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Ozguney B, Mohanty P, Mittal J. RNA binding tunes the conformational plasticity and intradomain stability of TDP-43 tandem RNA recognition motifs. Biophys J 2024:S0006-3495(24)00658-1. [PMID: 39354713 DOI: 10.1016/j.bpj.2024.09.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 07/26/2024] [Accepted: 09/27/2024] [Indexed: 10/03/2024] Open
Abstract
TAR DNA binding protein 43 (TDP-43) is a nuclear RNA/DNA-binding protein with pivotal roles in RNA-related processes such as splicing, transcription, transport, and stability. The high binding affinity and specificity of TDP-43 toward its cognate RNA sequences (GU-rich) is mediated by highly conserved residues in its tandem RNA recognition motif (RRM) domains (aa: 104-263). Importantly, the loss of RNA binding to the tandem RRMs caused by physiological stressors and chemical modifications promotes cytoplasmic mislocalization and pathological aggregation of TDP-43. Despite the substantial implications of RNA binding in TDP-43 function and pathology, its precise effects on the intradomain stability, and conformational dynamics of the tandem RRMs is not properly understood. Here, we employed all-atom molecular dynamics (MD) simulations to assess the effect of RNA binding on the conformational landscape and intradomain stability of TDP-43 tandem RRMs. RNA limits the overall conformational space of the tandem RRMs and promotes intradomain stability through a combination of specific base stacking interactions and transient electrostatic interactions. In contrast, tandem RRMs exhibit a high intrinsic conformational plasticity in the absence of RNA, which, surprisingly, is accompanied by a tendency of RRM1 to adopt partially unfolded conformations. Overall, our simulations reveal how RNA binding dynamically tunes the structural and conformational landscape of TDP-43 tandem RRMs, contributing to physiological function and mitigating pathological aggregation.
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Affiliation(s)
- Busra Ozguney
- Artie McFerrin Department of Chemical Engineering, Texas A&M College of Engineering, College Station, Texas
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M College of Engineering, College Station, Texas.
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M College of Engineering, College Station, Texas; Department of Chemistry, Texas A&M University, College Station, Texas; Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, Texas.
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2
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Huang Q, Liu L, Tan X, Wang S, Wang S, Luo J, Chen J, Yang N, Jiang J, Liu Y, Hong X, Guo S, Shen Y, Gao F, Feng H, Zhang J, Shen Q, Li C, Ji L. Empagliflozin alleviates neuroinflammation by inhibiting astrocyte activation in the brain and regulating gut microbiota of high-fat diet mice. J Affect Disord 2024; 360:229-241. [PMID: 38823591 DOI: 10.1016/j.jad.2024.05.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/26/2024] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
A high-fat diet can modify the composition of gut microbiota, resulting in dysbiosis. Changes in gut microbiota composition can lead to increased permeability of the gut barrier, allowing bacterial products like lipopolysaccharides (LPS) to enter circulation. This process can initiate systemic inflammation and contribute to neuroinflammation. Empagliflozin (EF), an SGLT2 inhibitor-type hypoglycemic drug, has been reported to treat neuroinflammation. However, there is a lack of evidence showing that EF regulates the gut microbiota axis to control neuroinflammation in HFD models. In this study, we explored whether EF could improve neuroinflammation caused by an HFD via regulation of the gut microbiota and the mechanism underlying this phenomenon. Our data revealed that EF alleviates pathological brain injury, reduces the reactive proliferation of astrocytes, and increases the expression of synaptophysin. In addition, the levels of inflammatory factors in hippocampal tissue were significantly decreased after EF intervention. Subsequently, the results of 16S rRNA gene sequencing showed that EF could change the microbial community structure of mice, indicating that the abundance of Lactococcus, Ligilactobacillus and other microbial populations decreased dramatically. Therefore, EF alleviates neuroinflammation by inhibiting gut microbiota-mediated astrocyte activation in the brains of high-fat diet-fed mice. Our study focused on the gut-brain axis, and broader research on neuroinflammation can provide a more holistic understanding of the mechanisms driving neurodegenerative diseases and inform the development of effective strategies to mitigate their impact on brain health. The results provide strong evidence supporting the larger clinical application of EF.
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Affiliation(s)
- Qiaoyan Huang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Liu Liu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xiaoyao Tan
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Shitong Wang
- Collaborative Innovation Center of Seafood Deep Processing, Zhejiang Province Joint Key Laboratory of Aquatic Products Processing, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China
| | - Sichen Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Jun Luo
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Jiayi Chen
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Na Yang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Jiajun Jiang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Yiming Liu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xiao Hong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Shunyuan Guo
- Center for Rehabilitation Medicine, Department of Neurology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou 314408, China
| | - Yuejian Shen
- Hangzhou Linping Hospital of Traditional Chinese Medicine, Linping 311106, China
| | - Feng Gao
- Hangzhou Linping Hospital of Traditional Chinese Medicine, Linping 311106, China
| | - Huina Feng
- Hangzhou Linping Hospital of Traditional Chinese Medicine, Linping 311106, China
| | - Jianliang Zhang
- Hangzhou Linping Hospital of Traditional Chinese Medicine, Linping 311106, China
| | - Qing Shen
- Collaborative Innovation Center of Seafood Deep Processing, Zhejiang Province Joint Key Laboratory of Aquatic Products Processing, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China.
| | - Changyu Li
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China; Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Liting Ji
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
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3
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Lang R, Hodgson RE, Shelkovnikova TA. TDP-43 in nuclear condensates: where, how, and why. Biochem Soc Trans 2024; 52:1809-1825. [PMID: 38958608 DOI: 10.1042/bst20231447] [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: 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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4
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Fernández Comaduran M, Minotti S, Jacob-Tomas S, Rizwan J, Larochelle N, Robitaille R, Sephton CF, Vera M, Nalbantoglu JN, Durham HD. Impact of histone deacetylase inhibition and arimoclomol on heat shock protein expression and disease biomarkers in primary culture models of familial ALS. Cell Stress Chaperones 2024; 29:359-380. [PMID: 38570009 PMCID: PMC11015512 DOI: 10.1016/j.cstres.2024.03.010] [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: 12/14/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024] Open
Abstract
Protein misfolding and mislocalization are common themes in neurodegenerative disorders, including motor neuron disease, and amyotrophic lateral sclerosis (ALS). Maintaining proteostasis is a crosscutting therapeutic target, including the upregulation of heat shock proteins (HSP) to increase chaperoning capacity. Motor neurons have a high threshold for upregulating stress-inducible HSPA1A, but constitutively express high levels of HSPA8. This study compared the expression of these HSPs in cultured motor neurons expressing three variants linked to familial ALS: TAR DNA binding protein 43 kDa (TDP-43)G348C, fused in sarcoma (FUS)R521G, or superoxide dismutase I (SOD1)G93A. All variants were poor inducers of Hspa1a, and reduced levels of Hspa8 mRNA and protein, indicating multiple compromises in chaperoning capacity. To promote HSP expression, cultures were treated with the putative HSP coinducer, arimoclomol, and class I histone deacetylase inhibitors, to promote active chromatin for transcription, and with the combination. Treatments had variable, often different effects on the expression of Hspa1a and Hspa8, depending on the ALS variant expressed, mRNA distribution (somata and dendrites), and biomarker of toxicity measured (histone acetylation, maintaining nuclear TDP-43 and the neuronal Brm/Brg-associated factor chromatin remodeling complex component Brg1, mitochondrial transport, FUS aggregation). Overall, histone deacetylase inhibition alone was effective on more measures than arimoclomol. As in the FUS model, arimoclomol failed to induce HSPA1A or preserve Hspa8 mRNA in the TDP-43 model, despite preserving nuclear TDP-43 and Brg1, indicating neuroprotective properties other than HSP induction. The data speak to the complexity of drug mechanisms against multiple biomarkers of ALS pathogenesis, as well as to the importance of HSPA8 for neuronal proteostasis in both somata and dendrites.
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Affiliation(s)
- Mario Fernández Comaduran
- Department of Neurology & Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Sandra Minotti
- Department of Neurology & Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | | - Javeria Rizwan
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Nancy Larochelle
- Department of Neurology & Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Richard Robitaille
- Département de Neurosciences and Groupe de Recherche sur le Système Nerveux Central, Université de Montréal, and Centre Interdisciplinaire de Recherche sur le Cerveau et l'apprentissage, Montreal, Quebec, Canada
| | - Chantelle F Sephton
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Josephine N Nalbantoglu
- Department of Neurology & Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Heather D Durham
- Department of Neurology & Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.
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Oliveira NAS, Pinho BR, Pinto J, Guedes de Pinho P, Oliveira JMA. Edaravone counteracts redox and metabolic disruptions in an emerging zebrafish model of sporadic ALS. Free Radic Biol Med 2024; 217:126-140. [PMID: 38531462 DOI: 10.1016/j.freeradbiomed.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/05/2024] [Accepted: 03/20/2024] [Indexed: 03/28/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease in which the death of motor neurons leads to loss of muscle function. Additionally, cognitive and circadian disruptions are common in ALS patients, contributing to disease progression and burden. Most ALS cases are sporadic, and environmental exposures contribute to their aetiology. However, animal models of these sporadic ALS cases are scarce. The small vertebrate zebrafish is a leading organism to model neurodegenerative diseases; previous studies have proposed bisphenol A (BPA) or β-methylamino-l-alanine (BMAA) exposure to model sporadic ALS in zebrafish, damaging motor neurons and altering motor responses. Here we characterise the face and predictive validity of sporadic ALS models, showing their potential for the mechanistic study of ALS drugs. We phenotypically characterise the BPA and BMAA-induced models, going beyond motor activity and motor axon morphology, to include circadian, redox, proteostasis, and metabolomic phenotypes, and assessing their predictive validity for ALS modelling. BPA or BMAA exposure induced concentration-dependent activity impairments. Also, exposure to BPA but not BMAA induced motor axonopathy and circadian alterations in zebrafish larvae. Our further study of the BPA model revealed loss of habituation to repetitive startles, increased oxidative damage, endoplasmic reticulum (ER) stress, and metabolome abnormalities. The BPA-induced model shows predictive validity, since the approved ALS drug edaravone counteracted BPA-induced motor phenotypes, ER stress, and metabolic disruptions. Overall, BPA exposure is a promising model of ALS-related redox and ER imbalances, contributing to fulfil an unmet need for validated sporadic ALS models.
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Affiliation(s)
- Nuno A S Oliveira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, 4050-313, Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Mitochondria and Neurobiology Lab, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Brígida R Pinho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, 4050-313, Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Mitochondria and Neurobiology Lab, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Joana Pinto
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, 4050-313, Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Faculty of Pharmacy, Laboratory of Toxicology, University of Porto, 4050-313, Porto, Portugal
| | - Paula Guedes de Pinho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, 4050-313, Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Faculty of Pharmacy, Laboratory of Toxicology, University of Porto, 4050-313, Porto, Portugal
| | - Jorge M A Oliveira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, 4050-313, Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Mitochondria and Neurobiology Lab, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal.
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6
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Dellar ER, Vendrell I, Talbot K, Kessler BM, Fischer R, Turner MR, Thompson AG. Data-independent acquisition proteomics of cerebrospinal fluid implicates endoplasmic reticulum and inflammatory mechanisms in amyotrophic lateral sclerosis. J Neurochem 2024; 168:115-127. [PMID: 38087504 PMCID: PMC10952667 DOI: 10.1111/jnc.16030] [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: 08/10/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 01/26/2024]
Abstract
While unbiased proteomics of human cerebrospinal fluid (CSF) has been used successfully to identify biomarkers of amyotrophic lateral sclerosis (ALS), high-abundance proteins mask the presence of lower abundance proteins that may have diagnostic and prognostic value. However, developments in mass spectrometry (MS) proteomic data acquisition methods offer improved protein depth. In this study, MS with library-free data-independent acquisition (DIA) was used to compare the CSF proteome of people with ALS (n = 40), healthy (n = 15) and disease (n = 8) controls. Quantified protein groups were subsequently correlated with clinical variables. Univariate analysis identified 7 proteins, all significantly upregulated in ALS versus healthy controls, and 9 with altered abundance in ALS versus disease controls (FDR < 0.1). Elevated chitotriosidase-1 (CHIT1) was common to both comparisons and was proportional to ALS disability progression rate (Pearson r = 0.41, FDR-adjusted p = 0.035) but not overall survival. Ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCHL1; upregulated in ALS versus healthy controls) was proportional to disability progression rate (Pearson r = 0.53, FDR-adjusted p = 0.003) and survival (Kaplan Meier log-rank p = 0.013) but not independently in multivariate proportional hazards models. Weighted correlation network analysis was used to identify functionally relevant modules of proteins. One module, enriched for inflammatory functions, was associated with age at symptom onset (Pearson r = 0.58, FDR-adjusted p = 0.005) and survival (Hazard Ratio = 1.78, FDR = 0.065), and a second module, enriched for endoplasmic reticulum proteins, was negatively correlated with disability progression rate (r = -0.42, FDR-adjusted p = 0.109). DIA acquisition methodology therefore strengthened the biomarker candidacy of CHIT1 and UCHL1 in ALS, while additionally highlighted inflammatory and endoplasmic reticulum proteins as novel sources of prognostic biomarkers.
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Affiliation(s)
| | - Iolanda Vendrell
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery InstituteUniversity of OxfordOxfordUK
- Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford InstituteUniversity of OxfordOxfordUK
| | - Kevin Talbot
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordOxfordUK
| | - Benedikt M. Kessler
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery InstituteUniversity of OxfordOxfordUK
- Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford InstituteUniversity of OxfordOxfordUK
| | - Roman Fischer
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery InstituteUniversity of OxfordOxfordUK
- Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford InstituteUniversity of OxfordOxfordUK
| | - Martin R. Turner
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
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Perlegos AE, Durkin J, Belfer SJ, Rodriguez A, Shcherbakova O, Park K, Luong J, Bonini NM, Kayser MS. TDP-43 impairs sleep in Drosophila through Ataxin-2-dependent metabolic disturbance. SCIENCE ADVANCES 2024; 10:eadj4457. [PMID: 38198547 PMCID: PMC10780954 DOI: 10.1126/sciadv.adj4457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
Neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia are associated with substantial sleep disruption, which may accelerate cognitive decline and brain degeneration. Here, we define a role for trans-activation response element (TAR) DNA binding protein 43 (TDP-43), a protein associated with human neurodegenerative disease, in regulating sleep using Drosophila. Expression of TDP-43 severely disrupts sleep, and the sleep deficit is rescued by Atx2 knockdown. Brain RNA sequencing revealed that Atx2 RNA interference regulates transcripts enriched for small-molecule metabolic signaling in TDP-43 brains. Focusing on these Atx2-regulated genes, we identified suppressors of the TDP-43 sleep phenotype enriched for metabolism pathways. Knockdown of Atx2 or treatment with rapamycin attenuated the sleep phenotype and mitigated the disruption of small-molecule glycogen metabolism caused by TDP-43. Our findings provide a connection between toxicity of TDP-43 and sleep disturbances and highlight key aspects of metabolism that interplay with TDP-43 toxicity upon Atx2 rescue.
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Affiliation(s)
- Alexandra E. Perlegos
- Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jaclyn Durkin
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- National Institute of Neurological Disorders & Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Samuel J. Belfer
- Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anyara Rodriguez
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Oksana Shcherbakova
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen Park
- Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jenny Luong
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nancy M. Bonini
- Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew S. Kayser
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Chronobiology Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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Geraci J, Bhargava R, Qorri B, Leonchyk P, Cook D, Cook M, Sie F, Pani L. Machine learning hypothesis-generation for patient stratification and target discovery in rare disease: our experience with Open Science in ALS. Front Comput Neurosci 2024; 17:1199736. [PMID: 38260713 PMCID: PMC10801647 DOI: 10.3389/fncom.2023.1199736] [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: 04/03/2023] [Accepted: 11/20/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Advances in machine learning (ML) methodologies, combined with multidisciplinary collaborations across biological and physical sciences, has the potential to propel drug discovery and development. Open Science fosters this collaboration by releasing datasets and methods into the public space; however, further education and widespread acceptance and adoption of Open Science approaches are necessary to tackle the plethora of known disease states. Motivation In addition to providing much needed insights into potential therapeutic protein targets, we also aim to demonstrate that small patient datasets have the potential to provide insights that usually require many samples (>5,000). There are many such datasets available and novel advancements in ML can provide valuable insights from these patient datasets. Problem statement Using a public dataset made available by patient advocacy group AnswerALS and a multidisciplinary Open Science approach with a systems biology augmented ML technology, we aim to validate previously reported drug targets in ALS and provide novel insights about ALS subpopulations and potential drug targets using a unique combination of ML methods and graph theory. Methodology We use NetraAI to generate hypotheses about specific patient subpopulations, which were then refined and validated through a combination of ML techniques, systems biology methods, and expert input. Results We extracted 8 target classes, each comprising of several genes that shed light into ALS pathophysiology and represent new avenues for treatment. These target classes are broadly categorized as inflammation, epigenetic, heat shock, neuromuscular junction, autophagy, apoptosis, axonal transport, and excitotoxicity. These findings are not mutually exclusive, and instead represent a systematic view of ALS pathophysiology. Based on these findings, we suggest that simultaneous targeting of ALS has the potential to mitigate ALS progression, with the plausibility of maintaining and sustaining an improved quality of life (QoL) for ALS patients. Even further, we identified subpopulations based on disease onset. Conclusion In the spirit of Open Science, this work aims to bridge the knowledge gap in ALS pathophysiology to aid in diagnostic, prognostic, and therapeutic strategies and pave the way for the development of personalized treatments tailored to the individual's needs.
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Affiliation(s)
- Joseph Geraci
- NetraMark Corp, Toronto, ON, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
- Centre for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
- Arthur C. Clarke Center for Human Imagination, School of Physical Sciences, University of California San Diego, San Diego, CA, United States
| | - Ravi Bhargava
- Department of Biomedical and Molecular Science, Queens University, Kingston, ON, Canada
- Science and Research, Roche Integrated Informatics, F. Hoffmann La-Roche, Toronto, ON, Canada
| | | | | | - Douglas Cook
- NetraMark Corp, Toronto, ON, Canada
- Department of Surgery, Queen's University, Kingston, ON, Canada
| | - Moses Cook
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Fanny Sie
- Science and Research, Roche Integrated Informatics, F. Hoffmann La-Roche, Toronto, ON, Canada
| | - Luca Pani
- NetraMark Corp, Toronto, ON, Canada
- Department of Psychiatry and Behavioral Sciences, Leonard M. Miller School of Medicine, University of Miami, Coral Gables, FL, United States
- Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
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9
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Flores-Montero K, Frontini-Lopez YR, Fontecilla-Escobar J, Ruete MC. Sperm proteostasis: Can-nabinoids be chaperone's partners? Life Sci 2023; 333:122167. [PMID: 37827231 DOI: 10.1016/j.lfs.2023.122167] [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: 08/16/2023] [Revised: 10/07/2023] [Accepted: 10/08/2023] [Indexed: 10/14/2023]
Abstract
The male gamete is a highly differentiated cell that aims to fuse with the oocyte in fertilization. Sperm have silenced the transcription and translational processes, maintaining proteostasis to guarantee male reproductive health. Despite the information about the implication of molecular chaperones as orchestrators of protein folding or aggregation, and the handling of body homeostasis by the endocannabinoid system, there is still a lack of basic investigation and random controlled clinical trials that deliver more evidence on the involvement of cannabinoids in reproductive function. Besides, we noticed that the information regarding whether recreational marijuana affects male fertility is controversial and requires further investigation. In other cell models, it has recently been evidenced that chaperones and cannabinoids are intimately intertwined. Through a literature review, we aim to explore the interaction between chaperones and cannabinoid signaling in sperm development and function. To untangle how or whether this dialogue happens within the sperm proteostasis. We discuss the action of chaperones, the endocannabinoid system and phytocannabinoids in sperm proteostasis. Reports of some heat shock and lipid proteins interacting with cannabinoid receptors prove that chaperones and the endocannabinoid system are in an intimate dialogue. Meanwhile, advancing the evidence to decipher these mechanisms for introducing innovative interventions into routine clinical settings becomes crucial. We highlight the potential interaction between chaperones and cannabinoid signaling in regulating proteostasis in male reproductive health.
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Affiliation(s)
- Karina Flores-Montero
- Instituto de Histología y Embriología de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Cuyo, Mendoza M5500, Argentina
| | - Yesica Romina Frontini-Lopez
- Instituto de Histología y Embriología de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Cuyo, Mendoza M5500, Argentina
| | - Javiera Fontecilla-Escobar
- Instituto de Histología y Embriología de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Cuyo, Mendoza M5500, Argentina
| | - María Celeste Ruete
- Instituto de Histología y Embriología de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Cuyo, Mendoza M5500, Argentina.
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De Marchi F, Franjkic T, Schito P, Russo T, Nimac J, Chami AA, Mele A, Vidatic L, Kriz J, Julien JP, Apic G, Russell RB, Rogelj B, Cannon JR, Baralle M, Agosta F, Hecimovic S, Mazzini L, Buratti E, Munitic I. Emerging Trends in the Field of Inflammation and Proteinopathy in ALS/FTD Spectrum Disorder. Biomedicines 2023; 11:1599. [PMID: 37371694 PMCID: PMC10295684 DOI: 10.3390/biomedicines11061599] [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: 04/28/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Proteinopathy and neuroinflammation are two main hallmarks of neurodegenerative diseases. They also represent rare common events in an exceptionally broad landscape of genetic, environmental, neuropathologic, and clinical heterogeneity present in patients. Here, we aim to recount the emerging trends in amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD) spectrum disorder. Our review will predominantly focus on neuroinflammation and systemic immune imbalance in ALS and FTD, which have recently been highlighted as novel therapeutic targets. A common mechanism of most ALS and ~50% of FTD patients is dysregulation of TAR DNA-binding protein 43 (TDP-43), an RNA/DNA-binding protein, which becomes depleted from the nucleus and forms cytoplasmic aggregates in neurons and glia. This, in turn, via both gain and loss of function events, alters a variety of TDP-43-mediated cellular events. Experimental attempts to target TDP-43 aggregates or manipulate crosstalk in the context of inflammation will be discussed. Targeting inflammation, and the immune system in general, is of particular interest because of the high plasticity of immune cells compared to neurons.
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Affiliation(s)
- Fabiola De Marchi
- Department of Neurology and ALS Centre, University of Piemonte Orientale, Maggiore Della Carità Hospital, Corso Mazzini 18, 28100 Novara, Italy; (F.D.M.); (A.M.)
| | - Toni Franjkic
- Laboratory for Molecular Immunology, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia;
- Metisox, Cambridge CB24 9NL, UK;
| | - Paride Schito
- Department of Neurology & Neuropathology Unit, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (P.S.); (T.R.)
| | - Tommaso Russo
- Department of Neurology & Neuropathology Unit, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (P.S.); (T.R.)
| | - Jerneja Nimac
- Department of Biotechnology, Jozef Stefan Institute, SI-1000 Ljubljana, Slovenia; (J.N.); (B.R.)
- Graduate School of Biomedicine, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Anna A. Chami
- CERVO Research Centre, Laval University, Quebec City, QC G1J 2G3, Canada; (A.A.C.); (J.K.); (J.-P.J.)
| | - Angelica Mele
- Department of Neurology and ALS Centre, University of Piemonte Orientale, Maggiore Della Carità Hospital, Corso Mazzini 18, 28100 Novara, Italy; (F.D.M.); (A.M.)
| | - Lea Vidatic
- Laboratory for Neurodegenerative Disease Research, Division of Molecular Medicine, Ruder Boskovic Institute, 10000 Zagreb, Croatia; (L.V.); (S.H.)
| | - Jasna Kriz
- CERVO Research Centre, Laval University, Quebec City, QC G1J 2G3, Canada; (A.A.C.); (J.K.); (J.-P.J.)
| | - Jean-Pierre Julien
- CERVO Research Centre, Laval University, Quebec City, QC G1J 2G3, Canada; (A.A.C.); (J.K.); (J.-P.J.)
| | | | | | - Boris Rogelj
- Department of Biotechnology, Jozef Stefan Institute, SI-1000 Ljubljana, Slovenia; (J.N.); (B.R.)
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jason R. Cannon
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, USA;
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | | | - Federica Agosta
- Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Silva Hecimovic
- Laboratory for Neurodegenerative Disease Research, Division of Molecular Medicine, Ruder Boskovic Institute, 10000 Zagreb, Croatia; (L.V.); (S.H.)
| | - Letizia Mazzini
- Department of Neurology and ALS Centre, University of Piemonte Orientale, Maggiore Della Carità Hospital, Corso Mazzini 18, 28100 Novara, Italy; (F.D.M.); (A.M.)
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Ivana Munitic
- Laboratory for Molecular Immunology, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia;
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Chaperone-Dependent Mechanisms as a Pharmacological Target for Neuroprotection. Int J Mol Sci 2023; 24:ijms24010823. [PMID: 36614266 PMCID: PMC9820882 DOI: 10.3390/ijms24010823] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 01/05/2023] Open
Abstract
Modern pharmacotherapy of neurodegenerative diseases is predominantly symptomatic and does not allow vicious circles causing disease development to break. Protein misfolding is considered the most important pathogenetic factor of neurodegenerative diseases. Physiological mechanisms related to the function of chaperones, which contribute to the restoration of native conformation of functionally important proteins, evolved evolutionarily. These mechanisms can be considered promising for pharmacological regulation. Therefore, the aim of this review was to analyze the mechanisms of endoplasmic reticulum stress (ER stress) and unfolded protein response (UPR) in the pathogenesis of neurodegenerative diseases. Data on BiP and Sigma1R chaperones in clinical and experimental studies of Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease are presented. The possibility of neuroprotective effect dependent on Sigma1R ligand activation in these diseases is also demonstrated. The interaction between Sigma1R and BiP-associated signaling in the neuroprotection is discussed. The performed analysis suggests the feasibility of pharmacological regulation of chaperone function, possibility of ligand activation of Sigma1R in order to achieve a neuroprotective effect, and the need for further studies of the conjugation of cellular mechanisms controlled by Sigma1R and BiP chaperones.
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Włodarczyk P, Witczak M, Gajewska A, Chady T, Piotrowski I. The role of TDP-43 protein in amyotrophic lateral sclerosis. JOURNAL OF MEDICAL SCIENCE 2022. [DOI: 10.20883/medical.e710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease where both upper and lower motoneurons are damaged. Even though the pathogenesis of ALS is unclear, the TDP-43 aggregations and non-nuclear localization may be crucial to understanding this process. Despite intensive research on ALS therapies, only two lifespan-prolonging medications have been approved: Riluzole and Edaravone. Unravelling the TDP-43 pathology could help develop new ALS therapies using mechanisms such as inhibition of nuclear export, autophagy, chaperones, or antisense oligonucleotides. Selective inhibitors of nuclear export (SINEs) are drugs that block Exportin 1 (XPO1) and cause the accumulation of not exported molecules inside the nucleus. SINEs that target XPO1 are shown to slightly extend the survival of neurons and soften motor symptoms. Dysfunctional proteins, including TDP-43, can be eliminated through autophagocytosis, which is regulated by the mTOR kinase. Stimulating the elimination of protein deposits may be an effective ALS therapy. Antisense oligonucleotides (ASO) are single-stranded, synthetic oligonucleotides that can bind and modulate specific RNA: via ribonuclease H, inducing their degradation or inducing alternative splicing via blocking primary RNA transcripts. Current ASOs therapies used in ALS focus on SOD1, C9ORF72, FUS, and ATXN2, and they may be used to slow the ALS progression. Reversing the aggregation is a promising therapeutic strategy. Chaperones control other proteins' quality and protect them against stress factors. Due to the irreversible character of ALS, it is essential to understand its complicated pathology better and to seek new therapies.
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Direito I, Gomes D, Monteiro FL, Carneiro I, Lobo J, Henrique R, Jerónimo C, Helguero LA. The Clinicopathological Significance of BiP/GRP-78 in Breast Cancer: A Meta-Analysis of Public Datasets and Immunohistochemical Detection. Curr Oncol 2022; 29:9066-9087. [PMID: 36547124 PMCID: PMC9777260 DOI: 10.3390/curroncol29120710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/24/2022] Open
Abstract
The endoplasmic reticulum chaperone BiP (also known as GRP-78 or HSPA5) maintains protein folding to allow cell proliferation and survival and has been implicated in carcinogenesis, tumor progression, and therapy resistance. BiP's association with clinical factors and prognostic potential in breast cancer remains unclear. In this work, three types of analysis were conducted to improve the knowledge of BiP's clinicopathological potential: (1) analysis of publicly available RNA-seq and proteomics datasets stratified as high and low quartiles; (2) a systematic review and meta-analysis of immunohistochemical detection of BIP; (3) confirmation of findings by BiP immunohistochemical detection in two luminal-like breast cancer small cohorts of paired samples (pre- vs. post-endocrine therapy, and primary pre- vs. metastasis post-endocrine therapy). The TCGA PanCancer dataset and CPTAC showed groups with high BiP mRNA and protein associated with HER2, basal-like subtypes, and higher immune scores. The meta-analysis of BiP immunohistochemistry disclosed an association between higher BiP positivity and reduced relapse-free survival. BiP immunohistochemistry confirmed increased BiP expression in metastasis, an association of BiP positivity with HER2 expression, and nuclear BiP localization with higher a tumor stage and poor outcome. Therefore, three independent approaches showed that BiP protein is associated with worse outcomes and holds prognostic potential for breast cancer.
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Affiliation(s)
- Inês Direito
- iBiMED—Institute of Biomedicine, University of Aveiro, Agra do Crasto 30, 3810-193 Aveiro, Portugal
| | - Daniela Gomes
- iBiMED—Institute of Biomedicine, University of Aveiro, Agra do Crasto 30, 3810-193 Aveiro, Portugal
| | - Fátima Liliana Monteiro
- iBiMED—Institute of Biomedicine, University of Aveiro, Agra do Crasto 30, 3810-193 Aveiro, Portugal
| | - Isa Carneiro
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC) & RISE@CI-IPOP (Health Research Network), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - João Lobo
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC) & RISE@CI-IPOP (Health Research Network), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC) & RISE@CI-IPOP (Health Research Network), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Carmen Jerónimo
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC) & RISE@CI-IPOP (Health Research Network), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Luisa Alejandra Helguero
- iBiMED—Institute of Biomedicine, University of Aveiro, Agra do Crasto 30, 3810-193 Aveiro, Portugal
- Correspondence: ; Tel.: +35-1-234-247-240 (ext. 22112)
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