Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation
Abstract Breast cancer is a major global health concern, and recent researches have highlighted the critical roles of non-coding RNAs in both cancer and the immune system. The competing endogenous RNA hypothesis suggests that various types of RNA, including coding and non-coding RNAs, compete for mi...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-11-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-47816-z |
| _version_ | 1797415387518730240 |
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| author | Alireza Shariatmadar Taleghani Yasaman Zohrab Beigi Fatemeh Zare-Mirakabad Ali Masoudi-Nejad |
| author_facet | Alireza Shariatmadar Taleghani Yasaman Zohrab Beigi Fatemeh Zare-Mirakabad Ali Masoudi-Nejad |
| author_sort | Alireza Shariatmadar Taleghani |
| collection | DOAJ |
| description | Abstract Breast cancer is a major global health concern, and recent researches have highlighted the critical roles of non-coding RNAs in both cancer and the immune system. The competing endogenous RNA hypothesis suggests that various types of RNA, including coding and non-coding RNAs, compete for microRNA targets, acting as molecular sponges. This study introduces the Pre_CLM_BCS pipeline to investigate the potential of long non-coding RNAs and circular RNAs as biomarkers in breast cancer subtypes. The pipeline identifies specific modules within each subtype that contain at least one long non-coding RNA or circular RNA exhibiting significantly distinct expression patterns when compared to other subtypes. The results reveal potential biomarker genes for each subtype, such as circ_001845, circ_001124, circ_003925, circ_000736, and circ_003996 for the basal-like subtype, circ_00306 and circ_00128 for the luminal B subtype, circ_000709 and NPHS1 for the normal-like subtype, CAMKV and circ_001855 for the luminal A subtype, and circ_00128 and circ_00173 for the HER2+ subtype. Additionally, certain long non-coding RNAs and circular RNAs, including RGS5-AS1, C6orf223, HHLA3-AS1, circ_000349, circ_003996, circ_003925, circ_002665, circ_001855, and DLEU1, are identified as potential regulators of T cell mechanisms, underscoring their importance in understanding breast cancer progression in various subtypes. This pipeline provides valuable insights into cancer and immune-related processes in breast cancer subtypes. |
| first_indexed | 2024-03-09T05:47:55Z |
| format | Article |
| id | doaj.art-2ab520fac3df42cba2661badb2181dd4 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-09T05:47:55Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-2ab520fac3df42cba2661badb2181dd42023-12-03T12:19:42ZengNature PortfolioScientific Reports2045-23222023-11-0113111610.1038/s41598-023-47816-zExploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulationAlireza Shariatmadar Taleghani0Yasaman Zohrab Beigi1Fatemeh Zare-Mirakabad2Ali Masoudi-Nejad3Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of TehranLaboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of TehranDepartment of Mathematics and Computer Science, Amirkabir University of Technology (Polytechnic Tehran)Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of TehranAbstract Breast cancer is a major global health concern, and recent researches have highlighted the critical roles of non-coding RNAs in both cancer and the immune system. The competing endogenous RNA hypothesis suggests that various types of RNA, including coding and non-coding RNAs, compete for microRNA targets, acting as molecular sponges. This study introduces the Pre_CLM_BCS pipeline to investigate the potential of long non-coding RNAs and circular RNAs as biomarkers in breast cancer subtypes. The pipeline identifies specific modules within each subtype that contain at least one long non-coding RNA or circular RNA exhibiting significantly distinct expression patterns when compared to other subtypes. The results reveal potential biomarker genes for each subtype, such as circ_001845, circ_001124, circ_003925, circ_000736, and circ_003996 for the basal-like subtype, circ_00306 and circ_00128 for the luminal B subtype, circ_000709 and NPHS1 for the normal-like subtype, CAMKV and circ_001855 for the luminal A subtype, and circ_00128 and circ_00173 for the HER2+ subtype. Additionally, certain long non-coding RNAs and circular RNAs, including RGS5-AS1, C6orf223, HHLA3-AS1, circ_000349, circ_003996, circ_003925, circ_002665, circ_001855, and DLEU1, are identified as potential regulators of T cell mechanisms, underscoring their importance in understanding breast cancer progression in various subtypes. This pipeline provides valuable insights into cancer and immune-related processes in breast cancer subtypes.https://doi.org/10.1038/s41598-023-47816-z |
| spellingShingle | Alireza Shariatmadar Taleghani Yasaman Zohrab Beigi Fatemeh Zare-Mirakabad Ali Masoudi-Nejad Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation Scientific Reports |
| title | Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation |
| title_full | Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation |
| title_fullStr | Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation |
| title_full_unstemmed | Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation |
| title_short | Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation |
| title_sort | exploring cerna networks for key biomarkers in breast cancer subtypes and immune regulation |
| url | https://doi.org/10.1038/s41598-023-47816-z |
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