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Zhang R, Chen L, Oliver LD, Voineskos AN, Park JY. SAN: mitigating spatial covariance heterogeneity in cortical thickness data collected from multiple scanners or sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.04.569619. [PMID: 38105933 PMCID: PMC10723364 DOI: 10.1101/2023.12.04.569619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
In neuroimaging studies, combining data collected from multiple study sites or scanners is becoming common to increase the reproducibility of scientific discoveries. At the same time, unwanted variations arise by using different scanners (inter-scanner biases), which need to be corrected before downstream analyses to facilitate replicable research and prevent spurious findings. While statistical harmonization methods such as ComBat have become popular in mitigating inter-scanner biases in neuroimaging, recent methodological advances have shown that harmonizing heterogeneous covariances results in higher data quality. In vertex-level cortical thickness data, heterogeneity in spatial autocorrelation is a critical factor that affects covariance heterogeneity. Our work proposes a new statistical harmonization method called SAN (Spatial Autocorrelation Normalization) that preserves homogeneous covariance vertex-level cortical thickness data across different scanners. We use an explicit Gaussian process to characterize scanner-invariant and scanner-specific variations to reconstruct spatially homogeneous data across scanners. SAN is computationally feasible, and it easily allows the integration of existing harmonization methods. We demonstrate the utility of the proposed method using cortical thickness data from the Social Processes Initiative in the Neurobiology of the Schizophrenia(s) (SPINS) study. SAN is publicly available as an R package.
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Affiliation(s)
- Rongqian Zhang
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - Linxi Chen
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | | | - Aristotle N. Voineskos
- Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Jun Young Park
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
- Department of Psychology, University of Toronto, Toronto, ON, Canada
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2
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Samet M, Yazdi M, Tajamolian M, Beygi M, Sheikhha MH, Hoseini SM. The Effect of Angiotensin-Converting Enzyme Insertion/Deletion Polymorphism on the Severity and Death Rate of COVID-19 in Iranian Patients. Biochem Genet 2023:10.1007/s10528-023-10614-3. [PMID: 38145438 DOI: 10.1007/s10528-023-10614-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023]
Abstract
The study was designed to assess the association of ACE I/D polymorphism with the severity and prognosis of COVID-19 in the Iranian population. Hence, 186 adult patients were categorized into three clinical groups based on the severity of COVID-19: 1) Outpatients or mildly symptomatic patients as control (n = 71); 2) Hospitalized patients or severe symptomatic cases (n = 53); 3) Inpatients led to ICU/death or critically ill patients needed mechanical ventilation (n = 62). The possible association of ACE I/D polymorphism with the risk of comorbidities and serum level of C-reactive protein was evaluated in two severe cases. The results showed that the frequency of D and I alleles are 69.35% and 30.65%, respectively, in the total population. The analysis of allelic frequencies via Fisher's exact test confirmed significantly higher frequency of D allele in both severe groups than that in the mild one, 78.31% in Hospitalized patients (OR = 2.56; 95% CI 1.46 to 4.46; p-value = 0.0011) and 74.19% in Inpatients led to ICU/death (OR = 2.04; 95% CI = 1.22 to 3.43; p-value = 0.0094) compared to 58.45% in Outpatients. The results of genotype proportions displayed an association between COVID-19 severity and DD genotype. Overall, our findings in Iranian patients supported the undeniable role of the DD genotype in the intensity of the disease, comparable to other populations. Furthermore, there is no definite evidence regarding the protective effect of the I allele in our inquiry.
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Affiliation(s)
- Mohammad Samet
- Departments of Internal Medicine, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Mehran Yazdi
- Departments of Internal Medicine, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Masoud Tajamolian
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mahdi Beygi
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Hasan Sheikhha
- Research and Clinical Center for Infertility, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Seyed Mehdi Hoseini
- Abortion Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran.
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Dery KJ, Wong Z, Wei M, Kupiec-Weglinski JW. Mechanistic Insights into Alternative Gene Splicing in Oxidative Stress and Tissue Injury. Antioxid Redox Signal 2023. [PMID: 37776178 DOI: 10.1089/ars.2023.0437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Significance: Oxidative stress (OS) and inflammation are inducers of tissue injury. Alternative splicing (AS) is an essential regulatory step for diversifying the eukaryotic proteome. Human diseases link AS to OS; however, the underlying mechanisms must be better understood. Recent Advances: Genome‑wide profiling studies identify new differentially expressed genes induced by OS-dependent ischemia/reperfusion injury. Overexpression of RNA-binding protein RBFOX1 protects against inflammation. Hypoxia-inducible factor-1α directs polypyrimidine tract binding protein 1 to regulate mouse carcinoembryonic antigen-related cell adhesion molecule 1 (Ceacam1) AS under OS conditions. Heterogeneous nuclear ribonucleoprotein L variant 1 contains an RGG/RG motif that coordinates with transcription factors to influence human CEACAM1 AS. Hypoxia intervention involving short interfering RNAs directed to long-noncoding RNA 260 polarizes M2 macrophages toward an anti-inflammatory phenotype and alleviates OS by inhibiting IL-28RA gene AS. Critical Issues: Protective mechanisms that eliminate reactive oxygen species (ROS) are important for resolving imbalances that lead to chronic inflammation. Defects in AS can cause ROS generation, cell death regulation, and the activation of innate and adaptive immune factors. We propose that AS pathways link redox regulation to the activation or suppression of the inflammatory response during cellular stress. Future Directions: Emergent studies using molecule-mediated RNA splicing are being conducted to exploit the immunogenicity of AS protein products. Deciphering the mechanisms that connect misspliced OS and pathologies should remain a priority. Controlled release of RNA directly into cells with clinical applications is needed as the demand for innovative nucleic acid delivery systems continues to be demonstrated.
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Affiliation(s)
- Kenneth J Dery
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Zeriel Wong
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Megan Wei
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Jerzy W Kupiec-Weglinski
- The Dumont-UCLA Transplantation Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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Saeliw T, Kanlayaprasit S, Thongkorn S, Songsritaya K, Sanannam B, Sae-Lee C, Jindatip D, Hu VW, Sarachana T. Epigenetic Gene-Regulatory Loci in Alu Elements Associated with Autism Susceptibility in the Prefrontal Cortex of ASD. Int J Mol Sci 2023; 24:ijms24087518. [PMID: 37108679 PMCID: PMC10139202 DOI: 10.3390/ijms24087518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/07/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Alu elements are transposable elements that can influence gene regulation through several mechanisms; nevertheless, it remains unclear whether dysregulation of Alu elements contributes to the neuropathology of autism spectrum disorder (ASD). In this study, we characterized transposable element expression profiles and their sequence characteristics in the prefrontal cortex tissues of ASD and unaffected individuals using RNA-sequencing data. Our results showed that most of the differentially expressed transposable elements belong to the Alu family, with 659 loci of Alu elements corresponding to 456 differentially expressed genes in the prefrontal cortex of ASD individuals. We predicted cis- and trans-regulation of Alu elements to host/distant genes by conducting correlation analyses. The expression level of Alu elements correlated significantly with 133 host genes (cis-regulation, adjusted p < 0.05) associated with ASD as well as the cell survival and cell death of neuronal cells. Transcription factor binding sites in the promoter regions of differentially expressed Alu elements are conserved and associated with autism candidate genes, including RORA. COBRA analyses of postmortem brain tissues showed significant hypomethylation in global methylation analyses of Alu elements in ASD subphenotypes as well as DNA methylation of Alu elements located near the RNF-135 gene (p < 0.05). In addition, we found that neuronal cell density, which was significantly increased (p = 0.042), correlated with the expression of genes associated with Alu elements in the prefrontal cortex of ASD. Finally, we determined a relationship between these findings and the ASD severity (i.e., ADI-R scores) of individuals with ASD. Our findings provide a better understanding of the impact of Alu elements on gene regulation and molecular neuropathology in the brain tissues of ASD individuals, which deserves further investigation.
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Affiliation(s)
- Thanit Saeliw
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Songphon Kanlayaprasit
- Systems Neuroscience of Autism and Psychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Surangrat Thongkorn
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Kwanjira Songsritaya
- The M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Bumpenporn Sanannam
- Division of Anatomy, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani 12120, Thailand
| | - Chanachai Sae-Lee
- Research Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Depicha Jindatip
- Systems Neuroscience of Autism and Psychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Valerie W Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20052, USA
| | - Tewarit Sarachana
- Systems Neuroscience of Autism and Psychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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Gupta K, Kaur G, Pathak T, Banerjee I. Systematic review and meta-analysis of human genetic variants contributing to COVID-19 susceptibility and severity. Gene 2022; 844:146790. [PMID: 35987511 PMCID: PMC9384365 DOI: 10.1016/j.gene.2022.146790] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/25/2022] [Accepted: 08/05/2022] [Indexed: 12/12/2022]
Abstract
The COVID-19 pandemic has spawned global health crisis of unprecedented magnitude, claiming millions of lives and pushing healthcare systems in many countries to the brink. Among several factors that contribute to an increased risk of COVID-19 and progression to exacerbated manifestations, host genetic landscape is increasingly being recognized as a critical determinant of susceptibility/resistance to infection and a prognosticator of clinical outcomes in infected individuals. Recently, several case-control association studies investigated the influence of human gene variants on COVID-19 susceptibility and severity to identify the culpable mutations. However, a comprehensive synthesis of the recent advances in COVID-19 host genetics research was lacking, and the inconsistent findings of the association studies required reliable evaluation of the strength of association with greater statistical power. In this study, we embarked on a systematic search of all possible reports of genetic association with COVID-19 till April 07, 2022, and performed meta-analyses of all the genetic polymorphisms that were examined in at least three studies. After identifying a total of 84 studies that investigated the association of 130 polymorphisms in 61 genes, we performed meta-analyses of all the eligible studies. Seven genetic polymorphisms involving 15,550 cases and 444,007 controls were explored for association with COVID-19 susceptibility, of which, ACE1 I/D rs4646994/rs1799752, APOE rs429358, CCR5 rs333, and IFITM3 rs12252 showed increased risk of infection. Meta-analyses of 11 gene variants involving 6702 patients with severe COVID-19 and 8640 infected individuals with non-severe manifestations revealed statistically significant association of ACE2 rs2285666, ACE2 rs2106809, ACE2 rs2074192, AGTR1 rs5186, and TNFA rs1800629 with COVID-19 severity. Overall, our study presents a synthesis of evidence on all the genetic determinants implicated in COVID-19 to date, and provides evidence of correlation between the above polymorphisms with COVID-19 susceptibility and severity.
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Affiliation(s)
| | | | | | - Indranil Banerjee
- Cellular Virology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali (IISER Mohali), Sector 81, S.A.S Nagar, Mohali 140306, India.
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Wang J, Weatheritt R, Voineagu I. Alu-minating the Mechanisms Underlying Primate Cortex Evolution. Biol Psychiatry 2022; 92:760-771. [PMID: 35981906 DOI: 10.1016/j.biopsych.2022.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/04/2022] [Accepted: 04/28/2022] [Indexed: 11/02/2022]
Abstract
The higher-order cognitive functions observed in primates correlate with the evolutionary enhancement of cortical volume and folding, which in turn are driven by the primate-specific expansion of cellular diversity in the developing cortex. Underlying these changes is the diversification of molecular features including the creation of human and/or primate-specific genes, the activation of specific molecular pathways, and the interplay of diverse layers of gene regulation. We review and discuss evidence for connections between Alu elements and primate brain evolution, the evolutionary milestones of which are known to coincide along primate lineages. Alus are repetitive elements that contribute extensively to the acquisition of novel genes and the expansion of diverse gene regulatory layers, including enhancers, alternative splicing, RNA editing, and microRNA pathways. By reviewing the impact of Alus on molecular features linked to cortical expansions or gyrification or implications in cognitive deficits, we suggest that future research focusing on the role of Alu-derived molecular events in the context of brain development may greatly advance our understanding of higher-order cognitive functions and neurologic disorders.
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Affiliation(s)
- Juli Wang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
| | - Robert Weatheritt
- St Vincent Clinical School, University of New South Wales, Sydney, Australia; Garvan Institute of Medical Research, EMBL Australia, Sydney, New South Wales, Australia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia; Cellular Genomics Futures Institute, University of New South Wales, Sydney, Australia.
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7
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Römer C. Viruses and Endogenous Retroviruses as Roots for Neuroinflammation and Neurodegenerative Diseases. Front Neurosci 2021; 15:648629. [PMID: 33776642 PMCID: PMC7994506 DOI: 10.3389/fnins.2021.648629] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/05/2021] [Indexed: 12/15/2022] Open
Abstract
Many neurodegenerative diseases are associated with chronic inflammation in the brain and periphery giving rise to a continuous imbalance of immune processes. Next to inflammation markers, activation of transposable elements, including long intrespersed nuclear elements (LINE) elements and endogenous retroviruses (ERVs), has been identified during neurodegenerative disease progression and even correlated with the clinical severity of the disease. ERVs are remnants of viral infections in the human genome acquired during evolution. Upon activation, they produce transcripts and the phylogenetically youngest ones are still able to produce viral-like particles. In addition, ERVs can bind transcription factors and modulate immune response. Being between own and foreign, ERVs are reviewed in the context of viral infections of the central nervous system, in aging and neurodegenerative diseases. Moreover, this review tests the hypothesis that viral infection may be a trigger at the onset of neuroinflammation and that ERVs sustain the inflammatory imbalance by summarizing existing data of neurodegenerative diseases associated with viruses and/or ERVs.
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Affiliation(s)
- Christine Römer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, The Berlin Institute for Medical Systems Biology, Berlin, Germany
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8
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Hsieh SW, Liu MW, Huang LC, Wu MN, Yang YH. The Impact of Angiotensin-Converting Enzyme Gene on Behavioral and Psychological Symptoms of Dementia in Alzheimer’s Disease. Curr Alzheimer Res 2020; 16:1269-1275. [DOI: 10.2174/1567205017666200103114550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 12/12/2019] [Accepted: 12/30/2019] [Indexed: 12/17/2022]
Abstract
Background:
The Angiotensin-Converting Enzyme (ACE) gene has drawn attention for its
possible role in regulating the degradation of β-amyloid (Aβ), yet its role in affecting the cognitive and
psychiatric symptoms of Alzheimer`s Disease (AD) patients has yet to be elucidated.
Objective:
This study aimed to investigate whether the ACE gene acts as a risk factor of Behavioral and
Psychological Symptoms of Dementia (BPSD) in the AD population.
Method:
The genotyping of ACE and Apolipoprotein E gene with allele ε4(APOEε4) was determined
among 360s clinically diagnosed AD patients. Symptoms and severity of BPSD were evaluated annually
via Neuropsychiatric Inventory (NPI).
Results:
At the base measurement of the first year of patient recruitment, there were no significant contributory
risk factors to NPI score. In the two-year follow-up, ACE insertion polymorphism showed a
significant risk (adjusted odds ratio=1.65, 95% CI=1.1- 2.5, p=0.019) of progression of NPI total score.
Conclusion:
ACE gene is involved in aggravating BPSD among AD patients.
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Affiliation(s)
- Sun-Wung Hsieh
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Wei Liu
- Department of Surgery, Cathay General Hospital, Taipei, Taiwan
| | - Ling-Chun Huang
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Meng-Ni Wu
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yuan-Han Yang
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
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Hwang YE, Baek YM, Baek A, Kim DE. Oxidative stress causes Alu RNA accumulation via PIWIL4 sequestration into stress granules. BMB Rep 2019. [PMID: 30103846 PMCID: PMC6476485 DOI: 10.5483/bmbrep.2019.52.3.146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The Alu element, the most abundant transposable element, is transcribed to Alu RNA. We hypothesized that the PIWI protein regulates the expression of Alu RNA in retinal pigment epithelial (RPE) cells, where accumulated Alu RNA leads to macular degeneration. Alu transcription was induced in RPE cells treated with H2O2. At an early stage of oxidative stress, PIWIL4 was translocated into the nucleus; however, subsequently it was sequestered into cytoplasmic stress granules, resulting in the accumulation of Alu RNA. An elevated amount of Alu RNA was positively correlated with the disruption of the epithelial features of RPE via induction of mesenchymal transition. Therefore, we suggest that oxidative stress causes Alu RNA accumulation via PIWIL4 sequestration into the cytoplasmic stress granules.
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Affiliation(s)
- Yeo Eun Hwang
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Yu Mi Baek
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Ahruem Baek
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea
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ALUminating the Path of Atherosclerosis Progression: Chaos Theory Suggests a Role for Alu Repeats in the Development of Atherosclerotic Vascular Disease. Int J Mol Sci 2018; 19:ijms19061734. [PMID: 29895733 PMCID: PMC6032270 DOI: 10.3390/ijms19061734] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 06/04/2018] [Accepted: 06/09/2018] [Indexed: 12/12/2022] Open
Abstract
Atherosclerosis (ATH) and coronary artery disease (CAD) are chronic inflammatory diseases with an important genetic background; they derive from the cumulative effect of multiple common risk alleles, most of which are located in genomic noncoding regions. These complex diseases behave as nonlinear dynamical systems that show a high dependence on their initial conditions; thus, long-term predictions of disease progression are unreliable. One likely possibility is that the nonlinear nature of ATH could be dependent on nonlinear correlations in the structure of the human genome. In this review, we show how chaos theory analysis has highlighted genomic regions that have shared specific structural constraints, which could have a role in ATH progression. These regions were shown to be enriched with repetitive sequences of the Alu family, genomic parasites that have colonized the human genome, which show a particular secondary structure and are involved in the regulation of gene expression. Here, we show the impact of Alu elements on the mechanisms that regulate gene expression, especially highlighting the molecular mechanisms via which the Alu elements alter the inflammatory response. We devote special attention to their relationship with the long noncoding RNA (lncRNA); antisense noncoding RNA in the INK4 locus (ANRIL), a risk factor for ATH; their role as microRNA (miRNA) sponges; and their ability to interfere with the regulatory circuitry of the (nuclear factor kappa B) NF-κB response. We aim to characterize ATH as a nonlinear dynamic system, in which small initial alterations in the expression of a number of repetitive elements are somehow amplified to reach phenotypic significance.
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Mafra FFP, Gattai PP, Macedo MM, Mori MA, Araujo RC. The angiotensin-I-converting enzyme insertion/deletion in polymorphic element codes for an AluYa5 RNA that downregulates gene expression. THE PHARMACOGENOMICS JOURNAL 2018; 18:517-527. [PMID: 29789676 DOI: 10.1038/s41397-018-0020-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 06/14/2017] [Accepted: 09/18/2017] [Indexed: 01/06/2023]
Abstract
Angiotensin-I-converting enzyme (ACE) is involved in the synthesis and degradation of important bioactive peptides. The ACE gene has a 287-bp insertion/deletion polymorphism that controls ACE expression through a mechanism that remains elusive. In this study, we found that the 287-bp polymorphic element of the ACE gene, a member of the AluYa5 sub-family of Alu elements, codes for an RNA molecule that controls the levels of ACE mRNA. Transient transfection of a plasmid containing a CMV promoter upstream of the ACE polymorphic element resulted in significant expression of an AluYa5 RNA and reduced ACE mRNA expression as well as ACE enzymatic activity in AD 293 cells. The AluYa5 element also independently reduced the expression of other genes, regardless of whether these genes harbored Alu elements within their genomic context. Interestingly, the CMV promoter was not required for the expression of the AluYa5 element in AD 293 cells. The 287-bp sequence was sufficient to produce AluYa5 RNA and led to a significant reduction in ACE gene expression. Moreover, the removal of an 11-bp fragment of the 3' end of the ACE polymorphic sequence, which is specific to this particular AluYa5 element, did not prevent this element from being expressed but did affect its ability to target ACE expression. Thus, the expression of the AluYa5 polymorphic element within the ACE gene could explain why patients carrying the ACE insertion polymorphism have reduced risk of developing several chronic diseases.
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Affiliation(s)
| | - Pedro P Gattai
- Dept. of Biophysics, Federal University of São Paulo, São Paulo, Brazil
| | - Michel M Macedo
- Dept. of Biophysics, Federal University of São Paulo, São Paulo, Brazil
| | - Marcelo A Mori
- Dept. of Biophysics, Federal University of São Paulo, São Paulo, Brazil
| | - Ronaldo C Araujo
- Dept. of Biophysics, Federal University of São Paulo, São Paulo, Brazil.
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12
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Larsen PA, Hunnicutt KE, Larsen RJ, Yoder AD, Saunders AM. Warning SINEs: Alu elements, evolution of the human brain, and the spectrum of neurological disease. Chromosome Res 2018; 26:93-111. [PMID: 29460123 PMCID: PMC5857278 DOI: 10.1007/s10577-018-9573-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/14/2018] [Accepted: 01/15/2018] [Indexed: 12/28/2022]
Abstract
Alu elements are a highly successful family of primate-specific retrotransposons that have fundamentally shaped primate evolution, including the evolution of our own species. Alus play critical roles in the formation of neurological networks and the epigenetic regulation of biochemical processes throughout the central nervous system (CNS), and thus are hypothesized to have contributed to the origin of human cognition. Despite the benefits that Alus provide, deleterious Alu activity is associated with a number of neurological and neurodegenerative disorders. In particular, neurological networks are potentially vulnerable to the epigenetic dysregulation of Alu elements operating across the suite of nuclear-encoded mitochondrial genes that are critical for both mitochondrial and CNS function. Here, we highlight the beneficial neurological aspects of Alu elements as well as their potential to cause disease by disrupting key cellular processes across the CNS. We identify at least 37 neurological and neurodegenerative disorders wherein deleterious Alu activity has been implicated as a contributing factor for the manifestation of disease, and for many of these disorders, this activity is operating on genes that are essential for proper mitochondrial function. We conclude that the epigenetic dysregulation of Alu elements can ultimately disrupt mitochondrial homeostasis within the CNS. This mechanism is a plausible source for the incipient neuronal stress that is consistently observed across a spectrum of sporadic neurological and neurodegenerative disorders.
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Affiliation(s)
- Peter A Larsen
- Department of Biology, Duke University, Durham, NC, 27708, USA.
- Duke Lemur Center, Duke University, Durham, NC, 27708, USA.
- Department of Biology, Duke University, 130 Science Drive, Box 90338, Durham, NC, 27708, USA.
| | | | - Roxanne J Larsen
- Duke University School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Duke Lemur Center, Duke University, Durham, NC, 27708, USA
| | - Ann M Saunders
- Zinfandel Pharmaceuticals Inc, Chapel Hill, NC, 27709, USA
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13
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Fekih-Mrissa N, Bedoui I, Sayeh A, Derbali H, Mrad M, Mrissa R, Nsiri B. Association between an angiotensin-converting enzyme gene polymorphism and Alzheimer's disease in a Tunisian population. Ann Gen Psychiatry 2017; 16:41. [PMID: 29176997 PMCID: PMC5693601 DOI: 10.1186/s12991-017-0164-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 11/08/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The angiotensin-converting enzyme gene (ACE) insertion/deletion (I/D or indel) polymorphism has long been linked to Alzheimer's disease (AD), but the interpretation of established data remains controversial. The aim of this study was to determine whether the angiotensin-converting enzyme is associated with the risk of Alzheimer's disease in Tunisian patients. METHODS We analyzed the genotype and allele frequency distribution of the ACE I/D gene polymorphism in 60 Tunisian AD patients and 120 healthy controls. RESULTS There is a significantly increased risk of AD in carriers of the D/D genotype (51.67% in patients vs. 31.67% in controls; p = .008, OR = 2.32). The D allele was also more frequently found in patients compared with controls (71.67% vs. 56.25%; p = .003, OR = 2.0). Moreover, as assessed by the Mini-Mental State Examination, patient D/D carriers were more frequently found to score in the severe category of dementia (65%) as compared to the moderate category (32%) or mild category (3%). CONCLUSIONS The D/D genotype and D allele of the ACE I/D polymorphism were associated with an increased risk in the development of AD in a Tunisian population. Furthermore, at the time of patient evaluation (average age 75 years), patients suffering with severe dementia were found predominantly in D/D carriers and, conversely, the D/D genotype and D allele were more frequently found in AD patients with severe dementia. These preliminary exploratory results should be confirmed in larger studies and further work is required to explore and interpret possible alternative findings in diverse populations.
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Affiliation(s)
- Najiba Fekih-Mrissa
- Laboratory of Molecular Biology, Department of Hematology, Military Hospital of Tunisia, Mont Fleury, 1008 Tunis, Tunisia
| | - Ines Bedoui
- Department of Neurology, Military Hospital of Tunisia, Montfleury, Tunis, 1008 Tunisia
| | - Aycha Sayeh
- Laboratory of Molecular Biology, Department of Hematology, Military Hospital of Tunisia, Mont Fleury, 1008 Tunis, Tunisia
| | - Hajer Derbali
- Department of Neurology, Military Hospital of Tunisia, Montfleury, Tunis, 1008 Tunisia
| | - Meriem Mrad
- Laboratory of Molecular Biology, Department of Hematology, Military Hospital of Tunisia, Mont Fleury, 1008 Tunis, Tunisia
| | - Ridha Mrissa
- Department of Neurology, Military Hospital of Tunisia, Montfleury, Tunis, 1008 Tunisia
| | - Brahim Nsiri
- Laboratory of Molecular Biology, Department of Hematology, Military Hospital of Tunisia, Mont Fleury, 1008 Tunis, Tunisia
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Kim S, Cho CS, Han K, Lee J. Structural Variation of Alu Element and Human Disease. Genomics Inform 2016; 14:70-77. [PMID: 27729835 PMCID: PMC5056899 DOI: 10.5808/gi.2016.14.3.70] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 01/04/2023] Open
Abstract
Transposable elements are one of major sources to cause genomic instability through various mechanisms including de novo insertion, insertion-mediated genomic deletion, and recombination-associated genomic deletion. Among them is Alu element which is the most abundant element, composing ~10% of the human genome. The element emerged in the primate genome 65 million years ago and has since propagated successfully in the human and non-human primate genomes. Alu element is a non-autonomous retrotransposon and therefore retrotransposed using L1-enzyme machinery. The 'master gene' model has been generally accepted to explain Alu element amplification in primate genomes. According to the model, different subfamilies of Alu elements are created by mutations on the master gene and most Alu elements are amplified from the hyperactive master genes. Alu element is frequently involved in genomic rearrangements in the human genome due to its abundance and sequence identity between them. The genomic rearrangements caused by Alu elements could lead to genetic disorders such as hereditary disease, blood disorder, and neurological disorder. In fact, Alu elements are associated with approximately 0.1% of human genetic disorders. The first part of this review discusses mechanisms of Alu amplification and diversity among different Alu subfamilies. The second part discusses the particular role of Alu elements in generating genomic rearrangements as well as human genetic disorders.
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Affiliation(s)
- Songmi Kim
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Korea.; BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
| | - Chun-Sung Cho
- Department of Neurosurgery, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Kyudong Han
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Korea.; BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
| | - Jungnam Lee
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Florida, Gainesville, FL 32610, USA
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15
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Wu SJ, Soulez M, Yang YH, Chu CS, Shih SC, Hébert MJ, Kuo MC, Hsieh YJ. Local Augmented Angiotensinogen Secreted from Apoptotic Vascular Endothelial Cells Is a Vital Mediator of Vascular Remodelling. PLoS One 2015; 10:e0132583. [PMID: 26147666 PMCID: PMC4492977 DOI: 10.1371/journal.pone.0132583] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 06/16/2015] [Indexed: 12/25/2022] Open
Abstract
Vascular remodelling is a critical vasculopathy found in atheromatous diseases and allograft failures. The local renin angiotensin system (RAS) has been implicated in vascular remodelling. However, the mechanisms by which the augmented local RAS is associated with the initial event of endothelial cell apoptosis in injured vasculature remain undefined. We induced the apoptosis of human umbilical vein endothelial cells (HUVECs) and vascular smooth muscle cells (VSMCs) through serum starvation (SS). After the cells were subjected to SS, we found that the mRNA expression of angiotensinogen (AGT) was increased by >3-fold in HUVECs and by approximately 2.5-fold in VSMCs. In addition, the expression of angiotensin-converting enzyme (ACE) mRNA was increased in VSMCs but decreased to 50% in HUVECs during the same apoptotic process. Increases in the expression of AGT protein and angiotensin II (Ang II) were found in a serum-free medium conditioned by HUVECs (SSC). The increased Ang II was suppressed using lisinopril (an ACE inhibitor) treatment. Moreover, the activation of ERK1/2 induced by the SSC in VSMCs was also suppressed by losartan. In conclusion, we first demonstrated that the augmented AGT released from apoptotic endothelial cells acts as a vital progenitor of Ang II to accelerate vascular remodelling, and we suggest that blocking local augmented Ang II might be an effective strategy for restraining intimal hyperplasia.
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Affiliation(s)
- Shyh-Jong Wu
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Mathilde Soulez
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Ya-Hui Yang
- Department of Occupational Safety and Hygiene, Fooyin University, Kaohsiung, Taiwan
| | - Chih-Sheng Chu
- Division of Cardiology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shih-Chuan Shih
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Marie-Josée Hébert
- Research Centre, Centre Hospitalier de l'Université de Montréal (CRCHUM), Hôpital Notre Dame and Université de Montréal, Montréal, QC, Canada
| | - Mei-Chuan Kuo
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ya-Ju Hsieh
- Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
- * E-mail:
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16
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Wang XB, Cui NH, Yang J, Qiu XP, Gao JJ, Yang N, Zheng F. Angiotensin-converting enzyme insertion/deletion polymorphism is not a major determining factor in the development of sporadic Alzheimer disease: evidence from an updated meta-analysis. PLoS One 2014; 9:e111406. [PMID: 25360660 PMCID: PMC4216072 DOI: 10.1371/journal.pone.0111406] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/23/2014] [Indexed: 11/19/2022] Open
Abstract
Angiotensin-converting enzyme gene (ACE) insertion/deletion (I/D) polymorphism have long been linked to sporadic Alzheimer disease (SAD), but the established data remained controversial. To clarify this inconsistency, a comprehensive meta-analysis was conducted. Through searching of Pubmed, Embase, Alzgene, China National Knowledge Infrastructure (CNKI) and manually searching relevant references, 53 independent studies from 48 articles were included, involving a total of 8153 cases and 14932 controls. The strength of association was assessed by using odds ratios (ORs) with 95% confidence intervals (CIs). Further stratified analyses and heterogeneity analyses were tested, as was publication bias. Overall, significant associations were revealed between I/D polymorphism and SAD risk using allelic comparison (OR = 1.09, 95%CI = 1.01–1.17, p = 0.030), homozygote comparison (OR = 1.17, 95%CI = 1.01–1.34, p = 0.030) and the dominant model (OR = 1.16, 95%CI = 1.04–1.29, p = 0.008), but they were not sufficiently robust to withstand the false-positive report probability (FPRP) analyses. Otherwise, in subgroup analyses restricted to the high quality studies, the large sample size studies and studies with population-based controls, no significant association was observed in any genetic models. In summary, the current meta-analysis suggested that the ACE I/D polymorphism is unlikely to be a major determining factor in the development of SAD.
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Affiliation(s)
- Xue-bin Wang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ning-hua Cui
- Department of Clinical Laboratory, Children's Hospital of Zhengzhou, Zhengzhou, Henan, China
| | - Jie Yang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xue-ping Qiu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jia-jia Gao
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Na Yang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Fang Zheng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- * E-mail:
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17
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Teranishi J, Yamamoto R, Nagasawa Y, Shoji T, Iwatani H, Okada N, Moriyama T, Yamauchi A, Tsubakihara Y, Imai E, Rakugi H, Isaka Y. ACE insertion/deletion polymorphism (rs1799752) modifies the renoprotective effect of renin-angiotensin system blockade in patients with IgA nephropathy. J Renin Angiotensin Aldosterone Syst 2014; 16:633-41. [DOI: 10.1177/1470320313515036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 11/01/2013] [Indexed: 11/15/2022] Open
Affiliation(s)
- Junya Teranishi
- Department of Geriatric Medicine and Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Ryohei Yamamoto
- Department of Geriatric Medicine and Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Yasuyuki Nagasawa
- Department of Geriatric Medicine and Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Tatsuya Shoji
- Department of Kidney Disease and Hypertension, Osaka General Medical Center, Japan
| | - Hirotsugu Iwatani
- Department of Geriatric Medicine and Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Noriyuki Okada
- Clinical Laboratory Medicine, Osaka General Medical Center, Japan
| | | | - Atsushi Yamauchi
- Division of Nephrology, Department of Internal Medicine, Osaka Rosai Hospital, Japan
| | - Yoshiharu Tsubakihara
- Department of Kidney Disease and Hypertension, Osaka General Medical Center, Japan
- Department of Comprehensive Kidney Disease Research, Osaka University Graduate School of Medicine, Japan
| | - Enyu Imai
- Department of Geriatric Medicine and Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Hiromi Rakugi
- Department of Geriatric Medicine and Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Yoshitaka Isaka
- Department of Geriatric Medicine and Nephrology, Osaka University Graduate School of Medicine, Japan
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Wright JW, Kawas LH, Harding JW. A Role for the Brain RAS in Alzheimer's and Parkinson's Diseases. Front Endocrinol (Lausanne) 2013; 4:158. [PMID: 24298267 PMCID: PMC3829467 DOI: 10.3389/fendo.2013.00158] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/09/2013] [Indexed: 12/30/2022] Open
Abstract
The brain renin-angiotensin system (RAS) has available the necessary functional components to produce the active ligands angiotensins II (AngII), angiotensin III, angiotensins (IV), angiotensin (1-7), and angiotensin (3-7). These ligands interact with several receptor proteins including AT1, AT2, AT4, and Mas distributed within the central and peripheral nervous systems as well as local RASs in several organs. This review first describes the enzymatic pathways in place to synthesize these ligands and the binding characteristics of these angiotensin receptor subtypes. We next discuss current hypotheses to explain the disorders of Alzheimer's disease (AD) and Parkinson's disease (PD), as well as research efforts focused on the use of angiotensin converting enzyme (ACE) inhibitors and angiotensin receptor blockers (ARBs), in their treatment. ACE inhibitors and ARBs are showing promise in the treatment of several neurodegenerative pathologies; however, there is a need for the development of analogs capable of penetrating the blood-brain barrier and acting as agonists or antagonists at these receptor sites. AngII and AngIV have been shown to play opposing roles regarding memory acquisition and consolidation in animal models. We discuss the development of efficacious AngIV analogs in the treatment of animal models of AD and PD. These AngIV analogs act via the AT4 receptor subtype which may coincide with the hepatocyte growth factor/c-Met receptor system. Finally, future research directions are described concerning new approaches to the treatment of these two neurological diseases.
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Affiliation(s)
- John W. Wright
- Departments of Psychology, Integrative Physiology and Neuroscience, Program in Biotechnology, Washington State University, Pullman, WA, USA
| | - Leen H. Kawas
- Departments of Psychology, Integrative Physiology and Neuroscience, Program in Biotechnology, Washington State University, Pullman, WA, USA
| | - Joseph W. Harding
- Departments of Psychology, Integrative Physiology and Neuroscience, Program in Biotechnology, Washington State University, Pullman, WA, USA
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