RNA-binding proteins (RBP) and noncoding RNAs (ncRNA), such as long noncoding RNAs (lncRNA) and microRNAs (miRNA), control co- and posttranscriptional gene regulation (PTR). At the PTR level, RBPs and ncRNAs contribute to pre-mRNA processing, mRNA maturation, transport, localization, turnover, and translation. Deregulation of RBPs and ncRNAs promotes the onset of cancer progression and metastasis. Both RBPs and ncRNAs are altered by signaling cascades to cooperate or compete with each other to bind their nucleic acid targets. Most importantly, transforming growth factor-beta (TGFβ) signaling plays a significant role in controlling gene expression patterns by targeting RBPs and ncRNAs. Because of TGFβ signaling in cancer, RBP-RNA or RNA-RNA interactions are altered and cause enhanced cell growth and tumor cell dissemination. This review focuses on the emerging concepts of TGFβ signaling on posttranscriptional gene regulation and highlights the implications of RBPs and ncRNAs in cancer progression and metastasis. Mol Cancer Res; 16(4); 567–79. ©2018 AACR.

The transforming growth factor beta (TGFβ) superfamily of secreted proteins are potent regulators of cellular development and differentiation. Once the TGFβ ligands bind to their cognate receptors, multitudes of downstream effector molecules are recruited to orchestrate a collective cellular response. The TGFβ signaling cascade is a tightly controlled process, and aberrant induction of this pathway is the driving mechanism underlying several human disorders (1, 2). Therefore, a comprehensive understanding of the molecular mediators controlling TGFβ-induced cellular transformation may provide novel targets for therapeutic intervention.

TGFβ possesses tumor suppressive and tumor-promoting attributes in multiple cancers. It is accepted that the strength, response, and source of TGFβ signaling in the context of cancer are highly dependent on the number of accrued driving oncogenic mutations in premalignant cells (3, 4). Traditionally, activation of the TGFβ signaling pathway is perceived as a transcriptional event, mediated through receptor phosphorylation and subsequent activation of downstream transcription factors, to promote or repress gene expression (3, 5). However, TGFβ signaling can also control posttranscriptional gene regulatory processes such as mRNA splicing and translation via RNA-binding proteins (RBP) and noncoding RNAs (ncRNA; refs. 6, 7).

RBPs are versatile regulators of gene expression. They control all aspects of messenger RNA maturation, including pre-mRNA splicing, mature mRNA export, localization, turnover, and translation. Due to their ability to regulate the expression of hundreds of coding and ncRNAs, the loss of a single RBP can dramatically alter cellular transcriptomic and proteomic landscapes, which could be detrimental to cellular development (8, 9). Therefore, signaling pathways, such as the TGFβ pathway, capable of altering RBP expression will have strong biological implications.

The noncoding class of RNAs (ribosomal RNA, transfer RNA, small nuclear RNA, piwi, micro, circular, and long noncoding) constitutes >90% of the total pool of transcribed RNAs in mammalian cells (10). Most extensively studied noncoding miRNAs have profound impact in cancer biology and also influenced by TGFβ (11). The long noncoding RNAs (lncRNA) are more than 200 nt in length, emerged as co- and posttranscriptional regulators of gene expression. Typically, miRNAs and lncRNAs are lowly abundant in cells, and evidence supports their role as contributors to many disease including cancer. In this review, we summarize the current field of ncRNA (miRNAs and lncRNAs) and RBP-mediated potentiation of TGFβ signaling in cancer. In addition, we discuss the potential avenues of research for the burgeoning field of TGFβ regulation of ncRNA expression in malignant cellular transformation.

TGFβ was originally identified and characterized as a factor central to the malignant transformation of fibroblasts (12). Since its discovery 40 years ago, TGFβ has emerged as a critical regulator of multiple biological processes, including epithelial–mesenchymal transition (EMT; ref. 13), stem cell regeneration (14), cell proliferation, and immune response (15). The TGFβ family consists of 33 secreted signaling molecules identified by their shared 3-dimensional cysteine knot motif (16). The 33 members are broadly subdivided into five classes: TGFβ, nodal, bone morphogenic proteins (BMP), activins/inhibins, and growth and differentiation factors (GDF; ref. 17). TGFβ is an obligate dimer that binds to heteromeric type-II and I serine/threonine kinase receptors and activates canonical or noncanonical downstream TGFβ signaling molecules. In the following section, we briefly describe the pathways of TGFβ canonical signaling.

There are seven type I (ALK1, ALK2, ALK3/BMPR1A, ALK4/ACVR1B, ALK5/TGFBR1, ALK6/BMPR1B, and ALK7) and five type II (TGFBR2, BMPR2, AMHR2, ACVR2, and ACVR2B) TGFβ receptors (3). These receptors form heteromeric complexes upon ligand binding, which induce type I signaling receptors undergo type II receptor-mediated phosphorylation, thus promoting intracellular adaptor protein binding. In canonical TGFβ signaling, type I receptors phosphorylate receptor regulated SMAD (R-SMADS) transcription factors. SMADs 1, 2, 3, 5, and 8 are R-SMADs and associate with the co-SMAD, SMAD4, to form a trimeric SMAD complex in the cytoplasm. The SMAD2/3/4 oligomers translocate from the cytoplasm to the nucleus and with the aid of additional cofactors alter transcription. For example, phosphorylated R-SMADs 2/3 associate with SMAD4 to activate TGFβ-responsive p21WAF1/Cip1 or repress c-MYC transcription (18). Attenuation of activated TGFβ signaling occurs through activation of inhibitory SMADs (I-SMADS) 6 and 7 (19).

SMAD6 solely functions in BMP signaling; however, SMAD7 can inhibit TGFβ signaling by either competing with SMAD-2 and -3 for type-I receptor binding or regulating the turnover of the TGFβ receptor through association with the ubiquitin ligase Smurf (20). Depending on the cellular context, the transcriptional events activated by canonical TGFβ signaling can enhance cell growth, promote programmed cell death, or facilitate malignant transformation. In addition to the canonical mode of activation, TGFβ can also stimulate ancillary intracellular signaling pathways via SMAD-dependent or independent mechanisms. The extent of TGFβ stimulation of the MAPK, PI3K/AKT, Wnt, and RhoGTPase signaling pathways and others is highly context dependent (21, 22). The TGFβ-mediated crosstalk between these noncanonical pathways is a complex, intricate network of signaling molecules whose concerted efforts promote epithelial-to-mesenchymal transition (EMT), cell proliferation, or apoptosis. For detailed discussions of noncanonical TGFβ signaling, we direct the readers to the following reviews (22, 23). Although TGFβ control of transcriptional events is important, there are several intermediate factors that are pivotal in the regulation of gene expression such as RBPs and ncRNAs. Below we discuss how TGFβ regulated RBPs, miRNAs, and lncRNAs activate or repress TGFβ-induced EMT and act as central signaling nodes for TGFβ-mediated malignant transformation in cancer.

Since its discovery in the late 1970s as a factor capable of transforming normal fibroblasts in vitro, TGFβ has emerged as an integral player in the development of cancer (12). Interestingly, TGFβ exhibits both protumorigenic and antitumorigenic activities. In early mouse models, to determine the effect of TGFβ signaling on tumorigenesis, it was observed that transgenic mice with reduced TGFβ signaling did not form spontaneous tumors. However, in the presence of carcinogenic stimuli, the loss of TGFβ signaling enhanced neoplastic lesions in the liver (24) and lung (24) compared with WT mice. These studies support a tumor suppressive role for TGFB signaling in cancer. In contrast, in a mammary carcinogenesis model, premalignant cells with an intact TGFβ signaling pathway exhibited a marked reduction in proliferation rates compared with the dominant-negative type II TGFβ receptor (DNR) expressing cells (25). However, TGFβ signaling enhanced lung colonization in metastatic cells, and loss of TGFβ signaling in the DNR expressing cells yielded a 60% reduction in metastatic lung lesions (25). This study demonstrated that the TGFβ signaling axis modifies its cellular response depending on the oncogenic mutational status of cells. Lastly, in a recent study, using a mouse model to track and manipulate TGFβ-responsive cells, Oshimori and colleagues identified that TGFβ promotes tumor heterogeneity and drug resistance in squamous cell carcinoma (26). The report demonstrated that TGFβ-responsive cancer stem cells had reduced proliferative rates and altered glutathione metabolism due to TGFβ-driven expression of proteins such as p21 and NRF2 (26). Altogether, these studies highlight the critical yet paradoxical role of TGFβ signaling in cancer.

EMT is an important biological process in the initiation of tumor metastasis. It is a developmental process co-opted by tumors, which helps tumor cell seeding and colonization of areas distant from the primary site of the tumor. EMT is characterized by the loss of epithelial cellular polarity, disruption of cell adhesion, and acquisition of protease production capacity resulting in increased cellular motility (27). Loss of E-cadherin, a potent tumor suppressor, has also been identified as a characteristic feature in the process of epithelial cellular EMT (28). The process of EMT is also governed by genetic alterations in tumor cells and their microenvironment. Also, cytokines, chemokines, extracellular matrix (ECM), and growth factors, which are altered by hypoxic conditions, are crucial for the development of EMT (29). Among these, members of the TGFβ family of cytokines are vital, because TGFβ signaling initiates EMT through the activation of EMT-inducing transcription factors (EMT-TF), including Snail/Slug, Twist, and zinc-finger E-box-binding homeobox 1/2 (ZEB1/2; ref. 28). EMT is also marked by the repression of E-cadherin by TFs including Snail, Slug, Twist, ZEB1, and ZEB2 via binding of its promoter (28).

Posttranscriptional mechanisms that regulate E-cadherin expression and EMT have gained much attention in recent years. The precise coordination between transcriptional, posttranscriptional, and posttranslational events is crucial for the regulation of protein expression and function. RBPs are one of the well-known posttranscriptional regulators and have been reported to regulate EMT through utilization of posttranscriptional gene control measures such as alternative splicing and translation (30, 31). In addition, the ncRNAs such as miRNAs and long noncoding RNAs (lncRNA) were also found to modulate gene expression at posttranscriptional levels. Specifically, ncRNA-mediated regulation of EMT was found to be mediated through EMT-TFs and EMT-associated signaling. In the following sections, we focus on RBPs, miRNAs, and lncRNAs involved both in the regulation of EMT and cancer progression, and we discuss the posttranscriptional mechanisms that contribute to regulation of cancer-associated EMT and tumorigenesis (Tables 1 and 2 and Figs. 1 and 2).

Table 1.

RBPs, miRNAs, and lncRNAs involved in TGFβ-induced EMT

SymbolNameFunctionReferences
RNA binding proteins 
 hnRNP E1 Heterogeneous ribonucleoprotein E1 Promotes EMT in breast cancer via translational repression of Dab2 and ILEI mRNAs (30) 
 ESRP 1 and 2 Epithelial splicing regulatory proteins 1 and 2 Upregulate E-cadherin expression and cause attenuation of EMT in breast cancer (6) 
 RBFOX2 RNA-binding Fox protein 2 Rbfox2 promoted EMT associated tissue invasiveness through splicing events (35) 
 RBFOX3 RNA-binding Fox protein 3 Plays an important role in TGFβ-induced EMT through posttranscriptional regulation of a subset of EMT-related genes (36) 
microRNAs 
 miR-200 family microRNA 200 family Inhibits EMT in breast cancer (40, 42) 
 miR-203 microRNA 203 Inhibits cancer invasion via upregulation of the transcription of SNAI2 (43, 44) 
 miR-181a microRNA 181a Promotes cell migration and invasion through abrogation of proper tight junction formation (45, 46) 
 miR-10b microRNA 10a Promotes TGFβ1-induced EMT in breast cancer cells (47, 48) 
Long noncoding RNAs 
 lncRNA Hotair Long intergenic noncoding RNA Hotair Promotes EMT via upregulation of EMT associated genes such as ZEB1, SNAI1, and TWIST (60) 
 lncRNA MALAT1 Long noncoding RNA metastasis associated lung adenocarcinoma transcript 1 Promotes EMT via repression of E-cadherin expression by associating with suz12 (63) 
 lncRNA ATB Long noncoding RNA activated by TGFβ Induces EMT in breast cancer, colorectal cancer and gastric cancer through the TGFβ/miR-200s/ZEB axis (64, 65) 
 lncRNA HULC Long noncoding RNA highly upregulated in cancer promotes TGFβ-induced EMT in HCC via reduction of E-Cad, and upregulation of N-Cadherin, Snail, and ZEB1 (66) 
 LINC01186 Long intergenic noncoding RNA 01186 Is regulated by TGFβ/SMAD3 and inhibits migration and invasion through EMT in lung cancer (67) 
 lncRNA PE Long noncoding RNA PE promotes invasion and EMT in HCC through the miR-200a/b-ZEB1 pathway (69) 
SymbolNameFunctionReferences
RNA binding proteins 
 hnRNP E1 Heterogeneous ribonucleoprotein E1 Promotes EMT in breast cancer via translational repression of Dab2 and ILEI mRNAs (30) 
 ESRP 1 and 2 Epithelial splicing regulatory proteins 1 and 2 Upregulate E-cadherin expression and cause attenuation of EMT in breast cancer (6) 
 RBFOX2 RNA-binding Fox protein 2 Rbfox2 promoted EMT associated tissue invasiveness through splicing events (35) 
 RBFOX3 RNA-binding Fox protein 3 Plays an important role in TGFβ-induced EMT through posttranscriptional regulation of a subset of EMT-related genes (36) 
microRNAs 
 miR-200 family microRNA 200 family Inhibits EMT in breast cancer (40, 42) 
 miR-203 microRNA 203 Inhibits cancer invasion via upregulation of the transcription of SNAI2 (43, 44) 
 miR-181a microRNA 181a Promotes cell migration and invasion through abrogation of proper tight junction formation (45, 46) 
 miR-10b microRNA 10a Promotes TGFβ1-induced EMT in breast cancer cells (47, 48) 
Long noncoding RNAs 
 lncRNA Hotair Long intergenic noncoding RNA Hotair Promotes EMT via upregulation of EMT associated genes such as ZEB1, SNAI1, and TWIST (60) 
 lncRNA MALAT1 Long noncoding RNA metastasis associated lung adenocarcinoma transcript 1 Promotes EMT via repression of E-cadherin expression by associating with suz12 (63) 
 lncRNA ATB Long noncoding RNA activated by TGFβ Induces EMT in breast cancer, colorectal cancer and gastric cancer through the TGFβ/miR-200s/ZEB axis (64, 65) 
 lncRNA HULC Long noncoding RNA highly upregulated in cancer promotes TGFβ-induced EMT in HCC via reduction of E-Cad, and upregulation of N-Cadherin, Snail, and ZEB1 (66) 
 LINC01186 Long intergenic noncoding RNA 01186 Is regulated by TGFβ/SMAD3 and inhibits migration and invasion through EMT in lung cancer (67) 
 lncRNA PE Long noncoding RNA PE promotes invasion and EMT in HCC through the miR-200a/b-ZEB1 pathway (69) 
Table 2.

TGFβ-regulated noncoding RNAs in cancer

SymbolNameFunctionReferences
miRNAs 
 miR-21 microRNA-21 Inhibited the expression of MutS homolog 2 (MSH2) and contribute to chemoresistance in cancer (7, 49) 
 miR-494 microRNA-494 Reduce cell proliferation, migration, and invasion in pancreatic ductal adenocarcinomas (50) 
 miR-34a microRNA-34a Induces tumor suppression in HBV positive HCC (52) 
 miR-584 microRNA-584 Inhibits cell migration in breast cancer (54) 
 miR-182 microRNA-182 Promotes NF-κB signaling pathway and causes aggressive phenotype in glioma (55) 
lncRNA 
 lncRNA ROR Long noncoding RNA-ROR lncRNA ROR was upregulated by TGFβ (70) 
 lncRNA Smad7 lncRNA Smad7 anti-apoptotic effect upon stimulation by TGFβ in mouse breast cancer cell line JygMC(A) (71) 
 HOXD-AS1 HOXD antisense growth-associated long noncoding RNA HOXD-AS1 is activated by the PI3K/Akt pathway and is involved in cell differentiation retinoid acid treatment induced cell differentiation in neuroblastoma (72) 
SymbolNameFunctionReferences
miRNAs 
 miR-21 microRNA-21 Inhibited the expression of MutS homolog 2 (MSH2) and contribute to chemoresistance in cancer (7, 49) 
 miR-494 microRNA-494 Reduce cell proliferation, migration, and invasion in pancreatic ductal adenocarcinomas (50) 
 miR-34a microRNA-34a Induces tumor suppression in HBV positive HCC (52) 
 miR-584 microRNA-584 Inhibits cell migration in breast cancer (54) 
 miR-182 microRNA-182 Promotes NF-κB signaling pathway and causes aggressive phenotype in glioma (55) 
lncRNA 
 lncRNA ROR Long noncoding RNA-ROR lncRNA ROR was upregulated by TGFβ (70) 
 lncRNA Smad7 lncRNA Smad7 anti-apoptotic effect upon stimulation by TGFβ in mouse breast cancer cell line JygMC(A) (71) 
 HOXD-AS1 HOXD antisense growth-associated long noncoding RNA HOXD-AS1 is activated by the PI3K/Akt pathway and is involved in cell differentiation retinoid acid treatment induced cell differentiation in neuroblastoma (72) 
Figure 1.

Regulation of TGFβ induced EMT by RBPs. RBPs such as hnRNPE1 and RB fox protein 2 (RBFOX2) are upregulated by TGFβ and promote EMT through posttranscriptional mechanisms such as translational regulation and splicing of EMT-associated target mRNAs. On the other hand, RBPs such as ESRP1 and ESRP2, RBFOX3, which have been reported to be repressed by TGFβ, repress the EMT process via the upregulation of E-cadherin. RBPs are denoted by dark blue rectangles, and RBP-mediated modulations of EMT are denoted by black arrows and lines.

Figure 1.

Regulation of TGFβ induced EMT by RBPs. RBPs such as hnRNPE1 and RB fox protein 2 (RBFOX2) are upregulated by TGFβ and promote EMT through posttranscriptional mechanisms such as translational regulation and splicing of EMT-associated target mRNAs. On the other hand, RBPs such as ESRP1 and ESRP2, RBFOX3, which have been reported to be repressed by TGFβ, repress the EMT process via the upregulation of E-cadherin. RBPs are denoted by dark blue rectangles, and RBP-mediated modulations of EMT are denoted by black arrows and lines.

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Figure 2.

Regulation of TGFβ induced EMT by microRNAs and lncRNAs. TGFβ upregulates miRNAs miR-10b, miR-181a, and miR-200 family, which in turn promote the EMT, process via repression of E-cadherin in various human cancers. In contrast, miR-203, which inhibits repressors of E-cadherin, is repressed by TGFβ to promote EMT. lncRNAs ATB, HULC, LINC01186, MALAT-1, and PE, which promote EMT either via repression of E-cadherin or through an E-cadherin–independent mechanism, are upregulated by TGFβ in order to promote EMT. However, lncRNAs Hotair, although upregulated by TGFβ, inhibits EMT via inhibition of one of the E-cadherin repressors such as ZEB1/2 or ZNF217. miRNAs are denoted by blue ovals and miRNA-mediated regulations of EMT are denoted by blue arrow and lines and lncRNAs are denoted red rectangles and lncRNA-mediated control of the EMT process is denoted by red arrows and lines. Transcription factors are denoted by dark yellow rounded rectangles and canonical TGFβ pathway members such as Smads and noncanonical TGFβ members such as PI3/Akt are denoted by light blue or yellow rectangles and dark green round single corner rectangles, respectively.

Figure 2.

Regulation of TGFβ induced EMT by microRNAs and lncRNAs. TGFβ upregulates miRNAs miR-10b, miR-181a, and miR-200 family, which in turn promote the EMT, process via repression of E-cadherin in various human cancers. In contrast, miR-203, which inhibits repressors of E-cadherin, is repressed by TGFβ to promote EMT. lncRNAs ATB, HULC, LINC01186, MALAT-1, and PE, which promote EMT either via repression of E-cadherin or through an E-cadherin–independent mechanism, are upregulated by TGFβ in order to promote EMT. However, lncRNAs Hotair, although upregulated by TGFβ, inhibits EMT via inhibition of one of the E-cadherin repressors such as ZEB1/2 or ZNF217. miRNAs are denoted by blue ovals and miRNA-mediated regulations of EMT are denoted by blue arrow and lines and lncRNAs are denoted red rectangles and lncRNA-mediated control of the EMT process is denoted by red arrows and lines. Transcription factors are denoted by dark yellow rounded rectangles and canonical TGFβ pathway members such as Smads and noncanonical TGFβ members such as PI3/Akt are denoted by light blue or yellow rectangles and dark green round single corner rectangles, respectively.

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hnRNP E1

Heterogeneous nuclear ribonucleoproteins (hnRNP) belong to a class of RBPs involved in mRNA processing such as alternative splicing, mRNA stability, and translational regulation. Recently, hnRNPE1 has been shown to repress EMT promoting diabled-2 (Dab2) and interleukin-like EMT inducer (ILEI), by binding the structural, 33 nucleotide long TGFβ-activated translation (BAT) element present in their 3′-UTRs (30). In addition, TGFβ-mediated phosphorylation of hnRNP E1 at Ser43 by protein kinase Bβ/Akt2 was found to enhance the translational activation of Dab2 and ILE1, by inducing the release of hnRNPE1 from the BAT element of these mRNAs (30). In addition to Dab2 and ILEI, several hnRNP E1 target mRNAs translationally regulated by hnRNPE1 were identified as mediators of EMT under TGFβ treatment (32). Specifically, a panel of 36 genes that possess BAT element in the 3′-UTR (termed BAT genes) including EMT-associated ZEB2, Eukaryotic initiation factor 5A2, Moesin, Egfr, and inhibin beta A was identified. Thus, TGFβ-inducible hnRNP E1 posttranscriptional regulon controls EMT process during development and metastatic progression of tumors (32).

ESRP 1 and 2

Epithelial splicing regulatory proteins (ESRP) 1 and 2 are RBPs that promote an epithelial phenotype by facilitating splicing of transcripts such as fibroblast growth factor receptor 2 (FGFR2) and ENAH, which have been shown to possess well-documented and essential roles in EMT (31). Recently, Horiguchi and colleagues demonstrated that TGFβ drives EMT via downregulation of ESRP1 and 2 (6). Specifically, in normal mammary gland, epithelial cell line NMuMG and EpRas cancer cell lines, TGFβ treatment increased the expression of EMT-inducing δEF1 family proteins, δEF1 and SIP1, which bound to the promoter regions of both ESRP1 and 2 and suppressed their transcription in response to TGFβ treatment. The authors also demonstrated that TGFβ induced downregulation of ESRPs in EpRas cells resulted in the upregulation of FGFR1IIIc, which is the mesenchymal isoform of FGFR1 and downregulation of FGFR2IIIb, which is the epithelial isoform of FGFR2, and both of these isoforms are the splicing targets of ESRP proteins. Importantly, ESRP 1 and 2 proteins have been reported to bind to the GU-rich, auxiliary cis-element ISE/ISS-3 of the FGFR2 gene to modulate its splicing (33). Furthermore, in breast cancer JygMC(A) cells, which autonomously secrete TGFβ, the expression of ESRP1 and 2 was shown to be increased upon treatment with a TGFβ type I receptor (TβR-I) inhibitor, SB431542. In addition, overexpression of ESRP 1 and 2 in human breast cancer MDA-MB-231 cells was found to upregulate E-cadherin expression thereby resulting in the attenuation of EMT (6). Therefore, the authors speculated that the alternative splicing events mediated by ESRP 1 and 2 may regulate unidentified E-cadherin inducers or epithelial regulators, causing a transition from mesenchymal-to-epithelial phenotype via increase in E-cadherin expression.

RBFOX family

The RNA-binding Fox (RBFOX) family of proteins is known to be a crucial player in the regulation of alternative splicing (AS) of pre-mRNA (34). The RBFOX family of proteins has been reported to regulate AS by specifically recognizing the (U)GCAUG sequence in regulated exons or flanking introns, and either promotes or represses the expression of the target exons (34). Recently, Rbfox2 (RNA binding Fox family protein 2) was found to regulate EMT-associated AS and mediate cellular invasion in a murine breast cancer cell line, PY2T, and its expression was shown to be increased by TGFβ treatment–induced EMT (35). Further, it was demonstrated that in PY2T cells, Rbfox2 regulated the splicing of its targets Cortactin (Cttn), Pard3 and dynamin 2 (Dnm2), which have been shown to control molecular events of EMT such as actin polymerization and regulation of cell polarity (35). Very recently, RBFOX3 (RNA binding Fox family protein 3), another well-known regulator of AS, was reported to be transcriptionally downregulated by TGFβ1 treatment in A549 lung cancer cells, and CRISPR-Cas9 mediated knockdown of RBFOX3 promoted EMT via the downregulation of both E-cadherin and Claudin1 (36). Although a reduction of RBFOX3 mRNA was observed upon treatment with TGFβ1, the authors did not identify the specific transcriptional regulator of RBFOX3; instead, they speculated that one of the Smad proteins might be involved in the TGFβ-mediated inhibition of RBFOX3. Furthermore, the authors only demonstrated that expression of RBFOX3 depleted lung cancer cells; however, the authors did not investigate the mechanism by which RBFOX3 controls E-cadherin and/or claudin (36). Taken together, data from the above studies suggest that several RBPs are either activated or repressed by TGFβ promote EMT in multiple cancers via some of the well-known PTR mechanisms as illustrated in Table 1 and Fig. 1.

MicroRNAs are a group of small (∼22 nucleotides) ncRNAs, which bind to complementary sequences within mRNA molecules and control mRNA translation. MicroRNAs influence several physiological conditions and their deregulation cause a myriad of diseases including cancer (37). TGFβ is well known for its dual role in cancer: In the early stages of carcinogenesis, TGFβ functions as a tumor suppressor, whereas in the advanced stages, it switches to promotion of cellular metastasis through the process EMT (38). The interplay between miRNAs, EMT and TGFβ signaling, has been studied extensively in the recent past, and studies have also reported that miRNA maturation can either be enhanced or inhibited by the TGFβ pathway (39). In the section below, we discuss how TGFβ-regulated miRNAs control cancer-associated EMT (Table 1 and Fig. 1).

miR-200

The miR200 family consists of five members—miR-200a, miR-200b, miR200c, miR-141, and miR-429—and are one of the well-known regulators of EMT. Interestingly, all the five miRNAs of the miR200 family have been reported to be markedly downregulated in cells that undergo TGFβ-induced EMT. Conversely, enforced expression of either miR-200b–200a–429 cluster or the miR-200c–141 cluster via a lentivirus system driven by cytomegalovirus (CMV) promoter prevented TGFβ-induced EMT. The authors also demonstrated that a cooperative regulation of E-cadherin transcriptional repressors ZEB1 and SIP1, by these five miRNAs, inhibited EMT in breast cancer (40). Although the authors of the above study did not show how TGFβ regulates the expression of miR-200, a later study by Gregory and colleagues demonstrated that prolonged exposure to TGFβ leads to DNA hypermethylation of the promoters of miR-200b and miR-200c, which resulted in the long-term repression of miR-200 expression (41). Recently, it was found that TGFβ-mediated downregulation of miR-200 induced the migration of triple-negative breast cancer (TNBC) cells through increasing the expression of ZEB2 (42).

miR-203

MicroRNA-203 (miR-203) is located on chromosome 14q32-33, and in breast cancer, it has recently been shown to inhibit cancer invasion via transcriptional downregulation of snail homolog 2 (SNAI2 or SLUG; ref. 43). Furthermore, the authors demonstrated that miR-203 is downregulated in metastatic breast cancer cells and promotes cell growth and invasion. The authors also indicated that miR-203 downregulation was mediated via methylation of its promoter, as observed in all the three metastatic breast cancer cell lines used in the study (43). Interestingly, a recent observation by Ding and colleagues demonstrated that TGFβ-induced SNAI2 repressed miR-203 by directly binding to its promoter, and SNAI2 expression promoted EMT in a group of both lowly invasive (MCF7, MDA-MB-468, BT474, and T47D) and highly invasive (MDA-MB-231, BT549, Hs578T, and SUM159) metastatic breast cancer cell lines (44). Conversely, miR-203 was also shown to directly target SNAI2 and inhibit metastasis in breast cancer cells. Thus, a negative feedback loop between miR-203 and SNAI2 was found to control EMT and tumor invasive growth and metastasis in a model of breast cancer.

miR-181a

miR-181a belongs to the miR-181 family, which consists of three other members, namely, miRs 181b, 181c, and 181d. In several of the metastatic breast tumor cell lines, miR-181a was significantly upregulated by TGFβ treatment, possibly via Smad4-independent processing of pre-miR-181a transcripts, and this upregulation enhanced the motility and invasion of breast cancer cells (45). Conversely, inhibition of miR-181a activity was shown to abrogate TGFβ-induced EMT, migration, invasion, and metastatic outgrowth of TNBC cells. Recently, Brockhausen and colleagues reported that TGFβ treatment significantly upregulated miR-181a in nontransformed PH5CH8 hepatocyte cell line and induced EMT. Importantly, miR-181a was shown to induce the expression of EMT-associated genes BMP1, MMP2/MMP9, and Snail in TGFβ-treated PH5CH8 cells. Moreover, the authors also observed increased levels of miR-181a in human HCC tissues compared with normal liver. Given the recent literature evidence for the involvement of TGFβ-mediated upregulation of miR-181a in the promotion of EMT in breast cancer, and in nontransformed PH5CH8 hepatocyte cell line in this study, it is reasonable to speculate that TGFβ-induced miR-181a upregulation might promote HCC metastasis via EMT (46).

miR-10b

Han and colleagues identified miR-10b as a target gene of TGFβ1 and found that expression of miR-10b was increased during TGFβ1-induced EMT in breast cancer cells. Conversely, inhibition of miR-10b increased the expression of E-cadherin while decreasing the expression of vimentin, with a concomitant decrease in the invasive potential of breast cancer cells (47). Furthermore, the expression of miR-10b was also found to be abundant in breast cancer in contrast to adjacent nontumor tissues and miR-10b expression was found to be closely correlated with breast cancer aggressiveness. These data suggested the possibility that miR-10b upregulation coupled with TGFβ1-induced EMT might be responsible for the promotion of invasion and metastasis in breast cancer cells. Unfortunately, the authors did not discuss the molecular mechanism by which TGFβ1 upregulated miR-10b expression. Interestingly, TGFβ1-induced upregulation of miR-10b has been shown to be involved in the regulation of glioblastoma (GBM) cell proliferation, migration, and EMT. Specifically, TGFβ1-induced miR-10b directly targeted E-cadherin, apoptotic protease activating factor 1 (Apaf-1), and phosphatase and tensin homolog (PTEN) genes (48).

miR-21

The miR-21 has been suggested to be a prognostic factor in cancer patients, based on the correlation between high miR-21 levels and poor overall survival in various carcinomas. Interestingly, a study by Yu and colleagues identified that TGFβ-induced miR-21 inhibited the expression of MutS homolog 2 (MSH2), by targeting its 3′-UTR region in HER2-transformed MCF10A mammary epithelial cells and in breast cancer cells (7). MSH2 is a central component of the DNA mismatch repair (MMR) system that recognizes chemotherapy drug-induced DNA adducts and triggers MMR at the damaged sites and causes cell-cycle arrest and apoptosis. The authors speculated that miRNA-mediated posttranscriptional inhibition of MSH2 might influence genomic instability and thereby contribute to chemoresistance in cancer (7). In human gliomas, TGFβ1-mediated upregulation of miR-21 was found to be inhibited by antitumor agent ursolic acid (UA), to promote apoptosis and attenuate proliferation of glioma cells. Specifically, UA was reported to suppress the attenuation of programmed cell death 4 (PDCD4) protein expression mediated by TGFβ1-induced miR-21, consequently promoting apoptosis of U251 glioma cells (49).

miR-494

The miR-494 is located in the Dlk1-Dio3–imprinted locus on human chromosome 14q32, a region containing 54 miRNAs, and is supposedly one of the largest miRNA clusters in the human genome. Myeloid-derived suppressor cells (MDSC) mediated suppression of antitumor immune responses favors tumor angiogenesis and metastasis. In a quest to identify the regulatory networks that govern the accumulation of tumor-expanded MDSCs, Liu and colleagues found that TGFβ-induced upregulation of miR-494 via the Smad3-dependent pathway inhibited the protein expression of phosphatase and tensin homolog (PTEN). The inhibition of PTEN was found to be essential for both the accumulation and activity of MDSCs (50). It was recently reported that TGFβ-mediated upregulation of miR-494, and miR-494-mediated negative regulation of FOXM1 protein expression could reduce cell proliferation, migration, and invasion in pancreatic ductal adenocarcinomas (PDAC). Precisely, the authors demonstrated that in PDAC, FOXM1 is a direct target of TGFβ-induced miR-494, and miR-494 affects FOXM1 expression through a direct interaction with FOXM1 3′-UTR (51).

miR-34a

The miR-34a belongs to the miR-34 family, which consists of miR-34a, miR-34b, and miR-34c. In hepatitis B virus (HBV)–positive HCC, a study by Yang and colleagues demonstrated that TGFβ-mediated suppression of miR-34a, possibly via the autocrine activity of the TGFβ produced by HepG2 cells, enhanced production of the chemokine CCL22 and promoted tumor growth of HCC cells (52). Conversely, the authors showed that ectopic expression of miR-34a reduced the mRNA and protein production of its predominant direct target CCL22, and suppressed HCC tumor growth, whereas overexpression of a nontargetable form of CCL22 largely eliminated miR-34a–induced tumor suppression in HBV-positive HCC (52).

miR-584

miR-584 is located at chromosomal region 5q32, and it was found to be tumor suppressive in clear cell renal carcinoma (ccRCC), via direct inhibition of the oncogene ROCK-1 mRNA by binding to its 3′-UTR (53). Recently, an investigation by Fils-Aime and colleagues identified miR-584 as a novel target of TGFβ in breast cancer and found that inhibition of miR-584 expression by TGFβ is required for cell migration. Importantly, overexpression of ectopic miR-584 was reported to reverse TGFβ-induced cell migration via inhibition of mRNA and protein expression of protein phosphatase and actin regulator 1 (PHACTR1; ref. 54).

miR-182

miR-182 is located on chromosome 7q32.1 and is often amplified in clinical gliomas. Recently, it was reported that in gliomas, TGFβ treatment markedly increased the expression of miR-182 and miR-182 directly targeted the 3′-UTR and suppressed the expression of multiple genes, including cylindromatosis (CYLD), which function as negative regulators of the NF-κB signaling pathway. Consequently, NF-κB hyperactivation mediated by TGFβ-induced miR-182 resulted in enhanced aggressiveness of gliomas (55). Interestingly, in normal cells, TGFβ has been shown to repress NF-κB activity, whereas in cancer cells, NF-κB has been reported to be activated by TGFβ, suggesting that NF-κB acts as an oncogenic mediator of TGFβ signaling in tumors. As demonstrated in this study, NF-κB is indeed activated by TGFβ via miR-182, leading to tumor aggressiveness in human gliomas (55).

Several miRNAs have been shown to target the components of the TGFβ signaling pathway, including TGFβ1 ligands and proteins in multiple cancers (56). For example, a recent study demonstrated that miR-744 binds directly to the 3′-UTR of TGFβ1 and posttranscriptionally inhibits the endogenous expression of TGFβ1 in human renal proximal tubule epithelial cells (reviewed in ref. 56). In multiple cancers, miRNAs have been shown to posttranscriptionally target SMAD proteins and regulate the TGFβ pathway, resulting in either tumor promotion or suppression. For example, in HCC, miR-148a was reported to attenuate the cancer stem cell properties of HepG2, Huh-7, and MHCC97H cell lines by targeting the 3′-UTR of SMAD2 protein and decreasing its expression and function (56). In gastric cancer, miR-424-5p was found to target and downregulate SMAD3 and promote the proliferation of gastric cancer cells (56). In addition to the SMAD proteins, miRNAs regulate the TGFβ pathway via direct targeting and controlling the expression of either TGFβ type I (TGFβ RI) or type II (TGFβ RII) receptors in cancers such as anaplastic thyroid carcinoma (ATC), glioblastoma, and non–small cell lung carcinoma (NSCLC). For detailed discussions on miRNA-mediated regulation of the TGFβ pathway via targeting either, one of the SMAD proteins or TGFβ receptors in cancer, we direct the readers to the review in ref. 56.

LncRNAs are ncRNA molecules greater than 200 nucleotides in length and can control gene expression via transcriptional and posttranscriptional regulatory mechanisms (57). Recent evidence suggests that lncRNAs play a crucial role in embryogenesis, cellular development, tumorigenesis, and EMT (58, 59). As a major inducer of EMT in several systems, the TGFβ pathway has also been shown to regulate several lncRNAs involved in EMT (Table 1 and Fig. 2).

Hotair

Hotair is a member of the subclass of lncRNA called large intergenic noncoding RNAs (lincRNA) and primarily is known for its ability to regulate epigenetic states through the recruitment of chromatin-modifying complexes to specific target sequences (60). Hotair expression is associated with breast cancer metastasis and poor outcomes in several neoplasia. Padua and colleagues demonstrated that TGFβ treatment increased the expression of Hotair in both colon and breast cancer cells, required for EMT. The authors observed that overexpression of Hotair in cancer cells upregulated EMT-associated genes such as ZEB1, SNAI1, TWIST, CTNNA1 (b-catenin), including the mesenchymal markers vimentin (VIM) and fibronectin (FN1; ref. 61). Although the authors demonstrated a positive correlation between TGFβ treatment and upregulation of Hotair, and induction of EMT, the mechanism involved in the TGFβ mediated upregulation of Hotair was not addressed in the study.

MALAT1

Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a lncRNA that was recently reported to be involved in bladder cancer cell migration, and its expression was found to be significantly increased in primary tumors that became subsequently metastatic compared with those that did not (62). Furthermore, downregulation of MALAT-1 resulted in impaired bladder cancer cell migration and inhibited the EMT process, which was associated with a decrease in ZEB1, ZEB2, and Slug expression levels (62). Importantly, a recent report by Fan and colleagues demonstrated the underlying mechanisms of TGFβ-induced MALAT1-mediated regulation of cancer metastasis in bladder cancer (63). The authors showed that TGFβ treatment induced MALAT1 expression by a yet unidentified mechanism, which was followed by reduction of E-cadherin mRNA and protein levels in RT4 bladder cancer cells. Of note, the authors also reported a significant negative correlation between the mRNA levels of E-cadherin and malat1 expression levels in vivo. On the other hand, mRNA and protein levels of mesenchymal markers N-cadherin and fibronectin were also increased by TGFβ treatment, but suppressed by malat1 silencing, indicating the induction of EMT by TGFβ and involvement of malat1 in TGFβ-induced EMT in bladder cancer. Interestingly, the authors also revealed that MALAT1 represses E-cadherin expression by associating with suz12, a member of the polycomb repressive complex 2 (PRC2). Also, the authors used RNA immuneprecipitation (RIP) assay with antibodies against EZH2 and SUZ12 and demonstrated that lncRNA MALAT1 association with SUZ12 but not EZH2.

LncRNA ATB

Long noncoding RNA activated by TGFβ (lncRNA ATB) was found to promote invasion and metastasis in gastric cancer through the TGFβ/miR-200s/ZEB axis leading to poor prognosis (64). More precisely, based on the expression level of lncRNA-ATB, patients (n = 183) were divided into high lncRNA ATB group (n = 105) and low lncRNA ATB group (n = 83). The expression level of miR-200c and ZEB1 was elevated in the high lncRNA ATB group compared with the low lncRNA ATB group, and the treatment of gastric cancer cell lines with TGFβ resulted in the upregulation of lncRNA ATB and ZEB1, and downregulation of miR-200c and CDH1. More recently, Yue and colleagues reported that lncRNA ATB was upregulated both in colon cancer and metastatic colon cancer tissues. In addition, relatively higher levels of lncRNA ATB and concurrent low levels of E-cadherin were also observed recently in three highly invasive colon cancer cell lines (65). Importantly, reduction of lncRNA ATB expression increased the expression of epithelial markers E-cadherin and ZO-1 and decreased expression of mesenchymal markers ZEB1 and N-cadherin (N-cad) in these colon cancer cell lines (65).

HULC

Highly upregulated in liver cancer (HULC), is a 500nt long lncRNA located on chromosome 6p24.3. Very recently, HULC was reported to promote TGFβ-induced EMT in HCC via reduction of E-Cadherin expression, and increased expressions of N-Cadherin, Snail, and ZEB1 in SMMC-7721 cancer cells (66). Specifically, HULC-mediated promotion of EMT occurred through the sequestration of miR-200a-3p, which positively regulates E-Cadherin and negatively regulates ZEB1 by binding to their 3′-UTR. Although the authors demonstrated that HULC functioned as ceRNA to upregulate ZEB1 by sequestering miR-200a-3p, the molecular mechanism by which TGFβ affected the expression level of HULC was not discussed in the study.

Linc01186

LINC01186 was originally identified in lung cancer tissues, as one of the 291 lncRNAs differentially expressed between lung cancer tissues and adjacent normal tissues (67). Interestingly, LINC01186 expression was found to be significantly downregulated in TGFβ1-treated A549 lung cancer cells. The authors demonstrated that overexpression of LINC01186 in A549 cells, inhibited migration, and the invasive capacity of lung cancer cells (67). The study also reported that SMAD3 repressed LINC01186, indicating that LINC01186 is a downstream target of SMAD3 in A549 lung cancer cells. Thus, the authors established a critical role for LINC01186 (a previously uncharacterized lncRNA) in TGFβ-induced EMT, in a model of lung cancer.

LincRNA PNUTS

We recently reported that a novel lncRNA PNUTS controlled by RBP hnRNP E1 is overexpressed in breast cancer tissues (68). In this report, Dr. Howe and colleagues demonstrate that in response to TGFβ, hnRNP E1 promotes alternative splicing and generates the noncoding lncRNA PNUTS. The lncRNA-PNUTS serves as a competitive sponge for miR-205 during EMT and appears to be tightly regulated by hnRNP E1 and tumor context. Thus, TGFβ cooperatively controls both RBP and lncRNA to modulate EMT.

LncRNA-PE

In a screen for lncRNAs that might promote EMT and HCC progression, Shen and colleagues identified a 1454-bp long lncRNA called lncRNA-PE (originally named as BC013423) in HCC cells (69). In addition, TGFβ treatment upregulated the expression of lncRNA-PE and lncRNA-PE in turn induced EMT in SK-Hep-1 HCC cells. More precisely, siRNA-mediated knockdown of lncRNA-PE in SK-Hep1 cells reduced the expression of N-cadherin and vimentin, whereas enhanced the protein levels of E-cadherin and ZO-1, consequently inhibiting HCC cell migration and invasion (69). In search of a mechanistic insight into the role of lncRNA-PE in the regulation of HCC associated EMT, the authors demonstrated that lncRNA-PE enhanced ZEB1 expression via downregulation of miR-200a/b. Importantly, an analysis of the distribution of lncRNA-PE in SK-Hep-1 cells revealed that it was localized both in the nucleus and the cytoplasm, indicating that lncRNA-PE might function as a miRNA sponge. Thus, lncRNA-PE might play a crucial role in the development of HCC via the miR-200a/b-ZEB1 pathway.

LncRNA-ROR

The lncRNA-ROR is a 2.6-kb long and is one of the most significantly upregulated lncRNA in HCC. Recently, it was reported that lncRNA-ROR, a stress-responsive and TGFβ-induced lncRNA, promoted chemo resistance of HCC cancer cells via CD133+ tumor-initiating cells (70). Importantly, TGFβ was found to reduce the chemosensitivity of HCC cells to the drugs sorafenib or doxorubicin and increased the expression of lnc-ROR, consequently reducing the chemotherapy induced cell death of HCC cells. In this study, although the authors have not demonstrated a direct association of lncRNA-ROR with its target genes, they showed that siRNA mediated knockdown of lncRNA-ROR in HepG2 cells significantly increased the expression of apoptosis associated genes caspase 8 and p53. Thus, the authors speculated that the effects of lncRNA-ROR in HCC could be mediated through p53 signaling (70).

LncRNA-Smad7

In epithelial cells, TGFβ has been shown to exhibit both proapoptotic and antiapoptotic effects. To study the downstream regulatory mechanisms governing the TGFβ-mediated antiapoptotic functions in breast cancer, Arase and colleagues conducted RNA sequencing in NmuMG cells and identified the antiapoptotic lncRNA-Smad7 as a target of TGFβ (71). LncRNA-Smad7 is located adjacent to the mouse Smad7 gene, found to be induced by TGFβ, and displays antiapoptotic functions in NMuMG and mouse breast cancer cell line JygMC (A). Interestingly, silencing lncRNA-Smad7 did not alter TGFβ-induced EMT or expression of Smad7 gene, suggesting that lncRNA-Smad7-mediated TGFβ functions may be restricted only to apoptosis (71). The identity of lncRNA-SMAD7 antiapoptotic targets is currently unknown.

HOXD-AS1

The HOXD-AS1 is a lncRNA located in the HOXD cluster, between HOXD1 and HOXD3 genes, and it is evolutionarily conserved among hominids (72). In a model of human metastatic neuroblastoma, HOXD-AS1 was activated by TGFβ induction of the PI3K/Akt pathway (72). Moreover, knockdown of HOXD-AS1 decreased the expression of several protein-coding genes associated with angiogenesis and inflammation, indicating that HOXD-AS1 controls these processes through regulation of the expression of its target genes (ref. 72; please see Fig. 3).

Figure 3.

TGFβ modulated miRNAs and lncRNAs in cancer. TGFβ-upregulated miR-21 inhibits cancer cell apoptosis via posttranscriptional repression of proteins such as MSH2 and PDCD4, which are known to induce apoptosis, whereas miR-494 upregulated by TGFβ promotes proliferation of cancer cells. TGFβ-downregulated miR-34a also promotes cancer cell proliferation. TGFβ-upregulated lncRNAs have been shown to play opposing roles in cancer cell apoptosis. For example, lnc-ROR promotes apoptosis whereas lncRNA-Smad7 inhibits apoptosis of cancer cells. LncRNA-HOX-D AS1 upregulated by TGFβ-activated PI3/Akt promotes angiogenesis. miRNAs are denoted by blue ovals, black arrow and lines denote miRNA-mediated regulations of target genes, and lncRNAs are denoted by red rectangles, and red arrows and lines denote lncRNA-mediated control of the EMT process. Transcription factors are denoted by yellow rounded rectangles and canonical TGFβ pathway members such as Smads and noncanonical TGFβ members such as PI3/Akt, JNK, and ERK1/2 are denoted by light blue or yellow rectangles and light green, respectively.

Figure 3.

TGFβ modulated miRNAs and lncRNAs in cancer. TGFβ-upregulated miR-21 inhibits cancer cell apoptosis via posttranscriptional repression of proteins such as MSH2 and PDCD4, which are known to induce apoptosis, whereas miR-494 upregulated by TGFβ promotes proliferation of cancer cells. TGFβ-downregulated miR-34a also promotes cancer cell proliferation. TGFβ-upregulated lncRNAs have been shown to play opposing roles in cancer cell apoptosis. For example, lnc-ROR promotes apoptosis whereas lncRNA-Smad7 inhibits apoptosis of cancer cells. LncRNA-HOX-D AS1 upregulated by TGFβ-activated PI3/Akt promotes angiogenesis. miRNAs are denoted by blue ovals, black arrow and lines denote miRNA-mediated regulations of target genes, and lncRNAs are denoted by red rectangles, and red arrows and lines denote lncRNA-mediated control of the EMT process. Transcription factors are denoted by yellow rounded rectangles and canonical TGFβ pathway members such as Smads and noncanonical TGFβ members such as PI3/Akt, JNK, and ERK1/2 are denoted by light blue or yellow rectangles and light green, respectively.

Close modal

The changes in gene expression and altered transcription under TGFβ signaling are well established (73); however, TGFβ signaling mediated posttranscriptional mechanisms that control pre-mRNA splicing, export, turnover, and translation are poorly understood. Understanding TGFβ-mediated posttranscriptional alterations in cancer may provide avenues for better therapeutic opportunities. Several studies have delineated the role of TGFβ-mediated miRNAs in cancer and discovered the possible mechanisms underlying the interaction between TGFβ and miRNAs. However, TGFB-mediated changes in lncRNAs and their contribution to cancer progression and metastasis remains understudied. Therefore, by better understanding of TGFβ-mediated changes in lncRNAs may provide an opportunity to modulate the expression of target genes and serve as a strategy for the treatment of cancer. On the other hand, silencing ncRNAs may have deleterious effects in cancer, which leads to overexpression of oncogenes or tumor-promoting effects. For such scenario, altering the expression of these ncRNAs or downregulating the expression of target genes may have beneficial effects. Thus, by understanding the molecular and epigenetic mechanisms, underlying the relationship between TGFβ and lncRNAs in cancer and their role in gene expression may facilitate the development of new therapeutic strategies targeting the tumor.

Using high-throughput transcriptomics and proteomics approach, one can identify novel TGFβ signaling mediated RNA transcripts and proteins altered at the posttranscriptional level. How the RNA transcripts are selectively regulated by TGFβ signaling is largely unknown, except HNRNP E1, which has been reported to utilize mRNA translation machinery (74). Although several attempts have been made to address TGFβ signaling mechanism, more in-depth understanding of TGFβ signaling mediated pre-mRNA processing is needed. For example, identifying a regulatory loop involving TGFβ, RBPs and ncRNAs will uncover innovative tools to target TGFβ-mediated cellular transitions from normal to benign and cancer. Likewise, the TGFβ signaling mediated posttranslational modifications of RBPs and their impact on gene expression patterns are largely unknown. In addition, there is a significant knowledge gap in TGFβ signaling mediated control of PTR in the tumor microenvironment and associated tumorigenesis.

Additional major consideration is whether TGFβ-initiated changes in gene expression patterns are coupled with co- and posttranscriptional changes during RNA processing. This interrogation is crucial because TGFβ promotes the expression of several transcription factors (75), which could serve as modifiers of transcriptional changes enhance the expression of ncRNAs and coding RNAs. One could assume establishment of the noncoding (intron or intergenic) transcript variant can act as a decoy or competitor for the same or different coding transcript (Fig. 4). Advances in genome sequencing, single-cell transcriptomics, and bioinformatic tools for investigating RNA expression are needed to dissect this pathway.

Figure 4.

LncRNAs can compete with or act as decoys for RBPs and RNAs. ia–ic, Long noncoding RNAs can be generated from (ia) intragenic, (ib) intergenic, (ic) or naturally occurring antisense sequences. In the nucleus, (ii) lncRNAs can bind to transcription factors, TFs, preventing specific gene transcription. In the cytoplasm, (iiia) lncRNAs can compete with miRNAs for mRNA binding sites or (iiib) or act as miRNA decoys affecting target mRNA stability and translation. Additionally, (iiic) lncRNAs can compete with or act as decoys for RBP regulation of mRNA fate. Lastly, (iv) naturally occurring antisense lncRNAs can regulate the stability and translation of the coding mRNA transcripts from which it was derived.

Figure 4.

LncRNAs can compete with or act as decoys for RBPs and RNAs. ia–ic, Long noncoding RNAs can be generated from (ia) intragenic, (ib) intergenic, (ic) or naturally occurring antisense sequences. In the nucleus, (ii) lncRNAs can bind to transcription factors, TFs, preventing specific gene transcription. In the cytoplasm, (iiia) lncRNAs can compete with miRNAs for mRNA binding sites or (iiib) or act as miRNA decoys affecting target mRNA stability and translation. Additionally, (iiic) lncRNAs can compete with or act as decoys for RBP regulation of mRNA fate. Lastly, (iv) naturally occurring antisense lncRNAs can regulate the stability and translation of the coding mRNA transcripts from which it was derived.

Close modal

Finally, as TGFβ signaling is strongly linked with metastasis, the RBPs, mRNAs, miRNAs, and lncRNAs associated with this process will allow us to identify several metastatic biomarkers. With better knowledge of TGFβ-driven posttranscriptional changes that target tumor progression and metastasis, the RBPs or RNA molecules that are involved in this process can be reengineered to fabricate novel drugs. A powerful search for posttranscriptional level effects of TGFβ on cancer cell progression and metastasis is warranted, as cancer cells constantly evolve for multidrug resistance and reoccurrence. Last but not least, a successful development of targeting TGFβ pathway members and its contribution to the control of single or multiple RBPs, miRNAs, and lncRNAs would be ideal to mechanistically understand the PTR and cancer progression.

No potential conflicts of interest were disclosed.

This study was supported by the grants from NIHDE022776 and DE025920 to V. Palanisamy, CA154664 and CA555536 to P.H. Howe, CA11360 to J.A. Diehl, and EY023427 to V. Gangaraju.Supported in part by pilot research funding, Hollings Cancer Center's Cancer Center Support Grant P30 CA138313 at the Medical University of South Carolina.

We sincerely apologize to colleagues whose work has been overlooked from this review owing to space limitations.

1.
Akhurst
RJ
,
Hata
A
. 
Targeting the TGF signalling pathway in disease
.
Nat Rev Drug Discov
2012
;
11
:
790
811
.
2.
Blobe
GC
,
Schiemann
WP
. 
Role of transforming growth factor β in human disease
.
N Engl J Med
2000
;
342
:
1350
8
.
3.
Massagué
J
. 
TGFβ signalling in context
.
Nat Rev Mol Cell Biol
2012
;
13
:
616
30
.
4.
Neuzillet
C
,
Tijeras-Raballand
A
,
Cohen
R
,
Cros
J
,
Faivre
S
,
Raymond
E
, et al
Targeting the TGFbeta pathway for cancer therapy
.
Pharmacol Ther
2015
;
147
:
22
31
.
5.
Massagué
J
. 
TGFbeta in cancer
.
Cell
2008
;
134
:
215
30
.
6.
Horiguchi
K
,
Sakamoto
K
,
Koinuma
D
,
Semba
K
,
Inoue
A
,
Inoue
S
, et al
TGF-β drives epithelial–mesenchymal transition through δEF1-mediated downregulation of ESRP
.
Oncogene
2012
;
31
:
3190
201
.
7.
Yu
Y
,
Wang
Y
,
Ren
X
,
Tsuyada
A
,
Li
A
,
Liu
LJ
, et al
Context-dependent bidirectional regulation of the MutS homolog 2 by transforming growth factor β contributes to chemoresistance in breast cancer cells
.
Mol Cancer Res
2010
;
8
:
1633
42
.
8.
Katsanou
V
,
Milatos
S
,
Yiakouvaki
A
,
Sgantzis
N
,
Kotsoni
A
,
Alexiou
M
, et al
The RNA-binding protein Elavl1/HuR is essential for placental branching morphogenesis and embryonic development
.
Mol Cell Biol
2009
;
29
:
2762
76
.
9.
Kress
C
,
Gautier-Courteille
C
,
Osborne
HB
,
Babinet
C
,
Paillard
L
. 
Inactivation of CUG-BP1/CELF1 causes growth, viability, and spermatogenesis defects in mice
.
Mol Cell Biol
2007
;
27
:
1146
57
.
10.
Palazzo
AF
,
Lee
ES
. 
Non-coding RNA: what is functional and what is junk?
Front Genet
2015
;
6
:
2
.
11.
Butz
H
,
Racz
K
,
Hunyady
L
,
Patocs
A
. 
Crosstalk between TGF-beta signaling and the microRNA machinery
.
Trends Pharmacol Sci
2012
;
33
:
382
93
.
12.
Moses
HL
,
Roberts
AB
,
Derynck
R
. 
The discovery and early days of TGF-β: a historical perspective
.
Cold Spring Harb Perspect Biol
. 
2016
;
8
. pii:
a021865
.
13.
Lamouille
S
,
Xu
J
,
Derynck
R
. 
Molecular mechanisms of epithelial–mesenchymal transition
.
Nat Rev Mol Cell Biol
2014
;
15
:
178
96
.
14.
Sakaki-Yumoto
M
,
Katsuno
Y
,
Derynck
R
. 
TGF-beta family signaling in stem cells
.
Biochim Biophys Acta
2013
;
1830
:
2280
96
.
15.
Johnston
CJ
,
Smyth
DJ
,
Dresser
DW
,
Maizels
RM
. 
TGF-beta in tolerance, development and regulation of immunity
.
Cell Immunol
2016
;
299
:
14
22
.
16.
Iyer
S
,
Acharya
KR
. 
Tying the knot: the cystine signature and molecular-recognition processes of the vascular endothelial growth factor family of angiogenic cytokines
.
FEBS J
2011
;
278
:
4304
22
.
17.
Morikawa
M
,
Derynck
R
,
Miyazono
K
. 
TGF-beta and the TGF-beta family: context-dependent roles in cell and tissue physiology
.
Cold Spring Harb Perspect Biol
2016
;
8
. pii:
a021873
.
18.
Chen
CR
,
Kang
Y
,
Siegel
PM
,
Massague
J
. 
E2F4/5 and p107 as Smad cofactors linking the TGFbeta receptor to c-myc repression
.
Cell
2002
;
110
:
19
32
.
19.
Massague
J
,
Seoane
J
,
Wotton
D
. 
Smad transcription factors
.
Genes Dev
2005
;
19
:
2783
810
.
20.
Suzuki
C
,
Murakami
G
,
Fukuchi
M
,
Shimanuki
T
,
Shikauchi
Y
,
Imamura
T
, et al
Smurf1 regulates the inhibitory activity of Smad7 by targeting Smad7 to the plasma membrane
.
J Biol Chem
2002
;
277
:
39919
25
.
21.
Zhang
L
,
Zhou
F
,
ten Dijke
P
. 
Signaling interplay between transforming growth factor-beta receptor and PI3K/AKT pathways in cancer
.
Trends Biochem Sci
2013
;
38
:
612
20
.
22.
Zhang
YE
. 
Non-Smad pathways in TGF-beta signaling
.
Cell Res
2009
;
19
:
128
39
.
23.
Margadant
C
,
Sonnenberg
A
. 
Integrin-TGF-beta crosstalk in fibrosis, cancer and wound healing
.
EMBO Rep
2010
;
11
:
97
105
.
24.
Tang
B
,
Bottinger
EP
,
Jakowlew
SB
,
Bagnall
KM
,
Mariano
J
,
Anver
MR
, et al
Transforming growth factor-beta1 is a new form of tumor suppressor with true haploid insufficiency
.
Nat Med
1998
;
4
:
802
7
.
25.
Tang
B
,
Vu
M
,
Booker
T
,
Santner
SJ
,
Miller
FR
,
Anver
MR
, et al
TGF-beta switches from tumor suppressor to prometastatic factor in a model of breast cancer progression
.
J Clin Invest
2003
;
112
:
1116
24
.
26.
Oshimori
N
,
Oristian
D
,
Fuchs
E
. 
TGF-beta promotes heterogeneity and drug resistance in squamous cell carcinoma
.
Cell
2015
;
160
:
963
76
.
27.
Thiery
JP
,
Acloque
H
,
Huang
RY
,
Nieto
MA
. 
Epithelial–mesenchymal transitions in development and disease
.
Cell
2009
;
139
:
871
90
.
28.
Garg
M
. 
Epithelial–mesenchymal transition - activating transcription factors - multifunctional regulators in cancer
.
World J Stem Cells
2013
;
5
:
188
95
.
29.
Philip
B
,
Ito
K
,
Moreno-Sánchez
R
,
Ralph
SJ
. 
HIF expression and the role of hypoxic microenvironments within primary tumours as protective sites driving cancer stem cell renewal and metastatic progression
.
Carcinogenesis
2013
;
34
:
1699
707
.
30.
Chaudhury
A
,
Hussey
GS
,
Ray
PS
,
Jin
G
,
Fox
PL
,
Howe
PH
. 
TGF-beta-mediated phosphorylation of hnRNP E1 induces EMT via transcript-selective translational induction of Dab2 and ILEI
.
Nat Cell Biol
2010
;
12
:
286
93
.
31.
Ishii
H
,
Saitoh
M
,
Sakamoto
K
,
Kondo
T
,
Katoh
R
,
Tanaka
S
, et al
Epithelial splicing regulatory proteins 1 (ESRP1) and 2 (ESRP2) suppress cancer cell motility via different mechanisms
.
J Biol Chem
2014
;
289
:
27386
99
.
32.
Hussey
GS
,
Link
LA
,
Brown
AS
,
Howley
BV
,
Chaudhury
A
,
Howe
PH
. 
Establishment of a TGFbeta-induced post-transcriptional EMT gene signature
.
PLoS One
2012
;
7
:
e52624
.
33.
Warzecha
CC
,
Sato
TK
,
Nabet
B
,
Hogenesch
JB
,
Carstens
RP
. 
ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing
.
Mol Cell
2009
;
33
:
591
601
.
34.
Kuroyanagi
H
. 
Fox-1 family of RNA-binding proteins
.
Cell Mol Life Sci
2009
;
66
:
3895
907
.
35.
Braeutigam
C
,
Rago
L
,
Rolke
A
,
Waldmeier
L
,
Christofori
G
,
Winter
J
. 
The RNA-binding protein Rbfox2: an essential regulator of EMT-driven alternative splicing and a mediator of cellular invasion
.
Oncogene
2014
;
33
:
1082
92
.
36.
Kim
YE
,
Kim
JO
,
Park
KS
,
Won
M
,
Kim
KE
,
Kim
KK
. 
Transforming growth factor-β-Induced RBFOX3 inhibition promotes epithelial–mesenchymal transition of lung cancer cells
.
Mol Cells
2016
;
39
:
625
30
.
37.
Lin
CW
,
Kao
SH
,
Yang
PC
. 
The miRNAs and epithelial–mesenchymal transition in cancers
.
Curr Pharm Des
2014
;
20
:
5309
18
.
38.
Akhurst
RJ
,
Derynck
R
. 
TGF-beta signaling in cancer–a double-edged sword
.
Trends Cell Biol
2001
;
11
:
S44
51
.
39.
Abba
ML
,
Patil
N
,
Leupold
JH
,
Allgayer
H
. 
MicroRNA regulation of epithelial to mesenchymal transition
.
J Clin Med
2016
;
5
:
8
.
40.
Gregory
PA
,
Bert
AG
,
Paterson
EL
,
Barry
SC
,
Tsykin
A
,
Farshid
G
, et al
The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1
.
Nat Cell Biol
2008
;
10
:
593
601
.
41.
Gregory
PA
,
Bracken
CP
,
Smith
E
,
Bert
AG
,
Wright
JA
,
Roslan
S
, et al
An autocrine TGF-beta/ZEB/miR-200 signaling network regulates establishment and maintenance of epithelial–mesenchymal transition
.
Mol Biol Cell
2011
;
22
:
1686
98
.
42.
Truong
HH
,
Xiong
J
,
Ghotra
VP
,
Nirmala
E
,
Haazen
L
,
Le Dévédec
SE
, et al
β1 integrin inhibition elicits a prometastatic switch through the TGFβ-miR-200-ZEB network in E-cadherin-positive triple-negative breast cancer
.
Sci Signal
2014
;
7
:
ra15
.
43.
Zhang
Z
,
Zhang
B
,
Li
W
,
Fu
L
,
Zhu
Z
,
Dong
JT
. 
Epigenetic silencing of miR-203 upregulates SNAI2 and contributes to the invasiveness of malignant breast cancer cells
.
Genes Cancer
2011
;
2
:
782
91
.
44.
Ding
X
,
Park
SI
,
McCauley
LK
,
Wang
CY
. 
Signaling between transforming growth factor β (TGF-β) and transcription factor SNAI2 represses expression of microRNA miR-203 to promote epithelial–mesenchymal transition and tumor metastasis
.
J Biol Chem
2013
;
288
:
10241
53
.
45.
Taylor
MA
,
Sossey-Alaoui
K
,
Thompson
CL
,
Danielpour
D
,
Schiemann
WP
. 
TGF-β upregulates miR-181a expression to promote breast cancer metastasis
.
J Clin Invest
2013
;
123
:
150
63
.
46.
Brockhausen
J
,
Tay
SS
,
Grzelak
CA
,
Bertolino
P
,
Bowen
DG
,
d'Avigdor
WM
, et al
miR-181a mediates TGF-β-induced hepatocyte EMT and is dysregulated in cirrhosis and hepatocellular cancer
.
Liver Int
2015
;
35
:
240
53
.
47.
Han
X
,
Yan
S
,
Weijie
Z
,
Feng
W
,
Liuxing
W
,
Mengquan
L
, et al
Critical role of miR-10b in transforming growth factor-β1-induced epithelial–mesenchymal transition in breast cancer
.
Cancer Gene Ther
2014
;
21
:
60
7
.
48.
Ma
C
,
Wei
F
,
Xia
H
,
Liu
H
,
Dong
X
,
Zhang
Y
, et al
MicroRNA-10b mediates TGF-β1-regulated glioblastoma proliferation, migration and epithelial–mesenchymal transition
.
Int J Oncol
2017
;
50
:
1739
48
.
49.
Wang
J
,
Li
Y
,
Wang
X
,
Jiang
C
. 
Ursolic acid inhibits proliferation and induces apoptosis in human glioblastoma cell lines U251 by suppressing TGF-β1/miR-21/PDCD4 pathway
.
Basic Clin Pharmacol Toxicol
2012
;
111
:
106
12
.
50.
Liu
Y
,
Lai
L
,
Chen
Q
,
Song
Y
,
Xu
S
,
Ma
F
, et al
MicroRNA-494 is required for the accumulation and functions of tumor-expanded myeloid-derived suppressor cells via targeting of PTEN
.
J Immunol
2012
;
188
:
5500
10
.
51.
Li
L
,
Li
Z
,
Kong
X
,
Xie
D
,
Jia
Z
,
Jiang
W
, et al
Down-regulation of microRNA-494 via loss of SMAD4 increases FOXM1 and beta-catenin signaling in pancreatic ductal adenocarcinoma cells
.
Gastroenterology
2014
;
147
:
485
97
e18
.
52.
Yang
P
,
Li
QJ
,
Feng
Y
,
Zhang
Y
,
Markowitz
GJ
,
Ning
S
, et al
TGF-β-miR-34a-CCL22 signaling-induced Treg cell recruitment promotes venous metastases of HBV-positive hepatocellular carcinoma
.
Cancer Cell
2012
;
22
:
291
303
.
53.
Ueno
K
,
Hirata
H
,
Shahryari
V
,
Chen
Y
,
Zaman
MS
,
Singh
K
, et al
Tumour suppressor microRNA-584 directly targets oncogene Rock-1 and decreases invasion ability in human clear cell renal cell carcinoma
.
Br J Cancer
2011
;
104
:
308
15
.
54.
Fils-Aimé
N
,
Dai
M
,
Guo
J
,
El-Mousawi
M
,
Kahramangil
B
,
Neel
JC
, et al
MicroRNA-584 and the protein phosphatase and actin regulator 1 (PHACTR1), a new signaling route through which transforming growth factor-β Mediates the migration and actin dynamics of breast cancer cells
.
J Biol Chem
2013
;
288
:
11807
23
.
55.
Song
L
,
Liu
L
,
Wu
Z
,
Li
Y
,
Ying
Z
,
Lin
C
, et al
TGF-β induces miR-182 to sustain NF-κB activation in glioma subsets
.
J Clin Invest
2012
;
122
:
3563
78
.
56.
Guo
L
,
Zhang
Y
,
Zhang
L
,
Huang
F
,
Li
J
,
Wang
S
. 
MicroRNAs, TGF-β signaling, and the inflammatory microenvironment in cancer
.
Tumour Biol
2016
;
37
:
115
25
.
57.
Guttman
M
,
Rinn
JL
. 
Modular regulatory principles of large non-coding RNAs
.
Nature
2012
;
482
:
339
46
.
58.
Pauli
A
,
Valen
E
,
Lin
MF
,
Garber
M
,
Vastenhouw
NL
,
Levin
JZ
, et al
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
.
Genome Res
2012
;
22
:
577
91
.
59.
Guttman
M
,
Donaghey
J
,
Carey
BW
,
Garber
M
,
Grenier
JK
,
Munson
G
, et al
lincRNAs act in the circuitry controlling pluripotency and differentiation
.
Nature
2011
;
477
:
295
300
.
60.
Gupta
RA
,
Shah
N
,
Wang
KC
,
Kim
J
,
Horlings
HM
,
Wong
DJ
, et al
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
.
Nature
2010
;
464
:
1071
6
.
61.
Pádua Alves
C
,
Fonseca
AS
,
Muys
BR
,
de Barros
E
,
Lima Bueno
R
,
Bürger
MC
,
de Souza
JE
, et al
Brief report: The lincRNA Hotair is required for epithelial-to-mesenchymal transition and stemness maintenance of cancer cell lines
.
Stem Cells
2013
;
31
:
2827
32
.
62.
Ying
L
,
Chen
Q
,
Wang
Y
,
Zhou
Z
,
Huang
Y
,
Qiu
F
. 
Upregulated MALAT-1 contributes to bladder cancer cell migration by inducing epithelial-to-mesenchymal transition
.
Mol Biosyst
2012
;
8
:
2289
94
.
63.
Fan
Y
,
Shen
B
,
Tan
M
,
Mu
X
,
Qin
Y
,
Zhang
F
, et al
TGF-β-induced upregulation of malat1 promotes bladder cancer metastasis by associating with suz12
.
Clin Cancer Res
2014
;
20
:
1531
41
.
64.
Saito
T
,
Kurashige
J
,
Nambara
S
,
Komatsu
H
,
Hirata
H
,
Ueda
M
, et al
A long non-coding RNA activated by transforming growth factor-β is an independent prognostic marker of gastric cancer
.
Ann Surg Oncol
2015
;
22
:
S915
22
.
65.
Yue
B
,
Qiu
S
,
Zhao
S
,
Liu
C
,
Zhang
D
,
Yu
F
, et al
LncRNA-ATB mediated E-cadherin repression promotes the progression of colon cancer and predicts poor prognosis
.
J Gastroenterol Hepatol
2016
;
31
:
595
603
.
66.
Li
SP
,
Xu
HX
,
Yu
Y
,
He
JD
,
Wang
Z
,
Xu
YJ
, et al
LncRNA HULC enhances epithelial–mesenchymal transition to promote tumorigenesis and metastasis of hepatocellular carcinoma via the miR-200a-3p/ZEB1 signaling pathway
.
Oncotarget
2016
;
7
:
42431
46
.
67.
Hao
Y
,
Yang
X
,
Zhang
D
,
Luo
J
,
Chen
R
. 
Long noncoding RNA LINC01186, regulated by TGF-β/SMAD3, inhibits migration and invasion through epithelial–mesenchymal-transition in lung cancer
.
Gene
2017
;
608
:
1
12
.
68.
Grelet
S
,
Link
LA
,
Howley
B
,
Obellianne
C
,
Palanisamy
V
,
Gangaraju
VK
, et al
A regulated PNUTS mRNA to lncRNA splice switch mediates EMT and tumour progression
.
Nat Cell Biol
2017
;
19
:
1105
15
.
69.
Shen
Y
,
Liu
S
,
Yuan
H
,
Ying
X
,
Fu
H
,
Zheng
X
. 
A long non-coding RNA lncRNA-PE promotes invasion and epithelial–mesenchymal transition in hepatocellular carcinoma through the miR-200a/b-ZEB1 pathway
.
Tumour Biol
2017
;
39
:
1010428317705756
.
70.
Takahashi
K
,
Yan
IK
,
Kogure
T
,
Haga
H
,
Patel
T
. 
Extracellular vesicle-mediated transfer of long non-coding RNA ROR modulates chemosensitivity in human hepatocellular cancer
.
FEBS Open Bio
2014
;
4
:
458
67
.
71.
Arase
M
,
Horiguchi
K
,
Ehata
S
,
Morikawa
M
,
Tsutsumi
S
,
Aburatani
H
, et al
Transforming growth factor-β-induced lncRNA-Smad7 inhibits apoptosis of mouse breast cancer JygMC(A) cells
.
Cancer Sci
2014
;
105
:
974
82
.
72.
Yarmishyn
AA
,
Batagov
AO
,
Tan
JZ
,
Sundaram
GM
,
Sampath
P
,
Kuznetsov
VA
, et al
HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome
.
BMC Genomics
2014
;
15
:
S7
.
73.
Cantelli
G
,
Crosas-Molist
E
,
Georgouli
M
,
Sanz-Moreno
V
. 
TGFB-induced transcription in cancer
.
Semin Cancer Biol
2017
;
42
:
60
9
.
74.
Chaudhury
A
,
Chander
P
,
Howe
PH
. 
Heterogeneous nuclear ribonucleoproteins (hnRNPs) in cellular processes: focus on hnRNP E1's multifunctional regulatory roles
.
RNA
2010
;
16
:
1449
62
.
75.
Gaarenstroom
T
,
Hill
CS
. 
TGF-β signaling to chromatin: how Smads regulate transcription during self-renewal and differentiation
.
Semin Cell Dev Biol
2014
;
32
:
107
18
.