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Wang H, Zeng R. Aberrant protein aggregation in amyotrophic lateral sclerosis. J Neurol 2024; 271:4826-4851. [PMID: 38869826 DOI: 10.1007/s00415-024-12485-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/14/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal disease. As its pathological mechanisms are not well understood, there are no efficient therapeutics for it at present. While it is highly heterogenous both etiologically and clinically, it has a common salient hallmark, i.e., aberrant protein aggregation (APA). The upstream pathogenesis and the downstream effects of APA in ALS are sophisticated and the investigation of this pathology would be of consequence for understanding ALS. In this paper, the pathomechanism of APA in ALS and the candidate treatment strategies for it are discussed.
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Affiliation(s)
- Huaixiu Wang
- Department Neurology, Shanxi Provincial Peoples Hospital: Fifth Hospital of Shanxi Medical University, Taiyuan, 030012, China.
- Beijing Ai-Si-Kang Medical Technology Co. Ltd., No. 18 11th St Economical & Technological Development Zone, Beijing, 100176, China.
| | - Rong Zeng
- Department Neurology, Shanxi Provincial Peoples Hospital: Fifth Hospital of Shanxi Medical University, Taiyuan, 030012, China
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2
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Lai JD, Berlind JE, Fricklas G, Lie C, Urenda JP, Lam K, Sta Maria N, Jacobs R, Yu V, Zhao Z, Ichida JK. KCNJ2 inhibition mitigates mechanical injury in a human brain organoid model of traumatic brain injury. Cell Stem Cell 2024; 31:519-536.e8. [PMID: 38579683 DOI: 10.1016/j.stem.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 11/21/2023] [Accepted: 03/06/2024] [Indexed: 04/07/2024]
Abstract
Traumatic brain injury (TBI) strongly correlates with neurodegenerative disease. However, it remains unclear which neurodegenerative mechanisms are intrinsic to the brain and which strategies most potently mitigate these processes. We developed a high-intensity ultrasound platform to inflict mechanical injury to induced pluripotent stem cell (iPSC)-derived cortical organoids. Mechanically injured organoids elicit classic hallmarks of TBI, including neuronal death, tau phosphorylation, and TDP-43 nuclear egress. We found that deep-layer neurons were particularly vulnerable to injury and that TDP-43 proteinopathy promotes cell death. Injured organoids derived from C9ORF72 amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) patients displayed exacerbated TDP-43 dysfunction. Using genome-wide CRISPR interference screening, we identified a mechanosensory channel, KCNJ2, whose inhibition potently mitigated neurodegenerative processes in vitro and in vivo, including in C9ORF72 ALS/FTD organoids. Thus, targeting KCNJ2 may reduce acute neuronal death after brain injury, and we present a scalable, genetically flexible cerebral organoid model that may enable the identification of additional modifiers of mechanical stress.
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Affiliation(s)
- Jesse D Lai
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Amgen Inc., Thousand Oaks, CA, USA; Neurological & Rare Diseases, Dewpoint Therapeutics, Boston, MA, USA.
| | - Joshua E Berlind
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Gabriella Fricklas
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Cecilia Lie
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Jean-Paul Urenda
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Kelsey Lam
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Naomi Sta Maria
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Russell Jacobs
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Violeta Yu
- Amgen Inc., Thousand Oaks, CA, USA; Neurological & Rare Diseases, Dewpoint Therapeutics, Boston, MA, USA
| | - Zhen Zhao
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Justin K Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA; Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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3
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Shih YC, Chen HF, Wu CY, Ciou YR, Wang CW, Chuang HC, Tan TH. The phosphatase DUSP22 inhibits UBR2-mediated K63-ubiquitination and activation of Lck downstream of TCR signalling. Nat Commun 2024; 15:532. [PMID: 38225265 PMCID: PMC10789758 DOI: 10.1038/s41467-024-44843-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
DUSP22 is a dual-specificity phosphatase that inhibits T cell activation by inactivating the kinase Lck. Here we show that the E3 ubiquitin ligase UBR2 is a positive upstream regulator of Lck during T-cell activation. DUSP22 dephosphorylates UBR2 at specific Serine residues, leading to ubiquitin-mediated UBR2 degradation. UBR2 is also modified by the SCF E3 ubiquitin ligase complex via Lys48-linked ubiquitination at multiple Lysine residues. Single-cell RNA sequencing analysis and UBR2 loss of function experiments showed that UBR2 is a positive regulator of proinflammatory cytokine expression. Mechanistically, UBR2 induces Lys63-linked ubiquitination of Lck at Lys99 and Lys276 residues, followed by Lck Tyr394 phosphorylation and activation as part of TCR signalling. Inflammatory phenotypes induced by TCR-triggered Lck activation or knocking out DUSP22, are attenuated by genomic deletion of UBR2. UBR2-Lck interaction and Lck Lys63-linked ubiquitination are induced in the peripheral blood T cells of human SLE patients, which demonstrate the relevance of the UBR2-mediated regulation of inflammation to human pathology. In summary, we show here an important regulatory mechanism of T cell activation, which finetunes the balance between T cell response and aggravated inflammation.
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Affiliation(s)
- Ying-Chun Shih
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Hsueh-Fen Chen
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Chia-Ying Wu
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Yi-Ru Ciou
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Chia-Wen Wang
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Huai-Chia Chuang
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan.
| | - Tse-Hua Tan
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan.
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4
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Rizzuti M, Sali L, Melzi V, Scarcella S, Costamagna G, Ottoboni L, Quetti L, Brambilla L, Papadimitriou D, Verde F, Ratti A, Ticozzi N, Comi GP, Corti S, Gagliardi D. Genomic and transcriptomic advances in amyotrophic lateral sclerosis. Ageing Res Rev 2023; 92:102126. [PMID: 37972860 DOI: 10.1016/j.arr.2023.102126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder and the most common motor neuron disease. ALS shows substantial clinical and molecular heterogeneity. In vitro and in vivo models coupled with multiomic techniques have provided important contributions to unraveling the pathomechanisms underlying ALS. To date, despite promising results and accumulating knowledge, an effective treatment is still lacking. Here, we provide an overview of the literature on the use of genomics, epigenomics, transcriptomics and microRNAs to deeply investigate the molecular mechanisms developing and sustaining ALS. We report the most relevant genes implicated in ALS pathogenesis, discussing the use of different high-throughput sequencing techniques and the role of epigenomic modifications. Furthermore, we present transcriptomic studies discussing the most recent advances, from microarrays to bulk and single-cell RNA sequencing. Finally, we discuss the use of microRNAs as potential biomarkers and promising tools for molecular intervention. The integration of data from multiple omic approaches may provide new insights into pathogenic pathways in ALS by shedding light on diagnostic and prognostic biomarkers, helping to stratify patients into clinically relevant subgroups, revealing novel therapeutic targets and supporting the development of new effective therapies.
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Affiliation(s)
- Mafalda Rizzuti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luca Sali
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Melzi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Simone Scarcella
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Gianluca Costamagna
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Quetti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lorenzo Brambilla
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Federico Verde
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Nicola Ticozzi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Giacomo Pietro Comi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania Corti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
| | - Delia Gagliardi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
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5
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Pun FW, Liu BHM, Long X, Leung HW, Leung GHD, Mewborne QT, Gao J, Shneyderman A, Ozerov IV, Wang J, Ren F, Aliper A, Bischof E, Izumchenko E, Guan X, Zhang K, Lu B, Rothstein JD, Cudkowicz ME, Zhavoronkov A. Identification of Therapeutic Targets for Amyotrophic Lateral Sclerosis Using PandaOmics – An AI-Enabled Biological Target Discovery Platform. Front Aging Neurosci 2022; 14:914017. [PMID: 35837482 PMCID: PMC9273868 DOI: 10.3389/fnagi.2022.914017] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/31/2022] [Indexed: 11/30/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative disease with ill-defined pathogenesis, calling for urgent developments of new therapeutic regimens. Herein, we applied PandaOmics, an AI-driven target discovery platform, to analyze the expression profiles of central nervous system (CNS) samples (237 cases; 91 controls) from public datasets, and direct iPSC-derived motor neurons (diMNs) (135 cases; 31 controls) from Answer ALS. Seventeen high-confidence and eleven novel therapeutic targets were identified and will be released onto ALS.AI (http://als.ai/). Among the proposed targets screened in the c9ALS Drosophila model, we verified 8 unreported genes (KCNB2, KCNS3, ADRA2B, NR3C1, P2RY14, PPP3CB, PTPRC, and RARA) whose suppression strongly rescues eye neurodegeneration. Dysregulated pathways identified from CNS and diMN data characterize different stages of disease development. Altogether, our study provides new insights into ALS pathophysiology and demonstrates how AI speeds up the target discovery process, and opens up new opportunities for therapeutic interventions.
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Affiliation(s)
- Frank W. Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Bonnie Hei Man Liu
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Xi Long
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Hoi Wing Leung
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Geoffrey Ho Duen Leung
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Quinlan T. Mewborne
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States
| | - Junli Gao
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States
| | - Anastasia Shneyderman
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Ivan V. Ozerov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Ju Wang
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Feng Ren
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Alexander Aliper
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
| | - Evelyne Bischof
- College of Clinical Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, China
- International Center for Multimorbidity and Complexity in Medicine (ICMC), Universität Zürich, Zurich, Switzerland
| | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, United States
| | - Xiaoming Guan
- 4B Technologies Limited, Suzhou BioBay, Suzhou, China
| | - Ke Zhang
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, United States
| | - Bai Lu
- School of Pharmaceutical Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Jeffrey D. Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Merit E. Cudkowicz
- Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- *Correspondence: Merit E. Cudkowicz,
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong, Hong Kong SAR, China
- Buck Institute for Research on Aging, Novato, CA, United States
- Alex Zhavoronkov,
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Biomarkers in Human Peripheral Blood Mononuclear Cells: The State of the Art in Amyotrophic Lateral Sclerosis. Int J Mol Sci 2022; 23:ijms23052580. [PMID: 35269723 PMCID: PMC8910056 DOI: 10.3390/ijms23052580] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease, characterized by the progressive loss of lower motor neurons, weakness and muscle atrophy. ALS lacks an effective cure and diagnosis is often made by exclusion. Thus, it is imperative to search for biomarkers. Biomarkers can help in understanding ALS pathomechanisms, identification of targets for treatment and development of effective therapies. Peripheral blood mononuclear cells (PBMCs) represent a valid source for biomarkers compared to cerebrospinal fluid, as they are simple to collect, and to plasma, because of the possibility of detecting lower expressed proteins. They are a reliable model for patients’ stratification. This review provides an overview on PBMCs as a potential source of biomarkers in ALS. We focused on altered RNA metabolism (coding/non-coding RNA), including RNA processing, mRNA stabilization, transport and translation regulation. We addressed protein abnormalities (aggregation, misfolding and modifications); specifically, we highlighted that SOD1 appears to be the most characterizing protein in ALS. Finally, we emphasized the correlation between biological parameters and disease phenotypes, as regards prognosis, severity and clinical features. In conclusion, even though further studies are needed to standardize the use of PBMCs as a tool for biomarker investigation, they represent a promising approach in ALS research.
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Baralle M, Romano M. Characterization of the human TARDBP gene promoter. Sci Rep 2021; 11:10438. [PMID: 34002018 PMCID: PMC8129075 DOI: 10.1038/s41598-021-89973-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 05/04/2021] [Indexed: 02/03/2023] Open
Abstract
The expression of TDP-43, the main component of neuronal intracellular inclusions across a broad spectrum of ALS and FTD disorders, is developmentally regulated and studies in vivo have shown that TDP-43 overexpression can be toxic, even before observation of pathological aggregates. Starting from these observations, the regulation of its expression at transcriptional level might represent a further key element for the pathogenesis of neurodegenerative diseases. Therefore, we have characterized the human TARDBP promoter, in order to study the transcriptional mechanisms of expression. Mapping of cis-acting elements by luciferase assays in different cell outlined that the activity of the promoter seems to be higher in SH-SY5Y, Neuro2A, and HeLa than in HEK293. In addition, we tested effects of two SNPs found in the promoter region of ALS patients and observed no significant effect on transcription levels in all tested cell lines. Lastly, while TDP-43 overexpression did not affect significantly the activity of its promoter (suggesting that TDP-43 does not influence its own transcription), the presence of the 5'UTR sequence and of intron-1 splicing seem to impact positively on TDP-43 expression without affecting transcript stability. In conclusion, we have identified the region spanning nucleotides 451-230 upstream from the transcription start site as the minimal region with a significant transcription activity. These results lay an important foundation for exploring the regulation of the TARDBP gene transcription by exogenous and endogenous stimuli and the implication of transcriptional mechanisms in the pathogenesis of TDP-43 proteinopathies.
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Affiliation(s)
- Marco Baralle
- grid.425196.d0000 0004 1759 4810International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, Padriciano, Trieste, Italy
| | - Maurizio Romano
- grid.5133.40000 0001 1941 4308Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy
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Vishwakarma GK, Bhattacharjee A, Banerjee S, Liquet B. Classification algorithm for high-dimensional protein markers in time-course data. Stat Med 2020; 39:4201-4217. [PMID: 32844489 DOI: 10.1002/sim.8720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 05/22/2020] [Accepted: 07/17/2020] [Indexed: 01/05/2023]
Abstract
Identification of biomarkers is an emerging area in oncology. In this article, we develop an efficient statistical procedure for the classification of protein markers according to their effect on cancer progression. A high-dimensional time-course dataset of protein markers for 80 patients motivates us for developing the model. The threshold value is formulated as a level of a marker having maximum impact on cancer progression. The classification algorithm technique for high-dimensional time-course data is developed and the algorithm is validated by comparing random components using both proportional hazard and accelerated failure time frailty models. The study elucidates the application of two separate joint modeling techniques using auto regressive-type model and mixed effect model for time-course data and proportional hazard model for survival data with proper utilization of Bayesian methodology. Also, a prognostic score is developed on the basis of few selected genes with application on patients. This study facilitates to identify relevant biomarkers from a set of markers.
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Affiliation(s)
- Gajendra K Vishwakarma
- Department of Mathematics & Computing, Indian Institute of Technology Dhanbad, Dhanbad, India
| | - Atanu Bhattacharjee
- Section of Biostatistics,Centre for Cancer Epidemiology, Tata Memorial Center, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
| | - Souvik Banerjee
- Department of Mathematics & Computing, Indian Institute of Technology Dhanbad, Dhanbad, India
| | - Benoit Liquet
- Laboratoire De Mathématiques et de leurs Applications de PAU, E2S-UPPA, CNRS, Pau, France.,ARC Centre of Excellence for Mathematical and Statistical Frontiers at School of Mathematical Science, Queensland University of Technology, Brisbane, Queensland, Australia.,Department of Mathematics and Statistics, Macquarie University, Sydney, Australia
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Le Gall L, Anakor E, Connolly O, Vijayakumar UG, Duddy WJ, Duguez S. Molecular and Cellular Mechanisms Affected in ALS. J Pers Med 2020; 10:E101. [PMID: 32854276 PMCID: PMC7564998 DOI: 10.3390/jpm10030101] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/17/2020] [Accepted: 08/22/2020] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a terminal late-onset condition characterized by the loss of upper and lower motor neurons. Mutations in more than 30 genes are associated to the disease, but these explain only ~20% of cases. The molecular functions of these genes implicate a wide range of cellular processes in ALS pathology, a cohesive understanding of which may provide clues to common molecular mechanisms across both familial (inherited) and sporadic cases and could be key to the development of effective therapeutic approaches. Here, the different pathways that have been investigated in ALS are summarized, discussing in detail: mitochondrial dysfunction, oxidative stress, axonal transport dysregulation, glutamate excitotoxicity, endosomal and vesicular transport impairment, impaired protein homeostasis, and aberrant RNA metabolism. This review considers the mechanistic roles of ALS-associated genes in pathology, viewed through the prism of shared molecular pathways.
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Affiliation(s)
- Laura Le Gall
- Northern Ireland Center for Stratified/Personalised Medicine, Biomedical Sciences Research Institute, Ulster University, Derry-Londonderry BT47, UK; (L.L.G.); (E.A.); (O.C.); (U.G.V.); (W.J.D.)
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London WC1N 1EH, UK
| | - Ekene Anakor
- Northern Ireland Center for Stratified/Personalised Medicine, Biomedical Sciences Research Institute, Ulster University, Derry-Londonderry BT47, UK; (L.L.G.); (E.A.); (O.C.); (U.G.V.); (W.J.D.)
| | - Owen Connolly
- Northern Ireland Center for Stratified/Personalised Medicine, Biomedical Sciences Research Institute, Ulster University, Derry-Londonderry BT47, UK; (L.L.G.); (E.A.); (O.C.); (U.G.V.); (W.J.D.)
| | - Udaya Geetha Vijayakumar
- Northern Ireland Center for Stratified/Personalised Medicine, Biomedical Sciences Research Institute, Ulster University, Derry-Londonderry BT47, UK; (L.L.G.); (E.A.); (O.C.); (U.G.V.); (W.J.D.)
| | - William J. Duddy
- Northern Ireland Center for Stratified/Personalised Medicine, Biomedical Sciences Research Institute, Ulster University, Derry-Londonderry BT47, UK; (L.L.G.); (E.A.); (O.C.); (U.G.V.); (W.J.D.)
| | - Stephanie Duguez
- Northern Ireland Center for Stratified/Personalised Medicine, Biomedical Sciences Research Institute, Ulster University, Derry-Londonderry BT47, UK; (L.L.G.); (E.A.); (O.C.); (U.G.V.); (W.J.D.)
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10
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Swindell WR, Kruse CPS, List EO, Berryman DE, Kopchick JJ. ALS blood expression profiling identifies new biomarkers, patient subgroups, and evidence for neutrophilia and hypoxia. J Transl Med 2019; 17:170. [PMID: 31118040 PMCID: PMC6530130 DOI: 10.1186/s12967-019-1909-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/07/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a debilitating disease with few treatment options. Progress towards new therapies requires validated disease biomarkers, but there is no consensus on which fluid-based measures are most informative. METHODS This study analyzed microarray data derived from blood samples of patients with ALS (n = 396), ALS mimic diseases (n = 75), and healthy controls (n = 645). Goals were to provide in-depth analysis of differentially expressed genes (DEGs), characterize patient-to-patient heterogeneity, and identify candidate biomarkers. RESULTS We identified 752 ALS-increased and 764 ALS-decreased DEGs (FDR < 0.10 with > 10% expression change). Gene expression shifts in ALS blood broadly resembled acute high altitude stress responses. ALS-increased DEGs had high exosome expression, were neutrophil-specific, associated with translation, and overlapped significantly with genes near ALS susceptibility loci (e.g., IFRD1, TBK1, CREB5). ALS-decreased DEGs, in contrast, had low exosome expression, were erythroid lineage-specific, and associated with anemia and blood disorders. Genes encoding neurofilament proteins (NEFH, NEFL) had poor diagnostic accuracy (50-53%). However, support vector machines distinguished ALS patients from ALS mimics and controls with 87% accuracy (sensitivity: 86%, specificity: 87%). Expression profiles were heterogeneous among patients and we identified two subgroups: (i) patients with higher expression of IL6R and myeloid lineage-specific genes and (ii) patients with higher expression of IL23A and lymphoid-specific genes. The gene encoding copper chaperone for superoxide dismutase (CCS) was most strongly associated with survival (HR = 0.77; P = 1.84e-05) and other survival-associated genes were linked to mitochondrial respiration. We identify a 61 gene signature that significantly improves survival prediction when added to Cox proportional hazard models with baseline clinical data (i.e., age at onset, site of onset and sex). Predicted median survival differed 2-fold between patients with favorable and risk-associated gene expression signatures. CONCLUSIONS Peripheral blood analysis informs our understanding of ALS disease mechanisms and genetic association signals. Our findings are consistent with low-grade neutrophilia and hypoxia as ALS phenotypes, with heterogeneity among patients partly driven by differences in myeloid and lymphoid cell abundance. Biomarkers identified in this study require further validation but may provide new tools for research and clinical practice.
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Affiliation(s)
- William R. Swindell
- Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
- Department of Internal Medicine, The Jewish Hospital, Cincinnati, OH 45236 USA
| | - Colin P. S. Kruse
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701 USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701 USA
| | - Edward O. List
- Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701 USA
- The Diabetes Institute, Ohio University, Athens, OH 45701 USA
| | - Darlene E. Berryman
- Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701 USA
- The Diabetes Institute, Ohio University, Athens, OH 45701 USA
| | - John J. Kopchick
- Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701 USA
- The Diabetes Institute, Ohio University, Athens, OH 45701 USA
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11
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Vijayakumar UG, Milla V, Cynthia Stafford MY, Bjourson AJ, Duddy W, Duguez SMR. A Systematic Review of Suggested Molecular Strata, Biomarkers and Their Tissue Sources in ALS. Front Neurol 2019; 10:400. [PMID: 31139131 PMCID: PMC6527847 DOI: 10.3389/fneur.2019.00400] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/02/2019] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease, is an incurable neurodegenerative condition, characterized by the loss of upper and lower motor neurons. It affects 1-1.8/100,000 individuals worldwide, and the number of cases is projected to increase as the population ages. Thus, there is an urgent need to identify both therapeutic targets and disease-specific biomarkers-biomarkers that would be useful to diagnose and stratify patients into different sub-groups for therapeutic strategies, as well as biomarkers to follow the efficacy of any treatment tested during clinical trials. There is a lack of knowledge about pathogenesis and many hypotheses. Numerous "omics" studies have been conducted on ALS in the past decade to identify a disease-signature in tissues and circulating biomarkers. The first goal of the present review was to group the molecular pathways that have been implicated in monogenic forms of ALS, to enable the description of patient strata corresponding to each pathway grouping. This strategy allowed us to suggest 14 strata, each potentially targetable by different pharmacological strategies. The second goal of this review was to identify diagnostic/prognostic biomarker candidates consistently observed across the literature. For this purpose, we explore previous biomarker-relevant "omics" studies of ALS and summarize their findings, focusing on potential circulating biomarker candidates. We systematically review 118 papers on biomarkers published during the last decade. Several candidate markers were consistently shared across the results of different studies in either cerebrospinal fluid (CSF) or blood (leukocyte or serum/plasma). Although these candidates still need to be validated in a systematic manner, we suggest the use of combinations of biomarkers that would likely reflect the "health status" of different tissues, including motor neuron health (e.g., pNFH and NF-L, cystatin C, Transthyretin), inflammation status (e.g., MCP-1, miR451), muscle health (miR-338-3p, miR-206) and metabolism (homocysteine, glutamate, cholesterol). In light of these studies and because ALS is increasingly perceived as a multi-system disease, the identification of a panel of biomarkers that accurately reflect features of pathology is a priority, not only for diagnostic purposes but also for prognostic or predictive applications.
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Affiliation(s)
| | | | | | | | | | - Stephanie Marie-Rose Duguez
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
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12
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Šoltić D, Bowerman M, Stock J, Shorrock HK, Gillingwater TH, Fuller HR. Multi-Study Proteomic and Bioinformatic Identification of Molecular Overlap between Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA). Brain Sci 2018; 8:brainsci8120212. [PMID: 30518112 PMCID: PMC6315439 DOI: 10.3390/brainsci8120212] [Citation(s) in RCA: 9] [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: 09/24/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 12/24/2022] Open
Abstract
Unravelling the complex molecular pathways responsible for motor neuron degeneration in amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA) remains a persistent challenge. Interest is growing in the potential molecular similarities between these two diseases, with the hope of better understanding disease pathology for the guidance of therapeutic development. The aim of this study was to conduct a comparative analysis of published proteomic studies of ALS and SMA, seeking commonly dysregulated molecules to be prioritized as future therapeutic targets. Fifteen proteins were found to be differentially expressed in two or more proteomic studies of both ALS and SMA, and bioinformatics analysis identified over-representation of proteins known to associate in vesicles and molecular pathways, including metabolism of proteins and vesicle-mediated transport—both of which converge on endoplasmic reticulum (ER)-Golgi trafficking processes. Calreticulin, a calcium-binding chaperone found in the ER, was associated with both pathways and we independently confirm that its expression was decreased in spinal cords from SMA and increased in spinal cords from ALS mice. Together, these findings offer significant insights into potential common targets that may help to guide the development of new therapies for both diseases.
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Affiliation(s)
- Darija Šoltić
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK; (D.S.); (M.B.)
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | - Melissa Bowerman
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK; (D.S.); (M.B.)
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | - Joanne Stock
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK; (D.S.); (M.B.)
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | - Hannah K. Shorrock
- Biomedical Sciences, Edinburgh Medical School, University of Edinburgh, Edinburgh EH8 9AG, UK; (H.K.S.); (T.H.G.)
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Thomas H. Gillingwater
- Biomedical Sciences, Edinburgh Medical School, University of Edinburgh, Edinburgh EH8 9AG, UK; (H.K.S.); (T.H.G.)
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Heidi R. Fuller
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK; (D.S.); (M.B.)
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
- Correspondence: ; Tel.: +44-169-140-4693; Fax: +44-169-140-4065
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Abstract
Background Gene set analysis is a valuable tool to summarize high-dimensional gene expression data in terms of biologically relevant sets. This is an active area of research and numerous gene set analysis methods have been developed. Despite this popularity, systematic comparative studies have been limited in scope. Methods In this study we present a semi-synthetic simulation study using real datasets in order to test and compare commonly used methods. Results A software pipeline, Flexible Algorithm for Novel Gene set Simulation (FANGS) develops simulated data based on a prostate cancer dataset where the KRAS and TGF-β pathways were differentially expressed. The FANGS software is compatible with other datasets and pathways. Comparisons of gene set analysis methods are presented for Gene Set Enrichment Analysis (GSEA), Significance Analysis of Function and Expression (SAFE), sigPathway, and Correlation Adjusted Mean RAnk (CAMERA) methods. All gene set analysis methods are tested using gene sets from the MSigDB knowledge base. The false positive rate and power are estimated and presented for comparison. Recommendations are made for the utility of the default settings of methods and each method’s sensitivity towards various effect sizes. Conclusions The results of this study provide empirical guidance to users of gene set analysis methods. The FANGS software is available for researchers for continued methods comparisons. Electronic supplementary material The online version of this article (10.1186/s13040-018-0166-8) contains supplementary material, which is available to authorized users.
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14
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Long non-coding and coding RNAs characterization in Peripheral Blood Mononuclear Cells and Spinal Cord from Amyotrophic Lateral Sclerosis patients. Sci Rep 2018; 8:2378. [PMID: 29402919 PMCID: PMC5799454 DOI: 10.1038/s41598-018-20679-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/22/2018] [Indexed: 12/12/2022] Open
Abstract
Alteration in RNA metabolism, concerning both coding and long non-coding RNAs (lncRNAs), may play an important role in Amyotrophic Lateral Sclerosis (ALS) pathogenesis. In this work, we performed a whole transcriptome RNA-seq analysis to investigate the regulation of non-coding and coding RNAs in Sporadic ALS patients (SALS), mutated ALS patients (FUS, TARDBP and SOD1) and matched controls in Peripheral Blood Mononuclear Cells (PBMC). Selected transcripts were validated in spinal cord tissues. A total of 293 differentially expressed (DE) lncRNAs was found in SALS patients, whereas a limited amount of lncRNAs was deregulated in mutated patients. A total of 87 mRNAs was differentially expressed in SALS patients; affected genes showed an association with transcription regulation, immunity and apoptosis pathways. Taken together our data highlighted the importance of extending the knowledge on transcriptomic molecular alterations and on the significance of regulatory lncRNAs classes in the understanding of ALS disease. Our data brought the light on the importance of lncRNAs and mRNAs regulation in central and peripheral systems, offering starting points for new investigations about pathogenic mechanism involved in ALS disease.
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15
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Danziger SA, Miller LR, Singh K, Whitney GA, Peskind ER, Li G, Lipshutz RJ, Aitchison JD, Smith JJ. An indicator cell assay for blood-based diagnostics. PLoS One 2017; 12:e0178608. [PMID: 28594877 PMCID: PMC5464608 DOI: 10.1371/journal.pone.0178608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 05/16/2017] [Indexed: 11/30/2022] Open
Abstract
We have established proof of principle for the Indicator Cell Assay Platform™ (iCAP™), a broadly applicable tool for blood-based diagnostics that uses specifically-selected, standardized cells as biosensors, relying on their innate ability to integrate and respond to diverse signals present in patients' blood. To develop an assay, indicator cells are exposed in vitro to serum from case or control subjects and their global differential response patterns are used to train reliable, disease classifiers based on a small number of features. In a feasibility study, the iCAP detected pre-symptomatic disease in a murine model of amyotrophic lateral sclerosis (ALS) with 94% accuracy (p-Value = 3.81E-6) and correctly identified samples from a murine Huntington's disease model as non-carriers of ALS. Beyond the mouse model, in a preliminary human disease study, the iCAP detected early stage Alzheimer's disease with 72% cross-validated accuracy (p-Value = 3.10E-3). For both assays, iCAP features were enriched for disease-related genes, supporting the assay's relevance for disease research.
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Affiliation(s)
- Samuel A. Danziger
- Institute for Systems Biology, Seattle, WA, United States of America
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, United States of America
| | - Leslie R. Miller
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Karanbir Singh
- Institute for Systems Biology, Seattle, WA, United States of America
| | | | - Elaine R. Peskind
- Northwest Network (VISN-20) Mental Illness, Research, Education, and Clinical Center (MIRECC), VA Puget Sound, Seattle, WA, United States of America
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, United States of America
| | - Ge Li
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, United States of America
- Geriatric Research, Education, and Clinical Center, Veterans Affairs (VA) Puget Sound Health Care System (VA Puget Sound), Seattle, WA, United States of America
| | - Robert J. Lipshutz
- Institute for Systems Biology, Seattle, WA, United States of America
- PreCyte Inc., Seattle, WA, United States of America
| | - John D. Aitchison
- Institute for Systems Biology, Seattle, WA, United States of America
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, United States of America
| | - Jennifer J. Smith
- Institute for Systems Biology, Seattle, WA, United States of America
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, United States of America
- PreCyte Inc., Seattle, WA, United States of America
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16
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Identifying a gene expression signature of cluster headache in blood. Sci Rep 2017; 7:40218. [PMID: 28074859 PMCID: PMC5225606 DOI: 10.1038/srep40218] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 12/05/2016] [Indexed: 12/12/2022] Open
Abstract
Cluster headache is a relatively rare headache disorder, typically characterized by multiple daily, short-lasting attacks of excruciating, unilateral (peri-)orbital or temporal pain associated with autonomic symptoms and restlessness. To better understand the pathophysiology of cluster headache, we used RNA sequencing to identify differentially expressed genes and pathways in whole blood of patients with episodic (n = 19) or chronic (n = 20) cluster headache in comparison with headache-free controls (n = 20). Gene expression data were analysed by gene and by module of co-expressed genes with particular attention to previously implicated disease pathways including hypocretin dysregulation. Only moderate gene expression differences were identified and no associations were found with previously reported pathogenic mechanisms. At the level of functional gene sets, associations were observed for genes involved in several brain-related mechanisms such as GABA receptor function and voltage-gated channels. In addition, genes and modules of co-expressed genes showed a role for intracellular signalling cascades, mitochondria and inflammation. Although larger study samples may be required to identify the full range of involved pathways, these results indicate a role for mitochondria, intracellular signalling and inflammation in cluster headache.
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17
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Hasegawa M, Hara-Miyauchi C, Ohta H, Sakimura K, Okano H, Okano HJ. Analysis of RNA metabolism in peripheral WBCs of TDP-43 KI mice identifies novel biomarkers of ALS. Neurosci Res 2015; 106:12-22. [PMID: 26672899 DOI: 10.1016/j.neures.2015.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/25/2015] [Accepted: 11/27/2015] [Indexed: 12/11/2022]
Abstract
Diagnostic biomarkers for amyotrophic lateral sclerosis (ALS) have yet to be identified. One of the causes of neuronal cell death in neurodegenerative diseases is abnormal RNA metabolism, although the mechanisms by which this occurs are unclear. Detection of abnormal RNA metabolism in white blood cells (WBCs) could lead to a new biomarker of ALS onset. TAR DNA-binding protein 43kDa (TDP-43) is an RNA-binding protein that regulates RNA metabolism. We previously developed a mouse model of ALS that exhibits adult-onset motor dysfunction; these mutant TDP-43 knock in (KI) mice heterozygously express mutant human TDP-43 (A382T or G348C). In the present study, we examined TDP-43 mRNA levels in WBCs of KI mice and found that A382T mutant mRNA is significantly higher than G348C. Our results suggest that each mutant TDP-43 induces distinct RNA metabolism, and that the expression of total TDP-43 alone in WBC is not suitable as an ALS biomarker. To identify additional candidates, we focused on survival and apoptosis-related factors and examined their mRNA metabolism in WBCs. mRNA levels of both Smn1 and Naip5 correlated with TDP-43 levels and also differed between A382T and G348C. Together, TDP-43 and these factors may enable detection of abnormalities in individual ALS pathologies.
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Affiliation(s)
- Minami Hasegawa
- Division of Regenerative Medicine, Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo 1058461, Japan; Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Chikako Hara-Miyauchi
- Division of Regenerative Medicine, Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo 1058461, Japan; Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Hiroki Ohta
- Division of Regenerative Medicine, Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo 1058461, Japan; Vascular Surgery, Department of Surgery, Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo 1058461, Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, 1-757 Asahimachidori Niigata Chuo-ku, Niigata 951-8585, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| | - Hirotaka James Okano
- Division of Regenerative Medicine, Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo 1058461, Japan; Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
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18
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Zhou W, Zhu Y, Chen S, Xu R, Wang K. Fibroblast growth factor receptor 1 promotes MG63 cell proliferation and is associated with increased expression of cyclin-dependent kinase 1 in osteosarcoma. Mol Med Rep 2015; 13:713-9. [PMID: 26648125 PMCID: PMC4686061 DOI: 10.3892/mmr.2015.4597] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 08/05/2015] [Indexed: 12/12/2022] Open
Abstract
Osteosarcoma is the most common type of malignant bone tumor in adolescents and young adults. However, current understanding of osteosarcomagenesis remains limited. In the present study, the role of fibroblast growth factor receptor 1 (FGFR1) in human osteosarcoma cell proliferation was investigated, and the possible pathways that contribute to FGFR1‑mediated osteosarcoma cell proliferation were examined using microarray analysis. The expression of FGFR1 in osteosarcoma tissues was assessed by reverse transcription-quantitative polymerase chain reaction and immunohistochemistry. The results demonstrated that FGFR1 was markedly increased in osteosarcoma tissues, and that the overexpression of FGFR1 in MG63 cells significantly promoted cell proliferation, as observed using the cell viability assay. In addition, FGFR1‑mediated cell proliferation was closely associated with cell cycle re‑distribution, as determined by microarray analysis. Western blotting identified that the expression of cyclin-dependent kinase 1 (CDK1) was correspondingly increased in response to the overexpression of FGFR1. These results indicated that FGFR1 contributes to cell proliferation in osteosarcoma MG63 cells, and FGFR1 mediated cell proliferation may be attributed to the regulation of the cell cycle regulator, CDK1. These findings provide evidence to support the potential use of molecule target therapy against FGFR1 as a promising strategy in osteosarcoma treatment and prevention.
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Affiliation(s)
- Wei Zhou
- Department of Orthopaedics, The Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Yue Zhu
- Department of Orthopaedics, The Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Song Chen
- Department of Orthopaedics, The Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Ruijun Xu
- Department of Orthopaedics, The Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Kunzheng Wang
- Department of Orthopaedics, The Second Hospital Affiliated to Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
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19
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Changes in TDP-43 expression in development, aging, and in the neurofilament light protein knockout mouse. Neurobiol Aging 2015; 36:1151-9. [DOI: 10.1016/j.neurobiolaging.2014.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/30/2014] [Accepted: 10/03/2014] [Indexed: 12/12/2022]
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20
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Blood biomarkers for amyotrophic lateral sclerosis: myth or reality? BIOMED RESEARCH INTERNATIONAL 2014; 2014:525097. [PMID: 24991560 PMCID: PMC4060749 DOI: 10.1155/2014/525097] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal condition primarily characterized by the selective loss of upper and lower motor neurons. At present, the diagnosis and monitoring of ALS is based on clinical examination, electrophysiological findings, medical history, and exclusion of confounding disorders. There is therefore an undeniable need for molecular biomarkers that could give reliable information on the onset and progression of ALS in clinical practice and therapeutic trials. From a practical point of view, blood offers a series of advantages, including easy handling and multiple testing at a low cost, that make it an ideal source of biomarkers. In this review, we revisited the findings of many studies that investigated the presence of systemic changes at the molecular and cellular level in patients with ALS. The results of these studies reflect the diversity in the pathological mechanisms contributing to disease (e.g., excitotoxicity, oxidative stress, neuroinflammation, metabolic dysfunction, and neurodegeneration, among others) and provide relatively successful evidence of the usefulness of a wide-ranging panel of molecules as potential biomarkers. More studies, hopefully internationally coordinated, would be needed, however, to translate the application of these biomarkers into benefit for patients.
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21
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Luque-Baena RM, Urda D, Gonzalo Claros M, Franco L, Jerez JM. Robust gene signatures from microarray data using genetic algorithms enriched with biological pathway keywords. J Biomed Inform 2014; 49:32-44. [PMID: 24480647 DOI: 10.1016/j.jbi.2014.01.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 01/09/2014] [Accepted: 01/16/2014] [Indexed: 12/12/2022]
Abstract
Genetic algorithms are widely used in the estimation of expression profiles from microarrays data. However, these techniques are unable to produce stable and robust solutions suitable to use in clinical and biomedical studies. This paper presents a novel two-stage evolutionary strategy for gene feature selection combining the genetic algorithm with biological information extracted from the KEGG database. A comparative study is carried out over public data from three different types of cancer (leukemia, lung cancer and prostate cancer). Even though the analyses only use features having KEGG information, the results demonstrate that this two-stage evolutionary strategy increased the consistency, robustness and accuracy of a blind discrimination among relapsed and healthy individuals. Therefore, this approach could facilitate the definition of gene signatures for the clinical prognosis and diagnostic of cancer diseases in a near future. Additionally, it could also be used for biological knowledge discovery about the studied disease.
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Affiliation(s)
- R M Luque-Baena
- Departmento de Lenguajes y Ciencias de la Computación, University of Málaga, Bulevar Louis Pasteur, 35, 29071 Málaga, Spain.
| | - D Urda
- Departmento de Lenguajes y Ciencias de la Computación, University of Málaga, Bulevar Louis Pasteur, 35, 29071 Málaga, Spain; Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain.
| | - M Gonzalo Claros
- Supercomputing and Bioinformatics Centre, University of Málaga, C/ Severo Ochoa, 34, 29590 Málaga, Spain.
| | - L Franco
- Departmento de Lenguajes y Ciencias de la Computación, University of Málaga, Bulevar Louis Pasteur, 35, 29071 Málaga, Spain; Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain.
| | - J M Jerez
- Departmento de Lenguajes y Ciencias de la Computación, University of Málaga, Bulevar Louis Pasteur, 35, 29071 Málaga, Spain; Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain.
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22
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Bayatti N, Cooper-Knock J, Bury JJ, Wyles M, Heath PR, Kirby J, Shaw PJ. Comparison of blood RNA extraction methods used for gene expression profiling in amyotrophic lateral sclerosis. PLoS One 2014; 9:e87508. [PMID: 24475299 PMCID: PMC3903649 DOI: 10.1371/journal.pone.0087508] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 12/26/2013] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that causes death within a mean of 2–3 years from symptom onset. There is no diagnostic test and the delay from symptom onset to diagnosis averages 12 months. The identification of prognostic and diagnostic biomarkers in ALS would facilitate earlier diagnosis and faster monitoring of treatments. Gene expression profiling (GEP) can help to identify these markers as well as therapeutic targets in neurological diseases. One source of genetic material for GEP in ALS is peripheral blood, which is routinely accessed from patients. However, a high proportion of globin mRNA in blood can mask important genetic information. A number of methods allow safe collection, storage and transport of blood as well as RNA stabilisation, including the PAXGENE and TEMPUS systems for the collection of whole blood and LEUKOLOCK which enriches for the leukocyte population. Here we compared these three systems and assess their suitability for GEP in ALS. We collected blood from 8 sporadic ALS patients and 7 controls. PAXGENE and TEMPUS RNA extracted samples additionally underwent globin depletion using GlobinClear. RNA was amplified and hybridised onto Affymetrix U133 Plus 2.0 arrays. Lists of genes differentially regulated in ALS patients and controls were created for each method using the R package PUMA, and RT-PCR validation was carried out on selected genes. TEMPUS/GlobinClear, and LEUKOLOCK produced high quality RNA with sufficient yield, and consistent array expression profiles. PAXGENE/GlobinClear yield and quality were lower. Globin depletion for PAXGENE and TEMPUS uncovered the presence of over 60% more transcripts than when samples were not depleted. TEMPUS/GlobinClear and LEUKOLOCK gene lists respectively contained 3619 and 3047 genes differentially expressed between patients and controls. Real-time PCR validation revealed similar reliability between these two methods and gene ontology analyses revealed similar pathways differentially regulated in disease compared to controls.
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Affiliation(s)
- Nadhim Bayatti
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Joanna J. Bury
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Matthew Wyles
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Paul R. Heath
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
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23
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Heath PR, Kirby J, Shaw PJ. Investigating cell death mechanisms in amyotrophic lateral sclerosis using transcriptomics. Front Cell Neurosci 2013; 7:259. [PMID: 24381542 PMCID: PMC3865770 DOI: 10.3389/fncel.2013.00259] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 11/28/2013] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a motor neuron disease characterized by degeneration and loss of upper and lower motor neurons from the motor cortex, brainstem and spinal cord although evidence is suggesting that there is further involvement of other cell types in the surrounding tissue. Transcriptomic analysis by gene expression profiling using microarray technology has enabled the determination of patterns of cell death in the degenerating tissues. This work has examined gene expression at the level of the tissue and individual cell types in both sporadic and familial forms of the disease. In addition, further studies have examined the differential vulnerability of neuronal cells in different regions of the central nervous system. Model systems have also provided further information to help unravel the mechanisms that lead to death of the motor neurons in disease and also provided novel insights. In this review we shall describe the methods that have been used in these investigations and describe how they have contributed to our knowledge of the cell death mechanisms in ALS.
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Affiliation(s)
- Paul R Heath
- Sheffield Institute for Translational Neuroscience, University of Sheffield Sheffield, UK
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience, University of Sheffield Sheffield, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience, University of Sheffield Sheffield, UK
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Milani P, Amadio M, Laforenza U, Dell'Orco M, Diamanti L, Sardone V, Gagliardi S, Govoni S, Ceroni M, Pascale A, Cereda C. Posttranscriptional regulation of SOD1 gene expression under oxidative stress: Potential role of ELAV proteins in sporadic ALS. Neurobiol Dis 2013; 60:51-60. [DOI: 10.1016/j.nbd.2013.08.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 07/05/2013] [Accepted: 08/07/2013] [Indexed: 11/28/2022] Open
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25
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Naughton BJ, Duncan FJ, Murrey D, Ware T, Meadows A, McCarty DM, Fu H. Amyloidosis, synucleinopathy, and prion encephalopathy in a neuropathic lysosomal storage disease: the CNS-biomarker potential of peripheral blood. PLoS One 2013; 8:e80142. [PMID: 24278249 PMCID: PMC3836978 DOI: 10.1371/journal.pone.0080142] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 09/30/2013] [Indexed: 12/12/2022] Open
Abstract
Mucopolysaccharidosis (MPS) IIIB is a devastating neuropathic lysosomal storage disease with complex pathology. This study identifies molecular signatures in peripheral blood that may be relevant to MPS IIIB pathogenesis using a mouse model. Genome-wide gene expression microarrays on pooled RNAs showed dysregulation of 2,802 transcripts in blood from MPS IIIB mice, reflecting pathological complexity of MPS IIIB, encompassing virtually all previously reported and as yet unexplored disease aspects. Importantly, many of the dysregulated genes are reported to be tissue-specific. Further analyses of multiple genes linked to major pathways of neurodegeneration demonstrated a strong brain-blood correlation in amyloidosis and synucleinopathy in MPS IIIB. We also detected prion protein (Prnp) deposition in the CNS and Prnp dysregulation in the blood in MPS IIIB mice, suggesting the involvement of Prnp aggregation in neuropathology. Systemic delivery of trans-BBB-neurotropic rAAV9-hNAGLU vector mediated not only efficient restoration of functional α-N-acetylglucosaminidase and clearance of lysosomal storage pathology in the central nervous system (CNS) and periphery, but also the correction of impaired neurodegenerative molecular pathways in the brain and blood. Our data suggest that molecular changes in blood may reflect pathological status in the CNS and provide a useful tool for identifying potential CNS-specific biomarkers for MPS IIIB and possibly other neurological diseases.
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Affiliation(s)
- Bartholomew J. Naughton
- Center for Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - F. Jason Duncan
- Center for Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Darren Murrey
- Center for Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Tierra Ware
- Center for Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Aaron Meadows
- Center for Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Douglas M. McCarty
- Center for Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
| | - Haiyan Fu
- Center for Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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26
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de Oliveira GP, Alves CJ, Chadi G. Early gene expression changes in spinal cord from SOD1(G93A) Amyotrophic Lateral Sclerosis animal model. Front Cell Neurosci 2013; 7:216. [PMID: 24302897 PMCID: PMC3831149 DOI: 10.3389/fncel.2013.00216] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/29/2013] [Indexed: 11/13/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is an adult-onset and fast progression neurodegenerative disease that leads to the loss of motor neurons. Mechanisms of selective motor neuron loss in ALS are unknown. The early events occurring in the spinal cord that may contribute to motor neuron death are not described, neither astrocytes participation in the pre-symptomatic phases of the disease. In order to identify ALS early events, we performed a microarray analysis employing a whole mouse genome platform to evaluate the gene expression pattern of lumbar spinal cords of transgenic SOD1G93A mice and their littermate controls at pre-symptomatic ages of 40 and 80 days. Differentially expressed genes were identified by means of the Bioconductor packages Agi4×44Preprocess and limma. FunNet web based tool was used for analysis of over-represented pathways. Furthermore, immunolabeled astrocytes from 40 and 80 days old mice were submitted to laser microdissection and RNA was extracted for evaluation of a selected gene by qPCR. Statistical analysis has pointed to 492 differentially expressed genes (155 up and 337 down regulated) in 40 days and 1105 (433 up and 672 down) in 80 days old ALS mice. KEGG analysis demonstrated the over-represented pathways tight junction, antigen processing and presentation, oxidative phosphorylation, endocytosis, chemokine signaling pathway, ubiquitin mediated proteolysis and glutamatergic synapse at both pre-symptomatic ages. Ube2i gene expression was evaluated in astrocytes from both transgenic ages, being up regulated in 40 and 80 days astrocytes enriched samples. Our data points to important early molecular events occurring in pre-symptomatic phases of ALS in mouse model. Early SUMOylation process linked to astrocytes might account to non-autonomous cell toxicity in ALS. Further studies on the signaling pathways presented here may provide new insights to better understand the events triggering motor neuron death in this devastating disorder.
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Affiliation(s)
- Gabriela P de Oliveira
- Department of Neurology, Neuroregeneration Center, University of São Paulo School of Medicine São Paulo, Brazil
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27
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Cereda C, Leoni E, Milani P, Pansarasa O, Mazzini G, Guareschi S, Alvisi E, Ghiroldi A, Diamanti L, Bernuzzi S, Ceroni M, Cova E. Altered intracellular localization of SOD1 in leukocytes from patients with sporadic amyotrophic lateral sclerosis. PLoS One 2013; 8:e75916. [PMID: 24155874 PMCID: PMC3796534 DOI: 10.1371/journal.pone.0075916] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 08/17/2013] [Indexed: 12/24/2022] Open
Abstract
Several lines of evidence support the hypothesis of a toxic role played by wild type SOD1 (WT-SOD1) in the pathogenesis of sporadic amyotrophic lateral sclerosis (SALS). In this study we investigated both distribution and expression profile of WT-SOD1 in leukocytes from 19 SALS patients and 17 healthy individuals. Immunofluorescence experiments by confocal microscopy showed that SOD1 accumulates in the nuclear compartment in a group of SALS subjects. These results were also confirmed by western blot carried out on soluble nuclear and cytoplasmic fractions, with increased nuclear SOD1 level (p<0.05). In addition, we observed the presence of cytoplasmic SOD1 aggregates in agreement with an increased amount of the protein recovered by the insoluble fraction. A further confirmation of the overall increased level of SOD1 has been obtained from single cells analysis using flow cytometry as cells from SALS patients showed an higher SOD1 protein content (p<0.05). These findings add further evidence to the hypothesis of an altered WT-SOD1 expression profile in peripheral blood mononuclear cells (PBMCs) from patients with ALS suggesting that WT-SOD1 species with different degrees of solubility could be involved in the pathogenesis of the disease.
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Affiliation(s)
- Cristina Cereda
- Laboratory of Experimental Neurobiology, “C. Mondino” National Neurological Institute, Pavia, Italy
| | - Emanuela Leoni
- Laboratory of Experimental Neurobiology, “C. Mondino” National Neurological Institute, Pavia, Italy
- Department of Brain and Behavioral Science, University of Pavia, Pavia, Italy
- * E-mail:
| | - Pamela Milani
- Laboratory of Experimental Neurobiology, “C. Mondino” National Neurological Institute, Pavia, Italy
- Department of Brain and Behavioral Science, University of Pavia, Pavia, Italy
| | - Orietta Pansarasa
- Laboratory of Experimental Neurobiology, “C. Mondino” National Neurological Institute, Pavia, Italy
| | - Giuliano Mazzini
- IGM-CNR, Histochemistry and Cytometry, Department of Animal Biology, University of Pavia, Pavia, Italy
| | - Stefania Guareschi
- Laboratory of Experimental Neurobiology, “C. Mondino” National Neurological Institute, Pavia, Italy
| | - Elena Alvisi
- Department of Brain and Behavioral Science, University of Pavia, Pavia, Italy
- Division of General Neurology, “C. Mondino” National Neurological Institute, Pavia, Italy
| | - Andrea Ghiroldi
- Laboratory of Experimental Neurobiology, “C. Mondino” National Neurological Institute, Pavia, Italy
- Department of Brain and Behavioral Science, University of Pavia, Pavia, Italy
| | - Luca Diamanti
- Department of Brain and Behavioral Science, University of Pavia, Pavia, Italy
- Division of General Neurology, “C. Mondino” National Neurological Institute, Pavia, Italy
| | - Stefano Bernuzzi
- Immunohematological and Transfusional Service and Centre of Transplantation Immunology, IRCCS Foundation “San Matteo”, Pavia, Italy
| | - Mauro Ceroni
- Department of Brain and Behavioral Science, University of Pavia, Pavia, Italy
- Division of General Neurology, “C. Mondino” National Neurological Institute, Pavia, Italy
| | - Emanuela Cova
- Laboratory of Experimental Neurobiology, “C. Mondino” National Neurological Institute, Pavia, Italy
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28
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White WM, Brost B, Sun Z, Rose C, Craici I, Wagner SJ, Turner ST, Garovic VD. Genome-wide methylation profiling demonstrates hypermethylation in maternal leukocyte DNA in preeclamptic compared to normotensive pregnancies. Hypertens Pregnancy 2013; 32:257-69. [PMID: 23782156 PMCID: PMC3741019 DOI: 10.3109/10641955.2013.796970] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To compare genome-wide methylation profiles in maternal leukocyte DNA between normotensive and preeclamptic pregnant women at delivery. METHODS Age, body mass index matched case-control comparison of methylation at 27,578 cytosine-- guanine sites in 14,495 genes in maternal leukocyte DNA in women with preeclampsia (PE; n = 14) and normotensive controls (n = 14). RESULTS PE was associated with widespread differential methylation favoring hypermethylation. Pathway analysis identified the best matched process as a neuropeptide signaling pathway (p < 10(-5)); best matched disease as eclampsia (p < 9.97 × 10(-20)). Significantly differentially methylated genes (GRIN2b. GABRA1. PCDHB7, and BEX1) are associated with seizures. CONCLUSION Altered maternal leukocyte DNA methylation is associated with PE at delivery, and differential methylation of certain neuronal genes may explain the risk for eclampsia.
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Affiliation(s)
- Wendy M White
- Department of OB/GYN, Division of Maternal Fetal Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
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29
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Abnormal regenerative responses and impaired axonal outgrowth after nerve crush in TDP-43 transgenic mouse models of amyotrophic lateral sclerosis. J Neurosci 2013; 32:18186-95. [PMID: 23238732 DOI: 10.1523/jneurosci.2267-12.2012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tar DNA binding protein 43 (TDP-43) mislocalization and aggregation is a hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia. Moreover, TDP-43 mRNA was found to be upregulated by ∼2.5-fold in the spinal cord of sporadic ALS subjects. Here we have examined the effects of nerve injury in new transgenic mouse models overexpressing by approximately threefold wild-type or mutant (G348C) TDP-43 species. Four weeks after axonal crush of sciatic nerve, TDP-43 transgenic mice remained paralyzed at the injured limb unlike control mice, which had regained most of their normal mobility. In contrast to normal mice, TDP-43 transgenic mice exhibited sustained elevation of TDP-43 cytoplasmic levels in motor neurons after nerve crush, and the relocalization of TDP-43 to the nucleus was delayed by several weeks. After crush, peripherin and ubiquitin levels remained also significantly elevated in TDP-43 transgenic mice compared with control mice. Analysis of the sciatic nerve at 11 d after nerve crush showed that the number of regenerating axons in the distal portion of the lesion was considerably reduced in TDP-43 transgenic mice, especially in TDP-43(G348C) mice, which exhibited a reduction of ∼40%. In addition, markers of neuroinflammation were detected at much higher levels in TDP-43 transgenic mice. These results suggest that a deregulation of TDP-43 expression in ALS is a phenomenon that can affect the regenerative responses to neuronal injury and regrowth potential of axons.
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Baciu C, Thompson KJ, Mougeot JL, Brooks BR, Weller JW. The LO-BaFL method and ALS microarray expression analysis. BMC Bioinformatics 2012; 13:244. [PMID: 23006766 PMCID: PMC3526454 DOI: 10.1186/1471-2105-13-244] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 09/05/2012] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Sporadic Amyotrophic Lateral Sclerosis (sALS) is a devastating, complex disease of unknown etiology. We studied this disease with microarray technology to capture as much biological complexity as possible. The Affymetrix-focused BaFL pipeline takes into account problems with probes that arise from physical and biological properties, so we adapted it to handle the long-oligonucleotide probes on our arrays (hence LO-BaFL). The revised method was tested against a validated array experiment and then used in a meta-analysis of peripheral white blood cells from healthy control samples in two experiments. We predicted differentially expressed (DE) genes in our sALS data, combining the results obtained using the TM4 suite of tools with those from the LO-BaFL method. Those predictions were tested using qRT-PCR assays. RESULTS LO-BaFL filtering and DE testing accurately predicted previously validated DE genes in a published experiment on coronary artery disease (CAD). Filtering healthy control data from the sALS and CAD studies with LO-BaFL resulted in highly correlated expression levels across many genes. After bioinformatics analysis, twelve genes from the sALS DE gene list were selected for independent testing using qRT-PCR assays. High-quality RNA from six healthy Control and six sALS samples yielded the predicted differential expression for 7 genes: TARDBP, SKIV2L2, C12orf35, DYNLT1, ACTG1, B2M, and ILKAP. Four of the seven have been previously described in sALS studies, while ACTG1, B2M and ILKAP appear in the context of this disease for the first time. Supplementary material can be accessed at: http://webpages.uncc.edu/~cbaciu/LO-BaFL/supplementary_data.html. CONCLUSION LO-BaFL predicts DE results that are broadly similar to those of other methods. The small healthy control cohort in the sALS study is a reasonable foundation for predicting DE genes. Modifying the BaFL pipeline allowed us to remove noise and systematic errors, improving the power of this study, which had a small sample size. Each bioinformatics approach revealed DE genes not predicted by the other; subsequent PCR assays confirmed seven of twelve candidates, a relatively high success rate.
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Affiliation(s)
- Cristina Baciu
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Kevin J Thompson
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jean-Luc Mougeot
- ALS Biomarker Laboratory, Carolinas Neuromuscular/ALS-MDA Center, Department of Neurology, Carolinas Medical Center, Charlotte, NC, 28207, USA
- University of North Carolina School of Medicine, Charlotte Campus, Charlotte, NC, 28203, USA
| | - Benjamin R Brooks
- ALS Biomarker Laboratory, Carolinas Neuromuscular/ALS-MDA Center, Department of Neurology, Carolinas Medical Center, Charlotte, NC, 28207, USA
- University of North Carolina School of Medicine, Charlotte Campus, Charlotte, NC, 28203, USA
| | - Jennifer W Weller
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
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31
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Cooper-Knock J, Kirby J, Ferraiuolo L, Heath PR, Rattray M, Shaw PJ. Gene expression profiling in human neurodegenerative disease. Nat Rev Neurol 2012; 8:518-30. [PMID: 22890216 DOI: 10.1038/nrneurol.2012.156] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcriptome study in neurodegenerative disease has advanced considerably in the past 5 years. Increasing scientific rigour and improved analytical tools have led to more-reproducible data. Many transcriptome analysis platforms assay the expression of the entire genome, enabling a complete biological context to be captured. Gene expression profiling (GEP) is, therefore, uniquely placed to discover pathways of disease pathogenesis, potential therapeutic targets, and biomarkers. This Review summarizes microarray human GEP studies in the common neurodegenerative diseases amyotrophic lateral sclerosis (ALS), Parkinson disease (PD) and Alzheimer disease (AD). Several interesting reports have compared pathological gene expression in different patient groups, disease stages and anatomical areas. In all three diseases, GEP has revealed dysregulation of genes related to neuroinflammation. In ALS and PD, gene expression related to RNA splicing and protein turnover is disrupted, and several studies in ALS support involvement of the cytoskeleton. GEP studies have implicated the ubiquitin-proteasome system in PD pathogenesis, and have provided evidence of mitochondrial dysfunction in PD and AD. Lastly, in AD, a possible role for dysregulation of intracellular signalling pathways, including calcium signalling, has been highlighted. This Review also provides a discussion of methodological considerations in microarray sample preparation and data analysis.
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Affiliation(s)
- Johnathan Cooper-Knock
- Academic Unit of Neurology, Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
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32
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From Transcriptome to Noncoding RNAs: Implications in ALS Mechanism. Neurol Res Int 2012; 2012:278725. [PMID: 22778949 PMCID: PMC3385659 DOI: 10.1155/2012/278725] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/27/2012] [Accepted: 05/11/2012] [Indexed: 12/12/2022] Open
Abstract
In the last years, numerous studies have focused on understanding the metabolism of RNA and its implication in disease processes but abnormal RNA metabolism is still unknown. RNA plays a central role in translating genetic information into proteins and in many other catalytic and regulatory tasks. Recent advances in the study of RNA metabolism revealed complex pathways for the generation and maintenance of functional RNA in amyotrophic lateral sclerosis (ALS). Interestingly, perturbations in RNA processing have been described in ALS at various levels such as gene transcription, mRNA stabilization, transport, and translational regulations. In this paper, we will discuss the alteration of RNA profile in ALS disease, starting from transcription, the first step leading to gene expression, through the posttranscriptional regulation, including RNA/DNA binding proteins and aberrant exon splicing to protein noncoding RNAs, as lncRNA and microRNA.
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