1
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Pocock J, Vasilopoulou F, Svensson E, Cosker K. Microglia and TREM2. Neuropharmacology 2024; 257:110020. [PMID: 38821351 DOI: 10.1016/j.neuropharm.2024.110020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/20/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
TREM2 is a membrane receptor solely expressed on microglia in normal brain. In this review we outline recent advances in TREM2 biology and its implications for microglial function, with particular emphasis on findings from iPSC-derived microglia (iMG) expressing TREM2 loss-of-function mutations. Alterations in receptor proximal and distal signalling underlie TREM2 risk variants linked to neurodegenerative disease, principally NH-linked FTD, and late-onset AD, but emerging data suggest roles for TREM2 in PD, MS and ALS. TREM2 downstream functions include phagocytosis of myelin debris, amyloid beta peptides, and phosphatidylserine-expressing cells (resulting from damage or stress). Microglial survival, migration, DAMP signalling, inflammasome activation, and intercellular signalling including tau spreading via exosomes, as well as roles for sTREM2 in protection and as a biomarker are discussed. The role of TREM2 in metabolic homeostasis, and immunometabolic switching are discussed regarding microglial responses to damage and protection. The use of iPSC models to investigate the role of TREM2 in AD, PD, MS, ALS, and other neurodegenerative diseases could prove invaluable due to their ability to recapitulate human pathology, allowing a full understanding of TREM2 and microglial involvement in the underlying disease mechanisms and progression. This article is part of the Special Issue on "Microglia".
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Affiliation(s)
- Jennifer Pocock
- Department of Neuroinflammation, And Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, 1 Wakefield Street, London, WC1N1PJ, UK.
| | - Foteini Vasilopoulou
- Department of Neuroinflammation, And Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, 1 Wakefield Street, London, WC1N1PJ, UK
| | - Elina Svensson
- Department of Neuroinflammation, And Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, 1 Wakefield Street, London, WC1N1PJ, UK
| | - Katharina Cosker
- Department of Neuroinflammation, And Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, 1 Wakefield Street, London, WC1N1PJ, UK
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2
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Frost B, Dubnau J. The Role of Retrotransposons and Endogenous Retroviruses in Age-Dependent Neurodegenerative Disorders. Annu Rev Neurosci 2024; 47:123-143. [PMID: 38663088 DOI: 10.1146/annurev-neuro-082823-020615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2024]
Abstract
Over 40% of the human genome is composed of retrotransposons, DNA species that hold the potential to replicate via an RNA intermediate and are evolutionarily related to retroviruses. Retrotransposons are most studied for their ability to jump within a genome, which can cause DNA damage and novel insertional mutations. Retrotransposon-encoded products, including viral-like proteins, double-stranded RNAs, and extrachromosomal circular DNAs, can also be potent activators of the innate immune system. A growing body of evidence suggests that retrotransposons are activated in age-related neurodegenerative disorders and that such activation causally contributes to neurotoxicity. Here we provide an overview of retrotransposon biology and outline evidence of retrotransposon activation in age-related neurodegenerative disorders, with an emphasis on those involving TAR-DNA binding protein-43 (TDP-43) and tau. Studies to date provide the basis for ongoing clinical trials and hold promise for innovative strategies to ameliorate the adverse effects of retrotransposon dysregulation in neurodegenerative disorders.
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Affiliation(s)
- Bess Frost
- Sam and Ann Barshop Institute for Longevity and Aging Studies, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, and Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas, USA;
| | - Josh Dubnau
- Department of Anesthesiology and Department of Neurobiology and Behavior, Stony Brook School of Medicine, Stony Brook, New York, USA;
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3
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He L, Zhou Q, Xiu C, Shao Y, Shen D, Meng H, Le W, Chen S. Circulating proteomic biomarkers for diagnosing sporadic amyotrophic lateral sclerosis: a cross-sectional study. Neural Regen Res 2024; 19:1842-1848. [PMID: 38103252 PMCID: PMC10960292 DOI: 10.4103/1673-5374.389357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/02/2023] [Accepted: 08/29/2023] [Indexed: 12/18/2023] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202408000-00039/figure1/v/2023-12-16T180322Z/r/image-tiff Biomarkers are required for the early detection, prognosis prediction, and monitoring of amyotrophic lateral sclerosis, a progressive disease. Proteomics is an unbiased and quantitative method that can be used to detect neurochemical signatures to aid in the identification of candidate biomarkers. In this study, we used a label-free quantitative proteomics approach to screen for substantially differentially regulated proteins in ten patients with sporadic amyotrophic lateral sclerosis compared with five healthy controls. Substantial upregulation of serum proteins related to multiple functional clusters was observed in patients with sporadic amyotrophic lateral sclerosis. Potential biomarkers were selected based on functionality and expression specificity. To validate the proteomics profiles, blood samples from an additional cohort comprising 100 patients with sporadic amyotrophic lateral sclerosis and 100 healthy controls were subjected to enzyme-linked immunosorbent assay. Eight substantially upregulated serum proteins in patients with sporadic amyotrophic lateral sclerosis were selected, of which the cathelicidin-related antimicrobial peptide demonstrated the best discriminative ability between patients with sporadic amyotrophic lateral sclerosis and healthy controls (area under the curve [AUC] = 0.713, P < 0.0001). To further enhance diagnostic accuracy, a multi-protein combined discriminant algorithm was developed incorporating five proteins (hemoglobin beta, cathelicidin-related antimicrobial peptide, talin-1, zyxin, and translationally-controlled tumor protein). The algorithm achieved an AUC of 0.811 and a P-value of < 0.0001, resulting in 79% sensitivity and 71% specificity for the diagnosis of sporadic amyotrophic lateral sclerosis. Subsequently, the ability of candidate biomarkers to discriminate between early-stage amyotrophic lateral sclerosis patients and controls, as well as patients with different disease severities, was examined. A two-protein panel comprising talin-1 and translationally-controlled tumor protein effectively distinguished early-stage amyotrophic lateral sclerosis patients from controls (AUC = 0.766, P < 0.0001). Moreover, the expression of three proteins (FK506 binding protein 1A, cathelicidin-related antimicrobial peptide, and hemoglobin beta-1) was found to increase with disease progression. The proteomic signatures developed in this study may help facilitate early diagnosis and monitor the progression of sporadic amyotrophic lateral sclerosis when used in combination with current clinical-based parameters.
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Affiliation(s)
- Lu He
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qinming Zhou
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaoyang Xiu
- Department of Neurology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, China
| | - Yaping Shao
- Center for Translational Research on Neurological Diseases, the First Affiliated Hospital, Dalian Medical University, Dalian, Liaoning Province, China
| | - Dingding Shen
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Huanyu Meng
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weidong Le
- Institute of Neurology, Sichuan Academy of Medical Sciences-Sichuan Provincial Hospital, Chengdu, Sichuan Province, China
| | - Sheng Chen
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
- Department of Neurology, Xinrui Hospital, Wuxi, Jiangsu Province, China
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4
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Pramanik S, Devi M H, Chakrabarty S, Paylar B, Pradhan A, Thaker M, Ayyadhury S, Manavalan A, Olsson PE, Pramanik G, Heese K. Microglia signaling in health and disease - Implications in sex-specific brain development and plasticity. Neurosci Biobehav Rev 2024; 165:105834. [PMID: 39084583 DOI: 10.1016/j.neubiorev.2024.105834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 07/21/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024]
Abstract
Microglia, the intrinsic neuroimmune cells residing in the central nervous system (CNS), exert a pivotal influence on brain development, homeostasis, and functionality, encompassing critical roles during both aging and pathological states. Recent advancements in comprehending brain plasticity and functions have spotlighted conspicuous variances between male and female brains, notably in neurogenesis, neuronal myelination, axon fasciculation, and synaptogenesis. Nevertheless, the precise impact of microglia on sex-specific brain cell plasticity, sculpting diverse neural network architectures and circuits, remains largely unexplored. This article seeks to unravel the present understanding of microglial involvement in brain development, plasticity, and function, with a specific emphasis on microglial signaling in brain sex polymorphism. Commencing with an overview of microglia in the CNS and their associated signaling cascades, we subsequently probe recent revelations regarding molecular signaling by microglia in sex-dependent brain developmental plasticity, functions, and diseases. Notably, C-X3-C motif chemokine receptor 1 (CX3CR1), triggering receptors expressed on myeloid cells 2 (TREM2), calcium (Ca2+), and apolipoprotein E (APOE) emerge as molecular candidates significantly contributing to sex-dependent brain development and plasticity. In conclusion, we address burgeoning inquiries surrounding microglia's pivotal role in the functional diversity of developing and aging brains, contemplating their potential implications for gender-tailored therapeutic strategies in neurodegenerative diseases.
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Affiliation(s)
- Subrata Pramanik
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| | - Harini Devi M
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Saswata Chakrabarty
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Berkay Paylar
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro 70182, Sweden
| | - Ajay Pradhan
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro 70182, Sweden
| | - Manisha Thaker
- Eurofins Lancaster Laboratories, Inc., 2425 New Holland Pike, Lancaster, PA 17601, USA
| | - Shamini Ayyadhury
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Arulmani Manavalan
- Department of Cariology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu 600077, India
| | - Per-Erik Olsson
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro 70182, Sweden
| | - Gopal Pramanik
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India.
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133791, the Republic of Korea.
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Pasternack N, Doucet-O'Hare T, Johnson K, Paulsen O, Nath A. Endogenous retroviruses are dysregulated in ALS. iScience 2024; 27:110147. [PMID: 38989463 PMCID: PMC11233923 DOI: 10.1016/j.isci.2024.110147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/25/2024] [Accepted: 05/27/2024] [Indexed: 07/12/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a universally fatal neurodegenerative disease with no cure. Human endogenous retroviruses (HERVs) have been implicated in its pathogenesis but their relevance to ALS is not fully understood. We examined bulk RNA-seq data from almost 2,000 ALS and unaffected control samples derived from the cortex and spinal cord. Using different methods of feature selection, including differential expression analysis and machine learning, we discovered that transcription of HERV-K loci 1q22 and 8p23.1 were significantly upregulated in the spinal cord of individuals with ALS. Additionally, we identified a subset of ALS patients with upregulated HERV-K expression in the cortex and spinal cord. We also found the expression of HERV-K loci 19q11 and 8p23.1 was correlated with protein coding genes previously implicated in ALS and dysregulated in ALS patients in this study. These results clarify the association of HERV-K and ALS and highlight specific genes in the pathobiology of late-stage ALS.
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Affiliation(s)
- Nicholas Pasternack
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Tara Doucet-O'Hare
- Neuro-Oncology Branch Stem Cell Team, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kory Johnson
- Bioinformatics Unit, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Ole Paulsen
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
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6
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Karagianni K, Dafou D, Xanthopoulos K, Sklaviadis T, Kanata E. RNA editing regulates glutamatergic synapses in the frontal cortex of a molecular subtype of Amyotrophic Lateral Sclerosis. Mol Med 2024; 30:101. [PMID: 38997636 PMCID: PMC11241978 DOI: 10.1186/s10020-024-00863-2] [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: 04/04/2024] [Accepted: 06/12/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Amyotrophic Lateral Sclerosis (ALS) is a highly heterogenous neurodegenerative disorder that primarily affects upper and lower motor neurons, affecting additional cell types and brain regions. Underlying molecular mechanisms are still elusive, in part due to disease heterogeneity. Molecular disease subtyping through integrative analyses including RNA editing profiling is a novel approach for identification of molecular networks involved in pathogenesis. METHODS We aimed to highlight the role of RNA editing in ALS, focusing on the frontal cortex and the prevalent molecular disease subtype (ALS-Ox), previously determined by transcriptomic profile stratification. We established global RNA editing (editome) and gene expression (transcriptome) profiles in control and ALS-Ox cases, utilizing publicly available RNA-seq data (GSE153960) and an in-house analysis pipeline. Functional annotation and pathway analyses identified molecular processes affected by RNA editing alterations. Pearson correlation analyses assessed RNA editing effects on expression. Similar analyses on additional ALS-Ox and control samples (GSE124439) were performed for verification. Targeted re-sequencing and qRT-PCR analysis targeting CACNA1C, were performed using frontal cortex tissue from ALS and control samples (n = 3 samples/group). RESULTS We identified reduced global RNA editing in the frontal cortex of ALS-Ox cases. Differentially edited transcripts are enriched in synapses, particularly in the glutamatergic synapse pathway. Bioinformatic analyses on additional ALS-Ox and control RNA-seq data verified these findings. We identified increased recoding at the Q621R site in the GRIK2 transcript and determined positive correlations between RNA editing and gene expression alterations in ionotropic receptor subunits GRIA2, GRIA3 and the CACNA1C transcript, which encodes the pore forming subunit of a post-synaptic L-type calcium channel. Experimental data verified RNA editing alterations and editing-expression correlation in CACNA1C, highlighting CACNA1C as a target for further study. CONCLUSIONS We provide evidence on the involvement of RNA editing in the frontal cortex of an ALS molecular subtype, highlighting a modulatory role mediated though recoding and gene expression regulation on glutamatergic synapse related transcripts. We report RNA editing effects in disease-related transcripts and validated editing alterations in CACNA1C. Our study provides targets for further functional studies that could shed light in underlying disease mechanisms enabling novel therapeutic approaches.
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Affiliation(s)
- Korina Karagianni
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece
| | - Dimitra Dafou
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece
| | - Konstantinos Xanthopoulos
- Laboratory of Pharmacology, Department of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001, Thermi, Greece
| | - Theodoros Sklaviadis
- Laboratory of Pharmacology, Department of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Eirini Kanata
- Laboratory of Pharmacology, Department of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
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7
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Lang R, Hodgson RE, Shelkovnikova TA. TDP-43 in nuclear condensates: where, how, and why. Biochem Soc Trans 2024:BST20231447. [PMID: 38958608 DOI: 10.1042/bst20231447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
TDP-43 is an abundant and ubiquitously expressed nuclear protein that becomes dysfunctional in a spectrum of neurodegenerative diseases. TDP-43's ability to phase separate and form/enter biomolecular condensates of varying size and composition is critical for its functionality. Despite the high density of phase-separated assemblies in the nucleus and the nuclear abundance of TDP-43, our understanding of the condensate-TDP-43 relationship in this cellular compartment is only emerging. Recent studies have also suggested that misregulation of nuclear TDP-43 condensation is an early event in the neurodegenerative disease amyotrophic lateral sclerosis. This review aims to draw attention to the nuclear facet of functional and aberrant TDP-43 condensation. We will summarise the current knowledge on how TDP-43 containing nuclear condensates form and function and how their homeostasis is affected in disease.
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Affiliation(s)
- Ruaridh Lang
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
| | - Rachel E Hodgson
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
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8
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Xie M, Miller AS, Pallegar PN, Umpierre A, Liang Y, Wang N, Zhang S, Nagaraj NK, Fogarty ZC, Ghayal NB, Oskarsson B, Zhao S, Zheng J, Qi F, Nguyen A, Dickson DW, Wu LJ. Rod-shaped microglia interact with neuronal dendrites to regulate cortical excitability in TDP-43 related neurodegeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.30.601396. [PMID: 39005475 PMCID: PMC11244918 DOI: 10.1101/2024.06.30.601396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Motor cortical hyperexcitability is well-documented in the presymptomatic stage of amyotrophic lateral sclerosis (ALS). However, the mechanisms underlying this early dysregulation are not fully understood. Microglia, as the principal immune cells of the central nervous system, have emerged as important players in sensing and regulating neuronal activity. Here we investigated the role of microglia in the motor cortical circuits in a mouse model of TDP-43 neurodegeneration (rNLS8). Utilizing multichannel probe recording and longitudinal in vivo calcium imaging in awake mice, we observed neuronal hyperactivity at the initial stage of disease progression. Spatial and single-cell RNA sequencing revealed that microglia are the primary responders to motor cortical hyperactivity. We further identified a unique subpopulation of microglia, rod-shaped microglia, which are characterized by a distinct morphology and transcriptional profile. Notably, rod-shaped microglia predominantly interact with neuronal dendrites and excitatory synaptic inputs to attenuate motor cortical hyperactivity. The elimination of rod-shaped microglia through TREM2 deficiency increased neuronal hyperactivity, exacerbated motor deficits, and further decreased survival rates of rNLS8 mice. Together, our results suggest that rod-shaped microglia play a neuroprotective role by attenuating cortical hyperexcitability in the mouse model of TDP-43 related neurodegeneration.
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9
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Limone F, Mordes DA, Couto A, Joseph BJ, Mitchell JM, Therrien M, Ghosh SD, Meyer D, Zhang Y, Goldman M, Bortolin L, Cobos I, Stevens B, McCarroll SA, Kadiu I, Burberry A, Pietiläinen O, Eggan K. Single-nucleus sequencing reveals enriched expression of genetic risk factors in extratelencephalic neurons sensitive to degeneration in ALS. NATURE AGING 2024; 4:984-997. [PMID: 38907103 PMCID: PMC11257952 DOI: 10.1038/s43587-024-00640-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/01/2024] [Indexed: 06/23/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by a progressive loss of motor function linked to degenerating extratelencephalic neurons/Betz cells (ETNs). The reasons why these neurons are selectively affected remain unclear. Here, to understand the unique molecular properties that may sensitize ETNs to ALS, we performed RNA sequencing of 79,169 single nuclei from cortices of patients and controls. In both patients and unaffected individuals, we found significantly higher expression of ALS risk genes in THY1+ ETNs, regardless of diagnosis. In patients, this was accompanied by the induction of genes involved in protein homeostasis and stress responses that were significantly induced in a wide collection of ETNs. Examination of oligodendroglial and microglial nuclei revealed patient-specific downregulation of myelinating genes in oligodendrocytes and upregulation of an endolysosomal reactive state in microglia. Our findings suggest that selective vulnerability of extratelencephalic neurons is partly connected to their intrinsic molecular properties sensitizing them to genetics and mechanisms of degeneration.
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Affiliation(s)
- Francesco Limone
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA.
| | - Daniel A Mordes
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Alexander Couto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Brian J Joseph
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Jana M Mitchell
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martine Therrien
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Sulagna Dia Ghosh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Yingying Zhang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Melissa Goldman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Laura Bortolin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Inma Cobos
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Beth Stevens
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Irena Kadiu
- Neuroinflammation Focus Area, UCB Pharma, Braine-l'Alleud, Belgium
| | - Aaron Burberry
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Olli Pietiläinen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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10
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Huang X, Lee S, Chen K, Kawaguchi R, Wiskow O, Ghosh S, Frost D, Perrault L, Pandey R, Klim JR, Boivin B, Hermawan C, Livak KJ, Geschwind DH, Wainger BJ, Eggan KC, Bean BP, Woolf CJ. Downregulation of the silent potassium channel Kv8.1 increases motor neuron vulnerability in amyotrophic lateral sclerosis. Brain Commun 2024; 6:fcae202. [PMID: 38911266 PMCID: PMC11191651 DOI: 10.1093/braincomms/fcae202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 04/10/2024] [Accepted: 06/07/2024] [Indexed: 06/25/2024] Open
Abstract
While voltage-gated potassium channels have critical roles in controlling neuronal excitability, they also have non-ion-conducting functions. Kv8.1, encoded by the KCNV1 gene, is a 'silent' ion channel subunit whose biological role is complex since Kv8.1 subunits do not form functional homotetramers but assemble with Kv2 to modify its ion channel properties. We profiled changes in ion channel expression in amyotrophic lateral sclerosis patient-derived motor neurons carrying a superoxide dismutase 1(A4V) mutation to identify what drives their hyperexcitability. A major change identified was a substantial reduction of KCNV1/Kv8.1 expression, which was also observed in patient-derived neurons with C9orf72 expansion. We then studied the effect of reducing KCNV1/Kv8.1 expression in healthy motor neurons and found it did not change neuronal firing but increased vulnerability to cell death. A transcriptomic analysis revealed dysregulated metabolism and lipid/protein transport pathways in KCNV1/Kv8.1-deficient motor neurons. The increased neuronal vulnerability produced by the loss of KCNV1/Kv8.1 was rescued by knocking down Kv2.2, suggesting a potential Kv2.2-dependent downstream mechanism in cell death. Our study reveals, therefore, unsuspected and distinct roles of Kv8.1 and Kv2.2 in amyotrophic lateral sclerosis-related neurodegeneration.
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Affiliation(s)
- Xuan Huang
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Seungkyu Lee
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Kuchuan Chen
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Riki Kawaguchi
- Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ole Wiskow
- Department of Stem Cell and Regenerative Biology and Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sulagna Ghosh
- Department of Stem Cell and Regenerative Biology and Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Devlin Frost
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Laura Perrault
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Roshan Pandey
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph R Klim
- Department of Stem Cell and Regenerative Biology and Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Bruno Boivin
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Crystal Hermawan
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Kenneth J Livak
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Daniel H Geschwind
- Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Brian J Wainger
- Department of Neurology, Mass General Brigham and Harvard Medical School, Boston, MA 02114, USA
| | - Kevin C Eggan
- Department of Stem Cell and Regenerative Biology and Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Bruce P Bean
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Clifford J Woolf
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
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11
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Caldi Gomes L, Hänzelmann S, Hausmann F, Khatri R, Oller S, Parvaz M, Tzeplaeff L, Pasetto L, Gebelin M, Ebbing M, Holzapfel C, Columbro SF, Scozzari S, Knöferle J, Cordts I, Demleitner AF, Deschauer M, Dufke C, Sturm M, Zhou Q, Zelina P, Sudria-Lopez E, Haack TB, Streb S, Kuzma-Kozakiewicz M, Edbauer D, Pasterkamp RJ, Laczko E, Rehrauer H, Schlapbach R, Carapito C, Bonetto V, Bonn S, Lingor P. Multiomic ALS signatures highlight subclusters and sex differences suggesting the MAPK pathway as therapeutic target. Nat Commun 2024; 15:4893. [PMID: 38849340 PMCID: PMC11161513 DOI: 10.1038/s41467-024-49196-y] [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: 08/03/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a debilitating motor neuron disease and lacks effective disease-modifying treatments. This study utilizes a comprehensive multiomic approach to investigate the early and sex-specific molecular mechanisms underlying ALS. By analyzing the prefrontal cortex of 51 patients with sporadic ALS and 50 control subjects, alongside four transgenic mouse models (C9orf72-, SOD1-, TDP-43-, and FUS-ALS), we have uncovered significant molecular alterations associated with the disease. Here, we show that males exhibit more pronounced changes in molecular pathways compared to females. Our integrated analysis of transcriptomes, (phospho)proteomes, and miRNAomes also identified distinct ALS subclusters in humans, characterized by variations in immune response, extracellular matrix composition, mitochondrial function, and RNA processing. The molecular signatures of human subclusters were reflected in specific mouse models. Our study highlighted the mitogen-activated protein kinase (MAPK) pathway as an early disease mechanism. We further demonstrate that trametinib, a MAPK inhibitor, has potential therapeutic benefits in vitro and in vivo, particularly in females, suggesting a direction for developing targeted ALS treatments.
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Affiliation(s)
- Lucas Caldi Gomes
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Sonja Hänzelmann
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabian Hausmann
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Robin Khatri
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sergio Oller
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mojan Parvaz
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Laura Tzeplaeff
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Laura Pasetto
- Research Center for ALS, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Marie Gebelin
- Laboratoire de Spectrométrie de Masse Bio-Organique, Université de Strasbourg, Infrastructure Nationale de Protéomique, Strasbourg, France
| | - Melanie Ebbing
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Constantin Holzapfel
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Serena Scozzari
- Research Center for ALS, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Johanna Knöferle
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Isabell Cordts
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Antonia F Demleitner
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Marcus Deschauer
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Claudia Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Qihui Zhou
- German Center for Neurodegenerative Diseases (DZNE), München, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Pavol Zelina
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Emma Sudria-Lopez
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Sebastian Streb
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | | | - Dieter Edbauer
- German Center for Neurodegenerative Diseases (DZNE), München, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Endre Laczko
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique, Université de Strasbourg, Infrastructure Nationale de Protéomique, Strasbourg, France
| | - Valentina Bonetto
- Research Center for ALS, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Stefan Bonn
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Paul Lingor
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany.
- German Center for Neurodegenerative Diseases (DZNE), München, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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12
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Castelli L, Vasta R, Allen SP, Waller R, Chiò A, Traynor BJ, Kirby J. From use of omics to systems biology: Identifying therapeutic targets for amyotrophic lateral sclerosis. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2024; 176:209-268. [PMID: 38802176 DOI: 10.1016/bs.irn.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a heterogeneous progressive neurodegenerative disorder with available treatments such as riluzole and edaravone extending survival by an average of 3-6 months. The lack of highly effective, widely available therapies reflects the complexity of ALS. Omics technologies, including genomics, transcriptomic and proteomics have contributed to the identification of biological pathways dysregulated and targeted by therapeutic strategies in preclinical and clinical trials. Integrating clinical, environmental and neuroimaging information with omics data and applying a systems biology approach can further improve our understanding of the disease with the potential to stratify patients and provide more personalised medicine. This chapter will review the omics technologies that contribute to a systems biology approach and how these components have assisted in identifying therapeutic targets. Current strategies, including the use of genetic screening and biosampling in clinical trials, as well as the future application of additional technological advances, will also be discussed.
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Affiliation(s)
- Lydia Castelli
- Sheffield Institute for Translational Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Rosario Vasta
- ALS Expert Center,'Rita Levi Montalcini' Department of Neuroscience, University of Turin, Turin, Italy; Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States
| | - Scott P Allen
- Sheffield Institute for Translational Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Rachel Waller
- Sheffield Institute for Translational Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Adriano Chiò
- ALS Expert Center,'Rita Levi Montalcini' Department of Neuroscience, University of Turin, Turin, Italy; Neurology 1, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza of Turin, Turin, Italy
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States; RNA Therapeutics Laboratory, National Center for Advancing Translational Sciences, NIH, Rockville, MD, United States; National Institute of Neurological Disorders and Stroke, Bethesda, MD, United States; Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, United States; Reta Lila Weston Institute, UCL Queen Square Institute of Neurology,University College London, London, United Kingdom
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom.
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13
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Prasad K, Hassan MI, Raghuvanshi S, Kumar V. Understanding the relationship between cerebellum and the frontal-cortex region of C9orf72-related amyotrophic lateral sclerosis: A comparative analysis of genetic features. PLoS One 2024; 19:e0301267. [PMID: 38753768 PMCID: PMC11098475 DOI: 10.1371/journal.pone.0301267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/13/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a relentlessly progressive and fatal neurodegenerative diseases for which at present no cure is available. Despite the extensive research the progress from diagnosis to prognosis in ALS and frontotemporal dementia (FTD) has been slow which represents suboptimal understanding of disease pathophysiological processes. In recent studies, several genes have been associated with the ALS and FTD diseases such as SOD1, TDP43, and TBK1, whereas the hexanucleotide GGGGCC repeat expansion (HRE) in C9orf72 gene is a most frequent cause of ALS and FTD, that has changed the understanding of these diseases. METHODS The goal of this study was to identify and spatially determine differential gene expression signature differences between cerebellum and frontal cortex in C9orf72-associated ALS (C9-ALS), to study the network properties of these differentially expressed genes, and to identify miRNAs targeting the common differentially expressed genes in both the tissues. This study thus highlights underlying differential cell susceptibilities to the disease mechanisms in C9-ALS and suggesting therapeutic target selection in C9-ALS. RESULTS In this manuscript, we have identified that the genes involved in neuron development, protein localization and transcription are mostly enriched in cerebellum of C9-ALS patients, while the UPR-related genes are enriched in the frontal cortex. Of note, UPR pathway genes were mostly dysregulated both in the C9-ALS cerebellum and frontal cortex. Overall, the data presented here show that defects in normal RNA processing and the UPR pathway are the pathological hallmarks of C9-ALS. Interestingly, the cerebellum showed more strong transcriptome changes than the frontal cortex. CONCLUSION Interestingly, the cerebellum region showed more significant transcriptomic changes as compared to the frontal cortex region suggesting its active participation in the disease process. This nuanced understanding may offer valuable insights for the development of targeted therapeutic strategies aimed at mitigating disease progression in C9-ALS.
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Affiliation(s)
- Kartikay Prasad
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP, India
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14
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Garcia-Montojo M, Fathi S, Rastegar C, Simula ER, Doucet-O'Hare T, Cheng YHH, Abrams RPM, Pasternack N, Malik N, Bachani M, Disanza B, Maric D, Lee MH, Wang H, Santamaria U, Li W, Sampson K, Lorenzo JR, Sanchez IE, Mezghrani A, Li Y, Sechi LA, Pineda S, Heiman M, Kellis M, Steiner J, Nath A. TDP-43 proteinopathy in ALS is triggered by loss of ASRGL1 and associated with HML-2 expression. Nat Commun 2024; 15:4163. [PMID: 38755145 PMCID: PMC11099023 DOI: 10.1038/s41467-024-48488-7] [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: 02/04/2023] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) proteinopathy in brain cells is the hallmark of amyotrophic lateral sclerosis (ALS) but its cause remains elusive. Asparaginase-like-1 protein (ASRGL1) cleaves isoaspartates, which alter protein folding and susceptibility to proteolysis. ASRGL1 gene harbors a copy of the human endogenous retrovirus HML-2, whose overexpression contributes to ALS pathogenesis. Here we show that ASRGL1 expression was diminished in ALS brain samples by RNA sequencing, immunohistochemistry, and western blotting. TDP-43 and ASRGL1 colocalized in neurons but, in the absence of ASRGL1, TDP-43 aggregated in the cytoplasm. TDP-43 was found to be prone to isoaspartate formation and a substrate for ASRGL1. ASRGL1 silencing triggered accumulation of misfolded, fragmented, phosphorylated and mislocalized TDP-43 in cultured neurons and motor cortex of female mice. Overexpression of ASRGL1 restored neuronal viability. Overexpression of HML-2 led to ASRGL1 silencing. Loss of ASRGL1 leading to TDP-43 aggregation may be a critical mechanism in ALS pathophysiology.
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Affiliation(s)
- Marta Garcia-Montojo
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Saeed Fathi
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Cyrus Rastegar
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Elena Rita Simula
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
- Struttura Complessa Microbiologia e Virologia, Azienda Ospedaliera Universitaria Sassari, Sassari, Italy
| | - Tara Doucet-O'Hare
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Y H Hank Cheng
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rachel P M Abrams
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nicholas Pasternack
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nasir Malik
- Translational Neuroscience Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Muzna Bachani
- Translational Neuroscience Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Brianna Disanza
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Myoung-Hwa Lee
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Herui Wang
- Neuro-Oncology Branch, National Cancer Institute (NIH), Bethesda, MD, USA
| | - Ulisses Santamaria
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Wenxue Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kevon Sampson
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Juan Ramiro Lorenzo
- Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CICPBA-UNCPBA, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro (FCV-UNCPBA), Tandil, Argentina
| | - Ignacio E Sanchez
- Protein Physiology Laboratory, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales and IQUIBICEN-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alexandre Mezghrani
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
- Centre de Biologie Structurale, Centre national de la recherche scientifique (CNRS), Montpellier, France
| | - Yan Li
- Protein/Peptide Sequencing Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Leonardo Antonio Sechi
- Struttura Complessa Microbiologia e Virologia, Azienda Ospedaliera Universitaria Sassari, Sassari, Italy
| | | | - Myriam Heiman
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manolis Kellis
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joseph Steiner
- Translational Neuroscience Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA.
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15
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Eisen A, Pioro EP, Goutman SA, Kiernan MC. Nanoplastics and Neurodegeneration in ALS. Brain Sci 2024; 14:471. [PMID: 38790450 PMCID: PMC11119293 DOI: 10.3390/brainsci14050471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Plastic production, which exceeds one million tons per year, is of global concern. The constituent low-density polymers enable spread over large distances and micro/nano particles (MNPLs) induce organ toxicity via digestion, inhalation, and skin contact. Particles have been documented in all human tissues including breast milk. MNPLs, especially weathered particles, can breach the blood-brain barrier, inducing neurotoxicity. This has been documented in non-human species, and in human-induced pluripotent stem cell lines. Within the brain, MNPLs initiate an inflammatory response with pro-inflammatory cytokine production, oxidative stress with generation of reactive oxygen species, and mitochondrial dysfunction. Glutamate and GABA neurotransmitter dysfunction also ensues with alteration of excitatory/inhibitory balance in favor of reduced inhibition and resultant neuro-excitation. Inflammation and cortical hyperexcitability are key abnormalities involved in the pathogenic cascade of amyotrophic lateral sclerosis (ALS) and are intricately related to the mislocalization and aggregation of TDP-43, a hallmark of ALS. Water and many foods contain MNPLs and in humans, ingestion is the main form of exposure. Digestion of plastics within the gut can alter their properties, rendering them more toxic, and they cause gut microbiome dysbiosis and a dysfunctional gut-brain axis. This is recognized as a trigger and/or aggravating factor for ALS. ALS is associated with a long (years or decades) preclinical period and neonates and infants are exposed to MNPLs through breast milk, milk substitutes, and toys. This endangers a time of intense neurogenesis and establishment of neuronal circuitry, setting the stage for development of neurodegeneration in later life. MNPL neurotoxicity should be considered as a yet unrecognized risk factor for ALS and related diseases.
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Affiliation(s)
- Andrew Eisen
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC V6S 1Z3, Canada;
| | - Erik P. Pioro
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC V6S 1Z3, Canada;
| | - Stephen A. Goutman
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA;
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16
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Sternberg Z. Neurodegenerative Etiology of Aromatic L-Amino Acid Decarboxylase Deficiency: a Novel Concept for Expanding Treatment Strategies. Mol Neurobiol 2024; 61:2996-3018. [PMID: 37953352 DOI: 10.1007/s12035-023-03684-2] [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: 02/07/2023] [Accepted: 09/29/2023] [Indexed: 11/14/2023]
Abstract
Aromatic l-amino acid decarboxylase deficiency (AADC-DY) is caused by one or more mutations in the DDC gene, resulting in the deficit in catecholamines and serotonin neurotransmitters. The disease has limited therapeutic options with relatively poor clinical outcomes. Accumulated evidence suggests the involvement of neurodegenerative mechanisms in the etiology of AADC-DY. In the absence of neurotransmitters' neuroprotective effects, the accumulation and the chronic presence of several neurotoxic metabolites including 4-dihydroxy-L-phenylalanine, 3-methyldopa, and homocysteine, in the brain of subjects with AADC-DY, promote oxidative stress and reduce the cellular antioxidant and methylation capacities, leading to glial activation and mitochondrial dysfunction, culminating to neuronal injury and death. These pathophysiological processes have the potential to hinder the clinical efficacy of treatments aimed at increasing neurotransmitters' synthesis and or function. This review describes in detail the mechanisms involved in AADC-DY neurodegenerative etiology, highlighting the close similarities with those involved in other neurodegenerative diseases. We then offer novel strategies for the treatment of the disease with the objective to either reduce the level of the metabolites or counteract their prooxidant and neurotoxic effects. These treatment modalities used singly or in combination, early in the course of the disease, will minimize neuronal injury, preserving the functional integrity of neurons, hence improving the clinical outcomes of both conventional and unconventional interventions in AADC-DY. These modalities may not be limited to AADC-DY but also to other metabolic disorders where a specific mutation leads to the accumulation of prooxidant and neurotoxic metabolites.
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Affiliation(s)
- Zohi Sternberg
- Jacobs School of Medicine and Biomedical Sciences, Buffalo Medical Center, Buffalo, NY, 14203, USA.
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17
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Wang W, Pan D, Liu Q, Chen X, Wang S. L-Carnitine in the Treatment of Psychiatric and Neurological Manifestations: A Systematic Review. Nutrients 2024; 16:1232. [PMID: 38674921 PMCID: PMC11055039 DOI: 10.3390/nu16081232] [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: 03/21/2024] [Revised: 04/13/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
OBJECTIVE L-carnitine (LC), a vital nutritional supplement, plays a crucial role in myocardial health and exhibits significant cardioprotective effects. LC, being the principal constituent of clinical-grade supplements, finds extensive application in the recovery and treatment of diverse cardiovascular and cerebrovascular disorders. However, controversies persist regarding the utilization of LC in nervous system diseases, with varying effects observed across numerous mental and neurological disorders. This article primarily aims to gather and analyze database information to comprehensively summarize the therapeutic potential of LC in patients suffering from nervous system diseases while providing valuable references for further research. METHODS A comprehensive search was conducted in PubMed, Web Of Science, Embase, Ovid Medline, Cochrane Library and Clinicaltrials.gov databases. The literature pertaining to the impact of LC supplementation on neurological or psychiatric disorders in patients was reviewed up until November 2023. No language or temporal restrictions were imposed on the search. RESULTS A total of 1479 articles were retrieved, and after the removal of duplicates through both automated and manual exclusion processes, 962 articles remained. Subsequently, a meticulous re-screening led to the identification of 60 relevant articles. Among these, there were 12 publications focusing on hepatic encephalopathy (HE), while neurodegenerative diseases (NDs) and peripheral nervous system diseases (PNSDs) were represented by 9 and 6 articles, respectively. Additionally, stroke was addressed in five publications, whereas Raynaud's syndrome (RS) and cognitive disorder (CD) each had three dedicated studies. Furthermore, migraine, depression, and amyotrophic lateral sclerosis (ALS) each accounted for two publications. Lastly, one article was found for other symptoms under investigation. CONCLUSION In summary, LC has demonstrated favorable therapeutic effects in the management of HE, Alzheimer's disease (AD), carpal tunnel syndrome (CTS), CD, migraine, neurofibromatosis (NF), PNSDs, RS, and stroke. However, its efficacy appears to be relatively limited in conditions such as ALS, ataxia, attention deficit hyperactivity disorder (ADHD), depression, chronic fatigue syndrome (CFS), Down syndrome (DS), and sciatica.
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Affiliation(s)
- Wenbo Wang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China; (W.W.); (D.P.); (X.C.)
| | - Da Pan
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China; (W.W.); (D.P.); (X.C.)
| | - Qi Liu
- Department of Public Health, School of Medicine, Xizang Minzu University, Xianyang 712082, China;
| | - Xiangjun Chen
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China; (W.W.); (D.P.); (X.C.)
- Department of Public Health, School of Medicine, Xizang Minzu University, Xianyang 712082, China;
| | - Shaokang Wang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China; (W.W.); (D.P.); (X.C.)
- Department of Public Health, School of Medicine, Xizang Minzu University, Xianyang 712082, China;
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18
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Wang X, Hu Y, Xu R. The pathogenic mechanism of TAR DNA-binding protein 43 (TDP-43) in amyotrophic lateral sclerosis. Neural Regen Res 2024; 19:800-806. [PMID: 37843214 PMCID: PMC10664110 DOI: 10.4103/1673-5374.382233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/19/2023] [Accepted: 07/03/2023] [Indexed: 10/17/2023] Open
Abstract
The onset of amyotrophic lateral sclerosis is usually characterized by focal death of both upper and/or lower motor neurons occurring in the motor cortex, basal ganglia, brainstem, and spinal cord, and commonly involves the muscles of the upper and/or lower extremities, and the muscles of the bulbar and/or respiratory regions. However, as the disease progresses, it affects the adjacent body regions, leading to generalized muscle weakness, occasionally along with memory, cognitive, behavioral, and language impairments; respiratory dysfunction occurs at the final stage of the disease. The disease has a complicated pathophysiology and currently, only riluzole, edaravone, and phenylbutyrate/taurursodiol are licensed to treat amyotrophic lateral sclerosis in many industrialized countries. The TAR DNA-binding protein 43 inclusions are observed in 97% of those diagnosed with amyotrophic lateral sclerosis. This review provides a preliminary overview of the potential effects of TAR DNA-binding protein 43 in the pathogenesis of amyotrophic lateral sclerosis, including the abnormalities in nucleoplasmic transport, RNA function, post-translational modification, liquid-liquid phase separation, stress granules, mitochondrial dysfunction, oxidative stress, axonal transport, protein quality control system, and non-cellular autonomous functions (e.g., glial cell functions and prion-like propagation).
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Affiliation(s)
- Xinxin Wang
- Medical College of Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, The Clinical College of Nanchang Medical College, Nanchang, Jiangxi Province, China
| | - Yushu Hu
- Medical College of Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, The Clinical College of Nanchang Medical College, Nanchang, Jiangxi Province, China
| | - Renshi Xu
- Medical College of Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, The Clinical College of Nanchang Medical College, Nanchang, Jiangxi Province, China
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19
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Marques C, Held A, Dorfman K, Sung J, Song C, Kavuturu AS, Aguilar C, Russo T, Oakley DH, Albers MW, Hyman BT, Petrucelli L, Lagier-Tourenne C, Wainger BJ. Neuronal STING activation in amyotrophic lateral sclerosis and frontotemporal dementia. Acta Neuropathol 2024; 147:56. [PMID: 38478117 PMCID: PMC10937762 DOI: 10.1007/s00401-024-02688-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/15/2023] [Accepted: 01/09/2024] [Indexed: 03/17/2024]
Abstract
The stimulator of interferon genes (STING) pathway has been implicated in neurodegenerative diseases, including Parkinson's disease and amyotrophic lateral sclerosis (ALS). While prior studies have focused on STING within immune cells, little is known about STING within neurons. Here, we document neuronal activation of the STING pathway in human postmortem cortical and spinal motor neurons from individuals affected by familial or sporadic ALS. This process takes place selectively in the most vulnerable cortical and spinal motor neurons but not in neurons that are less affected by the disease. Concordant STING activation in layer V cortical motor neurons occurs in a mouse model of C9orf72 repeat-associated ALS and frontotemporal dementia (FTD). To establish that STING activation occurs in a neuron-autonomous manner, we demonstrate the integrity of the STING signaling pathway, including both upstream activators and downstream innate immune response effectors, in dissociated mouse cortical neurons and neurons derived from control human induced pluripotent stem cells (iPSCs). Human iPSC-derived neurons harboring different familial ALS-causing mutations exhibit increased STING signaling with DNA damage as a main driver. The elevated downstream inflammatory markers present in ALS iPSC-derived neurons can be suppressed with a STING inhibitor. Our results reveal an immunophenotype that consists of innate immune signaling driven by the STING pathway and occurs specifically within vulnerable neurons in ALS/FTD.
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Affiliation(s)
- Christine Marques
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Aaron Held
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Katherine Dorfman
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Joon Sung
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Catherine Song
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Amey S Kavuturu
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Corey Aguilar
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Tommaso Russo
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Derek H Oakley
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Mark W Albers
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Alzheimer Disease Research Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Bradley T Hyman
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Alzheimer Disease Research Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | | | - Clotilde Lagier-Tourenne
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Brian J Wainger
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA.
- Department of Anesthesiology, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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20
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Tzeplaeff L, Jürs AV, Wohnrade C, Demleitner AF. Unraveling the Heterogeneity of ALS-A Call to Redefine Patient Stratification for Better Outcomes in Clinical Trials. Cells 2024; 13:452. [PMID: 38474416 PMCID: PMC10930688 DOI: 10.3390/cells13050452] [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: 01/31/2024] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Despite tremendous efforts in basic research and a growing number of clinical trials aiming to find effective treatments, amyotrophic lateral sclerosis (ALS) remains an incurable disease. One possible reason for the lack of effective causative treatment options is that ALS may not be a single disease entity but rather may represent a clinical syndrome, with diverse genetic and molecular causes, histopathological alterations, and subsequent clinical presentations contributing to its complexity and variability among individuals. Defining a way to subcluster ALS patients is becoming a central endeavor in the field. Identifying specific clusters and applying them in clinical trials could enable the development of more effective treatments. This review aims to summarize the available data on heterogeneity in ALS with regard to various aspects, e.g., clinical, genetic, and molecular.
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Affiliation(s)
- Laura Tzeplaeff
- Department of Neurology, Rechts der Isar Hospital, Technical University of Munich, 81675 München, Germany
| | - Alexandra V. Jürs
- Translational Neurodegeneration Section “Albrecht Kossel”, Department of Neurology, University Medical Center Rostock, 18057 Rostock, Germany
| | - Camilla Wohnrade
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany;
| | - Antonia F. Demleitner
- Department of Neurology, Rechts der Isar Hospital, Technical University of Munich, 81675 München, Germany
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21
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Jagaraj CJ, Shadfar S, Kashani SA, Saravanabavan S, Farzana F, Atkin JD. Molecular hallmarks of ageing in amyotrophic lateral sclerosis. Cell Mol Life Sci 2024; 81:111. [PMID: 38430277 PMCID: PMC10908642 DOI: 10.1007/s00018-024-05164-9] [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: 12/05/2023] [Revised: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, severely debilitating and rapidly progressing disorder affecting motor neurons in the brain, brainstem, and spinal cord. Unfortunately, there are few effective treatments, thus there remains a critical need to find novel interventions that can mitigate against its effects. Whilst the aetiology of ALS remains unclear, ageing is the major risk factor. Ageing is a slowly progressive process marked by functional decline of an organism over its lifespan. However, it remains unclear how ageing promotes the risk of ALS. At the molecular and cellular level there are specific hallmarks characteristic of normal ageing. These hallmarks are highly inter-related and overlap significantly with each other. Moreover, whilst ageing is a normal process, there are striking similarities at the molecular level between these factors and neurodegeneration in ALS. Nine ageing hallmarks were originally proposed: genomic instability, loss of telomeres, senescence, epigenetic modifications, dysregulated nutrient sensing, loss of proteostasis, mitochondrial dysfunction, stem cell exhaustion, and altered inter-cellular communication. However, these were recently (2023) expanded to include dysregulation of autophagy, inflammation and dysbiosis. Hence, given the latest updates to these hallmarks, and their close association to disease processes in ALS, a new examination of their relationship to pathophysiology is warranted. In this review, we describe possible mechanisms by which normal ageing impacts on neurodegenerative mechanisms implicated in ALS, and new therapeutic interventions that may arise from this.
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Affiliation(s)
- Cyril Jones Jagaraj
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sina Shadfar
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sara Assar Kashani
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sayanthooran Saravanabavan
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Fabiha Farzana
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Julie D Atkin
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia.
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22
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Rao Y, Peng B. Allogenic microglia replacement: A novel therapeutic strategy for neurological disorders. FUNDAMENTAL RESEARCH 2024; 4:237-245. [PMID: 38933508 PMCID: PMC11197774 DOI: 10.1016/j.fmre.2023.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/17/2022] [Accepted: 02/19/2023] [Indexed: 03/29/2023] Open
Abstract
Microglia are resident immune cells in the central nervous system (CNS) that play vital roles in CNS development, homeostasis and disease pathogenesis. Genetic defects in microglia lead to microglial dysfunction, which in turn leads to neurological disorders. The correction of the specific genetic defects in microglia in these disorders can lead to therapeutic effects. Traditional genetic defect correction approaches are dependent on viral vector-based genetic defect corrections. However, the viruses used in these approaches, including adeno-associated viruses, lentiviruses and retroviruses, do not primarily target microglia; therefore, viral vector-based genetic defect corrections are ineffective in microglia. Microglia replacement is a novel approach to correct microglial genetic defects via replacing microglia of genetic defects with allogenic healthy microglia. In this paper, we systematically review the history, rationale and therapeutic perspectives of microglia replacement, which would be a novel strategy for treating CNS disorders.
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Affiliation(s)
- Yanxia Rao
- Department of Laboratory Animal Science, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Bo Peng
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, MOE Innovative Center for New Drug Development of Immune Inflammatory Diseases, Fudan University, Shanghai 200000, China
- Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
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23
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Dopkins N, Nixon DF. Activation of human endogenous retroviruses and its physiological consequences. Nat Rev Mol Cell Biol 2024; 25:212-222. [PMID: 37872387 DOI: 10.1038/s41580-023-00674-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
Human endogenous retroviruses (HERVs) are abundant sequences that persist within the human genome as remnants of ancient retroviral infections. These sequences became fixed and accumulate mutations or deletions over time. HERVs have affected human evolution and physiology by providing a unique repertoire of coding and non-coding sequences to the genome. In healthy individuals, HERVs participate in immune responses, formation of syncytiotrophoblasts and cell-fate specification. In this Review, we discuss how endogenized retroviral motifs and regulatory sequences have been co-opted into human physiology and how they are tightly regulated. Infections and mutations can derail this regulation, leading to differential HERV expression, which may contribute to pathologies including neurodegeneration, pathological inflammation and oncogenesis. Emerging evidence demonstrates that HERVs are crucial to human health and represent an understudied facet of many diseases, and we therefore argue that investigating their fundamental properties could improve existing therapies and help develop novel therapeutic strategies.
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Affiliation(s)
- Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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24
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Zamani A, Thomas E, Wright DK. Sex biology in amyotrophic lateral sclerosis. Ageing Res Rev 2024; 95:102228. [PMID: 38354985 DOI: 10.1016/j.arr.2024.102228] [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: 08/31/2023] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024]
Abstract
Although sex differences in amyotrophic lateral sclerosis (ALS) have not been studied systematically, numerous clinical and preclinical studies have shown sex to be influential in disease prognosis. Moreover, with the development of advanced imaging tools, the difference between male and female brain in structure and function and their response to neurodegeneration are more definitive. As discussed in this review, ALS patients exhibit a sex bias pertaining to the features of the disease, and their clinical, pathological, (and pathophysiological) phenotypes. Several epidemiological studies have indicated that this sex disparity stems from various aetiologies, including sex-specific brain structure and neural functioning, genetic predisposition, age, gonadal hormones, susceptibility to traumatic brain injury (TBI)/head trauma and lifestyle factors.
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Affiliation(s)
- Akram Zamani
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia.
| | - Emma Thomas
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - David K Wright
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
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25
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Silvestri B, Mochi M, Mawrie D, de Turris V, Colantoni A, Borhy B, Medici M, Anderson EN, Garone MG, Zammerilla CP, Pandey UB, Rosa A. HuD (ELAVL4) gain-of-function impairs neuromuscular junctions and induces apoptosis in in vitro and in vivo models of amyotrophic lateral sclerosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.22.554258. [PMID: 38464028 PMCID: PMC10925158 DOI: 10.1101/2023.08.22.554258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Early defects at the neuromuscular junction (NMJ) are among the first hallmarks of the progressive neurodegenerative disease amyotrophic lateral sclerosis (ALS). According to the "dying back" hypothesis, disruption of the NMJ not only precedes, but is also a trigger for the subsequent degeneration of the motoneuron in both sporadic and familial ALS, including ALS caused by the severe FUS pathogenic variant P525L. However, the mechanisms linking genetic and environmental factors to NMJ defects remain elusive. By taking advantage of co-cultures of motoneurons and skeletal muscle derived from human induced pluripotent stem cells (iPSCs), we show that the neural RNA binding protein HuD (ELAVL4) may underlie NMJ defects and apoptosis in FUS-ALS. HuD overexpression in motoneurons phenocopies the severe FUSP525L mutation, while HuD knockdown in FUSP525L co-cultures produces phenotypic rescue. We validated these findings in vivo in a Drosophila FUS-ALS model. Neuronal-restricted overexpression of the HuD-related gene, elav, produces per se a motor phenotype, while neuronal-restricted elav knockdown significantly rescues motor dysfunction caused by FUS. Finally, we show that HuD levels increase upon oxidative stress in human motoneurons and in sporadic ALS patients with an oxidative stress signature. On these bases, we propose HuD as an important player downstream of FUS mutation in familial ALS, with potential implications for sporadic ALS related to oxidative stress.
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Affiliation(s)
- Beatrice Silvestri
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
- Center for Life Nano-& Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Michela Mochi
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Darilang Mawrie
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, PA, USA
| | - Valeria de Turris
- Center for Life Nano-& Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Alessio Colantoni
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
- Center for Life Nano-& Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Beatrice Borhy
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Margherita Medici
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Eric Nathaniel Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, PA, USA
| | - Maria Giovanna Garone
- Department of Stem Cell Biology, Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia
| | | | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, PA, USA
- Children's Neuroscience Institute, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA USA
| | - Alessandro Rosa
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
- Center for Life Nano-& Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
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26
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Le Breton A, Bettencourt MP, Gendrel AV. Navigating the brain and aging: exploring the impact of transposable elements from health to disease. Front Cell Dev Biol 2024; 12:1357576. [PMID: 38476259 PMCID: PMC10927736 DOI: 10.3389/fcell.2024.1357576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that constitute on average 45% of mammalian genomes. Their presence and activity in genomes represent a major source of genetic variability. While this is an important driver of genome evolution, TEs can also have deleterious effects on their hosts. A growing number of studies have focused on the role of TEs in the brain, both in physiological and pathological contexts. In the brain, their activity is believed to be important for neuronal plasticity. In neurological and age-related disorders, aberrant activity of TEs may contribute to disease etiology, although this remains unclear. After providing a comprehensive overview of transposable elements and their interactions with the host, this review summarizes the current understanding of TE activity within the brain, during the aging process, and in the context of neurological and age-related conditions.
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Affiliation(s)
| | | | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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27
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Scarian E, Viola C, Dragoni F, Di Gerlando R, Rizzo B, Diamanti L, Gagliardi S, Bordoni M, Pansarasa O. New Insights into Oxidative Stress and Inflammatory Response in Neurodegenerative Diseases. Int J Mol Sci 2024; 25:2698. [PMID: 38473944 DOI: 10.3390/ijms25052698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Oxidative stress (OS) and inflammation are two important and well-studied pathological hallmarks of neurodegenerative diseases (NDDs). Due to elevated oxygen consumption, the high presence of easily oxidizable polyunsaturated fatty acids and the weak antioxidant defenses, the brain is particularly vulnerable to oxidative injury. Uncertainty exists over whether these deficits contribute to the development of NDDs or are solely a consequence of neuronal degeneration. Furthermore, these two pathological hallmarks are linked, and it is known that OS can affect the inflammatory response. In this review, we will overview the last findings about these two pathways in the principal NDDs. Moreover, we will focus more in depth on amyotrophic lateral sclerosis (ALS) to understand how anti-inflammatory and antioxidants drugs have been used for the treatment of this still incurable motor neuron (MN) disease. Finally, we will analyze the principal past and actual clinical trials and the future perspectives in the study of these two pathological mechanisms.
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Affiliation(s)
- Eveljn Scarian
- Cellular Models and Neuroepigenetics Unit, IRCCS Mondino Foundation, Via Mondino 2, 27100 Pavia, Italy
| | - Camilla Viola
- Cellular Models and Neuroepigenetics Unit, IRCCS Mondino Foundation, Via Mondino 2, 27100 Pavia, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, Via Agostino Bassi 21, 27100 Pavia, Italy
| | - Francesca Dragoni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata, 9, 27100 Pavia, Italy
- Molecular Biology and Transcriptomics Unit, IRCCS Mondino Foundation, Via Mondino 2, 27100 Pavia, Italy
| | - Rosalinda Di Gerlando
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata, 9, 27100 Pavia, Italy
- Molecular Biology and Transcriptomics Unit, IRCCS Mondino Foundation, Via Mondino 2, 27100 Pavia, Italy
| | - Bartolo Rizzo
- Molecular Biology and Transcriptomics Unit, IRCCS Mondino Foundation, Via Mondino 2, 27100 Pavia, Italy
| | - Luca Diamanti
- Neuroncology Unit, IRCCS Mondino Foundation, Via Mondino 2, 27100 Pavia, Italy
| | - Stella Gagliardi
- Molecular Biology and Transcriptomics Unit, IRCCS Mondino Foundation, Via Mondino 2, 27100 Pavia, Italy
| | - Matteo Bordoni
- Cellular Models and Neuroepigenetics Unit, IRCCS Mondino Foundation, Via Mondino 2, 27100 Pavia, Italy
| | - Orietta Pansarasa
- Cellular Models and Neuroepigenetics Unit, IRCCS Mondino Foundation, Via Mondino 2, 27100 Pavia, Italy
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28
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Loh JS, Mak WQ, Tan LKS, Ng CX, Chan HH, Yeow SH, Foo JB, Ong YS, How CW, Khaw KY. Microbiota-gut-brain axis and its therapeutic applications in neurodegenerative diseases. Signal Transduct Target Ther 2024; 9:37. [PMID: 38360862 PMCID: PMC10869798 DOI: 10.1038/s41392-024-01743-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 01/02/2024] [Accepted: 01/14/2024] [Indexed: 02/17/2024] Open
Abstract
The human gastrointestinal tract is populated with a diverse microbial community. The vast genetic and metabolic potential of the gut microbiome underpins its ubiquity in nearly every aspect of human biology, including health maintenance, development, aging, and disease. The advent of new sequencing technologies and culture-independent methods has allowed researchers to move beyond correlative studies toward mechanistic explorations to shed light on microbiome-host interactions. Evidence has unveiled the bidirectional communication between the gut microbiome and the central nervous system, referred to as the "microbiota-gut-brain axis". The microbiota-gut-brain axis represents an important regulator of glial functions, making it an actionable target to ameliorate the development and progression of neurodegenerative diseases. In this review, we discuss the mechanisms of the microbiota-gut-brain axis in neurodegenerative diseases. As the gut microbiome provides essential cues to microglia, astrocytes, and oligodendrocytes, we examine the communications between gut microbiota and these glial cells during healthy states and neurodegenerative diseases. Subsequently, we discuss the mechanisms of the microbiota-gut-brain axis in neurodegenerative diseases using a metabolite-centric approach, while also examining the role of gut microbiota-related neurotransmitters and gut hormones. Next, we examine the potential of targeting the intestinal barrier, blood-brain barrier, meninges, and peripheral immune system to counteract glial dysfunction in neurodegeneration. Finally, we conclude by assessing the pre-clinical and clinical evidence of probiotics, prebiotics, and fecal microbiota transplantation in neurodegenerative diseases. A thorough comprehension of the microbiota-gut-brain axis will foster the development of effective therapeutic interventions for the management of neurodegenerative diseases.
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Affiliation(s)
- Jian Sheng Loh
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Wen Qi Mak
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Li Kar Stella Tan
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
- Digital Health & Medical Advancements, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
| | - Chu Xin Ng
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
| | - Hong Hao Chan
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Shiau Hueh Yeow
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Jhi Biau Foo
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
- Digital Health & Medical Advancements, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
| | - Yong Sze Ong
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Chee Wun How
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
| | - Kooi Yeong Khaw
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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Gomez N, Hsieh C, Li X, Dykstra M, Waksmacki J, Altheim C, Bechar Y, Klim J, Zaepfel B, Rothstein J, Tank EE, Barmada SJ. Counter-regulation of RNA stability by UPF1 and TDP43. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578310. [PMID: 38352350 PMCID: PMC10862862 DOI: 10.1101/2024.01.31.578310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
RNA quality control is crucial for proper regulation of gene expression. Disruption of nonsense mediated mRNA decay (NMD), the primary RNA decay pathway responsible for the degradation of transcripts containing premature termination codons (PTCs), can disrupt development and lead to multiple diseases in humans and other animals. Similarly, therapies targeting NMD may have applications in hematological, neoplastic and neurological disorders. As such, tools capable of accurately quantifying NMD status could be invaluable for investigations of disease pathogenesis and biomarker identification. Toward this end, we assemble, validate, and apply a next-generation sequencing approach (NMDq) for identifying and measuring the abundance of PTC-containing transcripts. After validating NMDq performance and confirming its utility for tracking RNA surveillance, we apply it to determine pathway activity in two neurodegenerative diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) characterized by RNA misprocessing and abnormal RNA stability. Despite the genetic and pathologic evidence implicating dysfunctional RNA metabolism, and NMD in particular, in these conditions, we detected no significant differences in PTC-encoding transcripts in ALS models or disease. Contrary to expectations, overexpression of the master NMD regulator UPF1 had little effect on the clearance of transcripts with PTCs, but rather restored RNA homeostasis through differential use and decay of alternatively poly-adenylated isoforms. Together, these data suggest that canonical NMD is not a significant contributor to ALS/FTD pathogenesis, and that UPF1 promotes neuronal survival by regulating transcripts with abnormally long 3'UTRs.
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30
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Seddighi S, Qi YA, Brown AL, Wilkins OG, Bereda C, Belair C, Zhang YJ, Prudencio M, Keuss MJ, Khandeshi A, Pickles S, Kargbo-Hill SE, Hawrot J, Ramos DM, Yuan H, Roberts J, Sacramento EK, Shah SI, Nalls MA, Colón-Mercado JM, Reyes JF, Ryan VH, Nelson MP, Cook CN, Li Z, Screven L, Kwan JY, Mehta PR, Zanovello M, Hallegger M, Shantaraman A, Ping L, Koike Y, Oskarsson B, Staff NP, Duong DM, Ahmed A, Secrier M, Ule J, Jacobson S, Reich DS, Rohrer JD, Malaspina A, Dickson DW, Glass JD, Ori A, Seyfried NT, Maragkakis M, Petrucelli L, Fratta P, Ward ME. Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD. Sci Transl Med 2024; 16:eadg7162. [PMID: 38277467 DOI: 10.1126/scitranslmed.adg7162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Functional loss of TDP-43, an RNA binding protein genetically and pathologically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), leads to the inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote the degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. Here, we show that mRNA transcripts harboring cryptic exons generated de novo proteins in TDP-43-depleted human iPSC-derived neurons in vitro, and de novo peptides were found in cerebrospinal fluid (CSF) samples from patients with ALS or FTD. Using coordinated transcriptomic and proteomic studies of TDP-43-depleted human iPSC-derived neurons, we identified 65 peptides that mapped to 12 cryptic exons. Cryptic exons identified in TDP-43-depleted human iPSC-derived neurons were predictive of cryptic exons expressed in postmortem brain tissue from patients with TDP-43 proteinopathy. These cryptic exons produced transcript variants that generated de novo proteins. We found that the inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Last, we showed that 18 de novo peptides across 13 genes were present in CSF samples from patients with ALS/FTD spectrum disorders. The demonstration of cryptic exon translation suggests new mechanisms for ALS/FTD pathophysiology downstream of TDP-43 dysfunction and may provide a potential strategy to assay TDP-43 function in patient CSF.
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Affiliation(s)
- Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Oscar G Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- Francis Crick Institute, London, UK
| | - Colleen Bereda
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Matthew J Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Aditya Khandeshi
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Sarah Pickles
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Sarah E Kargbo-Hill
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - James Hawrot
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Hebao Yuan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jessica Roberts
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Erika Kelmer Sacramento
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Syed I Shah
- Data Tecnica International, Washington, DC, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Jennifer M Colón-Mercado
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Joel F Reyes
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Veronica H Ryan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Matthew P Nelson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Casey N Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Ziyi Li
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Laurel Screven
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Justin Y Kwan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Puja R Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Martina Hallegger
- Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
| | | | - Lingyan Ping
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Yuka Koike
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Björn Oskarsson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Nathan P Staff
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Aisha Ahmed
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, UCL, London, UK
| | - Jernej Ule
- Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
| | - Steven Jacobson
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel S Reich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan D Rohrer
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Andrea Malaspina
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Jonathan D Glass
- Department of Neurology, Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, USA
| | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- Francis Crick Institute, London, UK
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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31
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Larson KC, Martens LH, Marconi M, Dejesus C, Bruhn S, Miller TA, Tate B, Levenson JM. Preclinical translational platform of neuroinflammatory disease biology relevant to neurodegenerative disease. J Neuroinflammation 2024; 21:37. [PMID: 38297405 PMCID: PMC10832185 DOI: 10.1186/s12974-024-03029-3] [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: 08/23/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
Neuroinflammation is a key driver of neurodegenerative disease, however the tools available to model this disease biology at the systems level are lacking. We describe a translational drug discovery platform based on organotypic culture of murine cortical brain slices that recapitulate disease-relevant neuroinflammatory biology. After an acute injury response, the brain slices assume a chronic neuroinflammatory state marked by transcriptomic profiles indicative of activation of microglia and astrocytes and loss of neuronal function. Microglia are necessary for manifestation of this neuroinflammation, as depletion of microglia prior to isolation of the brain slices prevents both activation of astrocytes and robust loss of synaptic function genes. The transcriptomic pattern of neuroinflammation in the mouse platform is present in published datasets derived from patients with amyotrophic lateral sclerosis, Huntington's disease, and frontotemporal dementia. Pharmacological utility of the platform was validated by demonstrating reversal of microglial activation and the overall transcriptomic signature with transforming growth factor-β. Additional anti-inflammatory targets were screened and inhibitors of glucocorticoid receptors, COX-2, dihydrofolate reductase, and NLRP3 inflammasome all failed to reverse the neuroinflammatory signature. Bioinformatics analysis of the neuroinflammatory signature identified protein tyrosine phosphatase non-receptor type 11 (PTPN11/SHP2) as a potential target. Three structurally distinct inhibitors of PTPN11 (RMC-4550, TN0155, IACS-13909) reversed the neuroinflammatory disease signature. Collectively, these results highlight the utility of this novel neuroinflammatory platform for facilitating identification and validation of targets for neuroinflammatory neurodegenerative disease drug discovery.
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Affiliation(s)
- Kelley C Larson
- Vigil Neuroscience, Watertown, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Lauren H Martens
- , Neumora Therapeutics, Watertown, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Michael Marconi
- Department of Molecular Pathology, Massachusetts General Hospital, Boston, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Christopher Dejesus
- Atalanta Therapeutics, Boston, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Suzanne Bruhn
- Charcot-Marie-Tooth Association, Glenolden, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Thomas A Miller
- Walden Biosciences, Cambridge, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Barbara Tate
- FARA, Homestead, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Jonathan M Levenson
- FireCyte Therapeutics, Beverly, USA.
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA.
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32
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Cha Y, Kagalwala MN, Ross J. Navigating the Frontiers of Machine Learning in Neurodegenerative Disease Therapeutics. Pharmaceuticals (Basel) 2024; 17:158. [PMID: 38399373 PMCID: PMC10891920 DOI: 10.3390/ph17020158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Recent advances in machine learning hold tremendous potential for enhancing the way we develop new medicines. Over the years, machine learning has been adopted in nearly all facets of drug discovery, including patient stratification, lead discovery, biomarker development, and clinical trial design. In this review, we will discuss the latest developments linking machine learning and CNS drug discovery. While machine learning has aided our understanding of chronic diseases like Alzheimer's disease and Parkinson's disease, only modest effective therapies currently exist. We highlight promising new efforts led by academia and emerging biotech companies to leverage machine learning for exploring new therapies. These approaches aim to not only accelerate drug development but to improve the detection and treatment of neurodegenerative diseases.
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Affiliation(s)
| | | | - Jermaine Ross
- Alleo Labs, San Francisco, CA 94105, USA; (Y.C.); (M.N.K.)
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33
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Hou Y, Li Y, Xiang JF, Tilahun K, Jiang J, Corces VG, Yao B. TDP-43 chronic deficiency leads to dysregulation of transposable elements and gene expression by affecting R-loop and 5hmC crosstalk. Cell Rep 2024; 43:113662. [PMID: 38184854 PMCID: PMC10857847 DOI: 10.1016/j.celrep.2023.113662] [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: 05/30/2023] [Revised: 10/30/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024] Open
Abstract
TDP-43 is an RNA/DNA-binding protein that forms aggregates in various brain disorders. TDP-43 engages in many aspects of RNA metabolism, but its molecular roles in regulating genes and transposable elements (TEs) have not been extensively explored. Chronic TDP-43 knockdown impairs cell proliferation and cellular responses to DNA damage. At the molecular level, TDP-43 chronic deficiency affects gene expression either locally or distally by concomitantly altering the crosstalk between R-loops and 5-hydroxymethylcytosine (5hmC) in gene bodies and long-range enhancer/promoter interactions. Furthermore, TDP-43 knockdown induces substantial disease-relevant TE activation by influencing their R-loop and 5hmC homeostasis in a locus-specific manner. Together, our findings highlight the genomic roles of TDP-43 in modulating R-loop-5hmC coordination in coding genes, distal regulatory elements, and TEs, presenting a general and broad molecular mechanism underlying the contributions of proteinopathies to the etiology of neurodegenerative disorders.
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Affiliation(s)
- Yingzi Hou
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yangping Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jian-Feng Xiang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kedamawit Tilahun
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jie Jiang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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34
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Bryce-Smith S, Brown AL, Mehta PR, Mattedi F, Mikheenko A, Barattucci S, Zanovello M, Dattilo D, Yome M, Hill SE, Qi YA, Wilkins OG, Sun K, Ryadnov E, Wan Y, Vargas JNS, Birsa N, Raj T, Humphrey J, Keuss M, Ward M, Secrier M, Fratta P. TDP-43 loss induces extensive cryptic polyadenylation in ALS/FTD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576625. [PMID: 38313254 PMCID: PMC10836071 DOI: 10.1101/2024.01.22.576625] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 is the hallmark of ALS, occurring in over 97% of cases. A key consequence of TDP-43 nuclear loss is the de-repression of cryptic exons. Whilst TDP-43 regulated cryptic splicing is increasingly well catalogued, cryptic alternative polyadenylation (APA) events, which define the 3' end of last exons, have been largely overlooked, especially when not associated with novel upstream splice junctions. We developed a novel bioinformatic approach to reliably identify distinct APA event types: alternative last exons (ALE), 3'UTR extensions (3'Ext) and intronic polyadenylation (IPA) events. We identified novel neuronal cryptic APA sites induced by TDP-43 loss of function by systematically applying our pipeline to a compendium of publicly available and in house datasets. We find that TDP-43 binding sites and target motifs are enriched at these cryptic events and that TDP-43 can have both repressive and enhancing action on APA. Importantly, all categories of cryptic APA can also be identified in ALS and FTD post mortem brain regions with TDP-43 proteinopathy underlining their potential disease relevance. RNA-seq and Ribo-seq analyses indicate that distinct cryptic APA categories have different downstream effects on transcript and translation. Intriguingly, cryptic 3'Exts occur in multiple transcription factors, such as ELK1, SIX3, and TLX1, and lead to an increase in wild-type protein levels and function. Finally, we show that an increase in RNA stability leading to a higher cytoplasmic localisation underlies these observations. In summary, we demonstrate that TDP-43 nuclear depletion induces a novel category of cryptic RNA processing events and we expand the palette of TDP-43 loss consequences by showing this can also lead to an increase in normal protein translation.
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Affiliation(s)
- Sam Bryce-Smith
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Puja R. Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Francesca Mattedi
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Alla Mikheenko
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Simone Barattucci
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Dario Dattilo
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matthew Yome
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Sarah E. Hill
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Yue A. Qi
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Oscar G. Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
| | - Kai Sun
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Eugeni Ryadnov
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Yixuan Wan
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | | | - Jose Norberto S. Vargas
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Nicol Birsa
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Michael Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
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35
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Arnold FJ, Cui Y, Michels S, Colwin MR, Stockford C, Ye W, Tam OH, Menon S, Situ WG, Ehsani KCK, Howard S, Hammell MG, Li W, La Spada AR. TDP-43 dysregulation of polyadenylation site selection is a defining feature of RNA misprocessing in ALS/FTD and related disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576709. [PMID: 38328178 PMCID: PMC10849549 DOI: 10.1101/2024.01.22.576709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Nuclear clearance and cytoplasmic aggregation of the RNA-binding protein TDP-43 are observed in many neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS) and fronto- temporal dementia (FTD). Although TDP-43 dysregulation of splicing has emerged as a key event in these diseases, TDP-43 can also regulate polyadenylation; yet, this has not been adequately studied. Here, we applied the dynamic analysis of polyadenylation from RNA-seq (DaPars) tool to ALS/FTD transcriptome datasets, and report extensive alternative polyadenylation (APA) upon TDP-43 alteration in ALS/FTD cell models and postmortem ALS/FTD neuronal nuclei. Importantly, many identified APA genes highlight pathways implicated in ALS/FTD pathogenesis. To determine the functional significance of APA elicited by TDP-43 nuclear depletion, we examined microtubule affinity regulating kinase 3 (MARK3). Nuclear loss of TDP-43 yielded increased expression of MARK3 transcripts with longer 3'UTRs, resulting in greater transcript stability and elevated MARK3 protein levels, which promotes increased neuronal tau S262 phosphorylation. Our findings define changes in polyadenylation site selection as a previously unrecognized feature of TDP-43-driven disease pathology in ALS/FTD and highlight a potentially novel mechanistic link between TDP-43 dysfunction and tau regulation.
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36
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Zhu Y, Burg T, Neyrinck K, Vervliet T, Nami F, Vervoort E, Ahuja K, Sassano ML, Chai YC, Tharkeshwar AK, De Smedt J, Hu H, Bultynck G, Agostinis P, Swinnen JV, Van Den Bosch L, da Costa RFM, Verfaillie C. Disruption of MAM integrity in mutant FUS oligodendroglial progenitors from hiPSCs. Acta Neuropathol 2024; 147:6. [PMID: 38170217 PMCID: PMC10764485 DOI: 10.1007/s00401-023-02666-x] [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: 07/26/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and fatal neurodegenerative disorder, characterized by selective loss of motor neurons (MNs). A number of causative genetic mutations underlie the disease, including mutations in the fused in sarcoma (FUS) gene, which can lead to both juvenile and late-onset ALS. Although ALS results from MN death, there is evidence that dysfunctional glial cells, including oligodendroglia, contribute to neurodegeneration. Here, we used human induced pluripotent stem cells (hiPSCs) with a R521H or a P525L mutation in FUS and their isogenic controls to generate oligodendrocyte progenitor cells (OPCs) by inducing SOX10 expression from a TET-On SOX10 cassette. Mutant and control iPSCs differentiated efficiently into OPCs. RNA sequencing identified a myelin sheath-related phenotype in mutant OPCs. Lipidomic studies demonstrated defects in myelin-related lipids, with a reduction of glycerophospholipids in mutant OPCs. Interestingly, FUSR521H OPCs displayed a decrease in the phosphatidylcholine/phosphatidylethanolamine ratio, known to be associated with maintaining membrane integrity. A proximity ligation assay further indicated that mitochondria-associated endoplasmic reticulum membranes (MAM) were diminished in both mutant FUS OPCs. Moreover, both mutant FUS OPCs displayed increased susceptibility to ER stress when exposed to thapsigargin, and exhibited impaired mitochondrial respiration and reduced Ca2+ signaling from ER Ca2+ stores. Taken together, these results demonstrate a pathological role of mutant FUS in OPCs, causing defects in lipid metabolism associated with MAM disruption manifested by impaired mitochondrial metabolism with increased susceptibility to ER stress and with suppressed physiological Ca2+ signaling. As such, further exploration of the role of oligodendrocyte dysfunction in the demise of MNs is crucial and will provide new insights into the complex cellular mechanisms underlying ALS.
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Affiliation(s)
- Yingli Zhu
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, 3000, Leuven, Belgium.
| | - Thibaut Burg
- Department of Neurosciences, Experimental Neurology, KU Leuven, Leuven Brain Institute (LBI), 3000, Leuven, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain and Disease Research, 3000, Leuven, Belgium
| | - Katrien Neyrinck
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, 3000, Leuven, Belgium
| | - Tim Vervliet
- Laboratory of Molecular and Cellular Signalling, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
| | - Fatemeharefeh Nami
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, 3000, Leuven, Belgium
| | - Ellen Vervoort
- Laboratory of Cell Death Research and Therapy, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
| | - Karan Ahuja
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, 3000, Leuven, Belgium
- Animal Physiology and Neurobiology Section, Department of Biology, Neural Circuit Development and Regeneration Research Group, 3000, Leuven, Belgium
| | - Maria Livia Sassano
- Laboratory of Cell Death Research and Therapy, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
| | - Yoke Chin Chai
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, 3000, Leuven, Belgium
| | - Arun Kumar Tharkeshwar
- Department of Neurosciences, Experimental Neurology, KU Leuven, Leuven Brain Institute (LBI), 3000, Leuven, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain and Disease Research, 3000, Leuven, Belgium
| | - Jonathan De Smedt
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, 3000, Leuven, Belgium
| | - Haibo Hu
- National Engineering Research Center for Modernization of Traditional Chinese Medicine-Hakka Medical Resources Branch, School of Pharmacy, Gannan Medical University, Ganzhou, China
| | - Geert Bultynck
- Laboratory of Molecular and Cellular Signalling, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
| | - Patrizia Agostinis
- Laboratory of Cell Death Research and Therapy, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
| | - Johannes V Swinnen
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology, KU Leuven, Leuven Brain Institute (LBI), 3000, Leuven, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain and Disease Research, 3000, Leuven, Belgium
| | | | - Catherine Verfaillie
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, 3000, Leuven, Belgium
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Marriott H, Kabiljo R, Hunt GP, Khleifat AA, Jones A, Troakes C, Pfaff AL, Quinn JP, Koks S, Dobson RJ, Schwab P, Al-Chalabi A, Iacoangeli A. Unsupervised machine learning identifies distinct ALS molecular subtypes in post-mortem motor cortex and blood expression data. Acta Neuropathol Commun 2023; 11:208. [PMID: 38129934 PMCID: PMC10734072 DOI: 10.1186/s40478-023-01686-8] [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: 09/19/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) displays considerable clinical and genetic heterogeneity. Machine learning approaches have previously been utilised for patient stratification in ALS as they can disentangle complex disease landscapes. However, lack of independent validation in different populations and tissue samples have greatly limited their use in clinical and research settings. We overcame these issues by performing hierarchical clustering on the 5000 most variably expressed autosomal genes from motor cortex expression data of people with sporadic ALS from the KCL BrainBank (N = 112). Three molecular phenotypes linked to ALS pathogenesis were identified: synaptic and neuropeptide signalling, oxidative stress and apoptosis, and neuroinflammation. Cluster validation was achieved by applying linear discriminant analysis models to cases from TargetALS US motor cortex (N = 93), as well as Italian (N = 15) and Dutch (N = 397) blood expression datasets, for which there was a high assignment probability (80-90%) for each molecular subtype. The ALS and motor cortex specificity of the expression signatures were tested by mapping KCL BrainBank controls (N = 59), and occipital cortex (N = 45) and cerebellum (N = 123) samples from TargetALS to each cluster, before constructing case-control and motor cortex-region logistic regression classifiers. We found that the signatures were not only able to distinguish people with ALS from controls (AUC 0.88 ± 0.10), but also reflect the motor cortex-based disease process, as there was perfect discrimination between motor cortex and the other brain regions. Cell types known to be involved in the biological processes of each molecular phenotype were found in higher proportions, reinforcing their biological interpretation. Phenotype analysis revealed distinct cluster-related outcomes in both motor cortex datasets, relating to disease onset and progression-related measures. Our results support the hypothesis that different mechanisms underpin ALS pathogenesis in subgroups of patients and demonstrate potential for the development of personalised treatment approaches. Our method is available for the scientific and clinical community at https://alsgeclustering.er.kcl.ac.uk .
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Affiliation(s)
- Heather Marriott
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Renata Kabiljo
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Guy P Hunt
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, 6150, Australia
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK
| | - Ashley Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK
| | - Claire Troakes
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK
- MRC London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, 6150, Australia
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, 6150, Australia
| | - Richard J Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR Maudsley Biomedical Research Centre (BRC), South London and Maudsley NHS Foundation Trust and King's College London, London, UK
- Institute of Health Informatics, University College London, London, UK
- NIHR Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, UK
| | - Patrick Schwab
- GlaxoSmithKline, Artificial Intelligence and Machine Learning, Durham, NC, USA
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK
- King's College Hospital, London, SE5 9RS, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King?s College London, London, SE5 9NU, UK.
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
- NIHR Maudsley Biomedical Research Centre (BRC), South London and Maudsley NHS Foundation Trust and King's College London, London, UK.
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Scopa C, Barnada SM, Cicardi ME, Singer M, Trotti D, Trizzino M. JUN upregulation drives aberrant transposable element mobilization, associated innate immune response, and impaired neurogenesis in Alzheimer's disease. Nat Commun 2023; 14:8021. [PMID: 38049398 PMCID: PMC10696058 DOI: 10.1038/s41467-023-43728-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 11/06/2023] [Indexed: 12/06/2023] Open
Abstract
Adult neurogenic decline, inflammation, and neurodegeneration are phenotypic hallmarks of Alzheimer's disease (AD). Mobilization of transposable elements (TEs) in heterochromatic regions was recently reported in AD, but the underlying mechanisms are still underappreciated. Combining functional genomics with the differentiation of familial and sporadic AD patient derived-iPSCs into hippocampal progenitors, CA3 neurons, and cerebral organoids, we found that the upregulation of the AP-1 subunit, c-Jun, triggers decondensation of genomic regions containing TEs. This leads to the cytoplasmic accumulation of HERVK-derived RNA-DNA hybrids, the activation of the cGAS-STING cascade, and increased levels of cleaved caspase-3, suggesting the initiation of programmed cell death in AD progenitors and neurons. Notably, inhibiting c-Jun effectively blocks all these downstream molecular processes and rescues neuronal death and the impaired neurogenesis phenotype in AD progenitors. Our findings open new avenues for identifying therapeutic strategies and biomarkers to counteract disease progression and diagnose AD in the early, pre-symptomatic stages.
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Affiliation(s)
- Chiara Scopa
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA.
| | - Samantha M Barnada
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Maria E Cicardi
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mo Singer
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Davide Trotti
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA.
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
- Department of Life Sciences, Imperial College London, London, UK.
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39
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Grima N, Liu S, Southwood D, Henden L, Smith A, Lee A, Rowe DB, D'Silva S, Blair IP, Williams KL. RNA sequencing of peripheral blood in amyotrophic lateral sclerosis reveals distinct molecular subtypes: Considerations for biomarker discovery. Neuropathol Appl Neurobiol 2023; 49:e12943. [PMID: 37818590 PMCID: PMC10946588 DOI: 10.1111/nan.12943] [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: 06/08/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/12/2023]
Abstract
AIM Amyotrophic lateral sclerosis (ALS) is a heterogeneous neurodegenerative disease with limited therapeutic options. A key factor limiting the development of effective therapeutics is the lack of disease biomarkers. We sought to assess whether biomarkers for diagnosis, prognosis or cohort stratification could be identified by RNA sequencing (RNA-seq) of ALS patient peripheral blood. METHODS Whole blood RNA-seq data were generated for 96 Australian sporadic ALS (sALS) cases and 48 healthy controls (NCBI GEO accession GSE234297). Differences in sALS-control gene expression, transcript usage and predicted leukocyte proportions were assessed, with pathway analysis used to predict the activity state of biological processes. Weighted Gene Co-expression Network Analysis (WGCNA) and machine learning algorithms were applied to search for diagnostic and prognostic gene expression patterns. Unsupervised clustering analysis was employed to determine whether sALS patient subgroups could be detected. RESULTS Two hundred and forty-five differentially expressed genes were identified in sALS patients relative to controls, with enrichment of immune, metabolic and stress-related pathways. sALS patients also demonstrated switches in transcript usage across a small set of genes. We established a classification model that distinguished sALS patients from controls with an accuracy of 78% (sensitivity: 79%, specificity: 75%) using the expression of 20 genes. Clustering analysis identified four patient subgroups with gene expression signatures and immune cell proportions reflective of distinct peripheral effects. CONCLUSIONS Our findings suggest that peripheral blood RNA-seq can identify diagnostic biomarkers and distinguish molecular subtypes of sALS patients however, its prognostic value requires further investigation.
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Affiliation(s)
- Natalie Grima
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Sidong Liu
- Centre for Health InformaticsFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Dean Southwood
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Lyndal Henden
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Andrew Smith
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Albert Lee
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Dominic B. Rowe
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Susan D'Silva
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Ian P. Blair
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Kelly L. Williams
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
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40
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Rifai OM, O’Shaughnessy J, Dando OR, Munro AF, Sewell MDE, Abrahams S, Waldron FM, Sibley CR, Gregory JM. Distinct neuroinflammatory signatures exist across genetic and sporadic amyotrophic lateral sclerosis cohorts. Brain 2023; 146:5124-5138. [PMID: 37450566 PMCID: PMC10690026 DOI: 10.1093/brain/awad243] [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: 03/26/2023] [Revised: 05/31/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive loss of upper and lower motor neurons. ALS is on a pathogenetic disease spectrum with frontotemporal dementia, referred to as ALS-frontotemporal spectrum disorder (ALS-FTSD). For mutations associated with ALS-FTSD, such as the C9orf72 hexanucleotide repeat expansion, the molecular factors associated with heterogeneity along this spectrum require further characterization. Here, using a targeted NanoString molecular barcoding approach, we interrogate neuroinflammatory dysregulation and heterogeneity at the level of gene expression in post-mortem motor cortex tissue from a cohort of clinically heterogeneous C9-ALS-FTSD cases. We identified 20 dysregulated genes in C9-ALS-FTSD, with enrichment of microglial and inflammatory response gene sets. Two genes with significant correlations to available clinical metrics were selected for validation: FKBP5, a correlate of cognitive function, and brain-derived neurotrophic factor (BDNF), a correlate of disease duration. FKBP5 and its signalling partner, NF-κB, appeared to have a cell type-specific staining distribution, with activated (i.e. nuclear) NF-κB immunoreactivity in C9-ALS-FTSD. Expression of BDNF, a correlate of disease duration, was confirmed to be higher in individuals with long compared to short disease duration using BaseScope™ in situ hybridization. Our analyses also revealed two distinct neuroinflammatory panel signatures (NPS), NPS1 and NPS2, delineated by the direction of expression of proinflammatory, axonal transport and synaptic signalling pathways. We compared NPS between C9-ALS-FTSD cases and those from sporadic ALS and SOD1-ALS cohorts and identified NPS1 and NPS2 across all cohorts. Moreover, a subset of NPS was also able to separate publicly available RNA sequencing data from independent C9-ALS and sporadic ALS cohorts into two inflammatory subgroups. Importantly, NPS subgroups did not clearly segregate with available demographic, genetic, clinical or pathological features, highlighting the value of molecular stratification in clinical trials for inflammatory subgroup identification. Our findings thus underscore the importance of tailoring therapeutic approaches based on distinct molecular signatures that exist between and within ALS-FTSD cohorts.
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Affiliation(s)
- Olivia M Rifai
- Translational Neuroscience PhD Programme, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, EH16 4SB, UK
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, EH16 4SB, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Judi O’Shaughnessy
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Owen R Dando
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, EH16 4SB, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, EH8 9XF, UK
| | - Alison F Munro
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Michael D E Sewell
- Translational Neuroscience PhD Programme, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Sharon Abrahams
- Human Cognitive Neuroscience-Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, Edinburgh, EH8 9AD, UK
| | - Fergal M Waldron
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Christopher R Sibley
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, EH16 4SB, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, EH8 9XF, UK
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3FF, UK
| | - Jenna M Gregory
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, UK
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41
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Boeke JD, Burns KH, Chiappinelli KB, Classon M, Coffin JM, DeCarvalho DD, Dukes JD, Greenbaum B, Kassiotis G, Knutson SK, Levine AJ, Nath A, Papa S, Rios D, Sedivy J, Ting DT. Proceedings of the inaugural Dark Genome Symposium: November 2022. Mob DNA 2023; 14:18. [PMID: 37990347 PMCID: PMC10664479 DOI: 10.1186/s13100-023-00306-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/08/2023] [Indexed: 11/23/2023] Open
Abstract
In November 2022 the first Dark Genome Symposium was held in Boston, USA. The meeting was hosted by Rome Therapeutics and Enara Bio, two biotechnology companies working on translating our growing understanding of this vast genetic landscape into therapies for human disease. The spirit and ambition of the meeting was one of shared knowledge, looking to strengthen the network of researchers engaged in the field. The meeting opened with a welcome from Rosana Kapeller and Kevin Pojasek followed by a first session of field defining talks from key academics in the space. A series of panels, bringing together academia and industry views, were then convened covering a wide range of pertinent topics. Finally, Richard Young and David Ting gave their views on the future direction and promise for patient impact inherent in the growing understanding of the Dark Genome.
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Affiliation(s)
- Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, 10016, USA
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Katherine B Chiappinelli
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Marie Classon
- Pfizer Centre for Therapeutic Innovation, San Diego, USA
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, 02111, USA
| | - Daniel D DeCarvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Joseph D Dukes
- Enara Bio Limited, Magdalen Centre, 1 Robert Robinson Avenue, The Oxford Science Park, Oxford, OX4 4GA, UK
| | - Benjamin Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Sarah K Knutson
- Rome Therapeutics, 201 Brookline Avenue, Suite 1001, Boston, MA, USA
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Avindra Nath
- Section for Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sophie Papa
- Enara Bio Limited, Magdalen Centre, 1 Robert Robinson Avenue, The Oxford Science Park, Oxford, OX4 4GA, UK.
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.
| | - Daniel Rios
- Rome Therapeutics, 201 Brookline Avenue, Suite 1001, Boston, MA, USA
| | - John Sedivy
- Center on the Biology of Aging, Brown University, Providence, RI, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - David T Ting
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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42
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Tam PLF, Leung D. The Molecular Impacts of Retrotransposons in Development and Diseases. Int J Mol Sci 2023; 24:16418. [PMID: 38003607 PMCID: PMC10671454 DOI: 10.3390/ijms242216418] [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: 10/07/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Retrotransposons are invasive genetic elements that constitute substantial portions of mammalian genomes. They have the potential to influence nearby gene expression through their cis-regulatory sequences, reverse transcription machinery, and the ability to mold higher-order chromatin structures. Due to their multifaceted functions, it is crucial for host fitness to maintain strict regulation of these parasitic sequences to ensure proper growth and development. This review explores how subsets of retrotransposons have undergone evolutionary exaptation to enhance the complexity of mammalian genomes. It also highlights the significance of regulating these elements, drawing on recent studies conducted in human and murine systems.
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Affiliation(s)
- Phoebe Lut Fei Tam
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China;
| | - Danny Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China;
- Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
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43
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Wilkins OG, Chien MZ, Wlaschin JJ, Pisliakova M, Thompson D, Digby H, Simkin RL, Diaz JA, Mehta PR, Keuss MJ, Zanovello M, Brown AL, Harley P, Darbey A, Karda R, Fisher EM, Cunningham TJ, Le Pichon CE, Ule J, Fratta P. Creation of de novo cryptic splicing for ALS/FTD precision medicine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.565967. [PMID: 38014203 PMCID: PMC10680699 DOI: 10.1101/2023.11.15.565967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
A system enabling the expression of therapeutic proteins specifically in diseased cells would be transformative, providing greatly increased safety and the possibility of pre-emptive treatment. Here we describe "TDP-REG", a precision medicine approach primarily for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), which exploits the cryptic splicing events that occur in cells with TDP-43 loss-of-function (TDP-LOF) in order to drive expression specifically in diseased cells. In addition to modifying existing cryptic exons for this purpose, we develop a deep-learning-powered algorithm for generating customisable cryptic splicing events, which can be embedded within virtually any coding sequence. By placing part of a coding sequence within a novel cryptic exon, we tightly couple protein expression to TDP-LOF. Protein expression is activated by TDP-LOF in vitro and in vivo, including TDP-LOF induced by cytoplasmic TDP-43 aggregation. In addition to generating a variety of fluorescent and luminescent reporters, we use this system to perform TDP-LOF-dependent genomic prime editing to ablate the UNC13A cryptic donor splice site. Furthermore, we design a panel of tightly gated, autoregulating vectors encoding a TDP-43/Raver1 fusion protein, which rescue key pathological cryptic splicing events. In summary, we combine deep-learning and rational design to create sophisticated splicing sensors, resulting in a platform that provides far safer therapeutics for neurodegeneration, potentially even enabling preemptive treatment of at-risk individuals.
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Affiliation(s)
- Oscar G. Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Max Z.Y.J. Chien
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Josette J. Wlaschin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892, USA
| | - Maria Pisliakova
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - David Thompson
- Mammalian Genetics Unit, MRC Harwell Institute; Oxfordshire, OX11 0RD, UK
| | - Holly Digby
- The Francis Crick Institute; London, NW1 1AT, UK
- UK Dementia Research Institute at King’s College London, Maurice Wohl Clinical Neuroscience Institute; London, SE5 9RX, UK
| | - Rebecca L. Simkin
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Juan Antinao Diaz
- EGA-Institute for Women’s Health, University College London; London, WC1E 6HX, UK
| | - Puja R. Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Matthew J. Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Peter Harley
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Annalucia Darbey
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Rajvinder Karda
- EGA-Institute for Women’s Health, University College London; London, WC1E 6HX, UK
| | - Elizabeth M.C. Fisher
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Tom J. Cunningham
- Mammalian Genetics Unit, MRC Harwell Institute; Oxfordshire, OX11 0RD, UK
| | - Claire E. Le Pichon
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892, USA
| | - Jernej Ule
- The Francis Crick Institute; London, NW1 1AT, UK
- UK Dementia Research Institute at King’s College London, Maurice Wohl Clinical Neuroscience Institute; London, SE5 9RX, UK
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
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Abstract
Although the past two decades have produced exciting discoveries in the genetics and pathology of amyotrophic lateral sclerosis (ALS), progress in developing an effective therapy remains slow. This review summarizes the critical discoveries and outlines the advances in disease characterization, diagnosis, imaging, and biomarkers, along with the current status of approaches to ALS care and treatment. Additional knowledge of the factors driving disease progression and heterogeneity will hopefully soon transform the care for patients with ALS into an individualized, multi-prong approach able to prevent disease progression sufficiently to allow for a dignified life with limited disability.
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Affiliation(s)
- Hristelina Ilieva
- Jefferson Weinberg ALS Center, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Justin Kwan
- National Institute of Neurological Disorders and Stroke, National Institute of Health, Bethesda, MD, USA
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45
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Xie M, Pallegar PN, Parusel S, Nguyen AT, Wu LJ. Regulation of cortical hyperexcitability in amyotrophic lateral sclerosis: focusing on glial mechanisms. Mol Neurodegener 2023; 18:75. [PMID: 37858176 PMCID: PMC10585818 DOI: 10.1186/s13024-023-00665-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder characterized by the loss of both upper and lower motor neurons, resulting in muscle weakness, atrophy, paralysis, and eventually death. Motor cortical hyperexcitability is a common phenomenon observed at the presymptomatic stage of ALS. Both cell-autonomous (the intrinsic properties of motor neurons) and non-cell-autonomous mechanisms (cells other than motor neurons) are believed to contribute to cortical hyperexcitability. Decoding the pathological relevance of these dynamic changes in motor neurons and glial cells has remained a major challenge. This review summarizes the evidence of cortical hyperexcitability from both clinical and preclinical research, as well as the underlying mechanisms. We discuss the potential role of glial cells, particularly microglia, in regulating abnormal neuronal activity during the disease progression. Identifying early changes such as neuronal hyperexcitability in the motor system may provide new insights for earlier diagnosis of ALS and reveal novel targets to halt the disease progression.
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Affiliation(s)
- Manling Xie
- Department of Neurology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Praveen N Pallegar
- Department of Neurology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN, USA
| | - Sebastian Parusel
- Department of Neurology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Aivi T Nguyen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Long-Jun Wu
- Department of Neurology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Department of Immunology, Mayo Clinic, Rochester, MN, USA.
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46
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Woo E, Bredvik K, Liu B, Fuchs TJ, Manfredi G, Konrad C. Machine learning approaches based on fibroblast morphometry do not predict ALS. Neurobiol Aging 2023; 130:80-83. [PMID: 37473581 DOI: 10.1016/j.neurobiolaging.2023.06.010] [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: 01/02/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neuromuscular disease with limited therapeutic options. Biomarkers are needed for early disease detection, clinical trial design, and personalized medicine. Early evidence suggests that specific morphometric features in ALS primary skin fibroblasts may be used as biomarkers; however, this hypothesis has not been rigorously tested in conclusively large fibroblast populations. Here, we imaged ALS-relevant organelles (mitochondria, endoplasmic reticulum, lysosomes) and proteins (TAR DNA-binding protein 43, Ras GTPase-activating protein-binding protein 1, heat-shock protein 60) at baseline and under stress perturbations and tested their predictive power on a total set of 443 human fibroblast lines from ALS and healthy individuals. Machine learning approaches were able to confidently predict stress perturbation states (ROC-AUC ∼0.99) but not disease groups or clinical features (ROC-AUC 0.58-0.64). Our findings indicate that multivariate models using patient-derived fibroblast morphometry can accurately predict different stressors but are insufficient to develop viable ALS biomarkers.
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Affiliation(s)
- Evan Woo
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Kirsten Bredvik
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Bangyan Liu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Thomas J Fuchs
- Hasso Plattner Institute for Digital Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giovanni Manfredi
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Csaba Konrad
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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47
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Gimenez J, Spalloni A, Cappelli S, Ciaiola F, Orlando V, Buratti E, Longone P. TDP-43 Epigenetic Facets and Their Neurodegenerative Implications. Int J Mol Sci 2023; 24:13807. [PMID: 37762112 PMCID: PMC10530927 DOI: 10.3390/ijms241813807] [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: 07/06/2023] [Revised: 07/31/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
Since its initial involvement in numerous neurodegenerative pathologies in 2006, either as a principal actor or as a cofactor, new pathologies implicating transactive response (TAR) DNA-binding protein 43 (TDP-43) are regularly emerging also beyond the neuronal system. This reflects the fact that TDP-43 functions are particularly complex and broad in a great variety of human cells. In neurodegenerative diseases, this protein is often pathologically delocalized to the cytoplasm, where it irreversibly aggregates and is subjected to various post-translational modifications such as phosphorylation, polyubiquitination, and cleavage. Until a few years ago, the research emphasis has been focused particularly on the impacts of this aggregation and/or on its widely described role in complex RNA splicing, whether related to loss- or gain-of-function mechanisms. Interestingly, recent studies have strengthened the knowledge of TDP-43 activity at the chromatin level and its implication in the regulation of DNA transcription and stability. These discoveries have highlighted new features regarding its own transcriptional regulation and suggested additional mechanistic and disease models for the effects of TPD-43. In this review, we aim to give a comprehensive view of the potential epigenetic (de)regulations driven by (and driving) this multitask DNA/RNA-binding protein.
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Affiliation(s)
- Juliette Gimenez
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
| | - Alida Spalloni
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
| | - Sara Cappelli
- Molecular Pathology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy; (S.C.); (E.B.)
| | - Francesca Ciaiola
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
- Department of Systems Medicine, University of Roma Tor Vergata, 00133 Rome, Italy
| | - Valerio Orlando
- KAUST Environmental Epigenetics Program, Biological Environmental Sciences and Engineering Division BESE, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia;
| | - Emanuele Buratti
- Molecular Pathology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy; (S.C.); (E.B.)
| | - Patrizia Longone
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
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48
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Krupp S, Hubbard I, Tam O, Hammell GM, Dubnau J. TDP-43 pathology in Drosophila induces glial-cell type specific toxicity that can be ameliorated by knock-down of SF2/SRSF1. PLoS Genet 2023; 19:e1010973. [PMID: 37747929 PMCID: PMC10553832 DOI: 10.1371/journal.pgen.1010973] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/05/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023] Open
Abstract
Accumulation of cytoplasmic inclusions of TAR-DNA binding protein 43 (TDP-43) is seen in both neurons and glia in a range of neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD) and Alzheimer's disease (AD). Disease progression involves non-cell autonomous interactions among multiple cell types, including neurons, microglia and astrocytes. We investigated the effects in Drosophila of inducible, glial cell type-specific TDP-43 overexpression, a model that causes TDP-43 protein pathology including loss of nuclear TDP-43 and accumulation of cytoplasmic inclusions. We report that TDP-43 pathology in Drosophila is sufficient to cause progressive loss of each of the 5 glial sub-types. But the effects on organismal survival were most pronounced when TDP-43 pathology was induced in the perineural glia (PNG) or astrocytes. In the case of PNG, this effect is not attributable to loss of the glial population, because ablation of these glia by expression of pro-apoptotic reaper expression has relatively little impact on survival. To uncover underlying mechanisms, we used cell-type-specific nuclear RNA sequencing to characterize the transcriptional changes induced by pathological TDP-43 expression. We identified numerous glial cell-type specific transcriptional changes. Notably, SF2/SRSF1 levels were found to be decreased in both PNG and in astrocytes. We found that further knockdown of SF2/SRSF1 in either PNG or astrocytes lessens the detrimental effects of TDP-43 pathology on lifespan, but extends survival of the glial cells. Thus TDP-43 pathology in astrocytes or PNG causes systemic effects that shorten lifespan and SF2/SRSF1 knockdown rescues the loss of these glia, and also reduces their systemic toxicity to the organism.
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Affiliation(s)
- Sarah Krupp
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, New York, United States of America
| | - Isabel Hubbard
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, New York, United States of America
| | - Oliver Tam
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Gale M. Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Josh Dubnau
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, New York, United States of America
- Department of Anesthesiology, Stony Brook School of Medicine, New York, United States of America
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49
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Cao MC, Ryan B, Wu J, Curtis MA, Faull RLM, Dragunow M, Scotter EL. A panel of TDP-43-regulated splicing events verifies loss of TDP-43 function in amyotrophic lateral sclerosis brain tissue. Neurobiol Dis 2023; 185:106245. [PMID: 37527763 DOI: 10.1016/j.nbd.2023.106245] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/13/2023] [Accepted: 07/28/2023] [Indexed: 08/03/2023] Open
Abstract
TDP-43 dysfunction is a molecular hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A major hypothesis of TDP-43 dysfunction in disease is the loss of normal nuclear function, resulting in impaired RNA regulation and the emergence of cryptic exons. Cryptic exons and differential exon usage are emerging as promising markers of lost TDP-43 function in addition to revealing biological pathways involved in neurodegeneration in ALS/FTD. In this brief report, we identified markers of TDP-43 loss of function by depleting TARDBP from post-mortem human brain pericytes, a manipulable in vitro primary human brain cell model, and identifying differential exon usage events with bulk RNA-sequencing analysis. We present these data in an interactive database (https://www.scotterlab.auckland.ac.nz/research-themes/tdp43-lof-db-v2/) together with seven other TDP-43-depletion datasets we meta-analysed previously, for user analysis of differential expression and splicing signatures. Differential exon usage events that were validated by qPCR were then compiled into a 'differential exon usage panel' with other well-established TDP-43 loss-of-function exon markers. This differential exon usage panel was investigated in ALS and control motor cortex tissue to verify whether, and to what extent, TDP-43 loss of function occurs in ALS. We find that profiles of TDP-43-regulated cryptic exons, changed exon usage and changed 3' UTR usage discriminate ALS brain tissue from controls, verifying that TDP-43 loss of function occurs in ALS. We propose that TDP-43-regulated splicing events that occur in brain tissue will have promise as predictors of disease.
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Affiliation(s)
- Maize C Cao
- Department of Pharmacology, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
| | - Brigid Ryan
- Department of Anatomy and Medical Imaging, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
| | - Jane Wu
- Department of Anatomy and Medical Imaging, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
| | - Maurice A Curtis
- Department of Anatomy and Medical Imaging, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
| | - Richard L M Faull
- Department of Anatomy and Medical Imaging, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
| | - Mike Dragunow
- Department of Pharmacology, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
| | - Emma L Scotter
- School of Biological Sciences, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
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50
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Lo Piccolo L, Umegawachi T, Yeewa R, Potikanond S, Nimlamool W, Prachayasittikul V, Gotoh Y, Yoshida H, Yamaguchi M, Jantrapirom S. A Novel Drosophila-based Drug Repurposing Platform Identified Fingolimod As a Potential Therapeutic for TDP-43 Proteinopathy. Neurotherapeutics 2023; 20:1330-1346. [PMID: 37493896 PMCID: PMC10480388 DOI: 10.1007/s13311-023-01406-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/27/2023] Open
Abstract
Pathogenic changes to TAR DNA-binding protein 43 (TDP-43) leading to alteration of its homeostasis are a common feature shared by several progressive neurodegenerative diseases for which there is no effective therapy. Here, we developed Drosophila lines expressing either wild type TDP-43 (WT) or that carrying an Amyotrophic Lateral Sclerosis /Frontotemporal Lobar Degeneration-associating G384C mutation that recapitulate several aspects of the TDP-43 pathology. To identify potential therapeutics for TDP-43-related diseases, we implemented a drug repurposing strategy that involved three consecutive steps. Firstly, we evaluated the improvement of eclosion rate, followed by the assessment of locomotive functions at early and late developmental stages. Through this approach, we successfully identified fingolimod, as a promising candidate for modulating TDP-43 toxicity. Fingolimod exhibited several beneficial effects in both WT and mutant models of TDP-43 pathology, including post-transcriptional reduction of TDP-43 levels, rescue of pupal lethality, and improvement of locomotor dysfunctions. These findings provide compelling evidence for the therapeutic potential of fingolimod in addressing TDP-43 pathology, thereby strengthening the rationale for further investigation and consideration of clinical trials. Furthermore, our study demonstrates the utility of our Drosophila-based screening pipeline in identifying novel therapeutics for TDP-43-related diseases. These findings encourage further scale-up screening endeavors using this platform to discover additional compounds with therapeutic potential for TDP-43 pathology.
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Affiliation(s)
- Luca Lo Piccolo
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Medicine, Musculoskeletal Science and Translational Research Centre (MSTR), Chiang Mai University, Chiang Mai, Thailand
| | | | - Ranchana Yeewa
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Saranyapin Potikanond
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Wutigri Nimlamool
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Virapong Prachayasittikul
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Chiang Mai, Thailand
| | - Yusuke Gotoh
- Platform Technology Research Unit, Sumitomo Pharma Co., Ltd, Kyoto, Japan
| | - Hideki Yoshida
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
| | | | - Salinee Jantrapirom
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
- Drosophila Centre for Human Diseases and Drug Discovery (DHD), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
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