1
|
Brancato D, Bruno F, Coniglio E, Sturiale V, Saccone S, Federico C. The Chromatin Organization Close to SNP rs12913832, Involved in Eye Color Variation, Is Evolutionary Conserved in Vertebrates. Int J Mol Sci 2024; 25:6602. [PMID: 38928306 PMCID: PMC11204186 DOI: 10.3390/ijms25126602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The most significant genetic influence on eye color pigmentation is attributed to the intronic SNP rs12913832 in the HERC2 gene, which interacts with the promoter region of the contiguous OCA2 gene. This interaction, through the formation of a chromatin loop, modulates the transcriptional activity of OCA2, directly affecting eye color pigmentation. Recent advancements in technology have elucidated the precise spatial organization of the genome within the cell nucleus, with chromatin architecture playing a pivotal role in regulating various genome functions. In this study, we investigated the organization of the chromatin close to the HERC2/OCA2 locus in human lymphocyte nuclei using fluorescence in situ hybridization (FISH) and high-throughput chromosome conformation capture (Hi-C) data. The 3 Mb of genomic DNA that belonged to the chromosomal region 15q12-q13.1 revealed the presence of three contiguous chromatin loops, which exhibited a different level of compaction depending on the presence of the A or G allele in the SNP rs12913832. Moreover, the analysis of the genomic organization of the genes has demonstrated that this chromosomal region is evolutionarily highly conserved, as evidenced by the analysis of syntenic regions in species from other Vertebrate classes. Thus, the role of rs12913832 variant is relevant not only in determining the transcriptional activation of the OCA2 gene but also in the chromatin compaction of a larger region, underscoring the critical role of chromatin organization in the proper regulation of the involved genes. It is crucial to consider the broader implications of this finding, especially regarding the potential regulatory role of similar polymorphisms located within intronic regions, which do not influence the same gene by modulating the splicing process, but they regulate the expression of adjacent genes. Therefore, caution should be exercised when utilizing whole-exome sequencing for diagnostic purposes, as intron sequences may provide valuable gene regulation information on the region where they reside. Thus, future research efforts should also be directed towards gaining a deeper understanding of the precise mechanisms underlying the role and mode of action of intronic SNPs in chromatin loop organization and transcriptional regulation.
Collapse
Affiliation(s)
| | | | | | | | - Salvatore Saccone
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (F.B.); (E.C.); (V.S.); (C.F.)
| | | |
Collapse
|
2
|
Garimberti E, Federico C, Ragusa D, Bruno F, Saccone S, Bridger JM, Tosi S. Alterations in Genome Organization in Lymphoma Cell Nuclei due to the Presence of the t(14;18) Translocation. Int J Mol Sci 2024; 25:2377. [PMID: 38397052 PMCID: PMC10889133 DOI: 10.3390/ijms25042377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/10/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Chromosomal rearrangements have been shown to alter genome organization, consequently having an impact on gene expression. Studies on certain types of leukemia have shown that gene expression can be exacerbated by the altered nuclear positioning of fusion genes arising from chromosomal translocations. However, studies on lymphoma have been, so far, very limited. The scope of this study was to explore genome organization in lymphoma cells carrying the t(14;18)(q32;q21) rearrangement known to results in over-expression of the BCL2 gene. In order to achieve this aim, we used fluorescence in situ hybridization to carefully map the positioning of whole chromosome territories and individual genes involved in translocation in the lymphoma-derived cell line Pfeiffer. Our data show that, although there is no obvious alteration in the positioning of the whole chromosome territories, the translocated genes may take the nuclear positioning of either of the wild-type genes. Furthermore, the BCL2 gene was looping out in a proportion of nuclei with the t(14;18) translocation but not in control nuclei without the translocation, indicating that chromosome looping may be an essential mechanism for BCL2 expression in lymphoma cells.
Collapse
Affiliation(s)
- Elisa Garimberti
- Clinical Genomics Laboratory, Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK;
| | - Concetta Federico
- Department of Biological, Geological, and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (C.F.); (F.B.); (S.S.)
| | - Denise Ragusa
- Centre for Genome Engineering and Maintenance (CenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK; (D.R.); (J.M.B.)
| | - Francesca Bruno
- Department of Biological, Geological, and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (C.F.); (F.B.); (S.S.)
| | - Salvatore Saccone
- Department of Biological, Geological, and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (C.F.); (F.B.); (S.S.)
| | - Joanna Mary Bridger
- Centre for Genome Engineering and Maintenance (CenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK; (D.R.); (J.M.B.)
| | - Sabrina Tosi
- Centre for Genome Engineering and Maintenance (CenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK; (D.R.); (J.M.B.)
- Leukaemia and Chromosome Research Laboratory, College of Health, Medicine and Life Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK
| |
Collapse
|
3
|
de Lima MF, Lisboa MDO, Terceiro LEL, Rangel-Pozzo A, Mai S. Chromosome Territories in Hematological Malignancies. Cells 2022; 11:1368. [PMID: 35456046 PMCID: PMC9028803 DOI: 10.3390/cells11081368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
Chromosomes are organized in distinct nuclear areas designated as chromosome territories (CT). The structural formation of CT is a consequence of chromatin packaging and organization that ultimately affects cell function. Chromosome positioning can identify structural signatures of genomic organization, especially for diseases where changes in gene expression contribute to a given phenotype. The study of CT in hematological diseases revealed chromosome position as an important factor for specific chromosome translocations. In this review, we highlight the history of CT theory, current knowledge on possible clinical applications of CT analysis, and the impact of CT in the development of hematological neoplasia such as multiple myeloma, leukemia, and lymphomas. Accumulating data on nuclear architecture in cancer allow one to propose the three-dimensional nuclear genomic landscape as a novel cancer biomarker for the future.
Collapse
Affiliation(s)
- Matheus Fabiao de Lima
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Mateus de Oliveira Lisboa
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná—PUCPR, Curitiba 80215-901, Brazil;
| | - Lucas E. L. Terceiro
- Department of Pathology, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 3P5, Canada;
| | - Aline Rangel-Pozzo
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Sabine Mai
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| |
Collapse
|
4
|
Bridger JM, Pereira RT, Pina C, Tosi S, Lewis A. Alterations to Genome Organisation in Stem Cells, Their Differentiation and Associated Diseases. Results Probl Cell Differ 2022; 70:71-102. [PMID: 36348105 DOI: 10.1007/978-3-031-06573-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The organisation of the genome in its home, the cell nucleus, is reliant on a number of different aspects to establish, maintain and alter its functional non-random positioning. The genome is dispersed throughout a cell nucleus in specific chromosome territories which are further divided into topologically associated domains (TADs), where regions of the genome from different and the same chromosomes come together. This organisation is both controlled by DNA and chromatin epigenetic modification and the association of the genome with nuclear structures such as the nuclear lamina, the nucleolus and nuclear bodies and speckles. Indeed, sequences that are associated with the first two structures mentioned are termed lamina-associated domains (LADs) and nucleolar-associated domains (NADs), respectively. The modifications and nuclear structures that regulate genome function are altered through a cell's life from stem cell to differentiated cell through to reversible quiescence and irreversible senescence, and hence impacting on genome organisation, altering it to silence specific genes and permit others to be expressed in a controlled way in different cell types and cell cycle statuses. The structures and enzymes and thus the organisation of the genome can also be deleteriously affected, leading to disease and/or premature ageing.
Collapse
Affiliation(s)
- Joanna M Bridger
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK.
| | - Rita Torres Pereira
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Cristina Pina
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Sabrina Tosi
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Annabelle Lewis
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| |
Collapse
|
5
|
Chromosomal Rearrangements and Altered Nuclear Organization: Recent Mechanistic Models in Cancer. Cancers (Basel) 2021; 13:cancers13225860. [PMID: 34831011 PMCID: PMC8616464 DOI: 10.3390/cancers13225860] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/09/2021] [Accepted: 11/19/2021] [Indexed: 01/07/2023] Open
Abstract
Simple Summary New methodologies and technologies developed in the last few decades have highlighted the precise spatial organization of the genome into the cell nucleus, with chromatin architecture playing a central role in controlling several genome functions. Genes are expressed in a well-defined way and at a well-defined time during cell differentiation, and alterations in genome organization can lead to genetic diseases, such as cancers. Here we review how the genome is organized in the cell nucleus and the evidence of genome misorganization leading to cancer diseases. Abstract The last decade has seen significant progress in understanding how the genome is organized spatially within interphase nuclei. Recent analyses have confirmed earlier molecular cytogenetic studies on chromosome positioning within interphase nuclei and provided new information about the topologically associated domains (TADs). Examining the nuances of how genomes are organized within interphase nuclei will provide information fundamental to understanding gene regulation and expression in health and disease. Indeed, the radial spatial positioning of individual gene loci within nuclei has been associated with up- and down-regulation of specific genes, and disruption of normal genome organization within nuclei will result in compromised cellular health. In cancer cells, where reorganization of the nuclear architecture may occur in the presence of chromosomal rearrangements such as translocations, inversions, or deletions, gene repositioning can change their expression. To date, very few studies have focused on radial gene positioning and the correlation to gene expression in cancers. Further investigations would improve our understanding of the biological mechanisms at the basis of cancer and, in particular, in leukemia initiation and progression, especially in those cases where the molecular consequences of chromosomal rearrangements are still unclear. In this review, we summarize the main milestones in the field of genome organization in the nucleus and the alterations to this organization that can lead to cancer diseases.
Collapse
|
6
|
Mehta IS, Riyahi K, Pereira RT, Meaburn KJ, Figgitt M, Kill IR, Eskiw CH, Bridger JM. Interphase Chromosomes in Replicative Senescence: Chromosome Positioning as a Senescence Biomarker and the Lack of Nuclear Motor-Driven Chromosome Repositioning in Senescent Cells. Front Cell Dev Biol 2021; 9:640200. [PMID: 34113611 PMCID: PMC8185894 DOI: 10.3389/fcell.2021.640200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/25/2021] [Indexed: 01/10/2023] Open
Abstract
This study demonstrates, and confirms, that chromosome territory positioning is altered in primary senescent human dermal fibroblasts (HDFs). The chromosome territory positioning pattern is very similar to that found in HDFs made quiescent either by serum starvation or confluence; but not completely. A few chromosomes are found in different locations. One chromosome in particular stands out, chromosome 10, which is located in an intermediate location in young proliferating HDFs, but is found at the nuclear periphery in quiescent cells and in an opposing location of the nuclear interior in senescent HDFs. We have previously demonstrated that individual chromosome territories can be actively and rapidly relocated, with 15 min, after removal of serum from the culture media. These chromosome relocations require nuclear motor activity through the presence of nuclear myosin 1β (NM1β). We now also demonstrate rapid chromosome movement in HDFs after heat-shock at 42°C. Others have shown that heat shock genes are actively relocated using nuclear motor protein activity via actin or NM1β (Khanna et al., 2014; Pradhan et al., 2020). However, this current study reveals, that in senescent HDFs, chromosomes can no longer be relocated to expected nuclear locations upon these two types of stimuli. This coincides with a entirely different organisation and distribution of NM1β within senescent HDFs.
Collapse
Affiliation(s)
- Ishita S Mehta
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom.,Tata Institute of Fundamental Research, Mumbai, India
| | - Kumars Riyahi
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom
| | - Rita Torres Pereira
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom
| | - Karen J Meaburn
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom
| | - Martin Figgitt
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom.,Department of Life Sciences, Birmingham City University, Birmingham, United Kingdom
| | - Ian R Kill
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom
| | - Christopher H Eskiw
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Joanna M Bridger
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom
| |
Collapse
|
7
|
Lassalle D, Tetreau G, Pinaud S, Galinier R, Crickmore N, Gourbal B, Duval D. Glabralysins, Potential New β-Pore-Forming Toxin Family Members from the Schistosomiasis Vector Snail Biomphalaria glabrata. Genes (Basel) 2020; 11:genes11010065. [PMID: 31936048 PMCID: PMC7016736 DOI: 10.3390/genes11010065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/20/2019] [Accepted: 12/27/2019] [Indexed: 12/11/2022] Open
Abstract
Biomphalaria glabrata is a freshwater Planorbidae snail. In its environment, this mollusk faces numerous microorganisms or pathogens, and has developed sophisticated innate immune mechanisms to survive. The mechanisms of recognition are quite well understood in Biomphalaria glabrata, but immune effectors have been seldom described. In this study, we analyzed a new family of potential immune effectors and characterized five new genes that were named Glabralysins. The five Glabralysin genes showed different genomic structures and the high degree of amino acid identity between the Glabralysins, and the presence of the conserved ETX/MTX2 domain, support the hypothesis that they are pore-forming toxins. In addition, tertiary structure prediction confirms that they are structurally related to a subset of Cry toxins from Bacillus thuringiensis, including Cry23, Cry45, and Cry51. Finally, we investigated their gene expression profiles in snail tissues and demonstrated a mosaic transcription. We highlight the specificity in Glabralysin expression following immune stimulation with bacteria, yeast or trematode parasites. Interestingly, one Glabralysin was found to be expressed in immune-specialized hemocytes, and two others were induced following parasite exposure.
Collapse
Affiliation(s)
- Damien Lassalle
- IHPE, University of Montpellier, CNRS, Ifremer, University of Perpignan Via Domitia, 66860 Perpignan France; (D.L.); (G.T.); (S.P.); (R.G.); (B.G.)
| | - Guillaume Tetreau
- IHPE, University of Montpellier, CNRS, Ifremer, University of Perpignan Via Domitia, 66860 Perpignan France; (D.L.); (G.T.); (S.P.); (R.G.); (B.G.)
| | - Silvain Pinaud
- IHPE, University of Montpellier, CNRS, Ifremer, University of Perpignan Via Domitia, 66860 Perpignan France; (D.L.); (G.T.); (S.P.); (R.G.); (B.G.)
| | - Richard Galinier
- IHPE, University of Montpellier, CNRS, Ifremer, University of Perpignan Via Domitia, 66860 Perpignan France; (D.L.); (G.T.); (S.P.); (R.G.); (B.G.)
| | - Neil Crickmore
- School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK;
| | - Benjamin Gourbal
- IHPE, University of Montpellier, CNRS, Ifremer, University of Perpignan Via Domitia, 66860 Perpignan France; (D.L.); (G.T.); (S.P.); (R.G.); (B.G.)
| | - David Duval
- IHPE, University of Montpellier, CNRS, Ifremer, University of Perpignan Via Domitia, 66860 Perpignan France; (D.L.); (G.T.); (S.P.); (R.G.); (B.G.)
- Correspondence:
| |
Collapse
|
8
|
Clements CS, Bikkul MU, Ofosu W, Eskiw C, Tree D, Makarov E, Kill IR, Bridger JM. Presence and distribution of progerin in HGPS cells is ameliorated by drugs that impact on the mevalonate and mTOR pathways. Biogerontology 2019; 20:337-358. [PMID: 31041622 PMCID: PMC6535420 DOI: 10.1007/s10522-019-09807-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/29/2019] [Indexed: 12/12/2022]
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare, premature ageing syndrome in children. HGPS is normally caused by a mutation in the LMNA gene, encoding nuclear lamin A. The classical mutation in HGPS leads to the production of a toxic truncated version of lamin A, progerin, which retains a farnesyl group. Farnesyltransferase inhibitors (FTI), pravastatin and zoledronic acid have been used in clinical trials to target the mevalonate pathway in HGPS patients to inhibit farnesylation of progerin, in order to reduce its toxicity. Some other compounds that have been suggested as treatments include rapamycin, IGF1 and N-acetyl cysteine (NAC). We have analysed the distribution of prelamin A, lamin A, lamin A/C, progerin, lamin B1 and B2 in nuclei of HGPS cells before and after treatments with these drugs, an FTI and a geranylgeranyltransferase inhibitor (GGTI) and FTI with pravastatin and zoledronic acid in combination. Confirming other studies prelamin A, lamin A, progerin and lamin B2 staining was different between control and HGPS fibroblasts. The drugs that reduced progerin staining were FTI, pravastatin, zoledronic acid and rapamycin. However, drugs affecting the mevalonate pathway increased prelamin A, with only FTI reducing internal prelamin A foci. The distribution of lamin A in HGPS cells was improved with treatments of FTI, pravastatin and FTI + GGTI. All treatments reduced the number of cells displaying internal speckles of lamin A/C and lamin B2. Drugs targeting the mevalonate pathway worked best for progerin reduction, with zoledronic acid removing internal progerin speckles. Rapamycin and NAC, which impact on the MTOR pathway, both reduced both pools of progerin without increasing prelamin A in HGPS cell nuclei.
Collapse
Affiliation(s)
- Craig S Clements
- Progeria Research Team, Ageing Studies Theme, Institute for Environment, Health and Societies, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Mehmet U Bikkul
- Progeria Research Team, Ageing Studies Theme, Institute for Environment, Health and Societies, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Wendy Ofosu
- Progeria Research Team, Ageing Studies Theme, Institute for Environment, Health and Societies, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK.,Department of Biomedical Sciences, University of Westminster, 115 New Cavendish Street, London, W1W 6UW, UK
| | - Christopher Eskiw
- Food and Bioproduct Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7B 5A8, Canada
| | - David Tree
- Progeria Research Team, Ageing Studies Theme, Institute for Environment, Health and Societies, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Evgeny Makarov
- Progeria Research Team, Ageing Studies Theme, Institute for Environment, Health and Societies, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Ian R Kill
- Progeria Research Team, Ageing Studies Theme, Institute for Environment, Health and Societies, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Joanna M Bridger
- Progeria Research Team, Ageing Studies Theme, Institute for Environment, Health and Societies, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK. .,Genome Engineering and Maintenance Network, Ageing Studies Theme, Institute of Environment, Health and Societies, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK.
| |
Collapse
|
9
|
Federico C, Owoka T, Ragusa D, Sturiale V, Caponnetto D, Leotta CG, Bruno F, Foster HA, Rigamonti S, Giudici G, Cazzaniga G, Bridger JM, Sisu C, Saccone S, Tosi S. Deletions of Chromosome 7q Affect Nuclear Organization and HLXB9Gene Expression in Hematological Disorders. Cancers (Basel) 2019; 11:cancers11040585. [PMID: 31027247 PMCID: PMC6521283 DOI: 10.3390/cancers11040585] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/03/2019] [Accepted: 04/19/2019] [Indexed: 12/22/2022] Open
Abstract
The radial spatial positioning of individual gene loci within interphase nuclei has been associated with up- and downregulation of their expression. In cancer, the genome organization may become disturbed due to chromosomal abnormalities, such as translocations or deletions, resulting in the repositioning of genes and alteration of gene expression with oncogenic consequences. In this study, we analyzed the nuclear repositioning of HLXB9 (also called MNX1), mapping at 7q36.3, in patients with hematological disorders carrying interstitial deletions of 7q of various extents, with a distal breakpoint in 7q36. We observed that HLXB9 remains at the nuclear periphery, or is repositioned towards the nuclear interior, depending upon the compositional properties of the chromosomal regions involved in the rearrangement. For instance, a proximal breakpoint leading the guanine-cytosine (GC)-poor band 7q21 near 7q36 would bring HLXB9 to the nuclear periphery, whereas breakpoints that join the GC-rich band 7q22 to 7q36 would bring HLXB9 to the nuclear interior. This nuclear repositioning is associated with transcriptional changes, with HLXB9 in the nuclear interior becoming upregulated. Here we report an in cis rearrangement, involving one single chromosome altering gene behavior. Furthermore, we propose a mechanistic model for chromatin reorganization that affects gene expression via the influences of new chromatin neighborhoods.
Collapse
Affiliation(s)
- Concetta Federico
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124 Catania CT, Italy.
| | - Temitayo Owoka
- Genome Engineering and Maintenance Network, Institute of Environment, Health and Societies, Brunel University London, Kingston Lane UB8 3PH, UK.
| | - Denise Ragusa
- Genome Engineering and Maintenance Network, Institute of Environment, Health and Societies, Brunel University London, Kingston Lane UB8 3PH, UK.
| | - Valentina Sturiale
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124 Catania CT, Italy.
| | - Domenica Caponnetto
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124 Catania CT, Italy.
| | - Claudia Giovanna Leotta
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124 Catania CT, Italy.
| | - Francesca Bruno
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124 Catania CT, Italy.
| | - Helen A Foster
- Department of Biological and Environmental Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.
- College of Health and Life Science, Brunel University London, Kingston Lane UB8 3PH, UK.
| | - Silvia Rigamonti
- Associazione Italiana Ematologia Oncologia Pediatrica (AIEOP), Centro Ricerca Tettamanti, Pediatric Department, University of Milano-Bicocca, 20900 Monza, Italy.
| | - Giovanni Giudici
- Associazione Italiana Ematologia Oncologia Pediatrica (AIEOP), Centro Ricerca Tettamanti, Pediatric Department, University of Milano-Bicocca, 20900 Monza, Italy.
| | - Giovanni Cazzaniga
- Associazione Italiana Ematologia Oncologia Pediatrica (AIEOP), Centro Ricerca Tettamanti, Pediatric Department, University of Milano-Bicocca, 20900 Monza, Italy.
| | - Joanna M Bridger
- Genome Engineering and Maintenance Network, Institute of Environment, Health and Societies, Brunel University London, Kingston Lane UB8 3PH, UK.
| | - Cristina Sisu
- College of Health and Life Science, Brunel University London, Kingston Lane UB8 3PH, UK.
| | - Salvatore Saccone
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124 Catania CT, Italy.
| | - Sabrina Tosi
- Genome Engineering and Maintenance Network, Institute of Environment, Health and Societies, Brunel University London, Kingston Lane UB8 3PH, UK.
| |
Collapse
|
10
|
Portet A, Pinaud S, Chaparro C, Galinier R, Dheilly NM, Portela J, Charriere GM, Allienne JF, Duval D, Gourbal B. Sympatric versus allopatric evolutionary contexts shape differential immune response in Biomphalaria / Schistosoma interaction. PLoS Pathog 2019; 15:e1007647. [PMID: 30893368 PMCID: PMC6443186 DOI: 10.1371/journal.ppat.1007647] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 04/01/2019] [Accepted: 02/19/2019] [Indexed: 12/22/2022] Open
Abstract
Selective pressures between hosts and their parasites can result in reciprocal evolution or adaptation of specific life history traits. Local adaptation of resident hosts and parasites should lead to increase parasite infectivity/virulence (higher compatibility) when infecting hosts from the same location (in sympatry) than from a foreign location (in allopatry). Analysis of geographic variations in compatibility phenotypes is the most common proxy used to infer local adaptation. However, in some cases, allopatric host-parasite systems demonstrate similar or greater compatibility than in sympatry. In such cases, the potential for local adaptation remains unclear. Here, we study the interaction between Schistosoma and its vector snail Biomphalaria in which such discrepancy in local versus foreign compatibility phenotype has been reported. Herein, we aim at bridging this gap of knowledge by comparing life history traits (immune cellular response, host mortality, and parasite growth) and molecular responses in highly compatible sympatric and allopatric Schistosoma/Biomphalaria interactions originating from different geographic localities (Brazil, Venezuela and Burundi). We found that despite displaying similar prevalence phenotypes, sympatric schistosomes triggered a rapid immune suppression (dual-RNAseq analyses) in the snails within 24h post infection, whereas infection by allopatric schistosomes (regardless of the species) was associated with immune cell proliferation and triggered a non-specific generalized immune response after 96h. We observed that, sympatric schistosomes grow more rapidly. Finally, we identify miRNAs differentially expressed by Schistosoma mansoni that target host immune genes and could be responsible for hijacking the host immune response during the sympatric interaction. We show that despite having similar prevalence phenotypes, sympatric and allopatric snail-Schistosoma interactions displayed strong differences in their immunobiological molecular dialogue. Understanding the mechanisms allowing parasites to adapt rapidly and efficiently to new hosts is critical to control disease emergence and risks of Schistosomiasis outbreaks. Schistosomiasis, the second most widespread human parasitic disease after malaria, is caused by helminth parasites of the genus Schistosoma. More than 200 million people in 74 countries suffer from the pathological, and societal consequences of this disease. To complete its life cycle, the parasite requires an intermediate host, a freshwater snail of the genus Biomphalaria for its transmission. Given the limited options for treating Schistosoma mansoni infections in humans, much research has focused on developing methods to control transmission by its intermediate snail host. Biomphalaria glabrata. Comparative studies have shown that infection of the snail triggers complex cellular and humoral immune responses resulting in significant variations in parasite infectivity and snail susceptibility, known as the so-called polymorphism of compatibility. However, studies have mostly focused on characterizing the immunobiological mechanisms in sympatric interactions. Herein we used a combination of molecular and phenotypic approaches to compare the effect of infection in various sympatric and allopatric evolutionary contexts, allowing us to better understand the mechanisms of host-parasite local adaptation. Learning more about the immunobiological interactions between B. glabrata and S. mansoni could have important socioeconomic and public health impacts by changing the way we attempt to eradicate parasitic diseases and prevent or control schistosomiasis in the field.
Collapse
Affiliation(s)
- Anaïs Portet
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Silvain Pinaud
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Cristian Chaparro
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Richard Galinier
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Nolwenn M. Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Julien Portela
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Guillaume M. Charriere
- Interactions Hôtes-Pathogènes-Environnements (IHPE), UMR 5244, CNRS, Ifremer, Université de Perpignan Via Domitia, Université de Montpellier, Montpellier, France
| | - Jean-François Allienne
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - David Duval
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Benjamin Gourbal
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
- * E-mail:
| |
Collapse
|
11
|
Fowler KE, Mandawala AA, Griffin DK. The role of chromosome segregation and nuclear organisation in human subfertility. Biochem Soc Trans 2019; 47:425-432. [DOI: 10.1042/bst20180231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Abstract
Spermatogenesis is central to successful sexual reproduction, producing large numbers of haploid motile male gametes. Throughout this process, a series of equational and reductional chromosome segregation precedes radical repackaging of the haploid genome. Faithful chromosome segregation is thus crucial, as is an ordered spatio-temporal ‘dance’ of packing a large amount of chromatin into a very small space. Ergo, when the process goes wrong, this is associated with an improper chromosome number, nuclear position and/or chromatin damage in the sperm head. Generally, screening for overall DNA damage is relatively commonplace in clinics, but aneuploidy assessment is less so and nuclear organisation studies form the basis of academic research. Several studies have focussed on the role of chromosome segregation, nuclear organisation and analysis of sperm morphometry in human subfertility observing significant alterations in some cases, especially of the sex chromosomes. Importantly, sperm DNA damage has been associated with infertility and both extrinsic (e.g. lifestyle) and intrinsic (e.g. reactive oxygen species levels) factors, and while some DNA-strand breaks are repaired, unexpected breaks can cause differential chromatin packaging and further breakage. A ‘healthy’ sperm nucleus (with the right number of chromosomes, nuclear organisation and minimal DNA damage) is thus an essential part of reproduction. The purpose of this review is to summarise state of the art in the fields of sperm aneuploidy assessment, nuclear organisation and DNA damage studies.
Collapse
Affiliation(s)
- Katie E. Fowler
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, U.K
| | - Anjali A. Mandawala
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, U.K
| | | |
Collapse
|
12
|
Olszewska M, Wiland E, Huleyuk N, Fraczek M, Midro AT, Zastavna D, Kurpisz M. Chromosome (re)positioning in spermatozoa of fathers and sons - carriers of reciprocal chromosome translocation (RCT). BMC Med Genomics 2019; 12:30. [PMID: 30709354 PMCID: PMC6359769 DOI: 10.1186/s12920-018-0470-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/28/2018] [Indexed: 01/05/2023] Open
Abstract
Background Non-random chromosome positioning has been observed in the nuclei of several different tissue types, including human spermatozoa. The nuclear arrangement of chromosomes can be altered in men with decreased semen parameters or increased DNA fragmentation and in males with chromosomal numerical or structural aberrations. An aim of this study was to determine whether and how the positioning of nine chromosome centromeres was (re)arranged in the spermatozoa of fathers and sons – carriers of the same reciprocal chromosome translocation (RCT). Methods Fluorescence in situ hybridization (FISH) was applied to analyse the positioning of sperm chromosomes in a group of 13 carriers of 11 RCTs, including two familial RCT cases: t(4;5) and t(7;10), followed by analysis of eight control individuals. Additionally, sperm chromatin integrity was evaluated using TUNEL and Aniline Blue techniques. Results In the analysed familial RCT cases, repositioning of the chromosomes occurred in a similar way when compared to the data generated in healthy controls, even if some differences between father and son were further observed. These differences might have arisen from various statuses of sperm chromatin disintegration. Conclusions Nuclear topology appears as another aspect of epigenetic genomic regulation that may influence DNA functioning. We have re-documented that chromosomal positioning is defined in control males and that a particular RCT is reflected in the individual pattern of chromosomal topology. The present study examining the collected RCT group, including two familial cases, additionally showed that chromosomal factors (karyotype and hyperhaploidy) have superior effects, strongly influencing the chromosomal topology, when confronted with sperm chromatin integrity components (DNA fragmentation or chromatin deprotamination). Electronic supplementary material The online version of this article (10.1186/s12920-018-0470-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Marta Olszewska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Ewa Wiland
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Nataliya Huleyuk
- National Academy of Medical Sciences of Ukraine, Institute of Hereditary Pathology, Lysenko Str. 31a, Lviv, 79000, Ukraine
| | - Monika Fraczek
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Alina T Midro
- Department of Clinical Genetics, Medical University of Bialystok, Waszyngtona 13, PO Box 22, 15-089, Bialystok, Poland
| | - Danuta Zastavna
- National Academy of Medical Sciences of Ukraine, Institute of Hereditary Pathology, Lysenko Str. 31a, Lviv, 79000, Ukraine.,Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Al. Powstancow Warszawy 6, 35-959, Rzeszow, Poland
| | - Maciej Kurpisz
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland.
| |
Collapse
|
13
|
Henry MP, Hawkins JR, Boyle J, Bridger JM. The Genomic Health of Human Pluripotent Stem Cells: Genomic Instability and the Consequences on Nuclear Organization. Front Genet 2019; 9:623. [PMID: 30719030 PMCID: PMC6348275 DOI: 10.3389/fgene.2018.00623] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/23/2018] [Indexed: 12/11/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are increasingly used for cell-based regenerative therapies worldwide, with embryonic and induced pluripotent stem cells as potential treatments for debilitating and chronic conditions, such as age-related macular degeneration, Parkinson's disease, spinal cord injuries, and type 1 diabetes. However, with the level of genomic anomalies stem cells generate in culture, their safety may be in question. Specifically, hPSCs frequently acquire chromosomal abnormalities, often with gains or losses of whole chromosomes. This review discusses how important it is to efficiently and sensitively detect hPSC aneuploidies, to understand how these aneuploidies arise, consider the consequences for the cell, and indeed the individual to whom aneuploid cells may be administered.
Collapse
Affiliation(s)
- Marianne P Henry
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom.,Laboratory of Nuclear and Genomic Health, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, United Kingdom
| | - J Ross Hawkins
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Jennifer Boyle
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Joanna M Bridger
- Laboratory of Nuclear and Genomic Health, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, United Kingdom
| |
Collapse
|
14
|
Bikkul MU, Faragher RGA, Worthington G, Meinke P, Kerr ARW, Sammy A, Riyahi K, Horton D, Schirmer EC, Hubank M, Kill IR, Anderson RM, Slijepcevic P, Makarov E, Bridger JM. Telomere elongation through hTERT immortalization leads to chromosome repositioning in control cells and genomic instability in Hutchinson-Gilford progeria syndrome fibroblasts, expressing a novel SUN1 isoform. Genes Chromosomes Cancer 2019; 58:341-356. [PMID: 30474255 PMCID: PMC6590296 DOI: 10.1002/gcc.22711] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 11/06/2018] [Accepted: 11/22/2018] [Indexed: 02/06/2023] Open
Abstract
Immortalizing primary cells with human telomerase reverse transcriptase (hTERT) has been common practice to enable primary cells to be of extended use in the laboratory because they avoid replicative senescence. Studying exogenously expressed hTERT in cells also affords scientists models of early carcinogenesis and telomere behavior. Control and the premature ageing disease—Hutchinson‐Gilford progeria syndrome (HGPS) primary dermal fibroblasts, with and without the classical G608G mutation have been immortalized with exogenous hTERT. However, hTERT immortalization surprisingly elicits genome reorganization not only in disease cells but also in the normal control cells, such that whole chromosome territories normally located at the nuclear periphery in proliferating fibroblasts become mislocalized in the nuclear interior. This includes chromosome 18 in the control fibroblasts and both chromosomes 18 and X in HGPS cells, which physically express an isoform of the LINC complex protein SUN1 that has previously only been theoretical. Additionally, this HGPS cell line has also become genomically unstable and has a tetraploid karyotype, which could be due to the novel SUN1 isoform. Long‐term treatment with the hTERT inhibitor BIBR1532 enabled the reduction of telomere length in the immortalized cells and resulted that these mislocalized internal chromosomes to be located at the nuclear periphery, as assessed in actively proliferating cells. Taken together, these findings reveal that elongated telomeres lead to dramatic chromosome mislocalization, which can be restored with a drug treatment that results in telomere reshortening and that a novel SUN1 isoform combined with elongated telomeres leads to genomic instability. Thus, care should be taken when interpreting data from genomic studies in hTERT‐immortalized cell lines.
Collapse
Affiliation(s)
- Mehmet U. Bikkul
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | | | - Gemma Worthington
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Peter Meinke
- Friedrich‐Baur‐InstitutKlinikum der Universität MünchenMünchenGermany
- The Wellcome Trust Centre for Cell BiologyInstitute of Cell Biology, and Centre for Translational and Chemical Biology, University of EdinburghEdinburghEngland
| | - Alastair R. W. Kerr
- The Wellcome Trust Centre for Cell BiologyInstitute of Cell Biology, and Centre for Translational and Chemical Biology, University of EdinburghEdinburghEngland
| | - Aakila Sammy
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Kumars Riyahi
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Daniel Horton
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Eric C. Schirmer
- The Wellcome Trust Centre for Cell BiologyInstitute of Cell Biology, and Centre for Translational and Chemical Biology, University of EdinburghEdinburghEngland
| | - Michael Hubank
- Centre for Molecular PathologyThe Royal Marsden HospitalLondonEngland
| | - Ian R. Kill
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Rhona M. Anderson
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Predrag Slijepcevic
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Evgeny Makarov
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Joanna M. Bridger
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| |
Collapse
|
15
|
Bridger JM, Brindley PJ, Knight M. The snail Biomphalaria glabrata as a model to interrogate the molecular basis of complex human diseases. PLoS Negl Trop Dis 2018; 12:e0006552. [PMID: 30091971 PMCID: PMC6084811 DOI: 10.1371/journal.pntd.0006552] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Joanna M. Bridger
- Institute of Environment, Health, and Societies, Brunel University London, Uxbridge, United Kingdom
| | - Paul J. Brindley
- Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington DC, United States of America
- Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington DC, United States of America
| | - Matty Knight
- Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington DC, United States of America
- Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington DC, United States of America
- Division of Science and Mathematics, University of the District of Columbia, Washington DC, United States of America
- * E-mail: ,
| |
Collapse
|
16
|
Bikkul MU, Clements CS, Godwin LS, Goldberg MW, Kill IR, Bridger JM. Farnesyltransferase inhibitor and rapamycin correct aberrant genome organisation and decrease DNA damage respectively, in Hutchinson-Gilford progeria syndrome fibroblasts. Biogerontology 2018; 19:579-602. [PMID: 29907918 PMCID: PMC6223735 DOI: 10.1007/s10522-018-9758-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/30/2018] [Indexed: 12/20/2022]
Abstract
Hutchinson–Gilford progeria syndrome (HGPS) is a rare and fatal premature ageing disease in children. HGPS is one of several progeroid syndromes caused by mutations in the LMNA gene encoding the nuclear structural proteins lamins A and C. In classic HGPS the mutation G608G leads to the formation of a toxic lamin A protein called progerin. During post-translational processing progerin remains farnesylated owing to the mutation interfering with a step whereby the farnesyl moiety is removed by the enzyme ZMPSTE24. Permanent farnesylation of progerin is thought to be responsible for the proteins toxicity. Farnesyl is generated through the mevalonate pathway and three drugs that interfere with this pathway and hence the farnesylation of proteins have been administered to HGPS children in clinical trials. These are a farnesyltransferase inhibitor (FTI), statin and a bisphosphonate. Further experimental studies have revealed that other drugs such as N-acetyl cysteine, rapamycin and IGF-1 may be of use in treating HGPS through other pathways. We have shown previously that FTIs restore chromosome positioning in interphase HGPS nuclei. Mis-localisation of chromosomes could affect the cells ability to regulate proper genome function. Using nine different drug treatments representing drug regimes in the clinic we have shown that combinatorial treatments containing FTIs are most effective in restoring specific chromosome positioning towards the nuclear periphery and in tethering telomeres to the nucleoskeleton. On the other hand, rapamycin was found to be detrimental to telomere tethering, it was, nonetheless, the most effective at inducing DNA damage repair, as revealed by COMET analyses.
Collapse
Affiliation(s)
- Mehmet U Bikkul
- Progeria Research Team, Healthy Ageing Theme, Institute for Environment, Health and Societies, College of Health and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Craig S Clements
- Progeria Research Team, Healthy Ageing Theme, Institute for Environment, Health and Societies, College of Health and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Lauren S Godwin
- Progeria Research Team, Healthy Ageing Theme, Institute for Environment, Health and Societies, College of Health and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Martin W Goldberg
- Department of Biosciences, Durham University, Science Laboratories, South Road, Durham, DH1 3LE, UK
| | - Ian R Kill
- Progeria Research Team, Healthy Ageing Theme, Institute for Environment, Health and Societies, College of Health and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Joanna M Bridger
- Progeria Research Team, Healthy Ageing Theme, Institute for Environment, Health and Societies, College of Health and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK.
| |
Collapse
|
17
|
Mandibuloacral dysplasia: A premature ageing disease with aspects of physiological ageing. Ageing Res Rev 2018; 42:1-13. [PMID: 29208544 DOI: 10.1016/j.arr.2017.12.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/09/2017] [Accepted: 12/01/2017] [Indexed: 01/12/2023]
Abstract
Mandibuloacral dysplasia (MAD) is a rare genetic condition characterized by bone abnormalities including localized osteolysis and generalized osteoporosis, skin pigmentation, lipodystrophic signs and mildly accelerated ageing. The molecular defects associated with MAD are mutations in LMNA or ZMPSTE24 (FACE1) gene, causing type A or type B MAD, respectively. Downstream of LMNA or ZMPSTE24 mutations, the lamin A precursor, prelamin A, is accumulated in cells and affects chromatin dynamics and stress response. A new form of mandibuloacral dysplasia has been recently associated with mutations in POLD1 gene, encoding DNA polymerase delta, a major player in DNA replication. Of note, involvement of prelamin A in chromatin dynamics and recruitment of DNA repair factors has been also determined under physiological conditions, at the border between stress response and cellular senescence. Here, we review current knowledge on MAD clinical and pathogenetic aspects and highlight aspects typical of physiological ageing.
Collapse
|
18
|
Ioannou D, Tempest HG. Does genome organization matter in spermatozoa? A refined hypothesis to awaken the silent vessel. Syst Biol Reprod Med 2018; 64:518-534. [DOI: 10.1080/19396368.2017.1421278] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Dimitrios Ioannou
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- IVF Florida Reproductive Associates, Margate, FL, USA
| | - Helen G. Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| |
Collapse
|
19
|
Portuguez AS, Schwartz M, Siersbaek R, Nielsen R, Sung MH, Mandrup S, Kaplan T, Hakim O. Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis. FEBS J 2017; 284:3230-3244. [PMID: 28755519 PMCID: PMC5626622 DOI: 10.1111/febs.14183] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/24/2017] [Accepted: 07/25/2017] [Indexed: 12/24/2022]
Abstract
The three dimensional folding of mammalian genomes is cell type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin-associating factors, the mechanisms driving the colocalization of active chromosomal domains and the role of this organization in regulating the transcription program in adipocytes are not clear. Analysis of genome-wide chromosomal associations revealed cell type-specific spatial clustering of adipogenic genes in 3T3-L1 cells. Time course analysis demonstrated that the adipogenic 'hub', sampled by PPARγ and Lpin1, undergoes orchestrated reorganization during adipogenesis. Coupling the dynamics of genome architecture with multiple chromatin datasets indicated that among all the transcription factors (TFs) tested, RXR is central to genome reorganization at the beginning of adipogenesis. Interestingly, at the end of differentiation, the adipogenic hub was shifted to an H3K27me3-repressive environment in conjunction with attenuation of gene transcription. We propose a stage-specific hierarchy for the activity of TFs contributing to the establishment of an adipogenic genome architecture that brings together the adipogenic genetic program. In addition, the repositioning of this network in a H3K27me3-rich environment at the end of differentiation may contribute to the stabilization of gene transcription levels and reduce the developmental plasticity of these specialized cells. DATABASE All sequence data reported in this paper have been deposited at GEO (http://www.ncbi.nlm.nih.gov/geo/) (GSE92475).
Collapse
Affiliation(s)
- Avital Sarusi Portuguez
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Michal Schwartz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Rasmus Siersbaek
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Ronni Nielsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, NIA, National Institutes of Health, Baltimore, MD 21224, USA
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
| |
Collapse
|
20
|
Ioannou D, Millan NM, Jordan E, Tempest HG. A new model of sperm nuclear architecture following assessment of the organization of centromeres and telomeres in three-dimensions. Sci Rep 2017; 7:41585. [PMID: 28139771 PMCID: PMC5282497 DOI: 10.1038/srep41585] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 12/21/2016] [Indexed: 01/01/2023] Open
Abstract
The organization of chromosomes in sperm nuclei has been proposed to possess a unique “hairpin-loop” arrangement, which is hypothesized to aid in the ordered exodus of the paternal genome following fertilization. This study simultaneously assessed the 3D and 2D radial and longitudinal organization of telomeres, centromeres, and investigated whether chromosomes formed the same centromere clusters in sperm cells. Reproducible radial and longitudinal non-random organization was observed for all investigated loci using both 3D and 2D approaches in multiple subjects. We report novel findings, with telomeres and centromeres being localized throughout the nucleus but demonstrating roughly a 1:1 distribution in the nuclear periphery and the intermediate regions with <15% occupying the nuclear interior. Telomeres and centromeres were observed to aggregate in sperm nuclei, forming an average of 20 and 7 clusters, respectively. Reproducible
longitudinal organization demonstrated preferential localization of telomeres and centromeres in the mid region of the sperm cell. Preliminary evidence is also provided to support the hypothesis that specific chromosomes preferentially form the same centromere clusters. The more segmental distribution of telomeres and centromeres as described in this study could more readily accommodate and facilitate the sequential exodus of paternal chromosomes following fertilization.
Collapse
Affiliation(s)
- Dimitrios Ioannou
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Nicole M Millan
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Elizabeth Jordan
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Helen G Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| |
Collapse
|
21
|
Sathitruangsak C, Righolt CH, Klewes L, Tung Chang D, Kotb R, Mai S. Distinct and shared three-dimensional chromosome organization patterns in lymphocytes, monoclonal gammopathy of undetermined significance and multiple myeloma. Int J Cancer 2017; 140:400-410. [PMID: 27711972 PMCID: PMC5132008 DOI: 10.1002/ijc.30461] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 07/11/2016] [Accepted: 09/29/2016] [Indexed: 12/24/2022]
Abstract
The consistent appearance of specific chromosomal translocations in multiple myeloma has suggested that the positioning of chromosomes in the interphase nucleus might play a role in the occurrence of particular chromosomal rearrangements associated with malignant transformation. Using fluorescence in situ hybridization, we have determined the positions of selected chromosome pairs (18 and 19, 9 and 22, 4 and 14, 14 and 16, 11 and 14) in interphase nuclei of myeloma cells compared to normal lymphocytes of treatment-naïve patients. All chromosome pairs were arranged in a nonrandom pattern. Chromosomes commonly involved in myeloma-associated translocations (4 and 14, 14 and 16, 11 and 14) were found in close spatial proximity, and this is correlated with the occurrence of overlapping chromosome territories. The spatial distribution of chromosomes may increase the possibility of chromosomal translocations in multiple myeloma.
Collapse
Affiliation(s)
- Chirawadee Sathitruangsak
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
- Division of Medical OncologyDepartment of Internal MedicinePrince of Songkla UniversitySongkhlaThailand
| | - Christiaan H. Righolt
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
| | - Ludger Klewes
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
- Department of Cell BiologyCancerCare Manitoba, Genomic Centre for Cancer Research and Diagnosis (GCCRD)WinnipegManitobaCanada
| | - Doris Tung Chang
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
| | - Rami Kotb
- Department of HaematologyCancerCare ManitobaWinnipegManitobaCanada
| | - Sabine Mai
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
- Department of Cell BiologyCancerCare Manitoba, Genomic Centre for Cancer Research and Diagnosis (GCCRD)WinnipegManitobaCanada
- Department of Physiology and PathophysiologyUniversity of ManitobaWinnipegManitobaCanada
| |
Collapse
|
22
|
Mitta G, Gourbal B, Grunau C, Knight M, Bridger J, Théron A. The Compatibility Between Biomphalaria glabrata Snails and Schistosoma mansoni: An Increasingly Complex Puzzle. ADVANCES IN PARASITOLOGY 2017; 97:111-145. [PMID: 28325369 DOI: 10.1016/bs.apar.2016.08.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
This review reexamines the results obtained in recent decades regarding the compatibility polymorphism between the snail, Biomphalaria glabrata, and the pathogen, Schistosoma mansoni, which is one of the agents responsible for human schistosomiasis. Some results point to the snail's resistance as explaining the incompatibility, while others support a "matching hypothesis" between the snail's immune receptors and the schistosome's antigens. We propose here that the two hypotheses are not exclusive, and that the compatible/incompatible status of a particular host/parasite couple probably reflects the balance of multiple molecular determinants that support one hypothesis or the other. Because these genes are involved in a coevolutionary arms race, we also propose that the underlying mechanisms can vary. Finally, some recent results show that environmental factors could influence compatibility. Together, these results make the compatibility between B. glabrata and S. mansoni an increasingly complex puzzle. We need to develop more integrative approaches in order to find targets that could potentially be manipulated to control the transmission of schistosomiasis.
Collapse
|
23
|
Meaburn KJ. Spatial Genome Organization and Its Emerging Role as a Potential Diagnosis Tool. Front Genet 2016; 7:134. [PMID: 27507988 PMCID: PMC4961005 DOI: 10.3389/fgene.2016.00134] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/13/2016] [Indexed: 12/12/2022] Open
Abstract
In eukaryotic cells the genome is highly spatially organized. Functional relevance of higher order genome organization is implied by the fact that specific genes, and even whole chromosomes, alter spatial position in concert with functional changes within the nucleus, for example with modifications to chromatin or transcription. The exact molecular pathways that regulate spatial genome organization and the full implication to the cell of such an organization remain to be determined. However, there is a growing realization that the spatial organization of the genome can be used as a marker of disease. While global genome organization patterns remain largely conserved in disease, some genes and chromosomes occupy distinct nuclear positions in diseased cells compared to their normal counterparts, with the patterns of reorganization differing between diseases. Importantly, mapping the spatial positioning patterns of specific genomic loci can distinguish cancerous tissue from benign with high accuracy. Genome positioning is an attractive novel biomarker since additional quantitative biomarkers are urgently required in many cancer types. Current diagnostic techniques are often subjective and generally lack the ability to identify aggressive cancer from indolent, which can lead to over- or under-treatment of patients. Proof-of-principle for the use of genome positioning as a diagnostic tool has been provided based on small scale retrospective studies. Future large-scale studies are required to assess the feasibility of bringing spatial genome organization-based diagnostics to the clinical setting and to determine if the positioning patterns of specific loci can be useful biomarkers for cancer prognosis. Since spatial reorganization of the genome has been identified in multiple human diseases, it is likely that spatial genome positioning patterns as a diagnostic biomarker may be applied to many diseases.
Collapse
Affiliation(s)
- Karen J. Meaburn
- Cell Biology of Genomes Group, National Cancer Institute, National Institutes of HealthBethesda, MD, USA
| |
Collapse
|
24
|
Loucas BD, Shuryak I, Cornforth MN. Three-Color Chromosome Painting as Seen through the Eyes of mFISH: Another Look at Radiation-Induced Exchanges and Their Conversion to Whole-Genome Equivalency. Front Oncol 2016; 6:52. [PMID: 27014627 PMCID: PMC4791380 DOI: 10.3389/fonc.2016.00052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/22/2016] [Indexed: 01/25/2023] Open
Abstract
Whole-chromosome painting (WCP) typically involves the fluorescent staining of a small number of chromosomes. Consequently, it is capable of detecting only a fraction of exchanges that occur among the full complement of chromosomes in a genome. Mathematical corrections are commonly applied to WCP data in order to extrapolate the frequency of exchanges occurring in the entire genome [whole-genome equivalency (WGE)]. However, the reliability of WCP to WGE extrapolations depends on underlying assumptions whose conditions are seldom met in actual experimental situations, in particular the presumed absence of complex exchanges. Using multi-fluor fluorescence in situ hybridization (mFISH), we analyzed the induction of simple exchanges produced by graded doses of 137Cs gamma rays (0–4 Gy), and also 1.1 GeV 56Fe ions (0–1.5 Gy). In order to represent cytogenetic damage as it would have appeared to the observer following standard three-color WCP, all mFISH information pertaining to exchanges that did not specifically involve chromosomes 1, 2, or 4 was ignored. This allowed us to reconstruct dose–responses for three-color apparently simple (AS) exchanges. Using extrapolation methods similar to those derived elsewhere, these were expressed in terms of WGE for comparison to mFISH data. Based on AS events, the extrapolated frequencies systematically overestimated those actually observed by mFISH. For gamma rays, these errors were practically independent of dose. When constrained to a relatively narrow range of doses, the WGE corrections applied to both 56Fe and gamma rays predicted genome-equivalent damage with a level of accuracy likely sufficient for most applications. However, the apparent accuracy associated with WCP to WGE corrections is both fortuitous and misleading. This is because (in normal practice) such corrections can only be applied to AS exchanges, which are known to include complex aberrations in the form of pseudosimple exchanges. When WCP to WGE corrections are applied to true simple exchanges, the results are less than satisfactory, leading to extrapolated values that underestimate the true WGE response by unacceptably large margins. Likely explanations for these results are discussed, as well as their implications for radiation protection. Thus, in seeming contradiction to notion that complex aberrations be avoided altogether in WGE corrections – and in violation of assumptions upon which these corrections are based – their inadvertent inclusion in three-color WCP data is actually required in order for them to yield even marginally acceptable results.
Collapse
Affiliation(s)
- Bradford D Loucas
- Department of Radiation Oncology, University of Texas Medical Branch , Galveston, TX , USA
| | - Igor Shuryak
- Center for Radiological Research, Columbia University , New York, NY , USA
| | - Michael N Cornforth
- Department of Radiation Oncology, University of Texas Medical Branch , Galveston, TX , USA
| |
Collapse
|
25
|
Clements CS, Bikkul U, Ahmed MH, Foster HA, Godwin LS, Bridger JM. Visualizing the Spatial Relationship of the Genome with the Nuclear Envelope Using Fluorescence In Situ Hybridization. Methods Mol Biol 2016; 1411:387-406. [PMID: 27147055 DOI: 10.1007/978-1-4939-3530-7_24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The genome has a special relationship with the nuclear envelope in cells. Much of the genome is anchored at the nuclear periphery, tethered by chromatin binding proteins such nuclear lamins and other integral membrane proteins. Even though there are global assays such as DAM-ID or ChIP to assess what parts of the genome are associated with the nuclear envelope, it is also essential to be able to visualize regions of the genome in order to reveal their individual relationships with nuclear structures in single cells. This is executed by fluorescence in situ hybridization (FISH) in 2-dimensional flattened nuclei (2D-FISH) or 3-dimensionally preserved cells (3D-FISH) in combination with indirect immunofluorescence to reveal structural proteins. This chapter explains the protocols for 2D- and 3D-FISH in combination with indirect immunofluorescence and discusses options for image capture and analysis. Due to the nuclear envelope proteins being part of the non-extractable nucleoskeleton, we also describe how to prepare DNA halos through salt extraction and how they can be used to study genome behavior and association when combined with 2D-FISH.
Collapse
Affiliation(s)
- Craig S Clements
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Ural Bikkul
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Mai Hassan Ahmed
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Helen A Foster
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Lauren S Godwin
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Joanna M Bridger
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK.
| |
Collapse
|
26
|
Abstract
The paternal contribution to fertilization and embryogenesis is frequently overlooked as the spermatozoon is often considered to be a silent vessel whose only function is to safely deliver the paternal genome to the maternal oocyte. In this article, we hope to demonstrate that this perception is far from the truth. Typically, infertile men have been unable to conceive naturally (or through regular IVF), and therefore, a perturbation of the genetic integrity of sperm heads in infertile males has been under-considered. The advent of intracytoplasmic sperm injection (ICSI) however has led to very successful treatment of male factor infertility and subsequent widespread use in IVF clinics worldwide. Until recently, little concern has been raised about the genetic quality of sperm in ICSI patients or the impact genetic aberrations could have on fertility and embryogenesis. This review highlights the importance of chromatin packaging in the sperm nucleus as essential for the establishment and maintenance of a viable pregnancy.
Collapse
|
27
|
Olszewska M, Wanowska E, Kishore A, Huleyuk N, Georgiadis AP, Yatsenko AN, Mikula M, Zastavna D, Wiland E, Kurpisz M. Genetic dosage and position effect of small supernumerary marker chromosome (sSMC) in human sperm nuclei in infertile male patient. Sci Rep 2015; 5:17408. [PMID: 26616419 PMCID: PMC4663790 DOI: 10.1038/srep17408] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/28/2015] [Indexed: 11/12/2022] Open
Abstract
Chromosomes occupy specific distinct areas in the nucleus of the sperm cell that may be altered in males with disrupted spermatogenesis. Here, we present alterations in the positioning of the human chromosomes 15, 18, X and Y between spermatozoa with the small supernumerary marker chromosome (sSMC; sSMC+) and spermatozoa with normal chromosome complement (sSMC−), for the first time described in the same ejaculate of an infertile, phenotypically normal male patient. Using classical and confocal fluorescent microscopy, the nuclear colocalization of chromosomes 15 and sSMC was analyzed. The molecular cytogenetic characteristics of sSMC delineated the karyotype as 47,XY,+der(15)(pter->p11.2::q11.1->q11.2::p11.2->pter)mat. Analysis of meiotic segregation showed a 1:1 ratio of sSMC+ to sSMC− spermatozoa, while evaluation of sperm aneuploidy status indicated an increased level of chromosome 13, 18, 21 and 22 disomy, up to 7 × (2.7 − 15.1). Sperm chromatin integrity assessment did not reveal any increase in deprotamination in the patient’s sperm chromatin. Importantly, we found significant repositioning of chromosomes X and Y towards the nuclear periphery, where both chromosomes were localized in close proximity to the sSMC. This suggests the possible influence of sSMC/XY colocalization on meiotic chromosome division, resulting in abnormal chromosome segregation, and leading to male infertility in the patient.
Collapse
Affiliation(s)
- Marta Olszewska
- Institute of Human Genetics, Polish Academy of Sciences, Department of Reproductive Biology and Stem Cells, Strzeszynska 32, 60-479 Poznan, Poland
| | - Elzbieta Wanowska
- Institute of Human Genetics, Polish Academy of Sciences, Department of Reproductive Biology and Stem Cells, Strzeszynska 32, 60-479 Poznan, Poland
| | - Archana Kishore
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh 15213, PA, USA
| | - Nataliya Huleyuk
- Institute of Hereditary Pathology, Ukrainian Academy of Medical Sciences, Lysenko Str. 31a, 79000 Lviv, Ukraine
| | - Andrew P Georgiadis
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh 15213, PA, USA
| | - Alexander N Yatsenko
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh 15213, PA, USA
| | - Mariya Mikula
- Institute of Hereditary Pathology, Ukrainian Academy of Medical Sciences, Lysenko Str. 31a, 79000 Lviv, Ukraine
| | - Danuta Zastavna
- Institute of Hereditary Pathology, Ukrainian Academy of Medical Sciences, Lysenko Str. 31a, 79000 Lviv, Ukraine
| | - Ewa Wiland
- Institute of Human Genetics, Polish Academy of Sciences, Department of Reproductive Biology and Stem Cells, Strzeszynska 32, 60-479 Poznan, Poland
| | - Maciej Kurpisz
- Institute of Human Genetics, Polish Academy of Sciences, Department of Reproductive Biology and Stem Cells, Strzeszynska 32, 60-479 Poznan, Poland
| |
Collapse
|
28
|
Popken J, Brero A, Koehler D, Schmid VJ, Strauss A, Wuensch A, Guengoer T, Graf A, Krebs S, Blum H, Zakhartchenko V, Wolf E, Cremer T. Reprogramming of fibroblast nuclei in cloned bovine embryos involves major structural remodeling with both striking similarities and differences to nuclear phenotypes of in vitro fertilized embryos. Nucleus 2015; 5:555-89. [PMID: 25482066 PMCID: PMC4615760 DOI: 10.4161/19491034.2014.979712] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Nuclear landscapes were studied during preimplantation development of bovine embryos, generated either by in vitro fertilization (IVF), or generated as cloned embryos by somatic cell nuclear transfer (SCNT) of bovine fetal fibroblasts, using 3-dimensional confocal laser scanning microscopy (3D-CLSM) and structured illumination microscopy (3D-SIM). Nuclear landscapes of IVF and SCNT embryonic nuclei were compared with each other and with fibroblast nuclei. We demonstrate that reprogramming of fibroblast nuclei in cloned embryos requires changes of their landscapes similar to nuclei of IVF embryos. On the way toward the 8-cell stage, where major genome activation occurs, a major lacuna, enriched with splicing factors, was formed in the nuclear interior and chromosome territories (CTs) were shifted toward the nuclear periphery. During further development the major lacuna disappeared and CTs were redistributed throughout the nuclear interior forming a contiguous higher order chromatin network. At all stages of development CTs of IVF and SCNT embryonic nuclei were built up from chromatin domain clusters (CDCs) pervaded by interchromatin compartment (IC) channels. Quantitative analyses revealed a highly significant enrichment of RNA polymerase II and H3K4me3, a marker for transcriptionally competent chromatin, at the periphery of CDCs. In contrast, H3K9me3, a marker for silent chromatin, was enriched in the more compacted interior of CDCs. Despite these striking similarities, we also detected major differences between nuclear landscapes of IVF and cloned embryos. Possible implications of these differences for the developmental potential of cloned animals remain to be investigated. We present a model, which integrates generally applicable structural and functional features of the nuclear landscape.
Collapse
Key Words
- 3D-CLSM, 3-dimensional confocal laser scanning microscopy
- 3D-SIM, 3-dimensional structured illumination microscopy
- B23, nucleophosmin B23
- BTA, Bos taurus
- CDC, chromatin domain cluster
- CT, chromosome territory
- EM, electron microscopy
- ENC, embryonic nuclei with conventional nuclear architecture
- ENP, embryonic nuclei with peripheral CT distribution
- H3K4me3
- H3K4me3, histone H3 with tri-methylated lysine 4
- H3K9me3
- H3K9me3, histone H3 with tri-methylated lysine 9
- H3S10p, histone H3 with phosphorylated serine 10
- IC, interchromatin compartment
- IVF, in vitro fertilization
- MCB, major chromatin body
- PR, perichromatin region
- RNA polymerase II
- RNA polymerase II-S2p, RNA polymerase II with phosphorylated serine 2 of its CTD domain
- RNA polymerase II-S5p, RNA polymerase II with phosphorylated serine 5 of its CTD domain
- SC-35, splicing factor SC-35
- SCNT, somatic cell nuclear transfer.
- bovine preimplantation development
- chromatin domain
- chromosome territory
- embryonic genome activation
- in vitro fertilization (IVF)
- interchromatin compartment
- major EGA, major embryonic genome activation
- somatic cell nuclear transfer (SCNT)
Collapse
Affiliation(s)
- Jens Popken
- a Division of Anthropology and Human Genetics ; Biocenter; LMU Munich ; Munich , Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Abstract
Chromatin, once thought to serve only as a means to package DNA, is now recognized as a major regulator of gene activity. As a result of the wide range of methods used to describe the numerous levels of chromatin organization, the terminology that has emerged to describe these organizational states is often imprecise and sometimes misleading. In this review, we discuss our current understanding of chromatin architecture and propose terms to describe the various biochemical and structural states of chromatin.
Collapse
Affiliation(s)
- Liron Even-Faitelson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | | | - Zahra Baghestani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | - David P Bazett-Jones
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada.
| |
Collapse
|
30
|
Ioannou D, Kandukuri L, Simpson JL, Tempest HG. Chromosome territory repositioning induced by PHA-activation of lymphocytes: A 2D and 3D appraisal. Mol Cytogenet 2015; 8:47. [PMID: 26146516 PMCID: PMC4490598 DOI: 10.1186/s13039-015-0146-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/14/2015] [Indexed: 11/26/2022] Open
Abstract
Background Genomes and by extension chromosome territories (CTs) in a variety of organisms exhibit nonrandom organization within interphase nuclei. CTs are susceptible to movement upon induction by a variety of stimuli, including: cell differentiation, growth factors, genotoxic agents, proliferating status, and stimulants that induce novel transcription profiles. These findings suggest nuclear architecture can undergo reorganization, providing support for a functional significance of CT organization. The effect of the initiation of transcription on global scale chromatin architecture has been underexplored. This study investigates the organization of all 24 human chromosomes in lymphocytes from two individuals in resting and phytohaemagglutinin activated lymphocytes using 2D and 3D approaches. Results The radial organization of CTs in lymphocytes in both resting and activated lymphocytes follows a gene-density pattern. However, CT organization in activated nuclei appears less constrained exhibiting a more random organization. We report differences in the spatial relationship between homologous and heterologous CTs in activated nuclei. In addition, a reproducible radial hierarchy of CTs was identified and evidence of a CT repositioning was observed in activated nuclei using both 2D and 3D approaches. Conclusions Alterations between resting and activated lymphocytes could be adaptation of CTs to the new transcription profile and possibly the formation of new neighborhoods of interest or interaction of CTs with nuclear landmarks. The increased distances between homologous and heterologous CTs in activated lymphocytes could be a reflection of a defensive mechanism to reduce potential interaction to prevent any structural chromosome abnormalities (e.g. translocations) as a result of DNA damage that increases during lymphocyte activation.
Collapse
Affiliation(s)
- Dimitrios Ioannou
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
| | - Lakshmi Kandukuri
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA ; Present address Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR) Uppal Road, Hyderabad, 500 007 India
| | - Joe Leigh Simpson
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
| | - Helen Ghislaine Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA ; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199 USA
| |
Collapse
|
31
|
Worman HJ, Schirmer EC. Nuclear membrane diversity: underlying tissue-specific pathologies in disease? Curr Opin Cell Biol 2015; 34:101-12. [PMID: 26115475 PMCID: PMC4522394 DOI: 10.1016/j.ceb.2015.06.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 06/05/2015] [Accepted: 06/10/2015] [Indexed: 11/16/2022]
Abstract
Human 'laminopathy' diseases result from mutations in genes encoding nuclear lamins or nuclear envelope (NE) transmembrane proteins (NETs). These diseases present a seeming paradox: the mutated proteins are widely expressed yet pathology is limited to specific tissues. New findings suggest tissue-specific pathologies arise because these widely expressed proteins act in various complexes that include tissue-specific components. Diverse mechanisms to achieve NE tissue-specificity include tissue-specific regulation of the expression, mRNA splicing, signaling, NE-localization and interactions of potentially hundreds of tissue-specific NETs. New findings suggest these NETs underlie tissue-specific NE roles in cytoskeletal mechanics, cell-cycle regulation, signaling, gene expression and genome organization. This view of the NE as 'specialized' in each cell type is important to understand the tissue-specific pathology of NE-linked diseases.
Collapse
Affiliation(s)
- Howard J Worman
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, USA; Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, USA
| | - Eric C Schirmer
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
32
|
Ioannou D, Kandukuri L, Quadri A, Becerra V, Simpson JL, Tempest HG. Spatial positioning of all 24 chromosomes in the lymphocytes of six subjects: evidence of reproducible positioning and spatial repositioning following DNA damage with hydrogen peroxide and ultraviolet B. PLoS One 2015; 10:e0118886. [PMID: 25756782 PMCID: PMC4355486 DOI: 10.1371/journal.pone.0118886] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 01/18/2015] [Indexed: 12/18/2022] Open
Abstract
The higher-order organization of chromatin is well-established, with chromosomes occupying distinct positions within the interphase nucleus. Chromatin is susceptible to, and constantly assaulted by both endogenous and exogenous threats. However, the effects of DNA damage on the spatial topology of chromosomes are hitherto, poorly understood. This study investigates the organization of all 24 human chromosomes in lymphocytes from six individuals prior to- and following in-vitro exposure to genotoxic agents: hydrogen peroxide and ultraviolet B. This study is the first to report reproducible distinct hierarchical radial organization of chromosomes with little inter-individual differences between subjects. Perturbed nuclear organization was observed following genotoxic exposure for both agents; however a greater effect was observed for hydrogen peroxide including: 1) More peripheral radial organization; 2) Alterations in the global distribution of chromosomes; and 3) More events of chromosome repositioning (18 events involving 10 chromosomes vs. 11 events involving 9 chromosomes for hydrogen peroxide and ultraviolet B respectively). Evidence is provided of chromosome repositioning and altered nuclear organization following in-vitro exposure to genotoxic agents, with notable differences observed between the two investigated agents. Repositioning of chromosomes following genotoxicity involved recurrent chromosomes and is most likely part of the genomes inherent response to DNA damage. The variances in nuclear organization observed between the two agents likely reflects differences in mobility and/or decondensation of chromatin as a result of differences in the type of DNA damage induced, chromatin regions targeted, and DNA repair mechanisms.
Collapse
Affiliation(s)
- Dimitrios Ioannou
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Lakshmi Kandukuri
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Ameer Quadri
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Victor Becerra
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Joe Leigh Simpson
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
- March of Dimes Foundation, White Plains, New York, United States of America
| | - Helen G. Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- * E-mail:
| |
Collapse
|
33
|
Arican-Goktas HD, Ittiprasert W, Bridger JM, Knight M. Differential spatial repositioning of activated genes in Biomphalaria glabrata snails infected with Schistosoma mansoni. PLoS Negl Trop Dis 2014; 8:e3013. [PMID: 25211244 PMCID: PMC4161332 DOI: 10.1371/journal.pntd.0003013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/20/2014] [Indexed: 11/18/2022] Open
Abstract
Schistosomiasis is an infectious disease infecting mammals as the definitive host and fresh water snails as the intermediate host. Understanding the molecular and biochemical relationship between the causative schistosome parasite and its hosts will be key to understanding and ultimately treating and/or eradicating the disease. There is increasing evidence that pathogens that have co-evolved with their hosts can manipulate their hosts' behaviour at various levels to augment an infection. Bacteria, for example, can induce beneficial chromatin remodelling of the host genome. We have previously shown in vitro that Biomphalaria glabrata embryonic cells co-cultured with schistosome miracidia display genes changing their nuclear location and becoming up-regulated. This also happens in vivo in live intact snails, where early exposure to miracidia also elicits non-random repositioning of genes. We reveal differences in the nuclear repositioning between the response of parasite susceptible snails as compared to resistant snails and with normal or live, attenuated parasites. Interestingly, the stress response gene heat shock protein (Hsp) 70 is only repositioned and then up-regulated in susceptible snails with the normal parasite. This movement and change in gene expression seems to be controlled by the parasite. Other differences in the behaviour of genes support the view that some genes are responding to tissue damage, for example the ferritin genes move and are up-regulated whether the snails are either susceptible or resistant and upon exposure to either normal or attenuated parasite. This is the first time host genome reorganisation has been seen in a parasitic host and only the second time for any pathogen. We believe that the parasite elicits a spatio-epigenetic reorganisation of the host genome to induce favourable gene expression for itself and this might represent a fundamental mechanism present in the human host infected with schistosome cercariae as well as in other host-pathogen relationships. Bilharzia is a parasitic disease endemic in many parts of the world. The schistosoma parasite that causes Bilharzia infects humans but uses a fresh water snail as a secondary host. These two organisms have co-evolved together, and as such the parasite will have mechanisms to overcome the host defences. Understanding this delicately balanced relationship is fundamental to controlling or eradicating the disease. We have studied how this parasite can influence how the DNA within the snail behaves. We have shown snail genes have specific locations within the cell nuclei. Further, we have revealed that specific snail genes related to a schistosome infection change to a new non-random nuclear location as they are turned on or up-regulated. We have snail strains that are susceptible or resistant to the infection of parasites and we can also take live parasites and make them unable to complete an infection by irradiating them. In this unique study, we have shown a gene that is involved in stress pathways moves to a new nuclear location and becomes turned on, but only in susceptible snails, infected with fully functional parasite. Our data suggest that this gene is regulated by the parasite, which has control over the host's DNA, so that the gene is moved to an area where it can be actively expressed. We have uncovered a novel mechanism whereby the spatial organization of a host organism is interfered with by a pathogen. This type of control is probably found in other host-pathogen relationships.
Collapse
Affiliation(s)
- Halime D. Arican-Goktas
- Lab of Nuclear and Genomic Health, Centre for Cell and Chromosome Biology, Biosciences, School of Health Sciences and Social Care, Brunel University, London, United Kingdom
| | | | - Joanna M. Bridger
- Lab of Nuclear and Genomic Health, Centre for Cell and Chromosome Biology, Biosciences, School of Health Sciences and Social Care, Brunel University, London, United Kingdom
- * E-mail: (JMB); (MK)
| | - Matty Knight
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Science, George Washington University, Washington, D.C., United States of America
- * E-mail: (JMB); (MK)
| |
Collapse
|