1
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Zhang S, Wang R, Zhu X, Zhang L, Liu X, Sun L. Characteristics and expression of lncRNA and transposable elements in Drosophila aneuploidy. iScience 2023; 26:108494. [PMID: 38125016 PMCID: PMC10730892 DOI: 10.1016/j.isci.2023.108494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/28/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Aneuploidy can globally affect the expression of the whole genome, which is detrimental to organisms. Dosage-sensitive regulators usually have multiple intermolecular interactions, and changes in their stoichiometry are responsible for the dysregulation of the regulatory network. Currently, studies on noncoding genes in aneuploidy are relatively rare. We studied the characteristics and expression profiles of long noncoding RNAs (lncRNAs) and transposable elements (TEs) in aneuploid Drosophila. It is found that lncRNAs and TEs are affected by genomic imbalance and appear to be more sensitive to an inverse dosage effect than mRNAs. Several dosage-sensitive lncRNAs and TEs were detected for their expression patterns during embryogenesis, and their biological functions in the ovary and testes were investigated using tissue-specific RNAi. This study advances our understanding of the noncoding sequences in imbalanced genomes and provides a novel perspective for the study of aneuploidy-related human diseases such as cancer.
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Affiliation(s)
- Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xilin Zhu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ludan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xinyu Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China
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2
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Zhegalova IV, Vasiluev PA, Flyamer IM, Shtompel AS, Glazyrina E, Shilova N, Minzhenkova M, Markova Z, Petrova NV, Dashinimaev EB, Razin SV, Ulianov SV. Trisomies Reorganize Human 3D Genome. Int J Mol Sci 2023; 24:16044. [PMID: 38003233 PMCID: PMC10671006 DOI: 10.3390/ijms242216044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 11/26/2023] Open
Abstract
Trisomy is the presence of one extra copy of an entire chromosome or its part in a cell nucleus. In humans, autosomal trisomies are associated with severe developmental abnormalities leading to embryonic lethality, miscarriage or pronounced deviations of various organs and systems at birth. Trisomies are characterized by alterations in gene expression level, not exclusively on the trisomic chromosome, but throughout the genome. Here, we applied the high-throughput chromosome conformation capture technique (Hi-C) to study chromatin 3D structure in human chorion cells carrying either additional chromosome 13 (Patau syndrome) or chromosome 16 and in cultured fibroblasts with extra chromosome 18 (Edwards syndrome). The presence of extra chromosomes results in systematic changes of contact frequencies between small and large chromosomes. Analyzing the behavior of individual chromosomes, we found that a limited number of chromosomes change their contact patterns stochastically in trisomic cells and that it could be associated with lamina-associated domains (LAD) and gene content. For trisomy 13 and 18, but not for trisomy 16, the proportion of compacted loci on a chromosome is correlated with LAD content. We also found that regions of the genome that become more compact in trisomic cells are enriched in housekeeping genes, indicating a possible decrease in chromatin accessibility and transcription level of these genes. These results provide a framework for understanding the mechanisms of pan-genome transcription dysregulation in trisomies in the context of chromatin spatial organization.
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Affiliation(s)
- Irina V. Zhegalova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127051 Moscow, Russia
| | | | - Ilya M. Flyamer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Anastasia S. Shtompel
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | | | | | | | - Zhanna Markova
- Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Natalia V. Petrova
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Erdem B. Dashinimaev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Sergey V. Razin
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Sergey V. Ulianov
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
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3
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Truong MA, Cané-Gasull P, Lens SMA. Modeling specific aneuploidies: from karyotype manipulations to biological insights. Chromosome Res 2023; 31:25. [PMID: 37640903 PMCID: PMC10462580 DOI: 10.1007/s10577-023-09735-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]
Abstract
An abnormal chromosome number, or aneuploidy, underlies developmental disorders and is a common feature of cancer, with different cancer types exhibiting distinct patterns of chromosomal gains and losses. To understand how specific aneuploidies emerge in certain tissues and how they contribute to disease development, various methods have been developed to alter the karyotype of mammalian cells and mice. In this review, we provide an overview of both classic and novel strategies for inducing or selecting specific chromosomal gains and losses in human and murine cell systems. We highlight how these customized aneuploidy models helped expanding our knowledge of the consequences of specific aneuploidies to (cancer) cell physiology.
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Affiliation(s)
- My Anh Truong
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands
| | - Paula Cané-Gasull
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands
| | - Susanne M A Lens
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands.
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4
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Nikolenko JV, Georgieva SG, Kopytova DV. Diversity of MLE Helicase Functions in the Regulation of Gene Expression in Higher Eukaryotes. Mol Biol 2023. [DOI: 10.1134/s0026893323010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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5
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Senger G, Santaguida S, Schaefer MH. Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors. eLife 2022; 11:75526. [PMID: 35575458 PMCID: PMC9135399 DOI: 10.7554/elife.75526] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
Aneuploidy, a state of chromosome imbalance, is a hallmark of human tumors, but its role in cancer still remains to be fully elucidated. To understand the consequences of whole-chromosome-level aneuploidies on the proteome, we integrated aneuploidy, transcriptomic, and proteomic data from hundreds of The Cancer Genome Atlas/Clinical Proteomic Tumor Analysis Consortium tumor samples. We found a surprisingly large number of expression changes happened on other, non-aneuploid chromosomes. Moreover, we identified an association between those changes and co-complex members of proteins from aneuploid chromosomes. This co-abundance association is tightly regulated for aggregation-prone aneuploid proteins and those involved in a smaller number of complexes. On the other hand, we observed that complexes of the cellular core machinery are under functional selection to maintain their stoichiometric balance in aneuploid tumors. Ultimately, we provide evidence that those compensatory and functional maintenance mechanisms are established through post-translational control, and that the degree of success of a tumor to deal with aneuploidy-induced stoichiometric imbalance impacts the activation of cellular protein degradation programs and patient survival.
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Affiliation(s)
- Gökçe Senger
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Stefano Santaguida
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Martin H Schaefer
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
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6
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Garribba L, Santaguida S. The Dynamic Instability of the Aneuploid Genome. Front Cell Dev Biol 2022; 10:838928. [PMID: 35265623 PMCID: PMC8899291 DOI: 10.3389/fcell.2022.838928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 02/02/2022] [Indexed: 11/30/2022] Open
Abstract
Proper partitioning of replicated sister chromatids at each mitosis is crucial for maintaining cell homeostasis. Errors in this process lead to aneuploidy, a condition in which daughter cells harbor genome imbalances. Importantly, aneuploid cells often experience DNA damage, which in turn could drive genome instability. This might be the product of DNA damage accumulation in micronuclei and/or a consequence of aneuploidy-induced replication stress in S-phase. Although high levels of genome instability are associated with cell cycle arrest, they can also confer a proliferative advantage in some circumstances and fuel tumor growth. Here, we review the main consequences of chromosome segregation errors on genome stability, with a special focus on the bidirectional relationship between aneuploidy and DNA damage. Also, we discuss recent findings showing how increased genome instability can provide a proliferation improvement under specific conditions, including chemotherapeutic treatments.
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Affiliation(s)
- Lorenza Garribba
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Stefano Santaguida
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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7
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Zhang S, Wang R, Huang C, Zhang L, Sun L. Modulation of Global Gene Expression by Aneuploidy and CNV of Dosage Sensitive Regulatory Genes. Genes (Basel) 2021; 12:genes12101606. [PMID: 34681000 PMCID: PMC8535535 DOI: 10.3390/genes12101606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/29/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022] Open
Abstract
Aneuploidy, which disrupts the genetic balance due to partial genome dosage changes, is usually more detrimental than euploidy variation. To investigate the modulation of gene expression in aneuploidy, we analyzed the transcriptome sequencing data of autosomal and sex chromosome trisomy in Drosophila. The results showed that most genes on the varied chromosome (cis) present dosage compensation, while the remainder of the genome (trans) produce widespread inverse dosage effects. Some altered functions and pathways were identified as the common characteristics of aneuploidy, and several possible regulatory genes were screened for an inverse dosage effect. Furthermore, we demonstrated that dosage changes of inverse regulator Inr-a/pcf11 can produce a genome-wide inverse dosage effect. All these findings suggest that the mechanism of genomic imbalance is related to the changes in the stoichiometric relationships of macromolecular complex members that affect the overall function. These studies may deepen the understanding of gene expression regulatory mechanisms.
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Affiliation(s)
- Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (C.H.); (L.Z.)
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (C.H.); (L.Z.)
| | - Cheng Huang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (C.H.); (L.Z.)
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100193, China
| | - Ludan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (C.H.); (L.Z.)
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (C.H.); (L.Z.)
- Correspondence:
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8
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Interaction of Male Specific Lethal complex and genomic imbalance on global gene expression in Drosophila. Sci Rep 2021; 11:19679. [PMID: 34608252 PMCID: PMC8490464 DOI: 10.1038/s41598-021-99268-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/20/2021] [Indexed: 02/04/2023] Open
Abstract
The inverse dosage effect caused by chromosome number variations shows global consequences in genomic imbalance including sexual dimorphism and an X chromosome-specific response. To investigate the relationship of the MSL complex to genomic imbalance, we over-expressed MSL2 in autosomal and sex chromosomal aneuploids, and analyzed the different transcriptomes. Some candidate genes involved in regulatory mechanisms have also been tested during embryogenesis using TSA-FISH. Here we show that the de novo MSL complex assembled on the X chromosomes in females further reduced the global expression level on the basis of 2/3 down-regulation caused by the inverse dosage effect in trisomy through epigenetic modulations rather than induced dosage compensation. Plus, the sexual dimorphism effect in unbalanced genomes was further examined due to the pre-existing of the MSL complex in males. All these results demonstrate the dynamic functions of the MSL complex on global gene expression in different aneuploid genomes.
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9
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Pal S, Nixon BR, Glennon MS, Shridhar P, Satterfield SL, Su YR, Becker JR. Replication Stress Response Modifies Sarcomeric Cardiomyopathy Remodeling. J Am Heart Assoc 2021; 10:e021768. [PMID: 34323119 PMCID: PMC8475701 DOI: 10.1161/jaha.121.021768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Background Sarcomere gene mutations lead to cardiomyocyte hypertrophy and pathological myocardial remodeling. However, there is considerable phenotypic heterogeneity at both the cellular and the organ level, suggesting modifiers regulate the effects of these mutations. We hypothesized that sarcomere dysfunction leads to cardiomyocyte genotoxic stress, and this modifies pathological ventricular remodeling. Methods and Results Using a murine model deficient in the sarcomere protein, Mybpc3−/− (cardiac myosin‐binding protein 3), we discovered that there was a surge in cardiomyocyte nuclear DNA damage during the earliest stages of cardiomyopathy. This was accompanied by a selective increase in ataxia telangiectasia and rad3‐related phosphorylation and increased p53 protein accumulation. The cause of the DNA damage and DNA damage pathway activation was dysregulated cardiomyocyte DNA synthesis, leading to replication stress. We discovered that selective inhibition of ataxia telangiectasia and rad3 related or cardiomyocyte deletion of p53 reduced pathological left ventricular remodeling and cardiomyocyte hypertrophy in Mybpc3−/− animals. Mice and humans harboring other types of sarcomere gene mutations also had evidence of activation of the replication stress response, and this was associated with cardiomyocyte aneuploidy in all models studied. Conclusions Collectively, our results show that sarcomere mutations lead to activation of the cardiomyocyte replication stress response, which modifies pathological myocardial remodeling in sarcomeric cardiomyopathy.
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Affiliation(s)
- Soumojit Pal
- Division of Cardiology Department of Medicine Heart, Lung Blood and Vascular Medicine InstituteSchool of MedicineUniversity of PittsburghUniversity of Pittsburgh Medical Center PA
| | - Benjamin R Nixon
- Division of Cardiology Department of Medicine Heart, Lung Blood and Vascular Medicine InstituteSchool of MedicineUniversity of PittsburghUniversity of Pittsburgh Medical Center PA
| | - Michael S Glennon
- Division of Cardiology Department of Medicine Heart, Lung Blood and Vascular Medicine InstituteSchool of MedicineUniversity of PittsburghUniversity of Pittsburgh Medical Center PA
| | - Puneeth Shridhar
- Division of Cardiology Department of Medicine Heart, Lung Blood and Vascular Medicine InstituteSchool of MedicineUniversity of PittsburghUniversity of Pittsburgh Medical Center PA.,Department of Bioengineering Swanson School of Engineering University of Pittsburgh PA
| | - Sidney L Satterfield
- Division of Cardiology Department of Medicine Heart, Lung Blood and Vascular Medicine InstituteSchool of MedicineUniversity of PittsburghUniversity of Pittsburgh Medical Center PA
| | - Yan Ru Su
- Division of Cardiology Department of Medicine Vanderbilt University Medical Center Nashville TN
| | - Jason R Becker
- Division of Cardiology Department of Medicine Heart, Lung Blood and Vascular Medicine InstituteSchool of MedicineUniversity of PittsburghUniversity of Pittsburgh Medical Center PA
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10
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Abstract
Introduction: Trisomy 8 is one of the most common cytogenetic alterations in acute myeloid leukemia (AML), with a frequency between 10% and 15%.Areas covered: The authors summarize the latest research regarding biological, translational and clinical aspects of trisomy 8 in AML.Expert opinion: Trisomy 8 can be found together with other karyotypes, although it also occurs as a sole aberration. The last decade's research has brought attention to molecular genetic alterations as strong contributors of leukemogenesis. AML with trisomy 8 seems to be associated with mutations in DNA methylation genes, spliceosome complex genes, and myeloid transcription factor genes, and these alterations probably have stronger implication for leukemic pathogenesis, treatment and hence prognosis, than the existence of trisomy 8 itself. Especially mutations in the RUNX1 and ASXL1 genes occur in high frequencies, and search for such mutations should be mandatory part of the diagnostic workup. AML with trisomy 8 is classified as intermediate-risk AML after recent European Leukemia Net (ELN) classification, and hence allogenic hematopoietic stem cell transplantation (Allo-HSCT) should be consider as consolidation therapy for this patient group.Trisomy 8 is frequently occurring in AML, although future molecular genetic workup should be performed, to optimize the diagnosis and treatment of these patients.
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Affiliation(s)
- Anette Lodvir Hemsing
- Division for Hematology, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Randi Hovland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Galina Tsykunova
- Division for Hematology, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Håkon Reikvam
- Division for Hematology, Department of Medicine, Haukeland University Hospital, Bergen, Norway.,Institute of Clinical Science, University of Bergen, Bergen, Norway
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11
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Chromosomal Density of Cancer Up-Regulated Genes, Aberrant Enhancer Activity and Cancer Fitness Genes Are Associated with Transcriptional Cis-Effects of Broad Copy Number Gains in Colorectal Cancer. Int J Mol Sci 2019; 20:ijms20184652. [PMID: 31546890 PMCID: PMC6770609 DOI: 10.3390/ijms20184652] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 12/31/2022] Open
Abstract
Broad Copy Number Gains (BCNGs) are copy-number increases of chromosomes or large segments of chromosomal arms. Publicly-available single-nucleotide polymorphism (SNP) array and RNA-Seq data of colon adenocarcinoma (COAD) samples from The Cancer Genome Atlas (TCGA) consortium allowed us to design better control groups in order to identify changes in expression due to highly recurrent BCNGs (in chromosomes 20, 8, 7, 13). We identified: (1) Overexpressed Transcripts (OverT), transcripts whose expression increases in "COAD groups bearing a specific BCNG" in comparison to "control COAD groups" not bearing it, and (2) up-regulated/down-regulated transcripts, transcripts whose expression increases/decreases in COAD groups in comparison to normal colon tissue. An analysis of gene expression reveals a correlation between the density of up-regulated genes per selected chromosome and the recurrence rate of their BCNGs. We report an enrichment of gained enhancer activity and of cancer fitness genes among OverT genes. These results support the hypothesis that the chromosomal density of overexpressed cancer fitness genes might play a significant role in the selection of gained chromosomes during cancer evolution. Analysis of functional pathways associated with OverT suggest that some multi-subunit protein complexes (eIF2, eIF3, CSTF and CPSF) are candidate targets for silencing transcriptional therapy.
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12
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Ried T, Meijer GA, Harrison DJ, Grech G, Franch-Expósito S, Briffa R, Carvalho B, Camps J. The landscape of genomic copy number alterations in colorectal cancer and their consequences on gene expression levels and disease outcome. Mol Aspects Med 2019; 69:48-61. [PMID: 31365882 DOI: 10.1016/j.mam.2019.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022]
Abstract
Aneuploidy, the unbalanced state of the chromosome content, represents a hallmark of most solid tumors, including colorectal cancer. Such aneuploidies result in tumor specific genomic imbalances, which emerge in premalignant precursor lesions. Moreover, increasing levels of chromosomal instability have been observed in adenocarcinomas and are maintained in distant metastases. A number of studies have systematically integrated copy number alterations with gene expression changes in primary carcinomas, cell lines, and experimental models of aneuploidy. In fact, chromosomal aneuploidies target a number of genes conferring a selective advantage for the metabolism of the cancer cell. Copy number alterations not only have a positive correlation with expression changes of the majority of genes on the altered genomic segment, but also have effects on the transcriptional levels of genes genome-wide. Finally, copy number alterations have been associated with disease outcome; nevertheless, the translational applicability in clinical practice requires further studies. Here, we (i) review the spectrum of genetic alterations that lead to colorectal cancer, (ii) describe the most frequent copy number alterations at different stages of colorectal carcinogenesis, (iii) exemplify their positive correlation with gene expression levels, and (iv) discuss copy number alterations that are potentially involved in disease outcome of individual patients.
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Affiliation(s)
- Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD, USA.
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - David J Harrison
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK
| | - Godfrey Grech
- Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Sebastià Franch-Expósito
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain
| | - Romina Briffa
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK; Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain; Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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Guo X, Ni J, Liang Z, Xue J, Fenech MF, Wang X. The molecular origins and pathophysiological consequences of micronuclei: New insights into an age-old problem. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 779:1-35. [PMID: 31097147 DOI: 10.1016/j.mrrev.2018.11.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 02/07/2023]
Abstract
Micronuclei (MN), the small nucleus-like bodies separated from the primary nucleus, can exist in cells with numerical and/or structural chromosomal aberrations in apparently normal tissues and more so in tumors in humans. While MN have been observed for over 100 years, they were merely and constantly considered as passive indicators of chromosome instability (CIN) for a long time. Relatively little is known about the molecular origins and biological consequences of MN. Rapid technological advances are helping to close these gaps. Very recent studies provide exciting evidence that MN act as key platform for chromothripsis and a trigger of innate immune response, suggesting that MN could affect cellular functions by both genetic and nongenetic means. These previously unappreciated findings have reawakened widespread interests in MN. In this review, the diverse mechanisms leading to MN generation and the complex fate profiles of MN are discussed, together with the evidence for their contribution to CIN, inflammation, senescence and cell death. Moreover, we put this knowledge together into a speculative perspective on how MN may be responsible for cancer development and how their presence may influence the choice of treatment. We suggest that the heterogeneous responses to MN may function physiological to ensure the arrestment, elimination and immune clearance of damaged cells, but pathologically, may enable the survival and oncogenic transformation of cells bearing CIN. These insights not only underscore the complexity of MN biology, but also raise a host of new questions and provide fertile ground for future research.
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Affiliation(s)
- Xihan Guo
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Juan Ni
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Ziqing Liang
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Jinglun Xue
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Michael F Fenech
- University of South Australia, Adelaide, SA, 5000, Australia; Genome Health Foundation, North Brighton, SA, 5048, Australia.
| | - Xu Wang
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China.
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14
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Cancer: a CINful evolution. Curr Opin Cell Biol 2018; 52:136-144. [DOI: 10.1016/j.ceb.2018.03.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 03/06/2018] [Accepted: 03/21/2018] [Indexed: 12/12/2022]
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15
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Zhang H, Yang X, Feng X, Xu H, Yang Q, Zou L, Yan M, Liu D, Su X, Jiao B. Chromosome-wide gene dosage rebalance may benefit tumor progression. Mol Genet Genomics 2018; 293:895-906. [DOI: 10.1007/s00438-018-1429-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 03/09/2018] [Indexed: 01/22/2023]
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16
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The deregulated microRNAome contributes to the cellular response to aneuploidy. BMC Genomics 2018; 19:197. [PMID: 29703144 PMCID: PMC6389165 DOI: 10.1186/s12864-018-4556-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/19/2018] [Indexed: 12/28/2022] Open
Abstract
Background Aneuploidy, or abnormal chromosome numbers, severely alters cell physiology and is widespread in cancers and other pathologies. Using model cell lines engineered to carry one or more extra chromosomes, it has been demonstrated that aneuploidy per se impairs proliferation, leads to proteotoxic as well as replication stress and triggers conserved transcriptome and proteome changes. Results In this study, we analysed for the first time miRNAs and demonstrate that their expression is altered in response to chromosome gain. The miRNA deregulation is independent of the identity of the extra chromosome and specific to individual cell lines. By cross-omics analysis we demonstrate that although the deregulated miRNAs differ among individual aneuploid cell lines, their known targets are predominantly associated with cell development, growth and proliferation, pathways known to be inhibited in response to chromosome gain. Indeed, we show that up to 72% of these targets are downregulated and the associated miRNAs are overexpressed in aneuploid cells, suggesting that the miRNA changes contribute to the global transcription changes triggered by aneuploidy. We identified hsa-miR-10a-5p to be overexpressed in majority of aneuploid cells. Hsa-miR-10a-5p enhances translation of a subset of mRNAs that contain so called 5’TOP motif and we show that its upregulation in aneuploids provides resistance to starvation-induced shut down of ribosomal protein translation. Conclusions Our work suggests that the changes of the microRNAome contribute on one hand to the adverse effects of aneuploidy on cell physiology, and on the other hand to the adaptation to aneuploidy by supporting translation under adverse conditions. Electronic supplementary material The online version of this article (10.1186/s12864-018-4556-6) contains supplementary material, which is available to authorized users.
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Knouse KA, Davoli T, Elledge SJ, Amon A. Aneuploidy in Cancer: Seq-ing Answers to Old Questions. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2017. [DOI: 10.1146/annurev-cancerbio-042616-072231] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kristin A. Knouse
- Howard Hughes Medical Institute, Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts 02115
| | - Teresa Davoli
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Stephen J. Elledge
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Angelika Amon
- Howard Hughes Medical Institute, Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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18
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Difference Makers: Chromosomal Instability versus Aneuploidy in Cancer. Trends Cancer 2016; 2:561-571. [DOI: 10.1016/j.trecan.2016.09.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/26/2016] [Accepted: 09/01/2016] [Indexed: 01/06/2023]
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Birchler JA. Parallel Universes for Models of X Chromosome Dosage Compensation in Drosophila: A Review. Cytogenet Genome Res 2016; 148:52-67. [PMID: 27166165 DOI: 10.1159/000445924] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2016] [Indexed: 11/19/2022] Open
Abstract
Dosage compensation in Drosophila involves an approximately 2-fold increase in expression of the single X chromosome in males compared to the per gene expression in females with 2 X chromosomes. Two models have been considered for an explanation. One proposes that the male-specific lethal (MSL) complex that is associated with the male X chromosome brings histone modifiers to the sex chromosome to increase its expression. The other proposes that the inverse effect which results from genomic imbalance would tend to upregulate the genome approximately 2-fold, but the MSL complex sequesters histone modifiers from the autosomes to the X to mute this autosomal male-biased expression. On the X, the MSL complex must override the high level of resulting histone modifications to prevent overcompensation of the X chromosome. Each model is evaluated in terms of fitting classical genetic and recent molecular data. Potential paths toward resolving the models are suggested.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Mo., USA
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Oshimura M, Uno N, Kazuki Y, Katoh M, Inoue T. A pathway from chromosome transfer to engineering resulting in human and mouse artificial chromosomes for a variety of applications to bio-medical challenges. Chromosome Res 2015; 23:111-33. [PMID: 25657031 PMCID: PMC4365188 DOI: 10.1007/s10577-014-9459-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Microcell-mediated chromosome transfer (MMCT) is a technique to transfer a chromosome from defined donor cells into recipient cells and to manipulate chromosomes as gene delivery vectors and open a new avenue in somatic cell genetics. However, it is difficult to uncover the function of a single specific gene via the transfer of an entire chromosome or fragment, because each chromosome or fragment contains a set of numerous genes. Thus, alternative tools are human artificial chromosome (HAC) and mouse artificial chromosome (MAC) vectors, which can carry a gene or genes of interest. HACs/MACs have been generated mainly by either a "top-down approach" (engineered creation) or a "bottom-up approach" (de novo creation). HACs/MACs with one or more acceptor sites exhibit several characteristics required by an ideal gene delivery vector, including stable episomal maintenance and the capacity to carry large genomic loci plus their regulatory elements, thus allowing the physiological regulation of the introduced gene in a manner similar to that of native chromosomes. The MMCT technique is also applied for manipulating HACs and MACs in donor cells and delivering them to recipient cells. This review describes the lessons learned and prospects identified from studies on the construction of HACs and MACs, and their ability to drive exogenous gene expression in cultured cells and transgenic animals via MMCT. New avenues for a variety of applications to bio-medical challenges are also proposed.
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Affiliation(s)
- Mitsuo Oshimura
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan,
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21
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Dürrbaum M, Storchová Z. Effects of aneuploidy on gene expression: implications for cancer. FEBS J 2015; 283:791-802. [DOI: 10.1111/febs.13591] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/02/2015] [Accepted: 11/05/2015] [Indexed: 01/23/2023]
Affiliation(s)
- Milena Dürrbaum
- Group Maintenance of Genome Stability; Max Planck Institute of Biochemistry; Martinsried Germany
- Center for Integrated Protein Science Munich; Ludwig-Maximilian-University Munich; Germany
| | - Zuzana Storchová
- Group Maintenance of Genome Stability; Max Planck Institute of Biochemistry; Martinsried Germany
- Center for Integrated Protein Science Munich; Ludwig-Maximilian-University Munich; Germany
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Giam M, Rancati G. Aneuploidy and chromosomal instability in cancer: a jackpot to chaos. Cell Div 2015; 10:3. [PMID: 26015801 PMCID: PMC4443636 DOI: 10.1186/s13008-015-0009-7] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/08/2015] [Indexed: 12/12/2022] Open
Abstract
Genomic instability (GIN) is a hallmark of cancer cells that facilitates the acquisition of mutations conferring aggressive or drug-resistant phenotypes during cancer evolution. Chromosomal instability (CIN) is a form of GIN that involves frequent cytogenetic changes leading to changes in chromosome copy number (aneuploidy). While both CIN and aneuploidy are common characteristics of cancer cells, their roles in tumor initiation and progression are unclear. On the one hand, CIN and aneuploidy are known to provide genetic variation to allow cells to adapt in changing environments such as nutrient fluctuations and hypoxia. Patients with constitutive aneuploidies are more susceptible to certain types of cancers, suggesting that changes in chromosome copy number could positively contribute to cancer evolution. On the other hand, chromosomal imbalances have been observed to have detrimental effects on cellular fitness and might trigger cell cycle arrest or apoptosis. Furthermore, mouse models for CIN have led to conflicting results. Taken together these findings suggest that the relationship between CIN, aneuploidy and cancer is more complex than what was previously anticipated. Here we review what is known about this complex ménage à trois, discuss recent evidence suggesting that aneuploidy, CIN and GIN together promote a vicious cycle of genome chaos. Lastly, we propose a working hypothesis to reconcile the conflicting observations regarding the role of aneuploidy and CIN in tumorigenesis.
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Affiliation(s)
- Maybelline Giam
- Institute for Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, 138648 Singapore
| | - Giulia Rancati
- Institute for Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, 138648 Singapore ; School of Biological Sciences, Nanyang Technological University, Singapore, 637551 Singapore ; Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Singapore, 117597 Singapore
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Saied MH, Marzec J, Khalid S, Smith P, Molloy G, Young BD. Trisomy 8 Acute Myeloid Leukemia Analysis Reveals New Insights of DNA Methylome with Identification of HHEX as Potential Diagnostic Marker. BIOMARKERS IN CANCER 2015; 7:1-6. [PMID: 25674022 PMCID: PMC4315123 DOI: 10.4137/bic.s19614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 11/09/2014] [Accepted: 11/13/2014] [Indexed: 01/17/2023]
Abstract
Trisomy 8 acute myeloid leukemia (AML) is the commonest numerical aberration in AML. Here we present a global analysis of trisomy 8 AML using methylated DNA immunoprecipitation-sequencing (MeDIP-seq). The study is based on three diagnostic trisomy 8 AML and their parallel relapse status in addition to nine non-trisomic AML and four normal bone marrows (NBMs). In contrast to non-trisomic DNA samples, trisomy 8 AML showed a characteristic DNA methylation distribution pattern because an increase in the frequency of the hypermethylation signals in chromosome 8 was associated with an increase in the hypomethylation signals in the rest of the chromosomes. Chromosome 8 hypermethylation signals were found mainly in the CpG island (CGI) shores and interspersed repeats. Validating the most significant differentially methylated CGI (P = 7.88 × 10(-11)) identified in trisomy 8 AML demonstrated a specific core region within the gene body of HHEX, which was significantly correlated with HHEX expression in both diagnostic and relapse trisomy 8 AMLs. Overall, the existence of extra chromosome 8 was associated with a global impact on the DNA methylation distribution with identification of HHEX gene methylation as a potential diagnostic marker for trisomy 8 AML.
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Affiliation(s)
- Marwa H Saied
- Centre for Haemato-Oncology, Barts Cancer Institute, Barts and the London School of Medicine, Queen Mary University of London, London, United Kingdom
- Clinical Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Jacek Marzec
- Centre for Haemato-Oncology, Barts Cancer Institute, Barts and the London School of Medicine, Queen Mary University of London, London, United Kingdom
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine, Queen Mary University of London, London, United Kingdom
| | - Sabah Khalid
- Centre for Haemato-Oncology, Barts Cancer Institute, Barts and the London School of Medicine, Queen Mary University of London, London, United Kingdom
| | - Paul Smith
- Centre for Haemato-Oncology, Barts Cancer Institute, Barts and the London School of Medicine, Queen Mary University of London, London, United Kingdom
| | - Gael Molloy
- Centre for Haemato-Oncology, Barts Cancer Institute, Barts and the London School of Medicine, Queen Mary University of London, London, United Kingdom
| | - Bryan D Young
- Centre for Haemato-Oncology, Barts Cancer Institute, Barts and the London School of Medicine, Queen Mary University of London, London, United Kingdom
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Abstract
Cancer cells differ from normal healthy cells in multiple aspects ranging from altered cellular signaling through metabolic changes to aberrant chromosome content, so called aneuploidy. The large-scale changes in copy numbers of chromosomes or large chromosomal regions due to aneuploidy alter significantly the gene expression, as several hundreds of genes are gained or lost. Comparison of quantitative genome, transcriptome and proteome data enables dissection of the molecular causes that underlie the gene expression changes observed in cancer cells and provides a new perspective on the molecular consequences of aneuploidy. Here, we will map to what degree aneuploidy affects the expression of genes located on the affected chromosomes. We will also address the effects of aneuploidy on global gene expression in cancer cells as well as whether and how it may contribute to the physiology of cancer cells.
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Affiliation(s)
- Milena Dürrbaum
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Center for Integrated Protein Science Munich, Ludwig-Maximilian-University Munich, 80336, Munich, Germany
| | - Zuzana Storchová
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
- Center for Integrated Protein Science Munich, Ludwig-Maximilian-University Munich, 80336, Munich, Germany.
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Potapova TA, Zhu J, Li R. Aneuploidy and chromosomal instability: a vicious cycle driving cellular evolution and cancer genome chaos. Cancer Metastasis Rev 2014; 32:377-89. [PMID: 23709119 DOI: 10.1007/s10555-013-9436-6] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aneuploidy and chromosomal instability frequently co-exist, and aneuploidy is recognized as a direct outcome of chromosomal instability. However, chromosomal instability is widely viewed as a consequence of mutations in genes involved in DNA replication, chromosome segregation, and cell cycle checkpoints. Telomere attrition and presence of extra centrosomes have also been recognized as causative for errors in genomic transmission. Here, we examine recent studies suggesting that aneuploidy itself can be responsible for the procreation of chromosomal instability. Evidence from both yeast and mammalian experimental models suggests that changes in chromosome copy number can cause changes in dosage of the products of many genes located on aneuploid chromosomes. These effects on gene expression can alter the balanced stoichiometry of various protein complexes, causing perturbations of their functions. Therefore, phenotypic consequences of aneuploidy will include chromosomal instability if the balanced stoichiometry of protein machineries responsible for accurate chromosome segregation is affected enough to perturb the function. The degree of chromosomal instability will depend on specific karyotypic changes, which may be due to dosage imbalances of specific genes or lack of scaling between chromosome segregation load and the capacity of the mitotic system. We propose that the relationship between aneuploidy and chromosomal instability can be envisioned as a "vicious cycle," where aneuploidy potentiates chromosomal instability leading to further karyotype diversity in the affected population.
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Affiliation(s)
- Tamara A Potapova
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA,
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Donnelly N, Passerini V, Dürrbaum M, Stingele S, Storchová Z. HSF1 deficiency and impaired HSP90-dependent protein folding are hallmarks of aneuploid human cells. EMBO J 2014; 33:2374-87. [PMID: 25205676 DOI: 10.15252/embj.201488648] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Aneuploidy is a hallmark of cancer and is associated with malignancy and poor prognosis. Recent studies have revealed that aneuploidy inhibits proliferation, causes distinct alterations in the transcriptome and proteome and disturbs cellular proteostasis. However, the molecular mechanisms underlying the changes in gene expression and the impairment of proteostasis are not understood. Here, we report that human aneuploid cells are impaired in HSP90-mediated protein folding. We show that aneuploidy impairs induction of the heat shock response suggesting that the activity of the transcription factor heat shock factor 1 (HSF1) is compromised. Indeed, increased levels of HSF1 counteract the effects of aneuploidy on HSP90 expression and protein folding, identifying HSF1 overexpression as the first aneuploidy-tolerating mutation in human cells. Thus, impaired HSF1 activity emerges as a critical factor underlying the phenotypes linked to aneuploidy. Finally, we demonstrate that deficient protein folding capacity directly shapes gene expression in aneuploid cells. Our study provides mechanistic insight into the causes of the disturbed proteostasis in aneuploids and deepens our understanding of the role of HSF1 in cytoprotection and carcinogenesis.
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Affiliation(s)
- Neysan Donnelly
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Verena Passerini
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Milena Dürrbaum
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany Center for Integrated Protein Science Munich, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Silvia Stingele
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Zuzana Storchová
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany Center for Integrated Protein Science Munich, Ludwig-Maximilian-University Munich, Munich, Germany
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Birchler JA. Facts and artifacts in studies of gene expression in aneuploids and sex chromosomes. Chromosoma 2014; 123:459-69. [DOI: 10.1007/s00412-014-0478-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/18/2022]
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Dürrbaum M, Kuznetsova AY, Passerini V, Stingele S, Stoehr G, Storchová Z. Unique features of the transcriptional response to model aneuploidy in human cells. BMC Genomics 2014; 15:139. [PMID: 24548329 PMCID: PMC3932016 DOI: 10.1186/1471-2164-15-139] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 02/14/2014] [Indexed: 02/08/2023] Open
Abstract
Background Aneuploidy, a karyotype deviating from multiples of a haploid chromosome set, affects the physiology of eukaryotes. In humans, aneuploidy is linked to pathological defects such as developmental abnormalities, mental retardation or cancer, but the underlying mechanisms remain elusive. There are many different types and origins of aneuploidy, but whether there is a uniform cellular response to aneuploidy in human cells has not been addressed so far. Results Here we evaluate the transcription profiles of eleven trisomic and tetrasomic cell lines and two cell lines with complex aneuploid karyotypes. We identify a characteristic aneuploidy response pattern defined by upregulation of genes linked to endoplasmic reticulum, Golgi apparatus and lysosomes, and downregulation of DNA replication, transcription as well as ribosomes. Strikingly, complex aneuploidy elicits the same transcriptional changes as trisomy. To uncover the triggers of the response, we compared the profiles with transcription changes in human cells subjected to stress conditions. Interestingly, we found an overlap only with the response to treatment with the autophagy inhibitor bafilomycin A1. Finally, we identified 23 genes whose expression is significantly altered in all aneuploids and which may thus serve as aneuploidy markers. Conclusions Our analysis shows that despite the variability in chromosome content, aneuploidy triggers uniform transcriptional response in human cells. A common response independent of the type of aneuploidy might be exploited as a novel target for cancer therapy. Moreover, the potential aneuploidy markers identified in our analysis might represent novel biomarkers to assess the malignant potential of a tumor.
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Affiliation(s)
| | | | | | | | | | - Zuzana Storchová
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany.
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Donnelly N, Storchová Z. Dynamic karyotype, dynamic proteome: buffering the effects of aneuploidy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:473-81. [DOI: 10.1016/j.bbamcr.2013.11.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/21/2013] [Accepted: 11/22/2013] [Indexed: 12/18/2022]
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Walen KH. Neoplastic-Like CELL Changes of Normal Fibroblast Cells Associated with Evolutionary Conserved Maternal and Paternal Genomic Autonomous Behavior (Gonomery). ACTA ACUST UNITED AC 2014. [DOI: 10.4236/jct.2014.59094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Gene expression analysis of induced pluripotent stem cells from aneuploid chromosomal syndromes. BMC Genomics 2013; 14 Suppl 5:S8. [PMID: 24564826 PMCID: PMC3852284 DOI: 10.1186/1471-2164-14-s5-s8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Human aneuploidy is the leading cause of early pregnancy loss, mental retardation, and multiple congenital anomalies. Due to the high mortality associated with aneuploidy, the pathophysiological mechanisms of aneuploidy syndrome remain largely unknown. Previous studies focused mostly on whether dosage compensation occurs, and the next generation transcriptomics sequencing technology RNA-seq is expected to eventually uncover the mechanisms of gene expression regulation and the related pathological phenotypes in human aneuploidy. Results Using next generation transcriptomics sequencing technology RNA-seq, we profiled the transcriptomes of four human aneuploid induced pluripotent stem cell (iPSC) lines generated from monosomy × (Turner syndrome), trisomy 8 (Warkany syndrome 2), trisomy 13 (Patau syndrome), and partial trisomy 11:22 (Emanuel syndrome) as well as two umbilical cord matrix iPSC lines as euploid controls to examine how phenotypic abnormalities develop with aberrant karyotype. A total of 466 M (50-bp) reads were obtained from the six iPSC lines, and over 13,000 mRNAs were identified by gene annotation. Global analysis of gene expression profiles and functional analysis of differentially expressed (DE) genes were implemented. Over 5000 DE genes are determined between aneuploidy and euploid iPSCs respectively while 9 KEGG pathways are overlapped enriched in four aneuploidy samples. Conclusions Our results demonstrate that the extra or missing chromosome has extensive effects on the whole transcriptome. Functional analysis of differentially expressed genes reveals that the genes most affected in aneuploid individuals are related to central nervous system development and tumorigenesis.
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Dosage compensation and inverse effects in triple X metafemales of Drosophila. Proc Natl Acad Sci U S A 2013; 110:7383-8. [PMID: 23589863 DOI: 10.1073/pnas.1305638110] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dosage compensation, the equalized X chromosome gene expression between males and females in Drosophila, has also been found in triple X metafemales. Inverse dosage effects, produced by genomic imbalance, are believed to account for this modulated expression, but they have not been studied on a global level. Here, we show a global expression comparison of metafemales (XXX; AA) with normal females (XX; AA) with high-throughput RNA-sequencing. We found that the majority of the X-linked genes in metafemales exhibit dosage compensation with an expression level similar to that of normal diploid females. In parallel, most of the autosomal genes were expressed at about two-thirds the level of normal females, the ratio of inverse dosage effects produced by the extra X chromosome. Both compensation and inverse effects were further confirmed by combination of X-linked and autosomally located miniwhite reporter genes in metafemales and relative quantitative PCR of selected genes. These data provide evidence for an inverse dosage component to X chromosome compensation.
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Abu-Amero KK, Kondkar AA, Salih MA, Al-Husain M, Al Shammari M, Zeidan G, Oystreck DT, Hellani AM, Kentab AY, Bosley TM. Ophthalmologic Observations in a Patient with Partial Mosaic Trisomy 8. Ophthalmic Genet 2013; 34:249-53. [DOI: 10.3109/13816810.2012.762933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Canel N, Bevacqua R, Hiriart MI, Salamone D. Replication of somatic micronuclei in bovine enucleated oocytes. Cell Div 2012; 7:23. [PMID: 23173571 PMCID: PMC3564703 DOI: 10.1186/1747-1028-7-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 11/15/2012] [Indexed: 11/24/2022] Open
Abstract
Background Microcell-mediated chromosome transfer (MMCT) was developed to introduce a low number of chromosomes into a host cell. We have designed a novel technique combining part of MMCT with somatic cell nuclear transfer, which consists of injecting a somatic micronucleus into an enucleated oocyte, and inducing its cellular machinery to replicate such micronucleus. It would allow the isolation and manipulation of a single or a low number of somatic chromosomes. Methods Micronuclei from adult bovine fibroblasts were produced by incubation in 0.05 μg/ml demecolcine for 46 h followed by 2 mg/ml mitomycin for 2 h. Cells were finally treated with 10 μg/ml cytochalasin B for 1 h. In vitro matured bovine oocytes were mechanically enucleated and intracytoplasmatically injected with one somatic micronucleus, which had been previously exposed [Micronucleus- injected (+)] or not [Micronucleus- injected (−)] to a transgene (50 ng/μl pCX-EGFP) during 5 min. Enucleated oocytes [Enucleated (+)] and parthenogenetic [Parthenogenetic (+)] controls were injected into the cytoplasm with less than 10 pl of PVP containing 50 ng/μl pCX-EGFP. A non-injected parthenogenetic control [Parthenogenetic (−)] was also included. Two hours after injection, oocytes and reconstituted embryos were activated by incubation in 5 μM ionomycin for 4 min + 1.9 mM 6-DMAP for 3 h. Cleavage stage and egfp expression were evaluated. DNA replication was confirmed by DAPI staining. On day 2, Micronucleus- injected (−), Parthenogenetic (−) and in vitro fertilized (IVF) embryos were karyotyped. Differences among treatments were determined by Fisher′s exact test (p≤0.05). Results All the experimental groups underwent the first cell divisions. Interestingly, a low number of Micronucleus-injected embryos showed egfp expression. DAPI staining confirmed replication of micronuclei in most of the evaluated embryos. Karyotype analysis revealed that all Micronucleus-injected embryos had fewer than 15 chromosomes per blastomere (from 1 to 13), while none of the IVF and Parthenogenetic controls showed less than 30 chromosomes per spread. Conclusions We have developed a new method to replicate somatic micronuclei, by using the replication machinery of the oocyte. This could be a useful tool for making chromosome transfer, which could be previously targeted for transgenesis.
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Affiliation(s)
- Natalia Canel
- Laboratorio Biotecnología Animal, Departamento de Producción Animal, Facultad Agronomía, Universidad de Buenos Aires, Av, San Martín 4453, C1417DSE, Buenos Aires, Argentina.
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Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc Natl Acad Sci U S A 2012; 109:14746-53. [PMID: 22908297 DOI: 10.1073/pnas.1207726109] [Citation(s) in RCA: 373] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We summarize, in this review, the evidence that genomic balance influences gene expression, quantitative traits, dosage compensation, aneuploid syndromes, population dynamics of copy number variants and differential evolutionary fate of genes after partial or whole-genome duplication. Gene balance effects are hypothesized to result from stoichiometric differences among members of macromolecular complexes, the interactome, and signaling pathways. The implications of gene balance are discussed.
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Abstract
Deviation from a balanced genome by either gain or loss of entire chromosomes is generally tolerated poorly in all eukaryotic systems studied to date. Errors in mitotic or meiotic cell division lead to aneuploidy, which places a burden of additional or insufficient gene products from the missegregated chromosomes on the daughter cells. The burden of aneuploidy often manifests itself as impaired fitness of individual cells and whole organisms, in which abnormal development is also characteristic. However, most human cancers, noted for their rapid growth, also display various levels of aneuploidy. Here we discuss the detrimental, potentially beneficial, and sometimes puzzling effects of aneuploidy on cellular and organismal fitness and tissue function as well as its role in diseases such as cancer and neurodegeneration.
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Affiliation(s)
- Jake J Siegel
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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Identification of Inverse Regulator-a (Inr-a) as Synonymous with Pre-mRNA Cleavage Complex II Protein (Pcf11) in Drosophila. G3-GENES GENOMES GENETICS 2012; 2:701-6. [PMID: 22690379 PMCID: PMC3362299 DOI: 10.1534/g3.112.002071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 04/11/2012] [Indexed: 11/18/2022]
Abstract
A common modulation of gene expression in aneuploids is an inverse correlation of the monitored gene with the dosage of another segment of the genome. Such effects can be reduced to the action of single genes. One gene previously found to modulate leaky alleles of the white eye color gene in Drosophila is Inverse regulator-a (Inr-a). Heterozygotes of mutations increase the expression of white about 2-fold, and trisomic regions surrounding the gene reduce the expression to about two-thirds of the normal diploid level. Further cytological definition of the location of this gene on the second chromosome led to a candidate pre-mRNA cleavege complex II protein (Pcf11) as the only gene in the remaining region whose mutations exhibit recessive lethality as do alleles of Inr-a. The product of Pcf11 has been implicated in transcriptional initiation, elongation, and termination reactions. Four mutant alleles showed molecular lesions predicted to lead to nonfunctional products of Pcf11. The identification of the molecular lesion of Inr-a provides insight into the basis of this common aneuploidy effect.
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Chromosomal instability and aneuploidy in cancer: from yeast to man. EMBO Rep 2012; 13:515-27. [PMID: 22614003 DOI: 10.1038/embor.2012.65] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 04/24/2012] [Indexed: 01/10/2023] Open
Abstract
Aneuploidy is frequently associated with disease and developmental abnormalities. It is also a key characteristic of cancer. Several model systems have been developed to study the role of chromosomal instability and aneuploidy in tumorigenesis. The results are surprisingly complex, with the conditions sometimes promoting and sometimes inhibiting tumour formation. Here, we review the effects of aneuploidy and chromosomal instability in cells and model systems of cancer, propose a model that could explain these complex findings and discuss how the aneuploid condition could be exploited in cancer therapy.
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