The responsive nucleus: morphological signatures of cellular state

ABSTRACT

Nuclear morphology is increasingly recognized as an integrative indicator of cellular state across diverse physiological and pathological conditions. Beyond storing genetic material, the nucleus also acts as a dynamic sensor responding to mechanical, biochemical, and epigenetic cues. These stimuli reshape nuclear size, architecture, chromatin organization, and envelope integrity providing valuable information about cell cycle progression, differentiation, senescence, and stress responses. Such features offer a scalable and non-invasive approach to assess cell fate. In this review, we position the nuclear envelope as a key sensor of nuclear morphology, outline major triggers of nuclear deformation, discuss the molecular and biophysical processes preserving nuclear integrity and highlight the diversity of nuclear phenotypes with diagnostic and prognostic value. This review provides a comprehensive and critical synthesis of the current knowledge on the regulation and functional relevance of nuclear morphology to serve as a resource and reference point for future interdisciplinary studies.

Introduction

Since the inception of cellular biology, enabled by breakthroughs in optical microscopy, the shape and structure of the nucleus have offered profound insights into cellular identity, tissue architecture, and the emergence of pathological states. In the 19th century, foundational contributions by Walther Flemming, Rudolf Virchow, and Ramón y Cajal, among others, have respectively characterized mitosis, cellular pathology, and neuronal structure, and have established morphological analysis as a central method in cell biology and biomedical science [1]. Even earlier, Alexander von Humboldt emphasized observation-driven approach to biology that laid conceptual groundwork for linking structure, form, and function. These early insights recognized nuclear morphology not as an aesthetic trait, but as a fundamental and functional readout of cellular state with diagnostic and mechanistic relevance.

In the current age of high-throughput omics and computational biology, direct observation is sometimes regarded as outdated – secondary to molecular and genomic data. Yet this view underestimates the integrative power of morphology. Nuclear morphology is shaped by a convergence of factors: chromatin architecture, envelope composition, cytoskeletal tension, and mitotic fidelity [2]. These inputs are not random, they are interpretable. In this way, nuclear shape serves as a real-time readout of both nuclear structure and cellular state. Importantly, nuclear morphology is not only a passive reflection of internal cell status; it plays an active and instructive role in dynamic cellular behaviors [3]. In contexts such as cancer and immunology, where cellular plasticity, invasion, migration, and metastasis are hallmarks of disease progression and immune function, nuclear deformation and morphological adaptation are closely tied to mechanotransduction, genome organization, and cellular fate decisions [4]. Abnormalities in nuclear shape often parallel – and sometimes predict – changes in transcriptional programs and epigenetic states that underline aggressive or immune-evasive phenotypes. Thus, a deeper understanding of nuclear morphology is essential for uncovering how cells adapt to stress and exploit mechanical and structural constraints during tumor progression and immune surveillance.

In this review, we revisit the nucleus through the lens of its morphology as a biologically meaningful phenotype, which reflects chromatin state, envelope integrity, mechanical forces, and genomic stability, to highlight its continuous value as a tool for interpreting cell state in both health and disease. To this end, this review is structured in five key sections:

1. The nuclear envelope – chromatin organization as the architectural control of nuclear shape.

2. The mechanisms and triggers that drive nuclear deformation.

3. An overview of the mechanisms implicated in nuclear envelope homeostasis.

4. An atlas of nuclear morphologies, charting their diversity across biology as a functional readout for cellular status.

5. Future perspectives and conclusions.

While we have aimed to provide a comprehensive overview of the field, space constraints have limited our ability to cite all relevant studies. We sincerely apologize to those authors whose important contributions may not be included.

The nuclear envelope – chromatin axis: architectural control of nuclear shape

The nuclear envelope (NE) is a dynamic and highly regulated double-membrane that separates the nucleus, containing the genetic material, from the cytoplasm of the cell. The NE is composed of two closely related lipid bilayers, referred to as the outer nuclear membrane (ONM) and the inner nuclear membrane (INM), which are formed as an extension of the endoplasmic reticulum (ER) and share many of its structural and functional properties (Figure 1) [5]. Beyond serving as a barrier, the NE plays a central role in maintaining nuclear architecture, positioning, and regulation of gene expression in response to mechanical cues through a network of integral proteins and associated scaffolding elements [6].

Figure 1.

Key structural and functional elements of nuclear envelope architecture.

The nuclear envelope (NE) consists of two concentric membranes, named the outer nuclear membrane (ONM) and the inner nuclear membrane (INM), formed as an extension of the endoplasmic reticulum (ER). The ONM interacts with the cytoskeleton through the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex, composed of SUN-domain proteins anchored to the INM and KASH-domain proteins embedded in the ONM. This complex physically bridges the nuclear membranes and connects them to actin filaments, microtubules (through kinesin and/or dynein binding), and intermediate filaments such as vimentin or desmin (via plectin engagement), facilitating the transmission of mechanical forces across the NE. Nuclear pore complexes (NPCs) perforate the NE to mediate selective bidirectional transport between nucleoplasm and cytoplasm. Additional regulators such as Torsin A, located in the perinuclear space, modulate NE structure, and regulate NPC assembly. Invaginations of the NE to the nucleoplasm, known as nucleoplasmic reticulum, may serve for calcium signaling and chromatin organization. The INM harbors integral membrane proteins such as the LEM-domain proteins Emerin, MAN1, and LAP2, and the lamin B receptor (LBR). The INM is closely associated with a meshwork of V type intermediate filaments formed by lamin A/C and lamin B. This network allows the anchorage of chromatin through lamin-associated domains (LADs) and the interaction with heterochromatin protein 1 (HP1), barrier-to-autointegration factor (BAF), and other chromatin-binding proteins. Whitin the nucleoplasm, nuclear actin, myosin, and spectrin contribute to nuclear mechanical plasticity, genome stability and chromatin dynamics.

At the cytoplasmic interface, the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex is a central architectural element of the NE that forms a continuous molecular bridge across the NE. The LINC complex is composed of KASH-domain proteins (Klarsicht, ANC-1 and SYNE/Nesprin-1 and −2) that are embedded in the ONM and interact with cytoskeletal elements such as actin filaments, microtubules – through a kinesin or dynein binding —, and intermediate filaments like vimentin or desmin. These KASH proteins are anchored across the perinuclear space to SUN-domain proteins (Sad1/UNC84) localized in the INM, which in turn connect to the nuclear lamina and chromatin (Figure 1) [7,8]. SUN1 and SUN2, the two main SUN-domain proteins, also play distinct roles during NE reassembly and nuclear pore complexes (NPC) organization. Through this configuration, the LINC complex transmits mechanical forces from the cytoskeleton into the nucleus, thus influencing nuclear shape, positioning, and even transcriptional activity [9–12]. Interestingly, during early mitosis, particularly in prophase, LINC is essential for establishing the timely recruitment of dynein to the NE, which provides spatial cues that guide centrosome positioning along the shortest nuclear axis. This coordination ensures robust centrosome alignment prior to nuclear envelope breakdown (NEBD), a critical step for accurate mitotic progression [13].

In addition to the LINC complex, NPCs are embedded at sites where the ONM and INM converge and therefore contribute to the physical and functional connection between the nucleus and the cytoplasm (Figure 1). These large assemblies, with a molecular mass ranging from 60 to 100 MDa, are composed of multiple copies of about 30 distinct nucleoporins (NUPs) and mediate selective nucleocytoplasmic transport of macromolecules. Transmembrane NUPs such as NDC1 and POM121 are essential for anchoring NPCs to the NE and coordinating their insertion and assembly during interphase and mitotic exit. Recent studies have revealed that other NUPs interact with chromatin and contribute to the spatial organization of the genome, thereby influencing gene expression [14]. This highlights a novel role for NPCs beyond their canonical function in nucleocytoplasmic transport.

Beneath the INM lies the nuclear lamina, a dense filamentous network composed primarily of type V intermediate filaments known as lamins (Figure 1). These include A-type lamins (lamin A and C, encoded by LMNA) and B-type lamins (lamin B1 and B2, encoded by LMNB1 and LMNB2) [15,16]. Lamin A and lamin B are synthesized as precursor proteins (prelamins) and undergo distinct post-translational modifications. For instance, lamin A is processed through farnesylation, carboxymethylation, and a final proteolytic cleavage that removes its C-terminal domain, resulting in the loss of its farnesyl group upon assembly. In contrast, Lamin B retains its farnesylated tail, anchoring it more stably to the INM [17,18]. In contrast, Lamin C does not require these modifications to reach its mature form. Together with INM-associated proteins such as Emerin, LAP2, and MAN1 (members of the LEM-domain family), lamins provide structural support to the NE. Nonetheless, lamins contribute differentially to nuclear mechanics: A-type lamins enhance nuclear stiffness, while B-type lamins provide elasticity, and the relative abundance of each lamin type varies across cell types, reflecting tissue-specific mechanical demands [19,20]. Among the INM proteins, Lamin B Receptor (LBR) plays a crucial role in anchoring heterochromatin to the nuclear periphery. LBR is a multi-pass transmembrane protein that binds directly to B-type lamins and chromatin-associated proteins, including the heterochromatin protein 1 (HP1) (Figure 1) [21]. Its interaction with chromatin is essential for the establishment and maintenance of peripheral heterochromatin domains, particularly during early development and in differentiated cells with low levels of lamin A/C. HP1 facilitates the tethering of H3K9-methylated chromatin to the NE by acting as a structural and regulatory scaffold, a process modulated by its phase separation properties and post-translational modifications [22,23]. Another key factor in NE-chromatin interactions is the Barrier-to-Autointegration Factor (BAF), a small DNA-binding protein that bridges chromatin to the NE by interacting with LEM-domain proteins (Figure 1). BAF plays a pivotal role during NE reassembly by targeting INM proteins to chromatin and facilitating the reformation of the nuclear lamina [24,25]. Its ability to bind both DNA and NE proteins makes it a central mediator of chromatin tethering and nuclear architecture. Alongside lamins and lamin-associated proteins, nuclear actin, myosins, and spectrins function as integral components of the nucleoskeleton, contributing to both nuclear mechanical plasticity and genome stability (Figure 1). Polymerized nuclear actin and myosin motor proteins assemble dynamic scaffolds stabilized by spectrins, which cross-link with chromatin and modulate gene expression (reviewed in [26,27]).

Additional components such as TorsinA, an AAA+ ATPase located in the perinuclear space, and its INM-associated cofactor LAP1 are involved in maintaining NE integrity and regulating NPC assembly (Figure 1) [28,29]. Furthermore, the NE can form invaginations into the nucleoplasm, known as the nucleoplasmic reticulum (NR), which may serve roles in calcium signaling and chromatin organization, although their precise functions remain under investigation (Figure 1) [30].

The nuclear lamina and associated INM proteins also play a pivotal role in genome organization [31]. They interact with specific chromatin regions known as lamin-associated domains (LADs), which are typically enriched in transcriptionally inactive heterochromatin [32]. These interactions help compartmentalize the genome and regulate gene expression. Importantly, LADs are not static; their organization can change during development or in response to environmental stimuli, highlighting the active role of the NE in mechanotransduction and genome regulation [33].

Within the nucleus, chromatin is organized into distinct, nonrandomly distributed regions known as chromosome territories. This spatial arrangement supports efficient gene regulation and contributes to genome stability. This organization is completely re-arranged during mitosis, in which chromatin undergoes extensive condensation into individual chromosomes, a process that ensures their accurate segregation and the faithful transmission of genetic material to each daughter cell during symmetric open cell division. This process requires a transient but highly orchestrated disassembly process known as NEBD [34]. This process begins in early prophase and is initiated by the activation of mitotic kinases, particularly cyclin-dependent kinase 1 (CDK1), which phosphorylates key structural components of the NE such as NUPs and lamins. These phosphorylation events trigger the disassembly of NPCs and the cessation of nucleocytoplasmic transport, promote the depolymerization of the lamina, and lead to the retraction of nuclear membranes into the ER [35,36]. After chromosome segregation, NE reassembly is initiated by the recruitment of INM proteins and lamins to decondensing chromatin, guided in part by BAF, followed by NPC reformation and restoration of nuclear compartmentalization [37].

In all, as a central integrator of mechanical signals, the nuclear envelope – chromatin interface is shaped by a dynamic interplay between cytoskeletal forces and chromatin organization, which together define nuclear morphology.

Triggers and mechanisms of nuclear deformation

Building upon the architectural principles outlined above, it becomes evident that nuclear shape is not merely a passive outcome of structural components, but a responsive feature shaped by diverse stimuli. We next examine the key triggers and mechanisms modifying nuclear morphology leading to variations in size, shape, and structural integrity of the nucleus. These can be broadly categorized into internal forces arising from chromatin organization and nuclear components, which contribute to nuclear pressure and osmotic balance; and external forces, transmitted through the cytoskeleton and extracellular environment, which impose mechanical tension on the NE.

Internal forces

Internal forces originate from within the nucleus and include chromatin organization, nuclear lamina composition, nucleoskeletal dynamics, and mitotic processes. These components collectively define the mechanical properties of the nucleus, which behaves as a viscoelastic material.

Chromatin structure and epigenetic regulation

Chromatin compaction and spatial organization play a central role in determining nuclear stiffness and shape. The compaction state of chromatin exerts internal pressure that influences nuclear volume, surface area, and curvature (Figure 2). For instance, constitutive heterochromatin, characterized by the histone modification H3K9me3, is essential for chromocenter compaction and contributes significantly to nuclear morphology [38]. Loss of this mark leads to reduced nuclear stiffness and increased susceptibility to blebbing and rupture. In contrast, H3K9me2 does not appear to exhibit comparable mechanical impact on nuclear integrity. Facultative heterochromatin, marked by H3K27me3, also contributes to nuclear stiffness, although its influence is restricted to chromatin-based mechanics and does not extend to lamina-associated stiffness. Thus, the depletion of constitutive heterochromatin affects both chromatin and lamina rigidity, whereas the loss of facultative heterochromatin primarily alters chromatin-level mechanical properties [38]. HP1 is crucial for recognizing and maintaining H3K9me2/3 marks [39], thus disruption of HP1 may therefore compromise heterochromatin stability and potentially affect NE stability. Among its isoforms, HP1γ has been specifically implicated in preserving NE structure [40]. Indeed, the depletion of HP1γ triggers aberrations in RNA splicing and induces the production of progerin, a mutant form of lamin A associated with nuclear abnormalities [41]. Global chromatin decompaction induced for instance by overexpression of HMGN5, a nucleosomal binding protein, significantly reduces nuclear stiffness and elasticity. In mice, HMGN5 depletion was shown to lead to misshapen nuclei resembling those appearing upon LMNA loss, ultimately triggering cardiac failure [42]. These findings underscore the importance of heterochromatin in resisting mechanical stress in contractile tissues.

Figure 2.

Overview of the main mechanisms driving nuclear deformation.

Various intracellular and extracellular triggers are known to modify nuclear morphology. Within the nucleus, alterations in chromatin organization and modifications, such as methylations (me), disruptions in lamin or nucleoskeletal integrity, and DNA damage can compromise the structure and function of the nuclear envelope (NE). The NE itself, composed of a lipid bilayer, is also sensitive to changes in lipid composition. The Nuclear Pore Complexes (NPCs) serve as mechanosensors of NE status. Upon deformation of the NPC or mechanical stress on actin fibers, transcription factors like Yes-associated protein (YAP), Transcriptional coactivator with PDZ-binding motif (TAZ) or Myocardin-Related Transcription Factor A (MRTF-A), respectively translocate into the nucleus to initiate stress-responsive gene expression. From the cytoplasm, the cytoskeleton, particularly actin filaments and microtubules (MTs), can exert mechanical forces on the NE either through LINC complexes or direct physical pressure. Extracellular forces, such as those arising from the extracellular matrix (ECM) stiffness, cell migration, or external pressure, can also transmit mechanical stress to the plasma membrane (PM), which in turn convey this stress to the NE and potentially lead its deformation.

Euchromatin, characterized by an open and transcriptionally active state, also influences nuclear morphology. Increased euchromatin content, which is often associated with histone acetylation, softens the nucleus and promotes nuclear flattening or irregular shapes under mechanical load. This decompacted state reduces internal pressure and weakens nuclear resistance to compression, making nuclei more deformable in 3D environments or during migration through confined spaces. Conversely, transitions toward a more compact chromatin state restore nuclear stiffness and help maintain spherical morphology [43]. These observations highlight that both heterochromatin and euchromatin act as dynamic internal forces shaping nuclear architecture.

Furthermore, changes in histones non-related to heterochromatin have been also shown to influence nuclear mechanics. WD repeat domain 5 (WDR5) and RbBP5, components of the H3K4 methyltransferase complex, regulate nuclear deformability and chromatin organization in 3D environments. Loss of WDR5 diminishes the nuclei mechanical adaptation normally observed during the transition from 2D to 3D growth [44]. Similarly, factors involved in chromatin remodeling such as complexes SWI/SNF ATPases (e.g. BRG1) have been shown to modulate nuclear shape independently of cytoskeletal forces [45]. These complexes reorganize chromatin architecture, and their activity can lead to chromatin decompaction, which in turn reduces nuclear resistance to compression and alters curvature [46]. Such changes directly impact nuclear morphology and may contribute to mechanical vulnerability in disease states. Pharmacological modulations of chromatin state further illustrate its mechanical role on nuclear morphology. Epigenetic modulators such as methylstat (an H3K9 demethylase inhibitor) and SAHA (a histone deacetylase inhibitor) exert opposing effects on the formation of toroidal nuclei, donut- or ring-shaped nuclei with central void encompassing cytosolic components [47]. Toroidal nuclei have recently emerged as a biomarker of chromosomal instability (CIN) further supporting the role of chromatin state in the regulation of nuclear morphology and genome stability.

Figure 3.

(Continued).

At the molecular level, nucleosome/nucleosome interactions are important for maintaining nuclear rigidity. Disruption of these interactions, due to histone tail acetylation or DNA digestions, reduces nuclear stiffness. Moreover, the ionic composition surrounding histones modify chromatin fiber strength, further tuning the mechanical properties of the nucleus [48].

Nuclear lamina integrity

The nuclear lamina, composed primarily of A-type and B-type lamins, forms a fibrous meshwork beneath the inner nuclear membrane and serves as a critical determinant of nuclear shape and mechanical resilience. The nucleus exhibits viscoelastic behavior, meaning its mechanical response depends on both the magnitude and duration of applied stress. Lamin A predominantly governs viscous resistance, enabling the nucleus to withstand sustained deformation, while lamin B1 contributes to elastic stiffness, facilitating recovery from transient mechanical perturbations [49]. Thus, any alterations in lamin expression are closely associated with changes in nuclear morphology. For instance, reduced levels of lamin B1 are observed in aging and senescent cells and are linked to irregular nuclear contours and increased invaginations [50]. Lamin A levels inversely correlate with nuclear area and roundness [51,52], and the ratio of lamin A/C to lamin B has been shown to negatively correlate with nuclear deformability, suggesting that a higher lamin A/C to lamin B ratio increases nuclear stiffness and reduces the ability to deform under mechanical stress [53]. Cells deficient in lamin A (mouse embryonic fibroblasts (MEFs) LMNA-/-) exhibit increased nuclear volume and irregular contours, underscoring the structural role of lamins in maintaining nuclear integrity (Figure 2) [54]. Besides, cells overexpressing lamin A present a higher incidence of toroidal nuclei [47]. Changes in nuclear stiffness mediated by lamin composition can also influence mechano-transduction pathways, thereby affecting gene expression and cellular behavior in response to mechanical cues [55]. These properties are essential for understanding how the nucleus adapts to diverse physiological contexts such as cell migration and differentiation and are equally relevant in pathological conditions where nuclear integrity is compromised. For instance, the role of lamin in cancer cell migration and metastatic potential remains context-dependent. Indeed, in some cancer types, reduced lamin A expression enhances nuclear deformability and facilitates migration through confined environments, while in other types of cancer, lamin A expression persists in metastatic cells [52,53]. Mutations in genes encoding lamins or associated envelope proteins lead to a class of disorders known as envelopathies, with laminopathies representing a subset characterized by altered nuclear mechanics and reduced stiffness [56,57].

Nucleoskeletal architecture

In addition to the lamina, the nucleoskeleton includes structural proteins such as nuclear actin and myosin, which contribute to the maintenance of nuclear shape. Actin within the nucleus exists in various conformations, including globular and filamentous forms. F-actin, polymerized by formins, has been shown to exert pressure on the NE, particularly in regions devoid of DNA and NPCs (Figure 2). The presence of lamin A counteracts the effects of F-actin, suggesting a mechanistic antagonism between these two components [51]. Indeed, in cells depleted for lamin A, this pressure participates in pronounced nuclear deformation. Importantly, these interactions occur independently of transcriptional activity and mitotic progression, highlighting a structural role for nuclear actin in shaping nuclear morphology. Spectrins and myosins also contribute to the nucleoskeletal framework, supporting nuclear shape and mechanical resilience. Spectrins form a flexible, membrane-associated scaffold that helps stabilize nuclear curvature and may interact with lamins and actin to buffer mechanical stress [58]. Within the nucleus, myosins – particularly nuclear isoforms of myosin I and II – play dual roles in chromatin remodeling and tension regulation. Working in concert with nuclear actin, myosins modulate internal force distribution and contribute to the dynamic organization of chromatin [59]. These components not only reinforce nuclear structure but also facilitate mechanical adaptability, especially under conditions of deformation or confinement.

DNA damage and mitosis

The DNA damage response (DDR) also influences nuclear mechanics, primarily through changes in chromatin compaction (Figure 2). Activation of the ataxia-telangiectasia mutated (ATM) kinase during DDR leads to chromatin relaxation, which reduces the resistance of the nucleus to deformation and increases the incidence of nuclear blebbing. These effects appear to be independent of lamin status [60,61]. However, the impact of DDR on nuclear morphology remains controversial, with conflicting results reported across different experimental systems [62]. In p53-deficient cells, DNA damage has been shown to activate ATM and Rad3-related kinase (ATR), leading to lamin A/C phosphorylation and subsequent changes in chromatin organization and cytoskeletal anchoring, which might culminate in NE rupture [63]. Beyond canonical DDR signaling, ATM and ATR also respond to mechanical stress independently of DNA damage. For instance, ATR localizes to the NE upon mechanical stress and could change the membrane fluidity [62]. ATR-deficient cells present nuclear abnormalities under basal conditions and catastrophic phenotypes under mechanical stress [64]. Similarly, ATM is activated by stretching and acts both at the chromatin level and through cytoskeleton remodeling. Cells lacking ATM display increased nuclear stiffness and enhanced nuclear translocation of yes-associated protein (YAP) or transcriptional coactivator with PDZ-binding motif (TAZ), key effectors of the Hippo pathway [62]. Given that YAP/TAZ activity is highly sensitive to nuclear mechanics and cytoskeletal tension, these observations raise the possibility of a functional interplay between DDR and Hippo signaling. Such crosstalk could influence transcriptional programs governing proliferation, survival, and repair, although the mechanistic basis remains to be fully elucidated. Additional triggers of nuclear rupture have been recently identified. For instance, micron-sized fat-filled lipid droplets can indent the perinuclear actomyosin network provoking a local dilution of lamin B1, but not of lamin A/C, and triggering local NE rupture [65]. This event was reported in mesenchymal stem cells as well as in cultured cells and is associated with the activation of DDR and subsequent cell cycle arrest. Further investigation is needed to clarify the mechanistic links between DNA damage signaling and nuclear mechanical properties. Finally, other processes, like replication stress, also directly affect DNA and nuclear morphology. Cells under replication stress have been observed to present nuclear hypertrophy and architectural changes through nuclear actin polymerization [66,67].

During open mitosis, the NE disassembles, exposing DNA and allowing it to interact directly with the cytoplasm. Accurate reassembly of the NE is essential for restoring nuclear integrity, including morphology, in daughter cells. Depletion of centromeric proteins such as CENP-A and CENP-C impairs chromosome segregation and leads to nuclear shape abnormalities during mitotic exit caused by the improper reestablishment of the nuclear lamina and anchoring of peripheral heterochromatin [68]. Such mitotic errors contribute to long-term alterations in nuclear morphology and may promote genomic instability, particularly in highly invasive cancer cells. Examples of altered nuclear morphologies upon mitotic defects include the presence in daughter cells of micronuclei and toroidal nuclei, both considered CIN biomarkers [69–72]. Independently, expression of progerin, a mutant form of lamin A associated with premature aging, was shown to disrupt nuclear architecture and mechanics but independently of chromosome mis-segregation. Importantly, both CENP-A-induced chromosome mis-segregation and progerin-induced lamina damage generate physical stress (softening and increased membrane tension) sufficient to activate the p53-mediated checkpoint. This shared outcome, despite independent upstream causes, suggested that the NE stress checkpoint responds to the mechanical state of the nucleus rather than to a specific initiating event such as CENP-A loss [68].

External forces

External forces predominantly arise from cytoskeletal interactions and mechanical signals transmitted from the extracellular environment, influencing nuclear shape, volume, and integrity.

Cytoskeletal coupling and mechanotransduction

The cytoskeleton exerts mechanical forces on the nucleus through the LINC complex, which physically connects cytoplasmic filaments to the nuclear lamina and chromatin (Figure 1). Disruption of this coupling alters nuclear volume and shape, underscoring its role in maintaining nuclear integrity [54,73,74]. Mechanical forces applied to the cell surface are transduced to the nucleus via cytoskeletal networks, initiating adaptive responses in nuclear architecture. The perinuclear actin cap, composed of apical actomyosin stress fibers anchored to focal adhesions, plays a key role in maintaining nuclear shape under mechanical stress (Figure 2). By exerting compressive forces, it flattens the nucleus and protects it from deformation. Its assembly depends on A-type lamins and myosin activity, and it is absent or disrupted in cells lacking functional lamina or LINC complex components. In mechanically stimulated cells, such as MEFs, the actin cap forms in response to stretch and induces nuclear flattening without altering nuclear volume [54]. While the actin cap contributes to nuclear shape stability, it is not essential to cell viability, as some proliferative cells lack this structure [51].

Microtubules (MTs) also contribute to nuclear deformation through their structural rigidity and dynamic reorganization (Figure 2). MTs interact with the nuclear lamina to shape nuclear morphology. In progeria cells lacking lamin A, nuclei often adopt a crescent shape associated with the microtubule-organizing center (MTOC) positioned at the center of the cell. The MTOC and the nucleus apply reciprocal forces onto each other. When lamin A is defective, the nucleus cannot withstand this pressure and deforms to accommodate MTOC positioning. In addition, treatment with nocodazole, a MT-targeting drug, in lamin A-positive cells reduces nuclear size, whereas taxol enlarges it, further indicating that MTs dynamics influence nuclear morphology through multiple mechanisms [75]. Mechanical forces likewise influence MTs organization, altering their orientation and stability. In neurons subjected to low mechanical forces via nano-pulling, MTs stabilize and reorient perpendicular to the NE. This reorganization disrupts the actin cap and induces surface grooves on the nuclear membrane, leading to increased nuclear sphericity and height [76]. MTs are also regulated by post-transcriptional modifications. C11ORF49, also known as CSTPP1, is a centriolar satellite-associated protein that stabilizes the tubulin polyglutamylase complex, which controls MTs polyglutamylation and nuclear shape [77]. Loss of C11ORF49/CSTPP1 induced a reduction of tubulin polyglutamylation, which led to increased MTs growth and MAPs recruitment during late telophase. At this stage, microtubules penetrate the newly formed NE, promoting nuclear polylobulation. Additionally, excessive MAP4 recruitment could exert abnormal mechanical forces on the nucleus.

These morphological changes are accompanied by chromatin decompaction and global transcriptional activation, suggesting that cytoskeletal remodeling can directly influence nuclear function.

Extracellular matrix (ECM) and mechanical microenvironment

Cells reside within a mechanically active ECM, which imposes external forces such as compressive, tensile, and shear stress. Variations in ECM stiffness modulate nuclear lamina organization: stiffer matrices promote smoother lamina phenotypes without altering nuclear volume [78]. This behavior supports the lamina drop model, where lamina tension responds to external mechanical cues independently of cytoskeletal input. Mechanical stimuli from the ECM are transduced to the nucleus via cytoskeletal elements, including the perinuclear actin cap. These forces alter cytoskeletal tension, which is transmitted to nucleoskeleton, influencing chromatin organization and nuclear mechanics [79]. Deformation of the nucleoskeleton has been shown to elicit diverse cellular responses. Cell migration, a common process across multiple cell types, often poses a challenge when cells traverse highly constricted regions. Interestingly, neutrophil-like cells present marked alterations in chromatin organization following confined migration. These nuclei display a global reduction in topologically associating domains (TADs) and disrupted chromatin contacts, while the A/B compartment switching remains relatively limited (A = euchromatin, B = heterochromatin). Although cells migrating through confined and narrow pores also present transcriptional changes, these changes do not consistently correlate with disrupted chromatin contacts. Importantly, confined migration is associated with an enrichment of disrupted contacts within transcriptionally inactive chromatin [80]. Similar results have been reported in tumor cells, where nuclear architecture is remodeled, including redistribution of lamin A/C and heterochromatin. In melanoma and breast cancer cells, repeated rounds of confined migration weaken the B compartment, a feature linked to nuclear morphological changes in melanoma cells. In these cells, chromatin reorganization has been associated with transcriptomic profiles that support migratory behavior. However, these transcriptional changes are less conserved than the alterations observed in A/B compartmentalization [81]. Of note, such nuclear adaptations also occur under physiological conditions. For instance, during C. elegans development, migrating cells pass through confined spaces and undergo nuclear modifications via the LINC complexes and heterochromatin [82]. Collectively, these results highlight the importance of heterochromatin as a mechanosensing component that contributes to cellular mechanical responses. Cellular migration through the ECM imposes physical constraints, and when proteolysis is absent, nuclear deformability becomes the critical determinant of successful migration [83]. Consequently, ECM pore size and composition strongly influence nuclear mechanics, chromatin organization, and overall cellular migratory capacity.

The nucleus as a mechanosensor

The nucleus functions as a mechanosensor through several interconnected mechanisms. The NE can directly sense mechanical stretch, wherein strain-induced alterations in the lipid bilayer of the nuclear membrane activate calcium channels and cytosolic phospholipase A2 (cPLA2), initiating signaling cascades that can modulate cellular migration and facilitate the escape from rigid microenvironments (Figure 2). Mechanical forces also regulate the nuclear translocation of well-characterized mechanotransducers, including transcriptional factors YAP/TAZ or myocardin-related transcription factor A (MRTF-A) (Figure 2). Notably, ATR, beyond its canonical role in DDR, contributes to nuclear actin assembly and polymerization by recruiting Filamin-A to the INM through ras association domain family member 1 (RASSF1A), a Hippo pathway scaffold for macrophage stimulating 1 and 2 (MST1/2) kinases [64,84]. This mechanism modulates YAP/TAZ activity in response to mechanical stress while preserving nuclear integrity. Additionally, nuclear stretching induces conformational changes in the NPC, altering its permeability and thus facilitating transport of these regulatory proteins (reviewed in [85]). Collectively, these processes enable the nucleus to sense and integrate mechanical cues to orchestrate adaptive cellular responses.

Mechanical forces in disease contexts

In cancer, mechanical forces fluctuate throughout the metastatic cascade (reviewed in [86,87]. Tumor growth increases internal pressure and ECM confinement. During invasion and transendothelial migration, cells encounter compressive and shear forces. Circulating tumor cells are exposed to fluid shear stress and must mechanically adapt to new tissue environments upon extravasation, further challenging nuclear integrity. These mechanical stresses reshape the cytoskeleton and, via the LINC complex, deform the nucleus. Of note, the NE can rupture for example during migration through confined spaces. Robust repair mechanisms exist to restore NE integrity following rupture, with LEM-domain proteins and CHMP7 playing pivotal roles [88–90]. In both yeast and mammals, the ESCRT machinery, in coordination with lipid synthesis, facilitates membrane resealing and structural recovery [91]. The ESCRT-III machinery rapidly repairs these ruptures, preserving nuclear integrity and preventing DNA damage. This repair mechanism is critical for cell survival in dense tissues and during metastasis [92].

Mechanical forces in transcriptional reprogramming and cell fate

Among the cellular changes discussed above, epigenetic modifications, chromatin remodeling, nuclear architecture disruption, and transcriptional factors translocation, play central roles in the regulation of transcriptional activity and the determination of cell fate.

The structural organization and mechanical properties of the nucleus influence the processes of cell differentiation. Key nuclear components such as lamin A/C and LBR are important to maintain chromatin organization, particularly heterochromatin. These proteins have partially redundant functions to preserve heterochromatin integrity [93]. When lamin A/C, lamin B and LBR are simultaneously depleted, heterochromatin detaches from the nuclear periphery. In mouse embryonic stem cells, this disruption impairs differentiation into epiblast-like cells due to the failure to expand the H3K9me2 mark. Furthermore, lamin A/C expression increases in differentiated cells, and contributes to enhanced nuclear stiffness. Consequently, stem cells and lamin A/C-deficient cells present greater nuclear deformability compared to differentiated cell types [94]. In somatic cells, lamin A/C dynamics was shown to have contrasting effects on cell plasticity: a transient loss of lamin A/C accelerates the kinetics of cellular reprogramming toward pluripotency, whereas expression of the lamin A mutant progerin triggers cellular senescence, thereby effectively inhibiting genetic reprogramming [95].

External mechanical forces, such as compressive stress, can also shape the epigenetic landscape and consequently influence cell fate decisions. For instance, compressive stress has been shown to induce a rejuvenation-like phenotype in human dermal fibroblasts. In addition, spheroids composed of aged cells subjected to external pressure undergo chromatin remodeling and activate regulatory pathways associated with cellular rejuvenation [96].

In all, beyond acute responses to internal and external forces, maintaining nuclear integrity over time remains a fundamental cellular challenge. To preserve NE homeostasis, cells rely on additional protective mechanisms.

Autophagy and lipid remodeling in the maintenance of NE homeostasis

The maintenance of NE homeostasis is a dynamic and tightly regulated process, essential for preserving nuclear architecture and cellular function. While the NE is generally robust, its integrity becomes increasingly compromised during aging and disease [97,98]. Interestingly, recent advances have characterized novel regulators of NE homeostasis. Among the newly identified regulators of NE dynamics and architecture, the autophagy – lysosome axis and lipid metabolism at the NE have emerged as particularly intriguing. In this section, we review how these processes contribute to maintain nuclear resilience and structural adaptation under both physiological and pathological conditions.

Cells rely on two major catabolic systems to maintain proteostasis and organelle integrity: the proteasome, which specializes in targeted protein degradation, and the autophagy-lysosome axis, capable of degrading a broad range of biological materials. Although these processes primarily operate in the cytoplasm, emerging evidence – largely from yeast studies – has highlighted their involvement in NE repair and homeostasis [99]. At the INM, protein quality control is governed by INM-associated degradation (INMAD), a proteasome-dependent pathway first characterized in yeast. INMAD selectively eliminates misfolded or excess INM proteins, thereby preserving NE integrity [97]. Although the full extent of INMAD in mammalian cells remains to be elucidated, SUN2 has been identified as a proteasomal substrate, and expression of non-degradable SUN2 mutants disrupts nuclear architecture [100]. The existence of additional, yet uncharacterized, proteasome-dependent mechanisms at the NE represents a promising avenue for future research.

Autophagy, a catabolic process encompassing microautophagy, chaperone-mediated autophagy (CMA), and macroautophagy, contributes to cellular homeostasis. In brief, microautophagy involves direct engulfment of cytoplasmic material by lysosomal or vacuolar membranes; CMA selectively translocates proteins across the lysosomal membrane via chaperone recognition; and macroautophagy (often simply referred to as autophagy) sequesters cargo within double-membrane autophagosomes that fuse with the vacuole or lysosomes for degradation (reviewed in [70,101–103]). While macroautophagy and CMA have been extensively studied, the mechanisms driving microautophagy remained largely understudied and was primarily explored in yeast. However, recent research has begun to uncover its mechanisms and functional relevance in mammalian cells, highlighting its role in homeostasis and disease [104]. For that manner, a recent expert consensus has refined the terminology for microautophagy, distinguishing vacuole-microautophagy (v-MI), lysosome-microautophagy (l-MI), and endosome-microautophagy (e-MI) [105], thus providing a clearer framework for mechanistic studies. Nuclear components are selectively degraded via nucleophagy, a specialized form of autophagy (reviewed recently in [106]). In yeast, macronucleophagy is orchestrated by the receptor Atg39, which localizes to the NE under stress and facilitates the formation of double-membrane nuclear-derived vesicles that are trafficked to the vacuole through coordinated fission of both the INM and ONM [107–109]. ONM fission was showed to be mediated by the GTPase dynamin-like 1 (Dnm1), which is recruited by Atg11 to Atg39-enriched sites on the ONM [110,111]. Dnm1, an ortholog of the mitochondrial fission factor DRP1, assembles at the ONM constriction site in a manner reminiscent of mitophagy and pexophagy, underscoring possible conserved principles of organelle remodeling. A related process, microONMphagy (class l-MI) mediates the selective clearance of ONM components following LINC complex disassembly and NE remodeling under ER stress conditions and involves the autophagic receptors SEC62 and TEX264 [106,112,113]. Micronucleophagy (v-MI), also known as piecemeal microautophagy of the nucleus, occurs at the nucleus-vacuole junction in yeast and involves the invagination of the NE into the vacuole for selective degradation. In mammalian cells, the core autophagy protein LC3 has been shown to interact with lamin A/C and lamin B1, suggesting that lamins may undergo autophagic turnover. Notably, NE blebs enriched in lamin B1 have been observed in IMR90 cells to bind LC3-family proteins under both normal conditions and oncogenic stimulation, and thus to be degraded via autophagy [114]. Furthermore, the presence of micronuclei in the cytosol can activate the autophagy-lysosome system to eliminate extranuclear DNA [115]. Inhibition of autophagy during mitosis, whether induced genetically or chemically, was shown to increase the formation of toroidal nuclei [69,116]. This effect is further amplified by LMNA overexpression, which interestingly, reduces the prevalence of micronuclei as previously reported [47,117]. Notably, LMNA overexpression did not alter autophagic flux, and conversely, inhibition of the autophagic flux did not modify LMNA processing. These findings suggest that the formation of toroidal nuclei and micronuclei is governed by distinct, independently regulated processes. Farnesyltransferase inhibitors (FTIs) such as lonafarnib, used clinically to treat Hutchinson – Gilford Progeria Syndrome, impair LMNA processing and have been reported to induce toroidal nuclei formation in HeLa cells, but not in U2OS cells, highlighting a cell-type-specific effect [47,69,118]. Importantly, this occurs without altering autophagic flux. These observations suggest that autophagy regulates nuclear morphology independently of LMNA processing and degradation, pointing to parallel and potentially synergistic regulatory pathways. Remodelin, a small molecule known to restore nuclear morphology in laminopathy models, acts via inhibition of the N-acetyltransferase NAT10, affecting cytoskeletal-lamina coupling and NE architecture [119]. While its role in autophagy-dependent nuclear remodeling in mammalian cells remains unexplored, remodelin represents a promising tool for investigating nuclear resilience. Despite growing insights, the molecular mechanisms underlying nucleophagy in mammals remain poorly understood, highlighting a significant gap in our knowledge of nuclear homeostasis. In particular, the balance between macro- and micronucleophagy, along with their substrate specificity, may play a critical role in maintaining NE integrity under both physiological and pathological conditions.

Beyond their structural contribution, lipids play dynamic and regulatory roles in maintaining NE homeostasis. Building on comprehensive reviews of lipid roles in NE homeostasis, this section highlights recent insights in yeast and higher eukaryotes (reviewed in [120,121]). The lipid composition of the NE plays a fundamental role in membrane curvature, flexibility, and NPC architecture [122]. Saturated lipids, particularly acyl-chain saturation, rigidify the NE and restrict membrane plasticity, while unsaturated lipids preserve flexibility and support NPC function under stress [122]. Sphingolipid synthesis during S/G2 phases ensures proper NE expansion and genome stability [123]. Inner nuclear membrane proteins such as Lem2, Bqt4, and Seipin act as lipid homeostasis guardians, coordinating metabolic pathways to preserve NE architecture [122,124]. Lipid droplets (LDs), enriched in cholesteryl esters, have been observed at NE invaginations, particularly during inflammatory responses, suggesting a functional link between lipid storage and NE remodeling [125]. LDs can supply fatty acids for phospholipid synthesis, buffering lipid demand during NE growth or recovery [126]. Glycerophospholipid biosynthesis, beyond its structural role, integrates metabolic signals to sustain phospholipid pools essential for NE maintenance [reviewed in [127]]. Nuclear phosphoinositides further contribute to NE homeostasis by modulating membrane dynamics and interacting with NE-associated protein complexes. Thus, their ability to respond to cellular stimuli positions them as regulators of NE remodeling and signaling [reviewed in [128]]. Autophagy may influence these lipid pools, although direct evidence in mammalian cells is currently lacking. Lysosomes, known for their role in plasma membrane repair and lipid exchange, may also contribute to NE maintenance, opening new avenues for investigation. With the advent of high-resolution lipidomic profiling, it is now possible to characterize the lipid landscapes of the ONM and INM, offering powerful tools to dissect the role of lipid remodeling in nuclear morphology.

Nuclear morphology in health and disease: a framework for diagnosis and intervention

The preceding sections delineated the biophysical and biochemical determinants that govern nuclear morphology, emphasizing how intracellular and extracellular stimuli converge to modulate NE architecture. In this section, we provide an overview of the most described nuclear phenotypes across physiological and pathological contexts (Figure 3).

Figure 3.

Nuclear phenotypes in health and disease.

Comprehensive overview of the principal nuclear phenotypes reported in the literature. Each phenotype is described by its morphological attributes, the underlying molecular or cellular mechanisms driving its formation, and the biological contexts in which it has been observed. For each nuclear phenotype, the stressors implicated in its emergence are color-coded to facilitate the association between the specific causes and the cellular states or tissues in which the phenotype has been documented.

Differentiation and lineage-specific nuclear shaping

Significant morphological changes occur during embryonic development, establishing nuclear appearances linked to tissue identity and specific cellular functions. Generally, pluripotent stem cells and undifferentiated cells possess larger, physically more plastic, and malleable nuclei than differentiated cells, which facilitates their migration into developing tissues. As a cell differentiates, its nucleus undergoes an increase in stiffness, which can intensify up to six-fold. This change is directly related to an increased expression of A-type lamin relative to B-type lamin [94]. This loss of nuclear plasticity is accompanied by changes in chromatin conformation. In pluripotent cells, chromatin is in an open state to accommodate the high demand for gene transcription. Conversely, differentiated cells experience a global decrease in transcription due to the silencing of a portion of the genome and a subsequent clustering into heterochromatin, which contributes to nuclear rigidity [129,130]. Indeed, one of the earliest steps in development is the formation of LADs, which help organize the heterochromatin [131].

The stoichiometric ratio between A-type and B-type lamins, along with other components of the NE, and the nuclear shape itself, act as lineage-driving factors that promote epigenetic changes determining cell fate commitment [132,133]. These factors are further influenced by the cellular microenvironment, which helps establish the unique morphology of each cell lineage. For example, the stiffness of the extracellular matrix and mechanical stress lead to an increase in A-type lamin expression, providing the appropriate rigidity to stabilize the nucleus in that environment and facilitating tissue-specific differentiation [134]. Another example of morphology dictated by tissue-specific mechanical stress is seen in endothelial cells. These cells, which line the inside of blood vessels, are highly sensitive to the mechanical forces of blood flow. Blood flow induces cell polarization and participates in morphogenetic changes that, through cytoskeletal reorganization, lead to the establishment of an elongated nuclear shape oriented in the direction of the flow (Figure 3.) [135].

While cellular differentiation generally leads to increased rigidity, certain cell types, like immune cells, maintain a high degree of plasticity. This is crucial for their function, as they must migrate through tissues. Neutrophils are a prime example: despite being terminally differentiated, they maintain low levels of A-type lamins, which enhance their migratory capacity. These cells exhibit diverse nuclear morphologies, often characterized by multi-lobed or segmented nuclei (Figure 3.). While it is commonly believed that this lobulated shape facilitates movement through confined environments, recent evidence suggests that nuclear deformability is more directly regulated by lamin expression [136]. The lobular phenotype is a feature more involved in migration speed of these cells rather than their ability to transit through tight interstitial spaces between tissues [137].

Cell cycle progression dictates the acquisition of the nuclear shape, with post-mitotic deformations being particularly influential. A proposed model suggests that, immediately after mitosis, the nucleus possesses an excess of surface area – primarily due to lamins – which allow it to mimic the shape of the cell. The surfaces of this compliant nucleus then tend to track the cell boundary due to the mechanical coupling of the two surfaces through the intervening cytoplasm, which is resistant to expansion or compression. Once the shape is established, the nucleus gradually stiffens [138]. Lamins then stabilize the acquired morphology, rendering it irreversible until the NEBD [94,139].

Beyond nuclear deformations, cell differentiation often involves the presence of polyploid cells. This increase in ploidy enhances the availability of DNA templates, thereby supporting more efficient protein production. This mechanism enables tissues to optimize their performance, respond to damage, or meet extreme metabolic demands. Cell ploidy can increase through three primary mechanisms. The first is endocycling, a process in which the cell repeatedly replicates its DNA without dividing, resulting in a single enlarged nucleus with increased genetic material. This is exemplified by trophoblast cells in the placenta. The second mechanism is endomitosis, an incomplete cell cycle where the cell enters mitosis but fails to complete cytokinesis, which can often lead to cells with multiple nuclei (binucleated), as observed in hepatocytes and cardiomyocytes (Figure 3). The third mechanism is cell fusion, where multiple mononucleated cells merge to form a large, multi-nucleated cell. This process is essential for the formation and development of specialized tissues like skeletal muscle fibers, osteoclasts, and the syncytiotrophoblast (Figure 3) [140].

Nuclear shape and size in tissue homeostasis

The tissues of an organism must maintain a dynamic and steady state to properly preserve their structure and function. This requires a strict balance between tissue renewal, which involves cell division to generate new cells, and the elimination of cells that are no longer able to function correctly, which occurs through apoptosis.

Tissue growth is driven by cell division, resulting in cellular proliferation under normal tissue development. During cell division, cells increase in size and double their biomass in the interphase stage (G1, S, G2). Just before cell division, the genetic material condenses into chromosomes and the nucleus reorganizes, becoming much more compact and disassembling its envelope. After division, the two daughter cells will have smaller nuclei that will gradually grow back to the characteristic interphase size after NE assembly.

The increase in cellular size may be explained by the nucleoskeletal theory, which proposes that the total amount of DNA and its associated proteins directly determine nuclear dimensions. Thus, genome size exerts a direct causal influence on nuclear size, a principle supported by the strong correlation observed between the species-specific differences in cell and their genome size [141], as well as by ploidy studies showing that polyploid cells typically exhibit enlarged nuclei and overall cell size [142]. However, the nucleoskeletal theory fails to explain the considerable variation in nuclear size observed among different adult tissues, as well as the marked reduction in nuclear size during early embryogenesis, despite an unchanged DNA content.

Studies in yeast have shown that the nucleocytoplasmic (N/C) ratio remains constant throughout the cell cycle. The lack of a significant increase in nuclear size during the S phase reinforces the idea that cell size is not proportional to DNA content [143,144]. The existence of this correlation between cell size and nuclear size, independent of DNA content, has been the subject of various explanatory studies. For instance, studies in Xenopus suggest that the levels of limiting factors decrease during development, causing cells to eventually scale the N/C ratio. These factors include proteins that influence chromatin organization, such as nucleoplasmin, and other factors involved in nuclear import of NE components like Importin-α and Ntf2 [145,146].

Another perspective attributes nuclear size scaling to underlying physical causes, known as the pump-leak principle. Size regulation is primarily governed by the balance of osmotic pressure across the NE. The dominant force driving nuclear expansion comes from the osmotic pressure generated by large macromolecules (proteins and RNA molecules) that are actively and differentially localized in the nucleoplasm or the cytoplasm via nucleocytoplasmic transport [147]. The N/C ratio is kept constant by a large pool of metabolites that freely diffuse across the NE to achieve osmotic equilibrium between nucleus and cytoplasm [148,149]

Mature tissue can increase in volume without cell division through cellular hypertrophy, which involves the expansion of individual existing cells in response to elevated metabolic demands [66]. This phenomenon is commonly observed in muscle tissue during intense exercise and is often accompanied by an enlargement of the nucleus and, in some cases, an increase in the number of nuclei per cell (Figure 3) (Reviewed in [150]). Moreover, hypertrophic nuclei typically feature a prominent nucleolus, reflecting enhanced ribosome synthesis activity (Figure 3) [151].

Apoptosis, or programmed cell death, is defined by a set of precise nuclear and cellular changes. Early in the process, the cell membrane begins to exhibit blebbing (forming dynamic, bubble-like protrusions) (Figure 3). Concurrently, the nucleus first undergoes pyknosis, a process where it shrinks and becomes extremely dense due to the tight compaction of its genetic material. Following this, the dense nucleus breaks apart in a process called karyorrhexis, fragmenting into small, membrane-bound sacs known as apoptotic bodies. These bodies are subsequently recognized and cleared by macrophages to prevent inflammation (reviewed in [152]).

Beyond cell division and cell death, aging or damaged cells can follow a third path: they may permanently exit the cell cycle while remaining viable and metabolically active within the tissue. This condition is known as cellular senescence. Senescence serves as a homeostatic function in tissues, contributing to processes such as tumor suppression, embryonic development, wound healing, tissue remodeling, regeneration, and vascular maintenance (reviewed in [153]). However, when these senescent cells accumulate and begin to replace the proliferative cells population, they can exert detrimental effects on the organism. Indeed, this buildup of senescent cells contributes to tissue dysfunction and the development of age-related diseases [154]. The nucleus of a senescent cell is typically enlarged, flattened, and irregular in shape (Figure 3). These morphological changes are driven by structural alterations such as the loss of lamin B1 protein and the accumulation of lysosomal bodies [155], and an extensive dynamic chromatin remodeling [156]. Importantly, these nuclear abnormalities are more than just biomarkers; they are active drivers of pathology. The disorganized NE compromises its integrity, leading to the formation of blebs and eventual rupture (Figure 3), a process that releases nuclear DNA fragments into the cytosol. This cytosolic DNA is detected by the innate immune sensor cGAS, which activates the cGAS-STING pathway [157,158]. This pathway, in turn, triggers the production and secretion of pro-inflammatory factors known as the Senescence-Associated Secretory Phenotype (SASP) (reviewed in [159]). Given the gradual and cell-type-specific nature of senescence, advanced deep learning approaches are essential for accurately profiling and characterizing senescent states [160,161].

Nuclear morphology as pathological biomarker

Diversity in the shape of cells and their nuclei is essential for the proper functioning of an organism. However, this variety has its limits; if the cellular or nuclear morphology deviates from what is considered normal for a specific cell type and tissue, it ceases to be a functional characteristic and becomes an indicator of disease or pathology.

Nuclear morphology is a cornerstone of cancer diagnosis and grading, routinely assessed in histopathological examinations of patient biopsies. The visual evaluation of nuclear features that deviate from normal architecture enables pathologists to differentiate malignant from benign lesions, classify tumor subtypes, and estimate disease aggressiveness. Although nuclear alterations are highly diverse in complex pathological processes like cancer, certain nuclear features are commonly observed [162]. For instance, hyperchromasia is characterized by increased nuclear staining intensity, and indicates dense chromatin packing and elevated transcriptional activity (Figure 3). Irregular nuclear contours and disrupted chromatin architecture further signal structural and functional aberrations in nuclear organization (Figure 3). Another key diagnostic parameter is the N/C ratio, which is typically elevated in cancer cells due to nuclear enlargement and cytoplasmic reduction (Figure 3). This shift is particularly prominent in high-grade tumors and correlates with increased proliferative capacity.

Chromosomal instability (CIN) is a hallmark of cancer, closely associated with tumor heterogeneity, progression, and therapeutic resistance [163,164]. Reliable biomarkers are essential for quantifying CIN and understanding its clinical implications. Among these, micronuclei are widely recognized and routinely used to assess CIN levels [71]. Micronuclei are extranuclear bodies that originate from acentric chromosomal fragments or whole chromosomes excluded from daughter nuclei during mitotic exit (Figure 3). Their presence reflects mitotic errors and DNA damage, and they are frequently observed in tumors with high CIN, such as triple-negative breast cancer and high-grade serous ovarian carcinoma [165]. More recently, toroidal nuclei have emerged as a novel nuclear phenotype relevant to cancer classification (Figure 3). Like micronuclei, toroidal nuclei arise from mitotic defects, but the mechanisms underlying their formation appear to differ, suggesting that these structures represent complementary biomarkers rather than redundant ones [69,116]. While micronuclei have been extensively studied and implicated in DNA damage responses and inflammatory signaling, the biological fate and functional significance of toroidal nuclei remain to be defined.

These alterations of the nuclear architecture are not only diagnostic but also prognostic. Their extend and distribution correlate with tumor grade, stage, and clinical outcome. For instance, poorly differentiated carcinomas often exhibit extreme pleomorphism and chromatin irregularities, which are predictive of aggressive behavior and poor therapeutic response. In breast, prostate, and lung cancers, nuclear grading remains a critical determinant of treatment planning and patient stratification. Importantly, the frequency and distribution of nuclear anomalies vary across cancer subtypes and are closely linked to clinical parameters. Their integration into diagnostic workflows, alongside traditional histological criteria, holds promise for refining prognostic models and guiding personalized treatment strategy.

As previously discussed, cellular morphology is significantly influenced by the protein meshwork situated along the nucleoplasmic surface of the INM. Therefore, alterations, whether mutations or changes in the expression levels of any of its constituents, can be linked to specific diseases characterized by an abnormal shape (Figure 3). Among the most extensively studied examples are laminopathies, a group of rare genetic disorders caused by mutations in the genes encoding nuclear lamins or their associated proteins (e.g., Emerin). Despite the affected proteins being ubiquitously expressed, laminopathies often affect specific tissues. These disorders include musculoskeletal and cardiac conditions, and thus primarily affect muscle and heart function, such as Emery-Dreifuss Muscular Dystrophy and Dilated Cardiomyopathy. Metabolic diseases, like Dunnigan-type Familial Partial Lipodystrophy, involve disruptions in adipose tissue and metabolic regulation. Neurological disorders, which are mainly associated with alterations in B-type lamins, include conditions such as Autosomal Dominant Leukodystrophy and Charcot – Marie – Tooth disease. Finally, progeroid syndromes are characterized by premature aging across multiple tissues, with Hutchinson-Gilford Progeria Syndrome being the most widely known example [166].

Most of the disease-causing mutations are distributed all along the LMNA gene, which encodes lamins A and C. More than 400 mutations have been documented across this gene, with missense mutations being the most common (www.umd.be/LMNA/). The most significant impact of the absence or disruption of A-type lamins is the drastic reduction in nuclear stiffness, which imparts greater fragility to the nucleus. This makes it vulnerable to deformation under physical stress and increases the frequency of NE rupture. Morphologically, this translates into an increase in the occurrence of nuclear phenotypes associated with these events, such as nuclear herniations (blebs), invaginations, lobulations, honeycomb-like structures, and donut-like shapes (Figure 3) [167–169].

Most pathological changes in nuclear morphology observed so far stem from genetic mutations affecting the NE or its regulatory proteins. However, external threats like viruses can also directly reshape the nucleus. Viral infections cause dramatic nuclear morphological alterations, including nuclear enlargement and chromatin marginalization, where the host genetic material is displaced toward the nuclear periphery to create a central space for viral replication or assembly (Figure 3) [170]. Furthermore, viruses can compromise the structural integrity of the NE. Disruption of the nuclear lamina is a critical step that facilitates the exit of large nucleocapsids from the nucleus, often resulting in membrane invaginations and irregularities (Figure 3). Some viral infections also lead to the formation of syncytia (multinucleated giant cells) by modifying viral fusion proteins to promote the fusion of the infected cell with neighboring uninfected cells. This process facilitates viral spread and helps the virus to evade immune surveillance (Figure 3) [171]. In relation to the latter, a similar phenotype can be observed in chronic infections by bacteria or fungi, or in the presence of persistent foreign bodies. When the immune system is unable to combat the pathogen, it may be preventively isolated, triggering a granulomatous reaction where a multinucleated structure, formed from fused macrophages, is created, known as a Multinucleated Giant Cell or Langhans Giant Cell (Figure 3) (reviewed in [172]).

Future directions and conclusions

As the field of cell biology continues to evolve, nuclear morphology is reemerging as a powerful readout of cellular state. Beyond its historical role in descriptive pathology, the nucleus is now recognized as a dynamic integrator of mechanical, genomic, and metabolic signals. Its shape is not merely a structural feature but a functional output of complex intracellular processes. Future research must move beyond static observations and embrace nuclear morphology as a dynamic, quantifiable, and mechanistically informative parameter. A key frontier lies in the development of high-resolution, real-time tools to monitor and manipulate nuclear architecture in living cells. Mechanogenetic platforms, including FRET-based force sensors and optogenetic probes, are beginning to reveal how mechanical forces shape the NE and influence chromatin organization [173,174]. These tools offer unprecedented opportunities to dissect how nuclear mechanics contribute to cell fate decisions, tissue remodeling, and disease progression. The spatial organization of the NE, particularly the nanoscale distance between the INM and ONM, has emerged as a putative determinant of nuclear flexibility and resilience [2]. However, its precise contribution remains to be fully elucidated. Future investigations integrating advanced imaging, biophysical modeling, and perturbation experiments will be essential to uncover how these spatial dynamics influence nuclear behavior under physiological and stress conditions. Modulating this spacing could become a strategy to tune nuclear mechanics in response to environmental stress. Given the structural continuity between the NE and the ER, it is plausible that autophagy initiation sites, such as omegasome-like structures [175], may also form at ER-NE junctions. If confirmed, this would represent a novel mechanism for initiating nucleophagy and regulating nuclear quality control in mammalian cells. Recent studies in yeast revealed that nucleophagy is not merely a degradative but a highly specialized and adaptive process [110,111]. Ultrastructural analyses demonstrated that nuclear material is cleared through a two-step fission mechanism involving both the INM and the OMN, ultimately delivering cargo to the vacuole. Remarkably, OMN fission occurs independently of phagophore formation and requires dynamin-like proteins, uncovering an unexpected role for these factors in NE remodeling. Beyond its canonical degradative function, nucleophagy operates as a selective surveillance system that targets discrete NE subdomains to preserve architecture and genome stability under stress. This dual role, in quality control and in structural remodeling, positions nucleophagy as a key contributor to nuclear resilience, particularly during aging and disease. These insights establish nucleophagy as a dynamic mechanism that integrates membrane remodeling with cellular homeostasis, opening new directions for investigating its regulation in mammalian cells. An important frontier is to determine whether nucleophagy actively remodels nuclear architecture beyond stress-induced clearance, shaping nuclear mechanics and chromatin organization in ways that intersect with mechanotransduction pathways. Another promising direction involves the integration of mechanical memory into models of nuclear adaptation [176]. Cells appear capable of encoding past mechanical experiences through stable changes in chromatin architecture and epigenetic marks. These imprints may influence nuclear morphology and gene expression long after the original stimulus has subsided, offering a new lens through which to study development, aging, and disease.

Computational modeling is also advancing our understanding of nuclear mechanics. Simulations now quantify how cytoskeletal forces, mediated by molecular motors like kinesin and dynein, deform the nucleus and influence its positioning [177,178]. These models are essential for predicting how perturbations in nuclear-cytoskeletal coupling – whether due to altered lamin expression, chromatin compaction, or cytoskeletal tension – translate into morphological abnormalities and functional consequences. Recent work has extended these approaches to explore chromatin phase separation and nuclear shape fluctuations in polymer models [179], as well as the role of chromatin-cytoskeletal tethering in determining nuclear morphology [180].

In parallel, the diagnostic and functional potential of nuclear morphology is being revisited through high-content imaging and artificial intelligence. Image-based phenotyping, when integrated with single-cell omics, will enable the mapping of nuclear features across diverse cell states and disease contexts. This convergence of imaging, computation, and molecular profiling calls for standardized, scalable metrics of nuclear shape and mechanics, and for frameworks that allow real-time interpretation of morphological changes. Looking ahead, the field must prioritize the mechanistic dissection of NE reformation, a process critical for genomic stability and cell identity, yet still under investigation [181,182]. Emerging technologies capable of probing lipid dynamics, membrane contact sites, autophagic flux, and mechanical forces at the nuclear periphery will be instrumental in this effort.

In all, by redefining nuclear morphology as a functional biomarker rather than a passive descriptor, future research can unlock new insights into how cells sense, respond to, and remember their physical and molecular environments. This shift holds the potential to transform our understanding of cellular plasticity, disease mechanisms, and therapeutic interventions.

Funding Statement

APV was supported by fellowship PREDOC-UB 2022 from the University of Barcelona. MBC was supported by fellowship FI [2024 FI-1 00315] from Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR). This study was supported by grants to CM from the Ministerio de Ciencia e Innovación and Agencia Estatal de Investigación [PID2020-118768RJ-I00 and PID2024-155897OB-I00], Ramon y Cajal fellowship [RYC2022-035576-I] and research grant from the Asociación Española Contra el Cáncer AECC [LABAE222994MAUV] and a grant from the Generalitat de Catalunya - AGAUR [2021SGR00284].

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

Data sharing is not applicable to this article as no new data were created or analyzed in this study.