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Karaglani M, Agorastos A, Panagopoulou M, Parlapani E, Athanasis P, Bitsios P, Tzitzikou K, Theodosiou T, Iliopoulos I, Bozikas VP, Chatzaki E. A novel blood-based epigenetic biosignature in first-episode schizophrenia patients through automated machine learning. Transl Psychiatry 2024; 14:257. [PMID: 38886359 PMCID: PMC11183091 DOI: 10.1038/s41398-024-02946-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
Schizophrenia (SCZ) is a chronic, severe, and complex psychiatric disorder that affects all aspects of personal functioning. While SCZ has a very strong biological component, there are still no objective diagnostic tests. Lately, special attention has been given to epigenetic biomarkers in SCZ. In this study, we introduce a three-step, automated machine learning (AutoML)-based, data-driven, biomarker discovery pipeline approach, using genome-wide DNA methylation datasets and laboratory validation, to deliver a highly performing, blood-based epigenetic biosignature of diagnostic clinical value in SCZ. Publicly available blood methylomes from SCZ patients and healthy individuals were analyzed via AutoML, to identify SCZ-specific biomarkers. The methylation of the identified genes was then analyzed by targeted qMSP assays in blood gDNA of 30 first-episode drug-naïve SCZ patients and 30 healthy controls (CTRL). Finally, AutoML was used to produce an optimized disease-specific biosignature based on patient methylation data combined with demographics. AutoML identified a SCZ-specific set of novel gene methylation biomarkers including IGF2BP1, CENPI, and PSME4. Functional analysis investigated correlations with SCZ pathology. Methylation levels of IGF2BP1 and PSME4, but not CENPI were found to differ, IGF2BP1 being higher and PSME4 lower in the SCZ group as compared to the CTRL group. Additional AutoML classification analysis of our experimental patient data led to a five-feature biosignature including all three genes, as well as age and sex, that discriminated SCZ patients from healthy individuals [AUC 0.755 (0.636, 0.862) and average precision 0.758 (0.690, 0.825)]. In conclusion, this three-step pipeline enabled the discovery of three novel genes and an epigenetic biosignature bearing potential value as promising SCZ blood-based diagnostics.
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Affiliation(s)
- Makrina Karaglani
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, GR-68132, Alexandroupolis, Greece
- Institute of Agri-food and Life Sciences, University Research & Innovation Center, H.M.U.R.I.C., Hellenic Mediterranean University, GR-71003, Crete, Greece
| | - Agorastos Agorastos
- Institute of Agri-food and Life Sciences, University Research & Innovation Center, H.M.U.R.I.C., Hellenic Mediterranean University, GR-71003, Crete, Greece
- II. Department of Psychiatry, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, GR-56430, Thessaloniki, Greece
| | - Maria Panagopoulou
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, GR-68132, Alexandroupolis, Greece
- Institute of Agri-food and Life Sciences, University Research & Innovation Center, H.M.U.R.I.C., Hellenic Mediterranean University, GR-71003, Crete, Greece
| | - Eleni Parlapani
- Ι. Department of Psychiatry, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, GR-56429, Thessaloniki, Greece
| | - Panagiotis Athanasis
- II. Department of Psychiatry, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, GR-56430, Thessaloniki, Greece
| | - Panagiotis Bitsios
- Department of Psychiatry and Behavioral Sciences, Faculty of Medicine, University of Crete, GR-71500, Heraklion, Greece
| | - Konstantina Tzitzikou
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, GR-68132, Alexandroupolis, Greece
| | - Theodosis Theodosiou
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, GR-68132, Alexandroupolis, Greece
- ABCureD P.C, GR-68131, Alexandroupolis, Greece
| | - Ioannis Iliopoulos
- Division of Basic Sciences, School of Medicine, University of Crete, GR-71003, Heraklion, Greece
| | - Vasilios-Panteleimon Bozikas
- II. Department of Psychiatry, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, GR-56430, Thessaloniki, Greece
| | - Ekaterini Chatzaki
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, GR-68132, Alexandroupolis, Greece.
- Institute of Agri-food and Life Sciences, University Research & Innovation Center, H.M.U.R.I.C., Hellenic Mediterranean University, GR-71003, Crete, Greece.
- ABCureD P.C, GR-68131, Alexandroupolis, Greece.
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 70013, Heraklion, Greece.
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Chataigner LMP, Thärichen L, Beugelink JW, Granneman JCM, Mokiem NJ, Snijder J, Förster F, Janssen BJC. Contactin 2 homophilic adhesion structure and conformational plasticity. Structure 2024; 32:60-73.e5. [PMID: 37992710 DOI: 10.1016/j.str.2023.10.012] [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: 06/21/2022] [Revised: 09/27/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023]
Abstract
The cell-surface attached glycoprotein contactin 2 is ubiquitously expressed in the nervous system and mediates homotypic cell-cell interactions to organize cell guidance, differentiation, and adhesion. Contactin 2 consists of six Ig and four fibronectin type III domains (FnIII) of which the first four Ig domains form a horseshoe structure important for homodimerization and oligomerization. Here we report the crystal structure of the six-domain contactin 2Ig1-6 and show that the Ig5-Ig6 combination is oriented away from the horseshoe with flexion in interdomain connections. Two distinct dimer states, through Ig1-Ig2 and Ig3-Ig6 interactions, together allow formation of larger oligomers. Combined size exclusion chromatography with multiangle light scattering (SEC-MALS), small-angle X-ray scattering (SAXS) and native MS analysis indicates contactin 2Ig1-6 oligomerizes in a glycan dependent manner. SAXS and negative-stain electron microscopy reveals inherent plasticity of the contactin 2 full-ectodomain. The combination of intermolecular binding sites and ectodomain plasticity explains how contactin 2 can function as a homotypic adhesion molecule in diverse intercellular environments.
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Affiliation(s)
- Lucas M P Chataigner
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3584 CG, the Netherlands
| | - Lena Thärichen
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3584 CG, the Netherlands
| | - J Wouter Beugelink
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3584 CG, the Netherlands
| | - Joke C M Granneman
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3584 CG, the Netherlands
| | - Nadia J Mokiem
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3584 CG, the Netherlands
| | - Bert J C Janssen
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3584 CG, the Netherlands.
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Qu M, Zhang Y, Gao Z, Zhang Z, Liu Y, Wan S, Wang X, Yu H, Zhang H, Liu Y, Schneider R, Meyer A, Lin Q. The genetic basis of the leafy seadragon's unique camouflage morphology and avenues for its efficient conservation derived from habitat modeling. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2317-6. [PMID: 37204606 DOI: 10.1007/s11427-022-2317-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/03/2023] [Indexed: 05/20/2023]
Abstract
The leafy seadragon certainly is among evolution's most "beautiful and wonderful" species aptly named for its extraordinary camouflage mimicking its coastal seaweed habitat. However, limited information is known about the genetic basis of its phenotypes and conspicuous camouflage. Here, we revealed genomic signatures of rapid evolution and positive selection in core genes related to its camouflage, which allowed us to predict population dynamics for this species. Comparative genomic analysis revealed that seadragons have the smallest olfactory repertoires among all ray-finned fishes, suggesting adaptations to the highly specialized habitat. Other positively selected and rapidly evolving genes that serve in bone development and coloration are highly expressed in the leaf-like appendages, supporting a recent adaptive shift in camouflage appendage formation. Knock-out of bmp6 results in dysplastic intermuscular bones with a significantly reduced number in zebrafish, implying its important function in bone formation. Global climate change-induced loss of seagrass beds now severely threatens the continued existence of this enigmatic species. The leafy seadragon has a historically small population size likely due to its specific habitat requirements that further exacerbate its vulnerability to climate change. Therefore, taking climate change-induced range shifts into account while developing future protection strategies.
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Affiliation(s)
- Meng Qu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingyi Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zexia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhixin Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- Global Ocean and Climate Research Center, South China Sea Institute of Oceanology, Guangzhou, 510301, China
| | - Yali Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiming Wan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Haiyan Yu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Yuhong Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Ralf Schneider
- Marine Evolutionary Ecology, Zoological Institute, Kiel University, 24118, Kiel, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany.
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China.
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Georgelou K, Saridaki EA, Karali K, Papagiannaki A, Charalampopoulos I, Gravanis A, Tzeranis DS. Microneurotrophin BNN27 Reduces Astrogliosis and Increases Density of Neurons and Implanted Neural Stem Cell-Derived Cells after Spinal Cord Injury. Biomedicines 2023; 11:biomedicines11041170. [PMID: 37189788 DOI: 10.3390/biomedicines11041170] [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: 03/04/2023] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Microneurotrophins, small-molecule mimetics of endogenous neurotrophins, have demonstrated significant therapeutic effects on various animal models of neurological diseases. Nevertheless, their effects on central nervous system injuries remain unknown. Herein, we evaluate the effects of microneurotrophin BNN27, an NGF analog, in the mouse dorsal column crush spinal cord injury (SCI) model. BNN27 was delivered systemically either by itself or combined with neural stem cell (NSC)-seeded collagen-based scaffold grafts, demonstrated recently to improve locomotion performance in the same SCI model. Data validate the ability of NSC-seeded grafts to enhance locomotion recovery, neuronal cell integration with surrounding tissues, axonal elongation and angiogenesis. Our findings also show that systemic administration of BNN27 significantly reduced astrogliosis and increased neuron density in mice SCI lesion sites at 12 weeks post injury. Furthermore, when BNN27 administration was combined with NSC-seeded PCS grafts, BNN27 increased the density of survived implanted NSC-derived cells, possibly addressing a major challenge of NSC-based SCI treatments. In conclusion, this study provides evidence that small-molecule mimetics of endogenous neurotrophins can contribute to effective combinatorial treatments for SCI, by simultaneously regulating key events of SCI and supporting grafted cell therapies in the lesion site.
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Affiliation(s)
- Konstantina Georgelou
- Department of Pharmacology, School of Medicine, University of Crete, 71003 Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 71003 Heraklion, Greece
| | | | - Kanelina Karali
- Department of Pharmacology, School of Medicine, University of Crete, 71003 Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 71003 Heraklion, Greece
| | - Argyri Papagiannaki
- Department of Pharmacology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Ioannis Charalampopoulos
- Department of Pharmacology, School of Medicine, University of Crete, 71003 Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 71003 Heraklion, Greece
| | - Achille Gravanis
- Department of Pharmacology, School of Medicine, University of Crete, 71003 Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 71003 Heraklion, Greece
| | - Dimitrios S Tzeranis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 71003 Heraklion, Greece
- Department of Mechanical and Manufacturing Engineering, University of Cyprus, Nicosia 2109, Cyprus
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Bizzoca A, Jirillo E, Flace P, Gennarini G. Overall Role of Contactins Expression in Neurodevelopmental Events and Contribution to Neurological Disorders. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2022; 22:CNSNDDT-EPUB-128217. [PMID: 36515028 DOI: 10.2174/1871527322666221212160048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/21/2022] [Accepted: 10/28/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Neurodegenerative disorders may depend upon a misregulation of the pathways which sustain neurodevelopmental control. In this context, this review article focuses on Friedreich ataxia (FA), a neurodegenerative disorder resulting from mutations within the gene encoding the Frataxin protein, which is involved in the control of mitochondrial function and oxidative metabolism. OBJECTIVE The specific aim of the present study concerns the FA molecular and cellular substrates, for which available transgenic mice models are proposed, including mutants undergoing misexpression of adhesive/morphoregulatory proteins, in particular belonging to the Contactin subset of the immunoglobulin supergene family. METHODS In both mutant and control mice, neurogenesis was explored by morphological/morphometric analysis through the expression of cell type-specific markers, including -tubulin, the Contactin-1 axonal adhesive glycoprotein, as well as the Glial Fibrillary Acidic Protein (GFAP). RESULTS Specific consequences were found to arise from the chosen misexpression approach, consisting of a neuronal developmental delay associated with glial upregulation. Protective effects against the arising phenotype resulted from antioxidants (essentially epigallocatechin gallate (EGCG)) administration, which was demonstrated through the profiles of neuronal (-tubulin and Contactin 1) as well as glial (GFAP) markers, in turn indicating the concomitant activation of neurodegeneration and neuro repair processes. The latter also implied activation of the Notch-1 signaling. CONCLUSION Overall, this study supports the significance of changes in morphoregulatory proteins expression in the FA pathogenesis and of antioxidant administration in counteracting it, which, in turn, allows to devise potential therapeutic approaches.
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Affiliation(s)
- Antonella Bizzoca
- Department of Basic Medical Sciences, Neurosciences, and Sensory Organs. Medical School. University of Bari. Piazza Giulio Cesare, 11. I-70124 Bari. Italy
| | - Emilio Jirillo
- Department of Basic Medical Sciences, Neurosciences, and Sensory Organs. Medical School. University of Bari. Piazza Giulio Cesare, 11. I-70124 Bari. Italy
| | - Paolo Flace
- Department of Basic Medical Sciences, Neurosciences, and Sensory Organs. Medical School. University of Bari. Piazza Giulio Cesare, 11. I-70124 Bari. Italy
| | - Gianfranco Gennarini
- Department of Basic Medical Sciences, Neurosciences, and Sensory Organs. Medical School. University of Bari. Piazza Giulio Cesare, 11. I-70124 Bari. Italy
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Prediction and Ranking of Biomarkers Using multiple UniReD. Int J Mol Sci 2022; 23:ijms231911112. [PMID: 36232413 PMCID: PMC9569535 DOI: 10.3390/ijms231911112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/06/2022] [Accepted: 09/17/2022] [Indexed: 11/23/2022] Open
Abstract
Protein–protein interactions (PPIs) are of key importance for understanding how cells and organisms function. Thus, in recent decades, many approaches have been developed for the identification and discovery of such interactions. These approaches addressed the problem of PPI identification either by an experimental point of view or by a computational one. Here, we present an updated version of UniReD, a computational prediction tool which takes advantage of biomedical literature aiming to extract documented, already published protein associations and predict undocumented ones. The usefulness of this computational tool has been previously evaluated by experimentally validating predicted interactions and by benchmarking it against public databases of experimentally validated PPIs. In its updated form, UniReD allows the user to provide a list of proteins of known implication in, e.g., a particular disease, as well as another list of proteins that are potentially associated with the proteins of the first list. UniReD then automatically analyzes both lists and ranks the proteins of the second list by their association with the proteins of the first list, thus serving as a potential biomarker discovery/validation tool.
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Kulchitsky VA, Zamaro AS, Shanko YG, Rubakhova VM. Mesenchymal Stem Cells and Activation of Reparative Processes in the Brain and Retina. J EVOL BIOCHEM PHYS+ 2021. [DOI: 10.1134/s0022093021050185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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