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Abbasi S, Sinha S, Labit E, Rosin NL, Yoon G, Rahmani W, Jaffer A, Sharma N, Hagner A, Shah P, Arora R, Yoon J, Islam A, Uchida A, Chang CK, Stratton JA, Scott RW, Rossi FMV, Underhill TM, Biernaskie J. Distinct Regulatory Programs Control the Latent Regenerative Potential of Dermal Fibroblasts during Wound Healing. Cell Stem Cell 2020; 27:396-412.e6. [PMID: 32755548 DOI: 10.1016/j.stem.2020.07.008] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/25/2020] [Accepted: 07/09/2020] [Indexed: 01/12/2023]
Abstract
Dermal fibroblasts exhibit considerable heterogeneity during homeostasis and in response to injury. Defining lineage origins of reparative fibroblasts and regulatory programs that drive fibrosis or, conversely, promote regeneration will be essential for improving healing outcomes. Using complementary fate-mapping approaches, we show that hair follicle mesenchymal progenitors make limited contributions to wound repair. In contrast, extrafollicular progenitors marked by the quiescence-associated factor Hic1 generated the bulk of reparative fibroblasts and exhibited functional divergence, mediating regeneration in the center of the wound neodermis and scar formation in the periphery. Single-cell RNA-seq revealed unique transcriptional, regulatory, and epithelial-mesenchymal crosstalk signatures that enabled mesenchymal competence for regeneration. Integration with scATAC-seq highlighted changes in chromatin accessibility within regeneration-associated loci. Finally, pharmacological modulation of RUNX1 and retinoic acid signaling or genetic deletion of Hic1 within wound-activated fibroblasts was sufficient to modulate healing outcomes, suggesting that reparative fibroblasts have latent but modifiable regenerative capacity.
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Bis-Brewer DM, Gan-Or Z, Sleiman P, Hakonarson H, Fazal S, Courel S, Cintra V, Tao F, Estiar MA, Tarnopolsky M, Boycott KM, Yoon G, Suchowersky O, Dupré N, Cheng A, Lloyd TE, Rouleau G, Schüle R, Züchner S. Assessing non-Mendelian inheritance in inherited axonopathies. Genet Med 2020; 22:2114-2119. [PMID: 32741968 PMCID: PMC7710562 DOI: 10.1038/s41436-020-0924-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 01/05/2023] Open
Abstract
PURPOSE Inherited axonopathies (IA) are rare, clinically and genetically heterogeneous diseases that lead to length-dependent degeneration of the long axons in central (hereditary spastic paraplegia [HSP]) and peripheral (Charcot-Marie-Tooth type 2 [CMT2]) nervous systems. Mendelian high-penetrance alleles in over 100 different genes have been shown to cause IA; however, about 50% of IA cases do not receive a genetic diagnosis. A more comprehensive spectrum of causative genes and alleles is warranted, including causative and risk alleles, as well as oligogenic multilocus inheritance. METHODS Through international collaboration, IA exome studies are beginning to be sufficiently powered to perform a pilot rare variant burden analysis. After extensive quality control, our cohort contained 343 CMT cases, 515 HSP cases, and 935 non-neurological controls. We assessed the cumulative mutational burden across disease genes, explored the evidence for multilocus inheritance, and performed an exome-wide rare variant burden analysis. RESULTS We replicated the previously described mutational burden in a much larger cohort of CMT cases, and observed the same effect in HSP cases. We identified a preliminary risk allele for CMT in the EXOC4 gene (p value= 6.9 × 10-6, odds ratio [OR] = 2.1) and explored the possibility of multilocus inheritance in IA. CONCLUSION Our results support the continuing emergence of complex inheritance mechanisms in historically Mendelian disorders.
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Stratton JA, Eaton S, Rosin NL, Jawad S, Holmes A, Yoon G, Midha R, Biernaskie J. Macrophages and Associated Ligands in the Aged Injured Nerve: A Defective Dynamic That Contributes to Reduced Axonal Regrowth. Front Aging Neurosci 2020; 12:174. [PMID: 32595489 PMCID: PMC7304384 DOI: 10.3389/fnagi.2020.00174] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/19/2020] [Indexed: 01/08/2023] Open
Abstract
The regenerative capacity of injured peripheral nerves is diminished with aging. To identify factors that contribute to this impairment, we compared the immune cell response in young vs. aged animals following nerve injury. First, we confirmed that macrophage accumulation is delayed in aged injured nerves which is due to defects in monocyte migration as a result of defects in site-specific recruitment signals in the aged nerve. Interestingly, impairment in both macrophage accumulation and functional recovery could be overcome by transplanting bone marrow from aged animals into young mice. That is, upon exposure to a youthful environment, monocytes/macrophages originating from the aged bone marrow behaved similarly to young cells. Transcriptional profiling of aged macrophages following nerve injury revealed that both pro- and anti-inflammatory genes were largely downregulated in aged compared to young macrophages. One ligand of particular interest was macrophage-associated secreted protein (MCP1), which exhibited a potent role in regulating aged axonal regrowth in vitro. Given that macrophage-derived MCP1 is significantly diminished in the aged injured nerve, our data suggest that age-associated defects in MCP1 signaling could contribute to the regenerative deficits that occur in the aged nervous system.
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Maio N, Ghosh MC, Costain G, Carnevale A, Si Y, Yoon G, Rouault TA. Reply: IREB2-associated neurodegeneration. Brain 2020; 142:e41. [PMID: 31243430 DOI: 10.1093/brain/awz185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Gauquelin L, Hawkins C, Tam EWY, Miller SP, Yoon G. Pearls & Oy-sters: Fatal brain edema is a rare complication of severe CACNA1A-related disorder. Neurology 2020; 94:631-634. [PMID: 32170034 DOI: 10.1212/wnl.0000000000009223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Costain G, Ghosh MC, Maio N, Carnevale A, Si YC, Rouault TA, Yoon G. Absence of iron-responsive element-binding protein 2 causes a novel neurodegenerative syndrome. Brain 2020; 142:1195-1202. [PMID: 30915432 DOI: 10.1093/brain/awz072] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/07/2019] [Accepted: 01/31/2019] [Indexed: 11/13/2022] Open
Abstract
Disruption of cellular iron homeostasis can contribute to neurodegeneration. In mammals, two iron-regulatory proteins (IRPs) shape the expression of the iron metabolism proteome. Targeted deletion of Ireb2 in a mouse model causes profoundly disordered iron metabolism, leading to functional iron deficiency, anemia, erythropoietic protoporphyria, and a neurodegenerative movement disorder. Using exome sequencing, we identified the first human with bi-allelic loss-of-function variants in the gene IREB2 leading to an absence of IRP2. This 16-year-old male had neurological and haematological features that emulate those of Ireb2 knockout mice, including neurodegeneration and a treatment-resistant choreoathetoid movement disorder. Cellular phenotyping at the RNA and protein level was performed using patient and control lymphoblastoid cell lines, and established experimental assays. Our studies revealed functional iron deficiency, altered post-transcriptional regulation of iron metabolism genes, and mitochondrial dysfunction, as observed in the mouse model. The patient's cellular abnormalities were reversed by lentiviral-mediated restoration of IRP2 expression. These results confirm that IRP2 is essential for regulation of iron metabolism in humans, and reveal a previously unrecognized subclass of neurodegenerative disease. Greater understanding of how the IRPs mediate cellular iron distribution may ultimately provide new insights into common and rare neurodegenerative processes, and could result in novel therapies.
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Xiong E, Lynch AE, Corben LA, Delatycki MB, Subramony SH, Bushara K, Gomez CM, Hoyle JC, Yoon G, Ravina B, Mathews KD, Wilmot G, Zesiewicz T, Susan Perlman M, Farmer JM, Rummey C, Lynch DR. Health related quality of life in Friedreich Ataxia in a large heterogeneous cohort. J Neurol Sci 2019; 410:116642. [PMID: 31901720 DOI: 10.1016/j.jns.2019.116642] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/09/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022]
Abstract
INTRODUCTION This study assessed the Health Related Quality of Life (HRQOL) of individuals with Friedreich Ataxia (FRDA) through responses to HRQOL questionnaires. METHODS The SF-36, a generic HRQOL instrument, and symptom specific scales examining vision, fatigue, pain and bladder function were administered to individuals with FRDA and analyzed by comparison with disease features. Multiple linear regression models were used to study independent effects of genetic severity and age. Assessments were performed at baseline then intermittently after that. RESULTS Subjects were on average young adults. For the SF36, the subscale with the lowest HRQOL score was the physical function scale, while the emotional well-being score was the highest. The physical function scale correlated with age of onset, duration, and subject age. In assessment of symptom specific scales, bladder control scores (BLCS) correlated with duration and age, while impact of visual impairment scores (IVIS) correlated with duration. In linear regression models, the BLCS, Pain Effect Score, and IVIS scores were predicted by age and GAA length; modified fatigue impact scale scores were predicted only by GAA length. Physical function and role limitation scores declined over time. No change was seen over time in other SF-36 subscores. Symptom specific scales also worsened over time, most notably the IVIS and BLCS. CONCLUSION The SF-36 and symptom specific scales capture dysfunction in FRDA in a manner that reflects disease status. HRQOL dysfunction was greatest on physically related scales; such scales correlated with disease duration, indicating that they worsen with progressing disease.
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Agabalyan NA, Sparks HD, Tarraf S, Rosin NL, Anker K, Yoon G, Burnett LN, Nickerson D, Di Martino ES, Gabriel VA, Biernaskie J. Adult Human Dermal Progenitor Cell Transplantation Modulates the Functional Outcome of Split-Thickness Skin Xenografts. Stem Cell Reports 2019; 13:1068-1082. [PMID: 31735655 PMCID: PMC6915850 DOI: 10.1016/j.stemcr.2019.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 02/01/2023] Open
Abstract
Following full-thickness skin injuries, epithelialization of the wound is essential. The standard of care to achieve this wound "closure" in patients is autologous split-thickness skin grafting (STSG). However, patients living with STSGs report significant chronic impairments leading to functional deficiencies such as itch, altered sensation, fragility, hypertrophic scarring, and contractures. These features are attributable to the absence of functional dermis combined with the formation of disorganized fibrotic extracellular matrix. Recent work has demonstrated the existence of dermal progenitor cells (DPCs) residing within hair follicles that function to continuously regenerate mesenchymal tissue. The present work examines whether cultured DPCs could regenerate dermis within an STSG and improve overall graft function. Adult human DPCs were transplanted into a full-thickness skin wound in immune-compromised mice and closed with a human STSG. At 3 months, human DPCs (hDPCs) had successfully integrated into the xenograft and differentiated into various regionally specified phenotypes, improving both viscoelastic properties of the graft and mitigating pruritus.
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Donkervoort S, Sabouny R, Yun P, Gauquelin L, Chao KR, Hu Y, Al Khatib I, Töpf A, Mohassel P, Cummings BB, Kaur R, Saade D, Moore SA, Waddell LB, Farrar MA, Goodrich JK, Uapinyoying P, Chan SS, Javed A, Leach ME, Karachunski P, Dalton J, Medne L, Harper A, Thompson C, Thiffault I, Specht S, Lamont RE, Saunders C, Racher H, Bernier FP, Mowat D, Witting N, Vissing J, Hanson R, Coffman KA, Hainlen M, Parboosingh JS, Carnevale A, Yoon G, Schnur RE, Boycott KM, Mah JK, Straub V, Foley AR, Innes AM, Bönnemann CG, Shutt TE. MSTO1 mutations cause mtDNA depletion, manifesting as muscular dystrophy with cerebellar involvement. Acta Neuropathol 2019; 138:1013-1031. [PMID: 31463572 PMCID: PMC6851037 DOI: 10.1007/s00401-019-02059-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/25/2019] [Accepted: 08/08/2019] [Indexed: 01/12/2023]
Abstract
MSTO1 encodes a cytosolic mitochondrial fusion protein, misato homolog 1 or MSTO1. While the full genotype–phenotype spectrum remains to be explored, pathogenic variants in MSTO1 have recently been reported in a small number of patients presenting with a phenotype of cerebellar ataxia, congenital muscle involvement with histologic findings ranging from myopathic to dystrophic and pigmentary retinopathy. The proposed underlying pathogenic mechanism of MSTO1-related disease is suggestive of impaired mitochondrial fusion secondary to a loss of function of MSTO1. Disorders of mitochondrial fusion and fission have been shown to also lead to mitochondrial DNA (mtDNA) depletion, linking them to the mtDNA depletion syndromes, a clinically and genetically diverse class of mitochondrial diseases characterized by a reduction of cellular mtDNA content. However, the consequences of pathogenic variants in MSTO1 on mtDNA maintenance remain poorly understood. We present extensive phenotypic and genetic data from 12 independent families, including 15 new patients harbouring a broad array of bi-allelic MSTO1 pathogenic variants, and we provide functional characterization from seven MSTO1-related disease patient fibroblasts. Bi-allelic loss-of-function variants in MSTO1 manifest clinically with a remarkably consistent phenotype of childhood-onset muscular dystrophy, corticospinal tract dysfunction and early-onset non-progressive cerebellar atrophy. MSTO1 protein was not detectable in the cultured fibroblasts of all seven patients evaluated, suggesting that pathogenic variants result in a loss of protein expression and/or affect protein stability. Consistent with impaired mitochondrial fusion, mitochondrial networks in fibroblasts were found to be fragmented. Furthermore, all fibroblasts were found to have depletion of mtDNA ranging from 30 to 70% along with alterations to mtDNA nucleoids. Our data corroborate the role of MSTO1 as a mitochondrial fusion protein and highlight a previously unrecognized link to mtDNA regulation. As impaired mitochondrial fusion is a recognized cause of mtDNA depletion syndromes, this novel link to mtDNA depletion in patient fibroblasts suggests that MSTO1-deficiency should also be considered a mtDNA depletion syndrome. Thus, we provide mechanistic insight into the disease pathogenesis associated with MSTO1 mutations and further define the clinical spectrum and the natural history of MSTO1-related disease.
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Nannini DR, Joyce BT, Zheng Y, Gao T, Liu L, Yoon G, Huan T, Ma J, Jacobs DR, Wilkins JT, Ren J, Zhang K, Khan SS, Allen NB, Horvath S, Lloyd-Jones DM, Greenland P, Hou L. Epigenetic age acceleration and metabolic syndrome in the coronary artery risk development in young adults study. Clin Epigenetics 2019; 11:160. [PMID: 31730017 PMCID: PMC6858654 DOI: 10.1186/s13148-019-0767-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/18/2019] [Indexed: 12/27/2022] Open
Abstract
Background The metabolic syndrome (MetS) is a collection of metabolic disturbances that can lead to various cardiovascular diseases. Previous studies have shown a more adverse metabolic risk profile is associated with more advanced biological aging. The associations between epigenetic biomarkers of age with MetS, however, are not well understood. We therefore investigated the associations between epigenetic age acceleration and MetS severity score and incident MetS. Results A subset of study participants with available whole blood at examination years 15 and 20 from the Coronary Artery Risk Development in Young Adults Study underwent epigenomic profiling using the Illumina MethylationEPIC Beadchip (~ 850,000 sites). Intrinsic and extrinsic epigenetic age acceleration (IEAA and EEAA) were calculated from DNA methylation levels. The MetS severity score was positively associated with IEAA at years 15 (P = 0.016) and 20 (P = 0.016) and EEAA at year 20 (P = 0.040) in cross-sectional analysis. IEAA at year 20 was significantly associated with incident MetS at year 30 (OR = 1.05 [95% CI 1.01, 1.10], P = 0.028). Conclusions To our knowledge, this is the first report of the longitudinal association between epigenetic age acceleration and MetS. These findings suggest that a higher MetS severity score is associated with accelerated epigenetic aging and such aging may play a role in the development of metabolic disorders, potentially serving as a useful biomarker of and early detection tool for future MetS.
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Gauquelin L, Cayami FK, Sztriha L, Yoon G, Tran LT, Guerrero K, Hocke F, van Spaendonk RML, Fung EL, D'Arrigo S, Vasco G, Thiffault I, Niyazov DM, Person R, Lewis KS, Wassmer E, Prescott T, Fallon P, McEntagart M, Rankin J, Webster R, Philippi H, van de Warrenburg B, Timmann D, Dixit A, Searle C, Thakur N, Kruer MC, Sharma S, Vanderver A, Tonduti D, van der Knaap MS, Bertini E, Goizet C, Fribourg S, Wolf NI, Bernard G. Clinical spectrum of POLR3-related leukodystrophy caused by biallelic POLR1C pathogenic variants. NEUROLOGY-GENETICS 2019; 5:e369. [PMID: 32042905 PMCID: PMC6927361 DOI: 10.1212/nxg.0000000000000369] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/18/2019] [Indexed: 11/15/2022]
Abstract
Objective To determine the clinical, radiologic, and molecular characteristics of RNA polymerase III-related leukodystrophy (POLR3-HLD) caused by biallelic POLR1C pathogenic variants. Methods A cross-sectional observational study involving 25 centers worldwide was conducted. Clinical and molecular information was collected on 23 unreported and previously reported patients with POLR3-HLD and biallelic pathogenic variants in POLR1C. Brain MRI studies were reviewed. Results Fourteen female and 9 male patients aged 7 days to 23 years were included in the study. Most participants presented early in life (birth to 6 years), and motor deterioration was seen during childhood. A notable proportion of patients required a wheelchair before adolescence, suggesting a more severe phenotype than previously described in POLR3-HLD. Dental, ocular, and endocrine features were not invariably present (70%, 50%, and 50%, respectively). Five patients (22%) had a combination of hypomyelinating leukodystrophy and abnormal craniofacial development, including 1 individual with clear Treacher Collins syndrome (TCS) features. Brain MRI revealed hypomyelination in all cases, often with areas of pronounced T2 hyperintensity corresponding to T1 hypointensity of the white matter. Twenty-nine different pathogenic variants (including 12 new disease-causing variants) in POLR1C were identified. Conclusions This study provides a comprehensive description of POLR3-HLD caused by biallelic POLR1C pathogenic variants based on the largest cohort of patients to date. These results suggest distinct characteristics of POLR1C-related disorder, with a spectrum of clinical involvement characterized by hypomyelinating leukodystrophy with or without abnormal craniofacial development reminiscent of TCS.
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Rummey C, Corben LA, Delatycki MB, Subramony SH, Bushara K, Gomez CM, Hoyle JC, Yoon G, Ravina B, Mathews KD, Wilmot G, Zesiewicz T, Perlman S, Farmer JM, Lynch DR. Psychometric properties of the Friedreich Ataxia Rating Scale. NEUROLOGY-GENETICS 2019; 5:371. [PMID: 32042904 PMCID: PMC6927357 DOI: 10.1212/nxg.0000000000000371] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/23/2019] [Indexed: 11/18/2022]
Abstract
Objective To investigate the psychometric properties of the Friedreich Ataxia Rating Scale neurologic examination (FARSn) and its subscores, as well as the influence of the modifications resulting in the now widely used modified FARS (mFARS) examination. Methods Based on cross-sectional FARS data from the FA–Clinical Outcome Measures cohort, we conducted correlation-based psychometric analyses to investigate the interplay of items and subscores within the FARSn/mFARS constructs. Results The results provide support for both the FARSn and the mFARS constructs, as well as individually for their upper limb and lower limb coordination components. The omission of the peripheral nervous system subscore (D) and 2 items of the bulbar subscore (A) in the mFARS strengthens the overall construct compared with the complete FARS. Conclusions A correlation-based psychometric analysis of the neurologic FARSn score justifies the overall validity of the scale. In addition, omission of items of limited functional significance as created in the mFARS improves the features of the measures. Such information is crucial to the ongoing application of the mFARS in natural history studies and clinical trials. Additional analyses of longitudinal changes will be necessary to fully ascertain its utility, especially in nonambulant patients.
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Yoon G, Estañ M, Fernandez-Nuñez E, Zak M, Esteban M, Donkervoort S, Hawkins C, Caparros-Martin J, Saade D, Hu Y, Bolduc V, Chao K, Otaify G, Temtamy S, Aglan M, Issa M, Bönnemann C, Lapunzina P, Ruiz-Perez V. NEW GENES AND DISEASES. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Mahjoub A, Cihlarova Z, Tétreault M, MacNeil L, Sondheimer N, Caldecott KW, Hanzlikova H, Yoon G. Homozygous pathogenic variant in BRAT1 associated with nonprogressive cerebellar ataxia. NEUROLOGY-GENETICS 2019; 5:e359. [PMID: 31742228 PMCID: PMC6773431 DOI: 10.1212/nxg.0000000000000359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/29/2019] [Indexed: 11/16/2022]
Abstract
Objective To investigate the pathogenicity of a novel homozygous BRAT1 variant in 2 siblings with nonprogressive cerebellar ataxia (NPCA) through functional studies on primary and immortalized patient cell lines. Methods BRAT1 protein levels and ataxia-telangiectasia mutated (ATM) kinase activity in patient-derived and control cell lines were assessed by Western blotting. The impact of the novel BRAT1 variants on mitochondrial function was also assessed, by comparing patient and control cell lines for rates of oxygen consumption and for phosphorylation (S293) of the E1⍺ subunit of pyruvate dehydrogenase (PDH). Results Two male siblings with NPCA, mild intellectual disability, and isolated cerebellar atrophy were found to be homozygous for a c.185T>A (p.Val62Glu) variant in BRAT1 by whole exome sequencing. Western blotting revealed markedly decreased BRAT1 protein levels in lymphocytes and/or fibroblast cells from both affected siblings compared to control cell lines. There were no differences between the patient and control cells in ATM kinase activation, following ionizing radiation. Mitochondrial studies were initially suggestive of a defect in regulation of PDH activity, but there was no evidence of increased phosphorylation of the E1⍺ subunit of the PDH complex. Measurement of oxygen consumption rates similarly failed to identify differences between patient and control cells. Conclusions Biallelic pathogenic variants in BRAT1 can be associated with NPCA, a phenotype considerably milder than previously reported. Surprisingly, despite the molecular role currently proposed for BRAT1 in ATM regulation, this disorder is unlikely to result from defective ATM kinase or mitochondrial dysfunction.
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Chong M, Yoon G, Susan-Resiga D, Chamberland A, Cheillan D, Paré G, Seidah NG. Hypolipidaemia among patients with PMM2-CDG is associated with low circulating PCSK9 levels: a case report followed by observational and experimental studies. J Med Genet 2019; 57:11-17. [PMID: 31391289 DOI: 10.1136/jmedgenet-2019-106102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/17/2019] [Accepted: 06/30/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors are novel therapeutics for reducing low-density lipoprotein cholesterol (LDLc). While serious side-effects have not been observed in short-term clinical trials, there remain concerns that long-term PCSK9 inhibition may cause neurocognitive side-effects. METHODS AND RESULTS An adult male with childhood-onset global developmental delay, cerebellar atrophy and severe hypolipidaemia underwent extensive biochemical and genetic investigations. Initial testing revealed low circulating PCSK9 levels and a common loss-of-function PCSK9 polymorphism, but these findings did not fully account for severe hypolipidaemia. Whole-exome sequencing was subsequently performed and identified two pathogenic phosphomannose mutase 2 (PMM2) variants (p.Arg141His and p.Pro69Ser) known to cause PMM2-associated congenital disorder of glycosylation (PMM2-CDG). A diagnosis of PMM2-CDG was consistent with the proband's neurological symptoms and severe hypolipidaemia. Given that PMM2-CDG is characterised by defective protein N-glycosylation and that PCSK9 is a negative regulator of LDLc, we postulated that loss of PCSK9 N-glycosylation mediates hypolipidaemia among patients with PMM2-CDG. First, in an independent cohort of patients with PMM2-CDG (N=8), we verified that circulating PCSK9 levels were significantly lower in patients than controls (p=0.0006). Second, we conducted in vitro experiments in hepatocyte-derived cells to evaluate the effects of PCSK9 N-glycosylation loss on LDL receptor (LDLR) activity. Experimental results suggest that defective PCSK9 N-glycosylation reduces the ability of circulating PCSK9 to degrade LDLR. CONCLUSION Life-long exposure to genetically lower PCSK9 per se is unlikely to cause neurocognitive impairment. Both observational and experimental findings suggest that hypolipidaemia in PMM2-CDG may be partially mediated by loss of PCSK9 N-glycosylation and/or its regulators.
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Yoon G, Gaynanova I, Müller CL. Microbial Networks in SPRING - Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data. Front Genet 2019; 10:516. [PMID: 31244881 PMCID: PMC6563871 DOI: 10.3389/fgene.2019.00516] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/13/2019] [Indexed: 12/15/2022] Open
Abstract
High-throughput microbial sequencing techniques, such as targeted amplicon-based and metagenomic profiling, provide low-cost genomic survey data of microbial communities in their natural environment, ranging from marine ecosystems to host-associated habitats. While standard microbiome profiling data can provide sparse relative abundances of operational taxonomic units or genes, recent advances in experimental protocols give a more quantitative picture of microbial communities by pairing sequencing-based techniques with orthogonal measurements of microbial cell counts from the same sample. These tandem measurements provide absolute microbial count data albeit with a large excess of zeros due to limited sequencing depth. In this contribution we consider the fundamental statistical problem of estimating correlations and partial correlations from such quantitative microbiome data. To this end, we propose a semi-parametric rank-based approach to correlation estimation that can naturally deal with the excess zeros in the data. Combining this estimator with sparse graphical modeling techniques leads to the Semi-Parametric Rank-based approach for INference in Graphical model (SPRING). SPRING enables inference of statistical microbial association networks from quantitative microbiome data which can serve as high-level statistical summary of the underlying microbial ecosystem and can provide testable hypotheses for functional species-species interactions. Due to the absence of verified microbial associations we also introduce a novel quantitative microbiome data generation mechanism which mimics empirical marginal distributions of measured count data while simultaneously allowing user-specified dependencies among the variables. SPRING shows superior network recovery performance on a wide range of realistic benchmark problems with varying network topologies and is robust to misspecifications of the total cell count estimate. To highlight SPRING's broad applicability we infer taxon-taxon associations from the American Gut Project data and genus-genus associations from a recent quantitative gut microbiome dataset. We believe that, as quantitative microbiome profiling data will become increasingly available, the semi-parametric estimators for correlation and partial correlation estimation introduced here provide an important tool for reliable statistical analysis of quantitative microbiome data.
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Yoon G, Jiang W, Liu L, Shih YCT. Simple Quasi-Bayes Approach for Modeling Mean Medical Costs. Int J Biostat 2019; 16:ijb-2018-0122. [PMID: 31194679 DOI: 10.1515/ijb-2018-0122] [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: 01/05/2018] [Accepted: 04/26/2019] [Indexed: 11/15/2022]
Abstract
AbstractSeveral statistical issues associated with health care costs, such as heteroscedasticity and severe skewness, make it challenging to estimate or predict medical costs. When the interest is modeling the mean cost, it is desirable to make no assumption on the density function or higher order moments. Another challenge in developing cost prediction models is the presence of many covariates, making it necessary to apply variable selection methods to achieve a balance of prediction accuracy and model simplicity. We propose Spike-or-Slab priors for Bayesian variable selection based on asymptotic normal estimates of the full model parameters that are consistent as long as the assumption on the mean cost is satisfied. In addition, the scope of model searching can be reduced by ranking the Z-statistics. This method possesses four advantages simultaneously: robust (due to avoiding assumptions on the density function or higher order moments), parsimonious (feature of variable selection), informative (due to its Bayesian flavor, which can compare posterior probabilities of candidate models) and efficient (by reducing model searching scope with the use of Z-ranking). We apply this method to the Medical Expenditure Panel Survey dataset.
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Nimmo GAM, Venkatesh S, Pandey AK, Marshall CR, Hazrati LN, Blaser S, Ahmed S, Cameron J, Singh K, Ray PN, Suzuki CK, Yoon G. Bi-allelic mutations of LONP1 encoding the mitochondrial LonP1 protease cause pyruvate dehydrogenase deficiency and profound neurodegeneration with progressive cerebellar atrophy. Hum Mol Genet 2019; 28:290-306. [PMID: 30304514 DOI: 10.1093/hmg/ddy351] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 09/28/2018] [Indexed: 12/30/2022] Open
Abstract
LonP1 is crucial for maintaining mitochondrial proteostasis and mitigating cell stress. We identified a novel homozygous missense LONP1 variant, c.2282 C > T, (p.Pro761Leu), by whole-exome and Sanger sequencing in two siblings born to healthy consanguineous parents. Both siblings presented with stepwise regression during infancy, profound hypotonia and muscle weakness, severe intellectual disability and progressive cerebellar atrophy on brain imaging. Muscle biopsy revealed the absence of ragged-red fibers, however, scattered cytochrome c oxidase-negative staining and electron dense mitochondrial inclusions were observed. Primary cultured fibroblasts from the siblings showed normal levels of mtDNA and mitochondrial transcripts, and normal activities of oxidative phosphorylation complexes I through V. Interestingly, fibroblasts of both siblings showed glucose-repressed oxygen consumption compared to their mother, whereas galactose and palmitic acid utilization were similar. Notably, the siblings' fibroblasts had reduced pyruvate dehydrogenase (PDH) activity and elevated intracellular lactate:pyruvate ratios, whereas plasma ratios were normal. We demonstrated that in the siblings' fibroblasts, PDH dysfunction was caused by increased levels of the phosphorylated E1α subunit of PDH, which inhibits enzyme activity. Blocking E1α phosphorylation activated PDH and reduced intracellular lactate concentrations. In addition, overexpressing wild-type LonP1 in the siblings' fibroblasts down-regulated phosphoE1α. Furthermore, in vitro studies demonstrated that purified LonP1-P761L failed to degrade phosphorylated E1α, in contrast to wild-type LonP1. We propose a novel mechanism whereby homozygous expression of the LonP1-P761L variant leads to PDH deficiency and energy metabolism dysfunction, which promotes severe neurologic impairment and neurodegeneration.
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Gauquelin L, Tétreault M, Thiffault I, Farrow E, Miller N, Yoo B, Bareke E, Yoon G, Suchowersky O, Dupré N, Tarnopolsky M, Brais B, Wolf NI, Majewski J, Rouleau GA, Gan-Or Z, Bernard G. POLR3A variants in hereditary spastic paraplegia and ataxia. Brain 2019; 141:e1. [PMID: 29228109 DOI: 10.1093/brain/awx290] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Sinha S, Nuñez Martinez CM, Hartley RL, Quintana Alvarez RJ, Yoon G, Biernaskie JA, Nickerson D, Gabriel VA. Epidemiological analysis of pediatric burns in the Dominican Republic reveals a demographic profile at significant risk for electrical burns. Burns 2018; 45:471-478. [PMID: 30573295 DOI: 10.1016/j.burns.2018.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/23/2018] [Indexed: 01/19/2023]
Abstract
OBJECTIVE Pediatric burns are preventable with legislative and infrastructural changes. Although retrospective audits of many low- and middle-income countries have aided preventative efforts, the epidemiological status of burns in the Caribbean is not known. This study characterizes pediatric burns in the Dominican Republic (DR) and compares these to age-matched North American records captured by the National Burn Repository. METHODS A retrospective audit of 1600 patients admitted to the Unidad de Niños Quemados Dra. Thelma Rosario Hospital, the island's only major pediatric burn center, between January 2010 to March 2017 was performed. Epidemiological variables analyzed included age, gender, burn mechanism, year, month, city, admission duration, nationality, mortality, and %TBSA. RESULTS Pediatric burn patients in the DR sustained larger burns (8.2% vs. 6.5% TBSA) and spent more days in the hospital (10 vs. 6 days). Females were overrepresented (M:F=1:1.5) and mortality amongst admitted patients was 4-fold higher (2.8% vs. 0.7%). Electrical burns were significantly overrepresented in DR (21%) compared to age-matched North American patients (2%). Although electrical burns were smaller (4% TBSA), compared to scald (14% TBSA), and flame (19% TBSA), these burns preferred hands and had a high mortality rate (3%). No significant seasonality in burn mechanisms were observed. Finally, we report geographical and age group differences in the distribution of burn mechanisms and highlight particularly vulnerable subpopulations. CONCLUSION This investigation identifies a demographical profile where electrical burns account for a significant percentage of the burn population. This provides a basis for concentrating preventative efforts in vulnerable populations.
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Leveille E, Gonorazky HD, Rioux MF, Hazrati LN, Ruskey JA, Carnevale A, Spiegelman D, Dionne-Laporte A, Rouleau GA, Yoon G, Gan-Or Z. Triple A syndrome presenting as complicated hereditary spastic paraplegia. Mol Genet Genomic Med 2018; 6:1134-1139. [PMID: 30381913 PMCID: PMC6305671 DOI: 10.1002/mgg3.492] [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: 08/14/2018] [Revised: 09/26/2018] [Accepted: 10/05/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Hereditary spastic paraplegia (HSP) is a group of rare disorders characterized by spastic paraparesis and other symptoms. Often, other diseases can mimic HSP, which may delay diagnosis and treatment. METHODS Whole exome sequencing was performed in families with clinically suspected HSP without a genetic diagnosis. RESULTS We report three patients from two families who presented with lower limb spasticity, muscular atrophy, and other neurological symptoms, who were clinically diagnosed with complicated HSP. Whole exome sequencing revealed bi-allelic AAAS nonsense mutations; one individual was homozygous for the p.(Arg478*) mutation, and two siblings were homozygous for the p.(Arg286*) mutation, leading to the diagnosis of triple A syndrome. This rare syndrome is typically characterized by a triad of symptoms: achalasia, adrenal insufficiency, and alacrima, and is often accompanied by other neurological abnormalities. CONCLUSIONS Our findings suggest that triple A syndrome should be suspected in complicated HSP patients without a known genetic cause, especially if at least one of the main triad of triple A syndrome symptoms is present.
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McMillan HJ, Telegrafi A, Singleton A, Cho MT, Lelli D, Lynn FC, Griffin J, Asamoah A, Rinne T, Erasmus CE, Koolen DA, Haaxma CA, Keren B, Doummar D, Mignot C, Thompson I, Velsher L, Dehghani M, Vahidi Mehrjardi MY, Maroofian R, Tchan M, Simons C, Christodoulou J, Martín-Hernández E, Guillen Sacoto MJ, Henderson LB, McLaughlin H, Molday LL, Molday RS, Yoon G. Recessive mutations in ATP8A2 cause severe hypotonia, cognitive impairment, hyperkinetic movement disorders and progressive optic atrophy. Orphanet J Rare Dis 2018; 13:86. [PMID: 30012219 PMCID: PMC6048855 DOI: 10.1186/s13023-018-0825-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/15/2018] [Indexed: 12/30/2022] Open
Abstract
Background ATP8A2 mutations have recently been described in several patients with severe, early-onset hypotonia and cognitive impairment. The aim of our study was to characterize the clinical phenotype of patients with ATP8A2 mutations. Methods An observational study was conducted at multiple diagnostic centres. Clinical data is presented from 9 unreported and 2 previously reported patients with ATP8A2 mutations. We compare their features with 3 additional patients that have been previously reported in the medical literature. Results Eleven patients with biallelic ATP8A2 mutations were identified, with a mean age of 9.4 years (range 2.5–28 years). All patients with ATP8A2 mutations (100%) demonstrated developmental delay, severe hypotonia and movement disorders, specifically chorea or choreoathetosis (100%), dystonia (27%) and facial dyskinesia (18%). Optic atrophy was observed in 78% of patients for whom funduscopic examination was performed. Symptom onset in all (100%) was noted before 6 months of age, with 70% having symptoms noted at birth. Feeding difficulties were common (91%) although most patients were able to tolerate pureed or thickened feeds, and 3 patients required gastrostomy tube insertion. MRI of the brain was normal in 50% of the patients. A smaller proportion was noted to have mild cortical atrophy (30%), delayed myelination (20%) and/or hypoplastic optic nerves (20%). Functional studies were performed on differentiated induced pluripotent cells from one child, which confirmed a decrease in ATP8A2 expression compared to control cells. Conclusions ATP8A2 gene mutations have emerged as the cause of a novel neurological phenotype characterized by global developmental delays, severe hypotonia and hyperkinetic movement disorders, the latter being an important distinguishing feature. Optic atrophy is common and may only become apparent in the first few years of life, necessitating repeat ophthalmologic evaluation in older children. Early recognition of the cardinal features of this condition will facilitate diagnosis of this complex neurologic disorder. Electronic supplementary material The online version of this article (10.1186/s13023-018-0825-3) contains supplementary material, which is available to authorized users.
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Ejaz R, Chen S, Isaacs CJ, Carnevale A, Wilson J, George K, Delatycki MB, Perlman SL, Mathews KD, Wilmot GR, Hoyle JC, Subramony SH, Zesiewicz T, Farmer JM, Lynch DR, Yoon G. Impact of Mobility Device Use on Quality of Life in Children With Friedreich Ataxia. J Child Neurol 2018; 33:397-404. [PMID: 29607705 DOI: 10.1177/0883073818764941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To determine how mobility device use impacts quality of life in children with Friedreich ataxia. STUDY DESIGN Data from 111 pediatric patients with genetically confirmed Friedreich ataxia were collected from a prospective natural history study utilizing standardized clinical evaluations, including health-related quality of life using the Pediatric Quality of Life Inventory (PedsQL) 4.0 Generic Core Module. RESULTS Mobility device use was associated with worse mean PedsQL total, physical, emotional, social, and academic subscores, after adjusting for gender, age of disease onset, and Friedreich Ataxia Rating Scale score. The magnitude of the difference was greatest for the physical subscore (-19.5 points, 95% CI = -30.00, -8.99, P < .001) and least for the emotional subscore (-10.61 points, 95% CI = -20.21, -1.02, P = .03). Transition to or between mobility devices trended toward worse physical subscore (-16.20 points, 95% CI = -32.07, -0.33, P = .05). CONCLUSIONS Mobility device use is associated with significant worsening of all domains of quality of life in children with Friedreich ataxia.
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Sinha S, Yoon G, Shin W, Biernaskie JA, Nickerson D, Gabriel VA. Burn clinical trials: A systematic review of registration and publications. Burns 2018; 44:263-271. [DOI: 10.1016/j.burns.2017.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/28/2017] [Accepted: 11/02/2017] [Indexed: 10/18/2022]
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Guerin A, Wilson G, Abdullah S, Mertens L, Yoon G, Carter M. Response to phenotypic hetergeneity of POMT2 variants. Am J Med Genet A 2018; 176:746-747. [DOI: 10.1002/ajmg.a.38591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 12/01/2017] [Indexed: 11/12/2022]
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