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Manzini V, Cappelletti P, Orefice NS, Brentari I, Rigby MJ, Lo Giudice M, Feligioni M, Rivabene R, Crestini A, Manfredi F, Talarico G, Bruno G, Corbo M, Puglielli L, Denti MA, Piscopo P. miR-92a-3p and miR-320a are Upregulated in Plasma Neuron-Derived Extracellular Vesicles of Patients with Frontotemporal Dementia. Mol Neurobiol 2024:10.1007/s12035-024-04386-z. [PMID: 39138758 DOI: 10.1007/s12035-024-04386-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 07/19/2024] [Indexed: 08/15/2024]
Abstract
Despite the efforts to identify fluid biomarkers to improve diagnosis of Frontotemporal dementia (FTD), only a few candidates have been described in recent years. In a previous study, we identified three circulating miRNAs (miR-92a-3p, miR-320a and miR-320b) differentially expressed in FTD patients with respect to healthy controls and/or Alzheimer's disease (AD) patients. Now, we investigated whether those changes could be due to miRNAs contained in neuron-derived extracellular vesicles (NDEVs). We also evaluated miRNAs content in total plasma EVs and in CSF samples. The analysis of plasma NDEVs carried out on 40 subjects including controls (n = 13), FTD (n = 13) and AD (n = 14) patients, showed that both miR-92a-3p and miR-320a levels were triplicated in the FTD group if compared with CT and AD patients. Increased levels of the same miRNAs were found also in CSF derived from FTD group compared to CTs. No differences were observed in expression levels of miR-320b among the three groups. Worthy of note, all miRNAs analysed were increased in an FTD cell model, MAPT IVS10 + 16 neurons. Our results suggest that miR-92a and miR-320a in NDEVs could be proposed as FTD biomarkers.
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Affiliation(s)
- Valeria Manzini
- Department of Neuroscience, Istituto Superiore Di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy
- Department of Biology and Biotechnology Charles Darwin, University of Rome "Sapienza", Rome, Italy
| | - Pamela Cappelletti
- Department of Neurorehabilitation Sciences, Casa Cura Igea, Milan, Italy
| | - Nicola S Orefice
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Feinberg School of Medicine, Department of Pharmacology, Northwestern University, Chicago, IL, 60611, USA
| | - Ilaria Brentari
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Michael J Rigby
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Maria Lo Giudice
- Need Institute, Foundation for Cure and Rehabilitation of Neurological Diseases, Milan, Italy
| | - Marco Feligioni
- Department of Neurorehabilitation Sciences, Casa Cura Igea, Milan, Italy
- Fondazione European Brain Research Institute (EBRI) Rita Levi-Montalcini, Rome, Italy
| | - Roberto Rivabene
- Department of Neuroscience, Istituto Superiore Di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy
| | - Alessio Crestini
- Department of Neuroscience, Istituto Superiore Di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy
| | - Francesco Manfredi
- National Center for Global Health, Istituto Superiore Di Sanità, Rome, Italy
| | - Giuseppina Talarico
- Department of Human Neuroscience, University of Rome "Sapienza", Rome, Italy
| | - Giuseppe Bruno
- Department of Human Neuroscience, University of Rome "Sapienza", Rome, Italy
| | - Massimo Corbo
- Department of Neurorehabilitation Sciences, Casa Cura Igea, Milan, Italy
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Geriatric Research Education Clinical Center, Veterans Affairs Medical Center, Madison, WI, 53705, USA
| | - Michela A Denti
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
| | - Paola Piscopo
- Department of Neuroscience, Istituto Superiore Di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy.
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2
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Matsuoka T, Yashiro M. Bioinformatics Analysis and Validation of Potential Markers Associated with Prediction and Prognosis of Gastric Cancer. Int J Mol Sci 2024; 25:5880. [PMID: 38892067 PMCID: PMC11172243 DOI: 10.3390/ijms25115880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
Gastric cancer (GC) is one of the most common cancers worldwide. Most patients are diagnosed at the progressive stage of the disease, and current anticancer drug advancements are still lacking. Therefore, it is crucial to find relevant biomarkers with the accurate prediction of prognoses and good predictive accuracy to select appropriate patients with GC. Recent advances in molecular profiling technologies, including genomics, epigenomics, transcriptomics, proteomics, and metabolomics, have enabled the approach of GC biology at multiple levels of omics interaction networks. Systemic biological analyses, such as computational inference of "big data" and advanced bioinformatic approaches, are emerging to identify the key molecular biomarkers of GC, which would benefit targeted therapies. This review summarizes the current status of how bioinformatics analysis contributes to biomarker discovery for prognosis and prediction of therapeutic efficacy in GC based on a search of the medical literature. We highlight emerging individual multi-omics datasets, such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics, for validating putative markers. Finally, we discuss the current challenges and future perspectives to integrate multi-omics analysis for improving biomarker implementation. The practical integration of bioinformatics analysis and multi-omics datasets under complementary computational analysis is having a great impact on the search for predictive and prognostic biomarkers and may lead to an important revolution in treatment.
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Affiliation(s)
- Tasuku Matsuoka
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 5458585, Japan;
- Institute of Medical Genetics, Osaka Metropolitan University, 1-4-3 Asahi-machi, Abeno-ku, Osaka 5458585, Japan
| | - Masakazu Yashiro
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 5458585, Japan;
- Institute of Medical Genetics, Osaka Metropolitan University, 1-4-3 Asahi-machi, Abeno-ku, Osaka 5458585, Japan
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3
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Lumi R, Petri S, Siwy J, Latosinska A, Raad J, Zürbig P, Skripuletz T, Mischak H, Beige J. Small peptide CSF fingerprint of amyotrophic lateral sclerosis. PLoS One 2024; 19:e0302280. [PMID: 38687737 PMCID: PMC11060592 DOI: 10.1371/journal.pone.0302280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by abnormal protein aggregation in the motor neurons. Present and earlier proteomic studies to characterize peptides in cerebrospinal fluid (CSF) associated with motoneuron pathology did not target low molecular weight proteins and peptides. We hypothesized that specific changes in CSF peptides or low molecular weight proteins are significantly altered in ALS, and that these changes may support deciphering molecular pathophysiology and even guide approaches towards therapeutic interventions. METHODS Cerebrospinal fluid (CSF) from 50 ALS patients and 50 non-ALS controls was collected, centrifuged immediately after collection, aliquoted into polypropylene test tubes, frozen within 30-40 min after the puncture, and stored at -80°C until use. Peptides were sequenced using capillary electrophoresis or liquid chromatography/mass spectrometry (CE-MS/MS or LC-MS/MS). FINDINGS In the CSF of 50 patients and 50 non-ALS controls 33 peptides were found, of which 14 could be sequenced using a non-lytic single-pot proteomic detection method, CE/MS. ALS deregulated peptides vs. controls included Integral membrane protein 2B, Neurosecretory protein VGF, Osteopontin, Neuroendocrine protein 7B2 (Secretogranin-V), EGF-containing fibulin-like extracellular matrix protein 1, Xylosyltransferase 1 XT-1, Chromogranin-A, Superoxide dismutase SOD-1, Secretogranin-1 (Chromogranin B), NR2F2 Nuclear Receptor Subfamily 2 Group F Member 2 and Collagen alpha-1(VII) chain. INTERPRETATION Most striking deregulations in CSF from ALS patients were found in VGF, Osteopontin, SOD-1 and EFEMP1 peptides. No associations of disease severity, duration and region of onset with sequenced peptides were found.
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Affiliation(s)
- Rea Lumi
- Department of Neurology, Hannover University Medical School, Hannover, Germany
| | - Susanne Petri
- Department of Neurology, Hannover University Medical School, Hannover, Germany
| | | | | | - Julia Raad
- Mosaiques Diagnostics GmbH, Hannover, Germany
| | | | - Thomas Skripuletz
- Department of Neurology, Hannover University Medical School, Hannover, Germany
| | | | - Joachim Beige
- Kuratorium for Dialysis and Kidney Transplantation, Neu-Isenburg, Germany
- Martin-Luther-University Halle/Wittenberg, Halle/Saale, Germany
- Hospital Sankt Georg gGmbH, Leipzig, Germany
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4
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Caggiano C, Morselli M, Qian X, Celona B, Thompson M, Wani S, Tosevska A, Taraszka K, Heuer G, Ngo S, Steyn F, Nestor P, Wallace L, McCombe P, Heggie S, Thorpe K, McElligott C, English G, Henders A, Henderson R, Lomen-Hoerth C, Wray N, McRae A, Pellegrini M, Garton F, Zaitlen N. Tissue informative cell-free DNA methylation sites in amyotrophic lateral sclerosis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.08.24305503. [PMID: 38645132 PMCID: PMC11030489 DOI: 10.1101/2024.04.08.24305503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Cell-free DNA (cfDNA) is increasingly recognized as a promising biomarker candidate for disease monitoring. However, its utility in neurodegenerative diseases, like amyotrophic lateral sclerosis (ALS), remains underexplored. Existing biomarker discovery approaches are tailored to a specific disease context or are too expensive to be clinically practical. Here, we address these challenges through a new approach combining advances in molecular and computational technologies. First, we develop statistical tools to select tissue-informative DNA methylation sites relevant to a disease process of interest. We then employ a capture protocol to select these sites and perform targeted methylation sequencing. Multi-modal information about the DNA methylation patterns are then utilized in machine learning algorithms trained to predict disease status and disease progression. We applied our method to two independent cohorts of ALS patients and controls (n=192). Overall, we found that the targeted sites accurately predicted ALS status and replicated between cohorts. Additionally, we identified epigenetic features associated with ALS phenotypes, including disease severity. These findings highlight the potential of cfDNA as a non-invasive biomarker for ALS.
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Affiliation(s)
- C Caggiano
- Department of Neurology, UCLA, Los Angeles, California
- Institute of Genomic Health, Icahn School of Medicine at Mt Sinai, New York, New York
| | - M Morselli
- Department of Molecular, Cell, and Developmental Biology, UCLA; Los Angeles, California
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - X Qian
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - B Celona
- Cardiovascular Research Institute, UCSF, San Francisco, California
| | - M Thompson
- Department of Neurology, UCLA, Los Angeles, California
- Systems and Synthetic Biology, Centre for Genomic Regulation, Barcelona, Spain
| | - S Wani
- Cardiovascular Research Institute, UCSF, San Francisco, California
| | - A Tosevska
- Department of Molecular, Cell, and Developmental Biology, UCLA; Los Angeles, California
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Vienna, Austria
| | - K Taraszka
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - G Heuer
- Computational and Systems Biology Interdepartmental Program, UCLA, Los Angeles, California
| | - S Ngo
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - F Steyn
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - P Nestor
- Queensland Brain Institute, Unviversity of Queensland, Brisbane, Australia
- Mater Public Hospital, Brisbane, Australia
| | - L Wallace
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - P McCombe
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - S Heggie
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - K Thorpe
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | | | - G English
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - A Henders
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - R Henderson
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - C Lomen-Hoerth
- Department of Neurology, UCSF, San Francisco, California
| | - N Wray
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - A McRae
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - M Pellegrini
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - F Garton
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - N Zaitlen
- Department of Neurology, UCLA, Los Angeles, California
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California
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5
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Matveeva A, Watters O, Rukhadze A, Khemka N, Gentile D, Perez IF, Llorente-Folch I, Farrell C, Lo Cacciato E, Jackson J, Piazzesi A, Wischhof L, Woods I, Halang L, Hogg M, Muñoz AG, Dillon ET, Matallanas D, Arijs I, Lambrechts D, Bano D, Connolly NMC, Prehn JHM. Integrated analysis of transcriptomic and proteomic alterations in mouse models of ALS/FTD identify early metabolic adaptions with similarities to mitochondrial dysfunction disorders. Amyotroph Lateral Scler Frontotemporal Degener 2024; 25:135-149. [PMID: 37779364 DOI: 10.1080/21678421.2023.2261979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/10/2023] [Indexed: 10/03/2023]
Abstract
OBJECTIVE Sporadic and familial amyotrophic lateral sclerosis (ALS) is a fatal progressive neurodegenerative disease that results in loss of motor neurons and, in some patients, associates with frontotemporal dementia (FTD). Apart from the accumulation of proteinaceous deposits, emerging literature indicates that aberrant mitochondrial bioenergetics may contribute to the onset and progression of ALS/FTD. Here we sought to investigate the pathophysiological signatures of mitochondrial dysfunction associated with ALS/FTD. METHODS By means of label-free mass spectrometry (MS) and mRNA sequencing (mRNA-seq), we report pre-symptomatic changes in the cortices of TDP-43 and FUS mutant mouse models. Using tissues from transgenic mouse models of mitochondrial diseases as a reference, we performed comparative analyses and extracted unique and common mitochondrial signatures that revealed neuroprotective compensatory mechanisms in response to early damage. RESULTS In this regard, upregulation of both Acyl-CoA Synthetase Long-Chain Family Member 3 (ACSL3) and mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) were the most representative change in pre-symptomatic ALS/FTD tissues, suggesting that fatty acid beta-oxidation and mitochondrial protein translation are mechanisms of adaptation in response to ALS/FTD pathology. CONCLUSIONS Together, our unbiased integrative analyses unveil novel molecular components that may influence mitochondrial homeostasis in the earliest phase of ALS.
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Affiliation(s)
- Anna Matveeva
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Orla Watters
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- SFI FutureNeuro Research Centre, Dublin 2, Ireland
| | - Ani Rukhadze
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Niraj Khemka
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Debora Gentile
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ivan Fernandez Perez
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Irene Llorente-Folch
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Cliona Farrell
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | | | - Joshua Jackson
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Antonia Piazzesi
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Lena Wischhof
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ina Woods
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Luise Halang
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Marion Hogg
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- SFI FutureNeuro Research Centre, Dublin 2, Ireland
- Department of Biosciences, Nottingham Trent University, Clifton Campus, Nottingham, UK
| | - Amaya Garcia Muñoz
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Belfield, Ireland
| | - Eugène T Dillon
- Mass Spectrometry Resource, Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - David Matallanas
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Belfield, Ireland
| | - Ingrid Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium, and
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium, and
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Niamh M C Connolly
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Jochen H M Prehn
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- SFI FutureNeuro Research Centre, Dublin 2, Ireland
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Guise AJ, Misal SA, Carson R, Chu JH, Boekweg H, Van Der Watt D, Welsh NC, Truong T, Liang Y, Xu S, Benedetto G, Gagnon J, Payne SH, Plowey ED, Kelly RT. TDP-43-stratified single-cell proteomics of postmortem human spinal motor neurons reveals protein dynamics in amyotrophic lateral sclerosis. Cell Rep 2024; 43:113636. [PMID: 38183652 PMCID: PMC10926001 DOI: 10.1016/j.celrep.2023.113636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/02/2023] [Accepted: 12/14/2023] [Indexed: 01/08/2024] Open
Abstract
A limitation of conventional bulk-tissue proteome studies in amyotrophic lateral sclerosis (ALS) is the confounding of motor neuron (MN) signals by admixed non-MN proteins. Here, we leverage laser capture microdissection and nanoPOTS single-cell mass spectrometry-based proteomics to query changes in protein expression in single MNs from postmortem ALS and control tissues. In a follow-up analysis, we examine the impact of stratification of MNs based on cytoplasmic transactive response DNA-binding protein 43 (TDP-43)+ inclusion pathology on the profiles of 2,238 proteins. We report extensive overlap in differentially abundant proteins identified in ALS MNs with or without overt TDP-43 pathology, suggesting early and sustained dysregulation of cellular respiration, mRNA splicing, translation, and vesicular transport in ALS. Together, these data provide insights into proteome-level changes associated with TDP-43 proteinopathy and begin to demonstrate the utility of pathology-stratified trace sample proteomics for understanding single-cell protein dynamics in human neurologic diseases.
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Affiliation(s)
| | - Santosh A Misal
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Richard Carson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | | | - Hannah Boekweg
- Biology Department, Brigham Young University, Provo, UT 84602, USA
| | | | | | - Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | | | | | | | - Samuel H Payne
- Biology Department, Brigham Young University, Provo, UT 84602, USA
| | | | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.
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7
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Geraci J, Bhargava R, Qorri B, Leonchyk P, Cook D, Cook M, Sie F, Pani L. Machine learning hypothesis-generation for patient stratification and target discovery in rare disease: our experience with Open Science in ALS. Front Comput Neurosci 2024; 17:1199736. [PMID: 38260713 PMCID: PMC10801647 DOI: 10.3389/fncom.2023.1199736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/20/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Advances in machine learning (ML) methodologies, combined with multidisciplinary collaborations across biological and physical sciences, has the potential to propel drug discovery and development. Open Science fosters this collaboration by releasing datasets and methods into the public space; however, further education and widespread acceptance and adoption of Open Science approaches are necessary to tackle the plethora of known disease states. Motivation In addition to providing much needed insights into potential therapeutic protein targets, we also aim to demonstrate that small patient datasets have the potential to provide insights that usually require many samples (>5,000). There are many such datasets available and novel advancements in ML can provide valuable insights from these patient datasets. Problem statement Using a public dataset made available by patient advocacy group AnswerALS and a multidisciplinary Open Science approach with a systems biology augmented ML technology, we aim to validate previously reported drug targets in ALS and provide novel insights about ALS subpopulations and potential drug targets using a unique combination of ML methods and graph theory. Methodology We use NetraAI to generate hypotheses about specific patient subpopulations, which were then refined and validated through a combination of ML techniques, systems biology methods, and expert input. Results We extracted 8 target classes, each comprising of several genes that shed light into ALS pathophysiology and represent new avenues for treatment. These target classes are broadly categorized as inflammation, epigenetic, heat shock, neuromuscular junction, autophagy, apoptosis, axonal transport, and excitotoxicity. These findings are not mutually exclusive, and instead represent a systematic view of ALS pathophysiology. Based on these findings, we suggest that simultaneous targeting of ALS has the potential to mitigate ALS progression, with the plausibility of maintaining and sustaining an improved quality of life (QoL) for ALS patients. Even further, we identified subpopulations based on disease onset. Conclusion In the spirit of Open Science, this work aims to bridge the knowledge gap in ALS pathophysiology to aid in diagnostic, prognostic, and therapeutic strategies and pave the way for the development of personalized treatments tailored to the individual's needs.
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Affiliation(s)
- Joseph Geraci
- NetraMark Corp, Toronto, ON, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
- Centre for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
- Arthur C. Clarke Center for Human Imagination, School of Physical Sciences, University of California San Diego, San Diego, CA, United States
| | - Ravi Bhargava
- Department of Biomedical and Molecular Science, Queens University, Kingston, ON, Canada
- Science and Research, Roche Integrated Informatics, F. Hoffmann La-Roche, Toronto, ON, Canada
| | | | | | - Douglas Cook
- NetraMark Corp, Toronto, ON, Canada
- Department of Surgery, Queen's University, Kingston, ON, Canada
| | - Moses Cook
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Fanny Sie
- Science and Research, Roche Integrated Informatics, F. Hoffmann La-Roche, Toronto, ON, Canada
| | - Luca Pani
- NetraMark Corp, Toronto, ON, Canada
- Department of Psychiatry and Behavioral Sciences, Leonard M. Miller School of Medicine, University of Miami, Coral Gables, FL, United States
- Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
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8
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Rajaratnam S, Pradhan SS, Naik AA, Sivaramakrishnan V. Integrated Multi-Omics Analysis and Validation in Yeast Model of Amyotrophic Lateral Sclerosis. Methods Mol Biol 2024; 2761:397-419. [PMID: 38427252 DOI: 10.1007/978-1-0716-3662-6_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Transcriptomics is a complex process that involves raw data extraction, normalization, differential gene expression, and analysis. The Gene Expression Omnibus (GEO) database at the National Center for Biotechnology Information (NCBI) is a repository of experimental datasets. Amyotrophic lateral sclerosis (ALS) datasets are deposited by various scientists and research investigators to expand the horizon of scientific knowledge. R-statistical tools are the most common ways for conducting these kinds of studies. The first step is the identification of appropriate datasets. Since the raw data is available in a variety of formats, a large array of software is used for extraction and analysis. Normalization is conducted for the datasets using NetworkAnalyst. Differential analysis is further conducted on the normalized data to identify significantly enriched genes. The significant genes are then grouped into pathways. The results were validated using yeast model of ALS in which the yeast is transformed with ALS plasmids encoding genes associated with ALS. The resulting GFP-tagged protein aggregates are imaged using fluorescence microscopy and subsequently validated using filter retardation assay and quantified using ImageJ software. Functional role of different genes is studied using metabolite treatment and knockout studies.
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Affiliation(s)
- Saiswaroop Rajaratnam
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
| | - Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
| | - Ashwin Ashok Naik
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India.
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9
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Shi X, Liu C, Zheng W, Cao X, Li W, Zhang D, Zhu J, Zhang X, Chen Y. Proteomic Analysis Revealed the Potential Role of MAGE-D2 in the Therapeutic Targeting of Triple-Negative Breast Cancer. Mol Cell Proteomics 2024; 23:100703. [PMID: 38128647 PMCID: PMC10835320 DOI: 10.1016/j.mcpro.2023.100703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Among all the molecular subtypes of breast cancer, triple-negative breast cancer (TNBC) is the most aggressive one. Currently, the clinical prognosis of TNBC is poor because there is still no effective therapeutic target. Here, we carried out a combined proteomic analysis involving bioinformatic analysis of the proteome database, label-free quantitative proteomics, and immunoprecipitation (IP) coupled with mass spectrometry (MS) to explore potential therapeutic targets for TNBC. The results of bioinformatic analysis showed an overexpression of MAGE-D2 (melanoma antigen family D2) in TNBC. In vivo and in vitro experiments revealed that MAGE-D2 overexpression could promote cell proliferation and metastasis. Furthermore, label-free quantitative proteomics revealed that MAGE-D2 acted as a cancer-promoting factor by activating the PI3K-AKT pathway. Moreover, the outcomes of IP-MS and cross-linking IP-MS demonstrated that MAGE-D2 could interact with Hsp70 and prevent Hsp70 degradation, but evidence for their direct interaction is still lacking. Nevertheless, MAGE-D2 is a potential therapeutic target for TNBC, and blocking MAGE-D2 may have important therapeutic implications.
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Affiliation(s)
- Xiaoyu Shi
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Chunyan Liu
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Weimin Zheng
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Xiao Cao
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Wan Li
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Dongxue Zhang
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Jianhua Zhu
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Xian Zhang
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, China; State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing, China; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Nanjing, China.
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10
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D’Ercole C, de Marco A. Native Agarose Gels and Contact Blotting as Means to Optimize the Protocols for the Formation of Antigen-Ligand Complexes. Bioengineering (Basel) 2023; 10:1111. [PMID: 37892841 PMCID: PMC10604731 DOI: 10.3390/bioengineering10101111] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Protein complexes provide valuable biological information, but can be difficult to handle. Therefore, technical advancements designed to improve their manipulation are always useful. METHODS We investigated the opportunity to exploit native agarose gels and the contact blot method for the transfer of native proteins to membranes as means for optimizing the conditions for obtaining stable complexes. As a simple model of protein-protein interactions, an antigen-ligand complex was used in which both proteins were fused to reporters. RESULTS At each step, it was possible to visualize both the antigen, fused to a fluorescent protein, and the ligand, fused to a monomeric ascorbate peroxidase (APEX) and, as such, a way to tune the protocol. The conditions for the complex formation were adapted by modifying the buffer conditions, the concentration of the proteins and of the cross-linkers. CONCLUSIONS The procedure is rapid, inexpensive, and the several detection opportunities allow for both the monitoring of complex stability and the preservation of the functionality of its components, which is critical for understanding their biomedical implications and supporting drug discovery. The overall protocol represents a handy alternative to gel filtration, uses very standard and ubiquitous equipment, and can be implemented rapidly and without specific training.
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Affiliation(s)
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, P.O. Box 301, SI-5000 Nova Gorica, Slovenia;
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11
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Morello G, La Cognata V, Guarnaccia M, La Bella V, Conforti FL, Cavallaro S. A Diagnostic Gene-Expression Signature in Fibroblasts of Amyotrophic Lateral Sclerosis. Cells 2023; 12:1884. [PMID: 37508548 PMCID: PMC10378077 DOI: 10.3390/cells12141884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/11/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, progressive neurodegenerative disease with limited treatment options. Diagnosis can be difficult due to the heterogeneity and non-specific nature of the initial symptoms, resulting in delays that compromise prompt access to effective therapeutic strategies. Transcriptome profiling of patient-derived peripheral cells represents a valuable benchmark in overcoming such challenges, providing the opportunity to identify molecular diagnostic signatures. In this study, we characterized transcriptome changes in skin fibroblasts of sporadic ALS patients (sALS) and controls and evaluated their utility as a molecular classifier for ALS diagnosis. Our analysis identified 277 differentially expressed transcripts predominantly involved in transcriptional regulation, synaptic transmission, and the inflammatory response. A support vector machine classifier based on this 277-gene signature was developed to discriminate patients with sALS from controls, showing significant predictive power in both the discovery dataset and in six independent publicly available gene expression datasets obtained from different sALS tissue/cell samples. Taken together, our findings support the utility of transcriptional signatures in peripheral cells as valuable biomarkers for the diagnosis of ALS.
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Affiliation(s)
- Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Vincenzo La Bella
- ALS Clinical Research Center and Neurochemistry Laboratory, BiND, University of Palermo, 90133 Palermo, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
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12
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Afridi R, Lee WH, Kim JH, Suk K. Utilizing databases for astrocyte secretome research. Expert Rev Proteomics 2023; 20:371-379. [PMID: 37978891 DOI: 10.1080/14789450.2023.2285311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
INTRODUCTION Astrocytes are the most abundant cell type in the central nervous system (CNS). They play a pivotal role in supporting neuronal function and maintaining homeostasis by releasing a variety of bioactive proteins, collectively known as the astrocyte secretome. Investigating secretome provides insights into the molecular mechanisms underlying astrocyte function and dysfunction, as well as novel strategies to prevent and treat diseases affecting the CNS. AREAS COVERED Proteomics databases are a valuable resource for studying the role of astrocytes in healthy and diseased brain function, as they provide information about gene expression, protein expression, and cellular function. In this review, we discuss existing databases that are useful for astrocyte secretome research. EXPERT OPINION Astrocyte secretomics is a field that is rapidly progressing, yet the availability of dedicated databases is currently limited. To meet the increasing demand for comprehensive omics data in glia research, developing databases specifically focused on astrocyte secretome is crucial. Such databases would allow researchers to investigate the intricate molecular landscape of astrocytes and comprehend their involvement in diverse physiological and pathological processes. Expanding resources through the development of databases dedicated to the astrocyte secretome may facilitate further advancements in this field.
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Affiliation(s)
- Ruqayya Afridi
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Won-Ha Lee
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Jong-Heon Kim
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Kyoungho Suk
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
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Khosla R, Bhagat H, Lal P, Anand A. ALS plasma reduces the viability of NSC34 cells via altering mRNA expression of VEGF: A short report. Heliyon 2023; 9:e18287. [PMID: 37519724 PMCID: PMC10372388 DOI: 10.1016/j.heliyon.2023.e18287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disorder that progressively leads to motor neuron degeneration at the neuromuscular junctions, resulting in paralysis in the patients. The clinical diagnosis of ALS is time taking and further delays the therapeutics that can be helpful if the disease is diagnosed at an early stage. Changes in plasma composition can be reflected upon CSF composition and hence, can be used to study the diagnosis and prognosis markers for the disease. Aim To develop a simple model system using motor neuron like cell line after plasma induction. Method Neuroblastoma × Spinal Cord hybridoma cell line (NSC34) was cultured under appropriate conditions. 10% ALS patients' plasma was added to the media, and cells were conditioned for 12 h. Cell survival analysis and differential gene expression of a panel of molecules (published previously, VEGF, VEGFR2, ANG, OPTN, TDP43, and MCP-1) were done. Results ALS patients' plasma impacted the life of the cells and reduced survival to nearly 50% after induction. VEGF was found to be significantly down-regulated in the cells, which can be explained as a reason for reduced cell survival. Conclusion ALS plasma altered the expression of an essential neuroprotective and growth factor VEGF in NSC34 cells leading to reduced viability.
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Affiliation(s)
| | - Hemant Bhagat
- Department of Anesthesia and Intensive Care, PGIMER, Chandigarh, India
| | - Parth Lal
- Advanced Paediatric Centre, PGIMER, Chandigarh, India
| | - Akshay Anand
- Neuroscience Research Lab, PGIMER, Chandigarh, India
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14
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Guise AJ, Misal SA, Carson R, Boekweg H, Watt DVD, Truong T, Liang Y, Chu JH, Welsh NC, Gagnon J, Payne SH, Plowey ED, Kelly RT. TDP-43-stratified single-cell proteomic profiling of postmortem human spinal motor neurons reveals protein dynamics in amyotrophic lateral sclerosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544233. [PMID: 37333094 PMCID: PMC10274884 DOI: 10.1101/2023.06.08.544233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Unbiased proteomics has been employed to interrogate central nervous system (CNS) tissues (brain, spinal cord) and fluid matrices (CSF, plasma) from amyotrophic lateral sclerosis (ALS) patients; yet, a limitation of conventional bulk tissue studies is that motor neuron (MN) proteome signals may be confounded by admixed non-MN proteins. Recent advances in trace sample proteomics have enabled quantitative protein abundance datasets from single human MNs (Cong et al., 2020b). In this study, we leveraged laser capture microdissection (LCM) and nanoPOTS (Zhu et al., 2018c) single-cell mass spectrometry (MS)-based proteomics to query changes in protein expression in single MNs from postmortem ALS and control donor spinal cord tissues, leading to the identification of 2515 proteins across MNs samples (>900 per single MN) and quantitative comparison of 1870 proteins between disease groups. Furthermore, we studied the impact of enriching/stratifying MN proteome samples based on the presence and extent of immunoreactive, cytoplasmic TDP-43 inclusions, allowing identification of 3368 proteins across MNs samples and profiling of 2238 proteins across TDP-43 strata. We found extensive overlap in differential protein abundance profiles between MNs with or without obvious TDP-43 cytoplasmic inclusions that together point to early and sustained dysregulation of oxidative phosphorylation, mRNA splicing and translation, and retromer-mediated vesicular transport in ALS. Our data are the first unbiased quantification of single MN protein abundance changes associated with TDP-43 proteinopathy and begin to demonstrate the utility of pathology-stratified trace sample proteomics for understanding single-cell protein abundance changes in human neurologic diseases.
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Affiliation(s)
| | - Santosh A. Misal
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Richard Carson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Hannah Boekweg
- Biology Department, Brigham Young University, Provo, UT 84602, USA
| | | | - Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | | | | | | | - Samuel H. Payne
- Biology Department, Brigham Young University, Provo, UT 84602, USA
| | | | - Ryan T. Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
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Luan W, Wright AL, Brown-Wright H, Le S, San Gil R, Madrid San Martin L, Ling K, Jafar-Nejad P, Rigo F, Walker AK. Early activation of cellular stress and death pathways caused by cytoplasmic TDP-43 in the rNLS8 mouse model of ALS and FTD. Mol Psychiatry 2023; 28:2445-2461. [PMID: 37012334 PMCID: PMC10611572 DOI: 10.1038/s41380-023-02036-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 04/05/2023]
Abstract
TAR DNA binding protein 43 (TDP-43) pathology is a key feature of over 95% of amyotrophic lateral sclerosis (ALS) and nearly half of frontotemporal dementia (FTD) cases. The pathogenic mechanisms of TDP-43 dysfunction are poorly understood, however, activation of cell stress pathways may contribute to pathogenesis. We, therefore, sought to identify which cell stress components are critical for driving disease onset and neurodegeneration in ALS and FTD. We studied the rNLS8 transgenic mouse model, which expresses human TDP-43 with a genetically-ablated nuclear localisation sequence within neurons of the brain and spinal cord resulting in cytoplasmic TDP-43 pathology and progressive motor dysfunction. Amongst numerous cell stress-related biological pathways profiled using qPCR arrays, several critical integrated stress response (ISR) effectors, including CCAAT/enhancer-binding homologous protein (Chop/Ddit3) and activating transcription factor 4 (Atf4), were upregulated in the cortex of rNLS8 mice prior to disease onset. This was accompanied by early up-regulation of anti-apoptotic gene Bcl2 and diverse pro-apoptotic genes including BH3-interacting domain death agonist (Bid). However, pro-apoptotic signalling predominated after onset of motor phenotypes. Notably, pro-apoptotic cleaved caspase-3 protein was elevated in the cortex of rNLS8 mice at later disease stages, suggesting that downstream activation of apoptosis drives neurodegeneration following failure of early protective responses. Unexpectedly, suppression of Chop in the brain and spinal cord using antisense oligonucleotide-mediated silencing had no effect on overall TDP-43 pathology or disease phenotypes in rNLS8 mice. Cytoplasmic TDP-43 accumulation therefore causes very early activation of ISR and both anti- and pro-apoptotic signalling that switches to predominant pro-apoptotic activation later in disease. These findings suggest that precise temporal modulation of cell stress and death pathways may be beneficial to protect against neurodegeneration in ALS and FTD.
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Affiliation(s)
- Wei Luan
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
| | - Amanda L Wright
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, Australia
| | - Heledd Brown-Wright
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
| | - Sheng Le
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, Australia
| | - Rebecca San Gil
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
| | - Lidia Madrid San Martin
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
| | - Karen Ling
- Ionis Pharmaceuticals, Carlsbad, CA, 90201, USA
| | | | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, 90201, USA
| | - Adam K Walker
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia.
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, Australia.
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Radford RAW, Rayner SL, Szwaja P, Morsch M, Cheng F, Zhu T, Widagdo J, Anggono V, Pountney DL, Chung R, Lee A. Identification of phosphorylated tau protein interactors in progressive supranuclear palsy (PSP) reveals networks involved in protein degradation, stress response, cytoskeletal dynamics, metabolic processes, and neurotransmission. J Neurochem 2023; 165:563-586. [PMID: 36847488 PMCID: PMC10953353 DOI: 10.1111/jnc.15796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/27/2023] [Accepted: 02/21/2023] [Indexed: 03/01/2023]
Abstract
Progressive supranuclear palsy (PSP) is a late-onset neurodegenerative disease defined pathologically by the presence of insoluble phosphorylated-Tau (p-Tau) in neurons and glia. Identifying co-aggregating proteins within p-Tau inclusions may reveal important insights into processes affected by the aggregation of Tau. We used a proteomic approach, which combines antibody-mediated biotinylation and mass spectrometry (MS) to identify proteins proximal to p-Tau in PSP. Using this proof-of-concept workflow for identifying interacting proteins of interest, we characterized proteins proximal to p-Tau in PSP cases, identifying >84% of previously identified interaction partners of Tau and known modifiers of Tau aggregation, while 19 novel proteins not previously found associated with Tau were identified. Furthermore, our data also identified confidently assigned phosphorylation sites that have been previously reported on p-Tau. Additionally, using ingenuity pathway analysis (IPA) and human RNA-seq datasets, we identified proteins previously associated with neurological disorders and pathways involved in protein degradation, stress responses, cytoskeletal dynamics, metabolism, and neurotransmission. Together, our study demonstrates the utility of biotinylation by antibody recognition (BAR) approach to answer a fundamental question to rapidly identify proteins in proximity to p-Tau from post-mortem tissue. The application of this workflow opens up the opportunity to identify novel protein targets to give us insight into the biological process at the onset and progression of tauopathies.
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Affiliation(s)
- Rowan A. W. Radford
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Stephanie L. Rayner
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Paulina Szwaja
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Marco Morsch
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Flora Cheng
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Tianyi Zhu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandQueenslandBrisbaneAustralia
| | - Jocelyn Widagdo
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandQueenslandBrisbaneAustralia
| | - Victor Anggono
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandQueenslandBrisbaneAustralia
| | - Dean L. Pountney
- School of Pharmacy and Medical SciencesGriffith UniversityQueenslandGold CoastAustralia
| | - Roger Chung
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Albert Lee
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
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Reilly L, Seddighi S, Singleton AB, Cookson MR, Ward ME, Qi YA. Variant biomarker discovery using mass spectrometry-based proteogenomics. FRONTIERS IN AGING 2023; 4:1191993. [PMID: 37168844 PMCID: PMC10165118 DOI: 10.3389/fragi.2023.1191993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/13/2023] [Indexed: 05/13/2023]
Abstract
Genomic diversity plays critical roles in risk of disease pathogenesis and diagnosis. While genomic variants-including single nucleotide variants, frameshift variants, and mis-splicing isoforms-are commonly detected at the DNA or RNA level, their translated variant protein or polypeptide products are ultimately the functional units of the associated disease. These products are often released in biofluids and could be leveraged for clinical diagnosis and patient stratification. Recent emergence of integrated analysis of genomics with mass spectrometry-based proteomics for biomarker discovery, also known as proteogenomics, have significantly advanced the understanding disease risk variants, precise medicine, and biomarker discovery. In this review, we discuss variant proteins in the context of cancers and neurodegenerative diseases, outline current and emerging proteogenomic approaches for biomarker discovery, and provide a comprehensive proteogenomic strategy for detection of putative biomarker candidates in human biospecimens. This strategy can be implemented for proteogenomic studies in any field of enquiry. Our review timely addresses the need of biomarkers for aging related diseases.
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Affiliation(s)
- Luke Reilly
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Andrew B. Singleton
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States
| | - Mark R. Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States
| | - Michael E. Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Yue A. Qi
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
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18
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Gawor A, Bulska E. A Standardized Protocol for Assuring the Validity of Proteomics Results from Liquid Chromatography-High-Resolution Mass Spectrometry. Int J Mol Sci 2023; 24:ijms24076129. [PMID: 37047102 PMCID: PMC10093877 DOI: 10.3390/ijms24076129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/14/2023] Open
Abstract
Significant advances in the technological development of mass spectrometry in the field of proteomics and the generation of extremely large amounts of data require a very critical approach to assure the validity of results. Commonly used procedures involved liquid chromatography followed by high-resolution mass spectrometry measurements. Proteomics analysis is used in many fields including the investigation of the metabolism of biologically active substances in organisms. Thus, there is a need to care about the validity of the obtained results. In this work, we proposed a standardized protocol for proteomic analysis using liquid chromatography-high-resolution mass spectrometry, which covers all of these analytical steps to ensure the validity of the results. For this purpose, we explored the requirements of the ISO/IEC 17025:2017 standard as a reference document for quality control in biochemistry research-based mass spectrometry.
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Affiliation(s)
- Andrzej Gawor
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Ewa Bulska
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
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Bridel C, van Gils JHM, Miedema SSM, Hoozemans JJM, Pijnenburg YAL, Smit AB, Rozemuller AJM, Abeln S, Teunissen CE. Clusters of co-abundant proteins in the brain cortex associated with fronto-temporal lobar degeneration. Alzheimers Res Ther 2023; 15:59. [PMID: 36949537 PMCID: PMC10035199 DOI: 10.1186/s13195-023-01200-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/28/2023] [Indexed: 03/24/2023]
Abstract
BACKGROUND Frontotemporal lobar degeneration (FTLD) is characterized pathologically by neuronal and glial inclusions of hyperphosphorylated tau or by neuronal cytoplasmic inclusions of TDP43. This study aimed at deciphering the molecular mechanisms leading to these distinct pathological subtypes. METHODS To this end, we performed an unbiased mass spectrometry-based proteomic and systems-level analysis of the middle frontal gyrus cortices of FTLD-tau (n = 6), FTLD-TDP (n = 15), and control patients (n = 5). We validated these results in an independent patient cohort (total n = 24). RESULTS The middle frontal gyrus cortex proteome was most significantly altered in FTLD-tau compared to controls (294 differentially expressed proteins at FDR = 0.05). The proteomic modifications in FTLD-TDP were more heterogeneous (49 differentially expressed proteins at FDR = 0.1). Weighted co-expression network analysis revealed 17 modules of co-regulated proteins, 13 of which were dysregulated in FTLD-tau. These modules included proteins associated with oxidative phosphorylation, scavenger mechanisms, chromatin regulation, and clathrin-mediated transport in both the frontal and temporal cortex of FTLD-tau. The most strongly dysregulated subnetworks identified cyclin-dependent kinase 5 (CDK5) and polypyrimidine tract-binding protein 1 (PTBP1) as key players in the disease process. Dysregulation of 9 of these modules was confirmed in independent validation data sets of FLTD-tau and control temporal and frontal cortex (total n = 24). Dysregulated modules were primarily associated with changes in astrocyte and endothelial cell protein abundance levels, indicating pathological changes in FTD are not limited to neurons. CONCLUSIONS Using this innovative workflow and zooming in on the most strongly dysregulated proteins of the identified modules, we were able to identify disease-associated mechanisms in FTLD-tau with high potential as biomarkers and/or therapeutic targets.
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Affiliation(s)
- Claire Bridel
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Neurodegeneration, Amsterdam UMC, Amsterdam, The Netherlands
- Department of Clinical Neurosciences, Division of Neurology, Geneva University Hospital, Geneva, Switzerland
| | - Juami H. M. van Gils
- Department of Computer Science, Bioinformatics group, VU University, Amsterdam, The Netherlands
| | - Suzanne S. M. Miedema
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Jeroen J. M. Hoozemans
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, The Netherlands
| | - Yolande A. L. Pijnenburg
- Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, The Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | | | - Sanne Abeln
- Department of Computer Science, Bioinformatics group, VU University, Amsterdam, The Netherlands
| | - Charlotte E. Teunissen
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Neurodegeneration, Amsterdam UMC, Amsterdam, The Netherlands
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Takahashi N, Akaike N, Nagamatsu T, Uchino H, Kudo Y. Effects of TND1128 (a 5-deazaflavin derivative), with self-redox ability, as a mitochondria activator on the mouse brain slice and its comparison with β-NMN. J Pharmacol Sci 2023; 151:93-109. [PMID: 36707184 DOI: 10.1016/j.jphs.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/22/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
We have no definitive treatment for dementia characterized by prolonged neuronal death due to the enormous accumulation of foreign matter, such as β-amyloid. Since Alzheimer's type dementia develops slowly, we may be able to delay the onset and improve neuronal dysfunction by enhancing the energy metabolism of individual neurons. TND1128, a derivative of 5-deazaflavin, is a chemical known to have an efficient self-redox ability. We expected TND1128 as an activator for mitochondrial energy synthesis. We used brain slices prepared from mice 22 ± 2 h pretreated with TND1128 or β-NMN. We measured Ca2+ concentrations in the cytoplasm ([Ca2+]cyt) and mitochondria ([Ca2+]mit) by using fluorescence Ca2+ indicators, Fura-4F, and X-Rhod-1, respectively, and examined the protective effects of drugs on [Ca2+]cyt and [Ca2+]mit overloading by repeating 80K exposure. TND1128 (0.01, 0.1, and 1 mg/kg s.c.) mitigates the dynamics of both [Ca2+]cyt and [Ca2+]mit in a dose-dependent manner. β-NMN (10, 30, and 100 mg/kg s.c.) also showed significant dose-dependent mitigating effects on [Ca2+]cyt, but the effect on the [Ca2+]mit dynamics was insignificant. We confirmed the mitochondria-activating potential of TND1128 in the present study. We expect TND1128 as a drug that rescues deteriorating neurons with aging or disease.
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Affiliation(s)
- Nanae Takahashi
- Department of Anesthesiology, Tokyo Medical University Hachioji Medical Center 1163 Tatemachi,Hachioji, Tokyo 193-0998, Japan.
| | - Norio Akaike
- Research Division for Clinical Pharmacology, Medical Corporation, Juryou Group, Kumamoto Kinoh Hospital, 6-8-1 Yamamuro, Kita-ku, Kumamoto 860-8518, Japan.
| | - Tomohisa Nagamatsu
- Laboratory of Curative Creation Study for Geriatric-diseases Prevention, Faculty of Pharmacological Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto, 860-0082, Japan.
| | - Hiroyuki Uchino
- Department of Anesthesiology, Tokyo Medical University, 6-7-1 Nishishinjuku, Sinjuku-ku, Tokyo 160-0023, Japan.
| | - Yoshihisa Kudo
- Department of Anesthesiology, Tokyo Medical University Hachioji Medical Center 1163 Tatemachi,Hachioji, Tokyo 193-0998, Japan.
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21
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Vignaroli F, Mele A, Tondo G, De Giorgis V, Manfredi M, Comi C, Mazzini L, De Marchi F. The Need for Biomarkers in the ALS-FTD Spectrum: A Clinical Point of View on the Role of Proteomics. Proteomes 2023; 11:proteomes11010001. [PMID: 36648959 PMCID: PMC9844364 DOI: 10.3390/proteomes11010001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are severely debilitating and progressive neurodegenerative disorders. A distinctive pathological feature of several neurodegenerative diseases, including ALS and FTD, is the deposition of aberrant protein inclusions in neuronal cells, which leads to cellular dysfunction and neuronal damage and loss. Despite this, to date, the biological process behind developing these protein inclusions must be better clarified, making the development of disease-modifying treatment impossible until this is done. Proteomics is a powerful tool to characterize the expression, structure, functions, interactions, and modifications of proteins of tissue and biological fluid, including plasma, serum, and cerebrospinal fluid. This protein-profiling characterization aims to identify disease-specific protein alteration or specific pathology-based mechanisms which may be used as markers of these conditions. Our narrative review aims to highlight the need for biomarkers and the potential use of proteomics in clinical practice for ALS-FTD spectrum disorders, considering the emerging rationale in proteomics for new drug development. Certainly, new data will emerge in the near future in this regard and support clinicians in the development of personalized medicine.
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Affiliation(s)
| | - Angelica Mele
- Neurology Unit, Maggiore della Carità Hospital, 28100 Novara, Italy
| | - Giacomo Tondo
- Department of Neurology, S. Andrea Hospital, University of Piemonte Orientale, 13100 Vercelli, Italy
| | - Veronica De Giorgis
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research and Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
| | - Marcello Manfredi
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research and Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
| | - Cristoforo Comi
- Department of Neurology, S. Andrea Hospital, University of Piemonte Orientale, 13100 Vercelli, Italy
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
| | - Letizia Mazzini
- Neurology Unit, Maggiore della Carità Hospital, 28100 Novara, Italy
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
| | - Fabiola De Marchi
- Neurology Unit, Maggiore della Carità Hospital, 28100 Novara, Italy
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Correspondence: ; Tel.: +39-0321-3733962
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22
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Allergy, asthma, and proteomics: opportunities with immediate impact. Allergol Immunopathol (Madr) 2023; 51:16-21. [PMID: 36617817 DOI: 10.15586/aei.v51i1.567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 09/08/2022] [Indexed: 01/03/2023]
Abstract
Allergy is widely discussed by researchers due to its complex mechanism that leads to disorders and injuries, but the reason behind the allergic status remains unclear. Current treatments are insufficient to improve the patient's quality of life significantly. New technologies in scientific and technological development are emerging. For instance, the union between allergy and peptidomics and bioinformatics tools may help fill the gaps in this field, diagnosis, and treatment. In this review, we look at peptidomics and address some findings, such as target proteins or biomarkers that help better understand mechanisms that lead to inflammation, organ damage, and, consequently, poor quality of life or even death.
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23
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Ng W, Ng SY. Remodeling of astrocyte secretome in amyotrophic lateral sclerosis: uncovering novel targets to combat astrocyte-mediated toxicity. Transl Neurodegener 2022; 11:54. [PMID: 36567359 PMCID: PMC9791755 DOI: 10.1186/s40035-022-00332-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/05/2022] [Indexed: 12/27/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an adult-onset paralytic disease characterized by progressive degeneration of upper and lower motor neurons in the motor cortex, brainstem and spinal cord. Motor neuron degeneration is typically caused by a combination of intrinsic neuronal (cell autonomous) defects as well as extrinsic (non-cell autonomous) factors such as astrocyte-mediated toxicity. Astrocytes are highly plastic cells that react to their microenvironment to mediate relevant responses. In neurodegeneration, astrocytes often turn reactive and in turn secrete a slew of factors to exert pro-inflammatory and neurotoxic effects. Various efforts have been carried out to characterize the diseased astrocyte secretome over the years, revealing that pro-inflammatory chemokines, cytokines and microRNAs are the main players in mediating neuronal death. As metabolomic technologies mature, these studies begin to shed light on neurotoxic metabolites such as secreted lipids. In this focused review, we will discuss changes in the astrocyte secretome during ALS. In particular, we will discuss the components of the reactive astrocyte secretome that contribute to neuronal death in ALS.
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Affiliation(s)
- Winanto Ng
- grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, 138673 Singapore
| | - Shi-Yan Ng
- grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, 138673 Singapore
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24
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Sai Swaroop R, Akhil PS, Sai Sanwid P, Bandana P, Raksha RK, Meghana M, Bibha C, Sivaramakrishnan V. Integrated multi-omic data analysis and validation with yeast model show oxidative phosphorylation modulates protein aggregation in amyotrophic lateral sclerosis. J Biomol Struct Dyn 2022:1-20. [PMID: 35749136 DOI: 10.1080/07391102.2022.2090441] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Amyotrophic Lateral Sclerosis is a progressive, incurable amyloid aggregating neurodegenerative disease involving the motor neurons. Identifying potential biomarkers and therapeutic targets can assist in the better management of the disease. We used an integrative approach encompassing analysis of transcriptomic datasets of human and mice from the GEO database. Our analysis of ALS patient datasets showed deregulation in Non-alcoholic fatty acid liver disease and oxidative phosphorylation. Transgenic mice datasets of SOD1, FUS and TDP-43 showed deregulation in oxidative phosphorylation and ribosome-associated pathways. Commonality analysis between the human and mice datasets showed oxidative phosphorylation as a major deregulated pathway. Further, protein-protein and protein-drug interaction network analysis of mitochondrial electron transport chain showed enrichment of proteins and inhibitors of mitochondrial Complex III and IV. The results were further validated using the yeast model system. Inhibitor studies using metformin (Complex-I inhibitor) and malonate (Complex-II inhibitor) did not show any effect in mitigating the amyloids, while antimycin (Complex-III inhibitor) and azide (Complex-IV inhibitor) reduced amyloidogenesis. Knock-out of QCR8 (Complex-III) or COX8 (Complex-IV) cleared the amyloids. Taken together, our results show a critical role for mitochondrial oxidative phosphorylation in amyloidogenesis and as a potential therapeutic target in ALS.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- R Sai Swaroop
- Disease Biology Lab, Dept. of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - P S Akhil
- Disease Biology Lab, Dept. of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India.,Scientist B, Central Water and Power Research Station, Khadakwasla, Pune
| | - Pradhan Sai Sanwid
- Disease Biology Lab, Dept. of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | | | - Rao K Raksha
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Manjunath Meghana
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Choudhary Bibha
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Dept. of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
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25
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Sanchez-Varo R, Mejias-Ortega M, Fernandez-Valenzuela JJ, Nuñez-Diaz C, Caceres-Palomo L, Vegas-Gomez L, Sanchez-Mejias E, Trujillo-Estrada L, Garcia-Leon JA, Moreno-Gonzalez I, Vizuete M, Vitorica J, Baglietto-Vargas D, Gutierrez A. Transgenic Mouse Models of Alzheimer's Disease: An Integrative Analysis. Int J Mol Sci 2022; 23:5404. [PMID: 35628216 PMCID: PMC9142061 DOI: 10.3390/ijms23105404] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/10/2022] [Indexed: 12/16/2022] Open
Abstract
Alzheimer's disease (AD) constitutes the most prominent form of dementia among elderly individuals worldwide. Disease modeling using murine transgenic mice was first initiated thanks to the discovery of heritable mutations in amyloid precursor protein (APP) and presenilins (PS) genes. However, due to the repeated failure of translational applications from animal models to human patients, along with the recent advances in genetic susceptibility and our current understanding on disease biology, these models have evolved over time in an attempt to better reproduce the complexity of this devastating disease and improve their applicability. In this review, we provide a comprehensive overview about the major pathological elements of human AD (plaques, tauopathy, synaptic damage, neuronal death, neuroinflammation and glial dysfunction), discussing the knowledge that available mouse models have provided about the mechanisms underlying human disease. Moreover, we highlight the pros and cons of current models, and the revolution offered by the concomitant use of transgenic mice and omics technologies that may lead to a more rapid improvement of the present modeling battery.
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Affiliation(s)
- Raquel Sanchez-Varo
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
- Departamento Fisiologia Humana, Histologia Humana, Anatomia Patologica y Educacion Fisica y Deportiva, Facultad de Medicina, Universidad de Malaga, 29071 Malaga, Spain
| | - Marina Mejias-Ortega
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Juan Jose Fernandez-Valenzuela
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Cristina Nuñez-Diaz
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Laura Caceres-Palomo
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Laura Vegas-Gomez
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Elisabeth Sanchez-Mejias
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Laura Trujillo-Estrada
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Juan Antonio Garcia-Leon
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Ines Moreno-Gonzalez
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Marisa Vizuete
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
- Departamento Bioquimica y Biologia Molecular, Facultad de Farmacia, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBIS)-Hospital Universitario Virgen del Rocio/CSIC, 41012 Seville, Spain
| | - Javier Vitorica
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
- Departamento Bioquimica y Biologia Molecular, Facultad de Farmacia, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBIS)-Hospital Universitario Virgen del Rocio/CSIC, 41012 Seville, Spain
| | - David Baglietto-Vargas
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Antonia Gutierrez
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
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Type 2 Diabetes Induced by Changes in Proteomic Profiling of Zebrafish Chronically Exposed to a Mixture of Organochlorine Pesticides at Low Concentrations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19094991. [PMID: 35564385 PMCID: PMC9100612 DOI: 10.3390/ijerph19094991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/07/2022] [Accepted: 04/15/2022] [Indexed: 02/04/2023]
Abstract
Effect of organochlorine pesticides (OCPs) mixtures on development of type 2 diabetes mellitus (T2DM) and the underlying mechanism, especially at protein levels, are largely unknown. We exposed a mixture of five OCPs to zebrafish at concentrations of 0, 0.05, 0.25, 2.5, and 25 μg/L for 12 weeks. Differentially expressed proteins (DEPs) were quantitatively identified in female zebrafish livers, and its functional study was conducted. The significantly high glucose and low insulin levels were observed only at 0.05 μg/L, linking to the different pattern of DEPs than other concentrations. A total of 1082 proteins was quantified, of which 321 proteins formed 6 clusters in protein dynamics analysis. The enriched pathways in cluster 3 showing distinct pattern of DEPs could explain the nonlinear response at 0.05 μg/L, indicating that OCP mixtures adversely affected proteins associated with mitochondrial function and energy metabolism. We proposed a feasible mechanism that decrease in expression of aldehyde dehydrogenase led to abnormal accumulation of aldehydes, reducing expression of glyceraldehyde 3-phosphate dehydrogenase, and resulting in disruption of glucose homeostasis. Our findings help to better understand the causality of T2DM by exposure to OCP mixtures and to identify biomarkers in the protein expression level.
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27
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Islam Khan MZ, Tam SY, Law HKW. Advances in High Throughput Proteomics Profiling in Establishing Potential Biomarkers for Gastrointestinal Cancer. Cells 2022; 11:973. [PMID: 35326424 PMCID: PMC8946849 DOI: 10.3390/cells11060973] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 12/24/2022] Open
Abstract
Gastrointestinal cancers (GICs) remain the most diagnosed cancers and accounted for the highest cancer-related death globally. The prognosis and treatment outcomes of many GICs are poor because most of the cases are diagnosed in advanced metastatic stages. This is primarily attributed to the deficiency of effective and reliable early diagnostic biomarkers. The existing biomarkers for GICs diagnosis exhibited inadequate specificity and sensitivity. To improve the early diagnosis of GICs, biomarkers with higher specificity and sensitivity are warranted. Proteomics study and its functional analysis focus on elucidating physiological and biological functions of unknown or annotated proteins and deciphering cellular mechanisms at molecular levels. In addition, quantitative analysis of translational proteomics is a promising approach in enhancing the early identification and proper management of GICs. In this review, we focus on the advances in mass spectrometry along with the quantitative and functional analysis of proteomics data that contributes to the establishment of biomarkers for GICs including, colorectal, gastric, hepatocellular, pancreatic, and esophageal cancer. We also discuss the future challenges in the validation of proteomics-based biomarkers for their translation into clinics.
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Affiliation(s)
| | | | - Helen Ka Wai Law
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China; (M.Z.I.K.); (S.Y.T.)
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28
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Chavda V, Patel C, Modh D, Ertas YN, Sonak SS, Munshi NK, Anand K, Soni A, Pandey S. Therapeutic Approaches to Amyotrophic Lateral Sclerosis from the Lab to the Clinic. Curr Drug Metab 2022; 23:200-222. [PMID: 35272595 DOI: 10.2174/1389200223666220310113110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 01/07/2022] [Accepted: 02/02/2022] [Indexed: 11/22/2022]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a terminal neuro-degenerative disorder that is clinically recognized as a gradual degeneration of the upper and lower motor neurons, with an average duration of 3 to 5 years from initiation of symptoms to death. The mechanisms underlying the pathogenesis and progression of the disease are multifactorial. Therefore, to find effective treatments, it is necessary to understand this heterogeneity underlying the progression of ALS. Recent developments in gene therapy have opened a new avenue to treat this condition, especially for the characterized genetic types. Gene therapy methods have been studied in a variety of pre-clinical settings and clinical trials, and they may be a promising path for developing an effective and safe ALS cure. A growing body of evidence demonstrates abnormalities in energy metabolism at the cellular and whole-body level in animal models and in people living with ALS. The use and incorporation of high-throughput "omics" methods has radically transformed our thought about ALS, strengthening our understanding of the disease's dynamic molecular architecture, differentiating distinct patient subtypes, and creating a reasonable basis for the identification of biomarkers and novel individualised treatments. Future clinical and laboratory trials would also focus on the diverse relationships between metabolism and ALS to address the issue of whether targeting deficient metabolism in ALS is an effective way to change disease progression. In this review, we focus on the detailed pathogenesis of ALS and highlight principal genes, i.e., SOD1, TDP-43, C9orf72, and FUS, targeted therapeutic approaches of ALS. An attempt is made to provide up-to-date information on clinical outcomes, including various biomarkers which are thought to be important players in early ALS detection.
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Affiliation(s)
- Vivek Chavda
- Department of Pharmaceutic, L M College of Pharmacy, Ahmedabad - 380009 (India)
| | - Chirag Patel
- Department of Pharmacology, L M College of Pharmacy, Ahmedabad - 380009 (India)
| | - Dharti Modh
- Department of pharmaceutical chemistry, Poona college of pharmacy, Bharti vidhyapith, Pune - 411030 (India)
| | - Yavuz Nuri Ertas
- Department of Biomedical Engineering at Erciyes University, Kayseri, Turkey
- ERNAM - Nanotechnology Research and Application Center, Erciyes University, Kayseri 38039, Turkey
| | - Shreya S Sonak
- Department of pharmaceutical chemistry, Poona college of pharmacy, Bharti vidhyapith, Pune - 411030 (India)
| | - Nafisa K Munshi
- Department of pharmaceutical chemistry, Poona college of pharmacy, Bharti vidhyapith, Pune - 411030 (India)
| | - Krishna Anand
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences and National Health Laboratory Service, University of the Free State, Bloemfontein 9300, South Africa
| | - Arun Soni
- Department of Pharmacology, SSR College of Pharmacy, Silvassa, Dadra and Nagar Haveli - 396230(India)
| | - Sonal Pandey
- Research and Development, Meril Diagnostic Pvt. Ltd, Vapi - 396191 (India)
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Wang F, Li S, Cheng KW, Rosencrans WM, Chou TF. The p97 Inhibitor UPCDC-30245 Blocks Endo-Lysosomal Degradation. Pharmaceuticals (Basel) 2022; 15:ph15020204. [PMID: 35215314 PMCID: PMC8880557 DOI: 10.3390/ph15020204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 01/23/2022] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
The diverse modes of action of small molecule inhibitors provide versatile tools to investigate basic biology and develop therapeutics. However, it remains a challenging task to evaluate their exact mechanisms of action. We identified two classes of inhibitors for the p97 ATPase: ATP competitive and allosteric. We showed that the allosteric p97 inhibitor, UPCDC-30245, does not affect two well-known cellular functions of p97, endoplasmic-reticulum-associated protein degradation and the unfolded protein response pathway; instead, it strongly increases the lipidated form of microtubule-associated proteins 1A/1B light chain 3B (LC3-II), suggesting an alteration of autophagic pathways. To evaluate the molecular mechanism, we performed proteomic analysis of UPCDC-30245 treated cells. Our results revealed that UPCDC-30245 blocks endo-lysosomal degradation by inhibiting the formation of early endosome and reducing the acidity of the lysosome, an effect not observed with the potent p97 inhibitor CB-5083. This unique effect allows us to demonstrate UPCDC-30245 exhibits antiviral effects against coronavirus by blocking viral entry.
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Affiliation(s)
- Feng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (K.-W.C.); (W.M.R.)
- Correspondence: (F.W.); (T.-F.C.); Tel.: +1 626-395-6772 (T.-F.C.)
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (K.-W.C.); (W.M.R.)
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (K.-W.C.); (W.M.R.)
| | - William M. Rosencrans
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (K.-W.C.); (W.M.R.)
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (K.-W.C.); (W.M.R.)
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
- Correspondence: (F.W.); (T.-F.C.); Tel.: +1 626-395-6772 (T.-F.C.)
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Agrawal I, Tripathi P, Biswas S. Mass Spectrometry Based Protein Biomarkers and Drug Target Discovery and Clinical Diagnosis in Age-Related Progressing Neurodegenerative Diseases. Drug Metab Rev 2022; 54:22-36. [PMID: 35038284 DOI: 10.1080/03602532.2022.2029475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Neurodegenerative diseases correspond to overly complex health disorders that are driven by intersecting pathophysiology that are often trapped in vicious cycles of degeneration and cognitive decline. The usual diagnostic route of these diseases is based on postmortem examination that involves identifying pathology that is specific to the disease in the brain. However, in such cases, accurate diagnosis of the specific disease is limited because clinical disease presentations are often complex that do not easily allow to discriminate patient's cognitive, behavioral, and functional impairment profiles. Additionally, an early identification and therapeutic intervention of these diseases is pivotal to slow the progression of neurodegeneration and extend healthy life span. Mass spectrometry-based techniques have proven to be hugely promising in biological sample analysis and discovery of biomarkers including protein and peptide biomarkers for potential drug target discovery. Recent studies on these biomarkers have demonstrated their potential for applications in early diagnostics and identifying therapeutic targets to battle against neurodegenerative diseases. In this review, we have presented principles of mass spectrometry (MS) and the associated workflows in analyzing and imaging biological samples for discovery of biomarkers. We have especially focused on age- related progressing neurodegenerative diseases such as Alzheimer's (AD) and Parkinson's disease (PD), Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal dementia (FTD) and the related MS-based biomarkers developments for these diseases. Finally, we present a future perspective discussing the potential research directions ahead.
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Affiliation(s)
- Ishita Agrawal
- Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Pallavi Tripathi
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK
| | - Shyamasri Biswas
- USA Prime Biotech LLC, 1330 NW 6th St., Suite A-2, Gainesville, FL 32601, USA
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Recent Developments in Clinical Plasma Proteomics—Applied to Cardiovascular Research. Biomedicines 2022; 10:biomedicines10010162. [PMID: 35052841 PMCID: PMC8773619 DOI: 10.3390/biomedicines10010162] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 01/27/2023] Open
Abstract
The human plasma proteome mirrors the physiological state of the cardiovascular system, a fact that has been used to analyze plasma biomarkers in routine analysis for the diagnosis and monitoring of cardiovascular diseases for decades. These biomarkers address, however, only a very limited subset of cardiovascular diseases, such as acute myocardial infarct or acute deep vein thrombosis, and clinical plasma biomarkers for the diagnosis and stratification cardiovascular diseases that are growing in incidence, such as heart failure and abdominal aortic aneurysm, do not exist and are urgently needed. The discovery of novel biomarkers in plasma has been hindered by the complexity of the human plasma proteome that again transforms into an extreme analytical complexity when it comes to the discovery of novel plasma biomarkers. This complexity is, however, addressed by recent achievements in technologies for analyzing the human plasma proteome, thereby facilitating the possibility for novel biomarker discoveries. The aims of this article is to provide an overview of the recent achievements in technologies for proteomic analysis of the human plasma proteome and their applications in cardiovascular medicine.
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Chelliah SS, Bhuvanendran S, Magalingam KB, Kamarudin MNA, Radhakrishnan AK. Identification of blood-based biomarkers for diagnosis and prognosis of Parkinson's disease: A systematic review of proteomics studies. Ageing Res Rev 2022; 73:101514. [PMID: 34798300 DOI: 10.1016/j.arr.2021.101514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/14/2021] [Accepted: 11/10/2021] [Indexed: 12/11/2022]
Abstract
Parkinson's Disease (PD), a neurodegenerative disorder, is characterised by the loss of motor function and dopamine neurons. Therapeutic avenues remain a challenge due to lack of accuracy in early diagnosis, monitoring of disease progression and limited therapeutic options. Proteomic platforms have been utilised to discover biomarkers for numerous diseases, a tool that may benefit the diagnosis and monitoring of disease progression in PD patients. Therefore, this systematic review focuses on analysing blood-based candidate biomarkers (CB) identified via proteomics platforms for PD. This study systematically reviewed articles across six databases (EMBASE, Cochrane, Ovid Medline, Scopus, Science Direct and PubMed) published between 2010 and 2020. Of the 504 articles identified, 12 controlled-PD studies were selected for further analysis. A total of 115 candidate biomarkers (CB) were identified across selected 12-controlled studies, of which 23 CB were found to be replicable in more than two cohorts. Using the PANTHER Go-Slim classification system and STRING network, the gene function and protein interactions between biomarkers were analysed. Our analysis highlights Apolipoprotein A-I (ApoA-I), which is essential in lipid metabolism, oxidative stress, and neuroprotection demonstrates high replicability across five cohorts with consistent downregulation across four cohorts. Since ApoA-I was highly replicable across blood fractions, proteomic platforms and continents, its relationship with cholesterol, statin and oxidative stress as PD biomarker, its role in the pathogenesis of PD is discussed in this paper. The present study identified ApoA-I as a potential biomarker via proteomics analysis of PD for the early diagnosis and prediction of disease progression.
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Affiliation(s)
- Shalini Sundramurthi Chelliah
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
| | - Saatheeyavaane Bhuvanendran
- Brain Research Institute Monash Sunway (BRIMS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia.
| | - Kasthuri Bai Magalingam
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
| | - Muhamad Noor Alfarizal Kamarudin
- Brain Research Institute Monash Sunway (BRIMS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
| | - Ammu Kutty Radhakrishnan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
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Lualdi M, Shafique A, Pedrini E, Pieroni L, Greco V, Castagnola M, Cucina G, Corrado L, Di Pierro A, De Marchi F, Camillo L, Colombrita C, D’Anca M, Alberio T, D’Alfonso S, Fasano M. C9ORF72 Repeat Expansion Affects the Proteome of Primary Skin Fibroblasts in ALS. Int J Mol Sci 2021; 22:ijms221910385. [PMID: 34638725 PMCID: PMC8508815 DOI: 10.3390/ijms221910385] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 12/16/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive degeneration of the corticospinal motor neurons, which ultimately leads to death. The repeat expansion in chromosome 9 open reading frame 72 (C9ORF72) represents the most common genetic cause of ALS and it is also involved in the pathogenesis of other neurodegenerative disorders. To offer insights into C9ORF72-mediated pathogenesis, we quantitatively analyzed the proteome of patient-derived primary skin fibroblasts from ALS patients carrying the C9ORF72 mutation compared with ALS patients who tested negative for it. Differentially expressed proteins were identified, used to generate a protein-protein interaction network and subjected to a functional enrichment analysis to unveil altered molecular pathways. ALS patients were also compared with patients affected by frontotemporal dementia carrying the C9ORF72 repeat expansion. As a result, we demonstrated that the molecular pathways mainly altered in fibroblasts (e.g., protein homeostasis) mirror the alterations observed in C9ORF72-mutated neurons. Moreover, we highlighted novel molecular pathways (nuclear and mitochondrial transports, vesicle trafficking, mitochondrial bioenergetics, glucose metabolism, ER-phagosome crosstalk and Slit/Robo signaling pathway) which might be further investigated as C9ORF72-specific pathogenetic mechanisms. Data are available via ProteomeXchange with the identifier PXD023866.
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Affiliation(s)
- Marta Lualdi
- Biochemistry and Functional Proteomics Laboratory, Department of Science and High Technology, Center of Bioinformatics and Center of Neuroscience, University of Insubria, I-21052 Busto Arsizio, Italy; (A.S.); (E.P.); (G.C.); (T.A.); (M.F.)
- Correspondence: ; Tel.: +39-0331-339-414
| | - Adeena Shafique
- Biochemistry and Functional Proteomics Laboratory, Department of Science and High Technology, Center of Bioinformatics and Center of Neuroscience, University of Insubria, I-21052 Busto Arsizio, Italy; (A.S.); (E.P.); (G.C.); (T.A.); (M.F.)
| | - Edoardo Pedrini
- Biochemistry and Functional Proteomics Laboratory, Department of Science and High Technology, Center of Bioinformatics and Center of Neuroscience, University of Insubria, I-21052 Busto Arsizio, Italy; (A.S.); (E.P.); (G.C.); (T.A.); (M.F.)
| | - Luisa Pieroni
- Proteomics and Metabolomic Laboratory, Experimental Neuroscience Department, S. Lucia Foundation IRCCS, I-00168 Rome, Italy; (L.P.); (M.C.)
| | - Viviana Greco
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, I-00168 Rome, Italy;
- Molecular and Genomic Diagnostics Unit, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, I-00168 Rome, Italy
| | - Massimo Castagnola
- Proteomics and Metabolomic Laboratory, Experimental Neuroscience Department, S. Lucia Foundation IRCCS, I-00168 Rome, Italy; (L.P.); (M.C.)
| | - Giorgia Cucina
- Biochemistry and Functional Proteomics Laboratory, Department of Science and High Technology, Center of Bioinformatics and Center of Neuroscience, University of Insubria, I-21052 Busto Arsizio, Italy; (A.S.); (E.P.); (G.C.); (T.A.); (M.F.)
| | - Lucia Corrado
- Department of Health Sciences, University of Eastern Piedmont “A. Avogadro”, I-28100 Novara, Italy; (L.C.); (A.D.P.); (L.C.); (S.D.)
| | - Alice Di Pierro
- Department of Health Sciences, University of Eastern Piedmont “A. Avogadro”, I-28100 Novara, Italy; (L.C.); (A.D.P.); (L.C.); (S.D.)
| | - Fabiola De Marchi
- Department of Translational Medicine, University of Eastern Piedmont “A. Avogadro”, I-28100 Novara, Italy;
- Department of Neurology and ALS Centre, “Maggiore della Carità” Hospital, I-28100 Novara, Italy
| | - Lara Camillo
- Department of Health Sciences, University of Eastern Piedmont “A. Avogadro”, I-28100 Novara, Italy; (L.C.); (A.D.P.); (L.C.); (S.D.)
| | - Claudia Colombrita
- Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, I-20149 Milan, Italy;
| | - Marianna D’Anca
- Neurodegenerative Disease Unit, Fondazione Ca’ Granda IRCCS, Policlinico Hospital, I-20122 Milan, Italy;
| | - Tiziana Alberio
- Biochemistry and Functional Proteomics Laboratory, Department of Science and High Technology, Center of Bioinformatics and Center of Neuroscience, University of Insubria, I-21052 Busto Arsizio, Italy; (A.S.); (E.P.); (G.C.); (T.A.); (M.F.)
| | - Sandra D’Alfonso
- Department of Health Sciences, University of Eastern Piedmont “A. Avogadro”, I-28100 Novara, Italy; (L.C.); (A.D.P.); (L.C.); (S.D.)
| | - Mauro Fasano
- Biochemistry and Functional Proteomics Laboratory, Department of Science and High Technology, Center of Bioinformatics and Center of Neuroscience, University of Insubria, I-21052 Busto Arsizio, Italy; (A.S.); (E.P.); (G.C.); (T.A.); (M.F.)
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Molecular Pathways Involved in Frontotemporal Lobar Degeneration with TDP-43 Proteinopathy: What Can We Learn from Proteomics? Int J Mol Sci 2021; 22:ijms221910298. [PMID: 34638637 PMCID: PMC8508653 DOI: 10.3390/ijms221910298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 12/14/2022] Open
Abstract
Frontotemporal lobar degeneration (FTLD) is a neurodegenerative disorder clinically characterized by behavioral, language, and motor symptoms, with major impact on the lives of patients and their families. TDP-43 proteinopathy is the underlying neuropathological substrate in the majority of cases, referred to as FTLD-TDP. Several genetic causes have been identified, which have revealed some components of its pathophysiology. However, the exact mechanisms driving FTLD-TDP remain largely unknown, forestalling the development of therapies. Proteomic approaches, in particular high-throughput mass spectrometry, hold promise to help elucidate the pathogenic molecular and cellular alterations. In this review, we describe the main findings of the proteomic profiling studies performed on human FTLD-TDP brain tissue. Subsequently, we address the major biological pathways implicated in FTLD-TDP, by reviewing these data together with knowledge derived from genomic and transcriptomic literature. We illustrate that an integrated perspective, encompassing both proteomic, genetic, and transcriptomic discoveries, is vital to unravel core disease processes, and to enable the identification of disease biomarkers and therapeutic targets for this devastating disorder.
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Schwab K, Melis V, Harrington CR, Wischik CM, Magbagbeolu M, Theuring F, Riedel G. Proteomic Analysis of Hydromethylthionine in the Line 66 Model of Frontotemporal Dementia Demonstrates Actions on Tau-Dependent and Tau-Independent Networks. Cells 2021; 10:2162. [PMID: 34440931 PMCID: PMC8391171 DOI: 10.3390/cells10082162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 12/21/2022] Open
Abstract
Abnormal aggregation of tau is the pathological hallmark of tauopathies including frontotemporal dementia (FTD). We have generated tau-transgenic mice that express the aggregation-prone P301S human tau (line 66). These mice present with early-onset, high tau load in brain and FTD-like behavioural deficiencies. Several of these behavioural phenotypes and tau pathology are reversed by treatment with hydromethylthionine but key pathways underlying these corrections remain elusive. In two proteomic experiments, line 66 mice were compared with wild-type mice and then vehicle and hydromethylthionine treatments of line 66 mice were compared. The brain proteome was investigated using two-dimensional electrophoresis and mass spectrometry to identify protein networks and pathways that were altered due to tau overexpression or modified by hydromethylthionine treatment. Overexpression of mutant tau induced metabolic/mitochondrial dysfunction, changes in synaptic transmission and in stress responses, and these functions were recovered by hydromethylthionine. Other pathways, such as NRF2, oxidative phosphorylation and protein ubiquitination were activated by hydromethylthionine, presumably independent of its function as a tau aggregation inhibitor. Our results suggest that hydromethylthionine recovers cellular activity in both a tau-dependent and a tau-independent fashion that could lead to a wide-spread improvement of homeostatic function in the FTD brain.
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Affiliation(s)
- Karima Schwab
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (K.S.); (V.M.); (C.R.H.); (C.M.W.)
- Charité—Universitätsmedizin Berlin, Hessische Str. 3-4, 10115 Berlin, Germany; (M.M.); (F.T.)
| | - Valeria Melis
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (K.S.); (V.M.); (C.R.H.); (C.M.W.)
| | - Charles R. Harrington
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (K.S.); (V.M.); (C.R.H.); (C.M.W.)
- TauRx Therapeutics Ltd., 395 King Street, Aberdeen AB24 5RP, UK
| | - Claude M. Wischik
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (K.S.); (V.M.); (C.R.H.); (C.M.W.)
- TauRx Therapeutics Ltd., 395 King Street, Aberdeen AB24 5RP, UK
| | - Mandy Magbagbeolu
- Charité—Universitätsmedizin Berlin, Hessische Str. 3-4, 10115 Berlin, Germany; (M.M.); (F.T.)
| | - Franz Theuring
- Charité—Universitätsmedizin Berlin, Hessische Str. 3-4, 10115 Berlin, Germany; (M.M.); (F.T.)
| | - Gernot Riedel
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (K.S.); (V.M.); (C.R.H.); (C.M.W.)
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Wrigglesworth J, Ward P, Harding IH, Nilaweera D, Wu Z, Woods RL, Ryan J. Factors associated with brain ageing - a systematic review. BMC Neurol 2021; 21:312. [PMID: 34384369 PMCID: PMC8359541 DOI: 10.1186/s12883-021-02331-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background Brain age is a biomarker that predicts chronological age using neuroimaging features. Deviations of this predicted age from chronological age is considered a sign of age-related brain changes, or commonly referred to as brain ageing. The aim of this systematic review is to identify and synthesize the evidence for an association between lifestyle, health factors and diseases in adult populations, with brain ageing. Methods This systematic review was undertaken in accordance with the PRISMA guidelines. A systematic search of Embase and Medline was conducted to identify relevant articles using search terms relating to the prediction of age from neuroimaging data or brain ageing. The tables of two recent review papers on brain ageing were also examined to identify additional articles. Studies were limited to adult humans (aged 18 years and above), from clinical or general populations. Exposures and study design of all types were also considered eligible. Results A systematic search identified 52 studies, which examined brain ageing in clinical and community dwelling adults (mean age between 21 to 78 years, ~ 37% were female). Most research came from studies of individuals diagnosed with schizophrenia or Alzheimer’s disease, or healthy populations that were assessed cognitively. From these studies, psychiatric and neurologic diseases were most commonly associated with accelerated brain ageing, though not all studies drew the same conclusions. Evidence for all other exposures is nascent, and relatively inconsistent. Heterogenous methodologies, or methods of outcome ascertainment, were partly accountable. Conclusion This systematic review summarised the current evidence for an association between genetic, lifestyle, health, or diseases and brain ageing. Overall there is good evidence to suggest schizophrenia and Alzheimer’s disease are associated with accelerated brain ageing. Evidence for all other exposures was mixed or limited. This was mostly due to a lack of independent replication, and inconsistency across studies that were primarily cross sectional in nature. Future research efforts should focus on replicating current findings, using prospective datasets. Trial registration A copy of the review protocol can be accessed through PROSPERO, registration number CRD42020142817. Supplementary Information The online version contains supplementary material available at 10.1186/s12883-021-02331-4.
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Affiliation(s)
- Jo Wrigglesworth
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia
| | - Phillip Ward
- Monash Biomedical Imaging, Monash University, Clayton, Victoria, 3168, Australia.,Turner Institute for Brain and Mental Health, Monash University, Clayton, Victoria, 3800, Australia.,Australian Research Council Centre of Excellence for Integrative Brain Function, Clayton, Victoria , 3800, , Australia
| | - Ian H Harding
- Monash Biomedical Imaging, Monash University, Clayton, Victoria, 3168, Australia.,Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
| | - Dinuli Nilaweera
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia
| | - Zimu Wu
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia
| | - Robyn L Woods
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia
| | - Joanne Ryan
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia.
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Kim JH, Park SH, Han J, Ko PW, Kwon D, Suk K. Gliome database: a comprehensive web-based tool to access and analyze glia secretome data. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5879255. [PMID: 32743661 PMCID: PMC7396318 DOI: 10.1093/database/baaa057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/12/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022]
Abstract
Glial cells are phenotypically heterogeneous non-neuronal components of the central and peripheral nervous systems. These cells are endowed with diverse functions and molecular machineries to detect and regulate neuronal or their own activities by various secreted mediators, such as proteinaceous factors. In particular, glia-secreted proteins form a basis of a complex network of glia-neuron or glia-glia interactions in health and diseases. In recent years, the analysis and profiling of glial secretomes have raised new expectations for the diagnosis and treatment of neurological disorders due to the vital role of glia in numerous physiological or pathological processes of the nervous system. However, there is no online database of glia-secreted proteins available to facilitate glial research. Here, we developed a user-friendly 'Gliome' database (available at www.gliome.org), a web-based tool to access and analyze glia-secreted proteins. The database provides a vast collection of information on 3293 proteins that are released from glia of multiple species and have been reported to have differential functions under diverse experimental conditions. It contains a web-based interface with the following four key features regarding glia-secreted proteins: (i) fundamental information, such as signal peptide, SecretomeP value, functions and Gene Ontology category; (ii) differential expression patterns under distinct experimental conditions; (iii) disease association; and (iv) interacting proteins. In conclusion, the Gliome database is a comprehensive web-based tool to access and analyze glia-secretome data obtained from diverse experimental settings, whereby it may facilitate the integration of bioinformatics into glial research.
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Affiliation(s)
- Jong-Heon Kim
- Brain Science and Engineering Institute, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Su-Hyeong Park
- Department of Pharmacology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea.,D&P BIOTECH, 807 Hoguk-ro, Buk-gu, Daegu, 41404, Republic of Korea
| | - Jin Han
- Department of Pharmacology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Pan-Woo Ko
- Department of Neurology, Kyungpook National University Chilgok Hospital, 807 Hoguk-ro, Buk-gu, Daegu, 41404, Republic of Korea
| | - Dongseop Kwon
- School of Software Convergence, Myongji University, 34 Geobukgol-ro, Seodaemun-gu, Seoul, 03674, Republic of Korea
| | - Kyoungho Suk
- Brain Science and Engineering Institute, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea.,Department of Pharmacology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
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Abstract
PURPOSE OF REVIEW This review draws together the most recent findings in ALS biomarker research from biochemical, imaging and neurophysiology techniques. RECENT FINDINGS The potential of circulating RNA is highlighted, including new retrieval techniques. With ongoing genetic clinical trials, the need for pharmacodynamic biomarkers is essential. There is a strong case for neurofilament proteins being validated in ALS; their biomarker profile is discussed. Oxidative stress and neuroinflammation studies offer insight into disease mechanisms and offer good biomarker potential. Recent metabolic studies include investigation of lipid profiles, creatinine and ferritin. The potential of chitinase proteins as pharmacodynamic and prognostic biomarkers is highlighted. The role of tau and amyloidβ is debated, as evidenced by the articles presented here. Proteomic approaches provide unbiased discoveries of novel biomarkers, together with confirmation of previous findings. The use of imaging techniques is outlined to demonstrate selective atrophy, volume loss, muscle and tract involvement. In-vivo imaging is discussed with reference to histone deacetylase, oxidative stress, neuroinflammation and metabolic changes. New applications of electrophysiology demonstrate objective muscle biomarkers and brain network perturbations. SUMMARY The biomarker research field continues to provide insight into the disease. Multicentre collaborations are needed to validate these promising recent findings.
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Bibyk MJ, Campbell MJ, Hummon AB. Mass spectrometric investigations of caloric restriction mimetics. Proteomics 2021; 21:e2000121. [PMID: 33460282 PMCID: PMC8262777 DOI: 10.1002/pmic.202000121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/17/2020] [Accepted: 12/07/2020] [Indexed: 11/11/2022]
Abstract
Caloric restriction (CR) is an innovative therapy used in tumor tissue and tumor model studies to promote cell death and decrease cell viability. Caloric restriction mimetics (CRMs) are a class of drugs that induce CR and starvation conditions within a cell. When used simultaneously with other chemotherapy agents, the effects are synergistic and effective at promoting tumor cell death. In this review, we discuss CRMs and their potential as cancer therapeutics. Firstly, we establish an overview of CR and its impacts on healthy and tumor cells. CR and CRM drugs have shown to decrease age-related diseases and can act as an anti-cancer agent. As it can be challenging for an individual to diligently stick to a diet that would induce CR, CRMs are even more desirable. Then, we discuss the drug class by highlighting three CRMs: resveratrol, (-)-hydroxycitric acid, and rapamycin. These CRMs are commonly known for their dietary effects, but the underlying mechanisms that drive cellular metabolic and proteomic changes show promise as a cancer therapeutic. Lastly, we highlight the use of mass spectrometry and proteomic techniques on experiments utilizing CRM drugs to understand the cellular pathways impacted by this drug class, leading to a better understanding of the anti-cancer properties and potentials of CRM.
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Affiliation(s)
- Michael J. Bibyk
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
| | - Melanie J. Campbell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Amanda B. Hummon
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
- The Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
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Cheng F, De Luca A, Hogan AL, Rayner SL, Davidson JM, Watchon M, Stevens CH, Muñoz SS, Ooi L, Yerbury JJ, Don EK, Fifita JA, Villalva MD, Suddull H, Chapman TR, Hedl TJ, Walker AK, Yang S, Morsch M, Shi B, Blair IP, Laird AS, Chung RS, Lee A. Unbiased Label-Free Quantitative Proteomics of Cells Expressing Amyotrophic Lateral Sclerosis (ALS) Mutations in CCNF Reveals Activation of the Apoptosis Pathway: A Workflow to Screen Pathogenic Gene Mutations. Front Mol Neurosci 2021; 14:627740. [PMID: 33986643 PMCID: PMC8111008 DOI: 10.3389/fnmol.2021.627740] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
The past decade has seen a rapid acceleration in the discovery of new genetic causes of ALS, with more than 20 putative ALS-causing genes now cited. These genes encode proteins that cover a diverse range of molecular functions, including free radical scavenging (e.g., SOD1), regulation of RNA homeostasis (e.g., TDP-43 and FUS), and protein degradation through the ubiquitin-proteasome system (e.g., ubiquilin-2 and cyclin F) and autophagy (TBK1 and sequestosome-1/p62). It is likely that the various initial triggers of disease (either genetic, environmental and/or gene-environment interaction) must converge upon a common set of molecular pathways that underlie ALS pathogenesis. Given the complexity, it is not surprising that a catalog of molecular pathways and proteostasis dysfunctions have been linked to ALS. One of the challenges in ALS research is determining, at the early stage of discovery, whether a new gene mutation is indeed disease-specific, and if it is linked to signaling pathways that trigger neuronal cell death. We have established a proof-of-concept proteogenomic workflow to assess new gene mutations, using CCNF (cyclin F) as an example, in cell culture models to screen whether potential gene candidates fit the criteria of activating apoptosis. This can provide an informative and time-efficient output that can be extended further for validation in a variety of in vitro and in vivo models and/or for mechanistic studies. As a proof-of-concept, we expressed cyclin F mutations (K97R, S195R, S509P, R574Q, S621G) in HEK293 cells for label-free quantitative proteomics that bioinformatically predicted activation of the neuronal cell death pathways, which was validated by immunoblot analysis. Proteomic analysis of induced pluripotent stem cells (iPSCs) derived from patient fibroblasts bearing the S621G mutation showed the same activation of these pathways providing compelling evidence for these candidate gene mutations to be strong candidates for further validation and mechanistic studies (such as E3 enzymatic activity assays, protein-protein and protein-substrate studies, and neuronal apoptosis and aberrant branching measurements in zebrafish). Our proteogenomics approach has great utility and provides a relatively high-throughput screening platform to explore candidate gene mutations for their propensity to cause neuronal cell death, which will guide a researcher for further experimental studies.
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Affiliation(s)
- Flora Cheng
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Alana De Luca
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Alison L Hogan
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Stephanie L Rayner
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Jennilee M Davidson
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Maxinne Watchon
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Claire H Stevens
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW, Australia.,School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Sonia Sanz Muñoz
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW, Australia.,School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW, Australia.,School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW, Australia.,School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Emily K Don
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Jennifer A Fifita
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Maria D Villalva
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Hannah Suddull
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Tyler R Chapman
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Thomas J Hedl
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
| | - Adam K Walker
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia.,Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
| | - Shu Yang
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Marco Morsch
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Bingyang Shi
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Angela S Laird
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Roger S Chung
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Albert Lee
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia
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Kim JA, Vetrivel P, Kim SM, Ha SE, Kim HH, Bhosale PB, Heo JD, Lee WS, Senthil K, Kim GS. Quantitative Proteomics Analysis for the Identification of Differential Protein Expression in Calf Muscles between Young and Old SD Rats Using Mass Spectrometry. ACS OMEGA 2021; 6:7422-7433. [PMID: 33778255 PMCID: PMC7992086 DOI: 10.1021/acsomega.0c05821] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/28/2021] [Indexed: 05/04/2023]
Abstract
Aging is associated with loss of muscle mass and strength that leads to a condition termed sarcopenia. Impaired conditions, morbidity, and malnutrition are the factors of devaluation of muscle fibers in aged animals. Satellite cells play an important role in maintaining muscle homeostasis during tissue regeneration and repair. Proteomic profiling on the skeletal muscle tissues of different age group rats helps to determine the differentially expressed (DE) proteins, which may eventually lead to the development of biomarkers in treating the conditions of sarcopenia. In this study, nanoscale liquid chromatography coupled to tandem mass spectrometry (nano-LC-MS/MS) analysis was implemented in the calf tissues of young and old groups of rats. The mass spectrometry (MS) analysis revealed the presence of 335 differentially expressed proteins between the two different age conditions, among which those based on log-fold change 25 proteins were upregulated and 77 were downregulated. The protein-protein interaction network analysis revealed 18 upregulated proteins with three distinct interconnected networks and 57 downregulated proteins with two networks. Further, gene ontology (GO) enrichment analysis showed the biological process, cellular component, and molecular function of the differential proteins. Pathway enrichment analysis of the DE proteins identified nine significantly enriched pathways with a list of eight significant genes (Cryab, Hspb2, Acat1, Ak1, Adssl1, Anxa5, Gys1, Ogdh, Gc, and Adssl1). Quantification of significant genes by quantitative real-time polymerase chain reaction (qRT-PCR) confirmed the downregulation at the mRNA level. Western blot analysis of their protein expression showed concordant results on two candidate proteins (Ogdh and annexin 5) confirming their differential regulation between the two age groups of rats. Thus, these proteomic approaches on young and aged rats provide insights into the development of protein targets in the treatment of sarcopenia (muscle loss).
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Affiliation(s)
- Jin A. Kim
- Department
of Physical Therapy, International University
of Korea, Jinju 52833, Republic of Korea
| | - Preethi Vetrivel
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Seong Min Kim
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Sang Eun Ha
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Hun Hwan Kim
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Jeong Doo Heo
- Gyeongnam
Department of Environment Toxicology and Chemistry, Toxicity Screening
Research Center, Korea Institute of Toxicology, Munsan-eup, Jinju, Gyeongnam 52834, Republic of Korea
| | - Won Sup Lee
- Department
of Internal Medicine, Institute of Health Sciences, Gyeongsang National
University Hospital, Gyeongsang National
University School of Medicine, Jinju 660-702, Republic
of Korea
| | - Kalaiselvi Senthil
- Department
of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for
Women, Coimbatore 641043, India
| | - Gon Sup Kim
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
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Rayner SL, Cheng F, Hogan AL, Grima N, Yang S, Ke YD, Au CG, Morsch M, De Luca A, Davidson JM, Molloy MP, Shi B, Ittner LM, Blair I, Chung RS, Lee A. ALS/FTD-causing mutation in cyclin F causes the dysregulation of SFPQ. Hum Mol Genet 2021; 30:971-984. [PMID: 33729478 DOI: 10.1093/hmg/ddab073] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 03/03/2021] [Accepted: 02/14/2021] [Indexed: 12/12/2022] Open
Abstract
Previously, we identified missense mutations in CCNF that are causative of familial and sporadic amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Hallmark features of these diseases include the build-up of insoluble protein aggregates as well as the mislocalization of proteins such as transactive response DNA binding protein 43 kDa (TDP-43). In recent years, the dysregulation of SFPQ (splicing factor proline and glutamine rich) has also emerged as a pathological hallmark of ALS/FTD. CCNF encodes for the protein cyclin F, a substrate recognition component of an E3 ubiquitin ligase. We have previously shown that ALS/FTD-linked mutations in CCNF cause disruptions to overall protein homeostasis that leads to a build-up of K48-linked ubiquitylated proteins as well as defects in autophagic machinery. To investigate further processes that may be affected by cyclin F, we used a protein-proximity ligation method, known as Biotin Identification (BioID), standard immunoprecipitations and mass spectrometry to identify novel interaction partners of cyclin F and infer further process that may be affected by the ALS/FTD-causing mutation. Results demonstrate that cyclin F closely associates with proteins involved with RNA metabolism as well as a number of RNA-binding proteins previously linked to ALS/FTD, including SFPQ. Notably, the overexpression of cyclin F(S621G) led to the aggregation and altered subcellular distribution of SFPQ in human embryonic kidney (HEK293) cells, while leading to altered degradation in primary neurons. Overall, our data links ALS/FTD-causing mutations in CCNF to converging pathological features of ALS/FTD and provides a link between defective protein degradation systems and the pathological accumulation of a protein involved in RNA processing and metabolism.
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Affiliation(s)
- Stephanie L Rayner
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Flora Cheng
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Alison L Hogan
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Natalie Grima
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Shu Yang
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Yazi D Ke
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Dementia Research Centre, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Carol G Au
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Dementia Research Centre, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Marco Morsch
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Alana De Luca
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Jennilee M Davidson
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Mark P Molloy
- Faculty of Medicine and Health, Sydney School of Medicine, Royal North Shore Hospital, Pacific Hwy, St Leonards, Sydney, NSW 2065, Australia
| | - Bingyang Shi
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Lars M Ittner
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Dementia Research Centre, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Ian Blair
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Roger S Chung
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Albert Lee
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
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Montalbano M, McAllen S, Cascio FL, Sengupta U, Garcia S, Bhatt N, Ellsworth A, Heidelman EA, Johnson OD, Doskocil S, Kayed R. TDP-43 and Tau Oligomers in Alzheimer's Disease, Amyotrophic Lateral Sclerosis, and Frontotemporal Dementia. Neurobiol Dis 2020; 146:105130. [PMID: 33065281 PMCID: PMC7703712 DOI: 10.1016/j.nbd.2020.105130] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/25/2020] [Accepted: 10/06/2020] [Indexed: 12/22/2022] Open
Abstract
Proteinaceous aggregates are major hallmarks of several neurodegenerative diseases. Aggregates of post-translationally modified transactive response (TAR)-DNA binding protein 43 (TDP-43) in cytoplasmic inclusion bodies are characteristic features in frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). Recent studies have also reported TDP-43 aggregation in Alzheimer's disease (AD). TDP-43 is an RNA/DNA binding protein (RBP) mainly present in the nucleus. In addition to several RBPs, TDP-43 has also been reported in stress granules in FTD and ALS pathologies. Despite knowledge of cytoplasmic mislocalization of TDP-43, the cellular effects of TDP-43 aggregates and their cytotoxic mechanism(s) remain to be clarified. We hypothesize that TDP-43 forms oligomeric assemblies that associate with tau, another key protein involved in ALS and FTD. However, no prior studies have investigated the interactions between TDP-43 oligomers and tau. It is therefore important to thoroughly investigate the cross-seeding properties and cellular localization of both TDP-43 and tau oligomers in neurodegenerative diseases. Here, we demonstrate the effect of tau on the cellular localization of TDP-43 in WT and P301L tau-inducible cell models (iHEK) and in WT HEK-293 cells treated exogenously with soluble human recombinant tau oligomers (Exo-rTauO). We observed cytoplasmic TDP-43 accumulation o in the presence of tau in these cell models. We also studied the occurrence of TDP-43 oligomers in AD, ALS, and FTD human brain tissue using novel antibodies generated against TDP-43 oligomers as well as generic TDP-43 antibodies. Finally, we examined the cross-seeding property of AD, ALS, and FTD brain-derived TDP-43 oligomers (BDT43Os) on tau aggregation using biochemical and biophysical assays. Our results allow us to speculate that TDP-43/tau interactions might play a role in AD, ALS, and FTD.
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Affiliation(s)
- Mauro Montalbano
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA; Departments of Neurology, Neuroscience, and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Salome McAllen
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA; Departments of Neurology, Neuroscience, and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Filippa Lo Cascio
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA; Departments of Neurology, Neuroscience, and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Urmi Sengupta
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA; Departments of Neurology, Neuroscience, and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Stephanie Garcia
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA; Departments of Neurology, Neuroscience, and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Nemil Bhatt
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA; Departments of Neurology, Neuroscience, and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Anna Ellsworth
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA; Departments of Neurology, Neuroscience, and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Eric A Heidelman
- School of Medicine, University of Texas Medical Branch, UTMB, Galveston, TX 77555, USA
| | - Omar D Johnson
- School of Medicine, University of Texas Medical Branch, UTMB, Galveston, TX 77555, USA
| | - Samantha Doskocil
- Neuroscience Summer Undergraduate Research Program, NSURP Program 2018, University of Texas Medical Branch, UTMB, Galveston, TX 77555, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA; Departments of Neurology, Neuroscience, and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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Lachén-Montes M, Mendizuri N, Ausin K, Andrés-Benito P, Ferrer I, Fernández-Irigoyen J, Santamaría E. Amyotrophic Lateral Sclerosis Is Accompanied by Protein Derangements in the Olfactory Bulb-Tract Axis. Int J Mol Sci 2020; 21:ijms21218311. [PMID: 33167591 PMCID: PMC7664257 DOI: 10.3390/ijms21218311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal disease characterized by progressive muscle paralysis due to the degeneration of upper and lower motor neurons. Recent studies point out an involvement of the non-motor axis during disease progression. Despite smell impairment being considered a potential non-motor finding in ALS, the pathobiochemistry at the olfactory level remains unknown. Here, we applied an olfactory quantitative proteotyping approach to analyze the magnitude of the olfactory bulb (OB) proteostatic imbalance in ALS subjects (n = 12) with respect to controls (n = 8). Around 3% of the quantified OB proteome was differentially expressed, pinpointing aberrant protein expression involved in vesicle-mediated transport, macroautophagy, axon development and gliogenesis in ALS subjects. The overproduction of olfactory marker protein (OMP) points out an imbalance in the olfactory signal transduction in ALS. Accompanying the specific overexpression of glial fibrillary acidic protein (GFAP) and Bcl-xL in the olfactory tract (OT), a tangled disruption of signaling routes was evidenced across the OB–OT axis in ALS. In particular, the OB survival signaling dynamics clearly differ between ALS and frontotemporal lobar degeneration (FTLD), two faces of TDP-43 proteinopathy. To the best of our knowledge, this is the first report on high-throughput molecular characterization of the olfactory proteostasis in ALS.
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Affiliation(s)
- Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain; (M.L.-M.); (N.M.)
- Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain;
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Naroa Mendizuri
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain; (M.L.-M.); (N.M.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Karina Ausin
- Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain;
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Pol Andrés-Benito
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain; (P.A.-B.); (I.F.)
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, 28031 Madrid, Spain
- Department of Pathology and Experimental Therapeutics, University of Barcelona, 08007 Hospitalet de Llobregat, Spain
- Institute of Neurosciences, University of Barcelona, 08007 Barcelona, Spain
| | - Isidro Ferrer
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain; (P.A.-B.); (I.F.)
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, 28031 Madrid, Spain
- Department of Pathology and Experimental Therapeutics, University of Barcelona, 08007 Hospitalet de Llobregat, Spain
- Institute of Neurosciences, University of Barcelona, 08007 Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain; (M.L.-M.); (N.M.)
- Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain;
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- Correspondence: (J.F.I.); (E.S.); Tel.: +34-848-425-740 (E.S.); Fax: +34-848-422-200 (E.S.)
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain; (M.L.-M.); (N.M.)
- Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain;
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- Correspondence: (J.F.I.); (E.S.); Tel.: +34-848-425-740 (E.S.); Fax: +34-848-422-200 (E.S.)
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Morello G, Salomone S, D’Agata V, Conforti FL, Cavallaro S. From Multi-Omics Approaches to Precision Medicine in Amyotrophic Lateral Sclerosis. Front Neurosci 2020; 14:577755. [PMID: 33192262 PMCID: PMC7661549 DOI: 10.3389/fnins.2020.577755] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating and fatal neurodegenerative disorder, caused by the degeneration of upper and lower motor neurons for which there is no truly effective cure. The lack of successful treatments can be well explained by the complex and heterogeneous nature of ALS, with patients displaying widely distinct clinical features and progression patterns, and distinct molecular mechanisms underlying the phenotypic heterogeneity. Thus, stratifying ALS patients into consistent and clinically relevant subgroups can be of great value for the development of new precision diagnostics and targeted therapeutics for ALS patients. In the last years, the use and integration of high-throughput "omics" approaches have dramatically changed our thinking about ALS, improving our understanding of the complex molecular architecture of ALS, distinguishing distinct patient subtypes and providing a rational foundation for the discovery of biomarkers and new individualized treatments. In this review, we discuss the most significant contributions of omics technologies in unraveling the biological heterogeneity of ALS, highlighting how these approaches are revealing diagnostic, prognostic and therapeutic targets for future personalized interventions.
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Affiliation(s)
- Giovanna Morello
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Catania, Italy
- Section of Pharmacology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Salvatore Salomone
- Section of Pharmacology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Velia D’Agata
- Human Anatomy and Histology, University of Catania, Catania, Italy
| | | | - Sebastiano Cavallaro
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Catania, Italy
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Deng S, Liu J, Wu X, Lu W. Golgi Apparatus: A Potential Therapeutic Target for Autophagy-Associated Neurological Diseases. Front Cell Dev Biol 2020; 8:564975. [PMID: 33015059 PMCID: PMC7509445 DOI: 10.3389/fcell.2020.564975] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
Autophagy has dual effects in human diseases: appropriate autophagy may protect cells from stress, while excessive autophagy may cause cell death. Additionally, close interactions exist between autophagy and the Golgi. This review outlines recent advances regarding the role of the Golgi apparatus in autophagy. The signaling processes of autophagy are dependent on the normal function of the Golgi. Specifically, (i) autophagy-related protein 9 is mainly located in the Golgi and forms new autophagosomes in response to stressors; (ii) Golgi fragmentation is induced by Golgi-related proteins and accompanied with autophagy induction; and (iii) the endoplasmic reticulum-Golgi intermediate compartment and the reticular trans-Golgi network play essential roles in autophagosome formation to provide a template for lipidation of microtubule-associated protein 1A/1B-light chain 3 and induce further ubiquitination. Golgi-related proteins regulate formation of autophagosomes, and disrupted formation of autophagy can influence Golgi function. Notably, aberrant autophagy has been demonstrated to be implicated in neurological diseases. Thus, targeted therapies aimed at protecting the Golgi or regulating Golgi proteins might prevent or ameliorate autophagy-related neurological diseases. Further studies are needed to investigate the potential application of Golgi therapy in autophagy-based neurological diseases.
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Affiliation(s)
- Shuwen Deng
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jia Liu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiaomei Wu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Lu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
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Blasco H, Lanznaster D, Veyrat-Durebex C, Hergesheimer R, Vourch P, Maillot F, Andres CR, Pradat PF, Corcia P. Understanding and managing metabolic dysfunction in Amyotrophic Lateral Sclerosis. Expert Rev Neurother 2020; 20:907-919. [PMID: 32583696 DOI: 10.1080/14737175.2020.1788389] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Amyotrophic Lateral Sclerosis (ALS) is a fatal motor neuron disease that leads to death after a median survival of 36 months. The development of an effective treatment has proven to be extremely difficult due to the inadequate understanding of the pathogenesis of ALS. Energy metabolism is thoroughly involved in the disease based on the discoveries of hypermetabolism, lipid/glucose metabolism, the tricarboxylic acid (TCA) cycle, and mitochondrial impairment. AREA COVERED Many perturbed metabolites within these processes have been identified as promising therapeutic targets. However, the therapeutic strategies targeting these pathways have failed to produce clinically significant results. The authors present in this review the metabolic disturbances observed in ALS and the derived-therapeutics. EXPERT OPINION The authors suggest that this is due to the insufficient knowledge of the relationship between the metabolic targets and the type of ALS of the patient, depending on genetic and environmental factors. We must improve our understanding of the pathological mechanisms and pay attention to the subtle hidden effects of changing diet, for example, and to use this strategy in addition to other drugs or to use metabolism status to determine subgroups of patients.
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Affiliation(s)
- Helene Blasco
- Unité INSERM U1253, équipe, neurogénomique et physiopathologie neuronale, Université de Tours , Tours, France.,Laboratoire de Biochimie et Biologie Moléculaire, CHRU de Tours , Tours, France
| | - Debora Lanznaster
- Unité INSERM U1253, équipe, neurogénomique et physiopathologie neuronale, Université de Tours , Tours, France
| | - Charlotte Veyrat-Durebex
- Unité INSERM U1253, équipe, neurogénomique et physiopathologie neuronale, Université de Tours , Tours, France.,Laboratoire de Biochimie et Biologie Moléculaire, CHRU de Tours , Tours, France
| | - Rudolf Hergesheimer
- Unité INSERM U1253, équipe, neurogénomique et physiopathologie neuronale, Université de Tours , Tours, France
| | - Patrick Vourch
- Unité INSERM U1253, équipe, neurogénomique et physiopathologie neuronale, Université de Tours , Tours, France.,Laboratoire de Biochimie et Biologie Moléculaire, CHRU de Tours , Tours, France
| | - Francois Maillot
- Unité INSERM U1253, équipe, neurogénomique et physiopathologie neuronale, Université de Tours , Tours, France.,Service de Médecine Interne, CHRU de Tours , Tours, France
| | - Christian R Andres
- Unité INSERM U1253, équipe, neurogénomique et physiopathologie neuronale, Université de Tours , Tours, France.,Laboratoire de Biochimie et Biologie Moléculaire, CHRU de Tours , Tours, France
| | - Pierre-François Pradat
- Unité INSERM U1253, équipe, neurogénomique et physiopathologie neuronale, Université de Tours , Tours, France.,Biomedical Imaging Laboratory, CNRS, INSERM, Sorbonne University , Paris, France.,APHP, Department of Neurology, Paris ALS Center, Pitié Salpêtrière Hospital , Paris, France
| | - Phillipe Corcia
- Unité INSERM U1253, équipe, neurogénomique et physiopathologie neuronale, Université de Tours , Tours, France.,Service de Neurologie, CHRU de Tours , Tours, France
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Jun F, Peng Z, Zhang Y, Shi D. Quantitative Proteomic Profiling Identifies SOX8 as Novel Regulator of Drug Resistance in Gestational Trophoblastic Neoplasia. Front Oncol 2020; 10:557. [PMID: 32411596 PMCID: PMC7198745 DOI: 10.3389/fonc.2020.00557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/27/2020] [Indexed: 12/15/2022] Open
Abstract
The development of drug resistance remains one of the major challenges to current chemotherapeutic regimens in gestational trophoblastic neoplasia (GTN). Further understanding on the mechanisms of drug resistance would help to develop more effective therapy to treat GTN. Herein, tandem mass tag-based (TMT) quantitative proteomic technique was used to establish drug resistance-related proteomic profiles in chemoresistant GTN cell models (JEG3/MTX, JEG3/VP16, JEG3/5-Fu). In total, we identified 5,704 protein groups, among which 4,997 proteins were quantified in JEG3 and its chemoresistant sublines. Bioinformatics analysis revealed that multiple biological processes/molecular pathways/signaling networks were involved in the regulation of drug resistance in chemoresistant JEG3 sublines. SOX8 was upregulated in all the three chemoresistant sublines, and its function was further investigated. Knockdown of SOX8 significantly reduced cell viability, impaired soft agar clonogenesis, and increased caspase-3 activities after drug treatment in JEG3 chemoresistant sublines. In addition, over-expression of SOX8 promoted cell survival, enhanced soft agar clonogenesis, and attenuated caspase-3 activities after drug treatment in GTN cells. Importantly, SOX8 might be a potential regulator of reactive oxygen species (ROS) homeostasis, as SOX8 regulated the expression of antioxidant enzymes (GPX1, HMOX1) and reduced drug-induced ROS accumulation in GTN cell models. Collectively, SOX8 might promote drug resistance through attenuating the accumulation of ROS induced by chemotherapeutic drugs in GTN cells. Targeting SOX8 might be useful to sensitize GTN cells to chemotherapy.
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Affiliation(s)
- Fu Jun
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Zheng Peng
- Department of Gynecology and Obstetrics, Xiangya Hospital, Central South University, Changsha, China.,Gynecological Oncology Research and Engineering Center of Hunan Province, Changsha, China
| | - Yi Zhang
- Department of Gynecology and Obstetrics, Xiangya Hospital, Central South University, Changsha, China.,Gynecological Oncology Research and Engineering Center of Hunan Province, Changsha, China
| | - Dazun Shi
- Department of Gynecology and Obstetrics, Xiangya Hospital, Central South University, Changsha, China.,Gynecological Oncology Research and Engineering Center of Hunan Province, Changsha, China
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Development of disease-modifying drugs for frontotemporal dementia spectrum disorders. Nat Rev Neurol 2020; 16:213-228. [PMID: 32203398 DOI: 10.1038/s41582-020-0330-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2020] [Indexed: 02/06/2023]
Abstract
Frontotemporal dementia (FTD) encompasses a spectrum of clinical syndromes characterized by progressive executive, behavioural and language dysfunction. The various FTD spectrum disorders are associated with brain accumulation of different proteins: tau, the transactive response DNA binding protein of 43 kDa (TDP43), or fused in sarcoma (FUS) protein, Ewing sarcoma protein and TATA-binding protein-associated factor 15 (TAF15) (collectively known as FET proteins). Approximately 60% of patients with FTD have autosomal dominant mutations in C9orf72, GRN or MAPT genes. Currently available treatments are symptomatic and provide limited benefit. However, the increased understanding of FTD pathogenesis is driving the development of potential disease-modifying therapies. Most of these drugs target pathological tau - this category includes tau phosphorylation inhibitors, tau aggregation inhibitors, active and passive anti-tau immunotherapies, and MAPT-targeted antisense oligonucleotides. Some of these therapeutic approaches are being tested in phase II clinical trials. Pharmacological approaches that target the effects of GRN and C9orf72 mutations are also in development. Key results of large clinical trials will be available in a few years. However, clinical trials in FTD pose several challenges, and the development of specific brain imaging and molecular biomarkers could facilitate the recruitment of clinically homogenous groups to improve the chances of positive clinical trial results.
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Hamza GM, Bergo VB, Mamaev S, Wojchowski DM, Toran P, Worsfold CR, Castaldi MP, Silva JC. Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics. Int J Mol Sci 2020; 21:E2016. [PMID: 32188029 PMCID: PMC7139916 DOI: 10.3390/ijms21062016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/10/2020] [Accepted: 03/13/2020] [Indexed: 02/06/2023] Open
Abstract
The ability to quantitatively probe diverse panels of proteins and their post-translational modifications (PTMs) across multiple samples would aid a broad spectrum of biological, biochemical and pharmacological studies. We report a novel, microarray analytical technology that combines immuno-affinity capture with Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS), which is capable of supporting highly multiplexed, targeted proteomic assays. Termed "Affinity-Bead Assisted Mass Spectrometry" (Affi-BAMS), this LC-free technology enables development of highly specific and customizable assay panels for simultaneous profiling of multiple proteins and PTMs. While affinity beads have been used previously in combination with MS, the Affi-BAMS workflow uses enrichment on a single bead that contains one type of antibody, generally capturing a single analyte (protein or PTM) while having enough binding capacity to enable quantification within approximately 3 orders of magnitude. The multiplexing capability is achieved by combining Affi-BAMS beads with different protein specificities. To enable screening of bead-captured analytes by MS, we further developed a novel method of performing spatially localized elution of targets from individual beads arrayed on a microscope slide. The resulting arrays of micro spots contain highly concentrated analytes localized within 0.5 mm diameter spots that can be directly measured using MALDI MS. While both intact proteins and protein fragments can be monitored by Affi-BAMS, we initially focused on applying this technology for bottom-up proteomics to enable screening of hundreds of samples per day by combining the robust magnetic bead-based workflow with the high throughput nature of MALDI MS acquisition. To demonstrate the variety of applications and robustness of Affi-BAMS, several studies are presented that focus on the response of 4EBP1, RPS6, ERK1/ERK2, mTOR, Histone H3 and C-MET to stimuli including rapamycin, H2O2, EPO, SU11274, Staurosporine and Vorinostat.
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Affiliation(s)
- Ghaith M. Hamza
- Discovery Sciences, BioPharmaceutical R&D, AstraZeneca, Boston, MA 02451, USA; (G.M.H.); (M.P.C.)
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (D.M.W.); (P.T.)
| | - Vladislav B. Bergo
- Adeptrix Corporation, Beverly, MA 01915, USA; (V.B.B.); (S.M.); (C.R.W.)
| | - Sergey Mamaev
- Adeptrix Corporation, Beverly, MA 01915, USA; (V.B.B.); (S.M.); (C.R.W.)
| | - Don M. Wojchowski
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (D.M.W.); (P.T.)
| | - Paul Toran
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (D.M.W.); (P.T.)
| | | | - M. Paola Castaldi
- Discovery Sciences, BioPharmaceutical R&D, AstraZeneca, Boston, MA 02451, USA; (G.M.H.); (M.P.C.)
| | - Jeffrey C. Silva
- Adeptrix Corporation, Beverly, MA 01915, USA; (V.B.B.); (S.M.); (C.R.W.)
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