Dysregulated Long Non-Coding RNAs in Colorectal Cancer: Identification and Validation Using RNA-seq and Real-Time Reverse Transcription Polymerase Chain Reaction
Objective: Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancerrelated deaths worldwide, posing a significant public health challenge. Recent advances in molecular research and technologies have highlighted the potential of long non-coding RNAs (lncRNAs) as...
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| Format: | Article |
| Language: | English |
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Royan Institute (ACECR), Tehran
2024-12-01
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| Series: | Cell Journal |
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| Online Access: | https://www.celljournal.org/article_723849_d41d8cd98f00b204e9800998ecf8427e.pdf |
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| author | Reyhaneh Dehghanzad Roghayeh Rahbar Parvaneh Mohammad Keramatipour Sepideh Kadkhoda Mohsen Aghajanpour Reza Taslimi Leyla Sahebi Abbas Shakoori Farahani |
| author_facet | Reyhaneh Dehghanzad Roghayeh Rahbar Parvaneh Mohammad Keramatipour Sepideh Kadkhoda Mohsen Aghajanpour Reza Taslimi Leyla Sahebi Abbas Shakoori Farahani |
| author_sort | Reyhaneh Dehghanzad |
| collection | DOAJ |
| description | Objective: Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancerrelated deaths worldwide, posing a significant public health challenge. Recent advances in molecular research and technologies have highlighted the potential of long non-coding RNAs (lncRNAs) as key players in CRC development and progression. High-throughput technologies, such as RNA sequencing (RNA-seq), enable comprehensive analysis of cancer omics data, providing valuable insights into CRC biology. This study aimed to identify and validate lncRNAs with potential roles in CRC pathogenesis.Materials and Methods: In this experimental study, we conducted RNA-seq analysis using data from The Cancer Genome Atlas (TCGA) to identify differentially expressed lncRNAs between 481 CRC and 41 healthy control samples. Using the Boruta feature selection algorithm, we identified statistically significant lncRNAs. Based on a comprehensive literature review, four lncRNAs (LINC01730, LINC02487, LINC01836, and LINC01594) were selected for experimental validation. Real-time reverse transcription polymerase chain reaction (RT-PCR) was performed on 10 primary CRC and 9 normal colorectal tissue samples to quantify the expression of these lncRNAs. Additionally, bioinformatic analyses were conducted to explore molecular pathways associated with these lncRNAs in CRC.Results: RNA-seq analysis identified 388 differentially expressed lncRNAs in CRC tissues compared to healthy controls. Among these, four lncRNAs (LINC01730, LINC02487, LINC01836, and LINC01594) were validated through real-time RT-PCR, confirming their significant upregulation in CRC tissues. Bioinformatic analysis revealed their potential involvement in molecular pathways critical to tumor growth and metastasis.Conclusion: This study identified and validated four significantly upregulated lncRNAs (LINC01730, LINC02487, LINC01836, and LINC01594) in CRC tissues, providing evidence of their potential roles in CRC pathogenesis. These lncRNAs could serve as promising candidates for future biomarker development and therapeutic research in colorectal cancer. |
| format | Article |
| id | doaj-art-c0b570e7149044b1be8d930812d0ffb9 |
| institution | OA Journals |
| issn | 2228-5806 2228-5814 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Royan Institute (ACECR), Tehran |
| record_format | Article |
| series | Cell Journal |
| spelling | doaj-art-c0b570e7149044b1be8d930812d0ffb92025-08-20T02:35:36ZengRoyan Institute (ACECR), TehranCell Journal2228-58062228-58142024-12-01261270071010.22074/cellj.2025.2042114.1684723849Dysregulated Long Non-Coding RNAs in Colorectal Cancer: Identification and Validation Using RNA-seq and Real-Time Reverse Transcription Polymerase Chain ReactionReyhaneh Dehghanzad0Roghayeh Rahbar Parvaneh1Mohammad Keramatipour2Sepideh Kadkhoda3Mohsen Aghajanpour4Reza Taslimi5Leyla Sahebi6Abbas Shakoori Farahani7Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, IranDepartment of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, IranWatson Genetic Laboratory, North Kargar Street, Tehran, IranDepartment of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, IranDepartment of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, IranDepartment of Gastroenterology, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, IranMaternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, IranDepartment of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, IranObjective: Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancerrelated deaths worldwide, posing a significant public health challenge. Recent advances in molecular research and technologies have highlighted the potential of long non-coding RNAs (lncRNAs) as key players in CRC development and progression. High-throughput technologies, such as RNA sequencing (RNA-seq), enable comprehensive analysis of cancer omics data, providing valuable insights into CRC biology. This study aimed to identify and validate lncRNAs with potential roles in CRC pathogenesis.Materials and Methods: In this experimental study, we conducted RNA-seq analysis using data from The Cancer Genome Atlas (TCGA) to identify differentially expressed lncRNAs between 481 CRC and 41 healthy control samples. Using the Boruta feature selection algorithm, we identified statistically significant lncRNAs. Based on a comprehensive literature review, four lncRNAs (LINC01730, LINC02487, LINC01836, and LINC01594) were selected for experimental validation. Real-time reverse transcription polymerase chain reaction (RT-PCR) was performed on 10 primary CRC and 9 normal colorectal tissue samples to quantify the expression of these lncRNAs. Additionally, bioinformatic analyses were conducted to explore molecular pathways associated with these lncRNAs in CRC.Results: RNA-seq analysis identified 388 differentially expressed lncRNAs in CRC tissues compared to healthy controls. Among these, four lncRNAs (LINC01730, LINC02487, LINC01836, and LINC01594) were validated through real-time RT-PCR, confirming their significant upregulation in CRC tissues. Bioinformatic analysis revealed their potential involvement in molecular pathways critical to tumor growth and metastasis.Conclusion: This study identified and validated four significantly upregulated lncRNAs (LINC01730, LINC02487, LINC01836, and LINC01594) in CRC tissues, providing evidence of their potential roles in CRC pathogenesis. These lncRNAs could serve as promising candidates for future biomarker development and therapeutic research in colorectal cancer.https://www.celljournal.org/article_723849_d41d8cd98f00b204e9800998ecf8427e.pdfcolorectal cancerlong non-coding rnasreal-time reverse transcription polymerase chain reactionrna sequencing analysis |
| spellingShingle | Reyhaneh Dehghanzad Roghayeh Rahbar Parvaneh Mohammad Keramatipour Sepideh Kadkhoda Mohsen Aghajanpour Reza Taslimi Leyla Sahebi Abbas Shakoori Farahani Dysregulated Long Non-Coding RNAs in Colorectal Cancer: Identification and Validation Using RNA-seq and Real-Time Reverse Transcription Polymerase Chain Reaction Cell Journal colorectal cancer long non-coding rnas real-time reverse transcription polymerase chain reaction rna sequencing analysis |
| title | Dysregulated Long Non-Coding RNAs in Colorectal Cancer: Identification and Validation Using RNA-seq and Real-Time Reverse Transcription Polymerase Chain Reaction |
| title_full | Dysregulated Long Non-Coding RNAs in Colorectal Cancer: Identification and Validation Using RNA-seq and Real-Time Reverse Transcription Polymerase Chain Reaction |
| title_fullStr | Dysregulated Long Non-Coding RNAs in Colorectal Cancer: Identification and Validation Using RNA-seq and Real-Time Reverse Transcription Polymerase Chain Reaction |
| title_full_unstemmed | Dysregulated Long Non-Coding RNAs in Colorectal Cancer: Identification and Validation Using RNA-seq and Real-Time Reverse Transcription Polymerase Chain Reaction |
| title_short | Dysregulated Long Non-Coding RNAs in Colorectal Cancer: Identification and Validation Using RNA-seq and Real-Time Reverse Transcription Polymerase Chain Reaction |
| title_sort | dysregulated long non coding rnas in colorectal cancer identification and validation using rna seq and real time reverse transcription polymerase chain reaction |
| topic | colorectal cancer long non-coding rnas real-time reverse transcription polymerase chain reaction rna sequencing analysis |
| url | https://www.celljournal.org/article_723849_d41d8cd98f00b204e9800998ecf8427e.pdf |
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