Alternative splicing of NF-YA promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients

Abstract Background Approaches based on expression signatures of prostate cancer (PCa) have been proposed to predict patient outcomes and response to treatments. The transcription factor NF-Y participates to the progression from benign epithelium to both localized and metastatic PCa and is associate...

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Autores principales:	Silvia Belluti, Valentina Semeghini, Giovanna Rigillo, Mirko Ronzio, Daniela Benati, Federica Torricelli, Luca Reggiani Bonetti, Gianluca Carnevale, Giulia Grisendi, Alessia Ciarrocchi, Massimo Dominici, Alessandra Recchia, Diletta Dolfini, Carol Imbriano
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	NF-Y Prostate cancer Alternative splicing Genome editing Transcriptome profiling Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282
Acceso en línea:	https://doaj.org/article/4a0867c853ee44289ffbdfc913f11aa3
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spelling	oai:doaj.org-article:4a0867c853ee44289ffbdfc913f11aa32021-11-21T12:12:54ZAlternative splicing of NF-YA promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients10.1186/s13046-021-02166-41756-9966https://doaj.org/article/4a0867c853ee44289ffbdfc913f11aa32021-11-01T00:00:00Zhttps://doi.org/10.1186/s13046-021-02166-4https://doaj.org/toc/1756-9966Abstract Background Approaches based on expression signatures of prostate cancer (PCa) have been proposed to predict patient outcomes and response to treatments. The transcription factor NF-Y participates to the progression from benign epithelium to both localized and metastatic PCa and is associated with aggressive transcriptional profile. The gene encoding for NF-YA, the DNA-binding subunit of NF-Y, produces two alternatively spliced transcripts, NF-YAs and NF-YAl. Bioinformatic analyses pointed at NF-YA splicing as a key transcriptional signature to discriminate between different tumor molecular subtypes. In this study, we aimed to determine the pathophysiological role of NF-YA splice variants in PCa and their association with aggressive subtypes. Methods Data on the expression of NF-YA isoforms were extracted from the TCGA (The Cancer Genome Atlas) database of tumor prostate tissues and validated in prostate cell lines. Lentiviral transduction and CRISPR-Cas9 technology allowed the modulation of the expression of NF-YA splice variants in PCa cells. We characterized 3D cell cultures through in vitro assays and RNA-seq profilings. We used the rank-rank hypergeometric overlap approach to identify concordant/discordant gene expression signatures of NF-YAs/NF-YAl-overexpressing cells and human PCa patients. We performed in vivo studies in SHO-SCID mice to determine pathological and molecular phenotypes of NF-YAs/NF-YAl xenograft tumors. Results NF-YA depletion affects the tumorigenic potential of PCa cells in vitro and in vivo. Elevated NF-YAs levels are associated to aggressive PCa specimens, defined by Gleason Score and TNM classification. NF-YAl overexpression increases cell motility, while NF-YAs enhances cell proliferation in PCa 3D spheroids and xenograft tumors. The transcriptome of NF-YAs-spheroids has an extensive overlap with localized and metastatic human PCa signatures. According to PCa PAM50 classification, NF-YAs transcript levels are higher in LumB, characterized by poor prognosis compared to LumA and basal subtypes. A significant decrease in NF-YAs/NF-YAl ratio distinguishes PCa circulating tumor cells from cancer cells in metastatic sites, consistently with pro-migratory function of NF-YAl. Stratification of patients based on NF-YAs expression is predictive of clinical outcome. Conclusions Altogether, our results indicate that the modulation of NF-YA isoforms affects prostate pathophysiological processes and contributes to cancer-relevant phenotype, in vitro and in vivo. Evaluation of NF-YA splicing may represent a new molecular strategy for risk assessment of PCa patients.Silvia BellutiValentina SemeghiniGiovanna RigilloMirko RonzioDaniela BenatiFederica TorricelliLuca Reggiani BonettiGianluca CarnevaleGiulia GrisendiAlessia CiarrocchiMassimo DominiciAlessandra RecchiaDiletta DolfiniCarol ImbrianoBMCarticleNF-YProstate cancerAlternative splicingGenome editingTranscriptome profilingNeoplasms. Tumors. Oncology. Including cancer and carcinogensRC254-282ENJournal of Experimental & Clinical Cancer Research, Vol 40, Iss 1, Pp 1-23 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	NF-Y Prostate cancer Alternative splicing Genome editing Transcriptome profiling Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282
spellingShingle	NF-Y Prostate cancer Alternative splicing Genome editing Transcriptome profiling Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282 Silvia Belluti Valentina Semeghini Giovanna Rigillo Mirko Ronzio Daniela Benati Federica Torricelli Luca Reggiani Bonetti Gianluca Carnevale Giulia Grisendi Alessia Ciarrocchi Massimo Dominici Alessandra Recchia Diletta Dolfini Carol Imbriano Alternative splicing of NF-YA promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients
description	Abstract Background Approaches based on expression signatures of prostate cancer (PCa) have been proposed to predict patient outcomes and response to treatments. The transcription factor NF-Y participates to the progression from benign epithelium to both localized and metastatic PCa and is associated with aggressive transcriptional profile. The gene encoding for NF-YA, the DNA-binding subunit of NF-Y, produces two alternatively spliced transcripts, NF-YAs and NF-YAl. Bioinformatic analyses pointed at NF-YA splicing as a key transcriptional signature to discriminate between different tumor molecular subtypes. In this study, we aimed to determine the pathophysiological role of NF-YA splice variants in PCa and their association with aggressive subtypes. Methods Data on the expression of NF-YA isoforms were extracted from the TCGA (The Cancer Genome Atlas) database of tumor prostate tissues and validated in prostate cell lines. Lentiviral transduction and CRISPR-Cas9 technology allowed the modulation of the expression of NF-YA splice variants in PCa cells. We characterized 3D cell cultures through in vitro assays and RNA-seq profilings. We used the rank-rank hypergeometric overlap approach to identify concordant/discordant gene expression signatures of NF-YAs/NF-YAl-overexpressing cells and human PCa patients. We performed in vivo studies in SHO-SCID mice to determine pathological and molecular phenotypes of NF-YAs/NF-YAl xenograft tumors. Results NF-YA depletion affects the tumorigenic potential of PCa cells in vitro and in vivo. Elevated NF-YAs levels are associated to aggressive PCa specimens, defined by Gleason Score and TNM classification. NF-YAl overexpression increases cell motility, while NF-YAs enhances cell proliferation in PCa 3D spheroids and xenograft tumors. The transcriptome of NF-YAs-spheroids has an extensive overlap with localized and metastatic human PCa signatures. According to PCa PAM50 classification, NF-YAs transcript levels are higher in LumB, characterized by poor prognosis compared to LumA and basal subtypes. A significant decrease in NF-YAs/NF-YAl ratio distinguishes PCa circulating tumor cells from cancer cells in metastatic sites, consistently with pro-migratory function of NF-YAl. Stratification of patients based on NF-YAs expression is predictive of clinical outcome. Conclusions Altogether, our results indicate that the modulation of NF-YA isoforms affects prostate pathophysiological processes and contributes to cancer-relevant phenotype, in vitro and in vivo. Evaluation of NF-YA splicing may represent a new molecular strategy for risk assessment of PCa patients.
format	article
author	Silvia Belluti Valentina Semeghini Giovanna Rigillo Mirko Ronzio Daniela Benati Federica Torricelli Luca Reggiani Bonetti Gianluca Carnevale Giulia Grisendi Alessia Ciarrocchi Massimo Dominici Alessandra Recchia Diletta Dolfini Carol Imbriano
author_facet	Silvia Belluti Valentina Semeghini Giovanna Rigillo Mirko Ronzio Daniela Benati Federica Torricelli Luca Reggiani Bonetti Gianluca Carnevale Giulia Grisendi Alessia Ciarrocchi Massimo Dominici Alessandra Recchia Diletta Dolfini Carol Imbriano
author_sort	Silvia Belluti
title	Alternative splicing of NF-YA promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients
title_short	Alternative splicing of NF-YA promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients
title_full	Alternative splicing of NF-YA promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients
title_fullStr	Alternative splicing of NF-YA promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients
title_full_unstemmed	Alternative splicing of NF-YA promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients
title_sort	alternative splicing of nf-ya promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients
publisher	BMC
publishDate	2021
url	https://doaj.org/article/4a0867c853ee44289ffbdfc913f11aa3
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Alternative splicing of NF-YA promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients

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