Mechanogenetic regulation of transcription

Simultaneous determination of the mechanical properties and turgor of a single bacterial cell using atomic force microscopy

Bacterial mechanical properties (cell wall stiffness and turgor) are important factors for bacterial survival in harsh environments. For an individual bacterial cell, it is challenging to determine the cell wall stiffness and turgor simultaneously. In this study, we adopted a combined finite element modelling and mathematical modelling approach to simultaneously determine bacterial cell wall stiffness and turgor of an individual bacterial cell based on atomic force microscopy (AFM) nanoindentation. The mechanical properties and turgor of Staphylococcus epidermidis, determined by our method are consistent with other independent studies. For a given aqueous environment, bacterial cell wall stiffness increased linearly with an increase in turgor. Higher osmolarity leads to a decrease in both cell wall stiffness and turgor. We also demonstrated that the change of turgor is associated with a change in viscosity of the bacterial cell.

Flow-enhanced priming of hESCs through H2B acetylation and chromatin decondensation

BACKGROUND

Distinct mechanical stimuli are known to manipulate the behaviors of embryonic stem cells (ESCs). Fundamental rationale of how ESCs respond to mechanical forces and the potential biological effects remain elusive. Here we conducted the mechanobiological study for hESCs upon mechanomics analysis to unravel typical mechanosensitive processes on hESC-specific fluid shear.

METHODS

hESC line H1 was subjected to systematically varied shear flow, and mechanosensitive proteins were obtained by mass spectrometry (MS) analysis. Then, function enrichment analysis was performed to identify the enriched gene sets. Under a steady shear flow of 1.1 Pa for 24 h, protein expressions were further detected using western blotting (WB), quantitative real-time PCR (qPCR), and immunofluorescence (IF) staining. Meanwhile, the cells were treated with 200 nM trichostatin (TSA) for 1 h as positive control to test chromatin decondensation. Actin, DNA, and RNA were then visualized with TRITC-labeled phalloidin, Hoechst 33342, and SYTO® RNASelect™ green fluorescent cell stain (Life Technologies), respectively. In addition, cell stiffness was determined with atomic force microscopy (AFM) and annexin V-PE was used to determine the apoptosis with a flow cytometer (FCM).

RESULTS

Typical mechanosensitive proteins were unraveled upon mechanomics analysis under fluid shear related to hESCs in vivo. Functional analyses revealed significant alterations in histone acetylation, nuclear size, and cytoskeleton for hESC under shear flow. Shear flow was able to induce H2B acetylation and nuclear spreading by CFL2/F-actin cytoskeletal reorganization. The resulting chromatin decondensation and a larger nucleus readily accommodate signaling molecules and transcription factors.

CONCLUSIONS

Shear flow regulated chromatin dynamics in hESCs via cytoskeleton and nucleus alterations and consolidated their primed state.

Validation of housekeeping gene and impact on normalized gene expression in clear cell renal cell carcinoma: critical reassessment of YBX3/ZONAB/CSDA expression

Background

YBX3/ZONAB/CSDA is an epithelial-specific transcription factor acting in the density-based switch between proliferation and differentiation. Our laboratory reported overexpression of YBX3 in clear cell renal cell arcinoma (ccRCC), as part of a wide study of YBX3 regulation in vitro and in vivo. The preliminary data was limited to 5 cases, of which only 3 could be compared to paired normal tissue, and beta-Actin was used as sole reference to normalize gene expression. We thus decided to re-evaluate YBX3 expression by real-time-PCR in a larger panel of ccRCC samples, and their paired healthy tissue, with special attention on experimental biases such as inter-individual variations, primer specificity, and reference gene for normalization.

Results

Gene expression was measured by RT-qPCR in 16 ccRCC samples, each compared to corresponding healthy tissue to minimize inter-individual variations. Eight potential housekeeping genes were evaluated for expression level and stability among the 16-paired samples. Among tested housekeeping genes, PPIA and RPS13, especially in combination, proved best suitable to normalize gene expression in ccRCC tissues as compared to classical reference genes such as beta-Actin, GAPDH, 18S or B2M. Using this pair as reference, YBX3 expression level among a collection of 16 ccRCC tumors was not significantly increased as compared to normal adjacent tissues. However, stratification according to Fuhrman grade disclosed higher YBX3 expression levels in low-grade tumors and lower in high-grade tumors. Immunoperoxidase confirmed homogeneous nuclear staining for YBX3 in low-grade but revealed nuclear heterogeneity in high-grade tumors.

Conclusions

This paper underlines that special attention to reference gene products in the design of real-time PCR analysis of tumoral tissue is crucial to avoid misleading conclusions.

Furthermore, we found that global YBX3/ZONAB/CSDA mRNA expression level may be considered within a “signature” of RCC grading.

Creatine increases IGF-I and myogenic regulatory factor mRNA in C(2)C(12) cells

Addition of creatine to the differentiation medium of C(2)C(12) cells leads to hypertrophy of the myotubes. To investigate the implication of insulin-like growth factor I (IGF-I) and myogenic regulatory factors (MRFs) in this hypertrophy, their mRNA levels were assessed during the first 72 h of differentiation. Creatine significantly increased the IGF-I mRNA level over the whole investigated period of time, whereas the MRF mRNA levels were only augmented at precise moments, suggesting a general activation mechanism for IGF-I and a specifically regulated mechanism for MRF transcription. Our results suggest therefore that creatine-induced hypertrophy of C(2)C(12) cells is at least partially mediated by overexpression of IGF-I and MRFs.

Bacterial turgor pressure can be measured by atomic force microscopy

We report a study of the deformability of a bacterial wall with an atomic force microscope (AFM). A theoretical expression is derived for the force exerted by the wall on the cantilever as a function of the depths of indentation generated by the AFM tip. Evidence is provided that this reaction force is a measure for the turgor pressure of the bacterium. The method was applied to magnetotactic bacteria of the species Magnetospirillum gryphiswaldense. Force curves were generated on the substrate and on the bacteria while scanning laterally. With the mechanical properties so gained we obtained the spring constant of the bacterium as a whole. Making use of our theoretical results we determined the turgor pressure to be in the range of 85 to 150 kPa.

Cardiac cell volume: crystal clear or murky waters? A comparison with other cell types

The osmolarity of bodily fluids is strictly controlled so that most cells do not experience changes in osmotic pressure under normal conditions, but osmotic changes can occur in pathological states such as ischemia, septic shock, and diabetic coma. The primary effect of a change in osmolarity is to acutely alter cell volume. If the osmolarity around a cell is decreased, the cell swells, and if increased, it shrinks. In order to tolerate changes in osmolarity, cells have evolved volume regulatory mechanisms activated by osmotic challenge to normalise cell volume and maintain normal function. In the heart, osmotic stress is encountered during a period of myocardial ischemia when metabolites such as lactate accumulate intracellularly and to a certain degree extracellularly, and cause cell swelling. This swelling may be exacerbated further on reperfusion when the hyperosmotic extracellular milieu is replaced by normosmotic blood. In this review, we describe the theory and mechanisms of volume regulation, and draw on findings in extracardiac tissues, such as kidney, whose responses to osmotic change are well characterised. We then describe cell volume regulation in the heart, with particular emphasis on the effect of myocardial ischemia. Finally, we describe the consequences of osmotic cell swelling for the cell and for the heart, and discuss the implications for antiarrhythmic drug efficacy. Using computer modelling, we have summated the changes induced by cell swelling, and predict that swelling will shorten the action potential. This finding indicates that cell swelling is an important component of the response to ischemia, a component modulating the excitability of the heart.

Microtubules are involved in early hypertrophic responses of myocardium during pressure overload

Mechanical overloading to cardiac muscle causes fetal contractile protein gene expression and acceleration of protein synthesis. Myocyte microtubules might be involved in these pressure overload-induced hypertrophic responses. We assessed c-fos and fetal contractile protein genes such as beta-myosin heavy chain (MHC) and alpha-skeletal actin using Northern blot analysis and quantified total cardiac protein, DNA, and RNA content in the left ventricular myocardium obtained from four groups of rats: sham-operated rats; sham-operated rats treated with colchicine, which depolymerized microtubules; rats in which acute pressure overload was imposed by abdominal aortic constriction for 3 days (AoC); and AoC rats treated with colchicine (AoC + colchicine). Systolic arterial pressure was elevated to a similar degree in AoC and AoC + colchicine rats. c-fos and beta-MHC mRNA levels were significantly upregulated in AoC rats, which was attenuated by microtubule inhibition. Both RNA content and RNA-to-DNA ratio, the index of the protein synthesis capacity, were increased in AoC rats, which effect was also abolished by colchicine. Furthermore, induction of nonfunctioning microtubules by taxol or deuterium oxide exerted the same inhibitory effects. Thus the hypertrophic responses of the myocardium during pressure overload might depend on the integrity of myocyte microtubules.

Increased c-fos mRNA expression by human fibroblasts contracting stressed collagen matrices

We studied early changes in gene expression during fibroblast contraction of stressed collagen matrices. The level of c-fos mRNA increased dramatically and peaked 50 to 60 min after matrix contraction was initiated. This response did not require serum and could not be accounted for simply by disruption of the actin cytoskeleton. Increased c-fos mRNA levels required Ca2+ influx but not the cyclic AMP or extracellular signal-regulated kinase (ERK 1/2) signaling pathways, both of which are activated when fibroblasts contract stressed collagen matrices. The levels of two other immediate-early genes, fosb and c-jun, also increased transiently after fibroblast contraction, whereas the levels of fra-1, fra-2, c-myc, and the transcription factor NF-kappaB remained the same, indicating that fibroblast contraction caused changes in a selective group of genes. The increase in c-fos mRNA during contraction of stressed collagen matrices may reflect a unique role for c-fos in mechanoregulated events at the end of wound repair.

Knockout and knockin of the beta1 exon D define distinct roles for integrin splice variants in heart function and embryonic development

The beta1D integrin is a recently characterized isoform of the beta1 subunit that is specifically expressed in heart and skeletal muscle. In this study we have assessed the function of the beta1D integrin splice variant in mice by generating, for the first time, Cre-mediated exon-specific knockout and knockin strains for this splice variant. We show that removal of the exon for beta1D leads to a mildly disturbed heart phenotype, whereas replacement of beta1A by beta1D results in embryonic lethality with a plethora of developmental defects, in part caused by the abnormal migration of neuroepithelial cells. Our data demonstrate that the splice variants A and D are not functionally equivalent. We propose that beta1D is less efficient than beta1A in mediating the signaling that regulates cell motility and responses of the cells to mechanical stress.

Identification of a regulatory protein required for pressure-responsive gene expression in the deep-sea bacterium Photobacterium species strain SS9

Here, we report the characterization of a gene necessary for hydrostatic pressure regulation of gene expression in the deep-sea bacterium Photobacterium species strain SS9. The deduced amino acid sequence of the gene product shares extensive similarity to ToxR, a transmembrane DNA-binding protein first discovered as a virulence determinant in the pathogenic bacterium Vibrio cholerae. Changes in hydrostatic pressure induce changes in both the abundance and the activity of the SS9 ToxR protein (or the activity of a ToxR-regulated protein). As with other high-pressure-inducible phenomena observed in higher organisms, anaesthetics antagonize high-pressure signalling mediated by ToxR. It is suggested that SS9 ToxR has evolved the ability to respond to pressure-mediated alterations in membrane structure. V. cholerae and SS9 also share similarity in a ToxR-regulated protein, indicating that part of the ToxR regulon is conserved in diverse members of the family Vibrionaceae. The SS9 ToxR system represents a useful model for studies of signal transduction and environmental adaptation in the largest portion of the biosphere, the deep sea.

Fibroblasts contracting collagen matrices form transient plasma membrane passages through which the cells take up fluorescein isothiocyanate-dextran and Ca2+

When fibroblasts contract collagen matrices, the cells activate a Ca(2+)-dependent cyclic AMP signaling pathway. We have found that contraction also stimulates uptake of fluorescein isothiocyanate-dextran molecules from the medium. Our results indicate that fluorescein isothiocyanate-dextran enters directly into the cell cytoplasm through 3- to 5-nm plasma membrane passages. These passages, which reseal in less than 5 s in the presence of divalent cations, also are likely sites of Ca2+ uptake during contraction and the first step in contraction-activated cyclic AMP signaling. The formation of plasma membrane passages during fibroblast contraction may reflect a general cellular response to rapid mechanical changes.

[Plasticity of the myocardium in pediatric cardiology]

The phenotypic adaptation of the myocardium to mechanical overload is a well known concept. The changes that occur into the myocardial structure in heart failure lead to new therapeutical approaches, particularly the use of ACE inhibitors in the treatment of dilated cardiomyopathies in order to prevent myocardial remodeling. In the hypoplastic left heart syndrome or in pulmonary atresia-intact septum, the pathogenetic process is supposed to be abnormal intra-cardiac blood flow during fetal life inducing abnormal cardiac remodeling. When the left ventricle ejects into the pulmonary circulation (double discordance, atrial repair of transposition of the great arteries), the surgical repair that consists to replace the left ventricule in the systemic circuit is based on the concept of ventricular remodeling and plasticity.

Enhanced cell attachment to anorganic bone mineral in the presence of a synthetic peptide related to collagen

We have examined the ability of a synthetic 15-residue peptide, P-15, related to a biologically active domain of type I collagen, to promote attachment of human dermal fibroblasts to anorganic bovine bone mineral (ABM) phase. The attachment of cells increased with increasing content of P-15 on the surface of ABM particles, as seen by the increased binding of radiolabeled cells, and by light microscopy and scanning electron microscopy. Incorporation of radioactive precursors of DNA and protein synthesis showed that cells on P-15-coated ABM synthesized over twofold the amount of DNA and protein than did cells on uncoated ABM. Fibroblasts attached to ABM in the presence of P-15 formed three-dimensional colonies. Cellular bridges formed between adjacent particles which aggregated in clusters with tissue-like structure. Cultures on ABM.P-15 stained for alkaline phosphatase. These observations suggest that P-15-coated ABM may be a useful matrix for bone repair.

Role of phospholipase D in the cAMP signal transduction pathway activated during fibroblast contraction of collagen matrices

Fibroblast contraction of stressed collagen matrices results in activation of a cAMP signal transduction pathway. This pathway involves influx of extracellular Ca2+ ions and increased production of arachidonic acid. We report that within 5 min after initiating contraction, a burst of phosphatidic acid release was detected. Phospholipase D was implicated in production of phosphatidic acid based on observation of a transphosphatidylation reaction in the presence of ethanol that resulted in formation of phosphatidylethanol at the expense of phosphatidic acid. Activation of phospholipase D required extracellular Ca2+ ions and was regulated by protein kinase C. Ethanol treatment of cells also inhibited by 60-70% contraction-dependent release of arachidonic acid and cAMP but had no effect on increased cAMP synthesis after addition of exogenous arachidonic acid or on phospholipase A2 activity measured in cell extracts. Moreover, other treatments that inhibited the burst of phosphatidic acid release after contraction--chelating extracellular Ca2+ or down-regulating protein kinase C--also blocked contraction activated cyclic AMP signaling. These results were consistent with the idea that phosphatidic acid production occurred upstream of arachidonic acid in the contraction-activated cAMP signaling pathway.

Stress relaxation of fibroblasts activates a cyclic AMP signaling pathway

Mechanical force regulates gene expression and cell proliferation in a variety of cell types, but the mechanotransducers and signaling mechanisms involved are highly speculative. We studied the fibroblast signaling mechanism that is activated when cells are switched from mechanically stressed to mechanically relaxed conditions, i.e., stress relaxation. Within 10 min after initiation of stress relaxation, we observed a transient 10-20-fold increase in cytoplasmic cyclic AMP (cAMP) and a threefold increase in protein kinase A activity. The increase in cAMP depended on stimulation of adenylyl cyclase rather than inhibition of phosphodiesterase. Generation of cAMP was inhibited by indomethacin, and release of arachidonic acid was found to be an upstream step of the pathway. Activation of signaling also depended on influx of extracellular Ca2+ because addition of EGTA to the incubations at concentrations just sufficient to exceed Ca2+ in the medium inhibited the stress relaxation-dependent increase in free arachidonic acid and cAMP. This inhibition was overcome by adding CaCl2 to the medium. On the other hand, treating fibroblasts in mechanically stressed cultures with the calcium ionophore A23187-stimulated arachidonic acid and cAMP production even without stress relaxation. In summary, our results show that fibroblast stress relaxation results in activation of a Ca(2+)-dependent, adenylyl cyclase signaling pathway. Overall, the effect of stress relaxation on cAMP and PKA levels was equivalent to that observed after treatment of cells with forskolin.

Molecular basis of regression of cardiac hypertrophy

Cardiac hypertrophy due to a chronic mechanical overload puts into play a biologic cascade, including a trigger (the mechanical stretch), a transmitter (very likely to be the phosphoinositol pathway), and the final target (which is the DNA). The permanent changes in genetic expression resulting from the activation of this cascade allows the heart to produce normal active tension at a lower cost in terms of energy expenditure. The process is reversible, providing the treatment reduces the real load on the heart--i.e., not only the peripheral resistances but also the aortic impedance--during a period of time that has to be several times the half-life of cardiac proteins, and also that the treatment has an effect on the detrimental consequences of cardiac hypertrophy, namely, the systolic and diastolic dysfunction and the incidence of arrhythmias. In this report semisenescent spontaneously hypertensive rats were treated for 3 months with the converting enzyme inhibitor trandolapril. The treatment had a rather modest effect on blood pressure but resulted in a pronounced reduction in cardiac hypertrophy and in cardiac fibrosis, an improved coronary reserve, and attenuated both the effects of anoxia on the left ventricular diastolic compliance and the incidence of ventricular arrhythmias.

Decreased level of PDGF-stimulated receptor autophosphorylation by fibroblasts in mechanically relaxed collagen matrices

The goal of our studies was to characterize the interrelationship between extracellular matrix organization and fibroblast proliferation in response to growth factors. We compared fibroblasts in monolayer culture with cells in contracted collagen matrices that were mechanically stressed or relaxed. In response to platelet-derived growth factor (PDGF), DNA synthesis by fibroblasts in mechanically relaxed collagen matrices was 80-90% lower than in monolayer culture and 50% lower than in mechanically stressed matrices. Fibroblasts in monolayer and contracted collagen matrix cultures contained similar levels of PDGF receptors, but differed in their autophosphorylation response. Cells in mechanically relaxed matrices showed lowest levels of autophosphorylation, 90% less than cells in monolayer culture. Experiments comparing receptor expression and capacity for PDGF-stimulated autophosphorylation showed that cells in mechanically relaxed collagen matrices never developed normal receptor autophosphorylation. Furthermore, when mechanically stressed collagen matrices were switched to mechanically relaxed conditions, capacity for receptor autophosphorylation decreased within 1-2 h and remained low. Based on immunomicroscopic observations and studies on down-regulation of receptors by PDGF binding, it appeared that most PDGF receptors in monolayer or contracted collagen matrix cultures were localized on the cell surface and accessible to PDGF binding. In related studies, we found that EGF receptors of fibroblasts in mechanically relaxed collagen matrices also showed low levels of autophosphorylation in response to EGF treatment. Based on these results, we suggest that mechanical interactions between cells and their surrounding matrix provide regulatory signals that modulate autophosphorylation of growth factor receptors and cell proliferation.

Stress-relaxation of fibroblasts in collagen matrices triggers ectocytosis of plasma membrane vesicles containing actin, annexins II and VI, and beta 1 integrin receptors

To learn about the effects of tension on fibroblast function, we have been studying initial cellular responses to stress-relaxation. Human foreskin fibroblasts were cultured in anchored collagen matrices for 2 days, during which time mechanical stress developed. Subsequently, the matrices were dislodged; thereby allowing stress to dissipate. Within 5 min after initiating stress-relaxation, fibroblasts retracted their pseudopodia. At this time, we observed the disappearance of cellular stress fibers and the formation of actin clusters along the cell margins. The actin was found to be located inside 200 nm diameter vesicles that were budding from the cell surface. Vesicles isolated from the matrix after stress-relaxation contained prominent 24 kDa, 36 kDa (doublet), 45 kDa, and 135 kDa polypeptides. The 45 kDa polypeptide was the major component in the Triton-insoluble vesicle fraction and appeared to be actin. The 36 kDa (doublet) polypeptide, which was found predominantly in the Triton-soluble vesicle fraction, was identified as annexin II. Vesicles also contained annexin VI and beta 1 integrin receptors but not tubulin, vimentin, vinculin or annexin I. The results suggest that stress-relaxation of fibroblasts induces a novel ectocytotic process involving transient budding of intact, plasma membrane vesicles from the cell cortex. On the basis of their morphological and biochemical features, these vesicles may be analogous to the ‘matrix vesicles’ released by chondrocytes and could play a role in extracellular matrix remodeling after wound contraction.

Stimulation of glucose transport in L6 muscle cells by long-term intermittent stretch-relaxation

Skeletal muscle stretch increases resting metabolism and causes hypertrophy. We have examined the effect of mechanical stretch in vitro on glucose transport activity and transporter contents in L6 muscle cells. Long-term (24-48 h) stretch-relaxation (25% maximal elongation at 30 cycles per min) of cell monolayers significantly increased glucose uptake by 1.6- to 2-fold in myotubes but not in myoblasts. The presence of serum was required for the stretch-relaxation induced increase in glucose uptake. Cycloheximide inhibited the mechanical stimulation of glucose uptake, and the latter response was not additive to the stimulatory effect of long-term exposure to insulin. GLUT1 and GLUT4 glucose transporter contents were not changed in total cell membranes from mechanically stimulated cells relative to controls. These results indicate that mechanical stimulation through passive stretch may be an important regulation of nutrient uptake in fetal myotubes independent of innervation.

Biological adaptation of the myocardium to a permanent change in loading conditions

Cardiac hypertrophy due to permanent mechanical overloading is only one example among thousands of the general process of biological adaptation. The process is randomly governed and results in at least one thermodynamical benefit: to be adaptational and to induce several changes in gene expression. Some of these changes are detrimental, some can even be useless. The cascade of events which finally leads to a permanent modification of the genetic expression involves an initial signal, likely to be the stretch, a pathway which transducts the signal, and a transient change in genetic expression which transmits competence to the cell to be transformed. The permanent modifications occur at all cellular levels including the sarcomere, sarcolemma, energy metabolism, and extra-cellular matrix, but they are species-specific and differ in the ventricles and the atria.