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Kuijpers L, Hornung B, van den Hout-van Vroonhoven MCGN, van IJcken WFJ, Grosveld F, Mulugeta E. Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison. BMC Genomics 2024; 25:361. [PMID: 38609853 PMCID: PMC11010347 DOI: 10.1186/s12864-024-10285-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Single-cell sequencing techniques are revolutionizing every field of biology by providing the ability to measure the abundance of biological molecules at a single-cell resolution. Although single-cell sequencing approaches have been developed for several molecular modalities, single-cell transcriptome sequencing is the most prevalent and widely applied technique. SPLiT-seq (split-pool ligation-based transcriptome sequencing) is one of these single-cell transcriptome techniques that applies a unique combinatorial-barcoding approach by splitting and pooling cells into multi-well plates containing barcodes. This unique approach required the development of dedicated computational tools to preprocess the data and extract the count matrices. Here we compare eight bioinformatic pipelines (alevin-fry splitp, LR-splitpipe, SCSit, splitpipe, splitpipeline, SPLiTseq-demultiplex, STARsolo and zUMI) that have been developed to process SPLiT-seq data. We provide an overview of the tools, their computational performance, functionality and impact on downstream processing of the single-cell data, which vary greatly depending on the tool used. RESULTS We show that STARsolo, splitpipe and alevin-fry splitp can all handle large amount of data within reasonable time. In contrast, the other five pipelines are slow when handling large datasets. When using smaller dataset, cell barcode results are similar with the exception of SPLiTseq-demultiplex and splitpipeline. LR-splitpipe that is originally designed for processing long-read sequencing data is the slowest of all pipelines. Alevin-fry produced different down-stream results that are difficult to interpret. STARsolo functions nearly identical to splitpipe and produce results that are highly similar to each other. However, STARsolo lacks the function to collapse random hexamer reads for which some additional coding is required. CONCLUSION Our comprehensive comparative analysis aids users in selecting the most suitable analysis tool for efficient SPLiT-seq data processing, while also detailing the specific prerequisites for each of these pipelines. From the available pipelines, we recommend splitpipe or STARSolo for SPLiT-seq data analysis.
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Affiliation(s)
- Lucas Kuijpers
- Department of Cell Biology, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, Rotterdam, 3015CN, The Netherlands.
| | - Bastian Hornung
- Center for Biomics, Erasmus University Medical Center Rotterdam (Erasmus MC), Rotterdam, The Netherlands
| | | | - Wilfred F J van IJcken
- Center for Biomics, Erasmus University Medical Center Rotterdam (Erasmus MC), Rotterdam, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, Rotterdam, 3015CN, The Netherlands
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, Rotterdam, 3015CN, The Netherlands.
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2
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Kulhankova L, Bindels E, Kayser M, Mulugeta E. Deconvoluting multi-person biological mixtures and accurate characterization and identification of separated contributors using non-targeted single-cell DNA sequencing. Forensic Sci Int Genet 2024; 71:103030. [PMID: 38513339 DOI: 10.1016/j.fsigen.2024.103030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/16/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
The genetic characterization and identification of individuals who contributed to biological mixtures are complex and mostly unresolved tasks. These tasks are relevant in various fields, particularly in forensic investigations, which frequently encounters crime scene stains generated by more than one person. Currently, forensic mixture deconvolution is mostly performed subsequent to forensic DNA profiling at the level of the mixed DNA profiles, which comes with several limitations. Some previous studies attempted at separating single cells prior to forensic DNA profiling. However, these approaches are biased at selection of the cells and, due to their targeted DNA analysis on low template DNA, provide incomplete and unreliable forensic DNA profiles. We recently demonstrated the feasibility of performing mixture deconvolution prior to forensic DNA profiling through the utilization of a non-targeted single-cell transcriptome sequencing (scRNA-seq). In addition to individual-specific mixture deconvolution, this approach also allowed accurate characterisation of biological sex, biogeographic ancestry and individual identification of the separated mixture contributors. However, RNA has the forensic disadvantage of being prone to degradation, and sequencing RNA - focussing on coding regions - limits the number of single nucleotide polymorphisms (SNPs) utilized for genetic mixture deconvolution, characterization, and identification. These limitations can be overcome by performing single-cell sequencing on the level of DNA instead of RNA. Here, for the first time, we applied non-targeted single-cell DNA sequencing (scDNA-seq) by applying the scATAC-seq (Assay for Transposase-Accessible Chromatin with sequencing) technique to address the challenges of mixture deconvolution in the forensic context. We demonstrated that scATAC-seq, together with our recently developed De-goulash data analysis pipeline, is capable of deconvoluting complex blood mixtures of five individuals from both sexes with varying biogeographic ancestries. We further showed that our approach achieved correct genetic characterization of the biological sex and the biogeographic ancestry of each of the separated mixture contributors and established their identity. Furthermore, by analysing in-silico generated scATAC-seq data mixtures, we demonstrated successful individual-specific mixture deconvolution of i) highly complex mixtures of 11 individuals, ii) balanced mixtures containing as few as 20 cells (10 per each individual), and iii) imbalanced mixtures with a ratio as low as 1:80. Overall, our proof-of-principle study demonstrates the general feasibility of scDNA-seq in general, and scATAC-seq in particular, for mixture deconvolution, genetic characterization and individual identification of the separated mixture contributors. Furthermore, it shows that compared to scRNA-seq, scDNA-seq detects more SNPs from fewer cells, providing higher sensitivity, that is valuable in forensic genetics.
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Affiliation(s)
- Lucie Kulhankova
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Eric Bindels
- Department of Haematology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.
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3
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Boers R, Boers J, Tan B, van Leeuwen ME, Wassenaar E, Sanchez EG, Sleddens E, Tenhagen Y, Mulugeta E, Laven J, Creyghton M, Baarends W, van IJcken WFJ, Gribnau J. Retrospective analysis of enhancer activity and transcriptome history. Nat Biotechnol 2023; 41:1582-1592. [PMID: 36823354 PMCID: PMC10635829 DOI: 10.1038/s41587-023-01683-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/20/2023] [Indexed: 02/25/2023]
Abstract
Cell state changes in development and disease are controlled by gene regulatory networks, the dynamics of which are difficult to track in real time. In this study, we used an inducible DCM-RNA polymerase subunit b fusion protein which labels active genes and enhancers with a bacterial methylation mark that does not affect gene transcription and is propagated in S-phase. This DCM-RNA polymerase fusion protein enables transcribed genes and active enhancers to be tagged and then examined at later stages of development or differentiation. We apply this DCM-time machine (DCM-TM) technology to study intestinal homeostasis, revealing rapid and coordinated activation of enhancers and nearby genes during enterocyte differentiation. We provide new insights in absorptive-secretory lineage decision-making in intestinal stem cell (ISC) differentiation and show that ISCs retain a unique chromatin landscape required to maintain ISC identity and delineate future expression of differentiation-associated genes. DCM-TM has wide applicability in tracking cell states, providing new insights in the regulatory networks underlying cell state changes.
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Affiliation(s)
- Ruben Boers
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Joachim Boers
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Beatrice Tan
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marieke E van Leeuwen
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Evelyne Wassenaar
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Erlantz Gonzalez Sanchez
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Esther Sleddens
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Yasha Tenhagen
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Joop Laven
- Department of Obstetrics and Gynaecology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Menno Creyghton
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Willy Baarends
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.
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Marion-Poll L, Roussarie JP, Taing L, Dard-Dascot C, Servant N, Jaszczyszyn Y, Jordi E, Mulugeta E, Hervé D, Bourc’his D, Greengard P, Thermes C, Girault JA. DNA methylation and hydroxymethylation characterize the identity of D1 and D2 striatal projection neurons. Commun Biol 2022; 5:1321. [PMID: 36456703 PMCID: PMC9715678 DOI: 10.1038/s42003-022-04269-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Neuronal DNA modifications differ from those in other cells, including methylation outside CpG context and abundant 5-hydroxymethylation whose relevance for neuronal identities are unclear. Striatal projection neurons expressing D1 or D2 dopamine receptors allow addressing this question, as they share many characteristics but differ in their gene expression profiles, connections, and functional roles. We compare translating mRNAs and DNA modifications in these two populations. DNA methylation differences occur predominantly in large genomic clusters including differentially expressed genes, potentially important for D1 and D2 neurons. Decreased gene body methylation is associated with higher gene expression. Hydroxymethylation differences are more scattered and affect transcription factor binding sites, which can influence gene expression. We also find a strong genome-wide hydroxymethylation asymmetry between the two DNA strands, particularly pronounced at expressed genes and retrotransposons. These results identify novel properties of neuronal DNA modifications and unveil epigenetic characteristics of striatal projection neurons heterogeneity.
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Affiliation(s)
- Lucile Marion-Poll
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France ,Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005 France ,grid.8591.50000 0001 2322 4988Present Address: Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, Geneva, 1211 Switzerland
| | - Jean-Pierre Roussarie
- grid.134907.80000 0001 2166 1519Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065 USA ,grid.189504.10000 0004 1936 7558Present Address: Department of Anatomy & Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118 USA
| | - Lieng Taing
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Present Address: UMR1166 Inserm and Sorbonne Université, Faculty of Medicine, Paris, 75013 France
| | - Cloelia Dard-Dascot
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198 France
| | - Nicolas Servant
- grid.440907.e0000 0004 1784 3645Institut Curie, INSERM U900, CBIO-Centre for Computational Biology, Mines Paris Tech, PSL-Research University, Paris, 75005 France
| | - Yan Jaszczyszyn
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198 France
| | - Emmanuelle Jordi
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France ,Present Address: Coave Therapeutics, Paris, 75014 France
| | - Eskeatnaf Mulugeta
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005 France ,grid.5645.2000000040459992XPresent Address: Erasmus University Medical Center (Erasmus MC), Department of Cell Biology, Rotterdam, 3000 CA The Netherlands
| | - Denis Hervé
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France
| | - Déborah Bourc’his
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005 France
| | - Paul Greengard
- grid.134907.80000 0001 2166 1519Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065 USA
| | - Claude Thermes
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198 France
| | - Jean-Antoine Girault
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France
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5
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Yousefi S, Deng R, Lanko K, Salsench EM, Nikoncuk A, van der Linde HC, Perenthaler E, van Ham TJ, Mulugeta E, Barakat TS. Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance. Genome Med 2021; 13:162. [PMID: 34663447 PMCID: PMC8524963 DOI: 10.1186/s13073-021-00980-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/29/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Non-coding regulatory elements (NCREs), such as enhancers, play a crucial role in gene regulation, and genetic aberrations in NCREs can lead to human disease, including brain disorders. The human brain is a complex organ that is susceptible to numerous disorders; many of these are caused by genetic changes, but a multitude remain currently unexplained. Understanding NCREs acting during brain development has the potential to shed light on previously unrecognized genetic causes of human brain disease. Despite immense community-wide efforts to understand the role of the non-coding genome and NCREs, annotating functional NCREs remains challenging. METHODS Here we performed an integrative computational analysis of virtually all currently available epigenome data sets related to human fetal brain. RESULTS Our in-depth analysis unravels 39,709 differentially active enhancers (DAEs) that show dynamic epigenomic rearrangement during early stages of human brain development, indicating likely biological function. Many of these DAEs are linked to clinically relevant genes, and functional validation of selected DAEs in cell models and zebrafish confirms their role in gene regulation. Compared to enhancers without dynamic epigenomic rearrangement, DAEs are subjected to higher sequence constraints in humans, have distinct sequence characteristics and are bound by a distinct transcription factor landscape. DAEs are enriched for GWAS loci for brain-related traits and for genetic variation found in individuals with neurodevelopmental disorders, including autism. CONCLUSION This compendium of high-confidence enhancers will assist in deciphering the mechanism behind developmental genetics of human brain and will be relevant to uncover missing heritability in human genetic brain disorders.
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Affiliation(s)
- Soheil Yousefi
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ruizhi Deng
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Kristina Lanko
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Eva Medico Salsench
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Anita Nikoncuk
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Herma C. van der Linde
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Elena Perenthaler
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Tjakko J. van Ham
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
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6
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de Haan W, Dheedene W, Apelt K, Décombas-Deschamps S, Vinckier S, Verhulst S, Conidi A, Deffieux T, Staring MW, Vandervoort P, Caluwé E, Lox M, Mannaerts I, Takagi T, Jaekers J, Berx G, Haigh J, Topal B, Zwijsen A, Higashi Y, van Grunsven LA, van IJcken WFJ, Mulugeta E, Tanter M, Lebrin FPG, Huylebroeck D, Luttun A. Endothelial Zeb2 preserves the hepatic angioarchitecture and protects against liver fibrosis. Cardiovasc Res 2021; 118:1262-1275. [PMID: 33909875 PMCID: PMC8953454 DOI: 10.1093/cvr/cvab148] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Aims Hepatic capillaries are lined with specialized liver sinusoidal endothelial cells (LSECs) which support macromolecule passage to hepatocytes and prevent fibrosis by keeping hepatic stellate cells (HSCs) quiescent. LSEC specialization is co-determined by transcription factors. The zinc-finger E-box-binding homeobox (Zeb)2 transcription factor is enriched in LSECs. Here, we aimed to elucidate the endothelium-specific role of Zeb2 during maintenance of the liver and in liver fibrosis. Methods and results To study the role of Zeb2 in liver endothelium we generated EC-specific Zeb2 knock-out (ECKO) mice. Sequencing of liver EC RNA revealed that deficiency of Zeb2 results in prominent expression changes in angiogenesis-related genes. Accordingly, the vascular area was expanded and the presence of pillars inside ECKO liver vessels indicated that this was likely due to increased intussusceptive angiogenesis. LSEC marker expression was not profoundly affected and fenestrations were preserved upon Zeb2 deficiency. However, an increase in continuous EC markers suggested that Zeb2-deficient LSECs are more prone to dedifferentiation, a process called ‘capillarization’. Changes in the endothelial expression of ligands that may be involved in HSC quiescence together with significant changes in the expression profile of HSCs showed that Zeb2 regulates LSEC–HSC communication and HSC activation. Accordingly, upon exposure to the hepatotoxin carbon tetrachloride (CCl4), livers of ECKO mice showed increased capillarization, HSC activation, and fibrosis compared to livers from wild-type littermates. The vascular maintenance and anti-fibrotic role of endothelial Zeb2 was confirmed in mice with EC-specific overexpression of Zeb2, as the latter resulted in reduced vascularity and attenuated CCl4-induced liver fibrosis. Conclusion Endothelial Zeb2 preserves liver angioarchitecture and protects against liver fibrosis. Zeb2 and Zeb2-dependent genes in liver ECs may be exploited to design novel therapeutic strategies to attenuate hepatic fibrosis.
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Affiliation(s)
- Willeke de Haan
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Wouter Dheedene
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Katerina Apelt
- Department of Internal Medicine (Nephrology), Einthoven Laboratory for Experimental Vascular Medicine. Leiden University Medical Center, . Leiden, The Netherlands
| | - Sofiane Décombas-Deschamps
- Physics for Medicine Paris, Inserm, CNRS, ESPCI Paris, Paris Sciences et Lettres University, Paris, France
| | - Stefan Vinckier
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, KU Leuven, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Stefaan Verhulst
- Liver Cell Biology research group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Thomas Deffieux
- Physics for Medicine Paris, Inserm, CNRS, ESPCI Paris, Paris Sciences et Lettres University, Paris, France
| | - Michael W Staring
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Petra Vandervoort
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Ellen Caluwé
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Marleen Lox
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Inge Mannaerts
- Liver Cell Biology research group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tsuyoshi Takagi
- Department of Disease Model, Institute of Developmental Research, Aichi Developmental Disability Center, Aichi, Japan
| | | | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jody Haigh
- Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.,Research Institute in Oncology and Hematology, Cancer Care Manitoba, Winnipeg, Manitoba, Canada
| | - Baki Topal
- Abdominal Surgery, UZ Leuven, Leuven, Belgium
| | - An Zwijsen
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Yujiro Higashi
- Department of Disease Model, Institute of Developmental Research, Aichi Developmental Disability Center, Aichi, Japan
| | - Leo A van Grunsven
- Liver Cell Biology research group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Wilfred F J van IJcken
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Center for Biomics-Genomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mickael Tanter
- Physics for Medicine Paris, Inserm, CNRS, ESPCI Paris, Paris Sciences et Lettres University, Paris, France
| | - Franck P G Lebrin
- Department of Internal Medicine (Nephrology), Einthoven Laboratory for Experimental Vascular Medicine. Leiden University Medical Center, . Leiden, The Netherlands.,Physics for Medicine Paris, Inserm, CNRS, ESPCI Paris, Paris Sciences et Lettres University, Paris, France
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Aernout Luttun
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
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7
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Groeneveldt LC, Herpelinck T, Maréchal M, Politis C, van IJcken WFJ, Huylebroeck D, Geris L, Mulugeta E, Luyten FP. The Bone-Forming Properties of Periosteum-Derived Cells Differ Between Harvest Sites. Front Cell Dev Biol 2020; 8:554984. [PMID: 33324630 PMCID: PMC7723972 DOI: 10.3389/fcell.2020.554984] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/22/2020] [Indexed: 12/16/2022] Open
Abstract
The development of alternatives for autologous bone grafts is a major focus of bone tissue engineering. To produce living bone-forming implants, skeletal stem and progenitor cells (SSPCs) are envisioned as key ingredients. SSPCs can be obtained from different tissues including bone marrow, adipose tissue, dental pulp, and periosteum. Human periosteum-derived cells (hPDCs) exhibit progenitor cell characteristics and have well-documented in vivo bone formation potency. Here, we have characterized and compared hPDCs derived from tibia with craniofacial hPDCs, from maxilla and mandible, respectively, each representing a potential source for cell-based tissue engineered implants for craniofacial applications. Maxilla and mandible-derived hPDCs display similar growth curves as tibial hPDCs, with equal trilineage differentiation potential toward chondrogenic, osteogenic, and adipogenic cells. These craniofacial hPDCs are positive for SSPC-markers CD73, CD164, and Podoplanin (PDPN), and negative for CD146, hematopoietic and endothelial lineage markers. Bulk RNA-sequencing identified genes that are differentially expressed between the three sources of hPDC. In particular, differential expression was found for genes of the HOX and DLX family, for SOX9 and genes involved in skeletal system development. The in vivo bone formation, 8 weeks after ectopic implantation in nude mice, was observed in constructs seeded with tibial and mandibular hPDCs. Taken together, we provide evidence that hPDCs show different profiles and properties according to their anatomical origin, and that craniofacial hPDCs are potential sources for cell-based bone tissue engineering strategies. The mandible-derived hPDCs display - both in vitro and in vivo - chondrogenic and osteogenic differentiation potential, which supports their future testing for use in craniofacial bone regeneration applications.
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Affiliation(s)
- Lisanne C Groeneveldt
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium.,Skeletal Biology and Engineering Research Center, KU Leuven, Leuven, Belgium.,OMFS IMPATH Research Group, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium.,Oral and Maxillofacial Surgery, University Hospitals Leuven, Leuven, Belgium.,Department of Cell Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Tim Herpelinck
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium.,Skeletal Biology and Engineering Research Center, KU Leuven, Leuven, Belgium
| | - Marina Maréchal
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium.,Skeletal Biology and Engineering Research Center, KU Leuven, Leuven, Belgium
| | - Constantinus Politis
- OMFS IMPATH Research Group, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium.,Oral and Maxillofacial Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Wilfred F J van IJcken
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, Netherlands.,Center for Biomics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Liesbet Geris
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium.,Skeletal Biology and Engineering Research Center, KU Leuven, Leuven, Belgium.,Biomechanics Research Unit, GIGA-R In Silico Medicine, Université de Liége, Liège, Belgium.,Biomechanics Section, KU Leuven, Leuven, Belgium
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Frank P Luyten
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium.,Skeletal Biology and Engineering Research Center, KU Leuven, Leuven, Belgium.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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8
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Parenti I, Diab F, Gil SR, Mulugeta E, Casa V, Berutti R, Brouwer RWW, Dupé V, Eckhold J, Graf E, Puisac B, Ramos F, Schwarzmayr T, Gines MM, van Staveren T, van IJcken WFJ, Strom TM, Pié J, Watrin E, Kaiser FJ, Wendt KS. MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome. Cell Rep 2020; 31:107647. [PMID: 32433956 DOI: 10.1016/j.celrep.2020.107647] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 09/30/2019] [Accepted: 04/24/2020] [Indexed: 12/26/2022] Open
Abstract
The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations in NIPBL account for most cases of the rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report a MAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus. Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable for normal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fatal outcome of an out-of-frame single nucleotide duplication in NIPBL, engineered in two different cell lines, alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interact with MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protective against out-of-frame mutations that is potentially relevant for other genetic conditions.
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Affiliation(s)
- Ilaria Parenti
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany; Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Farah Diab
- Centre National de la Recherche Scientifique, UMR6290, Rennes, France; Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Sara Ruiz Gil
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | | | - Valentina Casa
- Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands
| | - Riccardo Berutti
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Rutger W W Brouwer
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Center for Biomics, the Netherlands
| | - Valerie Dupé
- Centre National de la Recherche Scientifique, UMR6290, Rennes, France; Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Juliane Eckhold
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany; Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, 50009 Zaragoza, Spain
| | - Feliciano Ramos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, 50009 Zaragoza, Spain
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Wilfred F J van IJcken
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Center for Biomics, the Netherlands
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Juan Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, 50009 Zaragoza, Spain
| | - Erwan Watrin
- Centre National de la Recherche Scientifique, UMR6290, Rennes, France; Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Frank J Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany; Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany.
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands.
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9
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Dries R, Stryjewska A, Coddens K, Okawa S, Notelaers T, Birkhoff J, Dekker M, Verfaillie CM, Del Sol A, Mulugeta E, Conidi A, Grosveld FG, Huylebroeck D. Integrative and perturbation-based analysis of the transcriptional dynamics of TGFβ/BMP system components in transition from embryonic stem cells to neural progenitors. Stem Cells 2019; 38:202-217. [PMID: 31675135 PMCID: PMC7027912 DOI: 10.1002/stem.3111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/09/2019] [Indexed: 01/05/2023]
Abstract
Cooperative actions of extrinsic signals and cell‐intrinsic transcription factors alter gene regulatory networks enabling cells to respond appropriately to environmental cues. Signaling by transforming growth factor type β (TGFβ) family ligands (eg, bone morphogenetic proteins [BMPs] and Activin/Nodal) exerts cell‐type specific and context‐dependent transcriptional changes, thereby steering cellular transitions throughout embryogenesis. Little is known about coordinated regulation and transcriptional interplay of the TGFβ system. To understand intrafamily transcriptional regulation as part of this system's actions during development, we selected 95 of its components and investigated their mRNA‐expression dynamics, gene‐gene interactions, and single‐cell expression heterogeneity in mouse embryonic stem cells transiting to neural progenitors. Interrogation at 24 hour intervals identified four types of temporal gene transcription profiles that capture all stages, that is, pluripotency, epiblast formation, and neural commitment. Then, between each stage we performed esiRNA‐based perturbation of each individual component and documented the effect on steady‐state mRNA levels of the remaining 94 components. This exposed an intricate system of multilevel regulation whereby the majority of gene‐gene interactions display a marked cell‐stage specific behavior. Furthermore, single‐cell RNA‐profiling at individual stages demonstrated the presence of detailed co‐expression modules and subpopulations showing stable co‐expression modules such as that of the core pluripotency genes at all stages. Our combinatorial experimental approach demonstrates how intrinsically complex transcriptional regulation within a given pathway is during cell fate/state transitions.
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Affiliation(s)
- Ruben Dries
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Agata Stryjewska
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Kathleen Coddens
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Satoshi Okawa
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.,Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Tineke Notelaers
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Judith Birkhoff
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mike Dekker
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.,CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,IKERBASQUE, Basque, Foundation for Science, Bilbao, Spain
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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10
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Blomfield IM, Rocamonde B, Masdeu MDM, Mulugeta E, Vaga S, van den Berg DLC, Huillard E, Guillemot F, Urbán N. Id4 promotes the elimination of the pro-activation factor Ascl1 to maintain quiescence of adult hippocampal stem cells. eLife 2019; 8:e48561. [PMID: 31552825 PMCID: PMC6805120 DOI: 10.7554/elife.48561] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/24/2019] [Indexed: 12/22/2022] Open
Abstract
Quiescence is essential for the long-term maintenance of adult stem cells but how stem cells maintain quiescence is poorly understood. Here, we show that neural stem cells (NSCs) in the adult mouse hippocampus actively transcribe the pro-activation factor Ascl1 regardless of their activated or quiescent states. We found that the inhibitor of DNA binding protein Id4 is enriched in quiescent NSCs and that elimination of Id4 results in abnormal accumulation of Ascl1 protein and premature stem cell activation. Accordingly, Id4 and other Id proteins promote elimination of Ascl1 protein in NSC cultures. Id4 sequesters Ascl1 heterodimerization partner E47, promoting Ascl1 protein degradation and stem cell quiescence. Our results highlight the importance of non-transcriptional mechanisms for the maintenance of NSC quiescence and reveal a role for Id4 as a quiescence-inducing factor, in contrast with its role of promoting the proliferation of embryonic neural progenitors.
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Affiliation(s)
| | - Brenda Rocamonde
- Institut du Cerveau et de la Moelle EpinièreICM, Inserm U 1127, CNRS UMR 7225, Sorbonne UniversitéParisFrance
| | | | | | | | | | - Emmanuelle Huillard
- Institut du Cerveau et de la Moelle EpinièreICM, Inserm U 1127, CNRS UMR 7225, Sorbonne UniversitéParisFrance
| | | | - Noelia Urbán
- The Francis Crick InstituteLondonUnited Kingdom
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC)ViennaAustria
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11
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Redolfi J, Zhan Y, Valdes-Quezada C, Kryzhanovska M, Guerreiro I, Iesmantavicius V, Pollex T, Grand RS, Mulugeta E, Kind J, Tiana G, Smallwood SA, de Laat W, Giorgetti L. DamC reveals principles of chromatin folding in vivo without crosslinking and ligation. Nat Struct Mol Biol 2019; 26:471-480. [PMID: 31133702 PMCID: PMC6561777 DOI: 10.1038/s41594-019-0231-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/18/2019] [Indexed: 01/08/2023]
Abstract
Current understanding of chromosome folding largely relies on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after chromatin crosslinking. To measure chromosome structure in vivo, quantitatively and without crosslinking and ligation, we implemented a modified version of DamID named DamC, which combines DNA-methylation based detection of chromosomal interactions with next-generation sequencing and biophysical modelling of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of topologically associating domains (TADs), CTCF loops and confirms 3C-based measurements of the scaling of contact probabilities. Combining DamC with transposon-mediated genomic engineering shows that new loops can be formed between ectopic and endogenous CTCF sites, which redistributes physical interactions within TADs. DamC provides the first crosslinking- and ligation-free demonstration of the existence of key structural features of chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.
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Affiliation(s)
- Josef Redolfi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Christian Valdes-Quezada
- Oncode Institute, Hubrecht Institute-KNAW, Utrecht, the Netherlands.,University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Isabel Guerreiro
- Oncode Institute, Hubrecht Institute-KNAW, Utrecht, the Netherlands.,University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | - Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Jop Kind
- Oncode Institute, Hubrecht Institute-KNAW, Utrecht, the Netherlands.,University Medical Center Utrecht, Utrecht, the Netherlands
| | - Guido Tiana
- Università degli Studi di Milano and INFN, Milan, Italy
| | | | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW, Utrecht, the Netherlands.,University Medical Center Utrecht, Utrecht, the Netherlands
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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12
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Mulugeta E, Wassenaar E, Sleddens-Linkels E, van IJcken WFJ, Heard E, Grootegoed JA, Just W, Gribnau J, Baarends WM. Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes. Genome Res 2016; 26:1202-10. [PMID: 27510564 PMCID: PMC5052041 DOI: 10.1101/gr.201665.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 07/11/2016] [Indexed: 11/24/2022]
Abstract
The X and Y sex chromosomes of placental mammals show hallmarks of a tumultuous evolutionary past. The X Chromosome has a rich and conserved gene content, while the Y Chromosome has lost most of its genes. In the Transcaucasian mole vole Ellobius lutescens, the Y Chromosome including Sry has been lost, and both females and males have a 17,X diploid karyotype. Similarly, the closely related Ellobius talpinus, has a 54,XX karyotype in both females and males. Here, we report the sequencing and assembly of the E. lutescens and E. talpinus genomes. The results indicate that the loss of the Y Chromosome in E. lutescens and E. talpinus occurred in two independent events. Four functional homologs of mouse Y-Chromosomal genes were detected in both female and male E. lutescens, of which three were also detected in the E. talpinus genome. One of these is Eif2s3y, known as the only Y-derived gene that is crucial for successful male meiosis. Female and male E. lutescens can carry one and the same X Chromosome with a largely conserved gene content, including all genes known to function in X Chromosome inactivation. The availability of the genomes of these mole vole species provides unique models to study the dynamics of sex chromosome evolution.
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Affiliation(s)
- Eskeatnaf Mulugeta
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands; Institut Curie, Genetics and Developmental Biology Unit, 75248, Paris, France
| | - Evelyne Wassenaar
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | | | | | - Edith Heard
- Institut Curie, Genetics and Developmental Biology Unit, 75248, Paris, France
| | - J Anton Grootegoed
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | - Walter Just
- Institute of Human Genetics, University of Ulm, 89081, Ulm, Germany
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
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13
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Ferrari A, Vincent-Salomon A, Pivot X, Sertier AS, Thomas E, Tonon L, Boyault S, Mulugeta E, Treilleux I, MacGrogan G, Arnould L, Kielbassa J, Le Texier V, Blanché H, Deleuze JF, Jacquemier J, Mathieu MC, Penault-Llorca F, Bibeau F, Mariani O, Mannina C, Pierga JY, Trédan O, Bachelot T, Bonnefoi H, Romieu G, Fumoleau P, Delaloge S, Rios M, Ferrero JM, Tarpin C, Bouteille C, Calvo F, Gut IG, Gut M, Martin S, Nik-Zainal S, Stratton MR, Pauporté I, Saintigny P, Birnbaum D, Viari A, Thomas G. A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers. Nat Commun 2016; 7:12222. [PMID: 27406316 PMCID: PMC4947184 DOI: 10.1038/ncomms12222] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 06/12/2016] [Indexed: 02/06/2023] Open
Abstract
HER2-positive breast cancer has long proven to be a clinically distinct class of breast cancers for which several targeted therapies are now available. However, resistance to the treatment associated with specific gene expressions or mutations has been observed, revealing the underlying diversity of these cancers. Therefore, understanding the full extent of the HER2-positive disease heterogeneity still remains challenging. Here we carry out an in-depth genomic characterization of 64 HER2-positive breast tumour genomes that exhibit four subgroups, based on the expression data, with distinctive genomic features in terms of somatic mutations, copy-number changes or structural variations. The results suggest that, despite being clinically defined by a specific gene amplification, HER2-positive tumours melt into the whole luminal-basal breast cancer spectrum rather than standing apart. The results also lead to a refined ERBB2 amplicon of 106 kb and show that several cases of amplifications are compatible with a breakage-fusion-bridge mechanism.
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Affiliation(s)
- Anthony Ferrari
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Anne Vincent-Salomon
- Institut Curie, PSL Research University, Département de Pathologie, INSERM U934, 26 rue d'Ulm, 75248 Paris, France
| | - Xavier Pivot
- Centre Hospitalier Universitaire de Minjoz, UMR INSERM 1098, Boulevard A. Fleming, Besançon 25000, France
| | - Anne-Sophie Sertier
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Emilie Thomas
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Laurie Tonon
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Sandrine Boyault
- Plateforme de génomique des cancers, Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Eskeatnaf Mulugeta
- Institut Curie, UMR 3215 CNRS, Génétique et biologie du développement, Epigénèse et développement des mammifères, U934 Inserm, 26 rue d'Ulm, 75248 Paris, France
| | - Isabelle Treilleux
- Centre Léon Bérard, Département de Pathologie, 28 rue Laënnec, 69008 Lyon, France
| | - Gaëtan MacGrogan
- Département de Biopathologie, Unité Inserm U916, Institut Bergonié, 229 cours de l'Argonne, 33076 Bordeaux, France
| | - Laurent Arnould
- Centre Georges-François Leclerc et CRB Ferdinand Cabanne, 1 rue du Professeur Marion, Inserm U866-UBFC, 21000 Dijon, France
| | - Janice Kielbassa
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Vincent Le Texier
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Hélène Blanché
- Centre d'Etude du Polymorphisme Humain (CEPH), Fondation Jean Dausset, 27 rue Juliette Dodu, 75010 Paris, France
| | - Jean-François Deleuze
- Centre d'Etude du Polymorphisme Humain (CEPH), Fondation Jean Dausset, 27 rue Juliette Dodu, 75010 Paris, France
| | - Jocelyne Jacquemier
- Institut Paoli-Calmettes, Département de Pathologie, 232 Boulevard de Sainte-Marguerite, 13009 Marseille, France
| | - Marie-Christine Mathieu
- Institut Gustave Roussy, Comité de Pathologie Mammaire, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Frédérique Penault-Llorca
- Centre Jean Perrin, Département de Biopathologie, EA 4677 ERTICa, Université d'Auvergne, 58 rue Montalembert, 63000 Clermont-Ferrand, France
| | - Frédéric Bibeau
- Institut Régional du Cancer de Montpellier (ICM), Département de Pathologie, 208 Avenue des Apothicaires, 34298 Montpellier, France
| | - Odette Mariani
- Institut Curie, PSL Research University, Service de Pathologie, Centre de Ressources Biologiques, BRIF BB-0033-00048, 26 rue d'Ulm, 75248 Paris, France
| | - Cécile Mannina
- Département de Pathologie, Institut Bergonié, 229 cours de l'Argonne, CS 61283, 33076 Bordeaux, France
| | - Jean-Yves Pierga
- Institut Curie, PSL Research University, Département d'Oncologie Médicale, Université Paris Descartes, 26 rue d'Ulm, 75248 Paris, France
| | - Olivier Trédan
- Centre Léon Bérard, Département de Cancérologie Médicale, 28 rue Laënnec, 69008 Lyon, France
| | - Thomas Bachelot
- Centre Léon Bérard, Département de Cancérologie Médicale, 28 rue Laënnec, 69008 Lyon, France
| | - Hervé Bonnefoi
- Department of Medical Oncology, Institut Bergonié Unicancer, University of Bordeaux, INSERM U916, CIC1401, 229 cours de l'Argonne, CS 61283, 33076 Bordeaux, France
| | - Gilles Romieu
- Institut Régional du Cancer de Montpellier (ICM), Oncologie Sénologie, 208 Avenue des Apothicaires, 34298 Montpellier, France
| | - Pierre Fumoleau
- Centre Georges-François Leclerc et CRB Ferdinand Cabanne, 1 rue du Professeur Marion, Inserm U866-UBFC, 21000 Dijon, France
| | - Suzette Delaloge
- Institut Gustave Roussy, Comité de Pathologie Mammaire, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Maria Rios
- Centre Alexis Vautrin, Département d'Oncologie Médicale, 6 Avenue de Bourgogne, 54511 Vandoeuvre Les Nancy, France
| | - Jean-Marc Ferrero
- Centre Antoine Lacassagne, Département d'Oncologie Médicale, 33 Avenue de Valombrose, 06189 Nice, France
| | - Carole Tarpin
- Institut Paoli-Calmettes, Département d'Oncologie Médicale, 232 Boulevard de Sainte-Marguerite, 13009 Marseille, France
| | - Catherine Bouteille
- Clinique Mutualiste de Bellevue, Chirurgie Gynécologique et Mammaire, 3 rue le Verrier, 42100 Saint-Etienne, France
| | - Fabien Calvo
- Institut Gustave Roussy, Cancer Core Europe, 39 rue Camille Desmoulins, Villejuif 94805, France
| | - Ivo Glynne Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, UK
| | | | - Iris Pauporté
- Institut National du Cancer, Département de Recherche Clinique, 52 Avenue Morizet, 92513 Boulogne-Billancourt, France
| | - Pierre Saintigny
- INSERM U1052-CNRS 5286, Cancer Research Center of Lyon, F-69008 Lyon, France
- Université de Lyon, F-69622 Lyon, France
- Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Daniel Birnbaum
- Département d'Oncologie Moléculaire, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, INSERM, CNRS, Aix-Marseille Université, 232 boulevard de Sainte-Marguerite, 13009 Marseille, France
| | - Alain Viari
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
- Equipe Erable, INRIA Grenoble-Rhône-Alpes, 655 Avenue de l'Europe, 38330 Montbonnot-Saint Martin, France
| | - Gilles Thomas
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
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14
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Federici F, Mulugeta E, Schoenmakers S, Wassenaar E, Hoogerbrugge JW, van der Heijden GW, van Cappellen WA, Slotman JA, van IJcken WFJ, Laven JSE, Grootegoed JA, Baarends WM. Incomplete meiotic sex chromosome inactivation in the domestic dog. BMC Genomics 2015; 16:291. [PMID: 25884295 PMCID: PMC4399420 DOI: 10.1186/s12864-015-1501-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/30/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In mammalian meiotic prophase, homologous chromosome recognition is aided by formation and repair of programmed DNA double-strand breaks (DSBs). Subsequently, stable associations form through homologous chromosome synapsis. In male mouse meiosis, the largely heterologous X and Y chromosomes synapse only in their short pseudoautosomal regions (PARs), and DSBs persist along the unsynapsed non-homologous arms of these sex chromosomes. Asynapsis of these arms and the persistent DSBs then trigger transcriptional silencing through meiotic sex chromosome inactivation (MSCI), resulting in formation of the XY body. This inactive state is partially maintained in post-meiotic haploid spermatids (postmeiotic sex chromatin repression, PSCR). For the human, establishment of MSCI and PSCR have also been reported, but X-linked gene silencing appears to be more variable compared to mouse. To gain more insight into the regulation and significance of MSCI and PSCR among different eutherian species, we have performed a global analysis of XY pairing dynamics, DSB repair, MSCI and PSCR in the domestic dog (Canis lupus familiaris), for which the complete genome sequence has recently become available, allowing a thorough comparative analyses. RESULTS In addition to PAR synapsis between X and Y, we observed extensive self-synapsis of part of the dog X chromosome, and rapid loss of known markers of DSB repair from that part of the X. Sequencing of RNA from purified spermatocytes and spermatids revealed establishment of MSCI. However, the self-synapsing region of the X displayed higher X-linked gene expression compared to the unsynapsed area in spermatocytes, and was post-meiotically reactivated in spermatids. In contrast, genes in the PAR, which are expected to escape MSCI, were expressed at very low levels in both spermatocytes and spermatids. Our comparative analysis was then used to identify two X-linked genes that may escape MSCI in spermatocytes, and 21 that are specifically re-activated in spermatids of human, mouse and dog. CONCLUSIONS Our data indicate that MSCI is incomplete in the dog. This may be partially explained by extensive, but transient, self-synapsis of the X chromosome, in association with rapid completion of meiotic DSB repair. In addition, our comparative analysis identifies novel candidate male fertility genes.
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Affiliation(s)
- Federica Federici
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Eskeatnaf Mulugeta
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands. .,Present address: Institut Curie, Genetics and Developmental Biology, Unit 11 et 13 rue Pierre et Marie Curie, 75248, Paris, Cedex 05, France.
| | - Sam Schoenmakers
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands. .,Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Evelyne Wassenaar
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Jos W Hoogerbrugge
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Godfried W van der Heijden
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands. .,Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Wiggert A van Cappellen
- Department of Pathology, Erasmus Optical Imaging Centre, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Johan A Slotman
- Department of Pathology, Erasmus Optical Imaging Centre, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Joop S E Laven
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - J Anton Grootegoed
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
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Adeno F, Mulugeta E, Zewge F, Chebude Y. Adsorptive removal of fluoride from water using nanoscale aluminium oxide hydroxide (AlOOH). B CHEM SOC ETHIOPIA 2014. [DOI: 10.4314/bcse.v28i2.6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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16
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Mattsson N, Rosén E, Hansson O, Andreasen N, Parnetti L, Jonsson M, Herukka SK, van der Flier WM, Blankenstein MA, Ewers M, Rich K, Kaiser E, Verbeek MM, Olde Rikkert M, Tsolaki M, Mulugeta E, Aarsland D, Visser PJ, Schröder J, Marcusson J, de Leon M, Hampel H, Scheltens P, Wallin A, Eriksdotter-Jönhagen M, Minthon L, Winblad B, Blennow K, Zetterberg H. Age and diagnostic performance of Alzheimer disease CSF biomarkers. Neurology 2012; 78:468-76. [PMID: 22302554 DOI: 10.1212/wnl.0b013e3182477eed] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Core CSF changes in Alzheimer disease (AD) are decreased amyloid β(1-42), increased total tau, and increased phospho-tau, probably indicating amyloid plaque accumulation, axonal degeneration, and tangle pathology, respectively. These biomarkers identify AD already at the predementia stage, but their diagnostic performance might be affected by age-dependent increase of AD-type brain pathology in cognitively unaffected elderly. METHODS We investigated effects of age on the diagnostic performance of CSF biomarkers in a uniquely large multicenter study population, including a cross-sectional cohort of 529 patients with AD dementia (median age 71, range 43-89 years) and 304 controls (67, 44-91 years), and a longitudinal cohort of 750 subjects without dementia with mild cognitive impairment (69, 43-89 years) followed for at least 2 years, or until dementia diagnosis. RESULTS The specificities for subjects without AD and the areas under the receiver operating characteristics curves decreased with age. However, the positive predictive value for a combination of biomarkers remained stable, while the negative predictive value decreased only slightly in old subjects, as an effect of the high AD prevalence in older ages. CONCLUSION Although the diagnostic accuracies for AD decreased with age, the predictive values for a combination of biomarkers remained essentially stable. The findings highlight biomarker variability across ages, but support the use of CSF biomarkers for AD even in older populations.
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Affiliation(s)
- N Mattsson
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Neurochemistry and Psychiatry, The Sahlgrenska Academy at University of Gothenburg, Mo¨lndal, Sweden.
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17
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El-Bakri NK, Adem A, Suliman IA, Mulugeta E, Karlsson E, Lindgren JU, Winblad B, Islam A. Estrogen and progesterone treatment: effects on muscarinic M(4) receptor subtype in the rat brain. Brain Res 2002; 948:131-7. [PMID: 12383964 DOI: 10.1016/s0006-8993(02)02962-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We investigated the effect of ovariectomy (OVX) and hormonal treatment for 10 weeks by estradiol and progesterone on muscarinic M(4) receptor subtype in different brain areas of female rats. Moreover, motor activity of OVX and hormone-treated rats was measured by automated open field exploration boxes. Receptor quantification in the hippocampus, frontal cortex, parietal cortex, amygdala and hypothalamus was done by receptor autoradiography using a selective ligand for muscarinic M(4) receptors. Ovariectomy up-regulated M(4) receptors in the dentate gyrus, CA1, CA3, frontal cortex and hypothalamus whereas the estrogen treatment restored M(4) binding to that of the sham group. Progesterone treatment had no effect on the ovariectomy-induced up-regulation of M(4) receptors. Ovariectomy significantly decreased the exploratory activity of the rats compared to the sham group. Estrogen treatment restored the exploratory behavior of the ovariectomized rats to that of the sham group whereas the progesterone-treated rats were less alert to the surrounding when compared to the sham and estrogen supplemented rats. The effect of estrogen on the hippocampal muscarinic M(4) receptor subtype is a novel finding and may have functional significance for cholinergic receptors especially in relation to postmenopausal memory problems and neurodegenerative disease like Alzheimer's disease.
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Affiliation(s)
- Nahid K El-Bakri
- Department of Clinical Neuroscience, Karolinska Institute, Huddinge University Hospital, S-141 86 Huddinge, Sweden.
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Abstract
There are five subtypes of muscarinic acetylcholine receptors (M(1) to M(5)) which control a large number of physiological processes, such as the function of heart and smooth muscles, glandular secretion, release of neurotransmitters, gene expression and cognitive functions as learning and memory. A selective ligand is very useful for studying the function of a subtype in presence of other subtypes, which is the most common situation, since a cell or an organ usually has several subtypes. There are many non-selective muscarinic ligands, but only few selective ones. Mambas, African snakes of genus Dendroaspis have toxins, muscarinic toxins, that are selective for M(1), M(2) and M(4) receptors. They consist of 63-66 amino acids and four disulfides which form four loops. They are members of a large group of snake toxins, three-finger toxins; three loops are extended like the middle fingers of a hand and the disulfides and the shortest loop are in the palm of the hand. Some of the toxins target the allosteric site which is located in a cleft of the receptor molecule close to its extracellular part. A possible explanation to the good selectivity is that the toxins bind to the allosteric site, but because of their size they probably also bind to extracellular parts of the receptors which are rather different in the various subtypes. Some other allosteric ligands also have good selectivity, the alkaloid brucine and derivatives are selective for M(1), M(3) and M(4) receptors. Muscarinic toxins have been used in several types of experiments. For instance radioactively labeled M(1) and M(4) selective toxins were used in autoradiography of hippocampus from Alzheimer patients. One significant change in the receptor content was detected in one region of the hippocampus, dentate gyrus, where M(4) receptors were reduced by 50% in patients as compared to age-matched controls. Hippocampus is essential for memory consolidation. M(4) receptors in dentate gyrus may play a role, since they decreased in Alzheimers disease which destroys the memory. Another indication of the role of M(4) receptors for memory is that injection of the M(4) selective antagonist muscarinic toxin 3 (M(4)-toxin 1) into rat hippocampus produced amnesia.
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Affiliation(s)
- E Karlsson
- Department of Physiology, Biomedical Centre, Box 572, 751 23, Uppsala, Sweden.
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19
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Gessesse B, Mulugeta E. Multiforme skin lesions in Yekatit 12 Hospital, 1976-1994. Ethiop Med J 2000; 38:43-7. [PMID: 11144879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Because the number of cases of multiforme skin lesions encountered in the medical department of Yekatit 12 Hospital has increased in recent years, we conducted a retrospective study to identify the likely precipitating factors and the possible relationship of these with HIV infection. Forty-seven patients with Multiforme Skin Lesions (29 males, 18 females) were admitted between 1976 and January 1994, of whom 43 (92%) were admitted in the past 5 years. Most patients were aged 15-49 years. Thirty patients (64%) were discharged improved and 14 (30%) expired in hospital. The outcome of 3 patients are not known. The charts of only 16 patients could be retrieved for review. Fifteen of these (94%) gave a history of intake of streptomycin, isoniazed and thiacetazone prior to developing the skin manifestation. The anti-TB medications were discontinued initially; 14 patients were restarted on STM, INH and ethambutol without recurrence of the rash. All but 1 were discharged improved. HIV screening tests were done on 24 patients with multiforme skin lesion of whom 21 (88%) were seropositive. Our study suggested that the adverse effects of thiacetazone are increased in HIV associated tuberculous patients. We recommend that further studies be conducted in HIV seropositive and seronegative patients.
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Affiliation(s)
- B Gessesse
- Department of Internal Medicine, Yekatit 12 Hospital, Addis Ababa
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20
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Adem A, Blange I, Sylven C, Winblad B, Mulugeta E, Karlsson E, Mustafa A. Detection of muscarinic receptor subtypes in human heart using a reverse transcriptase-polymerase chain reaction (RT-PCR). Life Sci 1999. [DOI: 10.1016/s0024-3205(99)90536-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Mulugeta E, Kassaye M, Berhane Y. Prevalence and outcomes of sexual violence among high school students. Ethiop Med J 1998; 36:167-74. [PMID: 10214457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
A cross sectional, school-based survey using self administered anonymous questionnaire was conducted in Addis Ababa and Western Shoa among high school students to determine the prevalence, and reported outcomes of sexual violence. A total of 1401 female students were involved in the study. The prevalence of completed rape and attempted rape among female students was 5% and 10% respectively. The age range of completed rape was between 12-23 years and 61/72 (85%) of the rape victims were under 18 years of age. No significant linear trend was observed among the different age intervals (Chi Square for linear trend = 1.18; p-value = 0.27). Of the total respondents 78%, believed that rape was a major problem. Sexual harassment was reported in 74% of female students. Among the seventy two girls who reported to be raped 17(24%) had vaginal discharge and 12(17%) became pregnant. Social isolation, fear and phobia, hopelessness and suicide attempt were reported in 33%, 19%, 22%, 6% of rape victims, respectively. It is concluded that the prevalence of sexual violence among high school students is a serious problem and concern. Awareness creation to adolescents and the family need to be introduced and schools should also devise appropriate sex education regarding damaging effect of rape and educate youth on sexuality and responsible sexual decision making.
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Affiliation(s)
- E Mulugeta
- Department of Community Health, Faculty of Medicine, Addis Ababa University
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22
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Mulugeta E, Carnö S, Becker S, Hagman A, Mascher E. Rapid reversed-phase high-performance liquid chromatography method for quantitation, at high pH, of the recombinant apolipoprotein A-IMilano in Escherichia coli fermentation broth. J Chromatogr A 1998; 798:83-90. [PMID: 9542129 DOI: 10.1016/s0021-9673(97)01203-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An automated reversed-phase high-performance liquid chromatography method for quantitative determination of recombinant apolipoprotein A-IMilano (r-Apo A-IM) in E. coli fermentation broth has been developed and evaluated. The use of a unique matrix (Poros IIR/H) makes it possible to achieve rapid separation and good resolution at high pH. The r-Apo A-IM-containing fraction is well separated from other proteins allowing a reliable quantification. The automation and high sample throughput of this method makes it very useful for routine determination of r-Apo A-IM in fermentation broth and in eluates from the various purfication steps. With suitable modifications and adaptions this method is likely to be useful for similar rapid analytical determination of recombinant proteins in complex solutions.
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Affiliation(s)
- E Mulugeta
- Pharmacia & Upjohn AB, Process R&D, Stockholm, Sweden
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