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Jenne A, Soong R, Downey K, Biswas RG, Decker V, Busse F, Goerling B, Haber A, Simpson MJ, Simpson AJ. Brewing alcohol 101: An undergraduate experiment utilizing benchtop NMR for quantification and process monitoring. Magn Reson Chem 2024; 62:429-438. [PMID: 38230451 DOI: 10.1002/mrc.5428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024]
Abstract
In recent years there has been a renewed interest in benchtop NMR. Given their lower cost of ownership, smaller footprint, and ease of use, they are especially suited as an educational tool. Here, a new experiment targeted at upper-year undergraduates and first-year graduate students follows the conversion of D-glucose into ethanol at low-field. First, high and low-field data on D-glucose are compared and students learn both the Hz and ppm scales and how J-coupling is field-independent. The students then acquire their own quantitative NMR datasets and perform the quantification using an Electronic Reference To Access In Vivo Concentration (ERETIC) technique. To our knowledge ERETIC is not currently taught at the undergraduate level, but has an advantage in that internal standards are not required; ideal for following processes or with future use in flow-based benchtop monitoring. Using this quantitative data, students can relate a simple chemical process (fermentation) back to more complex topics such as reaction kinetics, bridging the gaps between analytical and physical chemistry. When asked to reflect on the experiment, students had an overwhelmingly positive experience, citing agreement with learning objectives, ease of understanding the protocol, and enjoyment. Each of the respondents recommended this experiment as a learning tool for others. This experiment has been outlined for other instructors to utilize in their own courses across institutions, with the hope that a continued expansion of low-field NMR will increase accessibility and learning opportunities at the undergraduate level.
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Affiliation(s)
- Amy Jenne
- Environmental NMR Center, University of Toronto Scarborough, Toronto, ON, Canada
| | - Ronald Soong
- Environmental NMR Center, University of Toronto Scarborough, Toronto, ON, Canada
| | - Katelyn Downey
- Environmental NMR Center, University of Toronto Scarborough, Toronto, ON, Canada
| | | | | | | | | | | | - Myrna J Simpson
- Environmental NMR Center, University of Toronto Scarborough, Toronto, ON, Canada
| | - Andre J Simpson
- Environmental NMR Center, University of Toronto Scarborough, Toronto, ON, Canada
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Pellizzari J, Soong R, Downey K, Biswas RG, Kock FC, Steiner K, Goerling B, Haber A, Decker V, Busse F, Simpson M, Simpson A. Slice through the water-Exploring the fundamental challenge of water suppression for benchtop NMR systems. Magn Reson Chem 2024; 62:463-473. [PMID: 38282484 DOI: 10.1002/mrc.5431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/01/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024]
Abstract
Benchtop NMR provides improved accessibility in terms of cost, space, and technical expertise. In turn, this encourages new users into the field of NMR spectroscopy. Unfortunately, many interesting samples in education and research, from beer to whole blood, contain significant amounts of water that require suppression in 1H NMR in order to recover sample information. However, due to the significant reduction in chemical shift dispersion in benchtop NMR systems, the sample signals are much closer to the water resonance compared to those in a corresponding high-field NMR spectrum. Therefore, simply translating solvent suppression experiments intended for high-field NMR instruments to benchtop NMR systems without careful consideration can be problematic. In this study, the effectiveness of several popular water suppression schemes was evaluated for benchtop NMR applications. Emphasis is placed on pulse sequences with no, or few, adjustable parameters making them easy to implement. These fall into two main categories: (1) those based on Pre-SAT including Pre-SAT, PURGE, NOESY-PR, and g-NOESY-PR and (2) those based on binomial inversion including JRS and W5-WATERGATE. Among these schemes, solvent suppression sequences based on Pre-SAT offer a general approach for easy solvent suppression for samples with higher analyte concentrations (sucrose standard and Redbull™). However, for human urine, binomial-like sequences were required. In summary, it is demonstrated that highly efficient water suppression approaches can be implemented on benchtop NMR systems in a simple manner, despite the limited spectral dispersion, further illustrating the potential for widespread implementation of these approaches in education and research.
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Affiliation(s)
| | - Ronald Soong
- University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Katelyn Downey
- University of Toronto Scarborough, Toronto, Ontario, Canada
| | | | - Flavio C Kock
- University of Toronto Scarborough, Toronto, Ontario, Canada
| | | | | | | | | | | | - Myrna Simpson
- University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Andre Simpson
- University of Toronto Scarborough, Toronto, Ontario, Canada
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Downey K, Bermel W, Soong R, Lysak DH, Ronda K, Steiner K, Costa PM, Wolff WW, Decker V, Busse F, Goerling B, Haber A, Simpson MJ, Simpson AJ. Low-field, not low quality: 1D simplification, selective detection, and heteronuclear 2D experiments for improving low-field NMR spectroscopy of environmental and biological samples. Magn Reson Chem 2024; 62:345-360. [PMID: 37811556 DOI: 10.1002/mrc.5401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023]
Abstract
Understanding environmental change is challenging and requires molecular-level tools to explain the physicochemical phenomena behind complex processes. Nuclear magnetic resonance (NMR) spectroscopy is a key tool that provides information on both molecular structures and interactions but is underutilized in environmental research because standard "high-field" NMR is financially and physically inaccessible for many and can be overwhelming to those outside of disciplines that routinely use NMR. "Low-field" NMR is an accessible alternative but has reduced sensitivity and increased spectral overlap, which is especially problematic for natural, heterogeneous samples. Therefore, the goal of this study is to investigate and apply innovative experiments that could minimize these challenges and improve low-field NMR analysis of environmental and biological samples. Spectral simplification (JRES, PSYCHE, singlet-only, multiple quantum filters), selective detection (GEMSTONE, DREAMTIME), and heteronuclear (reverse and CH3/CH2/CH-only HSQCs) NMR experiments are tested on samples of increasing complexity (amino acids, spruce resin, and intact water fleas) at-high field (500 MHz) and at low-field (80 MHz). A novel experiment called Doubly Selective HSQC is also introduced, wherein 1H signals are selectively detected based on the 1H and 13C chemical shifts of 1H-13C J-coupled pairs. The most promising approaches identified are the selective techniques (namely for monitoring), and the reverse and CH3-only HSQCs. Findings ultimately demonstrate that low-field NMR holds great potential for biological and environmental research. The multitude of NMR experiments available makes NMR tailorable to nearly any research need, and low-field NMR is therefore anticipated to become a valuable and widely used analytical tool moving forward.
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Affiliation(s)
- Katelyn Downey
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, Ontario, Canada
| | | | - Ronald Soong
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Daniel H Lysak
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Kiera Ronda
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Katrina Steiner
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Peter M Costa
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - William W Wolff
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, Ontario, Canada
| | | | | | | | | | - Myrna J Simpson
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Andre J Simpson
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, Ontario, Canada
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Croxall MP, Lawrence RT, Ghosh Biswas R, Soong R, Simpson AJ, Goh MC. Improved Photocatalytic Performance of TiO 2-Nitrogen-Doped Graphene Quantum Dot Composites Mediated by Heterogeneous Interactions. J Phys Chem Lett 2024; 15:3653-3657. [PMID: 38531047 PMCID: PMC11000646 DOI: 10.1021/acs.jpclett.4c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 03/28/2024]
Abstract
Photocatalysis is typically monitored via analysis of phases in isolation and focuses on the removal of a target analyte from the solution phase. Here we analyze the photocatalytic action of a TiO2-nitrogen-doped graphene quantum dot (NGQD) composite on a target analyte, phenol, using comprehensive multiphase NMR (CMP-NMR) which observes signals in solid, solution, and gel phases in situ. Phenol preferentially interacts with the composite photocatalyst compared to pure TiO2, increasing its effective concentration near the catalyst surface and its degradation rate. The presence of NGQDs in the composite reduced the fouling of the catalyst surface and caused a reduction of photogenerated intermediates. Increased heterogeneous interactions, likely mediated by π-π interactions, are hypothesized to cause each of these improvements in the observed photocatalytic performance by TiO2-NGQDs. CMP-NMR allows the elucidation of how the photocatalytic mechanism is enhanced via material design and provides a foundation for the development of efficient photocatalysts.
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Affiliation(s)
- Mark P. Croxall
- Department
of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Reece T. Lawrence
- Department
of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- Department
of Materials Science and Engineering, University
of Toronto, Toronto, ON M5S 3E4, Canada
| | - Rajshree Ghosh Biswas
- Department
of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- Department
of Physical and Environmental Science, University
of Toronto, Toronto, ON M1C 1A4, Canada
| | - Ronald Soong
- Department
of Physical and Environmental Science, University
of Toronto, Toronto, ON M1C 1A4, Canada
| | - Andre J. Simpson
- Department
of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- Department
of Physical and Environmental Science, University
of Toronto, Toronto, ON M1C 1A4, Canada
| | - M. Cynthia Goh
- Department
of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- Department
of Materials Science and Engineering, University
of Toronto, Toronto, ON M5S 3E4, Canada
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Bourmoum M, Radulovich N, Sharma A, Tkach JM, Tsao MS, Pelletier L. β-catenin mediates growth defects induced by centrosome loss in a subset of APC mutant colorectal cancer independently of p53. PLoS One 2024; 19:e0295030. [PMID: 38324534 PMCID: PMC10849215 DOI: 10.1371/journal.pone.0295030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 11/13/2023] [Indexed: 02/09/2024] Open
Abstract
Colorectal cancer is the third most common cancer and the second leading cause of cancer-related deaths worldwide. The centrosome is the main microtubule-organizing center in animal cells and centrosome amplification is a hallmark of cancer cells. To investigate the importance of centrosomes in colorectal cancer, we induced centrosome loss in normal and cancer human-derived colorectal organoids using centrinone B, a Polo-like kinase 4 (Plk4) inhibitor. We show that centrosome loss represses human normal colorectal organoid growth in a p53-dependent manner in accordance with previous studies in cell models. However, cancer colorectal organoid lines exhibited different sensitivities to centrosome loss independently of p53. Centrinone-induced cancer organoid growth defect/death positively correlated with a loss of function mutation in the APC gene, suggesting a causal role of the hyperactive WNT pathway. Consistent with this notion, β-catenin inhibition using XAV939 or ICG-001 partially prevented centrinone-induced death and rescued the growth two APC-mutant organoid lines tested. Our study reveals a novel role for canonical WNT signaling in regulating centrosome loss-induced growth defect/death in a subset of APC-mutant colorectal cancer independently of the classical p53 pathway.
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Affiliation(s)
- Mohamed Bourmoum
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Nikolina Radulovich
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Amit Sharma
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Johnny M. Tkach
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Ming-Sound Tsao
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Dang M, Shoichet MS. Long-Acting Ocular Injectables: Are We Looking In The Right Direction? Adv Sci (Weinh) 2024; 11:e2306463. [PMID: 38018313 PMCID: PMC10885661 DOI: 10.1002/advs.202306463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/24/2023] [Indexed: 11/30/2023]
Abstract
The complex anatomy and physiological barriers of the eye make delivering ocular therapeutics challenging. Generally, effective drug delivery to the eye is hindered by rapid clearance and limited drug bioavailability. Biomaterial-based approaches have emerged to enhance drug delivery to ocular tissues and overcome existing limitations. In this review, some of the most promising long-acting injectables (LAIs) in ocular drug delivery are explored, focusing on novel design strategies to improve therapeutic outcomes. LAIs are designed to enable sustained therapeutic effects, thereby extending local drug residence time and facilitating controlled and targeted drug delivery. Moreover, LAIs can be engineered to enhance drug targeting and penetration across ocular physiological barriers.
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Affiliation(s)
- Mickael Dang
- Department of Chemical Engineering and Applied ChemistryUniversity of Toronto200 College StreetTorontoONM5S 3E5Canada
- Donnelly Centre for Cellular and Biomolecular ResearchUniversity of Toronto160 College StreetTorontoONM5S 3E1Canada
| | - Molly S. Shoichet
- Department of Chemical Engineering and Applied ChemistryUniversity of Toronto200 College StreetTorontoONM5S 3E5Canada
- Donnelly Centre for Cellular and Biomolecular ResearchUniversity of Toronto160 College StreetTorontoONM5S 3E1Canada
- Institute of Biomedical Engineering164 College StreetTorontoONM5S 3G9Canada
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Koussiouris J, Looby N, Kotlyar M, Kulasingam V, Jurisica I, Chandran V. Classifying patients with psoriatic arthritis according to their disease activity status using serum metabolites and machine learning. Metabolomics 2024; 20:17. [PMID: 38267619 PMCID: PMC10810020 DOI: 10.1007/s11306-023-02079-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 12/06/2023] [Indexed: 01/26/2024]
Abstract
INTRODUCTION Psoriatic arthritis (PsA) is a heterogeneous inflammatory arthritis, affecting approximately a quarter of patients with psoriasis. Accurate assessment of disease activity is difficult. There are currently no clinically validated biomarkers to stratify PsA patients based on their disease activity, which is important for improving clinical management. OBJECTIVES To identify metabolites capable of classifying patients with PsA according to their disease activity. METHODS An in-house solid-phase microextraction (SPME)-liquid chromatography-high resolution mass spectrometry (LC-HRMS) method for lipid analysis was used to analyze serum samples obtained from patients classified as having low (n = 134), moderate (n = 134) or high (n = 104) disease activity, based on psoriatic arthritis disease activity scores (PASDAS). Metabolite data were analyzed using eight machine learning methods to predict disease activity levels. Top performing methods were selected based on area under the curve (AUC) and significance. RESULTS The best model for predicting high disease activity from low disease activity achieved AUC 0.818. The best model for predicting high disease activity from moderate disease activity achieved AUC 0.74. The best model for classifying low disease activity from moderate and high disease activity achieved AUC 0.765. Compounds confirmed by MS/MS validation included metabolites from diverse compound classes such as sphingolipids, phosphatidylcholines and carboxylic acids. CONCLUSION Several lipids and other metabolites when combined in classifying models predict high disease activity from both low and moderate disease activity. Lipids of key interest included lysophosphatidylcholine and sphingomyelin. Quantitative MS assays based on selected reaction monitoring, are required to quantify the candidate biomarkers identified.
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Affiliation(s)
- John Koussiouris
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Nikita Looby
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Osteoarthritis Research Program, Division of Orthopaedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopaedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Division of Clinical Biochemistry, Laboratory Medicine Program, University Health Network, Toronto, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopaedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Vinod Chandran
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Institute, University Health Network, Toronto, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, Canada.
- Institute of Medical Science, University of Toronto, Toronto, Canada.
- Krembil Research Institute, University Health Network, Toronto, Canada.
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Wolff WW, Pellizzari J, Soong R, Lysak DH, Steiner K, Ronda K, Costa P, Downey K, Moxley-Paquette V, Suszczynski C, Boehmer S, Prat JR, Simpson AJ. 13 C-depleted algae as food: Permitting background free in-vivo nuclear magnetic resonance of Daphnia magna at natural abundance. Magn Reson Chem 2024; 62:11-18. [PMID: 37984890 DOI: 10.1002/mrc.5409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023]
Affiliation(s)
- William W Wolff
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Jacob Pellizzari
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Ronald Soong
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Daniel H Lysak
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Katrina Steiner
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Kiera Ronda
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Peter Costa
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Katelyn Downey
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
| | | | - Chris Suszczynski
- ISOTEC Stable Isotope Division, Millipore Sigma, Burlington, Massachusetts, USA
| | - Steven Boehmer
- ISOTEC Stable Isotope Division, Millipore Sigma, Burlington, Massachusetts, USA
| | - Jacob R Prat
- ISOTEC Stable Isotope Division, Millipore Sigma, Burlington, Massachusetts, USA
| | - Andre J Simpson
- Environmental NMR Center, University of Toronto Scarborough, Toronto, Ontario, Canada
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Weaver DF. Thirty Risk Factors for Alzheimer's Disease Unified by a Common Neuroimmune-Neuroinflammation Mechanism. Brain Sci 2023; 14:41. [PMID: 38248256 PMCID: PMC10813027 DOI: 10.3390/brainsci14010041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/27/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024] Open
Abstract
One of the major obstacles confronting the formulation of a mechanistic understanding for Alzheimer's disease (AD) is its immense complexity-a complexity that traverses the full structural and phenomenological spectrum, including molecular, macromolecular, cellular, neurological and behavioural processes. This complexity is reflected by the equally complex diversity of risk factors associated with AD. However, more than merely mirroring disease complexity, risk factors also provide fundamental insights into the aetiology and pathogenesis of AD as a neurodegenerative disorder since they are central to disease initiation and subsequent propagation. Based on a systematic literature assessment, this review identified 30 risk factors for AD and then extended the analysis to further identify neuroinflammation as a unifying mechanism present in all 30 risk factors. Although other mechanisms (e.g., vasculopathy, proteopathy) were present in multiple risk factors, dysfunction of the neuroimmune-neuroinflammation axis was uniquely central to all 30 identified risk factors. Though the nature of the neuroinflammatory involvement varied, the activation of microglia and the release of pro-inflammatory cytokines were a common pathway shared by all risk factors. This observation provides further evidence for the importance of immunopathic mechanisms in the aetiopathogenesis of AD.
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Affiliation(s)
- Donald F Weaver
- Krembil Research Institute, University Health Network, Departments of Medicine, Chemistry, Pharmaceutical Sciences, University of Toronto, Toronto, ON M5T 0S8, Canada
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Jenne A, Soong R, Gruschke O, Bastawrous M, Monks P, Moloney C, Brougham DF, Busse F, Bermel W, Courtier-Murias D, Wu B, Simpson A. A holistic NMR framework to understand environmental impact: Examining the impacts of superparamagnetic iron oxide nanoparticles (SPIONs) in Daphnia magna via imaging, spectroscopy, and metabolomics. Magn Reson Chem 2023; 61:728-739. [PMID: 36137948 DOI: 10.1002/mrc.5315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) are a contaminant of emerging interest, often used in the medical field as an imaging contrast agent, with additional uses in wastewater treatment and as food additives. Although the use of SPIONs is increasing, little research has been conducted on the toxic impacts to living organisms beyond traditional lethal concentration endpoints. Daphnia magna are model organisms for aquatic toxicity testing with a well understood metabolome and high sensitivity to SPIONs. Thus, as environmental concentrations continue to increase, it is becoming critical to understand their sub-lethal toxicity. Due to the paramagnetic nature of SPIONs, a range of potential nuclear magnetic resonance spectroscopy (NMR) experiments are possible, offering the potential to probe the physical location (via imaging), binding (via relaxation weighted spectroscopy), and the biochemical pathways impacted (via in vivo metabolomics). Results indicate binding to carbohydrates, likely chitin in the exoskeleton, along with a decrease in energy metabolites and specific biomarkers of oxidative stress. The holistic NMR framework used here helps provide a more comprehensive understanding of SPIONs impacts on D. magna and showcases NMR's versatility in providing physical, chemical, and biochemical insights.
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Affiliation(s)
- Amy Jenne
- Environmental NMR Center, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - Ronald Soong
- Environmental NMR Center, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | | | - Monica Bastawrous
- Environmental NMR Center, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - Patricia Monks
- Department of Chemistry, RCSI University of Health Sciences, Dublin, Ireland
| | - Cara Moloney
- School of Medicine, BioDiscovery Institute-3, University of Nottingham, University Park, Nottingham, UK
| | | | | | | | - Denis Courtier-Murias
- Université Gustave Eiffel, GERS-LEE, Bouguenais, France
- Institut de Recherche en Sciences et Techniques de la Ville IRSTV, CNRS, Nantes, France
| | - Bing Wu
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Andre Simpson
- Environmental NMR Center, University of Toronto Scarborough, Scarborough, Ontario, Canada
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Vasilevskaya A, Martinez-Valbuena I, Anastassiadis C, Taghdiri F, Khodadadi M, Tarazi A, Green R, Colella B, Wennberg R, Mikulis D, Davis KD, Kovacs GG, Tator C, Tartaglia MC. Misfolded α-Synuclein in Cerebrospinal Fluid of Contact Sport Athletes. Mov Disord 2023; 38:2125-2131. [PMID: 37792643 DOI: 10.1002/mds.29621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/30/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Misfolded α-synuclein in Parkinson's disease (PD) and dementia with Lewy bodies (DLB) can be detected using the real-time quaking-induced conversion (RT-QuIC) technique in cerebrospinal fluid (CSF). OBJECTIVES The objectives are (1) to examine misfolded CSF α-synuclein incidence, and (2) to compare clinical presentation, sports history, brain volumes, and RT-QuIC α-synuclein positivity in former athletes. METHODS Thirty former athletes with magnetic resonance imaging, neuropsychological testing, and CSF analyzed for phosphorylated tau 181 (p-tau), total tau (t-tau), amyloid-β 42 (Aβ42), and neurofilament light chain (NfL). CSF α-synuclein was detected using RT-QuIC. RESULTS Six (20%) former athletes were α-synuclein positive. α-Synuclein positive athletes were similar to α-synuclein negative athletes on demographics, sports history, clinical features, CSF p-tau, t-tau, Aβ42, and NfL; however, had lower grey matter volumes in the right inferior orbitofrontal, right anterior insula and right olfactory cortices. CONCLUSIONS α-Synuclein RT-QuIC analysis of CSF may be useful as a prodromal biofluid marker of PD and DLB. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Anna Vasilevskaya
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Division of Neurology, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Ivan Martinez-Valbuena
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Anastassiadis
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Division of Neurology, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Foad Taghdiri
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Division of Neurology, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Mozhgan Khodadadi
- Canadian Concussion Centre, Toronto Western Hospital, Krembil Neuroscience Centre, University Health Network, Toronto, Ontario, Canada
| | - Apameh Tarazi
- Division of Neurology, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Canadian Concussion Centre, Toronto Western Hospital, Krembil Neuroscience Centre, University Health Network, Toronto, Ontario, Canada
| | - Robin Green
- Canadian Concussion Centre, Toronto Western Hospital, Krembil Neuroscience Centre, University Health Network, Toronto, Ontario, Canada
- KITE Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Brenda Colella
- Canadian Concussion Centre, Toronto Western Hospital, Krembil Neuroscience Centre, University Health Network, Toronto, Ontario, Canada
- KITE Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Richard Wennberg
- Division of Neurology, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Canadian Concussion Centre, Toronto Western Hospital, Krembil Neuroscience Centre, University Health Network, Toronto, Ontario, Canada
| | - David Mikulis
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Canadian Concussion Centre, Toronto Western Hospital, Krembil Neuroscience Centre, University Health Network, Toronto, Ontario, Canada
- Division of Neuroradiology, Joint Department of Medical Imaging, University Health Network, Toronto, Ontario, Canada
| | - Karen Deborah Davis
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Canadian Concussion Centre, Toronto Western Hospital, Krembil Neuroscience Centre, University Health Network, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Brain, Imaging, and Behaviour; Krembil Brain Institute, University Health Network, Toronto, Ontario, Canada
| | - Gabor G Kovacs
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine Program and Krembil Brain Institute, University Health Network, Toronto, Ontario, Canada
| | - Charles Tator
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Canadian Concussion Centre, Toronto Western Hospital, Krembil Neuroscience Centre, University Health Network, Toronto, Ontario, Canada
- Division of Neurosurgery, Toronto Western Hospital, Krembil Brain Institute, University Health Network, Toronto, Ontario, Canada
| | - Maria Carmela Tartaglia
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Division of Neurology, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Canadian Concussion Centre, Toronto Western Hospital, Krembil Neuroscience Centre, University Health Network, Toronto, Ontario, Canada
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12
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Gurdita A, Pham Truong VQB, Dolati P, Juric M, Tachibana N, Liu ZC, Ortín-Martínez A, Ibrahimi M, Pokrajac NT, Comanita L, Pacal M, Huang M, Sugita S, Bremner R, Wallace VA. Progenitor division and cell autonomous neurosecretion are required for rod photoreceptor sublaminar positioning. Proc Natl Acad Sci U S A 2023; 120:e2308204120. [PMID: 37812728 PMCID: PMC10589646 DOI: 10.1073/pnas.2308204120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/06/2023] [Indexed: 10/11/2023] Open
Abstract
Migration is essential for the laminar stratification and connectivity of neurons in the central nervous system. In the retina, photoreceptors (PRs) migrate to positions according to birthdate, with early-born cells localizing to the basal-most side of the outer nuclear layer. It was proposed that apical progenitor mitoses physically drive these basal translocations non-cell autonomously, but direct evidence is lacking, and whether other mechanisms participate is unknown. Here, combining loss- or gain-of-function assays to manipulate cell cycle regulators (Sonic hedgehog, Cdkn1a/p21) with an in vivo lentiviral labelling strategy, we demonstrate that progenitor division is one of two forces driving basal translocation of rod soma. Indeed, replacing Shh activity rescues abnormal rod translocation in retinal explants. Unexpectedly, we show that rod differentiation also promotes rod soma translocation. While outer segment function or formation is dispensable, Crx and SNARE-dependent synaptic function are essential. Thus, both non-cell and cell autonomous mechanisms underpin PR soma sublaminar positioning in the mammalian retina.
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Affiliation(s)
- Akshay Gurdita
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Victor Q. B. Pham Truong
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Parnian Dolati
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Matey Juric
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Nobuhiko Tachibana
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Zhongda C. Liu
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Arturo Ortín-Martínez
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Mostafa Ibrahimi
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Nenad T. Pokrajac
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Lacrimioara Comanita
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Marek Pacal
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ONM5G 1X5, Canada
| | - Mengjia Huang
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, University Health Network, Toronto, ONM5T 2S8, Canada
- Department of Physiology, University of Toronto, Toronto, ONM5S 1A8, Canada
| | - Shuzo Sugita
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, University Health Network, Toronto, ONM5T 2S8, Canada
- Department of Physiology, University of Toronto, Toronto, ONM5S 1A8, Canada
| | - Rod Bremner
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ONM5G 1X5, Canada
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ONM5T 3A9, Canada
| | - Valerie A. Wallace
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ONM5T 3A9, Canada
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13
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Trinh AT, Girardi-Schappo M, Béïque JC, Longtin A, Maler L. Adaptive spike threshold dynamics associated with sparse spiking of hilar mossy cells are captured by a simple model. J Physiol 2023; 601:4397-4422. [PMID: 37676904 DOI: 10.1113/jp283728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 08/17/2023] [Indexed: 09/09/2023] Open
Abstract
Hilar mossy cells (hMCs) in the dentate gyrus (DG) receive inputs from DG granule cells (GCs), CA3 pyramidal cells and inhibitory interneurons, and provide feedback input to GCs. Behavioural and in vivo recording experiments implicate hMCs in pattern separation, navigation and spatial learning. Our experiments link hMC intrinsic excitability to their synaptically evoked in vivo spiking outputs. We performed electrophysiological recordings from DG neurons and found that hMCs displayed an adaptative spike threshold that increased both in proportion to the intensity of injected currents, and in response to spiking itself, returning to baseline over a long time scale, thereby instantaneously limiting their firing rate responses. The hMC activity is additionally limited by a prominent medium after-hyperpolarizing potential (AHP) generated by small conductance K+ channels. We hypothesize that these intrinsic hMC properties are responsible for their low in vivo firing rates. Our findings extend previous studies that compare hMCs, CA3 pyramidal cells and hilar inhibitory cells and provide novel quantitative data that contrast the intrinsic properties of these cell types. We developed a phenomenological exponential integrate-and-fire model that closely reproduces the hMC adaptive threshold nonlinearities with respect to their threshold dependence on input current intensity, evoked spike latency and long-lasting spike-induced increase in spike threshold. Our robust and computationally efficient model is amenable to incorporation into large network models of the DG that will deepen our understanding of the neural bases of pattern separation, spatial navigation and learning. KEY POINTS: Previous studies have shown that hilar mossy cells (hMCs) are implicated in pattern separation and the formation of spatial memory, but how their intrinsic properties relate to their in vivo spiking patterns is still unknown. Here we show that the hMCs display electrophysiological properties that distinguish them from the other hilar cell types including a highly adaptive spike threshold that decays slowly. The spike-dependent increase in threshold combined with an after-hyperpolarizing potential mediated by a slow K+ conductance is hypothesized to be responsible for the low-firing rate of the hMC observed in vivo. The hMC's features are well captured by a modified stochastic exponential integrate-and-fire model that has the unique feature of a threshold intrinsically dependant on both the stimulus intensity and the spiking history. This computational model will allow future work to study how the hMCs can contribute to spatial memory formation and navigation.
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Affiliation(s)
- Anh-Tuan Trinh
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Trøndelag, Norway
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Mauricio Girardi-Schappo
- Departamento de Física, Universidade Federal de Santa Catarina, Santa Catarina, Florianópolis, Brazil
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Jean-Claude Béïque
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Brain and Mind Institute, University of Ottawa, Ottawa, Ontario, Canada
- Center for Neural Dynamics, University of Ottawa, Ottawa, Ontario, Canada
| | - André Longtin
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
- Brain and Mind Institute, University of Ottawa, Ottawa, Ontario, Canada
- Center for Neural Dynamics, University of Ottawa, Ottawa, Ontario, Canada
| | - Leonard Maler
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Brain and Mind Institute, University of Ottawa, Ottawa, Ontario, Canada
- Center for Neural Dynamics, University of Ottawa, Ottawa, Ontario, Canada
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14
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Weaver DF. Druggable targets for the immunopathy of Alzheimer's disease. RSC Med Chem 2023; 14:1645-1661. [PMID: 37731705 PMCID: PMC10507808 DOI: 10.1039/d3md00096f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/21/2023] [Indexed: 09/22/2023] Open
Abstract
Alzheimer's disease (AD) is one of the leading threats to the health and socioeconomic well-being of humankind. Though research to develop disease modifying therapies for AD has traditionally focussed on the misfolding and aggregation of proteins, this approach has failed to yield a definitively curative agent. Accordingly, the search for additional or alternative approaches is a medicinal chemistry priority. Dysfunction of the brain's neuroimmune-neuroinflammation axis has emerged as a leading contender. Neuroimmunity however is mechanistically complex, rendering the recognition of candidate receptors a challenging task. Herein, a review of the role of neuroimmunity in the biomolecular pathogenesis of AD is presented with the identification of a 'druggable dozen' targets; in turn, each identified target represents one or more discrete receptors centred on a common biochemical mechanism. The druggable dozen is composed of both cellular and molecular messenger targets, with a 'targetable ten' microglial targets as well as two cytokine-based targets. For each target, the underlying molecular basis, with a consideration of strengths and weaknesses, is considered.
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Affiliation(s)
- Donald F Weaver
- Krembil Research Institute, University Health Network, Department of Chemistry, University of Toronto 60 Leonard Avenue Toronto ON M5T 0S8 Canada
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15
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Eder L, Lee KA, Chandran V, Widdifield J, Drucker AM, Ritchlin C, Rosen CF, Cook RJ, Gladman DD. Derivation of a Multivariable Psoriatic Arthritis Risk Estimation Tool (PRESTO): A Step Towards Prevention. Arthritis Rheumatol 2023. [PMID: 37555242 DOI: 10.1002/art.42661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/28/2023] [Accepted: 06/14/2023] [Indexed: 08/10/2023]
Abstract
OBJECTIVE A simple, scalable tool that identifies psoriasis patients at high risk for developing psoriatic arthritis (PsA) could improve early diagnosis. We aimed to develop a risk prediction model for the development of PsA and to assess its performance among patients with psoriasis. METHODS We analyzed data from a prospective cohort of psoriasis patients without PsA at enrollment. Participants were assessed annually by a rheumatologist for the development of PsA. Information about their demographics, psoriasis characteristics, comorbidities, medications, and musculoskeletal symptoms was used to develop prediction models for PsA. Penalized binary regression models were used for variable selection while adjusting for psoriasis duration. Risks of developing PsA over 1- and 5-year time periods were estimated. Model performance was assessed by the area under the curve (AUC) and calibration plots. RESULTS Among 635 psoriasis patients, 51 and 71 developed PsA during the 1-year and 5-year follow-up periods, respectively. The risk of developing PsA within 1 year was associated with younger age, male sex, family history of psoriasis, back stiffness, nail pitting, joint stiffness, use of biologic medications, patient global health, and pain severity (AUC 72.3). The risk of developing PsA within 5 years was associated with morning stiffness, psoriatic nail lesion, psoriasis severity, fatigue, pain, and use of systemic nonbiologic medication or phototherapy (AUC 74.9). Calibration plots showed reasonable agreement between predicted and observed probabilities. CONCLUSIONS The development of PsA within clinically meaningful time frames can be predicted with reasonable accuracy for psoriasis patients using readily available clinical variables.
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Affiliation(s)
- Lihi Eder
- Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada, and Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ker-Ai Lee
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, Ontario, Canada
| | - Vinod Chandran
- Department of Medicine, University of Toronto, and Schroder Arthritis Institute, Krembil Research Institute, Toronto Western Hospital, Toronto, Ontario, Canada
| | - Jessica Widdifield
- Sunnybrook Research Institute, Sunnybrook Hospital, and Institute for Clinical Evaluative Sciences (ICES), and Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Aaron M Drucker
- Women's College Research Institute, Women's College Hospital, and Department of Medicine, University of Toronto, and ICES, and Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | | | - Cheryl F Rosen
- Department of Medicine, University of Toronto, and Schroder Arthritis Institute, Krembil Research Institute, Toronto Western Hospital, Toronto, Ontario, Canada
| | - Richard J Cook
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, Ontario, Canada
| | - Dafna D Gladman
- Department of Medicine, University of Toronto, and Schroder Arthritis Institute, Krembil Research Institute, Toronto Western Hospital, Toronto, Ontario, Canada
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16
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Inibhunu H, Moradi Chameh H, Skinner F, Rich S, Valiante TA. Hyperpolarization-Activated Cation Channels Shape the Spiking Frequency Preference of Human Cortical Layer 5 Pyramidal Neurons. eNeuro 2023; 10:ENEURO.0215-23.2023. [PMID: 37567768 PMCID: PMC10467019 DOI: 10.1523/eneuro.0215-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
Discerning the contribution of specific ionic currents to complex neuronal dynamics is a difficult, but important, task. This challenge is exacerbated in the human setting, although the widely characterized uniqueness of the human brain compared with preclinical models necessitates the direct study of human neurons. Neuronal spiking frequency preference is of particular interest given its role in rhythm generation and signal transmission in cortical circuits. Here, we combine the frequency-dependent gain (FDG), a measure of spiking frequency preference, and novel in silico analyses to dissect the contributions of individual ionic currents to the suprathreshold features of human layer 5 (L5) neurons captured by the FDG. We confirm that a contemporary model of such a neuron, primarily constrained to capture subthreshold activity driven by the hyperpolarization-activated cyclic nucleotide gated (h-) current, replicates key features of the in vitro FDG both with and without h-current activity. With the model confirmed as a viable approximation of the biophysical features of interest, we applied new analysis techniques to quantify the activity of each modeled ionic current in the moments before spiking, revealing unique dynamics of the h-current. These findings motivated patch-clamp recordings in analogous rodent neurons to characterize their FDG, which confirmed that a biophysically detailed model of these neurons captures key interspecies differences in the FDG. These differences are correlated with distinct contributions of the h-current to neuronal activity. Together, this interdisciplinary and multispecies study provides new insights directly relating the dynamics of the h-current to suprathreshold spiking frequency preference in human L5 neurons.
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Affiliation(s)
- Happy Inibhunu
- Division of Clinical and Computational Neuroscience, Krembil Brain Institute, University Health Network, Toronto, Ontario M5T 1M8, Canada
| | - Homeira Moradi Chameh
- Division of Clinical and Computational Neuroscience, Krembil Brain Institute, University Health Network, Toronto, Ontario M5T 1M8, Canada
| | - Frances Skinner
- Division of Clinical and Computational Neuroscience, Krembil Brain Institute, University Health Network, Toronto, Ontario M5T 1M8, Canada
- Departments of Medicine, Neurology and Physiology, University of Toronto, Toronto, Ontario M5S 3H2, Canada
| | - Scott Rich
- Division of Clinical and Computational Neuroscience, Krembil Brain Institute, University Health Network, Toronto, Ontario M5T 1M8, Canada
| | - Taufik A Valiante
- Division of Clinical and Computational Neuroscience, Krembil Brain Institute, University Health Network, Toronto, Ontario M5T 1M8, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E2, Canada
- Electrical and Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario M5T 1P5, Canada
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17
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Charlton CE, Karvelis P, McIntyre RS, Diaconescu AO. Suicide prevention and ketamine: insights from computational modeling. Front Psychiatry 2023; 14:1214018. [PMID: 37457775 PMCID: PMC10342546 DOI: 10.3389/fpsyt.2023.1214018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Suicide is a pressing public health issue, with over 700,000 individuals dying each year. Ketamine has emerged as a promising treatment for suicidal thoughts and behaviors (STBs), yet the complex mechanisms underlying ketamine's anti-suicidal effect are not fully understood. Computational psychiatry provides a promising framework for exploring the dynamic interactions underlying suicidality and ketamine's therapeutic action, offering insight into potential biomarkers, treatment targets, and the underlying mechanisms of both. This paper provides an overview of current computational theories of suicidality and ketamine's mechanism of action, and discusses various computational modeling approaches that attempt to explain ketamine's anti-suicidal effect. More specifically, the therapeutic potential of ketamine is explored in the context of the mismatch negativity and the predictive coding framework, by considering neurocircuits involved in learning and decision-making, and investigating altered connectivity strengths and receptor densities targeted by ketamine. Theory-driven computational models offer a promising approach to integrate existing knowledge of suicidality and ketamine, and for the extraction of model-derived mechanistic parameters that can be used to identify patient subgroups and personalized treatment approaches. Future computational studies on ketamine's mechanism of action should optimize task design and modeling approaches to ensure parameter reliability, and external factors such as set and setting, as well as psychedelic-assisted therapy should be evaluated for their additional therapeutic value.
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Affiliation(s)
- Colleen E. Charlton
- Krembil Center for Neuroinformatics, Center for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Povilas Karvelis
- Krembil Center for Neuroinformatics, Center for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Roger S. McIntyre
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Andreea O. Diaconescu
- Krembil Center for Neuroinformatics, Center for Addiction and Mental Health (CAMH), Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
- Department of Psychology, University of Toronto, Toronto, ON, Canada
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18
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Sifri C, Hoeg L, Durocher D, Setiaputra D. An AlphaFold2 map of the 53BP1 pathway identifies a direct SHLD3-RIF1 interaction critical for shieldin activity. EMBO Rep 2023:e56834. [PMID: 37306046 PMCID: PMC10398656 DOI: 10.15252/embr.202356834] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 05/28/2023] [Accepted: 05/31/2023] [Indexed: 06/13/2023] Open
Abstract
53BP1 is a chromatin-binding protein that promotes DNA double-strand break repair through the recruitment of downstream effectors including RIF1, shieldin, and CST. The structural basis of the protein-protein interactions within the 53BP1-RIF1-shieldin-CST pathway that are essential for its DNA repair activity is largely unknown. Here, we used AlphaFold2-Multimer (AF2) to predict all possible pairwise combinations of proteins within this pathway and provide structural models of seven previously characterized interactions. This analysis also predicted an entirely novel binding interface between the HEAT-repeat domain of RIF1 and the eIF4E-like domain of SHLD3. Extensive interrogation of this interface through both in vitro pulldown analysis and cellular assays supports the AF2-predicted model and demonstrates that RIF1-SHLD3 binding is essential for shieldin recruitment to sites of DNA damage, and for its role in antibody class switch recombination and PARP inhibitor sensitivity. Direct physical interaction between RIF1 and SHLD3 is therefore essential for 53BP1-RIF1-shieldin-CST pathway activity.
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Affiliation(s)
- Chérine Sifri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Lisa Hoeg
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Dheva Setiaputra
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
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19
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Savonije K, Meek A, Weaver DF. Indoleamine 2,3-Dioxygenase as a Therapeutic Target for Alzheimer's Disease and Geriatric Depression. Brain Sci 2023; 13:852. [PMID: 37371332 DOI: 10.3390/brainsci13060852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Neuroimmune-triggered neuroinflammation of the central nervous system is emerging as an important aetiopathogenic factor for multiple neurological disorders, including depression, dementia, Alzheimer's disease, multiple sclerosis and others. Tryptophan metabolism via the kynurenic pathway, which is initiated by the indoleamine-2,3-dioxygenase (IDO-1) enzyme, is a key regulator of the neuroimmune system and its associated neuroinflammatory effects. As discussed in this review, targeting the production of immunopathic and potentially neurotoxic kynurenine metabolites by inhibitory downregulation of IDO-1 may prove a viable target against inflammation-induced neurological conditions, particularly depression and dementia.
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Affiliation(s)
- Karl Savonije
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Autumn Meek
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Donald F Weaver
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Departments of Chemistry and Medicine, University of Toronto, Toronto, ON M5S 3M2, Canada
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20
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Boudreau-Pinsonneault C, David LA, Lourenço Fernandes JA, Javed A, Fries M, Mattar P, Cayouette M. Direct neuronal reprogramming by temporal identity factors. Proc Natl Acad Sci U S A 2023; 120:e2122168120. [PMID: 37126716 PMCID: PMC10175841 DOI: 10.1073/pnas.2122168120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Temporal identity factors are sufficient to reprogram developmental competence of neural progenitors and shift cell fate output, but whether they can also reprogram the identity of terminally differentiated cells is unknown. To address this question, we designed a conditional gene expression system that allows rapid screening of potential reprogramming factors in mouse retinal glial cells combined with genetic lineage tracing. Using this assay, we found that coexpression of the early temporal identity transcription factors Ikzf1 and Ikzf4 is sufficient to directly convert Müller glial (MG) cells into cells that translocate to the outer nuclear layer (ONL), where photoreceptor cells normally reside. We name these "induced ONL (iONL)" cells. Using genetic lineage tracing, histological, immunohistochemical, and single-cell transcriptome and multiome analyses, we show that expression of Ikzf1/4 in MG in vivo, without retinal injury, mostly generates iONL cells that share molecular characteristics with bipolar cells, although a fraction of them stain for Rxrg, a cone photoreceptor marker. Furthermore, we show that coexpression of Ikzf1 and Ikzf4 can reprogram mouse embryonic fibroblasts to induced neurons in culture by rapidly remodeling chromatin and activating a neuronal gene expression program. This work uncovers general neuronal reprogramming properties for temporal identity factors in terminally differentiated cells.
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Affiliation(s)
- Camille Boudreau-Pinsonneault
- Cellular Neurobiology Research Unit, Montreal Clinical Research Institute (IRCM), Montreal, QC H2W 1R7, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC H3A 1A1, Canada
| | - Luke Ajay David
- Cellular Neurobiology Research Unit, Montreal Clinical Research Institute (IRCM), Montreal, QC H2W 1R7, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC H3A 1A1, Canada
| | - José Alex Lourenço Fernandes
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Awais Javed
- Cellular Neurobiology Research Unit, Montreal Clinical Research Institute (IRCM), Montreal, QC H2W 1R7, Canada
- Molecular Biology Program, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Michel Fries
- Cellular Neurobiology Research Unit, Montreal Clinical Research Institute (IRCM), Montreal, QC H2W 1R7, Canada
- Molecular Biology Program, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Pierre Mattar
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Montreal Clinical Research Institute (IRCM), Montreal, QC H2W 1R7, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC H3A 1A1, Canada
- Molecular Biology Program, Université de Montréal, Montreal, QC H3C 3J7, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada
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21
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Hall EA, Kumar D, Prosser SL, Yeyati PL, Herranz-Pérez V, García-Verdugo JM, Rose L, McKie L, Dodd DO, Tennant PA, Megaw R, Murphy LC, Ferreira MF, Grimes G, Williams L, Quidwai T, Pelletier L, Reiter JF, Mill P. Centriolar satellites expedite mother centriole remodeling to promote ciliogenesis. eLife 2023; 12:e79299. [PMID: 36790165 PMCID: PMC9998092 DOI: 10.7554/elife.79299] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 02/14/2023] [Indexed: 02/16/2023] Open
Abstract
Centrosomes are orbited by centriolar satellites, dynamic multiprotein assemblies nucleated by Pericentriolar material 1 (PCM1). To study the requirement for centriolar satellites, we generated mice lacking PCM1, a crucial component of satellites. Pcm1-/- mice display partially penetrant perinatal lethality with survivors exhibiting hydrocephalus, oligospermia, and cerebellar hypoplasia, and variably expressive phenotypes such as hydronephrosis. As many of these phenotypes have been observed in human ciliopathies and satellites are implicated in cilia biology, we investigated whether cilia were affected. PCM1 was dispensable for ciliogenesis in many cell types, whereas Pcm1-/- multiciliated ependymal cells and human PCM1-/- retinal pigmented epithelial 1 (RPE1) cells showed reduced ciliogenesis. PCM1-/- RPE1 cells displayed reduced docking of the mother centriole to the ciliary vesicle and removal of CP110 and CEP97 from the distal mother centriole, indicating compromised early ciliogenesis. Similarly, Pcm1-/- ependymal cells exhibited reduced removal of CP110 from basal bodies in vivo. We propose that PCM1 and centriolar satellites facilitate efficient trafficking of proteins to and from centrioles, including the departure of CP110 and CEP97 to initiate ciliogenesis, and that the threshold to trigger ciliogenesis differs between cell types.
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Affiliation(s)
- Emma A Hall
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Dhivya Kumar
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of CaliforniaSan FranciscoUnited States
| | - Suzanna L Prosser
- Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Patricia L Yeyati
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Vicente Herranz-Pérez
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of ValenciaValenciaSpain
- Predepartamental Unit of Medicine, Jaume I UniversityCastelló de la PlanaSpain
| | | | - Lorraine Rose
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Lisa McKie
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Daniel O Dodd
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Peter A Tennant
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Roly Megaw
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Laura C Murphy
- Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Marisa F Ferreira
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Lucy Williams
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Tooba Quidwai
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
- Department of Molecular Genetics, University of TorontoUniversity of TorontoCanada
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of CaliforniaSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Pleasantine Mill
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
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22
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Harkin EF, Lynn MB, Payeur A, Boucher JF, Caya-Bissonnette L, Cyr D, Stewart C, Longtin A, Naud R, Béïque JC. Temporal derivative computation in the dorsal raphe network revealed by an experimentally driven augmented integrate-and-fire modeling framework. eLife 2023; 12:72951. [PMID: 36655738 PMCID: PMC9977298 DOI: 10.7554/elife.72951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/19/2022] [Indexed: 01/20/2023] Open
Abstract
By means of an expansive innervation, the serotonin (5-HT) neurons of the dorsal raphe nucleus (DRN) are positioned to enact coordinated modulation of circuits distributed across the entire brain in order to adaptively regulate behavior. Yet the network computations that emerge from the excitability and connectivity features of the DRN are still poorly understood. To gain insight into these computations, we began by carrying out a detailed electrophysiological characterization of genetically identified mouse 5-HT and somatostatin (SOM) neurons. We next developed a single-neuron modeling framework that combines the realism of Hodgkin-Huxley models with the simplicity and predictive power of generalized integrate-and-fire models. We found that feedforward inhibition of 5-HT neurons by heterogeneous SOM neurons implemented divisive inhibition, while endocannabinoid-mediated modulation of excitatory drive to the DRN increased the gain of 5-HT output. Our most striking finding was that the output of the DRN encodes a mixture of the intensity and temporal derivative of its input, and that the temporal derivative component dominates this mixture precisely when the input is increasing rapidly. This network computation primarily emerged from prominent adaptation mechanisms found in 5-HT neurons, including a previously undescribed dynamic threshold. By applying a bottom-up neural network modeling approach, our results suggest that the DRN is particularly apt to encode input changes over short timescales, reflecting one of the salient emerging computations that dominate its output to regulate behavior.
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Affiliation(s)
- Emerson F Harkin
- Brain and Mind Research Institute, Centre for Neural Dynamics, Department of Cellular and Molecular Medicine, University of OttawaOttawaCanada
| | - Michael B Lynn
- Brain and Mind Research Institute, Centre for Neural Dynamics, Department of Cellular and Molecular Medicine, University of OttawaOttawaCanada
| | - Alexandre Payeur
- Brain and Mind Research Institute, Centre for Neural Dynamics, Department of Cellular and Molecular Medicine, University of OttawaOttawaCanada
- Department of Physics, University of OttawaOttawaCanada
| | - Jean-François Boucher
- Brain and Mind Research Institute, Centre for Neural Dynamics, Department of Cellular and Molecular Medicine, University of OttawaOttawaCanada
| | - Léa Caya-Bissonnette
- Brain and Mind Research Institute, Centre for Neural Dynamics, Department of Cellular and Molecular Medicine, University of OttawaOttawaCanada
| | - Dominic Cyr
- Brain and Mind Research Institute, Centre for Neural Dynamics, Department of Cellular and Molecular Medicine, University of OttawaOttawaCanada
| | - Chloe Stewart
- Brain and Mind Research Institute, Centre for Neural Dynamics, Department of Cellular and Molecular Medicine, University of OttawaOttawaCanada
| | - André Longtin
- Brain and Mind Research Institute, Centre for Neural Dynamics, Department of Cellular and Molecular Medicine, University of OttawaOttawaCanada
- Department of Physics, University of OttawaOttawaCanada
| | - Richard Naud
- Brain and Mind Research Institute, Centre for Neural Dynamics, Department of Cellular and Molecular Medicine, University of OttawaOttawaCanada
- Department of Physics, University of OttawaOttawaCanada
| | - Jean-Claude Béïque
- Brain and Mind Research Institute, Centre for Neural Dynamics, Department of Cellular and Molecular Medicine, University of OttawaOttawaCanada
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23
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Stover KR, Stafford PM, Damian AC, Pasangulapati JP, Goodwin-Tindall J, López Vásquez LM, Lee S, Yang SP, Reed MA, Barden CJ, Weaver DF. Development and Optimization of a Target Engagement Model of Brain IDO Inhibition for Alzheimer's Disease. Curr Alzheimer Res 2023; 20:705-714. [PMID: 38288825 DOI: 10.2174/0115672050283199240111111801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 04/04/2024]
Abstract
BACKGROUND Indoleamine 2,3-dioxygenase (IDO1) inhibition is a promising target as an Alzheimer's disease (AD) Disease-modifying therapy capable of downregulating immunopathic neuroinflammatory processes. METHODS To aid in the development of IDO inhibitors as potential AD therapeutics, we optimized a lipopolysaccharide (LPS) based mouse model of brain IDO1 inhibition by examining the dosedependent and time-course of the brain kynurenine:tryptophan (K:T) ratio to LPS via intraperitoneal dosing. RESULTS We determined the optimal LPS dose to increase IDO1 activity in the brain, and the ideal time point to quantify the brain K:T ratio after LPS administration. We then used a brain penetrant tool compound, EOS200271, to validate the model, determine the optimal dosing profile and found that a complete rescue of the K:T ratio was possible with the tool compound. CONCLUSION This LPS-based model of IDO1 target engagement is a useful tool that can be used in the development of brain penetrant IDO1 inhibitors for AD. A limitation of the present study is the lack of quantification of potential clinically relevant biomarkers in this model, which could be addressed in future studies.
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Affiliation(s)
- Kurt R Stover
- Krembil Research Institute, University Health Network, 399 Bathurst Street, Toronto M5T 2S8, Canada
- Treventis Corporation, 60 Leonard Avenue, Toronto M5T 0S8, Canada
| | - Paul M Stafford
- Krembil Research Institute, University Health Network, 399 Bathurst Street, Toronto M5T 2S8, Canada
| | - Andreea C Damian
- Krembil Research Institute, University Health Network, 399 Bathurst Street, Toronto M5T 2S8, Canada
| | - Jagadeesh P Pasangulapati
- Krembil Research Institute, University Health Network, 399 Bathurst Street, Toronto M5T 2S8, Canada
- Treventis Corporation, 60 Leonard Avenue, Toronto M5T 0S8, Canada
| | - Jake Goodwin-Tindall
- Krembil Research Institute, University Health Network, 399 Bathurst Street, Toronto M5T 2S8, Canada
| | | | - Sanghyun Lee
- Treventis Corporation, 60 Leonard Avenue, Toronto M5T 0S8, Canada
| | - Seung-Pil Yang
- Treventis Corporation, 60 Leonard Avenue, Toronto M5T 0S8, Canada
| | - Mark A Reed
- Krembil Research Institute, University Health Network, 399 Bathurst Street, Toronto M5T 2S8, Canada
- Treventis Corporation, 60 Leonard Avenue, Toronto M5T 0S8, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, M5S1A8, ON, Canada
| | - Christopher J Barden
- Krembil Research Institute, University Health Network, 399 Bathurst Street, Toronto M5T 2S8, Canada
- Treventis Corporation, 60 Leonard Avenue, Toronto M5T 0S8, Canada
| | - Donald F Weaver
- Krembil Research Institute, University Health Network, 399 Bathurst Street, Toronto M5T 2S8, Canada
- Treventis Corporation, 60 Leonard Avenue, Toronto M5T 0S8, Canada
- Department of Chemistry, University of Toronto, Toronto M55 3H6, Canada
- Department of Medicine (Neurology), University of Toronto, Toronto M5G 2C4, Canada
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24
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Hussin AT, Abbaspoor S, Hoffman KL. Retrosplenial and Hippocampal Synchrony during Retrieval of Old Memories in Macaques. J Neurosci 2022; 42:7947-7956. [PMID: 36261267 PMCID: PMC9617609 DOI: 10.1523/jneurosci.0001-22.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 06/05/2022] [Accepted: 07/11/2022] [Indexed: 11/21/2022] Open
Abstract
Memory for events from the distant past relies on multiple brain regions, but little is known about the underlying neural dynamics that give rise to such abilities. We recorded neural activity in the hippocampus and retrosplenial cortex of two female rhesus macaques as they visually selected targets in year-old and newly acquired object-scene associations. Whereas hippocampal activity was unchanging with memory age, the retrosplenial cortex responded with greater magnitude alpha oscillations (10-15 Hz) and greater phase locking to memory-guided eye movements during retrieval of old events. A similar old-memory enhancement was observed in the anterior cingulate cortex but in a beta2/gamma band (28-35 Hz). In contrast, remote retrieval was associated with decreased gamma-band synchrony between the hippocampus and each neocortical area. The increasing retrosplenial alpha oscillation and decreasing hippocampocortical synchrony with memory age may signify a shift in frank memory allocation or, alternatively, changes in selection among distributed memory representations in the primate brain.SIGNIFICANCE STATEMENT Memory depends on multiple brain regions, whose involvement is thought to change with time. Here, we recorded neuronal population activity from the hippocampus and retrosplenial cortex as nonhuman primates searched for objects embedded in scenes. These memoranda were either newly presented or a year old. Remembering old material drove stronger oscillations in the retrosplenial cortex and led to a greater locking of neural activity to search movements. Remembering new material revealed stronger oscillatory synchrony between the hippocampus and retrosplenial cortex. These results suggest that with age, memories may come to rely more exclusively on neocortical oscillations for retrieval and search guidance and less on long-range coupling with the hippocampus.
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Affiliation(s)
- Ahmed T Hussin
- Department of Biology, Centre for Vision Research, York University, Toronto Ontario M3J 1P3, Canada
| | | | - Kari L Hoffman
- Department of Biology, Centre for Vision Research, York University, Toronto Ontario M3J 1P3, Canada
- Departments of Psychology
- Biomedical Engineering, Vanderbilt Vision Research Center, Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee 37240
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25
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Mehrabian M, Wang X, Eid S, Yan BQ, Grinberg M, Siegner M, Sackmann C, Sulman M, Zhao W, Williams D, Schmitt-Ulms G. Cardiac glycoside-mediated turnover of Na, K-ATPases as a rational approach to reducing cell surface levels of the cellular prion protein. PLoS One 2022; 17:e0270915. [PMID: 35776750 PMCID: PMC9249225 DOI: 10.1371/journal.pone.0270915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/17/2022] [Indexed: 01/16/2023] Open
Abstract
It is widely anticipated that a reduction of brain levels of the cellular prion protein (PrPC) can prolong survival in a group of neurodegenerative diseases known as prion diseases. To date, efforts to decrease steady-state PrPC levels by targeting this protein directly with small molecule drug-like compounds have largely been unsuccessful. Recently, we reported Na,K-ATPases to reside in immediate proximity to PrPC in the brain, unlocking an opportunity for an indirect PrPC targeting approach that capitalizes on the availability of potent cardiac glycosides (CGs). Here, we report that exposure of human co-cultures of neurons and astrocytes to non-toxic nanomolar levels of CGs causes profound reductions in PrPC levels. The mechanism of action underpinning this outcome relies primarily on a subset of CGs engaging the ATP1A1 isoform, one of three α subunits of Na,K-ATPases expressed in brain cells. Upon CG docking to ATP1A1, the ligand receptor complex, and PrPC along with it, is internalized by the cell. Subsequently, PrPC is channeled to the lysosomal compartment where it is digested in a manner that can be rescued by silencing the cysteine protease cathepsin B. These data signify that the repurposing of CGs may be beneficial for the treatment of prion disorders.
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Affiliation(s)
- Mohadeseh Mehrabian
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Xinzhu Wang
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shehab Eid
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Bei Qi Yan
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Mark Grinberg
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, Toronto, Ontario, Canada
| | - Murdock Siegner
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Christopher Sackmann
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, Toronto, Ontario, Canada
| | - Muhammad Sulman
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, Toronto, Ontario, Canada
| | - Wenda Zhao
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Declan Williams
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, Toronto, Ontario, Canada
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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26
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Suart C, Neuman K, Truant R. The impact of the COVID-19 pandemic on perceived publication pressure among academic researchers in Canada. PLoS One 2022; 17:e0269743. [PMID: 35731739 PMCID: PMC9216619 DOI: 10.1371/journal.pone.0269743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 05/27/2022] [Indexed: 12/23/2022] Open
Abstract
The phenomenon of “publish-or-perish” in academia, spurred on by limited funding and academic positions, has led to increased competition and pressure on academics to publish. Publication pressure has been linked with multiple negative outcomes, including increased academic misconduct and researcher burnout. COVID-19 has disrupted research worldwide, leading to lost research time and increased anxiety amongst researchers. The objective of this study was to examine how COVID-19 has impacted perceived publication pressure amongst academic researchers in Canada. We used the revised Publication Pressure Questionnaire, in addition to Likert-type questions to discern respondents’ beliefs and concerns about the impact of COVID-19 on academic publishing. We found that publication pressure increased across academic researchers in Canada following the pandemic, with respondents reporting increased stress, increased pessimism, and decreased access to support related to publishing. Doctoral students reported the highest levels of stress and pessimism, while principal investigators had the most access to publication support. There were no significant differences in publication pressure reported between different research disciplines. Women and non-binary or genderfluid respondents reported higher stress and pessimism than men. We also identified differences in perceived publication pressure based on respondents’ publication frequency and other demographic factors, including disability and citizenship status. Overall, we document a snapshot of perceived publication pressure in Canada across researchers of different academic career stages and disciplines. This information can be used to guide the creation of researcher supports, as well as identify groups of researchers who may benefit from targeted resources.
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Affiliation(s)
- Celeste Suart
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kaitlyn Neuman
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Ray Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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27
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Consens ME, Chen Y, Menon V, Wang Y, Schneider JA, De Jager PL, Bennett DA, Tripathy SJ, Felsky D. Bulk and Single-Nucleus Transcriptomics Highlight Intra-Telencephalic and Somatostatin Neurons in Alzheimer's Disease. Front Mol Neurosci 2022; 15:903175. [PMID: 35754708 PMCID: PMC9231610 DOI: 10.3389/fnmol.2022.903175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cortical neuron loss is a pathological hallmark of late-onset Alzheimer's disease (AD). However, it remains unclear which neuronal subtypes beyond broad excitatory and inhibitory classes are most vulnerable. Here, we analyzed cell subtype proportion differences in AD compared to non-AD controls using 1037 post-mortem brain samples from six neocortical regions. We identified the strongest associations of AD with fewer somatostatin (SST) inhibitory neurons (β = -0.48, p bonf = 8.98 × 10-9) and intra-telencephalic (IT) excitatory neurons (β = -0.45, p bonf = 4.32 × 10-7). Replication in three AD case-control single-nucleus RNAseq datasets most strongly supported the bulk tissue association of fewer SST neurons in AD. In depth analyses of cell type proportions with specific AD-related neuropathological and cognitive phenotypes revealed fewer SST neurons with greater brain-wide post-mortem tau and beta amyloid, as well as a faster rate of antemortem cognitive decline. In contrast, greater IT neuron proportions were associated with a slower rate of cognitive decline as well as greater residual cognition-a measure of cognitive resilience-but not canonical AD neuropathology. Our findings implicate somatostatin inhibitory and intra-telencephalic excitatory neuron subclasses in the pathogenesis of AD and in cognitive resilience to AD pathology, respectively.
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Affiliation(s)
- Micaela E. Consens
- The Krembil Centre for Neuroinformatics (KCNI), Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Yuxiao Chen
- The Krembil Centre for Neuroinformatics (KCNI), Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Vilas Menon
- The Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, United States
| | - Yanling Wang
- The Rush Alzheimer’s Disease Center, Rush University, Chicago, IL, United States
| | - Julie A. Schneider
- The Rush Alzheimer’s Disease Center, Rush University, Chicago, IL, United States
| | - Philip L. De Jager
- The Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, United States
| | - David A. Bennett
- The Rush Alzheimer’s Disease Center, Rush University, Chicago, IL, United States
| | - Shreejoy J. Tripathy
- The Krembil Centre for Neuroinformatics (KCNI), Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Daniel Felsky
- The Krembil Centre for Neuroinformatics (KCNI), Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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28
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Delignat-Lavaud B, Ducrot C, Kouwenhoven W, Feller N, Trudeau LÉ. Implication of synaptotagmins 4 and 7 in activity-dependent somatodendritic dopamine release in the ventral midbrain. Open Biol 2022; 12:210339. [PMID: 35232250 PMCID: PMC8889187 DOI: 10.1098/rsob.210339] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/31/2022] [Indexed: 01/07/2023] Open
Abstract
Dopamine (DA) neurons can release DA not just from axon terminals, but also from their somatodendritic (STD) compartment through a mechanism that is still incompletely understood. Using voltammetry in mouse mesencephalic brain slices, we find that STD DA release has low capacity and shows a calcium sensitivity that is comparable to that of axonal release. We find that the molecular mechanism of STD DA release differs from axonal release with regard to the implication of synaptotagmin (Syt) calcium sensors. While individual constitutive knockout of Syt4 or Syt7 is not sufficient to reduce STD DA release, the removal of both isoforms reduces this release by approximately 50%, leaving axonal release unimpaired. Our work unveils clear differences in the mechanisms of STD and axonal DA release.
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Affiliation(s)
- Benoît Delignat-Lavaud
- Department of Pharmacology and Physiology, Université de Montréal, QC, Canada H3T 1J4
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, QC, Canada H3T 1J4
- Neural Signaling and Circuitry Research Group (SNC), Montréal, QC, Canada H3C 3J7
| | - Charles Ducrot
- Department of Pharmacology and Physiology, Université de Montréal, QC, Canada H3T 1J4
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, QC, Canada H3T 1J4
- Neural Signaling and Circuitry Research Group (SNC), Montréal, QC, Canada H3C 3J7
| | - Willemieke Kouwenhoven
- Department of Pharmacology and Physiology, Université de Montréal, QC, Canada H3T 1J4
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, QC, Canada H3T 1J4
- Neural Signaling and Circuitry Research Group (SNC), Montréal, QC, Canada H3C 3J7
| | - Nina Feller
- Department of Pharmacology and Physiology, Université de Montréal, QC, Canada H3T 1J4
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, QC, Canada H3T 1J4
- Neural Signaling and Circuitry Research Group (SNC), Montréal, QC, Canada H3C 3J7
| | - Louis-Éric Trudeau
- Department of Pharmacology and Physiology, Université de Montréal, QC, Canada H3T 1J4
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, QC, Canada H3T 1J4
- Neural Signaling and Circuitry Research Group (SNC), Montréal, QC, Canada H3C 3J7
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29
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Li SH, Colson TLL, Abd-Elrahman KS, Ferguson SSG. Metabotropic Glutamate Receptor 5 Antagonism Reduces Pathology and Differentially Improves Symptoms in Male and Female Heterozygous zQ175 Huntington’s Mice. Front Mol Neurosci 2022; 15:801757. [PMID: 35185467 PMCID: PMC8847794 DOI: 10.3389/fnmol.2022.801757] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/07/2022] [Indexed: 12/11/2022] Open
Abstract
Huntington’s disease (HD) is an inherited autosomal dominant neurodegenerative disorder that leads to progressive motor and cognitive impairment. There are currently no available disease modifying treatments for HD patients. We have previously shown that pharmacological blockade of metabotropic glutamate receptor 5 (mGluR5) signaling rescues motor deficits, improves cognitive impairments and mitigates HD neuropathology in male zQ175 HD mice. Mounting evidence indicates that sex may influence HD progression and we have recently reported a sex-specific pathological mGluR5 signaling in Alzheimer’s disease (AD) mice. Here, we compared the outcomes of treatment with the mGluR5 negative allosteric modulator CTEP (2-chloro-4-[2-[2,5-dimethyl-1-[4-(trifluoromethoxy)phenyl]imidazol-4-yl]ethynyl]pyridine) in both male and female symptomatic zQ175 mice. We found that female zQ175 mice required a longer treatment duration with CTEP than male mice to show improvement in their rotarod performance. Unlike males, chronic CTEP treatment did not improve the grip strength nor reverse the cognitive decline of female zQ175 mice. However, CTEP reduced the number of huntingtin aggregates, improved neuronal survival and decreased microglia activation in the striatum of both male and female zQ175 mice. Together, our results indicate that mGluR5 antagonism can reduce HD neuropathology in both male and female zQ175 HD mice, but sex has a clear impact on the efficacy of the treatment and must be taken into consideration for future HD drug development.
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Affiliation(s)
- Si Han Li
- Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Tash-Lynn L. Colson
- Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Khaled S. Abd-Elrahman
- Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Stephen S. G. Ferguson
- Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- *Correspondence: Stephen S. G. Ferguson,
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30
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Liu J, Budylowski P, Samson R, Griffin BD, Babuadze G, Rathod B, Colwill K, Abioye JA, Schwartz JA, Law R, Yip L, Ahn SK, Chau S, Naghibosadat M, Arita Y, Hu Q, Yue FY, Banerjee A, Hardy WR, Mossman K, Mubareka S, Kozak RA, Pollanen MS, Martin Orozco N, Gingras AC, Marcusson EG, Ostrowski MA. Preclinical evaluation of a SARS-CoV-2 mRNA vaccine PTX-COVID19-B. Sci Adv 2022; 8:eabj9815. [PMID: 35044832 PMCID: PMC8769538 DOI: 10.1126/sciadv.abj9815] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/24/2021] [Indexed: 06/01/2023]
Abstract
Safe and effective vaccines are needed to end the COVID-19 pandemic. Here, we report the preclinical development of a lipid nanoparticle–formulated SARS-CoV-2 mRNA vaccine, PTX-COVID19-B. PTX-COVID19-B was chosen among three candidates after the initial mouse vaccination results showed that it elicited the strongest neutralizing antibody response against SARS-CoV-2. Further tests in mice and hamsters indicated that PTX-COVID19-B induced robust humoral and cellular immune responses and completely protected the vaccinated animals from SARS-CoV-2 infection in the lung. Studies in hamsters also showed that PTX-COVID19-B protected the upper respiratory tract from SARS-CoV-2 infection. Mouse immune sera elicited by PTX-COVID19-B vaccination were able to neutralize SARS-CoV-2 variants of concern, including the Alpha, Beta, Gamma, and Delta lineages. No adverse effects were induced by PTX-COVID19-B in either mice or hamsters. Based on these results, PTX-COVID19-B was authorized by Health Canada to enter clinical trials in December 2020 with a phase 2 clinical trial ongoing.
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MESH Headings
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Viral/blood
- CD4 Lymphocyte Count
- CD8-Positive T-Lymphocytes/immunology
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19 Vaccines/adverse effects
- COVID-19 Vaccines/immunology
- Canada
- Cell Line
- Cricetinae
- Drug Evaluation, Preclinical
- Female
- HEK293 Cells
- Humans
- Immunity, Cellular/immunology
- Immunity, Humoral/immunology
- Liposomes/pharmacology
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Nanoparticles
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Th1 Cells/immunology
- Vaccines, Synthetic/immunology
- mRNA Vaccines/immunology
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Affiliation(s)
- Jun Liu
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Patrick Budylowski
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Reuben Samson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | | | | | - Bhavisha Rathod
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Karen Colwill
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | | | | | - Ryan Law
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Lily Yip
- Sunnybrook Research Institute, Toronto, ON, Canada
| | - Sang Kyun Ahn
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Serena Chau
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | | | - Yuko Arita
- Providence Therapeutics Holdings Inc., Calgary, AB, Canada
| | - Queenie Hu
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Feng Yun Yue
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - W. Rod Hardy
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, ON, Canada
| | | | - Michael S. Pollanen
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, ON, Canada
| | | | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Eric G. Marcusson
- Providence Therapeutics Holdings Inc., Calgary, AB, Canada
- Marcusson Consulting, San Francisco, CA, USA
| | - Mario A. Ostrowski
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Keenan Research Centre for Biomedical Science of St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
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Abstract
Entry of SARS-CoV-2 into the central nervous system (CNS) activates microglia, triggering chronic neuroinflammation and possibly neurodegeneration. The complex transcriptome of SARS-CoV-2 shares molecular similarities with diverse human CNS protein epitopes, leading to a cytokine storm and various autoantibodies, potentially culminating in an autoimmune state. A COVID-19 initiated CNS autoimmune cascade may occur via multiple pathways including molecular mimicry, bystander activation, epitope spreading, production of autoantibodies, and immortalization of effector B-cells.
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Affiliation(s)
- Mayuri Gupta
- Krembil Research Institute, University
Health Network, 60 Leonard Avenue, Toronto M5T 0S8,
Canada
| | - Donald F. Weaver
- Krembil Research Institute, University
Health Network, 60 Leonard Avenue, Toronto M5T 0S8,
Canada
- Departments of Medicine, Chemistry, and Pharmaceutical
Sciences, University of Toronto, Toronto M55 3H6,
Canada
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32
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Pearson JD, Trcka D, Lu S, Hyduk SJ, Jen M, Aynaud MM, Hernández JJ, Peidis P, Barrios-Rodiles M, Chan K, Woodgett J, Mazzulli T, Attisano L, Pelletier L, Cybulsky MI, Wrana JL, Bremner R. Comparison of SARS-CoV-2 indirect and direct RT-qPCR detection methods. Virol J 2021; 18:99. [PMID: 34001180 PMCID: PMC8127261 DOI: 10.1186/s12985-021-01574-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/11/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Sensitive, rapid, and accessible diagnostics continue to be critical to track the COVID-19 pandemic caused by the SARS-CoV-2 virus. RT-qPCR is the gold standard test, and comparison of methodologies and reagents, utilizing patient samples, is important to establish reliable diagnostic pipelines. METHODS Here, we assessed indirect methods that require RNA extraction with direct RT-qPCR on patient samples. Four different RNA extraction kits (Qiagen, Invitrogen, BGI and Norgen Biotek) were compared. For detection, we assessed two recently developed Taqman-based modules (BGI and Norgen Biotek), a SYBR green-based approach (NEB Luna Universal One-Step Kit) with published and newly-developed primers, and clinical results (Seegene STARMag RNA extraction system and Allplex 2019-nCoV RT-qPCR assay). We also tested and optimized direct, extraction-free detection using these RT-qPCR systems and performed a cost analysis of the different methods evaluated here. RESULTS Most RNA isolation procedures performed similarly, and while all RT-qPCR modules effectively detected purified viral RNA, the BGI system provided overall superior performance (lower detection limit, lower Ct values and higher sensitivity), generating comparable results to original clinical diagnostic data, and identifying samples ranging from 65 copies to 2.1 × 105 copies of viral genome/μl. However, the BGI detection system is more expensive than other options tested here. With direct RT-qPCR, simply adding an RNase inhibitor greatly improved detection, without the need for any other treatments (e.g. lysis buffers or boiling). The best direct methods detected ~ 10 fold less virus than indirect methods, but this simplified approach reduced sample handling, as well as assay time and cost. CONCLUSIONS With extracted RNA, the BGI RT-qPCR detection system exhibited superior performance over the Norgen system, matching initial clinical diagnosis with the Seegene Allplex assay. The BGI system was also suitable for direct, extraction-free analysis, providing 78.4% sensitivity. The Norgen system, however, still accurately detected samples with a clinical Ct < 33 from extracted RNA, provided significant cost savings, and was superior to SYBR green assays that exhibited reduced specificity.
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Affiliation(s)
- Joel D Pearson
- Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, Canada
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Daniel Trcka
- Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, Canada
| | - Suying Lu
- Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, Canada
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Sharon J Hyduk
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Mark Jen
- Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, Canada
- Network Collaborative Biology Centre, Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Canada
| | - Marie-Ming Aynaud
- Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, Canada
| | - J Javier Hernández
- Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Philippos Peidis
- Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, Canada
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Miriam Barrios-Rodiles
- Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, Canada
- Network Collaborative Biology Centre, Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Canada
| | - Kin Chan
- Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, Canada
| | - Jim Woodgett
- Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Tony Mazzulli
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Microbiology, Sinai Health System/University Health Network, Toronto, Canada
| | - Liliana Attisano
- Department of Biochemistry, Donnelly Centre, University of Toronto, Toronto, Canada
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Myron I Cybulsky
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, Canada
- Network Collaborative Biology Centre, Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Rod Bremner
- Lunenfeld-Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, Canada.
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.
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33
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Aynaud MM, Hernandez JJ, Barutcu S, Braunschweig U, Chan K, Pearson JD, Trcka D, Prosser SL, Kim J, Barrios-Rodiles M, Jen M, Song S, Shen J, Bruce C, Hazlett B, Poutanen S, Attisano L, Bremner R, Blencowe BJ, Mazzulli T, Han H, Pelletier L, Wrana JL. A multiplexed, next generation sequencing platform for high-throughput detection of SARS-CoV-2. Nat Commun 2021; 12:1405. [PMID: 33658502 PMCID: PMC7930244 DOI: 10.1038/s41467-021-21653-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
Population scale sweeps of viral pathogens, such as SARS-CoV-2, require high intensity testing for effective management. Here, we describe "Systematic Parallel Analysis of RNA coupled to Sequencing for Covid-19 screening" (C19-SPAR-Seq), a multiplexed, scalable, readily automated platform for SARS-CoV-2 detection that is capable of analyzing tens of thousands of patient samples in a single run. To address strict requirements for control of assay parameters and output demanded by clinical diagnostics, we employ a control-based Precision-Recall and Receiver Operator Characteristics (coPR) analysis to assign run-specific quality control metrics. C19-SPAR-Seq coupled to coPR on a trial cohort of several hundred patients performs with a specificity of 100% and sensitivity of 91% on samples with low viral loads, and a sensitivity of >95% on high viral loads associated with disease onset and peak transmissibility. This study establishes the feasibility of employing C19-SPAR-Seq for the large-scale monitoring of SARS-CoV-2 and other pathogens.
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Affiliation(s)
- Marie-Ming Aynaud
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - J Javier Hernandez
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Seda Barutcu
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Ulrich Braunschweig
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
| | - Kin Chan
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Joel D Pearson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Daniel Trcka
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Suzanna L Prosser
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Jaeyoun Kim
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Miriam Barrios-Rodiles
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Mark Jen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Siyuan Song
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Jess Shen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Christine Bruce
- Department of Microbiology, Mount Sinai Hospital/University Health Network, Toronto, M5G 1X5, ON, Canada
| | - Bryn Hazlett
- Department of Microbiology, Mount Sinai Hospital/University Health Network, Toronto, M5G 1X5, ON, Canada
| | - Susan Poutanen
- Department of Microbiology, Mount Sinai Hospital/University Health Network, Toronto, M5G 1X5, ON, Canada
| | - Liliana Attisano
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Rod Bremner
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Benjamin J Blencowe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Tony Mazzulli
- Department of Microbiology, Mount Sinai Hospital/University Health Network, Toronto, M5G 1X5, ON, Canada
| | - Hong Han
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada.
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada.
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Grisé KN, Bautista NX, Jacques K, Coles BLK, van der Kooy D. Glucocorticoid agonists enhance retinal stem cell self-renewal and proliferation. Stem Cell Res Ther 2021; 12:83. [PMID: 33494791 PMCID: PMC7831262 DOI: 10.1186/s13287-021-02136-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/01/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Adult mammalian retinal stem cells (RSCs) readily proliferate, self-renew, and generate progeny that differentiate into all retinal cell types in vitro. RSC-derived progeny can be induced to differentiate into photoreceptors, making them a potential source for retinal cell transplant therapies. Despite their proliferative propensity in vitro, RSCs in the adult mammalian eye do not proliferate and do not have a regenerative response to injury. Thus, identifying and modulating the mechanisms that regulate RSC proliferation may enhance the capacity to produce RSC-derived progeny in vitro and enable RSC activation in vivo. METHODS Here, we used medium-throughput screening to identify small molecules that can expand the number of RSCs and their progeny in culture. In vitro differentiation assays were used to assess the effects of synthetic glucocorticoid agonist dexamethasone on RSC-derived progenitor cell fate. Intravitreal injections of dexamethasone into adult mouse eyes were used to investigate the effects on endogenous RSCs. RESULTS We discovered that high-affinity synthetic glucocorticoid agonists increase RSC self-renewal and increase retinal progenitor proliferation up to 6-fold without influencing their differentiation in vitro. Intravitreal injection of synthetic glucocorticoid agonist dexamethasone induced in vivo proliferation in the ciliary epithelium-the niche in which adult RSCs reside. CONCLUSIONS Together, our results identify glucocorticoids as novel regulators of retinal stem and progenitor cell proliferation in culture and provide evidence that GCs may activate endogenous RSCs.
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Affiliation(s)
- Kenneth N Grisé
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Nelson X Bautista
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Krystal Jacques
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Brenda L K Coles
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Derek van der Kooy
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada
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35
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Rich S, Moradi Chameh H, Sekulic V, Valiante TA, Skinner FK. Modeling Reveals Human-Rodent Differences in H-Current Kinetics Influencing Resonance in Cortical Layer 5 Neurons. Cereb Cortex 2021; 31:845-872. [PMID: 33068000 PMCID: PMC7906797 DOI: 10.1093/cercor/bhaa261] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 01/01/2023] Open
Abstract
While our understanding of human neurons is often inferred from rodent data, inter-species differences between neurons can be captured by building cellular models specifically from human data. This includes understanding differences at the level of ion channels and their implications for human brain function. Thus, we here present a full spiking, biophysically detailed multi-compartment model of a human layer 5 (L5) cortical pyramidal cell. Model development was primarily based on morphological and electrophysiological data from the same human L5 neuron, avoiding confounds of experimental variability. Focus was placed on describing the behavior of the hyperpolarization-activated cation (h-) channel, given increasing interest in this channel due to its role in pacemaking and differentiating cell types. We ensured that the model exhibited post-inhibitory rebound spiking considering its relationship with the h-current, along with other general spiking characteristics. The model was validated against data not used in its development, which highlighted distinctly slower kinetics of the human h-current relative to the rodent setting. We linked the lack of subthreshold resonance observed in human L5 neurons to these human-specific h-current kinetics. This work shows that it is possible and necessary to build human-specific biophysical neuron models in order to understand human brain dynamics.
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Affiliation(s)
- Scott Rich
- Division of Clinical and Computational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Homeira Moradi Chameh
- Division of Clinical and Computational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Vladislav Sekulic
- Division of Clinical and Computational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Taufik A Valiante
- Division of Clinical and Computational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 1A1, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A1, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON M5S 1A1, Canada
- Electrical and Computer Engineering, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Frances K Skinner
- Division of Clinical and Computational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Departments of Medicine (Neurology) and Physiology, University of Toronto, Toronto, ON M5S 1A1, Canada
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36
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Suart CE, Graham KJ, Suart TN, Truant R. Development of a knowledge translation platform for ataxia: Impact on readers and volunteer contributors. PLoS One 2020; 15:e0238512. [PMID: 32870931 PMCID: PMC7462291 DOI: 10.1371/journal.pone.0238512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/18/2020] [Indexed: 11/18/2022] Open
Abstract
Background Dissemination of accurate health research information to patients and families has become increasingly important with the rise of the internet as a means of finding health information. However, the public faces several barriers to accessing research information, including paywalls and technical jargon. One method to bridge this gap between patients, families, and research is using lay summaries. SCAsource is an online knowledge translation platform where peer-reviewed research papers on ataxia are translated into lay summaries. This online platform was launched in September 2018, with the goal of making ataxia research more accessible and understandable to patients and families. A secondary goal is to provide opportunities for ataxia researchers to develop and hone their knowledge translation skills, altogether improving the quality of patient communication in the ataxia community. Aim The aim of this study was to measure the impact of SCAsource on its readers and volunteer contributors after one year of activity. This is to ensure SCAsource is meeting its goals of (1) improving access and understanding of ataxia research to lay audiences, and (2) improving knowledge translation skills of volunteer contributors. Methods Two online surveys were launched, one for readers and one for volunteers. Each survey had a combination of multiple-choice, Likert-scale type, and open-ended short-answer questions. Descriptive quantitative analysis was used for respondent characteristics and Likert-type data. A grounded theory coding approach was used to analyze narrative feedback data. Results We found that SCAsource has mutually beneficial outcomes for both lay person readers and volunteer contributors. Readers have an increased understanding of ataxia research and access to up-to-date information on recent publications. Volunteers develop knowledge translation skills and have increased confidence in communicating results to lay audiences. Areas of improvement were identified to be incorporated into the platform. Conclusion We demonstrated that SCAsource improves access to information and understanding of research to lay audiences, while providing opportunities for researchers to develop knowledge translation skills. This framework can potentially be used by other rare disease organizations to launch and evaluate their own knowledge translation websites.
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Affiliation(s)
- Celeste Elisabeth Suart
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Katherine Jean Graham
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Theresa Nowlan Suart
- School of Medicine and Faculty of Education, Queen’s University, Kingston, Ontario, Canada
| | - Ray Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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Tsatskis Y, Rosenfeld R, Pearson JD, Boswell C, Qu Y, Kim K, Fabian L, Mohammad A, Wang X, Robson MI, Krchma K, Wu J, Gonçalves J, Hodzic D, Wu S, Potter D, Pelletier L, Dunham WH, Gingras AC, Sun Y, Meng J, Godt D, Schedl T, Ciruna B, Choi K, Perry JRB, Bremner R, Schirmer EC, Brill JA, Jurisicova A, McNeill H. The NEMP family supports metazoan fertility and nuclear envelope stiffness. Sci Adv 2020; 6:eabb4591. [PMID: 32923640 PMCID: PMC7455189 DOI: 10.1126/sciadv.abb4591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/17/2020] [Indexed: 05/06/2023]
Abstract
Human genome-wide association studies have linked single-nucleotide polymorphisms (SNPs) in NEMP1 (nuclear envelope membrane protein 1) with early menopause; however, it is unclear whether NEMP1 has any role in fertility. We show that whole-animal loss of NEMP1 homologs in Drosophila, Caenorhabditis elegans, zebrafish, and mice leads to sterility or early loss of fertility. Loss of Nemp leads to nuclear shaping defects, most prominently in the germ line. Biochemical, biophysical, and genetic studies reveal that NEMP proteins support the mechanical stiffness of the germline nuclear envelope via formation of a NEMP-EMERIN complex. These data indicate that the germline nuclear envelope has specialized mechanical properties and that NEMP proteins play essential and conserved roles in fertility.
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Affiliation(s)
- Yonit Tsatskis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Robyn Rosenfeld
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Joel D. Pearson
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Curtis Boswell
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Yi Qu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Kyunga Kim
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Physiology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Lacramioara Fabian
- Genome and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ariz Mohammad
- Department of Genetics, School of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xian Wang
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
- Institute of Biomaterials and Biomedical, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Michael I. Robson
- Wellcome Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Karen Krchma
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jun Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - João Gonçalves
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Didier Hodzic
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shu Wu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Daniel Potter
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Wade H. Dunham
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Yu Sun
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
- Institute of Biomaterials and Biomedical, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Jin Meng
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Dorothea Godt
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Tim Schedl
- Department of Genetics, School of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian Ciruna
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Kyunghee Choi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Graduate School of Biotechnology, Kyung Hee University, Yong In, South Korea
| | - John R. B. Perry
- MRC Epidemiology Unit, Cambridge Biomedical Campus, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Rod Bremner
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Departments of Ophthalmology and Visual Science and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eric C. Schirmer
- Wellcome Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Julie A. Brill
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Andrea Jurisicova
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Physiology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON M5G 1E2, Canada
| | - Helen McNeill
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
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Soong R, Liaghati Mobarhan Y, Tabatabaei M, Bastawrous M, Biswas RG, Simpson M, Simpson A. Flow-based in vivo NMR spectroscopy of small aquatic organisms. Magn Reson Chem 2020; 58:411-426. [PMID: 32239577 DOI: 10.1002/mrc.4886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/08/2019] [Accepted: 04/28/2019] [Indexed: 06/11/2023]
Abstract
NMR applied to living organisms is arguably the ultimate tool for understanding environmental stress responses and can provide desperately needed information on toxic mechanisms, synergistic effects, sublethal impacts, recovery, and biotransformation of xenobiotics. To perform in vivo NMR spectroscopy, a flow cell system is required to deliver oxygen and food to the organisms while maintaining optimal line shape for NMR spectroscopy. In this tutorial, two such flow cell systems and their constructions are discussed: (a) a single pump high-volume flow cell design is simple to build and ideal for organisms that do not require feeding (i.e., eggs) and (b) a more advanced low-volume double pump flow cell design that permits feeding, maintains optimal water height for water suppression, improves locking and shimming, and uses only a small recirculating volume, thus reducing the amount of xenobiotic required for testing. In addition, key experimental aspects including isotopic enrichment, water suppression, and 2D experiments for both 13 C enriched and natural abundance organisms are discussed.
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Affiliation(s)
- Ronald Soong
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Yalda Liaghati Mobarhan
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Maryam Tabatabaei
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Monica Bastawrous
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Rajshree Ghosh Biswas
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Myrna Simpson
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Andre Simpson
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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Liaghati Mobarhan Y, Soong R, Lane D, Simpson AJ. In vivo comprehensive multiphase NMR. Magn Reson Chem 2020; 58:427-444. [PMID: 32239574 DOI: 10.1002/mrc.4832] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/20/2018] [Accepted: 01/03/2019] [Indexed: 06/11/2023]
Abstract
Traditionally, due to different hardware requirements, nuclear magnetic resonance (NMR) has developed as two separate fields: one dealing with solids, and one with solutions. Comprehensive multiphase (CMP) NMR combines all electronics and hardware (magic angle spinning [MAS], gradients, high power Radio Frequency (RF) handling, lock, susceptibility matching) into a universal probe that permits a comprehensive study of all phases (i.e., liquid, gel-like, semisolid, and solid), in intact samples. When applied in vivo, it provides unique insight into the wide array of bonds in a living system from the most mobile liquids (blood, fluids) through gels (muscle, tissues) to the most rigid (exoskeleton, shell). In this tutorial, the practical aspects of in vivo CMP NMR are discussed including: handling the organisms, rotor preparation, sample spinning, water suppression, editing experiments, and finishes with a brief look at the potential of other heteronuclei (2 H, 15 N, 19 F, 31 P) for in vivo research. The tutorial is aimed as a general resource for researchers interested in developing and applying MAS-based approaches to living organisms. Although the focus here is CMP NMR, many of the approaches can be adapted (or directly applied) using conventional high-resolution magic angle spinning, and in some cases, even standard solid-state NMR probes.
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Affiliation(s)
- Yalda Liaghati Mobarhan
- Environmental NMR Center, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Ronald Soong
- Environmental NMR Center, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Lane
- Environmental NMR Center, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Andre J Simpson
- Environmental NMR Center, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
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Aubry A, Yu T, Bremner R. Preclinical studies reveal MLN4924 is a promising new retinoblastoma therapy. Cell Death Discov 2020; 6:2. [PMID: 32123578 PMCID: PMC7026052 DOI: 10.1038/s41420-020-0237-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/23/2019] [Accepted: 12/28/2019] [Indexed: 12/23/2022] Open
Abstract
RB1 loss (RB1 null ) or MYCN amplification (MYCN amp ) in fetal human retina causes retinoblastoma. SKP2 loss kills RB1 null cells, but small molecule SKP2 inhibitors remain unexplored therapeutically. Whether SKP2 is synthetic lethal in MYCN amp retinoblastoma is unclear. SKP2 is the substrate recognition component of two Cullin-RING Ligase complexes (CRL1SKP2/SCFSKP2, and CRL4SKP2), a family of multiprotein E3 ubiquitin ligases. NEDD8 activating enzyme (NAE) is required for Cullin neddylation and thus CRL activation. Here, we show that the NAE inhibitor, Pevonedistat (MLN4924), potently inhibits RB1 null and MYCN amp tumors. Intravitreal MLN4924 suppressed multiple human xenografts with EC80s from 20 ng to 3.5 μg. Maximum tolerated dose (MTD) was 10-30 μg, highlighting a favorable therapeutic window. Inhibition of Cullin neddylation was similar in all cases, but cellular effects ranged from G1 arrest with apoptosis to G2/M arrest with endoreplication. However, even in less sensitive lines (EC50 ≈ 1 μM), prolonged exposure was lethal or induced persistent cytostasis. Mechanistically, depleting any single Cullin did not fully recapitulate drug phenotypes, but sensitivity to SKP2 loss correlated with that of drug. Thus, intravitreal MLN4924 is a promising new retinoblastoma therapy, mimicking the cancer-specific lethality of eliminating SKP2 complexes.
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Affiliation(s)
- Arthur Aubry
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5 Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 27 King’s College Circle, Toronto, ON M5S 1A1 Canada
| | - Tao Yu
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5 Canada
| | - Rod Bremner
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5 Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 27 King’s College Circle, Toronto, ON M5S 1A1 Canada
- Department of Ophthalmology and Vision Science, University of Toronto, 27 King’s College Circle, Toronto, ON M5S 1A1 Canada
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Cook JL, Swart JC, Froböse MI, Diaconescu AO, Geurts DEM, den Ouden HEM, Cools R. Catecholaminergic modulation of meta-learning. eLife 2019; 8:e51439. [PMID: 31850844 PMCID: PMC6974360 DOI: 10.7554/elife.51439] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/18/2019] [Indexed: 01/03/2023] Open
Abstract
The remarkable expedience of human learning is thought to be underpinned by meta-learning, whereby slow accumulative learning processes are rapidly adjusted to the current learning environment. To date, the neurobiological implementation of meta-learning remains unclear. A burgeoning literature argues for an important role for the catecholamines dopamine and noradrenaline in meta-learning. Here, we tested the hypothesis that enhancing catecholamine function modulates the ability to optimise a meta-learning parameter (learning rate) as a function of environmental volatility. 102 participants completed a task which required learning in stable phases, where the probability of reinforcement was constant, and volatile phases, where probabilities changed every 10-30 trials. The catecholamine transporter blocker methylphenidate enhanced participants' ability to adapt learning rate: Under methylphenidate, compared with placebo, participants exhibited higher learning rates in volatile relative to stable phases. Furthermore, this effect was significant only with respect to direct learning based on the participants' own experience, there was no significant effect on inferred-value learning where stimulus values had to be inferred. These data demonstrate a causal link between catecholaminergic modulation and the adjustment of the meta-learning parameter learning rate.
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Affiliation(s)
- Jennifer L Cook
- School of PsychologyUniversity of BirminghamBirminghamUnited Kingdom
| | - Jennifer C Swart
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive NeuroimagingRadboud UniversityNijmegenNetherlands
| | - Monja I Froböse
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive NeuroimagingRadboud UniversityNijmegenNetherlands
| | - Andreea O Diaconescu
- Translational Neuromodeling Unit, Institute for Biomedical EngineeringUniversity of Zurich and ETH ZurichZurichSwitzerland
- Department of PsychiatryUniversity of BaselBaselSwitzerland
- Krembil Centre for Neuroinformatics,CAMHUniversity of TorontoTorontoCanada
| | - Dirk EM Geurts
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive NeuroimagingRadboud UniversityNijmegenNetherlands
- Department of PsychiatryRadboud University Medical CentreNijmegenNetherlands
| | - Hanneke EM den Ouden
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive NeuroimagingRadboud UniversityNijmegenNetherlands
| | - Roshan Cools
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive NeuroimagingRadboud UniversityNijmegenNetherlands
- Department of PsychiatryRadboud University Medical CentreNijmegenNetherlands
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Carlucci M, Kriščiūnas A, Li H, Gibas P, Koncevičius K, Petronis A, Oh G. DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity. Bioinformatics 2019; 36:btz834. [PMID: 31702788 PMCID: PMC7703757 DOI: 10.1093/bioinformatics/btz834] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/30/2019] [Accepted: 11/05/2019] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION Biological rhythmicity is fundamental to almost all organisms on Earth and plays a key role in health and disease. Identification of oscillating signals could lead to novel biological insights, yet its investigation is impeded by the extensive computational and statistical knowledge required to perform such analysis. RESULTS To address this issue, we present DiscoRhythm (Discovering Rhythmicity), a user-friendly application for characterizing rhythmicity in temporal biological data. DiscoRhythm is available as a web application or an R/Bioconductor package for estimating phase, amplitude, and statistical significance using four popular approaches to rhythm detection (Cosinor, JTK Cycle, ARSER, and Lomb-Scargle). We optimized these algorithms for speed, improving their execution times up to 30-fold to enable rapid analysis of -omic-scale datasets in real-time. Informative visualizations, interactive modules for quality control, dimensionality reduction, periodicity profiling, and incorporation of experimental replicates make DiscoRhythm a thorough toolkit for analyzing rhythmicity. AVAILABILITY AND IMPLEMENTATION The DiscoRhythm R package is available on Bioconductor (https://bioconductor.org/packages/DiscoRhythm), with source code available on GitHub (https://github.com/matthewcarlucci/DiscoRhythm) under a GPL-3 license. The web application is securely deployed over HTTPS (https://disco.camh.ca) and is freely available for use worldwide. Local instances of the DiscoRhythm web application can be created using the R package or by deploying the publicly available Docker container (https://hub.docker.com/r/mcarlucci/discorhythm). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthew Carlucci
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
| | - Algimantas Kriščiūnas
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Haohan Li
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
| | - Povilas Gibas
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Karolis Koncevičius
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Art Petronis
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Gabriel Oh
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
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Giguère N, Delignat-Lavaud B, Herborg F, Voisin A, Li Y, Jacquemet V, Anand-Srivastava M, Gether U, Giros B, Trudeau LÉ. Increased vulnerability of nigral dopamine neurons after expansion of their axonal arborization size through D2 dopamine receptor conditional knockout. PLoS Genet 2019; 15:e1008352. [PMID: 31449520 PMCID: PMC6730950 DOI: 10.1371/journal.pgen.1008352] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 09/06/2019] [Accepted: 08/07/2019] [Indexed: 01/20/2023] Open
Abstract
Parkinson’s disease (PD) is a neurodegenerative disorder characterized by the loss of dopamine (DA) neurons in the substantia nigra pars compacta (SNc). Rare genetic mutations in genes such as Parkin, Pink1, DJ-1, α-synuclein, LRRK2 and GBA are found to be responsible for the disease in about 15% of the cases. A key unanswered question in PD pathophysiology is why would these mutations, impacting basic cellular processes such as mitochondrial function and neurotransmission, lead to selective degeneration of SNc DA neurons? We previously showed in vitro that SNc DA neurons have an extremely high rate of mitochondrial oxidative phosphorylation and ATP production, characteristics that appear to be the result of their highly complex axonal arborization. To test the hypothesis in vivo that axon arborization size is a key determinant of vulnerability, we selectively labeled SNc or VTA DA neurons using floxed YFP viral injections in DAT-cre mice and showed that SNc DA neurons have a much more arborized axon than those of the VTA. To further enhance this difference, which may represent a limiting factor in the basal vulnerability of these neurons, we selectively deleted in mice the DA D2 receptor (D2-cKO), a key negative regulator of the axonal arbour of DA neurons. In these mice, SNc DA neurons have a 2-fold larger axonal arborization, release less DA and are more vulnerable to a 6-OHDA lesion, but not to α-synuclein overexpression when compared to control SNc DA neurons. This work adds to the accumulating evidence that the axonal arborization size of SNc DA neurons plays a key role in their vulnerability in the context of PD. Parkinson’s disease motor symptoms have been linked to age-dependent degeneration of a class of neurons in the brain that release the chemical messenger dopamine. The reason for the selective loss of these neurons represents a key unsolved mystery. One hypothesis is that the neurons most at risk in this disease are those with the most extensive and complex connectivity in the brain, which would make these cells most dependent on high rates of mitochondrial energy production and expose them to higher rates of oxidative stress. Here we selectively deleted in dopamine neurons a key gene providing negative feedback control of the axonal arbor size of these neurons, in the objective of producing mice in which dopamine neurons have more extensive connectivity. We found that deletion of the dopamine D2 receptor gene in dopamine neurons leads to dopamine neurons with a longer and more complex axonal domain. We also found that in these mice, dopamine neurons in a region of the brain called the substantia nigra show increased vulnerability to a neurotoxin often used to model Parkinson’s disease in rodents. Our findings provide support for the hypothesis that the scale of a neuron’s connectivity directly influences its vulnerability to cellular stressors that trigger Parkinson’s disease.
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Affiliation(s)
- Nicolas Giguère
- Departments of pharmacology and physiology, Department of neurosciences, Central Nervous System Research Group (GRSNC), Faculty of Medicine, Université de Montréal, Québec, Canada
| | - Benoît Delignat-Lavaud
- Departments of pharmacology and physiology, Department of neurosciences, Central Nervous System Research Group (GRSNC), Faculty of Medicine, Université de Montréal, Québec, Canada
| | - Freja Herborg
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Aurore Voisin
- Departments of pharmacology and physiology, Department of neurosciences, Central Nervous System Research Group (GRSNC), Faculty of Medicine, Université de Montréal, Québec, Canada
| | - Yuan Li
- Department of pharmacology and physiology, Faculty of Medicine, Université de Montréal, Québec, Canada
| | - Vincent Jacquemet
- Department of pharmacology and physiology, Research Center of the Hôpital de Sacré-Coeur de Montréal, Montréal, Québec, Canada
| | - Madhu Anand-Srivastava
- Department of pharmacology and physiology, Faculty of Medicine, Université de Montréal, Québec, Canada
| | - Ulrik Gether
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bruno Giros
- Department of Psychiatry, McGill University Faculty of Medicine, Douglas Mental Health University Institute, Montreal, Québec, Canada
| | - Louis-Éric Trudeau
- Departments of pharmacology and physiology, Department of neurosciences, Central Nervous System Research Group (GRSNC), Faculty of Medicine, Université de Montréal, Québec, Canada
- * E-mail:
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Gheiratmand L, Coyaud E, Gupta GD, Laurent EMN, Hasegan M, Prosser SL, Gonçalves J, Raught B, Pelletier L. Spatial and proteomic profiling reveals centrosome-independent features of centriolar satellites. EMBO J 2019; 38:e101109. [PMID: 31304627 PMCID: PMC6627244 DOI: 10.15252/embj.2018101109] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/19/2022] Open
Abstract
Centriolar satellites are small electron-dense granules that cluster in the vicinity of centrosomes. Satellites have been implicated in multiple critical cellular functions including centriole duplication, centrosome maturation, and ciliogenesis, but their precise composition and assembly properties have remained poorly explored. Here, we perform in vivo proximity-dependent biotin identification (BioID) on 22 human satellite proteins, to identify 2,113 high-confidence interactions among 660 unique polypeptides. Mining this network, we validate six additional satellite components. Analysis of the satellite interactome, combined with subdiffraction imaging, reveals the existence of multiple unique microscopically resolvable satellite populations that display distinct protein interaction profiles. We further show that loss of satellites in PCM1-depleted cells results in a dramatic change in the satellite interaction landscape. Finally, we demonstrate that satellite composition is largely unaffected by centriole depletion or disruption of microtubules, indicating that satellite assembly is centrosome-independent. Together, our work offers the first systematic spatial and proteomic profiling of human centriolar satellites and paves the way for future studies aimed at better understanding the biogenesis and function(s) of these enigmatic structures.
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Affiliation(s)
- Ladan Gheiratmand
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
| | - Etienne Coyaud
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoONCanada
| | - Gagan D Gupta
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
- Present address:
Department of Chemistry and BiologyRyerson UniversityTorontoONCanada
| | | | - Monica Hasegan
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
| | - Suzanna L Prosser
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
| | - João Gonçalves
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
| | - Brian Raught
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoONCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoONCanada
| | - Laurence Pelletier
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
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Pollock RA, Zaman L, Chandran V, Gladman DD. Epigenome-wide analysis of sperm cells identifies IL22 as a possible germ line risk locus for psoriatic arthritis. PLoS One 2019; 14:e0212043. [PMID: 30779748 PMCID: PMC6380582 DOI: 10.1371/journal.pone.0212043] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/20/2019] [Indexed: 01/06/2023] Open
Abstract
Psoriasis and its associated inflammatory arthritis, psoriatic arthritis (PsA), have a clear heritable component, but a large proportion of the heritable risk remains unexplained by gene sequence variation. This study aimed to determine if epigenetic factors contribute to the missing heritability in psoriatic disease. DNA methylation profiling was performed on sperm cells from 23 probands with psoriasis without PsA (PsC), 13 PsA probands, and 18 unaffected controls. Differentially methylated CpGs and regions (DMRs) were identified and validated by pyrosequencing. Underlying AluY and copy number variation (CNV) in the HCG26 and IL22 genes, respectively, were assessed by genotyping. Array, subject's age, age of psoriasis onset, psoriasis severity, and medication usage were found to influence methylation at many genes and were included as covariates in the analysis. Between PsC probands vs. controls, 169 DMRs were found; 754 DMRs were found between PsA probands vs. controls, and 86 between PsA and PsC probands (adjusted p<0.05). Differences in methylation across DMRs were generally subtle (<10%) but correlated well with pyrosequencing. Biological inference prioritized notable DMRs associated with skin disease (SIGLEC14, JAM3, PCOLCE, RXRB), skin and/or joint disease (MBP, OSBPL5, SNORD115, HCG26), and joint disease (IL22, ELF5, PPP2R2D, PTPRN2, HCG26). Hypermethylation of the DMR within the first exon of arthritis-associated IL22 showed significant correlation (rho = 0.34, 95% CI 0.06-0.57, p = 0.01) between paired sperm and blood samples, independent of a CNV within the same region. Further studies are needed to rule out underlying genetic causes and determine if these represent heritable, constitutional epimutations, or are the result of exposure of germ cells to endogenous or exogenous environmental factors.
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Affiliation(s)
- Remy A. Pollock
- Psoriatic Arthritis Program, Centre for Prognosis Studies in the Rheumatic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Laila Zaman
- Psoriatic Arthritis Program, Centre for Prognosis Studies in the Rheumatic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Vinod Chandran
- Psoriatic Arthritis Program, Centre for Prognosis Studies in the Rheumatic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Division of Rheumatology, Department of Medicine, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Institue of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Dafna D. Gladman
- Psoriatic Arthritis Program, Centre for Prognosis Studies in the Rheumatic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Division of Rheumatology, Department of Medicine, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Institue of Medical Science, University of Toronto, Toronto, ON, Canada
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Hassan Q, Dutta Majumdar R, Wu B, Lane D, Tabatabaei-Anraki M, Soong R, Simpson MJ, Simpson AJ. Improvements in lipid suppression for 1 H NMR-based metabolomics: Applications to solution-state and HR-MAS NMR in natural and in vivo samples. Magn Reson Chem 2018; 57:69-81. [PMID: 30520113 DOI: 10.1002/mrc.4814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
Proton nuclear magnetic resonance (NMR) spectra of intact biological samples often show strong contributions from lipids, which overlap with signals of interest from small metabolites. Pioneering work by Diserens et al. demonstrated that the relative differences in diffusivity and relaxation of lipids versus small metabolites could be exploited to suppress lipid signals, in high-resolution magic angle spinning (HR-MAS) NMR spectroscopy. In solution-state NMR, suspended samples can exhibit very broad water signals, which are challenging to suppress. Here, improved water suppression is incorporated into the sequence, and the Carr-Purcell-Meiboom-Gill sequence (CPMG) train is replaced with a low-power adiabatic spinlock that reduces heating and spectral artefacts seen with longer CPMG filters. The result is a robust sequence that works well in both HR-MAS as well as static solution-state samples. Applications are also extended to include in vivo organisms. For solution-state NMR, samples containing significant amount of fats such as milk and hemp hearts seeds are used to demonstrate the technique. For HR-MAS, living earthworms (Eisenia fetida) and freshwater shrimp (Hyalella azteca) are used for in vivo applications. Lipid suppression techniques are essential for non-invasive NMR-based analysis of biological samples with a high-lipid content and adds to the suite of experiments advantageous for in vivo environmental metabolomics.
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Affiliation(s)
- Qusai Hassan
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | | | - Bing Wu
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Lane
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Maryam Tabatabaei-Anraki
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Ronald Soong
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Myrna J Simpson
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Andre J Simpson
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
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Tabatabaei Anaraki M, Simpson MJ, Simpson AJ. Reducing impacts of organism variability in metabolomics via time trajectory in vivo NMR. Magn Reson Chem 2018; 56:1117-1123. [PMID: 29906816 DOI: 10.1002/mrc.4759] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/29/2018] [Accepted: 06/02/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Maryam Tabatabaei Anaraki
- Environmental NMR Center, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Myrna J Simpson
- Environmental NMR Center, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - André J Simpson
- Environmental NMR Center, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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