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Naseer QA, Malik A, Zhang F, Chen S. Exploring the enigma: history, present, and future of long non-coding RNAs in cancer. Discov Oncol 2024; 15:214. [PMID: 38847897 PMCID: PMC11161455 DOI: 10.1007/s12672-024-01077-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
Long noncoding RNAs (lncRNAs), which are more than 200 nucleotides in length and do not encode proteins, play crucial roles in governing gene expression at both the transcriptional and posttranscriptional levels. These molecules demonstrate specific expression patterns in various tissues and developmental stages, suggesting their involvement in numerous developmental processes and diseases, notably cancer. Despite their widespread acknowledgment and the growing enthusiasm surrounding their potential as diagnostic and prognostic biomarkers, the precise mechanisms through which lncRNAs function remain inadequately understood. A few lncRNAs have been studied in depth, providing valuable insights into their biological activities and suggesting emerging functional themes and mechanistic models. However, the extent to which the mammalian genome is transcribed into functional noncoding transcripts is still a matter of debate. This review synthesizes our current understanding of lncRNA biogenesis, their genomic contexts, and their multifaceted roles in tumorigenesis, highlighting their potential in cancer-targeted therapy. By exploring historical perspectives alongside recent breakthroughs, we aim to illuminate the diverse roles of lncRNA and reflect on the broader implications of their study for understanding genome evolution and function, as well as for advancing clinical applications.
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Affiliation(s)
- Qais Ahmad Naseer
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Abdul Malik
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Fengyuan Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Shengxia Chen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China.
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2
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Jiang J, Duan M, Wang Z, Lai Y, Zhang C, Duan C. RNA epigenetics in pulmonary diseases: Insights into methylation modification of lncRNAs in lung cancer. Biomed Pharmacother 2024; 175:116704. [PMID: 38749181 DOI: 10.1016/j.biopha.2024.116704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 06/03/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are pivotal controllers of gene expression through epigenetic mechanisms, Methylation, a prominent area of study in epigenetics, significantly impacts cellular processes. Various RNA base methylations, including m6A, m5C, m1A, and 2'-O-methylation, profoundly influence lncRNA folding, interactions, and stability, thereby shaping their functionality. LncRNAs and methylation significantly contribute to tumor development, especially in lung cancer. Their roles encompass cell differentiation, proliferation, the generation of cancer stem cells, and modulation of immune responses. Recent studies have suggested that dysregulation of lncRNA methylation can contribute to lung cancer development. Furthermore, methylation modifications of lncRNAs hold potential for clinical application in lung cancer. Dysregulated lncRNA methylation can promote lung cancer progression and may offer insights into potential biomarker or therapeutic target. This review summarizes the current knowledge of lncRNA methylation in lung cancer and its implications for RNA epigenetics and pulmonary diseases.
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Affiliation(s)
- Junjie Jiang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China
| | - Minghao Duan
- Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang, 412017, Hunan, People's Republic of China
| | - Zheng Wang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China
| | - Yuwei Lai
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China; Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China
| | - Chaojun Duan
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China; Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Institute of Medical Sciences, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; National Clinical Research Center for Geriatric Disorders, Changsha 410008, Hunan, People's Republic of China.
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3
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Nie Z, Gao M, Jin X, Rao Y, Zhang X. MFPINC: prediction of plant ncRNAs based on multi-source feature fusion. BMC Genomics 2024; 25:531. [PMID: 38816689 PMCID: PMC11137975 DOI: 10.1186/s12864-024-10439-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 05/21/2024] [Indexed: 06/01/2024] Open
Abstract
Non-coding RNAs (ncRNAs) are recognized as pivotal players in the regulation of essential physiological processes such as nutrient homeostasis, development, and stress responses in plants. Common methods for predicting ncRNAs are susceptible to significant effects of experimental conditions and computational methods, resulting in the need for significant investment of time and resources. Therefore, we constructed an ncRNA predictor(MFPINC), to predict potential ncRNA in plants which is based on the PINC tool proposed by our previous studies. Specifically, sequence features were carefully refined using variance thresholding and F-test methods, while deep features were extracted and feature fusion were performed by applying the GRU model. The comprehensive evaluation of multiple standard datasets shows that MFPINC not only achieves more comprehensive and accurate identification of gene sequences, but also significantly improves the expressive and generalization performance of the model, and MFPINC significantly outperforms the existing competing methods in ncRNA identification. In addition, it is worth mentioning that our tool can also be found on Github ( https://github.com/Zhenj-Nie/MFPINC ) the data and source code can also be downloaded for free.
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Affiliation(s)
- Zhenjun Nie
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - Mengqing Gao
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - Xiu Jin
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Yuan Rao
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Xiaodan Zhang
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China.
- Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China.
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4
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Chang H, Chen H, Ma T, Ma K, Li Y, Suo L, Liang X, Jia K, Ma J, Li J, Sun D. Multi-omics pan-cancer study of SPTBN2 and its value as a potential therapeutic target in pancreatic cancer. Sci Rep 2024; 14:9764. [PMID: 38684762 PMCID: PMC11059406 DOI: 10.1038/s41598-024-60780-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
SPTBN2 is a protein-coding gene that is closely related to the development of malignant tumors. However, its prognostic value and biological function in pan-cancer, especially pancreatic cancer (PAAD), have not been reported. In the present study, a novel exploration of the value and potential mechanism of SPTBN2 in PAAD was conducted using multi-omics in the background of pan-cancer. Via various database analysis, up-regulated expression of SPTBN2 was detected in most of the tumor tissues examined. Overexpression of SPTBN2 in PAAD and kidney renal clear cell cancer patients potentially affected overall survival, disease-specific survival, and progression-free interval. In PAAD, SPTBN2 can be used as an independent factor affecting prognosis. Mutations and amplification of SPTBN2 were detected, with abnormal methylation of SPTBN2 affecting its expression and the survival outcome of PAAD patients. Immunoassay results demonstrate that SPTBN2 was a potential biomarker for predicting therapeutic response in PAAD, and may influence the immunotherapy efficacy of PAAD by regulating levels of CD8 + T cells and neutrophil infiltration. Results from an enrichment analysis indicated that SPTBN2 may regulate the development of PAAD via immune pathways. Thus, SPTBN2 is a potential prognostic biomarker and immunotherapy target based on its crucial role in the development of PAAD.
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Affiliation(s)
- Hongliang Chang
- Division of Cholelithiasis Minimally Invasive Surgery, Department of General Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, 116001, China
| | - Hong Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Taiheng Ma
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Kexin Ma
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Yi Li
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Lida Suo
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Xiangnan Liang
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Kunyu Jia
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Jiahong Ma
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Jing Li
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Deguang Sun
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China.
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5
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Costa DL. Grandchildren's Longevity and Their Grandfathers' POW Trauma in the U.S. Civil War. Demography 2024; 61:337-361. [PMID: 38393987 DOI: 10.1215/00703370-11191183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
I document the transmission of a grandfather's net nutritional deprivation and psychosocial stress in young adulthood across multiple generations using the grandfather's ex-prisoner of war (ex-POW) status in the U.S. Civil War (1861-1865). Using a newly created dataset, I uncover an association between a grandfather's ex-POW status and the longevity after age 45 of his sons and male-line grandsons but not of his daughters, granddaughters, female-line grandsons, children-in-law, or grandchildren-in-law. Male-line grandsons lost roughly a year of life at age 45 (4% of remaining life expectancy) if descended from ex-POWs who suffered severe captivity conditions than if descended from non-POWs. If their grandfathers faced a less harsh captivity, male-line grandsons lost less than a year of life compared with those descended from non-POWs. I find that the grandfather's age at exposure and the grandson's education, as well as the son's and the grandson's poor late gestational conditions (proxied by season of birth), mediate this relationship. I rule out socioeconomic status, marriage and mortality selection, and cultural or psychological transmission from grandfathers to grandsons as explanations. I cannot rule out an epigenetic explanation.
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Affiliation(s)
- Dora L Costa
- Department of Economics, University of California, Los Angeles, Los Angeles, CA, USA
- National Bureau of Economic Research, Cambridge, MA, USA
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6
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Mohebbi H, Esbati R, Hamid RA, Akhavanfar R, Radi UK, Siri G, Yazdani O. EZH2-interacting lncRNAs contribute to gastric tumorigenesis; a review on the mechanisms of action. Mol Biol Rep 2024; 51:334. [PMID: 38393645 DOI: 10.1007/s11033-024-09237-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/10/2024] [Indexed: 02/25/2024]
Abstract
Gastric cancer (GC) remains one of the deadliest malignancies worldwide, demanding new targets to improve its diagnosis and treatment. Long non-coding RNAs (lncRNAs) are dysregulated through gastric tumorigenesis and play a significant role in GC progression and development. Recent studies have revealed that lncRNAs can interact with histone-modifying polycomb protein, enhance Zeste Homolog 2 (EZH2), and mediate its site-specific functioning. EZH2, which functions as an oncogene in GC, is the catalytic subunit of the PRC2 complex that induces H3K27 trimethylation and epigenetically represses gene expression. EZH2-interacting lncRNAs can recruit EZH2 to the promoter regions of various tumor suppressor genes and cause their transcriptional deactivation via histone methylation. The interactions between EZH2 and this lncRNA modulate different processes, such as cell cycle, cell proliferation and growth, migration, invasion, metastasis, and drug resistance, in vitro and in vivo GC models. Therefore, EZH2-interacting lncRNAs are exciting targets for developing novel targeted therapies for GC. Subsequently, this review aims to focus on the roles of these interactions in GC progression to understand the therapeutic value of EZH2-interacting lncRNAs further.
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Affiliation(s)
- Hossein Mohebbi
- Kermanshah University of medical sciences, International branch, Kermanshah, Iran
| | - Romina Esbati
- Department of Medicine, Shahid Beheshti University, Tehran, Iran
| | | | - Roozbeh Akhavanfar
- School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Usama Kadem Radi
- College of Pharmacy, National University of Science and Technology, Dhi Qar, Iraq
| | - Goli Siri
- Department of Internal Medicine, Amir Alam Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - Omid Yazdani
- Department of Medicine, Shahid Beheshti University, Tehran, Iran.
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7
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Malgundkar SH, Tamimi Y. The pivotal role of long non-coding RNAs as potential biomarkers and modulators of chemoresistance in ovarian cancer (OC). Hum Genet 2024; 143:107-124. [PMID: 38276976 DOI: 10.1007/s00439-023-02635-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024]
Abstract
Ovarian cancer (OC) is a fatal gynecological disease that is often diagnosed at later stages due to its asymptomatic nature and the absence of efficient early-stage biomarkers. Previous studies have identified genes with abnormal expression in OC that couldn't be explained by methylation or mutation, indicating alternative mechanisms of gene regulation. Recent advances in human transcriptome studies have led to research on non-coding RNAs (ncRNAs) as regulators of cancer gene expression. Long non-coding RNAs (lncRNAs), a class of ncRNAs with a length greater than 200 nucleotides, have been identified as crucial regulators of physiological processes and human diseases, including cancer. Dysregulated lncRNA expression has also been found to play a crucial role in ovarian carcinogenesis, indicating their potential as novel and non-invasive biomarkers for improving OC management. However, despite the discovery of several thousand lncRNAs, only one has been approved for clinical use as a biomarker in cancer, highlighting the importance of further research in this field. In addition to their potential as biomarkers, lncRNAs have been implicated in modulating chemoresistance, a major problem in OC. Several studies have identified altered lncRNA expression upon drug treatment, further emphasizing their potential to modulate chemoresistance. In this review, we highlight the characteristics of lncRNAs, their function, and their potential to serve as tumor markers in OC. We also discuss a few databases providing detailed information on lncRNAs in various cancer types. Despite the promising potential of lncRNAs, further research is necessary to fully understand their role in cancer and develop effective strategies to combat this devastating disease.
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Affiliation(s)
- Shika Hanif Malgundkar
- Biochemistry Department, College of Medicine and Health Sciences, Sultan Qaboos University, PC 123, PO Box 35, Muscat, Sultanate of Oman
| | - Yahya Tamimi
- Biochemistry Department, College of Medicine and Health Sciences, Sultan Qaboos University, PC 123, PO Box 35, Muscat, Sultanate of Oman.
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8
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Shehata AMF, Gohar SF, Muharram NM, Soliman SS, Shalaby HM, Kamal Eldin SM, El-Bassal FI. LncRNA CRNDE is downregulated and associated with poor prognostic markers in chronic lymphocytic leukemia. Int J Lab Hematol 2024; 46:107-112. [PMID: 37814899 DOI: 10.1111/ijlh.14186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/28/2023] [Indexed: 10/11/2023]
Abstract
INTRODUCTION Chronic lymphocytic leukemia (CLL) is characterized by a very heterogeneous clinical outcome. Thus, a plethora of prognostic factors and systems has been identified to place patients into different risk categories and to guide therapy decisions. The classic clinical staging models by Rai and Binet have been the cornerstone of patient management for several years. The greater insight into the molecular biology of CLL facilitated the advent of prognostic genetic biomarkers that are expected to impact clinical practice soon in the future. Therefore, we aimed to investigate the expression of long non-coding RNA (lncRNA) CRNDE in patients with CLL, and to analyze its relationship with the clinicopathological parameters of CLL. METHODS In this study, 40 untreated CLL patients and 30 age- and gender-matched controls were enrolled. The analysis of lncRNA CRNDE expression was determined using reverse transcription-quantitative polymerase chain reaction technique. RESULTS Our result confirmed the downregulated expression of LncRNA CRNDE in CLL patients compared to controls (p < 0.001). The low expression of CRNDE was significantly associated with poor prognostic markers including advanced stage of CLL, high levels of serum beta-2 microglobulin and lactic dehydrogenase, and the presence of del17p (p = 0.029, p = 0.013, p = 0.003, p = 0.028; respectively). CONCLUSION Our study demonstrated that LncRNA CRNDE is significantly downregulated and associated with poor prognostic markers in CLL. It provides a rationale to assess its biological and prognostic impact in CLL.
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Affiliation(s)
- Amira M F Shehata
- Clinical Pathology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Suzy F Gohar
- Clinical Oncology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Nashwa M Muharram
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Shaimaa Sherif Soliman
- Public Health and Community Medicine Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Hadeel M Shalaby
- Clinical Pathology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Samar M Kamal Eldin
- Clinical Pathology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Fathia I El-Bassal
- Clinical Pathology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
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9
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Akhouri V, Majumder S, Gaikwad AB. Targeting DNA methylation in diabetic kidney disease: A new perspective. Life Sci 2023; 335:122256. [PMID: 37949210 DOI: 10.1016/j.lfs.2023.122256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Diabetic kidney disease (DKD) is a leading diabetic complication causing significant mortality among people around the globe. People with poor glycemic control accompanied by hyperinsulinemia, dyslipidemia, hypertension, and obesity develop diabetic complications. These diabetic patients develop epigenetic changes and suffer from diabetic kidney complications even after subsequent glucose control, the phenomenon that is recognized as metabolic memory. DNA methylation is an essential epigenetic modification that contributes to the development and progression of several diabetic complications, including DKD. The aberrant DNA methylation pattern at CpGs sites within several genes, such as mTOR, RPTOR, IRS2, GRK5, SLC27A3, LCAT, and SLC1A5, associated with the accompanying risk factors exacerbate the DKD progression. Although drugs such as azacytidine and decitabine have been approved to target DNA methylation for diseases such as hematological malignancies, none have been approved for the treatment of DKD. More importantly, no DNA hypomethylation-targeting drugs have been approved for any disease conditions. Understanding the alteration in DNA methylation and its association with the disease risk factors is essential to target DKD effectively. This review has discussed the abnormal DNA methylation pattern and the kidney tissue-specific expression of critical genes involved in DKD onset and progression. Moreover, we also discuss the new possible therapeutic approach that can be exploited for treating DNA methylation aberrancy in a site-specific manner against DKD.
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Affiliation(s)
- Vivek Akhouri
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India
| | - Syamantak Majumder
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India
| | - Anil Bhanudas Gaikwad
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India.
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Hussain MS, Majami AA, Ali H, Gupta G, Almalki WH, Alzarea SI, Kazmi I, Syed RU, Khalifa NE, Bin Break MK, Khan R, Altwaijry N, Sharma R. The complex role of MEG3: An emerging long non-coding RNA in breast cancer. Pathol Res Pract 2023; 251:154850. [PMID: 37839358 DOI: 10.1016/j.prp.2023.154850] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/24/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023]
Abstract
MEG3, a significant long non-coding RNA (lncRNA), substantially functions in diverse biological processes, particularly breast cancer (BC) development. Within the imprinting DLK-MEG3 region on human chromosomal region 14q32.3, MEG3 spans 35 kb and encompasses ten exons. It exerts regulatory effects through intricate interactions with miRNAs, proteins, and epigenetic modifications. MEG3's multifaceted function in BC is evident in gene expression modulation, osteogenic tissue differentiation, and involvement in bone-related conditions. Its role as a tumor suppressor is highlighted by its influence on miR-182 and miRNA-29 expression in BC. Additionally, MEG3 is implicated in acute myocardial infarction and endothelial cell function, emphasising cell-specific regulatory mechanisms. MEG3's impact on gene activity encompasses transcriptional and post-translational adjustments, including DNA methylation, histone modifications, and interactions with transcription factors. MEG3 dysregulation is linked to unfavourable outcomes and drug resistance. Notably, higher MEG3 expression is associated with enhanced survival in BC patients. Overcoming challenges such as unravelling context-specific interactions, understanding epigenetic control, and translating findings into clinical applications is imperative. Prospective endeavours involve elucidating underlying mechanisms, exploring epigenetic alterations, and advancing MEG3-based diagnostic and therapeutic approaches. A comprehensive investigation into broader signaling networks and rigorous clinical trials are pivotal. Rigorous validation through functional and molecular analyses will shed light on MEG3's intricate contribution to BC progression.
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Affiliation(s)
- Md Sadique Hussain
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, 302017, Jaipur, Rajasthan, India
| | - Abdullah A Majami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haider Ali
- Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan.
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India; School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, 302017, Jaipur, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rahamat Unissa Syed
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia
| | - Nasrin E Khalifa
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia; Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, 11115, Sudan
| | - Mohammed Khaled Bin Break
- Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia; Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
| | - Ruqaiyah Khan
- Department of Basic Health Sciences, Deanship of Preparatory Year for the Health Colleges, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Najla Altwaijry
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint, Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Rahul Sharma
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, 302017, Jaipur, Rajasthan, India
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11
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Zhou C, Gan X, Sun S, Wang L, Zhang Y, Zhang J. Construction of an efferocytosis-related long non-coding ribonucleic acid scoring system to predict clinical outcome and immunotherapy response in pancreatic adenocarcinoma. Biochem Biophys Rep 2023; 35:101540. [PMID: 37692763 PMCID: PMC10482751 DOI: 10.1016/j.bbrep.2023.101540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/12/2023] Open
Abstract
Background Efferocytosis suppresses antitumour immune responses by inducing the release and secretion of cytokines. Long non-coding ribonucleic acids (lncRNAs) have various functions in different forms of programmed cell death and in immune regulation. This study aims to explore the potential role of efferocytosis-related lncRNAs as biomarkers in pancreatic adenocarcinoma (PAAD). Methods Transcriptome profiles, simple nucleotide variations and clinical data of patients with PAAD were extracted from The Cancer Genome Atlas (TCGA) database. Co-expression algorithms identified efferocytosis-related lncRNAs. The efferocytosis-related lncRNA scoring system (ERLncSys) was established using Cox regression and the Least Absolute Shrinkage and Selection Operator algorithm. Additionally, Kaplan-Meier (K-M) curves, Cox regression, receiver operating characteristic (ROC) curves and clinical parameter stratification analyses were used to evaluate ERlncSys. Moreover, ERlncSys was explored through Gene Set Variation Analysis, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. Furthermore, the TIMER platform, ESTIMATE algorithm, single sample Gene Set Enrichment Analysis and immune checkpoint analysis were utilised to explore the predictive power of ERlncSys for the tumour immune microenvironment (TIME). Finally, a consensus clustering algorithm identified distinct molecular profiles among patients with PAAD, aiding in the identification of potential beneficiaries for immunotherapy. Results K-M, Cox regression and ROC analyses confirmed the robust prognostic efficacy of ERlncSys. Clinical stratification analysis indicated the broad applicability of ERlncSys in PAAD. Additionally, mmunological analyses indicated that ERlncSys can determine immune cell infiltration status in the TIME. Furthermore, consensus clustering analysis based on ERlncSys divided the TCGA-PAAD cohort into two clusters. Cluster 1 exhibited characteristics consistent with an immune 'hot tumour' compared to cluster 2, suggesting cluster 1 is a more suitable population for immune checkpoint inhibitor therapy. Conclusion The established ErlncSys aids in predicting the prognosis and understanding the TIME landscape of patients with PAAD. In turn, it facilitates the identification of optimal candidates for immunotherapy. This study introduces novel insights into the potential value of efferocytosis-related lncRNAs as biomarkers in PAAD.
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Affiliation(s)
| | - Xiaoshuang Gan
- Suzhou Traditional Chinese Medicine Hospital of Anhui Province, Suzhou, 234000, China
| | - Shandong Sun
- Suzhou Traditional Chinese Medicine Hospital of Anhui Province, Suzhou, 234000, China
| | - Lei Wang
- Suzhou Traditional Chinese Medicine Hospital of Anhui Province, Suzhou, 234000, China
| | - Yong Zhang
- Suzhou Traditional Chinese Medicine Hospital of Anhui Province, Suzhou, 234000, China
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12
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Fenton CG, Ray MK, Meng W, Paulssen RH. Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis. Int J Mol Sci 2023; 24:10500. [PMID: 37445676 DOI: 10.3390/ijms241310500] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/26/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to play a role in the pathogenesis of ulcerative colitis (UC). Although epigenetic processes such as DNA methylation and lncRNA expression are well studied in UC, the importance of the interplay between the two processes has not yet been fully explored. It is, therefore, believed that interactions between environmental factors and epigenetics contribute to disease development. Mucosal biopsies from 11 treatment-naïve UC patients and 13 normal controls were used in this study. From each individual sample, both whole-genome bisulfite sequencing data (WGBS) and lncRNA expression data were analyzed. Correlation analysis between lncRNA expression and upstream differentially methylated regions (DMRs) was used to identify lncRNAs that might be regulated by DMRs. Furthermore, proximal protein-coding genes associated with DMR-regulated lncRNAs were identified by correlating their expression. The study identified UC-associated lncRNAs such as MIR4435-2HG, ZFAS1, IL6-AS1, and Pvt1, which may be regulated by DMRs. Several genes that are involved in inflammatory immune responses were found downstream of DMR-regulated lncRNAs, including SERPINB1, CCL18, and SLC15A4. The interplay between lncRNA expression regulated by DNA methylation in UC might improve our understanding of UC pathogenesis.
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Affiliation(s)
- Christopher G Fenton
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Mithlesh Kumar Ray
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Wei Meng
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Ruth H Paulssen
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
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13
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Al-Imam MJ, Hussein UAR, Sead FF, Faqri AMA, Mekkey SM, Khazel AJ, Almashhadani HA. The interactions between DNA methylation machinery and long non-coding RNAs in tumor progression and drug resistance. DNA Repair (Amst) 2023; 128:103526. [PMID: 37406581 DOI: 10.1016/j.dnarep.2023.103526] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023]
Abstract
DNA methylation is one of the main epigenetic mechanisms in cancer development and progression. Aberrant DNA methylation of CpG islands within promoter regions contributes to the dysregulation of various tumor suppressors and oncogenes; this leads to the appearance of malignant features, including rapid proliferation, metastasis, stemness, and drug resistance. The discovery of two important protein families, DNA methyltransferases (DNMTs) and Ten-eleven translocation (TET) dioxygenases, respectively, which are responsible for deregulated transcription of genes that play pivotal roles in tumorigenesis, led to further understanding of DNA methylation-related pathways. But how these enzymes can target specific genes in different malignancies; recent studies have highlighted the considerable role of Long Non-coding RNAs (LncRNAs). LncRNAs recruit these enzymes to promoter regions of genes and mediate their functions, showing great potential as therapeutic agents targeting the epigenetic regulation of various genes. Considering the importance of combining the current treatment methods, especially chemotherapies, with DNA methylation inhibitors in improving patients' outcomes, this review aimed to summarize the recent findings about the interaction between DNA methylation machinery and LncRNAs in regulating genes involved in tumorigenesis and drug resistance. So, these studies could provide insights toward developing novel strategies for cancer-targeted therapy.
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Affiliation(s)
- Mokhtar Jawad Al-Imam
- Department of Experimental Therapy, Iraqi Center for Cancer and Medical Genetics Research, Almustansiriyah University, Baghdad, Iraq
| | | | | | | | - Shereen M Mekkey
- Pharmacy Department, Al-Mustaqbal University College, 51001 Hilla, Babylon, Iraq
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14
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Kapinova A, Mazurakova A, Halasova E, Dankova Z, Büsselberg D, Costigliola V, Golubnitschaja O, Kubatka P. Underexplored reciprocity between genome-wide methylation status and long non-coding RNA expression reflected in breast cancer research: potential impacts for the disease management in the framework of 3P medicine. EPMA J 2023; 14:249-273. [PMID: 37275549 PMCID: PMC10236066 DOI: 10.1007/s13167-023-00323-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023]
Abstract
Breast cancer (BC) is the most common female malignancy reaching a pandemic scale worldwide. A comprehensive interplay between genetic alterations and shifted epigenetic regions synergistically leads to disease development and progression into metastatic BC. DNA and histones methylations, as the most studied epigenetic modifications, represent frequent and early events in the process of carcinogenesis. To this end, long non-coding RNAs (lncRNAs) are recognized as potent epigenetic modulators in pathomechanisms of BC by contributing to the regulation of DNA, RNA, and histones' methylation. In turn, the methylation status of DNA, RNA, and histones can affect the level of lncRNAs expression demonstrating the reciprocity of mechanisms involved. Furthermore, lncRNAs might undergo methylation in response to actual medical conditions such as tumor development and treated malignancies. The reciprocity between genome-wide methylation status and long non-coding RNA expression levels in BC remains largely unexplored. Since the bio/medical research in the area is, per evidence, strongly fragmented, the relevance of this reciprocity for BC development and progression has not yet been systematically analyzed. Contextually, the article aims at:consolidating the accumulated knowledge on both-the genome-wide methylation status and corresponding lncRNA expression patterns in BC andhighlighting the potential benefits of this consolidated multi-professional approach for advanced BC management. Based on a big data analysis and machine learning for individualized data interpretation, the proposed approach demonstrates a great potential to promote predictive diagnostics and targeted prevention in the cost-effective primary healthcare (sub-optimal health conditions and protection against the health-to-disease transition) as well as advanced treatment algorithms tailored to the individualized patient profiles in secondary BC care (effective protection against metastatic disease). Clinically relevant examples are provided, including mitochondrial health control and epigenetic regulatory mechanisms involved.
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Affiliation(s)
- Andrea Kapinova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Alena Mazurakova
- Department of Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Erika Halasova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Dietrich Büsselberg
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, 24144 Doha, Qatar
| | | | - Olga Golubnitschaja
- Predictive, Preventive, and Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
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Wozniak M, Czyz M. lncRNAs-EZH2 interaction as promising therapeutic target in cutaneous melanoma. Front Mol Biosci 2023; 10:1170026. [PMID: 37325482 PMCID: PMC10265524 DOI: 10.3389/fmolb.2023.1170026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023] Open
Abstract
Melanoma is the most lethal skin cancer with increasing incidence worldwide. Despite a great improvement of diagnostics and treatment of melanoma patients, this disease is still a serious clinical problem. Therefore, novel druggable targets are in focus of research. EZH2 is a component of the PRC2 protein complex that mediates epigenetic silencing of target genes. Several mutations activating EZH2 have been identified in melanoma, which contributes to aberrant gene silencing during tumor progression. Emerging evidence indicates that long non-coding RNAs (lncRNAs) are molecular "address codes" for EZH2 silencing specificity, and targeting lncRNAs-EZH2 interaction may slow down the progression of many solid cancers, including melanoma. This review summarizes current knowledge regarding the involvement of lncRNAs in EZH2-mediated gene silencing in melanoma. The possibility of blocking lncRNAs-EZH2 interaction in melanoma as a novel therapeutic option and plausible controversies and drawbacks of this approach are also briefly discussed.
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Affiliation(s)
- Michal Wozniak
- Department of Molecular Biology of Cancer, Medical University of Lodz, Lodz, Poland
| | - Malgorzata Czyz
- Department of Molecular Biology of Cancer, Medical University of Lodz, Lodz, Poland
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