Chromothripsis: potential origin in gametogenesis and preimplantation cell divisions. A review

Insights into embryonic chromosomal instability: mechanisms of DNA elimination during mammalian preimplantation development

Mammalian preimplantation embryos often contend with aneuploidy that arose either by the inheritance of meiotic errors from the gametes, or from mitotic mis-segregation events that occurred following fertilization. Regardless of the origin, mis-segregated chromosomes become encapsulated in micronuclei (MN) that are spatially isolated from the main nucleus. Much of our knowledge of MN formation comes from dividing somatic cells during tumorigenesis, but the error-prone cleavage-stage of early embryogenesis is fundamentally different. One unique aspect is that cellular fragmentation (CF), whereby small subcellular bodies pinch off embryonic blastomeres, is frequently observed. CF has been detected in both in vitro and in vivo-derived embryos and likely represents a response to chromosome mis-segregation since it only appears after MN formation. There are multiple fates for MN, including sequestration into CFs, but the molecular mechanism(s) by which this occurs remains unclear. Due to nuclear envelope rupture, the chromosomal material contained within MN and CFs becomes susceptible to double stranded-DNA breaks. Despite this damage, embryos may still progress to the blastocyst stage and exclude chromosome-containing CFs, as well as non-dividing aneuploid blastomeres, from participating in further development. Whether these are attempts to rectify MN formation or eliminate embryos with poor implantation potential is unknown and this review will discuss the potential implications of DNA removal by CF/blastomere exclusion. We will also extrapolate what is known about the intracellular pathways mediating MN formation and rupture in somatic cells to preimplantation embryogenesis and how nuclear budding and DNA release into the cytoplasm may impact overall development.

Breakpoints in complex chromosomal rearrangements correspond to transposase-accessible regions of DNA from mature sperm

Constitutional complex chromosomal rearrangements (CCRs) are rare cytogenetic aberrations arising in the germline via an unknown mechanism. Here we analyzed the breakpoint junctions of microscopically three-way or more complex translocations using comprehensive genomic and epigenomic analyses. All of these translocation junctions showed submicroscopic genomic complexity reminiscent of chromothripsis. The breakpoints were clustered within small genomic domains with junctions showing microhomology or microinsertions. Notably, all of the de novo cases were of paternal origin. The breakpoint distributions corresponded specifically to the ATAC-seq (assay for transposase-accessible chromatin with sequencing) read data peak of mature sperm and not to other chromatin markers or tissues. We propose that DNA breaks in CCRs may develop in an accessible region of densely packaged chromatin during post-meiotic spermiogenesis.

Chromosomal Instability in Genome Evolution: From Cancer to Macroevolution

The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures, and for this purpose use several mechanisms to diversify. Chromosomal instability (CIN) is one of the main mechanisms leading to the creation of genomic heterogeneity by altering the number of chromosomes and changing their structures. In this review, we will discuss the different chromosomal patterns and changes observed in speciation, in evolutional biology as well as during tumor progression. By nature, the human genome shows an induction of diversity during gametogenesis but as well during tumorigenesis that can conclude in drastic changes such as the whole genome doubling to more discrete changes as the complex chromosomal rearrangement chromothripsis. More importantly, changes observed during speciation are strikingly similar to the genomic evolution observed during tumor progression and resistance to therapy. The different origins of CIN will be treated as the importance of double-strand breaks (DSBs) or the consequences of micronuclei. We will also explain the mechanisms behind the controlled DSBs, and recombination of homologous chromosomes observed during meiosis, to explain how errors lead to similar patterns observed during tumorigenesis. Then, we will also list several diseases associated with CIN, resulting in fertility issues, miscarriage, rare genetic diseases, and cancer. Understanding better chromosomal instability as a whole is primordial for the understanding of mechanisms leading to tumor progression.

Chromoanagenesis in the asy1 meiotic mutant of Arabidopsis

Chromoanagenesis is a catastrophic event that involves localized chromosomal shattering and reorganization. In this study, we report a case of chromoanagenesis resulting from defective meiosis in the MEIOTIC ASYNAPTIC MUTANT 1 (asy1) background in Arabidopsis thaliana. We provide a detailed characterization of the genomic structure of this individual with a severely shattered segment of chromosome 1. We identified 260 novel DNA junctions in the affected region, most of which affect gene sequence on 1 or both sides of the junction. Our results confirm that asy1-related defective meiosis is a potential trigger for chromoanagenesis. This is the first example of chromoanagenesis associated with female meiosis and indicates the potential for genome evolution during oogenesis.

PLAIN LANGUAGE SUMMARY

Chromoanagenesis is a complex and catastrophic event that results in severely restructured chromosomes. It has been identified in cancer cells and in some plant samples, after specific triggering events. Here, we identified this kind of genome restructuring in a mutant that exhibits defective meiosis in the model plant system Arabidopsis thaliana.

On the origins and fate of chromosomal abnormalities in human preimplantation embryos: an unsolved riddle

About 8 out of 10 human embryos obtained in vitro harbour chromosomal abnormalities of either meiotic or mitotic origin. Abnormalities of mitotic origin lead to chromosomal mosaicism, a phenomenon which has sparked much debate lately as it confounds results obtained through preimplantation genetic testing for aneuploidy (PGT-A). PGT-A in itself is still highly debated, not only on the modalities of its execution, but also on whether it should be offered to patients at all.

We will focus on post-zygotic chromosomal abnormalities leading to mosaicism. First, we will summarize what is known of the rates of chromosomal abnormalities at different developmental stages. Next, based on the current understanding of the origin and cellular consequences of chromosomal abnormalities, which is largely based on studies on cancer cells and model organisms, we will offer a number of hypotheses on which mechanisms may be at work in early human development. Finally, and very briefly, we will touch upon the impact our current knowledge has on the practice of PGT-A. What is the level of abnormal cells that an embryo can tolerate before it loses its potential for full development? And is blastocyst biopsy as harmless as it seems?

Chromosome Changes in Soma and Germ Line: Heritability and Evolutionary Outcome

The origin and inheritance of chromosome changes provide the essential foundation for natural selection and evolution. The evolutionary fate of chromosome changes depends on the place and time of their emergence and is controlled by checkpoints in mitosis and meiosis. Estimating whether the altered genome can be passed to subsequent generations should be central when we consider a particular genome rearrangement. Through comparative analysis of chromosome rearrangements in soma and germ line, the potential impact of macromutations such as chromothripsis or chromoplexy appears to be fascinating. What happens with chromosomes during the early development, and which alterations lead to mosaicism are other poorly studied but undoubtedly essential issues. The evolutionary impact can be gained most effectively through chromosome rearrangements arising in male meiosis I and in female meiosis II, which are the last divisions following fertilization. The diversity of genome organization has unique features in distinct animals; the chromosome changes, their internal relations, and some factors safeguarding genome maintenance in generations under natural selection were considered for mammals.

Preimplantation genetic testing for aneuploidy (PGT-A)-a single-center experience

PURPOSE

The aim of this study was to determine the prevalence and nature of human embryonic aneuploidy based on the preimplantation genetic testing for aneuploidy (PGT-A), the distribution of aneuploidy across the individual chromosomes, and their relationship to maternal age.

METHODS

This is a retrospective cohort study conducted at a single center. The study includes subjects who opted for PGT-A in their in vitro fertilization (IVF) cycle from 2016 to 2020. PGT-A was performed on 1501 embryos from 488 patients in 535 cycles. PGT-A was performed using NGS-based technique on Ion Torrent PGM (Life Technologies). Analysis was performed to determine the (i) frequency of the aneuploidy, (ii) the chromosome most commonly affected, (iii) relationship between maternal age and the rate of aneuploidy, and (iv) incidence of segmental aneuploidy.

RESULTS

The overall frequency of aneuploidy was observed to be 46.8%. The incidence of aneuploidy rate was ~ 28% at maternal age < 30 years which steadily increased to ~ 67% in women above 40 years. High frequency of aneuploidy was observed in chromosomes 16, 22, 21, and 15. Segmental abnormalities, involving loss or gain of chromosomal fragments, were observed at a frequency of 5.3%, and highest incidence of segmental gain was observed on the q-arm of chromosome 9.

CONCLUSION

The study provides important information regarding the frequency of the aneuploidy in IVF cohort and the most frequent chromosomal abnormality. The study further emphasizes the relationship between maternal age and aneuploidy. This study has important implications which help clinicians and genetic counselors in providing information in patient counseling.

Giant cells: Linking McClintock's heredity to early embryogenesis and tumor origin throughout millennia of evolution on Earth

The "life code" theory postulates that egg cells, which are giant, are the first cells in reproduction and that damaged or aged giant somatic cells are the first cells in tumorigenesis. However, the hereditary basis for giant cells remains undefined. Here I propose that stress-induced genomic reorganization proposed by Nobel Laureate Barbara McClintock may represent the underlying heredity for giant cells, referred to as McClintock's heredity. Increase in cell size may serve as a response to environmental stress via switching proliferative mitosis to intranuclear replication for reproduction. Intranuclear replication activates McClintock's heredity to reset the genome following fertilization for reproduction or restructures the somatic genome for neoplastic transformation via formation of polyploid giant cancer cells (PGCCs). The genome-based McClintock heredity functions together with gene-based Mendel's heredity to regulate the genomic stability at two different stages of life cycle or tumorigenesis. Thus, giant cells link McClintock's heredity to both early embryogenesis and tumor origin. Cycling change in cell size together with ploidy number switch may represent the most fundamental mechanism on how both germ and soma for coping with environmental stresses for the survival across the tree of life which evolved over millions of years on Earth.

Rescuing monopronucleated-derived human blastocysts: a model to study chromosomal topography and fingerprinting

OBJECTIVE

To quantify the percentage of monopronuclear-derived blastocysts (MNBs) that are potentially useful for reproductive purposes using classic and state-of-the-art chromosome analysis approaches, and to study chromosomal distribution in the inner cell mass (ICM) and trophectoderm (TE) for intertissue/intratissue concordance comparison.

DESIGN

Prospective experimental study.

SETTING

Single-center in vitro fertilization clinic and reproductive genetics laboratory.

PATIENT(S)

A total of 1,128 monopronuclear zygotes were obtained between June 2016 and December 2018.

INTERVENTION(S)

MNBs were whole-fixed or biopsied to obtain a portion of ICM and 2 TE portions (TE1 and TE2) and were subsequently analyzed by fluorescence in situ hybridization, new whole-genome sequencing, and fingerprinting by single-nucleotide polymorphism array-based techniques (a-SNP).

MAIN OUTCOME MEASURE(S)

We assessed MNB rate, ploidy rate, and chromosomal constitution by new whole-genome sequencing, and parental composition by comparative a-SNP, performed in a "trio"-format (embryo/parents). The 24-chromosome distribution was compared between the TE and the ICM and within the TE.

RESULT(S)

A total of 18.4% of monopronuclear zygotes progressed to blastocysts; 77.6% of MNBs were diploid; 20% of MNBs were male and euploid, which might be reproductively useful. Seventy-five percent of MNBs were biparental and half of them were euploid, indicating that 40% might be reproductively useful. Intratissue concordance (TE1/TE2) was established for 93.3% and 73.3% for chromosome matching. Intertissue concordance (TE/ICM) was established for 78.8%, but 57.6% for chromosome matching. When segmental aneuploidy was not considered, intratissue concordance and chromosome matching increased to 100% and 80%, respectively, and intertissue concordance and chromosome matching increased to 84.8% and 75.8%, respectively.

CONCLUSION(S)

The a-SNP-trio strategy provides information about ploidy, euploidy, and parental origin in a single biopsy. This approach enabled us to identify 40% of MNBs with reproductive potential, which can have a significant effect in the clinical setting. Additionally, segmental aneuploidy is relevant for mismatched preimplantation genetic testing of aneuploidies, both within and between MNB tissues. Repeat biopsy might clarify whether segmental aneuploidy is a prone genetic character.

Uniparental disomy: Origin, frequency, and clinical significance

Uniparental disomy (UPD) is defined as two copies of a whole chromosome derived from the same parent. There can be multiple mechanisms that lead to UPD; these are reviewed in the context of contemporary views on the mechanism leading to aneuploidy. Recent studies indicate that UPD is rare in an apparently healthy population and also rare in spontaneous abortion tissues. The most common type of UPD is a maternal heterodisomy (both maternal allele sets present). Isodisomy (a duplicated single set of alleles) or segmental loss of heterozygosity is sometimes encountered in SNP-based microarray referrals. Decisions regarding the most appropriate follow-up testing should consider the possibility of consanguinity (that will generally involve multiple regions), an imprinted gene disorder (chromosomes 6, 7, 11, 14, 15, 20), expression of an autosomal recessive disorder, and an occult aneuploid cell line that may be confined to the placenta. Upd(16)mat, per se, does not appear to be associated with an abnormal phenotype. UPD provides an insight into the history of early chromosome segregation error and understanding the rates and fate of these events are of key importance in the provision of fertility management and prenatal healthcare.

Control of LINE-1 Expression Maintains Genome Integrity in Germline and Early Embryo Development

Maintenance of genome integrity in the germline and in preimplantation embryos is crucial for mammalian development. Epigenetic remodeling during primordial germ cell (PGC) and preimplantation embryo development may contribute to genomic instability in these cells, since DNA methylation is an important mechanism to silence retrotransposons. Long interspersed elements 1 (LINE-1 or L1) are the most common autonomous retrotransposons in mammals, corresponding to approximately 17% of the human genome. Retrotransposition events are more frequent in germ cells and in early stages of embryo development compared with somatic cells. It has been shown that L1 activation and expression occurs in germline and is essential for preimplantation development. In this review, we focus on the role of L1 retrotransposon in mouse and human germline and early embryo development and discuss the possible relationship between L1 expression and genomic instability during these stages. Although several studies have addressed L1 expression at different stages of development, the developmental consequences of this expression remain poorly understood. Future research is still needed to highlight the relationship between L1 retrotransposition events and genomic instability during germline and early embryo development.

Telomere aberrations, including telomere loss, doublets, and extreme shortening, are increased in patients with infertility

OBJECTIVE

To test the hypothesis that telomere shortening and/or loss are risk factors for infertility.

DESIGN

Retrospective analysis of the telomere status in patients with infertility using conventional cytogenetic data collected prospectively.

SETTING

Academic centers.

PATIENT(S)

Cytogenetic slides with cultured peripheral lymphocytes from 50 patients undergoing fertility treatment and 150 healthy donors, including 100 donors matched for age.

INTERVENTION(S)

Cytogenetic slides were used to detect chromosomal and telomere aberrations.

MAIN OUTCOME MEASURE(S)

Telomere length and telomere aberrations were analyzed after telomere and centromere staining.

RESULT(S)

The mean telomere length of patients consulting for infertility was significantly less than that of healthy donors of similar age. Moreover, patients with infertility showed significantly more extreme telomere loss and telomere doublet formation than healthy controls. Telomere shortening and/or telomere aberrations were more pronounced in patients with structural chromosomal aberrations. Dicentric chromosomes were identified in 6/13 patients, with constitutional chromosomal aberrations leading to chromosomal instability that correlated with chromosomal end-to-end fusions.

CONCLUSION(S)

Our findings demonstrate the feasibility of analyzing telomere aberrations in addition to chromosomal aberrations, using cytogenetic slides. Telomere attrition and/or dysfunction represent the main common cytogenetic characteristic of patients with infertility, leading to potential implications for fertility assessment. Pending further studies, these techniques that correlate the outcome of assisted reproduction and telomere integrity status may represent a novel and useful diagnostic and/or prognostic tool for medical care in this field.

Established and Novel Mechanisms Leading to de novo Genomic Rearrangements in the Human Germline

During gametogenesis, the human genome can acquire various de novo rearrangements. Most constitutional genomic rearrangements are created through 1 of the 4 well-known mechanisms, i.e., nonallelic homologous recombination, erroneous repair after double-strand DNA breaks, replication errors, and retrotransposition. However, recent studies have identified 2 types of extremely complex rearrangements that cannot be simply explained by these mechanisms. The first type consists of chaotic structural changes in 1 or a few chromosomes that result from “chromoanagenesis (an umbrella term that covers chromothripsis, chromoanasynthesis, and chromoplexy).” The other type is large independent rearrangements in multiple chromosomes indicative of “transient multifocal genomic crisis.” Germline chromoanagenesis (chromothripsis) likely occurs predominantly during spermatogenesis or postzygotic embryogenesis, while multifocal genomic crisis appears to be limited to a specific time window during oogenesis and early embryogenesis or during spermatogenesis. This review article introduces the current understanding of the molecular basis of de novo rearrangements in the germline.

Sperm DNA damage causes genomic instability in early embryonic development

Genomic instability is common in human embryos, but the underlying causes are largely unknown. Here, we examined the consequences of sperm DNA damage on the embryonic genome by single-cell whole-genome sequencing of individual blastomeres from bovine embryos produced with sperm damaged by γ-radiation. Sperm DNA damage primarily leads to fragmentation of the paternal chromosomes followed by random distribution of the chromosomal fragments over the two sister cells in the first cell division. An unexpected secondary effect of sperm DNA damage is the induction of direct unequal cleavages, which include the poorly understood heterogoneic cell divisions. As a result, chaotic mosaicism is common in embryos derived from fertilizations with damaged sperm. The mosaic aneuploidies, uniparental disomies, and de novo structural variation induced by sperm DNA damage may compromise fertility and lead to rare congenital disorders when embryos escape developmental arrest.

Chromoanagenesis: a piece of the macroevolution scenario

Over the last decade, new types of massive and complex chromosomal rearrangements based on the chaotic shattering and restructuring of chromosomes have been identified in cancer cells as well as in patients with congenital diseases and healthy individuals. These unanticipated phenomena are named chromothripsis, chromoanasynthesis and chromoplexy, and are grouped under the term of chromoanagenesis. As mechanisms for rapid and profound genome modifications in germlines and early development, these processes can be regarded as credible pathways for genomic evolution and speciation process. Their discovery confirms the importance of genome-centric investigations to fully understand organismal evolution.

Because they oppose the model of progressive acquisition of driver mutations or rearrangements, these phenomena conceptually give support to the concept of macroevolution, known through the models of “Hopeful Monsters” and the “Punctuated Equilibrium”. In this review, we summarize mechanisms underlying chromoanagenesis processes and we show that numerous cases of chromosomal speciation and short-term adaptation could be correlated to chromoanagenesis-related mechanisms.

In the frame of a modern and integrative analysis of eukaryote evolutionary processes, it seems important to consider the unexpected chromoanagenesis phenomena.

Segmental aneuploidy in human blastocysts: a qualitative and quantitative overview

BACKGROUND

Microarray-based and next generation sequencing (NGS) technologies have revealed that segmental aneuploidy is frequently present in human oocytes, cleavage-stage embryos and blastocysts. However, very little research has analyzed the type, size, chromosomal distribution and topography of the chromosomal segments at the different stages of development.

METHODS

This is a retrospective study of 822 PGT-A (preimplantation genetic test for aneuploidies) performed on trophectoderm samples from 3565 blastocysts biopsied between January 2016 and April 2017. The cycles in question had been initiated for varying clinical indications. Samples were analyzed by next generation sequencing-based technology. Segmental aneuploidies were evaluated when fragment size was > 5 Mb. Blastocysts presenting a single segmental aneuploidy (SSA), without any additional whole-chromosome gain/loss, were statistically analyzed for incidence, type, size and chromosomal emplacement. Segment sizes relative to the whole chromosome or arm (chromosome- and arm-ratios) were also studied.

RESULTS

8.4% (299/3565) of blastocysts exhibited segmental aneuploidy for one or more chromosomes, some of which were associated with whole-chromosome aneuploidy while others were not. Nearly half of them (4.5%: 159/3565 of blastocysts) exhibited pure-SSA, meaning that a single chromosome was affected by a SSA. Segments were more frequent in medium-sized metacentric or submetacentric chromosomes and particularly in q-chrmosome arms, variables that were related to trophectoderm quality. SSA size was related to a greater extent to chromosome number and the arm affected than it was to SSA type. In absolute values (Mb), SSA size was larger in large chromosomes. However, the SSA:chromosome ratio was constant across all chromosomes and never exceeded 50% of the chromosome.

CONCLUSIONS

SSA frequency is chromosome- and topographically dependent, and its incidence is not related to clinical or embryological factors, but rather to trophectoderm quality. SSA might be originated by chromosome instability in response to chromothripsis, bias introduced by the biopsy and/or iatrogenic effects.

TRIAL REGISTRATION

Retrospectively registered.

Transient multifocal genomic crisis creating chromothriptic and non-chromothriptic rearrangements in prezygotic testicular germ cells

Background

The co-occurrence of multiple de novo copy number variations (CNVs) is a rare phenomenon in the human genome. Recently, an “organismal CNV mutator phenotype” has been reported to result in transient genomic instability introducing multiple de novo CNVs in primary oocytes and early-stage zygotes. These findings opened a new area of human genome research.

Methods

We performed genome-wide copy number analysis for ~ 2100 individuals with various congenital defects. Furthermore, extensive molecular analyses, including synthetic long-read whole-genome sequencing and haplotype-phasing, were carried out for an individual with multiple de novo CNVs.

Results

A boy was found to have de novo rearrangements on five chromosomes. The rearrangements comprised simple duplication and inversion as well as chaotic changes, all of which affected paternally derived chromosomes. Postzygotic genomic instability was ruled out. The duplicated regions on 6q and 13q contained both diallelic and triallelic loci, indicating that the genomic rearrangements were initially created during premeiotic mitosis and subsequently modified by physiological cross-over during meiosis I. Breakpoints of the rearrangements were indicative of non-homologous end joining, replication-based errors, and/or chromothripsis. The mutagenic event was independent of specific local DNA motifs or de novo point mutations, but may be driven by spermatogenesis-specific factors.

Conclusions

These results indicate that during spermatogenesis, a transient multifocal genomic crisis can introduce several chromothriptic and non-chromothriptic changes into the genome. These findings broaden the concept of the “organismal CNV mutator phenotype”. This study provides insights into mechanisms for altering the global chromosomal architecture of human embryos.

Electronic supplementary material

The online version of this article (10.1186/s12920-019-0526-3) contains supplementary material, which is available to authorized users.

Inheritance of imbalances in recurrent chromosomal translocation t(11;22): clarification by PGT-SR and sperm-FISH analysis

RESEARCH QUESTION

To analyse why unbalanced viable offspring are derived mainly from the 3:1 segregation mode in t(11;22)(q23;q11.2) reciprocal translocation.

DESIGN

Retrospective analysis of 24 pre-implantation genetic testing for chromosomal structural re-arrangements (PGT-SR) cycles was performed on seven male and five female carriers of t(11;22) translocation. Sperm analysis was performed on each male carrier. These patients were directed to the study centre after several years of miscarriages and/or abortions, primary infertility for male carriers or birth of an affected child.

RESULTS

Twenty-four PGT-SR cycles were performed to exclude imbalances in both male and female carriers. The unbalanced embryos derived from the adjacent-1 segregation mode were the most represented in both male and female carriers (68.4% and 50%, respectively). These results were positively related with meiotic segregation analysis of reciprocal translocation in spermatozoa. A thorough analysis of the unbalanced embryo karyotypes determined that the expected viable +der22 karyotype resulting from 3:1 malsegregation was less represented at 5.3%.

CONCLUSIONS

These findings highlight the divergence that may exist between meiotic segregation and post-zygotic selection. Post-zygotic selection would be responsible for the elimination of unbalanced embryos derived from the adjacent-1 segregation mode. The combined action of several factors occurs at the beginning of post-zygotic selection. Genetic counselling must consider the risk of a birth related to the adjacent-1 segregation mode, irrespective of the sex of the translocation carrier. These results will allow deeper understanding of the PGT results of t(11;22) carriers, which often include a high number of aneuploid embryos.

Chromoanasynthesis: another way for the formation of complex chromosomal abnormalities in human reproduction

Chromoanasynthesis has been described as a novel cause of massive constitutional chromosomal rearrangements. Based on DNA replication machinery defects, chromoanasynthesis is characterized by the presence of chromosomal duplications and triplications locally clustered on one single chromosome, or a few chromosomes, associated with various other types of structural rearrangements. Two distinct mechanisms have been described for the formation of these chaotic genomic disorders, i.e. the fork stalling and template switching and the microhomology-mediated break-induced replication. Micronucleus-based processes have been evidenced as a causative mechanism, thus, highlighting the close connection between segregation errors and structural rearrangements. Accumulating data indicate that chromoanasynthesis is operating in human germline cells and during early embryonic development. The development of new tools for quantifying chromoanasynthesis events should provide further insight into the impact of this catastrophic cellular phenomenon in human reproduction.

On the Complexity of Mechanisms and Consequences of Chromothripsis: An Update

In the present review, we focus on the phenomenon of chromothripsis, a new type of complex chromosomal rearrangements. We discuss the challenges of chromothripsis detection and its distinction from other chromoanagenesis events. Along with already known causes and mechanisms, we introduce aberrant epigenetic regulation as a possible pathway to chromothripsis. We address the issue of chromothripsis characteristics in cancers and benign tumours, as well as chromothripsis inheritance in cases of its occurrence in germ cells, zygotes and early embryos. Summarising the presented data on different phenotypic effect of chromothripsis, we assume that its consequences are most likely determined not by the chromosome shattering and reassembly themselves, but by the genome regions involved in the rearrangement.

Ten new cases of Balanced Reciprocal Translocation Mosaicism (BRTM): Reproductive implications, frequency and mechanism

Chromosomal anomalies are well known to be an important cause of infertility, sterility and pregnancy loss. Balanced Reciprocal Translocation Mosaicism (BRTM) is an extremely rare phenomenon, mainly observed in subjects with a normal phenotype accompanied by reproductive failure. To date the mechanism of origin and the incidence of BRTM are poorly defined. Here we describe 10 new cases of BRTM. In 9 cases chromosome analysis revealed the presence of two different cell lines, one with a normal karyotype and the second with an apparently balanced reciprocal translocation. In the remaining case, both cell lines showed two different, but apparently balanced, reciprocal translocations. We document the clinical implications of BRTM, discuss its frequency in our referred population and suggest that carrier individuals might be more frequent than expected.

Double-stranded sperm DNA damage is a cause of delay in embryo development and can impair implantation rates

OBJECTIVE

To analyze the effect of single- and double-stranded sperm DNA fragmentation (ssSDF and dsSDF) on human embryo kinetics monitored under a time-lapse system.

DESIGN

Observational, double blind, prospective cohort study.

SETTING

University spin-off and private center.

PATIENT(S)

One hundred ninety-six embryos from 43 infertile couples were included prospectively.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

SsSDF and dsSDF were analyzed in the same semen sample used for intracytoplasmic sperm injection. Embryo kinetics was then monitored using time-lapse technology, and the timing of each embryo division was obtained.

RESULT(S)

When comparing embryos obtained from semen samples with low dsSDF and high dsSDF, splitting data using a statistically significant delay in high dsSDF was observed in second polar body extrusion, T4, T8, morula, and starting blastocyst and embryo implantation rates were impaired. Embryo kinetics and implantation rates are not significantly affected when high values of ssSDF are present. Different patterns of delay in embryo kinetics were observed for these different types of DNA damage: dsSDF caused a delay along all stages of embryo development; however, its major effect was observed at the second polar body extrusion and morula stages, coinciding with embryo DNA damage checkpoint activation as described before; ssSDF had its major effect at the pronucleus stage, but embryo kinetics was then restored at all following stages. The results show that dsSDF could be the main type of DNA damage that affects embryo development in intracytoplasmic sperm injection cycles, probably due to motility-based sperm selection in this assisted reproduction procedure.

CONCLUSION(S)

Double-stranded sperm DNA damage caused a delay in embryo development and impaired implantation, while single-stranded DNA damage did not significantly affect embryo kinetics and implantation.

Potential Role of Chromothripsis in the Genesis of Complex Chromosomal Rearrangements in Human Gametes and Preimplantation Embryo

The discovery of a new class of massive chromosomal rearrangement, baptized chromothripsis, in different cancers and congenital disorders has deeply modified our understanding on the genesis of complex genomic rearrangements. Several mechanisms, involving abortive apoptosis, telomere erosion, mitotic errors, micronuclei formation, and p53 inactivation, might cause chromothripsis. The remarkable point is that all these plausible mechanisms have been identified in the field of human reproduction as causal factors for reproductive failures and chromosomal abnormality genesis. Specific features of gametogenesis and early embryonic development may contribute to the emergence of chromothripsis. Multiple lines of evidence support the assumption that chromothripsis may arise more frequently than previously thought in both gametogenesis and early human embryogenesis.

Chromoanagenesis: cataclysms behind complex chromosomal rearrangements

Background

During the last decade, genome sequencing projects in cancer genomes as well as in patients with congenital diseases and healthy individuals have led to the identification of new types of massive chromosomal rearrangements arising during single chaotic cellular events. These unanticipated catastrophic phenomenon are termed chromothripsis, chromoanasynthesis and chromoplexis., and are grouped under the name of “chromoanagenesis”.

Results

For each process, several specific features have been described, allowing each phenomenon to be distinguished from each other and to understand its mechanism of formation and to better understand its aetiology. Thus, chromothripsis derives from chromosome shattering followed by the random restitching of chromosomal fragments with low copy-number change whereas chromoanasynthesis results from erroneous DNA replication of a chromosome through serial fork stalling and template switching with variable copy-number gains, and chromoplexy refers to the occurrence of multiple inter-and intra-chromosomal translocations and deletions with little or no copy-number alterations in prostate cancer. Cumulating data and experimental models have shown that chromothripsis and chromoanasynthesis may essentially result from lagging chromosome encapsulated in micronuclei or telomere attrition and end-to-end telomere fusion.

Conclusion

The concept of chromanagenesis has provided new insight into the aetiology of complex structural rearrangements, the connection between defective cell cycle progression and genomic instability, and the complexity of cancer evolution. Increasing reported chromoanagenesis events suggest that these chaotic mechanisms are probably much more frequent than anticipated.

Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion

Aneuploidy that arises during meiosis and/or mitosis is a major contributor to early embryo loss. We previously showed that human preimplantation embryos encapsulate missegregated chromosomes into micronuclei while undergoing cellular fragmentation and that fragments can contain chromosomal material, but the source of this DNA was unknown. Here, we leveraged the use of a nonhuman primate model and single-cell DNA-sequencing (scDNA-seq) to examine the chromosomal content of 471 individual samples comprising 254 blastomeres, 42 polar bodies, and 175 cellular fragments from a large number (N = 50) of disassembled rhesus cleavage-stage embryos. Our analysis revealed that the aneuploidy and micronucleation frequency is conserved between humans and macaques, and that fragments encapsulate whole and/or partial chromosomes lost from blastomeres. Single-cell/fragment genotyping showed that these chromosome-containing cellular fragments (CCFs) can be maternally or paternally derived and display double-stranded DNA breaks. DNA breakage was further indicated by reciprocal subchromosomal losses/gains between blastomeres and large segmental errors primarily detected at the terminal ends of chromosomes. By combining time-lapse imaging with scDNA-seq, we determined that multipolar divisions at the zygote or two-cell stage were associated with CCFs and generated a random mixture of chromosomally normal and abnormal blastomeres with uniparental or biparental origins. Despite frequent chromosome missegregation at the cleavage-stage, we show that CCFs and nondividing aneuploid blastomeres showing extensive DNA damage are prevented from incorporation into blastocysts. These findings suggest that embryos respond to chromosomal errors by encapsulation into micronuclei, elimination via cellular fragmentation, and selection against highly aneuploid blastomeres to overcome chromosome instability during preimplantation development.

The molecular origins and pathophysiological consequences of micronuclei: New insights into an age-old problem

Micronuclei (MN), the small nucleus-like bodies separated from the primary nucleus, can exist in cells with numerical and/or structural chromosomal aberrations in apparently normal tissues and more so in tumors in humans. While MN have been observed for over 100 years, they were merely and constantly considered as passive indicators of chromosome instability (CIN) for a long time. Relatively little is known about the molecular origins and biological consequences of MN. Rapid technological advances are helping to close these gaps. Very recent studies provide exciting evidence that MN act as key platform for chromothripsis and a trigger of innate immune response, suggesting that MN could affect cellular functions by both genetic and nongenetic means. These previously unappreciated findings have reawakened widespread interests in MN. In this review, the diverse mechanisms leading to MN generation and the complex fate profiles of MN are discussed, together with the evidence for their contribution to CIN, inflammation, senescence and cell death. Moreover, we put this knowledge together into a speculative perspective on how MN may be responsible for cancer development and how their presence may influence the choice of treatment. We suggest that the heterogeneous responses to MN may function physiological to ensure the arrestment, elimination and immune clearance of damaged cells, but pathologically, may enable the survival and oncogenic transformation of cells bearing CIN. These insights not only underscore the complexity of MN biology, but also raise a host of new questions and provide fertile ground for future research.

Stable transmission of an unbalanced chromosome 21 derived from chromoanasynthesis in a patient with a SYNGAP1 likely pathogenic variant

Background

Complex genomic structural variations, involving chromoanagenesis, have been implicated in multiple congenital anomalies and abnormal neurodevelopment. Familial inheritance of complex chromosomal structural alteration resulting from germline chromoanagenesis-type mechanisms are limited.

Case presentation

We report a two-year eleven-month old male presenting with epilepsy, ataxia and dysmorphic features of unknown etiology. Chromosomal microarray identified a complex unbalanced rearrangement involving chromosome 21. G-banding and FISH for targeted regions of chromosome 21 revealed that the copy number imbalances were limited to gains dispersed throughout the long arm of chromosome 21, characteristic of a chromosome derived from chromoanagenesis. Family studies showed that the unbalanced chromosome had been stably inherited, as it was present in both his healthy mother and maternal grandfather. Further molecular testing for non-syndromic intellectual disability genes found a likely pathogenic mutation in SYNGAP1 (NM_006772.2:c.3722_3723del).

Conclusions

This study indicates that complex rearrangements involving an unbalanced chromosome derived from chromoanasynthesis can be familial and should be not be presumed pathogenic.

The dualistic origin of human tumors

Life starts with a zygote, which is formed by the fusion of a haploid sperm and egg. The formation of a blastomere by cleavage division (nuclear division without an increase in cell size) is the first step in embryogenesis, after the formation of the zygote. Blastomeres are responsible for reprogramming the parental genome as a new embryonic genome for generation of the pluripotent stem cells which then differentiate by Waddington's epigenetic landscape to create a new life. Multiple authors over the past 150 years have proposed that tumors arises from development gone awry at a point within Waddington's landscape. Recent discoveries showing that differentiated somatic cells can be reprogrammed into induced pluripotent stem cells, and that somatic cell nuclear transfer can be used to successfully clone animals, have fundamentally reshaped our understanding of tumor development and origin. Differentiated somatic cells are plastic and can be induced to dedifferentiate into pluripotent stem cells. Here, I review the evidence that suggests somatic cells may have a previously overlooked endogenous embryonic program that can be activated to dedifferentiate somatic cells into stem cells of various potencies for tumor initiation. Polyploid giant cancer cells (PGCCs) have long been observed in cancer and were thought originally to be nondividing. Contrary to this belief, recent findings show that stress-induced PGCCs divide by endoreplication, which may recapitulate the pattern of cleavage-like division in blastomeres and lead to dedifferentiation of somatic cells by a programmed process known as "the giant cell cycle", which comprise four distinct but overlapping phases: initiation, self-renewal, termination and stability. Depending on the intensity and type of stress, different levels of dedifferentiation result in the formation of tumors of different grades of malignancy. Based on these results, I propose a unified dualistic model to demonstrate the origin of human tumors. The tenet of this model includes four points, as follows. 1. Tumors originate from a stem cell at a specific developmental hierarchy, which can be achieved by dualistic origin: dedifferentiation of the zygote formed by two haploid gametes (sexual reproduction) via the blastomere during normal development, or transformation from damaged or aged mature somatic cells via a blastomere-like embryonic program (asexual reproduction). 2. Initiation of the tumor begins with a stem cell that has uncoupled the differentiation from the proliferation program which results in stem cell maturation arrest. 3. The developmental hierarchy at which stem cells arrest determines the degree of malignancy: the more primitive the level at which stem cells arrest, the greater the likelihood of the tumor being malignant. 4. Environmental factors and intrinsic genetic or epigenetic alterations represent the risk factors or stressors that facilitate stem cell arrest and somatic cell dedifferentiation. However, they, per se, are not the driving force of tumorigenesis. Thus, the birth of a tumor can be viewed as a triad that originates from a stem cell via dedifferentiation through a blastomere or blastomere-like program, which then differentiates along Waddington's landscape, and arrests at a developmental hierarchy. Blocking the PGCC-mediated dedifferentiation process and inducing their differentiation may represent a novel alternative approach to eliminate the tumor occurrence and therapeutic resistance.

A Postgenomic Perspective on Molecular Cytogenetics

BACKGROUND

The postgenomic era is featured by massive data collection and analyses from various large scale-omics studies. Despite the promising capability of systems biology and bioinformatics to handle large data sets, data interpretation, especially the translation of -omics data into clinical implications, has been challenging.

DISCUSSION

In this perspective, some important conceptual and technological limitations of current systems biology are discussed in the context of the ultimate importance of the genome beyond the collection of all genes. Following a brief summary of the contributions of molecular cytogenetics/cytogenomics in the pre- and post-genomic eras, new challenges for postgenomic research are discussed. Such discussion leads to a call to search for a new conceptual framework and holistic methodologies.

CONCLUSION

Throughout this synthesis, the genome theory of somatic cell evolution is highlighted in contrast to gene theory, which ignores the karyotype-mediated higher level of genetic information. Since "system inheritance" is defined by the genome context (gene content and genomic topology) while "parts inheritance" is defined by genes/epigenes, molecular cytogenetics and cytogenomics (which directly study genome structure, function, alteration and evolution) will play important roles in this postgenomic era.

Experimental Induction of Genome Chaos

Genome chaos, or karyotype chaos, represents a powerful survival strategy for somatic cells under high levels of stress/selection. Since the genome context, not the gene content, encodes the genomic blueprint of the cell, stress-induced rapid and massive reorganization of genome topology functions as a very important mechanism for genome (karyotype) evolution. In recent years, the phenomenon of genome chaos has been confirmed by various sequencing efforts, and many different terms have been coined to describe different subtypes of the chaotic genome including "chromothripsis," "chromoplexy," and "structural mutations." To advance this exciting field, we need an effective experimental system to induce and characterize the karyotype reorganization process. In this chapter, an experimental protocol to induce chaotic genomes is described, following a brief discussion of the mechanism and implication of genome chaos in cancer evolution.

Genes, Proteins, and Biological Pathways Preventing Chromothripsis

The highly complex structural genome variations chromothripsis, chromoanasynthesis, and chromoplexy are subsumed under the term chromoanagenesis, which means chromosome rebirth. Precipitated by numerous DNA double-strand breaks, they differ in number of and distances between breakpoints, associated copy number variations, order and orientation of segments, and flanking sequences at joining points. Results from patients with the autosomal dominant cancer susceptibility disorder Li-Fraumeni syndrome implicated somatic TP53 mutations in chromothripsis. TP53 participates in the G2/M phase checkpoint, halting cell cycling after premature chromosome compaction during the second half of the S phase, thus preventing chromosome shattering. By experimental TP53 ablation and micronucleus induction, one or a few isolated chromosomes underwent desynchronized replication and chromothripsis. Secondly, chromothripsis occurred after experimental induction of telomere crisis after which dicentric chromosomes sustained TREX1-mediated resolution of chromosome bridges and kataegis. Third, DNA polymerase Polθ-dependent chromothripsis has been documented. Finally, a family with chromothripsis after L1 element-dependent retrotransposition and Alu/Alu homologous recombination has been reported. Human chromosomal instability syndromes share defects in responses to DNA double-strand breaks, characteristic cell cycle perturbations, elevated rates of micronucleus formation, premature chromosome compaction, and apoptosis. They are also associated with elevated susceptibility to malignant disease, such as medulloblastomas and gliomas in ataxia-telangiectasia, leukemia and lymphoma in Bloom syndrome, and osteosarcoma and soft tissue sarcoma in Werner syndrome. The latter syndrome is characterized by a premature aging-like progressive decline of mesenchymal tissues. In all thus far studied cases, constitutional chromothripsis occurred in the male germline and male patients with defects in the double-strand break response genes ATM, MRE11, BLM, LIG4, WRN, and Ku70 show impaired fertility. Conceivably, chromothripsis may, in a stochastic rather than deterministic way, be implicated in germline structural variation, malignant disease, premature aging, genome mosaicism in somatic tissues, and male infertility.

Detection of Chromothripsis in Plants

Chromothripsis, or chromosome shattering, occurs after chromosomes missegregate, are pulverized and subsequently repaired erroneously, leading to highly complex structural rearrangements. In plants, chromothripsis has been observed as a result of mitotic malfunction connected with the incomplete loss of haploid inducer chromosomes during uniparental genome elimination. Uniparental genome elimination, a process that results in haploid induction, is a phenomenon that typically results in the loss of an entire parental chromosome set in early embryos, resulting in haploid plants. In Arabidopsis thaliana, genome elimination can be achieved via the manipulation of the centromere-specific histone H3 variant, CENH3. Genomic characterization of F1 progeny resulting from CENH3-mediated genome elimination crosses in Arabidopsis revealed haploids (~39%), diploids (~25%), and aneuploids (~37%). Within the aneuploid class, ~11% show evidence for chromothripsis. Here, we present a protocol to identify Arabidopsis aneuploids that have inherited chromothriptic chromosomes during genome elimination crosses and describe in detail how to perform in silico reconstructions for individuals with chromothripsis using the somatic mutation finder (SMuFin) tool.

Clinical Consequences of Chromothripsis and Other Catastrophic Cellular Events

Chromothripsis was initially described as a novel cause of chromosomal rearrangements in cancer cells and was subsequently implicated in the development of gross chromosomal rearrangements in the germline. Other catastrophic cellular events such as chromoanasynthesis and chromoplexy have also been observed in human cells. Such events have been associated with various phenotypes including mental retardation and congenital malformations. Here, we introduce representative cases of human disorders arising from somatic or germline chromothripsis or similar catastrophic events. In this chapter, we use the term "chromoanagenesis" to indicate all catastrophic events including chromothripsis.

Time-Lapse Imaging for the Detection of Chromosomal Abnormalities in Primate Preimplantation Embryos

The use of time-lapse microscopic imaging has proven to be a powerful tool for the study of mitotic divisions and other cellular processes across diverse species and cell types. Although time-lapse monitoring (TLM) of human preimplantation development was first introduced to the in vitro fertilization (IVF) community several decades ago, it was not until relatively recently that TLM systems were commercialized for clinical embryology purposes. Traditionally, human IVF embryos are assessed by successful progression and morphology under a stereomicroscope at distinct time points prior to selection for transfer. Due to the high frequency of aneuploidy, embryos may also be biopsied at the cleavage or blastocyst stage for preimplantation genetic screening (PGS) of whole and/or partial chromosomal abnormalities. However, embryo biopsy is invasive and can hinder subsequent development, and there are additional concerns over chromosomal mosaicism and resolution with PGS. Moreover, embryos are typically outside of the incubator in suboptimal culture conditions for extended periods of time during these procedures. With TLM systems, embryos remain in the stable microenvironment of an incubator and are simultaneously imaged for noninvasive embryo evaluation using a fraction of the light exposure as compared to a stereomicroscope. Each image is then compiled into a time-lapse movie, the information from which can be extrapolated to correlate morphological, spatial, and temporal parameters with embryo quality and copy number status. Here, we describe the various TLM systems available for clinical and/or research use in detail and provide step-by-step instructions on how the measurement of specific timing intervals and certain morphological criteria can be implemented into IVF protocols to enhance embryo assessment and avoid the selection of aneuploid embryos. We also discuss the biological significance of processes unique to mitotically dividing embryos and the likelihood that complex chromosomal events such as chromothripsis occur during preimplantation development in humans and other mammals, particularly nonhuman primates.

Living Organisms Author Their Read-Write Genomes in Evolution

Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome

Background

Structural variation (SV) influences genome organization and contributes to human disease. However, the complete mutational spectrum of SV has not been routinely captured in disease association studies.

Results

We sequenced 689 participants with autism spectrum disorder (ASD) and other developmental abnormalities to construct a genome-wide map of large SV. Using long-insert jumping libraries at 105X mean physical coverage and linked-read whole-genome sequencing from 10X Genomics, we document seven major SV classes at ~5 kb SV resolution. Our results encompass 11,735 distinct large SV sites, 38.1% of which are novel and 16.8% of which are balanced or complex. We characterize 16 recurrent subclasses of complex SV (cxSV), revealing that: (1) cxSV are larger and rarer than canonical SV; (2) each genome harbors 14 large cxSV on average; (3) 84.4% of large cxSVs involve inversion; and (4) most large cxSV (93.8%) have not been delineated in previous studies. Rare SVs are more likely to disrupt coding and regulatory non-coding loci, particularly when truncating constrained and disease-associated genes. We also identify multiple cases of catastrophic chromosomal rearrangements known as chromoanagenesis, including somatic chromoanasynthesis, and extreme balanced germline chromothripsis events involving up to 65 breakpoints and 60.6 Mb across four chromosomes, further defining rare categories of extreme cxSV.

Conclusions

These data provide a foundational map of large SV in the morbid human genome and demonstrate a previously underappreciated abundance and diversity of cxSV that should be considered in genomic studies of human disease.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1158-6) contains supplementary material, which is available to authorized users.

Catastrophic cellular events leading to complex chromosomal rearrangements in the germline

Although complex chromosomal rearrangements were thought to reflect the accumulation of DNA damage over time, recent studies have shown that such rearrangements frequently arise from 'all-at-once' catastrophic cellular events. These events, designated chromothripsis, chromoanasynthesis, and chromoanagenesis, were first documented in the cancer genome and subsequently observed in the germline. These events likely result from micronucleus-mediated chromosomal shattering and subsequent random reassembly of DNA fragments, although several other mechanisms have also been proposed. Typically, only one or a few chromosomes of paternal origin are affected per event. These events can produce intrachromosomal deletions, duplications, inversions, and translocations, as well as interchromosomal translocations. Germline complex rearrangements of autosomes often result in developmental delay and dysmorphic features, whereas X chromosomal rearrangements are usually associated with relatively mild clinical manifestations. The concept of these catastrophic events provides novel insights into the etiology of human genomic disorders. This review introduces the molecular characteristics and phenotypic outcomes of catastrophic cellular events in the germline.

Heterogeneity of a Constitutional Complex Chromosomal Rearrangement in 2q

Complex chromosome rearrangements (CCRs) are unusual structural chromosome alterations found in humans, and to date only a few have been characterized molecularly. New mechanisms, such as chromothripsis, have been proposed to explain the presence of the CCRs in cancer cells and in patients with congenital disorders and/or mental retardation. The aim of the present study was the molecular characterization of a constitutional CCR in a girl with multiple congenital disorders and intellectual disability in order to determine the genotype-phenotype relation and to clarify whether the CCR could have been caused by chromosomal catastrophic events. The present CCR was characterized by G-banding, high-resolution CGH, multiplex ligation-dependent probe amplification and subtelomeric 2q-FISH analyses. Preliminary results indicate that the de novo CCR is unbalanced showing a 2q37.3 deletion and 2q34q37.2 partial trisomy. Our patient shows some of the typical traits and intellectual disability described in patients with 2q37 deletion and also in carriers of 2q34q37.2 partial trisomy; thus, the clinical disorders could be explained by additional effects of both chromosome alterations (deletions and duplications). A posterior, sequential FISH study using BAC probes revealed the unexpected presence of at least 17 different reorganizations affecting 2q34q37.2, suggesting the existence of chromosome instability in this region. The present CCR is the first case described in the literature of heterogeneity of unbalanced CCRs affecting a small region of 2q, indicating that the mechanisms involved in constitutional chromosome rearrangement may be more complex than previously thought.

Mapping Breakpoints of Complex Chromosome Rearrangements Involving a Partial Trisomy 15q23.1-q26.2 Revealed by Next Generation Sequencing and Conventional Techniques

Complex chromosome rearrangements (CCRs), which are rather rare in the whole population, may be associated with aberrant phenotypes. Next-generation sequencing (NGS) and conventional techniques, could be used to reveal specific CCRs for better genetic counseling. We report the CCRs of a girl and her mother, which were identified using a combination of NGS and conventional techniques including G-banding, fluorescence in situ hybridization (FISH) and PCR. The girl demonstrated CCRs involving chromosomes 3 and 8, while the CCRs of her mother involved chromosomes 3, 5, 8, 11 and 15. HumanCytoSNP-12 Chip analysis identified a 35.4 Mb duplication on chromosome 15q21.3-q26.2 in the proband and a 1.6 Mb microdeletion at chromosome 15q21.3 in her mother. The proband inherited the rearranged chromosomes 3 and 8 from her mother, and the duplicated region on chromosome 15 of the proband was inherited from the mother. Approximately one hundred genes were identified in the 15q21.3-q26.2 duplicated region of the proband. In particular, TPM1, SMAD6, SMAD3, and HCN4 may be associated with her heart defects, and HEXA, KIF7, and IDH2 are responsible for her developmental and mental retardation. In addition, we suggest that a microdeletion on the 15q21.3 region of the mother, which involved TCF2, TCF12, ADMA10 and AQP9, might be associated with mental retardation. We delineate the precise structures of the derivative chromosomes, chromosome duplication origin and possible molecular mechanisms for aberrant phenotypes by combining NGS data with conventional techniques.

Chromosomal instability in mammalian pre-implantation embryos: potential causes, detection methods, and clinical consequences

Formation of a totipotent blastocyst capable of implantation is one of the first major milestones in early mammalian embryogenesis, but less than half of in vitro fertilized embryos from most mammals will progress to this stage of development. Whole chromosomal abnormalities, or aneuploidy, are key determinants of whether human embryos will arrest or reach the blastocyst stage. Depending on the type of chromosomal abnormality, however, certain embryos still form blastocysts and may be morphologically indistinguishable from chromosomally normal embryos. Despite the implementation of pre-implantation genetic screening and other advanced in vitro fertilization (IVF) techniques, the identification of aneuploid embryos remains complicated by high rates of mosaicism, atypical cell division, cellular fragmentation, sub-chromosomal instability, and micro-/multi-nucleation. Moreover, several of these processes occur in vivo following natural human conception, suggesting that they are not simply a consequence of culture conditions. Recent technological achievements in genetic, epigenetic, chromosomal, and non-invasive imaging have provided additional embryo assessment approaches, particularly at the single-cell level, and clinical trials investigating their efficacy are continuing to emerge. In this review, we summarize the potential mechanisms by which aneuploidy may arise, the various detection methods, and the technical advances (such as time-lapse imaging, "-omic" profiling, and next-generation sequencing) that have assisted in obtaining this data. We also discuss the possibility of aneuploidy resolution in embryos via various corrective mechanisms, including multi-polar divisions, fragment resorption, endoreduplication, and blastomere exclusion, and conclude by examining the potential implications of these findings for IVF success and human fecundity.

Mammalian pre-implantation chromosomal instability: species comparison, evolutionary considerations, and pathological correlations

Pre-implantation embryo development in mammals begins at fertilization with the migration and fusion of the maternal and paternal pro-nuclei, followed by the degradation of inherited factors involved in germ cell specification and the activation of embryonic genes required for subsequent cell divisions, compaction, and blastulation. The majority of studies on early embryogenesis have been conducted in the mouse or non-mammalian species, often requiring extrapolation of the findings to human development. Given both conserved similarities and species-specific differences, however, even comparison between closely related mammalian species may be challenging as certain aspects, including susceptibility to chromosomal aberrations, varies considerably across mammals. Moreover, most human embryo studies are limited to patient samples obtained from in vitro fertilization (IVF) clinics and donated for research, which are generally of poorer quality and produced with germ cells that may be sub-optimal. Recent technical advances in genetic, epigenetic, chromosomal, and time-lapse imaging analyses of high quality whole human embryos have greatly improved our understanding of early human embryogenesis, particularly at the single embryo and cell level. This review summarizes the major characteristics of mammalian pre-implantation development from a chromosomal perspective, in addition to discussing the technological achievements that have recently been developed to obtain this data. We also discuss potential translation to clinical applications in reproductive medicine and conclude by examining the broader implications of these findings for the evolution of mammalian species and cancer pathology in somatic cells.

Mechanisms of Origin, Phenotypic Effects and Diagnostic Implications of Complex Chromosome Rearrangements

Complex chromosome rearrangements (CCRs) are currently defined as structural genome variations that involve more than 2 chromosome breaks and result in exchanges of chromosomal segments. They are thought to be extremely rare, but their detection rate is rising because of improvements in molecular cytogenetic technology. Their population frequency is also underestimated, since many CCRs may not elicit a phenotypic effect. CCRs may be the result of fork stalling and template switching, microhomology-mediated break-induced repair, breakage-fusion-bridge cycles, or chromothripsis. Patients with chromosomal instability syndromes show elevated rates of CCRs due to impaired DNA double-strand break responses during meiosis. Therefore, the putative functions of the proteins encoded by ATM, BLM, WRN, ATR, MRE11, NBS1, and RAD51 in preventing CCRs are discussed. CCRs may exert a pathogenic effect by either (1) gene dosage-dependent mechanisms, e.g. haploinsufficiency, (2) mechanisms based on disruption of the genomic architecture, such that genes, parts of genes or regulatory elements are truncated, fused or relocated and thus their interactions disturbed - these mechanisms will predominantly affect gene expression - or (3) mixed mutation mechanisms in which a CCR on one chromosome is combined with a different type of mutation on the other chromosome. Such inferred mechanisms of pathogenicity need corroboration by mRNA sequencing. Also, future studies with in vitro models, such as inducible pluripotent stem cells from patients with CCRs, and transgenic model organisms should substantiate current inferences regarding putative pathogenic effects of CCRs. The ramifications of the growing body of information on CCRs for clinical and experimental genetics and future treatment modalities are briefly illustrated with 2 cases, one of which suggests KDM4C (JMJD2C) as a novel candidate gene for mental retardation.