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Morales E, Prieto-Sánchez MT, Mendiola J, Cutillas-Tolín A, Adoamnei E, Valera-Gran D, Martínez-Graciá C, Santaella-Pascual M, Suárez-Martinez C, Vioque J, Castaños MJ, Del Castillo E, García-Marcos L. Maternal non-compliance with recommended folic acid supplement use alters global DNA methylation in cord blood of newborns: A cohort study. Clin Nutr 2024; 43:1191-1198. [PMID: 38631086 DOI: 10.1016/j.clnu.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND & AIMS Prenatal folate exposure may alter epigenetic marks in the offspring. We aimed to evaluate associations between prenatal exposure to folic acid (FA) in preconception and in utero with cord blood DNA methylation in long interspersed nuclear element 1 (LINE-1) and Alu short interspersed nuclear elements (SINEs) as markers of global DNA methylation levels. METHODS Data come from 325 mother-child pairs participating in the Nutrition in Early Life and Asthma (NELA) birth cohort (2015-2018). Pregnant women were asked about supplement use, including brand name and dose, one month before pregnancy (preconception) and through the trimesters of pregnancy. Maternal dietary folate intake was assessed using a validated food frequency questionnaire with additional questions for FA supplement use. Folate serum levels were measured in mothers at 24 weeks of gestation and in cord blood of newborns. DNA methylation was quantitatively assessed by bisulfite pyrosequencing on 5 LINE-1 and 3 Alu different elements. Associations were estimated using multivariable linear regression models. RESULTS A reduction in methylation levels of LINE-1 in newborns was associated with the use of FA supplements below the recommended doses (<400 ug/day) during preconception (-0.50; 95% CI: -0.91, -0.09; P = 0.016), and from preconception up to 12 weeks of gestation (-0.48; 95% CI: -0.88, -0.08; P = 0.018). Maternal use of FA supplements above the tolerable upper intake level of 1000 ug/day from preconception until 12 weeks of gestation was also related to lower methylation in LINE-1 at birth (-0.77; 95% CI: -1.52, -0.02; P = 0.044). Neither FA supplement use after 12 weeks of gestation nor maternal total folate intake (diet plus supplements) were associated with global DNA methylation levels at birth. CONCLUSIONS Maternal non-compliance with the use of FA supplement recommendations from preconception up to 12 weeks of gestation reduces offspring global DNA methylation levels at birth.
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Affiliation(s)
- Eva Morales
- Division of Preventive Medicine and Public Health, Department of Public Health Sciences, Faculty of Medicine, University of Murcia, Murcia, Spain; Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain.
| | - María Teresa Prieto-Sánchez
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain; Materno-Fetal Medicine Unit, Obstetrics and Gynaecology Service, "Virgen de la Arrixaca" University Clinical Hospital, University of Murcia, Murcia, Spain
| | - Jaime Mendiola
- Division of Preventive Medicine and Public Health, Department of Public Health Sciences, Faculty of Medicine, University of Murcia, Murcia, Spain; Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
| | - Ana Cutillas-Tolín
- Division of Preventive Medicine and Public Health, Department of Public Health Sciences, Faculty of Medicine, University of Murcia, Murcia, Spain; Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
| | - Evdochia Adoamnei
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain; Department of Nursing, University of Murcia School of Nursing, Murcia, Spain
| | - Desirée Valera-Gran
- Department of Surgery and Pathology, Miguel Hernandez University, 03550 Alicante, Spain; Grupo de Investigación en Terapia Ocupacional (InTeO), Miguel Hernandez University, 03550 Alicante, Spain; Health and Biomedical Research Institute of Alicante, University Miguel Hernandez (ISABIAL-UMH), Alicante, Spain
| | - Carmen Martínez-Graciá
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain; Department of Food Science and Technology, Faculty of Veterinary, University of Murcia, Murcia, Spain
| | - Marina Santaella-Pascual
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain; Department of Food Science and Technology, Faculty of Veterinary, University of Murcia, Murcia, Spain
| | - Clara Suárez-Martinez
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain; Department of Food Science and Technology, Faculty of Veterinary, University of Murcia, Murcia, Spain
| | - Jesús Vioque
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain; Health and Biomedical Research Institute of Alicante, University Miguel Hernandez (ISABIAL-UMH), Alicante, Spain
| | - María Jesús Castaños
- Obstetrics & Gynecology Service, Virgen de la Arrixaca University Clinical Hospital, University of Murcia, Murcia, Spain
| | - Eva Del Castillo
- Obstetrics & Gynecology Service, Virgen de la Arrixaca University Clinical Hospital, University of Murcia, Murcia, Spain
| | - Luis García-Marcos
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain; Paediatric Allergy and Pulmonology Units, Virgen de la Arrixaca University Children's Hospital, University of Murcia, Murcia, Spain; ARADyAL Allergy Network, Madrid, Spain
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Barington M, Bak M, Kjartansdóttir KR, Hansen TVO, Birkedal U, Østergaard E, Hove HB. Novel Alu insertion in the ZEB2 gene causing Mowat-Wilson syndrome. Am J Med Genet A 2024:e63581. [PMID: 38600862 DOI: 10.1002/ajmg.a.63581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/06/2024] [Accepted: 02/21/2024] [Indexed: 04/12/2024]
Abstract
Alu elements are short, interspersed elements located throughout the genome, playing a role in human diversity, and occasionally causing genetic diseases. Here, we report a novel Alu insertion causing Mowat-Wilson syndrome, a rare neurodevelopmental disorder, in an 8-year-old boy displaying the typical clinical features for Mowat-Wilson syndrome. The variant was not initially detected in genome sequencing data, but through deep phenotyping, which pointed to only one plausible candidate gene, manual inspection of genome sequencing alignment data enabled us to identify a de novo heterozygous Alu insertion in exon 8 of the ZEB2 gene. Nanopore long-read sequencing confirmed the Alu insertion, leading to the formation of a premature stop codon and likely haploinsufficiency of ZEB2. This underscores the importance of deep phenotyping and mobile element insertion analysis in uncovering genetic causes of monogenic disorders as these elements might be overlooked in standard next-generation sequencing protocols.
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Affiliation(s)
- Maria Barington
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mads Bak
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ulf Birkedal
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hanne Buciek Hove
- Center for Rare Diseases, Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital, Copenhagen, Denmark
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3
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Konečná K, Zapletalová P, Freiberger T, Tichý L. LDLR gene rearrangements in Czech FH patients likely arise from one mutational event. Lipids Health Dis 2024; 23:36. [PMID: 38308247 PMCID: PMC10835926 DOI: 10.1186/s12944-024-02013-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/09/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Large deletions and duplications within the low-density lipoprotein receptor (LDLR) gene make up approximately 10% of LDLR pathogenic variants found in Czech patients with familial hypercholesterolemia. The goal of this study was to test the hypothesis that all probands with each rearrangement share identical breakpoints inherited from a common ancestor and to determine the role of Alu repetitive elements in the generation of these rearrangements. METHODS The breakpoint sequence was determined by PCR amplification and Sanger sequencing. To confirm the breakpoint position, an NGS analysis was performed. Haplotype analysis of common LDLR variants was performed using PCR and Sanger sequencing. RESULTS The breakpoints of 8 rearrangements within the LDLR gene were analysed, including the four most common LDLR rearrangements in the Czech population (number of probands ranging from 8 to 28), and four less common rearrangements (1-4 probands). Probands with a specific rearrangement shared identical breakpoint positions and haplotypes associated with the rearrangement, suggesting a shared origin from a common ancestor. All breakpoints except for one were located inside an Alu element. In 6 out of 8 breakpoints, there was high homology (≥ 70%) between the two Alu repeats in which the break occurred. CONCLUSIONS The most common rearrangements of the LDLR gene in the Czech population likely arose from one mutational event. Alu elements likely played a role in the generation of the majority of rearrangements inside the LDLR gene.
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Affiliation(s)
- Kateřina Konečná
- Centre of Molecular Biology and Genetics, University Hospital Brno, Jihlavská 20, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Petra Zapletalová
- Centre of Molecular Biology and Genetics, University Hospital Brno, Jihlavská 20, Brno, 625 00, Czech Republic
| | - Tomáš Freiberger
- Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Centre for Cardiovascular Surgery and Transplantation, Pekařská 53, 656 91, Brno, Czech Republic
| | - Lukáš Tichý
- Centre of Molecular Biology and Genetics, University Hospital Brno, Jihlavská 20, Brno, 625 00, Czech Republic.
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Hall LL, Creamer KM, Byron M, Lawrence JB. Differences in Alu vs L1-rich chromosome bands underpin architectural reorganization of the inactive-X chromosome and SAHFs. bioRxiv 2024:2024.01.09.574742. [PMID: 38260534 PMCID: PMC10802495 DOI: 10.1101/2024.01.09.574742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The linear DNA sequence of mammalian chromosomes is organized in large blocks of DNA with similar sequence properties, producing a pattern of dark and light staining bands on mitotic chromosomes. Cytogenetic banding is essentially invariant between people and cell-types and thus may be assumed unrelated to genome regulation. We investigate whether large blocks of Alu-rich R-bands and L1-rich G-bands provide a framework upon which functional genome architecture is built. We examine two models of large-scale chromatin condensation: X-chromosome inactivation and formation of senescence-associated heterochromatin foci (SAHFs). XIST RNA triggers gene silencing but also formation of the condensed Barr Body (BB), thought to reflect cumulative gene silencing. However, we find Alu-rich regions are depleted from the L1-rich BB, supporting it is a dense core but not the entire chromosome. Alu-rich bands are also gene-rich, affirming our earlier findings that genes localize at the outer periphery of the BB. SAHFs similarly form within each territory by coalescence of syntenic L1 regions depleted for highly Alu-rich DNA. Analysis of senescent cell Hi-C data also shows large contiguous blocks of G-band and R-band DNA remodel as a segmental unit. Entire dark-bands gain distal intrachromosomal interactions as L1-rich regions form the SAHF. Most striking is that sharp Alu peaks within R-bands resist these changes in condensation. We further show that Chr19, which is exceptionally Alu rich, fails to form a SAHF. Collective results show regulation of genome architecture corresponding to large blocks of DNA and demonstrate resistance of segments with high Alu to chromosome condensation.
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Affiliation(s)
- Lisa L. Hall
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kevin M. Creamer
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Meg Byron
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Jeanne B. Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
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Brooks WH. Polyamine Dysregulation and Nucleolar Disruption in Alzheimer's Disease. J Alzheimers Dis 2024; 98:837-857. [PMID: 38489184 DOI: 10.3233/jad-231184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
A hypothesis of Alzheimer's disease etiology is proposed describing how cellular stress induces excessive polyamine synthesis and recycling which can disrupt nucleoli. Polyamines are essential in nucleolar functions, such as RNA folding and ribonucleoprotein assembly. Changes in the nucleolar pool of anionic RNA and cationic polyamines acting as counterions can cause significant nucleolar dynamics. Polyamine synthesis reduces S-adenosylmethionine which, at low levels, triggers tau phosphorylation. Also, polyamine recycling reduces acetyl-CoA needed for acetylcholine, which is low in Alzheimer's disease. Extraordinary nucleolar expansion and/or contraction can disrupt epigenetic control in peri-nucleolar chromatin, such as chromosome 14 with the presenilin-1 gene; chromosome 21 with the amyloid precursor protein gene; chromosome 17 with the tau gene; chromosome 19 with the APOE4 gene; and the inactive X chromosome (Xi; aka "nucleolar satellite") with normally silent spermine synthase (polyamine synthesis) and spermidine/spermine-N1-acetyltransferase (polyamine recycling) alleles. Chromosomes 17, 19 and the Xi have high concentrations of Alu elements which can be transcribed by RNA polymerase III if positioned nucleosomes are displaced from the Alu elements. A sudden flood of Alu RNA transcripts can competitively bind nucleolin which is usually bound to Alu sequences in structural RNAs that stabilize the nucleolar heterochromatic shell. This Alu competition leads to loss of nucleolar integrity with leaking of nucleolar polyamines that cause aggregation of phosphorylated tau. The hypothesis was developed with key word searches (e.g., PubMed) using relevant terms (e.g., Alzheimer's, lupus, nucleolin) based on a systems biology approach and exploring autoimmune disease tautology, gaining synergistic insights from other diseases.
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Herbert A. The Intransitive Logic of Directed Cycles and Flipons Enhances the Evolution of Molecular Computers by Augmenting the Kolmogorov Complexity of Genomes. Int J Mol Sci 2023; 24:16482. [PMID: 38003672 PMCID: PMC10671625 DOI: 10.3390/ijms242216482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Cell responses are usually viewed as transitive events with fixed inputs and outputs that are regulated by feedback loops. In contrast, directed cycles (DCs) have all nodes connected, and the flow is in a single direction. Consequently, DCs can regenerate themselves and implement intransitive logic. DCs are able to couple unrelated chemical reactions to each edge. The output depends upon which node is used as input. DCs can also undergo selection to minimize the loss of thermodynamic entropy while maximizing the gain of information entropy. The intransitive logic underlying DCs enhances their programmability and impacts their evolution. The natural selection of DCs favors the persistence, adaptability, and self-awareness of living organisms and does not depend solely on changes to coding sequences. Rather, the process can be RNA-directed. I use flipons, nucleic acid sequences that change conformation under physiological conditions, as a simple example and then describe more complex DCs. Flipons are often encoded by repeats and greatly increase the Kolmogorov complexity of genomes by adopting alternative structures. Other DCs allow cells to regenerate, recalibrate, reset, repair, and rewrite themselves, going far beyond the capabilities of current computational devices. Unlike Turing machines, cells are not designed to halt but rather to regenerate.
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Affiliation(s)
- Alan Herbert
- InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA
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Devine SE. Emerging Opportunities to Study Mobile Element Insertions and Their Source Elements in an Expanding Universe of Sequenced Human Genomes. Genes (Basel) 2023; 14:1923. [PMID: 37895272 PMCID: PMC10606232 DOI: 10.3390/genes14101923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/29/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Three mobile element classes, namely Alu, LINE-1 (L1), and SVA elements, remain actively mobile in human genomes and continue to produce new mobile element insertions (MEIs). Historically, MEIs have been discovered and studied using several methods, including: (1) Southern blots, (2) PCR (including PCR display), and (3) the detection of MEI copies from young subfamilies. We are now entering a new phase of MEI discovery where these methods are being replaced by whole genome sequencing and bioinformatics analysis to discover novel MEIs. We expect that the universe of sequenced human genomes will continue to expand rapidly over the next several years, both with short-read and long-read technologies. These resources will provide unprecedented opportunities to discover MEIs and study their impact on human traits and diseases. They also will allow the MEI community to discover and study the source elements that produce these new MEIs, which will facilitate our ability to study source element regulation in various tissue contexts and disease states. This, in turn, will allow us to better understand MEI mutagenesis in humans and the impact of this mutagenesis on human biology.
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Affiliation(s)
- Scott E Devine
- Institute for Genome Sciences, Department of Medicine, and Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Thongsroy J, Mutirangura A. Decreased Alu methylation in type 2 diabetes mellitus patients increases HbA1c levels. J Clin Lab Anal 2023; 37:e24966. [PMID: 37743692 PMCID: PMC10623537 DOI: 10.1002/jcla.24966] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/20/2023] [Accepted: 09/13/2023] [Indexed: 09/26/2023] Open
Abstract
INTRODUCTION Alu hypomethylation is a common epigenetic process that promotes genomic instability with aging phenotypes, which leads to type 2 diabetes mellitus (type 2 DM). Previously, our results showed significantly decreased Alu methylation levels in type 2 DM patients. In this study, we aimed to investigate the longitudinal changes in Alu methylation levels in these patients. RESULTS We observed significantly decreased Alu methylation levels in type 2 DM patients compared with normal (p = 0.0462). Moreover, our findings demonstrated changes in Alu hypomethylation over a follow-up period within the same individuals (p < 0.0001). A reduction in Alu methylation was found in patients with increasing HbA1c levels (p = 0.0013) and directly correlated with increased HbA1c levels in type 2 DM patients (r = -0.2273, p = 0.0387). CONCLUSIONS Alu methylation in type 2 DM patients progressively decreases with increasing HbA1c levels. This observation suggests a potential association between Alu hypomethylation and the underlying molecular mechanisms of elevated blood glucose. Furthermore, monitoring Alu methylation levels may serve as a valuable biomarker for assessing the clinical outcomes of type 2 DM.
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Affiliation(s)
- Jirapan Thongsroy
- School of MedicineWalailak UniversityNakhon Si ThammaratThailand
- Research Center in Tropical PathobiologyWalailak UniversityNakhon Si ThammaratThailand
| | - Apiwat Mutirangura
- Center for Excellence in Molecular Genetics of Cancer and Human DiseasesChulalongkorn UniversityBangkokThailand
- Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
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Helm BM, Smith AM, Schmit K, Landis BJ, Vatta M, Ware SM. Disruption of FBN1 by an Alu element insertion: A novel genetic cause of Marfan syndrome. Eur J Med Genet 2023; 66:104775. [PMID: 37264881 DOI: 10.1016/j.ejmg.2023.104775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 02/17/2023] [Accepted: 04/29/2023] [Indexed: 06/03/2023]
Abstract
Alu elements are retrotransposons with ubiquitous presence in the human genome that have contributed to human genomic diversity and health. These approximately 300-bp sequences can cause or mediate disease by disrupting coding/splicing regions in the germline, by insertional mutagenesis in somatic cells, and in promoting formation of copy-number variants. Alu elements may also disrupt epigenetic regulation by affecting non-coding regulatory regions. There are increasing reports of apparently sporadic and inherited genetic disorders caused by Alu-related gene disruption, but Marfan syndrome resulting from Alu element insertion has not been previously described. We report a family with classic features of Marfan syndrome whose previous FBN1 genetic testing was inconclusive. Using contemporary next-generation sequencing and bioinformatics analysis, a pathogenic/disruptive Alu insertion occurring in the coding region of the FBN1 gene was identified (c.6564_6565insAlu; p. Glu2189fs) and was confirmed and specified further with Sanger sequencing. This identified the molecular basis of disease in the family that was missed using previous genetic testing technologies and highlights a novel pathogenic mechanism for Marfan syndrome. This case adds to the growing literature of Mendelian diseases caused by Alu retrotransposition, and it also shows the growing capability of genomic technologies for detecting atypical mutation events.
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Affiliation(s)
- Benjamin M Helm
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Epidemiology, Indiana University Fairbanks School of Public Health, Indianapolis, IN, USA.
| | - Amanda M Smith
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kelly Schmit
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Benjamin J Landis
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.
| | | | - Stephanie M Ware
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.
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Dinh P, Tran C, Dinh T, Ali A, Pan S. Hsa_circRNA_0000284 acts as a ceRNA to participate in coronary heart disease progression by sponging miRNA-338-3p via regulating the expression of ETS1. J Biomol Struct Dyn 2023:1-14. [PMID: 37334706 DOI: 10.1080/07391102.2023.2225109] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Coronary heart disease (CHD) is a prevalent global cause of death. Research suggests that circular RNAs (circRNAs) play a role in the development of CHD. In this study, we investigated the expression of hsa_circRNA_0000284 in peripheral blood leukocytes (PBLs) obtained from a cohort of 94 CHD patients aged over 50 years, as well as 126 age-matched healthy controls (HC). An in vitro inflammatory and oxidative injury cell model that simulates CHD was used to evaluate changes in hsa_ circRNA _0000284 under stress. CRISPR/Cas9 technology was used to evaluate changes in hsa_circRNA_0000284 expression. An hsa_ circRNA_0000284 overexpression and silencing cell model was used to analyze the biological functions of hsa_circRNA_0000284. Bioinformatics, qRT-PCR, viral transfection technology, and luciferase assays were used to evaluate the potential hsa_circRNA_0000284/miRNA-338-3p/ETS1 axis. Western blotting analysis was performed to detect protein expression. Herein, PBLs from CHD patients exhibited downregulation of hsa_circRNA_0000284 expression. Exposure to oxidative stress and inflammation can induce damage to human umbilical endothelial cells, resulting in the downregulation of hsa_circRNA_0000284 expression. The expression of hsa_circRNA_0000284 in EA-hy926 cells was significantly reduced after the AluSq2 element of hsa_circRNA_0000284 had been knocked out. The expression of hsa_circRNA_0000284 affected proliferation, cycle distribution, aging, and apoptosis in EA-hy926 cells. Consistent with the results of cell transfection experiments and luciferase assays, Western blotting showed that hsa_circRNA_0000284 plays a role in the regulation of hsa-miRNA-338-3p expression. Subsequently, hsa-miRNA-338-3p was found to be involved in the regulation of ETS1 expression.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- PhongSon Dinh
- College of Medicine and Pharmacy, Duy Tan University, Danang, Vietnam
| | - ChauMyThanh Tran
- College of Medicine and Pharmacy, Duy Tan University, Danang, Vietnam
| | - ThiPhuongHoai Dinh
- Department of Neurosurgery, Hue University Hospital, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Awais Ali
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - ShangLing Pan
- Departments of Pathophysiology, Guangxi Medical University, Nanning, Guangxi, China
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Ravaioli F, Bacalini MG, Giuliani C, Pellegrini C, D’Silva C, De Fanti S, Pirazzini C, Giorgi G, Del Re B. Ev aluation of DNA Methylation Profiles of LINE-1, Alu and Ribosomal DNA Repeats in Human Cell Lines Exposed to Radiofrequency Radiation. Int J Mol Sci 2023; 24:9380. [PMID: 37298336 PMCID: PMC10253908 DOI: 10.3390/ijms24119380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
A large body of evidence indicates that environmental agents can induce alterations in DNA methylation (DNAm) profiles. Radiofrequency electromagnetic fields (RF-EMFs) are radiations emitted by everyday devices, which have been classified as "possibly carcinogenic"; however, their biological effects are unclear. As aberrant DNAm of genomic repetitive elements (REs) may promote genomic instability, here, we sought to determine whether exposure to RF-EMFs could affect DNAm of different classes of REs, such as long interspersed nuclear elements-1 (LINE-1), Alu short interspersed nuclear elements and ribosomal repeats. To this purpose, we analysed DNAm profiles of cervical cancer and neuroblastoma cell lines (HeLa, BE(2)C and SH-SY5Y) exposed to 900 MHz GSM-modulated RF-EMF through an Illumina-based targeted deep bisulfite sequencing approach. Our findings showed that radiofrequency exposure did not affect the DNAm of Alu elements in any of the cell lines analysed. Conversely, it influenced DNAm of LINE-1 and ribosomal repeats in terms of both average profiles and organisation of methylated and unmethylated CpG sites, in different ways in each of the three cell lines studied.
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Affiliation(s)
- Francesco Ravaioli
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Maria Giulia Bacalini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, 40126 Bologna, Italy;
| | - Camilla Pellegrini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Chiara D’Silva
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Sara De Fanti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Chiara Pirazzini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy;
| | - Gianfranco Giorgi
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy;
| | - Brunella Del Re
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy;
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12
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Colantoni A, Capauto D, Alfano V, D'Ambra E, D'Uva S, Tartaglia GG, Morlando M. FUS Alters circRNA Metabolism in Human Motor Neurons Carrying the ALS-Linked P525L Mutation. Int J Mol Sci 2023; 24. [PMID: 36834591 DOI: 10.3390/ijms24043181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Deregulation of RNA metabolism has emerged as one of the key events leading to the degeneration of motor neurons (MNs) in Amyotrophic Lateral Sclerosis (ALS) disease. Indeed, mutations on RNA-binding proteins (RBPs) or on proteins involved in aspects of RNA metabolism account for the majority of familiar forms of ALS. In particular, the impact of the ALS-linked mutations of the RBP FUS on many aspects of RNA-related processes has been vastly investigated. FUS plays a pivotal role in splicing regulation and its mutations severely alter the exon composition of transcripts coding for proteins involved in neurogenesis, axon guidance, and synaptic activity. In this study, by using in vitro-derived human MNs, we investigate the effect of the P525L FUS mutation on non-canonical splicing events that leads to the formation of circular RNAs (circRNAs). We observed altered levels of circRNAs in FUSP525L MNs and a preferential binding of the mutant protein to introns flanking downregulated circRNAs and containing inverted Alu repeats. For a subset of circRNAs, FUSP525L also impacts their nuclear/cytoplasmic partitioning, confirming its involvement in different processes of RNA metabolism. Finally, we assess the potential of cytoplasmic circRNAs to act as miRNA sponges, with possible implications in ALS pathogenesis.
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13
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Kraveishvili N, Kvaratskhelia E, Surmava S, Kvintradze M, Zarandia M, Gorgiladze T, Abzianidze E. DNA methylation status of interspersed repetitive sequences in patients with migraine. J Int Med Res 2023; 51:3000605231152109. [PMID: 36734246 PMCID: PMC9900668 DOI: 10.1177/03000605231152109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVE To analyse the methylation status of the Long Interspersed Nuclear Element-1 (LINE-1) and Short Interspersed Nuclear Element Alu (Alu) of peripheral blood mononuclear cells (PBMCs) from patients with migraine compared with healthy control subjects. METHODS This case-control study recruited patients with migraine without aura and age-matched healthy control subjects. PBMCs were purified from peripheral blood samples. Methylation levels and patterns of LINE-1 and Alu sequences were evaluated using combined bisulfite restriction analysis-interspersed repetitive sequences polymerase chain reaction. RESULTS A total of 84 patients with migraine and 82 age-matched healthy controls were enrolled in the study. High levels of unmethylated cytosines in both the LINE-1 and Alu repetitive elements were observed in the migraine group compared with the control subjects. In addition, a significant difference was detected in the methylation level of LINE-1 between TT and CC genotype groups of the methylenetetrahydrofolate reductase gene. CONCLUSIONS These results suggest that analysis of epigenetic biomarkers in PBMCs may help to identify patients at a higher risk of migraine development.
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Affiliation(s)
- Nino Kraveishvili
- Department of Molecular and Medical Genetics, Tbilisi State
Medical University, Tbilisi, Georgia,Department of Neurology, Tbilisi Institute of Medicine, Tbilisi,
Georgia
| | - Eka Kvaratskhelia
- Department of Molecular and Medical Genetics, Tbilisi State
Medical University, Tbilisi, Georgia,Eka Kvaratskhelia, Department of Molecular
and Medical Genetics, Tbilisi State Medical University, 5 Khvichia str., 0160
Tbilisi, Georgia.
| | - Sandro Surmava
- Department of Molecular and Medical Genetics, Tbilisi State
Medical University, Tbilisi, Georgia
| | - Merab Kvintradze
- Department of Molecular and Medical Genetics, Tbilisi State
Medical University, Tbilisi, Georgia
| | - Maia Zarandia
- Department of Molecular and Medical Genetics, Tbilisi State
Medical University, Tbilisi, Georgia
| | - Tinatin Gorgiladze
- Department of Dentistry, Batumi Shota Rustaveli State
University, Batumi, Georgia
| | - Elene Abzianidze
- Department of Molecular and Medical Genetics, Tbilisi State
Medical University, Tbilisi, Georgia
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14
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Beaumont R, Akam L, Singh P, Bhatti JS, Mastana S. Genomic diversity and differentiation of Alu insertion polymorphisms in a native British and four South Asian migrant populations. Ann Hum Biol 2023; 50:117-122. [PMID: 36786492 DOI: 10.1080/03014460.2023.2180091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
BACKGROUND Alu insertions are bi-allelic and primate-specific, this makes them a useful marker for studying genetic variation, migration patterns, forensic analyses, paternity, and evolutionary heritage; however, specific population studies are limited. AIM The objective of this study is to document the level and extent of genetic variation at 39 different Alu loci in five populations (British, Indian Punjabi, Indian Gujarati, Pakistani, and Bangladeshi) from the East Midlands region of the UK. Genetic data on migrant populations is currently limited. SUBJECTS AND METHODS DNA samples (n = 543) were analysed for 39 Alu insertion polymorphisms using specific primers and standard protocols. Data were analysed for population and forensic genetic parameters. RESULTS All studied Alus were polymorphic in the British White population while South Asian migrant populations had a variable number of loci which were monomorphic. Highest heterozygosities and lowest match probabilities were observed in the British sample, while the Bangladeshi sample had the lowest heterozygosity and higher match probability. CONCLUSION The analysed Alus insertions (TPA25, Ya5NBC123, Ya5NBC182, Ya5NBC241, and Ya5NBC242) are highly polymorphic and variable among migrant populations. These loci could be useful for population genomic and differentiation studies.
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Affiliation(s)
- Rebekah Beaumont
- Human Genomics Lab, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Liz Akam
- Human Genomics Lab, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Puneetpal Singh
- Department of Human Genetics, Punjabi University, Patiala, India
| | - Jasvinder Singh Bhatti
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Sarabjit Mastana
- Human Genomics Lab, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
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15
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Storer JM, Walker JA, Baker JN, Hossain S, Roos C, Wheeler TJ, Batzer MA. Framework of the Alu Subfamily Evolution in the Platyrrhine Three-Family Clade of Cebidae, Callithrichidae, and Aotidae. Genes (Basel) 2023; 14:249. [PMID: 36833175 PMCID: PMC9956951 DOI: 10.3390/genes14020249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/14/2023] [Indexed: 01/20/2023] Open
Abstract
The history of Alu retroposons has been choreographed by the systematic accumulation of inherited diagnostic nucleotide substitutions to form discrete subfamilies, each having a distinct nucleotide consensus sequence. The oldest subfamily, AluJ, gave rise to AluS after the split between Strepsirrhini and what would become Catarrhini and Platyrrhini. The AluS lineage gave rise to AluY in catarrhines and to AluTa in platyrrhines. Platyrrhine Alu subfamilies Ta7, Ta10, and Ta15 were assigned names based on a standardized nomenclature. However, with the subsequent intensification of whole genome sequencing (WGS), large scale analyses to characterize Alu subfamilies using the program COSEG identified entire lineages of subfamilies simultaneously. The first platyrrhine genome with WGS, the common marmoset (Callithrix jacchus; [caljac3]), resulted in Alu subfamily names sf0 to sf94 in an arbitrary order. Although easily resolved by alignment of the consensus sequences, this naming convention can become increasingly confusing as more genomes are independently analyzed. In this study, we reported Alu subfamily characterization for the platyrrhine three-family clade of Cebidae, Callithrichidae, and Aotidae. We investigated one species/genome from each recognized family of Callithrichidae and Aotidae and of both subfamilies (Cebinae and Saimiriinae) of the family Cebidae. Furthermore, we constructed a comprehensive network of Alu subfamily evolution within the three-family clade of platyrrhines to provide a working framework for future research. Alu expansion in the three-family clade has been dominated by AluTa15 and its derivatives.
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Affiliation(s)
- Jessica M. Storer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA; (J.M.S.); (J.A.W.)
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA; (J.M.S.); (J.A.W.)
| | - Jasmine N. Baker
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Shifat Hossain
- Department of Pharmacy Practice & Science, University of Arizona, Tucson, AZ 85721, USA; (S.H.); (T.J.W.)
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
| | - Travis J. Wheeler
- Department of Pharmacy Practice & Science, University of Arizona, Tucson, AZ 85721, USA; (S.H.); (T.J.W.)
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA; (J.M.S.); (J.A.W.)
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16
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Garcia-Cañadas M, Sanchez-Luque FJ, Sanchez L, Rojas J, Garcia Perez JL. LINE-1 Retrotransposition Assays in Embryonic Stem Cells. Methods Mol Biol 2023; 2607:257-309. [PMID: 36449167 DOI: 10.1007/978-1-0716-2883-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The ongoing mobilization of active non-long terminal repeat (LTR) retrotransposons continues to impact the genomes of most mammals, including humans and rodents. Non-LTR retrotransposons mobilize using an intermediary RNA and a copy-and-paste mechanism termed retrotransposition. Non-LTR retrotransposons are subdivided into long and short interspersed elements (LINEs and SINEs, respectively), depending on their size and autonomy; while active class 1 LINEs (LINE-1s or L1s) encode the enzymatic machinery required to mobilize in cis, active SINEs use the enzymatic machinery of active LINE-1s to mobilize in trans. The mobilization mechanism used by LINE-1s/SINEs was exploited to develop ingenious plasmid-based retrotransposition assays in cultured cells, which typically exploit a reporter gene that can only be activated after a round of retrotransposition. Retrotransposition assays, in cis or in trans, are instrumental tools to study the biology of mammalian LINE-1s and SINEs. In fact, these and other biochemical/genetic assays were used to uncover that endogenous mammalian LINE-1s/SINEs naturally retrotranspose during early embryonic development. However, embryonic stem cells (ESCs) are typically used as a cellular model in these and other studies interrogating LINE-1/SINE expression/regulation during early embryogenesis. Thus, human and mouse ESCs represent an excellent model to understand how active retrotransposons are regulated and how their activity impacts the germline. Here, we describe robust and quantitative protocols to study human/mouse LINE-1 (in cis) and SINE (in trans) retrotransposition using (human and mice) ESCs. These protocols are designed to study the mobilization of active non-LTR retrotransposons in a cellular physiologically relevant context.
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Affiliation(s)
- Marta Garcia-Cañadas
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain.
| | - Francisco J Sanchez-Luque
- Institute of Parasitology and Biomedicine "Lopez-Neyra" (IPBLN), Spanish National Research Council (CSIC), PTS Granada, Granada, Spain
| | - Laura Sanchez
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Johana Rojas
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Jose L Garcia Perez
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain.
- MRC Human Genetics Unit, Institute of Genetics and Cancer (IGC)/University of Edinburgh, Western General Hospital Campus, Edinburgh, UK.
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17
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Wang X, Liu Y, Li J, Wang G. StackCirRNAPred: computational classification of long circRNA from other lncRNA based on stacking strategy. BMC Bioinformatics 2022; 23:563. [PMID: 36575368 PMCID: PMC9793644 DOI: 10.1186/s12859-022-05118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND CircRNAs are essential for the regulation of post-transcriptional gene expression, including as miRNA sponges, and play an important role in disease development. Some computational tools have been proposed recently to predict circRNA, since only one classifier is used, there is still much that can be done to improve the performance. RESULTS StackCirRNAPred was proposed, the computational classification of long circRNA from other lncRNA based on stacking strategy. In order to cope with the potential problem that a single feature might not be able to distinguish circRNA well from other lncRNA, we first extracted features from different sources, including nucleic acid composition, sequence spatial features and physicochemical properties, Alu and tandem repeats. We innovatively apply the stacking strategy to integrate the more advantageous classifiers of RF, LightGBM, XGBoost. This allows the model to incorporate these features more flexibly. StackCirRNAPred was found to be significantly better than other tools, with precision, accuracy, F1, recall and MCC of 0.843, 0.833, 0.831, 0.819 and 0.666 respectively. We tested it directly on the mouse dataset. StackCirRNAPred was still significantly better than other methods, with precision, accuracy, F1, recall and MCC of 0.837, 0.839, 0.839, 0.841, 0.677. CONCLUSIONS We proposed StackCirRNAPred based on stacking strategy to distinguish long circRNAs from other lncRNAs. With the test results demonstrating the validity and robustness of StackCirRNAPred, we hope StackCirRNAPred will complement existing circRNA prediction methods and is helpful in down-stream research.
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Affiliation(s)
- Xin Wang
- grid.19373.3f0000 0001 0193 3564School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yadong Liu
- grid.19373.3f0000 0001 0193 3564School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jie Li
- grid.19373.3f0000 0001 0193 3564School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Guohua Wang
- grid.19373.3f0000 0001 0193 3564School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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18
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Cardelli M, Pierpaoli E, Marchegiani F, Marcheselli F, Piacenza F, Giacconi R, Recchioni R, Casoli T, Stripoli P, Provinciali M, Matacchione G, Giuliani A, Ramini D, Sabbatinelli J, Bonafè M, Di Rosa M, Cherubini A, Di Pentima C, Spannella F, Antonicelli R, Bonfigli AR, Olivieri F, Lattanzio F. Biomarkers of cell damage, neutrophil and macrophage activation associated with in-hospital mortality in geriatric COVID-19 patients. Immun Ageing 2022; 19:65. [PMID: 36522763 PMCID: PMC9751505 DOI: 10.1186/s12979-022-00315-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/10/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND The risk for symptomatic COVID-19 requiring hospitalization is higher in the older population. The course of the disease in hospitalised older patients may show significant variation, from mild to severe illness, ultimately leading to death in the most critical cases. The analysis of circulating biomolecules involved in mechanisms of inflammation, cell damage and innate immunity could lead to identify new biomarkers of COVID-19 severity, aimed to improve the clinical management of subjects at higher risk of severe outcomes. In a cohort of COVID-19 geriatric patients (n= 156) who required hospitalization we analysed, on-admission, a series of circulating biomarkers related to neutrophil activation (neutrophil elastase, LL-37), macrophage activation (sCD163) and cell damage (nuclear cfDNA, mithocondrial cfDNA and nuclear cfDNA integrity). The above reported biomarkers were tested for their association with in-hospital mortality and with clinical, inflammatory and routine hematological parameters. Aim of the study was to unravel prognostic parameters for risk stratification of COVID-19 patients. RESULTS Lower n-cfDNA integrity, higher neutrophil elastase and higher sCD163 levels were significantly associated with an increased risk of in-hospital decease. Median (IQR) values observed in discharged vs. deceased patients were: 0.50 (0.30-0.72) vs. 0.33 (0.22-0.62) for n-cfDNA integrity; 94.0 (47.7-154.0) ng/ml vs. 115.7 (84.2-212.7) ng/ml for neutrophil elastase; 614.0 (370.0-821.0) ng/ml vs. 787.0 (560.0-1304.0) ng/ml for sCD163. The analysis of survival curves in patients stratified for tertiles of each biomarker showed that patients with n-cfDNA integrity < 0.32 or sCD163 in the range 492-811 ng/ml had higher risk of in-hospital decease than, respectively, patients with higher n-cfDNA integrity or lower sCD163. These associations were further confirmed in multivariate models adjusted for age, sex and outcome-related clinical variables. In these models also high levels of neutrophil elastase (>150 ng/ml) appeared to be independent predictor of in-hospital death. An additional analysis of neutrophil elastase in patients stratified for n-cfDNA integrity levels was conducted to better describe the association of the studied parameters with the outcome. CONCLUSIONS On the whole, biomarkers of cell-free DNA integrity, neutrophil and macrophage activation might provide a valuable contribution to identify geriatric patients with high risk of COVID-19 in-hospital mortality.
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Affiliation(s)
- M. Cardelli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - E. Pierpaoli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - F. Marchegiani
- Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA, Ancona, Italy
| | - F. Marcheselli
- Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA, Ancona, Italy
| | - F. Piacenza
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - R. Giacconi
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - R. Recchioni
- Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA, Ancona, Italy
| | - T. Casoli
- Center for Neurobiology of Aging, Scientific Technological Area, IRCCS INRCA, Via Birarelli 8, 60121 Ancona, Italy
| | - P. Stripoli
- Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA, Ancona, Italy
| | - M. Provinciali
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - G. Matacchione
- grid.7010.60000 0001 1017 3210Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/a, 60126 Ancona, Italy
| | - A. Giuliani
- grid.7010.60000 0001 1017 3210Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/a, 60126 Ancona, Italy
| | - D. Ramini
- Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA, Ancona, Italy
| | - J. Sabbatinelli
- grid.411490.90000 0004 1759 6306SOD Medicina di Laboratorio, Azienda Ospedaliero Universitaria Ospedali Riuniti, Ancona, Italy
| | - M. Bonafè
- grid.6292.f0000 0004 1757 1758Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - M. Di Rosa
- Unit of Geriatric Pharmacoepidemiology and Biostatistics, IRCCS INRCA, Cosenza, Italy
| | - A. Cherubini
- Geriatria, Accettazione geriatrica e Centro di Ricerca per l’invecchiamento, IRCCS INRCA, Ancona, Italy
| | - C. Di Pentima
- Internal Medicine and Geriatrics, IRCCS INRCA, Via della Montagnola 81, 60127 Ancona, Italy
| | - F. Spannella
- Internal Medicine and Geriatrics, IRCCS INRCA, Via della Montagnola 81, 60127 Ancona, Italy
| | | | - A. R. Bonfigli
- Scientific Direction and Geriatric Unit, IRCCS INRCA, Ancona, Italy
| | - F. Olivieri
- grid.7010.60000 0001 1017 3210Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/a, 60126 Ancona, Italy
| | - F. Lattanzio
- Scientific Direction and Geriatric Unit, IRCCS INRCA, Ancona, Italy
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Savage AL, Iacoangeli A, Schumann GG, Rubio-Roldan A, Garcia-Perez JL, Al Khleifat A, Koks S, Bubb VJ, Al-Chalabi A, Quinn JP. Characterisation of retrotransposon insertion polymorphisms in whole genome sequencing data from individuals with amyotrophic lateral sclerosis. Gene 2022; 843:146799. [PMID: 35963498 DOI: 10.1016/j.gene.2022.146799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/15/2022] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The genetics of an individual is a crucial factor in understanding the risk of developing the neurodegenerative disease amyotrophic lateral sclerosis (ALS). There is still a large proportion of the heritability of ALS, particularly in sporadic cases, to be understood. Among others, active transposable elements drive inter-individual variability, and in humans long interspersed element 1 (LINE1, L1), Alu and SINE-VNTR-Alu (SVA) retrotransposons are a source of polymorphic insertions in the population. We undertook a pilot study to characterise the landscape of non-reference retrotransposon insertion polymorphisms (non-ref RIPs) in 15 control and 15 ALS individuals' whole genomes from Project MinE, an international project to identify potential genetic causes of ALS. The combination of two bioinformatics tools (mobile element locator tool (MELT) and TEBreak) identified on average 1250 Alu, 232 L1 and 77 SVA non-ref RIPs per genome across the 30 analysed. Further PCR validation of individual polymorphic retrotransposon insertions showed a similar level of accuracy for MELT and TEBreak. Our preliminary study did not identify a specific RIP or a significant difference in the total number of non-ref RIPs in ALS compared to control genomes. The use of multiple bioinformatic tools improved the accuracy of non-ref RIP detection and our study highlights the potential importance of studying these elements further in ALS.
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Affiliation(s)
- Abigail L Savage
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK; Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen 63225, Germany
| | - Alejandro Rubio-Roldan
- Department of Genomic Medicine and Department of Oncology, GENYO, Centre for Genomics & Oncology, PTS Granada, 18007, Spain
| | - Jose L Garcia-Perez
- Department of Genomic Medicine and Department of Oncology, GENYO, Centre for Genomics & Oncology, PTS Granada, 18007, Spain; MRC-HGU Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, Western Australia 6009, Australia; Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Western Australia 6150, Australia
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK; Department of Neurology, King's College Hospital, London SE5 9RS, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
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Storer JM, Walker JA, Rewerts LC, Brown MA, Beckstrom TO, Herke SW, Roos C, Batzer MA. Owl Monkey Alu Insertion Polymorphisms and Aotus Phylogenetics. Genes (Basel) 2022; 13:2069. [PMID: 36360306 PMCID: PMC9691001 DOI: 10.3390/genes13112069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 07/30/2023] Open
Abstract
Owl monkeys (genus Aotus), or "night monkeys" are platyrrhine primates in the Aotidae family. Early taxonomy only recognized one species, Aotus trivirgatus, until 1983, when Hershkovitz proposed nine unique species designations, classified into red-necked and gray-necked species groups based predominately on pelage coloration. Recent studies questioned this conventional separation of the genus and proposed designations based on the geographical location of wild populations. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. A scaffold-level genome assembly for one Aotus species, Aotus nancymaae [Anan_2.0], facilitated large-scale ascertainment of nearly 2000 young lineage-specific Alu insertions. This study provides candidate oligonucleotides for locus-specific PCR assays for over 1350 of these elements. For 314 Alu elements across four taxa with multiple specimens, PCR analyses identified 159 insertion polymorphisms, including 21 grouping A. nancymaae and Aotus azarae (red-necked species) as sister taxa, with Aotus vociferans and A. trivirgatus (gray-necked) being more basal. DNA sequencing identified five novel Alu elements from three different taxa. The Alu datasets reported in this study will assist in species identification and provide a valuable resource for Aotus phylogenetics, population genetics and conservation strategies when applied to wild populations.
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Affiliation(s)
- Jessica M. Storer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Lydia C. Rewerts
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Morgan A. Brown
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Thomas O. Beckstrom
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
- Department of Oral and Maxillofacial Surgery, University of Washington, 1959 NE Pacific Street, Health Sciences Building B-241, Seattle, WA 98195, USA
| | - Scott W. Herke
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
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22
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El-Ahwany E, Hassan M, Elzallat M, Abdelsalam L, El-Sawy MAH, Seyam M. Association of Sat-a and Alu methylation status with HCV-induced chronic liver disease and hepatocellular carcinoma. Virus Res 2022; 321:198928. [PMID: 36100006 DOI: 10.1016/j.virusres.2022.198928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 09/02/2022] [Accepted: 09/09/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The combination of epigenetic and genetic abnormalities contributes together to the development of liver cancer. The methylation status of the repetitive elements (REs) in DNA has been investigated in a variety of human illnesses. However, the methylation patterns of Sat-α and Alu REs in chronic liver disease (CLD) and hepatocellular carcinoma (HCC) caused by hepatitis C virus (HCV) have never been studied before. METHODOLOGY In this study, 3 groups of participants including 50 patients having HCV-induced CLD, 50 patients having HCV-induced HCC, and 46 healthy subjects were subjected to measurement of Sat-α and Alu methylation using the quantitative MethyLight assay. RESULTS Sat-α and Alu methylation percentages decreased significantly in both CLD and HCC, compared to control. Also, a significant Sat-α hypomethylation was detected in HCC, compared to CLD. In addition, Sat-α and Alu methylation showed a significant decline as lesion size grew. However, only Sat-α hypomethylation was significantly increased in association with portal vein thrombosis and the MELD score. Sat-α methylation percentage had the highest sensitivity and specificity for diagnosing HCC (100% and 84.4%) followed by α-fetoprotein (80% and 84.4%) and Alu methylation (66% and 61.5%). Furthermore, there was a strong positive correlation between Sat-α and Alu methylation. CONCLUSIONS Measuring Sat-α and Alu methylation provides us with a new tool for early detecting HCV-induced CLD and hepatocarcinogenesis. Sat-α has the potential to be utilized as an independent predictive parameter for HCC development and progression because of its ability to distinguish between CLD and HCC with their different MELD scores.
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Affiliation(s)
- Eman El-Ahwany
- Immunology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Marwa Hassan
- Immunology Department, Theodor Bilharz Research Institute, Giza, Egypt.
| | - Mohamed Elzallat
- Immunology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Lobna Abdelsalam
- Human Genetics Department, Faculty of Medicine, Cairo University, Cairo, Egypt; Human Genetics Department, Faculty of Medicine, University of North Carolina, USA
| | | | - Moataz Seyam
- Hepato-Gastroenterology Department, Theodor Bilharz Research Institute, Giza, Egypt
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23
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Storer JM, Walker JA, Brown MA, Batzer MA. Cebidae Alu Element Alignments and a Complex Non-Human Primate Radiation. Life (Basel) 2022; 12:1655. [PMID: 36295090 PMCID: PMC9605045 DOI: 10.3390/life12101655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022] Open
Abstract
Phylogenetic relationships among Cebidae species of platyrrhine primates are presently under debate. Studies prior to whole genome sequence (WGS) availability utilizing unidirectional Alu repeats linked Callithrix and Saguinus as sister taxa, based on a limited number of genetic markers and specimens, while the relative positions of Cebus, Saimiri and Aotus remained controversial. Multiple WGS allowed computational detection of Alu-genome junctions, however random mutation and evolutionary decay of these short-read segments prevented phylogenetic resolution. In this study, WGS for four Cebidae genomes of marmoset, squirrel monkey, owl monkey and capuchin were analyzed for full-length Alu elements and each locus was compared to the other three genomes in all possible combinations using orthologous region sequence alignments. Over 2000 candidates were aligned and subjected to visual inspection. Approximately 34% passed inspection and were considered shared in their respective category, 48% failed due to the target being present in all four genomes, having N's in the sequence or other sequence quality anomalies, and 18% were determined to represent near parallel insertions (NP). Wet bench locus specific PCR confirmed the presence of shared Alu insertions in all phylogenetically informative categories, providing evidence of extensive incomplete lineage sorting (ILS) and an abundance of Alu proliferation during the complex radiation of Cebidae taxa.
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Affiliation(s)
- Jessica M. Storer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Morgan A. Brown
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
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24
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Storer JM, Walker JA, Rockwell CE, Mores G, Beckstrom TO, Orkin JD, Melin AD, Phillips KA, Roos C, Batzer MA. Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/Sapajus Genomics. Genes (Basel) 2022; 13. [PMID: 35456378 DOI: 10.3390/genes13040572] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022] Open
Abstract
Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. Reported here are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships.
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25
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Lee JY, Lee WK, Kim DS. Particulate matter-induced hypomethylation of Alu and LINE1 in normal human bronchial epithelial cells and epidermal keratinocytes. Genes Environ 2022; 44:8. [PMID: 35172897 PMCID: PMC8848652 DOI: 10.1186/s41021-022-00235-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 01/20/2022] [Indexed: 11/25/2022] Open
Abstract
Background Airborne particulate matter (PM), a complex mixture of organic and inorganic compounds, is a major public health concern due to its adverse health effects. Understanding the biological action of PM is of particular importance in the improvement of public health. Differential methylation of repetitive elements (RE) by PM might have severe consequences for the structural integrity of the genome and on transcriptional activity, thereby affecting human health. This study aimed to evaluate the effect of inhaled and non-inhaled PM (PM2.5, PM10, and PM10-PAH) exposure on DNA methylation. We quantitatively measured the methylation content of Alu and LINE1 in PM-treated normal human bronchial epithelial cells (NHBE) and normal human epidermal keratinocytes (NHEK) by using whole-genome bisulfite sequencing and pyrosequencing. Results All PMs exposure significantly lowered Alu and LINE1 methylation in both cells than in mock-treated controls. Hypomethylation was more prominent in PM10-PAH exposed-NHBE and PM10 exposed-NHEK. Alu and LINE1 methylation change exhibited different sensitivity according to the subfamily evolutionary ages, with stronger effects on the oldest L1-M and Alu J in NHBE, and oldest L1-M and youngest Alu S in NHEK. Conclusions These results demonstrate that the differential susceptibility of PM-induced hypomethylation of Alu and LINE1 depends upon RE evolutionary age and PM type. Supplementary Information The online version contains supplementary material available at 10.1186/s41021-022-00235-4.
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Affiliation(s)
- Ji Yun Lee
- Department of Anatomy and BK21 Plus KNU Biomedical Convergence Program, Daegu, Republic of Korea
| | - Won Kee Lee
- Preventive Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Dong Sun Kim
- Department of Anatomy and BK21 Plus KNU Biomedical Convergence Program, Daegu, Republic of Korea. .,Department of Anatomy, School of Medicine, Kyungpook National University, 2-101 Dongin-dong, Jung-gu, 702-422, Daegu, Republic of Korea.
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26
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Hernandez-Landero F, Sanchez-Garcia E, Gomez-Crisostomo N, Contreras-Paredes A, Eduardo MA, de la Cruz-Hernandez E. Anthropometric, biochemical, and haematological indicators associated with hyperhomocysteinemia and their relation to global DNA methylation in a young adult population. Epigenetics 2021; 17:1269-1280. [PMID: 34923898 DOI: 10.1080/15592294.2021.2013420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Increased homocysteine (Hcy) levels have been associated with a higher risk of cardiovascular and neurodegenerative diseases. Passive DNA demethylation has been suggested as one of the mechanisms implicated in the development of these conditions, and most studies have investigated this relationship in older adult populations. Therefore, this study aimed to evaluate the relationship between corporal composition and biochemical and haematological indicators with plasma homocysteine levels and genome-wide methylation (Alu, LINE-1, and SAT2) in a population of healthy young adults (median age, 18 years). We showed that the prevalence of hyperhomocysteinemia was significantly higher in men (18.5%) than in women (6.6%) (P = 0.034). Increased Hcy level was substantially associated with higher levels of body mass index and visceral fat in females, whereas in males, it was significantly associated with reduced red cell distribution width and high-density lipoprotein (HDL) cholesterol (HDL-C) levels and increased low-density lipoprotein/HDL ratio. Hypomethylation of Alu was significantly associated with reduced levels of HDL-C (<40.0 mg dL-1), whereas hypomethylation of LINE-1 and SAT2 was significantly associated with higher levels of skeletal muscle (<39.3%) in males. These results highlight the participation of hormonal factors in regulating Hcy metabolism, primarily in the female population, whereas changes in DNA methylation observed in males might be associated with the consumption of a protein diet with high levels of methionine, independent of increased Hcy levels.
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Affiliation(s)
- Fernanda Hernandez-Landero
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
| | - Erika Sanchez-Garcia
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
| | - Nancy Gomez-Crisostomo
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
| | - Adriana Contreras-Paredes
- Laboratory of Molecular Biology of Oncogenic Viruses, Unit of Biomedical Research in Cancer, National Cancer Institute - Biomedical Research Institute, National Autonomous University of Mexico, Mexico City, Mexico
| | - Martínez Abundis Eduardo
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
| | - Erick de la Cruz-Hernandez
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
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27
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Głów D, Maire CL, Schwarze LI, Lamszus K, Fehse B. CRISPR-to-Kill (C2K)-Employing the Bacterial Immune System to Kill Cancer Cells. Cancers (Basel) 2021; 13:cancers13246306. [PMID: 34944926 PMCID: PMC8699370 DOI: 10.3390/cancers13246306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/01/2021] [Accepted: 12/10/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Reasoning that multiple DNA breaks will trigger programmed cell death, we generated lentiviral CRISPR-to-kill (C2K) vectors targeting highly repetitive SINE sequences for cancer gene therapy. In proof-of-concept experiments, C2K-Alu-vectors selectively killed human, but not murine cell lines, and efficiently inhibited the growth of patient-derived glioblastoma cell lines resistant to high-dose irradiation. In combination with tumor-targeting approaches, the C2K system might represent a promising tool for cancer gene therapy. Abstract CRISPR/Cas9 was described as a bacterial immune system that uses targeted introduction of DNA double-strand breaks (DSBs) to destroy invaders. We hypothesized that we can analogously employ CRISPR/Cas9 nucleases to kill cancer cells by inducing maximal numbers of DSBs in their genome and thus triggering programmed cell death. To do so, we generated CRISPR-to-kill (C2K) lentiviral particles targeting highly repetitive Short Interspersed Nuclear Element-Alu sequences. Our Alu-specific sgRNA has more than 15,000 perfectly matched target sites within the human genome. C2K-Alu-vectors selectively killed human, but not murine cell lines. More importantly, they efficiently inhibited the growth of cancer cells including patient-derived glioblastoma cell lines resistant to high-dose irradiation. Our data provide proof-of-concept for the potential of C2K as a novel treatment strategy overcoming common resistance mechanisms. In combination with tumor-targeting approaches, the C2K system might therefore represent a promising tool for cancer gene therapy.
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Affiliation(s)
- Dawid Głów
- Research Department, Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.G.); (L.I.S.)
| | - Cecile L. Maire
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (C.L.M.); (K.L.)
| | - Lea Isabell Schwarze
- Research Department, Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.G.); (L.I.S.)
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (C.L.M.); (K.L.)
| | - Boris Fehse
- Research Department, Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.G.); (L.I.S.)
- Correspondence: ; Tel.: +49-40-7410-55518; Fax: +49-40-7410-55468
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28
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Borges-Monroy R, Chu C, Dias C, Choi J, Lee S, Gao Y, Shin T, Park PJ, Walsh CA, Lee EA. Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder. Mob DNA 2021; 12:28. [PMID: 34838103 PMCID: PMC8627061 DOI: 10.1186/s13100-021-00256-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/02/2021] [Indexed: 12/30/2022] Open
Abstract
Background Retrotransposons have been implicated as causes of Mendelian disease, but their role in autism spectrum disorder (ASD) has not been systematically defined, because they are only called with adequate sensitivity from whole genome sequencing (WGS) data and a large enough cohort for this analysis has only recently become available. Results We analyzed WGS data from a cohort of 2288 ASD families from the Simons Simplex Collection by establishing a scalable computational pipeline for retrotransposon insertion detection. We report 86,154 polymorphic retrotransposon insertions—including > 60% not previously reported—and 158 de novo retrotransposition events. The overall burden of de novo events was similar between ASD individuals and unaffected siblings, with 1 de novo insertion per 29, 117, and 206 births for Alu, L1, and SVA respectively, and 1 de novo insertion per 21 births total. However, ASD cases showed more de novo L1 insertions than expected in ASD genes. Additionally, we observed exonic insertions in loss-of-function intolerant genes, including a likely pathogenic exonic insertion in CSDE1, only in ASD individuals. Conclusions These findings suggest a modest, but important, impact of intronic and exonic retrotransposon insertions in ASD, show the importance of WGS for their analysis, and highlight the utility of specific bioinformatic tools for high-throughput detection of retrotransposon insertions. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-021-00256-w.
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Affiliation(s)
- Rebeca Borges-Monroy
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Caroline Dias
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Division of Developmental Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jaejoon Choi
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, MA, Boston, USA
| | - Soohyun Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yue Gao
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Pediatrics, Harvard Medical School, MA, Boston, USA
| | - Taehwan Shin
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Pediatrics, Harvard Medical School, MA, Boston, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Department of Pediatrics, Harvard Medical School, MA, Boston, USA. .,Department of Neurology, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Department of Pediatrics, Harvard Medical School, MA, Boston, USA.
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29
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Bai X, Li F, Zhang Z. A hypothetical model of trans-acting R-loops-mediated promoter-enhancer interactions by Alu elements. J Genet Genomics 2021; 48:1007-19. [PMID: 34531149 DOI: 10.1016/j.jgg.2021.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
Enhancers modulate gene expression by interacting with promoters. Models of enhancer-promoter interactions (EPIs) in the literature involve the activity of many components, including transcription factors and nucleic acid. However, the role that sequence similarity plays in EPIs remains largely unexplored. Herein, we report that Alu-derived sequences dominate sequence similarity between enhancers and promoters. After rejecting alternative DNA:DNA and DNA:RNA triplex models, we propose that enhancer-associated RNAs (eRNAs) may directly contact their targeted promoters by forming trans-acting R-loops at those Alu sequences. We show how the characteristic distribution of functional genomic data, such as RNA-DNA proximate ligation reads, binding of transcription factors, and RNA-binding proteins, all align with the Alu sequences of EPIs. We also show that these aligned Alu sequences may be subject to the constraint of coevolution, further implying the functional significance of these R-loop hybrids. Finally, our results imply that eRNA and Alu elements associate in a manner previously unrecognized in EPIs and the evolution of gene regulation networks in mammals.
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30
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Vlachogiannis NI, Sachse M, Georgiopoulos G, Zormpas E, Bampatsias D, Delialis D, Bonini F, Galyfos G, Sigala F, Stamatelopoulos K, Gatsiou A, Stellos K. Adenosine-to-inosine Alu RNA editing controls the stability of the pro-inflammatory long noncoding RNA NEAT1 in atherosclerotic cardiovascular disease. J Mol Cell Cardiol 2021; 160:111-120. [PMID: 34302813 PMCID: PMC8585018 DOI: 10.1016/j.yjmcc.2021.07.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/21/2021] [Accepted: 07/16/2021] [Indexed: 12/24/2022]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as critical regulators in human disease including atherosclerosis. However, the mechanisms involved in the post-transcriptional regulation of the expression of disease-associated lncRNAs are not fully understood. Gene expression studies revealed that Nuclear Paraspeckle Assembly Transcript 1 (NEAT1) lncRNA expression was increased by >2-fold in peripheral blood mononuclear cells (PBMCs) derived from patients with coronary artery disease (CAD) or in carotid artery atherosclerotic plaques. We observed a linear association between NEAT1 lncRNA expression and prevalence of CAD which was independent of age, sex, cardiovascular traditional risk factors and renal function. NEAT1 expression was induced by TNF-α, while silencing of NEAT1 profoundly attenuated the TNF-α-induced vascular endothelial cell pro-inflammatory response as defined by the expression of CXCL8, CCL2, VCAM1 and ICAM1. Overexpression of the RNA editing enzyme adenosine deaminase acting on RNA-1 (ADAR1), but not of its editing-deficient mutant, upregulated NEAT1 levels. Conversely, silencing of ADAR1 suppressed the basal levels and the TNF-α-induced increase of NEAT1. NEAT1 lncRNA expression was strongly associated with ADAR1 in CAD and peripheral arterial vascular disease. RNA editing mapping studies revealed the presence of several inosines in close proximity to AU-rich elements within the AluSx3+/AluJo- double-stranded RNA complex. Silencing of the stabilizing RNA-binding protein AUF1 reduced NEAT1 levels while silencing of ADAR1 profoundly affected the binding capacity of AUF1 to NEAT1. Together, our findings propose a mechanism by which ADAR1-catalyzed A-to-I RNA editing controls NEAT1 lncRNA stability in ASCVD.
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Affiliation(s)
- Nikolaos I Vlachogiannis
- Biosciences Institute, Vascular Biology and Medicine Theme, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK; Department of Cardiology, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Marco Sachse
- Biosciences Institute, Vascular Biology and Medicine Theme, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK; Vascular Inflammation and RNA Metabolism Laboratory, Institute for Vascular Signalling, JW Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Georgios Georgiopoulos
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Eleftherios Zormpas
- Biosciences Institute, Vascular Biology and Medicine Theme, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Dimitrios Bampatsias
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Delialis
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Francesca Bonini
- Biosciences Institute, Vascular Biology and Medicine Theme, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK; Vascular Inflammation and RNA Metabolism Laboratory, Institute for Vascular Signalling, JW Goethe University Frankfurt, Frankfurt am Main, Germany
| | - George Galyfos
- First Propaedeutic Department of Surgery, National and Kapodistrian University of Athens, Hippocration Hospital, Athens, Greece
| | - Fragiska Sigala
- First Propaedeutic Department of Surgery, National and Kapodistrian University of Athens, Hippocration Hospital, Athens, Greece
| | - Kimon Stamatelopoulos
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Aikaterini Gatsiou
- Biosciences Institute, Vascular Biology and Medicine Theme, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK.
| | - Konstantinos Stellos
- Biosciences Institute, Vascular Biology and Medicine Theme, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK; Department of Cardiology, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK; Vascular Inflammation and RNA Metabolism Laboratory, Institute for Vascular Signalling, JW Goethe University Frankfurt, Frankfurt am Main, Germany.
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Yamamoto N, Nishida N, Yamamoto R, Gojobori T, Shimotohno K, Mizokami M, Ariumi Y. Angiotensin-Converting Enzyme (ACE) 1 Gene Polymorphism and Phenotypic Expression of COVID-19 Symptoms. Genes (Basel) 2021; 12:1572. [PMID: 34680966 DOI: 10.3390/genes12101572] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 12/25/2022] Open
Abstract
The renin–angiotensin–aldosterone system (RAAS) appears to play an important role in SARS-CoV-2 infection. Polymorphisms within the genes that control this enzymatic system are candidates for elucidating the pathogenesis of COVID-19, since COVID-19 is not only a pulmonary disease but also affects many organs and systems throughout the body in multiple ways. Most striking is the fact that ACE2, one of the major components of the RAAS, is a prerequisite for SARS-COV-2 infection. Recently, we and other groups reported an association between a polymorphism of the ACE1 gene (a homolog of ACE2) and the phenotypic expression of COVID-19, particularly in its severity. The ethnic difference in ACE1 insertion (I)/deletion (D) polymorphism seems to explain the apparent difference in mortality between the West and East Asia. The purpose of this review was to further evaluate the evidence linking ACE1 polymorphisms to COVID-19. We searched the Medline database (2019–2021) for reference citations of relevant articles and selected studies on the clinical outcome of COVID-19 related to ACE1 I/D polymorphism. Although the numbers of patients are not large enough yet, most available evidence supports the notion that the DD genotype adversely influences COVID-19 symptoms. Surprisingly, small studies conducted in several countries yielded opposite results, suggesting that the ACE1 II genotype is a risk factor. This contradictory result may be the case in certain geographic areas, especially in subgroups of patients. It may also be due to interactions with other genes or to yet unexplained biochemical mechanisms. According to our hypothesis, such candidates are genes that are functionally involved in the pathophysiology of COVID-19, can act in concert with the ACE1 DD genotype, and that show differences in their frequency between the West and East Asia. For this, we conducted research focusing on Alu-related genes. The current study on the ACE1 genotype will provide potentially new clues to the pathogenesis, treatment, and diagnosis of SARS-CoV-2 infections.
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Udomsinprasert W, Sakuntasri W, Jittikoon J, Chaikledkaew U, Honsawek S, Chantratita W, Wattanapokayakit S, Mahasirimongkol S. Global DNA hypomethylation of Alu and LINE-1 transposable elements as an epigenetic biomarker of anti-tuberculosis drug-induced liver injury. Emerg Microbes Infect 2021; 10:1862-1872. [PMID: 34467830 PMCID: PMC8451674 DOI: 10.1080/22221751.2021.1976079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite being highly effective, anti-tuberculosis (TB) drugs often induce adverse liver injury, anti-TB drug-induced liver injury (ATDILI), leading to treatment failure given no sensitive and selective ATDILI markers. Herein, we conducted a case–control association study to determine whether global DNA methylation of Alu and LINE-1 transposable elements responsible for genomic stability and transcriptional regulation was correlated with clinical parameters indicating ATDILI in TB patients and might serve as an ATDILI biomarker. Alu and LINE-1 methylation levels in blood leukocyte of 130 TB patients (80 ATDILI cases and 50 non-ATDILI cases) and 100 healthy controls were quantified using quantitative combined bisulfite restriction analysis. Both TB patients with and without ATDILI had significantly lower methylation levels of Alu and LINE-1 elements than healthy controls. Compared with non-ATDILI patients, Alu methylation levels were significantly decreased in ATDILI patients, commensurate with LINE-1 methylation analysis. Hypomethylation of Alu and LINE-1 measured within 1–7 days of TB treatment was independently associated with raised levels of serum aminotransferases assessed within 8–60 days of TB treatment. Receiver operating characteristic curve analysis uncovered that Alu and LINE-1 methylation levels were both more sensitive and specific for differentiating ATDILI cases from non-ATDILI cases than serum aminotransferases after starting TB treatment within 1–7 days. Kaplan-Meier analysis displayed a significant association between hypomethylation of Alu and LINE-1 elements and an increased rate of ATDILI occurrence in TB patients. Collectively, global DNA hypomethylation of Alu and LINE-1 elements would reflect ATDILI progression and might serve as novel sensitive and specific ATDILI biomarkers.
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Affiliation(s)
| | - Wanchaloem Sakuntasri
- Master of Science Program in Biopharmaceutical Sciences, Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Jiraphun Jittikoon
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Usa Chaikledkaew
- Social and Administrative Pharmacy Division, Department of Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand.,Mahidol University Health Technology Assessment (MUHTA) Graduate Program, Mahidol University, Bangkok, Thailand
| | - Sittisak Honsawek
- Department of Biochemistry, Osteoarthritis and Musculoskeleton Research Unit, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sukanya Wattanapokayakit
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Genomic Medicine Centre, Nonthaburi, Thailand
| | - Surakameth Mahasirimongkol
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Genomic Medicine Centre, Nonthaburi, Thailand
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Fukuda S, Varshney A, Fowler BJ, Wang SB, Narendran S, Ambati K, Yasuma T, Magagnoli J, Leung H, Hirahara S, Nagasaka Y, Yasuma R, Apicella I, Pereira F, Makin RD, Magner E, Liu X, Sun J, Wang M, Baker K, Marion KM, Huang X, Baghdasaryan E, Ambati M, Ambati VL, Pandey A, Pandya L, Cummings T, Banerjee D, Huang P, Yerramothu P, Tolstonog GV, Held U, Erwin JA, Paquola ACM, Herdy JR, Ogura Y, Terasaki H, Oshika T, Darwish S, Singh RK, Mozaffari S, Bhattarai D, Kim KB, Hardin JW, Bennett CL, Hinton DR, Hanson TE, Röver C, Parang K, Kerur N, Liu J, Werner BC, Sutton SS, Sadda SR, Schumann GG, Gelfand BD, Gage FH, Ambati J. Cytoplasmic synthesis of endogenous Alu complementary DNA via reverse transcription and implications in age-related macular degeneration. Proc Natl Acad Sci U S A 2021; 118:e2022751118. [PMID: 33526699 DOI: 10.1073/pnas.2022751118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Alu retroelements propagate via retrotransposition by hijacking long interspersed nuclear element-1 (L1) reverse transcriptase (RT) and endonuclease activities. Reverse transcription of Alu RNA into complementary DNA (cDNA) is presumed to occur exclusively in the nucleus at the genomic integration site. Whether Alu cDNA is synthesized independently of genomic integration is unknown. Alu RNA promotes retinal pigmented epithelium (RPE) death in geographic atrophy, an untreatable type of age-related macular degeneration. We report that Alu RNA-induced RPE degeneration is mediated via cytoplasmic L1-reverse-transcribed Alu cDNA independently of retrotransposition. Alu RNA did not induce cDNA production or RPE degeneration in L1-inhibited animals or human cells. Alu reverse transcription can be initiated in the cytoplasm via self-priming of Alu RNA. In four health insurance databases, use of nucleoside RT inhibitors was associated with reduced risk of developing atrophic macular degeneration (pooled adjusted hazard ratio, 0.616; 95% confidence interval, 0.493-0.770), thus identifying inhibitors of this Alu replication cycle shunt as potential therapies for a major cause of blindness.
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Reszka E, Jabłońska E, Lesicka M, Wieczorek E, Kapelski P, Szczepankiewicz A, Pawlak J, Dmitrzak-Węglarz M. An altered global DNA methylation status in women with depression. J Psychiatr Res 2021; 137:283-289. [PMID: 33730603 DOI: 10.1016/j.jpsychires.2021.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/10/2021] [Accepted: 03/02/2021] [Indexed: 12/23/2022]
Abstract
Sparse studies have shown that specific biomarkers of a global DNA methylation status may be related to various mental diseases and states, including: bipolar disorder (BD), anxiety and major depression disorder (MDD). The objective of this study was to analyze potential variation of the above mentioned global methylation status in women with depression. 38 women with a current and clinically confirmed depressive episode suffering from BD type I, type II or MDD and 71 women from the general population and at similar age were recruited for the study. Alu and LINE-1 methylation was assayed with the quantitative methylation-specific PCR technique with TaqMan probes, while the 5-mC and 5-hmC level was determined using the ELISA-based method. Significantly higher levels of 5-mC, Alu and LINE-1 methylation were observed in the women with depression as compared to the controls; while the 5-hmC level revealed to be significantly lower. The BD type I patients presented the highest level of 5-mC of all the women with a depressive episode. 5-mC level in the patients was positively and significantly correlated with the severity of the symptoms of depression. Relationships between Alu or LINE-1 methylation and 5-mC level were statistically significant only in the case of the control women. Alu and LINE-1 methylation do not constitute suitable biomarkers of global DNA methylation in the investigated patients. These findings require confirmation in case-control and prospective epidemiological studies.
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Affiliation(s)
- Edyta Reszka
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland.
| | - Ewa Jabłońska
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Monika Lesicka
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Edyta Wieczorek
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Paweł Kapelski
- Department of Psychiatric Genetics, Department of Psychiatry, University of Medical Sciences, Poznan, Poland
| | - Aleksandra Szczepankiewicz
- Department of Psychiatric Genetics, Department of Psychiatry, University of Medical Sciences, Poznan, Poland
| | - Joanna Pawlak
- Department of Psychiatric Genetics, Department of Psychiatry, University of Medical Sciences, Poznan, Poland
| | - Monika Dmitrzak-Węglarz
- Department of Psychiatric Genetics, Department of Psychiatry, University of Medical Sciences, Poznan, Poland
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35
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Affiliation(s)
- Walter Arancio
- Advanced Data Analysis Group, Fondazione Ri.MED, Palermo, 90133, Italy
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36
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Abstract
Short interspersed nuclear elements (SINEs) are nonautonomous retrotransposons that occupy approximately 13% of the human genome. They are transcribed by RNA polymerase III and can be retrotranscribed and inserted back into the genome with the help of other autonomous retroelements. Because they are preferentially located close to or within gene-rich regions, they can regulate gene expression by various mechanisms that act at both the DNA and the RNA levels. In this review, we summarize recent findings on the involvement of SINEs in different types of gene regulation and discuss the potential regulatory functions of SINEs that are in close proximity to genes, Pol III-transcribed SINE RNAs, and embedded SINE sequences within Pol II-transcribed genes in the human genome. These discoveries illustrate how the human genome has exapted some SINEs into functional regulatory elements.
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Affiliation(s)
- Xiao-Ou Zhang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; .,Current affiliation: School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Henry Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
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37
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Stenz L. The L1-dependant and Pol III transcribed Alu retrotransposon, from its discovery to innate immunity. Mol Biol Rep 2021; 48:2775-2789. [PMID: 33725281 PMCID: PMC7960883 DOI: 10.1007/s11033-021-06258-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
The 300 bp dimeric repeats digestible by AluI were discovered in 1979. Since then, Alu were involved in the most fundamental epigenetic mechanisms, namely reprogramming, pluripotency, imprinting and mosaicism. These Alu encode a family of retrotransposons transcribed by the RNA Pol III machinery, notably when the cytosines that constitute their sequences are de-methylated. Then, Alu hijack the functions of ORF2 encoded by another transposons named L1 during reverse transcription and integration into new sites. That mechanism functions as a complex genetic parasite able to copy-paste Alu sequences. Doing that, Alu have modified even the size of the human genome, as well as of other primate genomes, during 65 million years of co-evolution. Actually, one germline retro-transposition still occurs each 20 births. Thus, Alu continue to modify our human genome nowadays and were implicated in de novo mutation causing diseases including deletions, duplications and rearrangements. Most recently, retrotransposons were found to trigger neuronal diversity by inducing mosaicism in the brain. Finally, boosted during viral infections, Alu clearly interact with the innate immune system. The purpose of that review is to give a condensed overview of all these major findings that concern the fascinating physiology of Alu from their discovery up to the current knowledge.
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Affiliation(s)
- Ludwig Stenz
- Department of Genetic Medicine and Development, Faculty of Medicine, Geneva University, Geneva, Switzerland. .,Swiss Centre for Applied Human Toxicology, University of Basel, Basel, Switzerland.
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38
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Lagisquet J, Zuber K, Gramberg T. Recognize Yourself-Innate Sensing of Non-LTR Retrotransposons. Viruses 2021; 13:94. [PMID: 33445593 DOI: 10.3390/v13010094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022] Open
Abstract
Although mobile genetic elements, or transposons, have played an important role in genome evolution, excess activity of mobile elements can have detrimental consequences. Already, the enhanced expression of transposons-derived nucleic acids can trigger autoimmune reactions that may result in severe autoinflammatory disorders. Thus, cells contain several layers of protective measures to restrict transposons and to sense the enhanced activity of these “intragenomic pathogens”. This review focuses on our current understanding of immunogenic patterns derived from the most active elements in humans, the retrotransposons long interspersed element (LINE)-1 and Alu. We describe the role of known pattern recognition receptors in nucleic acid sensing of LINE-1 and Alu and the possible consequences for autoimmune diseases.
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Abstract
Background: Schizophrenia is a severe mental disorder, which has a major impact on the quality of life and imposes a huge burden on the family. However, the pathogenesis of schizophrenia remains unclear and there are no specific biomarkers. Therefore, we intend to explore whether cf-DNA levels are related to the occurrence and development of schizophrenia. Methods: We analyzed and compared the concentration of cf-DNA in 174 SZ patients and 100 matched healthy controls by using quantitative real-time PCR by amplifying the Alu repeats. Results: We found that cf-DNA levels in peripheral blood reliably distinguished SZ patients from healthy controls (P < 0.05). The ROC analysis also supports the above conclusion. By tracking the absolute concentration of serum cf-DNA in primary cases, we found a distinct increase before treatment with antipsychotics, which decreased progressively after treatment. Conclusions: The present work indicates that cf-DNA may improve the efficiency of disease diagnosis, and the level of cf-DNA plays a predictive role in the development of schizophrenia. By evaluating the level of cf-DNA, we might play a certain role in a more reasonable and standardized clinical treatment of schizophrenia.
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Affiliation(s)
- Ling-Yun Chen
- Center of Laboratory Medicine, Nantong Mental Health Center, Nantong, China
| | - Jing Qi
- Reaserch Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Hong-Lei Xu
- Neurology Laboratory, Affiliated Hospital of Nantong University, Nantong, China
| | - Xiang-Yun Lin
- School of Public Health, Nantong University, Nantong, China
| | - Ya-Jun Sun
- Center of Laboratory Medicine, Nantong Mental Health Center, Nantong, China
| | - Shao-Qing Ju
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
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40
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Abstract
Alu elements are repetitive short interspersed elements prevalent in the primate genome. These repeats account for over 10% of the genome with more than a million highly similar copies. A direct outcome of this is an enrichment in long structures of stable dsRNA, which are the target of adenosine deaminases acting on RNAs (ADARs), the enzymes catalyzing A-to-I RNA editing. Indeed, A-to-I editing by ADARs is extremely abundant in primates: over a hundred million editing sites exist in their genomes. However, despite the radical increase in ADAR targets brought on by the introduction of Alu elements, the few evolutionary conserved editing sites manage to retain their editing levels. Here, we review and discuss the cost of having an unusual amount of dsRNA and editing in the transcriptome, as well as the opportunities it presents, which possibly contributed to accelerating primate evolution.
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Affiliation(s)
- Amos A Schaffer
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
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41
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Shiromoto Y, Sakurai M, Qu H, Kossenkov AV, Nishikura K. Processing of Alu small RNAs by DICER/ADAR1 complexes and their RNAi targets. RNA 2020; 26:1801-1814. [PMID: 32817447 PMCID: PMC7668262 DOI: 10.1261/rna.076745.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/12/2020] [Indexed: 06/08/2023]
Abstract
In addition to adenosine-to-inosine RNA editing activities, ADAR1 has been shown to have various RNA editing-independent activities including modulation of RNAi efficacy. We previously reported that ADAR1 forms a heterodimer complex with DICER and facilitates processing of pre-miRNAs to mature miRNAs. In addition to miRNA synthesis, DICER is involved in processing of long dsRNAs into small RNAs (endo-siRNAs). Generation of retrotransposon-derived endo-siRNAs by DICER and their functions in regulation of transcripts in mouse oocytes has been previously reported. However, the synthesis and functions of endo-siRNAs in somatic cells remain largely unknown. Here, we report that ADAR1 together with DICER generates endogenous small RNAs, Alu endo-siRNAs by cleaving long double-stranded regions of inverted Alu repeats. We identified AGO2-loaded Alu endo-siRNAs, which are highly expressed in commonly used cell lines. These Alu endo-siRNAs carrying both sense and antisense Alu sequences seem to target a set of genes containing a single Alu sequence, either antisense or sense, respectively, within their 3'UTR. In silico screening identified potential RNA silencing target genes for these Alu endo-siRNAs. We present results of a proof-of-concept experiment, in which sense Alu endo-siRNAs derived from AluSz and AluJr family elements target CUB Domain Containing Protein 1 mRNAs containing an antisense copy of AluJb in their 3'UTRs and consequently induce apoptosis in HeLa cells. Our results clearly indicate that Alu endo-siRNAs are functional also in somatic cells.
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Affiliation(s)
| | | | - Helen Qu
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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42
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Booy EP, Gussakovsky D, Choi T, McKenna SA. The noncoding RNA BC200 associates with polysomes to positively regulate mRNA translation in tumor cells. J Biol Chem 2020; 296:100036. [PMID: 33410401 PMCID: PMC7949042 DOI: 10.1074/jbc.ra120.015775] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022] Open
Abstract
BC200 is a noncoding RNA elevated in a broad spectrum of tumor cells that is critical for cell viability, invasion, and migration. Overexpression studies have implicated BC200 and the rodent analog BC1 as negative regulators of translation in both cell-based and in vitro translation assays. Although these studies are consistent, they have not been confirmed in knockdown studies and direct evidence for this function is lacking. Herein, we have demonstrated that BC200 knockdown is correlated with a decrease in global translation rates. As this conflicts with the hypothesis that BC200 is a translational suppressor, we overexpressed BC200 by transfection of in vitro transcribed RNA and transient expression from transfected plasmids. In this context BC200 suppressed translation; however, an innate immune response confounded the data. To overcome this, breast cancer cells stably overexpressing BC200 and various control RNAs were developed by selection for genomic incorporation of a plasmid coexpressing BC200 and the neomycin resistance gene. Stable overexpression of BC200 was associated with elevated translation levels in pooled stable cell lines and isolated single-cell clones. Cross-linking sucrose density gradient centrifugation demonstrated an association of BC200 and its reported binding partners SRP9/14, CSDE1, DHX36, and PABPC1 with both ribosomal subunits and polysomal RNA, an association not previously observed owing to the labile nature of the interactions. In summary, these data present a novel understanding of BC200 function as well as optimized methodology that has far reaching implications in the study of noncoding RNAs, particularly within the context of translational regulatory mechanisms.
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Affiliation(s)
- Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Daniel Gussakovsky
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Taegi Choi
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
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43
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Ewing AD, Smits N, Sanchez-Luque FJ, Faivre J, Brennan PM, Richardson SR, Cheetham SW, Faulkner GJ. Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling. Mol Cell 2020; 80:915-928.e5. [PMID: 33186547 DOI: 10.1016/j.molcel.2020.10.024] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022]
Abstract
Transposable elements (TEs) drive genome evolution and are a notable source of pathogenesis, including cancer. While CpG methylation regulates TE activity, the locus-specific methylation landscape of mobile human TEs has to date proven largely inaccessible. Here, we apply new computational tools and long-read nanopore sequencing to directly infer CpG methylation of novel and extant TE insertions in hippocampus, heart, and liver, as well as paired tumor and non-tumor liver. As opposed to an indiscriminate stochastic process, we find pronounced demethylation of young long interspersed element 1 (LINE-1) retrotransposons in cancer, often distinct to the adjacent genome and other TEs. SINE-VNTR-Alu (SVA) retrotransposons, including their internal tandem repeat-associated CpG island, are near-universally methylated. We encounter allele-specific TE methylation and demethylation of aberrantly expressed young LINE-1s in normal tissues. Finally, we recover the complete sequences of tumor-specific LINE-1 insertions and their retrotransposition hallmarks, demonstrating how long-read sequencing can simultaneously survey the epigenome and detect somatic TE mobilization.
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Affiliation(s)
- Adam D Ewing
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia.
| | - Nathan Smits
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Francisco J Sanchez-Luque
- GENYO, Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Jamila Faivre
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
| | - Paul M Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, Edinburgh EH16 4SB, UK
| | - Sandra R Richardson
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Seth W Cheetham
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia.
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, St. Lucia, QLD 4067, Australia.
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44
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Abstract
In this review, Yeganeh et al. summarize different human diseases that have been linked to defects in the Pol III transcription apparatus or to Pol III products imbalance and discuss the possible underlying mechanisms. RNA polymerase (Pol) III is responsible for transcription of different noncoding genes in eukaryotic cells, whose RNA products have well-defined functions in translation and other biological processes for some, and functions that remain to be defined for others. For all of them, however, new functions are being described. For example, Pol III products have been reported to regulate certain proteins such as protein kinase R (PKR) by direct association, to constitute the source of very short RNAs with regulatory roles in gene expression, or to control microRNA levels by sequestration. Consistent with these many functions, deregulation of Pol III transcribed genes is associated with a large variety of human disorders. Here we review different human diseases that have been linked to defects in the Pol III transcription apparatus or to Pol III products imbalance and discuss the possible underlying mechanisms.
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Affiliation(s)
- Meghdad Yeganeh
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
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45
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Abstract
Background Genome-wide association studies have identified the CDC7-TGFBR3 intergenic region on chromosome 1 to be strongly associated with optic disc area size. The mechanism of its function remained unclear until new data on eQTL markers emerged from the Genotype-Tissue Expression project. The target region was found to contain a strong silencer of the distal (800 kb) Transcription Factor (TF) gene GFI1 (Growth Factor Independent Transcription Repressor 1) specifically in neuroendocrine cells (pituitary gland). GFI1 has also been reported to be involved in the development of sensory neurons and hematopoiesis. Therefore, GFI1, being a developmental gene, is likely to affect optic disc area size by altering the expression of the associated genes via long-range interactions. Results Distribution of haplotypes in the putative enhancer region has been assessed using the data on four continental supergroups generated by the 1000 Genomes Project. The East Asian (EAS) populations were shown to manifest a highly homogenous unimodal haplotype distribution pattern within the region with the major haplotype occurring with the frequency of 0.9. Another European specific haplotype was observed with the frequency of 0.21. The major haplotype appears to be involved in silencing GFI1repressor gene expression, which might be the cause of increased optic disc area characteristic of the EAS populations. The enhancer/eQTL region overlaps AluJo element, which implies that this particular regulatory element is primate-specific and confined to few tissues. Conclusion Population specific distribution of GFI1 enhancer alleles may predispose certain ethnic groups to glaucoma.
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Affiliation(s)
- Vladimir Babenko
- Institute of Cytology and Genetics, Lavrentyeva 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova Str 2, Novosibirsk, 630090, Russia.
| | - Roman Babenko
- Institute of Cytology and Genetics, Lavrentyeva 10, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova Str 2, Novosibirsk, 630090, Russia
| | - Yuri Orlov
- Institute of Cytology and Genetics, Lavrentyeva 10, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova Str 2, Novosibirsk, 630090, Russia.,I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Trubetskaya 8-2, Moscow, 119991, Russia
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Tang W, Liang P. Alu master copies serve as the drivers of differential SINE transposition in recent primate genomes. Anal Biochem 2020; 606:113825. [PMID: 32712063 DOI: 10.1016/j.ab.2020.113825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 12/25/2022]
Abstract
Alu elements, averaging ~300bp in length, are a family of primate-specific short intersperse nuclear elements (SINEs) with more than one million copies and contributing to ~11% of primate genomes. Despite mostly being shared among primates, our recent study revealed highly differential recent Alu transposition among the genomes of primates from Hominidae and Cercopithecidae families. To understand the underlying mechanism, we analyzed six primate genomes and revealed species- and lineage-specific Alu profile exclusively defined by AluY composition. Among all Alus from the 6 genomes, we identified 5401 Alu master copies with 99% being from the AluY subfamily. The numbers of Alu master copies are positively correlated to the number of AluY elements in the genomes with the baboon genome having the largest number of most recent Alu master copies at high activities, while the crab-eating macaque genome having a low number of Alu master copies with low activity. Furthermore, the expression level of Alu master copies is positively correlated with their transposition activity. Our results support the concept that Alu transposition in primate genomes is driven by a small number of master copies, the number and relative activity of which contribute to the differential Alu transposition in recent primate genomes.
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Affiliation(s)
- Wanxiangfu Tang
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada
| | - Ping Liang
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada.
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Pinheiro M, Peixoto A, Santos C, Escudeiro C, Bizarro S, Pinto P, Santos R, Pinto C, Guerra J, Silva J, Teixeira MR. Pathogenicity reclassification of two BRCA1/BRCA2 exonic duplications after identification of genomic breakpoints and tandem orientation. Cancer Genet 2020; 248-249:18-24. [PMID: 32971473 DOI: 10.1016/j.cancergen.2020.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 07/30/2020] [Accepted: 09/07/2020] [Indexed: 10/23/2022]
Abstract
The genomic consequence and clinical interpretation of large duplications are difficult to infer without determining the location and orientation of the duplicated sequence. We aimed to characterize two intragenic duplications detected in two hereditary breast and ovarian cancer syndrome (HBOC) families, namely BRCA1 exon 4 to 6 and BRCA2 exon 17 to 18, previously detected by multiplex ligation probe amplification and initially classified as variants of unknown significance. Using long range PCR, with duplication-specific primers, we were able to ascertain the genomic breakpoints and observed that the two rearrangements occurred in tandem and in direct orientation. The BRCA1 c.134+440_441+870dup and BRCA2 c.7806-2083_8332-1512dup duplications here identified are predicted to cause frameshifts that create a premature stop codon and were reclassified as pathogenic. Furthermore, both families present phenotypic traits typical of HBOC syndrome. We also observed that the genomic breakpoints of these two duplications occurred within highly homologous Alu elements. Concluding, we characterized two in tandem BRCA1 and BRCA2 duplications that likely occurred by Alu-mediated homologous recombination, allowing identification of the underlying cause of the HBOC syndrome in these families.
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Affiliation(s)
- Manuela Pinheiro
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Catarina Santos
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Carla Escudeiro
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Susana Bizarro
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Pedro Pinto
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Rui Santos
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Carla Pinto
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Joana Guerra
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - João Silva
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Largo Prof. Abel Salazar, Porto 4099-003, Portugal.
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48
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Choe SH, Park SJ, Cho HM, Park HR, Lee JR, Kim YH, Huh JW. A single mutation in the ACTR8 gene associated with lineage-specific expression in primates. BMC Evol Biol 2020; 20:66. [PMID: 32503430 PMCID: PMC7275561 DOI: 10.1186/s12862-020-01620-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/29/2020] [Indexed: 12/17/2022] Open
Abstract
Background Alternative splicing (AS) generates various transcripts from a single gene and thus plays a significant role in transcriptomic diversity and proteomic complexity. Alu elements are primate-specific transposable elements (TEs) and can provide a donor or acceptor site for AS. In a study on TE-mediated AS, we recently identified a novel AluSz6-exonized ACTR8 transcript of the crab-eating monkey (Macaca fascicularis). In the present study, we sought to determine the molecular mechanism of AluSz6 exonization of the ACTR8 gene and investigate its evolutionary and functional consequences in the crab-eating monkey. Results We performed RT-PCR and genomic PCR to analyze AluSz6 exonization in the ACTR8 gene and the expression of the AluSz6-exonized transcript in nine primate samples, including prosimians, New world monkeys, Old world monkeys, and hominoids. AluSz6 integration was estimated to have occurred before the divergence of simians and prosimians. The Alu-exonized transcript obtained by AS was lineage-specific and expressed only in Old world monkeys and apes, and humans. This lineage-specific expression was caused by a single G duplication in AluSz6, which provides a new canonical 5′ splicing site. We further identified other alternative transcripts that were unaffected by the AluSz6 insertion. Finally, we observed that the alternative transcripts were transcribed into new isoforms with C-terminus deletion, and in silico analysis showed that these isoforms do not have a destructive function. Conclusions The single G duplication in the TE sequence is the source of TE exonization and AS, and this mutation may suffer a different fate of ACTR8 gene expression during primate evolution.
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Affiliation(s)
- Se-Hee Choe
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea
| | - Hyeon-Mu Cho
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Hye-Ri Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Ja-Rang Lee
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56216, Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea.
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea.
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Abstract
Our genome is a historic record of successive invasions of mobile genetic elements. Like other eukaryotes, we have evolved mechanisms to limit their propagation and minimize the functional impact of new insertions. Although these mechanisms are vitally important, they are imperfect, and a handful of retroelement families remain active in modern humans. This review introduces the intrinsic functions of transposons, the tactics employed in their restraint, and the relevance of this conflict to human pathology. The most straightforward examples of disease-causing transposable elements are germline insertions that disrupt a gene and result in a monogenic disease allele. More enigmatic are the abnormal patterns of transposable element expression in disease states. Changes in transposon regulation and cellular responses to their expression have implicated these sequences in diseases as diverse as cancer, autoimmunity, and neurodegeneration. Distinguishing their epiphenomenal from their pathogenic effects may provide wholly new perspectives on our understanding of disease.
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Affiliation(s)
- Kathleen H Burns
- Department of Pathology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
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50
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Le Berre G, Hossard V, Riou JF, Guieysse-Peugeot AL. AP-TSS: A New Method for the Analysis of RNA Expression from Particular and Challenging Transcription Start Sites. Biomolecules 2020; 10:E827. [PMID: 32481529 DOI: 10.3390/biom10060827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/12/2020] [Accepted: 05/21/2020] [Indexed: 11/25/2022] Open
Abstract
Alternative promoter usage involved in the regulation of transcription, splicing, and translation contributes to proteome diversity and is involved in a large number of diseases, in particular, cancer. Epigenetic mechanisms and cis regulatory elements are involved in alternative promoter activity. Multiple transcript isoforms can be produced from a gene, due to the initiation of transcription at different transcription start sites (TSS). These transcripts may not have regions that allow discrimination during RT-qPCR, making quantification technically challenging. This study presents a general method for the relative quantification of a transcript synthesized from a particular TSS that we called AP-TSS (analysis of particular TSS). AP-TSS is based on the specific elongation of the cDNA of interest, followed by its quantification by qPCR. As proof of principle, AP-TSS was applied to two non-coding RNA: telomeric repeat-containing RNAs (TERRA) from a particular subtelomeric TSS, and Alu transcripts. The treatment of cells with a DNA methylation inhibitor was associated with a global increase of the total TERRA level, but the TERRA expression from the TSS of interest did not change in HT1080 cells, and only modestly increased in HeLa cells. This result suggests that TERRA upregulation induced by global demethylation of the genome is mainly due to activation from sites other than this particular TSS. For Alu RNA, the signal obtained by AP-TSS is specific for the RNA Polymerase III-dependent Alu transcript. In summary, our method provides a tool to study regulation of gene expression from a given transcription start site, in different conditions that could be applied to many genes. In particular, AP-TSS can be used to investigate the epigenetic regulation of alternative TSS usage that is of importance for the development of epigenetic-targeted therapies.
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