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Yoon JH, Seo Y, Jo YS, Lee S, Cho E, Cazenave-Gassiot A, Shin YS, Moon MH, An HJ, Wenk MR, Suh PG. Brain lipidomics: From functional landscape to clinical significance. SCIENCE ADVANCES 2022; 8:eadc9317. [PMID: 36112688 PMCID: PMC9481132 DOI: 10.1126/sciadv.adc9317] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/01/2022] [Indexed: 05/23/2023]
Abstract
Lipids are crucial components of cellular function owing to their role in membrane formation, intercellular signaling, energy storage, and homeostasis maintenance. In the brain, lipid dysregulations have been associated with the etiology and progression of neurodegeneration and other neurological pathologies. Hence, brain lipids are emerging as important potential targets for the early diagnosis and prognosis of neurological diseases. This review aims to highlight the significance and usefulness of lipidomics in diagnosing and treating brain diseases. We explored lipid alterations associated with brain diseases, paying attention to organ-specific characteristics and the functions of brain lipids. As the recent advances in brain lipidomics would have been impossible without advances in analytical techniques, we provide up-to-date information on mass spectrometric approaches and integrative analysis with other omic approaches. Last, we present the potential applications of lipidomics combined with artificial intelligence techniques and interdisciplinary collaborative research for treating brain diseases with clinical heterogeneities.
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Affiliation(s)
- Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Youngsuk Seo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Yeon Suk Jo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
- Department of Brain Sciences, Daegu-Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Seulah Lee
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Eunji Cho
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore
| | - Yong-Seung Shin
- Laboratory Solutions Sales, Agilent Technologies Korea Ltd., Seoul, 06621, Republic of Korea
| | - Myeong Hee Moon
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Markus R. Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore
| | - Pann-Ghill Suh
- Korea Brain Research Institute, Daegu 41062, Republic of Korea
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Baratta AM, Brandner AJ, Plasil SL, Rice RC, Farris SP. Advancements in Genomic and Behavioral Neuroscience Analysis for the Study of Normal and Pathological Brain Function. Front Mol Neurosci 2022; 15:905328. [PMID: 35813067 PMCID: PMC9259865 DOI: 10.3389/fnmol.2022.905328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
Psychiatric and neurological disorders are influenced by an undetermined number of genes and molecular pathways that may differ among afflicted individuals. Functionally testing and characterizing biological systems is essential to discovering the interrelationship among candidate genes and understanding the neurobiology of behavior. Recent advancements in genetic, genomic, and behavioral approaches are revolutionizing modern neuroscience. Although these tools are often used separately for independent experiments, combining these areas of research will provide a viable avenue for multidimensional studies on the brain. Herein we will briefly review some of the available tools that have been developed for characterizing novel cellular and animal models of human disease. A major challenge will be openly sharing resources and datasets to effectively integrate seemingly disparate types of information and how these systems impact human disorders. However, as these emerging technologies continue to be developed and adopted by the scientific community, they will bring about unprecedented opportunities in our understanding of molecular neuroscience and behavior.
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Affiliation(s)
- Annalisa M. Baratta
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Adam J. Brandner
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sonja L. Plasil
- Department of Pharmacology & Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rachel C. Rice
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sean P. Farris
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Sean P. Farris,
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Ryu CS, Bae J, Kim IJ, Kim J, Oh SH, Kim OJ, Kim NK. MPG and NPRL3 Polymorphisms are Associated with Ischemic Stroke Susceptibility and Post-Stroke Mortality. Diagnostics (Basel) 2020; 10:diagnostics10110947. [PMID: 33202874 PMCID: PMC7696846 DOI: 10.3390/diagnostics10110947] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/16/2020] [Accepted: 11/12/2020] [Indexed: 01/04/2023] Open
Abstract
Ischemic stroke is a complicated disease which is affected by environmental factors and genetic factors. In this field, various studies using whole-exome sequencing (WES) have focused on novel and linkage variants in diverse diseases. Thus, we have investigated the various novel variants, which focused on their linkages to each other, in ischemic stroke. Specifically, we analyzed the N-methylpurine DNA glycosylase (MPG) gene, which plays an initiating role in DNA repair, and the nitrogen permease regulator-like 3 (NPRL3) gene, which is involved in regulating the mammalian target of rapamycin pathway. We took blood samples of 519 ischemic stroke patients and 417 controls. Genetic polymorphisms were detected by polymerase chain reaction (PCR), real-time PCR, and restriction fragment length polymorphism (RFLP) analysis. We found that two NPRL3 polymorphisms (rs2541618 C>T and rs75187722 G>A), as well as the MPG rs2562162 C>T polymorphism, were significantly associated with ischemic stroke. In Cox proportional hazard regression models, the MPG rs2562162 was associated with the survival of small-vessel disease patients in ischemic stroke. Our study showed that NPRL3 and MPG polymorphisms are associated with ischemic stroke prevalence and ischemic stroke survival. Taken together, these findings suggest that NPRL3 and MPG genotypes may be useful clinical biomarkers for ischemic stroke development and prognosis.
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Affiliation(s)
- Chang Soo Ryu
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea;
| | - Jinkun Bae
- Department of Emergency Medicine, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Korea;
| | - In Jai Kim
- Department of Internal Medicine, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Korea;
| | - Jinkwon Kim
- Department of Neurology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Korea; (J.K.); (S.H.O.)
| | - Seung Hun Oh
- Department of Neurology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Korea; (J.K.); (S.H.O.)
| | - Ok Joon Kim
- Department of Neurology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Korea; (J.K.); (S.H.O.)
- Correspondence: (O.J.K.); (N.K.K.)
| | - Nam Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea;
- Correspondence: (O.J.K.); (N.K.K.)
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4
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Shademan B, Biray Avci C, Nikanfar M, Nourazarian A. Application of Next-Generation Sequencing in Neurodegenerative Diseases: Opportunities and Challenges. Neuromolecular Med 2020; 23:225-235. [PMID: 32399804 DOI: 10.1007/s12017-020-08601-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/01/2020] [Indexed: 12/28/2022]
Abstract
Genetic factors (gene mutations) lead to various rare and prevalent neurological diseases. Identification of underlying mutations in neurodegenerative diseases is of paramount importance due to the heterogeneous nature of the genome and different clinical manifestations. An early and accurate molecular diagnosis are cardinal for neurodegenerative patients to undergo proper therapeutic regimens. The next-generation sequencing (NGS) method examines up to millions of sequences at a time. As a result, the rare molecular diagnoses, previously presented with "unknown causes", are now possible in a short time. This method generates a large amount of data that can be utilized in patient management. Since each person has a unique genome, the NGS has transformed diagnostic and therapeutic strategies into sequencing and individual genomic mapping. However, this method has disadvantages like other diagnostic methods. Therefore, in this review, we aimed to briefly summarize the NGS method and correlated studies to unravel the genetic causes of neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, epilepsy, and MS. Finally, we discuss the NGS challenges and opportunities in neurodegenerative diseases.
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Affiliation(s)
- Behrouz Shademan
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey
| | - Cigir Biray Avci
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey.
| | - Masoud Nikanfar
- Department of Neurology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Nourazarian
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Golgasht St., 51666-16471, Tabriz, Iran. .,Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran.
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5
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Ilinca A, Martinez-Majander N, Samuelsson S, Piccinelli P, Truvé K, Cole J, Kittner S, Soller M, Kristoffersson U, Tatlisumak T, Puschmann A, Putaala J, Lindgren A. Whole-Exome Sequencing in 22 Young Ischemic Stroke Patients With Familial Clustering of Stroke. Stroke 2020; 51:1056-1063. [PMID: 32172663 DOI: 10.1161/strokeaha.119.027474] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Backgrounds and Purpose- Although new methods for genetic analyses are rapidly evolving, there are currently knowledge gaps in how to detect Mendelian forms of stroke. Methods- We performed whole-exome sequencing in 22 probands, under 56 years at their first ischemic stroke episode, from multi-incident stroke families. With the use of a comprehensive stroke-gene panel, we searched for variants in stroke-related genes. The probands' clinical stroke subtype was related to clinical characteristics previously associated with pathogenic variants in these genes. Relatives were genotyped in 7 families to evaluate stroke-gene variants of unknown significance. In 2 larger families with embolic stroke of unknown source, whole-exome sequencing was performed in additional members to examine the possibility of identifying new stroke genes. Results- Six of 22 probands carried pathogenic or possibly pathogenic variants in genes reported to be associated with their stroke subtype. A known pathogenic variant in NOTCH3 and a possibly pathogenic variant in ACAD9 gene were identified. A novel JAK2:c.3188G>A (p.Arg1063His) mutation was seen in a proband with embolic stroke of undetermined source and prothrombotic status. However, penetrance in the family was incomplete. COL4A2:c.3368A>G (p.Glu1123Gly) was detected in 2 probands but did not cosegregate with the disease in their families. Whole-exome sequencing in multiple members of 2 pedigrees with embolic stroke of undetermined source revealed possibly pathogenic variants in genes not previously associated with stroke, GPR142:c.148C>G (p.Leu50Val), and PTPRN2:c.2416A>G (p.Ile806Val); LRRC1 c.808A>G (p.Ile270Val), SLC7A10c.1294dupG (p.Val432fs), IKBKB: c.1070C>T (p.Ala357Val), and OXGR1 c.392G>A (p.Arg131His), respectively. Conclusions- Screening with whole-exome sequencing using a comprehensive stroke-gene panel may identify rare monogenic forms of stroke, but careful evaluation of clinical characteristics and potential pathogenicity of novel variants remain important. In our study, the majority of individuals with familial aggregation of stroke lacked any identified genetic causes.
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Affiliation(s)
- Andreea Ilinca
- From the Department of Clinical Sciences Lund, Neurology (A.I., A.P., A.L.), Lund University, Sweden.,Department of Neurology and Rehabilitation Medicine, Neurology, Skåne University Hospital, Sweden (A.L., A.P., A.L.)
| | | | - Sofie Samuelsson
- Department of Clinical Genetics and Pathology (S.S., P.P.), Lund University, Sweden
| | - Paul Piccinelli
- Department of Clinical Genetics and Pathology (S.S., P.P.), Lund University, Sweden
| | - Katarina Truvé
- Bioinformatics Core Facility, Sahlgrenska Academy at University of Gothenburg, Sweden (K.T.)
| | - John Cole
- Department of Neurology, Veterans Affairs Maryland Health Care System (J.C., S.K.), University of Maryland School of Medicine, Baltimore
| | - Steven Kittner
- Department of Neurology, Veterans Affairs Maryland Health Care System (J.C., S.K.), University of Maryland School of Medicine, Baltimore.,Department of Neurology (S.K.), University of Maryland School of Medicine, Baltimore
| | - Maria Soller
- Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden (M.S.)
| | - Ulf Kristoffersson
- Division of Clinical Genetics, Laboratory Medicine (U.K.), Lund University, Sweden
| | - Turgut Tatlisumak
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Sweden (T.T.)
| | - Andreas Puschmann
- From the Department of Clinical Sciences Lund, Neurology (A.I., A.P., A.L.), Lund University, Sweden.,Department of Neurology and Rehabilitation Medicine, Neurology, Skåne University Hospital, Sweden (A.L., A.P., A.L.)
| | - Jukka Putaala
- Department of Neurology, Helsinki University Hospital, Finland (N.M.-M., J.P.)
| | - Arne Lindgren
- From the Department of Clinical Sciences Lund, Neurology (A.I., A.P., A.L.), Lund University, Sweden.,Department of Neurology and Rehabilitation Medicine, Neurology, Skåne University Hospital, Sweden (A.L., A.P., A.L.)
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6
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Chen Y, Liao LD, Wu ZY, Yang Q, Guo JC, He JZ, Wang SH, Xu XE, Wu JY, Pan F, Lin DC, Xu LY, Li EM. Identification of key genes by integrating DNA methylation and next-generation transcriptome sequencing for esophageal squamous cell carcinoma. Aging (Albany NY) 2020; 12:1332-1365. [PMID: 31962291 PMCID: PMC7053602 DOI: 10.18632/aging.102686] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 12/25/2019] [Indexed: 02/05/2023]
Abstract
Aberrant DNA methylation leads to abnormal gene expression, making it a significant regulator in the progression of cancer and leading to the requirement for integration of gene expression with DNA methylation. Here, we identified 120 genes demonstrating an inverse correlation between DNA methylation and mRNA expression in esophageal squamous cell carcinoma (ESCC). Sixteen key genes, such as SIX4, CRABP2, and EHD3, were obtained by filtering 10 datasets and verified in paired ESCC samples by qRT-PCR. 5-Aza-dC as a DNA methyltransferase (DNMT) inhibitor could recover their expression and inhibit clonal growth of cancer cells in seven ESCC cell lines. Furthermore, 11 of the 16 genes were correlated with OS (overall survival) and DFS (disease-free survival) in 125 ESCC patients. ChIP-Seq data and WGBS data showed that DNA methylation and H3K27ac histone modification of these key genes displayed inverse trends, suggesting that there was collaboration between DNA methylation and histone modification in ESCC. Our findings illustrate that the integrated multi-omics data (transcriptome and epigenomics) can accurately obtain potential prognostic biomarkers, which may provide important insight for the effective treatment of cancers.
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Affiliation(s)
- Yang Chen
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Lian-Di Liao
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Zhi-Yong Wu
- Departments of Oncology Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-Sen University, Shantou 515041, Guangdong, P.R. China
| | - Qian Yang
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Jin-Cheng Guo
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Jian-Zhong He
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Shao-Hong Wang
- Departments of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-Sen University, Shantou 515041, Guangdong, P.R. China
| | - Xiu-E Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Jian-Yi Wu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Feng Pan
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
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7
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Pytel V, Matías-Guiu JA, Torre-Fuentes L, Montero-Escribano P, Maietta P, Botet J, Álvarez S, Gómez-Pinedo U, Matías-Guiu J. Exonic variants of genes related to the vitamin D signaling pathway in the families of familial multiple sclerosis using whole-exome next generation sequencing. Brain Behav 2019; 9:e01272. [PMID: 30900415 PMCID: PMC6456803 DOI: 10.1002/brb3.1272] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/27/2019] [Accepted: 03/06/2019] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Vitamin D (VD) deficiency has been associated with multiple sclerosis (MS) and other autoimmune diseases (AIDs). However, the effect of the genetics of VD on the risk of MS is subject to debate. This study focuses on genes linked to the VD signaling pathway in families with MS. The evaluation of gene variants in all the members of families could contribute to an additional knowledge on the information obtained from case-control studies that use nonrelated healthy people. MATERIAL AND METHODS We studied 94 individuals from 15 families including at least two patients with MS. We performed whole-exome next generation sequencing on all individuals and analyzed variants of the DHCR7, CYP2R1, CYP3A4, CYP27A1, GC, CYP27B1, LRP2, CUBN, DAB2, FCGR, RXR, VDR, CYP24A1, and PDIA3 genes. We also studied PTH, FGF23, METTL1, METTL21B, and the role of the linkage disequilibrium block on the long arm of chromosome 12, through analysis of the CDK4, TSFM, AGAP2, and AVIL genes. We compared patients with MS, other AIDs and unaffected members from different family types. RESULTS The study described the variants in the VD signaling pathway that appear in families with at least two patients with MS. Some infrequent variants were detected in these families, but no significant difference was observed between patients with MS and/or other AIDs and unaffected family members in the frequency of these variants. Variants previously associated with MS in the literature were not observed in these families or were distributed similarly in patients and unaffected family members. CONCLUSION The study of genes involved in the VD signaling pathway in families that include more than one patient with MS did not identify any variants that could explain the presence of the disease, suggesting that VD metabolism could probably play a role in MS more as an environmental factor rather than as a genetic factor. Our study also supports the analysis of cases and unaffected individuals within families in order to determine the influence of genetic factors.
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Affiliation(s)
- Vanesa Pytel
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain.,Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - Jordi A Matías-Guiu
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - Laura Torre-Fuentes
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - Paloma Montero-Escribano
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | | | | | | | - Ulises Gómez-Pinedo
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - Jorge Matías-Guiu
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain.,Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
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8
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Ungaro C, Citrigno L, Trojsi F, Sprovieri T, Gentile G, Muglia M, Monsurrò MR, Tedeschi G, Cavallaro S, Conforti FL. ALS and CHARGE syndrome: a clinical and genetic study. Acta Neurol Belg 2018; 118:629-635. [PMID: 30317490 PMCID: PMC6244742 DOI: 10.1007/s13760-018-1029-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/06/2018] [Indexed: 12/30/2022]
Abstract
Amyotrophic Lateral Sclerosis and CHARGE syndrome are complex neurological disorders, which never occurred together in the same family and, to date, no putative correlation between them has been described on PubMed Central. Due to our aim was to evaluate the presence of different genetic variants involved in these pathologies, we reported a clinical and genetic description of two sisters affected by these two different disorders. In the CHARGE patient, molecular analysis of the CHD7 gene revealed the c.8016G >A de novo variant in exon 37. The ALS patient had been screened negative for mutations in SOD1, TARDBP, FUS/TLS, C9orf72 and KIF5A genes. Anyway, targeted next generation sequencing analysis identified known and unknown genetic variations in 39 ALS-related genes: a total of 380 variants were reported, of which 194 in the ALS patient and 186 in the CHARGE patient. To date, although the results suggest that the occurrence of the two syndromes in the same family is co-incidental rather than based on a causative genetic variant, we could hypothesize that other factors might act as modulators in the pathogenesis of these different phenotypes.
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Affiliation(s)
- Carmine Ungaro
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Luigi Citrigno
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Francesca Trojsi
- Dipartimento di Scienze Mediche, Chirurgiche, Neurologiche, Metaboliche e dell'Invecchiamento, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Teresa Sprovieri
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Giulia Gentile
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Maria Muglia
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Maria Rosaria Monsurrò
- Dipartimento di Scienze Mediche, Chirurgiche, Neurologiche, Metaboliche e dell'Invecchiamento, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Gioacchino Tedeschi
- Dipartimento di Scienze Mediche, Chirurgiche, Neurologiche, Metaboliche e dell'Invecchiamento, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Sebastiano Cavallaro
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Francesca Luisa Conforti
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy.
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9
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Coarelli G, Brice A, Durr A. Recent advances in understanding dominant spinocerebellar ataxias from clinical and genetic points of view. F1000Res 2018; 7. [PMID: 30473770 PMCID: PMC6234732 DOI: 10.12688/f1000research.15788.1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/02/2018] [Indexed: 12/12/2022] Open
Abstract
Abstract Spinocerebellar ataxias (SCAs) are rare types of cerebellar ataxia with a dominant mode of inheritance. To date, 47 SCA subtypes have been identified, and the number of genes implicated in SCAs is continually increasing. Polyglutamine (polyQ) expansion diseases (
ATXN1/SCA1,
ATXN2/SCA2,
ATXN3/SCA3,
CACNA1A/SCA6,
ATXN7/SCA7,
TBP/SCA17, and
ATN1/DRPLA) are the most common group of SCAs. No preventive or curative treatments are currently available, but various therapeutic approaches, including RNA-targeting treatments, such as antisense oligonucleotides (ASOs), are being developed. Clinical trials of ASOs in SCA patients are already planned. There is, therefore, a need to identify valid outcome measures for such studies. In this review, we describe recent advances towards identifying appropriate biomarkers, which are essential for monitoring disease progression and treatment efficacy. Neuroimaging biomarkers are the most powerful markers identified to date, making it possible to reduce sample sizes for clinical trials. Changes on brain MRI are already evident at the premanifest stage in SCA1 and SCA2 carriers and are correlated with CAG repeat size. Other potential biomarkers have also been developed, based on neurological examination, oculomotor study, cognitive assessment, and blood and cerebrospinal fluid analysis. Longitudinal studies based on multimodal approaches are required to establish the relationships between parameters and to validate the biomarkers identified.
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Affiliation(s)
- Giulia Coarelli
- Assistance Publique-Hôpitaux de Paris (AP-HP), Department of Neurology, Avicenne Hospital, Paris 13 University, Bobigny, 93000, France.,Institut du Cerveau et de la Moelle épinière, ICM, Inserm U 1127, CNRS UMR 7225, Sorbonne University, Paris, 75013, France
| | - Alexis Brice
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm U 1127, CNRS UMR 7225, Sorbonne University, Paris, 75013, France.,Assistance Publique-Hôpitaux de Paris (AP-HP), Genetic department, Pitié-Salpêtrière University Hospital, Paris, 75013, France
| | - Alexandra Durr
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm U 1127, CNRS UMR 7225, Sorbonne University, Paris, 75013, France.,Assistance Publique-Hôpitaux de Paris (AP-HP), Genetic department, Pitié-Salpêtrière University Hospital, Paris, 75013, France
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10
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Abstract
Dear Editor Next generation sequencing (NGS) has changed the way we approach the diagnosis, prognosis and treatment of genetic disorders. It gave us base pair (bp) precision, multi-gene approach that can be executed in a timely and cost-effective manner. Despite some minor technical issues in NGS, it comes with great advantages. However, the clinical, and especially, genetic counseling profession will need to rise to the challenge to face some of the new issues, dilemmas and problems this new technology is bringing to the table. Some of the counseling guidelines predate the NGS era and will urgently need to be brought up to par with the technology.
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11
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Ilinca A, Samuelsson S, Piccinelli P, Soller M, Kristoffersson U, Lindgren AG. A stroke gene panel for whole-exome sequencing. Eur J Hum Genet 2018; 27:317-324. [PMID: 30356112 DOI: 10.1038/s41431-018-0274-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/19/2018] [Accepted: 08/28/2018] [Indexed: 12/21/2022] Open
Abstract
Extensive analyses of known monogenic causes of stroke by whole-exome/genome sequencing are technically possible today. We here aimed to compile a comprehensive panel of genes associated with monogenic causes of stroke for use in clinical and research situations. We systematically searched the publically available database Online Mendelian Inheritance in Man, and validated the entries against original peer-reviewed publications in PubMed. First, we selected known pathogenic or putatively pathogenic stroke genes reported in at least one person with stroke, and classified the stroke phenotype for each gene into eight subgroups: (1) large artery atherosclerotic, (2) large artery non-atherosclerotic (tortuosity, dolichoectasia, aneurysm, non-atherosclerotic dissection, occlusion), (3) cerebral small-vessel diseases, (4) cardioembolic (arrhythmia, heart defect, cardiomyopathy), (5) coagulation dysfunctions (venous thrombosis, arterial thrombosis, bleeding tendency), (6) intracerebral hemorrhage, (7) vascular malformations (cavernoma, arteriovenous malformations), and (8) metabolism disorders. Second, we selected other genes that may plausibly cause stroke through diseases related to stroke, but without any documented stroke patient description. A third section comprised SNPs associated with stroke in genome-wide association studies (GWAS). We identified in total 214 genes: 120 associated with stroke, 62 associated with diseases that may cause stroke, and 32 stroke-related genes from recent GWAS. We describe these 214 genes and the clinical stroke subtype(s) associated with each of them. The resulting gene panel can be used to interpret exome sequencing results regarding monogenic stroke. Based on the panel's clinical phenotype description, the pathogenicity of novel variants in these genes may be evaluated in specific situations.
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Affiliation(s)
- Andreea Ilinca
- Department of Clinical Sciences Lund, Neurology, Lund University, Lund, Sweden. .,Department of Neurology and Rehabilitation Medicine, Skåne University Hospital, Malmö, Sweden.
| | - Sofie Samuelsson
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Region Skåne and Lund University, Lund, Sweden
| | - Paul Piccinelli
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Region Skåne and Lund University, Lund, Sweden
| | - Maria Soller
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Region Skåne and Lund University, Lund, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Ulf Kristoffersson
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Region Skåne and Lund University, Lund, Sweden
| | - Arne G Lindgren
- Department of Clinical Sciences Lund, Neurology, Lund University, Lund, Sweden.,Department of Neurology and Rehabilitation Medicine, Skåne University Hospital, Lund, Sweden
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12
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Hurlimann T, Jaitovich Groisman I, Godard B. Exploring neurologists' perspectives on the return of next generation sequencing results to their patients: a needed step in the development of guidelines. BMC Med Ethics 2018; 19:81. [PMID: 30268121 PMCID: PMC6162934 DOI: 10.1186/s12910-018-0320-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 09/12/2018] [Indexed: 12/12/2022] Open
Abstract
Background The use of Next Generation Sequencing such as Whole Genome Sequencing (WGS) is a promising step towards a better understanding and treatment of neurological diseases. WGS can result into unexpected information (incidental findings, IFs), and information with uncertain clinical significance. In the context of a Genome Canada project on ‘Personalized Medicine in the Treatment of Epilepsy’, we intended to address these challenges surveying neurologists’ opinions about the type of results that should be returned, and their professional responsibility toward recontacting patients regarding new discovered mutations. Methods Potential participants were contacted through professional organizations or direct invitations. Results A total of 204 neurologists were recruited. Fifty nine percent indicated that to be conveyed, WGS results should have a demonstrated clinical utility for diagnosis, prognosis or treatment. Yet, 41% deemed appropriate to return results without clinical utility, when they could impact patients’ reproductive decisions, or on patients’ request. Current use of targeted genetic testing and age of patients influenced respondents’ answers. Respondents stated that analysis of genomics data resulting from WGS should be limited to the genes likely to be relevant for the patient’s specific medical condition (69%), so as to limit IFs. Respondents felt responsible to recontact patients and inform them about newly discovered mutations related to the medical condition that triggered the test (75%) for as long as they are following up on the patient (55%). Finally, 53.5% of the respondents felt responsible to recontact and inform patients of clinically significant, newly discovered IFs. Conclusion Our results show the importance of formulating professional guidelines sensitive to the various – and sometimes opposite – viewpoints that may prevail within a same community of practice, as well as flexible so as to be attuned to the characteristics of the neurological conditions that triggered a WGS.
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Affiliation(s)
- Thierry Hurlimann
- Institut de recherche en santé publique, Université de Montréal, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada.,Quebec Population Health Research Network, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada
| | - Iris Jaitovich Groisman
- Institut de recherche en santé publique, Université de Montréal, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada
| | - Béatrice Godard
- Institut de recherche en santé publique, Université de Montréal, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada. .,Department of Social and Preventive Medicine, Université de Montréal, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada. .,Quebec Population Health Research Network, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada.
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13
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George AJ, Hoffiz YC, Charles AJ, Zhu Y, Mabb AM. A Comprehensive Atlas of E3 Ubiquitin Ligase Mutations in Neurological Disorders. Front Genet 2018; 9:29. [PMID: 29491882 PMCID: PMC5817383 DOI: 10.3389/fgene.2018.00029] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/22/2018] [Indexed: 01/11/2023] Open
Abstract
Protein ubiquitination is a posttranslational modification that plays an integral part in mediating diverse cellular functions. The process of protein ubiquitination requires an enzymatic cascade that consists of a ubiquitin activating enzyme (E1), ubiquitin conjugating enzyme (E2) and an E3 ubiquitin ligase (E3). There are an estimated 600-700 E3 ligase genes representing ~5% of the human genome. Not surprisingly, mutations in E3 ligase genes have been observed in multiple neurological conditions. We constructed a comprehensive atlas of disrupted E3 ligase genes in common (CND) and rare neurological diseases (RND). Of the predicted and known human E3 ligase genes, we found ~13% were mutated in a neurological disorder with 83 total genes representing 70 different types of neurological diseases. Of the E3 ligase genes identified, 51 were associated with an RND. Here, we provide an updated list of neurological disorders associated with E3 ligase gene disruption. We further highlight research in these neurological disorders and discuss the advanced technologies used to support these findings.
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Affiliation(s)
- Arlene J. George
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | - Yarely C. Hoffiz
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | | | - Ying Zhu
- Creative Media Industries Institute & Department of Computer Science, Georgia State University, Atlanta, GA, United States
| | - Angela M. Mabb
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
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14
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Pang SYY, Teo KC, Hsu JS, Chang RSK, Li M, Sham PC, Ho SL. The role of gene variants in the pathogenesis of neurodegenerative disorders as revealed by next generation sequencing studies: a review. Transl Neurodegener 2017; 6:27. [PMID: 29046784 PMCID: PMC5639582 DOI: 10.1186/s40035-017-0098-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/02/2017] [Indexed: 12/13/2022] Open
Abstract
The clinical diagnosis of neurodegenerative disorders based on phenotype is difficult in heterogeneous conditions with overlapping symptoms. It does not take into account the disease etiology or the highly variable clinical course even amongst patients diagnosed with the same disorder. The advent of next generation sequencing (NGS) has allowed for a system-wide, unbiased approach to identify all gene variants in the genome simultaneously. With the plethora of new genes being identified, genetic rather than phenotype-based classification of Mendelian diseases such as spinocerebellar ataxia (SCA), hereditary spastic paraplegia (HSP) and Charcot-Marie-Tooth disease (CMT) has become widely accepted. It has also become clear that gene variants play a role in common and predominantly sporadic neurodegenerative diseases such as Parkinson’s disease (PD) and amyotrophic lateral sclerosis (ALS). The observation of pleiotropy has emerged, with mutations in the same gene giving rise to diverse phenotypes, which further increases the complexity of phenotype-genotype correlation. Possible mechanisms of pleiotropy include different downstream effects of different mutations in the same gene, presence of modifier genes, and oligogenic inheritance. Future directions include development of bioinformatics tools and establishment of more extensive public genotype/phenotype databases to better distinguish deleterious gene variants from benign polymorphisms, translation of genetic findings into pathogenic mechanisms through in-vitro and in-vivo studies, and ultimately finding disease-modifying therapies for neurodegenerative disorders.
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Affiliation(s)
- Shirley Yin-Yu Pang
- Division of Neurology, Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, People's Republic of China
| | - Kay-Cheong Teo
- Division of Neurology, Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, People's Republic of China
| | - Jacob Shujui Hsu
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, People's Republic of China
| | - Richard Shek-Kwan Chang
- Division of Neurology, Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, People's Republic of China
| | - Miaoxin Li
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, People's Republic of China.,Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China.,Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou, People's Republic of China
| | - Pak-Chung Sham
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, People's Republic of China
| | - Shu-Leong Ho
- Division of Neurology, Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, People's Republic of China
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15
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Abstract
Epilepsy is a common neurological problem, and there is a genetic basis in almost 50% of people with epilepsy. The diagnosis of genetic epilepsies makes the patient assured of the reasons of his/her seizures and avoids unnecessary, expensive, and invasive investigations. Last decade has shown tremendous growth in gene sequencing technologies, which have made genetic tests available at the bedside. Whole exome sequencing is now being routinely used in the clinical setting for making a genetic diagnosis. Genetic testing not only makes the diagnosis but also has an effect on the management of the patients, for example, the role of sodium channels blockers in SCN1A+ Dravet syndrome patients and usefulness of ketogenic diet therapy in SLC2A1+ generalized epilepsy patients. Many clinicians in our country have no or limited knowledge about the molecular genetics of epilepsies, types of genetic tests available, how to access them and how to interpret the results. The purpose of this review is to give an overview in this direction and encourage the clinicians to start considering genetic testing as an important investigation along with electroencephalogram and magnetic resonance imaging for better understanding and management of epilepsy in their patients.
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Affiliation(s)
- Vikas Dhiman
- Department of Neurology, Ivy Hospital, Panchkula, Haryana, India
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16
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Jaitovich Groisman I, Hurlimann T, Shoham A, Godard B. Practices and views of neurologists regarding the use of whole-genome sequencing in clinical settings: a web-based survey. Eur J Hum Genet 2017; 25:801-808. [PMID: 28488681 DOI: 10.1038/ejhg.2017.64] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/28/2017] [Accepted: 03/28/2017] [Indexed: 12/23/2022] Open
Abstract
The use of Whole-Genome Sequencing (WGS) in clinical settings has brought up a number of controversial scientific and ethical issues. The application of WGS is of particular relevance in neurology, as many conditions are difficult to diagnose. We conducted a worldwide, web-based survey to explore neurologists' views on the benefits of, and concerns regarding, the clinical use of WGS, as well as the resources necessary to implement it. Almost half of the 204 neurologists in the study treated mostly adult patients (48%), while the rest mainly children (37.3%), or both (14.7%). Epilepsy (73%) and headaches (57.8%) were the predominant conditions treated. Factor analysis brought out two profiles: neurologists who would offer WGS to their patients, and those who would not, or were not sure in which circumstances it should be offered. Neurologists considering the use of WGS as bringing more benefits than drawbacks currently used targeted genetic testing (P<0.05) or treated mainly children (P<0.05). WGS' benefits were directed towards the patients, while its risks were of a financial and legal nature. Furthermore, there was a correlation between respondents' current use of genetic tests and an anticipation of increased use in the future (P<0.001). However, over half of respondents did not feel sufficiently informed to use WGS in their practice (53.5%). Our results highlight gaps in education, organization, and funding to support the use of WGS in neurology, and draw attention to the need for resources that could strongly contribute to more straightforward diagnoses and possibly better treatment of neurological conditions.
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Affiliation(s)
- Iris Jaitovich Groisman
- Groupe de recherche Omics-Ethics, Institut de recherche en santé publique, Université de Montréal, Montreal, Quebec, Canada
| | - Thierry Hurlimann
- Groupe de recherche Omics-Ethics, Institut de recherche en santé publique, Université de Montréal, Montreal, Quebec, Canada
| | - Amir Shoham
- Département de psychologie, Faculté des arts et des sciences, Université de Montréal, Montreal, Quebec, Canada
| | - Béatrice Godard
- Groupe de recherche Omics-Ethics, Institut de recherche en santé publique, Université de Montréal, Montreal, Quebec, Canada
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17
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Chiabrando D, Castori M, di Rocco M, Ungelenk M, Gießelmann S, Di Capua M, Madeo A, Grammatico P, Bartsch S, Hübner CA, Altruda F, Silengo L, Tolosano E, Kurth I. Mutations in the Heme Exporter FLVCR1 Cause Sensory Neurodegeneration with Loss of Pain Perception. PLoS Genet 2016; 12:e1006461. [PMID: 27923065 PMCID: PMC5140052 DOI: 10.1371/journal.pgen.1006461] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 11/04/2016] [Indexed: 12/12/2022] Open
Abstract
Pain is necessary to alert us to actual or potential tissue damage. Specialized nerve cells in the body periphery, so called nociceptors, are fundamental to mediate pain perception and humans without pain perception are at permanent risk for injuries, burns and mutilations. Pain insensitivity can be caused by sensory neurodegeneration which is a hallmark of hereditary sensory and autonomic neuropathies (HSANs). Although mutations in several genes were previously associated with sensory neurodegeneration, the etiology of many cases remains unknown. Using next generation sequencing in patients with congenital loss of pain perception, we here identify bi-allelic mutations in the FLVCR1 (Feline Leukemia Virus subgroup C Receptor 1) gene, which encodes a broadly expressed heme exporter. Different FLVCR1 isoforms control the size of the cytosolic heme pool required to sustain metabolic activity of different cell types. Mutations in FLVCR1 have previously been linked to vision impairment and posterior column ataxia in humans, but not to HSAN. Using fibroblasts and lymphoblastoid cell lines from patients with sensory neurodegeneration, we here show that the FLVCR1-mutations reduce heme export activity, enhance oxidative stress and increase sensitivity to programmed cell death. Our data link heme metabolism to sensory neuron maintenance and suggest that intracellular heme overload causes early-onset degeneration of pain-sensing neurons in humans. Hereditary Sensory and Autonomic Neuropathy (HSAN) is a genetic disorder mainly characterized by the impairment of sensory neurons, which transmit information about sensations such as pain, temperature and touch. Therefore, unintentional self-injury, leading to ulcers and eventually amputations are common in affected individuals. Although mutations in several genes were previously associated with sensory neurodegeneration and pain insensitivity, the etiology of many cases remains unknown. We here identify mutations in the heme exporter protein FLVCR1 in patients with congenital inability to experience pain. We showed that FLVCR1 mutations results in reduced heme export activity, enhanced oxidative stress and increased sensitivity to programmed cell death. These data assign a surprising role for heme to sensory neuron maintenance.
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Affiliation(s)
- Deborah Chiabrando
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Torino, Italy
- * E-mail: (DC); (ET); (IK)
| | - Marco Castori
- Unit of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Maja di Rocco
- Unit of Rare Diseases, Department of Pediatrics, Gaslini Institute, Genoa, Italy
| | - Martin Ungelenk
- Institute of Human Genetics, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany
| | - Sebastian Gießelmann
- Institute of Human Genetics, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany
- Institute of Human Genetics, Uniklinik RWTH Aachen, Aachen, Germany
| | - Matteo Di Capua
- Unit of Neurophysiopathology, Department of Neuroscience, Bambino Gesù Children's Hospital, Rome, Italy
| | - Annalisa Madeo
- Unit of Rare Diseases, Department of Pediatrics, Gaslini Institute, Genoa, Italy
| | - Paola Grammatico
- Unit of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Sophie Bartsch
- Institute of Human Genetics, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany
| | - Christian A. Hübner
- Institute of Human Genetics, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany
| | - Fiorella Altruda
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Lorenzo Silengo
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Emanuela Tolosano
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Torino, Italy
- * E-mail: (DC); (ET); (IK)
| | - Ingo Kurth
- Institute of Human Genetics, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany
- Institute of Human Genetics, Uniklinik RWTH Aachen, Aachen, Germany
- * E-mail: (DC); (ET); (IK)
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18
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LoVerso PR, Cui F. Cell type-specific transcriptome profiling in mammalian brains. Front Biosci (Landmark Ed) 2016; 21:973-85. [PMID: 27100485 DOI: 10.2741/4434] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A mammalian brain contains numerous types of cells. Advances in neuroscience in the past decade allow us to identify and isolate neural cells of interest from mammalian brains. Recent developments in high-throughput technologies, such as microarrays and next-generation sequencing (NGS), provide detailed information on gene expression in pooled cells on a genomic scale. As a result, many novel genes have been found critical in cell type-specific transcriptional regulation. These differentially expressed genes can be used as molecular signatures, unique to a particular class of neural cells. Use of this gene expression-based approach can further differentiate neural cell types into subtypes, potentially linking some of them with neurological diseases. In this article, experimental techniques used to purify neural cells are described, followed by a review on recent microarray- or NGS-based transcriptomic studies of common neural cell types. The future prospects of cell type-specific research are also discussed.
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Affiliation(s)
- Peter R LoVerso
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, One Lomb Memorial Dr., Rochester, NY 14623
| | - Feng Cui
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, One Lomb Memorial Dr., Rochester, NY 14623,
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19
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Detection of a rare mutation in the ferroportin gene through targeted next generation sequencing. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2016; 14:531-534. [PMID: 27177411 DOI: 10.2450/2016.0286-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/04/2016] [Indexed: 12/20/2022]
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20
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Guio-Vega GP, Forero DA. Functional genomics of candidate genes derived from genome-wide association studies for five common neurological diseases. Int J Neurosci 2016; 127:118-123. [PMID: 26829381 DOI: 10.3109/00207454.2016.1149172] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AIM Recent genome-wide association studies (GWAS) are identifying novel candidate genes for several neurological diseases (NDs). However, a global functional analysis of those genes derived from GWAS for NDs is missing. We explored the genomic and functional features of novel candidate genes for five common NDs: Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, stroke and migraine. MATERIALS AND METHODS A functional enrichment analysis was performed for GWAS-derived genes, for categories such as Kyoto Encyclopedia of Genes and Genomes pathways, gene expression, InterPro domains, transcription factor binding sites, gene ontology (GO) terms and microRNA (miRNA) targets. An analysis of protein-protein interactions was carried out. RESULTS Six hundred and forty-two unique single nucleotide polymorphisms (SNPs) were identified for the five NDs and 2.3% of them were non-synonymous SNPs. There were no common SNPs for all five NDs and eight genes were associated with more than one ND. The enrichment analysis showed significant values for several GO categories, such as cell-cell adhesion and location in neurites and for expression in prefrontal cortex. An analysis of protein-protein interactions showed the evidence of a large component. Fifty-one of these GWAS-derived genes are known to be potentially druggable and twelve are known to harbor mutations for neuropsychiatric disorders. CONCLUSIONS Our results suggest that there is little overlap between the genes identified in GWAS for the five common NDs. Identification of functional categories in the GWAS-derived candidate genes for common NDs could lead to a better understanding of their functional consequences and could be useful for the future discovery of additional genetic risk factors for those diseases.
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Affiliation(s)
- Gina P Guio-Vega
- a Laboratory of NeuroPsychiatric Genetics, School of Medicine, Biomedical Sciences Research Group , Universidad Antonio Nariño , Bogotá , Colombia
| | - Diego A Forero
- a Laboratory of NeuroPsychiatric Genetics, School of Medicine, Biomedical Sciences Research Group , Universidad Antonio Nariño , Bogotá , Colombia
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21
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Gonorazky H, Liang M, Cummings B, Lek M, Micallef J, Hawkins C, Basran R, Cohn R, Wilson MD, MacArthur D, Marshall CR, Ray PN, Dowling JJ. RNAseq analysis for the diagnosis of muscular dystrophy. Ann Clin Transl Neurol 2015; 3:55-60. [PMID: 26783550 PMCID: PMC4704476 DOI: 10.1002/acn3.267] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 10/25/2015] [Indexed: 12/19/2022] Open
Abstract
The precise genetic cause remains elusive in nearly 50% of patients with presumed neurogenetic disease, representing a significant barrier for clinical care. This is despite significant advances in clinical genetic diagnostics, including the application of whole‐exome sequencing and next‐generation sequencing‐based gene panels. In this study, we identify a deep intronic mutation in the DMD gene in a patient with muscular dystrophy using both conventional and RNAseq‐based transcriptome analyses. The implications of our data are that noncoding mutations likely comprise an important source of unresolved genetic disease and that RNAseq is a powerful platform for detecting such mutations.
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Affiliation(s)
- Hernan Gonorazky
- Division of Neurology Hospital for Sick Children Toronto Ontario Canada M5G A04; Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Paediatrics University of Toronto Toronto Ontario Canada M5G AO4
| | - Minggao Liang
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4
| | - Beryl Cummings
- Analytic and Translational Genetics Unit Massachusetts General Hospital Boston Massachusetts 02114; Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge Massachusetts
| | - Monkol Lek
- Analytic and Translational Genetics Unit Massachusetts General Hospital Boston Massachusetts 02114; Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge Massachusetts
| | - Johann Micallef
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - Cynthia Hawkins
- Pediatric Laboratory Medicine Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - Raveen Basran
- Pediatric Laboratory Medicine Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - Ronald Cohn
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Paediatrics University of Toronto Toronto Ontario Canada M5G AO4; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4
| | - Michael D Wilson
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4
| | - Daniel MacArthur
- Analytic and Translational Genetics Unit Massachusetts General Hospital Boston Massachusetts 02114; Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge Massachusetts
| | - Christian R Marshall
- Pediatric Laboratory Medicine Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - Peter N Ray
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4; Pediatric Laboratory Medicine Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - James J Dowling
- Division of Neurology Hospital for Sick Children Toronto Ontario Canada M5G A04; Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Paediatrics University of Toronto Toronto Ontario Canada M5G AO4; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4
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Forlenza GP, Calhoun A, Beckman KB, Halvorsen T, Hamdoun E, Zierhut H, Sarafoglou K, Polgreen LE, Miller BS, Nathan B, Petryk A. Next generation sequencing in endocrine practice. Mol Genet Metab 2015; 115:61-71. [PMID: 25958132 PMCID: PMC4818590 DOI: 10.1016/j.ymgme.2015.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 05/02/2015] [Indexed: 11/23/2022]
Abstract
With the completion of the Human Genome Project and advances in genomic sequencing technologies, the use of clinical molecular diagnostics has grown tremendously over the last decade. Next-generation sequencing (NGS) has overcome many of the practical roadblocks that had slowed the adoption of molecular testing for routine clinical diagnosis. In endocrinology, targeted NGS now complements biochemical testing and imaging studies. The goal of this review is to provide clinicians with a guide to the application of NGS to genetic testing for endocrine conditions, by compiling a list of established gene mutations detectable by NGS, and highlighting key phenotypic features of these disorders. As we outline in this review, the clinical utility of NGS-based molecular testing for endocrine disorders is very high. Identifying an exact genetic etiology improves understanding of the disease, provides clear explanation to families about the cause, and guides decisions about screening, prevention and/or treatment. To illustrate this approach, a case of hypophosphatasia with a pathogenic mutation in the ALPL gene detected by NGS is presented.
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Affiliation(s)
- Gregory P Forlenza
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN 55454, USA
| | - Amy Calhoun
- Department of Pediatrics, Division of Genetics and Metabolism, University of Minnesota Masonic Children's Hospital, Minneapolis, MN 55454, USA
| | | | - Tanya Halvorsen
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN 55454, USA
| | - Elwaseila Hamdoun
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN 55454, USA
| | - Heather Zierhut
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kyriakie Sarafoglou
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN 55454, USA
| | - Lynda E Polgreen
- Division of Pediatric Endocrinology and Metabolism, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Bradley S Miller
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN 55454, USA
| | - Brandon Nathan
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN 55454, USA
| | - Anna Petryk
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN 55454, USA.
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