1
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Kaya IH, Al-Harazi O, Colak D. Transcriptomic data analysis coupled with copy number aberrations reveals a blood-based 17-gene signature for diagnosis and prognosis of patients with colorectal cancer. Front Genet 2023; 13:1031086. [PMID: 36685857 PMCID: PMC9854115 DOI: 10.3389/fgene.2022.1031086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/01/2022] [Indexed: 01/07/2023] Open
Abstract
Background: Colorectal cancer (CRC) is the third most common cancer and third leading cause of cancer-associated deaths worldwide. Diagnosing CRC patients reliably at an early and curable stage is of utmost importance to reduce the risk of mortality. Methods: We identified global differentially expressed genes with copy number alterations in patients with CRC. We then identified genes that are also expressed in blood, which resulted in a blood-based gene signature. We validated the gene signature's diagnostic and prognostic potential using independent datasets of gene expression profiling from over 800 CRC patients with detailed clinical data. Functional enrichment, gene interaction networks and pathway analyses were also performed. Results: The analysis revealed a 17-gene signature that is expressed in blood and demonstrated that it has diagnostic potential. The 17-gene SVM classifier displayed 99 percent accuracy in predicting the patients with CRC. Moreover, we developed a prognostic model and defined a risk-score using 17-gene and validated that high risk score is strongly associated with poor disease outcome. The 17-gene signature predicted disease outcome independent of other clinical factors in the multivariate analysis (HR = 2.7, 95% CI = 1.3-5.3, p = 0.005). In addition, our gene network and pathway analyses revealed alterations in oxidative stress, STAT3, ERK/MAPK, interleukin and cytokine signaling pathways as well as potentially important hub genes, including BCL2, MS4A1, SLC7A11, AURKA, IL6R, TP53, NUPR1, DICER1, DUSP5, SMAD3, and CCND1. Conclusion: Our results revealed alterations in various genes and cancer-related pathways that may be essential for CRC transformation. Moreover, our study highlights diagnostic and prognostic value of our gene signature as well as its potential use as a blood biomarker as a non-invasive diagnostic method. Integrated analysis transcriptomic data coupled with copy number aberrations may provide a reliable method to identify key biological programs associated with CRC and lead to improved diagnosis and therapeutic options.
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Affiliation(s)
- Ibrahim H. Kaya
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Olfat Al-Harazi
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Dilek Colak
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia,*Correspondence: Dilek Colak,
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2
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Lu G, Zhang Y, Xia H, He X, Xu P, Wu L, Li D, Ma L, Wu J, Peng Q. Identification of a de novo mutation of the FOXG1 gene and comprehensive analysis for molecular factors in Chinese FOXG1-related encephalopathies. Front Mol Neurosci 2022; 15:1039990. [PMID: 36568277 PMCID: PMC9768341 DOI: 10.3389/fnmol.2022.1039990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Background FOXG1-related encephalopathy, also known as FOXG1 syndrome or FOXG1-related disorder, affects most aspects of development and causes microcephaly and brain malformations. This syndrome was previously considered to be the congenital variant of Rett syndrome. The abnormal function or expression of FOXG1, caused by intragenic mutations, microdeletions or microduplications, was considered to be crucial pathological factor for this disorder. Currently, most of the FOXG1-related encephalopathies have been identified in Europeans and North Americans, and relatively few Chinese cases were reported. Methods Array-Comparative Genomic Hybridization (Array-CGH) and whole-exome sequencing (WES) were carried out for the proband and her parent to detect pathogenic variants. Results A de novo nonsense mutation (c.385G>T, p.Glu129Ter) of FOXG1 was identified in a female child in a cohort of 73 Chinese children with neurodevelopmental disorders/intellectual disorders (NDDs/IDs). In order to have a comprehensive view of FOXG1-related encephalopathy in China, relevant published reports were browsed and twelve cases with mutations in FOXG1 or copy number variants (CNVs) involving FOXG1 gene were involved in the analysis eventually. Feeding difficulties, seizures, delayed speech, corpus callosum hypoplasia and underdevelopment of frontal and temporal lobes occurred in almost all cases. Out of the 12 cases, eight patients (66.67%) had single-nucleotide mutations of FOXG1 gene and four patients (33.33%) had CNVs involving FOXG1 (3 microdeletions and 1 microduplication). The expression of FOXG1 could also be potentially disturbed by deletions of several brain-active regulatory elements located in intergenic FOXG1-PRKD1 region. Further analysis indicated that PRKD1 might be a cooperating factor to regulate the expression of FOXG1, MECP2 and CDKL5 to contribute the RTT/RTT-like disorders. Discussion This re-analysis would broaden the existed knowledge about the molecular etiology and be helpful for diagnosis, treatment, and gene therapy of FOXG1-related disorders in the future.
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Affiliation(s)
- Guanting Lu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Yan Zhang
- Department of Obstetrics and Gynecology, Strategic Support Force Medical Center, Beijing, China
| | - Huiyun Xia
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Xiaoyan He
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Pei Xu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Lianying Wu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Ding Li
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Liya Ma
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Jin Wu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Qiongling Peng
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
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Mahony C, O'Ryan C. A molecular framework for autistic experiences: Mitochondrial allostatic load as a mediator between autism and psychopathology. Front Psychiatry 2022; 13:985713. [PMID: 36506457 PMCID: PMC9732262 DOI: 10.3389/fpsyt.2022.985713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/07/2022] [Indexed: 11/27/2022] Open
Abstract
Molecular autism research is evolving toward a biopsychosocial framework that is more informed by autistic experiences. In this context, research aims are moving away from correcting external autistic behaviors and toward alleviating internal distress. Autism Spectrum Conditions (ASCs) are associated with high rates of depression, suicidality and other comorbid psychopathologies, but this relationship is poorly understood. Here, we integrate emerging characterizations of internal autistic experiences within a molecular framework to yield insight into the prevalence of psychopathology in ASC. We demonstrate that descriptions of social camouflaging and autistic burnout resonate closely with the accepted definitions for early life stress (ELS) and chronic adolescent stress (CAS). We propose that social camouflaging could be considered a distinct form of CAS that contributes to allostatic overload, culminating in a pathophysiological state that is experienced as autistic burnout. Autistic burnout is thought to contribute to psychopathology via psychological and physiological mechanisms, but these remain largely unexplored by molecular researchers. Building on converging fields in molecular neuroscience, we discuss the substantial evidence implicating mitochondrial dysfunction in ASC to propose a novel role for mitochondrial allostatic load in the relationship between autism and psychopathology. An interplay between mitochondrial, neuroimmune and neuroendocrine signaling is increasingly implicated in stress-related psychopathologies, and these molecular players are also associated with neurodevelopmental, neurophysiological and neurochemical aspects of ASC. Together, this suggests an increased exposure and underlying molecular susceptibility to ELS that increases the risk of psychopathology in ASC. This article describes an integrative framework shaped by autistic experiences that highlights novel avenues for molecular research into mechanisms that directly affect the quality of life and wellbeing of autistic individuals. Moreover, this framework emphasizes the need for increased access to diagnoses, accommodations, and resources to improve mental health outcomes in autism.
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Affiliation(s)
| | - Colleen O'Ryan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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4
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Daghestani MH, Alqahtani HA, AlBakheet A, Al Deery M, Awartani KA, Daghestani MH, Kaya N, Warsy A, Coskun S, Colak D. Global Transcriptional Profiling of Granulosa Cells from Polycystic Ovary Syndrome Patients: Comparative Analyses of Patients with or without History of Ovarian Hyperstimulation Syndrome Reveals Distinct Biomarkers and Pathways. J Clin Med 2022; 11:jcm11236941. [PMID: 36498516 PMCID: PMC9740016 DOI: 10.3390/jcm11236941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/09/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022] Open
Abstract
Ovarian hyperstimulation syndrome (OHSS) is often a complication of polycystic ovarian syndrome (PCOS), the most frequent disorder of the endocrine system, which affects women in their reproductive years. The etiology of OHSS is multifactorial, though the factors involved are not apparent. In an attempt to unveil the molecular basis of OHSS, we conducted transcriptome analysis of total RNA extracted from granulosa cells from PCOS patients with a history of OHSS (n = 6) and compared them to those with no history of OHSS (n = 18). We identified 59 significantly dysregulated genes (48 down-regulated, 11 up-regulated) in the PCOS with OHSS group compared to the PCOS without OHSS group (p-value < 0.01, fold change >1.5). Functional, pathway and network analyses revealed genes involved in cellular development, inflammatory and immune response, cellular growth and proliferation (including DCN, VIM, LIFR, GRN, IL33, INSR, KLF2, FOXO1, VEGF, RDX, PLCL1, PAPPA, and ZFP36), and significant alterations in the PPAR, IL6, IL10, JAK/STAT and NF-κB signaling pathways. Array findings were validated using quantitative RT-PCR. To the best of our knowledge, this is the largest cohort of Saudi PCOS cases (with or without OHSS) to date that was analyzed using a transcriptomic approach. Our data demonstrate alterations in various gene networks and pathways that may be involved in the pathophysiology of OHSS. Further studies are warranted to confirm the findings.
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Affiliation(s)
- Maha H. Daghestani
- Department of Zoology, College of Science, King Saud University, Riyadh 11495, Saudi Arabia
- Correspondence: (M.H.D.); (D.C.)
| | - Huda A. Alqahtani
- Department of Zoology, College of Science, King Saud University, Riyadh 11495, Saudi Arabia
| | - AlBandary AlBakheet
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mashael Al Deery
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Khalid A. Awartani
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mazin H. Daghestani
- Department of Obstetrics and Gynecology, Umm-Al-Qura University, Makkah 24382, Saudi Arabia
| | - Namik Kaya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Arjumand Warsy
- Central Laboratory, Center for Women Scientific and Medical Studies, King Saud University, Riyadh 11451, Saudi Arabia
| | - Serdar Coskun
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Dilek Colak
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
- Correspondence: (M.H.D.); (D.C.)
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5
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Gasparotto M, Lee YS, Palazzi A, Vacca M, Filippini F. Nuclear and Cytoplasmatic Players in Mitochondria-Related CNS Disorders: Chromatin Modifications and Subcellular Trafficking. Biomolecules 2022; 12:biom12050625. [PMID: 35625553 PMCID: PMC9138954 DOI: 10.3390/biom12050625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 12/10/2022] Open
Abstract
Aberrant mitochondrial phenotypes are common to many central nervous system (CNS) disorders, including neurodegenerative and neurodevelopmental diseases. Mitochondrial function and homeostasis depend on proper control of several biological processes such as chromatin remodeling and transcriptional control, post-transcriptional events, vesicle and organelle subcellular trafficking, fusion, and morphogenesis. Mutation or impaired regulation of major players that orchestrate such processes can disrupt cellular and mitochondrial dynamics, contributing to neurological disorders. The first part of this review provides an overview of a functional relationship between chromatin players and mitochondria. Specifically, we relied on specific monogenic CNS disorders which share features with mitochondrial diseases. On the other hand, subcellular trafficking is coordinated directly or indirectly through evolutionarily conserved domains and proteins that regulate the dynamics of membrane compartments and organelles, including mitochondria. Among these “building blocks”, longin domains and small GTPases are involved in autophagy and mitophagy, cell reshaping, and organelle fusion. Impairments in those processes significantly impact CNS as well and are discussed in the second part of the review. Hopefully, in filling the functional gap between the nucleus and cytoplasmic organelles new routes for therapy could be disclosed.
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Affiliation(s)
- Matteo Gasparotto
- Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Via Ugo Bassi 58/B, 35131 Padua, Italy;
| | - Yi-Shin Lee
- Institute of Genetics and Biophysics “A. Buzzati Traverso”, CNR, Via Pietro Castellino, 111, 80131 Naples, Italy; (Y.-S.L.); (A.P.); (M.V.)
- Pharmacology Division, Department of Neuroscience, Reproductive and Odontostomatological Sciences, Faculty of Medicine and surgery, University of Naples Federico II, Via Pansini 5, Building 19 (Biological Tower), 80131 Naples, Italy
| | - Alessandra Palazzi
- Institute of Genetics and Biophysics “A. Buzzati Traverso”, CNR, Via Pietro Castellino, 111, 80131 Naples, Italy; (Y.-S.L.); (A.P.); (M.V.)
| | - Marcella Vacca
- Institute of Genetics and Biophysics “A. Buzzati Traverso”, CNR, Via Pietro Castellino, 111, 80131 Naples, Italy; (Y.-S.L.); (A.P.); (M.V.)
| | - Francesco Filippini
- Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Via Ugo Bassi 58/B, 35131 Padua, Italy;
- Correspondence:
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6
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Benchoua A, Lasbareilles M, Tournois J. Contribution of Human Pluripotent Stem Cell-Based Models to Drug Discovery for Neurological Disorders. Cells 2021; 10:cells10123290. [PMID: 34943799 PMCID: PMC8699352 DOI: 10.3390/cells10123290] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 02/07/2023] Open
Abstract
One of the major obstacles to the identification of therapeutic interventions for central nervous system disorders has been the difficulty in studying the step-by-step progression of diseases in neuronal networks that are amenable to drug screening. Recent advances in the field of human pluripotent stem cell (PSC) biology offers the capability to create patient-specific human neurons with defined clinical profiles using reprogramming technology, which provides unprecedented opportunities for both the investigation of pathogenic mechanisms of brain disorders and the discovery of novel therapeutic strategies via drug screening. Many examples not only of the creation of human pluripotent stem cells as models of monogenic neurological disorders, but also of more challenging cases of complex multifactorial disorders now exist. Here, we review the state-of-the art brain cell types obtainable from PSCs and amenable to compound-screening formats. We then provide examples illustrating how these models contribute to the definition of new molecular or functional targets for drug discovery and to the design of novel pharmacological approaches for rare genetic disorders, as well as frequent neurodegenerative diseases and psychiatric disorders.
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Affiliation(s)
- Alexandra Benchoua
- Neuroplasticity and Therapeutics, CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France;
- High Throughput Screening Platform, CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France;
- Correspondence:
| | - Marie Lasbareilles
- Neuroplasticity and Therapeutics, CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France;
- UEVE UMR 861, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | - Johana Tournois
- High Throughput Screening Platform, CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France;
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7
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Al-Harazi O, Kaya IH, El Allali A, Colak D. A Network-Based Methodology to Identify Subnetwork Markers for Diagnosis and Prognosis of Colorectal Cancer. Front Genet 2021; 12:721949. [PMID: 34790220 PMCID: PMC8591094 DOI: 10.3389/fgene.2021.721949] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/28/2021] [Indexed: 12/30/2022] Open
Abstract
The development of reliable methods for identification of robust biomarkers for complex diseases is critical for disease diagnosis and prognosis efforts. Integrating multi-omics data with protein-protein interaction (PPI) networks to investigate diseases may help better understand disease characteristics at the molecular level. In this study, we developed and tested a novel network-based method to detect subnetwork markers for patients with colorectal cancer (CRC). We performed an integrated omics analysis using whole-genome gene expression profiling and copy number alterations (CNAs) datasets followed by building a gene interaction network for the significantly altered genes. We then clustered the constructed gene network into subnetworks and assigned a score for each significant subnetwork. We developed a support vector machine (SVM) classifier using these scores as feature values and tested the methodology in independent CRC transcriptomic datasets. The network analysis resulted in 15 subnetwork markers that revealed several hub genes that may play a significant role in colorectal cancer, including PTP4A3, FGFR2, PTX3, AURKA, FEN1, INHBA, and YES1. The 15-subnetwork classifier displayed over 98 percent accuracy in detecting patients with CRC. In comparison to individual gene biomarkers, subnetwork markers based on integrated multi-omics and network analyses may lead to better disease classification, diagnosis, and prognosis.
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Affiliation(s)
- Olfat Al-Harazi
- Biostatistics, Epidemiology and Scientific Computing Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Ibrahim H Kaya
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Dilek Colak
- Biostatistics, Epidemiology and Scientific Computing Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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8
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Golubiani G, Lagani V, Solomonia R, Müller M. Metabolomic Fingerprint of Mecp2-Deficient Mouse Cortex: Evidence for a Pronounced Multi-Facetted Metabolic Component in Rett Syndrome. Cells 2021; 10:cells10092494. [PMID: 34572143 PMCID: PMC8472238 DOI: 10.3390/cells10092494] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 01/10/2023] Open
Abstract
Using unsupervised metabolomics, we defined the complex metabolic conditions in the cortex of a mouse model of Rett syndrome (RTT). RTT, which represents a cause of mental and cognitive disabilities in females, results in profound cognitive impairment with autistic features, motor disabilities, seizures, gastrointestinal problems, and cardiorespiratory irregularities. Typical RTT originates from mutations in the X-chromosomal methyl-CpG-binding-protein-2 (Mecp2) gene, which encodes a transcriptional modulator. It then causes a deregulation of several target genes and metabolic alterations in the nervous system and peripheral organs. We identified 101 significantly deregulated metabolites in the Mecp2-deficient cortex of adult male mice; 68 were increased and 33 were decreased compared to wildtypes. Pathway analysis identified 31 mostly upregulated metabolic pathways, in particular carbohydrate and amino acid metabolism, key metabolic mitochondrial/extramitochondrial pathways, and lipid metabolism. In contrast, neurotransmitter-signaling is dampened. This metabolic fingerprint of the Mecp2-deficient cortex of severely symptomatic mice provides further mechanistic insights into the complex RTT pathogenesis. The deregulated pathways that were identified—in particular the markedly affected amino acid and carbohydrate metabolism—confirm a complex and multifaceted metabolic component in RTT, which in turn signifies putative therapeutic targets. Furthermore, the deregulated key metabolites provide a choice of potential biomarkers for a more detailed rating of disease severity and disease progression.
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Affiliation(s)
- Gocha Golubiani
- Institut für Neuro- und Sinnesphysiologie, Zentrum Physiologie und Pathophysiologie, Universitätsmedizin Göttingen, Georg-August-Universität Göttingen, D-37130 Göttingen, Germany;
- Institute of Chemical Biology, Ilia State University, 0162 Tbilisi, Georgia; (V.L.); (R.S.)
| | - Vincenzo Lagani
- Institute of Chemical Biology, Ilia State University, 0162 Tbilisi, Georgia; (V.L.); (R.S.)
| | - Revaz Solomonia
- Institute of Chemical Biology, Ilia State University, 0162 Tbilisi, Georgia; (V.L.); (R.S.)
| | - Michael Müller
- Institut für Neuro- und Sinnesphysiologie, Zentrum Physiologie und Pathophysiologie, Universitätsmedizin Göttingen, Georg-August-Universität Göttingen, D-37130 Göttingen, Germany;
- Correspondence: ; Tel.: +49-551-39-22933
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9
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Aldosary M, Baselm S, Abdulrahim M, Almass R, Alsagob M, AlMasseri Z, Huma R, AlQuait L, Al‐Shidi T, Al‐Obeid E, AlBakheet A, Alahideb B, Alahaidib L, Qari A, Taylor RW, Colak D, AlSayed MD, Kaya N. SLC25A42-associated mitochondrial encephalomyopathy: Report of additional founder cases and functional characterization of a novel deletion. JIMD Rep 2021; 60:75-87. [PMID: 34258143 PMCID: PMC8260478 DOI: 10.1002/jmd2.12218] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/09/2021] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
SLC25A42 is the main transporter of coenzyme A (CoA) into mitochondria. To date, 15 individuals have been reported to have one of two bi-allelic homozygous missense variants in the SLC25A42 as the cause of mitochondrial encephalomyopathy, of which 14 of them were of Saudi origin and share the same founder variant, c.871A > G:p.Asn291Asp. The other subject was of German origin with a variant at canonical splice site, c.380 + 2 T > A. Here, we describe the clinical manifestations and the disease course in additional six Saudi patients from four unrelated consanguineous families. While five patients have the Saudi founder p.Asn291Asp variant, one subject has a novel deletion. Functional analyses on fibroblasts obtained from this patient revealed that the deletion causes significant decrease in mitochondrial oxygen consumption and ATP production compared to healthy individuals. Moreover, extracellular acidification rate revealed significantly reduced glycolysis, glycolytic capacity, and glycolytic reserve as compared to control individuals. There were no changes in the mitochondrial DNA (mtDNA) content of patient fibroblasts. Immunoblotting experiments revealed significantly diminished protein expression due to the deletion. In conclusion, we report additional patients with SLC25A42-associated mitochondrial encephalomyopathy. Our study expands the molecular spectrum of this condition and provides further evidence of mitochondrial dysfunction as a central cause of pathology. We therefore propose that this disorder should be included in the differential diagnosis of any patient with an unexplained motor and speech delay, recurrent encephalopathy with metabolic acidosis, intermittent or persistent dystonia, lactic acidosis, basal ganglia lesions and, especially, of Arab ethnicity. Finally, deep brain stimulation should be considered in the management of patients with life altering dystonia.
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Affiliation(s)
- Mazhor Aldosary
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Shahad Baselm
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Maha Abdulrahim
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Rawan Almass
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Department of Medical GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Maysoon Alsagob
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- King Abdulaziz City for Science and TechnologyRiyadhSaudi Arabia
| | - Zainab AlMasseri
- Department of Medical GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Rozeena Huma
- Department of Medical GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Laila AlQuait
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Tarfa Al‐Shidi
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Eman Al‐Obeid
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Albandary AlBakheet
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Basma Alahideb
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Lujane Alahaidib
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Alya Qari
- Department of Medical GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Mitochondrial Diagnostic LaboratoryNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Dilek Colak
- Department of Biostatistics, Epidemiology, and Scientific ComputingKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Moeenaldeen D. AlSayed
- Department of Medical GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- College of MedicineAlfaisal UniversityRiyadhSaudi Arabia
| | - Namik Kaya
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
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10
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An mtDNA mutant mouse demonstrates that mitochondrial deficiency can result in autism endophenotypes. Proc Natl Acad Sci U S A 2021; 118:2021429118. [PMID: 33536343 PMCID: PMC8017921 DOI: 10.1073/pnas.2021429118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorders (ASDs) have increasingly been associated with mitochondrial dysfunction, corroborated by mitochondrial DNA (mtDNA) germline and somatic variants being found in ASD patients. If mitochondrial defects can generate ASD, then specific mtDNA mutations should induce ASD endophenotypes in mice. We tested this prediction by introduction of an mtDNA ND6 gene missense mutation (ND6P25L) into the mouse germline and found ASD endophenotypes. The ND6P25L mice exhibit impaired social interaction, compulsive behavior, and increased anxiety. They have reduced electroencephalographic delta and theta wave power, increased predilection to seizures, but without diminution of hippocampal interneurons. These endophenotypes correlate with impaired cortical and hippocampal mitochondrial respiration and increased reactive oxygen species production. Thus, mitochondrial defects can be sufficient to produce ASD phenotypes. Autism spectrum disorders (ASDs) are characterized by a deficit in social communication, pathologic repetitive behaviors, restricted interests, and electroencephalogram (EEG) aberrations. While exhaustive analysis of nuclear DNA (nDNA) variation has revealed hundreds of copy number variants (CNVs) and loss-of-function (LOF) mutations, no unifying hypothesis as to the pathophysiology of ASD has yet emerged. Based on biochemical and physiological analyses, it has been hypothesized that ASD may be the result of a systemic mitochondrial deficiency with brain-specific manifestations. This proposal has been supported by recent mitochondrial DNA (mtDNA) analyses identifying both germline and somatic mtDNA variants in ASD. If mitochondrial defects do predispose to ASD, then mice with certain mtDNA mutations should present with autism endophenotypes. To test this prediction, we examined a mouse strain harboring an mtDNA ND6 gene missense mutation (P25L). This mouse manifests impaired social interactions, increased repetitive behaviors and anxiety, EEG alterations, and a decreased seizure threshold, in the absence of reduced hippocampal interneuron numbers. EEG aberrations were most pronounced in the cortex followed by the hippocampus. Aberrations in mitochondrial respiratory function and reactive oxygen species (ROS) levels were also most pronounced in the cortex followed by the hippocampus, but absent in the olfactory bulb. These data demonstrate that mild systemic mitochondrial defects can result in ASD without apparent neuroanatomical defects and that systemic mitochondrial mutations can cause tissue-specific brain defects accompanied by regional neurophysiological alterations.
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Quach TT, Stratton HJ, Khanna R, Kolattukudy PE, Honnorat J, Meyer K, Duchemin AM. Intellectual disability: dendritic anomalies and emerging genetic perspectives. Acta Neuropathol 2021; 141:139-158. [PMID: 33226471 PMCID: PMC7855540 DOI: 10.1007/s00401-020-02244-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Intellectual disability (ID) corresponds to several neurodevelopmental disorders of heterogeneous origin in which cognitive deficits are commonly associated with abnormalities of dendrites and dendritic spines. These histological changes in the brain serve as a proxy for underlying deficits in neuronal network connectivity, mostly a result of genetic factors. Historically, chromosomal abnormalities have been reported by conventional karyotyping, targeted fluorescence in situ hybridization (FISH), and chromosomal microarray analysis. More recently, cytogenomic mapping, whole-exome sequencing, and bioinformatic mining have led to the identification of novel candidate genes, including genes involved in neuritogenesis, dendrite maintenance, and synaptic plasticity. Greater understanding of the roles of these putative ID genes and their functional interactions might boost investigations into determining the plausible link between cellular and behavioral alterations as well as the mechanisms contributing to the cognitive impairment observed in ID. Genetic data combined with histological abnormalities, clinical presentation, and transgenic animal models provide support for the primacy of dysregulation in dendrite structure and function as the basis for the cognitive deficits observed in ID. In this review, we highlight the importance of dendrite pathophysiology in the etiologies of four prototypical ID syndromes, namely Down Syndrome (DS), Rett Syndrome (RTT), Digeorge Syndrome (DGS) and Fragile X Syndrome (FXS). Clinical characteristics of ID have also been reported in individuals with deletions in the long arm of chromosome 10 (the q26.2/q26.3), a region containing the gene for the collapsin response mediator protein 3 (CRMP3), also known as dihydropyrimidinase-related protein-4 (DRP-4, DPYSL4), which is involved in dendritogenesis. Following a discussion of clinical and genetic findings in these syndromes and their preclinical animal models, we lionize CRMP3/DPYSL4 as a novel candidate gene for ID that may be ripe for therapeutic intervention.
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Affiliation(s)
- Tam T Quach
- Institute for Behavioral Medicine Research, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
- INSERM U1217/CNRS, UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Rajesh Khanna
- Department of Pharmacology, University of Arizona, Tucson, AZ, 85724, USA
| | | | - Jérome Honnorat
- INSERM U1217/CNRS, UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Lyon, France
- SynatAc Team, Institut NeuroMyoGène, Lyon, France
| | - Kathrin Meyer
- The Research Institute of Nationwide Children Hospital, Columbus, OH, 43205, USA
- Department of Pediatric, The Ohio State University, Columbus, OH, 43210, USA
| | - Anne-Marie Duchemin
- Department of Psychiatry and Behavioral Health, The Ohio State University, Columbus, OH, 43210, USA.
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12
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Bressan P, Kramer P. Mental Health, Mitochondria, and the Battle of the Sexes. Biomedicines 2021; 9:biomedicines9020116. [PMID: 33530498 PMCID: PMC7911591 DOI: 10.3390/biomedicines9020116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 01/12/2023] Open
Abstract
This paper presents a broad perspective on how mental disease relates to the different evolutionary strategies of men and women and to growth, metabolism, and mitochondria—the enslaved bacteria in our cells that enable it all. Several mental disorders strike one sex more than the other; yet what truly matters, regardless of one’s sex, is how much one’s brain is “female” and how much it is “male”. This appears to be the result of an arms race between the parents over how many resources their child ought to extract from the mother, hence whether it should grow a lot or stay small and undemanding. An uneven battle alters the child’s risk of developing not only insulin resistance, diabetes, or cancer, but a mental disease as well. Maternal supremacy increases the odds of a psychosis-spectrum disorder; paternal supremacy, those of an autism-spectrum one. And a particularly lopsided struggle may invite one or the other of a series of syndromes that come in pairs, with diametrically opposite, excessively “male” or “female” characteristics. By providing the means for this tug of war, mitochondria take center stage in steadying or upsetting the precarious balance on which our mental health is built.
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Ferrari A, Del'Olio S, Barrientos A. The Diseased Mitoribosome. FEBS Lett 2020; 595:1025-1061. [PMID: 33314036 DOI: 10.1002/1873-3468.14024] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 12/17/2022]
Abstract
Mitochondria control life and death in eukaryotic cells. Harboring a unique circular genome, a by-product of an ancient endosymbiotic event, mitochondria maintains a specialized and evolutionary divergent protein synthesis machinery, the mitoribosome. Mitoribosome biogenesis depends on elements encoded in both the mitochondrial genome (the RNA components) and the nuclear genome (all ribosomal proteins and assembly factors). Recent cryo-EM structures of mammalian mitoribosomes have illuminated their composition and provided hints regarding their assembly and elusive mitochondrial translation mechanisms. A growing body of literature involves the mitoribosome in inherited primary mitochondrial disorders. Mutations in genes encoding mitoribosomal RNAs, proteins, and assembly factors impede mitoribosome biogenesis, causing protein synthesis defects that lead to respiratory chain failure and mitochondrial disorders such as encephalo- and cardiomyopathy, deafness, neuropathy, and developmental delays. In this article, we review the current fundamental understanding of mitoribosome assembly and function, and the clinical landscape of mitochondrial disorders driven by mutations in mitoribosome components and assembly factors, to portray how basic and clinical studies combined help us better understand both mitochondrial biology and medicine.
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Affiliation(s)
- Alberto Ferrari
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA
| | - Samuel Del'Olio
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Molecular and Cellular Pharmacology Graduate Program, University of Miami Miller School of Medicine, FL, USA
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, FL, USA
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Adebayo OL, Dewenter I, Rinne L, Golubiani G, Solomonia R, Müller M. Intensified mitochondrial hydrogen peroxide release occurs in all brain regions, affects male as well as female Rett mice, and constitutes a life-long burden. Arch Biochem Biophys 2020; 696:108666. [PMID: 33160914 DOI: 10.1016/j.abb.2020.108666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/29/2020] [Accepted: 10/31/2020] [Indexed: 12/28/2022]
Abstract
The neurodevelopmental disorder Rett syndrome (RTT) affects mostly females. Upon an apparently normal initial development, cognitive impairment, irregular breathing, motor dysfunction, and epilepsy occur. The complex pathogenesis includes, among others, mitochondrial impairment, redox imbalance, and oxidative damage. As these arise already in neonatal Rett mice, they were proposed contributors of disease progression. Several mitochondrial studies in RTT used either full brains or selected brain regions only. Here, we mapped mitochondria-related ROS generation brain wide. Using sophisticated multi-sample spectrofluorimetry, H2O2 release by isolated mitochondria was quantified in a coupled reaction of Amplex UltraRed and horseradish peroxidase. All brain regions and the entire lifespan were characterized in male and female mice. In WT mice, mitochondrial H2O2 release was usually highest in cortex and lowest in hippocampus. Maximum rates occurred at postnatal day (PD) 10 and they slightly declined with further maturation. Already at PD 10, male and female Rett mice showed exaggerated mitochondrial H2O2 releases in first brain regions and persistent brain-wide increases from PD 50 on. Interestingly, female Rett mice were more intensely affected than male Rett mice, with their brainstem, midbrain and hippocampus being most severely struck. In conclusion, we used a reliable multi-sample cuvette-based assay on mitochondrial ROS release to perform brain-wide analyzes along the entire lifespan. Mitochondrial H2O2 release in Rett mice is intensified in all brain regions, affects hemizygous males and heterozygous females, and involves all maturational stages. Therefore, intensified mitochondrial H2O2 release seriously needs to be considered throughout RTT pathogenesis and may constitute a potential therapeutic target.
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Affiliation(s)
- Olusegun L Adebayo
- Georg-August-Universität Göttingen, Universitätsmedizin Göttingen, Zentrum Physiologie und Pathophysiologie, Institut für Neuro- und Sinnesphysiologie, Germany; Department of Biochemistry, Faculty of Basic Medical Sciences, Redeemer's University, P.M.B. 230, Ede, Osun State, Nigeria
| | - Ina Dewenter
- Georg-August-Universität Göttingen, Universitätsmedizin Göttingen, Zentrum Physiologie und Pathophysiologie, Institut für Neuro- und Sinnesphysiologie, Germany
| | - Lena Rinne
- Georg-August-Universität Göttingen, Universitätsmedizin Göttingen, Zentrum Physiologie und Pathophysiologie, Institut für Neuro- und Sinnesphysiologie, Germany
| | - Gocha Golubiani
- Georg-August-Universität Göttingen, Universitätsmedizin Göttingen, Zentrum Physiologie und Pathophysiologie, Institut für Neuro- und Sinnesphysiologie, Germany; Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
| | - Revaz Solomonia
- Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
| | - Michael Müller
- Georg-August-Universität Göttingen, Universitätsmedizin Göttingen, Zentrum Physiologie und Pathophysiologie, Institut für Neuro- und Sinnesphysiologie, Germany.
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Cicaloni V, Pecorelli A, Tinti L, Rossi M, Benedusi M, Cervellati C, Spiga O, Santucci A, Hayek J, Salvini L, Tinti C, Valacchi G. Proteomic profiling reveals mitochondrial alterations in Rett syndrome. Free Radic Biol Med 2020; 155:37-48. [PMID: 32445864 DOI: 10.1016/j.freeradbiomed.2020.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/14/2020] [Accepted: 05/16/2020] [Indexed: 12/11/2022]
Abstract
Rett syndrome (RTT) is a pervasive neurodevelopmental disorder associated with mutation in MECP2 gene. Despite a well-defined genetic cause, there is a growing consensus that a metabolic component could play a pivotal role in RTT pathophysiology. Indeed, perturbed redox homeostasis and inflammation, i.e. oxinflammation, with mitochondria dysfunction as the central hub between the two phenomena, appear as possible key contributing factors to RTT pathogenesis and its clinical features. While these RTT-related changes have been widely documented by transcriptomic profiling, proteomics studies supporting these evidences are still limited. Here, using primary dermal fibroblasts from control and patients, we perform a large-scale proteomic analysis that, together with data mining approaches, allow us to carry out the first comprehensive characterization of RTT cellular proteome, showing mainly changes in expression of proteins involved in the mitochondrial network. These findings parallel with an altered expression of key mediators of mitochondrial dynamics and mitophagy associated with abnormal mitochondrial morphology. In conclusion, our proteomic analysis confirms the pathological relevance of mitochondrial dysfunction in RTT pathogenesis and progression.
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Affiliation(s)
- Vittoria Cicaloni
- Toscana Life Science Foundation, Via Fiorentina 1, 53100, Siena, Italy
| | - Alessandra Pecorelli
- Plants for Human Health Institute, Animal Science Dept., NC Research Campus, NC State University, 600 Laureate Way, Kannapolis, NC, 28081, USA
| | - Laura Tinti
- Toscana Life Science Foundation, Via Fiorentina 1, 53100, Siena, Italy
| | - Marco Rossi
- Toscana Life Science Foundation, Via Fiorentina 1, 53100, Siena, Italy
| | - Mascia Benedusi
- Department of Biomedical and Specialist Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Carlo Cervellati
- Department of Morphology and Experimental Medicine University of Ferrara, via Borsari 46, 44121, Ferrara, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, Via Aldo Moro 2, University of Siena, Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, Via Aldo Moro 2, University of Siena, Siena, Italy
| | - Joussef Hayek
- Child Neuropsychiatry Unit, University General Hospital, Azienda Ospedaliera Universitaria Senese, Viale M. Bracci 16, 53100, Siena, Italy
| | - Laura Salvini
- Toscana Life Science Foundation, Via Fiorentina 1, 53100, Siena, Italy
| | - Cristina Tinti
- Toscana Life Science Foundation, Via Fiorentina 1, 53100, Siena, Italy
| | - Giuseppe Valacchi
- Plants for Human Health Institute, Animal Science Dept., NC Research Campus, NC State University, 600 Laureate Way, Kannapolis, NC, 28081, USA; Department of Biomedical and Specialist Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy; Kyung Hee University, Department of Food and Nutrition, Seoul, South Korea.
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