Uncoordinated centrosome cycle underlies the instability of non-diploid somatic cells in mammals

Structural Variants in the SMC1A Gene Associated With Near-Haploidy in Undifferentiated Pleomorphic Sarcomas

Near-haploidization, that is, loss of one copy of most chromosomes, is a relatively rare phenomenon in most tumors, but is enriched among certain soft tissue sarcomas, including undifferentiated pleomorphic sarcoma (UPS). Presumably, near-haploidization can arise through many mechanisms. This study aimed to identify gene rearrangements that could cause near-haploidization. We here present two UPS in which near-haploidization was an early event, identified through single nucleotide polymorphism (SNP) array analysis. One of the cases was studied further using whole genome and transcriptome sequencing, as well as cytogenetic and molecular cytogenetic methods. Both tumors had chromosomal rearrangements in the form of copy number shifts/structural variants affecting the SMC1A gene. These findings suggest that cohesin defects could contribute to mitotic errors resulting in massive loss of chromosomes. SMC1A encodes one of the components of the cohesin multiprotein complex, which is critical for proper alignment of the sister chromatids during S-phase and separation to opposite spindle poles. Further studies should explore the role of cohesin defects in near-haploidization in other sarcomas and to clarify its role in tumor development.

Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles

The CRISPR-Cas9 system is a powerful tool for studying gene functions and holds potential for disease treatment. However, precise genome editing requires thorough assessments to minimize unintended on- and off-target effects. Here, we report an unexpected 283-kb deletion on Chromosome 10 (10q23.31) in chronic myelogenous leukemia-derived HAP1 cells, which are frequently used in CRISPR screens. The deleted region encodes regulatory genes, including PAPSS2, ATAD1, KLLN, and PTEN We found that this deletion was not a direct consequence of CRISPR-Cas9 off-targeting but rather occurred frequently during the generation of CRISPR-Cas9-modified cells. The deletion was associated with global changes in histone acetylation and gene expression, affecting fundamental cellular processes such as cell cycle and DNA replication. We detected this deletion in cancer patient genomes. As in HAP1 cells, the deletion contributed to similar gene expression patterns among cancer patients despite interindividual differences. Our findings suggest that the unintended deletion of 10q23.31 can confound CRISPR-Cas9 studies and underscore the importance to assess unintended genomic changes in CRISPR-Cas9-modified cells, which could impact cancer research.

Cell shape instability during cytokinesis in tetraploid HCT116 cells

Tetraploidy is a hallmark of broad cancer types, but it remains largely unknown which aspects of cellular processes are influenced by tetraploidization in human cells. Here, we found that tetraploid HCT116 cells manifested severe cell shape instability during cytokinesis, unlike their diploid counterparts. The cell shape instability accompanied the formation of protrusive deformation at the cell poles, indicating ectopic contractile activity of the cell cortex. While cytokinesis regulators such as RhoA and anillin correctly accumulated at the equatorial cortex, myosin II was over-accumulated at the cell poles, specifically in tetraploid cells. Suppression of myosin II activity by Y27632 treatment restored smooth cell shape in tetraploids during cytokinesis, indicating dysregulation of myosin II as a primary cause of the cell shape instability in the tetraploid state. Our results demonstrate a new aspect of the dynamic cellular process profoundly affected by tetraploidization in human cells, which provides a clue to molecular mechanisms of tetraploidy-driven pathogenic processes.

Tetraploidy-linked sensitization to CENP-E inhibition in human cells

Tetraploidy is a hallmark of cancer cells, and tetraploidy-selective cell growth suppression is a potential strategy for targeted cancer therapy. However, how tetraploid cells differ from normal diploids in their sensitivity to anti-proliferative treatments remains largely unknown. In this study, we found that tetraploid cells are significantly more susceptible to inhibitors of a mitotic kinesin (CENP-E) than are diploids. Treatment with a CENP-E inhibitor preferentially diminished the tetraploid cell population in a diploid-tetraploid co-culture at optimum conditions. Live imaging revealed that a tetraploidy-linked increase in unsolvable chromosome misalignment caused substantially longer mitotic delay in tetraploids than in diploids upon moderate CENP-E inhibition. This time gap of mitotic arrest resulted in cohesion fatigue and subsequent cell death, specifically in tetraploids, leading to tetraploidy-selective cell growth suppression. In contrast, the microtubule-stabilizing compound paclitaxel caused tetraploidy-selective suppression through the aggravation of spindle multipolarization. We also found that treatment with a CENP-E inhibitor had superior generality to paclitaxel in its tetraploidy selectivity across a broader spectrum of cell lines. Our results highlight the unique properties of CENP-E inhibitors in tetraploidy-selective suppression and their potential use in the development of tetraploidy-targeting interventions in cancer.

The Centrosome: Conclusions and Perspectives

The centrosome consists of two centrioles surrounded by pericentriolar material [...].

Augmin-dependent microtubule self-organization drives kinetochore fiber maturation in mammals

Chromosome segregation in mammals relies on the maturation of a thick bundle of kinetochore-attached microtubules known as k-fiber. How k-fibers mature from initial kinetochore microtubule attachments remains a fundamental question. By combining molecular perturbations and phenotypic analyses in Indian muntjac fibroblasts containing the lowest known diploid chromosome number in mammals (2N = 6) and distinctively large kinetochores, with fixed/live-cell super-resolution coherent-hybrid stimulated emission depletion (CH-STED) nanoscopy and laser microsurgery, we demonstrate a key role for augmin in kinetochore microtubule self-organization and maturation, regardless of pioneer centrosomal microtubules. In doing so, augmin promotes kinetochore and interpolar microtubule turnover and poleward flux. Tracking of microtubule growth events within individual k-fibers reveals a wide angular dispersion, consistent with augmin-mediated branched microtubule nucleation. Augmin depletion reduces the frequency of kinetochore microtubule growth events and hampers efficient repair after acute k-fiber injury by laser microsurgery. Together, these findings underscore the contribution of augmin-mediated microtubule amplification for k-fiber self-organization and maturation in mammals.

The Use of Base Editing Technology to Characterize Single Nucleotide Variants

Single nucleotide variants (SNVs) represent the most common type of polymorphism in the human genome. However, in many cases the phenotypic impacts of such variants are not well understood. Intriguingly, while some SNVs cause debilitating diseases, other variants in the same gene may have no, or limited, impact. The mechanisms underlying these complex patterns are difficult to study at scale. Additionally, current data and research is mainly focused on European populations, and the mechanisms underlying genetic traits in other populations are poorly studied. Novel technologies may be able to mitigate this disparity and improve the applicability of personalized healthcare to underserved populations. In this review we discuss base editing technologies and their potential to accelerate progress in this field, particularly in combination with single-cell RNA sequencing. We further explore how base editing screens can help link SNVs to distinct disease phenotypes. We then highlight several studies that take advantage of single-cell RNA sequencing and CRISPR screens to emphasize the current limitations and future potential of this technique. Lastly, we consider the use of such approaches to potentially accelerate the study of genetic mechanisms in non-European populations.

Delayed DNA replication in haploid human embryonic stem cells

Haploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication. To test this, we profiled DNA replication timing in isogenic haploid and diploid ESCs. The greatest difference was the earlier replication of the X Chromosome in haploids, consistent with the lack of X-Chromosome inactivation. We also identified 21 autosomal regions that had delayed replication in haploids, extending beyond the normal S phase and into G2/M. Haploid-delays comprised a unique set of quiescent genomic regions that are also underreplicated in polyploid placental cells. The same delays were observed in female ESCs with two active X Chromosomes, suggesting that increased X-Chromosome dosage may cause delayed autosomal replication. We propose that incomplete replication at the onset of mitosis could prevent cell division and result in re-entry into the cell cycle and whole genome duplication.

Paralogous synthetic lethality underlies genetic dependencies of the cancer-mutated gene STAG2

STAG2, a component of the mitotically essential cohesin complex, is highly mutated in several different tumour types, including glioblastoma and bladder cancer. Whereas cohesin has roles in many cancer-related pathways, such as chromosome instability, DNA repair and gene expression, the complex nature of cohesin function has made it difficult to determine how STAG2 loss might either promote tumorigenesis or be leveraged therapeutically across divergent cancer types. Here, we have performed whole-genome CRISPR-Cas9 screens for STAG2-dependent genetic interactions in three distinct cellular backgrounds. Surprisingly, STAG1, the paralog of STAG2, was the only negative genetic interaction that was shared across all three backgrounds. We also uncovered a paralogous synthetic lethal mechanism behind a genetic interaction between STAG2 and the iron regulatory gene IREB2 Finally, investigation of an unusually strong context-dependent genetic interaction in HAP1 cells revealed factors that could be important for alleviating cohesin loading stress. Together, our results reveal new facets of STAG2 and cohesin function across a variety of genetic contexts.

Centrosomal-associated Proteins: Potential therapeutic targets for solid tumors?

The centrosome is a special organelle in human cells and an organizing unit for microtubules and signaling molecules. In addition, the centrosome is tightly restricted during the cell cycle and forms the basal body of the cilia in ciliated cells. Centrosome abnormality is frequently observed in malignant tumors. The dysregulation of centrosome-associated proteins leads to multipolar mitosis, aneuploidy, and nondirected cell migration, and therefore promotes cancer progression. The overduplication of primary centrosome and the accumulation of chromosome, comprise the majority cause of chromosomal mis-segregation in cancer cells. This review discusses the structure and function of the centrosome and the role of its associated proteins in the progression of solid tumors. We summarized the effects of centrosome amplification abnormalities and other centrosome-related phenotypes on tumors. The mechanism of the delineation of centrosome amplification with tumor malignancy remains to be decided. A better understanding of centrosome abnormality in tumorigenesis may be useful to screen novel therapeutic strategies for the treatment of solid tumors.

Quantitative live-cell imaging and computational modeling shed new light on endogenous WNT/CTNNB1 signaling dynamics

WNT/CTNNB1 signaling regulates tissue development and homeostasis in all multicellular animals, but the underlying molecular mechanism remains incompletely understood. Specifically, quantitative insight into endogenous protein behavior is missing. Here, we combine CRISPR/Cas9-mediated genome editing and quantitative live-cell microscopy to measure the dynamics, diffusion characteristics and absolute concentrations of fluorescently tagged, endogenous CTNNB1 in human cells under both physiological and oncogenic conditions. State-of-the-art imaging reveals that a substantial fraction of CTNNB1 resides in slow-diffusing cytoplasmic complexes, irrespective of the activation status of the pathway. This cytoplasmic CTNNB1 complex undergoes a major reduction in size when WNT/CTNNB1 is (hyper)activated. Based on our biophysical measurements, we build a computational model of WNT/CTNNB1 signaling. Our integrated experimental and computational approach reveals that WNT pathway activation regulates the dynamic distribution of free and complexed CTNNB1 across different subcellular compartments through three regulatory nodes: the destruction complex, nucleocytoplasmic shuttling, and nuclear retention.

Escape from mitotic catastrophe by actin-dependent nuclear displacement in fission yeast

Eukaryotic cells position the nucleus within the proper intracellular space, thereby safeguarding a variety of cellular processes. In fission yeast, the interphase nucleus is placed in the cell middle in a microtubule-dependent manner. By contrast, how the mitotic nucleus is positioned remains elusive. Here we show that several cell-cycle mutants that arrest in mitosis all displace the nucleus toward one end of the cell. Intriguingly, the actin cytoskeleton is responsible for nuclear movement. Time-lapse live imaging indicates that mitosis-specific F-actin cables possibly push the nucleus through direct interaction with the nuclear envelope, and subsequently actomyosin ring constriction further shifts the nucleus away from the center. This nuclear movement is beneficial, because if the nuclei were retained in the center, unseparated chromosomes would be intersected by the contractile actin ring and the septum, imposing the lethal cut phenotype. Thus, fission yeast escapes from mitotic catastrophe by means of actin-dependent nuclear movement.

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Actin-dependent mitotic nuclear positioning in fission yeast

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Actin cables and ring closure drive nuclear displacement upon mitotic arrest

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Nuclear displacement evades cut-mediated cell death

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Survivors resume cell division as diploids

CRISPR-Mediated Mutagenesis of Long Noncoding RNAs

Functional characterizations and molecular dissections of long noncoding RNAs (lncRNAs) are critical to understand their involvement in the cellular regulatory network. LncRNAs exert their effects through functional RNA domains that interact with other molecules, including proteins, DNA, and RNA. Here, we describe experimental procedures for generating genomic deletions in a human haploid cell line using the CRISPR/Cas9 system. This method can be applied to examine functions of lncRNAs and their domains by establishing knockout and partial deletion mutant cell lines. In addition, we describe a CRISPR-mediated knockin method for artificial tethering of partner RNA-binding proteins to lncRNAs and its use to validate lncRNA-mediated functions.

Efficient and crucial quality control of HAP1 cell ploidy status

The near-haploid human cell line HAP1 recently became a popular subject for CRISPR/Cas9 editing, since only one allele requires modification. Through the gene-editing service at Horizon Discovery, there are at present more than 7500 edited cell lines available and the number continuously increases. The haploid nature of HAP1 is unstable as cultures become diploid with time. Here, we demonstrated some fundamental differences between haploid and diploid HAP1 cells, hence underlining the need for taking control over ploidy status in HAP1 cultures prior to phenotyping. Consequently, we optimized a procedure to determine the ploidy of HAP1 by flow cytometry in order to obtain diploid cultures and avoid ploidy status as an interfering variable in experiments. Furthermore, in order to facilitate this quality control, we validated a size-based cell sorting procedure to obtain the diploid culture more rapidly. Hence, we provide here two streamlined protocols for quality controlling the ploidy of HAP1 cells and document their validity and necessity.

This article has an associated First Person interview with the co-first authors of the paper.

Summary: Sharing an effective procedure to quality control the near-haploid HAP1 cells for standardized comparison to CRISPR/Cas9 modified versions and demonstrating the need for controlling the spontaneous diploidization of HAP1 cultures.

The milestone of genetic screening: Mammalian haploid cells

Mammalian haploid cells provide insights into multiple genetics approaches as have been proved by advances in homozygous phenotypes and function as gametes. Recent achievements make ploidy of mammalian haploid cells stable and improve the developmental efficiency of embryos derived from mammalian haploid cells intracytoplasmic microinjection, which promise great potentials for using mammalian haploid cells in forward and reverse genetic screening. In this review, we introduce breakthroughs of mammalian haploid cells involving in mechanisms of self-diploidization, forward genetics for various targeting genes and imprinted genes related development.

Uncoupling of DNA Replication and Centrosome Duplication Cycles Is a Primary Cause of Haploid Instability in Mammalian Somatic Cells

Mammalian haploid somatic cells are unstable and prone to diploidize, but the cause of haploid instability remains largely unknown. Previously, we found that mammalian haploid somatic cells suffer chronic centrosome loss stemming from the uncoupling of DNA replication and centrosome duplication cycles. However, the lack of methodology to restore the coupling between DNA replication and centrosome duplication has precluded us from investigating the potential contribution of the haploidy-linked centrosome loss to haploid instability. In this study, we developed an experimental method that allows the re-coupling of DNA and centrosome cycles through the chronic extension of the G1/S phase without compromising cell proliferation using thymidine treatment/release cycles. Chronic extension of G1/S restored normal mitotic centrosome number and mitotic control, substantially improving the stability of the haploid state in HAP1 cells. Stabilization of the haploid state was compromised when cdk2 was inhibited during the extended G1/S, or when early G1 was chronically extended instead of G1/S, showing that the coupling of DNA and centrosome cycles rather than a general extension of the cell cycle is required for haploid stability. Our data indicate the chronic centriole loss arising from the uncoupling of centrosome and DNA cycles as a direct cause of genome instability in haploid somatic cells, and also demonstrate the feasibility of modulation of haploid stability through artificial coordination between DNA and centrosome cycles in mammalian somatic cells.

The Enigma of Centriole Loss in the 1182-4 Cell Line

The Drosophila melanogaster cell line 1182-4, which constitutively lacks centrioles, was established many years ago from haploid embryos laid by females homozygous for the maternal haploid (mh) mutation. This was the first clear example of animal cells regularly dividing in the absence of this organelle. However, the cause of the acentriolar nature of the 1182-4 cell line remained unclear and could not be clearly assigned to a particular genetic event. Here, we detail historically the longstanding mystery of the lack of centrioles in this Drosophila cell line. Recent advances, such as the characterization of the mh gene and the genomic analysis of 1182-4 cells, allow now a better understanding of the physiology of these cells. By combining these new data, we propose three reasonable hypotheses of the genesis of this remarkable phenotype.

The Centrosome Linker and Its Role in Cancer and Genetic Disorders

Centrosome cohesion, the joining of the two centrosomes of a cell, is increasingly appreciated as a major regulator of cell functions such as Golgi organization and cilia positioning. One major element of centrosome cohesion is the centrosome linker that consists of a growing number of proteins. The timely disassembly of the centrosome linker enables centrosomes to separate and assemble a functional bipolar mitotic spindle that is crucial for maintaining genomic integrity. Exciting new findings link centrosome linker defects to cell transformation and genetic disorders. We review recent data on the molecular mechanisms of the assembly and disassembly of the centrosome linker, and discuss how defects in the proper execution of these processes cause DNA damage and genomic instability leading to disease.

Mammalian haploid stem cells: establishment, engineering and applications

Haploid embryonic stem cells (haESCs) contain only one set of genomes inherited from the sperm or egg and are termed AG- or PG-haESCs, respectively. Mammalian haESCs show genome-wide hypomethylation and dysregulated imprinting, whereas they can sustain genome integrity during derivation and long-term propagation. In addition, haESCs exhibit similar pluripotency to traditional diploid ESCs but are unique because they function as gametes and have been used to produce semi-cloned animals. More strikingly, unisexual reproduction has been achieved in mice by using haESCs. In combination with a gene editing or screening system, haESCs represent a powerful tool for studies of underlying gene functions and explorations of mechanisms of genetic and epigenetic regulation not only at the cellular level in vitro but also at the animal level in vivo. More importantly, genetically edited AG-haESC lines may further serve as an ideal candidate for the establishment of a sperm bank, which is a highly cost-effective approach, and a wide range of engineered semi-cloned mice have been produced. Here, we review the historical development, characteristics, advantages and disadvantages of haESCs. Additionally, we present an in-depth discussion of the recent advances in haESCs and their potential applications.

Imbalance of the spindle-assembly checkpoint promotes spindle poison-mediated cytotoxicity with distinct kinetics

Disrupting microtubule dynamics with spindle poisons activates the spindle-assembly checkpoint (SAC) and induces mitotic cell death. However, mitotic exit can occur prematurely without proper chromosomal segregation or cytokinesis by a process termed mitotic slippage. It remains controversial whether mitotic slippage increases the cytotoxicity of spindle poisons or the converse. Altering the SAC induces either mitotic cell death or mitotic slippage. While knockout of MAD2-binding protein p31^comet strengthened the SAC and promoted mitotic cell death, knockout of TRIP13 had the opposite effect of triggering mitotic slippage. We demonstrated that mitotic slippage prevented mitotic cell death caused by spindle poisons, but reduced subsequent long-term survival. Weakening of the SAC also reduced cell survival in response to spindle perturbation insufficient for triggering mitotic slippage, of which mitotic exit was characterized by displaced chromosomes during metaphase. In either mitotic slippage or mitotic exit with missegregated chromosomes, cell death occurred only after one cell cycle following mitotic exit and increased progressively during subsequent cell cycles. Consistent with these results, transient inhibition of the SAC using an MPS1 inhibitor acted synergistically with spindle perturbation in inducing chromosome missegregation and cytotoxicity. The specific temporal patterns of cell death after mitotic exit with weakened SAC may reconcile the contradictory results from many previous studies.

Tetraploidy-associated centrosome overduplication in mouse early embryos

Recently, we observed that tetraploidization of certain types of human cancer cells resulted in upregulation of centrosome duplication cycles and chronic generation of the extra centrosome. Here, we investigated whether tetraploidy-linked upregulation of centrosome duplication also occurs in non-cancer cells using tetraploidized parthenogenetic mouse embryos. Cytokinesis blockage at early embryonic stage before de novo centriole biogenesis provided the unique opportunity in which tetraploidization can be induced without transient doubling of centrosome number. The extra numbers of the centrioles and the centrosomes were observed more frequently in tetraploidized embryos during the blastocyst stage than in their diploid counterparts, demonstrating the generality of the newly found tetraploidy-driven centrosome overduplication in mammalian non-cancer systems.