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Dolfini D, Gnesutta N, Mantovani R. Expression and function of NF-Y subunits in cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189082. [PMID: 38309445 DOI: 10.1016/j.bbcan.2024.189082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/05/2024]
Abstract
NF-Y is a Transcription Factor (TF) targeting the CCAAT box regulatory element. It consists of the NF-YB/NF-YC heterodimer, each containing an Histone Fold Domain (HFD), and the sequence-specific subunit NF-YA. NF-YA expression is associated with cell proliferation and absent in some post-mitotic cells. The review summarizes recent findings impacting on cancer development. The logic of the NF-Y regulome points to pro-growth, oncogenic genes in the cell-cycle, metabolism and transcriptional regulation routes. NF-YA is involved in growth/differentiation decisions upon cell-cycle re-entry after mitosis and it is widely overexpressed in tumors, the HFD subunits in some tumor types or subtypes. Overexpression of NF-Y -mostly NF-YA- is oncogenic and decreases sensitivity to anti-neoplastic drugs. The specific roles of NF-YA and NF-YC isoforms generated by alternative splicing -AS- are discussed, including the prognostic value of their levels, although the specific molecular mechanisms of activity are still to be deciphered.
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Affiliation(s)
- Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Nerina Gnesutta
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy.
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2
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Yamanaka T, Kurosawa M, Yoshida A, Shimogori T, Hiyama A, Maity SN, Hattori N, Matsui H, Nukina N. The transcription factor NF-YA is crucial for neural progenitor maintenance during brain development. J Biol Chem 2024; 300:105629. [PMID: 38199563 PMCID: PMC10839448 DOI: 10.1016/j.jbc.2024.105629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
In contrast to stage-specific transcription factors, the role of ubiquitous transcription factors in neuronal development remains a matter of scrutiny. Here, we demonstrated that a ubiquitous factor NF-Y is essential for neural progenitor maintenance during brain morphogenesis. Deletion of the NF-YA subunit in neural progenitors by using nestin-cre transgene in mice resulted in significant abnormalities in brain morphology, including a thinner cerebral cortex and loss of striatum during embryogenesis. Detailed analyses revealed a progressive decline in multiple neural progenitors in the cerebral cortex and ganglionic eminences, accompanied by induced apoptotic cell death and reduced cell proliferation. In neural progenitors, the NF-YA short isoform lacking exon 3 is dominant and co-expressed with cell cycle genes. ChIP-seq analysis from the cortex during early corticogenesis revealed preferential binding of NF-Y to the cell cycle genes, some of which were confirmed to be downregulated following NF-YA deletion. Notably, the NF-YA short isoform disappears and is replaced by its long isoform during neuronal differentiation. Forced expression of the NF-YA long isoform in neural progenitors resulted in a significant decline in neuronal count, possibly due to the suppression of cell proliferation. Collectively, we elucidated a critical role of the NF-YA short isoform in maintaining neural progenitors, possibly by regulating cell proliferation and apoptosis. Moreover, we identified an isoform switch in NF-YA within the neuronal lineage in vivo, which may explain the stage-specific role of NF-Y during neuronal development.
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Affiliation(s)
- Tomoyuki Yamanaka
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan; Laboratory of Structural Neuropathology, Doshisha University Graduate School of Brain Science, Kyoto, Japan; Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan; Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Masaru Kurosawa
- Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Aya Yoshida
- Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan
| | - Tomomi Shimogori
- Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan
| | - Akiko Hiyama
- Laboratory of Structural Neuropathology, Doshisha University Graduate School of Brain Science, Kyoto, Japan
| | - Sankar N Maity
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hideaki Matsui
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
| | - Nobuyuki Nukina
- Laboratory of Structural Neuropathology, Doshisha University Graduate School of Brain Science, Kyoto, Japan; Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan; Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan.
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3
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Liu J, Wu P, Lai S, Wang J, Wang J, Zhang Y. Identifying possible hub genes and biological mechanisms shared between bladder cancer and inflammatory bowel disease using machine learning and integrated bioinformatics. J Cancer Res Clin Oncol 2023; 149:16885-16904. [PMID: 37740761 DOI: 10.1007/s00432-023-05266-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/08/2023] [Indexed: 09/25/2023]
Abstract
BACKGROUND Recent studies have shown that inflammatory bowel disease (IBD) is associated with bladder cancer (BC) incidence. But there is still a lack of understanding regarding its pathogenesis. Thus, this study aimed to identify potential hub genes and their important pathways and pathological mechanisms of interactions between IBD and BC using bioinformatics methods. METHODS The data from Gene Expression Omnibus (GEO) and the cancer genome atlas (TCGA) were analyzed to screen common differentially expressed genes (DEGs) between IBD and BC. The "clusterProfiler" package was used to analyze GO term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment in DEGs. After that, we conducted a weighted gene co-expression network analysis (WGCNA) on these DEGs to determine the vital modules and genes significantly related to BC. Protein-protein interaction (PPI) networks was used to identify hub genes. Further, the hub genes were used to develop a prognostic signature by Cox analysis. The validity of the ten hub DEGs was tested using three classification algorithms. Finally, we analyzed the microRNAs (miRNA)-mRNA, transcription factors (TFs)-mRNA regulatory network. RESULTS Positive regulation of organelle fission, chromosomal region, tubulin binding, and cell cycle signaling pathway were the major enriched pathways for the common DEGs. PPI networks identified three hub proteins (AURKB, CDK1, and CCNA2) with high connectivity. Three machine-learning classification algorithms based on ten hub genes performed well for IBD and BC (accuracy > 0.80). The robust predictive model based on the ten hub genes could accurately classify BC cases with various clinical outcomes. Based on the gene-TFs and gene-miRNAs network construction, 9 TFs and 6 miRNAs were identified as potential critical TFs and miRNAs. There are 13 drugs that interact with the hub gene based on gene-drug interaction analysis. CONCLUSIONS This study explored common gene signatures and the potential pathogenesis of IBD and BC. We revealed that an unbalanced immune response, cell cycle pathway, and neutrophil infiltration might be the common pathogenesis of IBD and BC. Molecular mechanisms for the treatment of IBD and CC still require further investigation.
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Affiliation(s)
- Jianyong Liu
- Department of Urology, Institute of the Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Hospital Continence Center, Beijing, People's Republic of China
| | - Pengjie Wu
- Department of Urology, Institute of the Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Hospital Continence Center, Beijing, People's Republic of China
| | - Shicong Lai
- Department of Urology, Peking University People's Hospital, Beijing, 100044, People's Republic of China
| | - Jianye Wang
- Department of Urology, Institute of the Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
- Beijing Hospital Continence Center, Beijing, People's Republic of China.
- , No. 1 DaHua Road, Dong Dan, Beijing, 100730, China.
| | - Jianlong Wang
- Department of Urology, Institute of the Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
- Beijing Hospital Continence Center, Beijing, People's Republic of China.
- , No. 1 DaHua Road, Dong Dan, Beijing, 100730, China.
| | - Yaoguang Zhang
- Department of Urology, Institute of the Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
- Beijing Hospital Continence Center, Beijing, People's Republic of China.
- , No. 1 DaHua Road, Dong Dan, Beijing, 100730, China.
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4
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Moi D, Bonanni D, Belluti S, Linciano P, Citarella A, Franchini S, Sorbi C, Imbriano C, Pinzi L, Rastelli G. Discovery of potent pyrrolo-pyrimidine and purine HDAC inhibitors for the treatment of advanced prostate cancer. Eur J Med Chem 2023; 260:115730. [PMID: 37633202 DOI: 10.1016/j.ejmech.2023.115730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023]
Abstract
The development of drugs for the treatment of advanced prostate cancer (PCA) remains a challenging task. In this study we have designed, synthesized and tested twenty-nine novel HDAC inhibitors based on three different zinc binding groups (trifluoromethyloxadiazole, hydroxamic acid, and 2-mercaptoacetamide). These warheads were conveniently tethered to variously substituted phenyl linkers and decorated with differently substituted pyrrolo-pyrimidine and purine cap groups. Remarkably, most of the compounds showed nanomolar inhibitory activity against HDAC6. To provide structural insights into the Structure-Activity Relationships (SAR) of the investigated compounds, docking of representative inhibitors and molecular dynamics of HDAC6-inhibitor complexes were performed. Compounds of the trifluoromethyloxadiazole and hydroxamic acid series exhibited promising anti-proliferative activities, HDAC6 targeting in PCA cells, and in vitro tumor selectivity. Representative compounds of the two series were tested for solubility, cell permeability and metabolic stability, demonstrating favorable in vitro drug-like properties. The more interesting compounds were subjected to migration assays, which revealed that compound 13 and, to a lesser extent, compound 15 inhibited the invasive behaviour of androgen-sensitive and -insensitive advanced prostate cancer cells. Compound 13 was profiled against all HDACs and found to inhibit all members of class II HDACs (except for HDAC10) and to be selective with respect to class I and class IV HDACs. Overall, compound 13 combines potent inhibitory activity and class II selectivity with favorable drug-like properties, an excellent anti-proliferative activity and marked anti-migration properties on PCA cells, making it an excellent lead candidate for further optimization.
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Affiliation(s)
- Davide Moi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Davide Bonanni
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Andrea Citarella
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Silvia Franchini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Claudia Sorbi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy.
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy.
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Imbriano C, Moresi V, Belluti S, Renzini A, Cavioli G, Maretti E, Molinari S. Epitranscriptomics as a New Layer of Regulation of Gene Expression in Skeletal Muscle: Known Functions and Future Perspectives. Int J Mol Sci 2023; 24:15161. [PMID: 37894843 PMCID: PMC10606696 DOI: 10.3390/ijms242015161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Epitranscriptomics refers to post-transcriptional regulation of gene expression via RNA modifications and editing that affect RNA functions. Many kinds of modifications of mRNA have been described, among which are N6-methyladenosine (m6A), N1-methyladenosine (m1A), 7-methylguanosine (m7G), pseudouridine (Ψ), and 5-methylcytidine (m5C). They alter mRNA structure and consequently stability, localization and translation efficiency. Perturbation of the epitranscriptome is associated with human diseases, thus opening the opportunity for potential manipulations as a therapeutic approach. In this review, we aim to provide an overview of the functional roles of epitranscriptomic marks in the skeletal muscle system, in particular in embryonic myogenesis, muscle cell differentiation and muscle homeostasis processes. Further, we explored high-throughput epitranscriptome sequencing data to identify RNA chemical modifications in muscle-specific genes and we discuss the possible functional role and the potential therapeutic applications.
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Affiliation(s)
- Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Viviana Moresi
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), University of Rome “La Sapienza”, 00181 Rome, Italy;
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Alessandra Renzini
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Giorgia Cavioli
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Eleonora Maretti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Susanna Molinari
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
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6
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Duan C, Zhang Y, Li L, Liu K, Yao X, Wu X, Li B, Mao X, Wu H, Liu H, Zeng J, Li S, Gong Y, Hu Z, Xu H. Identification of alternative splicing associated with clinical features: from pan-cancers to genitourinary tumors. Front Oncol 2023; 13:1249932. [PMID: 37810965 PMCID: PMC10557043 DOI: 10.3389/fonc.2023.1249932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/17/2023] [Indexed: 10/10/2023] Open
Abstract
Background Alternative splicing events (ASEs) are vital causes of tumor heterogeneity in genitourinary tumors and many other cancers. However, the clinicopathological relevance of ASEs in cancers has not yet been comprehensively characterized. Methods By analyzing splicing data from the TCGA SpliceSeq database and phenotype data for all TCGA samples from the UCSC Xena database, we identified differential clinical feature-related ASEs in 33 tumors. CIBERSORT immune cell infiltration data from the TIMER2.0 database were used for differential clinical feature-related immune cell infiltration analysis. Gene function enrichment analysis was used to analyze the gene function of ASEs related to different clinical features in tumors. To reveal the regulatory mechanisms of ASEs, we integrated race-related ASEs and splicing quantitative trait loci (sQTLs) data in kidney renal clear cell carcinoma (KIRC) to comprehensively assess the impact of SNPs on ASEs. In addition, we predicted regulatory RNA binding proteins in bladder urothelial carcinoma (BLCA) based on the enrichment of motifs around alternative exons for ASEs. Results Alternative splicing differences were systematically analyzed between different groups of 58 clinical features in 33 cancers, and 30 clinical features in 24 cancer types were identified to be associated with more than 50 ASEs individually. The types of immune cell infiltration were found to be significantly different between subgroups of primary diagnosis and disease type. After integrating ASEs with sQTLs data, we found that 63 (58.9%) of the race-related ASEs were significantly SNP-correlated ASEs in KIRC. Gene function enrichment analyses showed that metastasis-related ASEs in KIRC mainly enriched Rho GTPase signaling pathways. Among those ASEs associated with metastasis, alternative splicing of GIT2 and TUBB3 might play key roles in tumor metastasis in KIRC patients. Finally, we identified several RNA binding proteins such as PCBP2, SNRNP70, and HuR, which might contribute to splicing differences between different groups of neoplasm grade in BLCA. Conclusion We demonstrated the significant clinical relevance of ASEs in multiple cancer types. Furthermore, we identified and validated alternative splicing of TUBB3 and RNA binding proteins such as PCBP2 as critical regulators in the progression of urogenital cancers.
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Affiliation(s)
- Chen Duan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yangjun Zhang
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Lu Li
- Department of Radiation Oncology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Kai Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiangyang Yao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiaoliang Wu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bo Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiongmin Mao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Huahui Wu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Haoran Liu
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Jin Zeng
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Sheng Li
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yan Gong
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhiquan Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hua Xu
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
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7
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Belluti S, Imbriano C, Casarini L. Nuclear Estrogen Receptors in Prostate Cancer: From Genes to Function. Cancers (Basel) 2023; 15:4653. [PMID: 37760622 PMCID: PMC10526871 DOI: 10.3390/cancers15184653] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Estrogens are almost ubiquitous steroid hormones that are essential for development, metabolism, and reproduction. They exert both genomic and non-genomic action through two nuclear receptors (ERα and ERβ), which are transcription factors with disregulated functions and/or expression in pathological processes. In the 1990s, the discovery of an additional membrane estrogen G-protein-coupled receptor augmented the complexity of this picture. Increasing evidence elucidating the specific molecular mechanisms of action and opposing effects of ERα and Erβ was reported in the context of prostate cancer treatment, where these issues are increasingly investigated. Although new approaches improved the efficacy of clinical therapies thanks to the development of new molecules targeting specifically estrogen receptors and used in combination with immunotherapy, more efforts are needed to overcome the main drawbacks, and resistance events will be a challenge in the coming years. This review summarizes the state-of-the-art on ERα and ERβ mechanisms of action in prostate cancer and promising future therapies.
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Affiliation(s)
- Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (C.I.)
| | - Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (C.I.)
| | - Livio Casarini
- Unit of Endocrinology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Ospedale di Baggiovara, 41126 Modena, Italy
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8
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Schertzer MD, Stirn A, Isaev K, Pereira L, Das A, Harbison C, Park SH, Wessels HH, Sanjana NE, Knowles DA. Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557474. [PMID: 37745416 PMCID: PMC10515814 DOI: 10.1101/2023.09.12.557474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Alternative splicing is an essential mechanism for diversifying proteins, in which mature RNA isoforms produce proteins with potentially distinct functions. Two major challenges in characterizing the cellular function of isoforms are the lack of experimental methods to specifically and efficiently modulate isoform expression and computational tools for complex experimental design. To address these gaps, we developed and methodically tested a strategy which pairs the RNA-targeting CRISPR/Cas13d system with guide RNAs that span exon-exon junctions in the mature RNA. We performed a high-throughput essentiality screen, quantitative RT-PCR assays, and PacBio long read sequencing to affirm our ability to specifically target and robustly knockdown individual RNA isoforms. In parallel, we provide computational tools for experimental design and screen analysis. Considering all possible splice junctions annotated in GENCODE for multi-isoform genes and our gRNA efficacy predictions, we estimate that our junction-centric strategy can uniquely target up to 89% of human RNA isoforms, including 50,066 protein-coding and 11,415 lncRNA isoforms. Importantly, this specificity spans all splicing and transcriptional events, including exon skipping and inclusion, alternative 5' and 3' splice sites, and alternative starts and ends.
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Affiliation(s)
- Megan D Schertzer
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
| | - Andrew Stirn
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
| | - Keren Isaev
- New York Genome Center, New York, NY
- Department of Systems Biology, Columbia University, New York, NY
| | | | - Anjali Das
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
| | | | - Stella H Park
- New York Genome Center, New York, NY
- Department of Biomedical Engineering, Columbia University, New York, NY
| | - Hans-Hermann Wessels
- New York Genome Center, New York, NY
- Department of Biology, New York University, New York, NY
| | - Neville E Sanjana
- New York Genome Center, New York, NY
- Department of Biology, New York University, New York, NY
| | - David A Knowles
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
- Department of Systems Biology, Columbia University, New York, NY
- Data Science Institute, Columbia University, New York, NY
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9
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Zhang H, Tian J, Ren S, Han B, Tian R, Zuo X, Liu H, Wang Z, Cui Y, Liu L, Guo H, Zhang F, Niu R. Comprehensively analysis of splicing factors to construct prognosis prediction classifier in prostate cancer. J Cell Mol Med 2023; 27:2684-2700. [PMID: 37559353 PMCID: PMC10494302 DOI: 10.1111/jcmm.17849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 08/11/2023] Open
Abstract
Splicing factors (SFs) are proteins that control the alternative splicing (AS) of RNAs, which have been recognized as new cancer hallmarks. Their dysregulation has been found to be involved in many biological processes of cancer, such as carcinogenesis, proliferation, metastasis and senescence. Dysregulation of SFs has been demonstrated to contribute to the progression of prostate cancer (PCa). However, a comprehensive analysis of the prognosis value of SFs in PCa is limited. In this work, we systematically analysed 393 SFs to deeply characterize the expression patterns, clinical relevance and biological functions of SFs in PCa. We identified 53 survival-related SFs that can stratify PCa into two de nove molecular subtypes with distinct mRNA expression and AS-event expression patterns and displayed significant differences in pathway activity and clinical outcomes. An SF-based classifier was established using LASSO-COX regression with six key SFs (BCAS1, LSM3, DHX16, NOVA2, RBM47 and SNRPN), which showed promising prognosis-prediction performance with a receiver operating characteristic (ROC) >0.700 in both the training and testing datasets, as well as in three external PCa cohorts (DKFZ, GSE70769 and GSE21035). CRISPR/CAS9 screening data and cell-level functional analysis suggested that LSM3 and DHX16 are essential factors for the proliferation and cell cycle progression in PCa cells. This study proposes that SFs and AS events are potential multidimensional biomarkers for the diagnosis, prognosis and treatment of PCa.
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Affiliation(s)
- He Zhang
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Jianfei Tian
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Sixin Ren
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Baoai Han
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Ruinan Tian
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Xiaoyan Zuo
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Hui Liu
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Zhiyong Wang
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Yanfen Cui
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Liming Liu
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Hui Guo
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Fei Zhang
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Ruifang Niu
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
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10
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Thakur N, Quazi S, Naik B, Jha SK, Singh P. New insights into molecular signaling pathways and current advancements in prostate cancer diagnostics & therapeutics. Front Oncol 2023; 13:1193736. [PMID: 37664036 PMCID: PMC10469924 DOI: 10.3389/fonc.2023.1193736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/18/2023] [Indexed: 09/05/2023] Open
Abstract
Prostate adenocarcinoma accounts for more than 20% of deaths among males due to cancer. It is the fifth-leading cancer diagnosed in males across the globe. The mortality rate is quite high due to prostate cancer. Despite the fact that advancements in diagnostics and therapeutics have been made, there is a lack of effective drugs. Metabolic pathways are altered due to the triggering of androgen receptor (AR) signaling pathways, and elevated levels of dihydrotestosterone are produced due to defects in AR signaling that accelerate the growth of prostate cancer cells. Further, PI3K/AKT/mTOR pathways interact with AR signaling pathway and act as precursors to promote prostate cancer. Prostate cancer therapy has been classified into luminal A, luminal B, and basal subtypes. Therapeutic drugs inhibiting dihydrotestosterone and PI3K have shown to give promising results to combat prostate cancer. Many second-generation Androgen receptor signaling antagonists are given either as single agent or with the combination of other drugs. In order to develop a cure for metastasized prostate cancer cells, Androgen deprivation therapy (ADT) is applied by using surgical or chemical methods. In many cases, Prostatectomy or local radiotherapy are used to control metastasized prostate cancer. However, it has been observed that after 1.5 years to 2 years of Prostatectomy or castration, there is reoccurrence of prostate cancer and high incidence of castration resistant prostate cancer is seen in population undergone ADT. It has been observed that Androgen derivation therapy combined with drugs like abiraterone acetate or docetaxel improve overall survival rate in metastatic hormone sensitive prostate cancer (mHSPC) patients. Scientific investigations have revealed that drugs inhibiting poly ADP Ribose polymerase (PARP) are showing promising results in clinical trials in the prostate cancer population with mCRPC and DNA repair abnormalities. Recently, RISUG adv (reversible inhibition of sperm under guidance) has shown significant results against prostate cancer cell lines and MTT assay has validated substantial effects of this drug against PC3 cell lines. Current review paper highlights the advancements in prostate cancer therapeutics and new drug molecules against prostate cancer. It will provide detailed insights on the signaling pathways which need to be targeted to combat metastasized prostate cancer and castration resistant prostate cancer.
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Affiliation(s)
- Neha Thakur
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, India
| | - Sameer Quazi
- Department of Chemistry, Akshara First Grade College, Bengaluru, India
- GenLab Biosolutions Private Limited, Bangalore, Karnataka, India
- Department of Biomedical Sciences, School of Life Sciences, Anglia Ruskin University, Cambridge, United Kingdom
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Solution Chemistry of Advanced Materials and Technologies (SCAMT) Institute, ITMO University, St. Petersburg, Russia
| | - Bindu Naik
- Department of Food Science and Technology, Graphic Era Deemed to be University, Dehradun, Uttarakhand, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, India
- Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun, India
| | - Pallavi Singh
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, India
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11
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Rigillo G, Belluti S, Campani V, Ragazzini G, Ronzio M, Miserocchi G, Bighi B, Cuoghi L, Mularoni V, Zappavigna V, Dolfini D, Mercatali L, Alessandrini A, Imbriano C. The NF-Y splicing signature controls hybrid EMT and ECM-related pathways to promote aggressiveness of colon cancer. Cancer Lett 2023:216262. [PMID: 37307894 DOI: 10.1016/j.canlet.2023.216262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/24/2023] [Accepted: 06/04/2023] [Indexed: 06/14/2023]
Abstract
Aberrant splicing events are associated with colorectal cancer (CRC) and provide new opportunities for tumor diagnosis and treatment. The expression of the splice variants of NF-YA, the DNA binding subunit of the transcription factor NF-Y, is deregulated in multiple cancer types compared to healthy tissues. NF-YAs and NF-YAl isoforms differ in the transactivation domain, which may result in distinct transcriptional programs. In this study, we demonstrated that the NF-YAl transcript is higher in aggressive mesenchymal CRCs and predicts shorter patients' survival. In 2D and 3D conditions, CRC cells overexpressing NF-YAl (NF-YAlhigh) exhibit reduced cell proliferation, rapid single cell amoeboid-like migration, and form irregular spheroids with poor cell-to-cell adhesion. Compared to NF-YAshigh, NF-YAlhigh cells show changes in the transcription of genes involved in epithelial-mesenchymal transition, extracellular matrix and cell adhesion. NF-YAl and NF-YAs bind similarly to the promoter of the E-cadherin gene, but oppositely regulate its transcription. The increased metastatic potential of NF-YAlhigh cells in vivo was confirmed in zebrafish xenografts. These results suggest that the NF-YAl splice variant could be a new CRC prognostic factor and that splice-switching strategies may reduce metastatic CRC progression.
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Affiliation(s)
- Giovanna Rigillo
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Virginia Campani
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Gregorio Ragazzini
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, via Campi 213/A, 41125, Modena, Italy
| | - Mirko Ronzio
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Giacomo Miserocchi
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Beatrice Bighi
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, via Campi 213/A, 41125, Modena, Italy
| | - Laura Cuoghi
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Valentina Mularoni
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Vincenzo Zappavigna
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Diletta Dolfini
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Laura Mercatali
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Andrea Alessandrini
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, via Campi 213/A, 41125, Modena, Italy; CNR-Nanoscience Institute-S3, Modena, Italy
| | - Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy.
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12
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Okada N, Ueki C, Shimazaki M, Tsujimoto G, Kohno S, Muranaka H, Yoshikawa K, Takahashi C. NFYA promotes malignant behavior of triple-negative breast cancer in mice through the regulation of lipid metabolism. Commun Biol 2023; 6:596. [PMID: 37268670 DOI: 10.1038/s42003-023-04987-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 05/26/2023] [Indexed: 06/04/2023] Open
Abstract
Two splicing variants exist in NFYA that exhibit high expression in many human tumour types. The balance in their expression correlates with prognosis in breast cancer, but functional differences remain unclear. Here, we demonstrate that NFYAv1, a long-form variant, upregulates the transcription of essential lipogenic enzymes ACACA and FASN to enhance the malignant behavior of triple-negative breast cancer (TNBC). Loss of the NFYAv1-lipogenesis axis strongly suppresses malignant behavior in vitro and in vivo, indicating that the NFYAv1-lipogenesis axis is essential for TNBC malignant behavior and that the axis might be a potential therapeutic target for TNBC. Furthermore, mice deficient in lipogenic enzymes, such as Acly, Acaca, and Fasn, exhibit embryonic lethality; however, Nfyav1-deficient mice exhibited no apparent developmental abnormalities. Our results indicate that the NFYAv1-lipogenesis axis has tumour-promoting effects and that NFYAv1 may be a safe therapeutic target for TNBC.
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Affiliation(s)
- Nobuhiro Okada
- Graduate School of Interdisciplinary Science & Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan.
- Department of Pharmacology, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan.
| | - Chihiro Ueki
- Graduate School of Interdisciplinary Science & Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
| | - Masahiro Shimazaki
- Laboratory for Malignancy Control Research, Medical Innovation Center, Kyoto University, Kyoto, 606-8501, Japan
| | - Goki Tsujimoto
- Graduate School of Interdisciplinary Science & Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
| | - Susumu Kohno
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Hayato Muranaka
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, 920-1192, Japan
- Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Kiyotsugu Yoshikawa
- Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts, Kyoto, 610-0395, Japan
| | - Chiaki Takahashi
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, 920-1192, Japan
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13
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Londero M, Gallo A, Cattaneo C, Ghilardi A, Ronzio M, Del Giacco L, Mantovani R, Dolfini D. NF-YAl drives EMT in Claudin low tumours. Cell Death Dis 2023; 14:65. [PMID: 36707502 PMCID: PMC9883497 DOI: 10.1038/s41419-023-05591-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/29/2023]
Abstract
NF-Y is a trimeric transcription factor whose binding site -the CCAAT box- is enriched in cancer-promoting genes. The regulatory subunit, the sequence-specificity conferring NF-YA, comes in two major isoforms, NF-YA long (NF-YAl) and short (NF-YAs). Extensive expression analysis in epithelial cancers determined two features: widespread overexpression and changes in NF-YAl/NF-YAs ratios (NF-YAr) in tumours with EMT features. We performed wet and in silico experiments to explore the role of the isoforms in breast -BRCA- and gastric -STAD- cancers. We generated clones of two Claudinlow BRCA lines SUM159PT and BT549 ablated of exon-3, thus shifting expression from NF-YAl to NF-YAs. Edited clones show normal growth but reduced migratory capacities in vitro and ability to metastatize in vivo. Using TCGA, including upon deconvolution of scRNA-seq data, we formalize the clinical importance of high NF-YAr, associated to EMT genes and cell populations. We derive a novel, prognostic 158 genes signature common to BRCA and STAD Claudinlow tumours. Finally, we identify splicing factors associated to high NF-YAr, validating RBFOX2 as promoting expression of NF-YAl. These data bring three relevant results: (i) the definition and clinical implications of NF-YAr and the 158 genes signature in Claudinlow tumours; (ii) genetic evidence of 28 amino acids in NF-YAl with EMT-promoting capacity; (iii) the definition of selected splicing factors associated to NF-YA isoforms.
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Affiliation(s)
- Michela Londero
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Alberto Gallo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Camilla Cattaneo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Anna Ghilardi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Mirko Ronzio
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Luca Del Giacco
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.
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14
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Li Z, You C, Huang J, Zhang M. NFYAv1 is a Tumor-Promoting Transcript Associated with Poor Prognosis of Hepatocellular Carcinoma. Med Sci Monit 2023; 29:e938410. [PMID: 36680333 PMCID: PMC9875548 DOI: 10.12659/msm.938410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Nuclear Transcription Factor Y Subunit Alpha (NFYA), together with NFYB and NFYC, form a sequence-specific heterotrimeric nuclear transcription factor (NFY), but their functional role in hepatocellular carcinoma (HCC) is still unclear. In this study, we explored the association between the NFY subunit genes and the survival of primary hepatocellular carcinoma (HCC) patients in The Cancer Genome Atlas (TCGA). The transcript-specific effect on HCC cell growth was studied. MATERIAL AND METHODS RNA-seq data from the Genotype-Tissue Expression Project (GTEx) and TCGA were analyzed in combination. In vitro cellular and molecular studies were conducted using SK-Hep-1 and Hep3B cells. Pearson's correlation coefficients were calculated to assess correlations. Welch's unpaired t test and one-way ANOVA with post hoc Tukey's multiple comparisons were performed. Kaplan-Meier (K-M) survival curves were assessed by conducting log-rank (Mantel-Cox) test. RESULTS NFYA was the only prognosis-related gene. Among the 2 splicing transcripts of NFYA, the long isoform (NFYAv1, NM_002505.5) but not the short-form (NFYAv2, NM_021705.4) was significantly associated with worse progression-free survival (PFS) (high [n=179] vs low [n=179], HR: 1.657, 95% CI: 1.228-2.235, P<0.001) and disease-specific survival (DSS) (high [n=175] vs low [n=175], HR: 1.986, 95% CI: 1.269-3.108, P<0.001) in HCC patients. GO/KEGG analysis in TCGA confirmed that NFYAv1 and NFYAv2 co-expressed (|Pearson's r|≥0.6) genes in primary HCC patients were enriched in quite different GO/KEGG terms. NFYAv1 knockdown significantly decreased cell viability and increased G0/G1 cell cycle arrest. The shRNA only targeting NFYAv1 had a significantly stronger growth-inhibiting effect than the shRNA targeting both NFYAv1 and NFYAv2. CONCLUSIONS This study showed that NFYAv1 is a tumor-promoting transcript associated with poor prognosis of HCC.
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Affiliation(s)
- Zigang Li
- Department of Hepatobiliary Surgery, The First People’s Hospital of Yibin, Yibin, Sichuan, PR China
| | - Chengshan You
- Department of Endocrinology, The Second People’s Hospital of Yibin, Yibin, Sichuan, PR China
| | - Jun Huang
- Department of Hepatobiliary Surgery, The First People’s Hospital of Yibin, Yibin, Sichuan, PR China
| | - Ming Zhang
- Department of Hepatobiliary Surgery, The First People’s Hospital of Yibin, Yibin, Sichuan, PR China
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15
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Imbriano C, Belluti S. Histone Marks-Dependent Effect on Alternative Splicing: New Perspectives for Targeted Splicing Modulation in Cancer? Int J Mol Sci 2022; 23:ijms23158304. [PMID: 35955433 PMCID: PMC9368390 DOI: 10.3390/ijms23158304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing (AS) is a tightly regulated mechanism that generates the complex human proteome from a small number of genes. Cis-regulatory RNA motifs in exons and introns control AS, recruiting positive and negative trans-acting splicing regulators. At a higher level, chromatin affects splicing events. Growing evidence indicates that the popular histone code hypothesis can be extended to RNA-level processes, such as AS. In addition to nucleosome positioning, which can generate transcriptional barriers to shape the final splicing outcome, histone post-translational modifications can contribute to the detailed regulation of single exon inclusion/exclusion. A histone-based system can identify alternatively spliced chromatin stretches, affecting RNAPII elongation locally or recruiting splicing components via adaptor complexes. In tumor cells, several mechanisms trigger misregulated AS events and produce cancer-associated transcripts. On a genome-wide level, aberrant AS can be the consequence of dysfunctional epigenetic splicing code, including altered enrichment in histone post-translational modifications. This review describes the main findings related to the effect of histone modifications and variants on splicing outcome and how a dysfunctional epigenetic splicing code triggers aberrant AS in cancer. In addition, it highlights recent advances in programmable DNA-targeting technologies and their possible application for AS targeted epigenetic modulation.
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16
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Curcumin-Based β-Diketo Ligands for Ga3+: Thermodynamic Investigation of Potential Metal-Based Drugs. Pharmaceuticals (Basel) 2022; 15:ph15070854. [PMID: 35890151 PMCID: PMC9321647 DOI: 10.3390/ph15070854] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 02/06/2023] Open
Abstract
Curcumin is known for its therapeutic properties; among these, antioxidant, anti-inflammatory and anti-cancer ones stand out. Besides, curcumin metal complexes have shown widespread application in medicine and can be exploited as lead structures for developing metal-based drugs. Unfortunately, curcumin is poorly bioavailable, mainly due to its instability in physiological conditions; this weakness is tightly connected to the presence of the β-diketo moiety undergoing tautomeric equilibrium. Stability and metal-chelating ability can be tuned by modulating the electronic effects and steric hindrance close to the β-diketo moiety; in addition, formation of a metal complex shifts the tautomeric equilibrium towards the β-keto–enol form and increases stability in biological media. Among the metals used in clinical therapy, gallium nitrate has shown to have significant antitumor activity against non-Hodgkin lymphoma and bladder cancer, thus indicating that gallium-based drugs have potential for further development as antineoplastic agents with improved therapeutic activity. Curcuminoids have demonstrated high affinity for gallium(III), allowing the formation of stable positively charged M:L 1:2 β-diketonate complexes that benefit from the therapeutic activity of both the metal and the ligand. Seven new curcumin derivatives were synthesized and completely characterized. The new derivatives retain the solvent-dependent keto–enol tautomerism, with the prevalence of the diketo form in aqueous solution. Enhanced stability in simulated physiological conditions was observed in comparison to the lead compound curcumin. The presence of Ga3+ anticipates the dissociation of the enolic proton, allowing chelate complex formation, and simultaneously it shifts the tautomeric equilibrium towards the keto–enol form. A complete 1H/13C NMR and UV–Vis study was performed to define the metal-to-ligand stoichiometry ratio and the overall stability constants. In addition, we demonstrated that some of the derivatives have increased antiproliferative activity on colon cancer cells compared to curcumin and antioxidant properties. On the whole, the synthesized curcumin-based molecules may act as new gallium(III) chelators with improved stability with respect to curcumin and could open interesting perspectives for the development of novel therapeutic agents for cancer.
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17
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Wang S, Wang S, Zhang X, Meng D, Xia Q, Xie S, Shen S, Yu B, Hu J, Liu H, Yan W. Comprehensive analysis of prognosis-related alternative splicing events in ovarian cancer. RNA Biol 2022; 19:1007-1018. [PMID: 35980273 PMCID: PMC9397453 DOI: 10.1080/15476286.2022.2113148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Ovarian cancer (OV) is characterized by high incidence and poor prognosis. Increasing evidence indicates that aberrant alternative splicing (AS) events are associated with the pathogenesis of cancer. We examined prognosis-related alternative splicing events and constructed a clinically applicable model to predict patients’ outcomes. Public database including The Cancer Genome Atlas (TCGA), TCGA SpliceSeq, and the Genomics of Drug Sensitivity in Cancer databases were used to detect the AS expression, immune cell infiltration and IC50. The prognosis-related AS model was constructed and validated by using Cox regression, LASSO regression, C-index, calibration plots, and ROC curves. A total of eight AS events (including FLT3LG|50942|AP) were selected to establish the prognosis-related AS model. Compared with high-risk group, low-risk group had a better outcome (P = 1.794e-06), was more sensitive to paclitaxel (P = 0.022), and higher proportions of plasma cells. We explored the upstream regulatory mechanisms of prognosis-related AS and found that two splicing factor and 156 tag single nucleotide polymorphisms may be involved in the regulation of prognosis-related AS. In order to assess patient prognosis more comprehensively, we constructed a clinically applicable model combining risk score and clinicopathological features, and the 1 -, and 3-year AUCs of the clinically applicable model were 0.812, and 0.726, which were 7.5% and 3.3% higher than that of the risk score. We constructed a prognostic signature for OV patients and comprehensively analysed the regulatory characteristics of the prognostic AS events in OV.
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Affiliation(s)
| | - Shiyuan Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Xing Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Dan Meng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Qianqian Xia
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Shuqian Xie
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Siyuan Shen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Bingjia Yu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Jing Hu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Haohan Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Wenjing Yan
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
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