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Shah PS, Hughes EG, Sukhadia SS, Green DC, Houde BE, Tsongalis GJ, Tafe LJ. Validation and Implementation of a Somatic-Only Tumor Exome for Routine Clinical Application. J Mol Diagn 2024; 26:815-824. [PMID: 38972591 DOI: 10.1016/j.jmoldx.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 05/13/2024] [Accepted: 05/30/2024] [Indexed: 07/09/2024] Open
Abstract
Next-generation sequencing-based genomic testing is standard of care for tumor workflows. However, its application across different institutions continues to be challenging given the diversity of needs and resource availability among different institutions globally. Moreover, the use of a variety of different panels, including those from a few individual genes to those involving hundreds of genes, results in a relatively skewed distribution of care for patients. It is imperative to obtain a higher level of standardization without having to be restricted to specific kits or requiring repeated validations, which are generally expensive. We show the validation and clinical implementation of the DH-CancerSeq assay, a tumor-only whole-exome-based sequencing assay with integrated informatics, while providing similar input requirements, sensitivity, and specificity to a previously validated targeted gene panel and maintaining similar turnaround times for patient care.
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Affiliation(s)
- Parth S Shah
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire; Genome Informatics, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire; Dartmouth Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Edward G Hughes
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Shrey S Sukhadia
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire; Genome Informatics, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Donald C Green
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Brianna E Houde
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Gregory J Tsongalis
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire; Dartmouth Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Laura J Tafe
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire; Dartmouth Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire.
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2
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Ormond C, Ryan NM, Hedman AM, Cannon TD, Sullivan PF, Gill M, Hultman C, Heron EA, Johansson V, Corvin A. Whole genome sequencing study of identical twins discordant for psychosis. Transl Psychiatry 2024; 14:313. [PMID: 39080272 PMCID: PMC11289105 DOI: 10.1038/s41398-024-02982-0] [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: 11/23/2023] [Revised: 06/14/2024] [Accepted: 06/18/2024] [Indexed: 08/02/2024] Open
Abstract
Monozygotic (MZ) twins are often thought to have identical genomes, but recent work has shown that early post-zygotic events can result in a spectrum of DNA variants that are different between MZ twins. Such variants may explain phenotypic discordance and contribute to disease etiology. Here we performed whole genome sequencing in 17 pairs of MZ twins discordant for a psychotic disorder (schizophrenia, schizoaffective disorder or bipolar disorder). We examined various classes of rare variants that are discordant within a twin pair. We identified four genes harboring rare, predicted deleterious missense variants that were private to an affected individual in the cohort. Variants in FOXN1 and FLOT2 would have been categorized as damaging from recent schizophrenia and bipolar exome sequencing studies. Additionally, we identified four rare genic copy number variants (CNVs) private to an affected sample, two of which overlapped genes that have shown evidence for association with schizophrenia or bipolar disorder. One such CNV was a 3q29 duplication previously implicated in autism and developmental delay. We have performed the largest MZ twin study for discordant psychotic phenotypes to date. These findings warrant further investigation using other analytical approaches.
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Affiliation(s)
- Cathal Ormond
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Dublin, Ireland
| | - Niamh M Ryan
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Dublin, Ireland
| | - Anna M Hedman
- Department of Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Tyrone D Cannon
- Departments of Psychology and Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Patrick F Sullivan
- Department of Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Michael Gill
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Dublin, Ireland
| | - Christina Hultman
- Department of Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Elizabeth A Heron
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Dublin, Ireland
| | - Viktoria Johansson
- Department of Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences, Psychiatry Unit, Umeå University, Umeå, Sweden
| | - Aiden Corvin
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Dublin, Ireland.
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3
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Shi L, Ju P, Meng X, Wang Z, Yao L, Zheng M, Cheng X, Li J, Yu T, Xia Q, Yan J, Zhu C, Zhang X. Intricate role of intestinal microbe and metabolite in schizophrenia. BMC Psychiatry 2023; 23:856. [PMID: 37978477 PMCID: PMC10657011 DOI: 10.1186/s12888-023-05329-z] [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: 12/26/2022] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The brain-gut axis has gained increasing attention due to its contribution to the etiology of various central nervous system disorders. This study aims to elucidate the hypothesis that schizophrenia is associated with disturbances in intestinal microflora and imbalance in intestinal metabolites. By exploring the intricate relationship between the gut and the brain, with the goal of offering fresh perspectives and valuable insights into the potential contribution of intestinal microbial and metabolites dysbiosis to the etiology of schizophrenia. METHODS In this study, we used a 16S ribosomal RNA (16S rRNA) gene sequence-based approach and an untargeted liquid chromatography-mass spectrometry-based metabolic profiling approach to measure the gut microbiome and microbial metabolites from 44 healthy controls, 41 acute patients, and 39 remission patients, to evaluate whether microbial dysbiosis and microbial metabolite biomarkers were linked with the severity of schizophrenic symptoms. RESULTS Here, we identified 20 dominant disturbances in the gut microbial composition of patients compared with healthy controls, with 3 orders, 4 families, 9 genera, and 4 species. Several unique bacterial taxa associated with schizophrenia severity. Compared with healthy controls, 145 unusual microflora metabolites were detected in the acute and remission groups, which were mainly involved in environmental information processing, metabolism, organismal systems, and human diseases in the Kyoto encyclopedia of genes and genomes pathway. The Sankey diagram showed that 4 abnormal intestinal and 4 anomalous intestinal microbial metabolites were associated with psychiatric clinical symptoms. CONCLUSIONS These findings suggest a possible interactive influence of the gut microbiota and their metabolites on the pathophysiology of schizophrenia.
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Affiliation(s)
- Li Shi
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230022, China
- Anhui Clinical Center for mental and psychological diseases, Hefei Fourth People's Hospital, 316 Mei shan Road, Hefei, Anhui, 230000, China
- Anhui Mental Health Center, Hefei, 230000, China
| | - Peijun Ju
- Shanghai Mental Health Center, Shanghai key Laboratory of Psychotic Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201108, China
| | - Xiaojing Meng
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230022, China
- Anhui Clinical Center for mental and psychological diseases, Hefei Fourth People's Hospital, 316 Mei shan Road, Hefei, Anhui, 230000, China
- Anhui Mental Health Center, Hefei, 230000, China
| | | | - Lihui Yao
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230022, China
- Anhui Clinical Center for mental and psychological diseases, Hefei Fourth People's Hospital, 316 Mei shan Road, Hefei, Anhui, 230000, China
- Anhui Mental Health Center, Hefei, 230000, China
| | - Mingming Zheng
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230022, China
- Anhui Clinical Center for mental and psychological diseases, Hefei Fourth People's Hospital, 316 Mei shan Road, Hefei, Anhui, 230000, China
- Anhui Mental Health Center, Hefei, 230000, China
| | - Xialong Cheng
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230022, China
- Anhui Clinical Center for mental and psychological diseases, Hefei Fourth People's Hospital, 316 Mei shan Road, Hefei, Anhui, 230000, China
- Anhui Mental Health Center, Hefei, 230000, China
| | - Jingwei Li
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230022, China
- Anhui Clinical Center for mental and psychological diseases, Hefei Fourth People's Hospital, 316 Mei shan Road, Hefei, Anhui, 230000, China
- Anhui Mental Health Center, Hefei, 230000, China
| | - Tao Yu
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230022, China
- Anhui Clinical Center for mental and psychological diseases, Hefei Fourth People's Hospital, 316 Mei shan Road, Hefei, Anhui, 230000, China
- Anhui Mental Health Center, Hefei, 230000, China
| | - Qingrong Xia
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230022, China
- Anhui Clinical Center for mental and psychological diseases, Hefei Fourth People's Hospital, 316 Mei shan Road, Hefei, Anhui, 230000, China
- Anhui Mental Health Center, Hefei, 230000, China
| | - Junwei Yan
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230022, China
- Anhui Clinical Center for mental and psychological diseases, Hefei Fourth People's Hospital, 316 Mei shan Road, Hefei, Anhui, 230000, China
- Anhui Mental Health Center, Hefei, 230000, China
| | - Cuizhen Zhu
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230022, China.
- Anhui Clinical Center for mental and psychological diseases, Hefei Fourth People's Hospital, 316 Mei shan Road, Hefei, Anhui, 230000, China.
- Anhui Mental Health Center, Hefei, 230000, China.
| | - Xulai Zhang
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230022, China.
- Anhui Clinical Center for mental and psychological diseases, Hefei Fourth People's Hospital, 316 Mei shan Road, Hefei, Anhui, 230000, China.
- Anhui Mental Health Center, Hefei, 230000, China.
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Singh M, Agarwal V, Jindal D, Pancham P, Agarwal S, Mani S, Tiwari RK, Das K, Alghamdi BS, Abujamel TS, Ashraf GM, Jha SK. Recent Updates on Corticosteroid-Induced Neuropsychiatric Disorders and Theranostic Advancements through Gene Editing Tools. Diagnostics (Basel) 2023; 13:diagnostics13030337. [PMID: 36766442 PMCID: PMC9914305 DOI: 10.3390/diagnostics13030337] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/28/2022] [Accepted: 10/16/2022] [Indexed: 01/19/2023] Open
Abstract
The vast use of corticosteroids (CCSs) globally has led to an increase in CCS-induced neuropsychiatric disorders (NPDs), a very common manifestation in patients after CCS consumption. These neuropsychiatric disorders range from depression, insomnia, and bipolar disorders to panic attacks, overt psychosis, and many other cognitive changes in such subjects. Though their therapeutic importance in treating and improving many clinical symptoms overrides the complications that arise after their consumption, still, there has been an alarming rise in NPD cases in recent years, and they are seen as the greatest public health challenge globally; therefore, these potential side effects cannot be ignored. It has also been observed that many of the neuronal functional activities are regulated and controlled by genomic variants with epigenetic factors (DNA methylation, non-coding RNA, and histone modeling, etc.), and any alterations in these regulatory mechanisms affect normal cerebral development and functioning. This study explores a general overview of emerging concerns of CCS-induced NPDs, the effective molecular biology approaches that can revitalize NPD therapy in an extremely specialized, reliable, and effective manner, and the possible gene-editing-based therapeutic strategies to either prevent or cure NPDs in the future.
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Affiliation(s)
- Manisha Singh
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT), Noida 201309, India
- Correspondence: (M.S.); (S.K.J.)
| | - Vinayak Agarwal
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT), Noida 201309, India
| | - Divya Jindal
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT), Noida 201309, India
| | - Pranav Pancham
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT), Noida 201309, India
| | - Shriya Agarwal
- Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Shalini Mani
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT), Noida 201309, India
| | - Raj Kumar Tiwari
- School of Health Sciences, Pharmaceutical Sciences, UPES, Dehradun 248007, India
| | - Koushik Das
- School of Health Sciences, Pharmaceutical Sciences, UPES, Dehradun 248007, India
| | - Badrah S. Alghamdi
- Department of Physiology, Neuroscience Unit, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Pre-Clinical Research Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Tukri S. Abujamel
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ghulam Md. Ashraf
- Pre-Clinical Research Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, University City, Sharjah 27272, United Arab Emirates
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida 201310, India
- Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun 248007, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali 140413, India
- Correspondence: (M.S.); (S.K.J.)
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5
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Sheardown E, Mech AM, Petrazzini MEM, Leggieri A, Gidziela A, Hosseinian S, Sealy IM, Torres-Perez JV, Busch-Nentwich EM, Malanchini M, Brennan CH. Translational relevance of forward genetic screens in animal models for the study of psychiatric disease. Neurosci Biobehav Rev 2022; 135:104559. [PMID: 35124155 PMCID: PMC9016269 DOI: 10.1016/j.neubiorev.2022.104559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/10/2021] [Accepted: 02/01/2022] [Indexed: 12/16/2022]
Abstract
Psychiatric disorders represent a significant burden in our societies. Despite the convincing evidence pointing at gene and gene-environment interaction contributions, the role of genetics in the etiology of psychiatric disease is still poorly understood. Forward genetic screens in animal models have helped elucidate causal links. Here we discuss the application of mutagenesis-based forward genetic approaches in common animal model species: two invertebrates, nematodes (Caenorhabditis elegans) and fruit flies (Drosophila sp.); and two vertebrates, zebrafish (Danio rerio) and mice (Mus musculus), in relation to psychiatric disease. We also discuss the use of large scale genomic studies in human populations. Despite the advances using data from human populations, animal models coupled with next-generation sequencing strategies are still needed. Although with its own limitations, zebrafish possess characteristics that make them especially well-suited to forward genetic studies exploring the etiology of psychiatric disorders.
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Affiliation(s)
- Eva Sheardown
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Aleksandra M Mech
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | | | - Adele Leggieri
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Agnieszka Gidziela
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Saeedeh Hosseinian
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Ian M Sealy
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jose V Torres-Perez
- UK Dementia Research Institute at Imperial College London and Department of Brain Sciences, Imperial College London, 86 Wood Lane, London W12 0BZ, UK
| | - Elisabeth M Busch-Nentwich
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Margherita Malanchini
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Caroline H Brennan
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK.
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6
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Yan J, Chen Y, Ju P, Gao J, Zhang L, Li J, Wang K, Zhang J, Li C, Xia Q, Zhu C, Zhang X. Network Association of Biochemical and Inflammatory Abnormalities With Psychiatric Symptoms in First-Episode Schizophrenia Patients. Front Psychiatry 2022; 13:834539. [PMID: 35273531 PMCID: PMC8901486 DOI: 10.3389/fpsyt.2022.834539] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/25/2022] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Cardiovascular disease (CVD) risk factors such as dyslipidemia and systemic aberrant inflammatory processes may occur in patients with psychotic disorders, which may cause increased mortality. The interplay between immune and metabolic markers and its contribution to the clinical symptoms of schizophrenia (SCZ) remain unclear. This study aimed to examine the association of a series of inflammatory factors, plasma biochemical indicators, and SCZ clinical symptomatology with the severity of SCZ symptoms. METHODS A total of 115 participants, including 79 first-episode drug-naïve patients with SCZ and 36 healthy controls, were enrolled in this study. Semi-structured interviews were used to collect sociodemographic data, family history of SCZ, and medical and psychiatric history. The Brief Psychiatric Rating Scale (BPRS) and the Positive and Negative Syndrome Scale (PANSS) were administered by a clinical psychiatrist to evaluate the symptom severity of patients with SCZ. Plasma inflammatory cytokines were measured by a fully automated electrochemiluminescent immunoassay (Meso Scale Discovery). RESULTS Blood routine, biochemical, and inflammation cytokine test results showed that the levels of white blood cell count, neutrophil count, natrium, CRP, IL-8, IL-6, IL-13, and IL-16 significantly increased in the case group than in the healthy controls (p < 0.05), whereas levels of red blood cell count, hemoglobin concentration, mean corpuscular hemoglobin concentration, total protein, albumin, total bile acid, high-density lipoprotein (HDL), apolipoprotein A1, blood urea nitrogen, kalium and IL-15 were lower than in the healthy controls (p < 0.05). Correlation network analysis results shown that the natrium, HDL and red blood cell count were the top 3 factors closely to with BPRS and PANSS related clinical symptoms among of correlation network (degree = 4). ROC curve analysis explored the IL-16, IL-8, IL-13, IL-15, natrium, and HDL had highly sensitivity and specificity to the predictive validity and effectiveness for SCZ symptoms. CONCLUSION Our study revealed a complex interactive network correlation among the cardiovascular risk factors, biological immunity profiles, and psychotic symptoms in first-episode patients. Abnormal inflammatory factors and CVD risk factors had high sensitivity and specificity for predicting SCZ symptoms. Generally, our study provided novel information on the immune-related mechanisms involved in early CVD risk in patients with psychotic disorders.
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Affiliation(s)
- Junwei Yan
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Department of Medical Education and Research, Hefei Fourth People's Hospital, Hefei, China.,Department of Medical Education and Research, Anhui Mental Health Center, Hefei, China.,Department of Medical Education and Research, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, China
| | - Yuanyuan Chen
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Department of Medical Education and Research, Hefei Fourth People's Hospital, Hefei, China.,Department of Medical Education and Research, Anhui Mental Health Center, Hefei, China.,Department of Medical Education and Research, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, China
| | - Peijun Ju
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai, China.,Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Psychiatry, Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Jianliang Gao
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Department of Medical Education and Research, Hefei Fourth People's Hospital, Hefei, China.,Department of Medical Education and Research, Anhui Mental Health Center, Hefei, China.,Department of Medical Education and Research, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, China
| | - Loufeng Zhang
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Department of Medical Education and Research, Hefei Fourth People's Hospital, Hefei, China.,Department of Medical Education and Research, Anhui Mental Health Center, Hefei, China.,Department of Medical Education and Research, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, China
| | - Jingwei Li
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Department of Medical Education and Research, Hefei Fourth People's Hospital, Hefei, China.,Department of Medical Education and Research, Anhui Mental Health Center, Hefei, China.,Department of Medical Education and Research, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, China
| | - Keming Wang
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Department of Medical Education and Research, Hefei Fourth People's Hospital, Hefei, China.,Department of Medical Education and Research, Anhui Mental Health Center, Hefei, China.,Department of Medical Education and Research, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, China
| | - Jie Zhang
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Department of Medical Education and Research, Hefei Fourth People's Hospital, Hefei, China.,Department of Medical Education and Research, Anhui Mental Health Center, Hefei, China.,Department of Medical Education and Research, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, China
| | - Chao Li
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Department of Medical Education and Research, Hefei Fourth People's Hospital, Hefei, China.,Department of Medical Education and Research, Anhui Mental Health Center, Hefei, China.,Department of Medical Education and Research, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, China
| | - Qingrong Xia
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Department of Medical Education and Research, Hefei Fourth People's Hospital, Hefei, China.,Department of Medical Education and Research, Anhui Mental Health Center, Hefei, China.,Department of Medical Education and Research, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, China
| | - Cuizhen Zhu
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Department of Medical Education and Research, Hefei Fourth People's Hospital, Hefei, China.,Department of Medical Education and Research, Anhui Mental Health Center, Hefei, China.,Department of Medical Education and Research, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, China
| | - Xulai Zhang
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Department of Medical Education and Research, Hefei Fourth People's Hospital, Hefei, China.,Department of Medical Education and Research, Anhui Mental Health Center, Hefei, China.,Department of Medical Education and Research, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, China
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7
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Systems biology analysis of human genomes points to key pathways conferring spina bifida risk. Proc Natl Acad Sci U S A 2021; 118:2106844118. [PMID: 34916285 PMCID: PMC8713748 DOI: 10.1073/pnas.2106844118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2021] [Indexed: 12/15/2022] Open
Abstract
Genetic investigations of most structural birth defects, including spina bifida (SB), congenital heart disease, and craniofacial anomalies, have been underpowered for genome-wide association studies because of their rarity, genetic heterogeneity, incomplete penetrance, and environmental influences. Our systems biology strategy to investigate SB predisposition controls for population stratification and avoids much of the bias inherent in candidate gene searches that are pervasive in the field. We examine both protein coding and noncoding regions of whole genomes to analyze sequence variants, collapsed by gene or regulatory region, and apply machine learning, gene enrichment, and pathway analyses to elucidate molecular pathways and genes contributing to human SB. Spina bifida (SB) is a debilitating birth defect caused by multiple gene and environment interactions. Though SB shows non-Mendelian inheritance, genetic factors contribute to an estimated 70% of cases. Nevertheless, identifying human mutations conferring SB risk is challenging due to its relative rarity, genetic heterogeneity, incomplete penetrance, and environmental influences that hamper genome-wide association studies approaches to untargeted discovery. Thus, SB genetic studies may suffer from population substructure and/or selection bias introduced by typical candidate gene searches. We report a population based, ancestry-matched whole-genome sequence analysis of SB genetic predisposition using a systems biology strategy to interrogate 298 case-control subject genomes (149 pairs). Genes that were enriched in likely gene disrupting (LGD), rare protein-coding variants were subjected to machine learning analysis to identify genes in which LGD variants occur with a different frequency in cases versus controls and so discriminate between these groups. Those genes with high discriminatory potential for SB significantly enriched pathways pertaining to carbon metabolism, inflammation, innate immunity, cytoskeletal regulation, and essential transcriptional regulation consistent with their having impact on the pathogenesis of human SB. Additionally, an interrogation of conserved noncoding sequences identified robust variant enrichment in regulatory regions of several transcription factors critical to embryonic development. This genome-wide perspective offers an effective approach to the interrogation of coding and noncoding sequence variant contributions to rare complex genetic disorders.
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8
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Zhu C, Zheng M, Ali U, Xia Q, Wang Z, Chenlong, Yao L, Chen Y, Yan J, Wang K, Chen J, Zhang X. Association Between Abundance of Haemophilus in the Gut Microbiota and Negative Symptoms of Schizophrenia. Front Psychiatry 2021; 12:685910. [PMID: 34393849 PMCID: PMC8362742 DOI: 10.3389/fpsyt.2021.685910] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/28/2021] [Indexed: 12/31/2022] Open
Abstract
Increasing evidence indicates an interaction between dysbiosis of the microbiota and the pathogenesis of schizophrenia. However, limited information is available on the specific microbial communities associated with symptoms of schizophrenia. Therefore, this study aimed to investigate gut microbiota dysbiosis and its relationship with psychopathologies in schizophrenia. We recruited 126 participants and divided them into three groups according to the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition, criteria-acute group (patients with acute schizophrenia), remission group (patients with schizophrenia in remission), and control group (healthy controls). Psychotic symptoms were evaluated using the Positive and Negative Syndrome Scale. Microbiota compositions, diversity and community structure were evaluated using 16S rRNA sequencing. Pearson's correlation analysis was used to evaluate the association between bacterial taxa and psychotic symptoms. The beta-diversity of microbiota composition in the acute group was distinct from that in the remission and control groups (PC1 = 21.11% vs. PC2 = 12.86%, P = 0.021). Furthermore, Pearson's correlation analysis revealed that abundance of Haemophilus was positively correlated with negative psychiatric symptoms (r = 0.303, P = 0.021), while abundance of Coprococcus was negatively correlated with negative psychiatric symptoms (r = -0.285, P = 0.025). Moreover, abundance of Haemophilus was positively correlated with cognition (r = 0.428, P = 0.009), excitement (r = 0.266, P = 0.037), and depression (r = 0.295, P = 0.020). The study findings suggest that alterations in certain gut microbiota may interfere with psychological symptoms in schizophrenia. Our results provide evidence that may help in the development of therapeutic strategies using microbial-based targets. The data that support the findings of this study have been deposited in the NCBI (https://submit.ncbi.nlm.nih.gov/) with accession number SUB9453991.
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Affiliation(s)
- Cuizhen Zhu
- Department of Science and Education, Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Anhui Clinical Center for Mental and Psychological Diseases, Hefei Fourth People's Hospital, Hefei, China.,Anhui Mental Health Center, Hefei, China
| | - Mingming Zheng
- Department of Science and Education, Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Anhui Clinical Center for Mental and Psychological Diseases, Hefei Fourth People's Hospital, Hefei, China.,Anhui Mental Health Center, Hefei, China
| | - Usman Ali
- Shanghai key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingrong Xia
- Department of Science and Education, Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Anhui Clinical Center for Mental and Psychological Diseases, Hefei Fourth People's Hospital, Hefei, China.,Anhui Mental Health Center, Hefei, China
| | - Zhongxian Wang
- Department of Science and Education, Affiliated Psychological Hospital of Anhui Medical University, Hefei, China
| | - Chenlong
- Department of Science and Education, Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Anhui Clinical Center for Mental and Psychological Diseases, Hefei Fourth People's Hospital, Hefei, China.,Anhui Mental Health Center, Hefei, China
| | - Lihui Yao
- Department of Science and Education, Affiliated Psychological Hospital of Anhui Medical University, Hefei, China
| | - Yuanyuan Chen
- Department of Science and Education, Affiliated Psychological Hospital of Anhui Medical University, Hefei, China
| | - Junwei Yan
- Department of Science and Education, Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Anhui Clinical Center for Mental and Psychological Diseases, Hefei Fourth People's Hospital, Hefei, China.,Anhui Mental Health Center, Hefei, China
| | - Keming Wang
- Department of Science and Education, Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Anhui Clinical Center for Mental and Psychological Diseases, Hefei Fourth People's Hospital, Hefei, China.,Anhui Mental Health Center, Hefei, China
| | - Jinghong Chen
- Shanghai key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xulai Zhang
- Department of Science and Education, Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,Anhui Clinical Center for Mental and Psychological Diseases, Hefei Fourth People's Hospital, Hefei, China.,Anhui Mental Health Center, Hefei, China
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9
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Abstract
Tourette syndrome (TS) is a complex disorder characterized by repetitive, sudden, and involuntary movements or vocalizations, called tics. Tics usually appear in childhood, and their severity varies over time. In addition to frequent tics, people with TS are at risk for associated problems including attention deficit hyperactivity disorder (ADHD), obsessive-compulsive disorder (OCD), anxiety, depression, and problems with sleep. TS occurs in most populations and ethnic groups worldwide, and it is more common in males than in females. Previous family and twin studies have shown that the majority of cases of TS are inherited. TS was previously thought to have an autosomal dominant pattern of inheritance. However, several decades of research have shown that this is unlikely the case. Instead, TS most likely results from a variety of genetic and environmental factors, not changes in a single gene. In the past decade, there has been a rapid development of innovative genetic technologies and methodologies, as well as significant progress in genetic studies of psychiatric disorders. In this review, we will briefly summarize previous genetic epidemiological studies of TS and related disorders. We will also review previous genetic studies based on genome-wide linkage analyses and candidate gene association studies to comment on problems of previous methodological and strategic issues. Our main purpose for this review will be to summarize the new genetic discoveries of TS based on novel genetic methods and strategies, such as genome-wide association studies (GWASs), whole exome sequencing (WES), and whole genome sequencing (WGS). We will also compare the new genetic discoveries of TS with other major psychiatric disorders in order to understand the current status of TS genetics and its relationship with other psychiatric disorders.
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10
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Rotenberg DJ, Chang Q, Potapova N, Wang A, Hon M, Sanches M, Bogetic N, Frias N, Liu T, Behan B, El-Badrawi R, Strother SC, Evans SG, Mikkelsen J, Gee T, Dong F, Arnott SR, Laing S, Dharsee M, Vaccarino AL, Javadi M, Evans KR, Jankowicz D. The CAMH Neuroinformatics Platform: A Hospital-Focused Brain-CODE Implementation. Front Neuroinform 2018; 12:77. [PMID: 30459587 PMCID: PMC6232622 DOI: 10.3389/fninf.2018.00077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 10/15/2018] [Indexed: 11/13/2022] Open
Abstract
Investigations of mental illness have been enriched by the advent and maturation of neuroimaging technologies and the rapid pace and increased affordability of molecular sequencing techniques, however, the increased volume, variety and velocity of research data, presents a considerable technical and analytic challenge to curate, federate and interpret. Aggregation of high-dimensional datasets across brain disorders can increase sample sizes and may help identify underlying causes of brain dysfunction, however, additional barriers exist for effective data harmonization and integration for their combined use in research. To help realize the potential of multi-modal data integration for the study of mental illness, the Centre for Addiction and Mental Health (CAMH) constructed a centralized data capture, visualization and analytics environment—the CAMH Neuroinformatics Platform—based on the Ontario Brain Institute (OBI) Brain-CODE architecture, towards the curation of a standardized, consolidated psychiatric hospital-wide research dataset, directly coupled to high performance computing resources.
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Affiliation(s)
- David J Rotenberg
- Krembil Center for Neuroinformatics, Center for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Qing Chang
- Krembil Center for Neuroinformatics, Center for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Natalia Potapova
- Krembil Center for Neuroinformatics, Center for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Andy Wang
- Krembil Center for Neuroinformatics, Center for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Marcia Hon
- Krembil Center for Neuroinformatics, Center for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Marcos Sanches
- Krembil Center for Neuroinformatics, Center for Addiction and Mental Health (CAMH), Toronto, ON, Canada.,Dalla Lana School of Public Health, Toronto, ON, Canada
| | - Nikola Bogetic
- Krembil Center for Neuroinformatics, Center for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Nathan Frias
- Business Intelligence, Center for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Tommy Liu
- Business Intelligence, Center for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | | | | | - Stephen C Strother
- Rotman Research Institute, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | | | | | - Tom Gee
- Indoc Research, Toronto, ON, Canada.,Rotman Research Institute, Toronto, ON, Canada
| | - Fan Dong
- Indoc Research, Toronto, ON, Canada.,Rotman Research Institute, Toronto, ON, Canada
| | - Stephen R Arnott
- Indoc Research, Toronto, ON, Canada.,Rotman Research Institute, Toronto, ON, Canada
| | - Shuai Laing
- Indoc Research, Toronto, ON, Canada.,Rotman Research Institute, Toronto, ON, Canada
| | | | - Anthony L Vaccarino
- Ontario Brain Institute, Toronto, ON, Canada.,Indoc Research, Toronto, ON, Canada
| | | | | | - Damian Jankowicz
- Krembil Center for Neuroinformatics, Center for Addiction and Mental Health (CAMH), Toronto, ON, Canada
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11
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Affiliation(s)
- Samet Kose
- Psychiatry and Clinical Psychopharmacology, Psychiatry and Behavioral Sciences, Franklin, TN, USA
| | - Mesut Cetin
- Psychiatry &Clinical Psychopharmacology and Psychiatry and Behavioral Sciences, Istanbul, Turkey
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12
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Qi Y, Zheng Y, Li Z, Xiong L. Progress in Genetic Studies of Tourette's Syndrome. Brain Sci 2017; 7:E134. [PMID: 29053637 PMCID: PMC5664061 DOI: 10.3390/brainsci7100134] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/03/2017] [Accepted: 10/17/2017] [Indexed: 12/23/2022] Open
Abstract
Tourette's Syndrome (TS) is a complex disorder characterized by repetitive, sudden, and involuntary movements or vocalizations, called tics. Tics usually appear in childhood, and their severity varies over time. In addition to frequent tics, people with TS are at risk for associated problems including attention deficit hyperactivity disorder (ADHD), obsessive-compulsive disorder (OCD), anxiety, depression, and problems with sleep. TS occurs in most populations and ethnic groups worldwide, and it is more common in males than in females. Previous family and twin studies have shown that the majority of cases of TS are inherited. TS was previously thought to have an autosomal dominant pattern of inheritance. However, several decades of research have shown that this is unlikely the case. Instead TS most likely results from a variety of genetic and environmental factors, not changes in a single gene. In the past decade, there has been a rapid development of innovative genetic technologies and methodologies, as well as significant progresses in genetic studies of psychiatric disorders. In this review, we will briefly summarize previous genetic epidemiological studies of TS and related disorders. We will also review previous genetic studies based on genome-wide linkage analyses and candidate gene association studies to comment on problems of previous methodological and strategic issues. Our main purpose for this review will be to summarize the new genetic discoveries of TS based on novel genetic methods and strategies, such as genome-wide association studies (GWASs), whole exome sequencing (WES) and whole genome sequencing (WGS). We will also compare the new genetic discoveries of TS with other major psychiatric disorders in order to understand the current status of TS genetics and its relationship with other psychiatric disorders.
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Affiliation(s)
- Yanjie Qi
- Laboratoire de Neurogénétique, Centre de Recherche, Institut Universitaire en Santé Mentale de Montréal, Montreal, QC H1N 3V2, Canada.
- Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China.
| | - Yi Zheng
- Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China.
- Center of Schizophrenia, Beijing Institute for Brain Disorders, Beijing 100088, China.
| | - Zhanjiang Li
- Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China.
- Center of Schizophrenia, Beijing Institute for Brain Disorders, Beijing 100088, China.
| | - Lan Xiong
- Laboratoire de Neurogénétique, Centre de Recherche, Institut Universitaire en Santé Mentale de Montréal, Montreal, QC H1N 3V2, Canada.
- Département de Psychiatrie, Faculté de Médecine, Université de Montréal, Montreal, QC H3C 3J7, Canada.
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A 2B4, Canada.
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13
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Demkow U, Wolańczyk T. Genetic tests in major psychiatric disorders-integrating molecular medicine with clinical psychiatry-why is it so difficult? Transl Psychiatry 2017; 7:e1151. [PMID: 28608853 PMCID: PMC5537634 DOI: 10.1038/tp.2017.106] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/29/2017] [Indexed: 02/06/2023] Open
Abstract
With the advent of post-genomic era, new technologies create extraordinary possibilities for diagnostics and personalized therapy, transforming todays' medicine. Rooted in both medical genetics and clinical psychiatry, the paper is designed as an integrated source of information of the current and potential future application of emerging genomic technologies as diagnostic tools in psychiatry, moving beyond the classical concept of patient approach. Selected approaches are presented, starting from currently used technologies (next-generation sequencing (NGS) and microarrays), followed by newer options (reverse phenotyping). Next, we describe an old concept in a new light (endophenotypes), subsequently coming up with a sophisticated and complex approach (gene networks) ending by a nascent field (computational psychiatry). The challenges and barriers that exist to translate genomic research to real-world patient assessment are further discussed. We emphasize the view that only a paradigm shift can bring a fundamental change in psychiatric practice, allowing to disentangle the intricacies of mental diseases. All the diagnostic methods, as described, are directed at uncovering the integrity of the system including many types of relations within a complex structure. The integrative system approach offers new opportunity to connect genetic background with specific diseases entities, or concurrently, with symptoms regardless of a diagnosis. To advance the field, we propose concerted cross-disciplinary effort to provide a diagnostic platform operating at the general level of genetic pathogenesis of complex-trait psychiatric disorders rather than at the individual level of a specific disease.
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Affiliation(s)
- U Demkow
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, Warsaw, Poland,Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, Zwirki i Wigury 63a, Warsaw 02-091, Poland. E-mail:
| | - T Wolańczyk
- Department of Child Psychiatry, Medical University of Warsaw, Warsaw, Poland
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14
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Whole-exome sequencing identifies two novel missense mutations (p.L111P and p.R3048C) of RYR3 in a Vietnamese patient with autism spectrum disorders. Genes Genomics 2017. [DOI: 10.1007/s13258-016-0495-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Rennert H, Eng K, Zhang T, Tan A, Xiang J, Romanel A, Kim R, Tam W, Liu YC, Bhinder B, Cyrta J, Beltran H, Robinson B, Mosquera JM, Fernandes H, Demichelis F, Sboner A, Kluk M, Rubin MA, Elemento O. Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care. NPJ Genom Med 2016; 1. [PMID: 28781886 PMCID: PMC5539963 DOI: 10.1038/npjgenmed.2016.19] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We describe Exome Cancer Test v1.0 (EXaCT-1), the first New York State-Department of Health-approved whole-exome sequencing (WES)-based test for precision cancer care. EXaCT-1 uses HaloPlex (Agilent) target enrichment followed by next-generation sequencing (Illumina) of tumour and matched constitutional control DNA. We present a detailed clinical development and validation pipeline suitable for simultaneous detection of somatic point/indel mutations and copy-number alterations (CNAs). A computational framework for data analysis, reporting and sign-out is also presented. For the validation, we tested EXaCT-1 on 57 tumours covering five distinct clinically relevant mutations. Results demonstrated elevated and uniform coverage compatible with clinical testing as well as complete concordance in variant quality metrics between formalin-fixed paraffin embedded and fresh-frozen tumours. Extensive sensitivity studies identified limits of detection threshold for point/indel mutations and CNAs. Prospective analysis of 337 cancer cases revealed mutations in clinically relevant genes in 82% of tumours, demonstrating that EXaCT-1 is an accurate and sensitive method for identifying actionable mutations, with reasonable costs and time, greatly expanding its utility for advanced cancer care.
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Affiliation(s)
- Hanna Rennert
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kenneth Eng
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Tuo Zhang
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Genomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Adrian Tan
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Genomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Jenny Xiang
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Genomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Alessandro Romanel
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Robert Kim
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Wayne Tam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yen-Chun Liu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Bhavneet Bhinder
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA
| | - Joanna Cyrta
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA
| | - Himisha Beltran
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Brian Robinson
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Juan Miguel Mosquera
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Helen Fernandes
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Andrea Sboner
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael Kluk
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mark A Rubin
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
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16
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Sener EF, Canatan H, Ozkul Y. Recent Advances in Autism Spectrum Disorders: Applications of Whole Exome Sequencing Technology. Psychiatry Investig 2016; 13:255-64. [PMID: 27247591 PMCID: PMC4878959 DOI: 10.4306/pi.2016.13.3.255] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 09/22/2015] [Accepted: 10/02/2015] [Indexed: 02/07/2023] Open
Abstract
Autism spectrum disorders (ASD) is characterized by three core symptoms with impaired reciprocal social interaction and communication, a pattern of repetitive behavior and/or restricted interests in early childhood. The prevalence is higher in male children than in female children. As a complex neurodevelopmental disorder, the phenotype and severity of autism are extremely heterogeneous with differences from one patient to another. Genetics has a key role in the etiology of autism. Environmental factors are also interacting with the genetic profile and cause abnormal changes in neuronal development, brain growth, and functional connectivity. The term of exome represents less than 1% of the human genome, but contains 85% of known disease-causing variants. Whole-exome sequencing (WES) is an application of the next generation sequencing technology to determine the variations of all coding regions, or exons of known genes. For this reason, WES has been extensively used for clinical studies in the recent years. WES has achieved great success in the past years for identifying Mendelian disease genes. This review evaluates the potential of current findings in ASD for application in next generation sequencing technology, particularly WES. WES and whole-genome sequencing (WGS) approaches may lead to the discovery of underlying genetic factors for ASD and may thereby identify novel therapeutic targets for this disorder.
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Affiliation(s)
- Elif Funda Sener
- Department of Medical Biology, Erciyes University Medical Faculty, Kayseri, Turkey
- Erciyes University Genome and Stem Cell Center, Kayseri, Turkey
| | - Halit Canatan
- Department of Medical Biology, Erciyes University Medical Faculty, Kayseri, Turkey
| | - Yusuf Ozkul
- Department of Medical Genetics, Erciyes University Medical Faculty, Kayseri, Turkey
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17
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McCammon JM, Sive H. Challenges in understanding psychiatric disorders and developing therapeutics: a role for zebrafish. Dis Model Mech 2016; 8:647-56. [PMID: 26092527 PMCID: PMC4486859 DOI: 10.1242/dmm.019620] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The treatment of psychiatric disorders presents three major challenges to the research and clinical community: defining a genotype associated with a disorder, characterizing the molecular pathology of each disorder and developing new therapies. This Review addresses how cellular and animal systems can help to meet these challenges, with an emphasis on the role of the zebrafish. Genetic changes account for a large proportion of psychiatric disorders and, as gene variants that predispose to psychiatric disease are beginning to be identified in patients, these are tractable for study in cellular and animal systems. Defining cellular and molecular criteria associated with each disorder will help to uncover causal physiological changes in patients and will lead to more objective diagnostic criteria. These criteria should also define co-morbid pathologies within the nervous system or in other organ systems. The definition of genotypes and of any associated pathophysiology is integral to the development of new therapies. Cell culture-based approaches can address these challenges by identifying cellular pathology and by high-throughput screening of gene variants and potential therapeutics. Whole-animal systems can define the broadest function of disorder-associated gene variants and the organismal impact of candidate medications. Given its evolutionary conservation with humans and its experimental tractability, the zebrafish offers several advantages to psychiatric disorder research. These include assays ranging from molecular to behavioural, and capability for chemical screening. There is optimism that the multiple approaches discussed here will link together effectively to provide new diagnostics and treatments for psychiatric patients. Summary: In this review, we discuss strengths and limitations of prevalent laboratory models that are used for understanding psychiatric disorders and developing therapeutics, with emphasis on the zebrafish.
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Affiliation(s)
- Jasmine M McCammon
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | - Hazel Sive
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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18
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Maj C, Minelli A, Giacopuzzi E, Sacchetti E, Gennarelli M. The Role of Metabotropic Glutamate Receptor Genes in Schizophrenia. Curr Neuropharmacol 2016; 14:540-50. [PMID: 27296644 PMCID: PMC4983747 DOI: 10.2174/1570159x13666150514232745] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/04/2015] [Accepted: 05/12/2015] [Indexed: 11/22/2022] Open
Abstract
Genomic studies revealed two main components in the genetic architecture of schizophrenia, one constituted by common variants determining a distributed polygenic effect and one represented by a large number of heterogeneous rare and highly disruptive mutations. These gene modifications often affect neural transmission and different studies proved an involvement of metabotropic glutamate receptors in schizophrenia phenotype. Through the combination of literature information with genomic data from public repositories, we analyzed the current knowledge on the involvement of genetic variations of the human metabotropic glutamate receptors in schizophrenia and related endophenotypes. Despite the analysis did not reveal a definitive connection, different suggestive associations have been identified and in particular a relevant role has emerged for GRM3 in affecting specific schizophrenia endophenotypes. This supports the hypothesis that these receptors are directly involved in schizophrenia disorder.
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Affiliation(s)
| | | | | | | | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11 - 25123 Brescia, Italy.
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19
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Levchenko A, Davtian S, Freylichman O, Zagrivnaya M, Kostareva A, Malashichev Y. Beta-catenin in schizophrenia: Possibly deleterious novel mutation. Psychiatry Res 2015; 228:843-8. [PMID: 26027441 DOI: 10.1016/j.psychres.2015.05.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/10/2015] [Accepted: 05/03/2015] [Indexed: 02/01/2023]
Abstract
Schizophrenia is a debilitating psychiatric disorder, affecting approximately 1% of the human population. Mostly genetic factors contribute to schizophrenia, but the genetics are complex and various aspects of brain functioning and structure, from development to synapse plasticity, seem to be involved in the pathogenesis. The goal of the study was to look for novel mutations in genes, implicated in molecular networks, important in schizophrenia. In the study four candidate genes taking part in the WNT signaling pathway were analyzed by sequencing in a cohort of 87 schizophrenia patients from Saint Petersburg, Russia. The gene list included CTNNB1 (beta-catenin), GSK3B, WNT2B and WNT7B. The impact of discovered variants on the protein function was analyzed in silico. We found three variants in the genes CTNNB1 and WNT7B, absent in healthy controls, including 212 controls from the same geographic area. The novel mutation c.1943A>G (p.N648S) in CTNNB1 seems to be the best candidate for disease-associated mutation in this study, as it damages the protein product in silico. This is the first study reporting mutations in CTNNB1 in schizophrenia.
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Affiliation(s)
- Anastasia Levchenko
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia.
| | - Stepan Davtian
- Department of Psychiatry and Addiction Medicine, Faculty of Medicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Olga Freylichman
- Institute of Molecular Biology and Genetics, Federal Almazov Medical Research Center, Saint Petersburg, Russia
| | - Maria Zagrivnaya
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Anna Kostareva
- Institute of Molecular Biology and Genetics, Federal Almazov Medical Research Center, Saint Petersburg, Russia; ITMO University, Institute of Translational Medicine, Saint Petersburg, Russia
| | - Yegor Malashichev
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia; Institute of Experimental Medicine, Northwestern Branch of the Russian Academy of Medical Sciences, Saint Petersburg, Russia.
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20
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Nascimento JM, Martins-de-Souza D. The proteome of schizophrenia. NPJ SCHIZOPHRENIA 2015; 1:14003. [PMID: 27336025 PMCID: PMC4849438 DOI: 10.1038/npjschz.2014.3] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 12/24/2022]
Abstract
On observing schizophrenia from a clinical point of view up to its molecular basis, one may conclude that this is likely to be one of the most complex human disorders to be characterized in all aspects. Such complexity is the reflex of an intricate combination of genetic and environmental components that influence brain functions since pre-natal neurodevelopment, passing by brain maturation, up to the onset of disease and disease establishment. The perfect function of tissues, organs, systems, and finally the organism depends heavily on the proper functioning of cells. Several lines of evidence, including genetics, genomics, transcriptomics, neuropathology, and pharmacology, have supported the idea that dysfunctional cells are causative to schizophrenia. Together with the above-mentioned techniques, proteomics have been contributing to understanding the biochemical basis of schizophrenia at the cellular and tissue level through the identification of differentially expressed proteins and consequently their biochemical pathways, mostly in the brain tissue but also in other cells. In addition, mass spectrometry-based proteomics have identified and precisely quantified proteins that may serve as biomarker candidates to prognosis, diagnosis, and medication monitoring in peripheral tissue. Here, we review all data produced by proteomic investigation in the last 5 years using tissue and/or cells from schizophrenic patients, focusing on postmortem brain tissue and peripheral blood serum and plasma. This information has provided integrated pictures of the biochemical systems involved in the pathobiology, and has suggested potential biomarkers, and warrant potential targets to alternative treatment therapies to schizophrenia.
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Affiliation(s)
- Juliana M Nascimento
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
- D’Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
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Apalasamy YD, Mohamed Z. Obesity and genomics: role of technology in unraveling the complex genetic architecture of obesity. Hum Genet 2015; 134:361-74. [PMID: 25687726 DOI: 10.1007/s00439-015-1533-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/02/2015] [Indexed: 01/15/2023]
Abstract
Obesity is a complex and multifactorial disease that occurs as a result of the interaction between "obesogenic" environmental factors and genetic components. Although the genetic component of obesity is clear from the heritability studies, the genetic basis remains largely elusive. Successes have been achieved in identifying the causal genes for monogenic obesity using animal models and linkage studies, but these approaches are not fruitful for polygenic obesity. The developments of genome-wide association approach have brought breakthrough discovery of genetic variants for polygenic obesity where tens of new susceptibility loci were identified. However, the common SNPs only accounted for a proportion of heritability. The arrival of NGS technologies and completion of 1000 Genomes Project have brought other new methods to dissect the genetic architecture of obesity, for example, the use of exome genotyping arrays and deep sequencing of candidate loci identified from GWAS to study rare variants. In this review, we summarize and discuss the developments of these genetic approaches in human obesity.
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Affiliation(s)
- Yamunah Devi Apalasamy
- Department of Pharmacology, Pharmacogenomics Laboratory, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia,
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Li X, Teng S. RNA Sequencing in Schizophrenia. Bioinform Biol Insights 2015; 9:53-60. [PMID: 27053919 PMCID: PMC4818022 DOI: 10.4137/bbi.s28992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/01/2016] [Accepted: 02/06/2016] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia (SCZ) is a serious psychiatric disorder that affects 1% of general population and places a heavy burden worldwide. The underlying genetic mechanism of SCZ remains unknown, but studies indicate that the disease is associated with a global gene expression disturbance across many genes. Next-generation sequencing, particularly of RNA sequencing (RNA-Seq), provides a powerful genome-scale technology to investigate the pathological processes of SCZ. RNA-Seq has been used to analyze the gene expressions and identify the novel splice isoforms and rare transcripts associated with SCZ. This paper provides an overview on the genetics of SCZ, the advantages of RNA-Seq for transcriptome analysis, the accomplishments of RNA-Seq in SCZ cohorts, and the applications of induced pluripotent stem cells and RNA-Seq in SCZ research.
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Affiliation(s)
- Xin Li
- Department of Biology, Howard University, Washington, DC, USA
| | - Shaolei Teng
- Department of Biology, Howard University, Washington, DC, USA
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Les nouvelles techniques de génétique moléculaire vont-elles révolutionner la psychiatrie ? Eur Psychiatry 2014. [DOI: 10.1016/j.eurpsy.2014.09.340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Durant longtemps, la psychiatrie et la génétique n’ont eu que de rares points de rencontre, essentiellement autour de travaux de recherche fondamentale, dans le cadre des études visant à déterminer un gène de vulnérabilité aux troubles mentaux. Aujourd’hui, un grand pas a été franchi qui amène à penser que la génétique fera partie du quotidien de la psychiatrie dans les années à venir et sortira du strict champ de la recherche. En effet, le développement et la diffusion de l’hybridation génomique comparative sur des puces à ADN ou CGH array est en train de bouleverser la pratique hospitalière du diagnostic des anomalies chromosomiques. Dans l’autisme, le déficit intellectuel et dans les troubles mentaux atypiques, la CGH array permet d’augmenter les potentialités diagnostiques syndromiques de plus de 15 % en comparaison aux moyens moléculaires classiques. C’est toute la pratique clinique quotidienne du psychiatre et du pédopsychiatre qui pourrait en être bouleversée. Cette révolution va être poussée plus loin encore avec le développement à venir du Next Generation Sequencing ou séquençage de nouvelle génération qui va permettre de séquencer l’ensemble du génome d’un individu. Encore à ses débuts, cette technique pourrait un jour expliquer l’origine de troubles mentaux comme la schizophrénie, les troubles bipolaires ou la dépression. Si le NGS promet d’éclairer sous un jour nouveau l’étiologie des maladies mentales, l’application au quotidien ne sera pas sans poser un certain nombre de questions, en particulier éthiques. La psychiatrie de demain doit donc se préparer au diagnostic génétique : ce qu’il implique en termes de soins, d’appréhension de la maladie et de conseil génétique. Cette rencontre avec l’expert permettra la présentation des principes et des limites de ces techniques, leurs potentielles indications en psychiatrie et les bouleversements attendus par leur introduction future en pratique clinique.
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Schmitt A, Malchow B, Keeser D, Falkai P, Hasan A. Neurobiologie der Schizophrenie. DER NERVENARZT 2014; 86:324-6, 328-31. [DOI: 10.1007/s00115-014-4115-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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