Amnon Buxboim

Nuclear Lamin-A Scales with Tissue Stiffness and Enhances Matrix-Directed Differentiation

Introduction Tissues can be soft like brain, bone marrow, and fat, which bear little mechanical stress, or stiff like muscle, cartilage, and bone, which sustain high levels of stress. Systematic relationships between tissue stiffness, protein abundance, and differential gene expression are unclear. Recent studies of stem cells cultured on matrices of different elasticity, E, have suggested that differentiation is mechanosensitive, but the molecular mechanisms involved in particular tissues remain elusive. Tissue micromechanics correlate with abundance of collagens and nuclear lamins, which influence cell differentiation. (Left) Collagen and lamin-A levels scale with E, consistent with matching tissue stress to nuclear mechanics. (Right) Matrix stiffness in tissue culture increases cell tension and stabilizes lamin-A, regulating its own transcription and that of stress fiber genes, enhancing differentiation. RA, retinoic acid, i.e., vitamin A; RARG, YAP1, and SRF, transcription factors. Methods We developed quantitative mass spectrometry algorithms to measure protein abundance, stoichiometry, conformation, and interactions within tissues and cells in relation to stiffness of tissues and extracellular matrix. Manipulations of lamin-A levels with small interfering RNA, overexpression, and retinoic acid or antagonist were applied to stem cells cultured on different matrices to assess lamin-A’s role in mechanosensitive differentiation. To characterize molecular mechanisms, promoter analyses, transcriptional profiling, and localization of transcription factors were complemented by measurements of nuclear mechanics and by modeling of the core gene circuit. Results Proteomic profiling of multiple adult solid tissues showed that widely varied levels of collagens in extracellular matrix and of lamin-A in nuclei followed power-law scaling versus E. Scaling for mechanoresponsive lamin-A conformed to predictions from polymer physics, whereas lamin-B’s varied weakly. Tumor xenograft studies further demonstrated that matrix determined tissue E, whereas lamin-A levels responded to changes in E. In tissue culture cells, both lamin-A conformation and expression were mechanosensitive, with phosphorylation and turnover of lamin-A correlating inversely with matrix E. Lamin-A knockdown enhanced mesenchymal stem cell differentiation on soft matrix that favored a low-stress, fat phenotype. Lamin-A overexpression or transcriptional induction with a retinoic acid (RA) antagonist enhanced differentiation on stiff matrix toward a high-stress, bone phenotype. Downstream of matrix stiffness, the RA pathway regulated lamin-A transcription, but feedback by lamin-A regulated RA receptor (RARG) translocation into nuclei. High lamin-A levels physically impeded nuclear remodeling under stress but also coregulated other key factors. These factors included both serum response factor (SRF), which promoted expression of stress fiber–associated proteins involved in differentiation, and a Hippo pathway factor (YAP1) involved in growth. Discussion The characteristic stress in normal tissue favors collagen accumulation and a characteristic stiffness that cells transduce through nuclear lamin-A to enhance tissue-specific differentiation. Tension-inhibited turnover of rope-like filaments of lamin-A provides sufficient mechanochemical control of a core gene circuit to explain the steady-state scaling of lamin-A with E. High lamin-A physically stabilizes the nucleus against stress and thereby stabilizes the nuclear lamina and chromatin, with implications for epigenetic stabilization and limiting of DNA breaks. Moreover, lamin-A levels directly or indirectly regulate many proteins involved in tissue-specific gene expression, and, because lamin-A levels can vary by a factor of 10 or more downstream of tissue mechanics, an important fraction of tissue-specific gene expression depends on tissue mechanics, which changes in development, injury, and many diseases. Lamins and Tissue Stiffness Microenvironment can influence cell fate and behavior; for example, extracellular matrix (ECM) stiffness increases cell proliferation, and ECM rigidity induces disorders in tissue morphogenesis by increasing cell tension. Swift et al. (1240104; see the Perspective by Bainer and Weaver) used proteomics to identify molecules that are mechanical sensors for tissue elasticity in the nucleus and discovered that expression of lamin-A levels apparently functions as a “mechanostat.” Tissues that need to remain stiff under stress rely on lamin-A to keep the cell nucleus whole. [Also see Perspective by Bainer and Weaver] Tissues can be soft like fat, which bears little stress, or stiff like bone, which sustains high stress, but whether there is a systematic relationship between tissue mechanics and differentiation is unknown. Here, proteomics analyses revealed that levels of the nucleoskeletal protein lamin-A scaled with tissue elasticity, E, as did levels of collagens in the extracellular matrix that determine E. Stem cell differentiation into fat on soft matrix was enhanced by low lamin-A levels, whereas differentiation into bone on stiff matrix was enhanced by high lamin-A levels. Matrix stiffness directly influenced lamin-A protein levels, and, although lamin-A transcription was regulated by the vitamin A/retinoic acid (RA) pathway with broad roles in development, nuclear entry of RA receptors was modulated by lamin-A protein. Tissue stiffness and stress thus increase lamin-A levels, which stabilize the nucleus while also contributing to lineage determination.

Matrix elasticity, cytoskeletal forces and physics of the nucleus: how deeply do cells ‘feel’ outside and in?

Cellular organization within a multicellular organism requires that a cell assess its relative location, taking in multiple cues from its microenvironment. Given that the extracellular matrix (ECM) consists of the most abundant proteins in animals and contributes both structure and elasticity to tissues, ECM probably provides key physical cues to cells. In vivo, in the vicinity of many tissue cell types, fibrous characteristics of the ECM are less discernible than the measurably distinct elasticity that characterizes different tissue microenvironments. As a cell engages matrix and actively probes, it senses the local elastic resistance of the ECM and nearby cells via their deformation, and — similar to the proverbial princess who feels a pea placed many mattresses below — the cell seems to possess feedback and recognition mechanisms that establish how far it can feel. Recent experimental findings and computational modeling of cell and matrix mechanics lend insight into the subcellular range of sensitivity. Continuity of deformation from the matrix into the cell and further into the cytoskeleton-caged and -linked nucleus also supports the existence of mechanisms that direct processes such as gene expression in the differentiation of stem cells. Ultimately, cells feel the difference between stiff or soft and thick or thin surroundings, regardless of whether or not they are of royal descent.

Matrix elasticity regulates lamin-A,C phosphorylation and turnover with feedback to actomyosin.

Tissue microenvironments are characterized not only in terms of chemical composition but also by collective properties such as stiffness, which influences the contractility of a cell, its adherent morphology, and even differentiation. The nucleoskeletal protein lamin-A,C increases with matrix stiffness, confers nuclear mechanical properties, and influences differentiation of mesenchymal stem cells (MSCs), whereas B-type lamins remain relatively constant. Here we show in single-cell analyses that matrix stiffness couples to myosin-II activity to promote lamin-A,C dephosphorylation at Ser22, which regulates turnover, lamina physical properties, and actomyosin expression. Lamin-A,C phosphorylation is low in interphase versus dividing cells, and its levels rise with states of nuclear rounding in which myosin-II generates little to no tension. Phosphorylated lamin-A,C localizes to nucleoplasm, and phosphorylation is enriched on lamin-A,C fragments and is suppressed by a cyclin-dependent kinase (CDK) inhibitor. Lamin-A,C knockdown in primary MSCs suppresses transcripts predominantly among actomyosin genes, especially in the serum response factor (SRF) pathway. Levels of myosin-IIA thus parallel levels of lamin-A,C, with phosphosite mutants revealing a key role for phosphoregulation. In modeling the system as a parsimonious gene circuit, we show that tension-dependent stabilization of lamin-A,C and myosin-IIA can suitably couple nuclear and cell morphology downstream of matrix mechanics.

Stem cells feel the difference

Arrays of microposts of different heights generate substrates with different flexibility, on which cells can be grown.

Contractile Forces Sustain and Polarize Hematopoiesis from Stem and Progenitor Cells

Self-renewal and differentiation of stem cells depend on asymmetric division and polarized motility processes that in other cell types are modulated by nonmuscle myosin-II (MII) forces and matrix mechanics. Here, mass spectrometry-calibrated intracellular flow cytometry of human hematopoiesis reveals MIIB to be a major isoform that is strongly polarized in hematopoietic stem cells and progenitors (HSC/Ps) and thereby downregulated in differentiated cells via asymmetric division. MIIA is constitutive and activated by dephosphorylation during cytokine-triggered differentiation of cells grown on stiff, endosteum-like matrix, but not soft, marrow-like matrix. In vivo, MIIB is required for generation of blood, while MIIA is required for sustained HSC/P engraftment. Reversible inhibition of both isoforms in culture with blebbistatin enriches for long-term hematopoietic multilineage reconstituting cells by 5-fold or more as assessed in vivo. Megakaryocytes also become more polyploid, producing 4-fold more platelets. MII is thus a multifunctional node in polarized division and niche sensing.

Fractal heterogeneity in minimal matrix models of scars modulates stiff-niche stem-cell responses via nuclear exit of a mechanorepressor

Scarring is a long-lasting problem in higher animals, and reductionist approaches could aid in developing treatments. Here, we show that co-polymerization of collagen-I with polyacrylamide produces minimal matrix models of scars (MMMS), in which fractal-fiber bundles segregate heterogeneously to the hydrogel subsurface. Matrix stiffens locally – as in scars – while allowing separate control over adhesive-ligand density. The MMMS elicits scar-like phenotypes from mesenchymal stem cells (MSCs): cells spread and polarize quickly, increasing nucleoskeletal lamin-A yet expressing the ‘scar marker’, smooth muscle actin (SMA) more slowly. Surprisingly, expression responses to MMMS exhibit less cell-to-cell noise than homogeneously stiff gels. Such differences from bulk-average responses arise because a strong SMA repressor, NKX2.5, slowly exits the nucleus on rigid matrices. NKX2.5 overexpression overrides rigid phenotypes, inhibiting SMA and cell spreading, while cytoplasm-localized NKX2.5 mutants degrade in well-spread cells. MSCs thus form a ‘mechanical memory’ of rigidity by progressively suppressing NKX2.5, thereby elevating SMA in a scar-like state.

Cell-free protein synthesis and assembly on a biochip

Biologically active complexes such as ribosomes and bacteriophages are formed through the self-assembly of proteins and nucleic acids. Recapitulating these biological self-assembly processes in a cell-free environment offers a way to develop synthetic biodevices. To visualize and understand the assembly process, a platform is required that enables simultaneous synthesis, assembly and imaging at the nanoscale. Here, we show that a silicon dioxide grid, used to support samples in transmission electron microscopy, can be modified into a biochip to combine in situ protein synthesis, assembly and imaging. Light is used to pattern the biochip surface with genes that encode specific proteins, and antibody traps that bind and assemble the nascent proteins. Using transmission electron microscopy imaging we show that protein nanotubes synthesized on the biochip surface in the presence of antibody traps efficiently assembled on these traps, but pre-assembled nanotubes were not effectively captured. Moreover, synthesis of green fluorescent protein from its immobilized gene generated a gradient of captured proteins decreasing in concentration away from the gene source. This biochip could be used to create spatial patterns of proteins assembled on surfaces.

Striated Acto-Myosin Fibers Can Reorganize and Register in Response to Elastic Interactions with the Matrix

The remarkable striation of muscle has fascinated many for centuries. In developing muscle cells, as well as in many adherent, nonmuscle cell types, striated, stress fiberlike structures with sarcomere-periodicity tend to register: Based on several studies, neighboring, parallel fibers at the basal membrane of cultured cells establish registry of their respective periodic sarcomeric architecture, but, to our knowledge, the mechanism has not yet been identified. Here, we propose for cells plated on an elastic substrate or adhered to a neighboring cell, that acto-myosin contractility in striated fibers close to the basal membrane induces substrate strain that gives rise to an elastic interaction between neighboring striated fibers, which in turn favors interfiber registry. Our physical theory predicts a dependence of interfiber registry on externally controllable elastic properties of the substrate. In developing muscle cells, registry of striated fibers (premyofibrils and nascent myofibrils) has been suggested as one major pathway of myofibrillogenesis, where it precedes the fusion of neighboring fibers. This suggests a mechanical basis for the optimal myofibrillogenesis on muscle-mimetic elastic substrates that was recently observed by several groups in cultures of mouse-, human-, and chick-derived muscle cells.

Mechanobiology of bone marrow stem cells: From myosin-II forces to compliance of matrix and nucleus in cell forms and fates

Adult stem cells and progenitors are of great interest for their clinical application as well as their potential to reveal deep sensitivities to microenvironmental factors. The bone marrow is a niche for at least two types of stem cells, and the prototype is the hematopoietic stem cell/progenitors (HSC/Ps), which have saved many thousands of patients for several decades now. In bone marrow, HSC/Ps interact functionally with marrow stromal cells that are often referred to as mesenchymal stem cells (MSCs) or derivatives thereof. Myosin and matrix elasticity greatly affect MSC function, and these mechanobiological factors are now being explored with HSC/Ps both in vitro and in vivo. Also emerging is a role for the nucleus as a mechanically sensitive organelle that is semi-permeable to transcription factors which are modified for nuclear entry by cytoplasmic mechanobiological pathways. Since therapies envisioned with induced pluripotent stem cells and embryonic stem cells generally involve in vitro commitment to an adult stem cell or progenitor, a very deep understanding of stem cell mechanobiology is essential to progress with these multi-potent cells.

Synthetic gene brushes: a structure–function relationship

We present the assembly of gene brushes by means of a photolithographic approach that allows us to control the density of end‐immobilized linear double‐stranded DNA polymers coding for entire genes. For 2 kbp DNAs, the mean distance varies from 300 nm, where DNAs are dilute and assume relaxed conformations, down to 30 nm, where steric repulsion at dense packing forces stretching out. We investigated the gene‐to‐protein relationship of firefly luciferase under the T7/E.Coli‐extract expression system, as well as transcription‐only reactions with T7 RNA polymerase, and found both systems to be highly sensitive to brush density, conformation, and orientation. A ‘structure–function’ picture emerges in which extension of genes induced by moderate packing exposes coding sequences and improves their interaction with the transcription/translation machinery. However, tighter packing impairs the penetration of the machinery into the brush. The response of expression to two‐dimensional gene crowding at the nanoscale identifies gene brushes as basic controllable units en route to multicomponent synthetic systems. In turn, these brushes could deepen our understanding of biochemical reactions taking place under confinement and molecular crowding in living cells.