Inducing segmental aneuploid mosaicism in the mouse through targeted asymmetric sister chromatid event of recombination

Loss or gain of whole chromosomes, or parts of chromosomes, is found in various pathological conditions, such as cancer and aneuploidy, and results from the missegregation of chromosomes during cellular division or abnormal mitotic recombination. We introduce a novel strategy for determining the consequences of segmental aneuploid mosaicism, called targeted asymmetric sister chromatin event of recombination (TASCER). We took advantage of the Cre/loxP system, used extensively in embryonic stem cells for generating deletions and duplications of regions of interest, to induce recombination during the G2 phase. Using two loxP sites in a Cis configuration, we generated in vivo cells harboring microdeletions and microduplications for regions of interest covering up to 2.2 Mb. Using this approach in the mouse provides insight into the consequences of segmental aneuploidy for homologous regions of the human chromosome 21 on cell survival. Furthermore, TASCER shows that Cre-induced recombination is more efficient after DNA replication in vivo and provides an opportunity to evaluate, through genetic mosaics, the outcome of copy number variation and segmental aneuploidy in the mouse.     

植物非整倍体研究进展

非整倍体(aneuploid)是指相对于正常个体(euploid)的染色体组增加、减少一条或若干条染色体的生物个体。由于非整倍体个体存在基因剂量效应的不平衡性(gene-dosage imbalance),非整倍体个体往往会表现严重的表型缺陷(aneuploid syndrom),如发育迟缓,个体矮小,难以繁殖后代等。在人类中,最为典型的例子为导致新生儿智力缺陷的唐氏综合症,由额外的一个21号染色体拷贝(部分拷贝)引起。此外,大多数癌细胞类型表型为严重的非整倍体。在大多情况下,非整倍体对于动物及人类是致命的,而植物对于非整倍体则往往表现出较强的耐受力,特别是在异源多倍体植物中。植物非整倍体对于植物的遗传、育种研究有重要意义,在基因及分子标记的物理位置确定,基因转移,连锁群与染色体的对应关系的确立上具有无可比拟的优势。该文综述了近些年来有关植物非整倍体研究的结果,介绍了非整倍体的几种重要成因和有关非整倍体鉴定手段的变迁,阐述了植物非整倍体对个体表型、基因表达以及表观遗传方面的影响,重点讨论了非整倍体在植物进化、基因组序列测定以及遗传改良方面的潜在作用。同时,探讨了植物非整倍体研究的新思路,以及利用非整倍体促进相关植物遗传改良、育种研究的新方法。     

Elevated Tolerance to Aneuploidy in Cancer Cells: Estimating the Fitness Effects of Chromosome Number Alterations by In Silico Modelling of Somatic Genome Evolution

An unbalanced chromosome number (aneuploidy) is present in most malignant tumours and has been attributed to mitotic mis-segregation of chromosomes. However, recent studies have shown a relatively high rate of chromosomal mis-segregation also in non-neoplastic human cells, while the frequency of aneuploid cells remains low throughout life in most normal tissues. This implies that newly formed aneuploid cells are subject to negative selection in healthy tissues and that attenuation of this selection could contribute to aneuploidy in cancer. To test this, we modelled cellular growth as discrete time branching processes, during which chromosome gains and losses were generated and their host cells subjected to selection pressures of various magnitudes. We then assessed experimentally the frequency of chromosomal mis-segregation as well as the prevalence of aneuploid cells in human non-neoplastic cells and in cancer cells. Integrating these data into our models allowed estimation of the fitness reduction resulting from a single chromosome copy number change to an average of ≈30% in normal cells. In comparison, cancer cells showed an average fitness reduction of only 6% (p = 0.0008), indicative of aneuploidy tolerance. Simulations based on the combined presence of chromosomal mis-segregation and aneuploidy tolerance reproduced distributions of chromosome aberrations in >400 cancer cases with higher fidelity than models based on chromosomal mis-segregation alone. Reverse engineering of aneuploid cancer cell development in silico predicted that aneuploidy intolerance is a stronger limiting factor for clonal expansion of aneuploid cells than chromosomal mis-segregation rate. In conclusion, our findings indicate that not only an elevated chromosomal mis-segregation rate, but also a generalised tolerance to novel chromosomal imbalances contribute to the genomic landscape of human tumours.     

Genomic organization and chromosomal distribution of rat ID elements.

Identifier (ID) elements are members of a family of short interspersed nuclear elements (SINEs) in rodents. We investigated the genomic organization and chromosomal distribution of the ID elements in the rat, mouse and Chinese hamster. Southern blot hybridization analysis revealed that the ID elements are widespread in the rat genome, but concentrated in the mouse and Chinese hamster genomes, and that the copy of ID elements in the rat is about 5 times and 50 times that in the mouse and Chinese hamster, respectively. FISH analysis showed that the ID elements are predominantly distributed in the R-band regions of rat chromosomes. In mouse and Chinese hamster chromosomes, no specific distribution pattern of the ID elements was found. Furthermore, we found a distinct group of derivative ID elements in the rat, which contain partially repeated ID core domains, by PCR amplification using an ID core sequence. Such derivatives were not found in either the mouse or Chinese hamster. These findings suggest that explosive amplification of the ID elements in the rat has been accompanied by the occurrence of derivative ID elements and a predominant localization to the R-band regions. Similar associations found in the Alu family, one of the human SINEs, allow us to speculate that the rat ID elements and the human Alu family have analogous functions in chromosomal organization.     

An approach for quantitative assessment of fluorescence in situ hybridization (FISH) signals for applied human molecular cytogenetics.

A number of applied molecular cytogenetic studies require the quantitative assessment of fluorescence in situ hybridization (FISH) signals (for example, interphase FISH analysis of aneuploidy by chromosome enumeration DNA probes; analysis of somatic pairing of homologous chromosomes in interphase nuclei; identification of chromosomal heteromorphism after FISH with satellite DNA probes for differentiation of parental origin of homologous chromosome, etc.). We have performed a pilot study to develop a simple technique for quantitative assessment of FISH signals by means of the digital capturing of microscopic images and the intensity measuring of hybridization signals using Scion Image software, commonly used for quantification of electrophoresis gels. We have tested this approach by quantitative analysis of FISH signals after application of chromosome-specific DNA probes for aneuploidy scoring in interphase nuclei in cells of different human tissues. This approach allowed us to exclude or confirm a low-level mosaic form of aneuploidy by quantification of FISH signals (for example, discrimination of pseudo-monosomy and artifact signals due to over-position of hybridization signals). Quantification of FISH signals was also used for analysis of somatic pairing of homologous chromosomes in nuclei of postmortem brain tissues after FISH with "classical" satellite DNA probes for chromosomes 1, 9, and 16. This approach has shown a relatively high efficiency for the quantitative registration of chromosomal heteromorphism due to variations of centromeric alphoid DNA in homologous parental chromosomes. We propose this approach to be efficient and to be considered as a useful tool in addition to visual FISH signal analysis for applied molecular cytogenetic studies.     

Chromosomal abnormalities and the morphology of mouse sperm heads.

In the mouse, numerous mutagens, teratogens and carcinogens have been shown to induce marked elevations in the fraction of sperm with head shape abnormalities. Since carcinogens and teratogens may act by causing genetic damage, a likely explanation of these results is that the sperm abnormalities are also caused by genetic damage. There are two more or less distinct classes of genetic damage, chromosomal aberrations and point mutations. In this paper, we provide evidence, that in general, chromosomal aberrations are not responsible for causing abnormally shaped sperm. Chromosomal aberrations could have caused abnormal sperm morphology in a number of ways. One possibility was that the mere presence of a translocated chromosome within the germ cell led to the malformation of the sperm head. A second possibility was that chromosomal imbalance, i.e., aneuploidy, duplications or deficiencies, within the spermatid or haploid cells caused abnormalities in shape. We tested these hypotheses by measuring the level of abnormally shaped sperm in mice homozygous and heterozygous for 24 various reciprocal and Robertsonian translocations. The diploid cells of these mice are known to be chromosomally balanced, containing translocated chromosomes. A predictable proportion of their gametes are, however, chromosomally unbalanced and carry translocated chromosomes. It was found that the levels of sperm abnormalities in these mice were convincingly unrelated to the levels predicted by any of the above hypotheses. Based on these results it seems that sperm abnormalities in mice are not due to the mere presence of translocated chromosomes in germ cells and also not due to chromosomal aneuploidy or duplication-deficiencies of chromosomal segments in the spermatid during development of the sperm.     

Estimation of Copy Number Alterations from Exome Sequencing Data

Exome sequencing constitutes an important technology for the study of human hereditary diseases and cancer. However, the ability of this approach to identify copy number alterations in primary tumor samples has not been fully addressed. Here we show that somatic copy number alterations can be reliably estimated using exome sequencing data through a strategy that we have termed exome2cnv. Using data from 86 paired normal and primary tumor samples, we identified losses and gains of complete chromosomes or large genomic regions, as well as smaller regions affecting a minimum of one gene. Comparison with high-resolution comparative genomic hybridization (CGH) arrays revealed a high sensitivity and a low number of false positives in the copy number estimation between both approaches. We explore the main factors affecting sensitivity and false positives with real data, and provide a side by side comparison with CGH arrays. Together, these results underscore the utility of exome sequencing to study cancer samples by allowing not only the identification of substitutions and indels, but also the accurate estimation of copy number alterations.     

A Simple Staining Method for the Analysis of Meiotic Metaphase II Divisions in the Male Mouse

During an investigation into the effects of X rays on meiosis in the male mouse (Szemere and Chandley 1975) a staining technique was required that would enable us to make an accurate analysis of dyads² at metaphase II. Not only were we interested in analysing chromosomal aberrations at this stage, but we also wished to identify with confidence the X and Y chromosomes, and to establish accurate counts of dyad numbers. Conventional staining with carbol fuchsin (Can and Walker 1961) provided adequate means for recognizing sex chromosomes, but centromere positions could not be identified and little morphological detail of autosomal dyads could be discerned. Staining by the BSG barium hydroxide/saline/Giemsa technique (Sumner 1972) as modified for use on meiotic cells of the mouse (Chandley and Fletcher 1973) gave excellent staining of centric heterochromatin, but dyad arms were often pale and indistinct. Other centromere staining methods for murine meiotic cells (Hsu, Cooper, Mace and Brinkley 1971, Polani 1972), gave unsatisfactory results in our hands. By combining carbol fuchsin staining with the BSG centromere staining technique, we have been able to produce a simple and quick technique which gives excellent staining of centromeres, easy identification of X and Y chromosomes and good staining of dyad arms at metaphase II. The technique has also been applied successfully to other meiotic stages of the mouse and to human somatic metaphase chromosomes.     

Aneuploidy in stem cells

Stem cells hold enormous promise for regenerative medicine as well as for engineering of model systems to study diseases and develop new drugs. The discovery of protocols that allow for generating induced pluripotent stem cells(IPSCs) from somatic cells has brought this promise steps closer to reality. However,as somatic cells might have accumulated various chromosomal abnormalities,including aneuploidies throughout their lives,the resulting IPSCs might no longer carry the perfect blueprint for the tissue to be generated,or worse,become at risk of adopting a malignant fate. In this review,we discuss the contribution of aneuploidy to healthy tissues and how aneuploidy can lead to disease. Furthermore,we review the differences between how somatic cells and stem cells respond to aneuploidy.     

Diversified chromosomal characteristics in Centropyge fishes (Pomacanthidae, Perciformes)

We studied karyotypes and other chromosomal markers such as C-banded heterochromatin and Ag-stained nucleolus organizer regions (Ag-NORs), in seven Centropyge fishes (Pomacanthidae, Perciformes). These results revealed diversified chromosomal characteristics in Centropyge species. Three species had 2n = 48 chromosomes, whereas four species had 2n = 52 chromosomes. Fundamental numbers showed a large variation from 48 to 82, particularly in the species with 2n = 52 chromosomes. In all the species, Ag-NORs were located in a single chromosome pair and C-bands were mainly distributed in the centromeric regions of most chromosomes, as commonly seen in teleostean fishes. However, these chromosomal markers showed species-specific variations and provided us with useful information that could help us in understanding chromosomal evolution. On the basis of these chromosomal characteristics, we infer the process of chromosomal evolution, which according to us involves an increase in chromosome number from 2n = 48 to 2n = 52 through centric fission or other mechanisms, and in fundamental number through pericentric inversion. In particular, karyotypic evolution involving the increase in chromosome number is an unusual event in the evolution of higher teleostean groups. Handling editor: K. Martens     

Genome sequence comparison between Chinese hamster ovary (CHO) DG44 cells and mouse using end sequences of CHO BAC clones based on BAC-FISH results

Chinese hamster ovary (CHO) cells have frequently been used in biotechnology as a mammalian host cell platform for expressing genes of interest. Previously, we constructed a detailed physical chromosomal map of the CHO DG44 cell line by fluorescence in situ hybridization (FISH) imaging using 303 bacterial artificial chromosome (BAC) clones as hybridization probes (BAC-FISH). BAC-FISH results revealed that the two longest chromosomes were completely paired. However, other chromosomes featured partial deletions or rearrangements. In this study, we determined the end sequences of 303 BAC clones (BAC end sequences), which were used for BAC-FISH probes. Among 606 BAC-end sequences (BESs) (forward and reverse ends), 558 could be determined. We performed a comparison between all determined BESs and mouse genome sequences using NCBI BLAST. Among these 558 BESs, 465 showed high homology to mouse chromosomal sequences. We analyzed the locations of these BACs in chromosomes of the CHO DG44 cell line using a physical chromosomal map. From the obtained results, we investigated the regional similarities among CHO chromosomes (A–T) and mouse chromosomes (1–19 and sex) about 217 BESs (46.7% of 465 high homologous BESs). Twenty-three specific narrow regions in 13 chromosomes of the CHO DG44 cell line showed high homology to mouse chromosomes, but most of other regions did not show significant correlations with the mouse genome. These results contribute to accurate alignments of chromosomes of Chinese hamster and its genome sequence, analysis of chromosomal instability in CHO cells, and the development of target locations for gene and/or genome editing techniques.     

Lack of detectable kinetochores on some chromosomes in mouse x human hybrids.

When treated with an anti-kinetochore antibody present in the sera of scleroderma (var. CREST) patients, most chromosomes exhibit kinetochore dots at the position of the centromere. In this paper we report that some chromosomes in the mouse x human somatic cell hybrid fail to show these dots. In the early passages in a hybrid, HYG-1, the frequency of such chromosomes was higher (0.85%) than in later passages (0.45%) studied after five months of continuous culturing. In parallel, the mean number of human chromosomes in the hybrid also dropped. The somewhat hypodiploid parental cell lines, when similarly treated, showed only a rare chromosome without kinetochore dots. Immunoblots of the proteins showed that the sera used for kinetochore detection recognized all major centromere proteins (CENPs). Electron microscopy of some offlying metaphase chromosomes in another hybrid, HR61, exhibited a lack of trilamellar kinetochores. This study suggests that akinetochoric chromosomes might provide a novel mechanism responsible for chromosome loss and genesis of aneuploidy. In early passages, some cells in the hybrid showed detached kinetochores. These autonomous kinetochores could be seen in clusters and involved some mouse chromosomes also. Potential significance of these autonomous kinetochores in generating compound centromeres is discussed.     

A Simple Staining Method for the Analysis of Meiotic Metaphase II Divisions in the Male Mouse

During an investigation into the effects of X rays on meiosis in the male mouse (Szemere and Chandley 1975) a staining technique was required that would enable us to make an accurate analysis of dyads² at metaphase II. Not only were we interested in analysing chromosomal aberrations at this stage, but we also wished to identify with confidence the X and Y chromosomes, and to establish accurate counts of dyad numbers. Conventional staining with carbol fuchsin (Can and Walker 1961) provided adequate means for recognizing sex chromosomes, but centromere positions could not be identified and little morphological detail of autosomal dyads could be discerned. Staining by the BSG barium hydroxide/saline/Giemsa technique (Sumner 1972) as modified for use on meiotic cells of the mouse (Chandley and Fletcher 1973) gave excellent staining of centric heterochromatin, but dyad arms were often pale and indistinct. Other centromere staining methods for murine meiotic cells (Hsu, Cooper, Mace and Brinkley 1971, Polani 1972), gave unsatisfactory results in our hands. By combining carbol fuchsin staining with the BSG centromere staining technique, we have been able to produce a simple and quick technique which gives excellent staining of centromeres, easy identification of X and Y chromosomes and good staining of dyad arms at metaphase II. The technique has also been applied successfully to other meiotic stages of the mouse and to human somatic metaphase chromosomes.     

A novel system for correcting large-scale chromosomal aberrations: ring chromosome correction via reprogramming into induced pluripotent stem cell (iPSC)

Approximately 1 in 500 newborns are born with chromosomal abnormalities that include trisomies, translocations, large deletions, and duplications. There is currently no therapeutic approach for correcting such chromosomal aberrations in vivo or in vitro. When we attempted to produce induced pluripotent stem cell (iPSC) models from patient-derived fibroblasts that contained ring chromosomes, we found that the ring chromosomes were eliminated and replaced by duplicated normal copies of chromosomes through a mechanism of uniparental isodisomy (Bershteyn et al. 2014, Nature 507:99). The discovery of this previously unforeseen system for aberrant chromosome correction during reprogramming enables us for the first time to model and understand this process of cell-autonomous correction of ring chromosomes during human patient somatic cell reprograming to iPSCs. This knowledge could lead to a potential therapeutic strategy to correct common large-scale chromosomal aberrations, termed “chromosome therapy”.     

Dynamic karyotype,dynamic proteome: buffering the effects of aneuploidy

Despite its ubiquity in cancer, link with other pathologies, and role in promoting adaptive evolution, the effects of aneuploidy or imbalanced chromosomal content on cellular physiology have remained incompletely characterized. Significantly, it appears that the detrimental as well as beneficial effects of aneuploidy are due to the altered gene expression elicited by the aneuploid state. In this review we examine the correlation between chromosome copy number changes and gene expression in aneuploid cells. We discuss the primary effects of aneuploidy on gene expression and describe the cellular response to altered mRNA and protein levels. Moreover, we consider compensatory mechanisms that may ameliorate imbalanced gene expression and restore protein homeostasis in aneuploid cells. Finally, we propose a novel hypothesis to explain the hitherto enigmatic abundance compensation of proteins encoded on supernumerary chromosomes.     

GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays

There is an increasing interest in using single nucleotide polymorphism (SNP) genotyping arrays for profiling chromosomal rearrangements in tumors, as they allow simultaneous detection of copy number and loss of heterozygosity with high resolution. Critical issues such as signal baseline shift due to aneuploidy, normal cell contamination, and the presence of GC content bias have been reported to dramatically alter SNP array signals and complicate accurate identification of aberrations in cancer genomes. To address these issues, we propose a novel Global Parameter Hidden Markov Model (GPHMM) to unravel tangled genotyping data generated from tumor samples. In contrast to other HMM methods, a distinct feature of GPHMM is that the issues mentioned above are quantitatively modeled by global parameters and integrated within the statistical framework. We developed an efficient EM algorithm for parameter estimation. We evaluated performance on three data sets and show that GPHMM can correctly identify chromosomal aberrations in tumor samples containing as few as 10% cancer cells. Furthermore, we demonstrated that the estimation of global parameters in GPHMM provides information about the biological characteristics of tumor samples and the quality of genotyping signal from SNP array experiments, which is helpful for data quality control and outlier detection in cohort studies.     

Applying Microsatellite Multiplex PCR Analysis (MMPA) for Determining Allele Copy-Number Status and Percentage of Normal Cells within Tumors

The study of somatic genetic alterations in tumors contributes to the understanding and management of cancer. Genetic alterations, such us copy number or copy neutral changes, generate allelic imbalances (AIs) that can be determined using polymorphic markers. Here we report the development of a simple set of calculations for analyzing microsatellite multiplex PCR data from control-tumor pairs that allows us to obtain accurate information not only regarding the AI status of tumors, but also the percentage of tumor-infiltrating normal cells, the locus copy-number status and the mechanism involved in AI. We validated this new approach by re-analyzing a set of Neurofibromatosis type 1-associated dermal neurofibromas and comparing newly generated data with results obtained for the same tumors in a previous study using MLPA, Paralog Ratio Analysis and SNP-array techniques.Microsatellite multiplex PCR analysis (MMPA) should be particularly useful for analyzing specific regions of the genome containing tumor suppressor genes and also for determining the percentage of infiltrating normal cells within tumors allowing them to be sorted before they are analyzed by more expensive techniques.     

Whole chromosome aneuploidy: Big mutations drive adaptation by phenotypic leap

Despite its widespread existence, the adaptive role of aneuploidy (the abnormal state of having an unequal number of different chromosomes) has been a subject of debate. Cellular aneuploidy has been associated with enhanced resistance to stress, whereas on the organismal level it is detrimental to multicellular species. Certain aneuploid karyotypes are deleterious for specific environments, but karyotype diversity in a population potentiates adaptive evolution. To reconcile these paradoxical observations, this review distinguishes the role of aneuploidy in cellular versus organismal evolution. Further, it proposes a population genetics perspective to examine the behavior of aneuploidy on a populational versus individual level. By altering the copy number of a significant portion of the genome, aneuploidy introduces large phenotypic leaps that enable small cell populations to explore a wide phenotypic landscape, from which adaptive traits can be selected. The production of chromosome number variation can be further increased by stress- or mutation-induced chromosomal instability, fueling rapid cellular adaptation.     

A new moderately repetitive DNA sequence family of novel organization.

In cloning adenovirus homologous sequences, from a human cosmid library, we identified a moderately repetitive DNA sequence family consisting of tandem arrays of 2.5 kb members. A member was sequenced and several non-adjacent, 15-20 bp G-C rich segments with homology to the left side of adenovirus were discovered. The copy number of 400 members is highly conserved among humans. Southern blots of partial digests of human DNA have verified the tandem array of the sequence family. The chromosomal location was defined by somatic cell genetics and in situ hybridization. Tandem arrays are found only on chromosomes 4 (4q31) and 19 (q13.1-q13.5). Homologous repetitive sequences are found in DNA of other primates but not in cat or mouse. Thus we have identified a new family of moderately repetitive DNA sequences, unique because of its organization in clustered tandem arrays, its length, its chromosomal location, and its lack of homology to other moderately repetitive sequence families.     

A model for genetic complementation controlling the chromosomal abnormalities and loss of heterozygosity formation in cancer

The relationship between the apparently random chromosomal changes found in aneuploidy and the genetic instability driving the progression of cancer is not clear. We report a test of the hypothesis that aneuploid chromosomal abnormalities might be selected to preserve cell-survival genes during loss of heterozygosity (LOH) formations which eliminate tumor suppressor genes. The LOHs and structurally abnormal chromosomes present in the aneuploid LoVo (colon), A549 (lung), SUIT-2 (pancreas), and LN-18 (glioma) cancer cell lines were identified by single nucleotide polymorphisms (SNPs) and Spectral Karyotyping (SKY). The Mann-Whitney U and chi square tests were used to evaluate possible differences in chromosome numbers and abnormalities between the cell lines, with two-tailed P values of <0.01 being considered significant. The cell lines differed significantly in chromosome numbers and frequency of structurally abnormal chromosomes. The SNP analysis revealed that each cell line contained at least a haploid set of somatic chromosomes, consistent with our hypothesis that cell-survival genes are widely scattered throughout the genome. Further, over 90% of the chromosomal abnormalities seemed to be selected, often after LOH formation, for gene-dosage compensation or to provide heterozygosity for specific chromosomal regions. These results suggest that the chromosomal changes of aneuploidy are not random, but may be selected to provide gene-dosage compensation and/or retain functional alleles of cell-survival genes during LOH formation.