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Duman ET, Sitte M, Conrads K, Mackay A, Ludewig F, Ströbel P, Ellenrieder V, Hessmann E, Papantonis A, Salinas G. A single-cell strategy for the identification of intronic variants related to mis-splicing in pancreatic cancer. NAR Genom Bioinform 2024; 6:lqae057. [PMID: 38800828 PMCID: PMC11127633 DOI: 10.1093/nargab/lqae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/24/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024] Open
Abstract
Most clinical diagnostic and genomic research setups focus almost exclusively on coding regions and essential splice sites, thereby overlooking other non-coding variants. As a result, intronic variants that can promote mis-splicing events across a range of diseases, including cancer, are yet to be systematically investigated. Such investigations would require both genomic and transcriptomic data, but there currently exist very few datasets that satisfy these requirements. We address this by developing a single-nucleus full-length RNA-sequencing approach that allows for the detection of potentially pathogenic intronic variants. We exemplify the potency of our approach by applying pancreatic cancer tumor and tumor-derived specimens and linking intronic variants to splicing dysregulation. We specifically find that prominent intron retention and pseudo-exon activation events are shared by the tumors and affect genes encoding key transcriptional regulators. Our work paves the way for the assessment and exploitation of intronic mutations as powerful prognostic markers and potential therapeutic targets in cancer.
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Affiliation(s)
- Emre Taylan Duman
- NGS-Core Unit for Integrative Genomics, Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Maren Sitte
- NGS-Core Unit for Integrative Genomics, Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Karly Conrads
- Clinic of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Göttingen, Germany
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Institute of Medical Bioinformatics, University Medical Center, Göttingen, Germany
| | - Adi Mackay
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Fabian Ludewig
- NGS-Core Unit for Integrative Genomics, Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Philipp Ströbel
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Volker Ellenrieder
- Clinic of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Göttingen, Germany
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Comprehensive Cancer Center Lower Saxony (CCC-N), Göttingen, Germany
| | - Elisabeth Hessmann
- Clinic of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Göttingen, Germany
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Comprehensive Cancer Center Lower Saxony (CCC-N), Göttingen, Germany
| | - Argyris Papantonis
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Institute of Pathology, University Medical Center, Göttingen, Germany
- Comprehensive Cancer Center Lower Saxony (CCC-N), Göttingen, Germany
| | - Gabriela Salinas
- NGS-Core Unit for Integrative Genomics, Institute of Pathology, University Medical Center, Göttingen, Germany
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
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Li X, Zhou X, Ping X, Zhao X, Kang H, Zhang Y, Ma Y, Ge H, Liu L, Li R, Guo L. Combined Plasma Olink Proteomics and Transcriptomics Identifies CXCL1 and TNFRSF12A as Potential Predictive and Diagnostic Inflammatory Markers for Acute Kidney Injury. Inflammation 2024:10.1007/s10753-024-01993-9. [PMID: 38472598 DOI: 10.1007/s10753-024-01993-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Acute kidney injury (AKI) poses a significant global public health challenge. Current methods for detecting AKI rely on monitoring changes in serum creatinine (Scr), blood urea nitrogen (BUN), urinary output and some commonly employed biomarkers. However, these indicators are usually neither specific nor sensitive to AKI, especially in cases of mild kidney injury. AKI is accompanied by severe inflammatory reactions, resulting in the upregulation of numerous inflammation-associated proteins in the plasma. Plasma biomarkers are a noninvasive method for detecting kidney injury, and to date, plasma inflammation-associated cytokines have not been adequately studied in AKI patients. The objective of our research was to identify novel inflammatory biomarkers for AKI. We utilized Olink proteomics to analyze the alterations in plasma inflammation-related proteins in the serum of healthy mice (n = 2) or mice treated with cisplatin (n = 6). Additionally, transcriptome datasets for the lipopolysaccharide (LPS), cisplatin, and ischemia‒reperfusion injury (IRI) groups were obtained from the National Center of Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. We calculated the intersection of differentially expressed proteins (DEPs) and genes (DEGs) from both datasets. In the Olink proteomics analysis, the AKI group had significantly greater levels of 11 DEPs than did the control group. In addition, 56 common upregulated DEGs were obtained from the transcriptome dataset. The expression of CXCL1 and TNFRSF12A overlapped across all the datasets. The transcription and protein expression levels of CXCL1 and TNFRSF12A were detected in vivo. The gene and protein levels of CXCL1 and TNFRSF12A were significantly increased in different AKI mouse models and clinical patients, suggesting that these genes and proteins could be potential specific biomarkers for the identification of AKI.
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Affiliation(s)
- Xiaoyang Li
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital, Yingze District, 29 Shuangta East Street, Taiyuan, 030000, People's Republic of China
| | - Xiangyang Zhou
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital, Yingze District, 29 Shuangta East Street, Taiyuan, 030000, People's Republic of China
- Basic-Medicine of Shanxi Medical University, Yingze District, 56 Xinjian South Road, Taiyuan, 030000, People's Republic of China
| | - Xinbo Ping
- Department of Nephrology, Shanxi Provincial People's Hospital, Taiyuan, China
| | - Xin Zhao
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital, Yingze District, 29 Shuangta East Street, Taiyuan, 030000, People's Republic of China
| | - Huixia Kang
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital, Yingze District, 29 Shuangta East Street, Taiyuan, 030000, People's Republic of China
- Second Department of Nephrology, Hospital of Traditional Chinese Medicine of Shanxi Province, Taiyuan, China
| | - Yue Zhang
- The Fifth Clinical Medical College of Shanxi Medical University, Fifth Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuehong Ma
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital, Yingze District, 29 Shuangta East Street, Taiyuan, 030000, People's Republic of China
| | - Haijun Ge
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital, Yingze District, 29 Shuangta East Street, Taiyuan, 030000, People's Republic of China
| | - Lili Liu
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital, Yingze District, 29 Shuangta East Street, Taiyuan, 030000, People's Republic of China
| | - Rongshang Li
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital, Yingze District, 29 Shuangta East Street, Taiyuan, 030000, People's Republic of China
- Department of Nephrology, Shanxi Provincial People's Hospital, Taiyuan, China
| | - Lili Guo
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital, Yingze District, 29 Shuangta East Street, Taiyuan, 030000, People's Republic of China.
- Basic-Medicine of Shanxi Medical University, Yingze District, 56 Xinjian South Road, Taiyuan, 030000, People's Republic of China.
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Cui Y, Zhang Z, Lv M, Duan Z, Liu W, Gao J, Xu R, Wan Q. Chromatin target of protein arginine methyltransferases alleviates cerebral ischemia/reperfusion-induced injury by regulating RNA alternative splicing. iScience 2024; 27:108688. [PMID: 38188517 PMCID: PMC10770728 DOI: 10.1016/j.isci.2023.108688] [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: 08/22/2023] [Revised: 11/01/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
RNA splicing is a post-transcriptional event that regulates many physiological and pathological events. However, whether RNA splicing regulates cerebral I/R-induced brain injury remains largely unknown. In this study, we found that the chromatin target of Prmts (CHTOP) was highly expressed in neurons, and anti-inflammatory cytokine interleukin-10 (IL-10) upregulates its expression after ischemia. In addition, overexpression or knockdown of CHTOP alleviated or exacerbated neuronal death in both experimental stroke mice and cultured neurons. Mechanistically, RNA alternative splicing is altered early after oxygen and glucose deprivation/reoxygenation (OGD/R). CHTOP interacted with nuclear speckle-related proteins to regulate alternative mRNA splicing of neuronal survival-related genes after OGD/R. In addition, I/R injury-induced cytokines IL-10 regulate CHTOP-mediated RNA splicing to alleviate ischemic brain injury. Taken together, this study reveals the alteration of RNA splicing after OGD/R and identifies the IL-10-CHTOP-RNA splicing axis as a modulator of brain injury, which may be promising therapeutic targets for ischemic stroke.
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Affiliation(s)
- Yu Cui
- Institute of Neuroregeneration and Neurorehabilitation, Qingdao University, 308 Ningxia Road, Qingdao, Shandong 266071, China
- Qingdao Medical College, Qingdao University, Qingdao 266071, China
| | - Zhaolong Zhang
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao, Shandong 266000, China
| | - Mengfei Lv
- Institute of Neuroregeneration and Neurorehabilitation, Qingdao University, 308 Ningxia Road, Qingdao, Shandong 266071, China
- Qingdao Medical College, Qingdao University, Qingdao 266071, China
| | - Zhongying Duan
- Institute of Neuroregeneration and Neurorehabilitation, Qingdao University, 308 Ningxia Road, Qingdao, Shandong 266071, China
- Qingdao Medical College, Qingdao University, Qingdao 266071, China
| | - Wenhao Liu
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao, Shandong 266000, China
| | - Jingchen Gao
- Institute of Neuroregeneration and Neurorehabilitation, Qingdao University, 308 Ningxia Road, Qingdao, Shandong 266071, China
| | - Rui Xu
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao, Shandong 266000, China
| | - Qi Wan
- Institute of Neuroregeneration and Neurorehabilitation, Qingdao University, 308 Ningxia Road, Qingdao, Shandong 266071, China
- Qingdao Medical College, Qingdao University, Qingdao 266071, China
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Xu K, Ren Y, Fan L, Zhao S, Feng J, Zhong Q, Tu D, Wu W, Chen J, Xie P. TCF4 and RBFOX1 as peripheral biomarkers for the differential diagnosis and treatment of major depressive disorder. J Affect Disord 2024; 345:252-261. [PMID: 37890537 DOI: 10.1016/j.jad.2023.10.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Recent genome-wide association studies on major depressive disorder (MDD) have indicated the involvement of LRFN5 and OLFM4; however, the expression levels and roles of these molecules in MDD remain unclear. The present study aimed to determine the serum levels of TCF4 and RBFOX1 in patients with MDD and to investigate whether these molecules could be used as biomarkers for MDD diagnosis. METHODS The study included 99 drug-naïve MDD patients, 90 drug-treated MDD patients, and 81 healthy controls (HCs). Serum TCF4 and RBFOX1 levels were measured by ELISA. Pearson's correlation analysis was conducted to determine the association between TCF4/RBFOX1 and clinical variables. Linear support vector machine classifier was used to evaluate the diagnostic capabilities of TCF4 and RBFOX1. RESULTS Serum TCF4 and RBFOX1 levels were substantially higher in MDD patients than in HCs and significantly lower in drug-treated MDD patients than in drug-naïve MDD patients. Moreover, serum TCF4 and RBFOX1 levels were associated with the Hamilton Depression Scale score, duration of illness, serum lipids levels, and hepatic function. Thus, both these molecules showed potential as biomarkers for MDD. TCF4 and RBFOX1 combination exhibited a higher diagnostic performance, with the mean area under the curve values of 0.9861 and 0.9936 in the training and testing sets, respectively. LIMITATIONS Small sample size and investigation of only the peripheral nervous system. CONCLUSIONS TCF4 and RBFOX1 may be involved in the pathogenesis of MDD, and their combination may serve as a diagnostic biomarker panel for MDD.
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Affiliation(s)
- Ke Xu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; National Health Commission Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yi Ren
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; National Health Commission Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Li Fan
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; National Health Commission Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Shuang Zhao
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China; Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing 400016, China
| | - Jinzhou Feng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Qi Zhong
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Dianji Tu
- Department of Clinical Laboratory, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Wentao Wu
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Jianjun Chen
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China.
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; National Health Commission Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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Zhang R, Zhao W, Zhu X, Liu Y, Ding Q, Yang C, Zou H. Identification of hub genes distinguishing subtypes in endometrial stromal sarcoma through comprehensive bioinformatics analysis. Sci Rep 2024; 14:37. [PMID: 38167455 PMCID: PMC10761685 DOI: 10.1038/s41598-023-47668-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 11/16/2023] [Indexed: 01/05/2024] Open
Abstract
Diagnosing low-grade and high-grade endometrial stromal sarcoma (LG-ESS and HG-ESS) is a challenge. This study aimed to identify biomarkers. 22 ESS cases were analyzed using Illumina microarrays. Differentially expressed genes (DEGs) were identified via Limma. DEGs were analyzed with String and Cytoscape. Core genes were enriched with GO and KEGG, their pan-cancer implications and immune aspects were studied. 413 DEGs were found by exome sequencing, 2174 by GSE85383 microarray. 36 common genes were identified by Venn analysis, and 10 core genes including RBFOX1, PCDH7, FAT1 were selected. Core gene GO enrichment included cell adhesion, T cell proliferation, and KEGG focused on related pathways. Expression was evaluated across 34 cancers, identifying immune DEGs IGF1 and AVPR1A. Identifying the DEGs not only helps improve our understanding of LG-ESS, HG-ESS but also promises to be potential biomarkers for differential diagnosis between LG-ESS and HG-ESS and new therapeutic targets.
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Affiliation(s)
- Ruiqi Zhang
- Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Weilin Zhao
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Hubei, 442000, China
| | - Xingyao Zhu
- Department of Pathology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang, 310009, China
| | - Yuhua Liu
- Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Qi Ding
- Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Caiyun Yang
- Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Hong Zou
- Department of Pathology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang, 310009, China.
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Wang P, Chen W, Zhao S, Cheng F. The role of LncRNA-regulated autophagy in AKI. Biofactors 2023; 49:1010-1021. [PMID: 37458310 DOI: 10.1002/biof.1980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/16/2023] [Indexed: 10/04/2023]
Abstract
Acute kidney injury (AKI) is a complex clinical syndrome involving a series of pathophysiological processes regulated by multiple pathways at the molecular and cellular level. Long noncoding RNAs (lncRNAs) play an important role in the regulation of epigenetics, and their regulation of autophagy-related genes in AKI has attracted increasing attention. However, the role of lncRNA-regulated autophagy in AKI has not been fully elucidated. Evidence indicated that lncRNAs play regulatory roles in most factors that induce AKI. LncRNAs can regulate autophagy in AKI via a complex network of regulatory pathways to affect the development and prognosis of AKI. This article reviewed and analyzed the pathways of lncRNA regulation of autophagy in AKI in recent years. The results provide new ideas for further study of the pathophysiological process and targeted therapy for AKI.
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Affiliation(s)
- Peihan Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wu Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Sheng Zhao
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Fan Cheng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
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7
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Wang S, Ma J, Qiu H, Liu S, Zhang S, Liu H, Zhang P, Ge RL, Li G, Cui S. Plasma exosomal microRNA expression profiles in patients with high-altitude polycythemia. Blood Cells Mol Dis 2023; 98:102707. [DOI: 10.1016/j.bcmd.2022.102707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
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Li B, Lin F, Xia Y, Ye Z, Yan X, Song B, Yuan T, Li L, Zhou X, Yu W, Cheng F. The Intersection of Acute Kidney Injury and Non-Coding RNAs: Inflammation. Front Physiol 2022; 13:923239. [PMID: 35755446 PMCID: PMC9218900 DOI: 10.3389/fphys.2022.923239] [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: 04/19/2022] [Accepted: 05/16/2022] [Indexed: 12/02/2022] Open
Abstract
Acute renal injury (AKI) is a complex clinical syndrome, involving a series of pathophysiological processes, in which inflammation plays a key role. Identification and verification of gene signatures associated with inflammatory onset and progression are imperative for understanding the molecular mechanisms involved in AKI pathogenesis. Non-coding RNAs (ncRNAs), involved in epigenetic modifications of inflammatory responses, are associated with the aberrant expression of inflammation-related genes in AKI. However, its regulatory role in gene expression involves precise transcriptional regulation mechanisms which have not been fully elucidated in the complex and volatile inflammatory response of AKI. In this study, we systematically review current research on the intrinsic molecular mechanisms of ncRNAs that regulate the inflammatory response in AKI. We aim to provide potential research directions and strategies for developing ncRNA-targeted gene therapies as an intervention for the inflammatory damage in AKI.
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Affiliation(s)
- Bojun Li
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fangyou Lin
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuqi Xia
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zehua Ye
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xinzhou Yan
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Baofeng Song
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tianhui Yuan
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lei Li
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiangjun Zhou
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weimin Yu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fan Cheng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
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