The relative composition of actin isoforms regulates cell surface biophysical features and cellular behaviors

Nuclear actin-dependent Meg3 expression suppresses metabolic genes by affecting the chromatin architecture at sites of elevated H3K27 acetylation levels

Nuclear actin mediates enhancer-dependent transcriptional regulation at compartment level, playing critical roles in 3D genome organization. In β-actin depleted cells, H3K27 acetylation is enhanced, directly affecting enhancer-dependent transcriptional regulation and gene expression changes during compartment-switching. Here, we report these mechanisms are influenced by the long non-coding RNA (lncRNA) Meg3. Bulk RNA-seq analysis and qPCR on wild-type (WT), heterozygous (HET), and β-actin knockout (KO) mouse embryonic fibroblasts (MEFs) show that β-actin depletion significantly alters expression of several lncRNAs, including Meg3. Results from ChIRP-seq, ChIRP-MS, and fRIP-qPCR revealed that in β-actin KO cells, Meg3 becomes enriched and binds to H3K27 acetylation marks within gene regulatory regions. By integrating RNA-seq, H3K27 acetylation ChIP-seq, ATAC-seq, and HiC-seq data through activity by contact (ABC) analysis, we discovered Meg3 binding disrupts promoter-enhancer interactions in β-actin KO cells. These results, combined with metabolomics in WT, HET, and β-actin KO MEFs, show Meg3 binding to regulatory regions at sites of increased H3K27 acetylation impairs the expression of genes involved in the synthesis of chondroitin, heparan, dermatan sulfate, and phospholipases. We propose that in β-actin KO cells Meg3 binds to H3K27 acetylation levels. This interferes with promoter-enhancer interactions, disrupts genome organization, and downregulates gene expression and key metabolic pathways.

Characterizing circulating tumor cells using affinity-based microfluidic capture and AFM-based biomechanics

Elasticity and bio-adhesiveness of circulating tumor cells (CTCs) are important biomarkers of cancer. CTCs are rare in blood, thus their capture and atomic force microscopy (AFM)-based biomechanical characterization require use of multifunctional microfluidic device. Here, we describe procedures for fabrication of such device, AFM-Chip, and give details on its use in affinity-based CTC capture, and integration with AFM via reversable physical assembly. In the AFM-Chip, CTC capture is efficient, and transition to AFM characterization is seamless with minimal cell loss.

For complete details on the use and execution of this protocol, please refer to Deliorman et al. (2020).

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Microfluidic device for isolation of CTCs from whole blood samples of cancer patients

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Reversable physical assembly in microfluidics enables seamless integration with AFM

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AFM-based biomechanics of CTCs for biophysical phenotyping

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AFM-Chip for liquid biopsy and biomechanical characterization of cancer cells

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Switching in the expression pattern of actin isoforms marks the onset of contractility and distinct mechanodynamic behavior during cardiomyocyte differentiation

Differentiation of cardiac progenitor cells (CPC) into cardiomyocytes is a fundamental step in cardiogenesis, which is marked by changes in gene expression responsible for remodeling of the cytoskeleton and in altering the mechanical properties of cells. Here we have induced the differentiation of CPC derived from human pluripotent stem cells into immature cardiomyocytes (iCM) which we compare with more differentiated cardiomyocytes (mCM). Using atomic force microscopy and real-time deformability cytometry, we describe the mechanodynamic changes that occur during the differentiation process and link our findings to protein expression data of cytoskeletal proteins. Increased levels of cardiac-specific markers as well as evolution of cytoskeletal morphology and contractility parameters correlated with the expected extent of cell differentiation that was accompanied by hypertrophic growth of cells. These changes were associated with switching in the balance of the different actin isoforms where β-actin is predominantly found in CPC, smooth muscle α-actin is dominant in iCM cells and sarcomeric α-actin is found in significantly higher levels in mCM. We link these cytoskeletal changes to differences in mechano-dynamic behavior of cells that translate to changes in Young's modulus that depend on the cell adherence. Our results demonstrate that the intracellular balance of actin isoform expression can be used as a sensitive ruler to determine the stage of differentiation during early phases of cardiomyocyte differentiation that correlates with an increased expression of sarcomeric proteins and is accompanied by changes in cellular elasticity.

Emerging roles of cytoskeletal proteins in regulating gene expression and genome organization during differentiation

In the eukaryotic cell nucleus, cytoskeletal proteins are emerging as essential players in nuclear function. In particular, actin regulates chromatin as part of ATP-dependent chromatin remodeling complexes, it modulates transcription and it is incorporated into nascent ribonucleoprotein complexes, accompanying them from the site of transcription to polyribosomes. The nuclear actin pool is undistinguishable from the cytoplasmic one in terms of its ability to undergo polymerization and it has also been implicated in the dynamics of chromatin, regulating heterochromatin segregation at the nuclear lamina and maintaining heterochromatin levels in the nuclear interiors. One of the next frontiers is, therefore, to determine a possible involvement of nuclear actin in the functional architecture of the cell nucleus by regulating the hierarchical organization of chromatin and, thus, genome organization. Here, we discuss the repertoire of these potential actin functions and how they are likely to play a role in the context of cellular differentiation.

Loss of β-Actin Leads to Accelerated Mineralization and Dysregulation of Osteoblast-Differentiation Genes during Osteogenic Reprogramming

Actin plays fundamental roles in both the cytoplasm and the cell nucleus. In the nucleus, β-actin regulates neuronal reprogramming by consolidating a heterochromatin landscape required for transcription of neuronal gene programs, yet it remains unknown whether it has a role in other differentiation models. To explore the potential roles of β-actin in osteogenesis, β-actin wild-type (WT) and β-actin knockout (KO) mouse embryonic fibroblasts (MEFs) are reprogrammed to osteoblast-like cells using small molecules in vitro. It is discovered that loss of β-actin leads to an accelerated mineralization phenotype (hypermineralization), accompanied with enhanced formation of extracellular hydroxyapatite microcrystals, which originate in the mitochondria in the form of microgranules. This phenotype is a consequence of rapid upregulation of mitochondrial genes including those involved in oxidative phosphorylation (OXPHOS) in reprogrammed KO cells. It is further found that osteogenic gene programs are differentially regulated between WT and KO cells, with clusters of genes exhibiting different temporal expression patterns. A novel function for β-actin in osteogenic reprogramming through a mitochondria-based mechanism that controls cell-mediated mineralization is proposed.

AFM-compatible microfluidic platform for affinity-based capture and nanomechanical characterization of circulating tumor cells

Circulating tumor cells (CTCs) carried by the patient's bloodstream are known to lead to the metastatic spread of cancer. It is becoming increasingly clear that an understanding of the nanomechanical characteristics of CTCs, such as elasticity and adhesiveness, represents advancements in tracking and monitoring cancer progression and metastasis. In the present work, we describe a combined microfluidic-atomic force microscopy (AFM) platform that uses antibody-antigen capture to routinely isolate and nanomechanically characterize CTCs present in blood samples from prostate cancer patients. We introduce the reversible assembly of a microfluidic device and apply refined and robust chemistry to covalently bond antibodies onto its glass substrate with high density and the desired orientation. As a result, we show that the device can efficiently capture CTCs from patients with localized and metastatic prostate cancer through anti-EpCAM, anti-PSA, and anti-PSMA antibodies, and it is suitable for AFM measurements of captured intact CTCs. When nanomechanically characterized, CTCs originating from metastatic cancer demonstrate decreased elasticity and increased deformability compared to those originating from localized cancer. While the average adhesion of CTCs to the AFM tip surface remained the same in both the groups, there were fewer multiple adhesion events in metastatic CTCs than there were in their counterparts. The developed platform is simple, robust, and reliable and can be useful in the diagnosis and prognosis of prostate cancer as well as other forms of cancer.

Responses of Acinetobacter baumannii Bound and Loose Extracellular Polymeric Substances to Hyperosmotic Agents Combined with or without Tobramycin: An Atomic Force Microscopy Study

In this work, contributions of extracellular polymeric substances (EPS) to the nanoscale mechanisms through which the multidrug-resistant Acinetobacter baumannii responds to antimicrobial and hyperosmotic treatments were investigated by atomic force microscopy. Specifically, the adhesion strengths to a control surface of silicon nitride (Si₃N₄) and the lengths of bacterial surface biopolymers of bound and loose EPS extracted from A. baumannii biofilms were quantified after individual or synergistic treatments with hyperosmotic agents (NaCl and maltodextrin) and an antibiotic (tobramycin). In the absence of any treatment, the loose EPS were significantly longer in length and higher in adhesion to Si₃N₄ than the bound EPS. When used individually, the hyperosmotic agents and tobramycin collapsed the A. baumannii bound and loose EPS. The combined treatment of maltodextrin with tobramycin collapsed only the loose EPS and did not alter the adhesion of both bound and loose EPS to Si₃N₄. In addition, the combined treatment was not as effective in collapsing the EPS molecules as when tobramycin was applied alone. Finally, the effects of treatments were dose-dependent. Altogether, our findings suggest that a sequential treatment could be effective in treating A. baumannii biofilms, in which a hyperosmotic agent is used first to collapse the EPS and limit the diffusion of nutrients into the biofilm, followed by the use of an antibiotic to kill the bacterial cells that escape from the biofilm because of starvation.

β-actin regulates a heterochromatin landscape essential for optimal induction of neuronal programs during direct reprograming

During neuronal development, β-actin serves an important role in growth cone mediated axon guidance. Consistent with this notion, in vivo ablation of the β-actin gene leads to abnormalities in the nervous system. However, whether β-actin is involved in the regulation of neuronal gene programs is not known. In this study, we directly reprogramed β-actin^+/+ WT, β-actin^+/- HET and β-actin^-/- KO mouse embryonic fibroblast (MEFs) into chemically induced neurons (CiNeurons). Using RNA-seq analysis, we profiled the transcriptome changes among the CiNeurons. We discovered that induction of neuronal gene programs was impaired in KO CiNeurons in comparison to WT ones, whereas HET CiNeurons showed an intermediate levels of induction. ChIP-seq analysis of heterochromatin markers demonstrated that the impaired expression of neuronal gene programs correlated with the elevated H3K9 and H3K27 methylation levels at gene loci in β-actin deficient MEFs, which is linked to the loss of chromatin association of the BAF complex ATPase subunit Brg1. Together, our study shows that heterochromatin alteration in β-actin null MEFs impedes the induction of neuronal gene programs during direct reprograming. These findings are in line with the notion that H3K9Me3-based heterochromatin forms a major epigenetic barrier during cell fate change.

Although β-actin plays an important role in growth cone mediated axon guidance in neurons, the potential role of β-actin in controlling neuron differentiation remains unknown. Here, we converted β-actin^+/+ WT, β-actin^+/- HET and β-actin^-/- KO mouse embryonic fibroblast (MEFs) into chemically induced neurons (CiNeurons) by direct reprograming. We found that the up-regulation of neuronal programs was impaired in β-actin^-/- CiNeurons in comparison to WT ones. β-actin^+/- HET CiNeurons showed an intermediate level of neuronal program expression, suggesting that β-actin dosage plays an important role during direct neuronal reprograming. Importantly, the impaired up-regulation of neuron-related genes was associated with the elevated H3K9 and H3K27 methylation levels at gene loci in KO MEFs. These epigenetic changes were accompanied by the impaired chromatin association of Brg1-containing chromatin remodeling BAF complex in β-actin null cells. Together our study demonstrates that β-actin is required for the optimal induction of neuronal gene programs during direct reprograming by presetting a favorable chromatin status.

Elevated transforming growth factor β signaling activation in β-actin-knockout mouse embryonic fibroblasts enhances myofibroblast features

Signaling by the transforming growth factor‐β (TGF‐β) is an essential pathway regulating a variety of cellular events. TGF‐β is produced as a latent protein complex and is required to be activated before activating the receptor. The mechanical force at the cell surface is believed to be a mechanism for latent TGF‐β activation. Using β‐actin null mouse embryonic fibroblasts as a model, in which actin cytoskeleton and cell‐surface biophysical features are dramatically altered, we reveal increased TGF‐β1 activation and the upregulation of TGF‐β target genes. In β‐actin null cells, we show evidence that the enhanced TGF‐β signaling relies on the active utilization of latent TGF‐β1 in the cell culture medium. TGF‐β signaling activation contributes to the elevated reactive oxygen species production, which is likely mediated by the upregulation of Nox4. The previously observed myofibroblast phenotype of β‐actin null cells is inhibited by TGF‐β signaling inhibition, while the expression of actin cytoskeleton genes and angiogenic phenotype are not affected. Together, our study shows a scenario that the alteration of the actin cytoskeleton and the consequent changes in cellular biophysical features lead to changes in cell signaling process such as TGF‐β activation, which in turn contributes to the enhanced myofibroblast phenotype.