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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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Zhong Y, Tubbs JD, Leung PBM, Zhan N, Hui TCK, Ho KKY, Hung KSY, Cheung EFC, So HC, Lui SSY, Sham PC. Whole-exome sequencing in a Chinese sample provides preliminary evidence for the link between rare/low-frequency immune-related variants and early-onset schizophrenia. Asian J Psychiatr 2024; 96:104046. [PMID: 38663229 DOI: 10.1016/j.ajp.2024.104046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/06/2024] [Indexed: 06/01/2024]
Abstract
Rare and low-frequency variants contribute to schizophrenia (SCZ), and may influence its age-at-onset (AAO). We examined the association of rare or low-frequency deleterious coding variants in Chinese patients with SCZ. We collected DNA samples in 197 patients with SCZ spectrum disorder and 82 healthy controls (HC), and performed exome sequencing. The AAO variable was ascertained in the majority of SCZ participants for identify the early-onset (EOS, AAO<=18) and adult-onset (AOS, AAO>18) subgroups. We examined the overall association of rare/low-frequency, damaging variants in SCZ versus HC, EOS versus HC, and AOS versus HC at the gene and gene-set levels using Sequence Kernel Association Test. The quantitative rare-variant association test of AAO was conducted. Resampling was used to obtain empirical p-values and to control for family-wise error rate (FWER). In binary-trait association tests, we identified 5 potential candidate risk genes and 10 gene ontology biological processes (GOBP) terms, among which PADI2 reached FWER-adjusted significance. In quantitative rare-variant association tests, we found marginally significant correlations of AAO with alterations in 4 candidate risk genes, and 5 GOBP pathways. Together, the biological and functional profiles of these genes and gene sets supported the involvement of perturbations of neural systems in SCZ, and altered immune functions in EOS.
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Affiliation(s)
- Yuanxin Zhong
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Justin D Tubbs
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China; Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Perry B M Leung
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China; Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Na Zhan
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Tomy C K Hui
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Karen K Y Ho
- Department of General Adult Psychiatry, Castle Peak Hospital, Hong Kong Special Administrative Region of China
| | - Karen S Y Hung
- Department of General Adult Psychiatry, Castle Peak Hospital, Hong Kong Special Administrative Region of China
| | - Eric F C Cheung
- Department of General Adult Psychiatry, Castle Peak Hospital, Hong Kong Special Administrative Region of China
| | - Hon-Cheong So
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China; Department of Psychiatry, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China.
| | - Simon S Y Lui
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China.
| | - Pak C Sham
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China; Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China; State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong Special Administrative Region of China.
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Grada S, Mihu AG, Oatis DA, Marc CC, Chicea LM, Petrescu C, Lupu AM, Olariu TR. Seroprevalence and Associated Risk Factors of Toxoplasma gondii in Patients Diagnosed with Schizophrenia: A Case-Control Cross Sectional Study. Biomedicines 2024; 12:998. [PMID: 38790960 PMCID: PMC11117935 DOI: 10.3390/biomedicines12050998] [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: 04/06/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
The protozoan parasite, Toxoplasma gondii, has been linked to several psychiatric disorders, including schizophrenia. The aim of this study was to assess the prevalence of T. gondii IgG antibodies and risk factors associated with seroprevalence in patients diagnosed with schizophrenia. This seroepidemiological study assessed 196 participants, divided into two groups. The study group consisted of 98 schizophrenic patients and was matched with 98 healthy blood donors. A questionnaire was used to gather information regarding potential risk factors associated with T. gondii seroprevalence. Results revealed a higher seroprevalence of T. gondii IgG antibodies in schizophrenic patients (69.39%, 68/98) when compared to healthy controls (51.02%, 50/98) (OR: 2.18; 95% CI: 1.21-3.9; p = 0.01). Patients with schizophrenia who consumed raw or undercooked meat (80.65%, 25/31) (OR: 3.75; 95% CI: 1.25-11.21, p = 0.02) and those with a lower educational level (77.59%, 45/58) (OR: 3.5; 95% CI: 1.59-7.54, p = 0.002) presented increased T. gondii seropositivity rates versus their control counterparts. Our findings indicate a high T. gondii IgG seroprevalence in patients diagnosed with schizophrenia compared to healthy blood donors. Factors associated with T. gondii seroprevalence were consumption of raw or uncooked meat and a lower educational attainment. This study provided the first data regarding the potential risk factors for toxoplasmosis in Romanian patients diagnosed with schizophrenia and may serve as a foundation for future research and the development of preventive strategies.
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Affiliation(s)
- Sebastian Grada
- Discipline of Parasitology, Department of Infectious Disease, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (S.G.); (T.R.O.)
- Center for Diagnosis and Study of Parasitic Diseases, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Alin Gabriel Mihu
- “Aurel Ardelean” Institute of Life Sciences, Vasile Goldis Western University of Arad, 86 Rebreanu, 310414 Arad, Romania;
- Department of Biology and Life Sciences, Vasile Goldis Western University, 310300 Arad, Romania
- Patogen Preventia, 300124 Timisoara, Romania
| | - Daniela Adriana Oatis
- “Aurel Ardelean” Institute of Life Sciences, Vasile Goldis Western University of Arad, 86 Rebreanu, 310414 Arad, Romania;
- Department of Infectious Disease, Faculty of Medicine, Vasile Goldis Western University, 310300 Arad, Romania
| | - Constantin Catalin Marc
- Center for Diagnosis and Study of Parasitic Diseases, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
- Department of Biology and Life Sciences, Vasile Goldis Western University, 310300 Arad, Romania
| | - Liana Maria Chicea
- Department II Medical Clinic, “Victor Papilian” Faculty of Medicine, Lucian Blaga University of Sibiu, 550024 Sibiu, Romania;
- Internal Medicine Department, Academic Emergency Hospital, 550245 Sibiu, Romania
| | - Cristina Petrescu
- Discipline of Hygiene, Department of Microbiology, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Alina Maria Lupu
- Discipline of Parasitology, Department of Infectious Disease, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (S.G.); (T.R.O.)
- Center for Diagnosis and Study of Parasitic Diseases, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
- Patogen Preventia, 300124 Timisoara, Romania
- Clinical Laboratory, Institute of Cardiovascular Diseases, 300310 Timisoara, Romania
| | - Tudor Rares Olariu
- Discipline of Parasitology, Department of Infectious Disease, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (S.G.); (T.R.O.)
- Center for Diagnosis and Study of Parasitic Diseases, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
- Patogen Preventia, 300124 Timisoara, Romania
- Clinical Laboratory, Municipal Clinical Emergency Teaching Hospital, 300254 Timisoara, Romania
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Kéri S, Kelemen O. Motion and Form Perception in Childhood-Onset Schizophrenia. Pediatr Rep 2024; 16:88-99. [PMID: 38251318 PMCID: PMC10801474 DOI: 10.3390/pediatric16010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/26/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
(1) Background: Childhood-onset schizophrenia (COS) is a rare type of psychotic disorder characterized by delusions, hallucinations, grossly disorganized behavior, and poor psychosocial functioning. The etiology of COS is unknown, but neurodevelopmental factors are likely to play a critical role. A potential neurodevelopmental anomaly marker is the dorsal visual system dysfunction, which is implicated in motion perception, spatial functions, and attention. (2) Methods: To elucidate the role of the dorsal visual system in COS, we investigated 21 patients with COS and 21 control participants matched for age, sex, education, IQ, and parental socioeconomic status. Participants completed a motion and form coherence task, during which one assesses an individual's ability to detect the direction of motion within a field of moving elements or dots and to recognize a meaningful form or object from a set of fragmented or disconnected visual elements, respectively. (3) Results: The patients with COS were impaired in both visual tasks compared to the control participants, but the evidence for the deficit was more substantial for motion perception than for form perception (form: BF10 = 27.22; motion: BF10 = 6.97 × 106). (4) Conclusions: These results highlight the importance of dorsal visual stream vulnerability in COS, a potential marker of neurodevelopmental anomalies.
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Affiliation(s)
- Szabolcs Kéri
- Sztárai Institute, University of Tokaj, 3944 Sárospatak, Hungary
- Department of Physiology, Albert Szent-Györgyi Medical School, University of Szeged, 6720 Szeged, Hungary
| | - Oguz Kelemen
- Department of Behavioral Science, Albert Szent Györgyi Medical School, University of Szeged, 6720 Szeged, Hungary;
- Department of Psychiatry, Bács-Kiskun County Hospital, 6000 Kecskemét, Hungary
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Zhong Y, Tubbs JD, Leung PBM, Zhan N, Hui TCK, Ho KKY, Hung KSY, Cheung EFC, So HC, Lui SSY, Sham PC. Early-onset schizophrenia is associated with immune-related rare variants in a Chinese sample. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.21.23298115. [PMID: 38045317 PMCID: PMC10690336 DOI: 10.1101/2023.11.21.23298115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Background Rare variants are likely to contribute to schizophrenia (SCZ), given the large discrepancy between the heritability estimated from twin and GWAS studies. Furthermore, the nature of the rare-variant contribution to SCZ may vary with the "age-at-onset" (AAO), since early-onset has been suggested as being indicative of neurodevelopment deviance. Objective To examine the association of rare deleterious coding variants in early- and adult-onset SCZ in a Chinese sample. Method Exome sequencing was performed on DNA from 197 patients with SCZ spectrum disorder and 82 healthy controls (HC) of Chinese ancestry recruited in Hong Kong. We also gathered AAO information in the majority of SCZ samples. Patients were classified into early-onset (EOS, AAO<18) and adult-onset (AOS, AAO>18). We collapsed the rare variants to improve statistical power and examined the overall association of rare variants in SCZ versus HC, EOS versus HC, and AOS versus HC at the gene and gene-set levels by Sequence Kernel Association Test. The quantitative rare-variant association test of AAO was also conducted. We focused on variants which were predicted to have a medium or high impact on the protein-encoding process as defined by Ensembl. We applied a 100000-time permutation test to obtain empirical p-values, with significance threshold set at p < 1e -3 to control family-wise error rates. Moreover, we compared the burden of targeted rare variants in significant risk genes and gene sets in cases and controls. Results Based on several binary-trait association tests (i.e., SCZ vs HC, EOS vs HC and AOS vs HC), we identified 7 candidate risk genes and 20 gene ontology biological processes (GOBP) terms, which exhibited higher burdens in SCZ than in controls. Based on quantitative rare-variant association tests, we found that alterations in 5 candidate risk genes and 7 GOBP pathways were significantly correlated with AAO. Based on biological and functional profiles of the candidate risk genes and gene sets, our findings suggested that, in addition to the involvement of perturbations in neural systems in SCZ in general, altered immune responses may be specifically implicated in EOS. Conclusion Disrupted immune responses may exacerbate abnormal perturbations during neurodevelopment and trigger the early onset of SCZ. We provided evidence of rare variants increasing SCZ risk in the Chinese population.
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