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Shirani N, Mahdi‐Esferizi R, Eshraghi Samani R, Tahmasebian S, Yaghoobi H. In silico identification and in vitro evaluation of MRPS30-DT lncRNA and MRPS30 gene expression in breast cancer. Cancer Rep (Hoboken) 2024; 7:e2114. [PMID: 38886335 PMCID: PMC11182701 DOI: 10.1002/cnr2.2114] [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: 10/24/2023] [Revised: 04/20/2024] [Accepted: 05/07/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND It has been reported that long non-coding RNAs (lncRNAs) can play important roles in a variety of biological processes and cancer regulatory networks, including breast cancer. AIMS This study aimed to identify a novel upregulated lncRNA in breast cancer and its associated gene using bioinformatics analysis, and then evaluate their potential roles in breast cancer. METHODS AND RESULTS Extensive in silico studies were performed using various bioinformatics databases and tools to identify a potential upregulated breast cancer-associated lncRNA and its co-expressed gene, and to predict their potential roles, functions, and interactions. The expression level of MRPS30-DT lncRNA and MRPS30 was assessed in both BC tissues and cell lines using qRT-PCR technology. MRPS30-DT lncRNA and MRPS30 were selected as target genes using bioinformatics analysis. We found that MRPS30-DT and MRPS30 were significantly overexpressed in BC tissues compared with normal tissues. Also, MRPS30 showed upregulation in all three BC cell lines compared with HDF. On the other hand, MRPS30-DT significantly increased in MDA-MB-231 compared with HDF. While the expression of MRPS30-DT was significantly dropped in the resistance cell line MCF/MX compared to HDF and MCF7. Moreover, bioinformatics analysis suggested that MRPS30-DT and MRPS30 may play a potential role in BC through their involvement in some cancer signaling pathways and processes, as well as through their interaction with TFs, genes, miRNAs, and proteins related to carcinogenesis. CONCLUSIONS Overall, our findings showed the dysregulation of MRPS30-DT lncRNA and MRPS30 may provide clues for exploring new therapeutic targets or molecular biomarkers in BC.
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Affiliation(s)
- Nooshafarin Shirani
- Clinical Biochemistry Research Center, Basic Health Sciences InstituteShahrekord University of Medical SciencesShahrekordIran
| | - Roohallah Mahdi‐Esferizi
- Clinical Biochemistry Research Center, Basic Health Sciences InstituteShahrekord University of Medical SciencesShahrekordIran
- Department of Medical BiotechnologySchool of Advanced Technologies, Shahrekord University of Medical SciencesShahrekordIran
| | - Reza Eshraghi Samani
- Department of General SurgerySchool of Medicine, Isfahan University of Medical SciencesIsfahanIran
| | - Shahram Tahmasebian
- Department of Medical BiotechnologySchool of Advanced Technologies, Shahrekord University of Medical SciencesShahrekordIran
| | - Hajar Yaghoobi
- Clinical Biochemistry Research Center, Basic Health Sciences InstituteShahrekord University of Medical SciencesShahrekordIran
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2
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Su X, Feng Y, Qu Y, Mu D. Association between methyltransferase-like 3 and non-small cell lung cancer: pathogenesis, therapeutic resistance, and clinical applications. Transl Lung Cancer Res 2024; 13:1121-1136. [PMID: 38854947 PMCID: PMC11157379 DOI: 10.21037/tlcr-24-85] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/22/2024] [Indexed: 06/11/2024]
Abstract
Non-small cell lung cancer (NSCLC) is a malignant cancer that with high incidence, recurrence, and mortality rates in human beings, posing significant threats to human health. Moreover, effective early diagnosis of NSCLC remains limited primarily by the lack of accurate biomarkers. Therefore, there is an urgent need to understand the mechanisms underlying NSCLC pathogenesis and treatment failure. Methyltransferase-like 3 (METTL3) is a prototypical member of a family of which its members transfer methyl groups. It has been implicated in modulating the pathogenesis of NSCLC, as well as conferring resistance to NSCLC therapeutics. The targeting of METTL3 for NSCLC treatment has been reported. However, the relationship between METTL3 and NSCLC remains to be demonstrated. In this review, we discuss relevant interrelationships by summarising the studies on METTL3 in NSCLC pathogenesis, therapeutic resistance, and clinical applications. Current research suggests that the upregulation of METTL3 expression propels the tumorigenesis, progression, and treatment resistance of NSCLC. Therefore, we propose that METTL3 is an excellent candidate biomarker for NSCLC diagnosis and prognosis. Therapeutic targeting of METTL3 has significant potential for NSCLC treatment. This review provides a summary of the association between METTL3 and NSCLC, which would be a valuable reference for both basic and clinical research.
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3
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Alzahrani AA, Saleh RO, Latypova A, Bokov DO, Kareem AH, Talib HA, Hameed NM, Pramanik A, Alawadi A, Alsalamy A. Therapeutic significance of long noncoding RNAs in estrogen receptor-positive breast cancer. Cell Biochem Funct 2024; 42:e3993. [PMID: 38532685 DOI: 10.1002/cbf.3993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
About 70% of cases of breast cancer are compromised by Estrogen-positive breast cancer. Through its regulation of several processes, including cell proliferation, cell cycle progression, and apoptosis, Estrogen signaling plays a pivotal role in the genesis and progression of this particular kind of breast cancer. One of the best treatment strategies for treating Estrogen-positive breast cancer is blocking Estrogen signaling. However, patients' treatment failure is mainly caused by the emergence of resistance and metastases, necessitating the development of novel therapeutic targets. Numerous studies have shown long noncoding RNAs (lncRNAs) to play a role in Estrogen-mediated carcinogenesis. These lncRNAs interact with co-regulators and the Estrogen signaling cascade components, primarily due to Estrogen activation. Vimentin and E-cadherin are examples of epithelial-to-mesenchymal transition markers, and they regulate genes involved in cell cycle progression, such as Cyclins, to affect the growth, proliferation, and metastasis of Estrogen-positive breast cancer. Furthermore, a few of these lncRNAs contribute to developing resistance to chemotherapy, making them more desirable targets for enhancing results. Thus, to shed light on the creation of fresh approaches for treating this cancer, this review attempts to compile recently conducted studies on the relationship between lncRNAs and the advancement of Estrogen-positive breast cancer.
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Affiliation(s)
| | - Raed Obaid Saleh
- Department of Medical Laboratory Techniques, Al-Maarif University College, Al-Anbar, Iraq
| | - Amaliya Latypova
- Department of Medical and Technical Information Technology, Bauman Moscow State Technical University, Moscow, Russia
- Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Mishref Campus, Kuwait
| | - Dmitry Olegovich Bokov
- Institute of Pharmacy, Sechenov First Moscow State Medical University, Moscow, Russian Federation
- Laboratory of Food Chemistry, Federal Research Center of Nutrition, Biotechnology and Food Safety, Moscow, Russian Federation
| | | | - Hayder Abdullah Talib
- College of Agriculture, National University of Science and Technology, Dhi Qar, Dhi Qar, Iraq
| | - Noora M Hameed
- Anesthesia techniques, Al-Nisour University College, Iraq
| | - Atreyi Pramanik
- Divison of Research and Innovation, School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Ahmed Alawadi
- College of Technical Engineering, the Islamic University, Najaf, Iraq
- College of Technical Engineering, the Islamic University of Al Diwaniyah, Iraq
- College of Technical Engineering, the Islamic University of Babylon, Iraq
| | - Ali Alsalamy
- College of Technical Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna, Iraq
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4
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Najafi D, Siri G, Sadri M, Yazdani O, Esbati R, Karimi P, Keshavarz A, Mehmandar-Oskuie A, Ilktac M. Combination MEG3 lncRNA and Ciprofloxacin dramatically decreases cell migration and viability as well as induces apoptosis in GC cells in vitro. Biotechnol Appl Biochem 2024. [PMID: 38499448 DOI: 10.1002/bab.2578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 02/25/2024] [Indexed: 03/20/2024]
Abstract
Gastric cancer (GC) is a prominent cause of cancer-related mortality worldwide. Long noncoding RNA (lncRNA) maternal expression gene3 (MEG3) participates in numerous signaling pathways by targeting the miRNA-mRNA axis. Studies on human tumors have demonstrated that the antibiotic Ciprofloxacin induces cell cycle changes, programmed cell death, and growth suppression. In this study, we transfected MEG3 lncRNA and Ciprofloxacin into the MKN-45 GC cell line. qRT-PCR was employed to evaluate the effects on the specific microRNA and mRNA. The wound healing test, MTT assay, and flow cytometry were used to assess the impact of their administration on cell migration, viability, and apoptosis, respectively. Research showed that miR-147 expression fell even more after MEG3 lncRNA transfection, leading to an increase in B-cell lymphoma 2 (BCL-2) levels. Ciprofloxacin transfection did not significantly affect the axis, except for MEG3, which led to its slight upregulation. MEG3 lncRNA inhibited the migration of MKN-45 cells compared to the control group. When MEG3 lncRNA was coupled with Ciprofloxacin, there was a significant reduction in cell migration compared to untreated groups and controls. MTT assay and flow cytometry demonstrated that MEG3 lncRNA decreased cell viability and triggered apoptosis. Simultaneous administration of MEG3 lncRNA and Ciprofloxacin revealed a significant reduction in cell viability caused by increased apoptosis obtained from MTT or flow cytometry assays. Modulating the miR-147-BCL-2 axis decreases cell migration and survival while promoting cell death. In conclusion, combining MEG3 lncRNA with Ciprofloxacin may be an effective therapeutic approach for GC treatment by influencing the miR-14-BCl-2 axis, resulting in reduced cell viability, migration, and increased apoptosis.
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Affiliation(s)
- Dena Najafi
- Faculty of Pharmacy, Eastern Mediterranean University, Famagusta, North Cyprus, Turkey
| | - Goli Siri
- Department of Internal Medicine, Amir Alam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Sadri
- Department of Internal Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Omid Yazdani
- Department of Medical Science, School of Medicine, Shahid Beheshti University, Tehran, Iran
| | - Romina Esbati
- Research Center for Social Determinants of Health, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parvin Karimi
- Fars Population-Based Cancer Registry, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Keshavarz
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirreza Mehmandar-Oskuie
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehmet Ilktac
- Faculty of Pharmacy, Eastern Mediterranean University, Famagusta, North Cyprus, Turkey
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5
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Wang Y, Bu N, Luan XF, Song QQ, Ma BF, Hao W, Yan JJ, Wang L, Zheng XL, Maimaitiyiming Y. Harnessing the potential of long non-coding RNAs in breast cancer: from etiology to treatment resistance and clinical applications. Front Oncol 2024; 14:1337579. [PMID: 38505593 PMCID: PMC10949897 DOI: 10.3389/fonc.2024.1337579] [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: 11/13/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Breast cancer (BC) is the most common malignancy among women and a leading cause of cancer-related deaths of females worldwide. It is a complex and molecularly heterogeneous disease, with various subtypes that require different treatment strategies. Despite advances in high-resolution single-cell and multinomial technologies, distant metastasis and therapeutic resistance remain major challenges for BC treatment. Long non-coding RNAs (lncRNAs) are non-coding RNAs with more than 200 nucleotides in length. They act as competing endogenous RNAs (ceRNAs) to regulate post-transcriptional gene stability and modulate protein-protein, protein-DNA, and protein-RNA interactions to regulate various biological processes. Emerging evidence suggests that lncRNAs play essential roles in human cancers, including BC. In this review, we focus on the roles and mechanisms of lncRNAs in BC progression, metastasis, and treatment resistance, and discuss their potential value as therapeutic targets. Specifically, we summarize how lncRNAs are involved in the initiation and progression of BC, as well as their roles in metastasis and the development of therapeutic resistance. We also recapitulate the potential of lncRNAs as diagnostic biomarkers and discuss their potential use in personalized medicine. Finally, we provide lncRNA-based strategies to promote the prognosis of breast cancer patients in clinical settings, including the development of novel lncRNA-targeted therapies.
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Affiliation(s)
- Yun Wang
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Na Bu
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-fei Luan
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qian-qian Song
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ba-Fang Ma
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Wenhui Hao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Jing-jing Yan
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Li Wang
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-ling Zheng
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yasen Maimaitiyiming
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Cancer Center, Zhejiang University School of Medicine, Hangzhou, China
- Women’s Hospital, Institute of Genetics, and Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, Urumqi, China
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Khojali WMA, Khalifa NE, Alshammari F, Afsar S, Aboshouk NAM, Khalifa AAS, Enrera JA, Elafandy NM, Abdalla RAH, Ali OHH, Syed RU, Nagaraju P. Pyroptosis-related non-coding RNAs emerging players in atherosclerosis pathology. Pathol Res Pract 2024; 255:155219. [PMID: 38401375 DOI: 10.1016/j.prp.2024.155219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/26/2024]
Abstract
Globally, atherosclerosis a persistent inflammatory condition of the artery walls continues to be the primary cause of cardiovascular illness and death. The ncRNAs are important regulators of important signalling pathways that affect pyroptosis and the inflammatory environment in atherosclerotic plaques. Comprehending the complex interaction between pyroptosis and non-coding RNAs (ncRNAs) offers fresh perspectives on putative therapeutic targets for ameliorating cardiovascular problems linked to atherosclerosis. The discovery of particular non-coding RNA signatures linked to the advancement of atherosclerosis could lead to the creation of novel biomarkers for risk assessment and customised treatment approaches. A thorough investigation of the regulatory networks regulated by these non-coding RNAs has been made possible by the combination of cutting-edge molecular methods and bioinformatics tools. Studying pyroptosis-related ncRNAs in detail appears to be a promising way to advance our understanding of disease pathophysiology and develop focused therapeutic methods as we work to unravel the complex molecular tapestry of atherosclerosis. This review explores the emerging significance of non-coding RNAs (ncRNAs) in the regulation of pyroptosis and their consequential impact on atherosclerosis pathology.
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Affiliation(s)
- Weam M A Khojali
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Omdurman 14415, Republic of the Sudan
| | - Nasrin E Khalifa
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, Khartoum 11115, Republic of the Sudan
| | - Farhan Alshammari
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
| | - S Afsar
- Department of Virology, Sri Venkateswara University, Tirupathi, Andhra Pradesh 517502, India.
| | - Nayla Ahmed Mohammed Aboshouk
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Amna Abakar Suleiman Khalifa
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Jerlyn Apatan Enrera
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Nancy Mohammad Elafandy
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Randa Abdeen Husien Abdalla
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Omar Hafiz Haj Ali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Rahamat Unissa Syed
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia.
| | - Potnuri Nagaraju
- Department of Pharmaceutics, Mandesh Institute of Pharmaceutical Science and Research Center, Maharashtra, India
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Nandagopal S, Choudhary G, Sankanagoudar S, Banerjee M, Elhence P, Jena R, Selvi MK, Shukla KK. Expression of stem cell markers as predictors of therapeutic response in metastatic prostate cancer patients. Urol Oncol 2024; 42:68.e21-68.e31. [PMID: 38278632 DOI: 10.1016/j.urolonc.2023.12.012] [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: 10/01/2023] [Revised: 12/09/2023] [Accepted: 12/17/2023] [Indexed: 01/28/2024]
Abstract
BACKGROUND Cancer stem cells (CSCs) have been implicated in prostate cancer (PCA) progression and therapeutic resistance. This study aimed to compare the expression levels of CSC CD (CD 44, CD 133, and CD 24) markers in treatment-naive patients with metastatic PCA before and after treatment. METHODS The study included 60 treatment-naïve patients with metastatic PCA who received androgen deprivation therapy (ADT) alone (n = 30) and ADT plus chemotherapy (n = 30). The level of CD44, CD133, and CD24 were obtained by flow cytometric analysis before and after treatment. Baseline characteristics were also assessed, including age, pretreatment testosterone levels, and pretreatment prostate-specific antigen (PSA) levels. RESULTS The baseline characteristics analysis showed no significant difference in pre-treatment testosterone levels between the ADT+ chemotherapy and ADT-alone groups. In the flow cytometric analysis, no significant difference was observed in pre-treatment CD44+ and CD133+ levels between the 2 treatment groups, although a trend towards higher pretreatment CD24- levels was observed in the ADT+ chemotherapy group. After treatment, significant reductions in testosterone and PSA levels were observed in both treatment arms. The ADT+ chemotherapy group showed a greater reduction in CD44+ and CD133+ levels compared to the ADT-alone group. Bioinformatic analysis using the UALCAN TCGA database also showed a similar trend of CD 44, CD 24, and CD 133 gene expression patterns. CONCLUSION Combination therapy involving chemotherapy and ADT appears to have a greater impact on suppressing CSCs compared to ADT alone. These findings highlight the potential of targeting CSCs as a prognostic and predictive marker therapeutic strategy in metastatic PCA.
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Affiliation(s)
- Srividhya Nandagopal
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India
| | - Gautam Choudhary
- Department of Urology, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India
| | | | - Mithu Banerjee
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India
| | - Poonam Elhence
- Department of Pathology and Lab Medicine, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India
| | - Rahul Jena
- Department of Urology, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India
| | - Maithili Karpaga Selvi
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India
| | - Kamla Kant Shukla
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India.
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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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Zabeti Touchaei A, Vahidi S, Samadani AA. Decoding the regulatory landscape of lncRNAs as potential diagnostic and prognostic biomarkers for gastric and colorectal cancers. Clin Exp Med 2024; 24:29. [PMID: 38294554 PMCID: PMC10830721 DOI: 10.1007/s10238-023-01260-5] [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: 08/30/2023] [Accepted: 12/12/2023] [Indexed: 02/01/2024]
Abstract
Colorectal cancer (CRC) and gastric cancer (GC) are major contributors to cancer-related mortality worldwide. Despite advancements in understanding molecular mechanisms and improved drug treatments, the overall survival rate for patients remains unsatisfactory. Metastasis and drug resistance are major challenges contributing to the high mortality rate in both CRC and GC. Recent research has shed light on the role of long noncoding RNAs (lncRNAs) in the development and progression of these cancers. LncRNAs regulate gene expression through various mechanisms, including epigenetic modifications and interactions with microRNAs (miRNAs) and proteins. They can serve as miRNA precursors or pseudogenes, modulating gene expression at transcriptional and post-transcriptional levels. Additionally, circulating lncRNAs have emerged as non-invasive biomarkers for the diagnosis, prognosis, and prediction of drug therapy response in CRC and GC. This review explores the intricate relationship between lncRNAs and CRC/GC, encompassing their roles in cancer development, progression, and chemoresistance. Furthermore, it discusses the potential of lncRNAs as therapeutic targets in these malignancies. The interplay between lncRNAs, miRNAs, and tumor microenvironment is also highlighted, emphasizing their impact on the complexity of cancer biology. Understanding the regulatory landscape and molecular mechanisms governed by lncRNAs in CRC and GC is crucial for the development of effective diagnostic and prognostic biomarkers, as well as novel therapeutic strategies. This review provides a comprehensive overview of the current knowledge and paves the way for further exploration of lncRNAs as key players in the management of CRC and GC.
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Affiliation(s)
| | - Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Trauma Institute, Guilan University of Medical Sciences, Rasht, Iran.
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10
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Cisneros-Villanueva M, Fonseca-Montaño MA, Ríos-Romero M, López-Camarillo C, Jiménez-Morales S, Langley E, Rosette-Rueda AS, Cedro-Tanda A, Hernández-Sotelo D, Hidalgo-Miranda A. LncRNA SOX9-AS1 triggers a transcriptional program involved in lipid metabolic reprogramming, cell migration and invasion in triple-negative breast cancer. Sci Rep 2024; 14:1483. [PMID: 38233470 PMCID: PMC10794186 DOI: 10.1038/s41598-024-51947-2] [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: 04/25/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024] Open
Abstract
At the molecular level, triple-negative breast cancer (TNBC) is frequently categorized as PAM50 basal-like subtype, but despite the advances in molecular analyses, the clinical outcome for these subtypes is uncertain. Long non-coding RNAs (lncRNAs) are master regulators of genes involved in hallmarks of cancer, which makes them suitable biomarkers for breast cancer (BRCA) diagnosis and prognosis. Here, we evaluated the regulatory role of lncRNA SOX9-AS1 in these subtypes. Using the BRCA-TCGA cohort, we observed that SOX9-AS1 was significantly overexpressed in basal-like and TNBC in comparison with other BRCA subtypes. Survival analyzes showed that SOX9-AS1 overexpression was associated with a favorable prognosis in TNBC and basal-like patients. To study the functions of SOX9-AS1, we determined the expression levels in a panel of nine BRCA cell lines finding increased levels in MDA-MB-468 and HCC1187 TNBC. Using subcellular fractionation in these cell lines, we ascertained that SOX9-AS1 was located in the cytoplasmic compartment. In addition, we performed SOX9-AS1 gene silencing using two short-harping constructs, which were transfected in both cell models and performed a genome-wide RNA-seq analysis. Data showed that 351 lncRNAs and 740 mRNAs were differentially expressed in MDA-MB-468 while 56 lncRNAs and 100 mRNAs were modulated in HCC1187 cells (Log2FC < - 1.5 and > 1.5, p.adj value < 0.05). Pathway analysis revealed that the protein-encoding genes potentially regulate lipid metabolic reprogramming, and epithelial-mesenchymal transition (EMT). Expression of lipid metabolic-related genes LIPE, REEP6, GABRE, FBP1, SCD1, UGT2B11, APOC1 was confirmed by RT-qPCR. Functional analysis demonstrated that the knockdown of SOX9-AS1 increases the triglyceride synthesis, cell migration and invasion in both two TNBC cell lines. In conclusion, high SOX9-AS1 expression predicts an improved clinical course in patients, while the loss of SOX9-AS1 expression enhances the aggressiveness of TNBC cells.
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Affiliation(s)
- Mireya Cisneros-Villanueva
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
- Programa de Doctorado en Ciencias Biomédicas, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero (UAGro), Chilpancingo de los Bravo, Guerrero, México
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero (UAGro), Chilpancingo de los Bravo, Guerrero, México
| | - Marco Antonio Fonseca-Montaño
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), 04510, Mexico, México
| | - Magdalena Ríos-Romero
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico, México
| | - Silvia Jiménez-Morales
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
| | - Elizabeth Langley
- Laboratorio de Cáncer Hormono Regulado, Instituto Nacional de Cancerología (INCan), 14080, Mexico, México
| | - Alan Sajid Rosette-Rueda
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
| | | | - Daniel Hernández-Sotelo
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero (UAGro), Chilpancingo de los Bravo, Guerrero, México.
| | - Alfredo Hidalgo-Miranda
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México.
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11
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Li W, Xu T, Jin H, Li M, Jia Q. Emerging role of cancer-associated fibroblasts in esophageal squamous cell carcinoma. Pathol Res Pract 2024; 253:155002. [PMID: 38056131 DOI: 10.1016/j.prp.2023.155002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
Esophageal carcinoma is the sixth leading cause of cancer death globally and the majority of global cases are esophageal squamous cell carcinoma (ESCC). Difficulty in diagnosis exists as more than 70% of ESCC patients are diagnosed at the intermediate or advanced stage. Cancer-associated fibroblasts (CAFs) have been considered one of the crucial components in the process of tumor growth, promoting communications between cancer cells and the tumor microenvironment (TME). CAFs grow alongside malignancies dynamically and interact with ESCC cells to promote their progression, proliferation, invasion, tumor escape, chemo- and radio-resistance, etc. It is believed that CAFs qualify as a promising direction for treatment. Analyzing CAFs' subtypes and functions will elucidate the involvement of CAFs in ESCC and aid in therapeutics. This review summarizes current information on CAFs in ESCC and focuses on the latest interaction between CAFs and ESCC cancer cell discoveries. The origin of CAFs and their communication with ESCC cells and TME are also demonstrated. On the foundation of a thorough analysis, we highlight the clinical prospects and CAFs-related therapies in ESCC in the future.
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Affiliation(s)
- Wenqing Li
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, China
| | - Tianqi Xu
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, China
| | - Hai Jin
- Department of Neurosurgery, General Hospital of Northern Theater Command, Shenyang, China.
| | - Mingyang Li
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, China.
| | - Qingge Jia
- Department of Reproductive Medicine, Xi'an International Medical Center Hospital, Northwest University, Xi'an, China.
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12
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He Y, Luan X, Lin Y, Dong C, Zhang J, Zhu Y. lncRNA AGAP11 Suppresses Lung Adenocarcinoma Progression by miR-494-3p and Predicts Prognosis. J Environ Pathol Toxicol Oncol 2024; 43:1-11. [PMID: 39016137 DOI: 10.1615/jenvironpatholtoxicoloncol.2024052122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is a subtype of lung cancer that occurs frequently and results in high mortality and morbidity, comprising almost 50% of all cases with the disease. Previously, long non-coding RNAs (lncRNAs) was evidenced to be helpful in the diagnosis and prognosis of LUAD. lncRNA AGAP11 was identified as a dysregulated lncRNA in LUAD. Whether AGAP11 is linked to the progression and prognosis of LUAD has not been known. The purpose was to probe the action of AGAP11 in the LUAD progression together with its intrinsic mechanism, with a view to supplying a perspective biomarker and therapeutic target for LUAD. AGAP11 expression in LUAD was analyzed by searching in the GEPIA database and conducting RT-qPCR. The significance of AGAP11 for the prognosis of LUAD was assessed by statistical analyses. The targeting relationship between AGAP11 and miR-494-3p was corroborated with Dual-luciferase reporter assay. The role of AGAP11 on cellular processes in LUAD cells was evaluated by CCK-8 and Transwell assays. AGAP11 was markedly down-regulated in LUAD and tightly correlated with TNM stage, lymph node metastasis, and tumor differentiation degree of patients. Down-regulation of AGAP11 was found to predict a dismal prognosis of LUAD. AGAP11 negatively modulated miR-494-3p expression by interacting with it. The growth, migration, and invasion of LUAD cells could be impaired by AGAP11 overexpression, which would be attenuated by the enhanced miR-494-3p expression. AGAP11 acted as a predictor for prognosis and curbed LUAD progression through modulating miR-494-3p.
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Affiliation(s)
- Ye He
- Department of Radiotherapy, The Second People's Hospital of Wuhu, Wuhu 241001, China
| | - Xinchi Luan
- Department of Oncology, Key Laboratory of Cancer Molecular and Translational Research, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Ya Lin
- The First People's Hospital of Wenling
| | - Chunge Dong
- Department of Pathology, The First People's Hospital of Wenling, Wenling 317500, China
| | - Jie Zhang
- Department of Pathology, The First People's Hospital of Wenling, Wenling 317500, China
| | - Yangli Zhu
- Department of Pathology, The First People's Hospital of Wenling, Wenling 317500, China
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13
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Modabber N, Mahboub SS, Khoshravesh S, Karimpour F, Karimi A, Goodarzi V. Evaluation of Long Non-coding RNA (LncRNA) in the Pathogenesis of Chemotherapy Resistance in Cervical Cancer: Diagnostic and Prognostic Approach. Mol Biotechnol 2023:10.1007/s12033-023-00909-6. [PMID: 37804407 DOI: 10.1007/s12033-023-00909-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/14/2023] [Indexed: 10/09/2023]
Abstract
Cervical cancer (CC), caused by human papillomavirus (HPV), is a leading cause of female malignancies worldwide. Therefore, understanding the underlying mechanisms of CC development and identifying novel therapeutic targets are significantly important. Cisplatin resistance is a significant challenge in the management of CC. Recent studies highlighted the critical role of long non-coding RNAs (lncRNAs) in modulation of cisplatin resistance. This comprehensive review aims to collect the current understanding roles of lncRNAs and their involvement in cisplatin resistance in CC by highlighting key processes of cancer progression, including apoptosis, proliferation, angiogenesis and epithelial-to-mesenchymal transition (EMT). We discussed the role of lncRNA in CC resistance to cisplatin through molecular pathways and examined gene expression changes. We also discussed treatment strategies and factors that reduce CC resistance to cisplatin by targeting them.
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Affiliation(s)
- Noushin Modabber
- Shahid Akbar-Abadi Clinical Research Development Unit (SHACRDU), School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sarah Sadat Mahboub
- Shahid Akbar-Abadi Clinical Research Development Unit (SHACRDU), School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Fatemeh Karimpour
- Cancer Reserch Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Anita Karimi
- Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Vahid Goodarzi
- Department of Anesthesiology, Rasoul-Akram Medical Center, Iran University of Medical Sciences (IUMS), Tehran, Iran.
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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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Jin Y, Jiang D. GATA6-AS1 via Sponging miR-543 to Regulate PTEN/AKT Signaling Axis Suppresses Cell Proliferation and Migration in Gastric Cancer. Mediators Inflamm 2023; 2023:9340499. [PMID: 37273453 PMCID: PMC10238141 DOI: 10.1155/2023/9340499] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/16/2022] [Accepted: 04/05/2023] [Indexed: 06/06/2023] Open
Abstract
Gastric cancer (GC) is one of the most common and lethal cancers worldwide. In view of the prominent roles of long noncoding RNAs (lncRNAs) in cancers, we investigated the specific role and underlying mechanism of GATA binding protein 6 antisense RNA 1 (GATA6-AS1) in GC. Quantitative real-time polymerase chain reaction (qRT-PCR) detected GATA6-AS1 expression in GC cell lines. Functional assays were conducted to explore the role of GATA6-AS1 in GC. Furthermore, mechanism investigations were implemented to uncover the interaction among GATA6-AS1, microRNA-543 (miR-543), and phosphatase and tensin homolog (PTEN). In the present study, it was found that GATA6-AS1 expression is significantly downregulated in GC cell lines. Functionally, GATA6-AS1 markedly suppresses GC cell growth and migration in vitro and in vivo tumorigenesis. Besides tumor suppressor, GATA6-AS1 serves as a miR-543 sponge. Specifically speaking, GATA6-AS1 acts as a competing endogenous RNA (ceRNA) of miR-543 to upregulate the expression of PTEN, thus inactivating AKT signaling pathway to inhibit GC progression. In conclusion, this study has manifested that GATA6-AS1 inhibits GC cell proliferation and migration as a sponge of miR-543 by regulating PTEN/AKT signaling axis, offering new perspective into developing novel GC therapies.
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Affiliation(s)
- Yi Jin
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110001 Liaoning, China
| | - Daqing Jiang
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110001 Liaoning, China
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16
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Fan YX, Andoh V, Chen L. Multi-omics study and ncRNA regulation of anti-BmNPV in silkworms, Bombyx mori: an update. Front Microbiol 2023; 14:1123448. [PMID: 37275131 PMCID: PMC10232802 DOI: 10.3389/fmicb.2023.1123448] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Bombyx mori silkworm is an important economic insect which has a significant contribution to the improvement of the economy. Bombyx mori nucleopolyhedrovirus (BmNPV) is a vitally significant purulent virus that impedes the sustainable and stable development of the silkworm industry, resulting in substantial economic losses. In recent years, with the development of biotechnology, transcriptomics, proteomics, metabolomics, and the related techniques have been used to select BmNPV-resistant genes, proteins, and metabolites. The regulatory networks between viruses and hosts have been gradually clarified with the discovery of ncRNAs, such as miRNA, lncRNA, and circRNA in cells. Thus, this paper aims to highlight the results of current multi-omics and ncRNA studies on BmNPV resistance in the silkworm, providing some references for resistant strategies in the silkworm to BmNPV.
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17
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Sabbir Ahmed CM, Canchola A, Paul B, Alam MRN, Lin YH. Altered long non-coding RNAs expression in normal and diseased primary human airway epithelial cells exposed to diesel exhaust particles. Inhal Toxicol 2023; 35:157-168. [PMID: 36877189 PMCID: PMC10424575 DOI: 10.1080/08958378.2023.2185703] [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: 06/24/2022] [Accepted: 02/24/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND Exposure to diesel exhaust particles (DEP) has been linked to a variety of adverse health effects, including increased morbidity and mortality from cardiovascular diseases, chronic obstructive pulmonary disease (COPD), metabolic syndrome, and lung cancer. The epigenetic changes caused by air pollution have been associated with increased health risks. However, the exact molecular mechanisms underlying the lncRNA-mediated pathogenesis induced by DEP exposure have not been revealed. METHODS Through RNA-sequencing and integrative analysis of both mRNA and lncRNA profiles, this study investigated the role of lncRNAs in altered gene expression in healthy and diseased human primary epithelial cells (NHBE and DHBE-COPD) exposed to DEP at a dose of 30 μg/cm2. RESULTS We identified 503 and 563 differentially expressed (DE) mRNAs and a total of 10 and 14 DE lncRNAs in NHBE and DHBE-COPD cells exposed to DEP, respectively. In both NHBE and DHBE-COPD cells, enriched cancer-related pathways were identified at mRNA level, and 3 common lncRNAs OLMALINC, AC069234.2, and LINC00665 were found to be associated with cancer initiation and progression. In addition, we identified two cis-acting (TMEM51-AS1 and TTN-AS1) and several trans-acting lncRNAs (e.g. LINC01278, SNHG29, AC006064.4, TMEM51-AS1) only differentially expressed in COPD cells, which could potentially play a role in carcinogenesis and determine their susceptibility to DEP exposure. CONCLUSIONS Overall, our work highlights the potential importance of lncRNAs in regulating DEP-induced gene expression changes associated with carcinogenesis, and individuals suffering from COPD are likely to be more vulnerable to these environmental triggers.
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Affiliation(s)
- C. M. Sabbir Ahmed
- Environmental Toxicology Graduate Program, University of California, Riverside, United States
| | - Alexa Canchola
- Environmental Toxicology Graduate Program, University of California, Riverside, United States
| | - Biplab Paul
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Md Rubaiat Nurul Alam
- Environmental Toxicology Graduate Program, University of California, Riverside, United States
| | - Ying-Hsuan Lin
- Environmental Toxicology Graduate Program, University of California, Riverside, United States
- Department of Environmental Sciences, University of California, Riverside, United States
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18
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Xie F, Yang Z, Song J, Dai Q, Duan X. DHNLDA: A Novel Deep Hierarchical Network Based Method for Predicting lncRNA-Disease Associations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3395-3403. [PMID: 34543201 DOI: 10.1109/tcbb.2021.3113326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Recent studies have found that lncRNA (long non-coding RNA) in ncRNA (non-coding RNA) is not only involved in many biological processes, but also abnormally expressed in many complex diseases. Identification of lncRNA-disease associations accurately is of great significance for understanding the function of lncRNA and disease mechanism. In this paper, a deep learning framework consisting of stacked autoencoder(SAE), multi-scale ResNet and stacked ensemble module, named DHNLDA, was constructed to predict lncRNA-disease associations, which integrates multiple biological data sources and constructing feature matrices. Among them, the biological data including the similarity and the interaction of lncRNAs, diseases and miRNAs are integrated. The feature matrices are obtained by node2vec embedding and feature extraction respectively. Then, the SAE and the multi-scale ResNet are used to learn the complementary information between nodes, and the high-level features of node attributes are obtained. Finally, the fusion of high-level feature is input into the stacked ensemble module to obtain the prediction results of lncRNA-disease associations. The experimental results of five-fold cross-validation show that the AUC of DHNLDA reaches 0.975 better than the existing methods. Case studies of stomach cancer, breast cancer and lung cancer have shown the great ability of DHNLDA to discover the potential lncRNA-disease associations.
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19
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Xia W, Zeng C, Zheng Z, Huang C, Zhou Y, Bai L. Development and Validation of a Novel Mitochondrion and Ferroptosis-Related Long Non-Coding RNA Prognostic Signature in Hepatocellular Carcinoma. Front Cell Dev Biol 2022; 10:844759. [PMID: 36036006 PMCID: PMC9413087 DOI: 10.3389/fcell.2022.844759] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/20/2022] [Indexed: 11/22/2022] Open
Abstract
Mitochondrion and ferroptosis are related to tumorigenesis and tumor progression of hepatocellular carcinoma (HCC). Therefore, this study focused on exploring the participation of lncRNAs in mitochondrial dysfunction and ferroptosis using public datasets from The Cancer Genome Atlas (TCGA) database. We identified the mitochondrion- and ferroptosis-related lncRNAs by Pearson’s analysis and lasso-Cox regression. Moreover, real-time quantitative reverse transcription PCR (RT-qPCR) was utilized to further confirm the abnormal expression of these lncRNAs. Based on eight lncRNAs, the MF-related lncRNA prognostic signature (LPS) with outstanding stratification ability and prognostic prediction capability was constructed. In addition, functional enrichment analysis and immune cell infiltration analysis were performed to explore the possible functions of lncRNAs and their impact on the tumor microenvironment. The pathways related to G2M checkpoint and MYC were activated, and the infiltration ratio of regulatory T cells and M0 and M2 macrophages was higher in the high-risk group. In conclusion, these lncRNAs may affect mitochondria functions, ferroptosis, and immune cell infiltration in HCC through specific pathways, which may provide valuable insight into the progression and therapies of HCC.
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Affiliation(s)
- Wuzheng Xia
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital/The First School of Clinical Medicine, Southem Medical University, Guangzhou, China
- Department of Organ Transplant, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Cong Zeng
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital/The First School of Clinical Medicine, Southem Medical University, Guangzhou, China
- Department of General Practice, Hospital of South China Normal University, Guangzhou, China
| | - Zehao Zheng
- Department of Organ Transplant, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Department of General Surger, Shantou University of Medical College, Shantou, China
| | - Chunwang Huang
- Department of Ultrasound, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Lan Bai, ; Yu Zhou, ; Chunwang Huang,
| | - Yu Zhou
- Department of Pancreatic Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Lan Bai, ; Yu Zhou, ; Chunwang Huang,
| | - Lan Bai
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital/The First School of Clinical Medicine, Southem Medical University, Guangzhou, China
- *Correspondence: Lan Bai, ; Yu Zhou, ; Chunwang Huang,
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Qiu L, Yue J, Ding L, Yin Z, Zhang K, Zhang H. Cancer-associated fibroblasts: An emerging target against esophageal squamous cell carcinoma. Cancer Lett 2022; 546:215860. [DOI: 10.1016/j.canlet.2022.215860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 11/02/2022]
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21
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Cai Y, Cui J, Wang Z, Wu H. Comprehensive bioinformatic analyses of lncRNA-mediated ceRNA network for uterine corpus endometrial carcinoma. Transl Cancer Res 2022; 11:1994-2012. [PMID: 35966302 PMCID: PMC9372196 DOI: 10.21037/tcr-22-249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/20/2022] [Indexed: 12/12/2022]
Abstract
Background Given that long non-coding RNAs (lncRNAs) involved in the tumor initiation or progression of the endometrium and that competing endogenous RNA (ceRNA) plays an important role in increasingly more biological processes, lncRNA-mediated ceRNA is likely to function in the pathogenesis of uterine corpus endometrial carcinoma (UCEC). Our present study aimed to explore the potential molecular mechanisms for the prognosis of UCEC through a lncRNA-mediated ceRNA network. Methods The transcriptome profiles and corresponding clinical profiles of UCEC dataset were retrieved from Clinical Proteomic Tumor Analysis Consortium (CPTAC) and The Cancer Genome Atlas (TCGA) databases respectively. Differentially expressed genes (DEGs) in UCEC samples were identified via "Edge R" package. Then, an integrated bioinformatics analysis including functional enrichment analysis, tumor infiltrating immune cell (TIIC) analysis, Kaplan-Meier curve, Cox regression analysis were conducted to analyze the prognostic biomarkers. Results In the CPTAC dataset of UCEC, a ceRNA network comprised of 36 miRNAs, 123 lncRNAs and 124 targeted mRNAs was established, and 8 of 123 prognostic-related Differentially Expressed long noncoding RNAs (DElncRNAs) were identified. While in the TCGA dataset, a ceRNA network comprised of 38 miRNAs, 83 lncRNAs and 110 targeted mRNAs was established, and 2 of 83 prognostic-related DElncRNAs were identified. After filtered by risk grouping and Cox regression analysis, 10 prognostic-related lncRNAs including LINC00443, LINC00483, C2orf48, TRBV11-2, MEG-8 were identified. In addition, 33 survival-related Differentially Expressed messenger RNA (DEmRNAs) in two ceRNA networks were further validated in the Human Protein Atlas Portal (HPA) database. Finally, six lncRNA/miRNA/mRNA axes were established to elucidate prognostic regulatory roles in UCEC. Conclusions Several prognostic lncRNAs are identified and prognostic model of lncRNA-mediated ceRNA network is constructed, which promotes the understanding of UCEC development mechanisms and potential therapeutic targets.
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Affiliation(s)
- Yiran Cai
- Medical School of Nantong University, Nantong, China
| | - Jin Cui
- Medical School of Nantong University, Nantong, China
| | - Zhisu Wang
- Medical School of Nantong University, Nantong, China
| | - Huiqun Wu
- Department of Medical Informatics, Medical School of Nantong University, Nantong, China
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22
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LncRNA-AP006284.1 promotes prostate cancer cell growth and motility by forming RNA-DNA triplexes and recruiting GNL3/SFPQ complex to facilitate RASSF7 transcription. Genes Dis 2022; 10:317-320. [DOI: 10.1016/j.gendis.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 11/18/2022] Open
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Shi R, Zhang Z, Zhu A, Xiong X, Zhang J, Xu J, Sy MS, Li C. Targeting Type I Collagen for Cancer Treatment. Int J Cancer 2022; 151:665-683. [PMID: 35225360 DOI: 10.1002/ijc.33985] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 11/07/2022]
Abstract
Collagen is the most abundant protein in animals. Interactions between tumor cells and collagen influence every step of tumor development. Type I collagen is the main fibrillar collagen in the extracellular matrix and is frequently up-regulated during tumorigenesis. The binding of type I collagen to its receptors on tumor cells promotes tumor cell proliferation, epithelial-mesenchymal transition, and metastasis. Type I collagen also regulates the efficacy of tumor therapies, such as chemotherapy, radiotherapy, and immunotherapy. Furthermore, type I collagen fragments are diagnostic markers of metastatic tumors and have prognostic value. Inhibition of type I collagen synthesis has been reported to have anti-tumor effects in animal models. However, collagen has also been shown to possess anti-tumor activity. Therefore, the roles that type I collagen plays in tumor biology are complex and tumor type-dependent. In this review, we discuss the expression and regulation of synthesis of type I collagen, as well as the role up-regulated type I collagen plays in various stages of cancer progression. We also discuss the role of collagen in tumor therapy. Finally, we highlight several recent approaches targeting type I collagen for cancer treatment. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Run Shi
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong High Education Institute, Guangzhou, China
| | - Zhe Zhang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong High Education Institute, Guangzhou, China
| | - Ankai Zhu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong High Education Institute, Guangzhou, China
| | - Xingxing Xiong
- Department of Operating Room, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
| | - Jie Zhang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong High Education Institute, Guangzhou, China
| | - Jiang Xu
- Department of Stomatology, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Man-Sun Sy
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Chaoyang Li
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong High Education Institute, Guangzhou, China
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Yu Y, Niu J, Zhang X, Wang X, Song H, Liu Y, Jiao X, Chen F. Identification and Validation of HOTAIRM1 as a Novel Biomarker for Oral Squamous Cell Carcinoma. Front Bioeng Biotechnol 2022; 9:798584. [PMID: 35087800 PMCID: PMC8787327 DOI: 10.3389/fbioe.2021.798584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/24/2021] [Indexed: 12/23/2022] Open
Abstract
ORAL squamous cell carcinoma (OSCC) is a malignant tumor with the highest incidence among tumors involving the oral cavity maxillofacial region, and is notorious for its high recurrence and metastasis potential. Long non-coding RNAs (lncRNAs), which regulate the genesis and evolution of cancers, are potential prognostic biomarkers. This study identified HOTAIRM1 as a novel significantly upregulated lncRNA in OSCC, which is strongly associated with unfavorable prognosis of OSCC. Systematic bioinformatics analyses demonstrated that HOTAIRM1 was closely related to tumor stage, overall survival, genome instability, the tumor cell stemness, the tumor microenvironment, and immunocyte infiltration. Using biological function prediction methods, including Weighted gene co-expression network analysis (WGCNA), Gene set enrichment analysis (GSEA), and Gene set variation analysis (GSVA), HOTAIRM1 plays a pivotal role in OSCC cell proliferation, and is mainly involved in the regulation of the cell cycle. In vitro, cell loss-functional experiments confirmed that HOTAIRM1 knockdown significantly inhibited the proliferation of OSCC cells, and arrested the cell cycle in G1 phase. At the molecular level, PCNA and CyclinD1 were obviously reduced after HOTAIRM1 knockdown. The expression of p53 and p21 was upregulated while CDK4 and CDK6 expression was decreased by HOTAIRM1 knockdown. In vivo, knocking down HOTAIRM1 significantly inhibited tumor growth, including the tumor size, weight, volume, angiogenesis, and hardness, monitored by ultrasonic imaging and magnetic resonance imaging In summary, our study reports that HOTAIRM1 is closely associated with tumorigenesis of OSCC and promotes cell proliferation by regulating cell cycle. HOTAIRM1 could be a potential prognostic biomarker and a therapeutic target for OSCC.
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Affiliation(s)
- Yixiu Yu
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiamei Niu
- Department of Abdominal Ultrasonography, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xingwei Zhang
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xue Wang
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongquan Song
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yingqun Liu
- Pediatric Dentistry Department, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaohui Jiao
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Xiaohui Jiao , ; Fuyang Chen,
| | - Fuyang Chen
- Department of Stomatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Xiaohui Jiao , ; Fuyang Chen,
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Huang X, Zhang W, Pu F, Zhang Z. LncRNA MEG3 promotes chemosensitivity of osteosarcoma by regulating antitumor immunity via miR-21-5p/p53 pathway and autophagy. Genes Dis 2021; 10:531-541. [DOI: 10.1016/j.gendis.2021.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/12/2021] [Accepted: 11/07/2021] [Indexed: 12/01/2022] Open
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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