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Alhazmi S, Alharthi M, Alzahrani M, Alrofaidi A, Basingab F, Almuhammadi A, Alkhatabi H, Ashi A, Chaudhary A, Elaimi A. Copy number variations in autistic children. Biomed Rep 2024; 21:107. [PMID: 38868529 PMCID: PMC11168027 DOI: 10.3892/br.2024.1795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/30/2024] [Indexed: 06/14/2024] Open
Abstract
Autism spectrum disorder (ASD) manifests as a neurodevelopmental condition marked by challenges in social communication, interaction and the performing of repetitive behaviors. The prevalence of autism increases markedly on an annual basis; however, the etiology remains incompletely understood. Cytogenetically visible chromosomal abnormalities, including copy number variations (CNVs), have been shown to contribute to the pathogenesis of ASD. More than 1% of ASD conditions can be explained based on a known genetic locus, whereas CNVs account for 5-10% of cases. However, there are no studies on the Saudi Arabian population for the detection of CNVs linked to ASD, to the best of our knowledge. Therefore, the aim of the present study was to explore the prevalence of CNVs in autistic Saudi Arabian children. Genomic DNA was extracted from the peripheral blood of 14 autistic children along with four healthy control children and then array-based comparative genomic hybridization (aCGH) was used to detect CNVs. Bioinformatics analysis of the aCGH results showed the presence of recurrent and non-recurrent deletion/duplication CNVs in several regions of the genome of autistic children. The most frequent CNVs were 1q21.2, 3p26.3, 4q13.2, 6p25.3, 6q24.2, 7p21.1, 7q34, 7q11.1, 8p23.2, 13q32.3, 14q11.1-q11.2 and 15q11.1-q11.2. In the present study, CNVs in autistic Saudi Arabian children were identified to improve the understanding of the etiology of autism and facilitate its diagnosis. Additionally, the present study identified certain possible pathogenic genes in the CNV region associated with several developmental and neurogenetic diseases.
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Affiliation(s)
- Safiah Alhazmi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Neuroscience and Geroscience Research Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Central Laboratory of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Maram Alharthi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Maryam Alzahrani
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Aisha Alrofaidi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fatemah Basingab
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Asma Almuhammadi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Heba Alkhatabi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Hematology Research Unit, King Fahad Medical Research Center, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Abrar Ashi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Adeel Chaudhary
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Aisha Elaimi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 22252, Saudi Arabia
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Izquierdo-Pujol J, Puertas MC, Martinez-Picado J, Morón-López S. Targeting Viral Transcription for HIV Cure Strategies. Microorganisms 2024; 12:752. [PMID: 38674696 PMCID: PMC11052381 DOI: 10.3390/microorganisms12040752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Combination antiretroviral therapy (ART) suppresses viral replication to undetectable levels, reduces mortality and morbidity, and improves the quality of life of people living with HIV (PWH). However, ART cannot cure HIV infection because it is unable to eliminate latently infected cells. HIV latency may be regulated by different HIV transcription mechanisms, such as blocks to initiation, elongation, and post-transcriptional processes. Several latency-reversing (LRA) and -promoting agents (LPA) have been investigated in clinical trials aiming to eliminate or reduce the HIV reservoir. However, none of these trials has shown a conclusive impact on the HIV reservoir. Here, we review the cellular and viral factors that regulate HIV-1 transcription, the potential pharmacological targets and genetic and epigenetic editing techniques that have been or might be evaluated to disrupt HIV-1 latency, the role of miRNA in post-transcriptional regulation of HIV-1, and the differences between the mechanisms regulating HIV-1 and HIV-2 expression.
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Affiliation(s)
- Jon Izquierdo-Pujol
- IrsiCaixa, 08916 Badalona, Spain; (J.I.-P.); (M.C.P.); (J.M.-P.)
- Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
| | - Maria C. Puertas
- IrsiCaixa, 08916 Badalona, Spain; (J.I.-P.); (M.C.P.); (J.M.-P.)
- Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
- CIBERINFEC, 28029 Madrid, Spain
| | - Javier Martinez-Picado
- IrsiCaixa, 08916 Badalona, Spain; (J.I.-P.); (M.C.P.); (J.M.-P.)
- Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
- CIBERINFEC, 28029 Madrid, Spain
- Department of Infectious Diseases and Immunity, School of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), 08500 Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Sara Morón-López
- IrsiCaixa, 08916 Badalona, Spain; (J.I.-P.); (M.C.P.); (J.M.-P.)
- Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
- CIBERINFEC, 28029 Madrid, Spain
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Gu R, Kim TD, Jiang H, Shin S, Oh S, Janknecht R. Methylation of the epigenetic JMJD2D protein by SET7/9 promotes prostate tumorigenesis. Front Oncol 2023; 13:1295613. [PMID: 38045004 PMCID: PMC10690936 DOI: 10.3389/fonc.2023.1295613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 11/06/2023] [Indexed: 12/05/2023] Open
Abstract
How the function of the JMJD2D epigenetic regulator is regulated or whether it plays a role in prostate cancer has remained elusive. We found that JMJD2D was overexpressed in prostate tumors, stimulated prostate cancer cell growth and became methylated by SET7/9 on K427. Mutation of this lysine residue in JMJD2D reduced the ability of DU145 prostate cancer cells to grow, invade and form tumors and elicited extensive transcriptomic changes. This included downregulation of CBLC, a ubiquitin ligase gene with hitherto unknown functions in prostate cancer, and upregulation of PLAGL1, a transcription factor with reported tumor suppressive characteristics in the prostate. Bioinformatic analyses indicated that CBLC expression was elevated in prostate tumors. Further, downregulation of CBLC largely phenocopied the effects of the K427 mutation on DU145 cells. In sum, these data have unveiled a novel mode of regulation of JMJD2D through lysine methylation, illustrated how this can affect oncogenic properties by influencing expression of the CBLC gene, and established a pro-tumorigenic role for CBLC in the prostate. A corollary is that JMJD2D and CBLC inhibitors could have therapeutic benefits in the treatment of prostate and possibly other cancers.
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Affiliation(s)
- Ruicai Gu
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Tae-Dong Kim
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Hanlin Jiang
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Sook Shin
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Stephenson Cancer Center, Oklahoma City, OK, United States
| | - Sangphil Oh
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Stephenson Cancer Center, Oklahoma City, OK, United States
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Stephenson Cancer Center, Oklahoma City, OK, United States
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Henry S, Kokity L, Pirity MK. Polycomb protein RYBP activates transcription factor Plagl1 during in vitro cardiac differentiation of mouse embryonic stem cells. Open Biol 2023; 13:220305. [PMID: 36751888 PMCID: PMC9905990 DOI: 10.1098/rsob.220305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
RING1 and YY1 binding protein (RYBP) is primarily known to function as a repressor being a core component of the non-canonical polycomb repressive complexes 1 (ncPRC1s). However, several ncPRC1-independent functions of RYBP have also been described. We previously reported that RYBP is essential for mouse embryonic development and that Rybp null mutant embryonic stem cells cannot form contractile cardiomyocytes (CMCs) in vitro. We also showed that PLAGL1, a cardiac transcription factor, which is often mutated in congenital heart diseases (CHDs), is not expressed in Rybp-null mutant CMCs. However, the underlying mechanism of how RYBP regulates Plagl1 expression was not revealed. Here, we demonstrate that RYBP cooperated with NKX2-5 to transcriptionally activate the P1 and P3 promoters of the Plagl1 gene and that this activation is ncPRC1-independent. We also show that two non-coding RNAs residing in the Plagl1 locus can also regulate the Plagl1 promoters. Finally, PLAGL1 was able to activate Tnnt2, a gene important for contractility of CMCs in transfected HEK293 cells. Our study shows that the activation of Plagl1 by RYBP is important for sarcomere development and contractility, and suggests that RYBP, via its regulatory functions, may contribute to the development of CHDs.
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Affiliation(s)
- Surya Henry
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Lilla Kokity
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Melinda Katalin Pirity
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary
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Shi Q, Liu X, Fan X, Wang R, Qi K. Paternal dietary ratio of n-6: n-3 polyunsaturated fatty acids programs offspring leptin expression and gene imprinting in mice. Front Nutr 2022; 9:1043876. [PMID: 36618698 PMCID: PMC9816484 DOI: 10.3389/fnut.2022.1043876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/08/2022] [Indexed: 12/25/2022] Open
Abstract
Background This study determined the effects of the paternal dietary ratio of n-6: n-3 polyunsaturated fatty acids (PUFAs) on leptin expression in the offspring and associated gene imprinting in a mouse model. Methods Three- to four-week-old male C57BL/6J mice (F0) were fed an n-3 PUFA-deficient (n-3 D) diet, a diet with normal n-3 PUFA content (n-3 N; n-6: n-3 = 4.3:1), or a diet with a high n-3 PUFA content (n-3 H; n-6: n-3 = 1.5:1) for 8 weeks. Two subsequent generations were generated by mating F0 and F1 male mice with 10-week-old virgin female C57 BL/6J mice, to produce F1 and F2 offspring. Results Compared to the paternal n-3 D diet, paternal n-3 N and n-3 H diets reduced adipose mRNA expression of leptin (Lep) and its plasma concentrations in juvenile F1 male and female offspring, and adult F1 male and F2 female offspring, with upregulated Lep receptor mRNA expression in the hypothalamus. Meanwhile, paternal n-3 N and n-3 H diets altered the expression of the imprinted genes H19, Igf2, Igf2r, Plagl1, Cdkn1c, Kcnq1ot1, Peg3, and Grb10 in the adipose tissue of juvenile and adult F1 males, with almost no effects on F1 females, while more effects were observed in the adult F2 females than F2 males. Principal component analysis verified that Plagl1, Cdkn1c, and Kcnq1ot1 contributed the most to variation in adipose tissue expression in all offspring. Some of these genes (Plagl1, Cdkn1c, Kcnq1ot1, Peg3, and Grb10) were altered by the paternal n-3 N and n-3 H diets in the F1 and F2 generation testes as well. Furthermore, adipose Lep expression was positively correlated with expressions of H19, Igf2r, Plagl1, and Kcnq1ot1 in juvenile F1 males and females, negatively correlated with the Kcnq1ot1 expression in adult F1 males, and positively correlated with the Plagl1 expression in adult F2 females. Conclusion These data imply that paternal Plagl1, Cdkn1c, and Kcnq1ot1 might be part of the pathways involved in offspring leptin programming. Therefore, a lower ratio of n-6: n-3 PUFAs, with higher intake of n-3 PUFAs in paternal pre-conception, may help maintain the offspring's optimal leptin pattern in a sex-specific manner through multiple generations, and thereby, be beneficial for the offspring's long-term health.
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Sécula A, Bluy LE, Chapuis H, Bonnet A, Collin A, Gress L, Cornuez A, Martin X, Bodin L, Bonnefont CMD, Morisson M. Maternal dietary methionine restriction alters hepatic expression of one-carbon metabolism and epigenetic mechanism genes in the ducklings. BMC Genomics 2022; 23:823. [PMID: 36510146 PMCID: PMC9746021 DOI: 10.1186/s12864-022-09066-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Embryonic and fetal development is very susceptible to the availability of nutrients that can interfere with the setting of epigenomes, thus modifying the main metabolic pathways and impacting the health and phenotypes of the future individual. We have previously reported that a 38% reduction of the methyl donor methionine in the diet of 30 female ducks reduced the body weight of their 180 mule ducklings compared to that of 190 ducklings from 30 control females. The maternal methionine-restricted diet also altered plasmatic parameters in 30 of their ducklings when compared to that of 30 ducklings from the control group. Thus, their plasma glucose and triglyceride concentrations were higher while their free fatty acid level and alanine transaminase activity were decreased. Moreover, the hepatic transcript level of 16 genes involved in pathways related to energy metabolism was significantly different between the two groups of ducklings. In the present work, we continued studying the liver of these newly hatched ducklings to explore the impact of the maternal dietary methionine restriction on the hepatic transcript level of 70 genes mostly involved in one-carbon metabolism and epigenetic mechanisms. RESULTS Among the 12 genes (SHMT1, GART, ATIC, FTCD, MSRA, CBS, CTH, AHCYL1, HSBP1, DNMT3, HDAC9 and EZH2) identified as differentially expressed between the two maternal diet groups (p-value < 0.05), 3 of them were involved in epigenetic mechanisms. Ten other studied genes (MTR, GLRX, MTHFR, AHCY, ADK, PRDM2, EEF1A1, ESR1, PLAGL1, and WNT11) tended to be differently expressed (0.05 < p-value < 0.10). Moreover, the maternal dietary methionine restriction altered the number and nature of correlations between expression levels of differential genes for one-carbon metabolism and epigenetic mechanisms, expression levels of differential genes for energy metabolism, and phenotypic traits of ducklings. CONCLUSION This avian model showed that the maternal dietary methionine restriction impacted both the mRNA abundance of 22 genes involved in one-carbon metabolism or epigenetic mechanisms and the mRNA abundance of 16 genes involved in energy metabolism in the liver of the newly hatched offspring, in line with the previously observed changes in their phenotypic traits.
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Affiliation(s)
- Aurélie Sécula
- grid.508721.9GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France
| | - Lisa E. Bluy
- grid.508721.9GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France
| | - Hervé Chapuis
- grid.508721.9GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France
| | - Agnès Bonnet
- grid.508721.9GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France
| | - Anne Collin
- grid.511104.0INRAE, Université de Tours, BOA, 37380 Nouzilly, France
| | - Laure Gress
- grid.508721.9GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France
| | - Alexis Cornuez
- UEPFG INRA Bordeaux-Aquitaine (Unité Expérimentale Palmipèdes à Foie Gras), Domaine d’Artiguères 1076, route de Haut Mauco, F-40280 Benquet, France
| | - Xavier Martin
- UEPFG INRA Bordeaux-Aquitaine (Unité Expérimentale Palmipèdes à Foie Gras), Domaine d’Artiguères 1076, route de Haut Mauco, F-40280 Benquet, France
| | - Loys Bodin
- grid.508721.9GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France
| | - Cécile M. D. Bonnefont
- grid.508721.9GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France
| | - Mireille Morisson
- grid.508721.9GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France
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Cell-of-Origin and Genetic, Epigenetic, and Microenvironmental Factors Contribute to the Intra-Tumoral Heterogeneity of Pediatric Intracranial Ependymoma. Cancers (Basel) 2021; 13:cancers13236100. [PMID: 34885210 PMCID: PMC8657076 DOI: 10.3390/cancers13236100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/24/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023] Open
Abstract
Intra-tumoral heterogeneity (ITH) is a complex multifaceted phenomenon that posits major challenges for the clinical management of cancer patients. Genetic, epigenetic, and microenvironmental factors are concurrent drivers of diversity among the distinct populations of cancer cells. ITH may also be installed by cancer stem cells (CSCs), that foster unidirectional hierarchy of cellular phenotypes or, alternatively, shift dynamically between distinct cellular states. Ependymoma (EPN), a molecularly heterogeneous group of tumors, shows a specific spatiotemporal distribution that suggests a link between ependymomagenesis and alterations of the biological processes involved in embryonic brain development. In children, EPN most often arises intra-cranially and is associated with an adverse outcome. Emerging evidence shows that EPN displays large intra-patient heterogeneity. In this review, after touching on EPN inter-tumoral heterogeneity, we focus on the sources of ITH in pediatric intra-cranial EPN in the framework of the CSC paradigm. We also examine how single-cell technology has shed new light on the complexity and developmental origins of EPN and the potential impact that this understanding may have on the therapeutic strategies against this deadly pediatric malignancy.
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Sievers P, Henneken SC, Blume C, Sill M, Schrimpf D, Stichel D, Okonechnikov K, Reuss DE, Benzel J, Maaß KK, Kool M, Sturm D, Zheng T, Ghasemi DR, Kohlhof-Meinecke P, Cruz O, Suñol M, Lavarino C, Ruf V, Boldt HB, Pagès M, Pouget C, Schweizer L, Kranendonk MEG, Akhtar N, Bunkowski S, Stadelmann C, Schüller U, Mueller WC, Dohmen H, Acker T, Harter PN, Mawrin C, Beschorner R, Brandner S, Snuderl M, Abdullaev Z, Aldape K, Gilbert MR, Armstrong TS, Ellison DW, Capper D, Ichimura K, Reifenberger G, Grundy RG, Jabado N, Krskova L, Zapotocky M, Vicha A, Varlet P, Wesseling P, Rutkowski S, Korshunov A, Wick W, Pfister SM, Jones DTW, von Deimling A, Pajtler KW, Sahm F. Recurrent fusions in PLAGL1 define a distinct subset of pediatric-type supratentorial neuroepithelial tumors. Acta Neuropathol 2021; 142:827-839. [PMID: 34355256 PMCID: PMC8500895 DOI: 10.1007/s00401-021-02356-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023]
Abstract
Ependymomas encompass a heterogeneous group of central nervous system (CNS) neoplasms that occur along the entire neuroaxis. In recent years, extensive (epi-)genomic profiling efforts have identified several molecular groups of ependymoma that are characterized by distinct molecular alterations and/or patterns. Based on unsupervised visualization of a large cohort of genome-wide DNA methylation data, we identified a highly distinct group of pediatric-type tumors (n = 40) forming a cluster separate from all established CNS tumor types, of which a high proportion were histopathologically diagnosed as ependymoma. RNA sequencing revealed recurrent fusions involving the pleomorphic adenoma gene-like 1 (PLAGL1) gene in 19 of 20 of the samples analyzed, with the most common fusion being EWSR1:PLAGL1 (n = 13). Five tumors showed a PLAGL1:FOXO1 fusion and one a PLAGL1:EP300 fusion. High transcript levels of PLAGL1 were noted in these tumors, with concurrent overexpression of the imprinted genes H19 and IGF2, which are regulated by PLAGL1. Histopathological review of cases with sufficient material (n = 16) demonstrated a broad morphological spectrum of tumors with predominant ependymoma-like features. Immunohistochemically, tumors were GFAP positive and OLIG2- and SOX10 negative. In 3/16 of the cases, a dot-like positivity for EMA was detected. All tumors in our series were located in the supratentorial compartment. Median age of the patients at the time of diagnosis was 6.2 years. Median progression-free survival was 35 months (for 11 patients with data available). In summary, our findings suggest the existence of a novel group of supratentorial neuroepithelial tumors that are characterized by recurrent PLAGL1 fusions and enriched for pediatric patients.
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Affiliation(s)
- Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sophie C Henneken
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christina Blume
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julia Benzel
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kendra K Maaß
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tuyu Zheng
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
| | - David R Ghasemi
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Ofelia Cruz
- Department of Pediatric Oncology, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Mariona Suñol
- Department of Pathology, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Cinzia Lavarino
- Laboratory of Molecular Oncology, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Viktoria Ruf
- Institute of Neuropathology, Ludwig-Maximilian University, Munich, Germany
| | - Henning B Boldt
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mélanie Pagès
- Department of Neuropathology, GHU Paris Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
- Laboratory of Translational Research in Pediatric Oncology, SIREDO, INSERM U830, Institut Curie, Paris Sciences Lettres University, Paris, France
| | | | - Leonille Schweizer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neuropathology, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mariëtte E G Kranendonk
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Noreen Akhtar
- Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
- Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Stephanie Bunkowski
- Institute for Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Christine Stadelmann
- Institute for Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Wolf C Mueller
- Paul-Flechsig Institute of Neuropathology, University Hospital and Faculty of Medicine, Leipzig, Germany
| | - Hildegard Dohmen
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Till Acker
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Patrick N Harter
- Frankfurt Cancer Institute (FCI), University Hospital, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Institute of Neurology (Edinger-Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner site Frankfurt/Mainz, Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Mawrin
- Department of Neuropathology, Otto-Von-Guericke University, Magdeburg, Germany
| | - Rudi Beschorner
- Department of Neuropathology, University of Tübingen, Tübingen, Germany
| | - Sebastian Brandner
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Matija Snuderl
- Department of Pathology, NYU Langone Medical Center, New York, NY, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, Bethesda, MD, USA
| | | | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David Capper
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neuropathology, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Koichi Ichimura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Richard G Grundy
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- Department of Pediatrics, McGill University, Montreal, QC, H4A 3J1, Canada
- The Research Institute of the McGill University Health Center, Montreal, QC, H4A 3J1, Canada
| | - Lenka Krskova
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Michal Zapotocky
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Ales Vicha
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Pascale Varlet
- Department of Neuropathology, GHU Paris Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
| | - Pieter Wesseling
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, Amsterdam University Medical Centers, Location VUmc and Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany.
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
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9
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Calcaterra V, Chiricosta L, Mazzon E, Gugnandolo A, Alberti D, Maestri L, Meroni M, Vestri E, Verduci E, Dilillo D, Zuccotti G, Pelizzo G. Determining oncogenic patterns and cancer predisposition through the transcriptomic profile in Mitchell-Riley syndrome with heterotopic gastric mucosa and duodenal atresia: a case report. Orphanet J Rare Dis 2021; 16:455. [PMID: 34715892 PMCID: PMC8556982 DOI: 10.1186/s13023-021-02093-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/17/2021] [Indexed: 11/25/2022] Open
Abstract
Background Homozygous mutations in the transcription factor RFX6 are the cause of the Mitchell–Riley syndrome (MRS) associating neonatal diabetes, congenital digestive system, such as biliary atresia, pancreatic hypoplasia, duodenal and/or jejunal atresia, intestinal malrotation, gallbladder aplasia, cholestasis. A constitutive inactivation of RFX6 leads also to gastric heterotopia. Application of RNA-seq in human diseases may help to better understand pathogenic mechanism of diseases and to predict the risk of developing chronic disorders and personalizing their prevention and treatment. We evaluated oncogenic patterns and cancer predisposition using the transcriptomic profile in a case of MRS with neonatal diabetes, duodenal atresia, and extensive intestinal tract gastric heterotopia. Results We signalled the interactors of RFX6 with other up and downregulated genes, that may be interested in severity of diabetic condition, in multi-organs impairment and cancer predisposition. Furthermore, several dysregulated genes are involved in biological processes that can lead to promote cancer including “Evading apoptosis” (BAD, BBC3, EGF, FGFR2, FLT3LG, HMOX1, HRAS, IFNAR2, IGF1R, IL12RB1, IL13RA1, IL15, IL2RB, IL2RG, IL6R, KEAP1, MGST1, PDGFA, PDGFRB, PIK3R3, RALB, RALGDS, RASSF1, SOS1, TGFA, TXNRD3), “Proliferation” (APC, BRAF, CCND2, CCND3, CCNE2, FGFR2, FLT3LG, FZD1, FZD6, HMOX1, HRAS, IGF1R, KEAP1, LRP6, MAPK3, MGST1, PDGFA, PDGFB, PDGFRB, RB1, SOS1, TGFA, TXNRD3, WNT10B), “Sustained angiogenesis” (BRAF, FGFR2, FLT3LG, HRAS, IGF1R, JAG1, MAPK3, NOTCH2, PDGFA, PDGFB, PDGFRB, SOS1, TGFA, TGFB1), “Genomic instability” (BAD, BBC3) and “Insensitivity to anti-growth signals” (SMAD2, TGFB1). We also inspected the signalings and their related genes in cancer, such as “PI3K signaling”, “ERK signaling”, “JAK-STAT signaling”, “Calcium signaling”, “Other RAS signaling”, “WNT signaling”. Conclusions In our MRS patient, we signaled the interactors of RFX6 with other up- and downregulated genes that may be related to severe diabetic condition, multi-organ impairment, and cancer predisposition. Notably, many dysregulated genes may lead to triggering carcinogenesis. The possibility of the patient developing cancer degeneration in heterotopic gastric mucosa and/or additional long-term tumoral sequelae is not excluded. Personalized prevention and treatment strategies should be proposed.
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Affiliation(s)
- Valeria Calcaterra
- Pediatrics and Adolescentology Unit, Department of Internal Medicine, University of Pavia, Pavia, Italy.,Pediatric Department, Children's Hospital "Vittore Buzzi", Milan, Italy
| | | | | | | | - Daniele Alberti
- Pediatric Surgery Department, "Spedali Civili" Children's Hospital, Brescia, Italy
| | - Luciano Maestri
- Pediatric Surgery Department, Children's Hospital "Vittore Buzzi", Via Lodovico Castelvetro n.32, 20154, Milan, Italy
| | - Milena Meroni
- Pediatric Surgery Department, Children's Hospital "Vittore Buzzi", Via Lodovico Castelvetro n.32, 20154, Milan, Italy
| | - Elettra Vestri
- Pediatric Surgery Department, Children's Hospital "Vittore Buzzi", Via Lodovico Castelvetro n.32, 20154, Milan, Italy
| | - Elvira Verduci
- Pediatric Department, Children's Hospital "Vittore Buzzi", Milan, Italy.,Department of Health Sciences, University of Milano, Milan, Italy
| | - Dario Dilillo
- Pediatric Department, Children's Hospital "Vittore Buzzi", Milan, Italy
| | - Gianvincenzo Zuccotti
- Pediatric Department, Children's Hospital "Vittore Buzzi", Milan, Italy.,Department of Biomedical and Clinical Science "L. Sacco", University of Milano, Milan, Italy
| | - Gloria Pelizzo
- Pediatric Surgery Department, Children's Hospital "Vittore Buzzi", Via Lodovico Castelvetro n.32, 20154, Milan, Italy. .,Department of Biomedical and Clinical Science "L. Sacco", University of Milano, Milan, Italy.
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10
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Rebendenne A, Roy P, Bonaventure B, Chaves VAL, Desmarets L, Rouillé Y, Tauziet M, Arnaud-Arnould M, Giovannini D, Lee Y, DeWeirdt P, Hegde M, Garcia de GF, McKellar J, Wencker M, Dubuisson J, Belouzard S, Moncorgé O, Doench JG, Goujon C. Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs. RESEARCH SQUARE 2021:rs.3.rs-555275. [PMID: 34075371 PMCID: PMC8168385 DOI: 10.21203/rs.3.rs-555275/v1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor. Additionally, such screens have yet to identify the protease TMPRSS2, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity of additional models to uncover the full landscape of SARS-CoV-2 host factors. We performed genome-wide knockout and activation CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. In addition to identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Moreover, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins, IL6R, and CD44 were identified. We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A orthomyxovirus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions.
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Affiliation(s)
| | - Priyanka Roy
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | | | | | - Lowiese Desmarets
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, France
| | - Yves Rouillé
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, France
| | | | | | | | - Yenarae Lee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Peter DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Mudra Hegde
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | | | | | | | - Jean Dubuisson
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, France
| | - Sandrine Belouzard
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, France
| | | | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
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11
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Rebendenne A, Roy P, Bonaventure B, Chaves Valadão AL, Desmarets L, Rouillé Y, Tauziet M, Arnaud-Arnould M, Giovannini D, Lee Y, DeWeirdt P, Hegde M, Garcia de Gracia F, McKellar J, Wencker M, Dubuisson J, Belouzard S, Moncorgé O, Doench JG, Goujon C. Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34031654 DOI: 10.1101/2021.05.19.444823] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor. Additionally, such screens have yet to identify the protease TMPRSS2, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity of additional models to uncover the full landscape of SARS-CoV-2 host factors. We performed genome-wide knockout and activation CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. In addition to identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Moreover, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins, IL6R, and CD44 were identified. We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A orthomyxovirus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions.
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12
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A functional screen identifies transcriptional networks that regulate HIV-1 and HIV-2. Proc Natl Acad Sci U S A 2021; 118:2012835118. [PMID: 33836568 DOI: 10.1073/pnas.2012835118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The molecular networks involved in the regulation of HIV replication, transcription, and latency remain incompletely defined. To expand our understanding of these networks, we performed an unbiased high-throughput yeast one-hybrid screen, which identified 42 human transcription factors and 85 total protein-DNA interactions with HIV-1 and HIV-2 long terminal repeats. We investigated a subset of these transcription factors for transcriptional activity in cell-based models of infection. KLF2 and KLF3 repressed HIV-1 and HIV-2 transcription in CD4+ T cells, whereas PLAGL1 activated transcription of HIV-2 through direct protein-DNA interactions. Using computational modeling with interacting proteins, we leveraged the results from our screen to identify putative pathways that define intrinsic transcriptional networks. Overall, we used a high-throughput functional screen, computational modeling, and biochemical assays to identify and confirm several candidate transcription factors and biochemical processes that influence HIV-1 and HIV-2 transcription and latency.
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13
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Baulina N, Kiselev I, Favorova O. Imprinted Genes and Multiple Sclerosis: What Do We Know? Int J Mol Sci 2021; 22:1346. [PMID: 33572862 PMCID: PMC7866243 DOI: 10.3390/ijms22031346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/23/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune neurodegenerative disease of the central nervous system that arises from interplay between non-genetic and genetic risk factors. The epigenetics functions as a link between these factors, affecting gene expression in response to external influence, and therefore should be extensively studied to improve the knowledge of MS molecular mechanisms. Among others, the epigenetic mechanisms underlie the establishment of parent-of-origin effects that appear as phenotypic differences depending on whether the allele was inherited from the mother or father. The most well described manifestation of parent-of-origin effects is genomic imprinting that causes monoallelic gene expression. It becomes more obvious that disturbances in imprinted genes at the least affecting their expression do occur in MS and may be involved in its pathogenesis. In this review we will focus on the potential role of imprinted genes in MS pathogenesis.
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Affiliation(s)
- Natalia Baulina
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Ivan Kiselev
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
| | - Olga Favorova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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14
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Villanueva-Hayes C, Millership SJ. Imprinted Genes Impact Upon Beta Cell Function in the Current (and Potentially Next) Generation. Front Endocrinol (Lausanne) 2021; 12:660532. [PMID: 33986727 PMCID: PMC8112240 DOI: 10.3389/fendo.2021.660532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/01/2021] [Indexed: 11/23/2022] Open
Abstract
Beta cell failure lies at the centre of the aetiology and pathogenesis of type 2 diabetes and the epigenetic control of the expression of critical beta cell genes appears to play a major role in this decline. One such group of epigenetically-controlled genes, termed 'imprinted' genes, are characterised by transgenerational monoallelic expression due to differential allelic DNA methylation and play key functional roles within beta cells. Here, we review the evidence for this functional importance of imprinted genes in beta cells as well as their nutritional regulation by the diet and their altered methylation and/or expression in rodent models of diabetes and in type 2 diabetic islets. We also discuss imprinted genes in the context of the next generation, where dietary overnutrition in the parents can lead to their deregulation in the offspring, alongside beta cell dysfunction and defective glucose handling. Both the modulation of imprinted gene expression and the likelihood of developing type 2 diabetes in adulthood are susceptible to the impact of nutritional status in early life. Imprinted loci, therefore, represent an excellent opportunity with which to assess epigenomic changes in beta cells due to the diet in both the current and next generation.
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15
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Ruggeri E, Lira-Albarrán S, Grow EJ, Liu X, Harner R, Maltepe E, Ramalho-Santos M, Donjacour A, Rinaudo P. Sex-specific epigenetic profile of inner cell mass of mice conceived in vivo or by IVF. Mol Hum Reprod 2020; 26:866-878. [PMID: 33010164 PMCID: PMC7821709 DOI: 10.1093/molehr/gaaa064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/10/2020] [Indexed: 12/12/2022] Open
Abstract
The preimplantation stage of development is exquisitely sensitive to environmental stresses, and changes occurring during this developmental phase may have long-term health effects. Animal studies indicate that IVF offspring display metabolic alterations, including hypertension, glucose intolerance and cardiac hypertrophy, often in a sexual dimorphic fashion. The detailed nature of epigenetic changes following in-vitro culture is, however, unknown. This study was performed to evaluate the epigenetic (using whole-genome bisulfite sequencing (WGBS) and assay for transposase-accessible chromatin using sequencing (ATAC-seq)) and transcriptomic changes (using RNA-seq) occurring in the inner cell mass (ICM) of male or female mouse embryos generated in vivo or by IVF. We found that the ICM of IVF embryos, compared to the in-vivo ICM, differed in 3% of differentially methylated regions (DMRs), of which 0.1% were located on CpG islands. ATAC-seq revealed that 293 regions were more accessible and 101 were less accessible in IVF embryos, while RNA-seq revealed that 21 genes were differentially regulated in IVF embryos. Functional enrichment analysis revealed that stress signalling (STAT and NF-kB signalling), developmental processes and cardiac hypertrophy signalling showed consistent changes in WGBS and ATAC-seq platforms. In contrast, male and female embryos showed minimal changes. Male ICM had an increased number of significantly hyper-methylated DMRs, while only 27 regions showed different chromatin accessibility and only one gene was differentially expressed. In summary, this study provides the first comprehensive analysis of DNA methylation, chromatin accessibility and RNA expression changes induced by IVF in male and female ICMs. This dataset can be of value to all researchers interested in the developmental origin of health and disease (DOHaD) hypothesis and might lead to a better understanding of how early embryonic manipulation may affect adult health.
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Affiliation(s)
- Elena Ruggeri
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
- San Diego Zoo Global, Institute for Conservation Research, Reproductive Sciences, Escondido, CA, 92027, USA
| | - Saúl Lira-Albarrán
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Edward J Grow
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Xiaowei Liu
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Royce Harner
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Emin Maltepe
- Department of Pediatrics, University of California, San Francisco, CA, 94143, USA
| | - Miguel Ramalho-Santos
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
- Lunenfeld-Tanenbaum Research Institute, University of Toronto, ON, M5G1X5, Canada
- Department of Molecular Genetics, University of Toronto, ON, M5S1A8, Canada
| | - Annemarie Donjacour
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Paolo Rinaudo
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
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16
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Axsom JE, Libonati JR. Impact of parental exercise on epigenetic modifications inherited by offspring: A systematic review. Physiol Rep 2020; 7:e14287. [PMID: 31758667 PMCID: PMC6874781 DOI: 10.14814/phy2.14287] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 01/07/2023] Open
Abstract
Performing regular exercise is associated with numerous health benefits including a reduction in all‐cause mortality. The mechanisms associated with exercise‐induced health improvements are wide ranging and benefit virtually every organ system in the body. Of significance, recent evidence has suggested that some of these protective benefits may also be passed to offspring through multiple generations via alterations in gamete presentation, changes to the in‐utero and offspring rearing environments, and epigenetic modifications. The purpose of this review was to systematically examine the current literature for evidence of exercise‐induced epigenetic modifications in offspring. A systematic search yielded four papers that met inclusion criteria. Parental exercise interventions were associated with differential DNA methylation patterns in offspring. These shifts in methylation patterns were consistent with concurrent changes in offspring mRNA levels, protein expression, and functional measures. Many of the observed changes were related to metabolic pathways. Hence, the evidence suggests that exercise‐induced epigenetic changes can be observed in offspring and may play a pivotal role among the multifactorial intergenerational‐health impact of exercise. A proposed mechanism for the wide‐ranging health benefits of exercise is epigenetic changes and there is potential for epigenetic changes to be passed on to offspring through intergenerational inheritance.![]()
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Affiliation(s)
- Jessie E Axsom
- Department of Nursing Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph R Libonati
- Department of Nursing Science, University of Pennsylvania, Philadelphia, PA, USA
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17
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Kore RA, Henson JC, Hamzah RN, Griffin RJ, Tackett AJ, Ding Z, Mehta JL. Molecular events in MSC exosome mediated cytoprotection in cardiomyocytes. Sci Rep 2019; 9:19276. [PMID: 31848380 PMCID: PMC6917778 DOI: 10.1038/s41598-019-55694-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/25/2019] [Indexed: 01/15/2023] Open
Abstract
A host of hormonal-metabolic alterations take place following exposure of cardiomyocytes to hypoxia and other noxious stimuli. Here, we demonstrate that exposure of cultured rat cardiomyocytes to lipopolysaccharide (LPS) resulted in upregulation (~1.5 fold) of oxidized low-density lipoprotein receptor-1 (LOX-1). There was also a marked increase in apoptosis 12 hrs after LPS treatment with caspase-3 levels being significantly elevated (~1.3 fold) and a significant increase in LDH release at 24 hrs. Interestingly, there was a ~1.4-fold upregulation of LC-3 expression post-LPS treatment indicating development of autophagy, which probably is a compensatory response to combat cellular injury induced by LPS. Treatment with LPS also reduced the size and morphology of cardiomyocyte spheroids. In an attempt to limit LPS-induced injury, cardiomyocytes were treated with exosomes derived from mesenchymal stromal cells (MSCs). We noted a significant suppression of LOX-1 expression that in turn suppressed apoptosis as well as autophagic response and restored spheroid morphology. Mass spectrophotometric analysis of MSC exosomes revealed a cargo rich in proteins which are involved in pathways negatively modulating cell death and apoptosis while promoting cell survival. This is first report to our knowledge on the initial molecular events in MSC exosome mediated cytoprotection of stressed cardiomyocytes.
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Affiliation(s)
- Rajshekhar A Kore
- Department of Medicine, Cardiology Division, University of Arkansas for Medical Sciences, Little Rock, AR and the Central Arkansas Veterans Healthcare system, Little Rock, AR, 72205, USA
| | - Jeffrey C Henson
- Department of Medicine, Cardiology Division, University of Arkansas for Medical Sciences, Little Rock, AR and the Central Arkansas Veterans Healthcare system, Little Rock, AR, 72205, USA
| | - Rabab N Hamzah
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.,Center for Integrative Nanotechnology Sciences, University of Arkansas at Little Rock, Little Rock, AR, 72204, USA
| | - Robert J Griffin
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Zufeng Ding
- Department of Medicine, Cardiology Division, University of Arkansas for Medical Sciences, Little Rock, AR and the Central Arkansas Veterans Healthcare system, Little Rock, AR, 72205, USA
| | - Jawahar L Mehta
- Department of Medicine, Cardiology Division, University of Arkansas for Medical Sciences, Little Rock, AR and the Central Arkansas Veterans Healthcare system, Little Rock, AR, 72205, USA.
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18
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Vega-Benedetti AF, Saucedo CN, Zavattari P, Vanni R, Royo F, Llavero F, Zugaza JL, Parada LA. PLAGL1 gene function during hepatoma cells proliferation. Oncotarget 2018; 9:32775-32794. [PMID: 30214684 PMCID: PMC6132347 DOI: 10.18632/oncotarget.25996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/31/2018] [Indexed: 01/15/2023] Open
Abstract
Hepatocellular carcinoma develops as a multistep process, in which cell cycle deregulation is a central feature, resulting in unscheduled proliferation. The PLAGL1 gene encodes a homonym zinc finger protein that is involved in cell-proliferation control. We determined the genomic profile and the transcription and expression level of PLAGL1, simultaneously with that of its molecular partners p53, PPARγ and p21, in cell-lines derived from patients with liver cancer, during in vitro cell growth. Our investigations revealed that genomic and epigenetic changes of PLAGL1 are also present in hepatoma cell-lines. Transcription of PLAGL1 in tumor cells is significantly lower than in normal fibroblasts, but no significant differences in terms of protein expression were detected between these two cell-types, indicating that there is not a direct relationship between the gene transcriptional activity and protein expression. RT-PCR analyses on normal fibroblasts, used as control, also showed that PLAGL1 and p53 genes transcription occurs as an apparent orchestrated process during normal cells proliferation, which gets disturbed in cancer cells. Furthermore, abnormal trafficking of the PLAGL1 protein may occur in hepatocarcinogenesis.
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Affiliation(s)
| | | | - Patrizia Zavattari
- Biochemistry, Biology and Genetics Unit, Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria di Monserrato SP 8, Monserrato, Cagliari, Italy
| | - Roberta Vanni
- Biochemistry, Biology and Genetics Unit, Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria di Monserrato SP 8, Monserrato, Cagliari, Italy
| | - Felix Royo
- CIC BioGUNE-CIBERehd, Bizkaia Technology Park, Derio, Spain
| | - Francisco Llavero
- Achucarro Basque Center for Neuroscience, UPV/EHU Technology Park, Leioa, Spain.,Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Dentistry, University of the Basque Country, Leioa, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - José L Zugaza
- Achucarro Basque Center for Neuroscience, UPV/EHU Technology Park, Leioa, Spain.,Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Dentistry, University of the Basque Country, Leioa, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Luis A Parada
- Institute of Experimental Pathology, CONICET-UNSa, Salta, Argentina
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19
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Smith CEL, Alexandraki A, Cordery SF, Parmar R, Bonthron DT, Valleley EMA. A tissue-specific promoter derived from a SINE retrotransposon drives biallelic expression of PLAGL1 in human lymphocytes. PLoS One 2017; 12:e0185678. [PMID: 28957425 PMCID: PMC5619815 DOI: 10.1371/journal.pone.0185678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 09/18/2017] [Indexed: 12/20/2022] Open
Abstract
The imprinted gene PLAGL1 is an important regulator of apoptosis and cell cycle arrest. Loss of its expression has been implicated in tumorigenesis in a range of different cancers, and overexpression during fetal development causes transient neonatal diabetes mellitus (TNDM). PLAGL1 lies within an imprinted region of chromosome 6q24, and monoallelic expression from the major, differentially methylated promoter (P1) occurs in most human tissues. However, in peripheral blood leukocytes, the active promoter (P2) is non-imprinted and drives biallelic transcription. We report here a novel PLAGL1 promoter (P5) derived from the insertion of a primate-specific, MIR3 SINE retrotransposon. P5 is highly utilized in lymphocytes, particularly in T cells, and like P2, directs biallelic transcription. Our results show that it is important to consider P5 in relation to PLAGL1 function in T cells when investigating the dysregulation of this gene.
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Affiliation(s)
- Claire E. L. Smith
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - Alexia Alexandraki
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - Sarah F. Cordery
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - Rekha Parmar
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - David T. Bonthron
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - Elizabeth M. A. Valleley
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
- * E-mail:
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20
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Soubry A, Hoyo C, Butt CM, Fieuws S, Price TM, Murphy SK, Stapleton HM. Human exposure to flame-retardants is associated with aberrant DNA methylation at imprinted genes in sperm. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx003. [PMID: 29492305 PMCID: PMC5804543 DOI: 10.1093/eep/dvx003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 02/15/2017] [Accepted: 02/27/2017] [Indexed: 05/18/2023]
Abstract
Emerging evidence suggests that early exposure to endocrine disrupting chemicals has long-term consequences that can influence disease risk in offspring. During gametogenesis, imprinted genes are reasonable epigenetic targets with the ability to retain and transfer environmental messages. We hypothesized that exposures to organophosphate (OP) flame-retardants can alter DNA methylation in human sperm cells affecting offspring's health. Sperm and urine samples were collected from 67 men in North Carolina, USA. Urinary metabolites of a chlorinated OP, tris(1,3-dichloro-2-propyl) phosphate, and two non-chlorinated OPs, triphenyl phosphate and mono-isopropylphenyl diphenyl phosphate, were measured using liquid-chromatography tandem mass-spectrometry. Sperm DNA methylation at multiple CpG sites of the regulatory differentially methylated regions (DMRs) of imprinted genes GRB10, H19, IGF2, MEG3, NDN, NNAT, PEG1/MEST, PEG3, PLAGL1, SNRPN, and SGCE/PEG10 was quantified using bisulfite pyrosequencing. Regression models were used to determine potential associations between OP concentrations and DNA methylation. We found that men with higher concentrations of urinary OP metabolites, known to originate from flame-retardants, have a slightly higher fraction of sperm cells that are aberrantly methylated. After adjusting for age, obesity-status and multiple testing, exposure to mono-isopropylphenyl diphenyl phosphate was significantly related to hypermethylation at the MEG3, NDN, SNRPN DMRs. Exposure to triphenyl phosphate was associated with hypermethylation at the GRB10 DMR; and tris(1,3-dichloro-2-propyl) phosphate exposure was associated with altered methylation at the MEG3 and H19 DMRs. Although measured methylation differences were small, implications for public health can be substantial. Interestingly, our data indicated that a multiplicity of OPs in the human body is associated with increased DNA methylation aberrancies in sperm, compared to exposure to few OPs. Further research is required in larger study populations to determine if our findings can be generalized.
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Affiliation(s)
- Adelheid Soubry
- Epidemiology Research Unit, Faculty of Medicine, Department of Public Health and Primary Care, KU Leuven, Kapucijnenvoer 35, Blok D, Box 7001, University of Leuven, Leuven, Belgium
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Campus Box 7633, Raleigh, NC 27633, USA
| | - Craig M. Butt
- Nicholas School of the Environment, Duke University, Box 90328, 450 Research Drive, Durham, NC 27708, USA
| | - Steffen Fieuws
- L-Biostat, Faculty of Medicine, Department of Public Health and Primary Care, KU Leuven - University of Leuven, Kapucijnenvoer 35, Leuven, Belgium
| | - Thomas M. Price
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Duke University Medical Center, Box 3143, Durham, NC 27713, USA
| | - Susan K. Murphy
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Box 91012, B223 LSRC, 450 Research Drive, Durham, NC 27708, USA
| | - Heather M. Stapleton
- Nicholas School of the Environment, Duke University, Box 90328, 450 Research Drive, Durham, NC 27708, USA
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