Abstract
The dysregulation of the splicing process has emerged as a novel hallmark of metabolic and tumor pathologies. In breast cancer (BCa), which represents the most diagnosed cancer type among women worldwide, the generation and/or dysregulation of several oncogenic splicing variants have been described. This is the case of the splicing variants of HER2, ER, BRCA1, or the recently identified by our group, In1-ghrelin and SST5TMD4, which exhibit oncogenic roles, increasing the malignancy, poor prognosis, and resistance to treatment of BCa. This altered expression of oncogenic splicing variants has been closely linked with the dysregulation of the elements belonging to the macromolecular machinery that controls the splicing process (spliceosome components and the associated splicing factors). In this review, we compile the current knowledge demonstrating the altered expression of splicing variants and spliceosomal components in BCa, showing the existence of a growing body of evidence supporting the close implication of the alteration in the splicing process in mammary tumorigenesis.
Introduction
Breast cancer epidemiology and risk factors
Breast cancer (BCa) accounts for about 30% of female cancers (Loibl et al. 2021) and represents the most prevalent cancer type among women in most countries (158 out of 185 countries with available information, according to the World Health Organization (WHO)). Worldwide incidence varies between 27 in 100,000 cases in Africa or Asia and 97 in 100,000 cases in Europe or North America. This different rate in BCa incidence may be associated with the degree of economic development and with the associated lifestyle and social factors. BCa has an estimated mortality rate of 15% (Siegel et al. 2020), but this parameter is also highly dependent on the country and risk factors (WHO). Fortunately, BCa death rates are steadily declining, especially in some developed regions. This decline in mortality seems to be associated with prevention programs, early detection, and the development of new therapeutic approaches (DeSantis et al. 2019).
Development of BCa is associated with a wide spectrum of risk factors (Loibl et al. 2021). Specifically, although 10% of BCa cases are related to genetic predisposition or family history, wherein the most common germline mutations are in BRCA1 and BRCA2 genes, a high percentage of cases are associated with other uncontrollable (age, race, and gender) and controllable factors such as lifestyle (i.e. obesity, physical inactivity, alcohol intake, low-fiber diet, and smoking), hormonal therapy, or pregnancy-associated, and other risk factors (Loibl et al. 2021). Indeed, in high-income countries, more than one-third of cases of BCa seem to be preventable through lifestyle changes.
Breast cancer subtyping
Several types of BCa have been described to date. Histologically, most BCa are adenocarcinomas, which are subclassified depending on the cells of origin (ductal or lobular) and the dissemination status (in situ or invasive). Ductal carcinomas, which comprise the vast majority of BCa cases, derive from cells of the milk ducts, while lobular carcinoma begins in the lobes or lobules of the gland. The most common type of BCa is the invasive ductal carcinoma (IDC), which seems to be the final stage of a pathological progression from ductal hyperplasia, atypical ductal hyperplasia, and ductal carcinoma in situ (DCIS), the most frequently diagnosed early-stage BCa (Casasent et al. 2017). DCIS is divided into several subtypes, mainly according to the appearance of the tumor. These subtypes include micropapillary, papillary, solid, cribriform, and comedo. Patients with DCIS are typically at higher risk of recurrence after treatment and of developing IDC, which can be subclassified into medullary, mucinous, papillary, or tubular IDC (Casasent et al. 2017).
BCas are clinically divided into four main subtypes based on the molecular profile, which consider the presence of hormone receptors (ER and PR) and human EGF-2 (HER2 or ERBB2). The main recognized subtypes include luminal A and B, HER2-positive, and triple-negative BCa (TNBC). The determination of these subtypes is established by a standardized diagnostic evaluation of ER, PR, and HER2 based on international guidelines (Hammond et al. 2011). Luminal cancers are positive for ER/PR, HER2, and BCa show increased HER2 expression, while TNBC lacks expression of hormonal receptors and HER2. Moreover, immunohistochemical staining for the proliferation marker Ki-67 (MKI67) can be used to differentiate between luminal A-like and B-like BCa (Hammond et al. 2011).
Altered splicing in breast cancer
Based on the above-mentioned information, it is nowadays well-accepted that BCa is a complex and heterogeneous disease that exhibits a wide spectrum of clinical, pathological, and molecular features, which show distinctive prognostic and therapeutic implications (Loibl et al. 2021). In addition, more recently, novel layers of heterogeneity and complexity have been added to this pathology. This is the case of the alteration in the physiologic RNA splicing process in BCa, which may lead to the generation of aberrant splicing variants with oncogenic potential. Indeed, this altered alternative RNA splicing process increases the repertoire of oncogenic proteins in cancer cells and has been revealed to be one of the important risk factors in BCa (Yang et al. 2019).
Constitutive RNA splicing is a crucial step in the cascade of RNA processing events, by which a nascent precursor mRNA (pre-mRNA) is transformed into a mature mRNA via the excision of introns and ligation of exons. However, the vast majority of mammalian genes (>90% of human genes) have been shown to undergo processes of alternative splicing, which implies the combinatorial rearrangement of exons, parts of exons, and/or even parts of introns into mature RNA to result in a multitude of transcripts and, thus, increasing proteome diversity (Kornblihtt et al. 2013). Specifically, seven different types of alternative splicing processes are generally recognized, including exon skipping or cassette exon (an exon can be spliced out or retained), alternative acceptor site (an alternative 3' splice junction is used), alternative donor site (an alternative 5' splice junction is used), intron retention (an intronic sequence is retained into the mature mRNA), alternative initial or terminal exons, and mutually exclusive exons (only one of two exons is retained) (Fig. 1).
Alternative splicing events. Schematic representation of the main events of alternative splicing described to date, named exon skipping, alternative 3′ splice-site selection, alternative 5′ splice-site selection, intron retention, alternative initial exons, alternative terminal exons, and mutually exclusive exons. Exons are shown in yellow boxes and introns in gray boxes. Green lines show constitutive splicing and red dotted lines show alternative splicing events. Green boxes indicate the alternative exon.
Citation: Endocrine-Related Cancer 29, 9; 10.1530/ERC-22-0019
Alternative splicing events. Schematic representation of the main events of alternative splicing described to date, named exon skipping, alternative 3′ splice-site selection, alternative 5′ splice-site selection, intron retention, alternative initial exons, alternative terminal exons, and mutually exclusive exons. Exons are shown in yellow boxes and introns in gray boxes. Green lines show constitutive splicing and red dotted lines show alternative splicing events. Green boxes indicate the alternative exon.
Citation: Endocrine-Related Cancer 29, 9; 10.1530/ERC-22-0019
Alternative splicing events. Schematic representation of the main events of alternative splicing described to date, named exon skipping, alternative 3′ splice-site selection, alternative 5′ splice-site selection, intron retention, alternative initial exons, alternative terminal exons, and mutually exclusive exons. Exons are shown in yellow boxes and introns in gray boxes. Green lines show constitutive splicing and red dotted lines show alternative splicing events. Green boxes indicate the alternative exon.
Citation: Endocrine-Related Cancer 29, 9; 10.1530/ERC-22-0019
However, the dysregulation of the normal, physiological alternative splicing pattern may lead to aberrant alternative splicing processes, which have been linked to a wide variety of human diseases (Gahete et al. 2018, del Río-Moreno et al. 2019, 2020, Ibáñez-Costa et al. 2022) and cancer (Vázquez-Borrego et al. 2019, Fuentes-Fayos et al. 2020, Jiménez-Vacas et al. 2020), including BCa (Yang et al. 2019). Indeed, dysregulated splicing processes have been found to be involved in different steps of the development and progression of tumors, including cell proliferation, apoptosis, invasion, tumor metastasis, angiogenesis, and chemo/radiotherapeutic resistance. Importantly, global analyses have discovered more than 15,000 cancer-specific splice variants in 27 types of cancers, including BCa (Kahles et al. 2018), wherein alterations in the landscape of splicing variants have been linked to dysregulations in the cellular machinery responsible for the modulation of the splicing process.
Dysregulation of spliceosomal components in breast cancer
The mRNA splicing process is catalyzed by a dynamic intracellular machinery composed of different macromolecular ribonucleoprotein (RNP) complexes called spliceosomes (Matera & Wang 2014). The spliceosome comprised five different RNP subunits and several associated proteins. The spliceosome is subdivided into major or U2-dependent spliceosomes, consisting of five uridine-rich small nuclear RNPs (RNU1, RNU2, RNU5, and RNU4/RNU6), and minor or U12-dependent spliceosome, consisting of other five snRNP (RNU11, RNU12, RNU5, and RNU4atac/RNU6atac). These macromolecular complexes include a central snRNA and a set of proteins that can be classified into two groups: the Sm proteins (B/B′, D1, D2, D3, E, F, and G) and the LSm proteins (LSm2, LSm3, LSm4, LSm5, LSm6, LSm7, and LSm8) that are common to each particle, and the specific proteins that associate only with a precise snRNP (Matera & Wang 2014). The activity of the components of the spliceosome is regulated by an ample repertoire of trans-acting elements named splicing factors, which bind to cis-acting RNA elements to regulate constitutive and alternative splicing (Matera & Wang 2014). In BCa, the alteration of certain spliceosomal components and splicing factors has been associated with altered splicing variants expression patterns and tumor development and progression. Some examples are described below, and a detailed list of spliceosomal components and splicing factors reported to be associated with breast carcinogenesis is presented in Table 1.
List of spliceosomal components and splicing factors found to be altered in breast cancer.
| Spliceosomal factor | Role in splicing process | Genes/pathways modulated | Cellular/tumoral processes implicated | Reference |
|---|---|---|---|---|
| SF3B1 | U2-snRNP component | 860 upregulated 776 down-regulated genes | Proliferation, invasion, migration, and apoptosis | (Zhang et al. 2020) |
| SRSF1 | SR family protein | Hundreds of AS events, including CASC4 and PTPMT1 DCUN1D5 | Proliferation, migration, apoptosis, metastasis | (Anczuków et al. 2015, Du et al. 2021b) |
| SRSF3 | SR family protein | GR (glucocorticoids receptor) HER2 | Migration HER2 signaling | (Gautrey et al. 2015, Buoso et al. 2019) |
| SRSF5 | SR family protein | CD44 | Epithelial-to-mesenchymal transition and metastasis | (Huang et al. 2007) |
| SRSF6 | SR family protein | CRH-R1 | Cellular response to CRH and invasion | (Lal et al. 2013) |
| Tra2-beta1 | SR family protein | CD44 | Epithelial-to-mesenchymal transition | (Watermann et al. 2006) |
| hnRNP A1 | hnRNP family protein | CD44, CEACAM1 | Invasion, migration, metastais, and epithelial-to-mesenchymal transition | (Dery et al. 2011, Loh et al. 2015) |
| hnRNP F | hnRNP family protein | MCL-1 | Apoptosis | (Tyson-Capper & Gautrey 2018) |
| hnRNP H1 | hnRNP family protein | MCL-1 HER2 | Apoptosis HER2 signaling | (Gautrey et al. 2015, Tyson-Capper & Gautrey 2018) |
| hnRNP K | hnRNP family protein | MCL-1 | Apoptosis | (Tyson-Capper & Gautrey (2018) |
| hnRNP A2B1 | hnRNP family protein | STAT3, ERK1/2 | Proliferation and apoptosis | (Hu et al. 2017) |
| hnRNP L | hnRNP family protein | CEACAM1 | Cell growth | (Dery et al. 2011) |
| hnRNP M | hnRNP family protein | CD44, CEACAM1 | Invasion, migration, metastasis, and epithelial-to-mesenchymal transition | (Dery et al. 2011, Xu et al. 2014, Zhang et al. 2018) |
| CDK12 | Splicing factor kinases | ATM, DNAJB6 | Cell invasion and tumorigenesis | (Tien et al. 2017) |
| CLK2 | Splicing factor kinases | MENA | Cell growth, migration, invasion, and epithelial-to-mesenchymal transition | (Yoshida et al. 2015) |
| SRPK1 | Splicing factor kinases | BARD1, BCL2L1 and MCL-1 | Drug resistance | (Lin et al. 2014, Wang et al. 2020) |
| CELF2 | CELF family protein | ULK1, CARD10 | Proliferation | (Piqué et al. 2019) |
| CUGBP | CELF family protein | INSR | Viability, migration, colony formation | (Huang et al. 2020) |
| RMB4 | RBM family protein | IR, MCL-1 | Apoptosis | (Lin et al. 2014) |
| RBFOX2 | RBFOX splicing factor | FLAT, PLOD2 | Epithelial-to-mesenchymal transition | (Shapiro et al. 2011) |
| SYF2 | NTC complex | ETC2 | Doxorubicin resistance | (Tanaka et al. 2020) |
| KHDRBS3 | STAR family protein | CD44 | Invasion, migration, metastasis, and epithelial-to-mesenchymal transition | (Matsumoto et al. 2018) |
| ESRP1 | Other splicing factor | FASN, SCD1, PHGDH | Epithelial-to-mesenchymal transition | (Shapiro et al. 2011, Gökmen‐Polar et al. 2019) |
| PRMT6 | Other splicing factor | Alternate splicing of 449 genes | Cell cycle and cell death | (Dowhan et al. 2012) |
| YB-1 | Other splicing factor | CD44 | Epithelial-to-mesenchymal transition | (Watermann et al. 2006) |
| ZRANB2 | Other splicing factor | ETC2 | Doxorubicin resistance | (Tanaka et al. 2020) |
Implication of SF3B1 in breast cancer
The splicing factor 3B subunit 1 (SF3B1) is a central spliceosome component that constitutes the U2 snRNP complex together with other factors, such as SF3a or the 12S RNA unit. SF3B1 is crucial for the appropriate splicing process, and it has been found to be frequently dysregulated (mutated or aberrantly expressed) in different pathologies, including myelodysplastic syndrome, chronic lymphocytic leukemia, and other solid tumors such as liver (López-Cánovas et al. 2021), pancreas (Alors-Perez et al. 2021), prostate (Jiménez-Vacas et al. 2019), or BCa (Maguire et al. 2015). SF3B1 is one of the spliceosomal components more frequently mutated in BCa, wherein SF3B1 mutations are significantly associated with ER-positive disease and AKT1 mutations (Maguire et al. 2015, Fu et al. 2017). These mutations seem to be especially relevant in some histological subtypes in that 16 and 6% of papillary and mucinous carcinomas harbored the SF3B1K700E mutation (Maguire et al. 2015). Also, SF3B1 mutations are a poor prognostic factor in luminal B and PR-negative BCa (Fu et al. 2017). In tumor cells, SF3B1 mutations are associated with altered transcriptome, proteome, and metabolome, leading to missplicing-associated downregulation of metabolic genes, decreased mitochondrial respiration, and suppression of the serine synthesis pathway, and with higher sensitivity to the SF3b complex inhibitor spliceostatin A (Maguire et al. 2015). In addition, SF3B1 has been also found to be overexpressed in BCa tissues compared with normal tissues, wherein it is associated with lymph node metastasis (Zhang et al. 2020). SF3B1 knockdown in BCa cells significantly induced the suppression of proliferation, migration, invasion, and increased apoptosis (Zhang et al. 2020). Similarly, changes in the in vitro expression of SF3B1 are associated with the differential expression of genes enriched in the Ras signaling pathway; cytokine receptor interaction; tight junction; MAPK signaling pathway; and glycine, serine, and threonine metabolism (Zhang et al. 2020). Therefore, alterations in SF3B1 (mutations or alterations in expression levels) result in alternative aberrant splicing events that contribute to breast tumorigenesis and may represent targetable vulnerabilities in BCa.
Role of SRSF1 in breast cancer
Serine-/arginine-rich splicing factor 1 (SRSF1 or SF2/ASF) is not only a prototypical SR protein implicated in constitutive and alternative splicing but also plays key roles in nonsense-mediated mRNA decay, mRNA export, and translation. SRSF1 is frequently overexpressed in cancer, including BCa, wherein it seems to play a role in the development of mammary tumors in humans and mice (Karni et al. 2007). SRSF1 overexpression promotes alternative splicing of hundreds of events, controlling exon inclusion or skipping depending on the location of the binding sites (Anczuków et al. 2015). In particular, SRSF1 can control the expression of the exon-9-included CASC4 variant, which increases acinar size and proliferation and decreases apoptosis (Anczuków et al. 2015). But SRSF1 can also regulate the splicing of BIM and BIN1 isoforms that lack pro-apoptotic functions and contribute to the malignant phenotype (Anczuków et al. 2012), or the PTPMT1 splice switching to modulate the AKT/C-MYC axis. In addition, it has also been shown that SRSF1 cooperates with MYC to transform mammary epithelial cells, in part by potentiating eIF4E activation (Anczuków et al. 2012).
Implication of hnRNPM in breast cancer
The RNA-binding protein heterogeneous nuclear RNP M (hnRNPM) is a splicing factor that belongs to the subfamily of ubiquitously expressed hnRNPs. These proteins are associated with pre-mRNAs splicing, processing, metabolism, and transport. In BCa, hnRNPM potentiates TGFβ signaling and promotes metastatic potential by activating the switch of alternative splicing that occurs during epithelial–mesenchymal transition (EMT) (Xu et al. 2014). hnRNPM acts in a mesenchymal-specific manner to precisely control CD44 splice isoform switching by competition with ESRP1, an epithelial splicing regulator that binds to the same cis-regulatory RNA elements and is repressed during EMT (Harvey et al. 2018). Indeed, hnRNPM correlates with increased CD44s in patient samples and is associated with aggressive BCa (Xu et al. 2014). hnRNPM may also mediate the tumorigenic effects of mutations in microrchidia family CW-type zinc finger 2 (MORC2), a chromatin remodeling protein whose mutations have been causally implicated in the metastatic progression of TNBC. Knockdown of hnRNPM reduced the binding of mutant MORC2 to CD44 pre-mRNA and reversed the mutant MORC2-induced CD44 splicing switch and EMT, impairing the migratory, invasive, and lung metastatic potential of mutant MORC2-expressing cells (Zhang et al. 2018). hnRNPM has also been involved in the alternative splicing of other oncogenes such as carcinoembryonic antigen-related cell adhesion molecule-1 (CEACAM1), which may generate two main splicing variants characterized by the inclusion (L-isoform) or exclusion (S-isoform) of exon 7 and implicated in breast carcinogenesis.
Splicing variants associated with breast cancer
Aberrant alternative splicing has been shown to be an important risk factor in BCa and may represent a potential target for cancer therapy (Read & Natrajan 2018). Different studies have demonstrated a widespread dysregulation of the alternative splicing landscape in BCa. For example, a recent study has shown up to 35,367 alternative splicing events and 973 differentially expressed alternative splicing events in BCa samples, wherein a total of 103 differentially expressed alternative splicing eventswere correlated with disease-free survival (Du et al. 2021). Similarly, another study has identified 546 recurrence-free survival-related alternative splicing events in TNBC (Wu et al. 2021). Indeed, the profile of the alternative splicing landscape has been shown to exhibit clinical implications in different BCa subtypes, wherein different alternative splicing signatures have been associated with invasive potential, metastasis, recurrence, or survival (Han et al. 2021, Wu et al. 2021), reinforcing the biological and clinical implication of the splicing process in the development and progression of BCa (Table 2).
List of splicing signatures found to be associated with breast cancer.
| Implication of splicing signature | Type of samples | Type of analysis | Reference | Publication title |
|---|---|---|---|---|
| AS pattern is altered in metastatic cells | Breast cancer cell lines | Global analysis of AS events in MDA-MB-231 and MCF-7 cells | Oh et al. 2021 | Widespread Alternative Splicing Changes in Metastatic Breast Cancer Cells. |
| DEAS signature predict disease-free survival | Breast cancer and paired normal tissues | Differentially expressed AS (DEAS) events from breast cancer patients from TCGA | Du et al. 2021a | Profiles of Alternative Splicing Landscape in Breast Cancer and Their Clinical Significance: An Integrative Analysis Based on Large-Sequencing Data. |
| AS events may predict survival of TNBC | TNBC tissues | AS events of 150 TNBC patients from TCGA | Wu et al. 2020 | The Functional Impact of Alternative Splicing on the Survival Prognosis of Triple-Negative Breast Cancer. |
| Survival-associated AS events and signatures may predict the survival outcomes of patients | Breast cancer samples | AS events of breast cancer samples from TCGA using SpliceSeq database | Han et al. 2021 | Characterization of Alternative Splicing Events and Prognostic Signatures in Breast Cancer. |
| AS events may represent a prognostic signature | Invasive breast cancer | AS events of invasive breast cancer from TCGA | Wang et al. 2020 | Transcriptome-wide Analysis and Modelling of Prognostic Alternative Splicing signatures in Invasive Breast Cancer: A Prospective Clinical Study. |
| A model with 15 AS events can predict overall survival | Breast cancer samples | AS events of breast cancer samples from TCGA using SpliceSeq database | Huang et al. 2020 | The Construction of Bone Metastasis-Specific Prognostic Model and Co-expressed Network of Alternative Splicing in Breast Cancer. |
| AS is related with the survival rate of TNBC patients | TNBC and normal breast tissues | AS event of TNBC and normal samples from TCGA using SpliceSeq database | Yu et al. 2020 | Comprehensive Analysis and Establishment of a Prediction Model of Alternative Splicing Events Reveal the Prognostic Predictor and Immune Microenvironment Signatures in Triple Negative Breast Cancer. |
| AS events in TNBC could uncover prognostic biomarkers and therapeutic targets | TNBC tissues | Percent spliced in (PIS) valuer for AS event of 151 TNBC samples from TCGA using SpliceSeq database | Gong et al. 2020 | Novel Insights Into Triple-Negative Breast Cancer Prognosis by Comprehensive Characterization of Aberrant Alternative Splicing. |
| An AS signature is capable of distinguishing epithelial and mesenchymal states of the tumors | Breast cancer samples | AS events in the breast cancer TCGA data set | Qiu et al. 2020 | A Combinatorially Regulated RNA Splicing Signature Predicts Breast Cancer EMT States and Patient Survival. |
| AS events may represent a prognostic signature | TNBC tissues | AS events of 150 TNBC patients from TCGA | Liu et al. 2020 | Prognostic Alternative mRNA Splicing Signature and a Novel Biomarker in Triple-Negative Breast Cancer. |
| AS events have a significant prognostic value in geriatric breast cancer | Geriatric breast cancer | AS event of geriatric breast cancer samples from TCGA using SpliceSeq database | Li et al. 2020 | Prognostic Value and Potential Regulatory Mechanism of Alternative Splicing in Geriatric Breast Cancer. |
| Inflammatory breast cancer has a specific spliced transcript profile associated to poor metastasis-free survival | Inflammatory breast cancer | Splicing variants by splice-sensitive array profiling using Affymetrix Exon Array in 177 IBC compared to 183 non-IBC | Lerebours et al. 2020 | Hemoglobin Overexpression and Splice Signature as New Features of Inflammatory Breast Cancer? |
| Splicing levels significantly contribute to the diversity of breast cancer molecular subtypes | Invasive breast carcinomas and normal breast tissues | AS in 176 invasive breast carcinomas and 9 normal breast tissues analyzd by Affymetrix GeneChip Exon 1.0 ST | Gracio et al. 2017 | Splicing Imbalances in Basal-like Breast Cancer Underpin Perturbation of Cell Surface and Oncogenic Pathways and Are Associated With Patients’ Survival. |
| Intronic and exonic changes in the transcriptional landscapes have therapeutic implications | ERBB2-amplified, ER-positive and triple-negative breast cancer samples | Splicing event in breast cancer samples using high-resolution next-generation transcriptome sequencing | Forootan et al. 2016 | Transcriptome Sequencing of Human Breast Cancer Reveals Aberrant Intronic Transcription in Amplicons and Dysregulation of Alternative Splicing With Major Therapeutic Implications. |
In addition to exhibit a prognostic potential in BCa, these altered splicing events may be also associated with the development, progression, and treatment response of BCa. A detailed list of identified splicing events associated with BCa can be found in Tables 3, 4 and 5. Indeed, aberrant splicing of several genes (Fig. 2), including HER2, ER, or BRCA1 as well as other regulators of the mammary gland pathophysiology, has been shown to contribute to breast carcinogenesis (Fig. 3). Some examples are described below.
List of transcription factors, nuclear receptors and DNA repair-associated genes with altered splicing pattern and splicing variants found to be altered in breast cancer.
| Gene | Name | Splicing variants | Type of alternative splicing process | Process modulated | Reference |
|---|---|---|---|---|---|
| AC3-33 | Chromosome 3 Open Reading Frame 33 | (sv)AC3-33 | Skipping of exon 2 | Cell proliferation | (Yuan et al. 2020) |
| AIB1 | Amplified In Breast Cancer 1 | AIB1Δ4 | N-terminally truncated isoform | Cell invasion and tumor growth, and metastasis | (Sharif et al. 2021) |
| AR | Androgen Receptor | AR-V1, -V3, -V4, -V7, and -V9 | Various alternative splicing events | Cell growth and proliferation | (Hu et al. 2014, 2016) |
| ATOH8 | Atonal BHLH Transcription Factor 8 | ATOH8 (fl) and ATOH8-V1 | Alternative usage of exons 4 and 3 | Metastasis | (Xu et al. 2021) |
| BRCA1 | Breast Cancer Type 1 Susceptibility Protein | BRCA1 (fl), BRCA1-Δ11 and BRCA1-Δ11q | Various alternative splicing events | Tumorigenesis | (Chai et al. 2001, Lixia et al. 2007) |
| CDC25 | Cell Division Cycle 25 | CDC25A, B and C | Various alternative splicing events | Cellular response to DNA damage | (Albert et al. 2011, 2012) |
| CPEB2 | Cytoplasmic Polyadenylation Element Binding Protein 2 | CPEB2A / CPEB2B | Inclusion/skipping of exon 4 | Anoikis resistance (AnR) and metastasis | (Johnson et al. 2015, DeLigio et al. 2017, 2019) |
| DCUN1D5 | Defective In Cullin Neddylation 1 Domain Containing 5 | DCUN1D5 exon 4-deleted | Skipping of exon 4 | Metastasis | (Oh et al. 2021) |
| ECT2 | MYB-like Transcription Factor ETC2 | ECT2-Ex5+ | Inclusion of exon 5 | Doxorubicin resistance | (Tanaka et al. 2020) |
| Ets1 | Transcription Factor Ets1 | fl-Ets1 / DeltaVII-Ets1 | Inclusion/skipping of exon 7 | Cell survival | (Ballschmieter et al. 2003) |
| hTERT | Human Telomerase Reverse Transcriptase | full length, alpha, beta, and alpha/beta | Various alternative splicing events | Genomic stability | (Rha et al. 2009, Bojesen et al. 2013) |
| MBD2 | Methyl-CpG Binding Domain Protein 2 | MBD2a, MBD2b, MBD2c | Various alternative splicing events | EMT and metastasis | (Teslow et al. 2019, Liu et al. 2021) |
| MCL-1 | Myeloid Cell Leukemia-1 | Mcl-1L / Mcl-1s | Inclusion/skipping of exon 2 | Apoptosis | (Gautrey & Tyson-Capper 2012, Lin et al. 2014) |
| MDM2 | Mouse Double Minute 2 Homolog | MDM2, P2-MDM2-10 and MDM2-Δ5 | Various alternative splicing events | Chemotherapy response | (Huun et al. 2017a,b) |
| NCOR2 | Nuclear Receptor Corepressor 2 | BQ323636.1 (BQ) | Skipping of exon 11 | Chemoresistance | (Zhang et al. 2013, Gong et al. 2018) |
| NF-YA | Nuclear Transcription Factor Y Subunit Alpha | NF-YAl / NF-YAs | Inclusion/skipping of exon 3 | Cell growth | (Dolfini et al. 2019) |
| NFIC | Nuclear factor IC | CTF5 | Skipping of exons 9 and 10 | Proliferation of TNBC | (Chen et al. 2021) |
| ORL-1 | Lectin-like Oxidized Low-density Lipoprotein Receptor | LOX-1 / LOX-1Δ4 | Skipping of exon 4 | Proliferation, apoptosis, and drug resistance | (Pucci et al. 2019) |
| PR | Progesterone Receptor | PR-A, PR-B and PR-C | Various alternative splicing events | Progestin response and cell growth | (Nagao et al. 2003, Cork et al. 2008) |
| PRMT2 | Protein Arginine Methyltransferase 2 | PRMT2/PRMT2β | Skippin og exons 7-9 | Cell cycle and apoptosis | (Zhong et al. 2017) |
| RAD51C | DNA Repair Protein RAD51 Homolog 3 | RAD51C c.571 + 4A > G | Skipping of exon 3 | Not determined | (Dawson et al. 2020, Sanoguera-Miralles et al. 2020) |
| SRA1 | Steroid Receptor RNA Activator 1 | SRAP | Inclusion of exon -1 | Steroid receptor activity | (Hube et al. 2006) |
| STAT3 | Signal Transducer and Activator of Transcription 3 | STAT3α/STAT3β | Alternative 3´SS | Cell growth, viability, and migration | (Tano et al. 2019) |
| Survivin | Survivin | Survivin-2a, -2b, -3b, -dEx3, -2b+32 | Various alternative splicing events | Cell apoptosis and drug resistance | (Ryan et al. 2005, Zheng et al. 2005) |
| uPAR | Urokinase Receptor | uPAR, uPAR-del4/5 | Delection of exons 4/5 | Cell adhesion and invasion | (Grismayer et al. 2012) |
| XBP-1 | X-box Binding Protein 1 | XBP-1U / XBP-1S | Alternative recognition sites in exon 4 | Estrogen independence and anti-estrogen resistance | (Davies et al. 2008, Hu et al. 2015, Ming et al. 2015) |
| ZNF217 | Zinc Finger Protein 217 | ZNF217/ZNF217-ΔE4 | Skipping of exon 4 | Aggressive phenotype | (Bellanger et al. 2021) |
List of membrane-related molecules with altered splicing pattern and splicing variants found to be altered in breast cancer.
| Gene | Name | Splicing variants | Type of alternative splicing process | Process modulated | Reference |
|---|---|---|---|---|---|
| CASC4 | Cancer Susceptibility Candidate 4 | Exon-9-included CASC4 | Inclusion of exon 9 | Proliferation and apoptosis | (Anczuków et al. 2015) |
| CD44 | CD44 Antigen | CD44v/CD44s | Inclusion/skipping of any of the nine variable exons | Invasion, migration, metastais, and EMT | (Tanabe et al. 1993, Brown et al. 2011) |
| CEACAM1 | Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 | CEACAM1-L/CEACAM1-S | Inclusion/skipping of exon 7 | Cell growth | (Gaur et al. 2008, Dery et al. 2011, 2014) |
| Cyr61 | Cysteine Rich 61 | Cyr61 IR / Cyr61 IS | Inclusion/skipping of exon 3 | Angiogenesis | (Hirschfeld et al. 2009) |
| DMP1 | Dentin Matrix Acidic Phosphoprotein 1 | DMP1α, DMP1β and DMP1γ | Various alternative splicing events | Cell proliferation | (Maglic et al. 2015) |
| FLNB | Filamin B | Large and short FLNB forms | Skipping of exon 30 | EMT | (Li et al. 2018) |
| GIRK1 (KCNJ3) | G-protein Activated Inwardly Rectifying K(+) Channel | GIRK1a, GIRK1c, GIRK1d | Various alternative splicing events | Cell migration, invasion, and angiogenesis | (Rezania et al. 2016) |
| ITGA6 | Integrin Alpha-6 | α6A integrin/α6β integrin | Inclusion/skipping of exon 25 | Cell proliferation and cancer cell stemness | (Goel et al. 2014) |
| KAI1 / CD82 | Cluster of Differentiation 82 | KAI1 / KAI1-SP | Skipping of exon 7 | Cellular migration | (Miller et al. 2018) |
| LMNA | Lamin A and C | Lamin A, Lamin C, Lamin AΔ10, and Lamin AΔ50 | Various alternative splicing events | Cell cycle, differentiation, and apoptosis | (Aljada et al. 2016) |
| MENA | Mammalian Ena | MENAΔ11a | Skipping of exon 11a | EMT | (di Modugno et al. 2012) |
| MTDH | Metadherin | MTDHΔ7 | Skipping of exon 7 | Cell proliferation, invasion, and EMT | (Neeli et al. 2020) |
| POSTN | Periostin | POSTN Ex17 | Skipping/inclusion of exon 17 | Cell growth and metastasis | (Hoersch & Andrade-Navarro 2010) |
| PTPMT1 | Protein Tyrosine Phosphatase Mitochondrial 1 | PTPMT1 exon 3 (E3) AS | Inclusion/skipping of exon 3 | Proliferation, migration, and apoptosis | (Du et al. 2021b) |
| RHAMM | Receptor of Hyaluronan-mediated Motility | RHAMMv1/v2/v3/v4 | Various alternative splicing events | Susceptibility to radiotherapy | (Schütze et al. 2016) |
| RHBDD2 | Rhomboid Domain Containing 2 | RHBDD2 variants 1 and 2 | Inclusion/skipping of exon 2 | Tumor progression | (Abba et al. 2009, Canzoneri et al. 2018) |
| SmgGDS | Smg GDP Dissociation Stimulator | SmgGDS-607 (fl) / SmgGDS-558 | Skipping of exon 5 | Cell cycle, proliferation, Rho activity | (Hauser et al. 2014, Schuld et al. 2014) |
| Syk | Spleen Tyrosine Kinase | Syk(L) / Syk(S) | Delection of 23aa | Cell invasion | (Wang et al. 2005) |
List of hormones and growth factors signaling-related genes with altered splicing pattern and splicing variants found to be altered in breast cancer.
| Gene | Name | Splicing variants | Type of alternative splicing process | Process modulated | Reference |
|---|---|---|---|---|---|
| CERS2 | Ceramide Synthase 2 | CERS2 AS1 | Skipping of exon 8 | Proliferation and migration | (Pani et al. 2021) |
| CRH-R1 | Corticotropin-releasing Hormone Receptor Type 1 | CRH-R1(Δ12) | Skipping of exon 12 | Cellular response to CRH and invasion | (Lal et al. 2013) |
| ERα | Estrogen Receptor α | ERα66 (fl), ERα46, and ERα36 | Various alternative splicing events | Estrogen signaling | (Klinge et al. 2010) |
| ERβ | Estrogen Receptor β | ERβ1 and ERβ2 | Various alternative splicing events | Estrogen signaling | (Iwao et al. 2000) |
| FGFR1 | Fibrobast Growth Factor Receptor 1 | FGFR1β/FGFR1α | Skipping/inclusion of exon 3 | Cell growth, motility, and resistance to treatment | (Zhao et al. 2019) |
| FGFR2 | Fibroblast Growth Factor Receptor 2 | FGFR2-IIIc | Inclusion of IIIc exon | FAST signaling | (Moffa & Ethier 2007, Zhu et al. 2009) |
| GHRL | Ghrelin | In1-ghrelin | Retention of intron 1 | Cell proliferation, migration, and stemness | (Gahete et al. 2011, Rincón-Fernández et al. 2018) |
| HER2 | Human Epidermal Growth Factor Receptor 2 | Herstatin, d15HER2, d16HER2, p100HER2, X5-HER2, HER2-PI9, and HER2-I12 | Various alternative splicing events | Cell proliferation and apoptosis | (Wan et al. 2009, Alajati et al. 2013, Hart et al. 2021) |
| IL-7 | Interleukin-7 | IL-7δ5 | Skipping of exon 5 | Growth, invasion, and EMT | (Pan et al. 2012, Yang et al. 2014) |
| INSR | Insulin Receptor | IR-A / IR-B | Inclusion/skipping of exon 11 | Insulin signaling, tumor growth, and progression | (Aljada et al. 2015, Huang et al. 2020) |
| PDGF-C | Platelet-derived Growth Factor C | FL-PDGF-C/t-PDGF-C | Alternative splicing of signal peptide and CUB domain | Anchorage-independent growth and invasion | (Bottrell et al. 2019) |
| RANK (TNFRSF11A) | Receptor Activator of Nuclear Factor-kB (NF-kB) | TNFRSF11A_Δ9, TNFRSF11A_Δ8,9 TNFRSF11A_Δ7,8,9 | Alternative splicing of exons 7 to 9 | Cell growth, migration, and apoptosis | (Papanastasiou et al. 2012, Sirinian et al. 2018) |
| SSTR5 | Somatostatin Receptor 5 | SSTR5 (fl)/SST5TMD4 | Splicing of cryptic intron | Cell proliferation, migration, invasion, and angiogenesis | (Durán-Prado et al. 2012, Gahete et al. 2016, del Rio-Moreno et al. 2019) |
| VEGF-A | Vascular Endothelial Growth Factor A | VEGF-A, VEGF-A165, VEGF-189, VEGF-206 | Various alternative splicing events | Therapy response | (Pentheroudakis et al. 2014) |
Key alternative splicing events in breast cancer pathogenesis. The constitutive and alternative mRNA processing of genes described in this review are represented. Exons are shown as boxes while introns are represented as lines between exons. For each gene, the pre-mRNA is depicted in the center of the scheme, while the full-length variant associated with constitutive splicing is represented on the top. The variants produced by alternative splicing events are shown in the bottom.
Citation: Endocrine-Related Cancer 29, 9; 10.1530/ERC-22-0019
Key alternative splicing events in breast cancer pathogenesis. The constitutive and alternative mRNA processing of genes described in this review are represented. Exons are shown as boxes while introns are represented as lines between exons. For each gene, the pre-mRNA is depicted in the center of the scheme, while the full-length variant associated with constitutive splicing is represented on the top. The variants produced by alternative splicing events are shown in the bottom.
Citation: Endocrine-Related Cancer 29, 9; 10.1530/ERC-22-0019
Key alternative splicing events in breast cancer pathogenesis. The constitutive and alternative mRNA processing of genes described in this review are represented. Exons are shown as boxes while introns are represented as lines between exons. For each gene, the pre-mRNA is depicted in the center of the scheme, while the full-length variant associated with constitutive splicing is represented on the top. The variants produced by alternative splicing events are shown in the bottom.
Citation: Endocrine-Related Cancer 29, 9; 10.1530/ERC-22-0019
Functional role of alternative splicing variants-generating genes in breast cancer pathogenesis. Genes with described breast cancer-associated alternative splicing variants are classified according to their implication in canonical cancer hallmarks, named cell growth/proliferation/apoptosis, migration/metastasis, drug resistance, angiogenesis, and hormonal signaling/intracellular events. The complete set of splicing variants is depicted in Table 2.
Citation: Endocrine-Related Cancer 29, 9; 10.1530/ERC-22-0019
Functional role of alternative splicing variants-generating genes in breast cancer pathogenesis. Genes with described breast cancer-associated alternative splicing variants are classified according to their implication in canonical cancer hallmarks, named cell growth/proliferation/apoptosis, migration/metastasis, drug resistance, angiogenesis, and hormonal signaling/intracellular events. The complete set of splicing variants is depicted in Table 2.
Citation: Endocrine-Related Cancer 29, 9; 10.1530/ERC-22-0019
Functional role of alternative splicing variants-generating genes in breast cancer pathogenesis. Genes with described breast cancer-associated alternative splicing variants are classified according to their implication in canonical cancer hallmarks, named cell growth/proliferation/apoptosis, migration/metastasis, drug resistance, angiogenesis, and hormonal signaling/intracellular events. The complete set of splicing variants is depicted in Table 2.
Citation: Endocrine-Related Cancer 29, 9; 10.1530/ERC-22-0019
Alternative splicing of HER2
One of the most paradigmatic cases of altered alternative splicing processes with a clear implication in BCa is HER2, a classic marker of BCa that can generate different splicing variants with clinical implications in BCa progression. HER2 is an oncogene encoding a tyrosine kinase receptor, whose amplification or overexpression defines the HER2-positive BCa subtype. These tumors are characterized by a high mitotic index and an elevated metastatic potential. Interestingly, the HER2 gene has been shown to generate at least seven splicing variants (Δ16HER2, Δ15HER2, Herstatin, p100HER2, X5-HER2, HER2-PI9, and HER2-I12 (Hart et al. 2020)) in addition to the canonical transcript, which are differently expressed in BCa samples and cell lines and can provide certain clinical characteristics to the patients, such as partial resistance to specific drugs. Δ16HER2 is a splice variant of HER2 that lacks exon 16, which encodes a small extracellular region (Inoue & Fry 2015). The resultant loss of cysteine residues in the extracellular domain of HER2 induces homodimerization via intermolecular disulfide bonds, resulting in a conformational change of HER2. This change has been shown to initiate key oncogenic signals with a significant impact on HER2-driven BCa stemness, tumorigenesis, and drug resistance (Jackson et al. 2013). Indeed, emerging evidence indicates that the co-expression of Δ16HER2 with HER2 significantly increases the heterogeneity of HER2-positive disease, affecting its biology, clinical progression, and treatment response (Hart et al. 2020). The secreted splicing variant Herstatin is produced by the retention of intron 8, which binds to the HER2 WT cysteine-rich domain 1 using its novel C-terminus, and blocks HER2 WT dimer formation, gaining an auto-inhibitory function and reducing the phosphorylation of its tyrosine residues and a reduction in Akt signaling (Azios et al. 2001). p100HER2 splicing variant lacks the intracellular domain of HER2 WT, owing to the retention of intron 15 and inducing a termination codon and poly (A) addition site, which triggers its truncation. It has been reported that p100HER2 could reduce the efficacy of treatments based on anti-HER2 monoclonal antibodies by sequestering HER2 outside the cell and reducing antibody binding. Moreover, p100HER2 can be secreted, and its production reduces downstream signaling via ERK1/2 and HER4 phosphorylation (Aigner et al. 2001).
Alternative splicing of ER
The ERα and ERβ types are nuclear receptors that act as hormone-inducible transcription factors to mediate the effects of estrogens. In BCa, the tumor-promoting actions exerted by ERα are well-known, while the exact role of ERβ in carcinogenesis and tumor progression is still unclear. Indeed, contradictory studies have shown highly variable, and even opposite, effects of ERβ in cancer, including both proliferative and growth-inhibitory actions (Sellitto et al. 2020). ERα (595 aa) and ERβ (530 aa) have been shown to coexist in different tissues, including BCa, wherein the presence of these ER-isoforms, together with the presence of PR, defines the luminal BCa subtype. However, ambiguous data concerning ERβ presence and role in BCa have been published (Sellitto et al. 2020), which could be related to the poor specificity of commercially available antibodies (Wu et al. 2012), as well as to the lack of standardization of IHC protocols and tissue samples preparation. Canonical ERα and ERβ are also usually co-expressed with alternative spliced variants, which exhibit pathological implications in BCa. In particular, the ERα gene can generate various alternative splicing isoforms in a tissue and in a disease-specific manner (Taylor et al. 2010). The canonical full-length ERα66 is characterized by the presence of two activation domains, one with a constitutive activation function (AF-1), and one with a hormone-dependent activation function (AF-2). Specifically, AF-2 (E domain) works by recruiting a large coactivator complex, composed of one or more p160s, CREB-binding protein (CBP)/p300, and p300 and CBP-associated factor (P/CAF) via direct contact with the p160s. In contrast, the splicing isoform ERα46 only contains the AF-1 domain, while the shortest isoform ERα36 lacks AF-1 and AF-2 domains and encodes a 29-aa protein. Among them, ERα46 has been shown to antagonize the function of the canonical ERα66 in mammary carcinoma cells and is involved in BCa development and drug resistance (Klinge et al. 2010). Similarly, ERβ, whose expression level is correlated to a better prognosis of BCa (Haldosén et al. 2014), has been shown to encode for, at least, five alternative splicing isoforms. These spliced variants have been named ERβ1, ERβ2, ERβ3, ERβ4, and ERβ5. For example, ERβ1 and ERβ2 seem to play different biological roles in normal and tumoral mammary tissues in as much as they exhibit differential expression patterns in normal epithelial and BCa cells and tissues (Iwao et al. 2000). In particular, ERβ1 has been shown to target the IRE1/XBP-1 pathway to promote apoptosis in BCa cells (Rajapaksa et al. 2016), while ERβ2 seems to be associated with poor disease-free survival and overall survival in BCa patients (Baek et al. 2015).
Alternative splicing of BRCA1
BRCA1 is a tumor suppressor gene involved in DNA repair by homologous recombination that interacts with different partners to maintain genomic stability. Mutations in BRCA1 constitute the largest proportion of genomic alterations found in BCa cases occurring in women who have a first-degree relative with a history of BCa (Semmler et al. 2019). However, dysregulation of BRCA1 alternative splicing has been also found to be involved in BCa development (Orban & Olah 2003). Indeed, several BRCA1 splice variants have been described in normal and tumoral tissues. Among them, the full-length BRCA1 and the splicing variants BRCA1-Δ11 and BRCA1-Δ11q are the most evolutionary conserved and the main isoforms involved in mammary carcinogenesis. These three major BRCA1 isoforms depend on the regulation of exon 11, which encodes the nuclear localization signal responsible for its translocation to the nucleus (Martínez-Montiel et al. 2017). While BRCA1 full-length exhibits the inclusion of all coding exons, BRCA1-Δ11 is generated by the skipping of exon 11, and BRCA1-Δ11q by the partial skipping of exon 11. In particular, the BRCA1-Δ11q isoform derives from the exclusion of most exon 11 sequences due to the usage of an alternative donor splice site in exon 11. Thus, both BRCA1-Δ11 and BRCA1-Δ11q isoforms are mainly retained in the cytoplasm, wherein they are unable to bind RAD51 for DNA repair.
The implication of BRCA1 splicing variants in BCa remains controversial. BRCA1-Δ11 show tumor-suppressive effects in vivo, as mice lacking this BRCA1 isoform spontaneously develop hyperplasia in the gynecological system. As BRCA1-Δ11 can translocate to the nucleus in a non-canonical way and partially compensate for the loss of full-length BRCA1 in DNA repair, the consequence of BRCA1-Δ11 elimination might be associated with a decrease in total nuclear BRCA1. However, BRCA1-Δ11 binds inefficiently to RAD51, leading to a decreased formation of RAD51 focus on damaged DNA compared to full-length BRCA1 (Huber et al. 2001). Strikingly, BCa patients bearing mutations in exon 11 have a worse overall survival compared to those lacking mutations in exon 11. Indeed, an exclusive expression of BRCA1-Δ11q promotes cancer cells growth and proliferation, and this splicing variant has been positively correlated to tumorigenesis and drug resistance in BCa (Nielsen et al. 2016). Moreover, Exon 11 mutations or higher expression of BRCA1-Δ11 and BRCA1-Δ11q compared to full-length BRCA1 lead to a decreased translocation of BRCA1. Thus, BRCA1 splicing pro- or anti-oncogenic effect seems to be associated with total BRCA1 presence in the nucleus.
Alternative splicing of SSTR5
Somatostatin receptors (SSTR) mediate the effects of somatostatin and cortistatin, two pleiotropic inhibitory hormones, in normal and cancer cells (Gahete et al. 2008). In particular, the SSTR5 has been shown to undergo processes of alternative splicing to generate two truncated, but functionally active and pathologically relevant, variants named SST5TMD4 and SST4TMD5 (Durán-Prado et al. 2010). These spliced mRNA variants generate shorter receptors (with less than seven transmembrane domains or TMD) that are practically absent in normal tissues but clearly overexpressed in different tumoral pathologies (Puig-Domingo et al. 2014, Luque et al. 2015a, Sampedro-Núñez et al. 2016, Hormaechea-Agulla et al. 2017a, Fuentes‐Fayos et al. 2022). The loss of two (SST5TMD5) or three (SST5TMD4) transmembrane domains after SSTR5 transcript splicing leads to the generation of shorter but functional receptors that exhibit a predominant cytoplasmatic location (Durán-Prado et al. 2012). This intracellular location together with its capacity to establish protein–protein interactions with other SSTRs can help to explain their oncogenic role in different cancers (Puig-Domingo et al. 2014, Luque et al. 2015a, Sampedro-Núñez et al. 2016, Hormaechea-Agulla et al. 2017a, Fuentes‐Fayos et al. 2022). In the case of BCa, the truncated SSTR5 receptor SST5TMD4 is overexpressed and associated with poor prognosis markers (Durán-Prado et al. 2012, Gahete et al. 2016). Particularly, this truncated receptor interacts with the canonical SSTR2 and SSTR5 isoforms to disrupt their actions and promote EMT, cell growth, migration, and invasion in BCa cells (Durán-Prado et al. 2012). Indeed, in vivo, xenograft tumors overexpress SST5TMD4 growth faster than controls. This spliced receptor also induces the expression of many angiogenic genes and, consistently, patients with higher SST5TMD4 levels exhibited higher metastatic potential and lower disease-free survival (Gahete et al. 2016). In a more recent publication, it has been demonstrated that the C-terminal tail of the spliced SST5TMD4 is exposed to the extracellular matrix, wherein it can be cleaved by matrix metalloproteinases to release soluble peptides with oncogenic potential (del Rio-Moreno et al. 2019). Indeed, these peptides derived from the C-terminal tail of the SST5TMD4 can increase the proliferation, migration, and capacity to form tumorospheres in BCa cell lines and are also implicated in the lack of response to somatostatin analogs observed in cells overexpression the SST5TMD4 variant (del Rio-Moreno et al. 2019).
Alternative splicing of ghrelin
Ghrelin is a 28-amino acid acylated hormone that regulates a plethora of relevant biological processes, including food intake, energy balance, hormonal secretions, learning, inflammation, etc (Gahete et al. 2014). However, ghrelin gene generates a growing number of alternative peptides, including splicing variants (e.g. obestatin, unacylated ghrelin, In1-ghrelin, etc.) that comprise a complex and intricate regulatory system (Gahete et al. 2014). Indeed, soon after the discovery of native ghrelin, several independent laboratories identified different alternative ghrelin gene-derived peptides and mRNA splice variants (Gahete et al. 2014). Particularly, the splicing variant In1-ghrelin shares the initial 13 amino acids with native ghrelin, including the first five amino acids, which is the minimum sequence required for ghrelin acylation by GOAT enzyme and for binding and activation of GHSR1a. In contrast, the In1-ghrelin C-terminal sequence is completely altered because of the retention of intron 1. In fact, In1-ghrelin can be proteolytically processed to generate In1-ghrelin derived peptides that may be secreted by cancer cells to act as oncogenic factors. For these reasons, the In1-ghrelin variant has been shown to be especially relevant in different tumor pathologies (Ibáñez-Costa et al. 2015, Luque et al. 2015b, Hormaechea-Agulla et al. 2017b, Jiménez-Vacas et al. 2021). Indeed, this splicing variant has been found to be overexpressed in BCa and associated with tumor progression and disease-free survival (Gahete et al. 2011, Rincón-Fernández et al. 2018). In vitro, the overexpression of this splicing variant or the exogenous treatment with the peptides derived from the In1-ghrelin can increase the proliferative and migrative capacity of BCa cells lines, as well as the ability to form tumorospheres (Rincón-Fernández et al. 2018), which reinforce the idea of the crucial implication of this splicing variant in BCa.
Alternative splicing of AIB1
Amplified in breast cancer 1 (AIB1), also known as steroid receptor coactivator 3 (SRC-3) or nuclear receptor coactivator 3 (NCOA3), was first identified by its amplification and/or overexpression in BCa (Anzick et al. 1997). AIB1 is a well-established oncogene in several model systems by coactivating transcription of hormone receptors such as ER and PR; however, AIB1 can also drive malignancy and invasion in ER/PR-negative cancers through other transcription factors (AP-1, TEADs, E2Fs, ETS, and NF-κB). In addition, miss-splicing of the AIB1 gene has also been associated with BCa malignancy. The mRNA splice isoform AIB1Δ4, which misses the first 223 amino acids from the N-terminus containing the PAS-HLH domains, is expressed in cancer cells together with full-length AIB1 (Sharif et al. 2021). This variant is generated by the skipping of exon 4, which generates a new translation start site on exon 7 in frame with the full-length AIB1 isoform, and leads to a truncated AIB1 variant. AIB1Δ4 expression in normal human mammary epithelium is negligible but is clearly upregulated in early-stage BCa and especially in BCa cell lines that metastasize to the lung and brain. In vitro and in vivo, AIB1Δ4 overexpression in the presence of endogenous AIB1 induced oncogenic potential and increased the malignancy of BCa cells via upregulation of different pathways such as cyclin D1, IGFI receptor signaling, NF-κB, or EGF-induced transcription. These actions of AIB1Δ4 have been attributed to the lack of an inhibitory domain on the missing N-terminus that binds the tumor suppressor ANCO1/ANKRD11. More recently, it has been demonstrated that cells that exclusively express the AIB1Δ4 variant show enhanced invasive and migratory behavior and exhibit an isoform-specific cistrome, which leads to a transcriptome pattern associated with poor outcome in BCa.
Concluding remarks
The dysregulation of the splicing process has emerged as a novel hallmark in BCa. Oncogenic splicing variants of HER2, ER, BRCA1, AIB1, and other tumor- and metabolic-associated genes have been described and associated with increased malignancy, poor prognosis, and resistance to treatment. Indeed, the alteration of splicing events has been shown to be useful in predicting the prognosis or the response to treatment in BCa patients, suggesting a putative utility in precision medicine. On the one hand, it could be suggested that the general pattern of dysregulation in the splicing process (the molecular signature of splicing events) could have clinical implications in this pathology. Indeed, several studies have recently reported that the landscape of alternative splicing changes has clinical implications in different BCa subtypes and are associated with invasive potential, metastasis, recurrence, or survival, suggesting a putative utility as prognostic biomarkers. On the other hand, individual cancer-associated splicing variants could be also of potential clinical utility. In fact, particular splicing variants that are mainly absent or at negligible levels in normal breast epithelium but overexpressed in tumor tissues (i.e. AB1, sst5TMD5, etc.) could be also postulated as diagnostic biomarkers. These splicing variants might be also used as more specific and personalized therapeutic targets, through the development of specific drugs (small molecules), or could represent a source for the identification of potential new targets (neo-antigens) for cancer immunotherapy. Consequently, targeting mis-spliced RNA transcripts during tumorigenesis through antisense oligonucleotides, shRNA interference, small interference RNA, CRISPR-Cas-directed gene editing, or single-base editors (BEs) cytosine-BEs, or adenine-BEs (ABEs) might represent novel and useful strategies to combat this pathology.
This altered expression of oncogenic splicing variants is tightly linked to the dysregulation of spliceosome components and splicing factors, which might be clinically relevant. Particularly, spliceosomal components shown to be dysregulated in BCa could also represent novel diagnostic, prognostic, and therapeutic targets. Indeed, a battery of compounds that affect global splicing efficiency or splicing sites selection has been identified and being pharmacologically tested in recent years. The first group of compounds act directly on the core spliceosomal component SF3B1 and include spliceostatins, sudemycins, FD-895, and pladienolides molecules or their derivatives (e.g. E7107 or FR901464). These SF3B1 inhibitors only affect a fraction of the splicing events, suggesting that some splicing sites are more sensitive than others to spliceosomal inhibitors. A second group of splicing inhibitors, such as isoginkgetin, act by preventing the recruitment of the U4/U5/U6 tri-snRNPs, which leads to the accumulation of the spliceosomal complex A405. A third group of small molecules alters the activity of splicing factors by targeting their regulatory kinases, including molecules such as NB-506, diospyrin D1, SRPIN34, and TG003. Of note, the exact mechanisms of action of these small molecules are not totally understood. However, in vitro and in vivo data suggest that cancer cells seem to be more sensitive than normal cells to global splicing inhibition (Fuentes-Fayos et al. 2020, López-Cánovas et al. 2021), thus providing a therapeutic window for these splicing inhibitors.
For all these reasons, although the spliceosomal landscape has not been comprehensively explored in BCa hitherto, this review supports the contention that the expression of splicing variants and spliceosomal components is drastically altered in BCa, and that may be implicated in mammary development and tumorigenesis.
Declaration of interest
The authors declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of this review.
Funding
This work did not receive any specific grant from any funding agency in the public, commercial, or not-for-profit sector.
Author contribution statement
M D G, J L L C, and R M L participated in the conception and design of the work. M D G, J L J C, A C F F, and N H S participated on the bibliography search, analysis, and interpretation of data. M D G and R M L have drafted and revised the work. All authors have approved the final version and have agreed both to be personally accountable for the author's own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature.
Acknowledgements
This work was funded by Instituto de Salud Carlos III, co-funded by European Union ((ERDF/ESF, ‘Investing in your future’) PI20/01301), MICINN (PID2019-105564RB-I00), Junta de Andalucía (BIO-0139), FSEOM, and CIBERobn.
References
Abba MC, Lacunza E, Nunez MI, Colussi A, Isla-Larrain M, Segal-Eiras A, Croce MV & Aldaz CM 2009 Rhomboid domain containing 2 (RHBDD2): a novel cancer-related gene over-expressed in breast cancer. Biochimica et Biophysica Acta 1792 988–997. (https://doi.org/10.1016/J.BBADIS.2009.07.006)
Aigner A, Juhl H, Malerczyk C, Tkybusch A, Benz CC & Czubayko F 2001 Expression of a truncated 100 kDa HER2 splice variant acts as an endogenous inhibitor of tumour cell proliferation. Oncogene 20 2101–2111. (https://doi.org/10.1038/sj.onc.1204305)
Alajati A, Sausgruber N, Aceto N, Duss S, Sarret S, Voshol H, Bonenfant D & Bentires-Alj M 2013 Mammary tumor formation and metastasis evoked by a HER2 splice variant. Cancer Research 73 5320–5327. (https://doi.org/10.1158/0008-5472.CAN-12-3186)
Albert H, Santos S, Battaglia E, Brito M, Monteiro C & Bagrel D 2011 Differential expression of CDC25 phosphatases splice variants in human breast cancer cells. Clinical Chemistry and Laboratory Medicine 49 1707–1714. (https://doi.org/10.1515/CCLM.2011.635)
Albert H, Battaglia E, Monteiro C & Bagrel D 2012 Genotoxic stress modulates CDC25C phosphatase alternative splicing in human breast cancer cell lines. Molecular Oncology 6 542–552. (https://doi.org/10.1016/j.molonc.2012.06.003)
Aljada A, Saleh AM, Al-Aqeel SM, Shamsa HB, Al-Bawab A, al Dubayee M & Ahmed AA 2015 Quantification of insulin receptor mRNA splice variants as a diagnostic tumor marker in breast cancer. Cancer Biomarkers: Section A of Disease Markers 15 653–661. (https://doi.org/10.3233/CBM-150505)
Aljada A, Doria J, Saleh AM, Al-Matar SH, AlGabbani S, Shamsa HB, Al-Bawab A & Ahmed AA 2016 Altered Lamin A/C splice variant expression as a possible diagnostic marker in breast cancer. Cellular Oncology 39 161–174. (https://doi.org/10.1007/s13402-015-0265-1)
Alors-Perez E, Blázquez-Encinas R, Alcalá S, Viyuela-García C, Pedraza-Arevalo S, Herrero-Aguayo V, Jiménez-Vacas JM, Mafficini A, Sánchez-Frías ME & Cano MT et al.2021 Dysregulated splicing factor SF3B1 unveils a dual therapeutic vulnerability to target pancreatic cancer cells and cancer stem cells with an anti-splicing drug. Journal of Experimental and Clinical Cancer Research 40 382. (https://doi.org/10.1186/S13046-021-02153-9)
Anczuków O, Rosenberg AZ, Akerman M, Das S, Zhan L, Karni R, Muthuswamy SK & Krainer AR 2012 The splicing factor SRSF1 regulates apoptosis and proliferation to promote mammary epithelial cell transformation. Nature Structural and Molecular Biology 19 220–228. (https://doi.org/10.1038/nsmb.2207)
Anczuków O, Akerman M, Cléry A, Wu J, Shen C, Shirole NH, Raimer A, Sun S, Jensen MA & Hua Y et al.2015 SRSF1-regulated alternative splicing in breast cancer. Molecular Cell 60 105–117. (https://doi.org/10.1016/J.MOLCEL.2015.09.005)
Anzick SL, Kononen J, Walker RL, Azorsa DO, Tanner MM, Guan XY, Sauter G, Kallioniemi OP, Trent JM & Meltzer PS 1997 AIB1, a steroid receptor coactivator amplified in breast and ovarian cancer. Science 277 965–968. (https://doi.org/10.1126/SCIENCE.277.5328.965)
Azios NG, Romero FJ, Denton MC, Doherty JK & Clinton GM 2001 Expression of herstatin, an autoinhibitor of HER-2/neu, inhibits transactivation of HER-3 by HER-2 and blocks EGF activation of the EGF receptor. Oncogene 20 5199–5209. (https://doi.org/10.1038/sj.onc.1204555)
Baek JM, Chae BJ, Song BJ & Jung SS 2015 The potential role of estrogen receptor β2 in breast cancer. International Journal of Surgery 14 17–22. (https://doi.org/10.1016/J.IJSU.2014.10.007)
Ballschmieter P, Braig M, Lindemann RK, Nordheim A & Dittmer J 2003 Splicing variant DeltaVII-Ets1 is downregulated in invasive Ets1-expressing breast cancer cells. International Journal of Oncology 22 849–853. (https://doi.org/10.3892/IJO.22.4.849/HTML)
Bellanger A, Le DT, Vendrell J, Wierinckx A, Pongor LS, Solassol J, Lachuer J, Clezardin P, Győrffy B & Cohen PA 2021 Exploring the significance of the exon 4-skipping isoform of the ZNF217 oncogene in breast cancer. Frontiers in Oncology 11 647269. (https://doi.org/10.3389/FONC.2021.647269)
Bojesen SE, Pooley KA, Johnatty SE, Beesley J, Michailidou K, Tyrer JP, Edwards SL, Pickett HA, Shen HC & Smart CE et al.2013 Multiple independent variants at the tert locus are associated with telomere length and risks of breast and ovarian cancer. Nature Genetics 45 371–384. (https://doi.org/10.1038/NG.2566)
Bottrell A, Meng YH, Najy AJ, Hurst N, Kim S, Kim CJ, Kim ES, Moon A, Kim EJ & Park SY et al.2019 An oncogenic activity of PDGF-C and its splice variant in human breast cancer. Growth Factors 37 131–145. (https://doi.org/10.1080/08977194.2019.1662415)
Brown RL, Reinke LM, Damerow MS, Perez D, Chodosh LA, Yang J & Cheng C 2011 CD44 splice isoform switching in human and mouse epithelium is essential for epithelial-mesenchymal transition and breast cancer progression. Journal of Clinical Investigation 121 1064–1074. (https://doi.org/10.1172/JCI44540)
Buoso E, Ronfani M, Galasso M, Ventura D, Corsini E & Racchi M 2019 Cortisol-induced SRSF3 expression promotes GR splicing, RACK1 expression and breast cancer cells migration. Pharmacological Research 143 17–26. (https://doi.org/10.1016/j.phrs.2019.03.008)
Canzoneri R, Rabassa ME, Gurruchaga A, Ferretti V, Palma S, Isla-Larrain M, Croce MV, Lacunza E & Abba MC 2018 Alternative splicing variant of RHBDD2 is associated with cell stress response and breast cancer progression. Oncology Reports 40 909–915. (https://doi.org/10.3892/or.2018.6489)
Casasent AK, Edgerton M & Navin NE 2017 Genome evolution in ductal carcinoma in situ: invasion of the clones. Journal of Pathology 241 208–218. (https://doi.org/10.1002/path.4840)
Chai Y, Chipitsyna G, Cui J, Liao B, Liu S, Aysola K, Yezdani M, Reddy ES & Rao VN 2001 c-Fos oncogene regulator Elk-1 interacts with BRCA1 splice variants BRCA1a/1b and enhances BRCA1a/1b-mediated growth suppression in breast cancer cells. Oncogene 20 1357–1367. (https://doi.org/10.1038/SJ.ONC.1204256)
Chen F, Wang Q, Yu X, Yang N, Wang Y, Zeng Y, Zheng Z, Zhou F & Zhou Y 2021 MCPIP1-mediated NFIC alternative splicing inhibits proliferation of triple-negative breast cancer via cyclin D1-Rb-E2F1 axis. Cell Death and Disease 12 370. (https://doi.org/10.1038/S41419-021-03661-4)
Cork DMW, Lennard TWJ & Tyson-Capper AJ 2008 Alternative splicing and the progesterone receptor in breast cancer. Breast Cancer Research 10 207. (https://doi.org/10.1186/BCR2097)
Davies MPA, Barraclough DL, Stewart C, Joyce KA, Eccles RM, Barraclough R, Rudland PS & Sibson DR 2008 Expression and splicing of the unfolded protein response gene XBP-1 are significantly associated with clinical outcome of endocrine-treated breast cancer. International Journal of Cancer 123 85–88. (https://doi.org/10.1002/IJC.23479)
Dawson LM, Smith KN, Werdyani S, Ndikumana R, Penney C, Wiede LL, Smith KL, Pater JA, MacMillan A & Green J et al.2020 A dominant RAD51C pathogenic splicing variant predisposes to breast and ovarian cancer in the Newfoundland population due to founder effect. Molecular Genetics and Genomic Medicine 8 e1070. (https://doi.org/10.1002/MGG3.1070)
del Rio-Moreno M, Alors-Perez E, Borges de Souza P, Prados-Gonzalez ME, Castaño JP, Luque RM & Gahete MD 2019 Peptides derived from the extracellular domain of the somatostatin receptor splicing variant SST5TMD4 increase malignancy in multiple cancer cell types. Translational Research 211 147–160. (https://doi.org/10.1016/j.trsl.2019.02.013)
del Río-Moreno M, Alors-Pérez E, González-Rubio S, Ferrín G, Reyes O, Rodríguez-Perálvarez M, Sánchez-Frías ME, Sánchez-Sánchez R, Ventura S & López-Miranda J et al.2019 Dysregulation of the splicing machinery is associated to the development of nonalcoholic fatty liver disease. Journal of Clinical Endocrinology and Metabolism 104 3389–3402. (https://doi.org/10.1210/jc.2019-00021)
del Río-Moreno M, Luque RM, Rangel-Zúñiga OA, Alors-Pérez E, Alcalá-Diaz JF, Roncero-Ramos I, Camargo A, Gahete MD, López-Miranda J & Castaño JP 2020 Dietary intervention modulates the expression of splicing machinery in cardiovascular patients at high risk of type 2 diabetes development: from the CORDIOPREV study. Nutrients 12 1–14. (https://doi.org/10.3390/NU12113528)
DeLigio JT, Lin G, Chalfant CE & Park MA 2017 Splice variants of cytosolic polyadenylation element-binding protein 2 (CPEB2) differentially regulate pathways linked to cancer metastasis. Journal of Biological Chemistry 292 17909–17918. (https://doi.org/10.1074/jbc.M117.810127)
DeLigio JT, Stevens SC, Nazario-Muñoz GS, MacKnight HP, Doe KK, Chalfant CE & Park MA 2019 Serine/arginine-rich splicing factor 3 modulates the alternative splicing of cytoplasmic polyadenylation element binding protein 2. Molecular Cancer Research 17 1920–1930. (https://doi.org/10.1158/1541-7786.MCR-18-1291)
Dery KJ, Gaur S, Gencheva M, Yen Y, Shively JE & Gaur RK 2011 Mechanistic control of carcinoembryonic antigen-related cell adhesion molecule-1 (CEACAM1) splice isoforms by the heterogeneous nuclear ribonuclear proteins hnRNP L, hnRNP A1, and hnRNP M. Journal of Biological Chemistry 286 16039–16051. (https://doi.org/10.1074/jbc.M110.204057)
Dery KJ, Kujawski M, Grunert D, Wu X, Ngyuen T, Cheung C, Yim JH & Shively JE 2014 IRF-1 regulates alternative mRNA splicing of carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) in breast epithelial cells generating an immunoreceptor tyrosine-based inhibition motif (ITIM) containing isoform. Molecular Cancer 13 64. (https://doi.org/10.1186/1476-4598-13-64)
DeSantis CE, Ma J, Gaudet MM, Newman LA, Miller KD, Goding Sauer A, Jemal A & Siegel RL 2019 Breast cancer statistics, 2019. CA: A Cancer Journal for Clinicians 69 438–451. (https://doi.org/10.3322/caac.21583)
di Modugno F, Iapicca P, Boudreau A, Mottolese M, Terrenato I, Perracchio L, Carstens RP, Santoni A, Bissell MJ & Nisticò P 2012 Splicing program of human MENA produces a previously undescribed isoform associated with invasive, mesenchymal-like breast tumors. PNAS 109 19280–19285. (https://doi.org/10.1073/PNAS.1214394109)
Dolfini D, Andrioletti V & Mantovani R 2019 Overexpression and alternative splicing of NF-YA in breast cancer. Scientific Reports 9 12955. (https://doi.org/10.1038/S41598-019-49297-5)
Dowhan DH, Harrison MJ, Eriksson NA, Bailey P, Pearen MA, Fuller PJ, Funder JW, Simpson ER, Leedman PJ & Tilley WD et al.2012 Protein arginine methyltransferase 6-dependent gene expression and splicing: association with breast cancer outcomes. Endocrine-Related Cancer 19 509–526. (https://doi.org/10.1530/ERC-12-0100)
Du JX, Liu YL, Zhu GQ, Luo YH, Chen C, Cai CZ, Zhang SJ, Wang B, Cai JL & Zhou J et al.2021a Profiles of alternative splicing landscape in breast cancer and their clinical significance: an integrative analysis based on large-sequencing data. Annals of Translational Medicine 9 58–58. (https://doi.org/10.21037/atm-20-7203)
Du JX, Luo YH, Zhang SJ, Wang B, Chen C, Zhu GQ, Zhu P, Cai CZ, Wan JL & Cai JL et al.2021b Splicing factor SRSF1 promotes breast cancer progression via oncogenic splice switching of PTPMT1. Journal of Experimental and Clinical Cancer Research 1 171. (https://doi.org/10.1186/S13046-021-01978-8)
Durán-Prado M, Saveanu A, Luque RM, Gahete MD, Gracia-Navarro F, Jaquet P, Dufour H, Malagón MM, Culler MD & Barlier A et al.2010 A potential inhibitory role for the new truncated variant of somatostatin receptor 5, sst5TMD4, in pituitary adenomas poorly responsive to somatostatin analogs. Journal of Clinical Endocrinology and Metabolism 95 2497–2502. (https://doi.org/10.1210/jc.2009-2247)
Durán-Prado M, Gahete MD, Hergueta-Redondo M, Martínez-Fuentes AJ, Córdoba-Chacón J, Palacios J, Gracia-Navarro F, Moreno-Bueno G, Malagón MM & Luque RM et al.2012 The new truncated somatostatin receptor variant sst5TMD4 is associated to poor prognosis in breast cancer and increases malignancy in MCF-7 cells. Oncogene 31 2049–2061. (https://doi.org/10.1038/onc.2011.389)
Forootan SS, Butler JM, Gardener D, Jones D, Baird AE, Dodson A, Darby A, Kenny J, Hall N, Cossins ARet al. 2016 Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications. International Journal of Oncology 48 130–144. (https://doi.org/10.3892/ijo.2015.3222)
Fu X, Tian M, Gu J, Cheng T, Ma D, Feng L, Xin X, Fu X, Tian M & Gu J 2017 SF3B1 mutation is a poor prognostic indicator in luminal B and progesterone receptor-negative breast cancer patients. Oncotarget 8 115018–115027. (https://doi.org/10.18632/ONCOTARGET.22983)
Fuentes-Fayos AC, Vazquez-Borrego MC, Jimenez-Vacas JM, Bejarano L, Pedraza-Arevalo S, Lopez FL, Blanco-Acevedo C, Sanchez-Sanchez R, Reyes O & Ventura S et al.2020 Splicing machinery dysregulation drives glioblastoma development/aggressiveness: oncogenic role of SRSF3. Brain 143 3273–3293. (https://doi.org/10.1093/BRAIN/AWAA273)
Fuentes‐Fayos AC, G-García ME, Pérez-Gómez JM, Peel A, Blanco-Acevedo C, Solivera J, Ibáñez-Costa A, Gahete MD, Castaño JP & Luque RM 2022 Somatostatin receptor splicing variant sst5TMD4 overexpression in glioblastoma is associated with poor survival, increased aggressiveness features, and somatostatin analogs resistance. International Journal of Molecular Sciences 23 1143. (https://doi.org/10.3390/IJMS23031143)
Gahete MD, Durán-Prado M, Luque RM, Martínez-Fuentes AJ, Vázquez-Martínez R, Malagón MM & Castaño JP 2008 Are somatostatin and cortistatin two siblings in regulating endocrine secretions? In vitro work ahead. Molecular and Cellular Endocrinology 286 128–134. (https://doi.org/10.1016/j.mce.2007.11.013)
Gahete MD, Córdoba-Chacón J, Hergueta-Redondo M, Martínez-Fuentes AJ, Kineman RD, Moreno-Bueno G, Luque RM & Castaño JP 2011 A novel human ghrelin variant (In1-ghrelin) and ghrelin-O-acyltransferase are overexpressed in breast cancer: potential pathophysiological relevance. PLoS ONE 6 e23302. (https://doi.org/10.1371/JOURNAL.PONE.0023302)
Gahete MD, Rincón-Fernández D, Villa-Osaba A, Hormaechea-Agulla D, Ibáñez-Costa A, Martínez-Fuentes AJ, Gracia-Navarro F, Castaño JP & Luque RM 2014 Ghrelin gene products, receptors, and goat enzyme: biological and pathophysiological insight. Journal of Endocrinology 220 R1–24. (https://doi.org/10.1530/JOE-13-0391)
Gahete MD, Rincón-Fernández D, Durán-Prado M, Hergueta-Redondo M, Ibáñez-Costa A, Rojo-Sebastián A, Gracia-Navarro F, Culler MD, Casanovas O & Moreno-Bueno G et al.2016 The truncated somatostatin receptor sst5TMD4 stimulates the angiogenic process and is associated to lymphatic metastasis and disease-free survival in breast cancer patients. Oncotarget 7 60110–60122. (https://doi.org/10.18632/ONCOTARGET.11076)
Gahete MD, del Rio-Moreno M, Camargo A, Alcala-Diaz JF, Alors-Perez E, Delgado-Lista J, Reyes O, Ventura S, Perez-Martínez P & Castaño JP et al.2018 Changes in splicing machinery components influence, precede, and early predict the development of type 2 diabetes: from the CORDIOPREV study. EBioMedicine 37 356–365. (https://doi.org/10.1016/J.EBIOM.2018.10.056)
Gaur S, Shively JE, Yen Y & Gaur RK 2008 Altered splicing of CEACAM1 in breast cancer: identification of regulatory sequences that control splicing of CEACAM1 into long or short cytoplasmic domain isoforms. Molecular Cancer 7 46. (https://doi.org/10.1186/1476-4598-7-46)
Gautrey HL & Tyson-Capper AJ 2012 Regulation of Mcl-1 by SRSF1 and SRSF5 in cancer cells. PLoS ONE 7 e51497. (https://doi.org/10.1371/JOURNAL.PONE.0051497)
Gautrey H, Jackson C, Dittrich AL, Browell D, Lennard T & Tyson-Capper A 2015 SRSF3 and hnRNP H1 regulate a splicing hotspot of HER2 in breast cancer cells. RNA Biology 12 1139–1151. (https://doi.org/10.1080/15476286.2015.1076610)
Goel HL, Gritsko T, Pursell B, Chang C, Shultz LD, Greiner DL, Norum JH, Toftgard R, Shaw LM & Mercurio AM 2014 Regulated splicing of the α6 integrin cytoplasmic domain determines the fate of breast cancer stem cells. Cell Reports 7 747–761. (https://doi.org/10.1016/j.celrep.2014.03.059)
Gökmen‐Polar Y, Neelamraju Y, Goswami CP, Gu Y, Gu X, Nallamothu G, Vieth E, Janga SC, Ryan M & Badve SS 2019 Splicing factor ESRP1 controls ER-positive breast cancer by altering metabolic pathways. EMBO Reports 20 e46078. (https://doi.org/10.15252/EMBR.201846078)
Gong C, Man EPS, Tsoi H, Lee TKW, Lee P, Ma ST, Wong LS, Luk MY, Rakha EA & Green AR et al.2018 BQ323636.1, a novel splice variant to NCOR 2, as a predictor for tamoxifen-resistant breast cancer. Clinical Cancer Research 24 3681–3691. (https://doi.org/10.1158/1078-0432.CCR-17-2259)
Gong S, Song Z, Spezia-Lindner D, Meng F, Ruan T, Ying G, Lai C, Wu Q & & Liang Y 2020 Novel insights into triple-negative breast cancer prognosis by comprehensive characterization of aberrant alternative splicing. Frontiers in Genetics 11 534. (https://doi.org/10.3389/fgene.2020.00534)
Gracio F, Burford B, Gazinska P, Mera A, Mohd Noor A, Marra P, Gillett C, Grigoriadis A, Pinder S, Tutt A & & de Rinaldis E 2017 Splicing imbalances in basal-like breast cancer underpin perturbation of cell surface and oncogenic pathways and are associated with patients' survival. Science Reports 7 40177. (https://doi.org/10.1038/srep40177)
Grismayer B, Sato S, Kopitz C, Ries C, Soelch S, Schmitt M, Baretton G, Kruger A, Luther T & Kotzsch M et al.2012 Overexpression of the urokinase receptor splice variant uPAR-del4/5 in breast cancer cells affects cell adhesion and invasion in a dose-dependent manner and modulates transcription of tumor-associated genes. Biological Chemistry 393 1449–1455. (https://doi.org/10.1515/hsz-2012-0206)
Haldosén LA, Zhao C & Dahlman-Wright K 2014 Estrogen receptor beta in breast cancer. Molecular and Cellular Endocrinology 382 665–672. (https://doi.org/10.1016/J.MCE.2013.08.005)
Hammond ME, Hayes DF & Wolff AC 2011 Clinical notice for American Society of Clinical Oncology-College of American Pathologists guideline recommendations on ER/PgR and HER2 testing in breast cancer. Journal of Clinical Oncology 29 e458. (https://doi.org/10.1200/JCO.2011.35.2245)
Han P, Zhu J, Feng G, Wang Z & Ding Y 2021 Characterization of alternative splicing events and prognostic signatures in breast cancer. BMC Cancer 21 587. (https://doi.org/10.1186/S12885-021-08305-6)
Hart V, Gautrey H, Kirby J & Tyson-Capper A 2020 HER2 splice variants in breast cancer: investigating their impact on diagnosis and treatment outcomes. Oncotarget 11 4338–4357. (https://doi.org/10.18632/ONCOTARGET.27789)
Hart V, Silipo M, Satam S, Gautrey H, Kirby J & Tyson-Capper A 2021 HER2-PI9 and HER2-I12: two novel and functionally active splice variants of the oncogene HER2 in breast cancer. Journal of Cancer Research and Clinical Oncology 147 2893–2912. (https://doi.org/10.1007/S00432-021-03689-1)
Harvey SE, Xu Y, Lin X, Gao XD, Qiu Y, Ahn J, Xiao X & Cheng C 2018 Coregulation of alternative splicing by hnRNPM and ESRP1 during EMT. RNA 24 1326–1338. (https://doi.org/10.1261/RNA.066712.118)
Hauser AD, Bergom C, Schuld NJ, Chen X, Lorimer EL, Huang J, Mackinnon AC & Williams CL 2014 The SmgGDS splice variant SmgGDS-558 is a key promoter of tumor growth and RhoA signaling in breast cancer. Molecular Cancer Research 12 130–142. (https://doi.org/10.1158/1541-7786.MCR-13-0362)
Hirschfeld M, Hausen zur A, Bettendorf H, Jäger M & Stickeier E 2009 Alternative splicing of Cyr61 is regulated by hypoxia and significantly changed in breast cancer. Cancer Research 69 2082–2090. (https://doi.org/10.1158/0008-5472.CAN-08-1997)
Hoersch S & Andrade-Navarro MA 2010 Periostin shows increased evolutionary plasticity in its alternatively spliced region. BMC Evolutionary Biology 10 30. (https://doi.org/10.1186/1471-2148-10-30)
Hormaechea-Agulla D, Jiménez-Vacas JM, Gómez-Gómez E, López FL, Carrasco-Valiente J, Valero-Rosa J, Moreno MM, Sánchez-Sánchez R, Ortega-Salas R & Gracia-Navarro F et al.2017a The oncogenic role of the spliced somatostatin receptor sst5TMD4 variant in prostate cancer. FASEB Journal 31 4682–4696. (https://doi.org/10.1096/fj.201601264RRR)
Hormaechea-Agulla D, Gahete M, Jiménez-Vacas J, Gómez-Gómez E, Ibáñez-Costa A, L-López F, Rivero-Cortés E, Sarmento-Cabral A, Valero-Rosa J & Carrasco-Valiente J et al.2017b The oncogenic role of the In1-ghrelin splicing variant in prostate cancer aggressiveness. Molecular Cancer 16 146. (https://doi.org/10.1186/S12943-017-0713-9)
Hu DG, Hickey TE, Irvine C, Wijayakumara DD, Lu L, Tilley WD, Selth LA & Mackenzie PI 2014 Identification of androgen receptor splice variant transcripts in breast cancer cell lines and human tissues. Hormones and Cancer 5 61–71. (https://doi.org/10.1007/S12672-014-0171-4)
Hu R, Warri A, Jin L, Zwart A, Riggins RB, Fang HB & Clarke R 2015 NF-κB signaling is required for XBP1 (unspliced and spliced)-mediated effects on antiestrogen responsiveness and cell fate decisions in breast cancer. Molecular and Cellular Biology 35 379–390. (https://doi.org/10.1128/MCB.00847-14)
Hu DG, McKinnon RA, Hulin JA, Mackenzie PI & Meech R 2016 Novel nine-exon AR transcripts (exon 1/exon 1b/exons 2–8) in normal and cancerous breast and prostate cells. International Journal of Molecular Sciences 18 40. (https://doi.org/10.3390/IJMS18010040)
Hu Y, Sun Z, Deng J, Hu B, Yan W, Wei H & Jiang J 2017 Splicing factor hnRNPA2B1 contributes to tumorigenic potential of breast cancer cells through STAT3 and ERK1/2 signaling pathway. Tumour Biology 39 1010428317694318. (https://doi.org/10.1177/1010428317694318)
Huang CS, Shen CY, Wang HW, Wu PE & Cheng CW 2007 Increased expression of SRp40 affecting CD44 splicing is associated with the clinical outcome of lymph node metastasis in human breast cancer. Clinica Chimica Acta: International Journal of Clinical Chemistry 384 69–74. (https://doi.org/10.1016/J.CCA.2007.06.001)
Huang G, Song C, Wang N, Qin T, Sui S, Obr A, Zeng L, Wood TL, Leroith D & Li M et al.2020 RNA-binding protein CUGBP1 controls the differential INSR splicing in molecular subtypes of breast cancer cells and affects cell aggressiveness. Carcinogenesis 41 1294–1305. (https://doi.org/10.1093/CARCIN/BGZ141)
Hube F, Guo J, Chooniedass-Kothari S, Cooper C, Hamedani MK, Dibrov AA, Blanchard AAA, Wang X, Deng G & Myal Y et al.2006 Alternative splicing of the first intron of the steroid receptor RNA activator (SRA) participates in the generation of coding and noncoding RNA isoforms in breast cancer cell lines. DNA and Cell Biology 25 418–428. (https://doi.org/10.1089/DNA.2006.25.418)
Huber LJ, Yang TW, Sarkisian CJ, Master SR, Deng CX & Chodosh LA 2001 Impaired DNA damage response in cells expressing an exon 11-deleted murine BRCA1 variant that localizes to nuclear foci. Molecular and Cellular Biology 21 4005–4015. (https://doi.org/10.1128/MCB.21.12.4005-4015.2001)
Huun J, Gansmo LB, Mannsåker B, Iversen GT, Øvrebø JI, Lønning PE & Knappskog S 2017a Impact of the MDM2 splice-variants MDM2-A, MDM2-B and MDM2-C on cytotoxic stress response in breast cancer cells. BMC Cell Biology 18 17. (https://doi.org/10.1186/S12860-017-0134-Z)
Huun J, Gansmo LB, Mannsåker B, Iversen GT, Sommerfelt-Pettersen J, Øvrebø JI, Lønning PE & Knappskog S 2017b The functional roles of the MDM2 splice variants P2-MDM2-10 and MDM2-∆5 in breast cancer cells. Translational Oncology 10 806–817. (https://doi.org/10.1016/J.TRANON.2017.07.006)
Ibáñez-Costa A, Córdoba-Chacón J, Gahete MD, Kineman RD, Castaño JP & Luque RM 2015 Melatonin regulates somatotrope and lactotrope function through common and distinct signaling pathways in cultured primary pituitary cells from female primates. Endocrinology 156 1100–1110. (https://doi.org/10.1210/en.2014-1819)
Ibáñez-Costa A, Perez-Sanchez C, Patiño-Trives AM, Luque-Tevar M, Font P, Arias de la Rosa I, Roman-Rodriguez C, Abalos-Aguilera MC, Conde C & Gonzalez A et al.2022 Splicing machinery is impaired in rheumatoid arthritis, associated with disease activity and modulated by anti-TNF therapy. Annals of the Rheumatic Diseases 81 56–67. (https://doi.org/10.1136/ANNRHEUMDIS-2021-220308)
Inoue K & Fry EA 2015 Aberrant splicing of estrogen receptor, HER2, and CD44 genes in breast cancer. Genetics and Epigenetics 7 19–32. (https://doi.org/10.4137/GEG.S35500)
Iwao K, Miyoshi Y, Egawa C, Ikeda N, Tsukamoto F & Noguchi S 2000 Quantitative analysis of estrogen receptor-alpha and -beta messenger RNA expression in breast carcinoma by real-time polymerase chain reaction. Cancer 89 1732–1738. (https://doi.org/10.1002/1097-0142(20001015)89:8<1732::AID-CNCR13>3.0.CO;2-2)
Jackson C, Browell D, Gautrey H & Tyson-Capper A 2013 Clinical significance of HER-2 splice variants in breast cancer progression and drug resistance. International Journal of Cell Biology 2013 973584. (https://doi.org/10.1155/2013/973584)
Jiménez-Vacas JM, Herrero-Aguayo V, Gómez-Gómez E, León-González AJ, Sáez-Martínez P, Alors-Pérez E, Fuentes-Fayos AC, Martínez-López A, Sánchez-Sánchez R & González-Serrano T et al.2019 Spliceosome component SF3B1 as novel prognostic biomarker and therapeutic target for prostate cancer. Translational Research 212 89–103. (https://doi.org/10.1016/J.TRSL.2019.07.001)
Jiménez-Vacas JM, Herrero-Aguayo V, Montero-Hidalgo AJ, Gómez-Gómez E, Fuentes-Fayos AC, León-González AJ, Sáez-Martínez P, Alors-Pérez E, Pedraza-Arévalo S & González-Serrano T et al.2020 Dysregulation of the splicing machinery is directly associated to aggressiveness of prostate cancer. EBioMedicine 51 102547. (https://doi.org/10.1016/J.EBIOM.2019.11.008)
Jiménez-Vacas JM, Montero-Hidalgo AJ, Gómez-Gómez E, Fuentes-Fayos AC, Ruiz-Pino F, Guler I, Camargo A, Anglada FJ, Carrasco-Valiente J & Tena-Sempere M et al.2021 In1-Ghrelin splicing variant as a key element in the pathophysiological association between obesity and prostate cancer. Journal of Clinical Endocrinology and Metabolism 106 e4956–e4968. (https://doi.org/10.1210/CLINEM/DGAB516)
Johnson RM, Vu NT, Griffin BP, Gentry AE, Archer KJ, Chalfant CE & Park MA 2015 The alternative splicing of cytoplasmic polyadenylation element binding protein 2 drives anoikis resistance and the metastasis of triple negative breast cancer. Journal of Biological Chemistry 290 25717–25727. (https://doi.org/10.1074/jbc.M115.671206)
Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C & GR et al.2018 Comprehensive analysis of alternative splicing across tumors from 8705 patients. Cancer Cell 34 211 .e6–224.e6. (https://doi.org/10.1016/J.CCELL.2018.07.001)
Karni R, Stanchina de E, Lowe SW, Sinha R, Mu D & Krainer AR 2007 The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nature Structural and Molecular Biology 14 185–193. (https://doi.org/10.1038/nsmb1209)
Klinge CM, Riggs KA, Wickramasinghe NS, Emberts CG, McConda DB, Barry PN & Magnusen JE 2010 Estrogen receptor alpha 46 is reduced in tamoxifen resistant breast cancer cells and re-expression inhibits cell proliferation and estrogen receptor alpha 66-regulated target gene transcription. Molecular and Cellular Endocrinology 323 268–276. (https://doi.org/10.1016/J.MCE.2010.03.013)
Kornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E & Muñoz MJ 2013 Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nature Reviews: Molecular Cell Biology 14 153–165. (https://doi.org/10.1038/NRM3525)
Lal S, Allan A, Markovic D, Walker R, Macartney J, Europe-Finner N, Tyson-Capper A & Grammatopoulos DK 2013 Estrogen alters the splicing of type 1 corticotropin-releasing hormone receptor in breast cancer cells. Science Signaling 6 ra53. (https://doi.org/10.1126/SCISIGNAL.2003926)
Lerebours F, Vacher S, Guinebretiere JM, Rondeau S, Caly M, Gentien D, Van Laere S, Bertucci F, de la Grange P, Bièche Let al. 2020 Hemoglobin overexpression and splice signature as new features of inflammatory breast cancer? Journal of Advanced Research 28 77–85. (https://doi.org/10.1016/j.jare.2020.08.009)
Li J, Choi PS, Chaffer CL, Labella K, Hwang JH, Giacomelli AO, Kim JW, Ilic N, Doench JG & Ly SH et al.2018 An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer. eLife 7 e37184. (https://doi.org/10.7554/eLife.37184)
Li X, Wang Y, Li B & & Ma W 2020 Prognostic value and potential regulatory mechanism of alternative splicing in geriatric breast cancer. Genes 11 200. (https://doi.org/10.3390/genes11020200)
Lin JC, Lin CY, Tarn WY & Li FY 2014 Elevated SRPK1 lessens apoptosis in breast cancer cells through RBM4-regulated splicing events. RNA 20 1621–1631. (https://doi.org/10.1261/RNA.045583.114)
Liu Q, Wang X, Kong X, Yang X, Cheng R, Zhang W, Gao P, Chen L, Wang Z, Fang Y & & Wang J 2020 Prognostic alternative mRNA splicing signature and a novel biomarker in triple-negative breast cancer. DNA and Cell Biology 39 1051–1063. (https://doi.org/10.1089/dna.2020.5460)
Liu Z, Sun L, Cai Y, Shen S, Zhang T, Wang N, Wu G, Ma W, Li ST & Suo C et al.2021 Hypoxia-induced suppression of alternative splicing of MBD2 promotes breast cancer metastasis via activation of FZD1. Cancer Research 81 1265–1278. (https://doi.org/10.1158/0008-5472.CAN-20-2876)
Lixia M, Zhijian C, Chao S, Chaojiang G & Congyi Z 2007 Alternative splicing of breast cancer associated gene BRCA1 from breast cancer cell line. Journal of Biochemistry and Molecular Biology 40 15–21. (https://doi.org/10.5483/BMBREP.2007.40.1.015)
Loh TJ, Moon H, Cho S, Jang H, Liu YC, Tai H, Jung DW, Williams DR, Kim HR & Shin MG et al.2015 CD44 alternative splicing and hnRNP A1 expression are associated with the metastasis of breast cancer. Oncology Reports 34 1231–1238. (https://doi.org/10.3892/OR.2015.4110)
Loibl S, Poortmans P, Morrow M, Denkert C & Curigliano G 2021 Breast cancer. Lancet 397 1750–1769. (https://doi.org/10.1016/S0140-6736(2032381-3)
López-Cánovas JL, del Rio-Moreno M, García-Fernandez H, Jiménez-Vacas JM, Moreno-Montilla MT, Sánchez-Frias ME, Amado V, L-López F, Fondevila MF & Ciria R et al.2021 Splicing factor SF3B1 is overexpressed and implicated in the aggressiveness and survival of hepatocellular carcinoma. Cancer Letters 496 72–83. (https://doi.org/10.1016/J.CANLET.2020.10.010)
Luque RM, Ibáñez-Costa A, Neto LV, Taboada GF, Hormaechea-Agulla D, Kasuki L, Venegas-Moreno E, Moreno-Carazo A, Gálvez MÁ & Soto-Moreno A et al.2015a Truncated somatostatin receptor variant sst5TMD4 confers aggressive features (proliferation, invasion and reduced octreotide response) to somatotropinomas. Cancer Letters 359 299–306. (https://doi.org/10.1016/j.canlet.2015.01.037)
Luque RM, Sampedro-Nuñez M, Gahete MD, Ramos-Levi A, Ibáñez-Costa A, Rivero-Cortés E, Serrano-Somavilla A, Adrados M, Culler MD & Castaño JP et al.2015b In1-ghrelin, a splice variant of ghrelin gene, is associated with the evolution and aggressiveness of human neuroendocrine tumors: evidence from clinical, cellular and molecular parameters. Oncotarget 6 19619–19633. (https://doi.org/10.18632/ONCOTARGET.4316)
Maglic D, Stovall DB, Cline JM, Fry EA, Mallakin A, Taneja P, Caudell DL, Willingham MC, Sui G & Inoue K 2015 DMP1β, a splice isoform of the tumour suppressor DMP1 locus, induces proliferation and progression of breast cancer. Journal of Pathology 236 90–102. (https://doi.org/10.1002/PATH.4504)
Maguire SL, Leonidou A, Wai P, Marchiò C, Ng CK, Sapino A, Salomon AV, Reis-Filho JS, Weigelt B & Natrajan RC 2015 SF3B1 mutations constitute a novel therapeutic target in breast cancer. Journal of Pathology 235 571–580. (https://doi.org/10.1002/PATH.4483)
Martínez-Montiel N, Anaya-Ruiz M, Pérez-Santos M & Martínez-Contreras RD 2017 Alternative splicing in breast cancer and the potential development of therapeutic tools. Genes 8 217. (https://doi.org/10.3390/GENES8100217)
Matera AG & Wang Z 2014 A day in the life of the spliceosome. Nature Reviews: Molecular Cell Biology 15 108–121. (https://doi.org/10.1038/NRM3742)
Matsumoto Y, Itou J, Sato F & Toi M 2018 SALL4 - KHDRBS3 network enhances stemness by modulating CD44 splicing in basal-like breast cancer. Cancer Medicine 7 454–462. (https://doi.org/10.1002/CAM4.1296)
Miller J, Dreyer TF, Benge AS, Sinner EK, Heinrich C, Benge A, Gross E, Preis S, Rother J & Roberts A et al.2018 Differential tumor biological role of the tumor suppressor KAI1 and its splice variant in human breast cancer cells. Oncotarget 9 6369–6390. (https://doi.org/10.18632/ONCOTARGET.23968)
Ming J, Ruan S, Wang M, Ye D, Fan N, Meng Q, Tian B & Huang T 2015 A novel chemical, STF-083010, reverses tamoxifen-related drug resistance in breast cancer by inhibiting IRE1/XBP1. Oncotarget 6 40692–40703. (https://doi.org/10.18632/ONCOTARGET.5827)
Moffa AB & Ethier SP 2007 Differential signal transduction of alternatively spliced FGFR2 variants expressed in human mammary epithelial cells. Journal of Cellular Physiology 210 720–731. (https://doi.org/10.1002/jcp.20880)
Nagao K, Kohno N, Wakita K, Hikiji K, Yamamoto S, Hirata H & Hisatomi H 2003 Expression of a novel splicing variant deleting exons 4 and 6 of the progesterone receptor gene is a rare event in breast cancer. Oncology Reports 10 305–308. (https://doi.org/10.3892/OR.10.2.305/HTML)
Neeli PK, Gollavilli PN, Mallappa S, Hari SG & Kotamraju S 2020 A novel metadherinΔ7 splice variant enhances triple negative breast cancer aggressiveness by modulating mitochondrial function via NFĸB-SIRT3 axis. Oncogene 39 2088–2102. (https://doi.org/10.1038/S41388-019-1126-6)
Nielsen FC, van Overeem Hansen T & Sørensen CS 2016 Hereditary breast and ovarian cancer: new genes in confined pathways. Nature Reviews: Cancer 16 599–612. (https://doi.org/10.1038/nrc.2016.72)
Oh J, Pradella D, Shao C, Li H, Choi N, Ha J, Ruggiero S, Fu XD, Zheng X & Ghigna C et al.2021 Widespread alternative splicing changes in metastatic breast cancer cells. Cells 10 858. (https://doi.org/10.3390/CELLS10040858)
Orban TI & Olah E 2003 Emerging roles of BRCA1 alternative splicing. Molecular Pathology 56 191–197. (https://doi.org/10.1136/MP.56.4.191)
Pan D, Liu B, Jin X & Zhu J 2012 IL-7 splicing variant IL-7δ5 induces human breast cancer cell proliferation via activation of PI3K/Akt pathway. Biochemical and Biophysical Research Communications 422 727–731. (https://doi.org/10.1016/J.BBRC.2012.05.070)
Pani T, Rajput K, Kar A, Sharma H, Basak R, Medatwal N, Saha S, Dev G, Kumar S & Gupta S et al.2021 Alternative splicing of ceramide synthase 2 alters levels of specific ceramides and modulates cancer cell proliferation and migration in luminal B breast cancer subtype. Cell Death and Disease 12 171. (https://doi.org/10.1038/S41419-021-03436-X)
Papanastasiou AD, Sirinian C & Kalofonos HP 2012 Identification of novel human receptor activator of nuclear factor-kB isoforms generated through alternative splicing: implications in breast cancer cell survival and migration. Breast Cancer Research 14 R112. (https://doi.org/10.1186/BCR3234)
Pentheroudakis G, Kotoula V, Kouvatseas G, Charalambous E, Dionysopoulos D, Zagouri F, Koutras A, Papazisis K, Pectasides D & Samantas E et al.2014 Association of VEGF-A splice variant mRNA expression with outcome in bevacizumab-treated patients with metastatic breast cancer. Clinical Breast Cancer 14 330–338. (https://doi.org/10.1016/J.CLBC.2014.02.009)
Piqué L, Martinez de Paz A, Piñeyro D, Martínez-Cardús A, Castro de Moura M, Llinàs-Arias P, Setien F, Gomez-Miragaya J, Gonzalez-Suarez E & Sigurdsson S et al.2019 Epigenetic inactivation of the splicing RNA-binding protein CELF2 in human breast cancer. Oncogene 38 7106–7112. (https://doi.org/10.1038/S41388-019-0936-X)
Pucci S, Polidoro C, Greggi C, Amati F, Morini E, Murdocca M, Biancolella M, Orlandi A, Sangiuolo F & Novelli G 2019 Pro-oncogenic action of LOX-1 and its splice variant LOX-1Δ4 in breast cancer phenotypes. Cell Death and Disease 10 53. (https://doi.org/10.1038/S41419-018-1279-1)
Puig-Domingo M, Luque RM, Reverter JL, López-Sánchez LM, Gahete MD, Culler MD, Díaz-Soto G, Lomeña F, Squarcia M & Mate JL et al.2014 The truncated isoform of somatostatin receptor5 (sst5TMD4) is associated with poorly differentiated thyroid cancer. PLoS ONE 9 e85527. (https://doi.org/10.1371/journal.pone.0085527)
Qiu Y, Lyu J, Dunlap M, Harvey SE & & Cheng C 2020 A combinatorially regulated RNA splicing signature predicts breast cancer EMT states and patient survival. RNA 26 1257–1267. (https://doi.org/10.1261/rna.074187.119)
Rajapaksa G, Thomas C & Gustafsson JÅ 2016 Estrogen signaling and unfolded protein response in breast cancer. Journal of Steroid Biochemistry and Molecular Biology 163 45–50. (https://doi.org/10.1016/J.JSBMB.2016.03.036)
Read A & Natrajan R 2018 Splicing dysregulation as a driver of breast cancer. Endocrine-Related Cancer 25 R467–R478. (https://doi.org/10.1530/ERC-18-0068)
Rezania S, Kammerer S, Li C, Steinecker-Frohnwieser B, Gorischek A, DeVaney TTJ, Verheyen S, Passegger CA, Tabrizi-Wizsy NG & Hackl H et al.2016 Overexpression of KCNJ3 gene splice variants affects vital parameters of the malignant breast cancer cell line MCF-7 in an opposing manner. BMC Cancer 16 628. (https://doi.org/10.1186/S12885-016-2664-8)
Rha SY, Jeung HC, Park KH, Kim JJ & Chung HC 2009 Changes of telomerase activity by alternative splicing of full-length and beta variants of hTERT in breast cancer patients. Oncology Research 18 213–220. (https://doi.org/10.3727/096504009X12596189659123)
Rincón-Fernández D, Culler MD, Tsomaia N, Moreno-Bueno G, Luque RM, Gahete MD & Castaño JP 2018 In1-ghrelin splicing variant is associated with reduced disease-free survival of breast cancer patients and increases malignancy of breast cancer cells lines. Carcinogenesis 39 447–457. (https://doi.org/10.1093/carcin/bgx146)
Ryan B, O’Donovan N, Browne B, O’Shea C, Crown J, Hill ADK, McDermott E, O’Higgins N & Duffy MJ 2005 Expression of survivin and its splice variants survivin-2B and survivin-DeltaEx3 in breast cancer. British Journal of Cancer 92 120–124. (https://doi.org/10.1038/SJ.BJC.6602314)
Sampedro-Núñez M, Luque RM, Ramos-Levi AM, Gahete MD, Serrano-Somavilla A, Villa-Osaba A, Adrados M, Ibáñez-Costa A, Martín-Pérez E & Culler MD et al.2016 Presence of sst5TMD4, a truncated splice variant of the somatostatin receptor subtype 5, is associated to features of increased aggressiveness in pancreatic neuroendocrine tumors. Oncotarget 7 6593–6608. (https://doi.org/10.18632/oncotarget.6565)
Sanoguera-Miralles L, Valenzuela-Palomo A, Bueno-Martínez E, Llovet P, Díez-Gómez B, Caloca MJ, Pérez-Segura P, Fraile-Bethencourt E, Colmena M & Carvalho S et al.2020 Comprehensive functional characterization and clinical interpretation of 20 splice-site variants of the RAD51C gene. Cancers 12 1–21. (https://doi.org/10.3390/CANCERS12123771)
Schuld NJ, Hauser AD, Gastonguay AJ, Wilson JM, Lorimer EL & Williams CL 2014 SmgGDS-558 regulates the cell cycle in pancreatic, non-small cell lung, and breast cancers. Cell Cycle 13 941–952. (https://doi.org/10.4161/CC.27804)
Schütze A, Vogeley C, Gorges T, Twarock S, Butschan J, Babayan A, Klein D, Knauer SK, Metzen E & Müller V et al.2016 RHAMM splice variants confer radiosensitivity in human breast cancer cell lines. Oncotarget 7 21428–21440. (https://doi.org/10.18632/ONCOTARGET.7258)
Sellitto A, D’agostino Y, Alexandrova E, Lamberti J, Pecoraro G, Memoli D, Rocco D, Coviello E, Giurato G & Nassa G et al.2020 Insights into the role of estrogen receptor β in triple-negative breast cancer. Cancers 12 1477. (https://doi.org/10.3390/CANCERS12061477)