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Piazzi M, Bavelloni A, Salucci S, Faenza I, Blalock WL. Alternative Splicing, RNA Editing, and the Current Limits of Next Generation Sequencing. Genes (Basel) 2023; 14:1386. [PMID: 37510291 PMCID: PMC10379330 DOI: 10.3390/genes14071386] [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: 06/08/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The advent of next generation sequencing (NGS) has fostered a shift in basic analytic strategies of a gene expression analysis in diverse pathologies for the purposes of research, pharmacology, and personalized medicine. What was once highly focused research on individual signaling pathways or pathway members has, from the time of gene expression arrays, become a global analysis of gene expression that has aided in identifying novel pathway interactions, the discovery of new therapeutic targets, and the establishment of disease-associated profiles for assessing progression, stratification, or a therapeutic response. But there are significant caveats to this analysis that do not allow for the construction of the full picture. The lack of timely updates to publicly available databases and the "hit and miss" deposition of scientific data to these databases relegate a large amount of potentially important data to "garbage", begging the question, "how much are we really missing?" This brief perspective aims to highlight some of the limitations that RNA binding/modifying proteins and RNA processing impose on our current usage of NGS technologies as relating to cancer and how not fully appreciating the limitations of current NGS technology may negatively affect therapeutic strategies in the long run.
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Affiliation(s)
- Manuela Piazzi
- "Luigi Luca Cavalli-Sforza" Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 40136 Bologna, Italy
- IRCCS, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Alberto Bavelloni
- Laboratorio di Oncologia Sperimentale, IRCCS, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Sara Salucci
- Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), Università di Bologna, 40126 Bologna, Italy
| | - Irene Faenza
- Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), Università di Bologna, 40126 Bologna, Italy
| | - William L Blalock
- "Luigi Luca Cavalli-Sforza" Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 40136 Bologna, Italy
- IRCCS, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
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Lu C, Chen X, Yan Y, Ren X, Wang X, Peng B, Cai Y, Liang Q, Xu Z, Peng J. Aberrant Expression of ADARB1 Facilitates Temozolomide Chemoresistance and Immune Infiltration in Glioblastoma. Front Pharmacol 2022; 13:768743. [PMID: 35177985 PMCID: PMC8844449 DOI: 10.3389/fphar.2022.768743] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/10/2022] [Indexed: 02/05/2023] Open
Abstract
Chemoresistance, especially temozolomide (TMZ) resistance, is a major clinical challenge in the treatment of glioblastoma (GBM). Exploring the mechanisms of TMZ resistance could help us identify effective therapies. Adenosine deaminases acting on RNA (ADARs) are very important in RNA modification through regulating the A-to-I RNA editing. Recent studies have shown that ADARs regulate multiple neurotransmitter receptors, which have been linked with the occurrence and progress of GBM. Here, data from several bioinformatics databases demonstrated that adenosine deaminase RNA specific B1 (ADARB1), also named ADAR2, was upregulated in both GBM tissues and cells, and had the prognostic value in GBM patients. Moreover, ADARB1 was found to be involved in AKT-mediated TMZ resistance in GBM cells. The KEGG analysis of ADARB1-associated co-expressed genes showed that ADARB1 was potentially involved in the mitochondrial respiratory chain complex. TISIDB and GEPIA databases were further used to analyze the role of ADARB1 in tumor-immune system interactions in GBM. These findings deepened our understanding of the function of ADARB1 in tumorigenesis and therapeutic response in GBM.
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Affiliation(s)
- Can Lu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Xi Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxin Ren
- Key Laboratory of Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Xiang Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,Department of Pathology, Xiangya Changde Hospital, Changde, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jinwu Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,Department of Pathology, Xiangya Changde Hospital, Changde, China
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Zhu W, Xu Z, Huang M, Wang X, Ren X, Cai Y, Peng B, Liang Q, Chen X, Yan Y. Downregulated ADARB1 Facilitates Cell Proliferation, Invasion and has Effect on the Immune Regulation in Ovarian Cancer. Front Bioeng Biotechnol 2022; 9:792911. [PMID: 35004651 PMCID: PMC8733684 DOI: 10.3389/fbioe.2021.792911] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/08/2021] [Indexed: 02/05/2023] Open
Abstract
Ovarian cancer (OC) is typically diagnosed at an advanced stage and poses a significant challenge to treatment and recovery. Rencently, Adenosine deaminase RNA-specific B1 (ADARB1), an adenosine-to-inosine (A-to-I) RNA-editing enzyme, has been found to play an essential role in the development of cancer. However, the specific function of ADARB1 in ovarian cancer is still not fully understood. Here, we investigated the effects of ADARB1 on OC biology. By conducting bioinformatics analyses of several public databases, we found significantly decreased ADARB1 expression in OC cells and tissues. Moreover, RT-PCR and western blot showed lower ADARB1 expression in OVCAR3, HO8910pm and A2780 OC cells compared to human normal ovarian epithelial cell IOSE. Cell proliferation assay and clone formation assay showed that overexpression of ADARB1 (ADARB1-OE) inhibited the proliferation of tumor cells. Wound healing and transwell assay indicated that ADARB1-OE could suppress OC cell invasion and metastasis. Kaplan-Meier methods revealed that the patients with low level of ADARB1 displayed poor prognosis. TISIDB databases were further used to analyze the roles of ADARB1 in tumor-immune system interactions in OC patients. Furthermore, ADARB1-OE down-regulated the expression of phosphorylated AKT. Combination of ADARB1-OE and AKT inhibitor MK2206 exerted stronger cell growth inhibition. Thus, our investigation demonstrated that low levels of ADARB1 might be a potential target in the tumorigenesis and prognostic evaluation of OC patients.
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Affiliation(s)
- Wei Zhu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Meiyuan Huang
- Department of Pathology, The Affiliated Zhuzhou Hospital Xiangya Medical College, Central South University, Zhuzhou, China
| | - Xiang Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxin Ren
- Key Laboratory of Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Xi Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
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Piazzi M, Bavelloni A, Faenza I, Blalock W. Glycogen synthase kinase (GSK)-3 and the double-strand RNA-dependent kinase, PKR: When two kinases for the common good turn bad. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118769. [PMID: 32512016 PMCID: PMC7273171 DOI: 10.1016/j.bbamcr.2020.118769] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 01/08/2023]
Abstract
Glycogen synthase kinase (GSK)-3α/β and the double-stranded RNA-dependent kinase PKR are two sentinel kinases that carry-out multiple similar yet distinct functions in both the cytosol and the nucleus. While these kinases belong to separate signal transduction cascades, they demonstrate an uncanny propensity to regulate many of the same proteins either through direct phosphorylation or by altering transcription/translation, including: c-MYC, NF-κB, p53 and TAU, as well as each another. A significant number of studies centered on the GSK3 kinases have led to the identification of the GSK3 interactome and a number of substrates, which link GSK3 activity to metabolic control, translation, RNA splicing, ribosome biogenesis, cellular division, DNA repair and stress/inflammatory signaling. Interestingly, many of these same pathways and processes are controlled by PKR, but unlike the GSK3 kinases, a clear picture of proteins interacting with PKR and a complete listing of its substrates is still missing. In this review, we take a detailed look at what is known about the PKR and GSK3 kinases, how these kinases interact to influence common cellular processes (innate immunity, alternative splicing, translation, glucose metabolism) and how aberrant activation of these kinases leads to diseases such as Alzheimer's disease (AD), diabetes mellitus (DM) and cancer. GSK3α/β and PKR are major regulators of cellular homeostasis and the response to stress/inflammation and infection. GSK3α/β and PKR interact with and/or modify many of the same proteins and affect the expression of similar genes. A balance between AKT and PKR nuclear signaling may be responsible for regulating the activation of nuclear GSK3β. GSK3α/β- and PKR-dependent signaling influence major molecular mechanisms of the cell through similar intermediates. Aberrant activation of GSK3α/β and PKR is highly involved in cancer, metabolic disorders, and neurodegenerative diseases.
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Affiliation(s)
- Manuela Piazzi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (IGM-CNR), Bologna, Italy; IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alberto Bavelloni
- Laboratoria di Oncologia Sperimentale, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Irene Faenza
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - William Blalock
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (IGM-CNR), Bologna, Italy; IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy.
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