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Abida, Imran M, Eltaib L, Ali A, Alanazi RAS, Singla N, Asdaq SMB, Al-Hajeili M, Alhakami FA, Al-Abdulhadi S, Abdulkhaliq AA, Rabaan AA. LncRNAs: Emerging biomarkers and therapeutic targets in rectal cancer. Pathol Res Pract 2024; 257:155294. [PMID: 38603843 DOI: 10.1016/j.prp.2024.155294] [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: 02/12/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024]
Abstract
According to findings, long non-coding RNAs (lncRNAs) have an important function in the onset and growth of various cancers, including rectal cancer (RC). RC offers unique issues in terms of diagnosis, treatment, and results, needing a full understanding of the cellular mechanisms that cause it to develop. This thorough study digs into the various functions that lncRNAs perform in RC, giving views into their multiple roles as well as possible therapeutic consequences. The function of lncRNAs in RC cell proliferation, apoptosis, migratory and infiltrating capacities, epithelial-mesenchymal shift, and therapy tolerance are discussed. Various lncRNA regulatory roles are investigated in depth, yielding information on their effect on essential cell functions such as angiogenesis, death, immunity, and growth. Systemic lncRNAs are currently acknowledged as potential indications for the initial stages of identification of cancer, with the ability to diagnose as well as forecast. Besides adding to their diagnostic utility, lncRNAs offer therapeutic opportunities as actors, contributing to the expanding landscape of cancer research. Moreover, the investigation looks into the assessment and predictive utility of lncRNAs as RC markers. The article also offers insight into lncRNAs as chemoresistance and drug resistance facilitators in the setting of RC.
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Affiliation(s)
- Abida
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Mohd Imran
- 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
| | - Akbar Ali
- Department of Pharmacy Practice, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | | | - Neelam Singla
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur 302017, India
| | | | - Marwan Al-Hajeili
- Department of Medicine, King Abdulaziz University, Jeddah 23624, Saudi Arabia
| | - Fatemah Abdulaziz Alhakami
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Saleh Al-Abdulhadi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Riyadh 11942, Saudi Arabia; Dr. Saleh Office for Medical Genetic and Genetic Counseling Services, The house of Expertise, Prince Sattam bin Abdulaziz University, Dammam 32411, Saudi Arabia
| | - Altaf A Abdulkhaliq
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
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Jayarathna DK, Rentería ME, Batra J, Gandhi NS. Integrative competing endogenous RNA network analyses identify novel lncRNA and genes implicated in metastatic breast cancer. Sci Rep 2023; 13:2423. [PMID: 36765262 PMCID: PMC9918521 DOI: 10.1038/s41598-023-29585-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Competing endogenous RNAs (ceRNAs) have gained attention in cancer research owing to their involvement in microRNA-mediated gene regulation. Previous studies have identified ceRNA networks of individual cancers. Nevertheless, none of these studies has investigated different cancer stages. We identify stage-specific ceRNAs in breast cancer using the cancer genome atlas data. Moreover, we investigate the molecular functions and prognostic ability of ceRNAs involved in stage I-IV networks. We identified differentially expressed candidate ceRNAs using edgeR and limma R packages. A three-step analysis was used to identify statistically significant ceRNAs of each stage. Survival analysis and functional enrichment analysis were conducted to identify molecular functions and prognostic ability. We found five genes and one long non-coding RNA unique to the stage IV ceRNA network. These genes have been described in previous breast cancer studies. Genes acted as ceRNAs are enriched in cancer-associated pathways. Two, three, and three microRNAs from stages I, II, and III were prognostic from the Kaplan-Meier survival analysis. Our results reveal a set of unique ceRNAs in metastatic breast cancer. Further experimental work is required to evaluate their role in metastasis. Moreover, identifying stage-specific ceRNAs will improve the understanding of personalised therapeutics in breast cancer.
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Affiliation(s)
- Dulari K Jayarathna
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Miguel E Rentería
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Kelvin Grove, Brisbane, QLD, 4059, Australia
| | - Jyotsna Batra
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Kelvin Grove, Brisbane, QLD, 4059, Australia
- Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Neha S Gandhi
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia.
- Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
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Jayarathna DK, Rentería ME, Batra J, Gandhi NS. A supervised machine learning approach identifies gene-regulating factor-mediated competing endogenous RNA networks in hormone-dependent cancers. J Cell Biochem 2022; 123:1394-1408. [PMID: 35757968 PMCID: PMC9542250 DOI: 10.1002/jcb.30300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022]
Abstract
Competing endogenous RNAs (ceRNAs) have become an emerging topic in cancer research due to their role in gene regulatory networks. To date, traditional ceRNA bioinformatic studies have investigated microRNAs as the only factor regulating gene expression. Growing evidence suggests that genomic (e.g., copy number alteration [CNA]), transcriptomic (e.g., transcription factors [TFs]), and epigenomic (e.g., DNA methylation [DM]) factors can influence ceRNA regulatory networks. Herein, we used the Least absolute shrinkage and selection operator regression, a machine learning approach, to integrate DM, CNA, and TFs data with RNA expression to infer ceRNA networks in cancer risk. The gene‐regulating factors‐mediated ceRNA networks were identified in four hormone‐dependent (HD) cancer types: prostate, breast, colorectal, and endometrial. The shared ceRNAs across HD cancer types were further investigated using survival analysis, functional enrichment analysis, and protein–protein interaction network analysis. We found two (BUB1 and EXO1) and one (RRM2) survival‐significant ceRNA(s) shared across breast‐colorectal‐endometrial and prostate–colorectal–endometrial combinations, respectively. Both BUB1 and BUB1B genes were identified as shared ceRNAs across more than two HD cancers of interest. These genes play a critical role in cell division, spindle‐assembly checkpoint signalling, and correct chromosome alignment. Furthermore, shared ceRNAs across multiple HD cancers have been involved in essential cancer pathways such as cell cycle, p53 signalling, and chromosome segregation. Identifying ceRNAs' roles across multiple related cancers will improve our understanding of their shared disease biology. Moreover, it contributes to the knowledge of RNA‐mediated cancer pathogenesis.
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Affiliation(s)
- Dulari K Jayarathna
- Centre for Genomics and Personalized Health, School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, Australia.,Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Miguel E Rentería
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jyotsna Batra
- Centre for Genomics and Personalized Health, School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, Australia.,School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia.,Australian Prostate Cancer Research Centre-Queensland, Woolloongabba, QLD, Australia
| | - Neha S Gandhi
- Centre for Genomics and Personalized Health, School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, Australia.,Cancer and Ageing Research Program, Translational Research Institute, Woolloongabba, QLD, Australia
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Le Y, Shi Y. MALAT1 regulates PCT expression in sepsis patients through the miR‐125b/STAT3 axis. J Clin Lab Anal 2022; 36:e24428. [PMID: 35426182 PMCID: PMC9102486 DOI: 10.1002/jcla.24428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 11/23/2022] Open
Abstract
Background Procalcitonin (PCT) is an important marker in diagnosing sepsis. However, some other diseases can also cause an increase in PCT. PCT still has some limitations in the clinical application of diagnosing sepsis. Therefore, it is of great significance to clarify the regulatory mechanism of PCT expression in sepsis and provide new therapeutic targets for sepsis. Methods Blood samples from clinical patients were collected, and peripheral blood monocytes were isolated. Bioinformatics was performed to find the ceRNA regulatory network of STAT3/PCT. MALAT1 and miR‐125b were detected by qRT‐PCR. MALAT1 was located by fluorescence in situ hybridization (FISH) in U937 cells, and the regulatory relationship between MALAT1, miR‐125b, and STAT3 was verified by double luciferase activity report and RNA pull‐down assay. U937 cells were transfected with miR‐125b, and the effects of the MALAT1/miR‐125b/STAT3 pathway on gene and protein secretion levels of PCT were verified by qRT‐PCR, western blot, and ELISA. Results In the serum of sepsis patients and lipopolysaccharide(LPS)‐induced U937 cells, MALAT1, STAT3, and PCT gene expression levels were significantly increased, while miR‐125b expression level was decreased. FISH results showed that the MALAT1 transcript was mainly located in the nucleus. The double luciferase activity report and RNA pull‐down assay results suggested a targeted regulatory relationship between MALAT1, miR‐125b, and STAT3. LPS‐induced U937 cells transfection with MALAT1 siRNA decreased STAT3 protein expression and phosphorylation level and the expression of PCT. Co‐transfection with miR‐125b inhibitor effectively reversed this phenomenon. Conclusions MALAT1 could upregulate the expressions of STAT3 and PCT by targeted adsorption of miR‐125b.
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Affiliation(s)
- Yuanjie Le
- Department of Emergency Hwamei Hospital University of Chinese Academy of Sciences Ningbo China
- Ningbo Institute of Life and Health Industry University of Chinese Academy of Sciences Ningbo China
| | - Yongwei Shi
- Department of Emergency Hwamei Hospital University of Chinese Academy of Sciences Ningbo China
- Ningbo Institute of Life and Health Industry University of Chinese Academy of Sciences Ningbo China
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