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Li J, Song M, Liu Z, Nan F, Wang B, Qian D, Hu M. Analysis of the mRNA export protein ZC3H11A in HCMV infection and pan-cancer. Front Microbiol 2023; 14:1296725. [PMID: 38033582 PMCID: PMC10684726 DOI: 10.3389/fmicb.2023.1296725] [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: 09/19/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Background We have previously reported that human cytomegalovirus (HCMV) infection could promote the progression of glioma. Here we discovered a stress-induced nuclear protein ZC3H11A (ZC3) through high-throughput sequencing after HCMV infection, which has been reported recently by our research group in regulating mRNA export under stress conditions. And also, a thorough analysis of ZC3 in pan-cancer and the omics data of ZC3 are yet to be conducted. Methods The transcriptomes of glioma cells after HCMV infection were assessed by RNA sequencing. ZC3 mRNA and protein level following HCMV infection were validated and measured by qRT-PCR and Western-blot. The RNA sequencing and protein expression information of ZC3 across pan-cancer were analyzed and visualized by R packages. The localization of ZC3 protein was assessed by IHC images from HPA. The ZC3 proteomics and transcriptomics data in different cancers were extracted through the CPTAC data portal, and comparisons were conducted with a Python script. The genetic alteration, survival prognosis, immune infiltration analysis of ZC3 in pan-cancer were analyzed by cBioPortal, TCGA, and TIMER2 databases. The protein interaction networks were revealed by STRING, GEPIA2 and TCGA. Results Genes in mRNA processing pathways were upregulated after HCMV infection and ZC3 expression in mRNA and protein level was validated. We also discovered that the status of ZC3 were generally at high levels in cancers, although varied among different cancer types. ZC3 protein in tumor cells localized to the nuclear whereas in normal cells it was mainly found in cytoplasmic/membranous. However, from ZC3 proteomics and transcriptomics data in some cancer types, the increase in ZC3 protein was not accompanied by a significant elevation in mRNA level. Additionally, our analysis indicated that elevated ZC3 expression was primarily linked to a negative prognosis in majority cancers but still varied depending on the cancer types. Our annotation analysis suggested that ZC3-related proteins are mainly involved in mRNA processing clusters. Conclusion We demonstrated that ZC3 significantly impacted by HCMV infection in gliomas. Furthermore, we identified a set of genes exhibiting analogous expression patterns to ZC3H11A in TCGA pan-cancer cohorts, implying a potential functional role for ZC3H11A in mRNA processing. Our study provided valuable insights into the role of a new mRNA export protein ZC3 in HCMV infection and pan-cancer progression. These results lay the foundation for our next research on the regulatory mechanism of ZC3 in virus-infected tumors.
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Affiliation(s)
- Jiawen Li
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Min Song
- Department of Digestive Endoscopy, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, China
| | - Zhen Liu
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Fulong Nan
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Bin Wang
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Dongmeng Qian
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Ming Hu
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
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Kases K, Schubert E, Hajikhezri Z, Larsson M, Devi P, Darweesh M, Andersson L, Akusjärvi G, Punga T, Younis S. The RNA-binding protein ZC3H11A interacts with the nuclear poly(A)-binding protein PABPN1 and alters polyadenylation of viral transcripts. J Biol Chem 2023; 299:104959. [PMID: 37356722 PMCID: PMC10371797 DOI: 10.1016/j.jbc.2023.104959] [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: 03/09/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023] Open
Abstract
Nuclear mRNA metabolism is regulated by multiple proteins, which either directly bind to RNA or form multiprotein complexes. The RNA-binding protein ZC3H11A is involved in nuclear mRNA export, NF-κB signaling, and is essential during mouse embryo development. Furthermore, previous studies have shown that ZC3H11A is important for nuclear-replicating viruses. However, detailed biochemical characterization of the ZC3H11A protein has been lacking. In this study, we established the ZC3H11A protein interactome in human and mouse cells. We demonstrate that the nuclear poly(A)-binding protein PABPN1 interacts specifically with the ZC3H11A protein and controls ZC3H11A localization into nuclear speckles. We report that ZC3H11A specifically interacts with the human adenovirus type 5 (HAdV-5) capsid mRNA in a PABPN1-dependent manner. Notably, ZC3H11A uses the same zinc finger motifs to interact with PABPN1 and viral mRNA. Further, we demonstrate that the lack of ZC3H11A alters the polyadenylation of HAdV-5 capsid mRNA. Taken together, our results suggest that the ZC3H11A protein may act as a novel regulator of polyadenylation of nuclear mRNA.
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Affiliation(s)
- Katharina Kases
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Schubert
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Zamaneh Hajikhezri
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mårten Larsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Priya Devi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mahmoud Darweesh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Department of Microbiology and Immunology, Al-Azhr University, Assiut, Egypt
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Göran Akusjärvi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Shady Younis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Division of Immunology and Rheumatology, Stanford University, Stanford, California, USA.
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Pavitra E, Kancharla J, Gupta VK, Prasad K, Sung JY, Kim J, Tej MB, Choi R, Lee JH, Han YK, Raju GSR, Bhaskar L, Huh YS. The role of NF-κB in breast cancer initiation, growth, metastasis, and resistance to chemotherapy. Biomed Pharmacother 2023; 163:114822. [PMID: 37146418 DOI: 10.1016/j.biopha.2023.114822] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/07/2023] Open
Abstract
Breast cancer (BC) is the second most fatal disease and is the prime cause of cancer allied female deaths. BC is caused by aberrant tumor suppressor genes and oncogenes regulated by transcription factors (TFs) like NF-κB. NF-κB is a pro-inflammatory TF that crucially alters the expressions of various genes associated with inflammation, cell progression, metastasis, and apoptosis and modulates a network of genes that underlie tumorigenesis. Herein, we focus on NF-κB signaling pathways, its regulators, and the rationale for targeting NF-κB. This review also includes TFs that maintain NF-κB crosstalk and their roles in promoting angiogenesis and metastasis. In addition, we discuss the importance of combination therapies, resistance to treatment, and potential novel therapeutic strategies including nanomedicine that targets NF-κB.
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Affiliation(s)
- Eluri Pavitra
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; 3D Convergence Center, Inha University, Incheon 22212, Republic of Korea
| | - Jyothsna Kancharla
- Department of Bioscience and Biotechnology, Banasthali University, Vanasthali, Rajasthan 304022, India
| | - Vivek Kumar Gupta
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Kiran Prasad
- Department of Zoology, Guru Ghasidas Vishwavidyalaya, Bilaspur- 495009, Chhattisgarh, India
| | - Ju Yong Sung
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Jigyeong Kim
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Mandava Bhuvan Tej
- Department of Health care informatics, Sacred Heart University, 5151Park Avenue, Fair fields, CT06825, USA
| | - Rino Choi
- 3D Convergence Center, Inha University, Incheon 22212, Republic of Korea; Department of Materials Science and Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Jeong-Hwan Lee
- 3D Convergence Center, Inha University, Incheon 22212, Republic of Korea; Department of Materials Science and Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Young-Kyu Han
- Department of Energy and Materials Engineering, Dongguk University-Seoul, Seoul 04620, Republic of Korea
| | - Ganji Seeta Rama Raju
- Department of Energy and Materials Engineering, Dongguk University-Seoul, Seoul 04620, Republic of Korea.
| | - Lvks Bhaskar
- Department of Zoology, Guru Ghasidas Vishwavidyalaya, Bilaspur- 495009, Chhattisgarh, India.
| | - Yun Suk Huh
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea.
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