Hypoxia-induced alternative splicing: the 11th Hallmark of Cancer

Abstract Hypoxia-induced alternative splicing is a potent driving force in tumour pathogenesis and progression. In this review, we update currents concepts of hypoxia-induced alternative splicing and how it influences tumour biology. Following brief descriptions of tumour-associated hypoxia and the pre-mRNA splicing process, we review the many ways hypoxia regulates alternative splicing and how hypoxia-induced alternative splicing impacts each individual hallmark of cancer. Hypoxia-induced alternative splicing integrates chemical and cellular tumour microenvironments, underpins continuous adaptation of the tumour cellular microenvironment responsible for metastatic progression and plays clear roles in oncogene activation and autonomous tumour growth, tumor suppressor inactivation, tumour cell immortalization, angiogenesis, tumour cell evasion of programmed cell death and the anti-tumour immune response, a tumour-promoting inflammatory response, adaptive metabolic re-programming, epithelial to mesenchymal transition, invasion and genetic instability, all of which combine to promote metastatic disease. The impressive number of hypoxia-induced alternative spliced protein isoforms that characterize tumour progression, classifies hypoxia-induced alternative splicing as the 11th hallmark of cancer, and offers a fertile source of potential diagnostic/prognostic markers and therapeutic targets.

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Exon definition facilitates reliable control of alternative splicing in the RON proto-oncogene

10.1101/714022 ◽

2019 ◽

Author(s):

M. Enculescu ◽

S. Braun ◽

S. T. Setty ◽

K. Zarnack ◽

J. König ◽

...

Keyword(s):

Alternative Splicing ◽

Epithelial To Mesenchymal Transition ◽

Intron Retention ◽

Regulatory Elements ◽

Protein Isoforms ◽

Splicing Regulation ◽

Exon Definition ◽

Mesenchymal Transition ◽

Mrna Maturation ◽

Exon 11

ABSTRACTAlternative splicing is a key step in eukaryotic gene expression that allows the production of multiple protein isoforms from the same gene. Even though splicing is perturbed in many diseases, we currently lack insights into regulatory mechanisms promoting its precision and efficiency. We analyse high-throughput mutagenesis data obtained for an alternatively spliced exon in the proto-oncogene RON and determine the functional units that control this splicing event. Using mathematical modeling of distinct splicing mechanisms, we show that alternative splicing is based in RON on a so-called ‘exon definition’ mechanism. Here, the recognition of the adjacent exons by the spliceosome is required for removal of an intron. We use our model to analyze the differences between the exon and intron definition scenarios and find that exon definition is crucial to prevent the accumulation of deleterious, partially spliced retention products during alternative splicing regulation. Furthermore, it modularizes splicing control, as multiple regulatory inputs are integrated into a common net input, irrespective of the location and nature of the corresponding cis-regulatory elements in the pre-mRNA. Our analysis suggests that exon definition promotes robust and reliable splicing outcomes in RON splicing.SIGNIFICANCEDuring mRNA maturation, pieces of the pre-mRNA (introns) are removed during splicing, and remaining parts (exons) are joined together. In alternative splicing, certain exons are either included or excluded, resulting in different splice products. Inclusion of RON alternative exon 11 leads to a functional receptor tyrosine kinase, while skipping results in a constitutively active receptor that promotes epithelial-to-mesenchymal transition and contributes to tumour invasiveness. Intron retention results in to deleterious isoforms that cannot be translated properly. Using kinetic modeling, we investigate the combinatorial regulation of this important splicing decision, and find that the experimental data supports a so-called exon definition mechanism. We show that this mechanism enhances the precision of alternative splicing regulation and prevents the retention of introns in the mature mRNA.

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TGF-β as Multifaceted Orchestrator in HCC Progression: Signaling, EMT, Immune Microenvironment, and Novel Therapeutic Perspectives

Seminars in Liver Disease ◽

10.1055/s-0038-1676121 ◽

2018 ◽

Vol 39 (01) ◽

pp. 053-069 ◽

Cited By ~ 17

Author(s):

Serena Mancarella ◽

Antonio Cigliano ◽

Annarita Chieti ◽

Gianluigi Giannelli ◽

Francesco Dituri

Keyword(s):

Epithelial To Mesenchymal Transition ◽

Transforming Growth Factor ◽

Ex Vivo ◽

Large Fraction ◽

Poor Response ◽

Tumor Promoter ◽

Molecular Heterogeneity ◽

Metastatic Progression ◽

Functional Link ◽

Mesenchymal Transition

AbstractTherapeutic attempts to treat hepatocellular carcinoma (HCC) frequently result in a poor response or treatment failure. The efficacy of approved drugs and survival expectancies is affected by an ample degree of variability that can be explained at least in part by the enormous between-patient cellular and molecular heterogeneity of this neoplasm. Transforming growth factor-β (TGF-β) is hyperactivated in a large fraction of HCCs, where it influences complex interactive networks covering multiple cell types and a plethora of other local soluble ligands, ultimately establishing several malignancy traits. This cytokine boosts the invasiveness of cancerous epithelial cells through promoting the epithelial-to-mesenchymal transition program, but also skews the phenotype of immune cells toward a tumor-supporting status. Here, we discuss recent strategies pursued to offset TGF-β-dependent processes that promote metastatic progression and immune surveillance escape in solid cancers, including HCC. Moreover, we report findings indicating that TGF-β reduces the expression of the proinflammatory factors CCL4 and interleukin-1β (IL-1β in human ex vivo treated HCC tissues. While this is consistent with the anti-inflammatory properties of TGF-β, whether it is an outright tumor promoter or suppressor is still a matter of some debate. Indeed, IL-1β has also been shown to support angiogenesis and cell invasiveness in some cancers. In addition, we describe an inhibitory effect of TGF-β on the secretion of CCL2 and CXCL1 by HCC-derived fibroblasts, which suggests the existence of an indirect stroma-mediated functional link between TGF-β and downstream immunity.

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RBM47-regulated alternative splicing of TJP1 promotes actin stress fiber assembly during epithelial-to-mesenchymal transition

Oncogene ◽

10.1038/s41388-019-0892-5 ◽

2019 ◽

Vol 38 (38) ◽

pp. 6521-6536 ◽

Cited By ~ 6

Author(s):

Yong-Eun Kim ◽

Minho Won ◽

Sung-Gwon Lee ◽

Chungoo Park ◽

Chang-Hwa Song ◽

...

Keyword(s):

Alternative Splicing ◽

Epithelial To Mesenchymal Transition ◽

Stress Fiber ◽

Actin Stress Fiber ◽

Mesenchymal Transition ◽

Fiber Assembly

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The Epithelial to Mesenchymal Transition and Metastatic Progression in Carcinoma

The Breast Journal ◽

10.1111/j.1524-4741.1996.tb00076.x ◽

1996 ◽

Vol 2 (1) ◽

pp. 83-96 ◽

Cited By ~ 51

Author(s):

Christine Gilles ◽

Erik W. Thompson

Keyword(s):

Epithelial To Mesenchymal Transition ◽

Metastatic Progression ◽

Mesenchymal Transition

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Hakin-1, a New Specific Small-Molecule Inhibitor for the E3 Ubiquitin-Ligase Hakai, Inhibits Carcinoma Growth and Progression

Cancers ◽

10.3390/cancers12051340 ◽

2020 ◽

Vol 12 (5) ◽

pp. 1340 ◽

Cited By ~ 2

Author(s):

Olaia Martinez-Iglesias ◽

Alba Casas-Pais ◽

Raquel Castosa ◽

Andrea Díaz-Díaz ◽

Daniel Roca-Lema ◽

...

Keyword(s):

Small Molecule ◽

Ubiquitin Ligase ◽

Epithelial To Mesenchymal Transition ◽

Tumour Progression ◽

E3 Ubiquitin Ligase ◽

Therapeutic Drug ◽

Mesenchymal Transition ◽

E Cadherin

The requirement of the E3 ubiquitin-ligase Hakai for the ubiquitination and subsequent degradation of E-cadherin has been associated with enhanced epithelial-to-mesenchymal transition (EMT), tumour progression and carcinoma metastasis. To date, most of the reported EMT-related inhibitors were not developed for anti-EMT purposes, but indirectly affect EMT. On the other hand, E3 ubiquitin-ligase enzymes have recently emerged as promising therapeutic targets, as their specific inhibition would prevent wider side effects. Given this background, a virtual screening was performed to identify novel specific inhibitors of Hakai, targeted against its phosphotyrosine-binding pocket, where phosphorylated-E-cadherin specifically binds. We selected a candidate inhibitor, Hakin-1, which showed an important effect on Hakai-induced ubiquitination. Hakin-1 also inhibited carcinoma growth and tumour progression both in vitro, in colorectal cancer cell lines, and in vivo, in a tumour xenograft mouse model, without apparent systemic toxicity in mice. Our results show for the first time that a small molecule putatively targeting the E3 ubiquitin-ligase Hakai inhibits Hakai-dependent ubiquitination of E-cadherin, having an impact on the EMT process. This represents an important step forward in a future development of an effective therapeutic drug to prevent or inhibit carcinoma tumour progression.

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Notch-Jagged signalling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype

Journal of The Royal Society Interface ◽

10.1098/rsif.2015.1106 ◽

2016 ◽

Vol 13 (118) ◽

pp. 20151106 ◽

Cited By ~ 67

Author(s):

Marcelo Boareto ◽

Mohit Kumar Jolly ◽

Aaron Goldman ◽

Mika Pietilä ◽

Sendurai A. Mani ◽

...

Keyword(s):

Epithelial To Mesenchymal Transition ◽

Tumour Progression ◽

Cell Communication ◽

Notch Signalling ◽

Circulating Tumour Cells ◽

Mesenchymal Phenotype ◽

Mesenchymal Transition ◽

Mesenchymal To Epithelial Transition ◽

Key Players

Metastasis can involve repeated cycles of epithelial-to-mesenchymal transition (EMT) and its reverse mesenchymal-to-epithelial transition. Cells can also undergo partial transitions to attain a hybrid epithelial/mesenchymal (E/M) phenotype that allows the migration of adhering cells to form a cluster of circulating tumour cells. These clusters can be apoptosis-resistant and possess an increased metastatic propensity as compared to the cells that undergo a complete EMT (mesenchymal cells). Hence, identifying the key players that can regulate the formation and maintenance of such clusters may inform anti-metastasis strategies. Here, we devise a mechanism-based theoretical model that links cell–cell communication via Notch-Delta-Jagged signalling with the regulation of EMT. We demonstrate that while both Notch-Delta and Notch-Jagged signalling can induce EMT in a population of cells, only Jagged-dominated Notch signalling, but not Delta-dominated signalling, can lead to the formation of clusters containing hybrid E/M cells. Our results offer possible mechanistic insights into the role of Jagged in tumour progression, and offer a framework to investigate the effects of other microenvironmental signals during metastasis.

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Bleomycin-enhanced alternative splicing of fibroblast growth factor receptor 2 induces epithelial to mesenchymal transition in lung fibrosis

Bioscience Reports ◽

10.1042/bsr20180445 ◽

2018 ◽

Vol 38 (6) ◽

Cited By ~ 5

Author(s):

Kui-Jun Chen ◽

Qing Li ◽

Chang-Mei Weng ◽

Zhao-Xia Duan ◽

Dong-Dong Zhang ◽

...

Keyword(s):

Alternative Splicing ◽

Growth Factor ◽

Fibroblast Growth Factor ◽

Lung Fibrosis ◽

Epithelial To Mesenchymal Transition ◽

Fibroblast Growth Factor Receptor ◽

Growth Factor Receptor ◽

Fibroblast Growth ◽

Transgenic Mouse Models ◽

Mesenchymal Transition

Idiopathic pulmonary fibrosis (IPF) is an important public health problem, and it has few treatment options given its poorly understood etiology; however, epithelial to mesenchymal transition (EMT) of pneumocytes has been implicated as a factor. Herein, we aimed to explore the underlying mechanisms of lung fibrosis mediated by EMT, with a focus on the alternative splicing of fibroblast growth factor receptor 2 (FGFR2), using bleomycin (BLM)-induced lung fibrotic and transgenic mouse models. We employed BLM-induced and surfactant protein C (SPC)-Cre and LacZ double transgenic mouse models. The results showed that EMT occurred during lung fibrosis. BLM inhibited the expression of epithelial splicing regulatory protein 1 (ESRP1), resulting in enhanced alternative splicing of FGFR2 to the mesenchymal isoform IIIc. BLM-induced lung fibrosis was also associated with the activation of TGF-β/Smad signaling. These findings have implications for rationally targetted strategies to therapeutically address IPF.

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PRPF6 Induces the Alternative Splicing of lncRNA SNHG16 To Promote Progression and Paclitaxel Resistance of Ovarian Cancer via Regulating GATA3 Transcription

10.21203/rs.3.rs-1045802/v1 ◽

2021 ◽

Author(s):

Han Wang ◽

Yingying Zhou ◽

Siyang Zhang ◽

Ya Qi ◽

Min Wang

Keyword(s):

Ovarian Cancer ◽

Alternative Splicing ◽

Epithelial To Mesenchymal Transition ◽

Binding Protein ◽

Luciferase Reporter ◽

Luciferase Reporter Gene ◽

Mesenchymal Transition ◽

Gene Assay

Abstract Background Small nucleolar RNA host gene 16 (SNHG16) and pre-mRNA processing factor 6(PRPF6) play vital roles in regulatory mechanisms of multiple cancers, but the mechanisms in ovarian cancer (OC) remains poorly understood. Methods The expression of SNHG16 transcripts-SNHG16-L/S in OC tissues were analyzed by real-time PCR (RT-PCR). The expression of PRPF6 in OC tissues were detected by Immunohistochemistry (IHC). Tumorigenesis, epithelial-to-mesenchymal transition (EMT) and PTX-resistance were detected by western blot, transwell, CCK-8 assays, colony formation assays and flow cytometry analyses. Molecular interactions were examined by dual-luciferase reporter gene assay, RNA immunoprecipitation (RIP) and chromatin immunoprecipitation (ChIP). Results The results indicated the expression of SNHG16-L/S was opposite in chemo-resistance and chemo-sensitivity tissues of OC. And SNHG16-L/S had different effects on the progression and PTX-resistance of OC cells. SNHG16-L inhibited GATA binding protein 3 (GATA3) transcription through CCAAT/enhancer-binding protein b (CEBPB) to further promote tumorigenesis, EMT and PTX-resistance of OC. Moreover, PRPF6 was upregulated in chemo-resistance tissues of OC. PRPF6 promoted tumorigenesis and PTX-resistance in vitro and in vivo. Mechanistically, PRPF6 induced the alternative splicing of SNHG16 to downregulate SNHG16-L, which further mediated progression and PTX-resistance through upregulating GATA3 in OC. Conclusions Totally, the results demonstrated that PRPF6 promoted progression and PTX-resistance in OC through SNHG16-L/CEBPB/GATA3 axis. Thus, PRPF6 may become a valuable target for OC therapy.

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Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling

Cancers ◽

10.3390/cancers12102823 ◽

2020 ◽

Vol 12 (10) ◽

pp. 2823

Author(s):

Ian M. Overton ◽

Andrew H. Sims ◽

Jeremy A. Owen ◽

Bret S. E. Heale ◽

Matthew J. Ford ◽

...

Keyword(s):

Transcription Factor ◽

Gene Networks ◽

Epithelial To Mesenchymal Transition ◽

Target Genes ◽

Cell Model ◽

Tumour Progression ◽

Mesenchymal Transition ◽

Transcription Factor Target ◽

Network Modules ◽

Conserved Gene

Cell identity is governed by gene expression, regulated by transcription factor (TF) binding at cis-regulatory modules. Decoding the relationship between TF binding patterns and gene regulation is nontrivial, remaining a fundamental limitation in understanding cell decision-making. We developed the NetNC software to predict functionally active regulation of TF targets; demonstrated on nine datasets for the TFs Snail, Twist, and modENCODE Highly Occupied Target (HOT) regions. Snail and Twist are canonical drivers of epithelial to mesenchymal transition (EMT), a cell programme important in development, tumour progression and fibrosis. Predicted “neutral” (non-functional) TF binding always accounted for the majority (50% to 95%) of candidate target genes from statistically significant peaks and HOT regions had higher functional binding than most of the Snail and Twist datasets examined. Our results illuminated conserved gene networks that control epithelial plasticity in development and disease. We identified new gene functions and network modules including crosstalk with notch signalling and regulation of chromatin organisation, evidencing networks that reshape Waddington’s epigenetic landscape during epithelial remodelling. Expression of orthologous functional TF targets discriminated breast cancer molecular subtypes and predicted novel tumour biology, with implications for precision medicine. Predicted invasion roles were validated using a tractable cell model, supporting our approach.

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A novel β2-AR/YB-1/β-catenin axis mediates chronic stress-associated metastasis in hepatocellular carcinoma

Oncogenesis ◽

10.1038/s41389-020-00268-w ◽

2020 ◽

Vol 9 (9) ◽

Author(s):

Jinxia Liu ◽

Lishuai Qu ◽

Chunhua Wan ◽

Mingbing Xiao ◽

Wenkai Ni ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Chronic Stress ◽

Adrenergic Receptor ◽

Epithelial To Mesenchymal Transition ◽

Tumour Progression ◽

Related Function ◽

Mesenchymal Transition ◽

Tumour Metastasis ◽

Clinicopathological Analysis ◽

Β2 Adrenergic Receptor

Abstract β-Adrenergic receptor (β-AR) signalling is strongly associated with tumour progression by the coupling of β-ARs with either a G protein or β-arrestin; however, the related mechanism underlying hepatocellular carcinoma (HCC) metastasis is not clear. Here, we reveal that the transcription factor Y-box binding protein 1 (YB-1) interacts with β2-adrenergic receptor (β2-AR) following stimulation with the agonist isoproterenol (ISO). Clinicopathological analysis demonstrated that β2-AR is significantly correlated with YB-1, which favours the progression of HCC. The binding of YB-1 with β2-AR resulted in YB-1 phosphorylation at serine 102 (S102) via the β-arrestin-1-dependent activation of the PI3K/AKT pathway, followed by the translocation of YB-1 to the nucleus to carry out its tumour-related function. β2-AR-mediated activation of YB-1 facilitated epithelial-to-mesenchymal transition (EMT) and HCC metastasis. The interference of YB-1 expression significantly attenuated liver tumour metastasis induced by chronic stress. Analysis of the transcriptional profile and chromatin immunoprecipitation (ChIP) identified β-catenin as a crucial target of YB-1. Our results unveiled a novel β2-AR-mediated regulatory axis in HCC metastasis that might be helpful for the development of HCC therapeutics.

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