پیوندهای مفید
آمار
| تعداد نشریات | 32 |
| تعداد شمارهها | 570 |
| تعداد مقالات | 5,520 |
| تعداد مشاهده مقاله | 8,416,885 |
| تعداد دریافت فایل اصل مقاله | 6,194,837 |
High-confidence Mapping and Clustered Patterns of LncRNA-associated SNP Reveal Recurrent Non-coding Variants in Colorectal Cancer Transcriptomes | ||
| Journal of Genetic Resources | ||
| دوره 12، شماره 1، 2026، صفحه 64-73 اصل مقاله (454.12 K) | ||
| نوع مقاله: Research Article | ||
| شناسه دیجیتال (DOI): 10.22080/jgr.2026.30992.1455 | ||
| نویسندگان | ||
| Maryam Esmaeili؛ Malek Hossein Asadi* | ||
| Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran | ||
| تاریخ دریافت: 05 آذر 1404، تاریخ بازنگری: 26 اردیبهشت 1405، تاریخ پذیرش: 07 دی 1404 | ||
| چکیده | ||
| Long non-coding RNAs (lncRNAs) are important regulators of gene expression and cellular homeostasis, yet sequence-level variation within these transcripts remains poorly characterized in colorectal cancer (CRC). Although evidence suggests that lncRNA-embedded variants influence transcriptional regulation and disease progression, the exact mechanistic function of these variants is not well understood. Publicly available CRC transcriptome sequencing libraries were systematically obtained and subjected to rigorous quality control to ensure high analytical reliability. Filtered libraries were aligned to a curated reference set of lncRNA transcripts derived from the RefSeq human genome assembly. Variant detection was carried out using RNA-seq-based variant-calling approaches, followed by stringent filtering based on alternate read depth and genotype confidence to minimize false-positive calls. Recurrence-based filtering, combined with hierarchical clustering of transcriptomes using shared variant profiles, was applied to identify reproducible patterns of sequence variation across independent datasets. Initial variant detection identified more than one hundred thousand candidate single nucleotide variants within lncRNA transcripts. Application of depth-, confidence-, and recurrence-based filtering substantially reduced this set to a focused catalogue of highly recurrent variants shared across multiple transcriptome clusters. In total, 549 high-confidence single nucleotide variants distributed across 99 lncRNAs were identified. Several of the transcript-embedded variants have been previously implicated in CRC biology, supporting the biological relevance of the detected variants. These findings demonstrated that expressed lncRNA-associated SNPs are non-randomly distributed in CRC transcriptomes and potentially accumulate in non-coding variant hotspots. This study provides a scalable framework for prioritizing recurrent lncRNA-associated sequence variants and offers a resource for future functional validation, biomarker-oriented analyses, and precision oncology studies in CRC. | ||
| کلیدواژهها | ||
| Colorectal cancer؛ Long non-coding RNA؛ Non-coding variants, RNA sequencing | ||
| مراجع | ||
|
Andrabi, M. Q., Kesavan, Y., & Ramalingam, S. (2024). Non-coding RNAs as biomarkers for survival in CRC patients. Current Aging Science, 17(1), 5-15. https://doi.org/10.2174/1874609816666230202101054
Bian, Z., Zhang, J., Li, M., Feng, Y., Wang, X., Zhang, J., ... & Huang, Z. (2018). LncRNA-FEZF1-AS1 promotes tumor proliferation and metastasis in colorectal cancer by regulating PKM2 signaling. Clinical Cancer Research, 24(19), 4808-4819. https://doi.org/10.1158/1078-0432.CCR-17-2967
Chen, W., Liu, X., Wu, Z., Tan, H., Yu, F., Wang, D., ... & Chen, Z. (2025). Unveiling the diagnostic power of lncRNAs in colorectal cancer: a meta-analysis. BioMedical Engineering OnLine, 24(1), 103. https://doi.org/10.1186/s12938-025-01431-3
Du, D., Shen, X., Zhang, Y., Yin, L., Pu, Y., & Liang, G. (2020). Expression of long non-coding RNA SFTA1P and its function in non-small cell lung cancer. Pathology-Research and Practice, 216(9), 153049. https://doi.org/10.1016/j.prp.2020.153049
He, F., Wei, R., Zhou, Z., Huang, L., Wang, Y., Tang, J., ... & Su, Z. (2019). Integrative analysis of somatic mutations in non-coding regions altering RNA secondary structures in cancer genomes. Scientific Reports, 9(1), 8205. https://doi.org/10.1038/s41598-019-44489-5
Hennig, E. E., Kluska, A., Piątkowska, M., Kulecka, M., Bałabas, A., Zeber-Lubecka, N., ... & Ostrowski, J. (2021). GWAS links new variant in long non-coding RNA LINC02006 with colorectal cancer susceptibility. Biology, 10(6), 465. https://doi.org/10.3390/biology10060465
Kerachian, M. A., & Azghandi, M. (2022). Identification of long non-coding RNA using single nucleotide epimutation analysis: A novel gene discovery approach. Cancer Cell International, 22(1), 337. https://doi.org/10.1186/s12935-022-02752-2
Liu, H., Li, Y., Karsidag, M., Tu, T., & Wang, P. (2025). Technical and biological biases in bulk transcriptomic data mining for cancer research. Journal of Cancer, 16(1), 34-43. https://doi.org/10.7150/jca.100922
Liu, Y., Liu, B., Jin, G., Zhang, J., Wang, X., Feng, Y., ... & Huang, Z. (2019). An integrated three-long non-coding RNA signature predicts prognosis in colorectal cancer patients. Frontiers in Oncology, 9, 1269. https://doi.org/10.3389/fonc.2019.01269
Lulli, M., Napoli, C., Landini, I., Mini, E., & Lapucci, A. (2022). Role of non-coding RNAs in colorectal cancer: Focus on long non-coding RNAs. International Journal of Molecular Sciences, 23(21), 13431. https://doi.org/10.3390/ijms232113431
Minotti, L., Agnoletto, C., Baldassari, F., Corra, F., & Volinia, S. (2018). SNPs and somatic mutations in long non-coding RNAs: a new frontier in cancer studies? High-Throughput, 7(4), 34. https://doi.org/10.3390/ht7040034
Tang, C., Liu, J., Hu, Q., Zeng, S., & Yu, L. (2021). Metastatic colorectal cancer: Perspectives on long non-coding RNAs and promising therapeutics. European Journal of Pharmacology, 908, 174367. https://doi.org/10.1016/j.ejphar.2021.174367
Tufail, M. (2023). HOTAIR in colorectal cancer: Structure, function, and therapeutic potential. Medical Oncology, 40(9), 259. https://doi.org/10.1007/s12032-023-02131-5
Wu, Y., & Xu, X. (2023). Long non-coding RNA signature in colorectal cancer: Research progression and clinical application. Cancer Cell International, 23(1), 28. https://doi.org/10.1186/s12935-023-02867-0
Yan, T., Shen, C., Jiang, P., Yu, C., Guo, F., Tian, X., ... & Fang, J. Y. (2021). Risk SNP-induced lncRNA-SLCC1 drives colorectal cancer through activating glycolysis signaling. Signal Transduction and Targeted Therapy, 6(1), 70. https://doi.org/10.1038/s41392-020-00446-7
Zhang, Z., Gu, M., Gu, Z., & Lou, Y. R. (2021). Role of long non-coding RNA polymorphisms in cancer chemotherapeutic response. Journal of Personalized Medicine, 11(6), 513. https://doi.org/10.3390/jpm11060513
Zhou, H., Hao, X., Zhang, P., & He, S. (2023). Noncoding RNA mutations in cancer. Wiley Interdisciplinary Reviews: RNA, 14(6), e1812. https://doi.org/10.1002/wrna.1812 | ||
|
آمار تعداد مشاهده مقاله: 2 تعداد دریافت فایل اصل مقاله: 1 |
||