, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China
| | - Huaye Pan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jing Guan
- Senior Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yangwei Jiang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Zexiao Jia
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Kaiwen Wu
- Senior Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Hui Zhou
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Qianqian Zhuang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Zhaoying Lei
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xue Ding
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Huajian Cai
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yufei Dong
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lei Yan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Aifu Lin
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yong Fu
- The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310052, China
| | - Dong Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Qingfeng Yan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
- Department of Pediatrics, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China.
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, Zhejiang, 310058, China.
| | - Qiuju Wang
- Senior Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
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7
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Bandyopadhyay A, Ghosh SK. Apoptosis-inducing factor-like protein-mediated stress and metronidazole-responsive programmed cell death pathway in Entamoeba histolytica. Mol Microbiol 2023; 119:640-658. [PMID: 37037799 DOI: 10.1111/mmi.15061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/12/2023]
Abstract
Apoptosis-inducing factor (AIF) is the major component of the caspase-independent cell death pathway that is considered to be evolutionarily ancient. Apoptosis is generally evolved with multicellularity as a prerequisite for the elimination of aged, stressed, or infected cells promoting the survival of the organism. Our study reports the presence of a putative AIF-like protein in Entamoeba histolytica, a caspase-deficient primitive protozoan, strengthening the concept of occurrence of apoptosis in unicellular organisms as well. The putative cytoplasmic EhAIF migrates to the nucleus on receiving stresses that precede its binding with DNA, following chromatin degradation and chromatin condensation as evident from both in vitro and in vivo experiments. Down-regulating the EhAIF expression attenuates the apoptotic features of insulted cells and increases the survival potency in terms of cell viability and vitality of the trophozoites, whereas over-expression of the EhAIF effectively enhances the phenomena. Interestingly, metronidazole, the most widely used drug for amoebiasis treatment, is also potent to elicit similar AIF-mediated cell death responses like other stresses indicating the AIF-mediated cell death could be the probable mechanism of trophozoite-death by metronidazole treatment. The occurrence of apoptosis in a unicellular organism is an interesting phenomenon that might signify the altruistic death that overall improves the population health.
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Affiliation(s)
| | - Sudip Kumar Ghosh
- Department of Biotechnology, IIT Kharagpur, Kharagpur, West Bengal, India
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8
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Cathepsin H Knockdown Reverses Radioresistance of Hepatocellular Carcinoma via Metabolic Switch Followed by Apoptosis. Int J Mol Sci 2023; 24:ijms24065257. [PMID: 36982347 PMCID: PMC10049059 DOI: 10.3390/ijms24065257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
Despite the wide application of radiotherapy in HCC, radiotherapy efficacy is sometimes limited due to radioresistance. Although radioresistance is reported with high glycolysis, the underlying mechanism between radioresistance and cancer metabolism, as well as the role of cathepsin H (CTSH) within it, remain unclear. In this study, tumor-bearing models and HCC cell lines were used to observe the effect of CTSH on radioresistance. Proteome mass spectrometry, followed by enrichment analysis, were used to investigate the cascades and targets regulated by CTSH. Technologies such as immunofluorescence co-localization flow cytometry and Western blot were used for further detection and verification. Through these methods, we originally found CTSH knockdown (KD) perturbed aerobic glycolysis and enhanced aerobic respiration, and thus promoted apoptosis through up-regulation and the release of proapoptotic factors such as AIFM1, HTRA2, and DIABLO, consequently reducing radioresistance. We also found that CTSH, together with its regulatory targets (such as PFKL, HK2, LDH, and AIFM1), was correlated with tumorigenesis and poor prognosis. In summary, our study found that the cancer metabolic switch and apoptosis were regulated by CTSH signaling, leading to the occurrence of radioresistance in HCC cells and suggesting the potential value of HCC diagnosis and therapy.
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9
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Baker MJ, Crameri JJ, Thorburn DR, Frazier AE, Stojanovski D. Mitochondrial biology and dysfunction in secondary mitochondrial disease. Open Biol 2022; 12:220274. [PMID: 36475414 PMCID: PMC9727669 DOI: 10.1098/rsob.220274] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial diseases are a broad, genetically heterogeneous class of metabolic disorders characterized by deficits in oxidative phosphorylation (OXPHOS). Primary mitochondrial disease (PMD) defines pathologies resulting from mutation of mitochondrial DNA (mtDNA) or nuclear genes affecting either mtDNA expression or the biogenesis and function of the respiratory chain. Secondary mitochondrial disease (SMD) arises due to mutation of nuclear-encoded genes independent of, or indirectly influencing OXPHOS assembly and operation. Despite instances of novel SMD increasing year-on-year, PMD is much more widely discussed in the literature. Indeed, since the implementation of next generation sequencing (NGS) techniques in 2010, many novel mitochondrial disease genes have been identified, approximately half of which are linked to SMD. This review will consolidate existing knowledge of SMDs and outline discrete categories within which to better understand the diversity of SMD phenotypes. By providing context to the biochemical and molecular pathways perturbed in SMD, we hope to further demonstrate the intricacies of SMD pathologies outside of their indirect contribution to mitochondrial energy generation.
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Affiliation(s)
- Megan J. Baker
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Jordan J. Crameri
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - David R. Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia,Victorian Clinical Genetics Services, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Ann E. Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
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10
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Wischhof L, Scifo E, Ehninger D, Bano D. AIFM1 beyond cell death: An overview of this OXPHOS-inducing factor in mitochondrial diseases. EBioMedicine 2022; 83:104231. [PMID: 35994922 PMCID: PMC9420475 DOI: 10.1016/j.ebiom.2022.104231] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022] Open
Abstract
Apoptosis-inducing factor (AIF) is a mitochondrial intermembrane space flavoprotein with diverse functions in cellular physiology. In this regard, a large number of studies have elucidated AIF's participation to chromatin condensation during cell death in development, cancer, cardiovascular and brain disorders. However, the discovery of rare AIFM1 mutations in patients has shifted the interest of biomedical researchers towards AIF's contribution to pathogenic mechanisms underlying inherited AIFM1-linked metabolic diseases. The functional characterization of AIF binding partners has rapidly advanced our understanding of AIF biology within the mitochondria and beyond its widely reported role in cell death. At the present time, it is reasonable to assume that AIF contributes to cell survival by promoting biogenesis and maintenance of the mitochondrial oxidative phosphorylation (OXPHOS) system. With this review, we aim to outline the current knowledge around the vital role of AIF by primarily focusing on currently reported human diseases that have been linked to AIFM1 deficiency.
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Affiliation(s)
- Lena Wischhof
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Enzo Scifo
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Dan Ehninger
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
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11
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Nowacki JC, Fields AM, Fu MM. Emerging cellular themes in leukodystrophies. Front Cell Dev Biol 2022; 10:902261. [PMID: 36003149 PMCID: PMC9393611 DOI: 10.3389/fcell.2022.902261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/30/2022] [Indexed: 11/18/2022] Open
Abstract
Leukodystrophies are a broad spectrum of neurological disorders that are characterized primarily by deficiencies in myelin formation. Clinical manifestations of leukodystrophies usually appear during childhood and common symptoms include lack of motor coordination, difficulty with or loss of ambulation, issues with vision and/or hearing, cognitive decline, regression in speech skills, and even seizures. Many cases of leukodystrophy can be attributed to genetic mutations, but they have diverse inheritance patterns (e.g., autosomal recessive, autosomal dominant, or X-linked) and some arise from de novo mutations. In this review, we provide an updated overview of 35 types of leukodystrophies and focus on cellular mechanisms that may underlie these disorders. We find common themes in specialized functions in oligodendrocytes, which are specialized producers of membranes and myelin lipids. These mechanisms include myelin protein defects, lipid processing and peroxisome dysfunction, transcriptional and translational dysregulation, disruptions in cytoskeletal organization, and cell junction defects. In addition, non-cell-autonomous factors in astrocytes and microglia, such as autoimmune reactivity, and intercellular communication, may also play a role in leukodystrophy onset. We hope that highlighting these themes in cellular dysfunction in leukodystrophies may yield conceptual insights on future therapeutic approaches.
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12
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Dong H, You J, Zhao Y, Zheng D, Zhong Y, Li G, Weng Z, Luo H, Jiang S. Study on the Characteristics of Small-Molecule Kinase Inhibitors-Related Drug-Induced Liver Injury. Front Pharmacol 2022; 13:838397. [PMID: 35529445 PMCID: PMC9068902 DOI: 10.3389/fphar.2022.838397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/11/2022] [Indexed: 11/30/2022] Open
Abstract
Background and Aim: More than half of the small-molecule kinase inhibitors (KIs) induced liver injury clinically. Meanwhile, studies have shown a close relationship between mitochondrial damage and drug-induced liver injury (DILI). We aimed to study KIs and the binding between drugs and mitochondrial proteins to find factors related to DILI occurrence. Methods: A total of 1,223 oral FDA-approved drugs were collected and analyzed, including 44 KIs. Fisher’s exact test was used to analyze DILI potential and risk of different factors. A total of 187 human mitochondrial proteins were further collected, and high-throughput molecular docking was performed between human mitochondrial proteins and drugs in the data set. The molecular dynamics simulation was used to optimize and evaluate the dynamic binding behavior of the selected mitochondrial protein/KI complexes. Results: The possibility of KIs to produce DILI is much higher than that of other types (OR = 46.89, p = 9.28E-13). A few DILI risk factors were identified, including molecular weight (MW) between 400 and 600, the defined daily dose (DDD) ≥ 100 mg/day, the octanol–water partition coefficient (LogP) ≥ 3, and the degree of liver metabolism (LM) more than 50%. Drugs that met this combination of rules were found to have a higher DILI risk than controls (OR = 8.28, p = 4.82E-05) and were more likely to cause severe DILI (OR = 8.26, p = 5.06E-04). The docking results showed that KIs had a significant higher affinity with human mitochondrial proteins (p = 4.19E-11) than other drug types. Furthermore, the five proteins with the lowest docking score were selected for molecular dynamics simulation, and the smallest fluctuation of the backbone RMSD curve was found in the protein 5FS8/KI complexes, which indicated the best stability of the protein 5FS8 bound to KIs. Conclusions: KIs were found to have the highest odds ratio of causing DILI. MW was significantly related to the production of DILI, and the average docking scores of KI drugs were found to be significantly different from other classes. Further analysis identified the top binding mitochondrial proteins for KIs, and specific binding sites were analyzed. The optimization of molecular docking results by molecular dynamics simulation may contribute to further studying the mechanism of DILI.
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Affiliation(s)
- Huiqun Dong
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Jia You
- Department of Hepatology, Hepatology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yu Zhao
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou, China
| | - Danhua Zheng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Yi Zhong
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou, China
| | - Gaozheng Li
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou, China
| | - Zuquan Weng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou, China
- *Correspondence: Zuquan Weng, ; Heng Luo, ; Shan Jiang,
| | - Heng Luo
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou, China
- MetaNovas Biotech Inc., Foster City, CA, United States
- *Correspondence: Zuquan Weng, ; Heng Luo, ; Shan Jiang,
| | - Shan Jiang
- Department of Vascular Thyroid Surgery, Affiliated Union Hospital, Fujian Medical University, Fuzhou, China
- *Correspondence: Zuquan Weng, ; Heng Luo, ; Shan Jiang,
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13
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Rex DAB, Arun Kumar ST, Rai AB, Kotimoole CN, Modi PK, Prasad TSK. Novel Post-Translational Modifications and Molecular Substrates in Glioma Identified by Bioinformatics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:463-473. [PMID: 34227895 DOI: 10.1089/omi.2021.0050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Glioma is the most common type of brain cancer that originates from the glial cells. It constitutes about one-third of all brain cancers. Recently, transcriptomics, proteomics, and multiomics approaches have been harnessed to discover potential biomarkers and therapeutic targets in glioma. Moreover, post-translational modifications (PTMs) of proteins play a major role in cell biology and function and offer new avenues of research in cancer. Using unbiased multi-PTM bioinformatics analyses of two proteomic datasets of glioma available in the public domain, we identified 866 proteins with common PTMs from both studies. Out of these 866 proteins, 19 proteins were identified with the common PTMs, with the same site modifications pertaining to glioma. Importantly, the identified PTMs belonged to proteins involved in integrin PI3K/Akt/mTOR, JAK/STAT, and Ras/Raf/MAPK pathways. These pathways are essential for cell proliferation in tumor cells and thus involved in glioma progression. Taken together, these findings call for validation in larger datasets in glioma and brain cancers and with an eye to future drug discovery and diagnostic innovation. Bioinformatics-guided discovery of novel PTMs from the publicly available proteomic data can offer new avenues for innovation in cancer research.
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Affiliation(s)
- Devasahayam Arokia Balaya Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sumaithangi Thattai Arun Kumar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Akhila Balakrishna Rai
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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14
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Molecular Insights into Mitochondrial Protein Translocation and Human Disease. Genes (Basel) 2021; 12:genes12071031. [PMID: 34356047 PMCID: PMC8305315 DOI: 10.3390/genes12071031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
In human mitochondria, mtDNA encodes for only 13 proteins, all components of the OXPHOS system. The rest of the mitochondrial components, which make up approximately 99% of its proteome, are encoded in the nuclear genome, synthesized in cytosolic ribosomes and imported into mitochondria. Different import machineries translocate mitochondrial precursors, depending on their nature and the final destination inside the organelle. The proper and coordinated function of these molecular pathways is critical for mitochondrial homeostasis. Here, we will review molecular details about these pathways, which components have been linked to human disease and future perspectives on the field to expand the genetic landscape of mitochondrial diseases.
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15
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Liu S, Zhou M, Ruan Z, Wang Y, Chang C, Sasaki M, Rajaram V, Lemoff A, Nambiar K, Wang JE, Hatanpaa KJ, Luo W, Dawson TM, Dawson VL, Wang Y. AIF3 splicing switch triggers neurodegeneration. Mol Neurodegener 2021; 16:25. [PMID: 33853653 PMCID: PMC8048367 DOI: 10.1186/s13024-021-00442-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 03/12/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Apoptosis-inducing factor (AIF), as a mitochondrial flavoprotein, plays a fundamental role in mitochondrial bioenergetics that is critical for cell survival and also mediates caspase-independent cell death once it is released from mitochondria and translocated to the nucleus under ischemic stroke or neurodegenerative diseases. Although alternative splicing regulation of AIF has been implicated, it remains unknown which AIF splicing isoform will be induced under pathological conditions and how it impacts mitochondrial functions and neurodegeneration in adult brain. METHODS AIF splicing induction in brain was determined by multiple approaches including 5' RACE, Sanger sequencing, splicing-specific PCR assay and bottom-up proteomic analysis. The role of AIF splicing in mitochondria and neurodegeneration was determined by its biochemical properties, cell death analysis, morphological and functional alterations and animal behavior. Three animal models, including loss-of-function harlequin model, gain-of-function AIF3 knockin model and conditional inducible AIF splicing model established using either Cre-loxp recombination or CRISPR/Cas9 techniques, were applied to explore underlying mechanisms of AIF splicing-induced neurodegeneration. RESULTS We identified a nature splicing AIF isoform lacking exons 2 and 3 named as AIF3. AIF3 was undetectable under physiological conditions but its expression was increased in mouse and human postmortem brain after stroke. AIF3 splicing in mouse brain caused enlarged ventricles and severe neurodegeneration in the forebrain regions. These AIF3 splicing mice died 2-4 months after birth. AIF3 splicing-triggered neurodegeneration involves both mitochondrial dysfunction and AIF3 nuclear translocation. We showed that AIF3 inhibited NADH oxidase activity, ATP production, oxygen consumption, and mitochondrial biogenesis. In addition, expression of AIF3 significantly increased chromatin condensation and nuclear shrinkage leading to neuronal cell death. However, loss-of-AIF alone in harlequin or gain-of-AIF3 alone in AIF3 knockin mice did not cause robust neurodegeneration as that observed in AIF3 splicing mice. CONCLUSIONS We identified AIF3 as a disease-inducible isoform and established AIF3 splicing mouse model. The molecular mechanism underlying AIF3 splicing-induced neurodegeneration involves mitochondrial dysfunction and AIF3 nuclear translocation resulting from the synergistic effect of loss-of-AIF and gain-of-AIF3. Our study provides a valuable tool to understand the role of AIF3 splicing in brain and a potential therapeutic target to prevent/delay the progress of neurodegenerative diseases.
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Affiliation(s)
- Shuiqiao Liu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Mi Zhou
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Zhi Ruan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Yanan Wang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Calvin Chang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Masayuki Sasaki
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Veena Rajaram
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Kalyani Nambiar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Jennifer E. Wang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Kimmo J. Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Weibo Luo
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Ted M. Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Valina L. Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Yingfei Wang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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16
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The Mia40/CHCHD4 Oxidative Folding System: Redox Regulation and Signaling in the Mitochondrial Intermembrane Space. Antioxidants (Basel) 2021; 10:antiox10040592. [PMID: 33921425 PMCID: PMC8069373 DOI: 10.3390/antiox10040592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022] Open
Abstract
Mitochondria are critical for several cellular functions as they control metabolism, cell physiology, and cell death. The mitochondrial proteome consists of around 1500 proteins, the vast majority of which (about 99% of them) are encoded by nuclear genes, with only 13 polypeptides in human cells encoded by mitochondrial DNA. Therefore, it is critical for all the mitochondrial proteins that are nuclear-encoded to be targeted precisely and sorted specifically to their site of action inside mitochondria. These processes of targeting and sorting are catalysed by protein translocases that operate in each one of the mitochondrial sub-compartments. The main protein import pathway for the intermembrane space (IMS) recognises proteins that are cysteine-rich, and it is the only import pathway that chemically modifies the imported precursors by introducing disulphide bonds to them. In this manner, the precursors are trapped in the IMS in a folded state. The key component of this pathway is Mia40 (called CHCHD4 in human cells), which itself contains cysteine motifs and is subject to redox regulation. In this review, we detail the basic components of the MIA pathway and the disulphide relay mechanism that underpins the electron transfer reaction along the oxidative folding mechanism. Then, we discuss the key protein modulators of this pathway and how they are interlinked to the small redox-active molecules that critically affect the redox state in the IMS. We present also evidence that the mitochondrial redox processes that are linked to iron–sulfur clusters biogenesis and calcium homeostasis coalesce in the IMS at the MIA machinery. The fact that the MIA machinery and several of its interactors and substrates are linked to a variety of common human diseases connected to mitochondrial dysfunction highlight the potential of redox processes in the IMS as a promising new target for developing new treatments for some of the most complex and devastating human diseases.
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17
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Overview of structurally homologous flavoprotein oxidoreductases containing the low M r thioredoxin reductase-like fold - A functionally diverse group. Arch Biochem Biophys 2021; 702:108826. [PMID: 33684359 DOI: 10.1016/j.abb.2021.108826] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/23/2021] [Accepted: 02/27/2021] [Indexed: 01/12/2023]
Abstract
Structural studies show that enzymes have a limited number of unique folds, although structurally related enzymes have evolved to perform a large variety of functions. In this review, we have focused on enzymes containing the low molecular weight thioredoxin reductase (low Mr TrxR) fold. This fold consists of two domains, both containing a three-layer ββα sandwich Rossmann-like fold, serving as flavin adenine dinucleotide (FAD) and, in most cases, pyridine nucleotide (NAD(P)H) binding-domains. Based on a search of the Protein Data Bank for all published structures containing the low Mr TrxR-like fold, we here present a comprehensive overview of enzymes with this structural architecture. These range from TrxR-like ferredoxin/flavodoxin NAD(P)+ oxidoreductases, through glutathione reductase, to NADH peroxidase. Some enzymes are solely composed of the low Mr TrxR-like fold, while others contain one or two additional domains. In this review, we give a detailed description of selected enzymes containing only the low Mr TrxR-like fold, however, catalyzing a diversity of chemical reactions. Our overview of this structurally similar, yet functionally distinct group of flavoprotein oxidoreductases highlights the fascinating and increasing number of studies describing the diversity among these enzymes, especially during the last decade(s).
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18
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Beijer D, Baets J. The expanding genetic landscape of hereditary motor neuropathies. Brain 2021; 143:3540-3563. [PMID: 33210134 DOI: 10.1093/brain/awaa311] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
Hereditary motor neuropathies are clinically and genetically diverse disorders characterized by length-dependent axonal degeneration of lower motor neurons. Although currently as many as 26 causal genes are known, there is considerable missing heritability compared to other inherited neuropathies such as Charcot-Marie-Tooth disease. Intriguingly, this genetic landscape spans a discrete number of key biological processes within the peripheral nerve. Also, in terms of underlying pathophysiology, hereditary motor neuropathies show striking overlap with several other neuromuscular and neurological disorders. In this review, we provide a current overview of the genetic spectrum of hereditary motor neuropathies highlighting recent reports of novel genes and mutations or recent discoveries in the underlying disease mechanisms. In addition, we link hereditary motor neuropathies with various related disorders by addressing the main affected pathways of disease divided into five major processes: axonal transport, tRNA aminoacylation, RNA metabolism and DNA integrity, ion channels and transporters and endoplasmic reticulum.
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Affiliation(s)
- Danique Beijer
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Belgium
| | - Jonathan Baets
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Belgium
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19
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CHCHD4 (MIA40) and the mitochondrial disulfide relay system. Biochem Soc Trans 2021; 49:17-27. [PMID: 33599699 PMCID: PMC7925007 DOI: 10.1042/bst20190232] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/19/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022]
Abstract
Mitochondria are pivotal for normal cellular physiology, as they perform a crucial role in diverse cellular functions and processes, including respiration and the regulation of bioenergetic and biosynthetic pathways, as well as regulating cellular signalling and transcriptional networks. In this way, mitochondria are central to the cell's homeostatic machinery, and as such mitochondrial dysfunction underlies the pathology of a diverse range of diseases including mitochondrial disease and cancer. Mitochondrial import pathways and targeting mechanisms provide the means to transport into mitochondria the hundreds of nuclear-encoded mitochondrial proteins that are critical for the organelle's many functions. One such import pathway is the highly evolutionarily conserved disulfide relay system (DRS) within the mitochondrial intermembrane space (IMS), whereby proteins undergo a form of oxidation-dependent protein import. A central component of the DRS is the oxidoreductase coiled-coil-helix-coiled-coil-helix (CHCH) domain-containing protein 4 (CHCHD4, also known as MIA40), the human homologue of yeast Mia40. Here, we summarise the recent advances made to our understanding of the role of CHCHD4 and the DRS in physiology and disease, with a specific focus on the emerging importance of CHCHD4 in regulating the cellular response to low oxygen (hypoxia) and metabolism in cancer.
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20
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W196 and the β-Hairpin Motif Modulate the Redox Switch of Conformation and the Biomolecular Interaction Network of the Apoptosis-Inducing Factor. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6673661. [PMID: 33510840 PMCID: PMC7822688 DOI: 10.1155/2021/6673661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/09/2020] [Accepted: 12/18/2020] [Indexed: 01/07/2023]
Abstract
The human apoptosis-inducing factor (hAIF) is a moonlight flavoprotein involved in mitochondrial respiratory complex assembly and caspase-independent programmed cell death. These functions might be modulated by its redox-linked structural transition that enables hAIF to act as a NAD(H/+) redox sensor. Upon reduction with NADH, hAIF undergoes a conformational reorganization in two specific insertions—the flexible regulatory C-loop and the 190-202 β-harpin—promoting protein dimerization and the stabilization of a long-life charge transfer complex (CTC) that modulates its monomer-dimer equilibrium and its protein interaction network in healthy mitochondria. In this regard, here, we investigated the precise function of the β-hairpin in the AIF conformation landscape related to its redox mechanism, by analyzing the role played by W196, a key residue in the interaction of this motif with the regulatory C-loop. Mutations at W196 decrease the compactness and stability of the oxidized hAIF, indicating that the β-hairpin and C-loop coupling contribute to protein stability. Kinetic studies complemented with computational simulations reveal that W196 and the β-hairpin conformation modulate the low efficiency of hAIF as NADH oxidoreductase, contributing to configure its active site in a noncompetent geometry for hydride transfer and to stabilize the CTC state by enhancing the affinity for NAD+. Finally, the β-hairpin motif contributes to define the conformation of AIF's interaction surfaces with its physiological partners. These findings improve our understanding on the molecular basis of hAIF's cellular activities, a crucial aspect for clarifying its associated pathological mechanisms and developing new molecular therapies.
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21
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Edgerley K, Barnicoat A, Offiah AC, Calder AD, Mankad K, Thomas NS, Bunyan DJ, Williams M, Buxton C, Majumdar A, Vijayakumar K, Hilliard T, Turner J, Burren CP, Monsell F, Smithson SF. AIFM1-associated X-linked spondylometaphyseal dysplasia with cerebral hypomyelination. Am J Med Genet A 2021; 185:1228-1235. [PMID: 33439541 DOI: 10.1002/ajmg.a.62072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/02/2020] [Accepted: 12/05/2020] [Indexed: 11/06/2022]
Abstract
Spondylometaphyseal dysplasia with cerebral hypomyelination (SMD-H) is a very rare but distinctive phenotype, unusually combining spondylometaphyseal dysplasia with hypomyelinating leukodystrophy. Recently, SMD-H has been associated with variants confined to a specific intra-genic locus involving Exon 7, suggesting that AIFM1 plays an important role in bone development and metabolism as well as cerebral myelination. Here we describe two further affected boys, one with a novel intronic variant associated with skipping of Exon 7 of AIFM1 and the other a synonymous variant within Exon 7 of AIFM1. We describe their clinical course and radiological and genetic findings, providing further insight into the natural history of this condition.
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Affiliation(s)
- Katharine Edgerley
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - Angela Barnicoat
- Department of Clinical Genetics, Great Ormond Street for Children NHS Foundation Trust, London, United Kingdom
| | - Amaka C Offiah
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Alistair D Calder
- Radiology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Kshitij Mankad
- Radiology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Nicholas Simon Thomas
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, United Kingdom
| | - David J Bunyan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, United Kingdom
| | - Maggie Williams
- Bristol Genetics Laboratory, South West Genomics Laboratory Hub, Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom
| | - Chris Buxton
- Bristol Genetics Laboratory, South West Genomics Laboratory Hub, Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom
| | - Arniban Majumdar
- Department of Paediatric Neurology, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - Kayal Vijayakumar
- Department of Paediatric Neurology, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - Tom Hilliard
- Department of Paediatric Respiratory Medicine, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - James Turner
- Department of Paediatric Orthopaedics, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - Christine P Burren
- Department of Paediatric Endocrinology and Diabetes, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - Fergal Monsell
- Department of Paediatric Orthopaedics, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - Sarah F Smithson
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
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22
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Ferroptosis-Related Flavoproteins: Their Function and Stability. Int J Mol Sci 2021; 22:ijms22010430. [PMID: 33406703 PMCID: PMC7796112 DOI: 10.3390/ijms22010430] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/14/2022] Open
Abstract
Ferroptosis has been described recently as an iron-dependent cell death driven by peroxidation of membrane lipids. It is involved in the pathogenesis of a number of diverse diseases. From the other side, the induction of ferroptosis can be used to kill tumor cells as a novel therapeutic approach. Because of the broad clinical relevance, a comprehensive understanding of the ferroptosis-controlling protein network is necessary. Noteworthy, several proteins from this network are flavoenzymes. This review is an attempt to present the ferroptosis-related flavoproteins in light of their involvement in anti-ferroptotic and pro-ferroptotic roles. When available, the data on the structural stability of mutants and cofactor-free apoenzymes are discussed. The stability of the flavoproteins could be an important component of the cellular death processes.
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Cocomazzi P, Tarantino D, Mastrangelo E, Aliverti A. Ligand Binding in Allosteric Flavoproteins: Part 2. Quantitative Analysis of the Redox-Dependent Interaction of the Apoptosis-Inducing Factor (AIF) with Its Protein Partner. Methods Mol Biol 2021; 2280:189-198. [PMID: 33751436 DOI: 10.1007/978-1-0716-1286-6_12] [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] [Indexed: 12/17/2023]
Abstract
To perform their action usually flavoproteins interact transiently with a variety of molecular partners, whose binding is reciprocally affected and often controlled by the redox state of the bound flavin cofactor. As a case study, here we describe an approach for the quantitative characterization of the redox-controlled interaction of the mammalian apoptosis inducing factor (AIF) with one of its known protein partners, namely, the mitochondrial coiled-coil-helix-coiled-coil-helix domain-containing protein 4 (CHCHD4). In particular, we report a protocol for the titration of the flavoprotein in both in its oxidized and reduced states with CHCHD4, using an implementation of the MicroScale Thermophoresis (MST) technique.
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Affiliation(s)
- Paolo Cocomazzi
- Department of Biosciences, University of Milan, Milan, Italy
| | - Delia Tarantino
- Department of Biosciences, University of Milan, Milan, Italy
| | - Eloise Mastrangelo
- CNR-IBF, Consiglio Nazionale delle Ricerche - Istituto di Biofisica, Milan, Italy
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24
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Cocomazzi P, Sorrentino L, Cossu F, Aliverti A. Ligand Binding in Allosteric Flavoproteins: Part 1. Quantitative Analysis of the Interaction with NAD + of the Apoptosis Inducing Factor (AIF) Harboring FAD in the Reduced State. Methods Mol Biol 2021; 2280:179-187. [PMID: 33751435 DOI: 10.1007/978-1-0716-1286-6_11] [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] [Indexed: 10/21/2022]
Abstract
To perform their action, flavoproteins usually interact with a variety of low molecular weight partners, including electron transporters, yielding transient complexes whose tightness is often controlled by the redox state of the bound flavin cofactor. As a case study, here we describe the quantitative analysis of the redox-dependent interaction of the mammalian apoptosis inducing factor (AIF) with its NAD+ ligand. In particular, we report a protocol for the spectrophotometric titration of AIF in its reduced state under anaerobic conditions with NAD+, in order to determine the dissociation constant of the resulting complex.
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Affiliation(s)
- Paolo Cocomazzi
- Department of Biosciences, University of Milan, Milan, Italy
| | - Luca Sorrentino
- Department of Biosciences, University of Milan, Milan, Italy
- Department of Chemistry, University of Milan, Milan, Italy
| | - Federica Cossu
- CNR-IBF, Consiglio Nazionale delle Ricerche - Istituto di Biofisica, Milan, Italy
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25
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Skeletal Phenotypes Due to Abnormalities in Mitochondrial Protein Homeostasis and Import. Int J Mol Sci 2020; 21:ijms21218327. [PMID: 33171986 PMCID: PMC7664180 DOI: 10.3390/ijms21218327] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/28/2020] [Accepted: 11/03/2020] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial disease represents a collection of rare genetic disorders caused by mitochondrial dysfunction. These disorders can be quite complex and heterogeneous, and it is recognized that mitochondrial disease can affect any tissue at any age. The reasons for this variability are not well understood. In this review, we develop and expand a subset of mitochondrial diseases including predominantly skeletal phenotypes. Understanding how impairment ofdiverse mitochondrial functions leads to a skeletal phenotype will help diagnose and treat patients with mitochondrial disease and provide additional insight into the growing list of human pathologies associated with mitochondrial dysfunction. The underlying disease genes encode factors involved in various aspects of mitochondrial protein homeostasis, including proteases and chaperones, mitochondrial protein import machinery, mediators of inner mitochondrial membrane lipid homeostasis, and aminoacylation of mitochondrial tRNAs required for translation. We further discuss a complex of frequently associated phenotypes (short stature, cataracts, and cardiomyopathy) potentially explained by alterations to steroidogenesis, a process regulated by mitochondria. Together, these observations provide novel insight into the consequences of impaired mitochondrial protein homeostasis.
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26
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Saneto RP. Mitochondrial diseases: expanding the diagnosis in the era of genetic testing. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2020; 4:384-428. [PMID: 33426505 PMCID: PMC7791531 DOI: 10.20517/jtgg.2020.40] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial diseases are clinically and genetically heterogeneous. These diseases were initially described a little over three decades ago. Limited diagnostic tools created disease descriptions based on clinical, biochemical analytes, neuroimaging, and muscle biopsy findings. This diagnostic mechanism continued to evolve detection of inherited oxidative phosphorylation disorders and expanded discovery of mitochondrial physiology over the next two decades. Limited genetic testing hampered the definitive diagnostic identification and breadth of diseases. Over the last decade, the development and incorporation of massive parallel sequencing has identified approximately 300 genes involved in mitochondrial disease. Gene testing has enlarged our understanding of how genetic defects lead to cellular dysfunction and disease. These findings have expanded the understanding of how mechanisms of mitochondrial physiology can induce dysfunction and disease, but the complete collection of disease-causing gene variants remains incomplete. This article reviews the developments in disease gene discovery and the incorporation of gene findings with mitochondrial physiology. This understanding is critical to the development of targeted therapies.
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Affiliation(s)
- Russell P. Saneto
- Center for Integrative Brain Research, Neuroscience Institute, Seattle, WA 98101, USA
- Department of Neurology/Division of Pediatric Neurology, Seattle Children’s Hospital/University of Washington, Seattle, WA 98105, USA
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27
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Tolomeo M, Nisco A, Leone P, Barile M. Development of Novel Experimental Models to Study Flavoproteome Alterations in Human Neuromuscular Diseases: The Effect of Rf Therapy. Int J Mol Sci 2020; 21:ijms21155310. [PMID: 32722651 PMCID: PMC7432027 DOI: 10.3390/ijms21155310] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
Inborn errors of Riboflavin (Rf) transport and metabolism have been recently related to severe human neuromuscular disorders, as resulting in profound alteration of human flavoproteome and, therefore, of cellular bioenergetics. This explains why the interest in studying the “flavin world”, a topic which has not been intensively investigated before, has increased much over the last few years. This also prompts basic questions concerning how Rf transporters and FAD (flavin adenine dinucleotide) -forming enzymes work in humans, and how they can create a coordinated network ensuring the maintenance of intracellular flavoproteome. The concept of a coordinated cellular “flavin network”, introduced long ago studying humans suffering for Multiple Acyl-CoA Dehydrogenase Deficiency (MADD), has been, later on, addressed in model organisms and more recently in cell models. In the frame of the underlying relevance of a correct supply of Rf in humans and of a better understanding of the molecular rationale of Rf therapy in patients, this review wants to deal with theories and existing experimental models in the aim to potentiate possible therapeutic interventions in Rf-related neuromuscular diseases.
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Pandolfo M, Rai M, Remiche G, Desmyter L, Vandernoot I. Cerebellar ataxia, neuropathy, hearing loss, and intellectual disability due to AIFM1 mutation. NEUROLOGY-GENETICS 2020; 6:e420. [PMID: 32337346 PMCID: PMC7164969 DOI: 10.1212/nxg.0000000000000420] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/07/2020] [Indexed: 11/30/2022]
Abstract
Objective To describe the clinical and molecular genetic findings in a family segregating a novel mutation in the AIFM1 gene on the X chromosome. Methods We studied the clinical features and performed brain MRI scans, nerve conduction studies, audiometry, cognitive testing, and clinical exome sequencing (CES) in the proband, his mother, and maternal uncle. We used in silico tools, X chromosome inactivation assessment, and Western blot analysis to predict the consequences of an AIFM1 variant identified by CES and demonstrate its pathogenicity. Results The proband and his maternal uncle presented with childhood-onset nonprogressive cerebellar ataxia, hearing loss, intellectual disability (ID), peripheral neuropathy, and mood and behavioral disorder. The proband's mother had mild cerebellar ataxia, ID, and mood and behavior disorder, but no neuropathy or hearing loss. The 3 subjects shared a variant (c.1195G>A; p.Gly399Ser) in exon 12 of the AIFM1 gene, which is not reported in the exome/genome sequence databases, affecting a critical amino acid for protein function involved in NAD(H) binding and predicted to be pathogenic with very high probability by variant analysis programs. X chromosome inactivation was highly skewed in the proband's mother. The mutation did not cause quantitative changes in protein abundance. Conclusions Our report extends the molecular and phenotypic spectrum of AIFM1 mutations. Specific findings include limited progression of neurologic abnormalities after the first decade and the coexistence of mood and behavior disorder. This family also shows the confounding effect on the phenotype of nongenetic factors, such as alcohol and drug use and side effects of medication.
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Affiliation(s)
- Massimo Pandolfo
- Neurology Service (M.P., G.R.), Hôpital Erasme; Laboratory of Experimental Neurology (M.P., M.R.); and Medical Genetics Service (L.D., I.V.), Hôpital Erasme, Université Libre de Bruxelles, Belgium
| | - Myriam Rai
- Neurology Service (M.P., G.R.), Hôpital Erasme; Laboratory of Experimental Neurology (M.P., M.R.); and Medical Genetics Service (L.D., I.V.), Hôpital Erasme, Université Libre de Bruxelles, Belgium
| | - Gauthier Remiche
- Neurology Service (M.P., G.R.), Hôpital Erasme; Laboratory of Experimental Neurology (M.P., M.R.); and Medical Genetics Service (L.D., I.V.), Hôpital Erasme, Université Libre de Bruxelles, Belgium
| | - Laurence Desmyter
- Neurology Service (M.P., G.R.), Hôpital Erasme; Laboratory of Experimental Neurology (M.P., M.R.); and Medical Genetics Service (L.D., I.V.), Hôpital Erasme, Université Libre de Bruxelles, Belgium
| | - Isabelle Vandernoot
- Neurology Service (M.P., G.R.), Hôpital Erasme; Laboratory of Experimental Neurology (M.P., M.R.); and Medical Genetics Service (L.D., I.V.), Hôpital Erasme, Université Libre de Bruxelles, Belgium
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AIF meets the CHCHD4/Mia40-dependent mitochondrial import pathway. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165746. [PMID: 32105825 DOI: 10.1016/j.bbadis.2020.165746] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 02/06/2023]
Abstract
In the mitochondria of healthy cells, Apoptosis-Inducing factor (AIF) is required for the optimal functioning of the respiratory chain machinery, mitochondrial integrity, cell survival, and proliferation. In all analysed species, it was revealed that the downregulation or depletion of AIF provokes mainly the post-transcriptional loss of respiratory chain Complex I protein subunits. Recent progress in the field has revealed that AIF fulfils its mitochondrial pro-survival function by interacting physically and functionally with CHCHD4, the evolutionarily-conserved human homolog of yeast Mia40. The redox-regulated CHCHD4/Mia40-dependent import machinery operates in the intermembrane space of the mitochondrion and controls the import of a set of nuclear-encoded cysteine-motif carrying protein substrates. In addition to their participation in the biogenesis of specific respiratory chain protein subunits, CHCHD4/Mia40 substrates are also implicated in the control of redox regulation, antioxidant response, translation, lipid homeostasis and mitochondrial ultrastructure and dynamics. Here, we discuss recent insights on the AIF/CHCHD4-dependent protein import pathway and review current data concerning the CHCHD4/Mia40 protein substrates in metazoan. Recent findings and the identification of disease-associated mutations in AIF or in specific CHCHD4/Mia40 substrates have highlighted these proteins as potential therapeutic targets in a variety of human disorders.
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Torres-Cuevas I, Corral-Debrinski M, Gressens P. Brain oxidative damage in murine models of neonatal hypoxia/ischemia and reoxygenation. Free Radic Biol Med 2019; 142:3-15. [PMID: 31226400 DOI: 10.1016/j.freeradbiomed.2019.06.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/26/2019] [Accepted: 06/10/2019] [Indexed: 02/08/2023]
Abstract
The brain is one of the main organs affected by hypoxia and reoxygenation in the neonatal period and one of the most vulnerable to oxidative stress. Hypoxia/ischemia and reoxygenation leads to impairment of neurogenesis, disruption of cortical migration, mitochondrial damage and neuroinflammation. The extent of the injury depends on the clinical manifestation in the affected regions. Preterm newborns are highly vulnerable, and they exhibit severe clinical manifestations such as intraventricular hemorrhage (IVH), retinopathy of prematurity (ROP) and diffuse white matter injury (DWMI) among others. In the neonatal period, the accumulation of high levels of reactive oxygen species exacerbated by the immature antioxidant defense systems in represents cellular threats that, if they exceed or bypass physiological counteracting mechanisms, are responsible of significant neuronal damage. Several experimental models in mice mimic the consequences of perinatal asphyxia and the use of oxygen in the reanimation process that produce brain injury. The aim of this review is to highlight brain damage associated with oxidative stress in different murine models of hypoxia/ischemia and reoxygenation.
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Affiliation(s)
| | | | - Pierre Gressens
- INSERM UMR1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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31
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Villanueva R, Romero-Tamayo S, Laplaza R, Martínez-Olivan J, Velázquez-Campoy A, Sancho J, Ferreira P, Medina M. Redox- and Ligand Binding-Dependent Conformational Ensembles in the Human Apoptosis-Inducing Factor Regulate Its Pro-Life and Cell Death Functions. Antioxid Redox Signal 2019; 30:2013-2029. [PMID: 30450916 DOI: 10.1089/ars.2018.7658] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Aims: The human apoptosis-inducing factor (hAIF) supports OXPHOS biogenesis and programmed cell death, with missense mutations producing neurodegenerative phenotypes. hAIF senses the redox environment of cellular compartments, stabilizing a charge transfer complex (CTC) dimer that modulates the protein interaction network. In this context, we aimed to evaluate the subcellular pH, CTC formation, and pathogenic mutations effects on hAIF stability, and a thermal denaturation high-throughput screening (HTS) assay to discover AIF binders. Results: Apoptotic hAIFΔ1-101 is not stable at intermembrane mitochondrial space (IMS) pH, but the 77-101 residues confer stability to the mitochondrial isoform. hAIF and its CTC populate different conformational ensembles with redox switch to the CTC producing a less stable and compact protein. The pathogenic G308E, ΔR201, and E493V mutations modulate hAIF stability; particularly, ΔR201 causes a population shift to a less stable conformation that remodels active site structure and dynamics. We have identified new molecules that modulate the hAIF reduced nicotinamide adenine dinucleotide (NADH)/oxidized nicotinamide adenine dinucleotide (NAD+) association/dissociation equilibrium and regulate its catalytic efficiency. Innovation: Biophysical methods allow evaluating the regulation of hAIF functional ensembles and to develop an HTS assay to discover small molecules that might modulate hAIF stability and activities. Conclusions: The mitochondrial soluble 54-77 portion stabilizes hAIF at the IMS pH. NADH-redox-linked conformation changes course with strong NAD+ binding and protein dimerization, but they produce a negative impact in overall hAIF stability. Loss of functionality in the R201 deletion is due to distortion of the active site architecture. We report molecules that may serve as leads in the development of hAIF bioactive compounds.
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Affiliation(s)
- Raquel Villanueva
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Silvia Romero-Tamayo
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Ruben Laplaza
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,2 Departamento de Química Física, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Juan Martínez-Olivan
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,3 Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain.,4 Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,5 Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid, Spain
| | - Javier Sancho
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,4 Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Patricia Ferreira
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Milagros Medina
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
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Wang Q, Xingxing L, Ding Z, Qi Y, Liu Y. Whole exome sequencing identifies a novel variant in an apoptosis-inducing factor gene associated with X-linked recessive hearing loss in a Chinese family. Genet Mol Biol 2019; 42:543-548. [PMID: 31188924 PMCID: PMC6905455 DOI: 10.1590/1678-4685-gmb-2018-0051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 01/30/2019] [Indexed: 11/22/2022] Open
Abstract
We report on the genetic analysis of a Chinese family in which four male patients presented with postlingual progressive hearing loss, associated with distal muscle wasting and unsteady ataxic gait. Using whole exome sequencing, we identified a new pathogenic variant (c.1463C>T, p.Pro488Leu) in the AIFM1 gene, which encodes the apoptosis-inducing factor mitochondrion-associated 1 precursor. AIFM1 is involved in the mitochondrial respiratory chain and cellular caspase-independent apoptosis pathway and has been reported to cause multiple phenotypes including hearing loss. The p.Pro488Leu missense variant segregated with symptoms in the pedigree. It was not found in the dbSNP database, databases of genomes and SNPs in the Chinese population, in 74 patients with sporadic hearing loss, or in 108 normal individuals.We also verified that this AIFM1variant enhanced cell apoptosis rates compared in 293T cells transfected with wild-type AIFM1. Different variations of AIFM1 give rise to different phenotypes in patients, and this is the second reported family with a variant in the C-terminal domain of AIFM1 showing the phenotype of hearing loss and peripheral neuropathy.
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Affiliation(s)
- Qi Wang
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, China.,Department of Otolaryngology-Head and Neck Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lu Xingxing
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, China
| | - Zhiwei Ding
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, China
| | - Yu Qi
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Yuhe Liu
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, China
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33
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Fan P, Wang N, Wang L, Xie X-Q. Autophagy and Apoptosis Specific Knowledgebases-guided Systems Pharmacology Drug Research. Curr Cancer Drug Targets 2019; 19:716-728. [PMID: 30727895 DOI: 10.2174/1568009619666190206122149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/20/2018] [Accepted: 01/30/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND Autophagy and apoptosis are the basic physiological processes in cells that clean up aged and mutant cellular components or even the entire cells. Both autophagy and apoptosis are disrupted in most major diseases such as cancer and neurological disorders. Recently, increasing attention has been paid to understand the crosstalk between autophagy and apoptosis due to their tightly synergetic or opposite functions in several pathological processes. OBJECTIVE This study aims to assist autophagy and apoptosis-related drug research, clarify the intense and complicated connections between two processes, and provide a guide for novel drug development. METHODS We established two chemical-genomic databases which are specifically designed for autophagy and apoptosis, including autophagy- and apoptosis-related proteins, pathways and compounds. We then performed network analysis on the apoptosis- and autophagy-related proteins and investigated the full protein-protein interaction (PPI) network of these two closely connected processes for the first time. RESULTS The overlapping targets we discovered show a more intense connection with each other than other targets in the full network, indicating a better efficacy potential for drug modulation. We also found that Death-associated protein kinase 1 (DAPK1) is a critical point linking autophagy- and apoptosis-related pathways beyond the overlapping part, and this finding may reveal some delicate signaling mechanism of the process. Finally, we demonstrated how to utilize our integrated computational chemogenomics tools on in silico target identification for small molecules capable of modulating autophagy- and apoptosis-related pathways. CONCLUSION The knowledge-bases for apoptosis and autophagy and the integrated tools will accelerate our work in autophagy and apoptosis-related research and can be useful sources for information searching, target prediction, and new chemical discovery.
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Affiliation(s)
- Peihao Fan
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, University of Pittsburgh, 3501 Terrace Street, PA, United States
| | - Nanyi Wang
- School of Pharmacy, University of Pittsburgh, 335 Sutherland Drive, 206 Salk Pavilion, PA, United States
| | - Lirong Wang
- School of Pharmacy, University of Pittsburgh, 335 Sutherland Drive, 206 Salk Pavilion, PA, United States
| | - Xie X-Q
- School of Pharmacy, University of Pittsburgh, 335 Sutherland Drive, 206 Salk Pavilion, PA, United States
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35
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Wischhof L, Gioran A, Sonntag-Bensch D, Piazzesi A, Stork M, Nicotera P, Bano D. A disease-associated Aifm1 variant induces severe myopathy in knockin mice. Mol Metab 2018; 13:10-23. [PMID: 29780003 PMCID: PMC6026322 DOI: 10.1016/j.molmet.2018.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE Mutations in the AIFM1 gene have been identified in recessive X-linked mitochondrial diseases. Functional and molecular consequences of these pathogenic AIFM1 mutations have been poorly studied in vivo. METHODS/RESULTS Here we provide evidence that the disease-associated apoptosis-inducing factor (AIF) deletion arginine 201 (R200 in rodents) causes pathology in knockin mice. Within a few months, posttranslational loss of the mutant AIF protein induces severe myopathy associated with a lower number of cytochrome c oxidase-positive muscle fibers. At a later stage, Aifm1 (R200 del) knockin mice manifest peripheral neuropathy, but they do not show neurodegenerative processes in the cerebellum, as observed in age-matched hypomorphic Harlequin (Hq) mutant mice. Quantitative proteomic and biochemical data highlight common molecular signatures of mitochondrial diseases, including aberrant folate-driven one-carbon metabolism and sustained Akt/mTOR signaling. CONCLUSION Our findings indicate metabolic defects and distinct tissue-specific vulnerability due to a disease-causing AIFM1 mutation, with many pathological hallmarks that resemble those seen in patients.
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Affiliation(s)
- Lena Wischhof
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Anna Gioran
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Antonia Piazzesi
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Miriam Stork
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
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Bano D, Prehn JHM. Apoptosis-Inducing Factor (AIF) in Physiology and Disease: The Tale of a Repented Natural Born Killer. EBioMedicine 2018; 30:29-37. [PMID: 29605508 PMCID: PMC5952348 DOI: 10.1016/j.ebiom.2018.03.016] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/05/2018] [Accepted: 03/13/2018] [Indexed: 12/12/2022] Open
Abstract
Apoptosis-inducing factor (AIF) is a mitochondrial oxidoreductase that contributes to cell death programmes and participates in the assembly of the respiratory chain. Importantly, AIF deficiency leads to severe mitochondrial dysfunction, causing muscle atrophy and neurodegeneration in model organisms as well as in humans. The purpose of this review is to describe functions of AIF and AIF-interacting proteins as regulators of cell death and mitochondrial bioenergetics. We describe how AIF deficiency induces pathogenic processes that alter metabolism and ultimately compromise cellular homeostasis. We report the currently known AIFM1 mutations identified in humans and discuss the variability of AIFM1-related disorders in terms of onset, organ involvement and symptoms. Finally, we summarize how the study of AIFM1-linked pathologies may help to further expand our understanding of rare inherited forms of mitochondrial diseases. AIF is a mitochondrial NADH-dependent oxidoreductase. Nuclear translocation of AIF occurs during cell death and has been associated with human disorders. Under physiological settings, AIF participates to the biogenesis of the respiratory complexes. AIFM1 mutations have been identified in patients with impaired mitochondrial bioenergetics. Inherited AIFM1 mutations lead to a variety of clinical manifestations, including severe childhood-onset mitochondrial diseases.
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Affiliation(s)
- Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin 2, Ireland
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37
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Wiraswati HL, Hangen E, Sanz AB, Lam NV, Reinhardt C, Sauvat A, Mogha A, Ortiz A, Kroemer G, Modjtahedi N. Apoptosis inducing factor (AIF) mediates lethal redox stress induced by menadione. Oncotarget 2018; 7:76496-76507. [PMID: 27738311 PMCID: PMC5363526 DOI: 10.18632/oncotarget.12562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 09/30/2016] [Indexed: 01/27/2023] Open
Abstract
Mitochondrial apoptosis inducing factor (AIF) is a redox-active enzyme that participates to the biogenesis/maintenance of complex I of the respiratory chain, yet also contributes to catabolic reactions in the context of regulated cell death when AIF translocates to the cytosol and to the nucleus. Here we explore the contribution of AIF to cell death induced by menadione (2-methyl-1,4-naphtoquinone; also called vitamin K3) in conditions in which this pro-oxidant does not cause the mitochondrial release of AIF, yet causes caspase-independent cell killing. Depletion of AIF from human cancer cells reduced the cytotoxicity of menadione. This cytoprotective effect was accompanied by the maintenance of high levels of reduced glutathione (GSH), which are normally depleted by menadione. In addition, AIF depletion reduced the arylation of cellular proteins induced by menadione. This menadione-triggered arylation, which can be measured by a fluorescence assay, is completely suppressed by addition of exogenous glutathione or N-acetyl cysteine. Complex I inhibition by Rotenone did not mimic the cytoprotective action of AIF depletion. Altogether, these results are compatible with the hypothesis that mitochondrion-sessile AIF facilitates lethal redox cycling of menadione, thereby precipitating protein arylation and glutathione depletion.
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Affiliation(s)
- Hesti Lina Wiraswati
- Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM, U1138, Paris, France.,Gustave Roussy Cancer Campus, Villejuif, France.,Faculty of Medicine, Université Paris-Saclay, Kremlin-Bicêtre, France.,Institut Teknologi Bandung (ITB), Bandung, Indonesia
| | - Emilie Hangen
- Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM, U1138, Paris, France.,Gustave Roussy Cancer Campus, Villejuif, France.,Faculty of Medicine, Université Paris-Saclay, Kremlin-Bicêtre, France
| | - Ana Belén Sanz
- Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM, U1138, Paris, France.,Gustave Roussy Cancer Campus, Villejuif, France.,Faculty of Medicine, Université Paris-Saclay, Kremlin-Bicêtre, France.,Laboratory of Nephrology, IIS-Fundacion Jimenez Diaz UAM and REDINREN, Madrid, Spain
| | - Ngoc-Vy Lam
- Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM, U1138, Paris, France.,Gustave Roussy Cancer Campus, Villejuif, France.,Faculty of Medicine, Université Paris-Saclay, Kremlin-Bicêtre, France
| | - Camille Reinhardt
- Gustave Roussy Cancer Campus, Villejuif, France.,Faculty of Medicine, Université Paris-Saclay, Kremlin-Bicêtre, France.,INSERM, U1030, Villejuif, France
| | - Allan Sauvat
- Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM, U1138, Paris, France.,Gustave Roussy Cancer Campus, Villejuif, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Ariane Mogha
- Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM, U1138, Paris, France.,Gustave Roussy Cancer Campus, Villejuif, France.,Faculty of Medicine, Université Paris-Saclay, Kremlin-Bicêtre, France
| | - Alberto Ortiz
- Laboratory of Nephrology, IIS-Fundacion Jimenez Diaz UAM and REDINREN, Madrid, Spain
| | - Guido Kroemer
- Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM, U1138, Paris, France.,Gustave Roussy Cancer Campus, Villejuif, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Université Pierre et Marie Curie, Paris, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.,Department of Women's and Children's Health, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Nazanine Modjtahedi
- Gustave Roussy Cancer Campus, Villejuif, France.,Faculty of Medicine, Université Paris-Saclay, Kremlin-Bicêtre, France.,INSERM, U1030, Villejuif, France
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38
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Hu Y, Hu L, Gong D, Lu H, Xuan Y, Wang R, Wu D, Chen D, Zhang K, Gao F, Che L. Genome-wide DNA methylation analysis in jejunum of Sus scrofa with intrauterine growth restriction. Mol Genet Genomics 2018; 293:807-818. [PMID: 29392408 PMCID: PMC6061055 DOI: 10.1007/s00438-018-1422-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/27/2018] [Indexed: 01/01/2023]
Abstract
Intrauterine growth restriction (IUGR) may elicit a series of postnatal body developmental and metabolic diseases due to their impaired growth and development in the mammalian embryo/fetus during pregnancy. In the present study, we hypothesized that IUGR may lead to abnormally regulated DNA methylation in the intestine, causing intestinal dysfunctions. We applied reduced representation bisulfite sequencing (RRBS) technology to study the jejunum tissues from four newborn IUGR piglets and their normal body weight (NBW) littermates. The results revealed extensively regional DNA methylation changes between IUGR/NBW pairs from different gilts, affecting dozens of genes. Hiseq-based bisulfite sequencing PCR (Hiseq-BSP) was used for validations of 19 genes with epigenetic abnormality, confirming three genes (AIFM1, MTMR1, and TWIST2) in extra samples. Furthermore, integrated analysis of these 19 genes with proteome data indicated that there were three main genes (BCAP31, IRAK1, and AIFM1) interacting with important immunity- or metabolism-related proteins, which could explain the potential intestinal dysfunctions of IUGR piglets. We conclude that IUGR can lead to disparate DNA methylation in the intestine and these changes may affect several important biological processes such as cell apoptosis, cell differentiation, and immunity, which provides more clues linking IUGR and its long-term complications.
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Affiliation(s)
- Yue Hu
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Liang Hu
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Desheng Gong
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hanlin Lu
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yue Xuan
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Ru Wang
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - De Wu
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Daiwen Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Keying Zhang
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Fei Gao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Lianqiang Che
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.
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Abstract
Impaired mitochondrial energy metabolism contributes to a wide range of pathologic conditions, including neurodegenerative diseases. Mitochondrial apoptosis-inducing factor (AIF) is required for the correct maintenance of mitochondrial electron transport chain. An emerging body of clinical evidence indicates that several mutations in the AIFM1 gene are causally linked to severe forms of mitochondrial disorders. Here we investigate the consequence of WAH-1/AIF deficiency in the survival of the nematode Caenorhabditis elegans. Moreover, we assess the survival of C. elegans strains expressing a disease-associated WAH-1/AIF variant. We demonstrate that wah-1 downregulation compromises the function of the oxidative phosphorylation system and reduces C. elegans lifespan. Notably, the loss of respiratory subunits induces a nuclear-encoded mitochondrial stress response independently of an evident increase of oxidative stress. Overall, our data pinpoint an evolutionarily conserved role of WAH-1/AIF in the maintenance of proper mitochondrial activity.
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40
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Heimer G, Eyal E, Zhu X, Ruzzo EK, Marek-Yagel D, Sagiv D, Anikster Y, Reznik-Wolf H, Pras E, Oz Levi D, Lancet D, Ben-Zeev B, Nissenkorn A. Mutations in AIFM1 cause an X-linked childhood cerebellar ataxia partially responsive to riboflavin. Eur J Paediatr Neurol 2018; 22:93-101. [PMID: 28967629 DOI: 10.1016/j.ejpn.2017.09.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/16/2017] [Accepted: 09/11/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND AIFM1 encodes a mitochondrial flavoprotein with a dual role (NADH oxidoreductase and regulator of apoptosis), which uses riboflavin as a cofactor. Mutations in the X-linked AIFM1 were reported in relation to two main phenotypes: a severe infantile mitochondrial encephalomyopathy and an early-onset axonal sensorimotor neuropathy with hearing loss. In this paper we report two unrelated males harboring AIFM1 mutations (one of which is novel) who display distinct phenotypes including progressive ataxia which partially improved with riboflavin treatment. METHODS For both patients trio whole exome sequencing was performed. Validation and segregation were performed with Sanger sequencing. Following the diagnosis, patients were treated with up to 200 mg riboflavin/day for 12 months. Ataxia was assessed by the ICARS scale at baseline, and 6 and 12 months following treatment. RESULTS Patient 1 presented at the age of 5 years with auditory neuropathy, followed by progressive ataxia, vermian atrophy and axonal neuropathy. Patient 2 presented at the age of 4.5 years with severe limb and palatal myoclonus, followed by ataxia, cerebellar atrophy, ophthalmoplegia, sensorineural hearing loss, hyporeflexia and cardiomyopathy. Two deleterious missense mutations were found in the AIFM1 gene: p. Met340Thr mutation located in the FAD dependent oxidoreductase domain and the novel p. Thr141Ile mutation located in a highly conserved DNA binding motif. Ataxia score, decreased by 39% in patient 1 and 20% in patient 2 following 12 months of treatment. CONCLUSION AIFM1 mutations cause childhood cerebellar ataxia, which may be partially treatable in some patients with high dose riboflavin.
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Affiliation(s)
- G Heimer
- Pediatric Neurology Unit, Edmond and Lilly Safra Children Hospital, Chaim Sheba Medical Center, 52621 Ramat Gan, Israel; Pinchas Borenstein Talpiot Medical Leadership Program, Chaim Sheba Medical Center, 52621 Ramat Gan, Israel; The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - E Eyal
- Cancer Research Center, Pediatric Hemato/oncology Unit, Edmond and Lily Children's Hospital, Chaim Sheba Medical Center, 52621 Ramat Gan, Israel
| | - X Zhu
- Institute for Genomic Medicine, Columbia University Medical School, Columbia University Medical Center, New York, NY 10032, USA
| | - E K Ruzzo
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, USA
| | - D Marek-Yagel
- The Metabolic Disorder Unit, Edmond and Lilly Safra Children Hospital, Chaim Sheba Medical Center, 52621 Ramat Gan, Israel
| | - Doron Sagiv
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Otolaryngology Head and Neck Surgery, Chaim Sheba Medical Center, 52621 Ramat Gan, Israel
| | - Y Anikster
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; The Metabolic Disorder Unit, Edmond and Lilly Safra Children Hospital, Chaim Sheba Medical Center, 52621 Ramat Gan, Israel
| | - H Reznik-Wolf
- Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, 52621 Ramat Gan, Israel
| | - E Pras
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, 52621 Ramat Gan, Israel
| | - D Oz Levi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - D Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - B Ben-Zeev
- Pediatric Neurology Unit, Edmond and Lilly Safra Children Hospital, Chaim Sheba Medical Center, 52621 Ramat Gan, Israel; The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - A Nissenkorn
- Pediatric Neurology Unit, Edmond and Lilly Safra Children Hospital, Chaim Sheba Medical Center, 52621 Ramat Gan, Israel; The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; The Service for Rare Disorders, Edmond and Lilly Safra Children Hospital, Chaim Sheba Medical Center, 52621 Ramat Gan, Israel.
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41
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A newly distal hereditary motor neuropathy caused by a rare AIFM1 mutation. Neurogenetics 2017; 18:245-250. [DOI: 10.1007/s10048-017-0524-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/14/2017] [Indexed: 11/25/2022]
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42
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Miyake N, Wolf NI, Cayami FK, Crawford J, Bley A, Bulas D, Conant A, Bent SJ, Gripp KW, Hahn A, Humphray S, Kimura-Ohba S, Kingsbury Z, Lajoie BR, Lal D, Micha D, Pizzino A, Sinke RJ, Sival D, Stolte-Dijkstra I, Superti-Furga A, Ulrick N, Taft RJ, Ogata T, Ozono K, Matsumoto N, Neubauer BA, Simons C, Vanderver A. X-linked hypomyelination with spondylometaphyseal dysplasia (H-SMD) associated with mutations in AIFM1. Neurogenetics 2017; 18:185-194. [PMID: 28842795 PMCID: PMC5705759 DOI: 10.1007/s10048-017-0520-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/04/2017] [Indexed: 01/12/2023]
Abstract
An X-linked condition characterized by the combination of hypomyelinating leukodystrophy and spondylometaphyseal dysplasia (H-SMD) has been observed in only four families, with linkage to Xq25-27, and recent genetic characterization in two families with a common AIFM1 mutation. In our study, 12 patients (6 families) with H-SMD were identified and underwent comprehensive assessment accompanied by whole-exome sequencing (WES). Pedigree analysis in all families was consistent with X-linked recessive inheritance. Presentation typically occurred between 12 and 36 months. In addition to the two disease-defining features of spondylometaphyseal dysplasia and hypomyelination on MRI, common clinical signs and symptoms included motor deterioration, spasticity, tremor, ataxia, dysarthria, cognitive defects, pulmonary hypertension, nystagmus, and vision loss due to retinopathy. The course of the disease was slowly progressive. All patients had maternally inherited or de novo mutations in or near exon 7 of AIFM1, within a region of 70 bp, including synonymous and intronic changes. AIFM1 mutations have previously been associated with neurologic presentations as varied as intellectual disability, hearing loss, neuropathy, and striatal necrosis, while AIFM1 mutations in this small region present with a distinct phenotype implicating bone. Analysis of cell lines derived from four patients identified significant reductions in AIFM1 mRNA and protein levels in osteoblasts. We hypothesize that AIFM1 functions in bone metabolism and myelination and is responsible for the unique phenotype in this condition.
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Affiliation(s)
- Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Nicole I Wolf
- Department of Child Neurology, and Amsterdam Neuroscience, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.
| | - Ferdy K Cayami
- Department of Child Neurology, and Amsterdam Neuroscience, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.,Department of Clinical Genetics, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.,Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Annette Bley
- University Children's Hospital, University Medical Center Hamburg Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Dorothy Bulas
- Department of Diagnostic Imaging and Radiology, Children's National Medical Center, Washington, DC, USA
| | - Alex Conant
- Department of Neurology, Children's National Medical Center, Suite 4800, Washington, DC, USA
| | - Stephen J Bent
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Karen W Gripp
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Andreas Hahn
- Department of Pediatric Neurology, Univ.-Klinikum Giessen/Marburg; Standort Giessen, Feulgenstr. 12, 35389, Giessen, Germany
| | - Sean Humphray
- Chesterford Research Park, Illumina, Inc., Little Chesterford, CB10 1XL, UK
| | - Shihoko Kimura-Ohba
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Zoya Kingsbury
- Chesterford Research Park, Illumina, Inc., Little Chesterford, CB10 1XL, UK
| | | | - Dennis Lal
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, USA
| | - Dimitra Micha
- Department of Clinical Genetics, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
| | - Amy Pizzino
- Department of Neurology, Children's National Medical Center, Suite 4800, Washington, DC, USA
| | - Richard J Sinke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Deborah Sival
- Department of Child Neurology, University Hospital Groningen, Groningen, Netherlands
| | - Irene Stolte-Dijkstra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne, Lausanne, Switzerland
| | - Nicole Ulrick
- Department of Neurology, Children's National Medical Center, Suite 4800, Washington, DC, USA
| | - Ryan J Taft
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.,Illumina, Inc, San Diego, CA, USA.,George Washington University School of Medicine, Washington, DC, USA
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Keiichi Ozono
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Bernd A Neubauer
- Department of Pediatric Neurology, Univ.-Klinikum Giessen/Marburg; Standort Giessen, Feulgenstr. 12, 35389, Giessen, Germany
| | - Cas Simons
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Adeline Vanderver
- Department of Neurology, Children's National Medical Center, Suite 4800, Washington, DC, USA.,Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne, Lausanne, Switzerland.,Children's Hospital of Philadelphia, Philadelphia, PA, USA
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Sorrentino L, Cossu F, Milani M, Aliverti A, Mastrangelo E. Structural bases of the altered catalytic properties of a pathogenic variant of apoptosis inducing factor. Biochem Biophys Res Commun 2017; 490:1011-1017. [PMID: 28666871 DOI: 10.1016/j.bbrc.2017.06.156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 10/19/2022]
Abstract
The apoptosis-inducing factor (AIF) is a FAD-containing protein playing critical roles in caspase-independent apoptosis and mitochondrial respiratory chain biogenesis and maintenance. While its lethal role is well known, the details of its mitochondrial function remain elusive. So far, nineteen allelic variants of AIF have been associated to human diseases, mainly affecting the nervous system. A strict correlation is emerging between the degree of impairment of its ability to stabilize the charge-transfer (CT) complex between FAD and NAD+ and the severity of the resulting pathology. Recently, we demonstrated that the G307E replacement in murine AIF (equivalent to the pathogenic G308E in the human protein) dramatically decreases the rate of CT complex formation through the destabilization of the flavoprotein interaction with NAD(H). To provide further insights into the structural bases of its altered functional properties, here we report the first crystal structure of an AIF pathogenic mutant variant in complex with NAD+ (murine AIF-G307ECT) in comparison with its oxidized form. With respect to wild type AIF, the mutation leads to an altered positioning of NAD+ adenylate moiety, which slows down CT complex formation. Moreover, the altered balance between the binding of the adenine/nicotinamide portions of the coenzyme determines a large drop in AIF-G307E ability to discriminate between NADH and NADPH.
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Affiliation(s)
- Luca Sorrentino
- Biophysics Institute, National Research Council c/o Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Federica Cossu
- Biophysics Institute, National Research Council c/o Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Mario Milani
- Biophysics Institute, National Research Council c/o Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Alessandro Aliverti
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - Eloise Mastrangelo
- Biophysics Institute, National Research Council c/o Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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44
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Murillo JR, Goto-Silva L, Sánchez A, Nogueira FCS, Domont GB, Junqueira M. Quantitative proteomic analysis identifies proteins and pathways related to neuronal development in differentiated SH-SY5Y neuroblastoma cells. EUPA OPEN PROTEOMICS 2017; 16:1-11. [PMID: 29900121 PMCID: PMC5965715 DOI: 10.1016/j.euprot.2017.06.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/07/2017] [Accepted: 06/21/2017] [Indexed: 02/04/2023]
Abstract
Differentiation analysis of SH-SY5Y cells with iTRAQ strategy is proposed. Differentiated SH-SY5Y cells are more appropriated as a neuronal model. Upregulated proteins are mainly related to ECM-interaction and apoptosis. Proteins to explore as differentiation markers: AGRN, EMILIM-1, AIFM, STMN1.
SH-SY5Y neuroblastoma cells are susceptible to differentiation using retinoic acid (RA) and brain-derived neurotrophic factor (BDNF), providing a model of neuronal differentiation. We compared SH-SY5Y cells proteome before and after RA/BDNF treatment using iTRAQ and phosphopeptide enrichment strategies. We identified 5587 proteins, 366 of them with differential abundance. Differentiated cells expressed proteins related to neuronal development, and, undifferentiated cells expressed proteins involved in cell proliferation. Interactive network covered focal adhesion, cytoskeleton dynamics and neurodegenerative diseases processes and regulation of mitogen-activated protein kinase-related signaling pathways; key proteins involved in those processes might be explored as markers for neuronal differentiation.
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Affiliation(s)
- Jimmy Rodriguez Murillo
- Proteomics Unit, Chemistry Institute, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
| | - Livia Goto-Silva
- D'Or Institute for Research and Education (IDOR), 22281-100, Rio de Janeiro, Brazil
| | - Aniel Sánchez
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden.,Center of Excellence in Biological and Medical Mass Spectrometry, Biomedical Center D13, Lund University, 221 84 Lund, Sweden
| | - Fábio C S Nogueira
- Proteomics Unit, Chemistry Institute, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
| | - Gilberto B Domont
- Proteomics Unit, Chemistry Institute, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
| | - Magno Junqueira
- Proteomics Unit, Chemistry Institute, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
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45
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Morton SU, Prabhu SP, Lidov HGW, Shi J, Anselm I, Brownstein CA, Bainbridge MN, Beggs AH, Vargas SO, Agrawal PB. AIFM1 mutation presenting with fatal encephalomyopathy and mitochondrial disease in an infant. Cold Spring Harb Mol Case Stud 2017; 3:a001560. [PMID: 28299359 PMCID: PMC5334471 DOI: 10.1101/mcs.a001560] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/29/2016] [Indexed: 12/11/2022] Open
Abstract
Apoptosis-inducing factor mitochondrion-associated 1 (AIFM1), encoded by the gene AIFM1, has roles in electron transport, apoptosis, ferredoxin metabolism, reactive oxygen species generation, and immune system regulation. Here we describe a patient with a novel AIFM1 variant presenting unusually early in life with mitochondrial disease, rapid deterioration, and death. Autopsy, at the age of 4 mo, revealed features of mitochondrial encephalopathy, myopathy, and involvement of peripheral nerves with axonal degeneration. In addition, there was microvesicular steatosis in the liver, thymic noninvolution, follicular bronchiolitis, and pulmonary arterial medial hypertrophy. This report adds to the clinical and pathological spectrum of disease related to AIFM1 mutations and provides insights into the role of AIFM1 in cellular function.
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Affiliation(s)
- Sarah U Morton
- Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sanjay P Prabhu
- Department of Radiology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hart G W Lidov
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jiahai Shi
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR
| | - Irina Anselm
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Matthew N Bainbridge
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
- Codified Genomics LLC, Houston, Texas 77004, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sara O Vargas
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Pankaj B Agrawal
- Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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46
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Brosey CA, Ho C, Long WZ, Singh S, Burnett K, Hura GL, Nix JC, Bowman GR, Ellenberger T, Tainer JA. Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor. Structure 2016; 24:2067-2079. [PMID: 27818101 DOI: 10.1016/j.str.2016.09.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/08/2016] [Accepted: 10/05/2016] [Indexed: 01/07/2023]
Abstract
Apoptosis-inducing factor (AIF) is critical for mitochondrial respiratory complex biogenesis and for mediating necroptotic parthanatos; these functions are seemingly regulated by enigmatic allosteric switching driven by NADH charge-transfer complex (CTC) formation. Here, we define molecular pathways linking AIF's active site to allosteric switching regions by characterizing dimer-permissive mutants using small-angle X-ray scattering (SAXS) and crystallography and by probing AIF-CTC communication networks using molecular dynamics simulations. Collective results identify two pathways propagating allostery from the CTC active site: (1) active-site H454 links to S480 of AIF's central β-strand to modulate a hydrophobic border at the dimerization interface, and (2) an interaction network links AIF's FAD cofactor, central β-strand, and Cβ-clasp whereby R529 reorientation initiates C-loop release during CTC formation. This knowledge of AIF allostery and its flavoswitch mechanism provides a foundation for biologically understanding and biomedically controlling its participation in mitochondrial homeostasis and cell death.
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Affiliation(s)
- Chris A Brosey
- Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
| | - Chris Ho
- Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Winnie Z Long
- Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sukrit Singh
- Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kathryn Burnett
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Greg L Hura
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jay C Nix
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Gregory R Bowman
- Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tom Ellenberger
- Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John A Tainer
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
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