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Yao F, Zhou S, Zhang R, Chen Y, Huang W, Yu K, Yang N, Qian X, Tie X, Xu J, Zhang Y, Baheti T, Xu J, Dai X, Hao X, Zhang L, Wang X, Li Q. CRISPR/Cas9 screen reveals that targeting TRIM34 enhances ferroptosis sensitivity and augments immunotherapy efficacy in hepatocellular carcinoma. Cancer Lett 2024; 593:216935. [PMID: 38704136 DOI: 10.1016/j.canlet.2024.216935] [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: 12/12/2023] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Hepatocellular carcinoma (HCC) is a prevalent malignancy characterized by complex heterogeneity and drug resistance. Resistance to ferroptosis is closely related to the progression of HCC. While HCC tumors vary in their sensitivity to ferroptosis, the precise factors underlying this heterogeneity remain unclear. In this study, we sought to elucidate the mechanisms that contribute to ferroptosis resistance in HCC. Whole-genome CRISPR/Cas9 screen using a subtoxic concentration (IC20) of ferroptosis inducer erastin in the HCC cell line Huh7 revealed TRIM34 as a critical driver of ferroptosis resistance in HCC. Further investigation revealed that TRIM34 suppresses ferroptosis in HCC cells, promoting their proliferation, migration, and invasion both in vitro and in vivo. Furthermore, TRIM34 expression is elevated in HCC tumor tissues, correlating with a poor prognosis. Mechanistically, TRIM34 directly interacts with Up-frameshift 1 (UPF1), a core component of the nonsense-mediated mRNA decay (NMD) pathway, to promote its ubiquitination and degradation. This interaction suppresses GPX4 transcript degradation, thus promoting the protein levels of this critical ferroptosis suppressor in HCC. In light of the close crosstalk between ferroptosis and the adaptive immune response in cancer, HCC cells with targeting knockdown of TRIM34 exhibited an improved response to anti-PD-1 treatment. Taken together, the TRIM34/UPF1/GPX4 axis mediates ferroptosis resistance in HCC, thereby promoting malignant phenotypes. Targeting TRIM34 may thus represent a promising new strategy for HCC treatment.
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Affiliation(s)
- Feifan Yao
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers (The First Affiliated Hospital of Nanjing Medical University), Nanjing, Jiangsu Province, China
| | - Suiqing Zhou
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers (The First Affiliated Hospital of Nanjing Medical University), Nanjing, Jiangsu Province, China
| | - Ruizhi Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers (The First Affiliated Hospital of Nanjing Medical University), Nanjing, Jiangsu Province, China
| | - Yining Chen
- Department of Anesthesiology and Perioperative Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Wei Huang
- Department of General Surgery, The Friendship Hospital of Ili Kazakh Autonomous Prefecture, Ili & Jiangsu Joint Institute of Health, Ili, China
| | - Kai Yu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers (The First Affiliated Hospital of Nanjing Medical University), Nanjing, Jiangsu Province, China
| | - Nanmu Yang
- Department of Hepatobiliopancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Xiangjun Qian
- Department of Hepatobiliopancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Xiaofeng Tie
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers (The First Affiliated Hospital of Nanjing Medical University), Nanjing, Jiangsu Province, China
| | - Jiali Xu
- Department of Anesthesiology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu Province, China
| | - Yu Zhang
- Department of General Surgery, The Friendship Hospital of Ili Kazakh Autonomous Prefecture, Ili & Jiangsu Joint Institute of Health, Ili, China
| | - Tasiken Baheti
- Department of General Surgery, The Friendship Hospital of Ili Kazakh Autonomous Prefecture, Ili & Jiangsu Joint Institute of Health, Ili, China
| | - Jing Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xinzheng Dai
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers (The First Affiliated Hospital of Nanjing Medical University), Nanjing, Jiangsu Province, China.
| | - Xiaopei Hao
- Department of Hepatobiliopancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, 450008, China.
| | - Liren Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers (The First Affiliated Hospital of Nanjing Medical University), Nanjing, Jiangsu Province, China.
| | - Xuehao Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers (The First Affiliated Hospital of Nanjing Medical University), Nanjing, Jiangsu Province, China; Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China.
| | - Qing Li
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers (The First Affiliated Hospital of Nanjing Medical University), Nanjing, Jiangsu Province, China; Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China.
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Temaj G, Chichiarelli S, Telkoparan-Akillilar P, Saha S, Nuhii N, Hadziselimovic R, Saso L. Advances in molecular function of UPF1 in Cancer. Arch Biochem Biophys 2024; 756:109989. [PMID: 38621446 DOI: 10.1016/j.abb.2024.109989] [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: 02/06/2024] [Revised: 03/23/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
It is known that more than 10 % of genetic diseases are caused by a mutation in protein-coding mRNA (premature termination codon; PTC). mRNAs with an early stop codon are degraded by the cellular surveillance process known as nonsense-mediated mRNA decay (NMD), which prevents the synthesis of C-terminally truncated proteins. Up-frameshift-1 (UPF1) has been reported to be involved in the downregulation of various cancers, and low expression of UPF1 was shown to correlate with poor prognosis. It is known that UPF1 is a master regulator of nonsense-mediated mRNA decay (NMD). UPF1 may also function as an E3 ligase and degrade target proteins without using mRNA decay mechanisms. Increasing evidence indicates that UPF1 could serve as a good biomarker for cancer diagnosis and treatment for future therapeutic applications. Long non-coding RNAs (lncRNAs) have the ability to bind different proteins and regulate gene expression; this role in cancer cells has already been identified by different studies. This article provides an overview of the aberrant expression of UPF1, its functional properties, and molecular processes during cancer for clinical applications in cancer. We also discussed the interactions of lncRNA with UPF1 for cell growth during tumorigenesis.
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Affiliation(s)
- Gazmend Temaj
- Faculty of Pharmacy, College UBT, 10000, Prishtina, Republic of Kosovo.
| | - Silvia Chichiarelli
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, 00185, Rome, Italy.
| | | | - Sarmistha Saha
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India.
| | - Nexhibe Nuhii
- Department of Pharmacy, Faculty of Medical Sciences, State University of Tetovo, 1200, Tetovo, Macedonia.
| | - Rifat Hadziselimovic
- Faculty of Science, University of Sarajevo, 71000, Sarajevo, Bosnia and Herzegovina.
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", La Sapienza University, 00185, Rome, Italy.
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Zhao J, Wang C, Zhao L, Zhou H, Wu R, Zhang T, Ding J, Zhou J, Zheng H, Zhang L, Kong T, Zhou J, Hu Z. A Novel Four-Gene Signature Based on Nonsense-Mediated RNA Decay for Predicting Prognosis in Hepatocellular Carcinoma: Bioinformatics Analysis and Functional Validation. J Hepatocell Carcinoma 2024; 11:747-766. [PMID: 38680213 PMCID: PMC11055534 DOI: 10.2147/jhc.s450711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/18/2024] [Indexed: 05/01/2024] Open
Abstract
Purpose Nonsense-mediated RNA decay (NMD), a surveillance pathway for selective degradation of aberrant mRNAs, is associated with cancer progression. Its potential as a predictor for aggressive hepatocellular carcinoma (HCC) is unclear. Here, we present an innovative NMD risk model for predicting HCC prognosis. Methods The Cancer Genome Atlas (TCGA) data of 374 liver HCC (LIHC) and 50 normal liver samples were extracted. A risk model based on NMD-related genes was developed through least absolute shrinkage and selection operator Cox (LASSO-Cox) regression of the LIHC-TCGA data. Prognostic validation was done using GSE54236, GSE116174, and GSE76427 data. Univariate and multivariate Cox regression analyses were conducted to assess the prognostic value of the model. We also constructed nomograms for survival prediction. Tumor immune infiltration was evaluated using the CIBERSORT algorithm, and the tumor cell phenotype was assessed. Finally, mouse experiments verified UPF3B knockdown effects on HCC tumor characteristics. Results We developed a risk model based on four NMD-related genes (PABPC1, RPL8, SMG5, and UPF3B) and validated it using GSE54236, GSE116174, and GSE76427 data. The model effectively distinguished high- and low-risk groups corresponding to unfavorable and favorable HCC outcomes. Its prognostic prediction accuracy was confirmed through time-dependent ROC analysis, and clinical-use nomograms with calibration curves were developed. Single-cell RNA sequencing results indicated significantly higher expression of SMG5 and UPF3B in tumor cells. Knockdown of SMG5 and UPF3B inhibited HCC cell proliferation, invasion, and migration, while affecting cell-cycle progression and apoptosis. In vivo, UPF3B knockdown delayed tumor growth and increased immune cell infiltration. Conclusion Our NMD-related gene-based risk model can help identify therapeutic targets and biomarkers for HCC. Additionally, it assists clinicians in predicting the prognosis of HCC patients.
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Affiliation(s)
- Jiaxin Zhao
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Cheng Wang
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Liang Zhao
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Huiying Zhou
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Rui Wu
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Tao Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Jiawei Ding
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Junjie Zhou
- Department of Radiology, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Huilin Zheng
- Zhejiang Provincial Collaborative Innovation Center of Agricultural Biological Resource Biochemical Manufacturing, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Lei Zhang
- Zhejiang Provincial Collaborative Innovation Center of Agricultural Biological Resource Biochemical Manufacturing, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Tianci Kong
- Zhejiang Provincial Collaborative Innovation Center of Agricultural Biological Resource Biochemical Manufacturing, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Jie Zhou
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Zhenhua Hu
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People’s Republic of China
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Das R, Panigrahi GK. Messenger RNA Surveillance: Current Understanding, Regulatory Mechanisms, and Future Implications. Mol Biotechnol 2024:10.1007/s12033-024-01062-4. [PMID: 38411790 DOI: 10.1007/s12033-024-01062-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/02/2024] [Indexed: 02/28/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved surveillance mechanism in eukaryotes primarily deployed to ensure RNA quality control by eliminating aberrant transcripts and also involved in modulating the expression of several physiological transcripts. NMD, the mRNA surveillance pathway, is a major form of gene regulation in eukaryotes. NMD serves as one of the most significant quality control mechanisms as it primarily scans the newly synthesized transcripts and differentiates the aberrant and non-aberrant transcripts. The synthesis of truncated proteins is restricted, which would otherwise lead to cellular dysfunctions. The up-frameshift factors (UPFs) play a central role in executing the NMD event, largely by recognizing and recruiting multiple protein factors that result in the decay of non-physiological mRNAs. NMD exhibits astounding variability in its ability across eukaryotes in an array of pathological and physiological contexts. The detailed understanding of NMD and the underlying molecular mechanisms remains blurred. This review outlines our current understanding of NMD, in regulating multifaceted cellular events during development and disease. It also attempts to identify unanswered questions that deserve further investigation.
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Affiliation(s)
- Rutupurna Das
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India
| | - Gagan Kumar Panigrahi
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India.
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5
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Cha H, Kim M, Ahn N, Jeong SD, Ignatova E, Chi SW, Kim HH, Hwang J. Role of UPF1 in lncRNA-HEIH regulation for hepatocellular carcinoma therapy. Exp Mol Med 2024; 56:344-354. [PMID: 38297160 PMCID: PMC10907594 DOI: 10.1038/s12276-024-01158-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 02/02/2024] Open
Abstract
UPF1, a novel posttranscriptional regulator, regulates the abundance of transcripts, including long noncoding RNAs (lncRNAs), and thus plays an important role in cell homeostasis. In this study, we revealed that UPF1 regulates the abundance of hepatocellular carcinoma upregulated EZH2-associated lncRNA (lncRNA-HEIH) by binding the CG-rich motif, thereby regulating hepatocellular carcinoma (HCC) tumorigenesis. UPF1-bound lncRNA-HEIH was susceptible to degradation mediated by UPF1 phosphorylation via SMG1 and SMG5. According to analysis of RNA-seq and public data on patients with liver cancer, the expression of lncRNA-HEIH increased the levels of miR-194-5p targets and was inversely correlated with miR-194-5p expression in HCC patients. Furthermore, UPF1 depletion upregulated lncRNA-HEIH, which acts as a decoy of miR-194-5p that targets GNA13, thereby promoting GNA13 expression and HCC proliferation. The UPF1/lncRNA-HEIH/miR-194-5p/GNA13 regulatory axis is suggested to play a crucial role in cell progression and may be a suitable target for HCC therapy.
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Affiliation(s)
- Hyunho Cha
- Graduate School for Biomedical Science & Engineering, Hanyang University, Seoul, Korea
| | - Minwoo Kim
- Graduate School for Biomedical Science & Engineering, Hanyang University, Seoul, Korea
| | - Narae Ahn
- Graduate School for Biomedical Science & Engineering, Hanyang University, Seoul, Korea
| | - Seong Dong Jeong
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | | | - Sung Wook Chi
- Department of Life Sciences, Korea University, Seoul, Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Korea
| | - Hyeon Ho Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
- Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | - Jungwook Hwang
- Graduate School for Biomedical Science & Engineering, Hanyang University, Seoul, Korea.
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Korea.
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Patro I, Sahoo A, Nayak BR, Das R, Majumder S, Panigrahi GK. Nonsense-Mediated mRNA Decay: Mechanistic Insights and Physiological Significance. Mol Biotechnol 2023:10.1007/s12033-023-00927-4. [PMID: 37930508 DOI: 10.1007/s12033-023-00927-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved surveillance mechanism across eukaryotes and also regulates the expression of physiological transcripts, thus involved in gene regulation. It essentially ensures recognition and removal of aberrant transcripts. Therefore, the NMD protects the cellular system by restricting the synthesis of truncated proteins, potentially by eliminating the faulty mRNAs. NMD is an evolutionarily conserved surveillance mechanism across eukaryotes and also regulates the expression of physiological transcripts, thus involved in gene regulation as well. Primarily, the NMD machinery scans and differentiates the aberrant and non-aberrant transcripts. A myriad of cellular dysfunctions arise due to production of truncated proteins, so the NMD core proteins, the up-frameshift factors (UPFs) recognizes the faulty mRNAs and further recruits factors resulting in the mRNA degradation. NMD exhibits astounding variability in its ability in regulating cellular mechanisms including both pathological and physiological events. But, the detailed underlying molecular mechanisms in NMD remains blurred and require extensive investigation to gain insights on cellular homeostasis. The complexity in understanding of NMD pathway arises due to the involvement of numerous proteins, molecular interactions and their functioning in different steps of this process. Moreover methods such as alternative splicing generates numerous isoforms of mRNA, so it makes difficulties in understanding the impact of alternative splicing on the efficiency of NMD functioning. Role of NMD in cancer development is very complex. Studies have shown that in some cases cancer cells use NMD pathway as a tool to exploit the NMD mechanism to maintain tumor microenvironment. A greater level of understanding about the intricate mechanism of how tumor used NMD pathway for their benefits, a strategy can be developed for targeting and inhibiting NMD factors involved in pro-tumor activity. There are very little amount of information available about the NMD pathway, how it discriminate mRNAs that are targeted by NMD from those that are not. This review highlights our current understanding of NMD, specifically the regulatory mechanisms and attempts to outline less explored questions that warrant further investigations. Taken as a whole, a detailed molecular understanding of the NMD mechanism could lead to wide-ranging applications for improving cellular homeostasis and paving out strategies in combating pathological disorders leaping forward toward achieving United Nations sustainable development goals (SDG 3: Good health and well-being).
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Affiliation(s)
- Ipsita Patro
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Annapurna Sahoo
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India.
| | - Bilash Ranjan Nayak
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Rutupurna Das
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Sanjoy Majumder
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Gagan Kumar Panigrahi
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India.
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Nasif S, Colombo M, Uldry AC, Schröder M, de Brot S, Mühlemann O. Inhibition of nonsense-mediated mRNA decay reduces the tumorigenicity of human fibrosarcoma cells. NAR Cancer 2023; 5:zcad048. [PMID: 37681034 PMCID: PMC10480688 DOI: 10.1093/narcan/zcad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/08/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic RNA decay pathway with roles in cellular stress responses, differentiation, and viral defense. It functions in both quality control and post-transcriptional regulation of gene expression. NMD has also emerged as a modulator of cancer progression, although available evidence supports both a tumor suppressor and a pro-tumorigenic role, depending on the model. To further investigate the role of NMD in cancer, we knocked out the NMD factor SMG7 in the HT1080 human fibrosarcoma cell line, resulting in suppression of NMD function. We then compared the oncogenic properties of the parental cell line, the SMG7-knockout, and a rescue cell line in which we re-introduced both isoforms of SMG7. We also tested the effect of a drug inhibiting the NMD factor SMG1 to distinguish NMD-dependent effects from putative NMD-independent functions of SMG7. Using cell-based assays and a mouse xenograft tumor model, we showed that suppression of NMD function severely compromises the oncogenic phenotype. Molecular pathway analysis revealed that NMD suppression strongly reduces matrix metalloprotease 9 (MMP9) expression and that MMP9 re-expression partially rescues the oncogenic phenotype. Since MMP9 promotes cancer cell migration and invasion, metastasis and angiogenesis, its downregulation may contribute to the reduced tumorigenicity of NMD-suppressed cells. Collectively, our results highlight the potential value of NMD inhibition as a therapeutic approach.
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Affiliation(s)
- Sofia Nasif
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland
| | - Martino Colombo
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research, University of Bern, Switzerland
| | - Markus S Schröder
- NCCR RNA & Disease Bioinformatics Support,Department of Biology, ETH Zürich, Switzerland
| | - Simone de Brot
- COMPATH, Institute of Animal Pathology, University of Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland
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de la Peña JB, Chase R, Kunder N, Smith PR, Lou TF, Stanowick A, Suresh P, Shukla T, Butcher SE, Price TJ, Campbell ZT. Inhibition of Nonsense-Mediated Decay Induces Nociceptive Sensitization through Activation of the Integrated Stress Response. J Neurosci 2023; 43:2921-2933. [PMID: 36894318 PMCID: PMC10124962 DOI: 10.1523/jneurosci.1604-22.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 02/20/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023] Open
Abstract
RNA stability is meticulously controlled. Here, we sought to determine whether an essential post-transcriptional regulatory mechanism plays a role in pain. Nonsense-mediated decay (NMD) safeguards against translation of mRNAs that harbor premature termination codons and controls the stability of ∼10% of typical protein-coding mRNAs. It hinges on the activity of the conserved kinase SMG1. Both SMG1 and its target, UPF1, are expressed in murine DRG sensory neurons. SMG1 protein is present in both the DRG and sciatic nerve. Using high-throughput sequencing, we examined changes in mRNA abundance following inhibition of SMG1. We confirmed multiple NMD stability targets in sensory neurons, including ATF4. ATF4 is preferentially translated during the integrated stress response (ISR). This led us to ask whether suspension of NMD induces the ISR. Inhibition of NMD increased eIF2-α phosphorylation and reduced the abundance of the eIF2-α phosphatase constitutive repressor of eIF2-α phosphorylation. Finally, we examined the effects of SMG1 inhibition on pain-associated behaviors. Peripheral inhibition of SMG1 results in mechanical hypersensitivity in males and females that persists for several days and priming to a subthreshold dose of PGE2. Priming was fully rescued by a small-molecule inhibitor of the ISR. Collectively, our results indicate that suspension of NMD promotes pain through stimulation of the ISR.SIGNIFICANCE STATEMENT Nociceptors undergo long-lived changes in their plasticity which may contribute to chronic pain. Translational regulation has emerged as a dominant mechanism in pain. Here, we investigate the role of a major pathway of RNA surveillance called nonsense-mediated decay (NMD). Modulation of NMD is potentially beneficial for a broad array of diseases caused by frameshift or nonsense mutations. Our results suggest that inhibition of the rate-limiting step of NMD drives behaviors associated with pain through activation of the ISR. This work reveals complex interconnectivity between RNA stability and translational regulation and suggests an important consideration in harnessing the salubrious benefits of NMD disruption.
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Affiliation(s)
- June Bryan de la Peña
- Department of Anesthesiology, University of Wisconsin-Madison, Madison, Wisconsin 53792
| | - Rebecca Chase
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080
| | - Nikesh Kunder
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080
| | - Patrick R Smith
- Department of Anesthesiology, University of Wisconsin-Madison, Madison, Wisconsin 53792
| | - Tzu-Fang Lou
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080
| | - Alexander Stanowick
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080
| | - Prarthana Suresh
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080
| | - Tarjani Shukla
- Department of Anesthesiology, University of Wisconsin-Madison, Madison, Wisconsin 53792
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53792
| | - Theodore J Price
- Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, Texas 75080
- Department of Neuroscience, University of Texas at Dallas, Richardson, Texas 75080
| | - Zachary T Campbell
- Department of Anesthesiology, University of Wisconsin-Madison, Madison, Wisconsin 53792
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53792
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9
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Nonsense-Mediated mRNA Decay as a Mediator of Tumorigenesis. Genes (Basel) 2023; 14:genes14020357. [PMID: 36833284 PMCID: PMC9956241 DOI: 10.3390/genes14020357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved and well-characterized biological mechanism that ensures the fidelity and regulation of gene expression. Initially, NMD was described as a cellular surveillance or quality control process to promote selective recognition and rapid degradation of erroneous transcripts harboring a premature translation-termination codon (PTC). As estimated, one-third of mutated and disease-causing mRNAs were reported to be targeted and degraded by NMD, suggesting the significance of this intricate mechanism in maintaining cellular integrity. It was later revealed that NMD also elicits down-regulation of many endogenous mRNAs without mutations (~10% of the human transcriptome). Therefore, NMD modulates gene expression to evade the generation of aberrant truncated proteins with detrimental functions, compromised activities, or dominant-negative effects, as well as by controlling the abundance of endogenous mRNAs. By regulating gene expression, NMD promotes diverse biological functions during development and differentiation, and facilitates cellular responses to adaptation, physiological changes, stresses, environmental insults, etc. Mutations or alterations (such as abnormal expression, degradation, post-translational modification, etc.) that impair the function or expression of proteins associated with the NMD pathway can be deleterious to cells and may cause pathological consequences, as implicated in developmental and intellectual disabilities, genetic defects, and cancer. Growing evidence in past decades has highlighted NMD as a critical driver of tumorigenesis. Advances in sequencing technologies provided the opportunity to identify many NMD substrate mRNAs in tumor samples compared to matched normal tissues. Interestingly, many of these changes are tumor-specific and are often fine-tuned in a tumor-specific manner, suggesting the complex regulation of NMD in cancer. Tumor cells differentially exploit NMD for survival benefits. Some tumors promote NMD to degrade a subset of mRNAs, such as those encoding tumor suppressors, stress response proteins, signaling proteins, RNA binding proteins, splicing factors, and immunogenic neoantigens. In contrast, some tumors suppress NMD to facilitate the expression of oncoproteins or other proteins beneficial for tumor growth and progression. In this review, we discuss how NMD is regulated as a critical mediator of oncogenesis to promote the development and progression of tumor cells. Understanding how NMD affects tumorigenesis differentially will pave the way for the development of more effective and less toxic, targeted therapeutic opportunities in the era of personalized medicine.
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Staszewski J, Lazarewicz N, Konczak J, Migdal I, Maciaszczyk-Dziubinska E. UPF1-From mRNA Degradation to Human Disorders. Cells 2023; 12:cells12030419. [PMID: 36766761 PMCID: PMC9914065 DOI: 10.3390/cells12030419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/07/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Up-frameshift protein 1 (UPF1) plays the role of a vital controller for transcripts, ready to react in the event of an incorrect translation mechanism. It is well known as one of the key elements involved in mRNA decay pathways and participates in transcript and protein quality control in several different aspects. Firstly, UPF1 specifically degrades premature termination codon (PTC)-containing products in a nonsense-mediated mRNA decay (NMD)-coupled manner. Additionally, UPF1 can potentially act as an E3 ligase and degrade target proteins independently from mRNA decay pathways. Thus, UPF1 protects cells against the accumulation of misfolded polypeptides. However, this multitasking protein may still hide many of its functions and abilities. In this article, we summarize important discoveries in the context of UPF1, its involvement in various cellular pathways, as well as its structural importance and mutational changes related to the emergence of various pathologies and disease states. Even though the state of knowledge about this protein has significantly increased over the years, there are still many intriguing aspects that remain unresolved.
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Affiliation(s)
- Jacek Staszewski
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Correspondence: (J.S.); (E.M.-D.)
| | - Natalia Lazarewicz
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Institute of Genetics and Development of Rennes, CNRS UMR 6290, University of Rennes 1, 35000 Rennes, France
| | - Julia Konczak
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Iwona Migdal
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Ewa Maciaszczyk-Dziubinska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Correspondence: (J.S.); (E.M.-D.)
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Palo A, Patel SA, Sahoo B, Chowdary TK, Dixit M. FRG1 is a direct transcriptional regulator of nonsense-mediated mRNA decay genes. Genomics 2023; 115:110539. [PMID: 36521634 DOI: 10.1016/j.ygeno.2022.110539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 12/04/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022]
Abstract
FRG1 is the primary candidate gene for Fascioscapulohumeral Muscular Dystrophy. So far, its role has been reported in muscle development, vasculogenesis, angiogenesis, and tumorigenesis. Mechanistically studies suggest FRG1's role in RNA biogenesis which may have implications in multiple physiological processes and diseases, including tumorigenesis. Its probable role as hnRNP and association with NMD-related genes prompted us to look into FRG1's effect on NMD gene expression and the mechanism. Using microarray profiling in cell lines, we found that FRG1 altered the mRNA surveillance pathway and associated pathways, such as RNA transport and spliceosome machinery molecules. Multiple sequence alignment of core factors, namely, UPF1, UPF3B, and SMG1, showed conserved stretches of nucleotide sequence 'CTGGG'. Structural modeling followed by EMSA, ChIP-qPCR, and luciferase reporter assays showed 'CTGGG' as a FRG1 binding site. Analysis of the publicly available datasets showed that the expression of FRG1 correlates with NMD genes in different tissue types. We validated the effect of FRG1 on NMD gene transcription by qRT-PCR. Overall, FRG1 might be a transcriptional regulator of NMD genes.
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Affiliation(s)
- Ananya Palo
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Saket Awadhesbhai Patel
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Bibekananda Sahoo
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Tirumala Kumar Chowdary
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Manjusha Dixit
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
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12
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Identification and Validation of UPF1 as a Novel Prognostic Biomarker in Renal Clear Cell Carcinoma. Genes (Basel) 2022; 13:genes13112166. [DOI: 10.3390/genes13112166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Up frameshift protein 1 (UPF1) is a key component of nonsense-mediated mRNA decay (NMD) of mRNA containing premature termination codons (PTCs). The dysregulation of UPF1 has been reported in various cancers. However, the expression profile of UPF1 and its clinical significance in clear cell renal cell carcinoma (ccRCC) remains unclear. Methods: In order to detect UPF1 expression in ccRCC and its relationship with the clinical features of ccRCC, bulk RNA sequencing data were analyzed from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and ArrayExpress databases. The impact of UPF1 on the immune microenvironment of ccRCC was evaluated by multiple immune scoring algorithms to identify the cell groups that typically express UPF1 using ccRCC single cell sequencing (scRNA) data. In addition, genes co-expressed with UPF1 were identified by the weighted gene correlation network analysis (WGCNA), followed by KEGG and Reactome enrichment analysis. A series of functional experiments were performed to assess the roles of UPF1 in renal cancer cells. Finally, pan-cancer analysis of UPF1 was also performed. Results: Compared with normal tissues, the expression levels of UPF1 mRNA and protein in tumor tissues of ccRCC patients decreased significantly. In addition, patients with low expression of UPF1 had a worse prognosis. Analysis of the immune microenvironment indicated that UPF1 immune cell infiltration was closely related and the ccRCC scRNA-seq data identified that UPF1 was mainly expressed in macrophages. WGCNA analysis suggested that the functions of co-expressed genes are mainly enriched in cell proliferation and cellular processes. Experimental tests showed that knockdown of UPF1 can promote the invasion, migration and proliferation of ccRCC cells. Lastly, pan-cancer analysis revealed that UPF1 disorders were closely associated with various cancer outcomes. Conclusions: UPF1 may play a tumor suppressive role in ccRCC and modulate the immune microenvironment. The loss of UPF1 can predict the prognosis of ccRCC, making it a promising biomarker and providing a new reference for prevention and treatment.
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FANG L, QI H, WANG P, WANG S, LI T, XIA T, PIAO H, GU C. UPF1 increases amino acid levels and promotes cell proliferation in lung adenocarcinoma via the eIF2α-ATF4 axis. J Zhejiang Univ Sci B 2022; 23:863-875. [PMID: 36226539 PMCID: PMC9561404 DOI: 10.1631/jzus.b2200144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Up-frameshift 1 (UPF1), as the most critical factor in nonsense-mediated messenger RNA (mRNA) decay (NMD), regulates tumor-associated molecular pathways in many cancers. However, the role of UPF1 in lung adenocarcinoma (LUAD) amino acid metabolism remains largely unknown. In this study, we found that UPF1 was significantly correlated with a portion of amino acid metabolic pathways in LUAD by integrating bioinformatics and metabolomics. We further confirmed that UPF1 knockdown inhibited activating transcription factor 4 (ATF4) and Ser51 phosphorylation of eukaryotic translation initiation factor 2α (eIF2α), the core proteins in amino acid metabolism reprogramming. In addition, UPF1 promotes cell proliferation by increasing the amino-acid levels of LUAD cells, which depends on the function of ATF4. Clinically, UPF1 mRNA expression is abnormal in LUAD tissues, and higher expression of UPF1 and ATF4 was significantly correlated with poor overall survival (OS) in LUAD patients. Our findings reveal that UPF1 is a potential regulator of tumor-associated amino acid metabolism and may be a therapeutic target for LUAD.
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Affiliation(s)
- Lei FANG
- Department of Thoracic Surgery, Lung Cancer Diagnosis and Treatment Center of Dalian, The First Affiliated Hospital of Dalian Medical University, Dalian116011, China
| | - Huan QI
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, China
| | - Peng WANG
- Department of Thoracic Surgery, Lung Cancer Diagnosis and Treatment Center of Dalian, The First Affiliated Hospital of Dalian Medical University, Dalian116011, China
| | - Shiqing WANG
- Department of Thoracic Surgery, Lung Cancer Diagnosis and Treatment Center of Dalian, The First Affiliated Hospital of Dalian Medical University, Dalian116011, China
| | - Tianjiao LI
- Department of Thoracic Surgery, Lung Cancer Diagnosis and Treatment Center of Dalian, The First Affiliated Hospital of Dalian Medical University, Dalian116011, China
| | - Tian XIA
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, China
| | - Hailong PIAO
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, China,Hailong PIAO,
| | - Chundong GU
- Department of Thoracic Surgery, Lung Cancer Diagnosis and Treatment Center of Dalian, The First Affiliated Hospital of Dalian Medical University, Dalian116011, China,Chundong GU,
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Li Y, Hu J, Guo D, Ma W, Zhang X, Zhang Z, Lu G, He S. LncRNA SNHG5 promotes the proliferation and cancer stem cell-like properties of HCC by regulating UPF1 and Wnt-signaling pathway. Cancer Gene Ther 2022; 29:1373-1383. [PMID: 35338348 PMCID: PMC9576592 DOI: 10.1038/s41417-022-00456-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 02/10/2022] [Accepted: 03/04/2022] [Indexed: 12/22/2022]
Abstract
The role of long noncoding RNA (lncRNAs) had been demonstrated in different types of cancer, including hepatocellular carcinoma. This study was intended to investigate the role of lncRNA small nucleolar RNA host gene 5 (SNHG5) in HCC proliferation and the liver CSC-like properties. Through functional experiments, we determined that knockdown of SNHG5 repressed HCC cell proliferation and CSC-like properties, while over-expression of SNHG5 promoted cell growth. At the same time, CSC markers (CD44, CD133, and ALDH1) and related transcription factors (OCT4, SOX2, and NANOG) were downregulated when SNHG5 was knocked down. Mechanically, RNA immunoprecipitation (RIP) and RNA pulldown assay showed that SNHG5 regulated the proliferation and CSC-like properties of HCC by binding UPF1. Further investigations showed that expression of critical components of Wnt/β-catenin pathway (β-catenin, TCF4, c-myc, cyclinD1, and c-Jun) were upregulated with depletion of UPF1 in liver CSCs, which were downregulated with depletion of SNHG5. After use of the inhibitor of Wnt/β-catenin pathway, the formation of liver CSCs sphere decreased. Taken together, SNHG5 plays a critical role to promote HCC cell proliferation and cancer stem cell-like properties via UPF1 and Wnt/β-catenin pathway.
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Affiliation(s)
- Yarui Li
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, P.R. China
| | - Junbi Hu
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, P.R. China
| | - Dan Guo
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, P.R. China
| | - Wenhui Ma
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, P.R. China
| | - Xu Zhang
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, P.R. China
| | - Zhiyong Zhang
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, P.R. China
| | - Guifang Lu
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, P.R. China
| | - Shuixiang He
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, P.R. China.
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Small Nucleolar RNAs and Their Comprehensive Biological Functions in Hepatocellular Carcinoma. Cells 2022; 11:cells11172654. [PMID: 36078062 PMCID: PMC9454744 DOI: 10.3390/cells11172654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are a class of highly conserved, stable non-coding RNAs involved in both post-transcriptional modification of RNA and in ribosome biogenesis. Recent research shows that the dysfunction of snoRNAs plays a pivotal role in hepatocellular carcinoma (HCC) and related etiologies, such as hepatitis B virus (HBV), hepatitis C virus (HCV), and non-alcoholic fatty liver disease (NAFLD). Growing evidence suggests that snoRNAs act as oncogenes or tumor suppressors in hepatocellular carcinoma (HCC) through multiple mechanisms. Furthermore, snoRNAs are characterized by their stability in body fluids and their clinical relevance and represent promising tools as diagnostic and prognostic biomarkers. SnoRNAs represent an emerging area of cancer research. In this review, we summarize the classification, biogenesis, activity, and functions of snoRNAs, as well as highlight the mechanism and roles of snoRNAs in HCC and related diseases. Our findings will aid in the understanding of complex processes of tumor occurrence and development, as well as suggest potential diagnostic markers and treatment targets. Furthermore, we discuss several limitations and suggest future research and application directions.
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Tan K, Stupack DG, Wilkinson MF. Nonsense-mediated RNA decay: an emerging modulator of malignancy. Nat Rev Cancer 2022; 22:437-451. [PMID: 35624152 PMCID: PMC11009036 DOI: 10.1038/s41568-022-00481-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that selectively degrades RNAs harbouring truncating mutations that prematurely terminate translation, including nonsense, frameshift and some splice-site mutations. Recent studies show that NMD shapes the mutational landscape of tumours by selecting for mutations that tend to downregulate the expression of tumour suppressor genes but not oncogenes. This suggests that NMD can benefit tumours, a notion further supported by the finding that mRNAs encoding immunogenic neoantigen peptides are typically targeted for decay by NMD. Together, this raises the possibility that NMD-inhibitory therapy could be of therapeutic benefit against many tumour types, including those with a high load of neoantigen-generating mutations. Complicating this scenario is the evidence that NMD can also be detrimental for many tumour types, and consequently tumours often have perturbed NMD. NMD may suppress tumour generation and progression by degrading subsets of specific normal mRNAs, including those encoding stress-response proteins, signalling factors and other proteins beneficial for tumours, as well as pro-tumour non-coding RNAs. Together, these findings suggest that NMD-modulatory therapy has the potential to provide widespread therapeutic benefit against diverse tumour types. However, whether NMD should be stimulated or repressed requires careful analysis of the tumour to be treated.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Dwayne G Stupack
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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Guo T, You K, Chen X, Sun Y, Wu Y, Wu P, Jiang Y. RBM47 inhibits hepatocellular carcinoma progression by targeting UPF1 as a DNA/RNA regulator. Cell Death Dis 2022; 8:320. [PMID: 35831298 PMCID: PMC9279423 DOI: 10.1038/s41420-022-01112-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022]
Abstract
The mechanisms by which the tumor behaviors of hepatocellular carcinoma (HCC) support growth and metastasis remain largely unknown, and it has become increasingly apparent that molecular dysregulation is of considerable importance for cellular signaling pathways. Recently, RNA-binding motif protein 47 (RBM47) has been suggested to function as a tumor regulator by acting as an RNA binding protein (RBP), but its role in HCC remains ambiguous. Here, in HCC, we identified that RBM47 had an inhibitory influence on tumor behaviors in vitro and accordingly suppressed the growth and metastasis of xenograft tumors in vivo. Additionally, RBM47 was verified to positively regulate Upframeshift 1 (UPF1), which is a crucial protein involved in the nonsense-mediated RNA decay (NMD) process and was previously determined to be an HCC suppressor. Mechanistically, the stability of UPF1 mRNA was demonstrated to be enhanced with its 3’UTR bound by RBM47, which acted as an RNA binding protein. Meanwhile, RBM47 was also proven to promote the transcription of UPF1 as a transcription factor. Taken together, we concluded that RBM47 functioned as a tumor suppressor by upregulating UPF1, acting as a DNA/RNA binding protein at the transcriptional and posttranscriptional levels.
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Affiliation(s)
- Tao Guo
- Department of Pathophysiology, School of Basic Medical Sciences, Weifang Medical University, Weifang, 261053, China
| | - Ke You
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Xi Chen
- School of Stomatology, Weifang Medical University, Weifang, 261053, China
| | - Yuqi Sun
- School of Clinical Medicine, Weifang Medical University, Weifang, 261031, China
| | - Ying Wu
- Liuzhou Key Laboratory of Infectious Disease Immunity Research, Guangxi Health Commission Key Laboratory of Clinical Biotechnology, Liuzhou People's Hospital affiliated to Guangxi Medical University, Liuzhou, 545006, China
| | - Ping Wu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510000, China
| | - Yingying Jiang
- School of Stomatology, Weifang Medical University, Weifang, 261053, China. .,Department of Dentistry, Affiliated Hospital of Weifang Medical University, Weifang, 261035, China.
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Lee S, Hwang Y, Kim TH, Jeong J, Choi D, Hwang J. UPF1 Inhibits Hepatocellular Carcinoma Growth through DUSP1/p53 Signal Pathway. Biomedicines 2022; 10:biomedicines10040793. [PMID: 35453543 PMCID: PMC9029930 DOI: 10.3390/biomedicines10040793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 12/21/2022] Open
Abstract
Human hepatocellular carcinoma (HCC) has a high mortality rate because of the dearth of effective treatments. Multiple studies have shown that overexpression of UPF1, a key nonsense-mediated mRNA decay (NMD) factor, reduces HCC growth through various cell signaling pathways. However, the mechanism by which UPF1 expression retards HCC proliferation through the regulation of RNA stability remains unclear. By employing various UPF1 variants and transcriptome analysis, we revealed that overexpression of UPF1 variants, not UPF1-mediated NMD, reduces HCC tumorigenesis. Additionally, UPF1 variant overexpression reduced tumorigenesis in xenografted mice. Transcriptome analysis indicated that the level of dual specificity phosphatase 1 (DUSP1) was increased by UPF1 variants via posttranscriptional regulation. The UPF1 overexpression-mediated increase of DUSP1 activated tumor suppressor signaling, ultimately inhibiting cell growth. In this study, we highlighted the function of UPF1 as a tumor suppressor in HCC growth.
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Affiliation(s)
- Suman Lee
- Graduate School for Biomedical Science & Engineering, Hanyang University, Seoul 04763, Korea; (S.L.); (Y.H.)
| | - Yukyung Hwang
- Graduate School for Biomedical Science & Engineering, Hanyang University, Seoul 04763, Korea; (S.L.); (Y.H.)
| | - Tae Hun Kim
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea; (T.H.K.); (J.J.); (D.C.)
| | - Jaemin Jeong
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea; (T.H.K.); (J.J.); (D.C.)
| | - Dongho Choi
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea; (T.H.K.); (J.J.); (D.C.)
| | - Jungwook Hwang
- Graduate School for Biomedical Science & Engineering, Hanyang University, Seoul 04763, Korea; (S.L.); (Y.H.)
- Correspondence: ; Tel.: +82-2-2220-2427; Fax: +82-2-2220-2422
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Lejeune F. Nonsense-Mediated mRNA Decay, a Finely Regulated Mechanism. Biomedicines 2022; 10:biomedicines10010141. [PMID: 35052820 PMCID: PMC8773229 DOI: 10.3390/biomedicines10010141] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 02/01/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is both a mechanism for rapidly eliminating mRNAs carrying a premature termination codon and a pathway that regulates many genes. This implies that NMD must be subject to regulation in order to allow, under certain physiological conditions, the expression of genes that are normally repressed by NMD. Therapeutically, it might be interesting to express certain NMD-repressed genes or to allow the synthesis of functional truncated proteins. Developing such approaches will require a good understanding of NMD regulation. This review describes the different levels of this regulation in human cells.
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Affiliation(s)
- Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France;
- Unité Tumorigenèse et Résistance aux Traitements, Institut Pasteur de Lille, F-59000 Lille, France
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20
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Bongiorno R, Colombo MP, Lecis D. Deciphering the nonsense-mediated mRNA decay pathway to identify cancer cell vulnerabilities for effective cancer therapy. J Exp Clin Cancer Res 2021; 40:376. [PMID: 34852841 PMCID: PMC8638473 DOI: 10.1186/s13046-021-02192-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/22/2021] [Indexed: 12/22/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a highly conserved cellular surveillance mechanism, commonly studied for its role in mRNA quality control because of its capacity of degrading mutated mRNAs that would produce truncated proteins. However, recent studies have proven that NMD hides more complex tasks involved in a plethora of cellular activities. Indeed, it can control the stability of mutated as well as non-mutated transcripts, tuning transcriptome regulation. NMD not only displays a pivotal role in cell physiology but also in a number of genetic diseases. In cancer, the activity of this pathway is extremely complex and it is endowed with both pro-tumor and tumor suppressor functions, likely depending on the genetic context and tumor microenvironment. NMD inhibition has been tested in pre-clinical studies showing favored production of neoantigens by cancer cells, which can stimulate the triggering of an anti-tumor immune response. At the same time, NMD inhibition could result in a pro-tumor effect, increasing cancer cell adaptation to stress. Since several NMD inhibitors are already available in the clinic to treat genetic diseases, these compounds could be redirected to treat cancer patients, pending the comprehension of these variegated NMD regulation mechanisms. Ideally, an effective strategy should exploit the anti-tumor advantages of NMD inhibition and simultaneously preserve its intrinsic tumor suppressor functions. The targeting of NMD could provide a new therapeutic opportunity, increasing the immunogenicity of tumors and potentially boosting the efficacy of the immunotherapy agents now available for cancer treatment.
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Affiliation(s)
- Roberta Bongiorno
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133, Milan, Italy
| | - Mario Paolo Colombo
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133, Milan, Italy
| | - Daniele Lecis
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133, Milan, Italy.
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21
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Palma M, Leroy C, Salomé-Desnoulez S, Werkmeister E, Kong R, Mongy M, Le Hir H, Lejeune F. A role for AKT1 in nonsense-mediated mRNA decay. Nucleic Acids Res 2021; 49:11022-11037. [PMID: 34634811 PMCID: PMC8565340 DOI: 10.1093/nar/gkab882] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a highly regulated quality control mechanism through which mRNAs harboring a premature termination codon are degraded. It is also a regulatory pathway for some genes. This mechanism is subject to various levels of regulation, including phosphorylation. To date only one kinase, SMG1, has been described to participate in NMD, by targeting the central NMD factor UPF1. Here, screening of a kinase inhibitor library revealed as putative NMD inhibitors several molecules targeting the protein kinase AKT1. We present evidence demonstrating that AKT1, a central player in the PI3K/AKT/mTOR signaling pathway, plays an essential role in NMD, being recruited by the UPF3X protein to phosphorylate UPF1. As AKT1 is often overactivated in cancer cells and as this should result in increased NMD efficiency, the possibility that this increase might affect cancer processes and be targeted in cancer therapy is discussed.
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Affiliation(s)
- Martine Palma
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France.,Unité tumorigenèse et résistance aux traitements, Institut Pasteur de Lille, F-59000 Lille, France
| | - Catherine Leroy
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France.,Unité tumorigenèse et résistance aux traitements, Institut Pasteur de Lille, F-59000 Lille, France
| | - Sophie Salomé-Desnoulez
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, F-59000 Lille, France
| | - Elisabeth Werkmeister
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Rebekah Kong
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France.,Unité tumorigenèse et résistance aux traitements, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marc Mongy
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, F-59000 Lille, France
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France.,Unité tumorigenèse et résistance aux traitements, Institut Pasteur de Lille, F-59000 Lille, France
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22
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UPF1 promotes chemoresistance to oxaliplatin through regulation of TOP2A activity and maintenance of stemness in colorectal cancer. Cell Death Dis 2021; 12:519. [PMID: 34021129 PMCID: PMC8140095 DOI: 10.1038/s41419-021-03798-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 02/04/2023]
Abstract
UPF1 is proved to dysregulate in multiple tumors and influence carcinogenesis. However, the role of UPF1 in oxaliplatin resistance in colorectal cancer (CRC) remains unknown. In our study, UPF1 is upregulated in CRC in mRNA and protein levels and overexpression of UPF1 predicts a poor overall survival (OS) and recurrence-free survival (RFS) in CRC patients and is an independent risk factor for recurrence. UPF1 promotes chemoresistance to oxaliplatin in vitro and in vivo. UPF1-induced oxaliplatin resistance can be associated with interaction between zinc finger of UPF1 and Toprim of TOP2A and increasing phosphorylated TOP2A in a SMG1-dependent manner. Moreover, UPF1 maintains stemness in a TOP2A-dependent manner in CRC. Taken together, UPF1 was overexpressed and predicted a poor prognosis in CRC. UPF1 enhanced chemoresistance to oxaliplatin in CRC, which may result from regulation of TOP2A activity and maintenance of stemness. Our findings could provide a new therapy strategy for chemoresistance to oxaliplatin in CRC patients.
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23
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Nogueira G, Fernandes R, García-Moreno JF, Romão L. Nonsense-mediated RNA decay and its bipolar function in cancer. Mol Cancer 2021; 20:72. [PMID: 33926465 PMCID: PMC8082775 DOI: 10.1186/s12943-021-01364-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/19/2021] [Indexed: 12/17/2022] Open
Abstract
Nonsense-mediated decay (NMD) was first described as a quality-control mechanism that targets and rapidly degrades aberrant mRNAs carrying premature termination codons (PTCs). However, it was found that NMD also degrades a significant number of normal transcripts, thus arising as a mechanism of gene expression regulation. Based on these important functions, NMD regulates several biological processes and is involved in the pathophysiology of a plethora of human genetic diseases, including cancer. The present review aims to discuss the paradoxical, pro- and anti-tumorigenic roles of NMD, and how cancer cells have exploited both functions to potentiate the disease. Considering recent genetic and bioinformatic studies, we also provide a comprehensive overview of the present knowledge of the advantages and disadvantages of different NMD modulation-based approaches in cancer therapy, reflecting on the challenges imposed by the complexity of this disease. Furthermore, we discuss significant advances in the recent years providing new perspectives on the implications of aberrant NMD-escaping frameshifted transcripts in personalized immunotherapy design and predictive biomarker optimization. A better understanding of how NMD differentially impacts tumor cells according to their own genetic identity will certainly allow for the application of novel and more effective personalized treatments in the near future.
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Affiliation(s)
- Gonçalo Nogueira
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Rafael Fernandes
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Juan F García-Moreno
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal. .,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal.
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24
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Abstract
Long non-coding RNAs (LncRNAs) can bind to other proteins or RNAs to regulate gene expression, and its role in tumors has been extensively studied. A common RNA binding protein, UPF1, is also a key factor in a variety of RNA decay pathways. RNA decay pathways serve to control levels of particular RNA molecules. The expression of UPF1 is often dysregulated in tumors, an observation which suggests that UPF1 contributes to development of a variety of tumors. Herein, we review evidence from studies of fourteen lncRNAs interact with UPF1. The interaction between lncRNA and UPFI provide fundamental basis for cell transformation and tumorigenic growth.
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Affiliation(s)
- Junjian He
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Xiaoxin Ma
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
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25
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Adylova A, Mukhanbetzhanovna AA, Attar R, Yulaevna IM, Farooqi AA. Regulation of TGFβ/SMAD signaling by long non-coding RNAs in different cancers: Dark Knight in the Castle of molecular oncology. Noncoding RNA Res 2021; 6:23-28. [PMID: 33511320 PMCID: PMC7814108 DOI: 10.1016/j.ncrna.2020.12.003] [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: 12/20/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 11/15/2022] Open
Abstract
One of the complex themes in recent years has been the multi-layered regulation of TGFβ signaling in cancer cells. TGFβ/SMAD signaling pathway is a highly complicated web of proteins which work spatio-temporally to regulate multiple steps of carcinogenesis. TGFβ/SMAD has been shown to dualistically regulate cancer progression. Therefore, TGFβ/SMAD signaling behaves as a “double-edged sword” in molecular oncology. Accordingly, regulation of TGFβ/SMAD is multi-layered because of oncogenic and tumor suppressor long non-coding RNAs (LncRNAs). In this review, we have summarized most recent breakthroughs in our understanding related to regulation of TGFβ/SMAD signaling by lncRNAs. We have comprehensively analyzed how different lncRNAs positively and negatively regulate TGFβ/SMAD signaling in different cancers. We have gathered missing pieces of an incomplete jig-saw puzzle of lncRNA-interactome ranging from “sponge effects” of lncRNAs to mechanistic modulation of TGFβ/SMAD signaling by lncRNAs.
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Affiliation(s)
- Aima Adylova
- Biomedical Engineering & Molecular Medicine PhD candidate, Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | | | - Rukset Attar
- Department of Obstetrics and Gynecology, Yeditepe University, Turkey
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26
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Zhang K, Zhang M, Luo Z, Wen Z, Yan X. The dichotomous role of TGF-β in controlling liver cancer cell survival and proliferation. J Genet Genomics 2020; 47:497-512. [PMID: 33339765 DOI: 10.1016/j.jgg.2020.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/14/2020] [Accepted: 09/29/2020] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is the major form of primary liver cancer and one of the most prevalent and life-threatening malignancies globally. One of the hallmarks in HCC is the sustained cell survival and proliferative signals, which are determined by the balance between oncogenes and tumor suppressors. Transforming growth factor beta (TGF-β) is an effective growth inhibitor of epithelial cells including hepatocytes, through induction of cell cycle arrest, apoptosis, cellular senescence, or autophagy. The antitumorigenic effects of TGF-β are bypassed during liver tumorigenesis via multiple mechanisms. Furthermore, along with malignant progression, TGF-β switches to promote cancer cell survival and proliferation. This dichotomous nature of TGF-β is one of the barriers to therapeutic targeting in liver cancer. Thereafter, understanding the underlying molecular mechanisms is a prerequisite for discovering novel antitumor drugs that may specifically disable the growth-promoting branch of TGF-β signaling or restore its tumor-suppressive arm. This review summarizes how TGF-β inhibits or promotes liver cancer cell survival and proliferation, highlighting the functional switch mechanisms during the process.
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Affiliation(s)
- Kegui Zhang
- School of Biological Engineering, Huainan Normal University, Huainan, 232001, China
| | - Meiping Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China
| | - Zhijun Luo
- School of Basic Medical Sciences, Nanchang University, Nanchang 330006, China
| | - Zhili Wen
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
| | - Xiaohua Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China; Institute of Biomedical Sciences, Nanchang University Medical College, Nanchang, 330031, China.
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27
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Zhang Z, Wang L, Wang Q, Zhang M, Wang B, Jiang K, Ye Y, Wang S, Shen Z. Molecular Characterization and Clinical Relevance of RNA Binding Proteins in Colorectal Cancer. Front Genet 2020; 11:580149. [PMID: 33193701 PMCID: PMC7597397 DOI: 10.3389/fgene.2020.580149] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/17/2020] [Indexed: 12/22/2022] Open
Abstract
Abnormal expression of RNA binding proteins (RBPs) has been reported across various cancers. However, the potential role of RBPs in colorectal cancer (CRC) remains unclear. In this study, we performed a systematic bioinformatics analysis of RBPs in CRC. We downloaded CRC data from The Cancer Genome Atlas (TCGA) database. Our analysis identified 242 differentially expressed RBPs between tumor and normal tissues, including 200 upregulated and 42 downregulated RBPs. Next, we found eight RBPs (RRS1, PABPC1L, TERT, SMAD6, UPF3B, RP9, NOL3, and PTRH1) related to the prognoses of CRC patients. Among these eight prognosis-related RBPs, four RBPs (NOL3, PTRH1, UPF3B, and SMAD6) were selected to construct a prognostic risk score model. Furthermore, our results indicated that the prognostic risk score model accurately predicted the prognosis of CRC patients [area under the receiver operating characteristic curve (AUC)for 3- and 5-year overall survival (OS) and was 0.645 and 0.672, respectively]. Furthermore, we developed a nomogram based on a prognostic risk score model. The nomogram was able to demonstrate the wonderful performance in predicting 3- and 5-year OS. Additionally, we validated the clinical value of four risk genes in the prognostic risk score model and identified that these risk genes were associated with tumorigenesis, lymph node metastasis, distant metastasis, clinical stage, and prognosis. Finally, we used the TIMER and Human Protein Atlas (HPA)database to validate the expression of four risk genes at the transcriptional and translational levels, respectively, and used a clinical cohort to validate the roles of NOL3 and UPF3B in predicting the prognosis of CRC patients. In summary, our study demonstrated that RBPs have an effect on CRC tumor progression and might be potential prognostic biomarkers for CRC patients.
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Affiliation(s)
- Zhen Zhang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Ling Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Hepatopancreatobiliary Surgery Department I, Peking University Cancer Hospital and Institute, Beijing, China
| | - Quan Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Mengmeng Zhang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Bo Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Kewei Jiang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Shan Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
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28
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Li C, Wu L, Liu P, Li K, Zhang Z, He Y, Liu Q, Jiang P, Yang Z, Liu Z, Yuan Y, Chang L. The C/D box small nucleolar RNA SNORD52 regulated by Upf1 facilitates Hepatocarcinogenesis by stabilizing CDK1. Am J Cancer Res 2020; 10:9348-9363. [PMID: 32802196 PMCID: PMC7415794 DOI: 10.7150/thno.47677] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
Rationale: Understanding the roles of small nucleolar RNAs (snoRNAs) in hepatocarcinogenesis will provide new avenues to identify diagnostic and therapeutic targets for hepatocellular carcinoma (HCC). Our previous research confirmed the tumor-suppressive effect of Up-frameshift 1 (Upf1) in HCC. Herein, we examined the expression profiles of snoRNAs regulated by Upf1 in hepatoma cells. Methods: We examined the expression profiles of snoRNAs regulated by Upf1 in hepatoma cells using RNA-sequencing analysis and then investigated the expression and significance of SNORD52 in HCC tissue and different cell lines. The protumorigenic effects of SNORD52 on HCC cells were confirmed both in vitro and in vivo by gain-of-function and loss-of-function assays. RNA pull-down assays and mass spectrometry were used to identify the RNA-binding protein that binds to SNORD52. Results: Many snoRNAs were identified; one of which, the human C/D box small nucleolar RNA SNORD52, was upregulated in HCC tissues and negatively correlated with Upf1 expression, and patients with higher SNORD52 expression had a poor clinical prognosis. SNORD52 promoted HCC tumorigenesis both in vitro and in vivo. Mechanistically, KEGG analysis showed that SNORD52 upregulated a series of cell cycle genes in HCC cells. We further confirmed that SNORD52 upregulated CDK1 by enhancing the stability of CDK1 proteins and that the function of SNORD52 depends on the presence of CDK1. Conclusion: Overall, the present study indicates that SNORD52 could be a potential biomarker for HCC. Targeting the Upf1/SNORD52/CDK1 pathway might have therapeutic potential for HCC.
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29
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Michalak M, Katzenmaier EM, Roeckel N, Woerner SM, Fuchs V, Warnken U, Yuan YP, Bork P, Neu-Yilik G, Kulozik A, von Knebel Doeberitz M, Kloor M, Kopitz J, Gebert J. (Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism Caused by Frameshift Mutation of NMD Regulator UPF3A. Int J Mol Sci 2020; 21:ijms21155234. [PMID: 32718059 PMCID: PMC7432364 DOI: 10.3390/ijms21155234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/13/2020] [Accepted: 07/20/2020] [Indexed: 12/13/2022] Open
Abstract
DNA mismatch repair-deficient colorectal cancers (CRCs) accumulate numerous frameshift mutations at repetitive sequences recognized as microsatellite instability (MSI). When coding mononucleotide repeats (cMNRs) are affected, tumors accumulate frameshift mutations and premature termination codons (PTC) potentially leading to truncated proteins. Nonsense-mediated RNA decay (NMD) can degrade PTC-containing transcripts and protect from such faulty proteins. As it also regulates normal transcripts and cellular physiology, we tested whether NMD genes themselves are targets of MSI frameshift mutations. A high frequency of cMNR frameshift mutations in the UPF3A gene was found in MSI CRC cell lines (67.7%), MSI colorectal adenomas (55%) and carcinomas (63%). In normal colonic crypts, UPF3A expression was restricted to single chromogranin A-positive cells. SILAC-based proteomic analysis of KM12 CRC cells revealed UPF3A-dependent down-regulation of several enzymes involved in cholesterol biosynthesis. Furthermore, reconstituted UPF3A expression caused alterations of 85 phosphosites in 52 phosphoproteins. Most of them (38/52, 73%) reside in nuclear phosphoproteins involved in regulation of gene expression and RNA splicing. Since UPF3A mutations can modulate the (phospho)proteomic signature and expression of enzymes involved in cholesterol metabolism in CRC cells, UPF3A may influence other processes than NMD and loss of UPF3A expression might provide a growth advantage to MSI CRC cells.
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Affiliation(s)
- Malwina Michalak
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Department of Pediatric Oncology, Hematology and Immunology, Children’s Hospital, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Eva-Maria Katzenmaier
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
| | - Nina Roeckel
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
| | - Stefan M. Woerner
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Department of Internal Medicine I, Endocrinology and Metabolism, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Vera Fuchs
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
| | - Uwe Warnken
- Clinical Cooperation Unit Neurooncology, DKFZ (German Cancer Research Center), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;
| | - Yan P. Yuan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany;
| | - Peer Bork
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany;
- Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Gabriele Neu-Yilik
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Department of Pediatric Oncology, Hematology and Immunology, Children’s Hospital, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Andreas Kulozik
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Department of Pediatric Oncology, Hematology and Immunology, Children’s Hospital, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jürgen Kopitz
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-564223
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30
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The Complex Relationship between HTLV-1 and Nonsense-Mediated mRNA Decay (NMD). Pathogens 2020; 9:pathogens9040287. [PMID: 32326562 PMCID: PMC7238105 DOI: 10.3390/pathogens9040287] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Accepted: 04/12/2020] [Indexed: 02/07/2023] Open
Abstract
Before the establishment of an adaptive immune response, retroviruses can be targeted by several cellular host factors at different stages of the viral replication cycle. This intrinsic immunity relies on a large diversity of antiviral processes. In the case of HTLV-1 infection, these active innate host defense mechanisms are debated. Among these mechanisms, we focused on an RNA decay pathway called nonsense-mediated mRNA decay (NMD), which can target multiple viral RNAs, including HTLV-1 unspliced RNA, as has been recently demonstrated. NMD is a co-translational process that depends on the RNA helicase UPF1 and regulates the expression of multiple types of host mRNAs. RNA sensitivity to NMD depends on mRNA organization and the ribonucleoprotein (mRNP) composition. HTLV-1 has evolved several means to evade the NMD threat, leading to NMD inhibition. In the early steps of infection, NMD inhibition favours the production of HTLV-1 infectious particles, which may contribute to the survival of the fittest clones despite genome instability; however, its direct long-term impact remains to be investigated.
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Xing TR, Chen P, Wu JM, Gao LL, Yang W, Cheng Y, Tong LB. UPF1 Participates in the Progression of Endometrial Cancer by Inhibiting the Expression of lncRNA PVT1. Onco Targets Ther 2020; 13:2103-2114. [PMID: 32210576 PMCID: PMC7074825 DOI: 10.2147/ott.s233149] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/18/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Endometrial carcinoma (EC) is the primary cause of death associated with cancer globally. Thus, the possible molecular mechanism of EC needs further exploration. Up-frameshift protein 1 (UPF1) is an ATPase depending on RNA/DNA and RNA helicase depending on ATP. Long noncoding RNA (lncRNA) plasmacytoma variant translocation 1 (PVT1) was dysregulated in diverse diseases. METHODS qRT-PCR and Western blot were applied to detect UPF1 and PVT1 in EC. CCK-8, colony formation, and Transwell assays were used to test the effects of UPF1/PVT1 on cell proliferation and migration. Cells were cultured with actinomycin D to observe mRNA stability, and RNA immunoprecipitation assay was applied to verified the relationship between UPF1 and PVT1. Glucose consumption and lactate generation were measured when cells were transfected with siRNA. RESULTS Results demonstrated that the expression of UPF1 exhibited a remarkable decrement in EC tissues relative to that in non-tumor tissues. Subsequent functional experiments suggested that UPF1 decrement stimulated EC cells to grow and migrate. Moreover, UPF1 was discovered to be linked to PVT1 and had an inverse correlation with PVT1. Besides, PVT1 expression affected EC growth and migration, and PVT1 decrement alleviated the influence of UPF1 decrement on EC growth and migration and strengthened glycolysis in EC. CONCLUSION In this study, we found that UPF1 was down-regulated in EC tissues, and UPF1 might exert its role by regulating the expression of PVT1.
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Affiliation(s)
- Tian-rong Xing
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
| | - Ping Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
| | - Jia-mei Wu
- Department of Pathophysiology, School of Basic Medicine, Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
| | - Li-li Gao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
| | - Wei Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
| | - Yu Cheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
| | - Li-bo Tong
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
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Kurosaki T, Popp MW, Maquat LE. Quality and quantity control of gene expression by nonsense-mediated mRNA decay. Nat Rev Mol Cell Biol 2020; 20:406-420. [PMID: 30992545 DOI: 10.1038/s41580-019-0126-2] [Citation(s) in RCA: 417] [Impact Index Per Article: 104.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is one of the best characterized and most evolutionarily conserved cellular quality control mechanisms. Although NMD was first found to target one-third of mutated, disease-causing mRNAs, it is now known to also target ~10% of unmutated mammalian mRNAs to facilitate appropriate cellular responses - adaptation, differentiation or death - to environmental changes. Mutations in NMD genes in humans are associated with intellectual disability and cancer. In this Review, we discuss how NMD serves multiple purposes in human cells by degrading both mutated mRNAs to protect the integrity of the transcriptome and normal mRNAs to control the quantities of unmutated transcripts.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.,Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Maximilian W Popp
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.,Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA. .,Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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Jin YJ, Byun S, Han S, Chamberlin J, Kim D, Kim MJ, Lee Y. Differential alternative splicing regulation among hepatocellular carcinoma with different risk factors. BMC Med Genomics 2019; 12:175. [PMID: 31856847 PMCID: PMC6923823 DOI: 10.1186/s12920-019-0635-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 11/25/2019] [Indexed: 12/11/2022] Open
Abstract
Background Hepatitis B virus (HBV), hepatitis C virus (HCV), and alcohol consumption are predominant causes of hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying how differently these causes are implicated in HCC development are not fully understood. Therefore, we investigated differential alternative splicing (AS) regulation among HCC patients with these risk factors. Methods We conducted a genome-wide survey of AS events associated with HCCs among HBV (n = 95), HCV (n = 47), or alcohol (n = 76) using RNA-sequencing data obtained from The Cancer Genome Atlas. Results In three group comparisons of HBV vs. HCV, HBV vs. alcohol, and HCV vs. alcohol for RNA seq (ΔPSI> 0.05, FDR < 0.05), 133, 93, and 29 differential AS events (143 genes) were identified, respectively. Of 143 AS genes, eight and one gene were alternatively spliced specific to HBV and HCV, respectively. Through functional analysis over the canonical pathways and gene ontologies, we identified significantly enriched pathways in 143 AS genes including immune system, mRNA splicing-major pathway, and nonsense-mediated decay, which may be important to carcinogenesis in HCC risk factors. Among eight genes with HBV-specific splicing events, HLA-A, HLA-C, and IP6K2 exhibited more differential expression of AS events (ΔPSI> 0.1). Intron retention of HLA-A was observed more frequently in HBV-associated HCC than HCV- or alcohol-associated HCC, and intron retention of HLA-C showed vice versa. Exon 3 (based on ENST00000432678) of IP6K2 was less skipped in HBV-associated in HCC compared to HCV- or alcohol-associated HCC. Conclusion AS may play an important role in regulating transcription differences implicated in HBV-, HCV-, and alcohol-related HCC development.
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Affiliation(s)
- Young-Joo Jin
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA.,Division of Gastroenterology, Department of Internal Medicine, Inha University School of Medicine, Incheon, South Korea
| | - Seyoun Byun
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Seonggyun Han
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - John Chamberlin
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Dongwook Kim
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Min Jung Kim
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA.,Pharmacy program, Massachusetts College of Pharmacy and Health Sciences, Worcester, MA, USA
| | - Younghee Lee
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA. .,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.
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Contextual Regulation of TGF-β Signaling in Liver Cancer. Cells 2019; 8:cells8101235. [PMID: 31614569 PMCID: PMC6829617 DOI: 10.3390/cells8101235] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 02/06/2023] Open
Abstract
Primary liver cancer is one of the leading causes for cancer-related death worldwide. Transforming growth factor beta (TGF-β) is a pleiotropic cytokine that signals through membrane receptors and intracellular Smad proteins, which enter the nucleus upon receptor activation and act as transcription factors. TGF-β inhibits liver tumorigenesis in the early stage by inducing cytostasis and apoptosis, but promotes malignant progression in more advanced stages by enhancing cancer cell survival, EMT, migration, invasion and finally metastasis. Understanding the molecular mechanisms underpinning the multi-faceted roles of TGF-β in liver cancer has become a persistent pursuit during the last two decades. Contextual regulation fine-tunes the robustness, duration and plasticity of TGF-β signaling, yielding versatile albeit specific responses. This involves multiple feedback and feed-forward regulatory loops and also the interplay between Smad signaling and non-Smad pathways. This review summarizes the known regulatory mechanisms of TGF-β signaling in liver cancer, and how they channel, skew and even switch the actions of TGF-β during cancer progression.
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A Humanized Yeast Phenomic Model of Deoxycytidine Kinase to Predict Genetic Buffering of Nucleoside Analog Cytotoxicity. Genes (Basel) 2019; 10:genes10100770. [PMID: 31575041 PMCID: PMC6826991 DOI: 10.3390/genes10100770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/17/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022] Open
Abstract
Knowledge about synthetic lethality can be applied to enhance the efficacy of anticancer therapies in individual patients harboring genetic alterations in their cancer that specifically render it vulnerable. We investigated the potential for high-resolution phenomic analysis in yeast to predict such genetic vulnerabilities by systematic, comprehensive, and quantitative assessment of drug–gene interaction for gemcitabine and cytarabine, substrates of deoxycytidine kinase that have similar molecular structures yet distinct antitumor efficacy. Human deoxycytidine kinase (dCK) was conditionally expressed in the Saccharomyces cerevisiae genomic library of knockout and knockdown (YKO/KD) strains, to globally and quantitatively characterize differential drug–gene interaction for gemcitabine and cytarabine. Pathway enrichment analysis revealed that autophagy, histone modification, chromatin remodeling, and apoptosis-related processes influence gemcitabine specifically, while drug–gene interaction specific to cytarabine was less enriched in gene ontology. Processes having influence over both drugs were DNA repair and integrity checkpoints and vesicle transport and fusion. Non-gene ontology (GO)-enriched genes were also informative. Yeast phenomic and cancer cell line pharmacogenomics data were integrated to identify yeast–human homologs with correlated differential gene expression and drug efficacy, thus providing a unique resource to predict whether differential gene expression observed in cancer genetic profiles are causal in tumor-specific responses to cytotoxic agents.
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Li Y, Guo D, Ren M, Zhao Y, Wang X, Chen Y, Liu Y, Lu G, He S. Long non-coding RNA SNAI3-AS1 promotes the proliferation and metastasis of hepatocellular carcinoma by regulating the UPF1/Smad7 signalling pathway. J Cell Mol Med 2019; 23:6271-6282. [PMID: 31264769 PMCID: PMC6714236 DOI: 10.1111/jcmm.14513] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 01/04/2023] Open
Abstract
Emerging evidence has indicated that deregulation of long non-coding RNAs (lncRNAs) can contribute to the progression of human cancers, including hepatocellular carcinoma (HCC). However, the role and exact mechanism of most lncRNAs in tumours remains largely unknown. In the current study, we found a novel long non-coding RNA termed SNAI3-AS1 which was generally up-regulated in HCC tissues compared with normal control. Higher expression of SNAI3-AS1 was significantly correlated with shorter overall survival of HCC patients. Knockdown of SNAI3-AS1 inhibited the proliferation and metastasis of HCC cells in vitro, whereas overexpression of SNAI3-AS1 promoted the proliferation and metastasis of HCC cells. Further investigations showed that SNAI3-AS1 could affect HCC tumorigenesis by binding up-frameshift protein 1 (UPF1), regulating Smad7 expression and activating TGF-β/Smad pathway. Functionally, SNAI3-AS1 promoted HCC growth and metastasis by inducing tumour epithelial to mesenchymal transition (EMT). Taken together, these findings showed that SNAI3-AS1 promotes the progression of HCC by regulating the UPF1 and activating TGF-β/Smad pathway.
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Affiliation(s)
- Yarui Li
- Department of GastroenterologyThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Dan Guo
- Department of GastroenterologyThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Mudan Ren
- Department of GastroenterologyThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Yan Zhao
- Department of GastroenterologyThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Xin Wang
- Department of GastroenterologyThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Yifei Chen
- Department of GastroenterologyThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Yaping Liu
- Department of GastroenterologyThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Guifang Lu
- Department of GastroenterologyThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Shuixiang He
- Department of GastroenterologyThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
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Xie X, Lin J, Liu J, Huang M, Zhong Y, Liang B, Song X, Gu S, Chang X, Huang D, Tang A. A novel lncRNA NR4A1AS up-regulates orphan nuclear receptor NR4A1 expression by blocking UPF1-mediated mRNA destabilization in colorectal cancer. Clin Sci (Lond) 2019; 133:1457-1473. [PMID: 31253658 DOI: 10.1042/cs20181061] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 06/19/2019] [Accepted: 06/27/2019] [Indexed: 02/05/2023]
Abstract
Long non-coding RNAs (lncRNAs) play important roles in tumorigenesis and cancer progression. The orphan nuclear receptor subfamily 4 group A member 1 (NR4A1) acts as an oncogene, and is involved in colorectal cancer (CRC) development. However, the mechanism through which lncRNA regulates NR4A1 expression remains unknown. We aimed to identify lncRNAs that regulate NR4A1 and assess their underlying mechanisms in CRC. We first identified an antisense lncRNA of NR4A1 that was up-regulated in CRC tissues and cells with rapid amplification of cDNA ends (RACE), and designated it as NR4A1AS. Spearman correlation analysis showed that NR4A1AS was positively correlated with NR4A1 mRNA levels in 37 CRC tissues. Mechanistically, NR4A1AS stabilized NR4A1 mRNA by forming RNA-RNA complexes via partial base-pairing and up-regulated NR4A1 expression in CRC cells. RNA immunoprecipitation (RIP) assays revealed that knockdown of NR4A1AS expression by siRNA enhanced up-frameshift 1 (UPF1) recruitment to NR4A1 mRNA, thereby decreasing NR4A1 mRNA stability. Moreover, depletion of NR4A1AS was found to mimic the effect of NR4A1 knockdown, specifically by suppressing cell proliferation, migration and invasion, and inducing apoptosis and cell cycle arrest. Accordingly, restoring NR4A1 expression ameliorated the effects of NR4A1AS knockdown on tumor growth and metastasis of CRC cells in vitro and in vivo Thus, we conclude that NR4A1AS up-regulates NR4A1 expression by forming RNA-RNA complexes and blocking UPF1-mediated mRNA destabilization, and it functions in tumor growth and metastasis of CRC cells at least partly through regulating NR4A1, suggesting that NR4A1AS might be as a potential target for RNA-based anti-CRC drug studies.
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MESH Headings
- Animals
- Apoptosis
- Caco-2 Cells
- Cell Cycle Checkpoints
- Cell Movement
- Cell Proliferation
- Colorectal Neoplasms/enzymology
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/pathology
- Gene Expression Regulation, Neoplastic
- HCT116 Cells
- Humans
- Male
- Mice, Inbred BALB C
- Mice, Nude
- Neoplasm Invasiveness
- Nuclear Receptor Subfamily 4, Group A, Member 1/genetics
- Nuclear Receptor Subfamily 4, Group A, Member 1/metabolism
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA Stability
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Signal Transduction
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Tumor Burden
- Up-Regulation
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Affiliation(s)
- Xina Xie
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Jiatian Lin
- Department of Minimally Invasive Intervention, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Jianlan Liu
- Department of Pathology, Shenzhen People's Hospital, Shenzhen 518000, China
| | - Meihui Huang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
- Department of Pathology and Central Laboratory, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, China
| | - Yuantang Zhong
- Department of Urinary Surgery, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen 518035, China
| | - Bin Liang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Xuhong Song
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Songgang Gu
- Department of General Surgery, First Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Xiaolan Chang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Dongyang Huang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China
| | - Aifa Tang
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China
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UPF1 inhibits the hepatocellular carcinoma progression by targeting long non-coding RNA UCA1. Sci Rep 2019; 9:6652. [PMID: 31040354 PMCID: PMC6491801 DOI: 10.1038/s41598-019-43148-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 03/05/2019] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the major causes of cancer-related death worldwide. However, the molecular mechanism underlying HCC carcinogenesis remains to be further elucidated. Up-frameshift protein 1 (UPF1) is a RNA/DNA-dependent ATPase and ATP-dependent RNA helicase. Here, we explored the expression and function of UPF1 in HCC. In this study, we demonstrated that UPF1 expression was significantly reduced in hepatocellular carcinoma (HCC) tissues compared with the adjacent normal tissues. And further functional assays revealed that knockdown of UPF1 promoted HCC cells growth and invasion. Furthermore, we found that UPF1 could bind to long non-coding RNA urothelial cancer associated 1 (UCA1) and was negatively correlated with UCA1. UCA1 expression also affected HCC growth and invasion. Knockdown of UCA1 ameliorated the effect of UPF1 knock down on HCC growth and invasion. Knockdown of UPF1 enhances glycolysis in HCC. Taken together, our results provided new insights for finding novel therapeutic targets for hepatocellular carcinoma progression.
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Li Y, Zhang T, Qin S, Wang R, Li Y, Zhou Z, Chen Y, Wu Q, Su F. Effects of UPF1 expression on EMT process by targeting E‑cadherin, N‑cadherin, Vimentin and Twist in a hepatocellular carcinoma cell line. Mol Med Rep 2019; 19:2137-2143. [PMID: 30628676 PMCID: PMC6390072 DOI: 10.3892/mmr.2019.9838] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 07/30/2018] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. It has been reported that HCC has a poor prognosis. In the majority of cases, once metastatic, HCC is incurable. To identify an effective treatment for HCC, it is important to understand the underlying molecular mechanisms of HCC-associated occurrence, proliferation, metastasis and carcinogenesis. In the present study, the role of Up-frameshift 1 (UPF1), a potential tumor suppressor, was investigated in the HCC cell lines. The expression levels of UPF1 in an HCC cell line were examined by reverse transcription-quantitative polymerase chain reaction. The expression levels of 19 key proteins in numerous signaling pathways were detected via protein array analysis in the presence of UPF1 overexpression. The present study further investigated the effects of UPF1 expression levels on the epithelial-mesenchymal transition (EMT) process by targeting E-cadherin, N-cadherin, Vimentin and Twist-related protein 1 (Twist). The results of the present study revealed that UPF1 was significantly downregulated in an HCC cell line. The majority of the proteins exhibited upregulated expression levels in the presence of UPF1 overexpression in the HCC cell line, Huh-7. Key proteins, including cluster of differentiation (CD)31 (platelet endothelial cell adhesion molecule-1), Vimentin, CD44, PCNA, Ki-67, N-Cadherin, Survivin, P53, Met and retinoblastoma exhibited a significant association with UPF1. Furthermore, western blotting indicated that the expression levels of N-cadherin, Vimentin and Twist were notably upregulated while UPF1 was overexpressed; however, E-cadherin was downregulated and opposing observations were reported with protein array analysis. In summary, E-cadherin expression levels were regulated by the manifold, and UPF1, a potential tumor suppressor, may promote the EMT process in Huh-7 HCC cells. The findings of the present study suggested that UPF1 expression levels affected the EMT process by targeting E-cadherin, N-cadherin, Vimentin and Twist.
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Affiliation(s)
- Yawei Li
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Tiantian Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Shukui Qin
- Department of Medical Oncology, PLA Cancer Center, Nanjing Bayi Hospital, Nanjing, Jiangsu 210002, P.R. China
| | - Rui Wang
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Yumei Li
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Zhengguang Zhou
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Yufo Chen
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Qiong Wu
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Fang Su
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
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Fernandes R, Nogueira G, da Costa PJ, Pinto F, Romão L. Nonsense-Mediated mRNA Decay in Development, Stress and Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:41-83. [DOI: 10.1007/978-3-030-19966-1_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Wang X, Lai Q, He J, Li Q, Ding J, Lan Z, Gu C, Yan Q, Fang Y, Zhao X, Liu S. LncRNA SNHG6 promotes proliferation, invasion and migration in colorectal cancer cells by activating TGF-β/Smad signaling pathway via targeting UPF1 and inducing EMT via regulation of ZEB1. Int J Med Sci 2019; 16:51-59. [PMID: 30662328 PMCID: PMC6332483 DOI: 10.7150/ijms.27359] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 10/18/2018] [Indexed: 12/29/2022] Open
Abstract
Background: Long noncoding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides in length. They drive many important cancer phenotypes through their interactions with other cellular macromolecules including DNA, RNA and protein. Recent studies have identified numerous lncRNAs active in colorectal cancer (CRC). The lncRNA small nucleolar RNA host gene 6 (SNHG6) has been reported to have an oncogenic role in multiple cancers. However, the biological role and mechanism of SNHG6 in the tumorigenesis of CRC has not been reported in-deep. Methods: The Cancer Genome Atlas (TCGA) database and GEO database were used to identify SNHG6 expression in different human cancers and explore the relationship between SNHG6 expression and patient prognosis using Kaplan-Meier method analysis. SNHG6 expression in 77 pairs of clinical CRC tissues and different CRC cell lines were analyzed by quantitative real-time PCR (qRT-PCR). A CCK-8 assay was used to assess cell proliferation, transwell assay to detect the cell metastasis, and tumor growth was investigated with a nude mice model in vivo. Whether UPF1 and ZEB1 are downstream targets of SNHG6 was verified by bioinformatics target gene prediction, qRT-PCR and western blot. Results: TCGA data showed that SNHG6 was significantly upregulated in colorectal cancer samples in comparison with healthy data samples (P < 0.01). CRC patients with high levels of SNHG6 had a significantly shorter overall survival than those with low levels of SNHG6 (P = 0.0162). qRT-PCR confirmed that the expression of SNHG6 was significantly upregulated in CRC tissues and cell lines. Upregulation of SNHG6 expression induced RKO and HCT116 cell proliferation as well as RKO cell metastasis, while downregulation of SNHG6 expression supressed the proliferation and metastasis of RKO cells and tumor growth in vivo. UPF1 was upregulated and ZEB1 was decreased when SNHG6 knockdown, regulating the TGF-β/Smad pathway and inducing EMT respectively. Conclusions: SNHG6 may play an oncogenic role in CRC cells by activating TGF-β/Smad signaling pathway via targeting of UPF1 and inducing EMT via regulating ZEB1. This could be a prognostic biomarker and therapeutic target for CRC.
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Affiliation(s)
- Xinke Wang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, No. 1838, Guangzhou Avenue North, Guangzhou, People's Republic of China
| | - Qiuhua Lai
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, No. 1838, Guangzhou Avenue North, Guangzhou, People's Republic of China
| | - Juan He
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, No. 1838, Guangzhou Avenue North, Guangzhou, People's Republic of China
| | - Qingyuan Li
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, No. 1838, Guangzhou Avenue North, Guangzhou, People's Republic of China
| | - Jian Ding
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, No. 1838, Guangzhou Avenue North, Guangzhou, People's Republic of China
| | - Zhixian Lan
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, No. 1838, Guangzhou Avenue North, Guangzhou, People's Republic of China
| | - Chuncai Gu
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, No. 1838, Guangzhou Avenue North, Guangzhou, People's Republic of China
| | - Qun Yan
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, No. 1838, Guangzhou Avenue North, Guangzhou, People's Republic of China
| | - Yuxin Fang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, No. 1838, Guangzhou Avenue North, Guangzhou, People's Republic of China
| | - Xinmei Zhao
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, No. 1838, Guangzhou Avenue North, Guangzhou, People's Republic of China
| | - Side Liu
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, No. 1838, Guangzhou Avenue North, Guangzhou, People's Republic of China
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Elbere I, Silamikelis I, Ustinova M, Kalnina I, Zaharenko L, Peculis R, Konrade I, Ciuculete DM, Zhukovsky C, Gudra D, Radovica-Spalvina I, Fridmanis D, Pirags V, Schiöth HB, Klovins J. Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals. Clin Epigenetics 2018; 10:156. [PMID: 30545422 PMCID: PMC6293577 DOI: 10.1186/s13148-018-0593-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 11/29/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Metformin is a widely prescribed antihyperglycemic agent that has been also associated with multiple therapeutic effects in various diseases, including several types of malignancies. There is growing evidence regarding the contribution of the epigenetic mechanisms in reaching metformin's therapeutic goals; however, the effect of metformin on human cells in vivo is not comprehensively studied. The aim of our study was to examine metformin-induced alterations of DNA methylation profiles in white blood cells of healthy volunteers, employing a longitudinal study design. RESULTS Twelve healthy metformin-naïve individuals where enrolled in the study. Genome-wide DNA methylation pattern was estimated at baseline, 10 h and 7 days after the start of metformin administration. The whole-genome DNA methylation analysis in total revealed 125 differentially methylated CpGs, of which 11 CpGs and their associated genes with the most consistent changes in the DNA methylation profile were selected: POFUT2, CAMKK1, EML3, KIAA1614, UPF1, MUC4, LOC727982, SIX3, ADAM8, SNORD12B, VPS8, and several differentially methylated regions as novel potential epigenetic targets of metformin. The main functions of the majority of top-ranked differentially methylated loci and their representative cell signaling pathways were linked to the well-known metformin therapy targets: regulatory processes of energy homeostasis, inflammatory responses, tumorigenesis, and neurodegenerative diseases. CONCLUSIONS Here we demonstrate for the first time the immediate effect of short-term metformin administration at therapeutic doses on epigenetic regulation in human white blood cells. These findings suggest the DNA methylation process as one of the mechanisms involved in the action of metformin, thereby revealing novel targets and directions of the molecular mechanisms underlying the various beneficial effects of metformin. TRIAL REGISTRATION EU Clinical Trials Register, 2016-001092-74. Registered 23 March 2017, https://www.clinicaltrialsregister.eu/ctr-search/trial/2016-001092-74/LV .
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Affiliation(s)
- Ilze Elbere
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Ivars Silamikelis
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Monta Ustinova
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Ineta Kalnina
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Linda Zaharenko
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Raitis Peculis
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Ilze Konrade
- Riga East Clinical University Hospital, 2 Hipokrata Street, Riga, LV-1038, Latvia
| | - Diana Maria Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden
| | - Christina Zhukovsky
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden
| | - Dita Gudra
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Ilze Radovica-Spalvina
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Davids Fridmanis
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Valdis Pirags
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia.
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Wang YG, Zheng DH, Shi M, Xu XM. T cell dysfunction in chronic hepatitis B infection and liver cancer: evidence from transcriptome analysis. J Med Genet 2018; 56:22-28. [PMID: 30518547 DOI: 10.1136/jmedgenet-2018-105570] [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: 06/26/2018] [Revised: 08/26/2018] [Accepted: 09/22/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND T cell dysfunction occurs in many diseases, especially in chronic virus infection and cancers. However, up to now, little is known on the distinctions in T cell exhaustion between cancer and chronic virus infection. The objective of this study is to explore the transcriptional similarities and differences in exhausted CD8 +T cell between chronic hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC). METHODS RNA sequencing was performed to compare the transcriptome of CD8 +T cells isolated from healthy donors' blood, tumour tissues of patients with HCC and chronic HBV infected HCC patients' paracancerous tissues. DESeq2 algorithm was used to determine differentially expressed genes. Gene ontology and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted for in-depth analysis of these differentially expressed genes. RESULTS A total number of 2109 and 2203 genes were differentially expressed in patients with chronic HBV infection and HCC, respectively. Comparing these two groups of differentially deregulated genes, we found that nearly half of them were shared, and these shared genes were further classified into several functional categories, such as metabolic process, binding and intracellular organelle. KEGG analysis revealed that these shared deregulated genes were involved in many important pathways such as Parkinson's disease, oxidative phosphorylation and messenger RNA surveillance. Interestingly, we reported that chronic HBV infection specific deregulated genes were mainly enriched in graft versus host disease, allograft rejection, phenylalanine, tyrosine and tryptophan biosynthesis pathways. Whereas, HCC-specific deregulated genes were highly enriched in oxidative phosphorylation, thyroid cancer and endometrial cancer pathways. CONCLUSION Our study demonstrated that T cell dysfunction associated with HCC and chronic HBV infection shares high similarities, however, each possesses its own features in terms of specific genes and signalling pathways. Uncovering the differences of T cells dysfunction would facilitate our understanding the diseases pathogenesis and developing innovative therapies in the future.
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Affiliation(s)
- Yu-Gang Wang
- Department of Gastroenterology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dong-Hui Zheng
- Department of Nephrology, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Min Shi
- Department of Gastroenterology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi-Ming Xu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
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Guo L, Smith JA, Abelson M, Vlasova-St. Louis I, Schiff LA, Bohjanen PR. Reovirus infection induces stabilization and up-regulation of cellular transcripts that encode regulators of TGF-β signaling. PLoS One 2018; 13:e0204622. [PMID: 30261045 PMCID: PMC6160134 DOI: 10.1371/journal.pone.0204622] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/11/2018] [Indexed: 12/24/2022] Open
Abstract
Reovirus infection induces dramatic changes in host mRNA expression. We utilized oligonucleotide microarrays to measure cellular mRNA decay rates in mock- or reovirus-infected murine L929 cells to determine if changes in host mRNA expression are a consequence of reovirus-induced alterations in cellular mRNA stability. Our analysis detected a subset of cellular transcripts that were coordinately induced and stabilized following infection with the reovirus isolates c87 and c8, strains that led to an inhibition of cellular translation, but not following infection with Dearing, a reovirus isolate that did not negatively impact cellular translation. The induced and stabilized transcripts encode multiple regulators of TGF- β signaling, including components of the Smad signaling network and apoptosis/survival pathways. The coordinate induction, through mRNA stabilization, of multiple genes that encode components of TGF-β signaling pathways represents a novel mechanism by which the host cell responds to reovirus infection.
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Affiliation(s)
- Liang Guo
- Program in Infection and Immunity, Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Institute for Molecular Virology Training Program, Graduate Program in Comparative and Molecular Bioscience, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jennifer A. Smith
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Michelle Abelson
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Irina Vlasova-St. Louis
- Program in Infection and Immunity, Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Leslie A. Schiff
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Paul R. Bohjanen
- Program in Infection and Immunity, Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Institute for Molecular Virology Training Program, Graduate Program in Comparative and Molecular Bioscience, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
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Liu Z, Wang Y, Dou C, Sun L, Li Q, Wang L, Xu Q, Yang W, Liu Q, Tu K. MicroRNA-1468 promotes tumor progression by activating PPAR-γ-mediated AKT signaling in human hepatocellular carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:49. [PMID: 29510736 PMCID: PMC5839011 DOI: 10.1186/s13046-018-0717-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 02/22/2018] [Indexed: 02/07/2023]
Abstract
Background Accumulating evidence confirm that aberrant microRNAs (miRNAs) expression contributes to hepatocellular carcinoma (HCC) development and progression. Previous study reported that miR-1468 showed an up-regulated tendency and might be a potential prognostic biomarker in HCC samples derived from TCGA database. However, the role of miR-1468 and its underlying mechanisms involved in the growth and metastasis of HCC remain poorly investigated. Methods CCK-8, EdU, colony formation and flow cytometry were used to determine proliferation, cell cycle progression and apoptosis of HCC cells in vitro. The subcutaneous tumor model in nude mice was established to detect tumor growth of HCC in vivo. The direct binding of miR-1468 to 3’UTR of Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 2 (CITED2) and Up-frameshift protein 1 (UPF1) was confirmed by luciferase reporter assay. Results Here, we demonstrated that miR-1468 expression was up-regulated in HCC tissues and cell lines. Clinical analysis revealed that increased miR-1468 level was significantly correlated with malignant prognostic features and shorter survival. Gain- and loss-of-function experiments indicated that miR-1468 promoted cell proliferation, colony formation, cell cycle progression and induced apoptosis of HCC cells in vitro and in vivo. Moreover, CITED2 and UPF1 were identified as direct downstream targets of miR-1468 in HCC cells, and mediated the functional effects of miR-1468 in HCC, resulting in peroxisome proliferator-activated receptor-γ (PPAR-γ)/AKT signaling activation. In clinical samples of HCC, miR-1468 inversely correlated with the levels of CITED2 and UPF1, which were confirmed to be down-regulated in HCC. Restoration of CITED2 or UPF1 expression at least partially abolished the biological effects of miR-1468 on HCC cells. Moreover, alteration of PPAR-γ or AKT phosphorylation could reverse the function of miR-1468 in HCC. Conclusions Taken together, this research supports the first evidence that miR-1468 plays an oncogenic role in HCC via activating PPAR-γ/AKT pathway by targeting CITED2 and UPF1, and represents a promising therapeutic strategy for HCC patients. Electronic supplementary material The online version of this article (10.1186/s13046-018-0717-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhikui Liu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, China
| | - Yufeng Wang
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, China
| | - Changwei Dou
- Department of Hepatobiliary Surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang, 310014, China
| | - Liankang Sun
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, China
| | - Qing Li
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, China
| | - Liang Wang
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, China
| | - Qiuran Xu
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang, 310014, China
| | - Wei Yang
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, China
| | - Qingguang Liu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, China.
| | - Kangsheng Tu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, China.
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Sokół E, Kędzierska H, Czubaty A, Rybicka B, Rodzik K, Tański Z, Bogusławska J, Piekiełko-Witkowska A. microRNA-mediated regulation of splicing factors SRSF1, SRSF2 and hnRNP A1 in context of their alternatively spliced 3'UTRs. Exp Cell Res 2018; 363:208-217. [PMID: 29331391 DOI: 10.1016/j.yexcr.2018.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/29/2017] [Accepted: 01/08/2018] [Indexed: 12/30/2022]
Abstract
SRSF1, SRSF2 and hnRNP A1 are splicing factors that regulate the expression of oncogenes and tumor suppressors. SRSF1 and SRSF2 contribute to the carcinogenesis in the kidney. Despite their importance, the mechanisms regulating their expression in cancer are not entirely understood. Here, we investigated the microRNA-mediated regulation of SRSF1, SRSF2 and hnRNP A1 in renal cancer. The expression of microRNAs predicted to target SRSF1, SRSF2 and hnRNP A1 was disturbed in renal tumors compared with controls. Using qPCR, Western blot/ICC and luciferase reporter system assays we identified microRNAs that contribute to the regulation of expression of SRSF1 (miR-10b-5p, miR-203a-3p), SRSF2 (miR-183-5p, miR-200c-3p), and hnRNP A1 (miR-135a-5p, miR-149-5p). Silencing of SRSF1 and SRSF2 enhanced the expression of their targeting microRNAs. miR-183-5p and miR-200c-3p affected the expression of SRSF2-target genes, TNFRSF1B, TNFRSF9, CRADD and TP53. 3'UTR variants of SRSF1 and SRSF2 differed by the presence of miRNA-binding sites. In conclusion, we identified a group of microRNAs that contribute to the regulation of expression of SRSF1, SRSF2 and hnRNP A1. The microRNAs targeting SRSF1 and SRSF2 are involved in a regulatory feedback loop. microRNAs miR-183-5p and miR-200c-3p that target SRSF2, affect the expression of genes involved in apoptotic regulation.
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Affiliation(s)
- Elżbieta Sokół
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Hanna Kędzierska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Alicja Czubaty
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Beata Rybicka
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Katarzyna Rodzik
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Zbigniew Tański
- Masovian Specialist Hospital in Ostrołęka, Ostrołęka, Poland
| | - Joanna Bogusławska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland.
| | - Agnieszka Piekiełko-Witkowska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland.
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Generation of Cell Lines Stably Expressing a Fluorescent Reporter of Nonsense-Mediated mRNA Decay Activity. Methods Mol Biol 2017. [PMID: 29236260 DOI: 10.1007/978-1-4939-7540-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a mechanism of mRNA surveillance ubiquitous among eukaryotes. Importantly, NMD not only removes aberrant transcripts with premature stop codons, but also regulates expression of many normal genes. A recently introduced dual-color fluorescent protein-based reporter enables analysis of NMD activity in live cells. In this chapter we describe the method to generate stable transgenic cell lines expressing the splicing-dependent NMD reporter using consecutive steps of lentivirus transduction and Tol2 transposition.
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48
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Lou CH, Chousal J, Goetz A, Shum EY, Brafman D, Liao X, Mora-Castilla S, Ramaiah M, Cook-Andersen H, Laurent L, Wilkinson MF. Nonsense-Mediated RNA Decay Influences Human Embryonic Stem Cell Fate. Stem Cell Reports 2017; 6:844-857. [PMID: 27304915 PMCID: PMC4912386 DOI: 10.1016/j.stemcr.2016.05.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/13/2016] [Accepted: 05/16/2016] [Indexed: 11/18/2022] Open
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved pathway that selectively degrades specific subsets of RNA transcripts. Here, we provide evidence that NMD regulates early human developmental cell fate. We found that NMD factors tend to be expressed at higher levels in human pluripotent cells than in differentiated cells, raising the possibility that NMD must be downregulated to permit differentiation. Loss- and gain-of-function experiments in human embryonic stem cells (hESCs) demonstrated that, indeed, NMD downregulation is essential for efficient generation of definitive endoderm. RNA-seq analysis identified NMD target transcripts induced when NMD is suppressed in hESCs, including many encoding signaling components. This led us to test the role of TGF-β and BMP signaling, which we found NMD acts through to influence definitive endoderm versus mesoderm fate. Our results suggest that selective RNA decay is critical for specifying the developmental fate of specific human embryonic cell lineages. The NMD RNA degradation pathway is highly active in pluripotent cells RNA-seq analysis identifies mRNA targets of NMD in human embryonic stem cells NMD degrades mRNAs encoding TGF-β/BMP, WNT, and FGF signaling components NMD acts through signaling pathways to influence endoderm versus mesoderm cell fate
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Affiliation(s)
- Chih-Hong Lou
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer Chousal
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Alexandra Goetz
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Eleen Y Shum
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - David Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Xiaoyan Liao
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sergio Mora-Castilla
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Madhuvanthi Ramaiah
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Heidi Cook-Andersen
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Louise Laurent
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Miles F Wilkinson
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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Popp MW, Maquat LE. Nonsense-mediated mRNA Decay and Cancer. Curr Opin Genet Dev 2017; 48:44-50. [PMID: 29121514 DOI: 10.1016/j.gde.2017.10.007] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/12/2017] [Accepted: 10/15/2017] [Indexed: 11/16/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a conserved mRNA surveillance pathway that cells use to ensure the quality of transcripts and to fine-tune transcript abundance. The role of NMD in cancer development is complex. In some cases, tumors have exploited NMD to downregulate gene expression by apparently selecting for mutations causing destruction of key tumor-suppressor mRNAs. In other cases, tumors adjust NMD activity to adapt to their microenvironment. Understanding how particular tumors exploit NMD for their benefit may augment the development of new therapeutic interventions.
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Affiliation(s)
- Maximilian W Popp
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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50
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Wang M, Zhang P, Zhu Y, Kong X, Zhang Z, Hu L. Assessing the activity of nonsense-mediated mRNA decay in lung cancer. BMC Med Genomics 2017; 10:55. [PMID: 28874147 PMCID: PMC5586017 DOI: 10.1186/s12920-017-0292-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 08/29/2017] [Indexed: 11/16/2022] Open
Abstract
Background Inhibition of nonsense-mediated mRNA decay (NMD) in tumor cells can suppress tumor growth through expressing new antigens whose mRNAs otherwise are degraded by NMD. Thus NMD inhibition is a promising approach for developing cancer therapies. Apparently, the success of this approach relies on the basal NMD activity in cancer cells. If NMD is already strongly inhibited in tumors, the approach would not work. Therefore, it is crucial to assess NMD activity in cancers to forecast the efficacy of NMD-inhibition based therapy. Methods Here we develop three metrics using RNA-seq data to measure NMD activity, and apply them to a dataset consisting of 72 lung cancer (adenocarcinoma) patients. Results We show that these metrics have good correlations, and that the NMD activities in adenocarcinoma samples vary among patients: some cancerous samples show significantly stronger NMD activities than the normal tissues while some others show the opposite pattern. The variation of NMD activities among these samples may be partly explained by the varying expression of NMD effectors. Conclusions In sum, NMD activity varies among lung cancerous samples, which forecasts varying efficacies of NMD-inhibition based therapy. The developed metrics can be further used in other cancer types to assess NMD activity. Electronic supplementary material The online version of this article (10.1186/s12920-017-0292-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Peiwei Zhang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Yufei Zhu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Xiangyin Kong
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Zhenguo Zhang
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA. .,, Present Address: 17062 Murphy Ave., Irvine, CA, 92614, USA.
| | - Landian Hu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.
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