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Li L, Yu S, Dou N, Wang X, Gao Y, Li Y. A new tandem repeat-enriched lncRNA XLOC_008672 promotes gastric carcinogenesis by regulating G3BP1 expression. Cancer Sci 2024. [PMID: 38581120 DOI: 10.1111/cas.16172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 03/11/2024] [Accepted: 03/23/2024] [Indexed: 04/08/2024] Open
Abstract
Aberrant expression of forkhead box transcription factor 1 (FOXM1) plays critical roles in a variety of human malignancies and predicts poor prognosis. However, little is known about the crosstalk between FOXM1 and long noncoding RNAs (lncRNAs) in tumorigenesis. The present study identifies a previously uncharacterized lncRNA XLOC_008672 in gastric cancer (GC), which is regulated by FOXM1 and possesses multiple copies of tandem repetitive sequences. LncRNA microarrays are used to screen differentially expressed lncRNAs in FOXM1 knockdown GC cells, and then the highest fold downregulation lncRNA XLOC_008672 is screened out. Sequence analysis reveals that the new lncRNA contains 62 copies of 37-bp tandem repeats. It is transcriptionally activated by FOXM1 and functions as a downstream effector of FOXM1 in GC cells through in vitro and in vivo functional assays. Elevated expression of XLOC_008672 is found in GC tissues and indicates worse prognosis. Mechanistically, XLOC_008672 can bind to small nuclear ribonucleoprotein polypeptide A (SNRPA), thereby enhancing mRNA stability of Ras-GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) and, consequently, facilitating GC cell proliferation and migration. Our study discovers a new uncharacterized lncRNA XLOC_008672 involved in GC carcinogenesis and progression. Targeting FOXM1/XLOC_008672/SNRPA/G3BP1 signaling axis might be a promising therapeutic strategy for GC.
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Affiliation(s)
- Li Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shijun Yu
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ning Dou
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiao Wang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yong Gao
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yandong Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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2
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Huang M, Zhao Z, Yang L. Long noncoding RNA small nucleolar RNA host genes as prognostic molecular biomarkers in hepatocellular carcinoma: A meta-analysis. Cancer Med 2024; 13:e7200. [PMID: 38634194 PMCID: PMC11024508 DOI: 10.1002/cam4.7200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 02/20/2024] [Accepted: 04/06/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Recently, increasing data have suggested that the lncRNA small nucleolar RNA host genes (SNHGs) were aberrantly expressed in hepatocellular carcinoma (HCC), but the association between the prognosis of HCC and their expression remained unclear. The purpose of this meta-analysis was to determine the prognostic significance of lncRNA SNHGs in HCC. METHODS We systematically searched Embase, Web of Science, PubMed, and Cochrane Library for eligible articles published up to February 2024. The prognostic significance of SNHGs in HCC was evaluated by hazard ratios (HRs) and 95% confidence intervals (CIs). Odds ratios (ORs) were used to assess the clinicopathological features of SNHGs. RESULTS This analysis comprised a total of 25 studies covering 2314 patients with HCC. The findings demonstrated that over-expressed SNHGs were associated with larger tumor size, multiple tumor numbers, poor histologic grade, earlier lymphatic metastasis, vein invasion, advanced tumor stage, portal vein tumor thrombosis (PVTT), and higher alpha-fetoprotein (AFP) level, but not with hepatitis B virus (HBV) infection, and cirrhosis. In terms of prognosis, patients with higher SNHG expression were more likely to have shorter overall survival (OS), relapse-free survival (RFS), and disease-free survival (DFS). CONCLUSIONS In conclusion, upregulation of SNHGs expression correlates with shorter OS, RFS, DFS, tumor size and numbers, histologic grade, lymphatic metastasis, vein invasion, tumor stage, PVTT, and AFP level, suggesting that SNHGs may serve as prognostic biomarkers in HCC.
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Affiliation(s)
- Meng Huang
- Medical Center for Digestive DiseaseThe Second Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsu ProvinceChina
| | - Zhiwen Zhao
- Medical Center for Digestive DiseaseThe Second Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsu ProvinceChina
| | - Lihua Yang
- Medical Center for Digestive DiseaseThe Second Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsu ProvinceChina
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3
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Sarfraz M, Abida, Eltaib L, Asdaq SMB, Guetat A, Alzahrani AK, Alanazi SS, Aaghaz S, Singla N, Imran M. Overcoming chemoresistance and radio resistance in prostate cancer: The emergent role of non-coding RNAs. Pathol Res Pract 2024; 255:155179. [PMID: 38320439 DOI: 10.1016/j.prp.2024.155179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/08/2024]
Abstract
Prostate cancer (PCa) continues to be a major health concern worldwide, with its resistance to chemotherapy and radiation therapy presenting major hurdles in successful treatment. While patients with localized prostate cancer generally have a good survival rate, those with metastatic prostate cancer often face a grim prognosis, even with aggressive treatments using various methods. The high mortality rate in severe cases is largely due to the lack of treatment options that can offer lasting results, especially considering the significant genetic diversity found in tumors at the genomic level. This comprehensive review examines the intricate molecular mechanisms governing resistance in PCa, emphasising the pivotal contributions of non-coding RNAs (ncRNAs). We delve into the diverse roles of microRNAs, long ncRNAs, and other non-coding elements as critical regulators of key cellular processes involved in CR & RR. The review emphasizes the diagnostic potential of ncRNAs as predictive biomarkers for treatment response, offering insights into patient stratification and personalized therapeutic approaches. Additionally, we explore the therapeutic implications of targeting ncRNAs to overcome CR & RR, highlighting innovative strategies to restore treatment sensitivity. By synthesizing current knowledge, this review not only provides a comprehension of the chemical basis of resistance in PCa but also identifies gaps in knowledge, paving the way for future research directions. Ultimately, this exploration of ncRNA perspectives offers a roadmap for advancing precision medicine in PCa, potentially transforming therapeutic paradigms and improving outcomes for patients facing the challenges of treatment resistance.
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Affiliation(s)
- Muhammad Sarfraz
- College of Pharmacy, Al Ain University, Al Ain Campus, Al Ain 64141, United Arab Emirates
| | - Abida
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Lina Eltaib
- Department of Pharmaceutics, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | | | - Arbi Guetat
- Department of Biological Sciences, College of Sciences, Northern Border University, Arar 73213, Saudi Arabia
| | - A Khuzaim Alzahrani
- Department of Medical Laboratory Technology, Faculty of Medical Applied Science, Northern Border University, Arar 91431, Saudi Arabia
| | | | - Shams Aaghaz
- Department of Pharmacy, School of Medical & Allied Sciences, Galgotias University, Greater Noida 203201, India
| | - Neelam Singla
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur 302017, India
| | - Mohd Imran
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia.
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4
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Alharbi KS. The ncRNA-TGF-β axis: Unveiling new frontiers in colorectal cancer research. Pathol Res Pract 2024; 254:155138. [PMID: 38266458 DOI: 10.1016/j.prp.2024.155138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/07/2024] [Accepted: 01/11/2024] [Indexed: 01/26/2024]
Abstract
Colorectal cancer (CRC) poses a substantial global challenge, necessitating a deeper understanding of the molecular underpinnings governing its onset and progression. The transforming growth factor beta (TGF-β) network has been a well-recognized cornerstone in advancing CRC. Nevertheless, a recent study has highlighted the growing importance of non-coding RNAs (ncRNAs) in this context. This comprehensive review aims to present an extensive examination of the interaction between ncRNAs and TGF-signaling. Noncoding RNAs (ncRNAs), encompassing circular RNAs (circRNAs), long-ncRNAs (lncRNAs), and microRNAs (miRNAs), have surfaced as pivotal modulators governing various aspects of TGF-β signaling. MiRNAs have been discovered to target elements within the TGF-β signaling, either enhancing or inhibiting signaling, depending on the context. LncRNAs have been associated with CRC progression, functioning as miRNA sponges or directly influencing TGF-β pathway elements. Even circRNAs, a relatively recent addition to the ncRNA family, have impacted CRC, affecting TGF-β signaling through diverse mechanisms. This review encompasses recent progress in comprehending specific ncRNAs involved in TGF-β signaling, their functional roles, and their clinical relevance in CRC. We investigate the possibility of ncRNAs as targets for detection, prognosis, and therapy. Additionally, we explore the interaction of TGF-β and other pathways in CRC and the role of ncRNAs within this intricate network. As we unveil the intricate regulatory function of ncRNAs in the TGF-β signaling in CRC, we gain valuable insights into the disease's pathogenesis. Incorporating these discoveries into clinical settings holds promise for more precise diagnosis, prognosis, and targeted therapeutic approaches, ultimately enhancing the care of CRC patients. This comprehensive review underscores the ever-evolving landscape of ncRNA research in CRC and the potential for novel interventions in the battle against this formidable disease.
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Affiliation(s)
- Khalid Saad Alharbi
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia.
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5
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Kazmi I, Altamimi ASA, Afzal M, Majami AA, AlGhamdi AS, Alkinani KB, Abbasi FA, Almalki WH, Alzera SI, Kukreti N, Fuloria NK, Sekar M, Abida. The emerging role of non-coding RNAs in the Wnt/β-catenin signaling pathway in Prostate Cancer. Pathol Res Pract 2024; 254:155134. [PMID: 38277746 DOI: 10.1016/j.prp.2024.155134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/28/2024]
Abstract
Prostate cancer (PCa) is an important worldwide medical concern, necessitating a greater understanding of the molecular processes driving its development. The Wnt/-catenin signaling cascade is established as a central player in PCa pathogenesis, and recent research emphasizes the critical involvement of non-coding RNAs (ncRNAs) in this scenario. This in-depth study seeks to give a thorough examination of the complex relationship between ncRNAs and the Wnt/β-catenin system in PCa. NcRNAs, such as circular RNAs (circRNAs), long ncRNAs (lncRNAs), and microRNAs (miRNAs), have been recognized as essential regulators that modulate numerous facets of the Wnt/β-catenin network. MiRNAs have been recognized as targeting vital elements of the process, either enhancing or inhibiting signaling, depending on their specific roles and targets. LncRNAs participate in fine-tuning the Wnt/β-catenin network as a result of complicated interplay with both upstream and downstream elements. CircRNAs, despite being a relatively recent addition to the ncRNA family, have been implicated in PCa, influencing the Wnt/β-catenin cascade through diverse mechanisms. This article encompasses recent advances in our comprehension of specific ncRNAs that participate in the Wnt/β-catenin network, their functional roles, and clinical relevance in PCa. We investigate their use as screening and predictive indicators, and targets for treatment. Additionally, we delve into the interplay between Wnt/β-catenin and other signaling networks in PCa and the role of ncRNAs within this complex network. As we unveil the intricate regulatory functions of ncRNAs in the Wnt/β-catenin cascade in PCa, we gain valuable insights into the disease's pathogenesis. The implementation of these discoveries in practical applications holds promise for more precise diagnosis, prognosis, and targeted therapeutic approaches, ultimately enhancing the care of PCa patients. This comprehensive review underscores the evolving landscape of ncRNA research in PCa and the potential for innovative interventions in the battle against this formidable malignancy.
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Affiliation(s)
- Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | | | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Abdullah A Majami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Abeer S AlGhamdi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Khadijah B Alkinani
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia; Department of Public Health, Faculty of Health Sciences, Umm Al-Qura University, 21955 Makkah, Saudi Arabia
| | - Fahad Al Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sami I Alzera
- Department of Pharmacology, College of Pharmacy, Jouf University, 72341, Sakaka, Aljouf, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | | | - Mahendran Sekar
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Subang Jaya 47500, Selangor, Malaysia
| | - Abida
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
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6
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Záveský L, Jandáková E, Weinberger V, Minář L, Kohoutová M, Slanař O. Long non-coding RNAs PTENP1, GNG12-AS1, MAGI2-AS3 and MEG3 as tumor suppressors in breast cancer and their associations with clinicopathological parameters. Cancer Biomark 2024:CBM230259. [PMID: 38277283 DOI: 10.3233/cbm-230259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
BACKGROUND Breast cancer is the most commonly occurring cancer worldwide and is the main cause of death from cancer in women. Novel biomarkers are highly warranted for this disease. OBJECTIVE Evaluation of novel long non-coding RNAs biomarkers for breast cancer. METHODS The study comprised the analysis of the expression of 71 candidate lncRNAs via screening, six of which (four underexpressed, two overexpressed) were validated and analyzed by qPCR in tumor tissues associated with NST breast carcinomas, compared with the benign samples and with respect to their clinicopathological characteristics. RESULTS The results indicated the tumor suppressor roles of PTENP1, GNG12-AS1, MEG3 and MAGI2-AS3. Low levels of both PTENP1 and GNG12-AS1 were associated with worsened progression-free and overall survival rates. The reduced expression of GNG12-AS1 was linked to the advanced stage. A higher grade was associated with the lower expression of PTENP1, GNG12-AS1 and MAGI2-AS3. Reduced levels of both MEG3 and PTENP1 were linked to Ki-67 positivity. The NRSN2-AS1 and UCA1 lncRNAs were overexpressed; higher levels of UCA1 were associated with multifocality. CONCLUSIONS The results suggest that the investigated lncRNAs may play important roles in breast cancer and comprise a potential factor that should be further evaluated in clinical studies.
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Affiliation(s)
- Luděk Záveský
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, and General University Hospital in Prague, Prague, Czech Republic
- Institute of Pharmacology, First Faculty of Medicine, Charles University, Prague, and General University Hospital in Prague, Prague, Czech Republic
| | - Eva Jandáková
- Department of Pathology, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Vít Weinberger
- Department of Obstetrics and Gynecology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Luboš Minář
- Department of Obstetrics and Gynecology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Milada Kohoutová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, and General University Hospital in Prague, Prague, Czech Republic
| | - Ondřej Slanař
- Institute of Pharmacology, First Faculty of Medicine, Charles University, Prague, and General University Hospital in Prague, Prague, Czech Republic
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7
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Avila Santos AP, de Almeida BLS, Bonidia RP, Stadler PF, Stefanic P, Mandic-Mulec I, Rocha U, Sanches DS, de Carvalho ACPLF. BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification. RNA Biol 2024; 21:1-12. [PMID: 38528797 DOI: 10.1080/15476286.2024.2329451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2024] [Indexed: 03/27/2024] Open
Abstract
The accurate classification of non-coding RNA (ncRNA) sequences is pivotal for advanced non-coding genome annotation and analysis, a fundamental aspect of genomics that facilitates understanding of ncRNA functions and regulatory mechanisms in various biological processes. While traditional machine learning approaches have been employed for distinguishing ncRNA, these often necessitate extensive feature engineering. Recently, deep learning algorithms have provided advancements in ncRNA classification. This study presents BioDeepFuse, a hybrid deep learning framework integrating convolutional neural networks (CNN) or bidirectional long short-term memory (BiLSTM) networks with handcrafted features for enhanced accuracy. This framework employs a combination of k-mer one-hot, k-mer dictionary, and feature extraction techniques for input representation. Extracted features, when embedded into the deep network, enable optimal utilization of spatial and sequential nuances of ncRNA sequences. Using benchmark datasets and real-world RNA samples from bacterial organisms, we evaluated the performance of BioDeepFuse. Results exhibited high accuracy in ncRNA classification, underscoring the robustness of our tool in addressing complex ncRNA sequence data challenges. The effective melding of CNN or BiLSTM with external features heralds promising directions for future research, particularly in refining ncRNA classifiers and deepening insights into ncRNAs in cellular processes and disease manifestations. In addition to its original application in the context of bacterial organisms, the methodologies and techniques integrated into our framework can potentially render BioDeepFuse effective in various and broader domains.
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Affiliation(s)
- Anderson P Avila Santos
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, Brazil
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research - UFZ GmbH, Leipzig, Saxony, Germany
| | - Breno L S de Almeida
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, Brazil
| | - Robson P Bonidia
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, Brazil
- Department of Computer Science, Federal University of Technology - Paraná, UTFPR, Cornélio Procópio, Brazil
| | - Peter F Stadler
- Department of Computer Science and Interdisciplinary Center of Bioinformatics, University of Leipzig, Leipzig, Saxony, Germany
| | - Polonca Stefanic
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ines Mandic-Mulec
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ulisses Rocha
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research - UFZ GmbH, Leipzig, Saxony, Germany
| | - Danilo S Sanches
- Department of Computer Science, Federal University of Technology - Paraná, UTFPR, Cornélio Procópio, Brazil
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8
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Sun J, Si S, Ru J, Wang X. DeepdlncUD: Predicting regulation types of small molecule inhibitors on modulating lncRNA expression by deep learning. Comput Biol Med 2023; 163:107226. [PMID: 37450966 DOI: 10.1016/j.compbiomed.2023.107226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/31/2023] [Accepted: 07/01/2023] [Indexed: 07/18/2023]
Abstract
Targeting lncRNAs by small molecules (SM-lncR) to alter their expression levels has emerged as an important therapeutic modality for disease treatment. To date, no computational tools have been dedicated to predicting small molecule-mediated upregulation or downregulation of lncRNA expression. Here, we introduce DeepdlncUD, which integrates predictions of nine deep learning algorithms together, to infer the regulation types of small molecules on modulating lncRNA expression. Through systematic optimization on a training set of 771 upregulation and 739 downregulation SM-lncR pairs, each encoding 1369 sequence, representational, and physiochemical features, this method outperforms a recently released program, DeepsmirUD, by achieving 0.674 in AUC (area under the receiver operating characteristic curve), 0.722 in AUCPR (area under the precision-recall curve), 0.681 in F1-score, and 0.516 in Jaccard Index on a test set of 222 SM-lncR pairs. By extracting 125 upregulation and 46 downregulation SM-lncR pairs that involve disease-associated lncRNAs, DeepdlncUD is shown to gain an accuracy of 0.700 in the pathological context. Using connectivity scores, around half of the small molecules are correctly estimated as drugs to treat lncRNA-regulated diseases. This tool can be run at a fast speed to assist the discovery of potential small molecule drugs of lncRNA targets on a large scale. DeepdlncUD is publicly available at https://github.com/2003100127/deepdlncud.
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Affiliation(s)
- Jianfeng Sun
- Botnar Research Centre, University of Oxford, Headington, Oxford, OX3 7LD, UK.
| | - Shuyue Si
- School of Mathematics and Physics, Xi'an Jiaotong-liverpool University, Renai, Suzhou, 215028, China
| | - Jinlong Ru
- Chair of Prevention of Microbial Diseases, School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Xia Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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9
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Aldayyeni H, Hjazi A, Shahab S, Gupta J, Alsaab HO, Motea YH, Alazbjee AAA, Romero-Parra RM, Obaid RF, Hussien BM, Hosseini-Fard SR. Functions, mechanisms, and clinical applications of lncRNA LINC00857 in cancer pathogenesis. Hum Cell 2023; 36:1656-1671. [PMID: 37378889 DOI: 10.1007/s13577-023-00936-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Emerging data indicated that long noncoding RNAs (lncRNAs) are crucial players in the biological processes via regulating epigenetics, transcription, and protein translation. A novel lncRNA, LINC00857, was indicated to upregulate in several types of cancer. In addition, LINC00857 was functionally related to the modulation of the cancer-linked behaviors, including invasion, migration, proliferation, epithelial-mesenchymal transition (EMT), cell cycle, and apoptosis. The importance of LINC00857 in cancer onset and development proposed that LINC00857 has major importance in the cancer progression and may be considered as a novel prognostic/diagnostic biomarker as well as a treatment target. Here, we retrospectively investigate the available progress in biomedical research investigating the functions of LINC00857 in cancer, focusing on finding the molecular mechanisms affecting various cancer-related behaviors and exploring its clinical applications.
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Affiliation(s)
| | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Sana Shahab
- Department of Business Administration, College of Business Administration, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Jitendra Gupta
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, Taif University, Taif, 21944, Saudi Arabia
| | | | | | | | - Rasha Fadhel Obaid
- Department of Biomedical Engineering, Al-Mustaqbal University College, Babylon, Iraq
| | - Beneen M Hussien
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Seyed Reza Hosseini-Fard
- Department of Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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10
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Huang LA, Lin C, Yang L. Plumbing mysterious RNAs in "dark genome" for the conquest of human diseases. Mol Ther 2023; 31:1577-1595. [PMID: 37165619 PMCID: PMC10278048 DOI: 10.1016/j.ymthe.2023.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Next-generation sequencing has revealed that less than 2% of transcribed genes are translated into proteins, with a large portion transcribed into noncoding RNAs (ncRNAs). Among these, long noncoding RNAs (lncRNAs) represent the largest group and are pervasively transcribed throughout the genome. Dysfunctions in lncRNAs have been found in various diseases, highlighting their potential as therapeutic, diagnostic, and prognostic targets. However, challenges, such as unknown molecular mechanisms and nonspecific immune responses, and issues of drug specificity and delivery present obstacles in translating lncRNAs into clinical applications. In this review, we summarize recent publications that have explored lncRNA functions in human diseases. We also discuss challenges and future directions for developing lncRNA treatments, aiming to bridge the gap between functional studies and clinical potential and inspire further exploration in the field.
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Affiliation(s)
- Lisa A Huang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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11
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Jacksi M, Schad E, Buday L, Tantos A. Absence of Scaffold Protein Tks4 Disrupts Several Signaling Pathways in Colon Cancer Cells. Int J Mol Sci 2023; 24:ijms24021310. [PMID: 36674824 PMCID: PMC9861885 DOI: 10.3390/ijms24021310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
Tks4 is a large scaffold protein in the EGFR signal transduction pathway that is involved in several cellular processes, such as cellular motility, reactive oxygen species-dependent processes, and embryonic development. It is also implicated in a rare developmental disorder, Frank-ter Haar syndrome. Loss of Tks4 resulted in the induction of an EMT-like process, with increased motility and overexpression of EMT markers in colorectal carcinoma cells. In this work, we explored the broader effects of deletion of Tks4 on the gene expression pattern of HCT116 colorectal carcinoma cells by transcriptome sequencing of wild-type and Tks4 knockout (KO) cells. We identified several protein coding genes with altered mRNA levels in the Tks4 KO cell line, as well as a set of long non-coding RNAs, and confirmed these changes with quantitative PCR on a selected set of genes. Our results show a significant perturbation of gene expression upon the deletion of Tks4, suggesting the involvement of different signal transduction pathways over the well-known EGFR signaling.
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Affiliation(s)
- Mevan Jacksi
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Department of Molecular Biology, Semmelweis University Medical School, 1094 Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Correspondence:
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12
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Alfieri M, Meo L, Ragno P. Posttranscriptional Regulation of the Plasminogen Activation System by Non-Coding RNA in Cancer. Int J Mol Sci 2023; 24:ijms24020962. [PMID: 36674481 PMCID: PMC9860977 DOI: 10.3390/ijms24020962] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/07/2023] Open
Abstract
Various species of non-coding RNAs (ncRNAs) may act as functional molecules regulating diverse biological processes. In cancer cell biology, ncRNAs include RNAs that regulate the expression of oncogenes and tumor suppressor genes through various mechanisms. The urokinase (uPA)-mediated plasminogen activation system (PAS) includes uPA, its inhibitors PAI-1 and PAI-2 and its specific cellular receptor uPAR; their increased expression represents a negative prognostic factor in several cancers. Here, we will briefly describe the main uPA-mediated PAS components and ncRNA species; then, we will review more recent evidence of the roles that ncRNAs may play in regulating the expression and functions of uPA-mediated PAS components in cancer.
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Affiliation(s)
- Mariaevelina Alfieri
- Clinical Pathology, Pausilipon Hospital, A.O.R.N Santobono-Pausilipon, 80123 Naples, Italy
| | - Luigia Meo
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Pia Ragno
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
- Correspondence: ; Tel.: +39-089-969456
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13
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Yang W, Lyu Y, Xiang R, Yang J. Long Noncoding RNAs in the Pathogenesis of Insulin Resistance. Int J Mol Sci 2022; 23:ijms232416054. [PMID: 36555704 PMCID: PMC9785789 DOI: 10.3390/ijms232416054] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Insulin resistance (IR), designated as the blunted response of insulin target tissues to physiological level of insulin, plays crucial roles in the development and progression of diabetes, nonalcoholic fatty liver disease (NAFLD) and other diseases. So far, the distinct mechanism(s) of IR still needs further exploration. Long non-coding RNA (lncRNA) is a class of non-protein coding RNA molecules with a length greater than 200 nucleotides. LncRNAs are widely involved in many biological processes including cell differentiation, proliferation, apoptosis and metabolism. More recently, there has been increasing evidence that lncRNAs participated in the pathogenesis of IR, and the dysregulated lncRNA profile played important roles in the pathogenesis of metabolic diseases including obesity, diabetes and NAFLD. For example, the lncRNAs MEG3, H19, MALAT1, GAS5, lncSHGL and several other lncRNAs have been shown to regulate insulin signaling and glucose/lipid metabolism in various tissues. In this review, we briefly introduced the general features of lncRNA and the methods for lncRNA research, and then summarized and discussed the recent advances on the roles and mechanisms of lncRNAs in IR, particularly focused on liver, skeletal muscle and adipose tissues.
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Affiliation(s)
- Weili Yang
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yixiang Lyu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
| | - Rui Xiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
| | - Jichun Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
- Correspondence:
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14
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Wu K, Tsai Y, Huang Y, Wu Y, Chang C, Liu Y, Hsu Y, Hung J. LINC02323 facilitates development of lung squamous cell carcinoma by miRNA sponge and RBP dysregulation and links to poor prognosis. Thorac Cancer 2022; 14:407-418. [PMID: 36516959 PMCID: PMC9891863 DOI: 10.1111/1759-7714.14760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The poor outcome of patients with lung squamous cell carcinoma (LUSC) highlights the importance of the identification of novel effective prognostic markers and therapeutic targets. Long noncoding RNAs (lncRNAs) have generally been considered to serve important roles in tumorigenesis and the development of various types of cancer, including LUSC. METHODS Here, we aimed to investigate the role of LINC02323 in LUSC and its potential mechanisms by performing comprehensive bioinformatic analyses. RESULTS LINC02323 was elevated and positively associated with unfavorable prognosis of LUSC patients. LINC02323 exerted oncogenic function by competitively binding to miR-1343-3p and miR-6783-3p, thereby upregulating L1CAM expression. Indeed, we also determined that LINC02323 could interact with the RNA-binding protein DDX3X, which regulates various stages of RNA expression and processing. CONCLUSION Taken together, we identified that LINC02323 and its indirect target L1CAM can act as novel biomarkers for determining the prognosis of patients with LUSC and thus deserves further study.
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Affiliation(s)
- Kuan‐Li Wu
- Graduate Institute of Medicine, College of MedicineKaohsiung Medical UniversityKaohsiungTaiwan,Division of Pulmonary and Critical Care MedicineKaohsiung Medical University Hospital, Kaohsiung Medical UniversityKaohsiungTaiwan,Drug Development and Value Creation Research CenterKaohsiung Medical UniversityKaohsiungTaiwan
| | - Ying‐Ming Tsai
- Graduate Institute of Medicine, College of MedicineKaohsiung Medical UniversityKaohsiungTaiwan,Division of Pulmonary and Critical Care MedicineKaohsiung Medical University Hospital, Kaohsiung Medical UniversityKaohsiungTaiwan,Drug Development and Value Creation Research CenterKaohsiung Medical UniversityKaohsiungTaiwan
| | - Yung‐Chi Huang
- Graduate Institute of Medicine, College of MedicineKaohsiung Medical UniversityKaohsiungTaiwan,Drug Development and Value Creation Research CenterKaohsiung Medical UniversityKaohsiungTaiwan
| | - Yu‐Yuan Wu
- School of Medicine, College of MedicineKaohsiung Medical UniversityKaohsiungTaiwan
| | - Chao‐Yuan Chang
- Graduate Institute of Medicine, College of MedicineKaohsiung Medical UniversityKaohsiungTaiwan,Department of AnatomyKaohsiung Medical UniversityKaohsiungTaiwan
| | - Yu‐Wei Liu
- Division of Thoracic Surgery, Department of Surgery, Kaohsiung Medical University HospitalKaohsiung Medical UniversityKaohsiungTaiwan
| | - Ya‐Ling Hsu
- Graduate Institute of Medicine, College of MedicineKaohsiung Medical UniversityKaohsiungTaiwan,Drug Development and Value Creation Research CenterKaohsiung Medical UniversityKaohsiungTaiwan
| | - Jen‐Yu Hung
- Graduate Institute of Medicine, College of MedicineKaohsiung Medical UniversityKaohsiungTaiwan,Division of Pulmonary and Critical Care MedicineKaohsiung Medical University Hospital, Kaohsiung Medical UniversityKaohsiungTaiwan,Drug Development and Value Creation Research CenterKaohsiung Medical UniversityKaohsiungTaiwan,Department of Internal MedicineKaohsiung Municipal Ta‐Tung HospitalKaohsiungTaiwan
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Tossetta G. Metformin Improves Ovarian Cancer Sensitivity to Paclitaxel and Platinum-Based Drugs: A Review of In Vitro Findings. Int J Mol Sci 2022; 23:12893. [PMID: 36361682 PMCID: PMC9654053 DOI: 10.3390/ijms232112893] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 07/30/2023] Open
Abstract
Ovarian cancer is one of the most dangerous gynecologic cancers worldwide, showing a high fatality rate and recurrence due to diagnosis at an advanced stage of the disease and the occurrence of chemoresistance, which weakens the therapeutic effects of the chemotherapeutic treatments. In fact, although paclitaxel and platinum-based drugs (carboplatin or cisplatin) are widely used alone or in combination to treat ovarian cancer, the occurrence of chemoresistance significantly reduces the effects of these drugs. Metformin is a hypoglycemic agent that is commonly used for the treatment of type 2 diabetes mellitus and non-alcoholic fatty liver disease. However, this drug also shows anti-tumor activity, reducing cancer risk and chemoresistance. This review analyzes the current literature regarding the role of metformin in ovarian cancer and investigates what is currently known about its effects in reducing paclitaxel and platinum resistance to restore sensitivity to these drugs.
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Affiliation(s)
- Giovanni Tossetta
- Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, 60126 Ancona, Italy; ; Tel.: +39-0712206270
- Clinic of Obstetrics and Gynaecology, Department of Clinical Sciences, Università Politecnica delle Marche, Salesi Hospital, Azienda Ospedaliero Universitaria, 60126 Ancona, Italy
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