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Liu H, Ye Z, Wang X, Wu Y, Deng C. Comprehensive analysis of the functions, prognostic and diagnostic values of RNA binding proteins in head and neck squamous cell carcinoma. JOURNAL OF STOMATOLOGY, ORAL AND MAXILLOFACIAL SURGERY 2024:101937. [PMID: 38844022 DOI: 10.1016/j.jormas.2024.101937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND Accumulating evidence has suggested that RNA binding protein (RBP) dysregulation plays an essential role during tumorigenesis. Here, we sought to explore the potential biological functions and clinical significance of RBP and develop diagnostic and prognostic signatures based on RBP in patients with head and neck squamous cell carcinoma (HNSCC). METHODS The differently expressed RBPs between HNSCC samples and their normal counterparts were identified using the Limma package. The immunohistochemistry (IHC) images of several RBPs were collected from the Human Protein Atlas database. The diagnostic signature based on RBP was built by LASSO-logistic regression and random forest. The prognostic signature based on RBP was constructed by LASSO and stepwise Cox regression analysis in the training cohort and validated in the validation cohort. RESULTS Eighty-four aberrantly expressed RBPs were obtained, comprising 41 up-regulated and 43 down-regulated RBPs. Seven RBP genes (CPEB3, PDCD4, ENDOU, PARP12, DNMT3B, IGF2BP1, EXO1) were identified as diagnostic-related hub genes. They were used to establish a diagnostic RBP signature risk score (DRBPS) model by the coefficients in least absolute shrinkage and selection operator (LASSO)-logistic regression analysis and showed high specificity and sensitivity in the training (area under the receiver operating characteristic curve (AUC) = 0.998), and in all validation cohorts (AUC > 0.95 for all). Similarly, seven RBP genes (MKRN3, ZC3H12D, EIF5A2, AFF3, SIDT1, RBM24, and NR0B1) were identified as prognosis-associated hub genes by LASSO and stepwise multiple Cox regression analyses and were used to construct the prognostic model named as PRBPS. The AUC of the time-dependent receiver operator characteristic curve of the prognostic model was 0.664 at 3 years and 0.635 at 5 years in the training cohort and 0.720, 0.777 in the validation cohort, showing a favorable predictive efficacy for prognosis in HNSCC. CONCLUSIONS Our results demonstrate the value of consideration of RBP in the diagnosis and prognosis for HNSCC and provide a novel insight into understanding the potential role of dysregulated RBP in HNSCC.
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Affiliation(s)
- Hai Liu
- School of Stomatology, Wannan Medical College, Wuhu, China; Anhui Provincial Engineering Research Center for Dental Materials and Application, Wannan Medical College, Wuhu, China
| | - Zhenqi Ye
- School of Stomatology, Wannan Medical College, Wuhu, China; Anhui Provincial Engineering Research Center for Dental Materials and Application, Wannan Medical College, Wuhu, China
| | - Xiaoying Wang
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Yaping Wu
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China; Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.
| | - Chao Deng
- School of Stomatology, Wannan Medical College, Wuhu, China; Anhui Provincial Engineering Research Center for Dental Materials and Application, Wannan Medical College, Wuhu, China.
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Zhang H, Lin J, Yahaya BH. Comprehensive analysis of co-expressed genes with TDP-43: prognostic and therapeutic potential in lung adenocarcinoma. J Cancer Res Clin Oncol 2024; 150:44. [PMID: 38281298 PMCID: PMC10822823 DOI: 10.1007/s00432-023-05554-9] [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: 07/24/2023] [Accepted: 11/09/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Transactivating DNA-binding protein 43 (TDP-43) is intimately associated with tumorigenesis and progression by regulating mRNA splicing, transport, stability, and non-coding RNA molecules. The exact role of TDP-43 in lung adenocarcinoma (LUAD) has not yet been fully elucidated, despite extensive research on its function in various cancer types. An imperative aspect of comprehending the underlying biological characteristics associated with TDP-43 involves investigating the genes that are co-expressed with this protein. This study assesses the prognostic significance of these co-expressed genes in LUAD and subsequently explores potential therapeutic strategies based on these findings. METHODS Transcriptomic and clinical data pertaining to LUAD were retrieved from open-access databases to establish an association between mRNA expression profiles and the presence of TDP-43. A risk-prognosis model was developed to compare patient survival rates across various groups, and its accuracy was also assessed. Additionally, differences in tumor stemness, mutational profiles, tumor microenvironment (TME) characteristics, immune checkpoints, and immune cell infiltration were analyzed in the different groups. Moreover, the study entailed predicting the potential response to immunotherapy as well as the sensitivity to commonly employed chemotherapeutic agents and targeted drugs for each distinct group. RESULTS The TDP-43 Co-expressed Gene Risk Score (TCGRS) model was constructed utilizing four genes: Kinesin Family Member 20A (KIF20A), WD Repeat Domain 4 (WDR4), Proline Rich 11 (PRR11), and Glia Maturation Factor Gamma (GMFG). The value of this model in predicting LUAD patient survival is effectively illustrated by both the Kaplan-Meier (K-M) survival curve and the area under the receiver operating characteristic curve (AUC-ROC). The Gene Set Enrichment Analysis (GSEA) revealed that the high TCGRS group was primarily enriched in biological pathways and functions linked to DNA replication and cell cycle; the low TCGRS group showed primary enrichment in immune-related pathways and functions. The high and low TCGRS groups showed differences in tumor stemness, mutational burden, TME, immune infiltration level, and immune checkpoints. The predictions analysis of immunotherapy indicates that the Tumor Immune Dysfunction and Exclusion (TIDE) score (p < 0.001) and non-response rate (74% vs. 51%, p < 0.001) in the high TCGRS group are higher than those in the low TCGRS group. The Immune Phenotype Score (IPS) in the high TCGRS group is lower than in the low TCGRS group (p < 0.001). The drug sensitivity analysis revealed that the half-maximal inhibitory concentration (IC50) values for cisplatin, docetaxel, doxorubicin, etoposide, gemcitabine, paclitaxel, vincristine, erlotinib, and gefitinib (all p < 0.01) in the high TCGRS group are lower than those in the low TCGRS group. CONCLUSIONS The TCGRS derived from the model exhibits a reliable biomarker for evaluating both prognosis and treatment effectiveness among patients with LUAD. This study is anticipated to offer valuable insights into developing effective treatment strategies for this patient population. It is believed that this study is anticipated to contribute significantly to clinical diagnostics, the development of therapeutic drugs, and the enhancement of patient care.
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Affiliation(s)
- Hao Zhang
- Lung Stem Cell and Gene Therapy Group (LSCGT), Department of Biomedical Sciences, Advanced Medical and Dental Institute (IPPT), Universiti Sains Malaysia, SAINS@Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Juntang Lin
- Henan Joint International Research Laboratory of Stem Cell Medicine, School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, China
| | - Badrul Hisham Yahaya
- Lung Stem Cell and Gene Therapy Group (LSCGT), Department of Biomedical Sciences, Advanced Medical and Dental Institute (IPPT), Universiti Sains Malaysia, SAINS@Bertam, 13200, Kepala Batas, Penang, Malaysia.
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Chen J, Li X, Liu H, Zhong D, Yin K, Li Y, Zhu L, Xu C, Li M, Wang C. Bone marrow stromal cell-derived exosomal circular RNA improves diabetic foot ulcer wound healing by activating the nuclear factor erythroid 2-related factor 2 pathway and inhibiting ferroptosis. Diabet Med 2022:e15031. [PMID: 36537855 DOI: 10.1111/dme.15031] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Diabetic foot ulcer (DFU) remains a serious chronic diabetic complication that can lead to disability. CircRNA-itchy E3 ubiquitin protein ligase (circ-ITCH) was observed to be down-regulated in diabetic retinopathy and diabetic nephropathy, and overexpression of circ-ITCH could inhibit the processes of these diseases. However, the detailed physiological and pathological functions of circ-ITCH in wound healing of DFU remain undetermined. METHODS Exosomes derived from bone marrow stromal cells (BMSCs) were isolated and identified. Cell viability and angiogenesis of human umbilical vein endothelial cells (HUVECs) were evaluated by cell counting kit-8 (CCK-8) and tube formation assays, respectively. The interplays of circ-ITCH, TATA-Box-binding protein associated factor 15 (TAF15) and nuclear factor erythroid 2-related factor 2 (Nrf2) mRNA were analysed by RNA immunoprecipitation (RIP), fluorescence in situ hybridization (FISH) combined immunofluorescent staining and RNA pull-down assays. qRT-PCR, western blot or immunohistochemistry (IHC) were used to measure the expression of circ-ITCH, TAF15, Nrf2, vascular endothelial growth factor (VEGFR) and ferroptosis-related makers. The mice DFU model was established to verify the in vitro results. RESULTS Circ-ITCH was down-regulated in in vitro and in vivo models of DFU. Deferoxamine (DFO), an iron chelating agent, improved the viability and angiogenic ability of high glucose (HG)-treated HUVECs. Overexpression of circ-ITCH or co-cultured with exosomal circ-ITCH from BMSCs could alleviate HG-induced ferroptosis and improve the angiogenesis ability of HUVECs. Circ-ITCH in HUVECs recruited TAF15 protein to stabilize Nrf2 mRNA, thus activating the Nrf2 signalling pathway and suppressing ferroptosis. Exosomal circ-ITCH from BMSCs also accelerated the wound healing process by inhibiting ferroptosis in the DFU mice in a time-dependent manner. CONCLUSION Exosomal circ-ITCH from BMSCs inhibited ferroptosis and improved the angiogenesis of HUVECs through activation of the Nrf2 signalling pathway by recruiting TAF15 protein, ultimately accelerating the wound healing process in DFU.
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Affiliation(s)
- Juehao Chen
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
| | - Xi Li
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
| | - Hua Liu
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
| | - Da Zhong
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Ke Yin
- Department of Orthopedics, The First Affiliated Hospital of Hengyang Medical School, University of South China, Hengyang, China
| | - Yusheng Li
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
| | - Lemei Zhu
- School of Public Health, Changsha Medical University, Changsha, China
| | - Can Xu
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
| | - Mingqing Li
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
| | - Chenggong Wang
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
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Prasad K, Gour P, Raghuvanshi S, Kumar V. The SARS-CoV-2 targeted human RNA binding proteins network biology to investigate COVID-19 associated manifestations. Int J Biol Macromol 2022; 217:853-863. [PMID: 35907451 PMCID: PMC9328843 DOI: 10.1016/j.ijbiomac.2022.07.200] [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] [Received: 02/06/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022]
Abstract
The global coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 virus has had unprecedented social and economic ramifications. Identifying targets for drug repurposing could be an effective means to present new and fast treatments. Furthermore, the risk of morbidity and mortality from COVID-19 goes up when there are coexisting medical conditions, however, the underlying mechanisms remain unclear. In the current study, we have adopted a network-based systems biology approach to investigate the RNA binding proteins (RBPs)-based molecular interplay between COVID-19, various human cancers, and neurological disorders. The network based on RBPs commonly involved in the three disease conditions consisted of nine RBPs connecting 10 different cancer types, 22 brain disorders, and COVID-19 infection, ultimately hinting at the comorbidities and complexity of COVID-19. Further, we underscored five miRNAs with reported antiviral properties that target all of the nine shared RBPs and are thus therapeutically valuable. As a strategy to improve the clinical conditions in comorbidities associated with COVID-19, we propose perturbing the shared RBPs by drug repurposing. The network-based analysis presented hereby contributes to a better knowledge of the molecular underpinnings of the comorbidities associated with COVID-19.
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Affiliation(s)
- Kartikay Prasad
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP 201303, India
| | - Pratibha Gour
- Dept. of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
| | - Saurabh Raghuvanshi
- Dept. of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India.
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP 201303, India.
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Examples of Inverse Comorbidity between Cancer and Neurodegenerative Diseases: A Possible Role for Noncoding RNA. Cells 2022; 11:cells11121930. [PMID: 35741059 PMCID: PMC9221903 DOI: 10.3390/cells11121930] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/25/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023] Open
Abstract
Cancer is one of the most common causes of death; in parallel, the incidence and prevalence of central nervous system diseases are equally high. Among neurodegenerative diseases, Alzheimer’s dementia is the most common, while Parkinson’s disease (PD) is the second most frequent neurodegenerative disease. There is a significant amount of evidence on the complex biological connection between cancer and neurodegeneration. Noncoding RNAs (ncRNAs) are defined as transcribed nucleotides that perform a variety of regulatory functions. The mechanisms by which ncRNAs exert their functions are numerous and involve every aspect of cellular life. The same ncRNA can act in multiple ways, leading to different outcomes; in fact, a single ncRNA can participate in the pathogenesis of more than one disease—even if these seem very different, as cancer and neurodegenerative disorders are. The ncRNA activates specific pathways leading to one or the other clinical phenotype, sometimes with obvious mechanisms of inverse comorbidity. We aimed to collect from the existing literature examples of inverse comorbidity in which ncRNAs seem to play a key role. We also investigated the example of mir-519a-3p, and one of its target genes Poly (ADP-ribose) polymerase 1, for the inverse comorbidity mechanism between some cancers and PD. We believe it is very important to study the inverse comorbidity relationship between cancer and neurodegenerative diseases because it will help us to better assess these two major areas of human disease.
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Zhang Q, Zhang Y, Guo Y, Tang H, Li M, Liu L. A novel machine learning derived RNA-binding protein gene-based score system predicts prognosis of hepatocellular carcinoma patients. PeerJ 2022; 9:e12572. [PMID: 35036125 PMCID: PMC8697767 DOI: 10.7717/peerj.12572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/09/2021] [Indexed: 01/01/2023] Open
Abstract
Background Although the expression of RNA-binding protein (RBP) genes in hepatocellular carcinoma (HCC) varies and is associated with tumor progression, there has been no overview study with multiple cohorts and large samples. The HCC-associated RBP genes need to be more accurately identified, and their clinical application value needs to be further explored. Methods First, we used the robust rank aggregation (RRA) algorithm to extract HCC-associated RBP genes from nine HCC microarray datasets and verified them in The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) cohort and International Cancer Genome Consortium (ICGC) Japanese liver cancer (ICGC-LIRI-JP) cohort. In addition, the copy number variation (CNV), single-nucleotide variant (SNV), and promoter-region methylation data of HCC-associated RBP genes were analyzed. Using the random forest algorithm, we constructed an RBP gene–based prognostic score system (RBP-score). We then evaluated the ability of RBP-score to predict the prognosis of patients. The relationships between RBP-score and other clinical characteristics of patients were analyzed. Results The RRA algorithm identified 30 RBP mRNAs with consistent expression patterns across the nine HCC microarray datasets. These 30 RBP genes were defined as HCC-associated RBP genes. Their mRNA expression patterns were further verified in the TCGA-LIHC and ICGC-LIRI-JP cohorts. Among these 30 RBP genes, some showed significant copy number gain or loss, while others showed differences in the methylation levels of their promoter regions. Some RBP genes were risk factors or protective factors for the prognosis of patients. We extracted 10 key HCC-associated RBP genes using the random forest algorithm and constructed an RBP-score system. RBP-score effectively predicted the overall survival (OS) and disease-free survival (DFS) of HCC patients and was associated with the tumor, node, metastasis (TNM) stage, α-fetoprotein (AFP), and metastasis risk. The clinical value of RBP-score was validated in datasets from different platforms. Cox analysis suggested that a high RBP-score was an independent risk factor for poor prognosis in HCC patients. We also successfully established a combined RBP-score+TNM LASSO-Cox model that more accurately predicted the prognosis. Conclusion The RBP-score system constructed based on HCC-associated RBP genes is a simple and highly effective prognostic evaluation tool. It is suitable for different subgroups of HCC patients and has cross-platform characteristics. Combining RBP-score with the TNM staging system or other clinical parameters can lead to an even greater clinical benefit. In addition, the identified HCC-associated RBP genes may serve as novel targets for HCC treatment.
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Affiliation(s)
- Qiangnu Zhang
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital).,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | | | | | | | - Mingyue Li
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital).,Shenzhen People's Hospital, Shenzhen, China
| | - Liping Liu
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital).,Shenzhen People's Hospital, Shenzhen, China
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Zhao S, Liu Q, Li J, Hu C, Cao F, Ma W, Gao J. Construction and Validation of Prognostic Regulation Network Based on RNA-Binding Protein Genes in Lung Squamous Cell Carcinoma. DNA Cell Biol 2021; 40:1563-1583. [PMID: 34931870 DOI: 10.1089/dna.2021.0145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC) is a common histologic subtype of non-small cell lung cancer with a poor prognosis. RNA-binding proteins (RBPs) are key modulators in the posttranscriptional regulation and RBP alterations are commonly found in various cancer types. However, its roles in predicting the tumorigenesis and prognosis have not been identified in LUSC. To identify the roles of RBPs in the tumorigenesis and prognosis of LUSC, the RNA sequencing data of patients with LUSC were retrieved from The Cancer Genome Atlas (TCGA) databases. The differential expressed genes (DEGs) were evaluated and identified. The intersection of manually curated RBPs and tumorigenesis-related DEGs was filtered to the univariate Cox regression analysis. The intersection genes with prognostic value were defined as prognostic RNA-binding protein genes (PRBPGs). Based on them, the predicted model was constructed. Its accuracy was tested by the area under the curve (AUC) of the receiver operator characteristic curve and the risk score. In addition, to explore the key regulatory network, the relationship among PRBPGs, target RNA, and absolute quantification of 50 hallmarks of cancer was also identified by Pearson correlation analysis. A total of 311 genes were filtered as the intersection of 1542 manually curated RBPs and tumorigenesis-related DEGs and the results revealed 17 PRBPGs. Based on them, we constructed the predict model with a relatively high accuracy (AUC: 0.739). The Kaplan-Meier survival curve showed the significant prognostic value of risk score (p < 0.001). Moreover, we uncovered the regulatory networks of PHF5A-TOMM22-oxidative phosphorylation, TLR3-CTSO inflammation-related pathway, SECISBP2L-targeted RNA (ADGRF5, TGFBR2, CD302, AC096921.2, AHCYL2, RPS6KA2, SLC34A2, and SFTPB) angiogenesis, and SECISBP2L-AKAP13 signaling (DNA repair, MTORC1 signaling, and MYC targets). The regulation mechanisms and cellular location of key PRBPGs were validated by assay for targeting accessible chromatin with high-throughput sequencing and single-cell RNA sequencing. Our study identifies PRBPGs as reliable indexes in predicting the tumorigenesis and prognosis of patients with LUSC and provides a well-applied model for predicting the overall survival for patients with LUSC. Besides, we also identified the regulatory network among PRBPGs, target RNA, and cancer gene sets in mediating the LUSC tumorigenesis.
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Affiliation(s)
- Shilong Zhao
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiuhong Liu
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junlu Li
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunling Hu
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fengan Cao
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wentao Ma
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jing Gao
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Pandini C, Garofalo M, Rey F, Garau J, Zucca S, Sproviero D, Bordoni M, Berzero G, Davin A, Poloni TE, Pansarasa O, Carelli S, Gagliardi S, Cereda C. MINCR: A long non-coding RNA shared between cancer and neurodegeneration. Genomics 2021; 113:4039-4051. [PMID: 34662711 DOI: 10.1016/j.ygeno.2021.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 08/20/2021] [Accepted: 10/12/2021] [Indexed: 01/21/2023]
Abstract
The multitasking nature of lncRNAs allows them to play a central role in both physiological and pathological conditions. Often the same lncRNA can participate in different diseases. Specifically, the MYC-induced Long non-Coding RNA MINCR is upregulated in various cancer types, while downregulated in Amyotrophic Lateral Sclerosis patients. Therefore, this work aims to investigate MINCR potential mechanisms of action and its implications in cancer and neurodegeneration in relation to its expression levels in SH-SY5Y cells through RNA-sequencing approach. Our results show that MINCR overexpression causes massive alterations in cancer-related genes, leading to disruption in many fundamental processes, such as cell cycle and growth factor signaling. On the contrary, MINCR downregulation influences a small number of genes involved in different neurodegenerative disorders, mostly concerning RNA metabolism and inflammation. Thus, understanding the cause and functional consequences of MINCR deregulation gives important insights on potential pathogenetic mechanisms both in cancer and in neurodegeneration.
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Affiliation(s)
- Cecilia Pandini
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy
| | - Maria Garofalo
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy; Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Federica Rey
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan 20157, Italy; Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milano, Milano 20157, Italy
| | - Jessica Garau
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy
| | | | - Daisy Sproviero
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy
| | - Matteo Bordoni
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di Milano, Milano 20157, Italy
| | - Giulia Berzero
- Neuroncology Unit, IRCCS Mondino Foundation, Pavia 27100, Italy
| | - Annalisa Davin
- Laboratory of Neurobiology and Neurogenetic, Golgi Cenci Foundation, Abbiategrasso, Milan 20081, Italy
| | - Tino Emanuele Poloni
- Neurology and Neuropathololgy Department Golgi-Cenci Foundation & ASP Golgi-Redaelli, Abbiategrasso, Milan 20081, Italy
| | - Orietta Pansarasa
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy
| | - Stephana Carelli
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan 20157, Italy; Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milano, Milano 20157, Italy
| | - Stella Gagliardi
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy.
| | - Cristina Cereda
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy.
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Luo H, Zhang Y, Hu N, He Y, He C. Systematic Construction and Validation of an RNA-Binding Protein-Associated Prognostic Model for Acute Myeloid Leukemia. Front Genet 2021; 12:715840. [PMID: 34630514 PMCID: PMC8498117 DOI: 10.3389/fgene.2021.715840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022] Open
Abstract
Background: The abnormal expression of RNA-binding proteins (RBPs) in various malignant tumors is closely related to the occurrence and development of tumors. However, the role of RBPs in acute myeloid leukemia (AML) is unclear. Methods: We downloaded harmonized RNA-seq count data and clinical data for AML from UCSC Xena, including The Cancer Genome Atlas (TCGA), The Genotype-Tissue Expression (GTEx), and Therapeutically Applicable Research to Generate Effective Treatments (TARGET) cohorts. R package edgeR was used for differential expression analysis of 337 whole-blood data and 173 AML data. The prognostic value of these RBPs was systematically investigated by using univariate Cox regression analysis, least absolute shrinkage and selection operator (LASSO)-Cox regression analysis, and multivariate Cox regression analysis. C-index and calibration diagram were used to judge the accuracy of the model, and decision curve analysis (DCA) was used to judge the net benefit. The biological pathways involved were revealed by gene set enrichment analysis (GSEA). The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and the protein-protein interaction (PPI) network performed lateral verification on the selected gene set and LASSO results. Results: A prognostic model of 12-RBP signature was established. In addition, the net benefit and prediction accuracy of the prognostic model and the mixed model based on it were significantly higher than that of cytogenetics. It is verified in the TARGET cohort and shows good prediction effect. Both the selection of our gene set and the LASSO results have high credibility. Most of these pathways are involved in the development of the disease, and they also accumulate in leukemia and RNA-related pathways. Conclusion: The prognosis model of the 12-RBP signature found in this study is an optimized biomarker that can effectively stratify the risk of AML patients. Nomogram based on this prognostic model is a reliable method to predict the median survival time of patients. This study expands our current understanding of the role of RBPs in the occurrence of AML and may lay the foundation for future treatment of the disease.
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Affiliation(s)
| | | | - Nan Hu
- Southwest Medical University, Luzhou, China
| | - Yancheng He
- Jiangyang City Construction College, Luzhou, China
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Tabbì G, Cucci LM, Pinzino C, Munzone A, Marzo T, Pizzanelli S, Satriano C, Magrì A, La Mendola D. Peptides Derived from Angiogenin Regulate Cellular Copper Uptake. Int J Mol Sci 2021; 22:9530. [PMID: 34502439 PMCID: PMC8430698 DOI: 10.3390/ijms22179530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 12/31/2022] Open
Abstract
The angiogenin protein (ANG) is one of the most potent endogenous angiogenic factors. In this work we characterized by means of potentiometric, spectroscopic and voltammetric techniques, the copper complex species formed with peptide fragments derived from the N-terminal domain of the protein, encompassing the sequence 1-17 and having free amino, Ang1-17, or acetylated N-terminus group, AcAng1-17, so to explore the role of amino group in metal binding and cellular copper uptake. The obtained data show that amino group is the main copper anchoring site for Ang1-17. The affinity constant values, metal coordination geometry and complexes redox-potentials strongly depend, for both peptides, on the number of copper equivalents added. Confocal laser scanning microscope analysis on neuroblastoma cells showed that in the presence of one equivalent of copper ion, the free amino Ang1-17 increases cellular copper uptake while the acetylated AcAng1-17 strongly decreases the intracellular metal level. The activity of peptides was also compared to that of the protein normally present in the plasma (wtANG) as well as to the recombinant form (rANG) most commonly used in literature experiments. The two protein isoforms bind copper ions but with a different coordination environment. Confocal laser scanning microscope data showed that the wtANG induces a strong increase in intracellular copper compared to control while the rANG decreases the copper signal inside cells. These data demonstrate the relevance of copper complexes' geometry to modulate peptides' activity and show that wtANG, normally present in the plasma, can affect cellular copper uptake.
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Affiliation(s)
- Giovanni Tabbì
- Institute of Crystallography—National Council of Research—CNR, via Paolo Gaifami 18, 95126 Catania, Italy;
| | - Lorena Maria Cucci
- Nano Hybrid BioInterfaces Lab (NHBIL), Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy;
| | - Calogero Pinzino
- Institute for the Chemistry of OrganoMetallic Compounds (ICCOM), National Council of Research—CNR, via G. Moruzzi 1, 56124 Pisa, Italy;
| | - Alessia Munzone
- Aix-Marseille Univesité, 52 Avenue Escadrille Normandie Niemen, 13013 Marseille, France;
| | - Tiziano Marzo
- Department of Pharmacy, University of Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy;
| | - Silvia Pizzanelli
- Institute for the Chemistry of OrganoMetallic Compounds (ICCOM), National Council of Research—CNR, via G. Moruzzi 1, 56124 Pisa, Italy;
| | - Cristina Satriano
- Nano Hybrid BioInterfaces Lab (NHBIL), Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy;
| | - Antonio Magrì
- Institute of Crystallography—National Council of Research—CNR, via Paolo Gaifami 18, 95126 Catania, Italy;
| | - Diego La Mendola
- Department of Pharmacy, University of Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy;
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11
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Wu ZH, Huang HM, Yang DL. Integrated analysis of the functions and prognostic values of RNA binding proteins in hepatocellular carcinoma. BMC Gastroenterol 2021; 21:265. [PMID: 34130650 PMCID: PMC8204501 DOI: 10.1186/s12876-021-01843-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 06/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC), one of the most common malignant tumors worldwide, ranks as the fifth most common cancer and has been the second most frequent cause of cancer-related death. RNA binding proteins (RBPs) are proteins that interact with different classes of RNA and are commonly detected in cells. Methods We used RNA sequencing data from TCGA to display dysfunctional RBPs microenvironments and provide potential useful biomarkers for HCC diagnosis and prognosis. Results 330 differently expressed RBPs (208 upregulated and 122 downregulated) were identified. KEGG were mainly enriched in RNA degradation, Influenza A, Hepatitis C, RIG-I-like receptor signaling pathway, Herpes simplex virus 1 infection and RNA transport. CBioPortal results demonstrated that these genes were altered in 50 samples out of 357 HCC patients (14%) and the amplification of BRCA1 was the largest frequent copy-number alteration. Conclusion Based on the online database, we identified novel RBPs markers for the prognosis of hepatocellular carcinoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-021-01843-0.
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Affiliation(s)
- Zeng-Hong Wu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hong-Ming Huang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Dong-Liang Yang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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12
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Campos-Melo D, Hawley ZCE, Droppelmann CA, Strong MJ. The Integral Role of RNA in Stress Granule Formation and Function. Front Cell Dev Biol 2021; 9:621779. [PMID: 34095105 PMCID: PMC8173143 DOI: 10.3389/fcell.2021.621779] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Stress granules (SGs) are phase-separated, membraneless, cytoplasmic ribonucleoprotein (RNP) assemblies whose primary function is to promote cell survival by condensing translationally stalled mRNAs, ribosomal components, translation initiation factors, and RNA-binding proteins (RBPs). While the protein composition and the function of proteins in the compartmentalization and the dynamics of assembly and disassembly of SGs has been a matter of study for several years, the role of RNA in these structures had remained largely unknown. RNA species are, however, not passive members of RNA granules in that RNA by itself can form homo and heterotypic interactions with other RNA molecules leading to phase separation and nucleation of RNA granules. RNA can also function as molecular scaffolds recruiting multivalent RBPs and their interactors to form higher-order structures. With the development of SG purification techniques coupled to RNA-seq, the transcriptomic landscape of SGs is becoming increasingly understood, revealing the enormous potential of RNA to guide the assembly and disassembly of these transient organelles. SGs are not only formed under acute stress conditions but also in response to different diseases such as viral infections, cancer, and neurodegeneration. Importantly, these granules are increasingly being recognized as potential precursors of pathological aggregates in neurodegenerative diseases. In this review, we examine the current evidence in support of RNA playing a significant role in the formation of SGs and explore the concept of SGs as therapeutic targets.
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Affiliation(s)
- Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Zachary C E Hawley
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Cristian A Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael J Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Pathology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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13
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Non-coding RNA suppresses FUS aggregation caused by mechanistic shear stress on pipetting in a sequence-dependent manner. Sci Rep 2021; 11:9523. [PMID: 33947944 PMCID: PMC8096841 DOI: 10.1038/s41598-021-89075-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/20/2021] [Indexed: 11/29/2022] Open
Abstract
Fused in sarcoma/translocated in liposarcoma (FUS/TLS) is a multitasking RNA/DNA binding protein. FUS aggregation is implicated in various neurodegenerative diseases. RNA was suggested to modulate phase transition of FUS. Here, we found that FUS transforms into the amorphous aggregation state as an instant response to the shear stress caused by usual pipetting even at a low FUS concentration, 100 nM. It was revealed that non-coding RNA can suppress the transformation of FUS into aggregates. The suppressive effect of RNA on FUS aggregation is sequence-dependent. These results suggested that the non-coding RNA could be a prospective suppressor of FUS aggregation caused by mechanistic stress in cells. Our finding might pave the way for more research on the role of RNAs as aggregation inhibitors, which could facilitate the development of therapies for neurodegenerative diseases.
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14
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Wu ZH, Yue JX, Zhou T, Xiao HJ. Integrated analysis of the prognostic values of RNA-binding proteins in head and neck squamous cell carcinoma. Biofactors 2021; 47:478-488. [PMID: 33651487 DOI: 10.1002/biof.1722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/16/2021] [Indexed: 12/11/2022]
Abstract
Head and neck squamous cell carcinoma is a malignant tumor of the upper aerodigestive tract. These RNA-binding proteins (RBPs) influence post-transcriptional in cells and regulate cell physiology, participate in regulating RNA stability, alternative splicing, translation, modification, localization, and apoptosis. We used RNA sequencing data from The Cancer Genome Atlas to display dysfunctional RBPs microenvironments and provide potential useful biomarkers for head and neck squamous cell carcinoma (HNSCC) diagnosis and prognosis. Six RBPs (DNMT1, PCF11, EIF5A2, RNASE10, PSMA6, and IGF2BP2) were selected as independent prognosis factors of HNSCC patients. The Kyoto Encyclopedia of Genes and Genomes were mainly enriched in RNA transport, Spliceosome, RNA degradation, mRNA surveillance pathway, and Epstein-Barr virus infection. cBioPortal results demonstrated that these six genes were altered in 150 samples out of 504 HNSCC patients (30%) and the amplification of IGF2BP2 was the largest frequent copy-number alteration. Based on the online database, we identified novel RBPs markers for the prognosis of HNSCC.
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Affiliation(s)
- Zeng-Hong Wu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jian-Xin Yue
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tao Zhou
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hong-Jun Xiao
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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15
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Yamaguchi M, Lee IS, Jantrapirom S, Suda K, Yoshida H. Drosophila models to study causative genes for human rare intractable neurological diseases. Exp Cell Res 2021; 403:112584. [PMID: 33812867 DOI: 10.1016/j.yexcr.2021.112584] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/25/2021] [Accepted: 03/27/2021] [Indexed: 12/11/2022]
Abstract
Drosophila is emerging as a convenient model for investigating human diseases. Functional homologues of almost 75% of human disease-related genes are found in Drosophila. Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative disease that causes defects in motoneurons. Charcot-Marie-Tooth disease (CMT) is one of the most commonly found inherited neuropathies affecting both motor and sensory neurons. No effective therapy has been established for either of these diseases. In this review, after overviewing ALS, Drosophila models targeting several ALS-causing genes, including TDP-43, FUS and Ubiquilin2, are described with their genetic interactants. Then, after overviewing CMT, examples of Drosophila models targeting several CMT-causing genes, including mitochondria-related genes and FIG 4, are also described with their genetic interactants. In addition, we introduce Sotos syndrome caused by mutations in the epigenetic regulator gene NSD1. Lastly, several genes and pathways that commonly interact with ALS- and/or CMT-causing genes are described. In the case of ALS and CMT that have many causative genes, it may be not practical to perform gene therapy for each of the many disease-causing genes. The possible uses of the common genes and pathways as novel diagnosis markers and effective therapeutic targets are discussed.
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Affiliation(s)
- Masamitsu Yamaguchi
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan; Kansai Gakken Laboratory, Kankyo Eisei Yakuhin Co. Ltd., Seika-cho, Kyoto, 619-0237, Japan
| | - Im-Soon Lee
- Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
| | - Salinee Jantrapirom
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Kojiro Suda
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Hideki Yoshida
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
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16
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Listro R, Rossino G, Della Volpe S, Stabile R, Boiocchi M, Malavasi L, Rossi D, Collina S. Enantiomeric Resolution and Absolute Configuration of a Chiral δ-Lactam, Useful Intermediate for the Synthesis of Bioactive Compounds. Molecules 2020; 25:E6023. [PMID: 33352660 PMCID: PMC7766352 DOI: 10.3390/molecules25246023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 12/30/2022] Open
Abstract
During the past several years, the frequency of discovery of new molecular entities based on γ- or δ-lactam scaffolds has increased continuously. Most of them are characterized by the presence of at least one chiral center. Herein, we present the preparation, isolation and the absolute configuration assignment of enantiomeric 2-(4-bromophenyl)-1-isobutyl-6-oxopiperidin-3-carboxylic acid (trans-1). For the preparation of racemic trans-1, the Castagnoli-Cushman reaction was employed. (Semi)-preparative enantioselective HPLC allowed to obtain enantiomerically pure trans-1 whose absolute configuration was assigned by X-ray diffractometry. Compound (+)-(2R,3R)-1 represents a reference compound for the configurational study of structurally related lactams.
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Affiliation(s)
- Roberta Listro
- Department of Drug Sciences, University of Pavia, via Taramelli 12, 27100 Pavia, Italy; (R.L.); (G.R.); (S.D.V.); (R.S.); (S.C.)
| | - Giacomo Rossino
- Department of Drug Sciences, University of Pavia, via Taramelli 12, 27100 Pavia, Italy; (R.L.); (G.R.); (S.D.V.); (R.S.); (S.C.)
| | - Serena Della Volpe
- Department of Drug Sciences, University of Pavia, via Taramelli 12, 27100 Pavia, Italy; (R.L.); (G.R.); (S.D.V.); (R.S.); (S.C.)
| | - Rita Stabile
- Department of Drug Sciences, University of Pavia, via Taramelli 12, 27100 Pavia, Italy; (R.L.); (G.R.); (S.D.V.); (R.S.); (S.C.)
| | - Massimo Boiocchi
- Centro Grandi Strumenti, University of Pavia, via Bassi 21, 27100 Pavia, Italy;
| | - Lorenzo Malavasi
- Department of Chemistry, University of Pavia, via Taramelli 12, 27100 Pavia, Italy;
| | - Daniela Rossi
- Department of Drug Sciences, University of Pavia, via Taramelli 12, 27100 Pavia, Italy; (R.L.); (G.R.); (S.D.V.); (R.S.); (S.C.)
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, via Taramelli 12, 27100 Pavia, Italy; (R.L.); (G.R.); (S.D.V.); (R.S.); (S.C.)
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17
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Malecki C, Hambly BD, Jeremy RW, Robertson EN. The RNA-binding fragile-X mental retardation protein and its role beyond the brain. Biophys Rev 2020; 12:903-916. [PMID: 32654068 DOI: 10.1007/s12551-020-00730-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022] Open
Abstract
It is well-established that variations of a CGG repeat expansion in the gene FMR1, which encodes the fragile-X mental retardation protein (FMRP), cause the neurocognitive disorder, fragile-X syndrome (FXS). However, multiple observations suggest a general and complex regulatory role of FMRP in processes outside the brain: (1) FMRP is ubiquitously expressed in the body, suggesting it functions in multiple organ systems; (2) patients with FXS can exhibit a physical phenotype that is consistent with an underlying abnormality in connective tissue; (3) different CGG repeat expansion lengths in FMR1 result in different clinical outcomes due to different pathogenic mechanisms; (4) the function of FMRP as an RNA-binding protein suggests it has a general regulatory role. This review details the complex nature of FMRP and the different CGG repeat expansion lengths and the evidence supporting the essential role of the protein in a variety of biological and pathological processes.
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Affiliation(s)
- Cassandra Malecki
- Discipline of Pathology and Bosch Institute, The University of Sydney, Level 4 West, Charles Perkins Centre D17, Sydney, NSW, 2006, Australia.
| | - Brett D Hambly
- Discipline of Pathology and Bosch Institute, The University of Sydney, Level 4 West, Charles Perkins Centre D17, Sydney, NSW, 2006, Australia
| | - Richmond W Jeremy
- Discipline of Pathology and Bosch Institute, The University of Sydney, Level 4 West, Charles Perkins Centre D17, Sydney, NSW, 2006, Australia.,Cardiology Department, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Elizabeth N Robertson
- Discipline of Pathology and Bosch Institute, The University of Sydney, Level 4 West, Charles Perkins Centre D17, Sydney, NSW, 2006, Australia.,Cardiology Department, Royal Prince Alfred Hospital, Sydney, NSW, Australia
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18
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Meldolesi J. Alternative Splicing by NOVA Factors: From Gene Expression to Cell Physiology and Pathology. Int J Mol Sci 2020; 21:ijms21113941. [PMID: 32486302 PMCID: PMC7312376 DOI: 10.3390/ijms21113941] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/24/2022] Open
Abstract
NOVA1 and NOVA2, the two members of the NOVA family of alternative splicing factors, bind YCAY clusters of pre-mRNAs and assemble spliceosomes to induce the maintenance/removal of introns and exons, thus governing the development of mRNAs. Members of other splicing families operate analogously. Activity of NOVAs accounts for up to 700 alternative splicing events per cell, taking place both in the nucleus (co-transcription of mRNAs) and in the cytoplasm. Brain neurons express high levels of NOVAs, with NOVA1 predominant in cerebellum and spinal cord, NOVA2 in the cortex. Among brain physiological processes NOVAs play critical roles in axon pathfinding and spreading, structure and function of synapses, as well as the regulation of surface receptors and voltage-gated channels. In pathology, NOVAs contribute to neurodegenerative diseases and epilepsy. In vessel endothelial cells, NOVA2 is essential for angiogenesis, while in adipocytes, NOVA1 contributes to regulation of thermogenesis and obesity. In many cancers NOVA1 and also NOVA2, by interacting with specific miRNAs and by additional mechanisms, activate oncogenic roles promoting cell proliferation, colony formation, migration, and invasion. In conclusion, NOVAs regulate cell functions of physiological and pathological nature. Single cell identification and distinction, and new therapies addressed to NOVA targets might be developed in the near future.
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Affiliation(s)
- Jacopo Meldolesi
- Department of Neuroscience, San Raffaele Institute and San Raffaele University, via Olgettina 58, 20132 Milan, Italy
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19
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Volpe SD, Listro R, Parafioriti M, Di Giacomo M, Rossi D, Ambrosio FA, Costa G, Alcaro S, Ortuso F, Hirsch AKH, Vasile F, Collina S. BOPC1 Enantiomers Preparation and HuR Interaction Study. From Molecular Modeling to a Curious DEEP-STD NMR Application. ACS Med Chem Lett 2020; 11:883-888. [PMID: 32435400 DOI: 10.1021/acsmedchemlett.9b00659] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 01/28/2020] [Indexed: 01/13/2023] Open
Abstract
The Hu family of RNA-binding proteins plays a crucial role in post-transcriptional processes; indeed, Hu-RNA complexes are involved in various dysfunctions (i.e., inflammation, neurodegeneration, and cancer) and have been recently proposed as promising therapeutic targets. Intrigued by this concept, our research efforts aim at identifying small molecules able to modulate HuR-RNA interactions, with a focus on subtype HuR, upregulated and dysregulated in several cancers. By applying structure-based design, we had already identified racemic trans-BOPC1 as promising HuR binder. In this Letter, we accomplished the enantio-resolution, the assignment of the absolute configuration, and the recognition study with HuR of enantiomerically pure trans-BOPC1. For the first time, we apply DEEP (differential epitope mapping)-STD NMR to study the interaction of BOPC1 with HuR and compare its enantiomers, gaining information on ligand orientation and amino acids involved in the interaction, and thus increasing focus on the in silico binding site model.
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Affiliation(s)
- Serena Della Volpe
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy
| | - Roberta Listro
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Michela Parafioriti
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Marcello Di Giacomo
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | | | - Giosuè Costa
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, Germaneto, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, Germaneto, 88100 Catanzaro, Italy
| | - Francesco Ortuso
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, Germaneto, 88100 Catanzaro, Italy
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization, Campus Building E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Francesca Vasile
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy
| | - Simona Collina
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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20
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Droppelmann CA, Campos-Melo D, Moszczynski AJ, Amzil H, Strong MJ. TDP-43 aggregation inside micronuclei reveals a potential mechanism for protein inclusion formation in ALS. Sci Rep 2019; 9:19928. [PMID: 31882736 PMCID: PMC6934605 DOI: 10.1038/s41598-019-56483-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating progressive neurodegenerative disease with no known etiology. The formation of pathological protein inclusions, including RNA-binding proteins such as TDP-43 and rho guanine nucleotide exchange factor (RGNEF) are a hallmark of ALS. Despite intensive research, the mechanisms behind protein aggregate formation in ALS remains unclear. We have investigated the role of metabolic stress in protein aggregate formation analyzing how it is relevant to the co-aggregation observed between RGNEF and TDP-43 in motor neurons of ALS patients. Metabolic stress was able to induce formation of micronuclei, small nuclear fragments, in cultured cells. Notably, we observed the formation TDP-43 protein inclusions within micronuclei that co-aggregate with RGNEF and can be released to the cytoplasm. We observed that the leucine-rich domain of RGNEF is critical for its interaction with TDP-43 and localization in micronuclei. Finally, we described that micronuclei-like structures can be found in brain and spinal cord of ALS patients. This work is the first description of protein inclusion formation within micronuclei which also is linked with a neurodegenerative disease. The formation of TDP-43 inclusions within micronuclei induced by metabolic stress is a novel mechanism of protein aggregate formation which may have broad relevance for ALS and other neurodegenerative diseases.
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Affiliation(s)
- Cristian A Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada.
| | - Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Alexander J Moszczynski
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Hind Amzil
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Michael J Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada.
- Department of Clinical Neurological Sciences, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada.
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21
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Della Volpe S, Nasti R, Queirolo M, Unver MY, Jumde VK, Dömling A, Vasile F, Potenza D, Ambrosio FA, Costa G, Alcaro S, Zucal C, Provenzani A, Di Giacomo M, Rossi D, Hirsch AKH, Collina S. Novel Compounds Targeting the RNA-Binding Protein HuR. Structure-Based Design, Synthesis, and Interaction Studies. ACS Med Chem Lett 2019; 10:615-620. [PMID: 30996806 DOI: 10.1021/acsmedchemlett.8b00600] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/21/2019] [Indexed: 12/14/2022] Open
Abstract
The key role of RNA-binding proteins (RBPs) in regulating post-transcriptional processes and their involvement in several pathologies (i.e., cancer and neurodegeneration) have highlighted their potential as therapeutic targets. In this scenario, Embryonic Lethal Abnormal Vision (ELAV) or Hu proteins and their complexes with target mRNAs have been gaining growing attention. Compounds able to modulate the complex stability could constitute an innovative pharmacological strategy for the treatment of numerous diseases. Nevertheless, medicinal-chemistry efforts aimed at developing such compounds are still at an early stage. As part of our ongoing research in this field, we hereby present the rational design and synthesis of structurally novel HuR ligands, potentially acting as HuR-RNA interferers. The following assessment of the structural features of their interaction with HuR, combining saturation-transfer difference NMR and in silico studies, provides a guide for further research on the development of new effective interfering compounds of the HuR-RNA complex.
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Affiliation(s)
- Serena Della Volpe
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Rita Nasti
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Michele Queirolo
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - M. Yagiz Unver
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization and Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747 AG, Groningen, The Netherlands
| | - Varsha K. Jumde
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization and Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747 AG, Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Francesca Vasile
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy
| | - Donatella Potenza
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy
| | | | - Giosué Costa
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Chiara Zucal
- Department of CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, TN, Italy
| | | | - Marcello Di Giacomo
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization and Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747 AG, Groningen, The Netherlands
| | - Simona Collina
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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22
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Wang K, Li L, Fu L, Yuan Y, Dai H, Zhu T, Zhou Y, Yuan F. Integrated Bioinformatics Analysis the Function of RNA Binding Proteins (RBPs) and Their Prognostic Value in Breast Cancer. Front Pharmacol 2019; 10:140. [PMID: 30881302 PMCID: PMC6405693 DOI: 10.3389/fphar.2019.00140] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/06/2019] [Indexed: 02/06/2023] Open
Abstract
Background and Purpose: Breast cancer is one of the leading causes of death among women. RNA binding proteins (RBPs) play a vital role in the progression of many cancers. Functional investigation of RBPs may contribute to elucidating the mechanisms underlying tumor initiation, progression, and invasion, therefore providing novel insights into future diagnosis, treatment, and prognosis. Methods: We downloaded RNA sequencing data from the cancer genome atlas (TCGA) by UCSC Xena and identified relevant RBPs through an integrated bioinformatics analysis. We then analyzed biological processes of differentially expressed genes (DEGs) by DAVID, and established their interaction networks and performed pathway analysis through the STRING database to uncover potential biological effects of these RBPs. We also explored the relationship between these RBPs and the prognosis of breast cancer patients. Results: In the present study, we obtained 1092 breast tumor samples and 113 normal controls. After data analysis, we identified 90 upregulated and 115 downregulated RBPs in breast cancer. GO and KEGG pathway analysis indicated that these significantly changed genes were mainly involved in RNA processing, splicing, localization and RNA silencing, DNA transposition regulation and methylation, alkylation, mitochondrial gene expression, and transcription regulation. In addition, some RBPs were related to histone H3K27 methylation, estrogen response, inflammatory mediators, and translation regulation. Our study also identified five RBPs associated with breast cancer prognosis. Survival analysis found that overexpression of DCAF13, EZR, and MRPL13 showed worse survival, but overexpression of APOBEC3C and EIF4E3 showed better survival. Conclusion: In conclusion, we identified key RBPs of breast cancer through comprehensive bioinformatics analysis. These RBPs were involved in a variety of biological and molecular pathways in breast cancer. Furthermore, we identified five RBPs as a potential prognostic biomarker of breast cancer. Our study provided novel insights to understand breast cancer at a molecular level.
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Affiliation(s)
- Ke Wang
- Clinical Laboratory, Yongchuan People's Hospital of Chongqing, Chongqing, China
| | - Ling Li
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Liang Fu
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Yongqiang Yuan
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Hongying Dai
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Tianjin Zhu
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Yuxi Zhou
- Yidu Cloud (Beijing) Technology Co., Ltd., Beijing, China
| | - Fang Yuan
- Yidu Cloud (Beijing) Technology Co., Ltd., Beijing, China
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23
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Gomez-Verjan JC, Vazquez-Martinez ER, Rivero-Segura NA, Medina-Campos RH. The RNA world of human ageing. Hum Genet 2018; 137:865-879. [DOI: 10.1007/s00439-018-1955-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/29/2018] [Indexed: 12/15/2022]
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24
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Chen X, Fan Z, McGee W, Chen M, Kong R, Wen P, Xiao T, Chen X, Liu J, Zhu L, Chen R, Wu JY. TDP-43 regulates cancer-associated microRNAs. Protein Cell 2018; 9:848-866. [PMID: 28952053 PMCID: PMC6160384 DOI: 10.1007/s13238-017-0480-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 08/31/2017] [Indexed: 12/14/2022] Open
Abstract
Aberrant regulation of miRNA genes contributes to pathogenesis of a wide range of human diseases, including cancer. The TAR DNA binding protein 43 (TDP-43), a RNA/DNA binding protein associated with neurodegeneration, is involved in miRNA biogenesis. Here, we systematically examined miRNAs regulated by TDP-43 using RNA-Seq coupled with an siRNA-mediated knockdown approach. TDP-43 knockdown affected the expression of a number of miRNAs. In addition, TDP-43 down-regulation led to alterations in the patterns of different isoforms of miRNAs (isomiRs) and miRNA arm selection, suggesting a previously unknown role of TDP-43 in miRNA processing. A number of TDP-43 associated miRNAs, and their candidate target genes, are associated with human cancers. Our data reveal highly complex roles of TDP-43 in regulating different miRNAs and their target genes. Our results suggest that TDP-43 may promote migration of lung cancer cells by regulating miR-423-3p. In contrast, TDP-43 increases miR-500a-3p expression and binds to the mature miR-500a-3p sequence. Reduced expression of miR-500a-3p is associated with poor survival of lung cancer patients, suggesting that TDP-43 may have a suppressive role in cancer by regulating miR-500a-3p. Cancer-associated genes LIF and PAPPA are possible targets of miR-500a-3p. Our work suggests that TDP-43-regulated miRNAs may play multifaceted roles in the pathogenesis of cancer.
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Affiliation(s)
- Xiaowei Chen
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Guangdong Geneway Decoding Bio-Tech Co. Ltd, Foshan, 528316, China
| | - Zhen Fan
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Warren McGee
- Department of Neurology, Center for Genetic Medicine, Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Mengmeng Chen
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Department of Neurology, Center for Genetic Medicine, Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Ruirui Kong
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pushuai Wen
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tengfei Xiao
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaomin Chen
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianghong Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Runsheng Chen
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- Research Network of Computational Biology, RNCB, Beijing, 100101, China.
- Guangdong Geneway Decoding Bio-Tech Co. Ltd, Foshan, 528316, China.
| | - Jane Y Wu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- Department of Neurology, Center for Genetic Medicine, Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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25
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Exploration of ligand binding modes towards the identification of compounds targeting HuR: a combined STD-NMR and Molecular Modelling approach. Sci Rep 2018; 8:13780. [PMID: 30214075 PMCID: PMC6137155 DOI: 10.1038/s41598-018-32084-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/29/2018] [Indexed: 12/18/2022] Open
Abstract
Post-transcriptional processes have been recognised as pivotal in the control of gene expression, and impairments in RNA processing are reported in several pathologies (i.e., cancer and neurodegeneration). Focusing on RNA-binding proteins (RBPs), the involvement of Embryonic Lethal Abnormal Vision (ELAV) or Hu proteins and their complexes with target mRNAs in the aetiology of various dysfunctions, has suggested the great potential of compounds able to interfere with the complex stability as an innovative pharmacological strategy for the treatment of numerous diseases. Here, we present a rational follow-up investigation of the interaction between ELAV isoform HuR and structurally-related compounds (i.e., flavonoids and coumarins), naturally decorated with different functional groups, by means of STD-NMR and Molecular Modelling. Our results represent the foundation for the development of potent and selective ligands able to interfere with ELAV–RNA complexes.
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26
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Ernst EH, Nielsen J, Ipsen MB, Villesen P, Lykke-Hartmann K. Transcriptome Analysis of Long Non-coding RNAs and Genes Encoding Paraspeckle Proteins During Human Ovarian Follicle Development. Front Cell Dev Biol 2018; 6:78. [PMID: 30087896 PMCID: PMC6066568 DOI: 10.3389/fcell.2018.00078] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/02/2018] [Indexed: 12/11/2022] Open
Abstract
Emerging evidence indicated that many long non-coding (lnc)RNAs function in multiple biological processes and dysregulation of their expression can cause diseases. Most regulatory lncRNAs interact with biological macromolecules such as DNA, RNA, and protein. LncRNAs regulate gene expression through epigenetic modification, transcription, and posttranscription, through DNA methylation, histone modification, and chromatin remodeling. Interestingly, differential lncRNA expression profiles in human oocytes and cumulus cells was recently assessed, however, lncRNAs in human follicle development has not previously been described. In this study, transcriptome dynamics in human primordial, primary and small antral follicles were interrogated and revealed information of lncRNA genes. It is known that some lncRNAs form a complex with paraspeckle proteins and therefore, we extended our transcriptional analysis to include genes encoding paraspeckle proteins. Primordial, primary follicles and small antral follicles was isolated using laser capture micro-dissection from ovarian tissue donated by three women having ovarian tissue cryopreserved before chemotherapy. After RN sequencing, a bioinformatic class comparison was performed and primordial, primary and small antral follicles were found to express several lncRNA and genes encoding paraspeckle proteins. Of particular interest, we detected the lncRNAs XIST, NEAT1, NEAT2 (MALAT1), and GAS5. Moreover, we noted a high expression of FUS, TAF15, and EWS components of the paraspeckles, proteins that belong to the FET (previously TET) family of RNA-binding proteins and are implicated in central cellular processes such as regulation of gene expression, maintenance of genomic integrity, and mRNA/microRNA processing. We also interrogated the intra-ovarian localization of the FUS, TAF15, and EWS proteins using immunofluorescence. The presence and the dynamics of genes that encode lncRNA and paraspeckle proteins may suggest that these may mediate functions in the cyclic recruitment and differentiation of human follicles and could participate in biological processes known to be associated with lncRNAs and paraspeckle proteins, such as gene expression control, scaffold formation and epigenetic control through human follicle development. This comprehensive transcriptome analysis of lncRNAs and genes encoding paraspeckle proteins expressed in human follicles could potentially provide biomarkers of oocyte quality for the development of non-invasive tests to identify embryos with high developmental potential.
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Affiliation(s)
- Emil H. Ernst
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Julie Nielsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Malene B. Ipsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Palle Villesen
- Bioinformatic Research Centre, Aarhus University, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karin Lykke-Hartmann
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
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27
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The EGF/hnRNP Q1 axis is involved in tumorigenesis via the regulation of cell cycle-related genes. Exp Mol Med 2018; 50:1-14. [PMID: 29884818 PMCID: PMC5994831 DOI: 10.1038/s12276-018-0101-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 01/10/2023] Open
Abstract
Heterogeneous nuclear ribonucleoprotein (hnRNP) Q1, an RNA-binding protein, has been implicated in many post-transcriptional processes, including RNA metabolism and mRNA splicing and translation. However, the role of hnRNP Q1 in tumorigenesis remains unclear. We previously performed RNA immunoprecipitation (RIP)-seq analysis to identify hnRNP Q1-interacting mRNAs and found that hnRNP Q1 targets a group of genes that are involved in mitotic regulation, including Aurora-A. Here, we demonstrate that altering the hnRNP Q1 level influences the expression of the Aurora-A protein, but not its mRNA. Stimulation with epidermal growth factor (EGF) enhances both binding between hnRNP Q1 and Aurora-A mRNA as well as the efficacy of the hnRNP Q1-induced translation of Aurora-A mRNA. The EGF/hnRNP Q1-induced translation of Aurora-A mRNA is mediated by the mTOR and ERK pathways. In addition, we show that hnRNP Q1 up-regulates the translation of a group of spindle assembly checkpoint (SAC) genes. hnRNP Q1 overexpression is positively correlated with the levels of Aurora-A and the SAC genes in human colorectal cancer tissues. In summary, our data suggest that hnRNP Q1 plays an important role in regulating the expression of a group of cell cycle-related genes. Therefore, it may contribute to tumorigenesis by up-regulating the translation of these genes in colorectal cancer. An RNA-binding protein contributes to cancer by boosting the protein-making potential of various genes involved in the cell cycle and cell division. Researchers in Taiwan led by Liang-Yi Hung from the National Cheng Kung University in Tainan, Taiwan, previously showed that a cancer-causing protein implicated in tumors of the colon and elsewhere gets induced by both an RNA-binding protein called hnRNP Q1 and a growth factor called EGF. Now, they have demonstrated that these two molecules work in concert to boost the efficiency by which the RNA encoding the cancer-causing protein gets translated into the protein. They also showed that hnRNP Q1 serves a similar RNA-modulating function for several genes involved in spindle checkpoint during cell division. Together, the findings point to hnRNP Q1 as a potential target for future anti-cancer drugs.
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28
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Xiong D, Wu YB, Jin C, Li JJ, Gu J, Liao YF, Long X, Zhu SQ, Wu HB, Xu JJ, Ding JY. Elevated FUS/TLS expression is negatively associated with E-cadherin expression and prognosis of patients with non-small cell lung cancer. Oncol Lett 2018; 16:1791-1800. [PMID: 30008867 DOI: 10.3892/ol.2018.8816] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 11/23/2017] [Indexed: 01/02/2023] Open
Abstract
Fused in sarcoma/translocated in liposarcoma (FUS/TLS), a ubiquitous and multifunctional DNA and RNA-binding protein, contributes an important function in cancer and neurodegenerative disease; however, its role in lung cancer remains unclear. In the present study, the expression of FUS/TLS in non-small cell lung cancer (NSCLC) and the significance of FUS/TLS for predicting the clinical outcome of patients with NSCLC, was examined. FUS/TLS expression was investigated in NSCLC tissues and their matched adjacent non-tumorous tissues by reverse transcription-quantitative polymerase chain reaction, western blotting, and immunohistochemistry. Tissue microarrays representing 208 patients with NSCLC were used to determine the expression pattern and associations with FUS/TLS using immunohistochemistry. Prognostic significance was assessed by Kaplan-Meier survival estimates and log-rank tests. Data revealed that FUS/TLS expression was elevated in NSCLC tissues compared with corresponding normal tissue mRNA (9.27±0.73 vs. 6.15±0.60) and protein (3.32±0.75 vs. 0.30±0.07) levels. In tissue microarrays, FUS/TLS was highly expressed in 103 (49.5%, 103/208) NSCLC tissues compared with adjacent normal lung tissues (28.4%, 59/208). Overexpression of FUS/TLS was associated with higher tumor node metastasis stage (P=0.016), poorer differentiation (P=0.008), large tumor size (P=0.019) and predicted poor prognosis (P=0.005) in patients with NSCLC. Notably, correlation analysis revealed a significant inverse association between the expression of FUS/TLS and E-cadherin (r2=0.51; P=0.036). Furthermore, patients with NSCLC with high FUS/TLS and impaired E-cadherin expression had a notably poor prognosis (P=4.01×10-4). Thus, the results from the present study indicate that elevated FUS/TLS expression promotes NSCLC progression. FUS/TLS, alone or in combination with E-cadherin, is a novel prognostic predictor for patients with NSCLC.
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Affiliation(s)
- Dian Xiong
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China.,Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Yong-Bing Wu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Chun Jin
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Ji-Jun Li
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China.,Department of Cardio-Thoracic Surgery, Kashgar Prefecture Second People's Hospital, Kashgar, Xinjiang 844000, P.R. China
| | - Jie Gu
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Yun-Fei Liao
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Xiang Long
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Shu-Qiang Zhu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Hai-Bo Wu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Jian-Jun Xu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Jian-Yong Ding
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
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29
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Zalfa F, Panasiti V, Carotti S, Zingariello M, Perrone G, Sancillo L, Pacini L, Luciani F, Roberti V, D'Amico S, Coppola R, Abate SO, Rana RA, De Luca A, Fiers M, Melocchi V, Bianchi F, Farace MG, Achsel T, Marine JC, Morini S, Bagni C. The fragile X mental retardation protein regulates tumor invasiveness-related pathways in melanoma cells. Cell Death Dis 2017; 8:e3169. [PMID: 29144507 PMCID: PMC5775405 DOI: 10.1038/cddis.2017.521] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/24/2017] [Accepted: 08/25/2017] [Indexed: 02/06/2023]
Abstract
The fragile X mental retardation protein (FMRP) is lacking or mutated in patients with the fragile X syndrome (FXS), the most frequent form of inherited intellectual disability. FMRP affects metastasis formation in a mouse model for breast cancer. Here we show that FMRP is overexpressed in human melanoma with high Breslow thickness and high Clark level. Furthermore, meta-analysis of the TCGA melanoma data revealed that high levels of FMRP expression correlate significantly with metastatic tumor tissues, risk of relapsing and disease-free survival. Reduction of FMRP in metastatic melanoma cell lines impinges on cell migration, invasion and adhesion. Next-generation sequencing in human melanoma cells revealed that FMRP regulates a large number of mRNAs involved in relevant processes of melanoma progression. Our findings suggest an association between FMRP levels and the invasive phenotype in melanoma and might open new avenues towards the discovery of novel therapeutic targets.
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Affiliation(s)
- Francesca Zalfa
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Vincenzo Panasiti
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Simone Carotti
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Maria Zingariello
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Giuseppe Perrone
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Laura Sancillo
- Department of Medicine and Science of Aging, University of Chieti 'G d'Annunzio', via dei Vestini 31, 66100 Chieti-Pescara, Italy
| | - Laura Pacini
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', via Montpellier 1, 00133 Rome, Italy
| | - Flavie Luciani
- VIB/Center for the Biology of Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, 3000, Leuven, Belgium.,Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, Leuven, 3000, Belgium
| | - Vincenzo Roberti
- Department of Dermatology, University of Rome 'La Sapienza', viale dell'Università 1, 00185 Rome, Italy
| | - Silvia D'Amico
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', via Montpellier 1, 00133 Rome, Italy
| | - Rosa Coppola
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Simona Osella Abate
- Department of Medical Science and Human Oncology, Section of Dermato-Oncology, University of Turin, via Verdi 8, 10124 Turin, Italy
| | - Rosa Alba Rana
- Department of Medicine and Science of Aging, University of Chieti 'G d'Annunzio', via dei Vestini 31, 66100 Chieti-Pescara, Italy
| | - Anastasia De Luca
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', via Montpellier 1, 00133 Rome, Italy
| | - Mark Fiers
- VIB/Center for the Biology of Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, 3000, Leuven, Belgium.,Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, Leuven, 3000, Belgium
| | - Valentina Melocchi
- ISBREMIT, Institute for Stem-cell Biology, Regenerative Medicine and Innovative Therapies, IRCCS Casa Sollievo della Sofferenza, viale Padre Pio 7, 71013 San Giovanni Rotondo (FG), Italy
| | - Fabrizio Bianchi
- ISBREMIT, Institute for Stem-cell Biology, Regenerative Medicine and Innovative Therapies, IRCCS Casa Sollievo della Sofferenza, viale Padre Pio 7, 71013 San Giovanni Rotondo (FG), Italy
| | - Maria Giulia Farace
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', via Montpellier 1, 00133 Rome, Italy
| | - Tilmann Achsel
- VIB/Center for the Biology of Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, 3000, Leuven, Belgium.,Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, Leuven, 3000, Belgium
| | - Jean-Christophe Marine
- VIB/Center for the Biology of Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, 3000, Leuven, Belgium.,Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, Leuven, 3000, Belgium
| | - Sergio Morini
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Claudia Bagni
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', via Montpellier 1, 00133 Rome, Italy.,VIB/Center for the Biology of Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, 3000, Leuven, Belgium.,Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, Leuven, 3000, Belgium.,Department of Fundamental Neuroscience, University of Lausanne, Rue du Bugnon 9, 1005 Lausanne, Switzerland
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30
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Appocher C, Mohagheghi F, Cappelli S, Stuani C, Romano M, Feiguin F, Buratti E. Major hnRNP proteins act as general TDP-43 functional modifiers both in Drosophila and human neuronal cells. Nucleic Acids Res 2017; 45:8026-8045. [PMID: 28575377 PMCID: PMC5570092 DOI: 10.1093/nar/gkx477] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 05/16/2017] [Indexed: 12/13/2022] Open
Abstract
Nuclear factor TDP-43 is known to play an important role in several neurodegenerative pathologies. In general, TDP-43 is an abundant protein within the eukaryotic nucleus that binds to many coding and non-coding RNAs and influence their processing. Using Drosophila, we have performed a functional screening to establish the ability of major hnRNP proteins to affect TDP-43 overexpression/depletion phenotypes. Interestingly, we observed that lowering hnRNP and TDP-43 expression has a generally harmful effect on flies locomotor abilities. In parallel, our study has also identified a distinct set of hnRNPs that is capable of powerfully rescuing TDP-43 toxicity in the fly eye (Hrb27c, CG42458, Glo and Syp). Most importantly, removing the human orthologs of Hrb27c (DAZAP1) in human neuronal cell lines can correct several pre-mRNA splicing events altered by TDP-43 depletion. Moreover, using RNA sequencing analysis we show that DAZAP1 and TDP-43 can co-regulate an extensive number of biological processes and molecular functions potentially important for the neuron/motor neuron pathophysiology. Our results suggest that changes in hnRNP expression levels can significantly modulate TDP-43 functions and affect pathological outcomes.
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Affiliation(s)
- Chiara Appocher
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Fatemeh Mohagheghi
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Sara Cappelli
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy
| | - Fabian Feiguin
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
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31
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Nasti R, Rossi D, Amadio M, Pascale A, Unver MY, Hirsch AKH, Collina S. Compounds Interfering with Embryonic Lethal Abnormal Vision (ELAV) Protein–RNA Complexes: An Avenue for Discovering New Drugs. J Med Chem 2017; 60:8257-8267. [DOI: 10.1021/acs.jmedchem.6b01871] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Rita Nasti
- Department of Drug
Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department of Drug
Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Marialaura Amadio
- Department of Drug
Sciences, Pharmacology Section, University of Pavia, Via Taramelli
14, 27100 Pavia, Italy
| | - Alessia Pascale
- Department of Drug
Sciences, Pharmacology Section, University of Pavia, Via Taramelli
14, 27100 Pavia, Italy
| | - M. Yagiz Unver
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747
AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747
AG Groningen, The Netherlands
| | - Simona Collina
- Department of Drug
Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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32
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Tallaksen CME, Müller U. Cancer and neurodegeneration: Time to move beyond Janus? Neurology 2017; 88:1106-1107. [PMID: 28202693 DOI: 10.1212/wnl.0000000000003727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Chantal M E Tallaksen
- From the Department of Neurology (C.M.E.T.), Oslo University Hospital; Faculty of Medicine (U.M.), University of Oslo, Norway; and Institute of Human Genetics (U.M.), Justus-Liebig-University, Giessen, Germany
| | - Ulrich Müller
- From the Department of Neurology (C.M.E.T.), Oslo University Hospital; Faculty of Medicine (U.M.), University of Oslo, Norway; and Institute of Human Genetics (U.M.), Justus-Liebig-University, Giessen, Germany
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33
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Ratti A, Buratti E. Physiological functions and pathobiology of TDP-43 and FUS/TLS proteins. J Neurochem 2016; 138 Suppl 1:95-111. [PMID: 27015757 DOI: 10.1111/jnc.13625] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/19/2016] [Accepted: 03/22/2016] [Indexed: 12/12/2022]
Abstract
The multiple roles played by RNA binding proteins in neurodegeneration have become apparent following the discovery of TAR DNA binding protein 43 kDa (TDP-43) and fused in sarcoma/translocated in liposarcoma (FUS/TLS) involvement in amyotrophic lateral sclerosis and frontotemporal lobar dementia. In these two diseases, the majority of patients display the presence of aggregated forms of one of these proteins in their brains. The study of their functional properties currently represents a very promising target for developing the effective therapeutic options that are still lacking. This aim, however, must be preceded by an accurate evaluation of TDP-43 and FUS/TLS biological functions, both in physiological and disease conditions. Recent findings have uncovered several aspects of RNA metabolism that can be affected by misregulation of these two proteins. Progress has also been made in starting to understand how the aggregation of these proteins occurs and spreads from cell to cell. The aim of this review will be to provide a general overview of TDP-43 and FUS/TLS proteins and to highlight their physiological functions. At present, the emerging picture is that TDP-43 and FUS/TLS control several aspects of an mRNA's life, but they can also participate in DNA repair processes and in non-coding RNA metabolism. Although their regulatory activities are similar, they regulate mainly distinct RNA targets and show different pathogenetic mechanisms in amyotrophic lateral sclerosis/frontotemporal lobar dementia diseases. The identification of key events in these processes represents today the best chance of finding targetable options for therapeutic approaches that might actually make a difference at the clinical level. The two major RNA Binding Proteins involved in Amyotrophic Lateral Sclerosisi and Frontotemporal Dementia are TDP-43 and FUST/TLS. Both proteins are involved in regulating all aspects of RNA and RNA life cycle within neurons, from transcription, processing, and transport/stability to the formation of cytoplasmic and nuclear stress granules. For this reason, the aberrant aggregation of these factors during disease can impair multiple RNA metabolic pathways and eventually lead to neuronal death/inactivation. The purpose of this review is to provide an up-to-date perspective on what we know about this issue at the molecular level. This article is part of the Frontotemporal Dementia special issue.
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Affiliation(s)
- Antonia Ratti
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, Milan, Italy.,Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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34
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De Conti L, Akinyi MV, Mendoza-Maldonado R, Romano M, Baralle M, Buratti E. TDP-43 affects splicing profiles and isoform production of genes involved in the apoptotic and mitotic cellular pathways. Nucleic Acids Res 2015; 43:8990-9005. [PMID: 26261209 PMCID: PMC4605304 DOI: 10.1093/nar/gkv814] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 12/13/2022] Open
Abstract
In recent times, high-throughput screening analyses have broadly defined the RNA cellular targets of TDP-43, a nuclear factor involved in neurodegeneration. A common outcome of all these studies is that changing the expression levels of this protein can alter the expression of several hundred RNAs within cells. What still remains to be clarified is which changes represent direct cellular targets of TDP-43 or just secondary variations due to the general role played by this protein in RNA metabolism. Using an HTS-based splicing junction analysis we identified at least six bona fide splicing events that are consistent with being controlled by TDP-43. Validation of the data, both in neuronal and non-neuronal cell lines demonstrated that TDP-43 substantially alters the levels of isoform expression in four genes potentially important for neuropathology: MADD/IG20, STAG2, FNIP1 and BRD8. For MADD/IG20 and STAG2, these changes could also be confirmed at the protein level. These alterations were also observed in a cellular model that successfully mimics TDP-43 loss of function effects following its aggregation. Most importantly, our study demonstrates that cell cycle alterations induced by TDP-43 knockdown can be recovered by restoring the STAG2, an important component of the cohesin complex, normal splicing profile.
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Affiliation(s)
- Laura De Conti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
| | - Maureen V Akinyi
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
| | | | - Maurizio Romano
- LNCIB-Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie, Laboratorio di Oncologia Molecolare, 34012 Trieste, Italy
| | - Marco Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
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