1
|
Gudra D, Valdovska A, Jonkus D, Kairisa D, Galina D, Ustinova M, Viksne K, Fridmanis D, Kalnina I. Genetic characterization of the Latvian local goat breed and genetic traits associated with somatic cell count. Animal 2024; 18:101154. [PMID: 38703755 DOI: 10.1016/j.animal.2024.101154] [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: 10/28/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 05/06/2024] Open
Abstract
The Latvian local goat (LVK) breed represents the only native domestic goat breed in Latvia, but its limited population places it within the endangered category. However, the LVK breed has not yet undergone a comprehensive genetic characterization. Therefore, we completed whole genome sequencing to reveal the genetic foundation of the LVK breed while identifying genetic traits linked to the somatic cell count (SCC) levels. The study included 40 genomes of LVK goats sequenced to acquire at least 35x or 10x coverage. A Principal component analysis, a genetic distance tree, and an admixture analysis showed LVK's similarity to some European breeds, such as Finnish Landrace, Alpine, and Saanen, which aligns with the breed's history. An analysis of genome-wide heterozygosity, nucleotide diversity, and LD analysis indicated that the LVK population exhibits substantial levels of genetic diversity. LVK genome was dominated by short runs of homozygosity (ROHs, ≤ 500 kb) with a median length of 25 kb. With FROH 2.49%, average inbreeding levels were low; however, FROH ranged broadly from 0.13 to 12.2%. With the exception of one pure-blood breeding buck exhibiting FROH of 9.3% and FSNP of 8.5%, animals with at least 66% LVK ancestry showed moderate or no inbreeding. Overall, this study demonstrated that the LVK goats can be differentiated from imported breeds, although the population has a complex genetic structure. We were able to identify potential genetic traits associated with SCC levels, although the kinship of the animals and the heterogenic substructure of the population might have largely influenced the association analysis. We identified 26 genetic variants associated with SCC levels, which included the potentially relevant SNP rs662053371 in the OSBPL8 gene, indicating a potential signal linked to lipid metabolism in goats. To conclude, these findings present valuable insight into the genetic structure of the LVK breed for the conservation of local genetic resources.
Collapse
Affiliation(s)
- D Gudra
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - A Valdovska
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, Helmana iela 8 K, LV-3004 Jelgava, Latvia; Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia.
| | - D Jonkus
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - D Kairisa
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - D Galina
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, Helmana iela 8 K, LV-3004 Jelgava, Latvia; Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - M Ustinova
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - K Viksne
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - D Fridmanis
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - I Kalnina
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| |
Collapse
|
2
|
Vacca V, Rossi C, Pieroni L, De Angelis F, Giacovazzo G, Cicalini I, Ciavardelli D, Pavone F, Coccurello R, Marinelli S. Sex-specific adipose tissue's dynamic role in metabolic and inflammatory response following peripheral nerve injury. iScience 2023; 26:107914. [PMID: 37817933 PMCID: PMC10561049 DOI: 10.1016/j.isci.2023.107914] [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: 05/02/2023] [Revised: 08/30/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
Epidemiological data and research highlight increased neuropathy and chronic pain prevalence among females, spanning metabolic and normometabolic contexts, including murine models. Prior findings demonstrated diverse immune and neuroimmune responses between genders in neuropathic pain (NeP), alongside distinct protein expression in sciatic nerves. This study unveils adipose tissue's (AT) role in sex-specific NeP responses after peripheral nerve injury. Metabolic assessments, metabolomics, energy expenditure evaluations, AT proteomic analyses, and adipokine mobilization depict distinct AT reactions to nerve damage. Females exhibit altered lipolysis, fatty acid oxidation, heightened energy expenditure, and augmented steroids secretion affecting glucose and insulin metabolism. Conversely, male neuropathy prompts glycolysis, reduced energy expenditure, and lowered unsaturated fatty acid levels. Males' AT promotes regenerative molecules, oxidative stress defense, and stimulates peroxisome proliferator-activated receptors (PPAR-γ) and adiponectin. This study underscores AT's pivotal role in regulating gender-specific inflammatory and metabolic responses to nerve injuries, shedding light on female NeP susceptibility determinants.
Collapse
Affiliation(s)
- Valentina Vacca
- National Council of Research - Institute of Biochemistry and Cell Biology, Monterotondo (RM), Italy
| | - Claudia Rossi
- Department of Innovative Technologies in Medicine and Dentistry, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
- Center for Advanced Studies and Technology (CAST), "G. D'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Luisa Pieroni
- Departmental Faculty of Medicine, UniCamillus - Saint Camillus International University of Health Sciences, 00131 Rome, Italy
- European Center for Brain Research/Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Federica De Angelis
- National Council of Research - Institute of Biochemistry and Cell Biology, Monterotondo (RM), Italy
- European Center for Brain Research/Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Giacomo Giacovazzo
- European Center for Brain Research/Santa Lucia Foundation IRCCS, 00143 Rome, Italy
- Università degli studi di Teramo (UniTE) - Facoltà di Medicina Veterinaria, 64100 Teramo, Italy
| | - Ilaria Cicalini
- Department of Innovative Technologies in Medicine and Dentistry, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
- Center for Advanced Studies and Technology (CAST), "G. D'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Domenico Ciavardelli
- Center for Advanced Studies and Technology (CAST), "G. D'Annunzio" University of Chieti-Pescara, Chieti, Italy
- School of Medicine, University Kore of Enna, Enna, Italy
| | - Flaminia Pavone
- National Council of Research - Institute of Biochemistry and Cell Biology, Monterotondo (RM), Italy
| | - Roberto Coccurello
- European Center for Brain Research/Santa Lucia Foundation IRCCS, 00143 Rome, Italy
- Institute for Complex Systems (ISC), National Council of Research (CNR), 00185 Rome, Italy
| | - Sara Marinelli
- National Council of Research - Institute of Biochemistry and Cell Biology, Monterotondo (RM), Italy
| |
Collapse
|
3
|
Castelo Rueda MP, Zanon A, Gilmozzi V, Lavdas AA, Raftopoulou A, Delcambre S, Del Greco M F, Klein C, Grünewald A, Pramstaller PP, Hicks AA, Pichler I. Molecular phenotypes of mitochondrial dysfunction in clinically non-manifesting heterozygous PRKN variant carriers. NPJ Parkinsons Dis 2023; 9:65. [PMID: 37072441 PMCID: PMC10113363 DOI: 10.1038/s41531-023-00499-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 03/23/2023] [Indexed: 04/20/2023] Open
Abstract
Homozygous or compound heterozygous (biallelic) variants in PRKN are causal for PD with highly penetrant symptom expression, while the much more common heterozygous variants may predispose to PD with highly reduced penetrance, through altered mitochondrial function. In the presence of pathogenic heterozygous variants, it is therefore important to test for mitochondrial alteration in cells derived from variant carriers to establish potential presymptomatic molecular markers. We generated lymphoblasts (LCLs) and human induced pluripotent stem cell (hiPSC)-derived neurons from non-manifesting heterozygous PRKN variant carriers and tested them for mitochondrial functionality. In LCLs, we detected hyperactive mitochondrial respiration, and, although milder compared to a biallelic PRKN-PD patient, hiPSC-derived neurons of non-manifesting heterozygous variant carriers also displayed several phenotypes of altered mitochondrial function. Overall, we identified molecular phenotypes that might be used to monitor heterozygous PRKN variant carriers during the prodromal phase. Such markers might also be useful to identify individuals at greater risk of eventual disease development and for testing potential mitochondrial function-based neuroprotective therapies before neurodegeneration advances.
Collapse
Affiliation(s)
- Maria Paulina Castelo Rueda
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
| | - Alessandra Zanon
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Valentina Gilmozzi
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Alexandros A Lavdas
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Athina Raftopoulou
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
- Department of Economics, University of Patras, Patras, Greece
| | - Sylvie Delcambre
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esche-sur-Alzette, Luxembourg
| | - Fabiola Del Greco M
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esche-sur-Alzette, Luxembourg
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
- Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| |
Collapse
|
4
|
Shafique A, Brughera M, Lualdi M, Alberio T. The Role of Rab Proteins in Mitophagy: Insights into Neurodegenerative Diseases. Int J Mol Sci 2023; 24:ijms24076268. [PMID: 37047239 PMCID: PMC10094445 DOI: 10.3390/ijms24076268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Mitochondrial dysfunction and vesicular trafficking alterations have been implicated in the pathogenesis of several neurodegenerative diseases. It has become clear that pathogenetic pathways leading to neurodegeneration are often interconnected. Indeed, growing evidence suggests a concerted contribution of impaired mitophagy and vesicles formation in the dysregulation of neuronal homeostasis, contributing to neuronal cell death. Among the molecular factors involved in the trafficking of vesicles, Ras analog in brain (Rab) proteins seem to play a central role in mitochondrial quality checking and disposal through both canonical PINK1/Parkin-mediated mitophagy and novel alternative pathways. In turn, the lack of proper elimination of dysfunctional mitochondria has emerged as a possible causative/early event in some neurodegenerative diseases. Here, we provide an overview of major findings in recent years highlighting the role of Rab proteins in dysfunctional mitochondrial dynamics and mitophagy, which are characteristic of neurodegenerative diseases. A further effort should be made in the coming years to clarify the sequential order of events and the molecular factors involved in the different processes. A clear cause–effect view of the pathogenetic pathways may help in understanding the molecular basis of neurodegeneration.
Collapse
|
5
|
Li C, Zhu Y, Liu W, Xiang W, He S, Hayashi T, Mizuno K, Hattori S, Fujisaki H, Ikejima T. Impaired mitophagy causes mitochondrial DNA leakage and STING activation in ultraviolet B-irradiated human keratinocytes HaCaT. Arch Biochem Biophys 2023; 737:109553. [PMID: 36842493 DOI: 10.1016/j.abb.2023.109553] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 02/27/2023]
Abstract
Ultraviolet B (UVB) irradiation causes skin damages. In this study, we focus on the involvement of mitochondrial disorders in UVB injury. Surprisingly, UVB irradiation increases the amounts of mitochondria in human immortalized keratinocytes HaCaT. However, further analysis shows that ATP levels decreased by UVB treatment in accordance with the collapse of mitochondrial membrane potential (MMP), suggesting an accumulation of dysfunctional mitochondria in UVB-irradiated HaCaT cells. Mitophagy, mainly mediated by PINK1 and parkin, is critical for the elimination of damaged mitochondria. Western blot results show that the levels of both PINK1 and parkin are decreased in UVB-irradiated cells, indicating the impairment of mitophagy. Silencing the expression of PINK1 or parkin by transfection of siRNA shows essentially the same damage to the cells as UVB irradiation does, including increased mitochondrial amount, decreased MMP and ATP production, and enhanced apoptosis, evidencing that repression of PINK1/parkin-mediated mitophagy plays a primary cause of UVB-caused cells damages. We previously found that HaCaT cells exposed to UVB showed activation of the cGAS-STING pathway and apoptosis. Here, silencing PINK1 or parkin also increases the protein levels of cGAS and STING, facilitates nuclear accumulation of NF-κB, and promotes the transcription of IFNβ, suggesting for the activation of STING pathway. Mitophagy impairment either by UVB-irradiation or by PINK1/parkin silencing initiates caspase-3-mediated apoptosis, as shown by the activation of caspase-3 and cleavage of PARP, as well as the increase of Hoechst-positive stained cells and Annexin V-positive cells. Further studies find that Bax-mediated permeabilization of mitochondrial membrane is critical for cell apoptosis, as well as the cytosolic leakage of mtDNA in UVB-treated cells, which results in cGAS-STING activation, and these processes are negatively-regulated by PINK1/parkin-mediated mitophagy. This study reveals the involvement of dysfunctional mitochondria due to impaired mitophagy in the damaging effect of UVB irradiation on HaCaT cells. Restoring the mitophagy has the potential to be developed as a new strategy to protect skin from UVB damages.
Collapse
Affiliation(s)
- Can Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China
| | - Yuying Zhu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China
| | - Weiwei Liu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China
| | - Wendie Xiang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China
| | - Sijun He
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China
| | - Toshihiko Hayashi
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China; Nippi Research Institute of Biomatrix, Toride, Ibaraki, 302-0017, Japan
| | - Kazunori Mizuno
- Nippi Research Institute of Biomatrix, Toride, Ibaraki, 302-0017, Japan
| | - Shunji Hattori
- Nippi Research Institute of Biomatrix, Toride, Ibaraki, 302-0017, Japan
| | - Hitomi Fujisaki
- Nippi Research Institute of Biomatrix, Toride, Ibaraki, 302-0017, Japan
| | - Takashi Ikejima
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning, China.
| |
Collapse
|
6
|
Li JJ, Wang YJ, Wang CM, Li YJ, Yang Q, Cai WY, Chen Y, Zhu XX. Shenlian extract decreases mitochondrial autophagy to regulate mitochondrial function in microvascular to alleviate coronary artery no-reflow. Phytother Res 2023; 37:1864-1882. [PMID: 36740450 DOI: 10.1002/ptr.7703] [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: 06/24/2022] [Revised: 10/31/2022] [Accepted: 11/19/2022] [Indexed: 02/07/2023]
Abstract
Shenlian (SL) extract has been proven to be effective in the prevention and treatment of atherosclerosis and myocardial ischemia. However, the function and molecular mechanisms of SL on coronary artery no-reflow have not been fully elucidated. This study was designed to investigate the contribution of SL extract in repressing excessive mitochondrial autophagy to protect the mitochondrial function and prevent coronary artery no-reflow. The improvement of SL on coronary artery no-reflow was observed in vivo experiments and the molecular mechanisms were further explored through vitro experiments. First, a coronary artery no-reflow rat model was built by ligating the left anterior descending coronary artery for 2 hr of ischemia, followed by 24 hr of reperfusion. Thioflavin S (6%, 1 ml/kg) was injected into the inferior vena cava to mark the no-reflow area. Transmission electron microscopy was performed to observe the cellular structure, mitochondrial structure, and mitochondrial autophagy of the endothelial cells. Immunofluorescence was used to observe the microvascular barrier function and microvascular inflammation. Cardiac microvascular endothelial cells (CMECs) were isolated from rats. The CMECs were deprived of oxygen-glucose deprivation (OGD) for 2 hr and reoxygenated for 4 hr to mimic the Myocardial ischemia-reperfusion (MI/R) injury-induced coronary artery no-reflow in vitro. Mitochondrial membrane potential was assessed using JC-1 dye. Intracellular adenosine triphosphate (ATP) levels were determined using an ATP assay kit. The cell total reactive oxygen species (ROS) levels and cell apoptosis rate were analyzed by flow cytometry. Colocalization of mitochondria and lysosomes indirectly indicated mitophagy. The representative ultrastructural morphologies of the autophagosomes and autolysosomes were also observed under transmission electron microscopy. The mitochondrial autophagy-related proteins (LC3II/I, P62, PINK, and Parkin) were analyzed using Western blot analysis. In vivo, results showed that, compared with the model group, SL could reduce the no-reflow area from 37.04 ± 9.67% to 18.31 ± 4.01% (1.08 g·kg-1 SL), 13.79 ± 4.77% (2.16 g·kg-1 SL), and 12.67 ± 2.47% (4.32 g·kg-1 SL). The extract also significantly increased the left ventricular ejection fraction (EF) and left ventricular fractional shortening (FS) (p < 0.05 or p < 0.01). The fluorescence intensities of VE-cadherin, which is a junctional protein that preserves the microvascular barrier function, decreased to ~74.05% of the baseline levels in the no-reflow rats and increased to 89.87%(1.08 g·kg-1 SL), 82.23% (2.16 g·kg-1 SL), and 89.69% (4.32 g·kg-1 SL) of the baseline levels by SL treatment. SL administration repressed the neutrophil migration into the myocardium. The oxygen-glucose deprivation/reoxygenation (OGD/R) model was induced in vitro to mimic microvascular ischemia-reperfusion injury. The impaired mitochondrial function after OGD/R injury led to decreased ATP production, calcium overload, the excessive opening of the Mitochondrial Permeability Transition Pore, decreased mitochondrial membrane potential, and reduced ROS scavenging ability (p < 0.05 or p < 0.01). The normal autophagosomes (double-membrane vacuoles with autophagic content) in the sham group were rarely found. The large morphology and autophagosomes were frequently observed in the model group. By contrast, SL inhibited the excessive activation of mitochondrial autophagy. The mitochondrial autophagy regulated by the PINK/Parkin pathway was excessively activated. However, administration of SL prevented the activation of the PINK/Parkin pathway and inhibited excessive mitochondrial autophagy to regulate mitochondrial dysfunction. Results also demonstrated that mitochondrial dysfunction stimulated endothelial cell barrier dysfunction, but Evans blue transmission was significantly decreased and transmembrane resistance was increased significantly by SL treatment (p < 0.05 or p < 0.01). Carbonylcyanide-3-chlorophenylhydrazone (CCCP) could activate the PINK/Parkin pathway. CCCP reversed the regulation of SL on mitochondrial autophagy and mitochondrial function. SL could alleviate coronary artery no-reflow by protecting the microvasculature by regulating mitochondrial function. The underlying mechanism was related to decreased mitochondrial autophagy by the PINK/Parkin pathway.
Collapse
Affiliation(s)
- Jing-Jing Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, China
| | - Ya-Jie Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, China
| | - Chun-Miao Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, China
| | - Yu-Jie Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, China
| | - Qing Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, China
| | - Wei-Yan Cai
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, China
| | - Ying Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, China
| | - Xiao-Xin Zhu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, China
| |
Collapse
|
7
|
Alberio T, Brughera M, Lualdi M. Current Insights on Neurodegeneration by the Italian Proteomics Community. Biomedicines 2022; 10:biomedicines10092297. [PMID: 36140397 PMCID: PMC9496271 DOI: 10.3390/biomedicines10092297] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/29/2022] [Accepted: 09/13/2022] [Indexed: 12/02/2022] Open
Abstract
The growing number of patients affected by neurodegenerative disorders represents a huge problem for healthcare systems, human society, and economics. In this context, omics strategies are crucial for the identification of molecular factors involved in disease pathobiology, and for the discovery of biomarkers that allow early diagnosis, patients’ stratification, and treatment response prediction. The integration of different omics data is a required step towards the goal of personalized medicine. The Italian proteomics community is actively developing and applying proteomics approaches to the study of neurodegenerative disorders; moreover, it is leading the mitochondria-focused initiative of the Human Proteome Project, which is particularly important given the central role of mitochondrial impairment in neurodegeneration. Here, we describe how Italian research groups in proteomics have contributed to the knowledge of many neurodegenerative diseases, through the elucidation of the pathobiology of these disorders, and through the discovery of disease biomarkers. In particular, we focus on the central role of post-translational modifications analysis, the implementation of network-based approaches in functional proteomics, the integration of different omics in a systems biology view, and the development of novel platforms for biomarker discovery for the high-throughput quantification of thousands of proteins at a time.
Collapse
|
8
|
Olesen MA, Villavicencio-Tejo F, Quintanilla RA. The use of fibroblasts as a valuable strategy for studying mitochondrial impairment in neurological disorders. Transl Neurodegener 2022; 11:36. [PMID: 35787292 PMCID: PMC9251940 DOI: 10.1186/s40035-022-00308-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/26/2022] [Indexed: 11/10/2022] Open
Abstract
Neurological disorders (NDs) are characterized by progressive neuronal dysfunction leading to synaptic failure, cognitive impairment, and motor injury. Among these diseases, Alzheimer's disease (AD), Parkinson's disease (PD), Huntington’s disease (HD), and amyotrophic lateral sclerosis (ALS) have raised a significant research interest. These disorders present common neuropathological signs, including neuronal dysfunction, protein accumulation, oxidative damage, and mitochondrial abnormalities. In this context, mitochondrial impairment is characterized by a deficiency in ATP production, excessive production of reactive oxygen species, calcium dysregulation, mitochondrial transport failure, and mitochondrial dynamics deficiencies. These defects in mitochondrial health could compromise the synaptic process, leading to early cognitive dysfunction observed in these NDs. Interestingly, skin fibroblasts from AD, PD, HD, and ALS patients have been suggested as a useful strategy to investigate and detect early mitochondrial abnormalities in these NDs. In this context, fibroblasts are considered a viable model for studying neurodegenerative changes due to their metabolic and biochemical relationships with neurons. Also, studies of our group and others have shown impairment of mitochondrial bioenergetics in fibroblasts from patients diagnosed with sporadic and genetic forms of AD, PD, HD, and ALS. Interestingly, these mitochondrial abnormalities have been observed in the brain tissues of patients suffering from the same pathologies. Therefore, fibroblasts represent a novel strategy to study the genesis and progression of mitochondrial dysfunction in AD, PD, HD, and ALS. This review discusses recent evidence that proposes fibroblasts as a potential target to study mitochondrial bioenergetics impairment in neurological disorders and consequently to search for new biomarkers of neurodegeneration.
Collapse
Affiliation(s)
- Margrethe A Olesen
- Laboratory of Neurodegenerative Diseases, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Francisca Villavicencio-Tejo
- Laboratory of Neurodegenerative Diseases, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Rodrigo A Quintanilla
- Laboratory of Neurodegenerative Diseases, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile.
| |
Collapse
|
9
|
Angelopoulou E, Bougea A, Papageorgiou SG, Villa C. Psychosis in Parkinson's Disease: A Lesson from Genetics. Genes (Basel) 2022; 13:genes13061099. [PMID: 35741861 PMCID: PMC9222985 DOI: 10.3390/genes13061099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 02/06/2023] Open
Abstract
Psychosis in Parkinson's disease (PDP) represents a common and debilitating condition that complicates Parkinson's disease (PD), mainly in the later stages. The spectrum of psychotic symptoms are heterogeneous, ranging from minor phenomena of mild illusions, passage hallucinations and sense of presence to severe psychosis consisting of visual hallucinations (and rarely, auditory and tactile or gustatory) and paranoid delusions. PDP is associated with increased caregiver stress, poorer quality of life for patients and carers, reduced survival and risk of institutionalization with a significant burden on the healthcare system. Although several risk factors for PDP development have been identified, such as aging, sleep disturbances, long history of PD, cognitive impairment, depression and visual disorders, the pathophysiology of psychosis in PD is complex and still insufficiently clarified. Additionally, several drugs used to treat PD can aggravate or even precipitate PDP. Herein, we reviewed and critically analyzed recent studies exploring the genetic architecture of psychosis in PD in order to further understand the pathophysiology of PDP, the risk factors as well as the most suitable therapeutic strategies.
Collapse
Affiliation(s)
- Efthalia Angelopoulou
- Department of Neurology, Eginition University Hospital, National and Kapodistrian University of Athens, 11528 Athens, Greece; (E.A.); (A.B.); (S.G.P.)
| | - Anastasia Bougea
- Department of Neurology, Eginition University Hospital, National and Kapodistrian University of Athens, 11528 Athens, Greece; (E.A.); (A.B.); (S.G.P.)
| | - Sokratis G. Papageorgiou
- Department of Neurology, Eginition University Hospital, National and Kapodistrian University of Athens, 11528 Athens, Greece; (E.A.); (A.B.); (S.G.P.)
| | - Chiara Villa
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- Correspondence: ; Tel.: +39-02-6448-8138
| |
Collapse
|
10
|
Parkin beyond Parkinson’s Disease—A Functional Meaning of Parkin Downregulation in TDP-43 Proteinopathies. Cells 2021; 10:cells10123389. [PMID: 34943897 PMCID: PMC8699658 DOI: 10.3390/cells10123389] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022] Open
Abstract
Parkin and PINK1 are key regulators of mitophagy, an autophagic pathway for selective elimination of dysfunctional mitochondria. To this date, parkin depletion has been associated with recessive early onset Parkinson’s disease (PD) caused by loss-of-function mutations in the PARK2 gene, while, in sporadic PD, the activity and abundance of this protein can be compromised by stress-related modifications. Intriguingly, research in recent years has shown that parkin depletion is not limited to PD but is also observed in other neurodegenerative diseases—especially those characterized by TDP-43 proteinopathies, such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Here, we discuss the evidence of parkin downregulation in these disease phenotypes, its emerging connections with TDP-43, and its possible functional implications.
Collapse
|
11
|
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.
Collapse
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.)
| |
Collapse
|
12
|
Choong CJ, Okuno T, Ikenaka K, Baba K, Hayakawa H, Koike M, Yokota M, Doi J, Kakuda K, Takeuchi T, Kuma A, Nakamura S, Nagai Y, Nagano S, Yoshimori T, Mochizuki H. Alternative mitochondrial quality control mediated by extracellular release. Autophagy 2020; 17:2962-2974. [PMID: 33218272 PMCID: PMC8525996 DOI: 10.1080/15548627.2020.1848130] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial quality control, which is crucial for maintaining cellular homeostasis, has been considered to be achieved exclusively through mitophagy. Here we report an alternative mitochondrial quality control pathway mediated by extracellular mitochondria release. By performing time-lapse confocal imaging on a stable cell line with fluorescent-labeled mitochondria, we observed release of mitochondria from cells into the extracellular space. Correlative light-electron microscopy revealed that majority of the extracellular mitochondria are in free form and, on rare occasions, some are enclosed in membrane-surrounded vesicles. Rotenone- and carbonyl cyanide m-chlorophenylhydrazone-induced mitochondrial quality impairment promotes the extracellular release of depolarized mitochondria. Overexpression of PRKN (parkin RBR E3 ubiquitin protein ligase), which has a pivotal role in mitophagy regulation, suppresses the extracellular mitochondria release under basal and stress condition, whereas its knockdown exacerbates it. Correspondingly, overexpression of PRKN-independent mitophagy regulators, BNIP3 (BCL2 interacting protein 3) and BNIP3L/NIX (BCL2 interacting protein 3 like), suppress extracellular mitochondria release. Autophagy-deficient cell lines show elevated extracellular mitochondria release. These results imply that perturbation of mitophagy pathway prompts mitochondria expulsion. Presence of mitochondrial protein can also be detected in mouse sera. Sera of PRKN-deficient mice contain higher level of mitochondrial protein compared to that of wild-type mice. More importantly, fibroblasts and cerebrospinal fluid samples from Parkinson disease patients carrying loss-of-function PRKN mutations show increased extracellular mitochondria compared to control subjects, providing evidence in a clinical context. Taken together, our findings suggest that extracellular mitochondria release is a comparable yet distinct quality control pathway from conventional mitophagy. Abbreviations: ACTB: actin beta; ANXA5: annexin A5; ATP5F1A/ATP5A: ATP synthase F1 subunit alpha; ATG: autophagy related; BNIP3: BCL2 interacting protein 3; BNIP3L/NIX: BCL2 interacting protein 3 like; CCCP: carbonyl cyanide m-chlorophenylhydrazone; CM: conditioned media; CSF: cerebrospinal fluid; DMSO: dimethyl sulfoxide; EM: electron microscopy; HSPD1/Hsp60: heat shock protein family D (Hsp60) member 1; KD: knockdown; KO: knockout; MAP1LC3A/LC3: microtubule associated protein 1 light chain 3 alpha; MT-CO1: mitochondrially encoded cytochrome c oxidase I; NDUFB8: NADH:ubiquinone oxidoreductase subunit B8; OE: overexpression; OPA1: OPA1 mitochondrial dynamin like GTPase; OXPHOS: oxidative phosphorylation; PBS: phosphate-buffered saline; PB: phosphate buffer; PD: Parkinson disease; PINK1: PTEN induced kinase 1; PRKN: parkin RBR E3 ubiquitin protein ligase; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SDHB: succinate dehydrogenase complex iron sulfur subunit B; TOMM20: translocase of outer mitochondrial membrane 20; TOMM40: translocase of outer mitochondrial membrane 40; UQCRC2: ubiquinol-cytochrome c reductase core protein 2; WT: wild-type
Collapse
Affiliation(s)
- Chi-Jing Choong
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Tatsusada Okuno
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kensuke Ikenaka
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kousuke Baba
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hideki Hayakawa
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Masato Koike
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mutsumi Yokota
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Junko Doi
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Keita Kakuda
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Toshihide Takeuchi
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Akiko Kuma
- Department of Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Shuhei Nakamura
- Department of Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshitaka Nagai
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Seiichi Nagano
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Tamotsu Yoshimori
- Department of Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| |
Collapse
|