Biology subjects

Pavin, N.

Publications and source records attributed to Pavin, N..

14 recordsLinked to original sources

bioRxiv2026

Coordinated control of both microtubule ends regulates mitotic spindle length

The mitotic spindle is a biomechanical structure whose length must be precisely controlled to ensure faithful chromosome segregation. The treadmilling of microtubules towards centrosomes, termed poleward flux, is involved in spindle length control. However, poleward flux has been shown to be both inversely and directly proportional to spindle length, a contradiction that remains unexplained by current mechanisms. Here we introduce a model which demonstrates that length-dependent regulation at both microtubule ends allows plus- and minus-end dynamics to synchronize with one another, enabling pathways of poleward flux-based spindle length control which can rectify previous results. Moreover, our model predicts that spindle length and poleward flux can vary independently via simultaneous perturbations at both microtubule ends, which we experimentally validate with combinations of KIF18A, KIF2A, and KATNB1 depletions in human cells. Our results thus resolve a longstanding paradox and provide mechanistic insight into the reciprocal control of spindle length and poleward flux.

biophysics↗

bioRxiv2025

Slowdown of microtubule retrograde flow enables axon and dendrite development and maintenance

Distinct microtubule arrays form in axons and dendrites defining their functions in neurons. These arrays are thought to develop through separate processes. Here we challenge this view by showing that axons and dendrites develop by a unifying process: slowdown of microtubule retrograde flow (MT-RF), a recently discovered mechanism of microtubule dynamics. By integrating quantitative data of microtubule dynamics and distributions into a newly developed biophysical model of microtubules across developmental stages, we uncover that MT-RF interacts with microtubule stability and nucleation. Without MT-RF slowdown, this interaction suppresses development and maintenance of axonal and dendritic microtubule arrays. In axons, MT-RF slowdown enables microtubules to reach the tip, even at long distances, supporting axon growth. In dendrites, late MT-RF slowdown facilitates an efficient increase in stable microtubules. Thus, our data-integrated model reveals MT-RF slowdown as central for the development of distinct neuronal compartments, providing a unifying mechanism for microtubule-related physiology.

neuroscience↗

bioRxiv2025

Distinct aneuploid karyotypes are universally selected for across cancers

Aneuploid karyotype evolution leads to immense variability in cancer patient prognosis, so characterizing relevant trends has been an important objective (1-9). Recurrent chromosome gains and losses as well as oncogenic mutations have been associated with specific cancers (10-14), but a general trend in aneuploidy evolution has not yet been identified. Here we show a universal selection principle for karyotypes composed entirely of disomies and trisomies that is conserved across many different cancer types and even in yeast. This finding is surprising enough on its own, as cancers do not typically have generalized trends, but we also see that these karyotypes exhibit a 3 times lower mutation rate of the cancer suppressor gene TP53 compared to other aneuploid karyotypes. We find that, in general, karyotypes composed of combinations of any two chromosome copy numbers, termed binary karyotypes, make up over three-quarters of the Mitelman database, which we explain by a 15% increased fitness relative to other aneuploid karyotypes. In conclusion, our results reveal binary karyotypes as a distinct category of aneuploid karyotypes that are tolerated by p53 and universally selected for independent of encoded genes or any other chromosome-specific feature, shifting the current paradigm of aneuploid cell classification.

cancer biology↗

bioRxiv2025

A Universal Scaling Law for Mitotic Spindles Driven by Chromosome Crowding

Cells regulate the size of their internal structures to maintain function in diverse biological settings1. The mitotic spindle, a molecular micro-machine responsible for chromosome segregation2, must scale to accommodate genomes varying in size by over 10,000-fold across eukaryotes3. Yet, how spindle biomechanics adapts to vastly different genome sizes remains unknown. Here, we uncover a universal spindle scaling law, where metaphase plate width scales with genome size following a power law with an exponent of [~]1/3. We hypothesize that chromosome crowding within the metaphase plate generates compressive forces as chromosomes push against each other, thereby determining spindle size and shape. Our experiments with altered chromosome number and mechanical properties in healthy and cancerous human and mouse cells, together with a theoretical model based on inter-chromosome pushing forces and mechanical manipulations of cells, confirm this hypothesis. Extending these insights across eukaryotes, we demonstrate that chromosome crowding predicts the observed power-law scaling. The biophysical constraint of chromosome crowding offers a mechanistic explanation for the evolution of open mitosis and mitotic cell rounding, enabling the division of larger genomes. Spindle adaptability to larger genomes may promote the proliferation of polyploid cells, driving not only tumor progression but also speciation during evolution.

biophysics↗

bioRxiv2024

Motor proteins in antiparallel microtubule overlaps drive chromosome congression during mitotic spindle assembly

Mitotic spindle, a micromachine composed of microtubules and associated proteins, plays a pivotal role in ensuring the accurate segregation of chromosomes. During spindle assembly, initially randomly distributed chromosomes are transported toward the equatorial plate and experiments suggest that several competing mechanisms can contribute to this process of chromosome congression. However, a systematic theoretical study of forces relevant to chromosome congression is still lacking. Here we show, by introducing a physical model, that length-dependent forces generated by motor proteins transport chromosomes toward the spindle equator. Passive crosslinkers, on the other hand, can generate off-centering forces that impair chromosome congression. Our mean-field approach also reveals that stable points can exist in the vicinity of spindle poles, in addition to the one in the center, and thus provides an explanation for erroneous spindles with polar chromosomes. Taken together, our study provides a comprehensive approach to understanding how different spindle components interact with each other and generate forces that drive chromosome congression.

biophysics↗

bioRxiv2024

Oscillatory dynamics of Rac1 activity in Dictyostelium discoideum amoebae

Small GTPases of the Rho family play a central role in the regulation of cell motility by controlling the remodeling of the actin cytoskeleton. In the amoeboid cells of Dictyostelium discoideum, the active form of the Rho GTPase Rac1 regulates actin polymerases at the leading edge and actin filament bundling proteins at the posterior cortex of polarized cells. However, constitutive Rac1 dynamics in D. discoideum have not yet been systematically investigated. Therefore, we monitored the spatiotemporal dynamics of Rac1 activity in vegetative amoebae using a specific fluorescent probe. We observed that plasma membrane domains enriched in active Rac1 not only exhibited stable polarization, but also showed rotations and oscillations. To simulate the observed dynamics, we developed a mass-conserving reaction-diffusion model based on the circulation of Rac1 between the membrane and the cytoplasm in conjunction with its activation by GEFs, deactivation by GAPs and interaction with the Rac1 effector DGAP1. Our theoretical model accurately reproduced the experimentally observed dynamic patterns, including the predominant anti-correlation between active Rac1 and DGAP1. Significantly, the model predicted a new colocalization regime of these two proteins in polarized cells, which we confirmed experimentally. In summary, our results improve the understanding of Rac1 dynamics and reveal how the occurrence and transitions between different regimes depend on biochemical reaction rates, protein levels and cell size. This study not only expands our knowledge of the behavior of small GTPases in D. discoideum amoebae, but also provides a simple modeling framework that can be adapted to study similar dynamics in other cell types.

systems biology↗

bioRxiv2023

Mechanical Dissociation of Tissues for Single Cell Analysis Using a Simple Motorized Device

ABSTRACT/SUMMARYThe use of single cell analysis methods has grown rapidly in the last two decades and has led to rapid discoveries in cell biology and beyond. Single cell analysis requires complex systems like tissues to be dissociated, separating individual cells from extracellular tissue materials. This requires manual processing of tissues and materials through chopping, pipetting, and suspension with enzymes for degradation of the structural elements of the tissue. Manual processing can be time consuming and lead to variability between scientists. Automating this process through motorized dissociation could thus improve reproducibility of research and reduce time of cell manipulation prior to analysis. Here, we have designed a low-cost, customizable automatic tissue dissociator device that can be easily assembled by research groups for individual use. Our device allows for customizable programmed dissociation protocols for ease of use and reproducibility between researchers and can be placed into heat or cold environments based on the protocol need. We have found this device comparable in cell viability and reproducibility to manual dissociation, while significantly reducing time spent and even enhancing cells extracted from more fibrous tissues. Broad dissemination and use of this device could enhance single cell analysis reproducibility and provide a time-saving alternative to the currently used manual dissociation protocols.

cell biology↗

bioRxiv2022

Proliferative advantage of specific aneuploid cells drives evolution of tumor karyotypes

Most tumors have abnormal karyotypes, which arise from mistakes during mitotic division of healthy euploid cells and evolve through numerous complex mechanisms. In a recent mouse model with high levels of chromosome missegregation, chromosome gains dominate over losses both in pretumor and tumor tissues, whereas tumors are characterized by gains of chromosomes 14 and 15. However, the mechanisms driving clonal selection leading to tumor karyotype evolution remain unclear. Here we show, by introducing a mathematical model based on a concept of a macro-karyotype, that tumor karyotypes can be explained by proliferation-driven evolution of aneuploid cells. In pretumor cells, increased apoptosis and slower proliferation of cells with monosomies lead to predominant chromosome gains over losses. Tumor karyotypes with gain of one chromosome can be explained by karyotype-dependent proliferation, while for those with two chromosomes an interplay with karyotype-dependent apoptosis is an additional possible pathway. Thus, evolution of tumor-specific karyotypes requires proliferative advantage of specific aneuploid karyotypes. SignificanceMost tumors have an erroneous number of chromosomes, which arise from mistakes during division of healthy cells and evolve through numerous complex mechanisms, including chromosome missegregation, cell proliferation and cell death. However, understanding the mechanisms leading to tumor evolution from healthy cells is a hot topic. Here we show, by introducing a "macro-karyotype model", that perturbed number of chromosomes in tumor cells arises predominantly from faster division of cells characterized by a specific combination of chromosomes, or together with irregular cell death. This finding, strengthened by comparison of our theory with experimentally observed combination of chromosomes in different stages of tumor development, gives a direction for future experiments in identifying the key processes underlying tumor development.

biophysics↗

bioRxiv2022

Kinetochore- and chromosome-driven transition of microtubules into bundles promotes spindle assembly

Mitotic spindle assembly is crucial for chromosome segregation and relies on bundles of microtubules that extend from the poles and overlap in the middle. However, how these structures form remains poorly understood. Here we show that overlap bundles arise through a network-to-bundles transition driven by kinetochores and chromosomes. STED super-resolution microscopy revealed that PRC1-crosslinked microtubules initially form loose arrays, which become rearranged into bundles. Kinetochores promote microtubule bundling by lateral binding via CENP-E/kinesin-7 in an Aurora B-regulated manner. Bundle separation is driven by steric interactions of the bundle-associated chromosomes at the spindle midplane since spindles with uncondensed or uncongressed chromosomes are narrower. In agreement with experiments, theoretical modeling suggests that bundles arise through competing attractive and repulsive mechanisms. Finally, perturbation of overlap bundles led to inefficient correction of erroneous kinetochore-microtubule attachments. Thus, kinetochores and chromosomes drive coarsening of a uniform microtubule array into overlap bundles, which promote not only spindle formation but also chromosome segregation fidelity.

cell biology↗

bioRxiv2021

Measurement of curvature and twist of microtubule bundles in the mitotic spindle

The highly ordered spatial organization of microtubule bundles in the mitotic spindle is crucial for its proper functioning. The recent discovery of twisted shapes of microtubule bundles and spindle chirality suggests that the bundles extend along curved paths in three dimensions, rather than being confined to a plane. This in turn implies that rotational forces exist in the spindle in addition to the widely studied linear forces. However, studies of spindle architecture and forces are impeded by a lack of a robust method for the geometric quantification of microtubule bundles in the spindle. In this paper, we describe a simple method for measuring and evaluating the shapes of microtubule bundles, by characterizing them in terms of their curvature and twist. By using confocal microscopy, we obtain three-dimensional images of spindles, which allow us to trace the entire microtubule bundles. For each traced bundle, we first fit a plane, and then fit a circle lying in that plane. With this easily reproducible method, we extract the curvature and twist, which represent the geometric information characteristic for each bundle. As the bundle shapes reflect the forces within them, this method is valuable for the understanding of forces that act on chromosomes during mitosis.

biophysics↗

bioRxiv2018

Pivoting of microtubules driven by minus end directed motors leads to their alignment to form an interpolar bundle

At the beginning of mitosis, the cell forms a spindle made of microtubules and associated proteins to segregate chromosomes. An important part of spindle architecture is a set of antiparallel microtubule bundles connecting the two spindle poles. A key question is how microtubules extending at arbitrary angles form an antiparallel interpolar bundle. Here we show that microtubules meet at an oblique angle and subsequently rotate into antiparallel alignment. By combining experiments with theory, we show that microtubules from each pole search for those from the opposite pole by performing random angular movement. Upon contact of two microtubules, they slide sideways along each other towards the minus end, which we interpret as the action of minus end directed Cut7/kinesin-5 motors. In conclusion, random rotational motion helps microtubules from the opposite poles to find each other and subsequent accumulation of motors allows them to generate forces that drive interpolar bundle formation.

cell biology↗

bioRxiv2017

Chromosome loss rate in cells of different ploidy can be explained by spindle self-organization

The mitotic spindle segregates chromosomes and minimizes chromosome loss for the specific number of chromosomes present in an organism. In Saccharomyces cerevisiae, for example, haploid and diploid cells are part of the sexual life cycle and have a thousand times lower rate of chromosome loss than tetraploid cells. Currently it is unclear what constrains the number of chromosomes that can be segregated with high fidelity in an organism. Here we developed a mathematical model to study if different rates of chromosome loss in cells with different ploidy can arise from changes in (1) spindle dynamics and (2) a maximum duration of mitotic arrest, after which cells enter anaphase. Our model reveals how small increases in spindle assembly time can result in exponential differences in rate of chromosomes loss between cells of increasing ploidy and predicts the maximum duration of mitotic arrest.

evolutionary biology↗

bioRxiv2017

The mitotic spindle is chiral due to torques generated by motor proteins

Mitosis relies on forces generated in the spindle, a micro-machine composed of microtubules and associated proteins1,2. Forces are required for the congression of chromosomes to the metaphase plate and separation of chromatids in anaphase3-6. However, torques may also exist in the spindle, yet they have not been investigated. Here we show that the spindle is chiral. Chirality is evident from the finding that microtubule bundles follow a left-handed helical path, which cannot be explained by forces but rather by torques acting in the bundles. STED super-resolution microscopy, as well as confocal microscopy, of human spindles shows that the bundles have complex curved shapes. The average helicity of the bundles with respect to the spindle axis is 1.2{degrees}/m. Inactivation of kinesin-5 (Eg5/Kif11) abolished the chirality of the spindle, suggesting that this motor generates the helical shape of microtubule bundles. To explain the observed shapes, we introduce a theoretical model for the balance of forces and torques acting in the spindle, and show that torque is required to generate the helical shapes. We conclude that torques generated by motor proteins, in addition to forces, exist in the spindle and determine its architecture.

cell biology↗

bioRxiv2017

Pivot-and-bond model explains microtubule bundle formation

During mitosis, bundles of microtubules form a spindle, but the physical mechanism of bundle formation is still not known. Here we show that random angular movement of microtubules around the spindle pole and forces exerted by passive cross-linking proteins are sufficient for the formation of stable microtubule bundles. We test these predictions by experiments in wild-type and ase1{Delta} fission yeast cells. In conclusion, the angular motion drives the alignment of microtubules, which in turn allows the cross-linking proteins to connect the microtubules into a stable bundle.

biophysics↗