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Jackson WS, Bauer S, Kaczmarczyk L, Magadi SS. Selective Vulnerability to Neurodegenerative Disease: Insights from Cell Type-Specific Translatome Studies. BIOLOGY 2024; 13:67. [PMID: 38392286 PMCID: PMC10886597 DOI: 10.3390/biology13020067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/24/2024]
Abstract
Neurodegenerative diseases (NDs) manifest a wide variety of clinical symptoms depending on the affected brain regions. Gaining insights into why certain regions are resistant while others are susceptible is vital for advancing therapeutic strategies. While gene expression changes offer clues about disease responses across brain regions, the mixture of cell types therein obscures experimental results. In recent years, methods that analyze the transcriptomes of individual cells (e.g., single-cell RNA sequencing or scRNAseq) have been widely used and have provided invaluable insights into specific cell types. Concurrently, transgene-based techniques that dissect cell type-specific translatomes (CSTs) in model systems, like RiboTag and bacTRAP, offer unique advantages but have received less attention. This review juxtaposes the merits and drawbacks of both methodologies, focusing on the use of CSTs in understanding conditions like amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), Alzheimer's disease (AD), and specific prion diseases like fatal familial insomnia (FFI), genetic Creutzfeldt-Jakob disease (gCJD), and acquired prion disease. We conclude by discussing the emerging trends observed across multiple diseases and emerging methods.
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Affiliation(s)
- Walker S Jackson
- Wallenberg Center for Molecular Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Susanne Bauer
- Wallenberg Center for Molecular Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Lech Kaczmarczyk
- Wallenberg Center for Molecular Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Srivathsa S Magadi
- Wallenberg Center for Molecular Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
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Reflections on Cerebellar Neuropathology in Classical Scrapie. Biomolecules 2021; 11:biom11050649. [PMID: 33924986 PMCID: PMC8146067 DOI: 10.3390/biom11050649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 01/15/2023] Open
Abstract
In this review, the most important neuropathological changes found in the cerebella of sheep affected by classical natural scrapie are discussed. This disease is the oldest known of a group of unconventional “infections” caused by toxic prions of different origins. Scrapie is currently considered a “transmissible spongiform encephalopathy” (due to its neuropathological characteristics and its transmission), which is the paradigm of prion pathologies as well as many encephalopathies (prion-like) that present aberrant deposits of insoluble protein with neurotoxic effects due to errors in their catabolization (“misfolding protein diseases”). The study of this disease is, therefore, of great relevance. Our work data from the authors’ previous publications as well as other research in the field. The four most important types of neuropathological changes are neuron abnormalities and loss, neurogliosis, tissue vacuolization (spongiosis) and pathological or abnormal prion protein (PrP) deposits/deposition. These findings were analyzed and compared to other neuropathologies. Various aspects related to the presentation and progression of the disease, the involution of different neuronal types, the neuroglial responses and the appearance of abnormal PrP deposits are discussed. The most important points of controversy in scrapie neuropathology are presented.
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Calbindin-D28k in the Brain Influences the Expression of Cellular Prion Protein. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018. [PMID: 29541346 PMCID: PMC5818940 DOI: 10.1155/2018/4670210] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The phenotypes of calbindin-D9k- (CaBP-9k-) knockout (KO), calbindin-D28k- (CaBP-28k-) KO, and CaBP-9k/28k-KO mice are similar to those of wild-type (WT) mice due to the compensatory action of other calcium transport proteins. In this study, we investigated the expression of cellular prion protein (PrPC) in the brains of CaBP-9k-, CaBP-28k-, and CaBP-9k/28k-KO mice. PrPC expression was significantly upregulated in the brain of all three strains. Levels of phospho-Akt (Ser473) and phospho-Bad (Ser136) were significantly elevated, but those of phospho-ERK and phospho-Bad (Ser155 and 112) were significantly reduced in the brains of CaBP-9k-, CaBP-28k-, and CaBP-9k/28k-KO mice. The expressions of the Bcl-2, p53, Bax, Cu/Zn-SOD, and Mn-SOD proteins were decreased in the brains of all KO mice. Expression of the endoplasmic reticulum marker protein BiP/GRP78 was decreased, and that of the CHOP protein was increased in the brains of those KO mice. To identify the roles of CaBP-28k, we transfected PC12 cells with siRNA for CaBP-28k and found increased expression of the PrPC protein compared to the levels in control cells. These results suggest that CaBP-28k expression may regulate PrPC protein expression and these mice may be vulnerable to the influence of prion disease.
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Marrone A, Re N, Storchi L. The Effects of Ca2+ Concentration and E200K Mutation on the Aggregation Propensity of PrPC: A Computational Study. PLoS One 2016; 11:e0168039. [PMID: 27959938 PMCID: PMC5154561 DOI: 10.1371/journal.pone.0168039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/23/2016] [Indexed: 11/18/2022] Open
Abstract
The propensity of cellular prion protein to aggregation is reputed essential for the initiation of the amyloid cascade that ultimately lead to the accumulation of neurotoxic aggregates. In this paper, we extended and applied an already reported computational workflow [Proteins 2015; 83: 1751–1765] to elucidate in details the aggregation propensity of PrP protein systems including wild type, wild type treated at different [Ca2+] and E200K mutant. The application of the computational procedure to two segments of PrPC, i.e. 125–228 and 120–231, allowed to emphasize how the inclusion of complete C-terminus and last portion (120–126) of the neurotoxic segment 106–126 may be crucial to unveil significant and unexpected interaction properties. Indeed, the anchoring of N-terminus on H2 domain detected in the wild type resulted to be disrupted upon either E200K mutation or Ca2+ binding, and to unbury hydrophobic spots on the PrPC surface. A peculiar dinuclear Ca2+ binding motif formed by the C-terminus and the S2-H2 loop was detected for [Ca2+] > 5 mM and showed similarities with binding motifs retraced in other protein systems, thus suggesting a possible functional meaning for its formation. Therefore, we potentiated the computational procedure by including a tool that clusterize the minima of molecular interaction fields of a proteinand delimit the regions of space with higher hydrophobic or higher hydrophilic character, hence, more likely involved in the self-assembly process. Plausible models for the self-assembly of either the E200K mutated or Ca2+-bound PrPC were sketched and discussed. The present investigation provides for structure-based information and new prompts that may represent a starting point for future experimental or computational works on the PrPC aggregation.
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Affiliation(s)
- Alessandro Marrone
- Università “G d’Annunzio” di Chieti-Pescara, Department of Pharmacy, Chieti, Italy
- * E-mail:
| | - Nazzareno Re
- Università “G d’Annunzio” di Chieti-Pescara, Department of Pharmacy, Chieti, Italy
| | - Loriano Storchi
- Università “G d’Annunzio” di Chieti-Pescara, Department of Pharmacy, Chieti, Italy
- Molecular Discovery Limited, Middlesex, London, United Kingdom
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Storchi L, Paciotti R, Re N, Marrone A. Investigation of the molecular similarity in closely related protein systems: The PrP case study. Proteins 2015; 83:1751-65. [PMID: 26018750 DOI: 10.1002/prot.24836] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/04/2015] [Accepted: 05/19/2015] [Indexed: 12/24/2022]
Abstract
The amyloid conversion is a massive detrimental modification affecting several proteins upon specific physical or chemical stimuli characterizing a plethora of diseases. In many cases, the amyloidogenic stimuli induce specific structural features to the protein conferring the propensity to misfold and form amyloid deposits. The investigation of mutants, structurally similar to their native isoform but inherently prone to amyloid conversion, may be a viable strategy to elucidate the structural features connected with amyloidogenesis. In this article, we present a computational protocol based on the combination of molecular dynamics (MD) and grid-based approaches suited for the pairwise comparison of closely related protein structures. This method was applied on the cellular prion protein (PrP(C)) as a case study and, in particular, addressed to the quali/quantification of the structural features conferred by either E200K mutations and treatment with CaCl(2), both able to induce the scrapie conversion of PrP. Several schemes of comparison were developed and applied to this case study, and made up suitable of application to other protein systems. At this purpose an in-house python codes has been implemented that, together with the parallelization of the GRID force fields program, will spread the applicability of the proposed computational procedure.
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Affiliation(s)
- Loriano Storchi
- Department of Pharmacy, Università "G D'annunzio" Di Chieti-Pescara, 66100, Italy.,Molecular Discovery Limited, Pinner, Middlesex, UK-Ha5 5NE, London, United Kingdom
| | - Roberto Paciotti
- Department of Pharmacy, Università "G D'annunzio" Di Chieti-Pescara, 66100, Italy
| | - Nazzareno Re
- Department of Pharmacy, Università "G D'annunzio" Di Chieti-Pescara, 66100, Italy
| | - Alessandro Marrone
- Department of Pharmacy, Università "G D'annunzio" Di Chieti-Pescara, 66100, Italy
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The use of transgenic mouse models to reveal the functions of Ca2+ buffer proteins in excitable cells. Biochim Biophys Acta Gen Subj 2012; 1820:1294-303. [DOI: 10.1016/j.bbagen.2011.11.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 11/14/2011] [Accepted: 11/15/2011] [Indexed: 12/19/2022]
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Basu U, Almeida LM, Dudas S, Graham CE, Czub S, Moore SS, Guan LL. Gene expression alterations in Rocky Mountain elk infected with chronic wasting disease. Prion 2012; 6:282-301. [PMID: 22561165 DOI: 10.4161/pri.19915] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Chronic wasting disease (CWD) is an invariably fatal neurologic disease that naturally infects mule deer, white tailed deer and elk. The understanding of CWD neurodegeneration at a molecular level is very limited. In this study, microarray analysis was performed to determine changes in the gene expression profiles in six different tissues including brain, midbrain, thalamus, spleen, RPLN and tonsil of CWD-infected elk in comparison to non-infected healthy elk, using 24,000 bovine specific oligo probes. In total, 329 genes were found to be differentially expressed (> 2.0-fold) between CWD negative and positive brain tissues, with 132 genes upregulated and 197 genes downregulated. There were 249 DE genes in the spleen (168 up- and 81 downregulated), 30 DE genes in the retropharyngeal lymph node (RPLN) (18 up- and 12 downregulated), and 55 DE genes in the tonsil (21 up- and 34 downregulated). Using Gene Ontology (GO), the DE genes were assigned to functional groups associated with cellular process, biological regulation, metabolic process, and regulation of biological process. For all brain tissues, the highest ranking networks for DE genes identified by Ingenuity Pathway Analysis (IPA) were associated with neurological disease, cell morphology, cellular assembly and organization. Quantitative real-time PCR (qRT-PCR) validated the expression of DE genes primarily involved in different regulatory pathways, including neuronal signaling and synapse function, calcium signaling, apoptosis and cell death and immune cell trafficking and inflammatory response. This is the first study to evaluate altered gene expression in multiple organs including brain from orally infected elk and the results will improve our understanding of CWD neurodegeneration at the molecular level.
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Affiliation(s)
- Urmila Basu
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB, Canada
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Almeida LM, Basu U, Khaniya B, Taniguchi M, Williams JL, Moore SS, Guan LL. Gene expression in the medulla following oral infection of cattle with bovine spongiform encephalopathy. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2011; 74:110-126. [PMID: 21218340 DOI: 10.1080/15287394.2011.529061] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The identification of variations in gene expression in response to bovine spongiform encephalopathy (BSE) may help to elucidate the mechanisms of neuropathology and prion replication and discover biomarkers for disease. In this study, genes that are differentially expressed in the caudal medulla tissues of animals infected with different doses of PrP(BSE) at 12 and 45 mo post infection were compared using array containing 24,000 oligonucleotide probes. Data analysis identified 966 differentially expressed (DE) genes between control and infected animals. Genes identified in at least two of four experiments (control versus 1-g infected animals at 12 and 45-mo; control versus 100-g infected animals at 12 and 45 mo) were considered to be the genes that may be associated with BSE disease. From the 176 DE genes associated with BSE, 84 had functions described in the Gene Ontology (GO) database. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of 14 genes revealed that prion infection may cause dysfunction of several different networks, including extracellular matrix (ECM), cell adhesion, neuroactive ligand-receptor interaction, complement and coagulation cascades, MAPK signaling, neurodegenerative disorder, SNARE interactions in vesicular transport, and the transforming growth factor (TGF) beta signaling pathways. The identification of DE genes will contribute to a better understanding of the molecular mechanisms of neuropathology in bovine species. Additional studies on larger number of animals are in progress in our laboratory to investigate the roles of these DE genes in pathogenesis of BSE.
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Affiliation(s)
- Luciane M Almeida
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
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Arif SH. A Ca(2+)-binding protein with numerous roles and uses: parvalbumin in molecular biology and physiology. Bioessays 2009; 31:410-21. [PMID: 19274659 DOI: 10.1002/bies.200800170] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Parvalbumins (PVs) are acidic, intracellular Ca(2+)-binding proteins of low molecular weight. They are associated with several Ca(2+)-mediated cellular activities and physiological processes. It has been suggested that PV might function as a "Ca2+ shuttle" transporting Ca2+ from troponin-C (TnC) to the sarcoplasmic reticulum (SR) Ca2+ pump during muscle relaxation. Thus, PV may contribute to the performance of rapid, phasic movements by accelerating the contraction-relaxation cycle of fast-twitch muscle fibers. Interestingly, PVs promote the generation of power stroke in fish by speeding up the rate of relaxation and thus provide impetus to attain maximal sustainable speeds. However, immunological monitoring of diverse tissues demonstrated that PVs are also present in non-muscle cells. The axoplasmic transport and various intracellular secretory mechanisms including the endocrine secretions seem to be controlled by the Ca2+ regulation machinery. Any defect in the Ca2+ handling apparatus may cause several clinical problems; for instance, PV deficiency alters the neuronal activity, a key mechanism leading to epileptic seizures. Moreover, atypical relaxation of the heart results in diastolic dysfunction, which is a major cause of heart failure predominantly among the aged people. PV may offer a unique potential to correct defective relaxation in energetically compromised failing hearts through PV gene transfer. Consequently, PV gene transfer may present a new therapeutic approach to correct cellular disturbances in Ca2+ signaling pathways of diseased organs. Hence, PVs appear to be amazingly useful candidate proteins regulating a variety of cellular functions through action on Ca2+ flux management.
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Affiliation(s)
- Syed Hasan Arif
- Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, UP, India.
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Jia Y, Pérez JC. Recombinant expression and affinity purification of snake venom gland parvalbumin in Escherichia coli. Comp Biochem Physiol A Mol Integr Physiol 2009; 153:303-8. [PMID: 19275943 DOI: 10.1016/j.cbpa.2009.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Revised: 02/25/2009] [Accepted: 03/03/2009] [Indexed: 10/21/2022]
Abstract
Parvalbumins (PV) are small, acidic, water soluble and calcium-binding proteins generally present in muscular and nervous tissues. In the present study, we identified and characterized a cDNA clone encoding PV, named AplPV, from a snake (Agkistrodon piscivorus leucostoma) venom gland cDNA library. AplPV belongs to EF-hand proteins with six alpha-helices constituting three EF-hand domains. The deduced amino acid sequence of AplPV is 91% and 68% identical to the previously characterized PVs of Boa constrictor and Cyprinus carpio, respectively. The full-length cDNA was subcloned into the expression vector pGEX and transformed into Escherichia coli (E.coli) to produce recombinant protein. The bacterially expressed GST-AplPV fusion protein was highly expressed, and effectively purified by Glutathione-Sepharose affinity chromatography. A high concentration of thrombin protease specifically cleaved and removed the GST tag from fusion protein, and further purified by Benzamidine column for removal of thrombin protease. As a result, the 12 kDa AplPV recombinant protein alone was purified. To investigate the tissue-specific biological occurrence of AplPV, a polyclonal antibody (anti-AplPV-antibody) was raised against GST-AplPV fusion protein in rabbit. Western blot analysis revealed that immunoreactive bands were exhibited in both recombinant protein and samples of venom glands, but not in any crude venom. This specific occurrence indicates a specialized function of AplPV in snake venom glands.
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Affiliation(s)
- Ying Jia
- Natural Toxins Research Center, College of Arts and Sciences, Texas A&M University-Kingsville, Kingsville, Texas 78363, USA
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