Tetraploid Cells Research Articles

Kinesins regulate the heterogeneity in centrosome clustering after whole-genome duplication.

After whole-genome duplication (WGD), tetraploid cells can undergo multipolar mitosis or pseudo-bipolar mitosis with clustered centrosomes. Kinesins play a crucial role in regulating spindle formation. However, the contribution of kinesin expression levels to the heterogeneity in centrosome clustering observed across different cell lines after WGD remains unclear. We identified two subsets of cell lines: "BP" cells efficiently cluster extra centrosomes for pseudo-bipolar mitosis, and "MP" cells primarily undergo multipolar mitosis after WGD. Diploid MP cells contained higher levels of KIF11 and KIF15 compared with BP cells and showed reduced sensitivity to centrosome clustering induced by KIF11 inhibitors. Moreover, partial inhibition of KIF11 or depletion of KIF15 converted MP cells from multipolar to bipolar mitosis after WGD. Multipolar spindle formation involved microtubules but was independent of kinetochore-microtubule attachment. Silencing KIFC1, but not KIFC3, promoted multipolar mitosis in BP cells, indicating the involvement of specific kinesin-14 family members in counteracting the forces from KIF11/KIF15 after WGD. These findings highlight the collective role of KIF11, KIF15, and KIFC1 in determining the polarity of the mitotic spindle after WGD.

Central Role of the Actomyosin Ring in Coordinating Cytokinesis Steps in Budding Yeast.

Eukaryotic cells must accurately transfer their genetic material and cellular components to their daughter cells. Initially, cells duplicate their chromosomes and subsequently segregate them toward the poles. The actomyosin ring, a crucial molecular machinery normally located in the middle of the cells and underneath the plasma membrane, then physically divides the cytoplasm and all components into two daughter cells, each ready to start a new cell cycle. This process, known as cytokinesis, is conserved throughout evolution. Defects in cytokinesis can lead to the generation of genetically unstable tetraploid cells, potentially initiating uncontrolled proliferation and cancer. This review focuses on the molecular mechanisms by which budding yeast cells build the actomyosin ring and the preceding steps involved in forming a scaffolding structure that supports the challenging structural changes throughout cytokinesis. Additionally, we describe how cells coordinate actomyosin ring contraction, plasma membrane ingression, and extracellular matrix deposition to successfully complete cytokinesis. Furthermore, the review discusses the regulatory roles of Cyclin-Dependent Kinase (Cdk1) and the Mitotic Exit Network (MEN) in ensuring the precise timing and execution of cytokinesis. Understanding these processes in yeast provides insights into the fundamental aspects of cell division and its implications for human health.

Nucleolin acute degradation reveals novel functions in cell cycle progression and division in TNBC.

Nucleoli are large nuclear sub-compartments where vital processes, such as ribosome assembly, take place. Technical obstacles still limit our understanding of the biological functions of nucleolar proteins in cell homeostasis and cancer pathogenesis. Since most nucleolar proteins are essential, their abrogation cannot be achieved through conventional approaches. Additionally, the biological activities of many nucleolar proteins are connected to their physiological concentration. Thus, artificial overexpression might not fully recapitulate their endogenous functions. Proteolysis-based approaches, such as the Auxin Inducible Degron (AID) system paired with CRISPR/Cas9 knock-in gene-editing, have the potential to overcome these limitations, providing unprecedented characterization of the biological activities of endogenous nucleolar proteins. We applied this system to endogenous nucleolin (NCL), one of the most abundant nucleolar proteins, and characterized the impact of its acute depletion on Triple-Negative Breast Cancer (TNBC) cell behavior. Abrogation of endogenous NCL reduced proliferation and caused defective cytokinesis, resulting in bi-nucleated tetraploid cells. Bioinformatic analysis of patient data, and quantitative proteomics using our experimental NCL-depleted model, indicated that NCL levels are correlated with the abundance of proteins involved in chromosomal segregation. In conjunction with its effects on sister chromatid dynamics, NCL abrogation enhanced the anti-proliferative effects of chemical inhibitors of mitotic modulators such as the Anaphase Promoting Complex. In summary, using the AID system in combination with CRISPR/Cas9 for endogenous gene editing, our findings indicate a novel role for NCL in supporting the completion of the cell division in TNBC models, and that its abrogation could enhance the therapeutic activity of mitotic-progression inhibitors.

Beyond Death: Unmasking the Intricacies of Apoptosis Escape.

Apoptosis, or programmed cell death, maintains tissue homeostasis by eliminating damaged or unnecessary cells. However, cells can evade this process, contributing to conditions such as cancer. Escape mechanisms include anoikis, mitochondrial DNA depletion, cellular FLICE inhibitory protein (c-FLIP), endosomal sorting complexes required for transport (ESCRT), mitotic slippage, anastasis, and blebbishield formation. Anoikis, triggered by cell detachment from the extracellular matrix, is pivotal in cancer research due to its role in cellular survival and metastasis. Mitochondrial DNA depletion, associated with cellular dysfunction and diseases such as breast and prostate cancer, links to apoptosis resistance. The c-FLIP protein family, notably CFLAR, regulates cell death processes as a truncated caspase-8 form. The ESCRT complex aids apoptosis evasion by repairing intracellular damage through increased Ca2+ levels. Antimitotic agents induce mitotic arrest in cancer treatment but can lead to mitotic slippage and tetraploid cell formation. Anastasis allows cells to resist apoptosis induced by various triggers. Blebbishield formation suppresses apoptosis indirectly in cancer stem cells by transforming apoptotic cells into blebbishields. In conclusion, the future of apoptosis research offers exciting possibilities for innovative therapeutic approaches, enhanced diagnostic tools, and a deeper understanding of the complex biological processes that govern cell fate. Collaborative efforts across disciplines, including molecular biology, genetics, immunology, and bioinformatics, will be essential to realize these prospects and improve patient outcomes in diverse disease contexts.

Sustained ERK signaling promotes G2 cell cycle exit and primes cells for whole-genome duplication

Whole-genome duplication (WGD) is a frequent event in cancer evolution that fuels chromosomal instability. WGD can result from mitotic errors or endoreduplication, yet the molecular mechanisms that drive WGD remain unclear. Here, we use live single-cell analysis to characterize cell-cycle dynamics upon aberrant Ras-ERK signaling. We find that sustained ERK signaling in human cells leads to reactivation of the APC/C in G2, resulting in tetraploid G0-like cells that are primed for WGD. This process is independent of DNA damage or p53 but dependent on p21. Transcriptomics analysis and live-cell imaging showed that constitutive ERK activity promotes p21 expression, which is necessary and sufficient to inhibit CDK activity and which prematurely activates the anaphase-promoting complex (APC/C). Finally, either loss of p53 or reduced ERK signaling allowed for endoreduplication, completing a WGD event. Thus, sustained ERK signaling-induced G2 cell cycle exit represents an alternative path to WGD.

Abstract 7419: Seq2Karyotype (S2K): A method for deconvoluting heterogeneity of copy number alterations using single-sample whole-genome sequencing data

Abstract Broad copy number alterations (CNAs) at chromosomal band resolution have been used as cancer diagnostic and prognostic biomarkers for decades. These events have been characterized by cytogenetic imaging, an approach which is powerful for assessing heterogeneity but limited for locus fine mapping. While CNA detection by next-generation sequencing has become a standard analysis, existing methods rarely model CNA heterogeneity in bulk tumor samples and often require a paired normal sample for control. To overcome these limitations, we developed Seq2Karyotype (S2K, https://github.com/chenlab-sj/Seq2Karyotype), a new algorithm for in-silico karyotyping using single-sample whole-genome sequencing (WGS) data. S2K performs joint modeling of read-depth and allelic imbalance (AI) of high-quality heterozygous SNPs to identify reference diploid regions, followed by modeling and segmenting the deviation from the reference. Empirical coverage and AI of segmented regions are fitted to models of single and admixed CNAs to estimate clonality. The final karyotyping considers both the model fitness and minimization of evolution steps.To evaluate S2K’s performance, we analyzed two cell lines commonly used for benchmark test: COLO829 (melanoma) and HCT1395 (breast cancer); both had single-cell (sc) WGS for validation. For COLO829, S2K replicated the four populations detected by scWGS but derived a different clonality estimate. The predominant clone, defined by loss of 1p, 10p, and chr18, was estimated to have 67% cellular fraction (CF) by bulk sample analysis of S2K in contrast to the 10% CF by scWGS analysis. In HCT1395, S2K identified three new CNAs present in >50% of the cells of the matching germline sample which were subsequently validated by FISH, karyotyping and SKY mapping.To demonstrate S2K’s utility, we analyzed three diverse data sets: 17 neuroblastoma cell lines, 24 pediatric AML samples with karyotyping data, and two blood samples from children with myelodysplastic syndromes (MDS) known to harbor mosaic uniparental disomy (UPD). CNA-based intra-tumor heterogeneity was detected in 88% (15/17) of the neuroblastoma cell lines, comprised of 2-4 distinct populations with diverse ranges of CF (~10%-90%) and varying CNA patterns (e.g. admixture of tetraploid and diploid cells), which were validated by cytogenetics or scWGS. In the patient AML samples, S2K detected >95% of the previously reported cytogenetic events and 30% of additional copy-neutral loss-of-heterozygosity events. The mosaic UPD events in MDS patients were detected with projected clonality of 60% and 25%, respectively. These results not only demonstrate the accuracy of in-silico karyotyping performed by S2K but also reveal the dynamic intra-tumor heterogeneity in cancer cell lines, which may impact the design and interpretation of future experiments using these cell lines. Citation Format: Limeng Pu, Karol Szlachta, Virginia Valentine, Xiaolong Chen, Jian Wang, Dennis Kennetz, Daniel Putnam, Sivaraman Natarajan, Li Dong, Thomas Look, Marcin Wlodarski, Lu Wang, Steven Burden, John Easton, Xiang Chen, Jinghui Zhang. Seq2Karyotype (S2K): A method for deconvoluting heterogeneity of copy number alterations using single-sample whole-genome sequencing data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7419.

Tumor acidosis-induced DNA damage response and tetraploidy enhance sensitivity to ATM and ATR inhibitors

Tumor acidosis is associated with increased invasiveness and drug resistance. Here, we take an unbiased approach to identify vulnerabilities of acid-exposed cancer cells by combining pH-dependent flow cytometry cell sorting from 3D colorectal tumor spheroids and transcriptomic profiling. Besides metabolic rewiring, we identify an increase in tetraploid cell frequency and DNA damage response as consistent hallmarks of acid-exposed cancer cells, supported by the activation of ATM and ATR signaling pathways. We find that regardless of the cell replication error status, both ATM and ATR inhibitors exert preferential growth inhibitory effects on acid-exposed cancer cells. The efficacy of a combination of these drugs with 5-FU is further documented in 3D spheroids as well as in patient-derived colorectal tumor organoids. These data position tumor acidosis as a revelator of the therapeutic potential of DNA repair blockers and as an attractive clinical biomarker to predict the response to a combination with chemotherapy.

Persistence of Chronic Lymphocytic Leukemia Stem-like Populations under Simultaneous In Vitro Treatment with Curcumin, Fludarabine, and Ibrutinib: Implications for Therapy Resistance.

Leukemic stem cells (LSCs) possess similar characteristics to normal hematopoietic stem cells, including self-renewal capacity, quiescence, ability to initiate leukemia, and drug resistance. These cells play a significant role in leukemia relapse, persisting even after apparent remission. LSCs were first described in 1994 by Lapidot et al. Although they have been extensively studied in acute leukemia, more LSC research is still needed in chronic lymphocytic leukemia (CLL) to understand if reduced apoptosis in mature cells should still be considered as the major cause of this disease. Here, we provide new evidence suggesting the existence of stem-like cell populations in CLL, which may help to understand the disease as well as to develop effective treatments. In this study, we identified a potential leukemic stem cell subpopulation using the tetraploid CLL cell line I83. This subpopulation is characterized by diploid cells that were capable of generating the I83 tetraploid population. Furthermore, we adapted a novel flow cytometry analysis protocol to detect CLL subpopulations with stem cell properties in peripheral blood samples and primary cultures from CLL patients. These cells were identified by their co-expression of CD19 and CD5, characteristic markers of CLL cells. As previously described, increased alkaline phosphatase (ALP) activity is indicative of stemness and pluripotency. Moreover, we used this method to investigate the potential synergistic effect of curcumin in combination with fludarabine and ibrutinib to deplete this subpopulation. Our results confirmed the effectiveness of this ALP-based analysis protocol in detecting and monitoring leukemic stem-like cells in CLL. This analysis also identified limitations in eradicating these populations using in vitro testing. Furthermore, our findings demonstrated that curcumin significantly enhanced the effects of fludarabine and ibrutinib on the leukemic fraction, exhibiting synergistic effects (combination drug index, CDI 0.97 and 0.37, respectively). Our results lend support to the existence of potential stem-like populations in CLL cell lines, and to the idea that curcumin could serve as an effective adjuvant in therapies aimed at eliminating these populations and improving treatment efficacy.

Abstract A024: Ploidy as a predictive biomarker for gemcitabine sensitivity in triple-negative breast cancers

Abstract The polyploid giant cancer cell (PGCC) state is a common response of cancer cells to various stressors including chemotherapy, irradiation, hypoxia and viral infection. Upon stress, PGCCs adopt an endoreplication in which the genome replicates, mitosis is omitted, and cells grow in size, causing drug resistance. How accessible endoreplication is to a cell, therefore, directly translates to its resistance to therapy. In this study, we hypothesized that endoreplication and PGCC state are more accessible to cancer cells that already have a higher ploidy content prior to therapy. To test this hypothesis, we developed a comprehensive three-tier framework consisting of i) computational, ii) in-vitro and iii) in silico components. First, we designed a set of ordinary differential equations (ODEs) to mathematically model how cells enter and exit the PGCC state in response to a given stressor. We engineered how this in silico approach interacts with in vitro experiments into a broadly applicable software solution called CLONEID. The software uses computer vision to monitor phenotypic changes in cell and nuclear size from standard bright-field microscopy and classify cells into PGCC and non-PGCC states. We used CLONEID to test various therapeutic agents for their ability to select for a stable near-tetraploid (4N) population in a set of near-diploid (2N) cell lines. Through spontaneous cell fusions, we also obtained tetraploid breast cancer cells matched with their parental lines. Altogether, this framework enabled us to i) monitor the PGCC state experimentally in ii) two sets of matched isogenic cell lines with 2N and 4N DNA content to iii) model the successful entry and exit rates to and from the endoreplication state, respectively. As the first application of this framework, we tested the ability of our 2N and 4N TNBC lines (SUM159 and MDA-MB-231) to access the PGCC state upon treatment with 18 chemotherapy agents. Among those drugs, we observed that only gemcitabine caused continued cell growth without cell division in both tetraploid SUM159 and MDA-MB-231 cells whereas near-diploid parental lines were hypersensitive to the treatment. Consequently, tetraploid cancer cells continued to safely grow in the presence of gemcitabine. Furthermore, these PGCCs re-entered the proliferative cell cycle and grew in cell number when treatment is terminated. Gemcitabine-based chemotherapy is a standard treatment for patients with TNBC although its efficacy is limited mainly due to drug resistance. We expect our findings and three-component framework strategy to help stratify the TNBC patient population by their response to gemcitabine. In addition, our mathematical modelling approach has the promising potential to inform personalized dose optimization and to effectively decrease administered gemcitabine dose for a subset of patients, which would alleviate severe therapy-associated side effects and co-morbidities. Citation Format: Vural Tagal, Jackson Cole, Daria Miroshnychenko, Andriy Marusyk, Noemi Andor. Ploidy as a predictive biomarker for gemcitabine sensitivity in triple-negative breast cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr A024.

Abstract PR010: Linking proliferation rate to the evolution of single-cell primary and metastatic tumor clones

Abstract Proliferation is a key phenotypic feature of cancer, with higher rates associated with poorer clinical outcomes. Thus far, proliferation rates have been measured using pathological or experimental techniques on bulk tumor samples. However, tumors are heterogeneous compositions of distinct clones. Measuring the proliferation of individual clones has been unfeasible to date since proliferation and clonal diversity cannot easily be measured for the same set of cells, but it is potentially important as it may allow the identification of clones that develop more aggressive phenotypes (e.g., metastatic potential or treatment resistance). We have developed SPRINTER, a novel algorithm that uses single-cell whole-genome DNA sequencing (scDNA-seq) data to enable the accurate identification of actively replicating cells in both the S and G2 phases of the cell cycle and their assignment to distinct tumor clones, thus providing a proxy to estimate clone-specific proliferation rates. To evaluate SPRINTER’s accuracy, we generated a ground truth dataset of 8,844 diploid and tetraploid cancer cells by coupling scDNA-seq with 5-Ethynyl-2-deoxyuridine (EdU) labeling, and demonstrated that SPRINTER can accurately distinguish clone proliferation rates in contrast to previous approaches. We further generated a longitudinal, primary-metastasis matched dataset of 23,001 cancer cells obtained from 5 samples from the primary tumor and 5 samples from distinct metastases from a patient with non-small cell lung cancer, allowing us to integrate analyses of proliferation and cancer evolution through the metastatic disease course. We revealed widespread heterogeneity in clone proliferation rates both between and within samples, supported by multiple orthogonal analyses including Ki-67 pathology, nuclei microscopy imaging, and patient clinical imaging, with high proliferation seen in fast-growing metastatic lesions. We demonstrated an association between clones with high proliferation and increased metastatic potential, as well as increased shedding of circulating tumor DNA. We further illustrated SPRINTER’s broad applicability on previous datasets of 42,009 breast cancer cells and 19,905 ovarian cancer cells, revealing an association between high proliferation and increased rates of different genetic variants. In conclusion, SPRINTER infers the proliferation rates of distinct tumor clones from scDNA-seq data, allowing the identification of clones with potentially aggressive phenotypes, such as metastatic potential. Citation Format: Olivia Lucas, Sophia Ward, Rija Zaidi, Abigail Bunkum, Alexander M. Frankell, David A. Moore, Mark S. Hill, Wing Kin Liu, Daniele Marinelli, Emilia L. Lim, Sonya Hessey, Cristina Naceur-Lombardelli, Andrew Rowan, Sukhveer Mann, Haoran Zhai, Michelle Dietzen, Boyue Ding, Gary Royle, Nicholas McGranahan, Mariam Jamal-Hanjani, Nnennaya Kanu, Charles Swanton, Simone Zaccaria. Linking proliferation rate to the evolution of single-cell primary and metastatic tumor clones [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr PR010.

Aurora A Kinase Plays a Key Role in Mitosis Skip during Senescence Induced by Ionizing Radiation

ObjectiveTo investigate the fate and underlying mechanisms of G2 phase arrest in cancer cells elicited by ionizing radiation (IR). MethodsHuman melanoma A375 and 92-1 cells were treated with X-rays radiation or Aurora A inhibitor MLN8237 (MLN) and/or p21 depletion by small interfering RNA (siRNA). Cell cycle distribution was determined using flow cytometry and a fluorescent ubiquitin-based cell cycle indicator (FUCCI) system combined with histone H3 phosphorylation at Ser10 (pS10 H3) detection. Senescence was assessed using senescence-associated-β-galactosidase (SA-β-Gal), Ki67, and γH2AX staining. Protein expression levels were determined using western blotting. ResultsTumor cells suffered severe DNA damage and underwent G2 arrest after IR treatment. The damaged cells did not successfully enter M phase nor were they stably blocked at G2 phase but underwent mitotic skipping and entered G1 phase as tetraploid cells, ultimately leading to senescence in G1. During this process, the p53/p21 pathway is hyperactivated. Accompanying p21 accumulation, Aurora A kinase levels declined sharply. MLN treatment confirmed that Aurora A kinase activity is essential for mitosis skipping and senescence induction. ConclusionPersistent p21 activation during IR-induced G2 phase blockade drives Aurora A kinase degradation, leading to senescence via mitotic skipping.

Tetraploidization Increases the Motility and Invasiveness of Cancer Cells.

Polyploidy and metastasis are associated with a low probability of disease-free survival in cancer patients. Polyploid cells are known to facilitate tumorigenesis. However, few data associate polyploidization with metastasis. Here, by generating and using diploid (2n) and tetraploid (4n) clones from malignant fibrous histiocytoma (MFH) and colon carcinoma (RKO), we demonstrate the migration and invasion advantage of tetraploid cells in vitro using several assays, including the wound healing, the OrisTM two-dimensional cell migration, single-cell migration tracking by video microscopy, the Boyden chamber, and the xCELLigence RTCA real-time cell migration. Motility advantage was observed despite tetraploid cell proliferation weakness. We could also demonstrate preferential metastatic potential in vivo for the tetraploid clone using the tail vein injection in mice and tracking metastatic tumors in the lung. Using the Mitelman Database of Chromosome Aberrations in Cancer, we found an accumulation of polyploid karyotypes in metastatic tumors compared to primary ones. This work reveals the clinical relevance of the polyploid subpopulation and the strategic need to highlight polyploidy in preclinical studies as a therapeutic target for metastasis.

High-Frequency Dielectrophoresis Reveals That Distinct Bio-Electric Signatures of Colorectal Cancer Cells Depend on Ploidy and Nuclear Volume.

Aneuploidy, or an incorrect chromosome number, is ubiquitous among cancers. Whole-genome duplication, resulting in tetraploidy, often occurs during the evolution of aneuploid tumors. Cancers that evolve through a tetraploid intermediate tend to be highly aneuploid and are associated with poor patient prognosis. The identification and enrichment of tetraploid cells from mixed populations is necessary to understand the role these cells play in cancer progression. Dielectrophoresis (DEP), a label-free electrokinetic technique, can distinguish cells based on their intracellular properties when stimulated above 10 MHz, but DEP has not been shown to distinguish tetraploid and/or aneuploid cancer cells from mixed tumor cell populations. Here, we used high-frequency DEP to distinguish cell subpopulations that differ in ploidy and nuclear size under flow conditions. We used impedance analysis to quantify the level of voltage decay at high frequencies and its impact on the DEP force acting on the cell. High-frequency DEP distinguished diploid cells from tetraploid clones due to their size and intracellular composition at frequencies above 40 MHz. Our findings demonstrate that high-frequency DEP can be a useful tool for identifying and distinguishing subpopulations with nuclear differences to determine their roles in disease progression.

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.

Abstract P2063: Cellular Fusion Drives Polyploidization In Human Cardiomyocytes

Polyploidization is the roadblock to cardiac regeneration. Although endoreplication has been considered to be the main source of polyploidization in cardiomyocytes, recent evidence indicates transient cardiomyocyte fusion and its potential role in cardiac development in zebrafish. To understand polyploidization, it is essential to trace the lineage of cardiomyocytes. The existing lineage method is not suitable for studying the lineage in human heart cardiomyocytes. However, the accumulation of clonal somatic DNA mutation can be traced, and the clonal structure of these somatic mutations can be used for lineage reconstruction of human cardiomyocytes as these non-inherited clonal somatic mutations record the unique history of each somatic cell originating from a zygote and can be used as “endogenous barcodes.” Our analysis of ultra-deep targeted sequencing of ≈500 single cardiomyocyte nuclei using a panel of 253 validated clonal sSNVs revealed that 75.7% of the sequenced cardiomyocytes could be classified into one of the nine clades categorized based on the presence or absence of these mutations. Interestingly, we found that cardiomyocytes can have mutations from more than one clade, indicating the possibilities of cellular fusion in cardiomyocytes. Our results suggest that at least ~10% of tetraploid cardiomyocytes are generated from the fusion mechanism during development, whereas 60% higher ploidy cardiomyocytes are generated from the fusion. Further, we performed ATAC Seq and transcriptome analysis to find out the types of cells that are fused to generate polyploid cardiomyocytes in the human heart. Analysis of the transcriptome and chromatin peaks of tetraploid and higher ploidy cells unraveled a population of cells (cluster 7) that expressed chromatin peaks for endothelial markers (EGFL7) as well as cardiomyocyte-specific markers like TBX5, PLN, etc. Our study demonstrates cellular fusion in the adult human heart and the cell types involved in this fusion event. Understanding the generation of polyploid cardiomyocytes in the human heart might enable us to advance the mechanistic understanding of cardiomyocyte regeneration with the long-term goal of stimulating therapeutic cardiac regeneration.

The fate of extra centrosomes in newly formed tetraploid cells: should I stay, or should I go?

An increase in centrosome number is commonly observed in cancer cells, but the role centrosome amplification plays along with how and when it occurs during cancer development is unclear. One mechanism for generating cancer cells with extra centrosomes is whole genome doubling (WGD), an event that occurs in over 30% of human cancers and is associated with poor survival. Newly formed tetraploid cells can acquire extra centrosomes during WGD, and a generally accepted model proposes that centrosome amplification in tetraploid cells promotes cancer progression by generating aneuploidy and chromosomal instability. Recent findings, however, indicate that newly formed tetraploid cells in vitro lose their extra centrosomes to prevent multipolar cell divisions. Rather than persistent centrosome amplification, this evidence raises the possibility that it may be advantageous for tetraploid cells to initially restore centrosome number homeostasis and for a fraction of the population to reacquire additional centrosomes in the later stages of cancer evolution. In this review, we explore the different evolutionary paths available to newly formed tetraploid cells, their effects on centrosome and chromosome number distribution in daughter cells, and their probabilities of long-term survival. We then discuss the mechanisms that may alter centrosome and chromosome numbers in tetraploid cells and their relevance to cancer progression following WGD.

A fine balance among key biophysical factors is required for recovery of bipolar mitotic spindle from monopolar and multipolar abnormalities.

During mitosis, equal partitioning of chromosomes into two daughter cells requires assembly of a bipolar mitotic spindle. Because the spindle poles are each organized by a centrosome in animal cells, centrosome defects can lead to monopolar or multipolar spindles. However, the cell can effectively recover the bipolar spindle by separating the centrosomes in monopolar spindles and clustering them in multipolar spindles. To interrogate how a cell can separate and cluster centrosomes as needed to form a bipolar spindle, we developed a biophysical model, based on experimental data, which uses effective potential energies to describe key mechanical forces driving centrosome movements during spindle assembly. Our model identified general biophysical factors crucial for robust bipolarization of spindles that start as monopolar or multipolar. These factors include appropriate force fluctuation between centrosomes, balance between repulsive and attractive forces between centrosomes, exclusion of the centrosomes from the cell center, proper cell size and geometry, and a limited centrosome number. Consistently, we found experimentally that bipolar centrosome clustering is promoted as mitotic cell aspect ratio and volume decrease in tetraploid cancer cells. Our model provides mechanistic explanations for many more experimental phenomena and a useful theoretical framework for future studies of spindle assembly.

Polyploidy as a strategy to increase taxane production in yew cell cultures: Obtaining and characterizing a Taxus baccata tetraploid cell line

Novel approaches to optimize the production of plant specialized metabolites are crucial to reach maximum productivity of plant biofactories. Plant polyploidization frequently enhances protein synthesis and thereby increases the biosynthesis of specialized metabolites. Paclitaxel is a valuable anticancer agent scarcely produced in nature. Therefore, plant biofactories represent a sustainable alternative source of this compound and related taxanes. With the aim of improving the productivity of Taxus spp. cell cultures, we induced polyploidy in vitro by treating immature embryos of Taxus baccata with colchicine. To obtain the polyploid cell lines, calli were induced from T. baccata plantlets previously treated with colchicine and ploidy levels were accurately identified using flow cytometry. In terms of cell morphology, tetraploid cells were about 3-fold bigger than the diploid cells. The expression of taxane pathway genes was higher in the tetraploid cell line compared to the diploid cells. Moreover, taxane production was 6.2-fold higher and the production peak was achieved 8 days earlier than in the diploid cell line, indicating a higher productivity. The obtained tetraploid cell line proved to be highly productive, constituting a step forward towards the development of a bio-sustainable production system for this chemotherapeutic drug.

Abstract LB175: Ploidy as a predictive biomarker for gemcitabine sensitivity in triple-negative breast cancers

Abstract Polyploid giant cancer (PGCC) state is a common response of cancer cells to various stressors including chemotherapy, irradiation, hypoxia and viral infection. Upon stress, PGCCs adopt an endoreplication in which the genome replicates, mitosis is omitted, and cells grow in size, leading to resistance. How accessible endoreplication is to a cell, therefore, directly translates to its resistance to therapy. In this study, we hypothesized that endoreplication and PGCC state are more plausible to cancer cells that already have a higher ploidy content prior to therapy. To test this hypothesis, we developed a comprehensive three-tier framework consisting of i) computational, ii) in vitro and iii) in silico components. We designed a set of ordinary differential equations (ODEs) to model how cells enter and exit the PGCC state in response to a given stressor. We engineered how this in silico approach interacts with in vitro experiments into a broadly applicable software solution called CLONEID. The software uses computer vision to monitor phenotypic changes in cell and nuclear size from standard bright-field microscopy and classify cells into PGCC and non-PGCC states. We used CLONEID to test various therapeutic agents for their ability to select for a stable near-tetraploid population in a set of near-diploid cell lines. Through spontaneous cell fusions, we also obtained tetraploid breast cancer cells matched with their parental lines. Altogether, this framework, now, enables us i) to monitor the PGCC state experimentally ii) in matched cell lines with differential DNA content iii) to model the successful entrance and exit rates to and from the endoreplication state, respectively. As the first application of this framework, we tested the ability of our matched triple-negative breast cancer (TNBC) lines (SUM-159 and MDA-MB-231) to access the PGCC state upon treatment with 18 commonly-used chemotherapy agents. We observed that gemcitabine caused continued cell growth without cell division in both tetraploid SUM-159 and MDA-MB-231 cells whereas near-diploid parental cells were hypersensitive to the treatment. Consequently, tetraploid cancer cells continued to safely grow in the presence of gemcitabine. Furthermore, these PGCCs re-entered the proliferative cell cycle and grew in cell number when treatment is terminated. Gemcitabine (GEM)-based chemotherapy is a standard treatment for patients with TNBC although its efficacy is limited mainly due to drug resistance. Moreover, such poor response rate is coupled with severe side effects that frequently leads to the failure of vital organs, serious secondary diseases, and co-morbidities. Our findings suggest that ploidy is a predictive biomarker for gemcitabine sensitivity. Thus, we expect our findings and three-component framework strategy to help stratify the TNBC patient population by their response to gemcitabine. In addition, our mathematical modelling approach has the promising potential to inform personalized dose optimization and to effectively decrease administered gemcitabine dose for a subset of patients, which would alleviate therapy-associated side effects and lethalities. Citation Format: Vural Tagal, Jackson P. Cole, Daria Miroshnychenko, Andriy Marusyk, Noemi Andor. Ploidy as a predictive biomarker for gemcitabine sensitivity in triple-negative breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB175.

Abstract 3171: Detecting ploidy specific vulnerability to resource restriction: An integrated in vitro and in silico approach

Abstract Changes in the number of copies of the genome, i.e. changes in ploidy are widespread among cancer cells. Increased ploidy is thought to benefit cancer cells by conferring robustness against deleterious consequences of genomic instability. However, whether there are any potential costs associated with increased ploidy has not been sufficiently investigated. One hypothesis holds that high ploidy cells may exhibit increased sensitivity to limitations in resources, due to the extra energy required for the replication of a larger genome. To address this hypothesis, we developed an integrated in vitro and in silico system to investigate the response to glucose restriction in diploid and tetraploid cells. Near diploid (2N) SUM159 breast cancer cells were fused to generate an isogenic tetraploid (4N) cell line. 2N or 4N cells were plated with varying initial concentrations of glucose. Cells grew for five days and media was not refreshed, so cells depleted the glucose in the media until they eventually died. Throughout the experiments, glucose concentration was measured at 24 hour intervals, and images were taken at 8 hour intervals allowing quantification of the number of alive or dead cells over time. These in vitro data were then used as inputs to the in silico portion of our system, which consists of an Ordinary Differential Equation (ODE) model of cancer cell growth. ODE model parameters were estimated using the measured outputs from the in vitro experiments. Parameters estimated from the ODE model gave insight into differences between the 2N and 4N cell lines. We found that 4N cells outcompeted 2N cells at high glucose concentrations, due to their ability to divide more rapidly when glucose was abundant. However, 2N cells were able to outcompete 4N cells at lower glucose concentrations. The advantage of 2N cells at low glucose was not due to an increased proliferative capacity. Instead, 2N cells were more resistant to cell death when glucose was limited. Our next steps will be to expand our system to assess ploidy specific sensitivity to other resources, such as phosphate or oxygen. The ODE model we have developed allows us to identify resource conditions that will select for tumor cells based on ploidy. In future this knowledge can be used to suggest therapeutics that can modulate resource availability within tumors, in order to steer tumor evolution towards less aggressive phenotypes. Citation Format: Richard J. Beck, Didem Ilter, Ana P. Gomes, Noemi Andor. Detecting ploidy specific vulnerability to resource restriction: An integrated in vitro and in silico approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3171.