Splicing factor 3b subunit 1 (SF3B1) was frequently reported to be significantly mutated in breast cancer. However, the status of SF3B1 expression, its function and molecular consequence in breast cancer remained unreported.
Immunohistochemistry was used to assess SF3B1expression in 110 breast cancer samples. SF3B1 knock‑down in ZR-75-30 and MDA-MB-231 cells was performed by shRNA transfection. The expression of SF3B1 in cells was detected by quantitative real‑time PCR and western blot. Cell proliferation ability was determined by MTT and colony formation assay. Migration and invasion were determined by transwell assay. Flow cytometry was performed to investigate cell cycle and apoptosis. RNA-sequencing was performed to examine differentially expressed genes and affected alternative splicing events.
SF3B1 is overexpressed in breast cancer tissues compared with normal tissues. Overexpression of SF3B1 is associated with lymph node metastasis. SF3B1 knockdown in MDA-MB-231 and ZR-75-30 breast cancer cells significantly induced the suppression of proliferation, migration, invasion and also enhancement of apoptosis. RNA-sequencing data revealed that 860 genes were significantly up-regulated and 776 genes were significantly down-regulated upon SF3B1 knockdown. Differentially expressed genes enriched in the signaling pathways including Ras signaling pathway; cytokine receptor interaction; tight junction; MAPK signaling pathway, Glycine, serine and threonine metabolism. Alternative splicing analysis revealed that exon skipping (SKIP) and cassette exons (MSKIP) were the most common molecular effect upon SF3B1 knockdown.
Our study suggests that SF3B1 may be an important molecular target for breast cancer treatment and provides a new clue for clinical treatment of breast cancer.
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El Marabti E, Younis I. The cancer spliceome: reprograming of alternative splicing in cancer. Front Mol Biosci. 2018;5:80.
Slansky JE, Spellman PT. Alternative splicing in tumors-a path to immunogenicity? N Engl J Med. 2019;380:877–80.
Maguire SL, Leonidou A, Wai P, Marchiò C, Ng CK, Sapino A, et al. SF3B1 mutations constitute a novel therapeutic target in breast cancer. J Pathol. 2015;235:571–80.
Newell F, Kong Y, Wilmott JS, Johansson PA, Ferguson PM, Cui C, et al. Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets. Nat Commun. 2019;10:3163.
Jiménez-Vacas JM, Herrero-Aguayo V, Gómez-Gómez E, León-González AJ, Sáez-Martínez P, Alors-Pérez E, et al. Spliceosome component SF3B1 as novel prognostic biomarker and therapeutic target for prostate cancer. Transl Res. 2019;S1931–5244:30134–43.
Wang L, Lawrence MS, Wan Y, Stojanov P, Sougnez C, Stevenson K, et al. SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med. 2011;365:2497–506.
Chang YS, Huang HD, Yeh KT, Chang JG. Genetic alterations in endometrial cancer by targeted next-generation sequencing. Exp Mol Pathol. 2016;100:8–12.
Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature. 2014;505:495–501.
Network CGA. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490:61–70.
Effenberger KA, Urabe VK, Prichard BE, Ghosh AK, Jurica MS. Interchangeable SF3B1 inhibitors interfere with pre-mRNA splicing at multiple stages. RNA. 2016;22:350–9.
Paolella BR, Gibson WJ, Urbanski LM, Alberta JA, Zack TI, Bandopadhayay P, et al. Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. Elife. 2017;6:e23268.
Mortera-Blanco T, Dimitriou M, Woll PS, Karimi M, Elvarsdottir E, Conte S, et al. SF3B1-initiating mutations in MDS-RSs target lymphomyeloid hematopoietic stem cells. Blood. 2017;130:881–90.
Zhang L, Zhou Y, Cheng C, Cui H, Cheng L, Kong P, et al. Genomic analyses reveal mutational signatures and frequently altered genes in esophageal squamous cell carcinoma. Am J Hum Genet. 2015;96:597–611.
Gökmen-Polar Y, Neelamraju Y, Goswami CP, Gu X, Nallamothu G, Janga SC, et al. Expression levels of SF3B3 correlate with prognosis and endocrine resistance in estrogen receptor-positive breast cancer. Mod Pathol. 2015;28:677–85.
Guo S, Yang J, Wu M, Xiao G. Clinical value screening, prognostic significance and key pathway identification of miR-204-5p in endometrial carcinoma: A study based on the Cancer Genome Atlas (TCGA), and bioinformatics analysis. Pathol Res Pract. 2019;215:1003–111.
Hwang HM, Heo CK, Lee HJ, Kwak SS, Lim WH, Yoo JS, et al. Identification of anti-SF3B1 autoantibody as a diagnostic marker in patients with hepatocellular carcinoma. J Transl Med. 2018;16:177.
Ohashi R, Schraml P, Batavia A, Angori S, Simmler P, Rupp N, et al. Allele loss and reduced expression of CYCLOPS genes is a characteristic feature of chromophobe renal cell carcinoma. Transl Oncol. 2019;12:1131–7.
Neelamraju Y, Gonzalez-Perez A, Bhat-Nakshatri P, Nakshatri H, Janga SC. Mutational landscape of RNA-binding proteins in human cancers. RNA Biol. 2018;15:115–29.
Dalton WB, Helmenstine E, Walsh N, Gondek LP, Kelkar DS, Read A, et al. Hotspot SF3B1 mutations induce metabolic reprogramming and vulnerability to serine deprivation. J Clin Invest. 2019;130:4708–23.
Samanta D, Semenza GL. Serine synthesis helps hypoxic cancer stem cells regulate redox. Cancer Res. 2016;76:6458–62.
Zhang X, Bai W. Repression of phosphoglycerate dehydrogenase sensitizes triple-negative breast cancer to doxorubicin. Cancer Chemother Pharmacol. 2016;78:655–9.
DeBoever C, Ghia EM, Shepard PJ, Rassenti L, Barrett CL, Jepsen K, et al. Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers. PLoS Comput Biol. 2015;11:e1004105.
Alsafadi S, Houy A, Battistella A, Popova T, Wassef M, Henry E. Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage. Nat Commun. 2016;7:10615.
Wu G, Fan L, Edmonson MN, Shaw T, Boggs K, Easton J, et al. Inhibition of SF3B1 by molecules targeting the spliceosome results in massive aberrant exon skipping. RNA. 2018;24:1056–66.
Yoshimoto R, Kaida D, Furuno M, Burroughs AM, Noma S, Suzuki H, et al. Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A. RNA. 2017;23:47–57.
Sciarrillo R, Wojtuszkiewicz A, El Hassouni B, Funel N, Gandellini P, Lagerweij T, et al. Splicing modulation as novel therapeutic strategy against diffuse malignant peritoneal mesothelioma. EBioMedicine. 2019;39:215–25.
Iwata M, Ozawa Y, Uenaka T, Shimizu H, Niijima J, et al. E7107, a new 7-urethane derivative of pladienolide D, displays curative effect against several human tumor xenografts [abstract 2989]. Proc Am Assoc Cancer Res. 2004;45:691.
Eskens FA, Ramos FJ, Burger H, O'Brien JP, Piera A, Piera A, et al. Phase I pharmacokinetic and pharmacodynamic study of the first-in-class spliceosome inhibitor E7107 in patients with advanced solid tumors. Clin Cancer Res. 2013;19:6296–304.
Desterro J, Bak-Gordon P, Carmo-Fonseca M. Targeting mRNA processing as an anticancer strategy. Nat Rev Drug Discov. 2019. https://doi.org/10.1038/s41573-019-0042-3.
This work was supported by funding from the National Natural Science Foundation of China (81773150 to LZ.), Natural Science Foundation of Shanxi Province (201801D121339 to JL.), the Program for the Outstanding Innovative Teams of Higher Learning Institutions of Shanxi (OIT 2017 to LZ.), the Doctoral Start up Research Fund of Shanxi Medical University (03201508 to LZ.).
Conflict of interest
The authors declare no conflict of interest.
The present study was approved by the Ethics Committee of the Shanxi Medical University (approval No. 2018LL0115) and was conducted in accordance with the ethical standards. All procedures performed in studies involving human participants were in accordance the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration.
Informed consent was obtained from all individual participants included in this study.
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Zhang, L., Zhang, X., Zhang, H. et al. Knockdown of SF3B1 inhibits cell proliferation, invasion and migration triggering apoptosis in breast cancer via aberrant splicing. Breast Cancer (2020). https://doi.org/10.1007/s12282-020-01045-8
- Breast cancer