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Article ; Online: Chromothripsis, DNA repair and checkpoints defects.

Simovic, Milena / Ernst, Aurélie

Seminars in cell & developmental biology

2021 Volume 123, Page(s) 110–114

Abstract: Chromothripsis is a unique form of genome instability characterized by tens to hundreds of DNA double-strand breaks on one or very few chromosomes, followed by error-prone repair. The derivative chromosome(s) display massive rearrangements, which lead to ...

Abstract	Chromothripsis is a unique form of genome instability characterized by tens to hundreds of DNA double-strand breaks on one or very few chromosomes, followed by error-prone repair. The derivative chromosome(s) display massive rearrangements, which lead to the loss of tumor suppressor function and to the activation of oncogenes. Chromothripsis plays a major role in cancer as well as in other conditions, such as congenital diseases. In this review, we discuss the repair processes involved in the rejoining of the chromosome fragments, the role of DNA repair and checkpoint defects as a cause for chromothripsis as well as DNA repair defects resulting from chromothripsis. Finally, we consider clinical implications and potential therapeutic vulnerabilities that could be utilized to eliminate tumor cells with chromothripsis.
MeSH term(s)	Chromothripsis ; DNA Breaks, Double-Stranded ; DNA Repair/genetics ; Gene Rearrangement ; Genomic Instability/genetics ; Humans
Language	English
Publishing date	2021-02-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1312473-0
ISSN	1096-3634 ; 1084-9521
ISSN (online)	1096-3634
ISSN	1084-9521
DOI	10.1016/j.semcdb.2021.02.001
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Zs.A 2918: Show issues

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Article ; Online: Cell-based model systems for genome instability: Dissecting the mechanistic basis of chromothripsis in cancer.

Kolb, Thorsten / Ernst, Aurélie

International journal of cancer

2021

Abstract: Chromothripsis is a form of genomic instability that was shown to play a major role in cancer. Beyond cancer, this type of catastrophic event is also involved in germline structural variation, genome mosaicism in somatic tissues, infertility, mental ... ...

Abstract	Chromothripsis is a form of genomic instability that was shown to play a major role in cancer. Beyond cancer, this type of catastrophic event is also involved in germline structural variation, genome mosaicism in somatic tissues, infertility, mental retardation, congenital malformations and reproductive development in plants. Several assays have been developed to model chromothripsis in vitro and to dissect the mechanistic basis of this phenomenon. Cell-based model systems are designed with different strategies, such as the formation of nuclear structures called micronuclei, telomere fusions or the induction of exogenous DNA double-strand breaks. Here, we review a range of model systems for chromothripsis and the mechanistic insights gained from these assays, with a particular focus on chromothripsis in cancer.
Language	English
Publishing date	2021-05-01
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	218257-9
ISSN	1097-0215 ; 0020-7136
ISSN (online)	1097-0215
ISSN	0020-7136
DOI	10.1002/ijc.33618
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Zs.A 478: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Adult neurogenesis in humans- common and unique traits in mammals.

Ernst, Aurélie / Frisén, Jonas

PLoS biology

2015 Volume 13, Issue 1, Page(s) e1002045

Abstract: New neurons are continuously generated in specific regions in the adult brain. Studies in rodents have demonstrated that adult-born neurons have specific functional features and mediate neural plasticity. Data on the extent and dynamics of adult ... ...

Abstract	New neurons are continuously generated in specific regions in the adult brain. Studies in rodents have demonstrated that adult-born neurons have specific functional features and mediate neural plasticity. Data on the extent and dynamics of adult neurogenesis in adult humans are starting to emerge, and there are clear similarities and differences compared to other mammals. Why do these differences arise? And what do they mean?
MeSH term(s)	Adult ; Animals ; Biological Evolution ; Corpus Striatum/physiology ; Hippocampus/physiology ; Humans ; Lateral Ventricles/physiology ; Models, Neurological ; Neocortex/physiology ; Neurogenesis ; Neuronal Plasticity ; Olfactory Bulb/physiology ; Organ Specificity ; Transcriptome
Language	English
Publishing date	2015-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.1002045
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Article ; Online: Cancer Hallmarks: Piecing the Puzzle Together.

Alcolea, Maria P / Alonso-Curbelo, Direna / Ambrogio, Chiara / Bullman, Susan / Correia, Ana Luísa / Ernst, Aurélie / Halbrook, Christopher J / Kelly, Gemma L / Lund, Amanda W / Quail, Daniela F / Ruscetti, Marcus / Shema, Efrat / Stromnes, Ingunn M / Tam, Wai Leong

Cancer discovery

2024 Volume 14, Issue 4, Page(s) 674–682

MeSH term(s)	Humans ; Neoplasms/epidemiology
Language	English
Publishing date	2024-04-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2625242-9
ISSN	2159-8290 ; 2159-8274
ISSN (online)	2159-8290
ISSN	2159-8274
DOI	10.1158/2159-8290.CD-24-0097
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Article ; Online: Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures.

Rausch, Tobias / Snajder, Rene / Leger, Adrien / Simovic, Milena / Giurgiu, Mădălina / Villacorta, Laura / Henssen, Anton G / Fröhling, Stefan / Stegle, Oliver / Birney, Ewan / Bonder, Marc Jan / Ernst, Aurelie / Korbel, Jan O

Cell genomics

2023 Volume 3, Issue 4, Page(s) 100281

Abstract: Cancer genomes harbor a broad spectrum of structural variants (SVs) driving tumorigenesis, a relevant subset of which escape discovery using short-read sequencing. We employed Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic ...

Abstract	Cancer genomes harbor a broad spectrum of structural variants (SVs) driving tumorigenesis, a relevant subset of which escape discovery using short-read sequencing. We employed Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic and post-therapy medulloblastoma to unravel the haplotype-resolved somatic genetic and epigenetic landscape. We assembled complex rearrangements, including a 1.55-Mbp chromothripsis event, and we uncover a complex SV pattern termed templated insertion (TI) thread, characterized by short (mostly <1 kb) insertions showing prevalent self-concatenation into highly amplified structures of up to 50 kbp in size. TI threads occur in 3% of cancers, with a prevalence up to 74% in liposarcoma, and frequent colocalization with chromothripsis. We also perform long-read-based methylome profiling and discover allele-specific methylation (ASM) effects, complex rearrangements exhibiting differential methylation, and differential promoter methylation in cancer-driver genes. Our study shows the advantage of long-read sequencing in the discovery and characterization of complex somatic rearrangements.
Language	English
Publishing date	2023-03-22
Publishing country	United States
Document type	Journal Article
ISSN	2666-979X
ISSN (online)	2666-979X
DOI	10.1016/j.xgen.2023.100281
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Article ; Online: Comparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states.

Jaber, Mohammad / Radwan, Ahmed / Loyfer, Netanel / Abdeen, Mufeed / Sebban, Shulamit / Khatib, Areej / Yassen, Hazar / Kolb, Thorsten / Zapatka, Marc / Makedonski, Kirill / Ernst, Aurelie / Kaplan, Tommy / Buganim, Yosef

Nature communications

2022 Volume 13, Issue 1, Page(s) 3475

Abstract: Following fertilization, it is only at the 32-64-cell stage when a clear segregation between cells of the inner cell mass and trophectoderm is observed, suggesting a 'T'-shaped model of specification. Here, we examine whether the acquisition of these two ...

Abstract	Following fertilization, it is only at the 32-64-cell stage when a clear segregation between cells of the inner cell mass and trophectoderm is observed, suggesting a 'T'-shaped model of specification. Here, we examine whether the acquisition of these two states in vitro, by nuclear reprogramming, share similar dynamics/trajectories. Using a comparative parallel multi-omics analysis (i.e., bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, RRBS and CNVs) on cells undergoing reprogramming to pluripotency and TSC state we show that each reprogramming system exhibits specific trajectories from the onset of the process, suggesting 'V'-shaped model. We describe in detail the various trajectories toward the two states and illuminate reprogramming stage-specific markers, blockers, facilitators and TSC subpopulations. Finally, we show that while the acquisition of the TSC state involves the silencing of embryonic programs by DNA methylation, during the acquisition of pluripotency these regions are initially defined but retain inactive by the elimination of H3K27ac.
MeSH term(s)	Blastocyst/metabolism ; Cells, Cultured ; Cellular Reprogramming/genetics ; DNA Methylation
Language	English
Publishing date	2022-06-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-31131-8
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Article ; Online: Chromothripsis in cancer cells: An update.

Rode, Agata / Maass, Kendra Korinna / Willmund, Karolin Viktoria / Lichter, Peter / Ernst, Aurélie

International journal of cancer

2016 Volume 138, Issue 10, Page(s) 2322–2333

Abstract: In 2011, a novel form of genome instability was reported by Stephens et al., characterized by tens to hundreds of locally clustered rearrangements affecting one or a few chromosome(s) in cancer cells. This phenomenon, termed chromothripsis, is likely due ...

Abstract	In 2011, a novel form of genome instability was reported by Stephens et al., characterized by tens to hundreds of locally clustered rearrangements affecting one or a few chromosome(s) in cancer cells. This phenomenon, termed chromothripsis, is likely due to a single catastrophic event leading to the simultaneous formation of multiple double-strand breaks, which are repaired by error-prone mechanisms. Since then, the occurrence of chromothripsis was detected in a wide range of tumor entities. In this review, we will discuss potential mechanisms of chromothripsis initiation in cancer and outline the prevalence of chromothripsis across entities. Furthermore, we will examine how chromothriptic events may promote cancer development and how they may affect cancer therapy.
MeSH term(s)	Animals ; Cell Transformation, Neoplastic/genetics ; Chromosome Aberrations ; Genomic Instability ; Humans ; Neoplasms/genetics ; Neoplasms/therapy
Language	English
Publishing date	2016-05-15
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	218257-9
ISSN	1097-0215 ; 0020-7136
ISSN (online)	1097-0215
ISSN	0020-7136
DOI	10.1002/ijc.29888
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Article: Evidence for a pre-malignant cell line in a skin biopsy from a patient with Nijmegen breakage syndrome.

Habib, Raneem / Neitzel, Heidemarie / Ernst, Aurelie / Wong, John K L / Goryluk-Kozakiewicz, Bozenna / Gerlach, Antje / Demuth, Ilja / Sperling, Karl / Chrzanowska, Krystyna

Molecular cytogenetics

2018 Volume 11, Page(s) 17

Abstract: Background: Nijmegen breakage syndrome is an autosomal recessive disorder characterized by microcephaly, immunodeficiency, hypersensitivity to X-irradiation, and a high predisposition to cancer. Nibrin, the product of the : Case presentation: Here we ...

Abstract	Background: Nijmegen breakage syndrome is an autosomal recessive disorder characterized by microcephaly, immunodeficiency, hypersensitivity to X-irradiation, and a high predisposition to cancer. Nibrin, the product of the Case presentation: Here we present an incidental finding. Skin fibroblasts, derived from a 9 year old NBS patient, showed a mosaic of normal diploid cells (46,XY) and those with a complex, unbalanced translocation. The aberrant karyotype was analysed by G-banding, comparative genomic hybridization, and whole chromosome painting. The exact breakpoints of the derivative chromosome were mapped by whole genome sequencing: 45,XY,der(6)(6pter → 6q11.1::13q11 → 13q21.33::20q11.22 → 20qter),-13. The deleted region of chromosomes 6 harbors almost 1.400 and that of chromosome 13 more than 500 genes, the duplicated region of chromosome 20 contains about 700 genes. Such unbalanced translocations are regularly incompatible with cellular survival, except in malignant cells. The aberrant cells, however, showed a high proliferation potential and could even be clonally expanded. Telomere length was significantly reduced, Conclusions: The aberrant cells had a significant selective advantage in vitro. It is therefore tempting to speculate that this highly unbalanced translocation could be a primary driver of cancer cell growth.
Language	English
Publishing date	2018-02-07
Publishing country	England
Document type	Case Reports
ZDB-ID	2420849-8
ISSN	1755-8166
ISSN	1755-8166
DOI	10.1186/s13039-018-0364-6
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Article ; Online: Altered nuclear envelope structure and proteasome function of micronuclei.

Maass, Kendra K / Rosing, Fabian / Ronchi, Paolo / Willmund, Karolin V / Devens, Frauke / Hergt, Michaela / Herrmann, Harald / Lichter, Peter / Ernst, Aurélie

Experimental cell research

2018 Volume 371, Issue 2, Page(s) 353–363

Abstract: Micronuclei are extra-nuclear bodies containing whole chromosomes that were not incorporated into the nucleus after cell division or damaged chromosome fragments. Even though the link between micronuclei and DNA damage is described for a long time, ... ...

Abstract	Micronuclei are extra-nuclear bodies containing whole chromosomes that were not incorporated into the nucleus after cell division or damaged chromosome fragments. Even though the link between micronuclei and DNA damage is described for a long time, little is known about the functional organization of micronuclei and their contribution to tumorigenesis. We showed fusions between micronuclear membranes and lysosomes by electron microscopy and linked lysosome function to DNA damage levels in micronuclei. In addition, micronuclei drastically differ from primary nuclei in nuclear envelope composition, with a significant increase in the relative amount of nuclear envelope proteins LBR and emerin and a decrease in nuclear pore proteins. Strikingly, micronuclei lack active proteasomes, as the processing subunits and other factors of the ubiquitin proteasome system. Moreover, micronuclear chromatin shows a higher degree of compaction as compared to primary nuclei. The specific aberrations identified in micronuclei and the potential functional consequences of these defects may contribute to the role of micronuclei in catastrophic genomic rearrangements.
MeSH term(s)	Cell Line ; Cell Nucleus/metabolism ; Cell Nucleus/pathology ; Cell Nucleus/ultrastructure ; Chromatin/chemistry ; Chromatin/ultrastructure ; Chromothripsis ; DNA Damage ; Epithelial Cells/drug effects ; Epithelial Cells/metabolism ; Epithelial Cells/ultrastructure ; Fibroblasts/drug effects ; Fibroblasts/metabolism ; Fibroblasts/ultrastructure ; Gene Expression ; Genomic Instability ; Humans ; Lysosomes/metabolism ; Lysosomes/ultrastructure ; Membrane Fusion ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Micronucleus Tests ; Nocodazole/pharmacology ; Nuclear Envelope/chemistry ; Nuclear Envelope/metabolism ; Nuclear Envelope/pathology ; Nuclear Envelope/ultrastructure ; Nuclear Pore Complex Proteins/genetics ; Nuclear Pore Complex Proteins/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Proteasome Endopeptidase Complex/physiology ; Proteasome Endopeptidase Complex/ultrastructure ; Receptors, Cytoplasmic and Nuclear/genetics ; Receptors, Cytoplasmic and Nuclear/metabolism ; Retinal Pigment Epithelium/drug effects ; Retinal Pigment Epithelium/metabolism ; Retinal Pigment Epithelium/ultrastructure ; Lamin B Receptor
Chemical Substances	Chromatin ; Membrane Proteins ; Nuclear Pore Complex Proteins ; Nuclear Proteins ; Receptors, Cytoplasmic and Nuclear ; emerin ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Nocodazole (SH1WY3R615)
Language	English
Publishing date	2018-08-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1493-x
ISSN	1090-2422 ; 0014-4827
ISSN (online)	1090-2422
ISSN	0014-4827
DOI	10.1016/j.yexcr.2018.08.029
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Zs.A 563: Show issues

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Article ; Online: Pilocytic astrocytoma demethylation and transcriptional landscapes link bZIP transcription factors to immune response.

Aichmüller, Christian F / Iskar, Murat / Jones, David T W / Korshunov, Andrey / Radlwimmer, Bernhard / Kool, Marcel / Ernst, Aurelie / Pfister, Stefan M / Lichter, Peter / Zapatka, Marc

Neuro-oncology

2020 Volume 22, Issue 9, Page(s) 1327–1338

Abstract: Background: Pilocytic astrocytoma (PA) is the most common pediatric brain tumor. While genome and transcriptome landscapes are well studied, data of the complete methylome, tumor cell composition, and immune infiltration are scarce.: Methods: We ... ...

Abstract	Background: Pilocytic astrocytoma (PA) is the most common pediatric brain tumor. While genome and transcriptome landscapes are well studied, data of the complete methylome, tumor cell composition, and immune infiltration are scarce. Methods: We generated whole genome bisulfite sequence (WGBS) data of 9 PAs and 16 control samples and integrated available 154 PA and 57 control methylation array data. RNA sequence data of 49 PAs and 11 control samples as well as gene expression arrays of 248 PAs and 28 controls were used to assess transcriptional activity. Results: DNA-methylation patterns of partially methylated domains suggested high stability of the methylomes during tumorigenesis. Comparing tumor and control tissues of infra- and supratentorial location using methylation arrays revealed a site specific pattern. Analysis of WGBS data revealed 9381 significantly differentially methylated regions (DMRs) in PA versus control tissue. Enhancers and transcription factor (TF) motifs of five distinct TF families were found to be enriched in DMRs. Methylation together with gene expression data-based in silico tissue deconvolution analysis indicated a striking variation in the immune cell infiltration in PA. A TF network analysis showed a regulatory relation between basic leucine zipper (bZIP) transcription factors and genes involved in immune-related processes. Conclusion: We provide evidence for a link of focal methylation differences and differential gene expression to immune infiltration.
MeSH term(s)	Astrocytoma/genetics ; Basic-Leucine Zipper Transcription Factors ; Child ; DNA Methylation ; Demethylation ; Humans ; Immunity
Chemical Substances	Basic-Leucine Zipper Transcription Factors
Language	English
Publishing date	2020-02-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2028601-6
ISSN	1523-5866 ; 1522-8517
ISSN (online)	1523-5866
ISSN	1522-8517
DOI	10.1093/neuonc/noaa035
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