Tehran University of Medical Sciences

Science Communicator Platform

Stay connected! Follow us on X network (Twitter):
Share this content! On (X network) By
Heterogeneous Expression of Long Noncoding Rna Rp11-109D20.2: Insights Into Regulatory Gene Expression Roles in Colon Cancer Publisher



Chitgaran S1 ; Mahmoudian RA2 ; Khatami SS1 ; Nasrabadi F1 ; Soltani E3 ; Razavi AE4 ; Kamali F4 ; Bahrami AR1, 5 ; Matin MM1, 6 ; Farshchian M7
Authors
Show Affiliations
Authors Affiliations
  1. 1. Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
  2. 2. Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
  3. 3. Department of Cancer Surgery, Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
  4. 4. Iran National Tumor Bank, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
  5. 5. Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
  6. 6. Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
  7. 7. Stem Cell and Regenerative Medicine Research Group, Academic Center for Education, Culture, and Research (ACECR), Khorasan Razavi, Mashhad, Iran

Source: Iranian Journal of Basic Medical Sciences Published:2025


Abstract

Objective(s): Colorectal cancer is one of the deadliest cancers worldwide, which can be prevented and even cured by early diagnosis and more efficient treatment modalities. Comprehensive transcriptional analysis has highlighted the importance of lncRNAs in CRC tumorigenesis. In this study, we identified co-expressed lncRNA networks based on public RNA sequencing data for biomarker prediction in CRC and then verified the best candidate experimentally. Materials and Methods: Publicly available RNA-sequencing data (BioProject PRJEB27536) of CRC samples and normal adjacent tissues were reanalyzed using the DESeq2 package in R to find differentially expressed lncRNAs. Pathway enrichment and gene network analysis were accomplished using GSEA and WGCNA to identify potential functions of lncRNAs with possible roles in tumorigenesis pathways. Subsequently, the expression of RP11-109D20.2 (lnc-Duox2-1:1) was assessed in fresh/frozen tissues obtained from 46 CRC patients by quantitative RT-PCR. Results: A total of 17939 DElncRNAs were identified between CRC and normal tissues via bioinformatics analyses. A significant up-regulation of RP11-109D20.2 (48%) was observed in CRC samples. Functional enrichment analysis showed that RP11-109D20.2 was mainly related to pathways like phosphoric ester hydrolase, oxidoreductase, phosphoric diester hydrolase, and cyclic-nucleotide phosphodiester activities. Moreover, elevated expression of DUOX2 in tumors with high levels of RP11-109D20.2 suggests a link between these genes. Conclusion: Our data revealed that RP11-109D20.2 may have a considerable role in CRC progression. However, further functional analyses are essential to evaluate the probable role of RP11-109D20.2 as a potential diagnostic marker and its potential role in the dysregulation of cyclic nucleotide phosphodiesterase genes in CRC. © 2025 Mashhad University of Medical Sciences. All rights reserved.
Related Docs
View other Related Docs
1. Deciphering the Oncogenic Landscape: Unveiling the Molecular Machinery and Clinical Significance of Lncrna Tmpo-As1 in Human Cancers, Pathology Research and Practice (2024)
2. Identification of Key Lncrnas Associated With Oxaliplatin Resistance in Colorectal Cancer Cells and Isolated Exosomes: From In-Silico Prediction to In-Vitro Validation, PLoS ONE (2024)
3. 3D Hydrogel-Based Microcapsules As an in Vitro Model to Study Tumorigenicity, Cell Migration and Drug Resistance, Acta Biomaterialia (2022)
4. Prdm12 Is Transcriptionally Active and Required for Nociceptor Function Throughout Life, Frontiers in Molecular Neuroscience (2021)
5. Core Liver Homeostatic Co-Expression Networks Are Preserved But Respond to Perturbations in an Organism- and Disease-Specific Manner, Cell Systems (2021)
6. Hepatogenesis and Hepatocarcinogenesis: Alignment of the Main Signaling Pathways, Journal of Cellular Physiology (2022)
7. Evaluation of the Expression Level of Some Coding and Non-Coding Genes in Breast Cancer Samples Based on Bioinformatics and Laboratory Studies, International Journal of Cancer Management (2024)
8. The Potential of Pik3ca, Kras, Braf, and Apc Hotspot Mutations As a Non-Invasive Detection Method for Colorectal Cancer, Molecular and Cellular Probes (2022)
Experts (# of related papers)
View all Related Experts
Reza Malekzadeh (2)
Habibollah Mahmoodzadeh (2)
Other Related Docs
9. Overexpression of Ddit4 and Tptep1 Are Associated With Metastasis and Advanced Stages in Colorectal Cancer Patients: A Study Utilizing Bioinformatics Prediction and Experimental Validation, Cancer Cell International (2021)
10. Identification of Dysregulated Pathways Underlying Htlv-1-Associated Myelopathy/Tropical Spastic Paraparesis Through Co-Expression Network Analysis, Journal of NeuroVirology (2021)
11. Naringenin: A Potential Flavonoid Phytochemical for Cancer Therapy, Life Sciences (2022)
12. Exploring the Therapeutic Potential of Quercetin in Cancer Treatment: Targeting Long Non-Coding Rnas, Pathology Research and Practice (2024)
13. Integrated Analysis of the Genetic Basis of Suicidal Behavior: What Has Been Shown by Structural Genetic Studies so Far, Psychiatric Genetics (2018)
14. Mrna–Mirna Bipartite Networks Reconstruction in Different Tissues of Bladder Cancer Based on Gene Co-Expression Network Analysis, Scientific Reports (2022)
15. Nlrp3 Inflammasome Pathway in Atherosclerosis: Focusing on the Therapeutic Potential of Non-Coding Rnas, Pathology Research and Practice (2023)
16. Pattern of Participation in Colorectal Cancer Screening From a Population-Based Screening Program in Iran, Archives of Iranian Medicine (2024)
17. Association Between Probiotics and Modulation of Gut Microbial Community Composition in Colorectal Cancer Animal Models: A Systematic Review (2010-2021), Canadian Journal of Infectious Diseases and Medical Microbiology (2023)
18. Constructing Mrna, Mirna, Circrna and Lncrna Regulatory Network by Analysis of Microarray Data in Breast Cancer, Gene Reports (2022)
19. An Overview of Long Noncoding Rnas: Biology, Functions, Therapeutics, Analysis Methods, and Bioinformatics Tools, Cell Biochemistry and Function (2022)
20. Opium Use and Risk of Colorectal Cancer: A Multi-Center Case-Referent Study in Iran, Acta Oncologica (2023)
21. Ube2c: A Pan-Cancer Diagnostic and Prognostic Biomarker Revealed Through Bioinformatics Analysis, Cancer Reports (2024)
22. Colorectal Cancer Screening Program Results in Iran, Medical Journal of the Islamic Republic of Iran (2022)
23. Metformin and Long Non-Coding Rnas in Breast Cancer, Journal of Translational Medicine (2023)
24. Analysis of Sdc2 Gene Promoter Methylation in Whole Blood for Noninvasive Early Detection of Colorectal Cancer, Journal of Cancer Research and Therapeutics (2022)
25. The Role of Long Non-Coding Rna Linc00839 in Oral Squamous Cell Carcinoma Based on Bioinformatics and Experimental Research, Scientific Reports (2024)
26. Identification of Antisense and Sense Rnas of Intracrine Fibroblast Growth Factor Components As Novel Biomarkers in Colorectal Cancer and in Silico Studies for Drug and Nanodrug Repurposing, Environmental Research (2023)
27. Integrative Analysis of Patient-Derived Tumoroids and Ex Vivo Organoid Modelling of Arid1a Loss in Bladder Cancer Reveals Therapeutic Molecular Targets, Cancer Letters (2025)
28. Dysregulation of Ribosome-Related Genes in Ankylosing Spondylitis: A Systems Biology Approach and Experimental Method, BMC Musculoskeletal Disorders (2021)
29. The Dysregulation and Clinical Relevance of Lncrnas Myoslid and Sfta1p in Colorectal Cancer Patients, Molecular Biology Reports (2024)
30. What Do the Genetic Association Data Say About the High Risk of Suicide in People With Depression? a Novel Network-Based Approach to Find Common Molecular Basis for Depression and Suicidal Behavior and Related Therapeutic Targets, Journal of Affective Disorders (2018)
31. Cancer in Iran 2008 to 2025: Recent Incidence Trends and Short-Term Predictions of the Future Burden, International Journal of Cancer (2021)
32. Tissue-Specific Down-Regulation of the Long Non-Coding Rnas Pcat18 and Linc01133 in Gastric Cancer Development, International Journal of Molecular Sciences (2018)
33. Incidence and Risk Factors of Colorectal Cancer in the Iranian Population: A Systematic Review, Journal of Gastrointestinal Cancer (2021)
34. Downregulation of Itm2a Gene Expression in Macrophages of Patients With Ankylosing Spondylitis, International Archives of Allergy and Immunology (2021)
35. Differential Expression Analysis in Epithelial Ovarian Cancer Using Functional Genomics and Integrated Bioinformatics Approaches, Informatics in Medicine Unlocked (2023)
36. Low Expression of Isocitrate Dehydrogenase 1 (Idh1) R132h Is Associated With Advanced Pathological Features in Laryngeal Squamous Cell Carcinoma, Journal of Cancer Research and Clinical Oncology (2023)
37. Identification of Joint Gene Players Implicated in the Pathogenesis of Htlv-1 and Blv Through a Comprehensive System Biology Analysis, Microbial Pathogenesis (2021)
38. Comprehensive Analysis of the Role of Ubiquitin-Specific Peptidases in Colorectal Cancer: A Systematic Review, World Journal of Gastrointestinal Oncology (2024)
39. A Novel Link Between the Oxytocin Receptor Gene and Impulsivity, Neuroscience (2020)
40. Impaired Il-23–Dependent Induction of Ifn-Γ Underlies Mycobacterial Disease in Patients With Inherited Tyk2 Deficiency, Journal of Experimental Medicine (2022)
41. An Integrative Gene Network-Based Approach to Uncover the Cellular and Molecular Infrastructures of Schizophrenia, Life Sciences (2020)
42. Mir-17-92A-1 Cluster Host Gene: A Key Regulator in Colorectal Cancer Development and Progression, Clinical and Experimental Medicine (2024)
43. The Burden of Colorectal Cancer in Yazd Province in 2016, Iranian Journal of Epidemiology (2022)
44. Novel Targets in Rectal Cancer by Considering Lncrna–Mirna–Mrna Network in Response to Lactobacillus Acidophilus Consumption: A Randomized Clinical Trial, Scientific Reports (2022)
45. Nanotopographical Cues of Electrospun Plla Efficiently Modulate Non-Coding Rna Network to Osteogenic Differentiation of Mesenchymal Stem Cells During Bmp Signaling Pathway, Materials Science and Engineering C (2018)
46. Melatonin Targeting Non-Coding Rnas in Cancer: Focus on Mechanisms and Potential Therapeutic Targets, European Journal of Pharmacology (2023)
47. Naturally Nutrient Rich (Nnr) Score and the Risk of Colorectal Cancer: A Case-Control Study, BMJ Open Gastroenterology (2023)
48. Modulation of Colorectal Tumor Behavior Via Lncrna Tp53tg1-Lipidic Nanosystem, Pharmaceutics (2021)
49. Guca2a Dysregulation As a Promising Biomarker for Accurate Diagnosis and Prognosis of Colorectal Cancer, Clinical and Experimental Medicine (2024)
50. Dysregulated Linc01133 Expression in Laryngeal Carcinoma: Prognostic Implications and Predicted Cerna Interactome, Molecular Biology Research Communications (2025)