CRISPR screens in 3D tumourspheres identified miR-4787-3p as a transcriptional start site miRNA essential for breast tumour-initiating cell growth.
Humans
MicroRNAs
/ genetics
Breast Neoplasms
/ genetics
Female
Gene Expression Regulation, Neoplastic
Transcription Initiation Site
Neoplastic Stem Cells
/ metabolism
Cell Proliferation
/ genetics
Cell Line, Tumor
Ribonuclease III
/ genetics
Clustered Regularly Interspaced Short Palindromic Repeats
Spheroids, Cellular
/ pathology
DEAD-box RNA Helicases
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
13 Jul 2024
13 Jul 2024
Historique:
received:
07
12
2023
accepted:
04
07
2024
medline:
14
7
2024
pubmed:
14
7
2024
entrez:
13
7
2024
Statut:
epublish
Résumé
Our study employs pooled CRISPR screens, integrating 2D and 3D culture models, to identify miRNAs critical in Breast Cancer (BC) tumoursphere formation. These screens combine with RNA-seq experiments allowing identification of miRNA signatures and targets essential for tumoursphere growth. miR-4787-3p exhibits significant up-regulation in BC, particularly in basal-like BCs, suggesting its association with aggressive disease. Surprisingly, despite its location within the 5'UTR of a protein coding gene, which defines DROSHA-independent transcription start site (TSS)-miRNAs, we find it dependant on both DROSHA and DICER1 for maturation. Inhibition of miR-4787-3p hinders tumoursphere formation, highlighting its potential as a therapeutic target in BC. Our study proposes elevated miR-4787-3p expression as a potential prognostic biomarker for adverse outcomes in BC. We find that protein-coding genes positively selected in the CRISPR screens are enriched of miR-4787-3p targets. Of these targets, we select ARHGAP17, FOXO3A, and PDCD4 as known tumour suppressors in cancer and experimentally validate the interaction of miR-4787-3p with their 3'UTRs. Our work illuminates the molecular mechanisms underpinning miR-4787-3p's oncogenic role in BC. These findings advocate for clinical investigations targeting miR-4787-3p and underscore its prognostic significance, offering promising avenues for tailored therapeutic interventions and prognostic assessments in BC.
Identifiants
pubmed: 39003349
doi: 10.1038/s42003-024-06555-1
pii: 10.1038/s42003-024-06555-1
doi:
Substances chimiques
MicroRNAs
0
Ribonuclease III
EC 3.1.26.3
DICER1 protein, human
EC 3.1.26.3
DEAD-box RNA Helicases
EC 3.6.4.13
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
859Informations de copyright
© 2024. Crown.
Références
Harbeck, N. et al. Breast cancer. Nat. Rev. Dis. Prim. 5, 66 (2019).
doi: 10.1038/s41572-019-0111-2
pubmed: 31548545
Sorlie, T. et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl Acad. Sci. USA 98, 10869–10874 (2001).
doi: 10.1073/pnas.191367098
pubmed: 11553815
pmcid: 58566
Meacham, C. E. & Morrison, S. J. Tumour heterogeneity and cancer cell plasticity. Nature 501, 328–337 (2013).
doi: 10.1038/nature12624
pubmed: 24048065
pmcid: 4521623
Wang, R. et al. Comparison of mammosphere formation from breast cancer cell lines and primary breast tumors. J. Thorac. Dis. 6, 829–837 (2014).
pubmed: 24977009
pmcid: 4073404
Dontu, G. et al. In vitro propagation and transcriptional profiling of human mammary stem/progenitor cells. Genes Dev. 17, 1253–1270 (2003).
doi: 10.1101/gad.1061803
pubmed: 12756227
pmcid: 196056
Scioli, M. G. et al. The role of breast cancer stem cells as a prognostic marker and a target to improve the efficacy of breast cancer therapy. Cancers (Basel) 11, 1021 (2019).
doi: 10.3390/cancers11071021
pubmed: 31330794
Lombardo, Y., de Giorgio, A., Coombes, C. R., Stebbing, J. & Castellano, L. Mammosphere formation assay from human breast cancer tissues and cell lines. J. Vis. Exp. 97, 52671 (2015)
Zagorac, S. et al. SCIRT lncRNA restrains tumorigenesis by opposing transcriptional programs of tumor-initiating cells. Cancer Res. 81, 580–593 (2021).
doi: 10.1158/0008-5472.CAN-20-2612
pubmed: 33172932
Gebert, L. F. R. & MacRae, I. J. Regulation of microRNA function in animals. Nat. Rev. Mol. Cell Biol. 20, 21–37 (2019).
doi: 10.1038/s41580-018-0045-7
pubmed: 30108335
pmcid: 6546304
Shang, R., Lee, S., Senavirathne, G. & Lai, E. C. microRNAs in action: biogenesis, function and regulation. Nat. Rev. Genet. 24, 816–813 (2023).
Li, Z. & Rana, T. M. Therapeutic targeting of microRNAs: current status and future challenges. Nat. Rev. Drug Discov. 13, 622–638 (2014).
doi: 10.1038/nrd4359
pubmed: 25011539
Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20 (2005).
doi: 10.1016/j.cell.2004.12.035
pubmed: 15652477
Munker, R. & Calin, G. A. MicroRNA profiling in cancer. Clin. Sci. (Lond.) 121, 141–158 (2011).
doi: 10.1042/CS20110005
pubmed: 21526983
Katti, A., Diaz, B. J., Caragine, C. M., Sanjana, N. E. & Dow, L. E. CRISPR in cancer biology and therapy. Nat. Rev. Cancer 22, 259–279 (2022).
doi: 10.1038/s41568-022-00441-w
pubmed: 35194172
Han, K. et al. CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities. Nature 580, 136–141 (2020).
doi: 10.1038/s41586-020-2099-x
pubmed: 32238925
pmcid: 7368463
Takahashi, N. et al. 3D culture models with CRISPR screens reveal hyperactive NRF2 as a prerequisite for spheroid formation via regulation of proliferation and ferroptosis. Mol. Cell 80, 828–844.e6 (2020).
doi: 10.1016/j.molcel.2020.10.010
pubmed: 33128871
pmcid: 7718371
Sanjana, N. E., Shalem, O. & Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Methods 11, 783–784 (2014).
doi: 10.1038/nmeth.3047
pubmed: 25075903
pmcid: 4486245
Li, W. et al. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 15, 554 (2014).
doi: 10.1186/s13059-014-0554-4
pubmed: 25476604
pmcid: 4290824
Xie, Z. et al. Gene set knowledge discovery with Enrichr. Curr. Protoc. 1, e90 (2021).
doi: 10.1002/cpz1.90
pubmed: 33780170
pmcid: 8152575
Varlakhanova, N. V. et al. myc maintains embryonic stem cell pluripotency and self-renewal. Differentiation 80, 9–19 (2010).
doi: 10.1016/j.diff.2010.05.001
pubmed: 20537458
pmcid: 2916696
Yin, S., Cheryan, V. T., Xu, L., Rishi, A. K. & Reddy, K. B. Myc mediates cancer stem-like cells and EMT changes in triple negative breast cancers cells. PLoS ONE 12, e0183578 (2017).
doi: 10.1371/journal.pone.0183578
pubmed: 28817737
pmcid: 5560738
Nguyen, V. T. et al. Differential epigenetic reprogramming in response to specific endocrine therapies promotes cholesterol biosynthesis and cellular invasion. Nat. Commun. 6, 10044 (2015).
doi: 10.1038/ncomms10044
pubmed: 26610607
Ehmsen, S. et al. Increased Cholesterol Biosynthesis Is a Key Characteristic of Breast Cancer Stem Cells Influencing Patient Outcome. Cell Rep. 27, 3927–3938.e6 (2019).
doi: 10.1016/j.celrep.2019.05.104
pubmed: 31242424
Kavakiotis, I., Alexiou, A., Tastsoglou, S., Vlachos, I. S. & Hatzigeorgiou, A. G. DIANA-miTED: a microRNA tissue expression database. Nucleic Acids Res. 50, D1055–D1061 (2022).
doi: 10.1093/nar/gkab733
pubmed: 34469540
Sokilde, R. et al. Refinement of breast cancer molecular classification by miRNA expression profiles. BMC Genomics 20, 503 (2019).
doi: 10.1186/s12864-019-5887-7
pubmed: 31208318
pmcid: 6580620
Xie, M. et al. Mammalian 5’-capped microRNA precursors that generate a single microRNA. Cell 155, 1568–1580 (2013).
doi: 10.1016/j.cell.2013.11.027
pubmed: 24360278
pmcid: 3899828
Zamudio, J. R., Kelly, T. J. & Sharp, P. A. Argonaute-bound small RNAs from promoter-proximal RNA polymerase II. Cell 156, 920–934 (2014).
doi: 10.1016/j.cell.2014.01.041
pubmed: 24581493
pmcid: 4111103
Zheng, J. Z. et al. Elevated miR-301a expression indicates a poor prognosis for breast cancer patients. Sci. Rep. 8, 2225 (2018).
doi: 10.1038/s41598-018-20680-y
pubmed: 29396508
pmcid: 5797194
Jia, Y., Zhao, J., Yang, J., Shao, J. & Cai, Z. miR-301 regulates the SIRT1/SOX2 pathway via CPEB1 in the breast cancer progression. Mol. Ther. Oncolytics 22, 13–26 (2021).
doi: 10.1016/j.omto.2021.03.007
pubmed: 34377766
pmcid: 8313741
Liu, H. & Wang, G. MicroRNA-301a-3p promotes triple-negative breast cancer progression through downregulating MEOX2. Exp. Ther. Med. 22, 945 (2021).
doi: 10.3892/etm.2021.10377
pubmed: 34306209
pmcid: 8281382
Farina, N. H. et al. Development of a predictive miRNA signature for breast cancer risk among high-risk women. Oncotarget 8, 112170–112183 (2017).
doi: 10.18632/oncotarget.22750
pubmed: 29348816
pmcid: 5762501
Ramanto, K. N., Widianto, K. J., Wibowo, S. S. H. & Agustriawan, D. The regulation of microRNA in each of cancer stage from two different ethnicities as potential biomarker for breast cancer. Comput Biol. Chem. 93, 107497 (2021).
doi: 10.1016/j.compbiolchem.2021.107497
pubmed: 34029828
Yerukala Sathipati, S. & Ho, S. Y. Identifying a miRNA signature for predicting the stage of breast cancer. Sci. Rep. 8, 16138 (2018).
doi: 10.1038/s41598-018-34604-3
pubmed: 30382159
pmcid: 6208346
Lytle, N. K., Barber, A. G. & Reya, T. Stem cell fate in cancer growth, progression and therapy resistance. Nat. Rev. Cancer 18, 669–680 (2018).
doi: 10.1038/s41568-018-0056-x
pubmed: 30228301
pmcid: 8388042
Pantelaiou-Prokaki, G. et al. Basal-like mammary carcinomas stimulate cancer stem cell properties through AXL-signaling to induce chemotherapy resistance. Int J. Cancer 152, 1916–1932 (2023).
doi: 10.1002/ijc.34429
pubmed: 36637144
Guo, Q., Xiong, Y., Song, Y., Hua, K. & Gao, S. ARHGAP17 suppresses tumor progression and up-regulates P21 and P27 expression via inhibiting PI3K/AKT signaling pathway in cervical cancer. Gene 692, 9–16 (2019).
doi: 10.1016/j.gene.2019.01.004
pubmed: 30641218
Sun, L. et al. Progress in the study of FOXO3a interacting with microRNA to regulate tumourigenesis development. Front. Oncol. 13, 1293968 (2023).
doi: 10.3389/fonc.2023.1293968
pubmed: 37965449
pmcid: 10641706
Cai, Q., Yang, H. S., Li, Y. C. & Zhu, J. Dissecting the Roles of PDCD4 in Breast Cancer. Front. Oncol. 12, 855807 (2022).
doi: 10.3389/fonc.2022.855807
pubmed: 35795053
pmcid: 9251513