1
|
Kolipaka R, Magesh I, Bharathy MA, Karthik S, Saranya I, Selvamurugan N. A potential function for MicroRNA-124 in normal and pathological bone conditions. Noncoding RNA Res 2024; 9:687-694. [PMID: 38577015 PMCID: PMC10990750 DOI: 10.1016/j.ncrna.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/22/2024] [Accepted: 02/25/2024] [Indexed: 04/06/2024] Open
Abstract
Cells produce short single-stranded non-coding RNAs (ncRNAs) called microRNAs (miRNAs), which actively regulate gene expression at the posttranscriptional level. Several miRNAs have been observed to exert significant impacts on bone health and bone-related disorders. One of these, miR-124, is observed in bone microenvironments and is conserved across species. It affects bone cell growth and differentiation by activating different transcription factors and signaling pathways. In-depth functional analyses of miR-124 have revealed several physiological and pathological roles exerted through interactions with other ncRNAs. Deciphering these RNA-mediated signaling networks and pathways is essential for understanding the potential impacts of dysregulated miRNA functions on bone biology. In this review, we aim to provide a comprehensive analysis of miR-124's involvement in bone physiology and pathology. We highlight the importance of miR-124 in controlling transcription factors and signaling pathways that promote bone growth. This review reveals therapeutic implications for the treatment of bone-related diseases.
Collapse
Affiliation(s)
- Rushil Kolipaka
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - Induja Magesh
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - M.R. Ashok Bharathy
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - S. Karthik
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - I. Saranya
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - N. Selvamurugan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| |
Collapse
|
2
|
Dunn-Davies H, Dudnakova T, Nogara A, Rodor J, Thomas AC, Parish E, Gautier P, Meynert A, Ulitsky I, Madeddu P, Caporali A, Baker A, Tollervey D, Mitić T. Control of endothelial cell function and arteriogenesis by MEG3:EZH2 epigenetic regulation of integrin expression. Mol Ther Nucleic Acids 2024; 35:102173. [PMID: 38617973 PMCID: PMC11015509 DOI: 10.1016/j.omtn.2024.102173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
Epigenetic processes involving long non-coding RNAs regulate endothelial gene expression. However, the underlying regulatory mechanisms causing endothelial dysfunction remain to be elucidated. Enhancer of zeste homolog 2 (EZH2) is an important rheostat of histone H3K27 trimethylation (H3K27me3) that represses endothelial targets, but EZH2 RNA binding capacity and EZH2:RNA functional interactions have not been explored in post-ischemic angiogenesis. We used formaldehyde/UV-assisted crosslinking ligation and sequencing of hybrids and identified a new role for maternally expressed gene 3 (MEG3). MEG3 formed the predominant RNA:RNA hybrid structures in endothelial cells. Moreover, MEG3:EZH2 assists recruitment onto chromatin. By EZH2-chromatin immunoprecipitation, following MEG3 depletion, we demonstrated that MEG3 controls recruitment of EZH2/H3K27me3 onto integrin subunit alpha4 (ITGA4) promoter. Both MEG3 knockdown or EZH2 inhibition (A-395) promoted ITGA4 expression and improved endothelial cell migration and adhesion to fibronectin in vitro. The A-395 inhibitor re-directed MEG3-assisted chromatin remodeling, offering a direct therapeutic benefit by increasing endothelial function and resilience. This approach subsequently increased the expression of ITGA4 in arterioles following ischemic injury in mice, thus promoting arteriogenesis. Our findings show a context-specific role for MEG3 in guiding EZH2 to repress ITGA4. Novel therapeutic strategies could antagonize MEG3:EZH2 interaction for pre-clinical studies.
Collapse
Affiliation(s)
- Hywel Dunn-Davies
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building Max Born Crescent, King’s Buildings, Edinburgh EH9 3BF, UK
| | - Tatiana Dudnakova
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Antonella Nogara
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Julie Rodor
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Anita C. Thomas
- Bristol Medical School, Translational Health Sciences, University of Bristol, Research and Teaching Floor Level 7, Queens Building, Bristol Royal Infirmary, Bristol BS2 8HW, UK
| | - Elisa Parish
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Alison Meynert
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann-UK Building rm. 007, Weizmann Institute of Science Rehovot 76100, Israel
| | - Paolo Madeddu
- Bristol Medical School, Translational Health Sciences, University of Bristol, Research and Teaching Floor Level 7, Queens Building, Bristol Royal Infirmary, Bristol BS2 8HW, UK
| | - Andrea Caporali
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Andrew Baker
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building Max Born Crescent, King’s Buildings, Edinburgh EH9 3BF, UK
| | - Tijana Mitić
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| |
Collapse
|
3
|
Aghaei-Zarch SM. Crosstalk between MiRNAs/ lncRNAs and PI3K/AKT signaling pathway in diabetes mellitus: Mechanistic and therapeutic perspectives. Noncoding RNA Res 2024; 9:486-507. [PMID: 38511053 PMCID: PMC10950585 DOI: 10.1016/j.ncrna.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/24/2023] [Accepted: 01/09/2024] [Indexed: 03/22/2024] Open
Abstract
Diabetes as a fastest growing diseases worldwide is characterized by elevated blood glucose levels. There's an enormous financial burden associated with this endocrine disorder, with unequal access to health care between developed and developing countries. PI3Ks (phosphoinositide 3-kinases) have been demonstrated to be crucial for glucose homeostasis, and malfunctioning of these molecules can contribute to an increase in glucose serum levels, the main pathophysiological feature of diabetes. Additionally, recent evidence suggests that miRNAs and lncRNAs are reciprocally interacting with this signaling pathway. It is therefore evident that abnormal regulation of miRNAs/lncRNAs in the lncRNAs/miRNAs/PI3K/AKT axis is related to clinicopathological characteristics and plays a crucial role in the regulation of biological processes. It has therefore been attempted in this review to describe the interaction between PI3K/AKT signaling pathway and various miRNAs/lncRNAs and their importance in DM biology. We also presented the clinical applications of PI3K/AKT-related ncRNAs/herbal medicine in patients with DM.
Collapse
Affiliation(s)
- Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
4
|
Yu S, Li Y, Lu X, Han Z, Li C, Yuan X, Guo D. The regulatory role of miRNA and lncRNA on autophagy in diabetic nephropathy. Cell Signal 2024; 118:111144. [PMID: 38493883 DOI: 10.1016/j.cellsig.2024.111144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/09/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Diabetic nephropathy (DN) is a serious complication of diabetes that causes glomerular sclerosis and end-stage renal disease, leading to ascending morbidity and mortality in diabetic patients. Excessive accumulation of aberrantly modified proteins or damaged organelles, such as advanced glycation end-products, dysfunctional mitochondria, and inflammasomes is associated with the pathogenesis of DN. As one of the main degradation pathways, autophagy recycles toxic substances to maintain cellular homeostasis and autophagy dysregulation plays a crucial role in DN progression. MicroRNA (miRNA) and long non-coding RNA (lncRNA) are non-coding RNA (ncRNA) molecules that regulate gene expression and have been implicated in both physiological and pathological conditions. Recent studies have revealed that autophagy-regulating miRNA and lncRNA have been involved in pathological processes of DN, including renal cell injury, mitochondrial dysfunction, inflammation, and renal fibrosis. This review summarizes the role of autophagy in DN and emphasizes the modulation of miRNA and lncRNA on autophagy during disease progression, for the development of promising interventions by targeting these ncRNAs in this disease.
Collapse
Affiliation(s)
- Siming Yu
- Department of Nephrology II, First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin 150036, China
| | - Yue Li
- Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Xinxin Lu
- Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Zehui Han
- Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Chunsheng Li
- Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Xingxing Yuan
- Heilongjiang University of Chinese Medicine, Harbin 150040, China; Department of Gastroenterology, Heilongjiang Academy of Traditional Chinese Medicine, Harbin 150006, China
| | - Dandan Guo
- Department of Cardiology, Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin 150001, China.
| |
Collapse
|
5
|
Rajendran P, Sekar R, Abdallah BM, Fathima JH S, Ali EM, Jayaraman S, Abdelsalam SA, Veeraraghavan V. Epigenetic modulation of long noncoding RNA H19 in oral squamous cell carcinoma-A narrative review. Noncoding RNA Res 2024; 9:602-611. [PMID: 38532798 PMCID: PMC10963247 DOI: 10.1016/j.ncrna.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 03/28/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) showed a seemingly increasing incidence in the last decade. In India, despite the use of tobacco decreased rapidly, in the past five years, the incidence pattern of OSCC over gender and age showed a drastic shift. About 51 % of the head and neck cancers are not associated with habits. Studies exploring various contributing factors in the incidence of this malignancy have documented. Recently, the epigenetic factors associated with the induction and progression of OSCC were explored. More than 90 % of the human genome is made up of non-coding transcriptome, which believed to be noises. However, these non-coding RNAs were identified to be the major epigenetic modulators, which raises concern over incidence of carcinoma in non-habit patients. H19 is a long non coding RNA which proved to be an effective biomarker in various carcinoma. Its role in oral squamous cell cancer was not investigated in depth. This review discusses in detail the various epigenetic role of H19 in inducing oral carcinogenesis.
Collapse
Affiliation(s)
- Peramaiyan Rajendran
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
| | - Ramya Sekar
- Department of Oral Pathology & Microbiology, Meenakshi Ammal Dental College & Hospital, Alapakkam Main Road, Maduravoyal, Chennai, 95, TN, India
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
| | - Basem M. Abdallah
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Shazia Fathima JH
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
- Department of Oral Pathology and Microbiology, Ragas Dental College and Hospitals, Chennai, 600119, Tamil Nadu, India
| | - Enas M. Ali
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Cairo, 12613, Egypt
| | - Selvaraj Jayaraman
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
| | - Salaheldin Abdelraouf Abdelsalam
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Department of Zoology, Faculty of Science, Assiut University, Assiut, 71515, Egypt
| | - Vishnupriya Veeraraghavan
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
| |
Collapse
|
6
|
Xiao T, Yan A, Tan L, Zhu H, Gao W. LncRNA HOXA‑AS2 is a prognostic and clinicopathological predictor in patients with cancer: A meta‑analysis. Oncol Lett 2024; 27:226. [PMID: 38586205 PMCID: PMC10996033 DOI: 10.3892/ol.2024.14359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/23/2024] [Indexed: 04/09/2024] Open
Abstract
Elevated expression of long non-coding RNA homeobox A cluster antisense RNA 2 (lncRNA HOXA-AS2) is known to have prognostic value in various solid tumors. The present meta-analysis aimed to comprehensively quantify its prognostic significance across a wider spectrum of malignancies and to provide an updated synthesis of evidence that could refine prognostic models. To achieve this aim, multiple databases were carefully searched for lncRNA HOXA-AS2-related articles published in the past 10 years. Hazard ratios (HRs) or odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to demonstrate the prognostic value of lncRNA HOXA-AS2 using Stata 15.0 software. The function of lncRNA HOXA-AS2 was inferred from its associations with key clinical outcomes such as lymph node metastasis, distant metastasis, tumor stage and tumor size, which may reflect its role in tumor biology. In the present systematic review and meta-analysis of 454 patients across 7 studies, it was found that high lncRNA HOXA-AS2 expression was significantly associated with a shorter overall survival (OS) time in patients with cancer (HR=2.14; 95% CI, 1.40-3.27; P<0.001). High lncRNA HOXA-AS2 expression was also associated with lymph node metastasis [odds ratio (OR)=2.06; 95% CI, 1.07-3.99; P=0.032], distant metastasis (OR=2.11; 95% CI, 1.15-3.88; P=0.016), advanced tumor stage (OR=2.71; 95% CI, 1.50-4.89; P=0.001) and larger tumor size (OR=2.02; 95% CI, 0.86-4.78; P=0.006). However, no significant association was observed with age (OR=1.00; 95% CI, 0.63-1.59; P=0.991) or sex (OR=1.55; 95% CI, 0.72-3.34; P=0.258). In conclusion, elevated expression of lncRNA HOXA-AS2 was significantly related to poor clinical outcomes in various cancer types, such as osteosarcoma, non-small cell lung cancer and papillary thyroid carcinoma, a finding that was further confirmed by the present study. Specifically, the potential of lncRNAHOXA-AS2 as a biomarker in assessing tumor stage, metastasis risk and OS in patients was demonstrated. However, the results of the present study also indicated that the expression of lncRNA HOXA-AS2 was not significantly associated with age or sex, suggesting its role in cancer progression might be independent of these factors. This insight may direct future research to place more focus on the relationship between lncRNA HOXA-AS2 and specific cancer types and clinical characteristics.
Collapse
Affiliation(s)
- Tijun Xiao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Shaoyang University, Shaoyang, Hunan 422000, P.R. China
| | - An Yan
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Lifang Tan
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Shaoyang University, Shaoyang, Hunan 422000, P.R. China
| | - Hongwei Zhu
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Wenzhe Gao
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| |
Collapse
|
7
|
Qiu H, Jiang B, Chen Y, Lin Z, Zheng W, Cao X. Featured lncRNA-based signature for discriminating prognosis and progression of hepatocellular carcinoma. J Appl Genet 2024; 65:355-366. [PMID: 38347289 DOI: 10.1007/s13353-024-00836-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 02/20/2024]
Abstract
Long non-coding RNAs (lncRNAs) have been implicated in carcinogenesis and progression of hepatocellular carcinoma (HCC). This study aimed to identify a robust lncRNA signature for predicting the survival of HCC patients. We performed an integrated analysis of the lncRNA expression profiling in The Cancer Genome Atlas (TCGA)-liver hepatocellular carcinoma database to identify the prognosis-related lncRNA for the HCC. The HCC cohort was randomly divided into a training set (n = 250) and a testing set (n = 113). Following a two-step screening, we identified an 18-lncRNA signature risk score. The high-risk subgroups had significantly shorter survival time than the low-risk group in both the training set (P < 0.0001) and the testing set (P = 0.005). Stratification analysis revealed that the prognostic value of the lncRNA-based signature was independent of the tumor stage and pathologic stage. The area under the receiver operating characteristic curve (AUROC) of the 18-lncRNA signature risk score was 0.826 (95%CI, 0.764-0.888), 0.817 (95%CI, 0.759-0.876), and 0.799 (95%CI, 0.731-0.867) for 1-year, 3-year, and 5-year follow-up, respectively. Bioinformatics analyses indicated that the 18 lncRNA might mediate cell cycle, DNA replication processes, and canonical cancer-related pathways, in which MCM3AP-AS1 was a potential target for HCC. In conclusion, the 18-lncRNA signature was a robust predictive biomarker for the prognosis and progression of HCC.
Collapse
Affiliation(s)
- Huiyuan Qiu
- Medical School of Nantong University, Nantong, 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Bo Jiang
- Department of Gastroenterology, Suqian First People's Hospital, Suqian, Jiangsu, China
| | - Yinqi Chen
- Medical School of Nantong University, Nantong, 226001, China
| | - Zhaoyi Lin
- Medical School of Nantong University, Nantong, 226001, China
| | - Wenjie Zheng
- Medical School of Nantong University, Nantong, 226001, China.
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.
| | - Xiaolei Cao
- Medical School of Nantong University, Nantong, 226001, China.
| |
Collapse
|
8
|
Jiang F, Tao Z, Zhang Y, Xie X, Bao Y, Hu Y, Ding J, Wu C. Machine learning combined with single-cell analysis reveals predictive capacity and immunotherapy response of T cell exhaustion-associated lncRNAs in uterine corpus endometrial carcinoma. Cell Signal 2024; 117:111077. [PMID: 38311301 DOI: 10.1016/j.cellsig.2024.111077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/24/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND The exhaustion of T-cells is a primary factor contributing to immune dysfunction in cancer. Long non-coding RNAs (lncRNAs) play a significant role in the advancement, survival, and treatment of Uterine Corpus Endometrial Carcinoma (UCEC). Nevertheless, there has been no investigation into the involvement of lncRNAs associated with T-cell exhaustion (TEXLs) in UCEC. The goal of this work is to establish predictive models for TEXLs in UCEC and study their related immune features. METHODS Using transcriptome and single-cell sequencing data from The Cancer Genome Atlas and Gene Expression Omnibus databases, we employed co-expression analysis and univariate Cox regression to identify prognostic-associated TEXLs (pTEXLs). The prognostic model was developed using the Least Absolute Contraction and Selection Operator. The immunotherapy characteristics of the prognostic model risk score were studied. Then molecular subgroups were identified through non-negative Matrix Factorization based on pTEXLs. The identification of co-expressed genes was done using a weighted correlation network analysis. Subsequently, a diagnostic model for UCEC was created. In-depth investigations, both in vitro and in vivo, were carried out to elucidate the molecular mechanism of the key gene within the diagnostic model. RESULTS Receiver operating characteristic curve, calibration curve, and decision curve analysis proved the validity of the predictive models established according to pTEXLs. The subgroup with lower risk scores in the prognostic model has better responses to blocking immune checkpoint therapy. Single-cell analysis suggests that the expression level of MIEN1 is relatively high in immune cells among diagnostic genes. Furthermore, the targeted suppression of MIEN1 via sh-MIEN1 diminishes the proliferative, migratory, and invasive capacities of UCEC cells, potentially associated with CD8+ T cell exhaustion. CONCLUSIONS The association between TEXLs and UCEC was methodically elucidated by our investigation. A stable pTEXLs risk prediction model and a diagnosis model for UCEC were also established.
Collapse
Affiliation(s)
- Feng Jiang
- Department of Neonatology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Ziyu Tao
- Department of Ultrasound, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yun Zhang
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoyan Xie
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yunlei Bao
- Department of Neonatology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yifang Hu
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Jingxin Ding
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China; Shanghai Key Laboratory of Female Reproductive Endocrine-Related Disease, Shanghai, China.
| | - Chuyan Wu
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| |
Collapse
|
9
|
Liu Z, Yang J, Wang N, Liu J, Geng J, Zhu J, Cong B, Sun H, Wu R. Integrative lncRNA, circRNA, and mRNA analysis reveals expression profiles of six forensic body fluids/tissue. Int J Legal Med 2024; 138:731-742. [PMID: 37994925 DOI: 10.1007/s00414-023-03131-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023]
Abstract
RNAs have attracted much attention in forensic body fluid/tissue identification (BFID) due to their tissue-specific expression characteristics. Among RNAs, long RNAs (e.g., mRNA) have a higher probability of containing more polymorphic sites that can be used to assign the specific donor of the body fluid/tissue. However, few studies have characterized their overall profiles in forensic science. In this study, we sequenced the transcriptomes of 30 samples from venous blood, menstrual blood, semen, saliva, vaginal secretion, and skin tissue, obtaining a comprehensive picture of mRNA, lncRNA, and circRNA profiles. A total of 90,305 mRNAs, 102,906 lncRNAs (including 19,549 novel lncRNAs), and 40,204 circRNAs were detected. RNA type distribution, length distribution, and expression distribution were presented according to their annotation and expression level, and many novel body fluid/tissue-specific RNA markers were identified. Furthermore, the cognate relations among the three RNAs were analyzed according to gene annotations. Finally, SNPs and InDels from RNA transcripts were genotyped, and 21,611 multi-SNP and 4,471 multi-InDel transcriptomic microhaplotypes (tMHs) were identified. These results provide a comprehensive understanding of transcriptome profiles, which could provide new avenues for tracing the origin of the body fluid/tissue and identifying an individual.
Collapse
Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jianzhang Zhu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, China.
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China.
| |
Collapse
|
10
|
Ageeli Hakami M. Diabetes and diabetic associative diseases: An overview of epigenetic regulations of TUG1. Saudi J Biol Sci 2024; 31:103976. [PMID: 38510528 PMCID: PMC10951089 DOI: 10.1016/j.sjbs.2024.103976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
The epigenetic regulation of lncRNA TUG1 has garnered significant attention in the context of diabetes and its associated disorders. TUG1's multifaceted roles in gene expression modulation, and cellular differentiation, and it plays a major role in the growth of diabetes and the issues that are related to it due to pathological processes. In diabetes, aberrant epigenetic modifications can lead to dysregulation of TUG1 expression, contributing to disrupted insulin signaling, impaired glucose metabolism, and beta-cell dysfunction. Moreover, it has been reported that TUG1 contributes to the development of problems linked to diabetes, such as nephropathy, retinopathy, and cardiovascular complications, through epigenetically mediated mechanisms. Understanding the epigenetic regulations of TUG1 offers novel insights into the primary molecular mechanisms of diabetes and provides a possible path for healing interventions. Targeting epigenetic modifications associated with TUG1 holds promise for restoring proper gene expression patterns, ameliorating insulin sensitivity, and mitigating the inception and development of diabetic associative diseases. This review highlights the intricate epigenetic landscape that governs TUG1 expression in diabetes, encompassing DNA methylation and alterations in histone structure, as well as microRNA interactions.
Collapse
Affiliation(s)
- Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah, Riyadh, Saudi Arabia
| |
Collapse
|
11
|
Chang M, Cui X, Sun Q, Wang Y, Liu J, Sun Z, Ren J, Sun Y, Han L, Li W. Lnc-PLCB1 is stabilized by METTL14 induced m6A modification and inhibits Helicobacter pylori mediated gastric cancer by destabilizing DDX21. Cancer Lett 2024; 588:216746. [PMID: 38387756 DOI: 10.1016/j.canlet.2024.216746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/19/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Helicobacter pylori (H. pylori) infection is considered to be an important factor in gastric cancer (GC). Long noncoding RNA (lncRNA) and m6A modification are involved in the occurrence and development of GC, but the role of lncRNA m6A modification in the development of GC mediated by H. pylori is still unclear. Here, we found that H. pylori infection downregulated the expression of lnc-PLCB1 through METTL14-mediated m6A modification and IRF2-mediated transcriptional regulation. Overexpression of lnc-PLCB1 inhibited the proliferation and migration of GC cells, while downregulation of lnc-PLCB1 promoted the proliferation and migration ability of GC cells. In addition, clinical analysis showed that lnc-PLCB1 is lower in GC tissues than in normal tissues. Further study found that lnc-PLCB1 reduced the protein stability of its binding protein DEAD-box helicase 21 (DDX21) and then downregulated the expression of CCND1 and Slug, thereby playing tumour suppressing role in the occurrence and development of GC. In conclusion, the METTL14/lnc-PLCB1/DDX21 axis plays an important role in H. pylori-mediated GC, and lnc-PLCB1 can be used as a new target for GC treatment.
Collapse
Affiliation(s)
- Mingjie Chang
- Key Laboratory for Experimental Teratology of Chinese Ministry of Education, The Shandong Provincial Key Laboratory of Infection and Immunology, Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Xixi Cui
- Key Laboratory for Experimental Teratology of Chinese Ministry of Education, The Shandong Provincial Key Laboratory of Infection and Immunology, Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Qiyu Sun
- Key Laboratory for Experimental Teratology of Chinese Ministry of Education, The Shandong Provincial Key Laboratory of Infection and Immunology, Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Yuqiong Wang
- Key Laboratory for Experimental Teratology of Chinese Ministry of Education, The Shandong Provincial Key Laboratory of Infection and Immunology, Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Jiayi Liu
- Key Laboratory for Experimental Teratology of Chinese Ministry of Education, The Shandong Provincial Key Laboratory of Infection and Immunology, Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Zenghui Sun
- Key Laboratory for Experimental Teratology of Chinese Ministry of Education, The Shandong Provincial Key Laboratory of Infection and Immunology, Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Juchao Ren
- Department of Urology, Qilu Hospital, Shandong University, Jinan, PR China
| | - Yundong Sun
- Key Laboratory for Experimental Teratology of Chinese Ministry of Education, The Shandong Provincial Key Laboratory of Infection and Immunology, Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Lihui Han
- Shandong Provincial Key Laboratory of Infection and Immunology, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Wenjuan Li
- Key Laboratory for Experimental Teratology of Chinese Ministry of Education, The Shandong Provincial Key Laboratory of Infection and Immunology, Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China.
| |
Collapse
|
12
|
Tang H, Lu K, Wang Y, Shi Y, Ma W, Chen X, Li B, Shao Y. Analyses of lncRNA and mRNA profiles in recurrent atrial fibrillation after catheter ablation. Eur J Med Res 2024; 29:244. [PMID: 38643140 PMCID: PMC11031869 DOI: 10.1186/s40001-024-01799-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/17/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Atrial fibrillation (AF) is the most common cardiac arrhythmia worldwide. Catheter ablation has become a crucial treatment for AF. However, there is a possibility of atrial fibrillation recurrence after catheter ablation. Our study sought to elucidate the role of lncRNA‒mRNA regulatory networks in late AF recurrence after catheter ablation. METHODS We conducted RNA sequencing to profile the transcriptomes of 5 samples from the presence of recurrence after AF ablation (P-RAF) and 5 samples from the absence of recurrence after AF ablation (A-RAF). Differentially expressed genes (DEGs) and long noncoding RNAs (DE-lncRNAs) were analyzed using the DESeq2 R package. The functional correlations of the DEGs were assessed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. A protein‒protein interaction (PPI) network was constructed using STRING and Cytoscape. We also established a lncRNA‒mRNA regulatory network between DE-lncRNAs and DEGs using BEDTools v2.1.2 software and the Pearson correlation coefficient method. To validate the high-throughput sequencing results of the hub genes, we conducted quantitative real-time polymerase chain reaction (qRT‒PCR) experiments. RESULTS A total of 28,528 mRNAs and 42,333 lncRNAs were detected. A total of 96 DEGs and 203 DE-lncRNAs were identified between the two groups. GO analysis revealed that the DEGs were enriched in the biological processes (BPs) of "regulation of immune response" and "regulation of immune system process", the cellular components (CCs) of "extracellular matrix" and "cell‒cell junction", and the molecular functions (MFs) of "signaling adaptor activity" and "protein-macromolecule adaptor activity". According to the KEGG analysis, the DEGs were associated with the "PI3K-Akt signaling pathway" and "MAPK signaling pathway." Nine hub genes (MMP9, IGF2, FGFR1, HSPG2, GZMB, PEG10, GNLY, COL6A1, and KCNE3) were identified through the PPI network. lncRNA-TMEM51-AS1-201 was identified as a core regulator in the lncRNA‒mRNA regulatory network, suggesting its potential impact on the recurrence of AF after catheter ablation through the regulation of COL6A1, FGFR1, HSPG2, and IGF2. CONCLUSIONS The recurrence of atrial fibrillation after catheter ablation may be associated with immune responses and fibrosis, with the extracellular matrix playing a crucial role. TMEM51-AS1-201 has been identified as a potential key target for AF recurrence after catheter ablation.
Collapse
Affiliation(s)
- Huaiguang Tang
- Department of Cardiology, Qingdao Municipal Hospital, Qingdao University, No. 5, Donghai Middle Road, Qingdao, 266071, Shandong, China
| | - Kongmiao Lu
- Department of Pulmonary and Critical Care Medicine, Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, No. 5, Donghai Middle Road, Qingdao, 266071, Shandong, China
| | - Yan Wang
- Department of Cardiology, Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, No. 5, Donghai Middle Road, Qingdao, 266071, Shandong, China
| | - Yue Shi
- Department of Cardiology, Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, No. 5, Donghai Middle Road, Qingdao, 266071, Shandong, China
| | - Wansheng Ma
- Department of Cardiology, Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, No. 5, Donghai Middle Road, Qingdao, 266071, Shandong, China
| | - Xiaomeng Chen
- Department of Cardiology, Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, No. 5, Donghai Middle Road, Qingdao, 266071, Shandong, China.
| | - Bingong Li
- Department of Cardiology, Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, No. 5, Donghai Middle Road, Qingdao, 266071, Shandong, China.
| | - Yibing Shao
- Department of Cardiology, Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, No. 5, Donghai Middle Road, Qingdao, 266071, Shandong, China.
| |
Collapse
|
13
|
Deng Y, Zhang C, Yu H, Chen G, Peng X, Li Y, Feng Z, Shi W, Bai X, Gou X, Liu N. AAT resistance-related AC007405.2 and AL354989.1 as novel diagnostic and prognostic markers in prostate cancer. Aging (Albany NY) 2024; 16:205754. [PMID: 38643469 DOI: 10.18632/aging.205754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/28/2024] [Indexed: 04/22/2024]
Abstract
OBJECTIVE Prostate cancer (PCa) is the second disease threatening men's health, and anti-androgen therapy (AAT) is a primary approach for treating this condition. Increasing evidence suggests that long non-coding RNAs (lncRNAs) play crucial roles in the development of PCa and the process of AAT resistance. The objective of this study is to utilize bioinformatics methods to excavate lncRNAs association with AAT resistance and investigate their biological functions. METHODS AAT resistance-related risk score model (ARR-RSM) was established by multivariate Cox analysis. Paired clinical tissue samples of 36 PCa patients and 42 blood samples from patients with PSA over 4 ng/ml were collected to verify the ARR-RSM. In vitro, RT-qPCR, CCK-8 and clone formation assays were displayed to verify the expression and function of AL354989.1 and AC007405.2. RESULTS Pearson correlation analysis identified 996 lncRNAs were associated with AAT resistance (ARR-LncRs). ARR-RSM was established using multivariate Cox regression analysis, and PCa patients were divided into high-risk and low-risk groups. High-risk patients showed increased expression of AL354989.1 and AC007405.2 had poorer prognoses. The high-risk score correlated with advanced T-stage and N-stage. The AUC of ARR-RSM outperformed tPSA in diagnosing PCa. Silencing of AC007405.2 and AL354989.1 inhibited PCa cells proliferation and AAT resistance. CONCLUSIONS In this study, we have discovered the clinical significance of AC007405.2 and AL354989.1 in predicting the prognosis and diagnosing PCa patients. Furthermore, we have confirmed their correlation with various clinical features. These findings provide potential targets for PCa treatment and a novel diagnostic and predictive indicator for precise PCa diagnosis.
Collapse
Affiliation(s)
- Yuanzhong Deng
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, China
| | - Chunlin Zhang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Yuzhong, Chongqing, China
| | - Haitao Yu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Yuzhong, Chongqing, China
| | - Guo Chen
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Yuzhong, Chongqing, China
| | - Xiang Peng
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Yuzhong, Chongqing, China
| | - Yang Li
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Yuzhong, Chongqing, China
| | - Zhenwei Feng
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Yuzhong, Chongqing, China
| | - Wei Shi
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Yuzhong, Chongqing, China
| | - Xuesong Bai
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Yuzhong, Chongqing, China
| | - Xin Gou
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, China
| | - Nian Liu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, China
| |
Collapse
|
14
|
Zong K, Lin C, Luo K, Deng Y, Wang H, Hu J, Chen S, Li R. Ferroptosis-related lncRNA NRAV affects the prognosis of hepatocellular carcinoma via the miR-375-3P/SLC7A11 axis. BMC Cancer 2024; 24:496. [PMID: 38637761 PMCID: PMC11027313 DOI: 10.1186/s12885-024-12265-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/15/2024] [Indexed: 04/20/2024] Open
Abstract
Ferroptosis has important value in cancer treatment. It is significant to explore the new ferroptosis-related lncRNAs prediction model in Hepatocellular carcinoma (HCC) and the potential molecular mechanism of ferroptosis-related lncRNAs. We constructed a prognostic multi-lncRNA signature based on ferroptosis-related differentially expressed lncRNAs in HCC. qRT-PCR was applied to determine the expression of lncRNA in HCC cells. The biological roles of NRAV in vitro and in vivo were determined by performing a series of functional experiments. Furthermore, dual-luciferase reporter and RNA immunoprecipitation (RIP) assays were used to confirm the interaction of NRAV with miR-375-3P. We identified 6 differently expressed lncRNAs associated with the prognosis of HCC. Kaplan-Meier analyses revealed the high-risk lncRNAs signature associated with poor prognosis of HCC. Moreover, the AUC of the lncRNAs signature showed utility in predicting HCC prognosis. Further functional experiments show that the high expression of NRAV can strengthen the viciousness of HCC. Interestingly, we found that NRAV can enhance iron export and ferroptosis resistance. Further study showed that NRAV competitively binds to miR-375-3P and attenuates the inhibitory effect of miR-375-3P on SLC7A11, affecting the prognosis of patients with HCC. In conclusion, We developed a novel ferroptosis-related lncRNAs prognostic model with important predictive value for the prognosis of HCC. NRAV is important in ferroptosis induction through the miR-375-3P/SLC7A11 axis.
Collapse
Affiliation(s)
- Ke Zong
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Caifeng Lin
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, Fujian Province, 350001, PR China
- Department of Hepatopancreatobiliary Surgery, Fujian Provincial Hospital, No. 134, East Street, Fuzhou, Fujian Province, 350001, PR China
| | - Kai Luo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yilei Deng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Hongfei Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Jianfei Hu
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, Fujian Province, 350001, PR China
- Department of Hepatopancreatobiliary Surgery, Fujian Provincial Hospital, No. 134, East Street, Fuzhou, Fujian Province, 350001, PR China
| | - Shi Chen
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, Fujian Province, 350001, PR China.
- Department of Hepatopancreatobiliary Surgery, Fujian Provincial Hospital, No. 134, East Street, Fuzhou, Fujian Province, 350001, PR China.
| | - Renfeng Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
| |
Collapse
|
15
|
Ha JH, Radhakrishnan R, Nadhan R, Gomathinayagam R, Jayaraman M, Yan M, Kashyap S, Fung KM, Xu C, Bhattacharya R, Mukherjee P, Isidoro C, Song YS, Dhanasekaran DN. Deciphering a GPCR- lncRNA-miRNA Nexus: Identification of an Aberrant Therapeutic Target in Ovarian Cancer. Cancer Lett 2024:216891. [PMID: 38642607 DOI: 10.1016/j.canlet.2024.216891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/30/2024] [Accepted: 04/11/2024] [Indexed: 04/22/2024]
Abstract
Ovarian cancer ranks as a leading cause of mortality among gynecological malignancies, primarily due to the lack of early diagnostic tools, effective targeted therapy, and clear understanding of disease etiology. Previous studies have identified the pivotal role of Lysophosphatidic acid (LPA)-signaling in ovarian cancer pathobiology. Our earlier transcriptomic analysis identified Urothelial Carcinoma Associated-1 (UCA1) as an LPA-stimulated long non-coding RNA (lncRNA). In this study, we elucidate the tripartite interaction between LPA-signaling, UCA1, and let-7 miRNAs in ovarian cancer progression. Results show that the elevated expression of UCA1 enhances cell proliferation, invasive migration, and therapy resistance in high-grade serous ovarian carcinoma cells, whereas silencing UCA1 reverses these oncogenic phenotypes. UCA1 expression inversely correlates with survival outcomes and therapy response in ovarian cancer clinical samples, underscoring its prognostic significance. Mechanistically, UCA1 sequesters let-7 miRNAs, effectively neutralizing their tumor-suppressive functions involving key oncogenes such as Ras and c-Myc. More significantly, intratumoral delivery of UCA1-specific siRNAs inhibits the growth of cisplatin-refractory ovarian cancer xenografts, demonstrating the therapeutic potential of targeting LPAR-UCA1-let-7 axis in ovarian cancer. Thus, our results identify LPAR-UCA1-let-7 axis as a novel avenue for targeted treatment strategies.
Collapse
Affiliation(s)
- Ji Hee Ha
- Stephenson Cancer Center; Department of Cell Biology
| | | | | | | | | | | | | | | | - Chao Xu
- Department of Biostatistics and Epidemiology
| | - Resham Bhattacharya
- Stephenson Cancer Center; Department of Obstetrics and Gynecology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | | | - Ciro Isidoro
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Yong Sang Song
- Seoul National University, College of Medicine, Seoul 151-921, Korea
| | | |
Collapse
|
16
|
Chen D, Zhao H, Guo Z, Dong Z, Yu Y, Zheng J, Ma Y, Sun H, Zhang Q, Zhang J, He Y, Song T. Identification of m6A-related lncRNAs LINC02471 and DOCK9-DT as potential biomarkers for thyroid cancer. Int Immunopharmacol 2024; 133:112050. [PMID: 38636370 DOI: 10.1016/j.intimp.2024.112050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/29/2024] [Accepted: 04/06/2024] [Indexed: 04/20/2024]
Abstract
Thyroid cancer (THCA) is the most common endocrine malignancy worldwide and has been rising at the fastest rate in recent years. Long-stranded non-coding RNAs (lncRNAs) and N6-methyladenosine (m6A) have been associated with immunotherapy efficacy and cancer prognosis. However, how m6A-associated lncRNAs (mrlncRNAs) affect the prognosis of patients with thyroid cancer is unclear. Therefore, this study utilized The Cancer Genome Atlas (TCGA) database to provide thyroid cancer-related transcriptomic data and related clinical data. The R program was used to identify m6A-related lncRNAs, and a risk model consisting of two lncRNAs (LINC02471 and DOCK9-DT) was obtained using least absolute shrinkage and selection operator (LASSO) Cox regression analysis. Kaplan-Meier survival analysis and transient subject operating characteristics (ROC) were used for analysis. The results showed a substantial association between immune cell infiltration and risk scores. Independent analyses confirmed that the expression of LINC02471 and DOCK9-DT was significantly higher in thyroid cancer tissues than in normal tissues, suggesting that they may be useful biomarkers for thyroid cancer.
Collapse
Affiliation(s)
- Dengwang Chen
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Hongyuan Zhao
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zhanwen Guo
- School of Medical Information Engineering, Zunyi Medical University, Zunyi, China
| | - Zixuan Dong
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Yuanning Yu
- Department of Immunology, Zunyi Medical University, Zunyi, China.
| | - Jishan Zheng
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Yunyan Ma
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Hongqin Sun
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Qian Zhang
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Jidong Zhang
- Department of Immunology, Zunyi Medical University, Zunyi, China; Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, China; Special Key Laboratory of Gene Detection & Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Yuqi He
- School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Tao Song
- Department of Immunology, Zunyi Medical University, Zunyi, China; Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, China; Special Key Laboratory of Gene Detection & Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China.
| |
Collapse
|
17
|
Abedi Kichi Z, Dini N, Rojhannezhad M, Shirvani Farsani Z. Noncoding RNAs in B cell non-Hodgkins lymphoma. Gene 2024; 917:148480. [PMID: 38636814 DOI: 10.1016/j.gene.2024.148480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
B-cell non-Hodgkins lymphomas (BCNHLs) are a category of B-cell cancers that show heterogeneity. These blood disorders are derived from different levels of B-cell maturity. Among NHL cases, ∼80-90 % are derived from B-cells. Recent studies have demonstrated that noncoding RNAs (ncRNAs) contribute to almost all parts of mechanisms and are essential in tumorigenesis, including B-cell non-Hodgkins lymphomas. The study of ncRNA dysregulations in B-cell lymphoma unravels important mysteries in lymphoma's molecular etiology. It seems also necessary for discovering novel trials as well as investigating the potential of ncRNAs as markers for their diagnosis and prognosis. In the current study, we summarize the role of ncRNAs involving miRNAs, long noncoding RNAs, as well as circular RNAs in the development or progression of BCNHLs.
Collapse
Affiliation(s)
- Zahra Abedi Kichi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IR Iran; Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University Munich, Germany
| | - Niloofar Dini
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Mahbubeh Rojhannezhad
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IR Iran
| | - Zeinab Shirvani Farsani
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| |
Collapse
|
18
|
Ren W, Wang J, Zeng Y, Wang T, Meng J, Yao X. Transcriptome identification of differential mammary genes of Kazakh horses during early pregnancy. Gene 2024; 902:148189. [PMID: 38246578 DOI: 10.1016/j.gene.2024.148189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/06/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
Kazakh mares have attracted widespread attention with their outstanding lactation traits. Lactation is a complex dynamic process regulated by multiple factors. The extensive application of transcriptome sequencing technology enables researchers to further explore this biological issue. This study selected three pregnant and three non-pregnant Kazakh mares as the research subject. Their mammary glands were taken for transcriptome sequencing. The results show that there are 9 lncRNAs and 122 mRNAs differentially expressed between the two groups. GO enrichment analysis shows that there are 175 molecular functions, 59 cellular components, and 555 biological processes, including cellular hormone metabolic process, hormone catabolic process, and I-kappaB kinase/NF-kappaB signaling. KEGG enrichment analysis exhibits that these differential genes are mainly enriched in the NF-kappa B signaling pathway, steroid hormone biosynthesis, breast cancer, ECM-receptor interaction, and MAPK signaling pathway. WNT4, DPP4, and NFKBIA are key nodes regulating breast activation. Conclusions: Through the comparative analysis of the transcriptome data of mammary tissues of pregnant and non-pregnant mares, relevant differentially expressed genes are screened and analyzed. This study provides valuable fundamental data for investigating candidate genes related to the lactation regulation and mammogenesis of Kazakh horses.
Collapse
Affiliation(s)
- Wanlu Ren
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Jianwen Wang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; Xinjiang Key Laboratory of Equine Breeding and Exercise Physiology, Urumqi 830052, China
| | - Yaqi Zeng
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Tongliang Wang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Jun Meng
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Xinkui Yao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; Xinjiang Key Laboratory of Equine Breeding and Exercise Physiology, Urumqi 830052, China.
| |
Collapse
|
19
|
Huang Y, Lv Y, Yang B, Zhang S, Bixia liu, Zhang C, Hu W, Jiang L, Chen C, Ji D, Xiong C, Liang Y, Liu M, Ying X, Ji W. Enhancing m 6A modification of lncRNA through METTL3 and RBM15 to promote malignant progression in bladder cancer. Heliyon 2024; 10:e28165. [PMID: 38560117 PMCID: PMC10979072 DOI: 10.1016/j.heliyon.2024.e28165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/10/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Objective Bladder cancer is one of the most prominent malignancies affecting the urinary tract, characterized by a poor prognosis. Our previous research has underscored the pivotal role of m6A methylation in the progression of bladder cancer. Nevertheless, the precise relationship between N6-methyladenosine (m6A) regulation of long non-coding RNA (lncRNA) and bladder cancer remains elusive. Methods This study harnessed sequencing data and clinical records from 408 bladder cancer patients in the TCGA database. Employing R software, we conducted bioinformatics analysis to establish an m6A-lncRNA co-expression network. Analyzing the differences between high and low-risk groups, particularly at the immunological level, and subsequently investigating the primary regulatory factors of these lncRNA, validating the findings through experiments, and exploring their specific cellular functions. Results We identified 50 m6A-related lncRNA with prognostic significance through univariate Cox regression analysis. In parallel, we employed a LASSO-Cox regression model to pinpoint 11 lncRNA and calculate risk scores for bladder cancer patients. Based on the median risk score, patients were categorized into low-risk and high-risk groups. The high-risk cohort exhibited notably lower survival rates than their low-risk counterparts. Further analysis pointed to RBM15 and METTL3 as potential master regulators of these m6A-lncRNA. Experimental findings also shed light on the upregulated expression of METTlL3 and RBM15 in bladder cancer, where they contributed to the malignant progression of tumors. The experimental findings demonstrated a significant upregulation of METTL3 and RBM15 in bladder cancer specimens, implicating their contributory role in the oncogenic progression. Knockdown of METTL3 and RBM15 resulted in a marked attenuation of tumor cell proliferation, invasion, and migration, which was concomitant with a downregulation in the cellular m6A methylation status. Moreover, these results revealed that RBM15 and METTL3 function in a synergistic capacity, positing their involvement in cancer promotion via the upregulation of m6A modifications in long non-coding RNAs. Additionally, this study successfully developed an N-methyl-N-nitrosourea (MNU)-induced rat model of in situ bladder carcinoma, confirming the elevated expression of RBM15 and METTL3, which paralleled the overexpression of m6A-related- lncRNAs observed in bladder cancer cell lines. This congruence underscores the potential utility of these molecular markers in in vivo models that mirror human malignancies. Conclusion This study not only offers novel molecular targets,but also enriches the research on m6A modification in bladder cancer, thereby facilitating its clinical translation.
Collapse
Affiliation(s)
- Yapeng Huang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yifan Lv
- Guangdong Provincial Key Laboratory of Urology, Guangzhou, 510230, China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Baotong Yang
- Guangdong Provincial Key Laboratory of Urology, Guangzhou, 510230, China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shike Zhang
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bixia liu
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chengcheng Zhang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenyu Hu
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | | | - Cong Chen
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ding Ji
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chang Xiong
- Guangdong Provincial People's Hospital, China
| | - Yaoming Liang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Mingrui Liu
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaoling Ying
- Guangdong Provincial Key Laboratory of Urology, Guangzhou, 510230, China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510220, China
| | - Weidong Ji
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| |
Collapse
|
20
|
Galus Ł, Kolenda T, Michalak M, Mackiewicz J. Diagnostic and prognostic role of long non-coding RNAs ( lncRNAs) in metastatic melanoma patients with BRAF gene mutation receiving BRAF and MEK inhibitors. Heliyon 2024; 10:e29071. [PMID: 38601651 PMCID: PMC11004874 DOI: 10.1016/j.heliyon.2024.e29071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
Melanoma is a cancer with a high incidence rate that, despite the significant development of therapeutic options, still remains a major problem. The identification of biomarkers to select the right therapy for the right patient is one of the possibilities to improve the prognosis of patients. Potentially, the function of biomarkers could be played long non-coding RNAs (lncRNAs). The expression of selected 90 lncRNAs in serum from 30 metastatic melanoma patients with confirmed mutations in the BRAF V600 E or K gene was studied. Serum was collected prior to BRAF and MEK inhibitor therapy. The control group consisted of 16 healthy volunteers. A total of 41 lncRNAs were identified the expression of which differed statistically significantly between the patient group and the healthy volunteers. In addition, it was shown that the expression of HOXA3as (p = 0.033), PRINS (p = 0.036) and RNCR3 (p = 0.045) is higher in patients with the presence of CNS metastases, PFS inhibiting RNA (p = 0.048) is higher among patients with the presence of hepatic metastases, UCA1 (p = 0.008) expression is lower in patients with increased lactate dehydrogenase levels, while HOTAIRM1 (p = 0.044) and E2F4 antisense (p = 0.040) expression is lower in patients over 60 years of age. In addition, patients with high lincRNASFMBT2 expression showed longer median PFS (8.75 vs. 17.5 months, p = 0.0319) and OS (9.75 vs. 38 months (open observation, p = 0.0253). The obtained results require validation on a larger group of patients. If the results are confirmed, the indicated lncRNAs may play an important role as diagnostic and prognostic markers.
Collapse
Affiliation(s)
- Łukasz Galus
- Department of Medical and Experimental Oncology, Institute of Oncology, Poznan University of Medical Sciences, Poland
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Michał Michalak
- Department of Computer Science and Statistics, Poznan University of Medical Sciences, Poland
| | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, Institute of Oncology, Poznan University of Medical Sciences, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland
| |
Collapse
|
21
|
Sun X, Yuan Y, Li S, Gan L, Xu M, Li Q, Liu M, Hu K, Nan K, Zhang J, Dong Y, Lin Y, Zhang X, Hou P, Liu T. Prostate cancer-associated transcript 6 (PCAT6) promotes epithelial-mesenchymal transition and stemness and worsens prognosis in patients with colorectal cancer. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 38606479 DOI: 10.3724/abbs.2024031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024] Open
Abstract
Approximately 20% of colorectal cancer (CRC) patients are first diagnosed with metastatic colorectal cancer (mCRC) because they develop symptoms at an advanced stage. Despite advancements in treatment, patients with metastatic disease still experience inferior survival rates. Our objective is to investigate the association between long noncoding RNAs (lncRNAs) and prognosis and to explore their role in mCRC. In this study, we find that elevated expression of PCAT6 is independently linked to unfavourable survival outcomes in The Cancer Genome Atlas (TCGA) data, and this finding is further confirmed in CRC samples obtained from Fudan University Shanghai Cancer Center. Cell lines and xenograft mouse models are used to examine the impact of PCAT6 on tumor metastasis. Knockdown of PCAT6 is observed to impede the metastatic phenotype of CRC, as evidenced by functional assays, demonstrating the suppression of epithelial-mesenchymal transition (EMT) and stemness. Our findings show the significance of PCAT6 in mCRC and its potential use as a prognostic biomarker.
Collapse
Affiliation(s)
- Xun Sun
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yitao Yuan
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Suyao Li
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lu Gan
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Fudan Zhangjiang Institute, Shanghai 201203, China
| | - Midie Xu
- Department of Pathology and Tissue Bank, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Qingguo Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Mengling Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Keshu Hu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ke Nan
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiayu Zhang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yu Dong
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yufu Lin
- Department of Oncology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen 361015, China
| | - Xiuping Zhang
- Xiamen Clinical Research Center for Cancer Therapy, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen 361015, China
| | - Pengcong Hou
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Tianshu Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| |
Collapse
|
22
|
Xu WB, Guo QH, Liu P, Dai S, Wu CA, Yang GD, Huang JG, Zhang SZ, Song JM, Zheng CC, Yan K. A long non-coding RNA functions as a competitive endogenous RNA to modulate TaNAC018 by acting as a decoy for tae-miR6206. Plant Mol Biol 2024; 114:36. [PMID: 38598012 DOI: 10.1007/s11103-024-01448-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
Increasing evidence indicates a strong correlation between the deposition of cuticular waxes and drought tolerance. However, the precise regulatory mechanism remains elusive. Here, we conducted a comprehensive transcriptome analysis of two wheat (Triticum aestivum) near-isogenic lines, the glaucous line G-JM38 rich in cuticular waxes and the non-glaucous line NG-JM31. We identified 85,143 protein-coding mRNAs, 4,485 lncRNAs, and 1,130 miRNAs. Using the lncRNA-miRNA-mRNA network and endogenous target mimic (eTM) prediction, we discovered that lncRNA35557 acted as an eTM for the miRNA tae-miR6206, effectively preventing tae-miR6206 from cleaving the NAC transcription factor gene TaNAC018. This lncRNA-miRNA interaction led to higher transcript abundance for TaNAC018 and enhanced drought-stress tolerance. Additionally, treatment with mannitol and abscisic acid (ABA) each influenced the levels of tae-miR6206, lncRNA35557, and TaNAC018 transcript. The ectopic expression of TaNAC018 in Arabidopsis also improved tolerance toward mannitol and ABA treatment, whereas knocking down TaNAC018 transcript levels via virus-induced gene silencing in wheat rendered seedlings more sensitive to mannitol stress. Our results indicate that lncRNA35557 functions as a competing endogenous RNA to modulate TaNAC018 expression by acting as a decoy target for tae-miR6206 in glaucous wheat, suggesting that non-coding RNA has important roles in the regulatory mechanisms responsible for wheat stress tolerance.
Collapse
Affiliation(s)
- Wei-Bo Xu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Qian-Huan Guo
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Peng Liu
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Shuang Dai
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, People's Republic of China
| | - Chang-Ai Wu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Guo-Dong Yang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Jin-Guang Huang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Shi-Zhong Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Jian-Min Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, People's Republic of China.
| | - Cheng-Chao Zheng
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China.
| | - Kang Yan
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China.
| |
Collapse
|
23
|
Tan Y, Huang Y, Xu C, Huang X, Li S, Yin Z. Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson). BMC Genomics 2024; 25:357. [PMID: 38600449 PMCID: PMC11005167 DOI: 10.1186/s12864-024-10281-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Broodiness significantly impacts poultry egg production, particularly notable in specific breeds such as the black-boned Silky, characterized by pronounced broodiness. An understanding of the alterations in ovarian signaling is essential for elucidating the mechanisms that influence broodiness. However, comparative research on the characteristics of long non-coding RNAs (lncRNAs) in the ovaries of broody chickens (BC) and high egg-laying chickens (GC) remains scant. In this investigation, we employed RNA sequencing to assess the ovarian transcriptomes, which include both lncRNAs and mRNAs, in eight Taihe Black-Bone Silky Fowls (TBsf), categorized into broody and high egg-laying groups. This study aims to provide a clearer understanding of the genetic underpinnings associated with broodiness and egg production. RESULTS We have identified a total of 16,444 mRNAs and 18,756 lncRNAs, of which 349 mRNAs and 651 lncRNAs exhibited significantly different expression (DE) between the BC and GC groups. Furthermore, we have identified the cis-regulated and trans-regulated target genes of differentially abundant lncRNA transcripts and have constructed an lncRNA-mRNA trans-regulated interaction network linked to ovarian follicle development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses have revealed that DE mRNAs and the target genes of DE lncRNAs are associated with pathways including neuroactive ligand-receptor interaction, CCR6 chemokine receptor binding, G-protein coupled receptor binding, cytokine-cytokine receptor interaction, and ECM-receptor interaction. CONCLUSION Our research presents a comprehensive compilation of lncRNAs and mRNAs linked to ovarian development. Additionally, it establishes a predictive interaction network involving differentially abundant lncRNAs and differentially expressed genes (DEGs) within TBsf. This significantly contributes to our understanding of the intricate interactions between lncRNAs and genes governing brooding behavior.
Collapse
Affiliation(s)
- Yuting Tan
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Yunyan Huang
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Chunhui Xu
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Xuan Huang
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Shibao Li
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Zhaozheng Yin
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
24
|
Wang J, Ren H, Xu C, Yu B, Cai Y, Wang J, Ni X. Identification of m6A/m5C-related lncRNA signature for prediction of prognosis and immunotherapy efficacy in esophageal squamous cell carcinoma. Sci Rep 2024; 14:8238. [PMID: 38589454 PMCID: PMC11001862 DOI: 10.1038/s41598-024-58743-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/02/2024] [Indexed: 04/10/2024] Open
Abstract
N6-methyladenosine (m6A) and 5-methylcytosine (m5C) RNA modifications have garnered significant attention in the field of epigenetic research due to their close association with human cancers. This study we focus on elucidating the expression patterns of m6A/m5C-related long non-coding RNAs (lncRNAs) in esophageal squamous cell carcinoma (ESCC) and assessing their prognostic significance and therapeutic potential. Transcriptomic profiles of ESCC were derived from public resources. m6A/m5C-related lncRNAs were obtained from TCGA using Spearman's correlations analysis. The m6A/m5C-lncRNAs prognostic signature was selected to construct a RiskScore model for survival prediction, and their correlation with the immune microenvironment and immunotherapy response was analyzed. A total of 606 m6A/m5C-lncRNAs were screened, and ESCC cases in the TCGA cohort were stratified into three clusters, which showed significantly distinct in various clinical features and immune landscapes. A RiskScore model comprising ten m6A/m5C-lncRNAs prognostic signature were constructed and displayed good independent prediction ability in validation datasets. Patients in the low-RiskScore group had a better prognosis, a higher abundance of immune cells (CD4 + T cell, CD4 + naive T cell, class-switched memory B cell, and Treg), and enhanced expression of most immune checkpoint genes. Importantly, patients with low-RiskScore were more cline benefit from immune checkpoint inhibitor treatment (P < 0.05). Our findings underscore the potential of RiskScore system comprising ten m6A/m5C-related lncRNAs as effective biomarkers for predicting survival outcomes, characterizing the immune landscape, and assessing response to immunotherapy in ESCC.
Collapse
Affiliation(s)
- Jianlin Wang
- Department of Radiotherapy, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213003, Jiangsu, China
- Center for Medical Physics, Nanjing Medical University, Changzhou, 213003, Jiangsu, China
| | - Huiwen Ren
- Department of Radiotherapy, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213003, Jiangsu, China
| | - Chao Xu
- Department of Radiotherapy, Jiangyin People's Hospital, Jiangyin, 214400, Jiangsu, China
| | - Bo Yu
- Department of Radiotherapy, Jiangyin People's Hospital, Jiangyin, 214400, Jiangsu, China
| | - Yiling Cai
- Department of Radiotherapy, Jiangyin People's Hospital, Jiangyin, 214400, Jiangsu, China
| | - Jian Wang
- Department of Radiotherapy, Jiangyin People's Hospital, Jiangyin, 214400, Jiangsu, China.
| | - Xinye Ni
- Department of Radiotherapy, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213003, Jiangsu, China.
- Center for Medical Physics, Nanjing Medical University, Changzhou, 213003, Jiangsu, China.
| |
Collapse
|
25
|
Chong ZX, Ho WY, Yeap SK. Tumour-regulatory role of long non-coding RNA HOXA-AS3. Prog Biophys Mol Biol 2024:S0079-6107(24)00037-3. [PMID: 38593905 DOI: 10.1016/j.pbiomolbio.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
Dysregulation of long non-coding RNA (lncRNA) HOXA-AS3 has been shown to contribute to the development of multiple cancer types. Several studies have presented the tumour-modulatory role or prognostic significance of this lncRNA in various kinds of cancer. Overall, HOXA-AS3 can act as a competing endogenous RNA (ceRNA) that inhibits the activity of seven microRNAs (miRNAs), including miR-29a-3p, miR-29 b-3p, miR-29c, miR-218-5p, miR-455-5p, miR-1286, and miR-4319. This relieves the downstream messenger RNA (mRNA) targets of these miRNAs from miRNA-mediated translational repression, allowing them to exert their effect in regulating cellular activities. Examples of the pathways regulated by lncRNA HOXA-AS3 and its associated downstream targets include the WNT/β-catenin and epithelial-to-mesenchymal transition (EMT) activities. Besides, HOXA-AS3 can interact with other cellular proteins like homeobox HOXA3 and HOXA6, influencing the oncogenic signaling pathways associated with these proteins. Generally, HOXA-AS3 is overexpressed in most of the discussed human cancers, making this lncRNA a potential candidate to diagnose cancer or predict the clinical outcomes of cancer patients. Hence, targeting HOXA-AS3 could be a new therapeutic approach to slowing cancer progression or as a potential biomarker and therapeutic target. A drawback of using lncRNA HOXA-AS3 as a biomarker or therapeutic target is that most of the studies that have reported the tumour-regulatory roles of lncRNA HOXA-AS3 are single observational, in vitro, or in vivo studies. More in-depth mechanistic and large-scale clinical trials must be conducted to confirm the tumour-modulatory roles of lncRNA HOXA-AS3 further. Besides, no lncRNA HOXA-AS3 inhibitor has been tested preclinically and clinically, and designing such an inhibitor is crucial as it may potentially slow cancer progression.
Collapse
Affiliation(s)
- Zhi Xiong Chong
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Wan Yong Ho
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia.
| |
Collapse
|
26
|
Liu T, Su X, Kong X, Dong H, Wei Y, Wang Y, Wang C. Whole transcriptome sequencing identifies key lncRNAs,circRNAs, and mRNAs for exploring the pathogenesis and therapeutic target of mouse pneumoconiosis. Gene 2024; 901:148169. [PMID: 38242381 DOI: 10.1016/j.gene.2024.148169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/17/2023] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND Pneumoconiosis is a kind of lung dysfunction caused by the inhalation of mineral dust. However, the potential molecular mechanism of pneumoconiosis have not been fully elucidated. METHODS In this study, the silica-treated pneumoconiosis mice model was constructed and the transcriptome sequencing data including lncRNA, circRNA, and mRNA were obtained. Firstly, differentially expressed lncRNA, circRNA, and mRNA (DElncRNA, DEcircRNA, DEGs) between control and pneumoconiosis/silicosis samples were screened, the target miRNAs (co-pre-miRNAs) were obtained by intersecting the miRNAs predicted by DElncRNA and DEcircRNA, respectively, and the target mRNAs (co-mRNA) were obtained by intersecting the mRNAs predicted by target miRNA and DEGs. Then, the lncRNA/circRNA-miRNA-mRNA networks were constructed by Cytoscape. Next, the key mRNAs were obtained by protein-protein interaction (PPI) analysis, and the key lncRNAs/circRNAs were selected by correlation analysis. Moreover, the expression of the key lncRNAs, circRNAs and mRNAs on chromosome were studied by the "circlize" package. Furthermore, the TFs-miRNA-mRNA network was constructed and the function of DEGs were explored by Ingenuity Pathway Analysis (IPA). To demonstrate the feasibility and value of the constructed ceRNA networks, we validated key genes and mmu-miR-682 pathway. Finally, We used the Drug-Gene Interaction database to predict potential drugs that could interfere with key genes,which may help to find promising treatment. RESULTS There were 427 DElncRNAs, 107 DEcircRNAs and 1,597 DEGs between silicosis and control groups. Totals of 77 co-pre-miRNAs and 96 co-mRNA were screened, and the lncRNA/circRNA-miRNA-mRNA networks were constructed with 27 lncRNA/25 circRNAs, 74 miRNAs and 96 mRNAs. Then, 6 key mRNAs including Igf1, Klf4, Ptgs2, Epas1, Gnao1, and Il1a were obtained by PPI, and all of these key mRNAs and 10 key lncRNAs and 8 circRNAs were significantly different between the pneumoconiosis and normal groups, in which 10 lncRNAs and 9 circRNA that have not been previously studied in pneumoconiosis/silicosis can be used as new potential therapeutic targets. Moreover, the TFs-miRNA-mRNA network were constructed with 11 TFs, 1 key miRNA (mmu-miR-682) and 3 key mRNAs (Igf1, Epas1, Ptgs2). And the validation of key genes revealing by RNA-seq through experimental approaches shows the the predictive power of this study. Finally, IPA results indicated that 41 pathways were activated and 2 pathways were suppressed in pneumoconiosis/silicosis groups, and Pathogen Induced Cytokine Storm Signaling Pathway was the most significant pathway affected by pneumoconiosis/silicosis. In addition, 93 drugs were screened out by Drug-Gene Interaction database. Among them, Hydroxychloroquine was a kind of drug which associated with Il1a and Ptgs2, may be a promising treatment. CONCLUSION This study constructed the lncRNA/circRNA-miRNA-mRNA and TFs-miRNA-mRNA networks, which could deepen the potential molecular regulatory mechanism of pneumoconiosis/silicosis.
Collapse
Affiliation(s)
- Ting Liu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, The First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xuesen Su
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, The First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaomei Kong
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, The First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Hantian Dong
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, The First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yangyang Wei
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, The First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yan Wang
- Medical School of Shanxi Datong University, Datong, Shanxi Province, China
| | - Chen Wang
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, The First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China.
| |
Collapse
|
27
|
Liao B, Wang J, Xie Y, Luo H, Min J. LINK-A: unveiling its functional role and clinical significance in human tumors. Front Cell Dev Biol 2024; 12:1354726. [PMID: 38645412 PMCID: PMC11032015 DOI: 10.3389/fcell.2024.1354726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/20/2024] [Indexed: 04/23/2024] Open
Abstract
LINK-A, also recognized as LINC01139, has emerged as a key oncological lncRNA in cancer. LINK-A is upregulated in solid and liquid tumor samples, including breast cancer, ovarian cancer, glioma, non-small-cell lung cancer, and mantle cell lymphoma. Notably, LINK-A is involved in regulating critical cancer-related pathways, such as AKT and HIF1α signaling, and is implicated in a range of oncogenic activities, including cell proliferation, apoptosis, epithelial-mesenchymal transition (EMT), cell invasion and migration, and glycolysis reprogramming. LINK-A's differential expression and its correlation with clinical features enable it to be a promising biomarker for cancer diagnosis, prognosis, and the stratification of tumor progression. Additionally, LINK-A's contribution to the development of resistance to cancer therapies, including AKT inhibitors and immunotherapy, underscores its potential as a therapeutic target. This review provides a comprehensive overview of the available data on LINK-A, focusing on its molecular regulatory pathways and clinical significance. By exploring the multifaceted nature of LINK-A in cancer, the review aims to offer a valuable resource for future research directions, potentially guiding the development of novel therapeutic strategies targeting this lncRNA in cancer treatment.
Collapse
Affiliation(s)
- Bing Liao
- Department of Otorhinolaryngology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Jialing Wang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Yilin Xie
- Second School of Clinical Medicine, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Hongliang Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Jun Min
- Department of Neurology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| |
Collapse
|
28
|
Mahyari E, Vigh-Conrad KA, Daube C, Lima AC, Guo J, Carrell DT, Hotaling JM, Aston KI, Conrad DF. The human infertility single-cell testis atlas (HISTA): an interactive molecular scRNA-Seq reference of the human testis. Andrology 2024. [PMID: 38577799 DOI: 10.1111/andr.13637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 02/03/2024] [Accepted: 03/08/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Single-cell RNA-seq (scRNA-Seq) has been widely adopted to study gene expression of the human testis. Several datasets of scRNA-Seq from human testis have been generated from different groups processed with different informatics pipelines. An integrated atlas of scRNA-Seq expression constructed from multiple donors, developmental ages, and fertility states would be widely useful for the testis research community. OBJECTIVE To describe the generation and use of the human infertility single-cell testis atlas (HISTA), an interactive web tool for understanding human spermatogenesis through scRNA-Seq analysis. METHODS We obtained scRNA-Seq datasets derived from 12 donors, including healthy adult controls, juveniles, and several infertility cases, and reprocessed these data using methods to remove batch effects. Using Shiny, an open-source environment for data visualization, we created numerous interactive tools for exploring the data, some of which support simple statistical hypothesis testing. We used the resulting HISTA browser and its underlying data to demonstrate HISTA's value for testis researchers. RESULTS A primary application of HISTA is to search by a single gene or a set of genes; thus, we present various analyses that quantify and visualize gene expression across the testis cells and pathology. HISTA also contains machine-learning-derived gene modules ("components") that capture the entire transcriptional landscape of the testis tissue. We show how the use of these components can simplify the highly complex data in HISTA and assist with the interpretation of genes with unknown functions. Finally, we demonstrate the diverse ways HISTA can be used for new data analysis, including hypothesis testing. DISCUSSION AND CONCLUSIONS HISTA is a research environment that can help scientists organize and understand the high-dimensional transcriptional landscape of the human testis. HISTA has already contributed to published testis research and can be updated as needed with input from the research community or downloaded and modified for individual needs.
Collapse
Affiliation(s)
- Eisa Mahyari
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, USA
| | - Katinka A Vigh-Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, USA
| | - Clément Daube
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, USA
| | - Ana C Lima
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, USA
| | - Jingtao Guo
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Douglas T Carrell
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - James M Hotaling
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Kenneth I Aston
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, USA
| |
Collapse
|
29
|
Wang H, Wang W. Unlocking the future of hepatocellular carcinoma treatment: A comprehensive analysis of disulfidptosis-related lncRNAs for prognosis and drug screening. Open Med (Wars) 2024; 19:20240919. [PMID: 38584823 PMCID: PMC10998672 DOI: 10.1515/med-2024-0919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 04/09/2024] Open
Abstract
Background The disulfide stress-induced cell death known as disulfidptosis is characterized by the disintegration of cytoskeletal proteins and F-actin as a result of an excessive buildup of disulfides within the cell. The relationship between disulfidptosis-associated long non-coding RNA (lncRNA) in hepatocellular carcinoma (HCC) progression is still not clearly understood. In this article, we aim to explore the crucial role of lncRNA in HCC. Methods We initially obtained lncRNA related to HCC and clinical data from TCGA. The genes associated with disulfidptosis were identified through co-expression analysis, Cox regression, and Lasso regression. Additionally, we established a prognostic model for verification. Results The risk model constructed with disulfidptosis-related lncRNA has been confirmed to be a good predictor of high and low-risk groups of HCC patients through survival curves, independent prognostic analysis, concordance index (C-index), ROC curves, and Kaplan-Meier plots. We also discovered differences in the response to immune targets and anticancer drugs between the two groups of patients, with GDC0810, Osimertinib, Paclitaxel, and YK-4-279 being more effective for patients in the high-risk group. Conclusion In conclusion, we have developed a risk model that can guide future efforts to diagnose and treat HCC.
Collapse
Affiliation(s)
- Haojun Wang
- Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China
- Capital Medical University, Beijing, 100071, China
| | - Wei Wang
- Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China
- Capital Medical University, Beijing, 100071, China
| |
Collapse
|
30
|
Murugan AK, Al-Hindi H, Alzahrani AS. LncRNA GAS8-AS1 dinucleotide genetic variant n.713A>G, n.714T>C is associated with early-stage disease, lymph node, and distant metastasis in differentiated thyroid cancer. Endocrine 2024:10.1007/s12020-024-03802-7. [PMID: 38580894 DOI: 10.1007/s12020-024-03802-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/24/2024] [Indexed: 04/07/2024]
Abstract
PURPOSE Long noncoding RNAs (lncRNAs) play an essential role in the epigenetic regulation of various key genes involved in vital cellular functions. A somatic dinucleotide mutation in the lncRNA GAS8-AS1 was reported in Chinese papillary thyroid cancer. However, GAS8-AS1 dinucleotide alteration and its impact have never been explored in differentiated thyroid cancers and other populations. METHODS We extracted genomic DNA from 265 DTCs and 97 normal healthy subjects, PCR amplified and Sanger sequenced to examine the GAS8-AS1 dinucleotide alteration. Calculated genotype/allele frequency to test Hardy-Weinberg Equilibrium (HWE) and performed a genetic model of inheritance to determine its association with DTC risk. Correlated the GAS8-AS1 dinucleotide variant distribution with clinical characteristics to find the association. Predicted GAS8-AS1 RNA secondary structure for wild type and variant using RemuRNA and RNAfold to assess the conformational changes. RESULTS GAS8-AS1 dinucleotide alteration (n.713A > G, rs55742939; n.714T > C, rs61118444) identified in DTCs is a germline variant not somatic. The GAS8-AS1 genotype and allele frequency significantly deviated for HWE in DTCs (χ2 = 37.954; p = 0.0001) though not associated with its risk. Dinucleotide variant distribution was remarkably associated with early-stage disease (p = 0.002), lymph node (p = 0.01), and distant metastasis (p = 0.01) in DTCs. The GAS8-AS1 bearing dinucleotide variant markedly showed conformational change compared to that of its wild type. CONCLUSIONS These findings indicate that GAS8-AS1 is genetically deregulated and implicated in several stages of DTC tumorigenesis suggesting it could be a promising prognostic biomarker in DTCs.
Collapse
Affiliation(s)
- Avaniyapuram Kannan Murugan
- Division of Molecular Endocrinology, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia.
| | - Hindi Al-Hindi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Ali S Alzahrani
- Division of Molecular Endocrinology, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia.
- Department of Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia.
| |
Collapse
|
31
|
Zhu Y, Liu C, Hallajzadeh J. Understanding the Roles of Non-coding RNAs and Exosomal Non-Coding RNAs in Diabetic Nephropathy. Curr Mol Med 2024; 24:CMM-EPUB-139623. [PMID: 38591211 DOI: 10.2174/0115665240287631240321072504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/18/2024] [Accepted: 02/27/2024] [Indexed: 04/10/2024]
Abstract
One of the greatest serious side effects of diabetes is diabetic nephropathy (DN), which is also the key factor in the sometimes-deadly diabetic end-stage renal disease. Progressive renal interstitial fibrosis is closely associated with oxidative stress, and the extracellular matrix is typically a feature of DN. Some RNAs formed by genome transcription that are not translated into proteins are recognized as noncoding RNAs. It has been shown that ncRNAs control apoptosis, inflammatory response, cell proliferation, autophagy, and other pathogenic processes, contributing to the pathogenesis of DN. Exosomes are nano-carriers vesicles that variety in size from 40 to 160 nm. Exosomes are widely present and dispersed in different bodily fluids, plentiful in nucleic acids, lipids, and proteins (microRNA, mRNA, tRNA, lncRNA, circRNA, etc.). Exosomes play a crucial role as messengers for cellular communication. They transport and transmit key signaling molecules, participate in the transfer of information and materials between cells, control cellular physiological processes, and are carefully linked to the beginning and development of many diseases. Herein, we summarized the role of different ncRNAs in DN. Moreover, we highlighted the role of the exosomal form of ncRNAs in the DN pathogenesis.
Collapse
Affiliation(s)
- Yuye Zhu
- Xianyang Vocational Technical College, XianYang, ShaanXi, 725000, China
| | - Chunying Liu
- The First Clinical Medical College of Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine, Xian Yang, ShaanXi, 712000
| | - Jamal Hallajzadeh
- Department of Biochemistry and Nutrition, Research Center for Evidence-Based Health Management, Maragheh University of Medical Science, Maragheh, Iran
| |
Collapse
|
32
|
Forabosco P, Pala M, Crobu F, Diana MA, Marongiu M, Cusano R, Angius A, Steri M, Orrù V, Schlessinger D, Fiorillo E, Devoto M, Cucca F. Transcriptome organization of white blood cells through gene co-expression network analysis in a large RNA-seq dataset. Front Immunol 2024; 15:1350111. [PMID: 38629067 PMCID: PMC11018966 DOI: 10.3389/fimmu.2024.1350111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Gene co-expression network analysis enables identification of biologically meaningful clusters of co-regulated genes (modules) in an unsupervised manner. We present here the largest study conducted thus far of co-expression networks in white blood cells (WBC) based on RNA-seq data from 624 individuals. We identify 41 modules, 13 of them related to specific immune-related functions and cell types (e.g. neutrophils, B and T cells, NK cells, and plasmacytoid dendritic cells); we highlight biologically relevant lncRNAs for each annotated module of co-expressed genes. We further characterize with unprecedented resolution the modules in T cell sub-types, through the availability of 95 immune phenotypes obtained by flow cytometry in the same individuals. This study provides novel insights into the transcriptional architecture of human leukocytes, showing how network analysis can advance our understanding of coding and non-coding gene interactions in immune system cells.
Collapse
Affiliation(s)
- Paola Forabosco
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Mauro Pala
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Francesca Crobu
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Maria Antonietta Diana
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Mara Marongiu
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Roberto Cusano
- CRS4-Next Generation Sequencing (NGS) Core, Parco POLARIS, Cagliari, Italy
| | - Andrea Angius
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - David Schlessinger
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health (NIH), Baltimore, MA, United States
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Marcella Devoto
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
- Dipartimento di Medicina Traslazionale e di Precisione, Università Sapienza, Roma, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| |
Collapse
|
33
|
Xu Y, Mao S, Fan H, Wan J, Wang L, Zhang M, Zhu S, Yuan J, Lu Y, Wang Z, Yu B, Jiang Z, Huang Y. LINC MIR503HG Controls SC-β Cell Differentiation and Insulin Production by Targeting CDH1 and HES1. Adv Sci (Weinh) 2024; 11:e2305631. [PMID: 38243869 PMCID: PMC10987150 DOI: 10.1002/advs.202305631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/03/2024] [Indexed: 01/22/2024]
Abstract
Stem cell-derived pancreatic progenitors (SC-PPs), as an unlimited source of SC-derived β (SC-β) cells, offers a robust tool for diabetes treatment in stem cell-based transplantation, disease modeling, and drug screening. Whereas, PDX1+/NKX6.1+ PPs enhances the subsequent endocrine lineage specification and gives rise to glucose-responsive SC-β cells in vivo and in vitro. To identify the regulators that promote induction efficiency and cellular function maturation, single-cell RNA-sequencing is performed to decipher the transcriptional landscape during PPs differentiation. The comprehensive evaluation of functionality demonstrated that manipulating LINC MIR503HG using CRISPR in PP cell fate decision can improve insulin synthesis and secretion in mature SC-β cells, without effects on liver lineage specification. Importantly, transplantation of MIR503HG-/- SC-β cells in recipients significantly restored blood glucose homeostasis, accompanied by serum C-peptide release and an increase in body weight. Mechanistically, by releasing CtBP1 occupying the CDH1 and HES1 promoters, the decrease in MIR503HG expression levels provided an excellent extracellular niche and appropriate Notch signaling activation for PPs following differentiation. Furthermore, this exhibited higher crucial transcription factors and mature epithelial markers in CDH1High expressed clusters. Altogether, these findings highlighted MIR503HG as an essential and exclusive PP cell fate specification regulator with promising therapeutic potential for patients with diabetes.
Collapse
Affiliation(s)
- Yang Xu
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
- Center of Gallbladder DiseaseShanghai East HospitalInstitute of Gallstone DiseaseSchool of MedicineTongji UniversityShanghai200092China
- Research Center of Clinical MedicineAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Susu Mao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of EducationNMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology ProductsCo‐innovation Center of NeuroregenerationNantong UniversityNantong226001China
| | - Haowen Fan
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
- Research Center of Clinical MedicineAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Jian Wan
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
- Research Center of Clinical MedicineAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Lin Wang
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
- Department of Graduate SchoolDalian Medical UniversityDalianLiaoning116000China
| | - Mingyu Zhang
- Department of Nuclear MedicineBeijing Friendship HospitalAffiliated to Capital Medical UniversityBeijing100050China
| | - Shajun Zhu
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Jin Yuan
- Department of Endocrinology and MetabolismAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Yuhua Lu
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Zhiwei Wang
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
| | - Bin Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of EducationNMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology ProductsCo‐innovation Center of NeuroregenerationNantong UniversityNantong226001China
| | - Zhaoyan Jiang
- Center of Gallbladder DiseaseShanghai East HospitalInstitute of Gallstone DiseaseSchool of MedicineTongji UniversityShanghai200092China
| | - Yan Huang
- Department of Hepatobiliary and Pancreatic SurgeryAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
- Research Center of Clinical MedicineAffiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of EducationNMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology ProductsCo‐innovation Center of NeuroregenerationNantong UniversityNantong226001China
| |
Collapse
|
34
|
Olazagoitia‐Garmendia A, Rojas‐Márquez H, Sebastian‐delaCruz M, Agirre‐Lizaso A, Ochoa A, Mendoza‐Gomez LM, Perugorria MJ, Bujanda L, Madrigal AH, Santin I, Castellanos‐Rubio A. m 6A Methylated Long Noncoding RNA LOC339803 Regulates Intestinal Inflammatory Response. Adv Sci (Weinh) 2024; 11:e2307928. [PMID: 38273714 PMCID: PMC10987157 DOI: 10.1002/advs.202307928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/20/2023] [Indexed: 01/27/2024]
Abstract
Cytokine mediated sustained inflammation increases the risk to develop different complex chronic inflammatory diseases, but the implicated mechanisms remain unclear. Increasing evidence shows that long noncoding RNAs (lncRNAs) play key roles in the pathogenesis of inflammatory disorders, while inflammation associated variants are described to affect their function or essential RNA modifications as N6-methyladenosine (m6A) methylation, increasing predisposition to inflammatory diseases. Here, the functional implication of the intestinal inflammation associated lncRNA LOC339803 in the production of cytokines by intestinal epithelial cells is described. Allele-specific m6A methylation is found to affect YTHDC1 mediated protein binding affinity. LOC339803-YTHDC1 interaction dictates chromatin localization of LOC339803 ultimately inducing the expression of NFκB mediated proinflammatory cytokines and contributing to the development of intestinal inflammation. These findings are confirmed using human intestinal biopsy samples from different intestinal inflammatory conditions and controls. Additionally, it is demonstrated that LOC339803 targeting can be a useful strategy for the amelioration of intestinal inflammation in vitro and ex vivo. Overall, the results support the importance of the methylated LOC339803 lncRNA as a mediator of intestinal inflammation, explaining genetic susceptibility and presenting this lncRNA as a potential novel therapeutic target for the treatment of inflammatory intestinal disorders.
Collapse
Affiliation(s)
- Ane Olazagoitia‐Garmendia
- Department of Biochemistry and Molecular BiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Henar Rojas‐Márquez
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Maialen Sebastian‐delaCruz
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Aloña Agirre‐Lizaso
- Department of Liver and Gastrointestinal DiseasesBiogipuzkoa Health Research InstituteDonostia University HospitalDonostia‐San Sebastian20014Spain
| | - Anne Ochoa
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Luis Manuel Mendoza‐Gomez
- Department of Biochemistry and Molecular BiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Biobizkaia Health Research InstituteBarakaldo48903Spain
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal DiseasesBiogipuzkoa Health Research InstituteDonostia University HospitalDonostia‐San Sebastian20014Spain
- Department of MedicineFaculty of Medicine and NursingUniversity of the Basque CountryUPV/EHUDonostia‐San Sebastián20014Spain
- CIBERehdInstituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - Luis Bujanda
- Department of Liver and Gastrointestinal DiseasesBiogipuzkoa Health Research InstituteDonostia University HospitalDonostia‐San Sebastian20014Spain
- Department of MedicineFaculty of Medicine and NursingUniversity of the Basque CountryUPV/EHUDonostia‐San Sebastián20014Spain
- CIBERehdInstituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - Alain Huerta Madrigal
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of MedicineMedicine FacultyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Gastroenterology DepartmentHospital Universitario de GaldakaoGaldakao48960Spain
| | - Izortze Santin
- Department of Biochemistry and Molecular BiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas CIBERDEMInstituto de Salud Carlos IIIMadrid28029Spain
| | - Ainara Castellanos‐Rubio
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas CIBERDEMInstituto de Salud Carlos IIIMadrid28029Spain
- IkerbasqueBasque Foundation for ScienceBilbao48011Spain
| |
Collapse
|
35
|
Duan W, Yang L, Liu J, Dai Z, Wang Z, Zhang H, Zhang X, Liang X, Luo P, Zhang J, Liu Z, Zhang N, Mo H, Qu C, Xia Z, Cheng Q. A TGF-β signaling-related lncRNA signature for prediction of glioma prognosis, immune microenvironment, and immunotherapy response. CNS Neurosci Ther 2024; 30:e14489. [PMID: 37850692 PMCID: PMC11017415 DOI: 10.1111/cns.14489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 07/27/2023] [Accepted: 09/24/2023] [Indexed: 10/19/2023] Open
Abstract
AIMS The dysregulation of TGF-β signaling is a crucial pathophysiological process in tumorigenesis and progression. LncRNAs have diverse biological functions and are significant participants in the regulation of tumor signaling pathways. However, the clinical value of lncRNAs related to TGF-β signaling in glioma is currently unclear. METHODS Data on glioma's RNA-seq transcriptome, somatic mutation, DNA methylation data, and clinicopathological information were derived from the CGGA and TCGA databases. A prognostic lncRNA signature was constructed by Cox and LASSO regression analyses. TIMER2.0 database was utilized to deduce immune infiltration characteristics. "ELMER v.2" was used to reconstruct TF-methylation-gene regulatory network. Immunotherapy and chemotherapy response predictions were implemented by the TIDE algorithm and GDSC database, respectively. In vitro and in vivo experiments were conducted to verify the results and clarify the regulatory mechanism of lncRNA. RESULTS In glioma, a TGF-β signaling-related 15-lncRNA signature was constructed, including AC010173.1, HOXA-AS2, AC074286.1, AL592424.1, DRAIC, HOXC13-AS, AC007938.1, AC010729.1, AC013472.3, AC093895.1, AC131097.4, AL606970.4, HOXC-AS1, AGAP2-AS1, and AC002456.1. This signature proved to be a reliable prognostic tool, with high risk indicating an unfavorable prognosis and being linked to malignant clinicopathological and genomic mutation traits. Risk levels were associated with different immune infiltration landscapes, where high risk was indicative of high levels of macrophage infiltration. In addition, high risk also suggested better immunotherapy and chemotherapy response. cg05987823 was an important methylation site in glioma progression, and AP-1 transcription factor family participated in the regulation of signature lncRNA expression. AGAP2-AS1 knockdown in in vitro and in vivo experiments inhibited the proliferation, migration, and invasion of glioma cells, as well as the growth of glioma, by downregulating the expression levels of NF-κB and ERK 1/2 in the TGF-β signaling pathway. CONCLUSIONS A prognostic lncRNA signature of TGF-β signaling was established in glioma, which can be used for prognostic judgment, immune infiltration status inference, and immunotherapy response prediction. AGAP2-AS1 plays an important role in glioma progression.
Collapse
Affiliation(s)
- Wei‐Wei Duan
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Li‐Ting Yang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Jian Liu
- Experiment Center of Medical InnovationThe First Hospital of Hunan University of Chinese MedicineChangshaHunanChina
| | - Zi‐Yu Dai
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Ze‐Yu Wang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- MRC Centre for Regenerative Medicine, Institute for Regeneration and RepairUniversity of EdinburghEdinburghUK
| | - Hao Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xun Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xi‐Song Liang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Peng Luo
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Jian Zhang
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Zao‐Qu Liu
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Nan Zhang
- One‐third Lab, College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinHei LongjiangChina
| | - Hao‐Yang Mo
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Chun‐Run Qu
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zhi‐Wei Xia
- Department of NeurologyHunan Aerospace HospitalChangshaHunanChina
| | - Quan Cheng
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaHunanChina
| |
Collapse
|
36
|
Miller MJ, Gries KJ, Marcotte GR, Ryan Z, Strub MD, Kunz HE, Arendt BK, Dasari S, Ebert SM, Adams CM, Lanza IR. Human myofiber-enriched aging-induced lncRNA FRAIL1 promotes loss of skeletal muscle function. Aging Cell 2024; 23:e14097. [PMID: 38297807 PMCID: PMC11019130 DOI: 10.1111/acel.14097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 02/02/2024] Open
Abstract
The loss of skeletal muscle mass during aging is a significant health concern linked to adverse outcomes in older individuals. Understanding the molecular basis of age-related muscle loss is crucial for developing strategies to combat this debilitating condition. Long noncoding RNAs (lncRNAs) are a largely uncharacterized class of biomolecules that have been implicated in cellular homeostasis and dysfunction across a many tissues and cell types. To identify lncRNAs that might contribute to skeletal muscle aging, we screened for lncRNAs whose expression was altered in vastus lateralis muscle from older compared to young adults. We identified FRAIL1 as an aging-induced lncRNA with high abundance in human skeletal muscle. In healthy young and older adults, skeletal muscle FRAIL1 was increased with age in conjunction with lower muscle function. Forced expression of FRAIL1 in mouse tibialis anterior muscle elicits a dose-dependent reduction in skeletal muscle fiber size that is independent of changes in muscle fiber type. Furthermore, this reduction in muscle size is dependent on an intact region of FRAIL1 that is highly conserved across non-human primates. Unbiased transcriptional and proteomic profiling of the effects of FRAIL1 expression in mouse skeletal muscle revealed widespread changes in mRNA and protein abundance that recapitulate age-related changes in pathways and processes that are known to be altered in aging skeletal muscle. Taken together, these findings shed light on the intricate molecular mechanisms underlying skeletal muscle aging and implicate FRAIL1 in age-related skeletal muscle phenotypes.
Collapse
Affiliation(s)
- Matthew J. Miller
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- University of IowaIowa CityIowaUSA
| | | | - George R. Marcotte
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- University of IowaIowa CityIowaUSA
| | - Zachary Ryan
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
| | | | - Hawley E. Kunz
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
| | | | - Surendra Dasari
- Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | - Scott M. Ebert
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- Emmyon, Inc.RochesterMinnesotaUSA
| | - Christopher M. Adams
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- Emmyon, Inc.RochesterMinnesotaUSA
| | - Ian R. Lanza
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
| |
Collapse
|
37
|
Qian HG, Wu Q, Wu JH, Tian XY, Xu W, Hao CY. [Corrigendum] Long non‑coding RNA LINC00238 suppresses the malignant phenotype of liver cancer by sponging miR‑522. Mol Med Rep 2024; 29:65. [PMID: 38426568 PMCID: PMC10926094 DOI: 10.3892/mmr.2024.13189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/13/2021] [Indexed: 03/02/2024] Open
Abstract
Subsequently to the publication of the above article, an interested reader drew to the authors' attention that two pairs of data panels featured in Figs. 2E and 6D, portraying the results from cell invasion and migration assay experiments, appeared to contain overlapping sections, such that data which were intended to show the results from differently performed experiments had apparently been derived from a smaller number of original sources. The authors were able to re‑examine their original data (which was also presented to the Editorial Office), and realized that errors has been made in the compilation of Fig. 2. The proposed revised version of Fig. 2, now showing the results from the 'field 1' view of the data, is shown on the next page. Note that these errors did not significantly affect either the results or the conclusions reported in this paper,.All the authors agree to the publication of this Corrigendum, and are grateful to the Editor of Molecular Medicine Reports for allowing them the opportunity to correct this error; furthermore, they apologize to the readership for any inconvenience caused. [Molecular Medicine Reports 25: 71, 2022; DOI: 10.3892/mmr.2022.12587].
Collapse
Affiliation(s)
- Hong-Gang Qian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Hepato‑Pancreato‑Biliary Surgery, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Qiong Wu
- MOE Key Lab, Bioinformatics, School of Life Sciences; 3Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, P.R. China
| | - Jian-Hui Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Hepato‑Pancreato‑Biliary Surgery, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Xiu-Yun Tian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Hepato‑Pancreato‑Biliary Surgery, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Wei Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Hepato‑Pancreato‑Biliary Surgery, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Chun-Yi Hao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Hepato‑Pancreato‑Biliary Surgery, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| |
Collapse
|
38
|
Yin Q, Qu Z, Mathew R, Zeng L, Du Z, Xue Y, Liu D, Zheng X. Epitranscriptomic orchestrations: Unveiling the regulatory paradigm of m6A, A-to-I editing, and m5C in breast cancer via long noncoding RNAs and microRNAs. Cell Biochem Funct 2024; 42:e3996. [PMID: 38561942 DOI: 10.1002/cbf.3996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/09/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Breast cancer (BC) poses a persistent global health challenge, particularly in countries with elevated human development indices linked to factors such as increased life expectancy, education, and wealth. Despite therapeutic progress, challenges persist, and the role of epitranscriptomic RNA modifications in BC remains inadequately understood. The epitranscriptome, comprising diverse posttranscriptional modifications on RNA molecules, holds the potential to intricately modulate RNA function and regulation, implicating dysregulation in various diseases, including BC. Noncoding RNAs (ncRNAs), acting as posttranscriptional regulators, influence physiological and pathological processes, including cancer. RNA modifications in long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) add an extra layer to gene expression control. This review delves into recent insights into epitranscriptomic RNA modifications, such as N-6-methyladenosine (m6A), adenine-to-inosine (A-to-I) editing, and 5-methylcytosine (m5C), specifically in the context of lncRNA and miRNAs in BC, highlighting their potential implications in BC development and progression. Understanding this intricate regulatory landscape is vital for deciphering the molecular mechanisms underlying BC and identifying potential therapeutic targets.
Collapse
Affiliation(s)
- Qinan Yin
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Zhifeng Qu
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Regina Mathew
- Department of Chemistry and Biochemistry, California State University, Los Angeles, California, USA
| | - Li Zeng
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Zhe Du
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Yun Xue
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Dechun Liu
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Xuewei Zheng
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| |
Collapse
|
39
|
Zhang ZY, Zhang Z, Ye X, Sakurai T, Lin H. A BERT-based model for the prediction of lncRNA subcellular localization in Homo sapiens. Int J Biol Macromol 2024; 265:130659. [PMID: 38462114 DOI: 10.1016/j.ijbiomac.2024.130659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/19/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
Understanding the subcellular localization of lncRNAs is crucial for comprehending their regulation activities. The conventional detection of lncRNA subcellular location usually uses in situ detection techniques, which are resource intensive. Some machine learning-based algorithms have been proposed for lncRNA subcellular location prediction in mammals. However, due to the low level of conservation of lncRNA sequence, the performance of cross-species models remains unsatisfactory. In this study, we curated a novel dataset containing subcellular location information of lncRNAs in Homo sapiens. Subsequently, based on the BERT pre-trained language algorithm, we developed a model for lncRNA subcellular location prediction. Our model achieved a micro-average area under the receiver operating characteristic (AUROC) of 0.791 on the training set and an AUROC of 0.700 on the testing nucleus set. Additionally, we conducted cross-species validation and motif discovery to further investigate underlying patterns. In summary, our study provides valuable guidance and computational analysis tools for exploring the mechanisms of lncRNA subcellular localization and the dynamic spatial changes of RNA in abnormal physiological states.
Collapse
Affiliation(s)
- Zhao-Yue Zhang
- Tsukuba Life Science Innovation Program, University of Tsukuba, Tsukuba 3058577, Japan
| | - Zheng Zhang
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL 36849, USA
| | - Xiucai Ye
- Department of Computer Science, University of Tsukuba, Tsukuba 3058577, Japan.
| | - Tetsuya Sakurai
- Department of Computer Science, University of Tsukuba, Tsukuba 3058577, Japan
| | - Hao Lin
- Center for Information Biology, University of Electronic Science and Technology of China, Chengdu 611731, China.
| |
Collapse
|
40
|
Darmadi D, Chugaeva UY, Saleh RO, Hjazi A, Saleem HM, Ghildiyal P, Alwaily ER, Alawadi A, Alnajar MJ, Ihsan A. Critical roles of long noncoding RNA H19 in cancer. Cell Biochem Funct 2024; 42:e4018. [PMID: 38644608 DOI: 10.1002/cbf.4018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 03/18/2024] [Accepted: 04/06/2024] [Indexed: 04/23/2024]
Abstract
Long noncoding RNAs (lncRNAs) are a category of noncoding RNAs characterized by their length, often exceeding 200 nucleotides. There is a growing body of data that indicate the significant involvement of lncRNAs in a wide range of disorders, including cancer. lncRNA H19 was among the initial lncRNAs to be identified and is transcribed from the H19 gene. The H19 lncRNA exhibits significant upregulation in a diverse range of human malignancies, such as breast, colorectal, pancreatic, glioma, and gastric cancer. Moreover, the overexpression of H19 is frequently associated with a worse prognosis among individuals diagnosed with cancer. H19 has been shown to have a role in facilitating several cellular processes, including cell proliferation, invasion, migration, epithelial-mesenchymal transition, metastasis, and apoptosis. This article summarizes the aberrant upregulation of H19 in human malignancies, indicating promising avenues for future investigations on cancer diagnostics and therapeutic interventions.
Collapse
Affiliation(s)
- Darmadi Darmadi
- Department of Internal Medicine, Faculty of Medicine, Universitas Sumatera Utara, Medan, North Sumatera, Indonesia
| | - Uliana Y Chugaeva
- Department of Pediatric, Preventive Dentistry and Orthodontics, Institute of Dentistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Raed Obaid Saleh
- Department of Medical Laboratory Techniques, Al-Maarif University College, Al-Anbar, Iraq
| | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Hiba Muwafaq Saleem
- Department of Biology, College of Science, University of Anbar, Ramadi, Iraq
| | - Pallavi Ghildiyal
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Enas R Alwaily
- Microbiology Research Group, College of Pharmacy, Al-Ayen University, Thi-Qar, Iraq
| | - Ahmed Alawadi
- College of Technical Engineering, The Islamic University, Najaf, Iraq
- College of Technical Engineering, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- College of Technical Engineering, The Islamic University of Babylon, Hillah, Iraq
| | | | - Ali Ihsan
- College of Technical Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna, Iraq
| |
Collapse
|
41
|
Pan Y, Wu Y, Liu Y, Wang P, Huang H, Jin J, Fang Y, Huang S, Fan Z, Yu H. Long non-coding RNA ENSMUST00000197208 promotes a shift in the Th17/Treg ratio via the P2X7R-NLRP3 inflammasome axis in collagen-induced arthritis. Immunol Res 2024; 72:347-360. [PMID: 38066380 DOI: 10.1007/s12026-023-09439-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/15/2023] [Indexed: 04/20/2024]
Abstract
Recently, long non‑coding RNAs (lncRNAs) have been implicated in several human diseases, including arthritis. However, the role of lncRNAs in regulating the Th17/Treg ratio during the progression of collagen-induced arthritis (CIA) is poorly understood. Therefore, the aim of this study was to determine the role of the lncRNA ENSMUST00000197208 and the P2X7R-NLRP3 inflammasome axis in changes in the Th17/Treg ratio in CIA. To achieve this, the distribution of T cell subgroups in the spleen cells of a CIA mouse model and control mice was examined. Additionally, we examined the expression profile of ENSMUST00000197208 in a CIA mouse model and healthy mice. The results showed that ENSMUST00000197208 expression was significantly upregulated in the CIA models compared with the control group. Additionally, the P2X7R-NLRP3 inflammasome axis participated in the pathogenesis of CIA and knockdown of ENSMUST00000197208 inhibited CD4+ T cell differentiation into Th17 cells. Compared with the control group, joint inflammation was less visible in NLRP3 knockout mice. Additionally, the P2X7R-NLRP3 inflammasome axis, which is downstream of ENSMUST00000197208, can be positively targeted and regulated by ENSMUST00000197208 through miR-107. Overall, the findings of this study showed that the "lncRNA ENSMUST00000197208-miR 107-P2X7R/NLRP3" axis plays an important role in CIA and knocking down ENSMUST00000197208 can efficiently inhibit Th17 differentiation by suppressing the P2X7R-NLRP3 inflammasome axis. Therefore, targeting this axis may represent a novel strategy for arthritis treatment.
Collapse
Affiliation(s)
- Yuting Pan
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China
| | - Yan Wu
- Department of Child Health Care, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China
| | - Yingying Liu
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China
| | - Panpan Wang
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China
| | - Hui Huang
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China
| | - Jing Jin
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China
| | - Yuying Fang
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China
| | - Shuoyin Huang
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China
| | - Zhidan Fan
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China.
| | - Haiguo Yu
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China.
| |
Collapse
|
42
|
Xu J, Liu C, Qu K, Zhang J, Liu S, Meng F, Wan Y. m6A methyltransferase METTL14‑mediated RP1‑228H13.5 promotes the occurrence of liver cancer by targeting hsa‑miR‑205/ZIK1. Oncol Rep 2024; 51:59. [PMID: 38426536 PMCID: PMC10926101 DOI: 10.3892/or.2024.8718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 01/25/2024] [Indexed: 03/02/2024] Open
Abstract
The aim of the present study was to explore the association between N6‑methyladenosine (m6A) modification regulatory gene‑related long noncoding (lnc)RNA RP1‑228H13.5 and cancer prognosis through bioinformatics analysis, as well as the impact of RP1‑228H13.5 on cell biology‑related behaviors and specific molecular mechanisms. Bioinformatics analysis was used to construct a risk model consisting of nine genes. This model can reflect the survival time and differentiation degree of cancer. Subsequently, a competing endogenous RNA network consisting of 3 m6A‑related lncRNAs, six microRNAs (miRs) and 201 mRNAs was constructed. A cell assay confirmed that RP1‑228H13.5 is significantly upregulated in liver cancer cells, which can promote liver cancer cell proliferation, migration and invasion, and inhibit liver cancer cell apoptosis. The specific molecular mechanism may be the regulation of the expression of zinc finger protein interacting with K protein 1 (ZIK1) by targeting the downstream hsa‑miR‑205. Further experiments found that the m6A methyltransferase 14, N6‑adenosine‑methyltransferase subunit mediates the regulation of miR‑205‑5p expression by RP1‑228H13.5. m6A methylation regulatory factor‑related lncRNA has an important role in cancer. The targeting of hsa‑miR‑205 by RP1‑228H13.5 to regulate ZIK1 may serve as a potential mechanism in the occurrence and development of liver cancer.
Collapse
Affiliation(s)
- Jia Xu
- Department of Hepatobiliary Pancreatic and Liver Transplantation Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
- Department of General Surgery, Leping People's Hospital, Jingdezhen, Jiangxi 333300, P.R. China
| | - Chang Liu
- Department of Hepatobiliary Pancreatic and Liver Transplantation Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Kai Qu
- Department of Hepatobiliary Pancreatic and Liver Transplantation Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Jingyao Zhang
- Department of SICU, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Sinan Liu
- Department of SICU, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Fandi Meng
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yong Wan
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| |
Collapse
|
43
|
Li N, Yu K, Huang D, Li S, Zeng D, Li J, Fan L. Molecular Characterization of Cuproptosis-related lncRNAs: Defining Molecular Subtypes and a Prognostic Signature of Ovarian Cancer. Biol Trace Elem Res 2024; 202:1428-1445. [PMID: 37528285 DOI: 10.1007/s12011-023-03780-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023]
Abstract
Cuproptosis, a newly discovered form of programmed cell death, relies on mitochondrial respiration, the chain of which has been found to be altered in ovarian cancer (OC). The current work probed into the effects of Cuproptosis on the prognosis, immune microenvironment and therapeutic response of OC based on Cuproptosis-related lncRNAs. Data on OC gene expression and clinical characteristics were collected from TCGA, ICGC and GEO databases, and mRNA and lncRNA were distinguished. Cuproptosis-related lncRNAs were screened for consensus clustering analysis. Differentially expressed lncRNAs (DElncRNAs) were identified between clusters, and least absolute shrinkage and selection operator (LASSO) and Cox regression analysis were performed to establish a prognostic signature. Its potential value in OC was evaluated by Gene Set Enrichment Analysis (GSEA), tumor cell mutation and immune microenvironment analysis, and response to immunotherapy and antineoplastic drugs. According to the classification scheme of Cuproptosis-related lncRNAs, OC was divided into four molecular subtypes, which were different in survival time, immune characteristics and somatic mutation. The prognostic signature between subtypes included 10 lncRNAs, which were significantly correlated with the prognosis, immune microenvironment related indexes, the expression of immune checkpoint molecules and the sensitivity of antineoplastic drug Paclitaxel and Gefitinib of OC. We examined the expression of ten LncRNAs in OC cell lines and found that LINC00189, ZFHX4-AS1, RPS6KA2-IT1 and C9orf106 were expressed elevated in OC cell lines, and LINC00861, LINC00582, DEPDC1-AS1, LINC01556, LEMD1-AS1, TYMSOS expression was decreased in OC cell lines. The results of CCK8 showed that the cell viability of OC cells decreased after inhibition of C9orf106, whereas the cell viability of OC cells increased after inhibition of LEMD1-AS1. This work revealed new Cuproptosis-related lncRNA molecular subtypes exhibiting tumor microenvironment (TME) heterogeneity for OC and proposed a prognostic signature that may have benefits in understanding the prognosis, pathological features and immune microenvironment of OC patients.
Collapse
Affiliation(s)
- Nan Li
- Reproductive Medicine Center, Liuzhou Maternity and Child Health Care Hospital, Liuzhou, 545001, China
- Liuzhou Institute of Reproduction and Genetics, Liuzhou, 545001, China
- Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi, University of Science and Technology, Liuzhou, 545001, China
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, 545001, China
| | - Kai Yu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Delun Huang
- Department of Physiology, Guangxi University of Chinese Medicine, Nanning, 530001, China
| | - Shu Li
- Reproductive Medicine Center, Liuzhou Maternity and Child Health Care Hospital, Liuzhou, 545001, China
- Liuzhou Institute of Reproduction and Genetics, Liuzhou, 545001, China
- Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi, University of Science and Technology, Liuzhou, 545001, China
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, 545001, China
| | - Dingyuan Zeng
- Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi, University of Science and Technology, Liuzhou, 545001, China
- The Department of Obstetrics and Gynecology, Liuzhou Maternity and Child Health Care Hospital, Liuzhou, 545001, China
| | - Jingjing Li
- Reproductive Medicine Center, Liuzhou Maternity and Child Health Care Hospital, Liuzhou, 545001, China.
- Liuzhou Institute of Reproduction and Genetics, Liuzhou, 545001, China.
- Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi, University of Science and Technology, Liuzhou, 545001, China.
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, 545001, China.
| | - Li Fan
- Reproductive Medicine Center, Liuzhou Maternity and Child Health Care Hospital, Liuzhou, 545001, China.
- Liuzhou Institute of Reproduction and Genetics, Liuzhou, 545001, China.
- Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi, University of Science and Technology, Liuzhou, 545001, China.
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, 545001, China.
| |
Collapse
|
44
|
Zhang J, Li S, Zhang M, Wang Z, Xing Z. Targeting HOXA11-AS to mitigate prostate cancer via the glycolytic metabolism: In vitro and in vivo. J Cell Mol Med 2024; 28:e18227. [PMID: 38520207 PMCID: PMC10960170 DOI: 10.1111/jcmm.18227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/10/2024] [Accepted: 02/26/2024] [Indexed: 03/25/2024] Open
Abstract
As oncogenes or oncogene suppressors, long-stranded non-coding RNAs are essential for the formation and progression of human tumours. However, the mechanisms behind the regulatory role of RNA HOXA11-AS in prostate cancer (PCa) are unclear. PCa is a common malignant tumour worldwide, and an increasing number of studies have focused on its metabolic profile. Studies have shown that the long non-coding RNA (lncRNA) HOXA11-AS is aberrantly expressed in many tumours. However, the role of HOXA11-AS in PCa is unclear. This work aimed to determine how HOXA11-AS regulated PCa in vitro and in vivo. We first explored the clinical role of HOXA11-AS in PCa using bioinformatics methods, including single sample gene set enrichment analysis (ssGSEA), weighted gene co-expression network analysis (WGCNA), and least absolute shrinkage and selection operator (LASSO)-logistics systematically. In this study, PCa cell lines were selected to assess the PCa regulatory role of HOXA11-AS overexpression versus silencing in vitro, and tumour xenografts were performed in nude mice to assess tumour suppression by HOXA11-AS silencing in vivo. HOXA11-AS expression was significantly correlated with clinicopathological factors, epithelial-mesenchymal transition (EMT) and glycolysis. Moreover, key genes downstream of HOXA11-AS exhibited good clinical diagnostic properties for PCa. Furthermore, we studied both in vitro and in vivo effects of HOXA11-AS expression on PCa. Overexpression of HOXA11-AS increased PCa cell proliferation, migration and EMT, while silencing HOXA11-AS had the opposite effect on PCa cells. In addition, multiple metabolites were downregulated by silencing HOXA11-AS via the glycolytic pathway. HOXA11-AS silencing significantly inhibited tumour development in vivo. In summary, silencing HOXA11-AS can inhibit PCa by regulating glucose metabolism and may provide a future guidance for the treatment of PCa.
Collapse
Affiliation(s)
- Jiankang Zhang
- Department of UrologyAffiliated Haikou Hospital of Xiangya Medical School, Central South UniversityHaikouChina
| | - Sailian Li
- Department of GastroenterologyAffiliated Haikou Hospital of Xiangya Medical School, Central South UniversityHaikouChina
| | - Mengyu Zhang
- Department of UrologyAffiliated Haikou Hospital of Xiangya Medical School, Central South UniversityHaikouChina
| | - Zhenting Wang
- Department of UrologyAffiliated Haikou Hospital of Xiangya Medical School, Central South UniversityHaikouChina
| | - Zengshu Xing
- Department of UrologyAffiliated Haikou Hospital of Xiangya Medical School, Central South UniversityHaikouChina
| |
Collapse
|
45
|
Liu Y, Wang Y, Liu B, Liu W, Ma Y, Cao Y, Yan S, Zhang P, Zhou L, Zhan Q, Wu N. Targeting lncRNA16 by GalNAc-siRNA conjugates facilitates chemotherapeutic sensibilization via the HBB/NDUFAF5/ROS pathway. Sci China Life Sci 2024; 67:663-679. [PMID: 38155279 DOI: 10.1007/s11427-023-2434-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 12/30/2023]
Abstract
Chemoresistance is a significant barrier to effective cancer treatment. Potential mechanisms for chemoresistance include reactive oxygen species (ROS) accumulation and expression of chemoresistance-promoting genes. Here, we report a novel function of lncRNA16 in the inhibition of ROS generation and the progression of chemoresistance. By analyzing the serum levels of lncRNA16 in a cohort of 35 patients with non-small cell lung cancer (NSCLC) and paired serum samples pre- and post-treatment from 10 NSCLC patients receiving neoadjuvant platinum-based chemotherapy, performing immunohistochemistry (IHC) assays on 188 NSCLC tumor samples, using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) assays, as well as RNA immunoprecipitation (RIP) and RNA pull-down analyses, we discovered that patients with increased serum levels of lncRNA16 exhibited a poor response to platinum-based chemotherapy. The expression of hemoglobin subunit beta (HBB) and NDUFAF5 significantly increases with the development of chemoresistance. LncRNA16 binds to HBB and promotes HBB accumulation by inhibiting autophagy. LncRNA16 can also inhibit ROS generation via the HBB/NDUFAF5 axis and function as a scaffold to facilitate the colocalization of HBB and NDUFAF5 in the mitochondria. Importantly, preclinical studies in mouse models of chemo-resistant NSCLC have suggested that lncRNA16 targeting by trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNA restores chemosensitivity and results in tumor growth inhibition with no detectable toxicity in vivo. Overall, lncRNA16 is a promising therapeutic target for overcoming chemoresistance, and the combination of first-line platinum-based chemotherapy with lncRNA16 intervention can substantially enhance anti-tumor efficacy.
Collapse
Affiliation(s)
- Yanfang Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Bing Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Wenzhong Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yuanyuan Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yiren Cao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Shi Yan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Panpan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Oncology II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Lixin Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Qimin Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
- Peking University International Cancer Institute, Beijing, 100191, China.
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
| | - Nan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
| |
Collapse
|
46
|
Bau DT, Tsai CW, Chang WS, Yang JS, Liu TY, Lu HF, Wang YW, Tsai FJ. Genetic susceptibility to prostate cancer in Taiwan: A genome-wide association study. Mol Carcinog 2024; 63:617-628. [PMID: 38390760 DOI: 10.1002/mc.23676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/02/2023] [Accepted: 12/15/2023] [Indexed: 02/24/2024]
Abstract
We conducted the first genome-wide association study (GWAS) of prostate cancer (PCa) in Taiwan with 1844 cases and 80,709 controls. Thirteen independent single-nucleotide polymorphisms (SNPs) reached genome-wide significance (p < 5 × 10-8 ). Among these, three were distinct from previously identified loci: rs76072851 in CORO2B gene (15q23), odds ratio (OR) = 1.54, 95% confidence interval (CI), 1.36-1.76, p = 5.30 × 10-11 ; rs7837051, near two long noncoding RNA (lncRNA) genes, PRNCR1 and PCAT2 (8q24.21), OR = 1.41 (95% CI, 1.31-1.51), p = 8.77 × 10-21 ; and rs56339048, near an lncRNA gene, CASC8 (8q24.21), OR = 1.25 (95% CI, 1.16-1.35), p = 2.14 × 10-8 . We refined the lead SNPs for two previously identified SNPs in Taiwanese: rs13255059 (near CASC8), p = 9.02 × 10-43 , and rs1456315 (inside PRNCR1), p = 4.33 × 10-42 . We confirmed 35 out of 49 GWAS-identified East Asian PCa susceptibility SNPs. In addition, we identified two SNPs more specific to Taiwanese than East Asians: rs34295433 in LAMC1 (1q25.3) and rs6853490 in PDLIM5 (4q22.3). A weighted genetic risk score (GRS) was developed using the 40 validated SNPs and the area under the receiver-operating characteristic curve for the GRS to predict PCa was 0.67 (95% CI, 0.63-0.71). These identified SNPs provide valuable insights into the molecular mechanisms of prostate carcinogenesis in Taiwan and underscore the significant role of genetic susceptibility in regional differences in PCa incidence.
Collapse
Affiliation(s)
- Da-Tian Bau
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
| | - Chia-Wen Tsai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Wen-Shin Chang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Jai-Sing Yang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Ting-Yuan Liu
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Hsing-Fang Lu
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Yu-Wen Wang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Fuu-Jen Tsai
- Human Genetics Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- Department of Medical Genetics, China Medical University Hospital, Taichung, Taiwan
| |
Collapse
|
47
|
Zhang X, Zhu R, Jiao Y, Simayi H, He J, Shen Z, Wang H, He J, Zhang S, Yang F. Expression profiles and gene set enrichment analysis of the transcriptomes from the cancer tissue, white adipose tissue and paracancer tissue with colorectal cancer. PeerJ 2024; 12:e17105. [PMID: 38563016 PMCID: PMC10984182 DOI: 10.7717/peerj.17105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/22/2024] [Indexed: 04/04/2024] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common cancers worldwide and is related to diet and obesity. Currently, crosstalk between lipid metabolism and CRC has been reported; however, the specific mechanism is not yet understood. In this study, we screened differentially expressed long non-coding RNAs (lncRNAs) and mRNAs from primary cancer, paracancer, and white adipose tissue of CRC patients. We screened and analyzed the genes differentially expressed between primary and paracancer tissue and between paracancer and white adipose tissue but not between primary and white adipose tissue. According to the results of the biological analysis, we speculated a lncRNA (MIR503HG) that may be involved in the crosstalk between CRC and lipid metabolism through exosome delivery. Methods We screened differentially expressed long non-coding RNAs (lncRNAs) and mRNAs from primary cancer, paracancer, and white adipose tissue of CRC patients. We screened and analyzed the genes differentially expressed between primary and paracancer tissue and between paracancer and white adipose tissue but not between primary and white adipose tissue. Results We speculated a lncRNA (MIR503HG) that may be involved in the crosstalk between CRC and lipid metabolism through exosome delivery. Conclusions In this study, the findings raise the possibility of crosstalk between lipid metabolism and CRC through the exosomal delivery of lncRNAs.
Collapse
Affiliation(s)
- Xiufeng Zhang
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Provincial Clinical Research Center, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Rui Zhu
- Affiliated XiaoShan Hospital, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Ye Jiao
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Halizere Simayi
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jialing He
- Department of Colorectal Surgery, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhong Shen
- Department of Colorectal Surgery, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Houdong Wang
- Department of Colorectal Surgery, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun He
- Department of Colorectal Surgery, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Suzhan Zhang
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Provincial Clinical Research Center, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Fei Yang
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| |
Collapse
|
48
|
Ding Y, Zhang C, Zuo Q, Jin K, Li B. lncCPSET1 acts as a scaffold for MLL2/COMPASS to regulate Bmp4 and promote the formation of chicken primordial germ cells. Mol Genet Genomics 2024; 299:41. [PMID: 38551742 DOI: 10.1007/s00438-024-02127-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/15/2024] [Indexed: 04/02/2024]
Abstract
Primordial germ cells (PGCs) are the ancestors of female and male germ cells. Recent studies have shown that long non-coding RNA (lncRNA) and histone methylation are key epigenetic factors affecting PGC formation; however, their joint regulatory mechanisms have rarely been studied. Here, we explored the mechanism by which lncCPSET1 and H3K4me2 synergistically regulate the formation of chicken PGCs for the first time. Combined with chromatin immunoprecipitation (CHIP) sequencing and RNA-seq of PGCs transfected with the lncCPSET1 overexpression vector, GO annotation and KEGG enrichment analysis revealed that Wnt and TGF-β signaling pathways were significantly enriched, and Fzd2, Id1, Id4, and Bmp4 were identified as candidate genes. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that ASH2L, DPY30, WDR5, and RBBP5 overexpression significantly increased the expression of Bmp4, which was up-regulated after lncCPSET1 overexpression as well. It indicated that Bmp4 is a target gene co-regulated by lncCPSET1 and MLL2/COMPASS. Interestingly, co-immunoprecipitation results showed that ASH2L, DPY30 and WDR5 combined and RBBP5 weakly combined with DPY30 and WDR5. lncCPSET1 overexpression significantly increased Dpy30 expression and co-immunoprecipitation showed that interference/overexpression of lncCPSET1 did not affect the binding between the proteins in the complexes, but interference with lncCPSET1 inhibited DPY30 expression, which was confirmed by RNA immunoprecipitation that lncCPSET1 binds to DPY30. Additionally, CHIP-qPCR results showed that DPY30 enriched in the Bmp4 promoter region promoted its transcription, thus promoting the formation of PGCs. This study demonstrated that lncCPSET1 and H3K4me2 synergistically promote PGC formation, providing a reference for the study of the regulatory mechanisms between lncRNA and histone methylation, as well as a molecular basis for elucidating the formation mechanism of PGCs in chickens.
Collapse
Affiliation(s)
- Ying Ding
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Chen Zhang
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
- RNA Medicine Center, International Institutes of Medicine, Zhejiang University, Hangzhou, China
| | - Qisheng Zuo
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Kai Jin
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou University, Yangzhou, 225009, China
| | - Bichun Li
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China.
| |
Collapse
|
49
|
Čáp M, Palková Z. Non-Coding RNAs: Regulators of Stress, Ageing, and Developmental Decisions in Yeast? Cells 2024; 13:599. [PMID: 38607038 PMCID: PMC11012152 DOI: 10.3390/cells13070599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Cells must change their properties in order to adapt to a constantly changing environment. Most of the cellular sensing and regulatory mechanisms described so far are based on proteins that serve as sensors, signal transducers, and effectors of signalling pathways, resulting in altered cell physiology. In recent years, however, remarkable examples of the critical role of non-coding RNAs in some of these regulatory pathways have been described in various organisms. In this review, we focus on all classes of non-coding RNAs that play regulatory roles during stress response, starvation, and ageing in different yeast species as well as in structured yeast populations. Such regulation can occur, for example, by modulating the amount and functional state of tRNAs, rRNAs, or snRNAs that are directly involved in the processes of translation and splicing. In addition, long non-coding RNAs and microRNA-like molecules are bona fide regulators of the expression of their target genes. Non-coding RNAs thus represent an additional level of cellular regulation that is gradually being uncovered.
Collapse
Affiliation(s)
- Michal Čáp
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
| |
Collapse
|
50
|
Patel A, Dharap A. An Emerging Role for Enhancer RNAs in Brain Disorders. Neuromolecular Med 2024; 26:7. [PMID: 38546891 DOI: 10.1007/s12017-024-08776-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/23/2024] [Indexed: 04/02/2024]
Abstract
Noncoding DNA undergoes widespread context-dependent transcription to produce noncoding RNAs. In recent decades, tremendous advances in genomics and transcriptomics have revealed important regulatory roles for noncoding DNA elements and the RNAs that they produce. Enhancers are one such element that are well-established drivers of gene expression changes in response to a variety of factors such as external stimuli, cellular responses, developmental cues, and disease states. They are known to act at long distances, interact with multiple target gene loci simultaneously, synergize with other enhancers, and associate with dynamic chromatin architectures to form a complex regulatory network. Recent advances in enhancer biology have revealed that upon activation, enhancers transcribe long noncoding RNAs, known as enhancer RNAs (eRNAs), that have been shown to play important roles in enhancer-mediated gene regulation and chromatin-modifying activities. In the brain, enhancer dysregulation and eRNA transcription has been reported in numerous disorders from acute injuries to chronic neurodegeneration. Because this is an emerging area, a comprehensive understanding of eRNA function has not yet been achieved in brain disorders; however, the findings to date have illuminated a role for eRNAs in activity-driven gene expression and phenotypic outcomes. In this review, we highlight the breadth of the current literature on eRNA biology in brain health and disease and discuss the challenges as well as focus areas and strategies for future in-depth research on eRNAs in brain health and disease.
Collapse
Affiliation(s)
- Ankit Patel
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
- Byrd Alzheimer's Center & Research Institute, USF Health Neuroscience Institute, Tampa, FL, USA
| | - Ashutosh Dharap
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA.
- Byrd Alzheimer's Center & Research Institute, USF Health Neuroscience Institute, Tampa, FL, USA.
| |
Collapse
|