BMB Reports 2024; 57(6): 293-298
Genetic disruption of ATAT1 causes RhoA downregulation through abnormal truncation of C/EBPβ
Jee-Hye Choi1,#, Jangho Jeong1,#, Jaegu Kim1, Eunae You1, Seula Keum1, Seongeun Song1, Ye Eun Hwang1, Minjoo Ji1, Kwon-Sik Park2 & Sangmyung Rhee1,*
1Department of Life Science, Chung-Ang University, Seoul 06974, Korea, 2Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA
Correspondence to: Tel: +82-2-820-5818; Fax: +82-2-825-5206; E-mail:
#These authors contributed equally to this work.
Received: December 1, 2023; Revised: January 3, 2024; Accepted: February 1, 2024; Published online: May 3, 2024.
© Korean Society for Biochemistry and Molecular Biology. All rights reserved.

cc This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Microtubule acetylation has been shown to regulate actin filament dynamics by modulating signaling pathways that control actin organization, although the precise mechanisms remain unknown. In this study, we found that the downregulation of microtubule acetylation via the disruption ATAT1 (which encodes α-tubulin N-acetyltransferase 1) inhibited the expression of RhoA, a small GTPase involved in regulating the organization of actin filaments and the formation of stress fibers. Analysis of RHOA promoter and chromatin immunoprecipitation assays revealed that C/EBPβ is a major regulator of RHOA expression. Interestingly, the majority of C/EBPβ in ATAT1 knockout (KO) cells was found in the nucleus as a 27-kDa fragment (referred to as C/EBPβp27) lacking the N-terminus of C/EBPβ. Overexpression of a gene encoding a C/EBPβp27-mimicking protein via an N-terminal deletion in C/EBPβ led to competitive binding with wild-type C/EBPβ at the C/EBPβ binding site in the RHOA promoter, resulting in a significant decrease of RHOA expression. We also found that cathepsin L (CTSL), which is overexpressed in ATAT1 KO cells, is responsible for C/EBPβp27 formation in the nucleus. Treatment with a CTSL inhibitor led to the restoration of RHOA expression by downregulation of C/EBPβp27 and the invasive ability of ATAT1 KO MDA-MB-231 breast cancer cells. Collectively, our findings suggest that the downregulation of microtubule acetylation associated with ATAT1 deficiency suppresses RHOA expression by forming C/EBPβp27 in the nucleus through CTSL. We propose that CTSL and C/EBPβp27 may represent a novel therapeutic target for breast cancer treatment.
Keywords: Breast cancer, C/EBPβ, Focal adhesion, Microtubule acetylation, RhoA

Tissue homeostasis and function are maintained through a complex combination of cellular activities. These activities ensure the stability of the tissue, enable it to react to external factors, and allow it to carry out its unique roles. At the cellular level, these processes include cell adhesion, migration, proliferation, and differentiation, as well as the organization and regulation of the cytoskeleton and extracellular matrix (ECM) (1). The synchronization of actin and microtubule dynamics, in particular, is critical for cell adhesion and migration (2). Microtubules, for example, can control the localization and activity of actin-binding proteins by transporting them to specific locations within the cell (3). Actin filaments, in turn, can alter microtubule architecture and dynamics by exerting mechanical forces on microtubule growth and orientation (4). As a result, dysregulation of this cooperation can lead to a variety of diseases, including cancer and neurological disorders (5, 6).

Ras homolog family member A (RhoA) regulates actin dynamics during cell migration by driving retraction at the trailing edge and promoting membrane protrusions at the leading edge via processes such as membrane ruffling, lamellae formation, and membrane blebbing (7). Despite the understanding of RhoA’s activation mechanism and its significance in cell migration, an understanding of the transcriptional regulation of RhoA in cancer cells remains elusive. While several transcription factors are known to regulate RhoA expression (8), they fail to comprehensively explain the diverse regulatory mechanisms observed in various cancer cells, particularly in terms of how microtubule acetylation in response to ECM stiffness impacts RhoA expression. Recent research has identified the CCAAT box within the RHOA promoter as a critical regulatory element, with CCAAT/enhancer-binding protein β (C/EBPβ), a well-known transcription factor in cancer progression, emerging as a likely candidate involved in RHOA’s transcriptional regulation (9). Since C/EBPβ is known to exist in various protein isoforms with varied transactivation potential (10), their interplay and response to microtubule acetylation, as well as their specific role in modulating RHOA’s transcriptional activity, are unexplored areas that require further investigation.

We have previously reported that the genetic disruption of alpha-tubulin N-acetyltransferase 1 (α-TAT1), a major α-tubulin acetyltransferase, inhibits colorectal and breast cancers invasion through dysregulation of actin-related adherent junctions and focal adhesions (11, 12). However, the molecular mechanisms leading to the inhibition of actin-related signaling by ATAT1 depletion has not been identified. In this study, we demonstrated that ATAT1 knockout (KO) MDA-MB-231 cells reduced actin-dependent signaling through inhibition of RhoA expression. We also found that ATAT1 KO cells generate a variant of C/EBPβ lacking the N-terminal deletion by cathepsin L (CTSL), which ultimately competes with normal C/EBPβ at the RHOA promoter and represses RhoA expression. Together, these results suggest that the introduction of the gene encoding nuclear CTSL or N-terminal deleted C/EBPβ may be a promising therapeutic target for microtubule acetylation-mediated invasive cancer.


Downregulation of RhoA by genetic disruption of ATAT1

Quantitative analysis of actin-related morphology in ATAT1 KO MDA-MB-231 cells revealed a significant decrease in the size of vinculin-positive focal adhesions in the peripheral region and the length of stress fibers compared with control cells, indicating that microtubule acetylation is involved in the formation of cellular tension (Fig. 1A).

To determine the underlying causes of the morphological changes observed in the ATAT1 KO cells, we conducted functional analysis on differentially expressed genes (DEGs) using RNA-seq raw data obtained from mock and ATAT1 KO cells. We performed a ShinyGO enrichment analysis ( using 3,644 genes that were downregulated in ATAT1 KO cells compared to wild-type (WT) cells, (fold change > 0.66 and adjusted P-values < 0.05). Fig. 1B shows the top 5 significantly downregulated categories according to the PANTHER database and Gene Ontology (GO) database for cellular components. Notably, RHOA was found to belong to all three categories, being most downregulated in ATAT1 KO cells in the following area: microtubule cytoskeleton, anchoring junction and integrin signaling pathway (Fig. 1B).

To confirm RhoA expression in ATAT1 KO cells, we examined the expression level of RhoA in both mock and ATAT1 KO cells by RT-qPCR and Western blot analysis. Fig. 1C shows that significant reductions in RHOA transcript levels were observed in ATAT1 KO cells compared with mock cells. Consistently, RhoA protein expression levels also decreased in ATAT1 KO cells (Fig. 1D). Additionally, when the amount of active RhoA is normalized to GAPDH, it is evident that the absolute amount of intracellular active RhoA in ATAT1 KO cells is up to three times lower than that in mock cells (Fig. 1E). These findings suggest that genetic disruption of ATAT1 disrupts the formation of stress fibers and focal adhesions by inhibiting RhoA signaling.

Identification of C/EBPβ as a RHOA transcriptional activator

To explore the transcriptional regulation of RHOA, we analyzed the promoter region, up to 2 kb from the transcription start site, using the web-based program PROMO 3.0 and AliBaBa2.1. There were 140 cis-acting element sites predicted as candidates for potential competitive binders to the RHOA promoter region. Among them, we sorted out several binding proteins that met both the criteria of being reduced in ATAT1 KO cells (fold change > 0.66, adjusted P-values < 0.05) relative to control cells and having a high hazard ratio (HR ≥ 1.0) in breast cancer patients (Supplementary Fig. 1A).

To ascertain the pivotal promoter region responsible for the transcriptional activation of RHOA, five progressive truncations of the RHOA promoter region were integrated into the pGL3 luciferase vector, as illustrated in Fig. 2A. The transcription efficacies of these varied RHOA promoter fragments (P1 to P5) were compared to that of pGL3-Basic vector in HEK293T cells. Notably, when the P2 construct (−1482 to +1) was introduced into the HEK293T cells, its transcriptional activity declined markedly compared with the P1 construct (−1972 to +1). Additionally, excising 381 bp from the P4 construct (−597 to +1) resulted in a significant decrease in luciferase activity, as seen in Fig. 2A. These results suggest the potential presence of positive regulatory elements within the −1972 bp to −1482 bp and −597 bp to −261 bp regions.

Given that the two defined regions contain potential binding sites for C/EBPβ, we investigated the influence of C/EBPβ on RHOA promoter activity. To this end, we co-transfected C/EBPβ expression vector with pGL3-P1 promoter vector into HEK293T cells and subsequently assessed the ensuing luciferase activity. Remarkably, the transcriptional activity of the P1 promoter exhibited significant elevation (by 6 and 10 times, respectively) in a dose-dependent relationship with C/EBPβ expression, as shown in Fig. 2B, C. To further investigate whether the putative C/EBPβ binding site is indispensable for RHOA promoter activity, we constructed RHOA promoter variant (ΔC/EBPβ) that specifically deleted three putative C/EBPβ binding sites (−1745, −1646 and −261). As shown in Fig. 2D, following co-transfection with C/EBPβ expression vector, the transcriptional activity of the ΔC/EBPβ promoter was significantly attenuated relative to the native RHOA promoter. To corroborate this result, we performed chromatin immunoprecipitation (ChIP) assays to discern the possibility that C/EBPβ binds to the RHOA promoter region. The ChIP assay revealed that C/EBPβ preferentially binds with the −1808/−1686 and −323/−191 regions, while it appears to abstain from the −1050/−795 region (Fig. 2E). We also examined RhoA expression in cells treated with C/EBPβ shRNA to ascertain whether C/EBPβ regulates the expression of RhoA. Our findings demonstrated that the shRNA significantly reduced cellular RhoA protein expression (Supplementary Fig. 1B). Collectively, these results suggest that C/EBPβ functions as a potent transcriptional activator for RHOA transcription.

Reduced expression of RHOA by C/EBPβ lacking the N-terminus

To verify whether reduced expression of C/EBPβ in ATAT1 KO cells downregulates RHOA expression, we confirmed RNA levels of C/EBPβ in mock and ATAT1 KO cells. Contrary to the results obtained from the RNA sequencing analysis, the RNA and protein levels of C/EBPβ in ATAT1 KO cells remained unchanged relative to the mock cells, as indicated in Fig. 3A, B. However, a notable increase was observed in a band of novel size—approximately 27 kDa—which was identified using a C/EBPβ-specific antibody in the ATAT1 KO cells (Fig. 3B). Additionally, the ChIP assay using C/EBPβ antibody also showed that more C/EBPβ protein was bound to the RHOA promoter in ATAT1 KO cells than in mock cells (Supplementary Fig. 2A). Given that C/EBPβ undergoes fragmentary processing during protein expression (13), these results raised the possibility that a 27-kDa protein detected with a C/EBPβ antibody exclusively in ATAT1 KO cells could be a novel derivative with the ability to bind to the C/EBPβ cis-acting element.

To test this hypothesis, we first determined whether the 27-kDa protein originated from the C/EBPβ protein. Transfection with shRNA targeting C/EBPβ not only reduced the levels of the WT C/EBPβ protein—including well-known derivatives of C/EBPβ (liver-enriched activator protein [LAP] and liver-enriched inhibitory protein [LIP])—but also diminished the levels of the 27-kDa protein, which is predominantly found in the nuclear fraction of ATAT1 KO cells (Supplementary Fig. 2B). Next, to determine whether the 27-kDa protein represents a fragment commonly produced through alternative translation or protein processing of C/EBPβ, such as the LIP fragment, we tagged the N-terminal and C-terminal ends of the C/EBPβ protein with Myc and Flag tags, respectively (Fig. 3C). We then assessed whether the 27-kDa band was included in the N- or C-terminus of C/EBPβ. Interestingly, the 27-kDa band was absent in the Western blot probed with the Myc antibody but was evident in the blot probed with the Flag antibody in ATAT1 KO cells (Fig. 3C). Collectively, these results indicate that the 27-kDa protein, detected using C/EBPβ antibody predominantly in the nuclei of ATAT1 KO cells, is a protein missing the N-terminus of C/EBPβ (hereafter referred to as C/EBPβp27).

Based on the molecular weight of C/EBPβp27, it is likely that it possesses a partial deletion of the transcriptional activation domain in the N-terminal region of C/EBPβ while retaining an intact DNA binding domain in the C-terminus. Consequently, C/EBPβp27 likely exerts a negative regulatory effect upon binding to the C/EBPβ cis-acting element within the cell. To test this possibility, we engineered a truncated C/EBPβ fragment corresponding to approximately 27 kDa that contained both the intact DNA-binding and dimerization domains (referred to as ∆N-C/EBPβ; shown in Fig. 3D). Ectopic expression of ∆N-C/EBPβ significantly reduced the expression of RhoA in MDA-MB-231 cells (Fig. 3D). Additionally, we performed a pGL3-RHOA promoter activity assay in HEK293T cells after co-expression of ∆N-C/EBPβ and WT C/EBPβ vectors. As shown in Fig 3E, F, the activity of the RHOA promoter, which is dependent on WT C/EBPβ, decreased proportionately to the ∆N-C/EBPβ levels. These results suggest that C/EBPβp27 competes with native C/EBPβ for binding at the RHOA promoter, ultimately acting to inhibit the transcriptional expression of RHOA.

C/EBPβp27 formation by nuclear CTSL in ATAT1 KO cells

To elucidate how ATAT1 KO MDA-MB-231 cells produce C/EBPβp27, we used RNA sequencing data to examine the expression levels of various proteinases that could target nuclear C/EBPβ. Among the proteases, CTSL expression was significantly increased (5-fold) in ATAT1 KO cells relative to the expression in mock cells, both at the transcript and protein levels (Fig. 4A, B). Notably, CTSL was discernible in the nuclear fraction of ATAT1 KO cells (Fig. 4C).

To determine whether CTSL plays a role in the production of C/EBPβp27, we treated ATAT1 KO cells with a CTSL inhibitor and then analyzed the C/EBPβp27 expression pattern. Following this treatment, there was a significant decrease in C/EBPβp27 and an increase in native C/EBPβ (Fig. 4D). CTSL inhibitor treatment also restored RHOA expression in ATAT1 KO cells (Fig. 4E). The findings from the 3D invasion analysis indicated that the invasive ability of ATAT1 KO cells was restored after CTSL inhibitor treatment (Fig. 4F). Collectively, these results suggest that abnormal CTSL induction in ATAT1 KO cells promotes C/EBPβp27 formation, which in turn suppresses cancer cell mobility by downregulating RHOA expression (Fig. 4G).


Many diseases are associated with increased ECM stiffness. RhoA plays a crucial role in actin-dependent signaling and becomes abnormally active in cells responding to alternations in ECM stiffness (14). For these reasons, RhoA has been considered an attractive target for cancer interventions. However, extensive efforts have been made to develop inhibitors targeting Rho GTPases themselves, none have achieved clinical utility. Fig. 4G summarizes the results of our studies. we identified a series of molecular mechanisms involved in the inhibition of RhoA expression. First, we found that C/EBPβ is a transcription factor for the RHOA gene. Second, CSTL can truncate the N-terminus of C/EBPβ in the nuclei of ATAT1-depleted cancer cells to form C/EBPβp27, a 27-kDa variant. This variant functions as a negative regulatory factor for native C/EBPβ, leading to the inhibition of RHOA gene expression. These results indicate that CSTL, C/EBPβ, and ATAT1 could serve as promising therapeutic targets for ECM stiffening and/or RhoA-dependent cancer treatment.

C/EBPβ is a well-known transcription factor required for tumor progression (10). It is processed into three proteins from a single transcript: LAP1, LAP2, and LIP (13). Interestingly, the LAP2 isoform is a more powerful transcriptional activator than full-length LAP1 (15). The LIP isoform, given its absence of an N-terminal activation domain, acts to inhibit the transcriptional activity of other C/EBP proteins, either through competing for C/EBP consensus binding sites or by forming inactivating heterodimers with other C/EBPs, thereby serving as a dominant negative (13). The C/EBPβp27 investigated in this research shares similarities with LIP in that it lacks the N-terminal transcriptional activation domain. This protein subtype also competes with the native LAP2 protein, inhibiting its binding to the RhoA promoter, thus suppressing its transcriptional activity (Fig. 3E, F). Though the in vivo existence of C/EBPβp27 remains unconfirmed, our findings hint at its potential role as a novel C/EBPβ-dependent gene regulator in certain cancers, like triple-negative breast cancer. Thus, these findings emphasize the potential significance of studying the mechanisms that promote C/EBPβp27 generation in cancer cells. Such insights could pave the way for developing novel therapeutic agents that target C/EBPβ-dependent cancer cell activities, particularly those associated with breast cancer.

CTSL, a member of the cathepsin family, is essential for protein degradation within lysosomes, and it promotes cancer cell migration and invasion via ECM breakdown (16). Its ectopic expression is especially problematic, as it frequently correlates with a poor prognosis (17). Recent findings highlight an intriguing short CTSL isoform without a signal peptide that regulates gene expression by processing the CCAAT-displacement protein/cut homeobox transcription factor (18). In ATAT1 KO cells, we found an increase in the mature CTSL form (25 kDa) in the nucleus, but nuclear CTSL (35 kDa) remained unaffected (Supplementary Fig. 3). The presence of mature CTSL in the nuclei of ATAT1 KO cells raised intriguing questions about the cellular trafficking mechanism of CTSL. While CTSL is typically known to be in lysosomes, our results suggest that mature CTSL also could exist in nuclei and play a critical role in regulating cancer cell progression. One possible explanation lies in the dynamics of acetylated microtubules. In the context of ATAT1 KO cells, there is a decrease in microtubule acetylation, which weakens the binding affinity between these acetylated microtubules and motor proteins such as kinesins (19). Under normal conditions, this interaction facilitates the transportation of intracellular vesicles, including in the contexts of endocytosis and exocytosis. However, given the decreased binding in ATAT1 KO cells, CTSL’s typical egression processes may be disrupted, making it less capable of escaping the cellular region. As a result, there is a propensity for CTSL to accumulate within the nucleus, likely facilitated by simple diffusion through the nuclear pore complex. This novel localization pattern underscores the multifaceted roles CTSL might play in cellular contexts where microtubule dynamics are altered, such as in ATAT1 KO cells.

Each of α-TAT1, RhoA, C/EBPβ, and CTSL is already well known as an important protein in cancer processing. Bioinformatic analysis using Oncomine database of breast cancer patients showed that the expression of α-TAT1, RhoA and C/EBPβ had a strong clinical relevance to the progression of breast cancer (Supplementary Fig. 4). Here, we showed that α-TAT1, RhoA, C/EBPβ, and CTSL interact with each other to affect each other’s activity and transcriptional regulation. The results suggest that the interactions of these proteins may affect cancer development differently from each individual function. This will be of great help in predicting the potential side effects that may arise from regulating the expression of these proteins, which are widely recognized as anticancer targets, on the development and behavior of cancer cells. Our results were observed in the limited context of the ATAT1 KO MDA-MB-231 cell line. Therefore, additional research involving other breast cancer cell lines or animal models is essential for further validation. Additionally, our hypothesis about the regulation of CTSL activity by microtubule acetylation needs to be addressed through further research. Nevertheless, our results clearly showed that the downregulation of microtubule acetylation by ATAT1 deficiency suppresses RHOA expression by forming nuclear C/EBPβp27 through increased CTSL expression, resulting in a loss of motility in MDA-MB-231 cancer cells. The results of this study collectively suggest that regulating RhoA expression via the regulation of ATAT1 activity or through the overexpression of the C/EBPβp27could represent a novel therapeutic strategy for combating breast cancer.


Materials and methods are available in the supplemental material.


This research was supported by grants from the National Research Foundation of Korea (NRF), funded by the Korean government (MSIT) (No. RS-2023-00220089), the MOTIE (Ministry of Trade, Industry, and Energy) in Korea, under the Fostering Global Talents for Innovative Growth Program (P0017308) supervised by the Korea Institute for Advancement of Technology and the Chung-Ang University Research Scholarship Grants in 2022.


The authors have no conflicting interests.

Fig. 1. Genetic disruption of ATAT1 inhibits stress fiber and focal adhesion formation and reduces RhoA expression and activity. (A) Immunocytochemistry analysis of acetylated α-tubulin, focal adhesions and F-actin in mock and ATAT1 KO cells. Scale bar, 10 μm. Graphs show the lengths of actin stress fibers between two focal adhesions and area of focal adhesions at the marginal region (n > 100). (B) Functional annotation of 3,644 genes downregulated in ATAT1 KO cells using PANTHER and GO database and schematic diagram of the identification of the RHOA gene. (C) Results from qPCR analysis of the transcriptional expression of RHOA in mock and ATAT1 KO (clones #1 and #2) MDA-MB-231 cells. (D) Immunoblotting analysis showing the protein level of RhoA in mock and ATAT1 KO cells. (E) A RhoA activity assay was performed on mock and ATAT1 KO cells. All error bars represent the standard deviation (SD) of the data.
Fig. 2. C/EBPβ binds to the RHOA promoter and acts as an activator to increase RHOA expression. (A) Schematic representation of RHOA promoter-luciferase constructs and luciferase activity results. The schematic representation shows the one intact RHOA promoter (P1) and four truncated RHOA promoters from which the following regions had been deleted. (B) Luciferase assay results showing RHOA promoter activity according to the expression of C/EBPβ. (C) Immunoblotting analysis showing the protein level of Flag-C/EBPβ for samples used in (B). (D) Schematic representation of ΔC/EBPβ-RHOA promoter construct and luciferase assay results showing RHOA promoter activity according to the expression of C/EBPβ. (E) Results from ChIP analysis showing C/EBPβ binding to RHOA promoter. All data represent the means of independent experiments ± SD.
Fig. 3. C-terminal fragment of C/EBPβ found in ATAT1 KO MDA-MB-231 cells causes a decrease in RhoA expression. (A) Results from qPCR analysis of the transcriptional expression of C/EBPβ in mock and ATAT1 KO cells. (B) Immunoblotting analysis showing the protein level of C/EBPβ in the cytosolic and nuclear fractions of mock and ATAT1 KO cell lines. Asterisk indicates the newly detected C/EBPβ band (C/EBPβp27). α-tubulin and H3 were used as markers of the cytoplasmic and nuclear factions, respectively. (C) Schematic representation of Myc-C/EBPβ-Flag construct and immunoblotting results using anti-Myc and anti-Flag antibodies. (D) Schematic representation of ΔN-C/EBPβ construct and immunoblot result showing the RhoA protein level according to the over-expression of ΔN-C/EBPβ in MDA-MB-231 cells. Arrowhead indicates ΔN-C/EBPβ band. (E) Luciferase assay results showing RhoA promoter activity according to the expression of C/EBPβ. (F) Immunoblotting analysis showing Flag-C/EBPβ and ΔN-C/EBPβ protein levels in the samples used in (E).
Fig. 4. Increased cathepsin L in the nuclei of ATAT1 KO MDA-MB-231 cells inhibits cancer cell invasion by inducing the production of C/EBPβ C-terminal fragments. (A) Results from qPCR analysis of the transcriptional expression of CTSL in mock and ATAT1 KO cells. (B) Immunoblotting analysis showing the protein levels of cathepsin L and cathepsin D in mock and ATAT1 KO cells. (C) Immunoblotting analysis showing the protein levels of cathepsin L, cathepsin D, and Ac-α-tubulin in the different cellular fractions (total, cytosol and nuclear) of mock and ATAT1 KO cell lines; α-tubulin and H3 were used as cytosolic and nuclear markers, respectively. (D, E) Immunoblotting analysis showing the protein levels of C/EBPβ and RhoA following the pharmacological inhibition of CTSL in mock and ATAT1 KO cell lines. The nuclear fraction was used for analyzing the expression of C/EBPβ, and the level of lamin A/C was used as an internal control (D). Arrowhead indicates C/EBPβp27. The total fraction used for analyzing the expression of RhoA and α-tubulin was analyzed as a loading control (E). (F) 3D cell spheroid invasion assay of ATAT1 KO cells with or without CTSL inhibitor. The yellow solid line represents the spheroid size on day 0. The yellow dotted line indicates invading cells observed on day 4 under each condition. Scale bar, 250 μm. The quantitative analysis results for the relative invasion area are expressed in the graph on the right. Data represent the means of independent triplicate experiments ± SD. (G) Graphical summary of the molecular mechanism involving the inhibition of RhoA expression.
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