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Wang ZY, Ge LP, Ouyang Y, Jin X, Jiang YZ. Targeting transposable elements in cancer: developments and opportunities. Biochim Biophys Acta Rev Cancer 2024; 1879:189143. [PMID: 38936517 DOI: 10.1016/j.bbcan.2024.189143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
Transposable elements (TEs), comprising nearly 50% of the human genome, have transitioned from being perceived as "genomic junk" to key players in cancer progression. Contemporary research links TE regulatory disruptions with cancer development, underscoring their therapeutic potential. Advances in long-read sequencing, computational analytics, single-cell sequencing, proteomics, and CRISPR-Cas9 technologies have enriched our understanding of TEs' clinical implications, notably their impact on genome architecture, gene regulation, and evolutionary processes. In cancer, TEs, including long interspersed element-1 (LINE-1), Alus, and long terminal repeat (LTR) elements, demonstrate altered patterns, influencing both tumorigenic and tumor-suppressive mechanisms. TE-derived nucleic acids and tumor antigens play critical roles in tumor immunity, bridging innate and adaptive responses. Given their central role in oncology, TE-targeted therapies, particularly through reverse transcriptase inhibitors and epigenetic modulators, represent a novel avenue in cancer treatment. Combining these TE-focused strategies with existing chemotherapy or immunotherapy regimens could enhance efficacy and offer a new dimension in cancer treatment. This review delves into recent TE detection advancements, explores their multifaceted roles in tumorigenesis and immune regulation, discusses emerging diagnostic and therapeutic approaches centered on TEs, and anticipates future directions in cancer research.
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Affiliation(s)
- Zi-Yu Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Li-Ping Ge
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yang Ouyang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xi Jin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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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] [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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Kondratov K, Nikitin Y, Fedorov A, Kostareva A, Mikhailovskii V, Isakov D, Ivanov A, Golovkin A. Heterogeneity of the nucleic acid repertoire of plasma extracellular vesicles demonstrated using high-sensitivity fluorescence-activated sorting. J Extracell Vesicles 2020; 9:1743139. [PMID: 32341769 PMCID: PMC7170328 DOI: 10.1080/20013078.2020.1743139] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 02/12/2020] [Accepted: 03/05/2020] [Indexed: 12/13/2022] Open
Abstract
The aim of this study was to investigate cell source-dependent nucleic acids repertoire of diverse subpopulations of plasma extracellular vesicles (EVs). Blood plasma from nine healthy volunteers was used for the analysis. Samples of EVs were obtained by differential centrifugation of plasma. The application of high-sensitivity fluorescence-activated vesicles sorting (hs-FAVS) using fluorophore-conjugated anti-CD41-FITC (Fluorescein isothiocyanate) and anti-CD235a-PE antibodies allowed the isolation of three subpopulations of EVs, namely CD41+ CD235a-, CD41-CD235a+ and CD41-CD235a dim. The high purity (>97%) of the sorted subpopulations was verified by high-sensitivity flow cytometry. Presence of nanosized objects in sorted samples was confirmed by combination of low-voltage scanning electron microscopy and dynamic light scattering. The amount of material in sorted samples was enough to perform Quantitative polymerase chain reaction (qPCR)-based nucleic acid quantification. The most prominent differences in the nucleic acid repertoire were noted between CD41+ CD235- vs. CD41-CD235a+ vesicles: the former contained significantly (p = 0.004) higher amount of mitochondrial DNA, and platelet enriched miR-21-5p (4-fold), miR-223-3p (38-fold) and miR-199a-3p (187-fold), but lower amount of erythrocyte enriched miR-451a (90-fold). CD41-CD235a+ and CD41-CD235a dim vesicles differed in levels of miR-451a (p = 0.016) and miR-21-5p (p = 0.031). Nuclear DNA was below the limit of detection in all EV subpopulations. The hs-FCM-based determination of the number of sorted EVs allowed the calculation of per single-event miRNA concentrations. It was demonstrated that the most abundant marker in CD41+ CD235a- subpopulation was miR-223-3p, reaching 38.2 molecules per event. In the CD41-CD235+ subpopulation, the most abundant marker was miR-451a, reaching 24.7 molecules per event. Taken together, our findings indicate that erythrocyte- and platelet-derived EVs carry different repertoires of nucleic acids, which were similar to the composition of their cellular sources.
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Affiliation(s)
- Kirill Kondratov
- Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Yuri Nikitin
- Department of Clinical Biochemistry and Laboratory Diagnostics, Military Medical Academy N.a. S.M. Kirov, St. Petersburg, Russia
| | - Anton Fedorov
- Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Anna Kostareva
- Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, St. Petersburg, Russia
- Department of Woman and Child Health, Karolinska Institute, Stockholm, Sweden
| | - Vladimir Mikhailovskii
- Interdisciplinary Resource Center for Nanotechnology, Saint-Petersburg State University, St. Petersburg, Russia
| | - Dmitry Isakov
- Department of Immunology, Institution of Experimental Medicine, St. Petersburg, Russia
- Department of Immunology, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Andrey Ivanov
- Department of Clinical Biochemistry and Laboratory Diagnostics, Military Medical Academy N.a. S.M. Kirov, St. Petersburg, Russia
| | - Alexey Golovkin
- Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, St. Petersburg, Russia
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Arroyo M, Bautista R, Larrosa R, Cobo MÁ, Claros MG. Biomarker potential of repetitive-element transcriptome in lung cancer. PeerJ 2019; 7:e8277. [PMID: 31875158 PMCID: PMC6925957 DOI: 10.7717/peerj.8277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/22/2019] [Indexed: 12/11/2022] Open
Abstract
Since repetitive elements (REs) account for nearly 53% of the human genome, profiling its transcription after an oncogenic change might help in the search for new biomarkers. Lung cancer was selected as target since it is the most frequent cause of cancer death. A bioinformatic workflow based on well-established bioinformatic tools (such as RepEnrich, RepBase, SAMTools, edgeR and DESeq2) has been developed to identify differentially expressed RNAs from REs. It was trained and tested with public RNA-seq data from matched sequencing of tumour and healthy lung tissues from the same patient to reveal differential expression within the RE transcriptome. Healthy lung tissues express a specific set of REs whose expression, after an oncogenic process, is strictly and specifically changed. Discrete sets of differentially expressed REs were found for lung adenocarcinoma, for small-cell lung cancer, and for both cancers. Differential expression affects more HERV-than LINE-derived REs and seems biased towards down-regulation in cancer cells. REs behaving consistently in all patients were tested in a different patient cohort to validate the proposed biomarkers. Down-regulation of AluYg6 and LTR18B was confirmed as potential lung cancer biomarkers, while up-regulation of HERVK11D-Int is specific for lung adenocarcinoma and up-regulation of UCON88 is specific for small cell lung cancer. Hence, the study of RE transcriptome might be considered another research target in cancer, making REs a promising source of lung cancer biomarkers.
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Affiliation(s)
- Macarena Arroyo
- U.G.C. Médico-Quirúrgica de Enfermedades Respiratorias, Hospital Regional Universitario de Málaga, Málaga, Spain.,Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, Spain
| | - Rocío Bautista
- Andalusian Platform for Bioinformatics-SCBI, Universidad de Málaga, Málaga, Spain
| | - Rafael Larrosa
- Andalusian Platform for Bioinformatics-SCBI, Universidad de Málaga, Málaga, Spain.,Department of Computer Architecture, Universidad de Málaga, Málaga, Spain
| | - Manuel Ángel Cobo
- Area of Oncology and Rare Diseases (IBIMA), Hospital Regional Universitario de Málaga, Málaga, Spain
| | - M Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, Spain.,Andalusian Platform for Bioinformatics-SCBI, Universidad de Málaga, Málaga, Spain.,Area of Oncology and Rare Diseases (IBIMA), Hospital Regional Universitario de Málaga, Málaga, Spain
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TDP-43 regulates transcription at protein-coding genes and Alu retrotransposons. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194434. [PMID: 31655156 DOI: 10.1016/j.bbagrm.2019.194434] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022]
Abstract
The 43-kDa transactive response DNA-binding protein (TDP-43) is an example of an RNA-binding protein that regulates RNA metabolism at multiple levels from transcription and splicing to translation. Its role in post-transcriptional RNA processing has been a primary focus of recent research, but its role in regulating transcription has been studied for only a few human genes. We characterized the effects of TDP-43 on transcription genome-wide and found that TDP-43 broadly affects transcription of protein-coding and noncoding RNA genes. Among protein-coding genes, the effects of TDP-43 were greatest for genes <30 thousand base pairs in length. Surprisingly, we found that the loss of TDP-43 resulted in increased evidence for transcription activity near repetitive Alu elements found within expressed genes. The highest densities of affected Alu elements were found in the shorter genes, whose transcription was most affected by TDP-43. Thus, in addition to its role in post-transcriptional RNA processing, TDP-43 plays a critical role in maintaining the transcriptional stability of protein-coding genes and transposable DNA elements.
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Jiang Y, Zong W, Ju S, Jing R, Cui M. Promising member of the short interspersed nuclear elements ( Alu elements): mechanisms and clinical applications in human cancers. J Med Genet 2019; 56:639-645. [PMID: 30852527 DOI: 10.1136/jmedgenet-2018-105761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/13/2019] [Accepted: 01/31/2019] [Indexed: 12/11/2022]
Abstract
Alu elements are one of most ubiquitous repetitive sequences in human genome, which were considered as the junk DNA in the past. Alu elements have been found to be associated with human diseases including cancers via events such as amplification, insertion, recombination or RNA editing, which provide a new perspective of oncogenesis at both DNA and RNA levels. Due to the prevalent distribution, Alu elements are widely used as target molecule of liquid biopsy. Alu-based cell-free DNA shows feasible application value in tumour diagnosis, postoperative monitoring and adjuvant therapy. In this review, the special tumourigenesis mechanism of Alu elements in human cancers is discussed, and the application of Alu elements in various tumour liquid biopsy is summarised.
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Affiliation(s)
- Yun Jiang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Medical college, Nantong University, Nantong, Jiangsu, China
| | - Wei Zong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Medical college, Nantong University, Nantong, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Rongrong Jing
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Ming Cui
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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Epigenetic variation at the SLC6A4 gene promoter in mother-child pairs with major depressive disorder. J Affect Disord 2019; 245:716-723. [PMID: 30447571 DOI: 10.1016/j.jad.2018.10.369] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 10/05/2018] [Accepted: 10/31/2018] [Indexed: 01/16/2023]
Abstract
BACKGROUND Genetic and epigenetic variations of the serotonin transporter gene (SLC6A4) have been related to the etiology of depression. The 5-HTTLPR polymorphism at the SLC6A4 promoter region has two variants, a short allele (S) and a long allele (L), in which the S allele results in lower gene transcription and has been associated with depression. The short S-allele of 5-HTTLPR polymorphism of this gene has been associated with depression. In addition to molecular mechanisms, exposure to early life risk factors such as maternal depression seems to affect the development of depression in postnatal life. The present study investigated the association of 5-HTTLPR polymorphism and CpG DNA methylation (5mC) levels of an AluJb repeat element at the SLC6A4 promoter region in mother-child pairs exposed to maternal depression. METHODS We analyzed DNA samples from 60 subjects (30 mother-child pairs) split into three groups, with and without major depression disorder (DSM-IV) among children and mothers. The genotyping of 5-HTTLPR polymorphism and quantification of 5mC levels was performed by qualitative PCR and methylation-sensitive restriction enzyme digestion, and real-time quantitative PCR (MSRED-qPCR), respectively. RESULTS The sample analyzed presented a higher frequency of S allele of 5-HTTLPR (67.5%). Despite the high frequency of this allele, we did not find statistically significant differences between individuals carrying at least one S allele between the depression and healthy control subjects, or among the mother-child pair groups with different patterns of occurrence of depression. In the group where the mother and child were both diagnosed with depression, we found a statistically significant decrease of the 5mC level at the SLC6A4 promoter region. LIMITATIONS The limitations are the relatively small sample size and lack of gene expression data available for comparison with methylation data. CONCLUSION In this study, we demonstrated a repeat element specific 5mC level reduction in mother-child pairs, concordant for the diagnosis of depression.
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Saito S, Lin YC, Nakamura Y, Eckner R, Wuputra K, Kuo KK, Lin CS, Yokoyama KK. Potential application of cell reprogramming techniques for cancer research. Cell Mol Life Sci 2019; 76:45-65. [PMID: 30283976 PMCID: PMC6326983 DOI: 10.1007/s00018-018-2924-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 09/15/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023]
Abstract
The ability to control the transition from an undifferentiated stem cell to a specific cell fate is one of the key techniques that are required for the application of interventional technologies to regenerative medicine and the treatment of tumors and metastases and of neurodegenerative diseases. Reprogramming technologies, which include somatic cell nuclear transfer, induced pluripotent stem cells, and the direct reprogramming of specific cell lineages, have the potential to alter cell plasticity in translational medicine for cancer treatment. The characterization of cancer stem cells (CSCs), the identification of oncogene and tumor suppressor genes for CSCs, and the epigenetic study of CSCs and their microenvironments are important topics. This review summarizes the application of cell reprogramming technologies to cancer modeling and treatment and discusses possible obstacles, such as genetic and epigenetic alterations in cancer cells, as well as the strategies that can be used to overcome these obstacles to cancer research.
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Affiliation(s)
- Shigeo Saito
- Saito Laboratory of Cell Technology, Yaita, Tochigi, 329-1571, Japan
- College of Engineering, Nihon University, Koriyama, Fukushima, 963-8642, Japan
| | - Ying-Chu Lin
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Richard Eckner
- Department of Biochemistry and Molecular Biology, Rutgers, New Jersey Medical School-Rutgers, The State University of New Jersey, Newark, NJ, 07101, USA
| | - Kenly Wuputra
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Kung-Kai Kuo
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, 807, Taiwan
| | - Chang-Shen Lin
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.
| | - Kazunari K Yokoyama
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Faculty of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan.
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Exaptation at the molecular genetic level. SCIENCE CHINA-LIFE SCIENCES 2018; 62:437-452. [PMID: 30798493 DOI: 10.1007/s11427-018-9447-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 12/01/2018] [Indexed: 12/22/2022]
Abstract
The realization that body parts of animals and plants can be recruited or coopted for novel functions dates back to, or even predates the observations of Darwin. S.J. Gould and E.S. Vrba recognized a mode of evolution of characters that differs from adaptation. The umbrella term aptation was supplemented with the concept of exaptation. Unlike adaptations, which are restricted to features built by selection for their current role, exaptations are features that currently enhance fitness, even though their present role was not a result of natural selection. Exaptations can also arise from nonaptations; these are characters which had previously been evolving neutrally. All nonaptations are potential exaptations. The concept of exaptation was expanded to the molecular genetic level which aided greatly in understanding the enormous potential of neutrally evolving repetitive DNA-including transposed elements, formerly considered junk DNA-for the evolution of genes and genomes. The distinction between adaptations and exaptations is outlined in this review and examples are given. Also elaborated on is the fact that such distinctions are sometimes more difficult to determine; this is a widespread phenomenon in biology, where continua abound and clear borders between states and definitions are rare.
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10
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Schneider I, Kugel H, Redlich R, Grotegerd D, Bürger C, Bürkner PC, Opel N, Dohm K, Zaremba D, Meinert S, Schröder N, Straßburg AM, Schwarte K, Schettler C, Ambrée O, Rust S, Domschke K, Arolt V, Heindel W, Baune BT, Zhang W, Dannlowski U, Hohoff C. Association of Serotonin Transporter Gene AluJb Methylation with Major Depression, Amygdala Responsiveness, 5-HTTLPR/rs25531 Polymorphism, and Stress. Neuropsychopharmacology 2018; 43:1308-1316. [PMID: 29114103 PMCID: PMC5916353 DOI: 10.1038/npp.2017.273] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/23/2017] [Accepted: 10/27/2017] [Indexed: 12/16/2022]
Abstract
DNA methylation profiles of the serotonin transporter gene (SLC6A4) have been shown to alter SLC6A4 expression, drive antidepressant treatment response and modify brain functions. This study investigated whether methylation of an AluJb element in the SLC6A4 promotor was associated with major depressive disorder (MDD), amygdala reactivity to emotional faces, 5-HTTLPR/rs25531 polymorphism, and recent stress. MDD patients (n=122) and healthy controls (HC, n=176) underwent fMRI during an emotional face-matching task. Individual SLC6A4 AluJb methylation profiles were ascertained and associated with MDD, amygdala reactivity, 5-HTTLPR/rs25531, and stress. SLC6A4 AluJb methylation was significantly lower in MDD compared to HC and in stressed compared to less stressed participants. Lower AluJb methylation was particularly found in 5-HTTLPR/rs25531 risk allele carriers under stress and correlated with less depressive episodes. fMRI analysis revealed a significant interaction of AluJb methylation and diagnosis in the amygdala, with MDD patients showing lower AluJb methylation associated with decreased amygdala reactivity. While no joint effect of AluJb methylation and 5-HTTLPR/rs25531 existed, risk allele carriers showed significantly increased bilateral amygdala activation. These findings suggest a role of SLC6A4 AluJb methylation in MDD, amygdala reactivity, and stress reaction, partly interwoven with 5-HTTLPR/rs25531 effects. Patients with low methylation in conjunction with a shorter MDD history and decreased amygdala reactivity might feature a more stress-adaptive epigenetic process, maybe via theoretically possible endogenous antidepressant-like effects. In contrast, patients with higher methylation might possibly suffer from impaired epigenetic adaption to chronic stress. Further, the 5-HTTLPR/rs25531 association with amygdala activation was confirmed in our large sample.
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Affiliation(s)
- Ilona Schneider
- Department of Psychiatry, University of Münster, Münster, Germany,Otto Creutzfeldt Center for Cognitive and Behavioral Neuroscience, University of Münster, Münster, Germany
| | - Harald Kugel
- Department of Clinical Radiology, University of Münster, Münster, Germany
| | - Ronny Redlich
- Department of Psychiatry, University of Münster, Münster, Germany
| | | | - Christian Bürger
- Department of Psychiatry, University of Münster, Münster, Germany
| | | | - Nils Opel
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Katharina Dohm
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Dario Zaremba
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Susanne Meinert
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Nina Schröder
- Department of Psychiatry, University of Münster, Münster, Germany
| | | | - Kathrin Schwarte
- Department of Psychiatry, University of Münster, Münster, Germany
| | | | - Oliver Ambrée
- Department of Psychiatry, University of Münster, Münster, Germany,Department of Behavioural Biology, University of Osnabrück, Osnabrück, Germany
| | - Stephan Rust
- Department of Pediatrics, University of Münster, Münster, Germany
| | - Katharina Domschke
- Department of Psychiatry, University of Münster, Münster, Germany,Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Volker Arolt
- Department of Psychiatry, University of Münster, Münster, Germany,Otto Creutzfeldt Center for Cognitive and Behavioral Neuroscience, University of Münster, Münster, Germany
| | - Walter Heindel
- Department of Clinical Radiology, University of Münster, Münster, Germany
| | - Bernhard T Baune
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Weiqi Zhang
- Department of Psychiatry, University of Münster, Münster, Germany,Otto Creutzfeldt Center for Cognitive and Behavioral Neuroscience, University of Münster, Münster, Germany
| | - Udo Dannlowski
- Department of Psychiatry, University of Münster, Münster, Germany,Otto Creutzfeldt Center for Cognitive and Behavioral Neuroscience, University of Münster, Münster, Germany
| | - Christa Hohoff
- Department of Psychiatry, University of Münster, Münster, Germany,Department of Psychiatry, University of Münster, Albert-Schweitzer-Campus 1, Building A9, Münster 48149 Germany, Tel: +49-251-8357122, Fax: +49-251-8357123, E-mail:
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Hausmann M, Ilić N, Pilarczyk G, Lee JH, Logeswaran A, Borroni AP, Krufczik M, Theda F, Waltrich N, Bestvater F, Hildenbrand G, Cremer C, Blank M. Challenges for Super-Resolution Localization Microscopy and Biomolecular Fluorescent Nano-Probing in Cancer Research. Int J Mol Sci 2017; 18:E2066. [PMID: 28956810 PMCID: PMC5666748 DOI: 10.3390/ijms18102066] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 09/21/2017] [Accepted: 09/23/2017] [Indexed: 11/17/2022] Open
Abstract
Understanding molecular interactions and regulatory mechanisms in tumor initiation, progression, and treatment response are key requirements towards advanced cancer diagnosis and novel treatment procedures in personalized medicine. Beyond decoding the gene expression, malfunctioning and cancer-related epigenetic pathways, investigations of the spatial receptor arrangements in membranes and genome organization in cell nuclei, on the nano-scale, contribute to elucidating complex molecular mechanisms in cells and tissues. By these means, the correlation between cell function and spatial organization of molecules or molecular complexes can be studied, with respect to carcinogenesis, tumor sensitivity or tumor resistance to anticancer therapies, like radiation or antibody treatment. Here, we present several new applications for bio-molecular nano-probes and super-resolution, laser fluorescence localization microscopy and their potential in life sciences, especially in biomedical and cancer research. By means of a tool-box of fluorescent antibodies, green fluorescent protein (GFP) tagging, or specific oligonucleotides, we present tumor relevant re-arrangements of Erb-receptors in membranes, spatial organization of Smad specific ubiquitin protein ligase 2 (Smurf2) in the cytosol, tumor cell characteristic heterochromatin organization, and molecular re-arrangements induced by radiation or antibody treatment. The main purpose of this article is to demonstrate how nano-scaled distance measurements between bio-molecules, tagged by appropriate nano-probes, can be applied to elucidate structures and conformations of molecular complexes which are characteristic of tumorigenesis and treatment responses. These applications open new avenues towards a better interpretation of the spatial organization and treatment responses of functionally relevant molecules, at the single cell level, in normal and cancer cells, offering new potentials for individualized medicine.
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Affiliation(s)
- Michael Hausmann
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Nataša Ilić
- Laboratory of Molecular and Cellular Cancer Biology, Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold ST, Safed 1311502, Israel.
| | - Götz Pilarczyk
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Jin-Ho Lee
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Abiramy Logeswaran
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Aurora Paola Borroni
- Laboratory of Molecular and Cellular Cancer Biology, Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold ST, Safed 1311502, Israel.
| | - Matthias Krufczik
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Franziska Theda
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Nadine Waltrich
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Felix Bestvater
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
- Department of Radiation Oncology, Universitätsmedizin Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 3-5, 68159 Mannheim, Germany.
| | - Christoph Cremer
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.
| | - Michael Blank
- Laboratory of Molecular and Cellular Cancer Biology, Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold ST, Safed 1311502, Israel.
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12
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Krufczik M, Sievers A, Hausmann A, Lee JH, Hildenbrand G, Schaufler W, Hausmann M. Combining Low Temperature Fluorescence DNA-Hybridization, Immunostaining, and Super-Resolution Localization Microscopy for Nano-Structure Analysis of ALU Elements and Their Influence on Chromatin Structure. Int J Mol Sci 2017; 18:ijms18051005. [PMID: 28481278 PMCID: PMC5454918 DOI: 10.3390/ijms18051005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/25/2017] [Accepted: 05/02/2017] [Indexed: 01/12/2023] Open
Abstract
Immunostaining and fluorescence in situ hybridization (FISH) are well established methods for specific labelling of chromatin in the cell nucleus. COMBO-FISH (combinatorial oligonucleotide fluorescence in situ hybridization) is a FISH method using computer designed oligonucleotide probes specifically co-localizing at given target sites. In combination with super resolution microscopy which achieves spatial resolution far beyond the Abbe Limit, it allows new insights into the nano-scaled structure and organization of the chromatin of the nucleus. To avoid nano-structural changes of the chromatin, the COMBO-FISH labelling protocol was optimized omitting heat treatment for denaturation of the target. As an example, this protocol was applied to ALU elements—dispersed short stretches of DNA which appear in different kinds in large numbers in primate genomes. These ALU elements seem to be involved in gene regulation, genomic diversity, disease induction, DNA repair, etc. By computer search, we developed a unique COMBO-FISH probe which specifically binds to ALU consensus elements and combined this DNA–DNA labelling procedure with heterochromatin immunostainings in formaldehyde-fixed cell specimens. By localization microscopy, the chromatin network-like arrangements of ALU oligonucleotide repeats and heterochromatin antibody labelling sites were simultaneously visualized and quantified. This novel approach which simultaneously combines COMBO-FISH and immunostaining was applied to chromatin analysis on the nanoscale after low-linear-energy-transfer (LET) radiation exposure at different doses. Dose-correlated curves were obtained from the amount of ALU representing signals, and the chromatin re-arrangements during DNA repair after irradiation were quantitatively studied on the nano-scale. Beyond applications in radiation research, the labelling strategy of immunostaining and COMBO-FISH with localization microscopy will also offer new potentials for analyses of subcellular elements in combination with other specific chromatin targets.
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Affiliation(s)
- Matthias Krufczik
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Aaron Sievers
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Annkathrin Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Jin-Ho Lee
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
- Department of Radiation Oncology, University Medical Center Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 3-5, 68159 Mannheim, Germany.
| | - Wladimir Schaufler
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
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13
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Zhu W, Mitsuhashi S, Yonekawa T, Noguchi S, Huei JCY, Nalini A, Preethish-Kumar V, Yamamoto M, Murakata K, Mori-Yoshimura M, Kamada S, Yahikozawa H, Karasawa M, Kimura S, Yamashita F, Nishino I. Missing genetic variations in GNE myopathy: rearrangement hotspots encompassing 5'UTR and founder allele. J Hum Genet 2016; 62:159-166. [PMID: 27829678 DOI: 10.1038/jhg.2016.134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 09/17/2016] [Accepted: 09/30/2016] [Indexed: 01/07/2023]
Abstract
GNE myopathy is an autosomal recessive distal myopathy caused by loss-of-function mutations in the GNE gene, which encodes UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE), a key enzyme in sialic-acid biosynthesis. By comprehensive screening of manifesting patients using a fine-mapped targeted next-generation sequencing (NGS), we identified copy number variations (CNVs) in 13 patients from 11 unrelated families. The nine unique CNVs largely vary in size from 0.3 to 72 kb. Over half of the cases carry different deletions spanning merely exon 2, which contains the 5' untranslated region (5'UTR) of the muscle major transcript hGNE1. Of most unique CNVs, either the telomeric or the centromeric breakpoint locates within intron 2, indicating rearrangement hotspots. Haplotype analysis suggested the existence of a founder allele with exon 2 deletion. The breakpoints for all CNVs were determined by long-range PCR and sequencing. All of the breakpoints of gross deletion/duplications reside within directly oriented pairs of Alu repeats. The results of this study firstly widen the spectra of mutations to CNVs encompassing 5'UTR, underscoring the pivotal role of the hGNE1 transcript. Alu-mediated non-recurrent CNVs may have been overlooked in a wide variety of recessive phenotypes, especially in those associated with genomic Alu-rich genes such as GNE.
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Affiliation(s)
- Wenhua Zhu
- Department of Neuromuscular Research, National Institute of Neuroscience, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center (MGC), National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Satomi Mitsuhashi
- Department of Neuromuscular Research, National Institute of Neuroscience, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center (MGC), National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Takahiro Yonekawa
- Department of Neuromuscular Research, National Institute of Neuroscience, Tokyo, Japan
| | - Satoru Noguchi
- Department of Neuromuscular Research, National Institute of Neuroscience, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center (MGC), National Center of Neurology and Psychiatry, Tokyo, Japan
| | | | | | - Veeramani Preethish-Kumar
- Department of Clinical Neurosciences, National Institute of Mental Health and Neurosciences, Bangalore, India
| | | | - Kenji Murakata
- Department of Neurology, Kansai Electric Power Hospital, Osaka, Japan
| | - Madoka Mori-Yoshimura
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Sachiko Kamada
- Department of Neurology, Akita University Graduate School of Medicine, Akita, Japan
| | | | | | - Seigo Kimura
- Department of Neurology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | | | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center (MGC), National Center of Neurology and Psychiatry, Tokyo, Japan
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14
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Bouttier M, Laperriere D, Memari B, Mangiapane J, Fiore A, Mitchell E, Verway M, Behr MA, Sladek R, Barreiro LB, Mader S, White JH. Alu repeats as transcriptional regulatory platforms in macrophage responses to M. tuberculosis infection. Nucleic Acids Res 2016; 44:10571-10587. [PMID: 27604870 PMCID: PMC5159539 DOI: 10.1093/nar/gkw782] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 12/19/2022] Open
Abstract
To understand the epigenetic regulation of transcriptional response of macrophages during early-stage M. tuberculosis (Mtb) infection, we performed ChIPseq analysis of H3K4 monomethylation (H3K4me1), a marker of poised or active enhancers. De novo H3K4me1 peaks in infected cells were associated with genes implicated in host defenses and apoptosis. Our analysis revealed that 40% of de novo regions contained human/primate-specific Alu transposable elements, enriched in the AluJ and S subtypes. These contained several transcription factor binding sites, including those for members of the MEF2 and ATF families, and LXR and RAR nuclear receptors, all of which have been implicated in macrophage differentiation, survival, and responses to stress and infection. Combining bioinformatics, molecular genetics, and biochemical approaches, we linked genes adjacent to H3K4me1-associated Alu repeats to macrophage metabolic responses against Mtb infection. In particular, we show that LXRα signaling, which reduced Mtb viability 18-fold by altering cholesterol metabolism and enhancing macrophage apoptosis, can be initiated at response elements present in Alu repeats. These studies decipher the mechanism of early macrophage transcriptional responses to Mtb, highlighting the role of Alu element transposition in shaping human transcription programs during innate immunity.
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Affiliation(s)
- Manuella Bouttier
- Department of Physiology, Montréal, Québec, Canada .,McGill University, Montréal, Québec, Canada
| | - David Laperriere
- Département de Biochimie, Montréal, Québec, Canada.,Institut de Recherche en Immunologie et Cancérologie (IRIC), Montréal, Québec, Canada.,Université de Montréal, Montréal, Québec, Canada
| | - Babak Memari
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Joseph Mangiapane
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Amanda Fiore
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Eric Mitchell
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Mark Verway
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Marcel A Behr
- McGill University, Montréal, Québec, Canada.,Division of Infectious Diseases and Medical Microbiology, Montréal, Québec, Canada.,McGill International TB Centre, Montréal, Québec, Canada
| | - Robert Sladek
- McGill University, Montréal, Québec, Canada.,School of Computer Science, Montréal, Québec, Canada.,Genome Quebec Innovation Centre, Montréal, Québec, Canada
| | - Luis B Barreiro
- Université de Montréal, Montréal, Québec, Canada.,Department of Pediatrics, Montréal, Québec, Canada
| | - Sylvie Mader
- Département de Biochimie, Montréal, Québec, Canada.,Institut de Recherche en Immunologie et Cancérologie (IRIC), Montréal, Québec, Canada.,Université de Montréal, Montréal, Québec, Canada
| | - John H White
- Department of Physiology, Montréal, Québec, Canada .,McGill University, Montréal, Québec, Canada.,Department of Medecine, Montréal, Québec, Canada
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15
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Kim DS, Kim YH, Lee WK, Na YK, Hong HS. Effect of alcohol consumption on peripheral blood Alu methylation in Korean men. Biomarkers 2016; 21:243-8. [PMID: 26846433 DOI: 10.3109/1354750x.2015.1134661] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Alcohol use disorders (AUD) are defined as alcohol abuse and alcohol dependence, which create a substantial public health problem worldwide. To date, no therapeutic can effectively solve these problems. They are complex diseases characterized by both genetic and environmental factors. DNA methylation can act as a downstream effector of environmental signals and account for multi-factorial nature of the disease. Global DNA methylation of peripheral blood cells has recently been proposed as a potential biomarker for disease risk. Alu elements host one-quarter of CpG dinucelotides in the genome to function as proxies for global DNA methylation. In this study, we evaluated the Alu methylation in the peripheral blood DNA of healthy volunteers and AUD patients using the pyrosequencing technology. The Alu methylation level is significantly higher in AUD compared to healthy controls (23.4 ± 1.6 versus 22.1 ± 1.0, t = 7.83, p < 0.0001). Moreover, significant correlation was found between Alu methylation and alcohol use disorders identification test score (r = 0.250, p < 0.0001), alcohol problem (r = 0.294, p < 0.0001), and life position (r = -0.205, p = 0.0005). Overall, these novel findings indicate that alcohol-related increase in Alu methylation might play a complex role in the etiology and pathogenesis of AUD. Further studies are required to elucidate the mechanisms underlying this relationship.
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Affiliation(s)
| | | | - Won Kee Lee
- b Department of Preventive Medicine , College of Nursing, Kyungpook National University , Daegu , Republic of Korea , and
| | - Yeon Kyung Na
- c School of Medicine, College of Nursing, Kyungpook National University , Daegu , Republic of Korea
| | - Hae Sook Hong
- c School of Medicine, College of Nursing, Kyungpook National University , Daegu , Republic of Korea
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16
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Caillet-Boudin ML, Buée L, Sergeant N, Lefebvre B. Regulation of human MAPT gene expression. Mol Neurodegener 2015; 10:28. [PMID: 26170022 PMCID: PMC4499907 DOI: 10.1186/s13024-015-0025-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/30/2015] [Indexed: 12/12/2022] Open
Abstract
The number of known pathologies involving deregulated Tau expression/metabolism is increasing. Indeed, in addition to tauopathies, which comprise approximately 30 diseases characterized by neuronal aggregation of hyperphosphorylated Tau in brain neurons, this protein has also been associated with various other pathologies such as cancer, inclusion body myositis, and microdeletion/microduplication syndromes, suggesting its possible function in peripheral tissues. In addition to Tau aggregation, Tau deregulation can occur at the expression and/or splicing levels, as has been clearly demonstrated in some of these pathologies. Here, we aim to review current knowledge regarding the regulation of human MAPT gene expression at the DNA and RNA levels to provide a better understanding of its possible deregulation. Several aspects, including repeated motifs, CpG island/methylation, and haplotypes at the DNA level, as well as the key regions involved in mRNA expression and stability and the splicing patterns of different mRNA isoforms at the RNA level, will be discussed.
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Affiliation(s)
| | - Luc Buée
- Univ. Lille, UMR-S 1172, Inserm, CHU, 59000, Lille, France
| | | | - Bruno Lefebvre
- Univ. Lille, UMR-S 1172, Inserm, CHU, 59000, Lille, France
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17
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Olins AL, Ishaque N, Chotewutmontri S, Langowski J, Olins DE. Retrotransposon Alu is enriched in the epichromatin of HL-60 cells. Nucleus 2014; 5:237-46. [PMID: 24824428 DOI: 10.4161/nucl.29141] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epichromatin, the surface of chromatin facing the nuclear envelope in an interphase nucleus, reveals a "rim" staining pattern with specific mouse monoclonal antibodies against histone H2A/H2B/DNA and phosphatidylserine epitopes. Employing a modified ChIP-Seq procedure on undifferentiated and differentiated human leukemic (HL-60/S4) cells,>95% of assembled epichromatin regions overlapped with Alu retrotransposons. They also exhibited enrichment of the AluS subfamily and of Alu oligomers. Furthermore, mapping epichromatin regions to the human chromosomes revealed highly similar localization patterns in the various cell states and with the different antibodies. Comparisons with available epigenetic databases suggested that epichromatin is neither "classical" heterochromatin nor highly expressing genes, implying another function at the surface of interphase chromatin. A modified chromatin immunoprecipitation procedure (xxChIP) was developed because the studied antibodies react generally with mononucleosomes and lysed chromatin. A second fixation is necessary to securely attach the antibodies to the epichromatin epitopes of the intact nucleus.
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Affiliation(s)
- Ada L Olins
- Department of Pharmaceutical Sciences; College of Pharmacy; University of New England; Portland, ME USA
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg, Germany; Heidelberg Center for Personalized Oncology; German Cancer Research Center (DKFZ); Heidelberg, Germany
| | - Sasithorn Chotewutmontri
- German Cancer Research Center; Genomics and Proteomics Core Facility, High Throughput Sequencing Unit; Heidelberg, Germany
| | - Jörg Langowski
- Biophysik der Makromoleküle; German Cancer Research Center; Heidelberg, Germany
| | - Donald E Olins
- Department of Pharmaceutical Sciences; College of Pharmacy; University of New England; Portland, ME USA
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