Inferences of Individual Drug Response-Related Long Non-coding RNAs Based on Integrating Multi-omics Data in Breast Cancer
Differences in individual drug responses are obstacles in breast cancer (BRCA) treatment, so predicting responses would help to plan treatment strategies. The accumulation of cancer molecular profiling and drug response data provide opportunities and challenges to identify novel molecular signatures...
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| Format: | Article |
| Language: | English |
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Elsevier
2020-06-01
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| Series: | Molecular Therapy: Nucleic Acids |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2162253120300810 |
| _version_ | 1818216171950833664 |
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| author | Hao Cui Hanqing Kong Fuhui Peng Chunjing Wang Dandan Zhang Jiawei Tian Lei Zhang |
| author_facet | Hao Cui Hanqing Kong Fuhui Peng Chunjing Wang Dandan Zhang Jiawei Tian Lei Zhang |
| author_sort | Hao Cui |
| collection | DOAJ |
| description | Differences in individual drug responses are obstacles in breast cancer (BRCA) treatment, so predicting responses would help to plan treatment strategies. The accumulation of cancer molecular profiling and drug response data provide opportunities and challenges to identify novel molecular signatures and mechanisms of tumor responsiveness to drugs in BRCA. This study evaluated drug responses with a multi-omics integrated system that depended on long non-coding RNAs (lncRNAs). We identified drug response-related lncRNAs (DRlncs) by combining expression data of lncRNA, microRNA, messenger RNA, methylation levels, somatic mutations, and the survival data of cancer patients treated with drugs. We constructed an integrated and computational multi-omics approach to identify DRlncs for diverse chemotherapeutic drugs in BRCA. Some DRlncs were identified with Adriamycin, Cytoxan, Tamoxifen, and all samples for BRCA patients. These DRlncs showed specific features regarding both expression and computational accuracies. The DRlnc-gene co-expression networks were constructed and analyzed. Key DRlncs, such as HOXA-AS2 (Ensembl: ENSG00000253552), in the drug Adriamycin were characterized. The experimental analysis also suggested that HOXA-AS2 (Ensembl: ENSG00000253552) was a key DRlnc in Adriamycin drug resistance in BRCA patients. Some DRlncs were associated with survival and some specific functions. A possible mechanism of DRlnc HOXA-AS2 (Ensembl: ENSG00000253552) in the Adriamycin drug response for BRCA resistance was inferred. In summary, this study provides a framework for lncRNA-based evaluation of clinical drug responses in BRCA. Understanding the underlying molecular mechanisms of drug responses will facilitate improved responses to chemotherapy and outcomes of BRCA treatment. |
| first_indexed | 2024-12-12T06:47:44Z |
| format | Article |
| id | doaj.art-940844be64dd44b599dd61c57b75feac |
| institution | Directory Open Access Journal |
| issn | 2162-2531 |
| language | English |
| last_indexed | 2024-12-12T06:47:44Z |
| publishDate | 2020-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Molecular Therapy: Nucleic Acids |
| spelling | doaj.art-940844be64dd44b599dd61c57b75feac2022-12-22T00:34:08ZengElsevierMolecular Therapy: Nucleic Acids2162-25312020-06-0120128139Inferences of Individual Drug Response-Related Long Non-coding RNAs Based on Integrating Multi-omics Data in Breast CancerHao Cui0Hanqing Kong1Fuhui Peng2Chunjing Wang3Dandan Zhang4Jiawei Tian5Lei Zhang6Department of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, ChinaDepartment of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, ChinaDepartment of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, ChinaDepartment of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, ChinaDepartment of Ultrasound, Heilongjiang Provincial Hospital, Harbin 150081, ChinaDepartment of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China; Corresponding author: Jiawei Tian, Department of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China.Department of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China; Corresponding author: Lei Zhang, Department of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China.Differences in individual drug responses are obstacles in breast cancer (BRCA) treatment, so predicting responses would help to plan treatment strategies. The accumulation of cancer molecular profiling and drug response data provide opportunities and challenges to identify novel molecular signatures and mechanisms of tumor responsiveness to drugs in BRCA. This study evaluated drug responses with a multi-omics integrated system that depended on long non-coding RNAs (lncRNAs). We identified drug response-related lncRNAs (DRlncs) by combining expression data of lncRNA, microRNA, messenger RNA, methylation levels, somatic mutations, and the survival data of cancer patients treated with drugs. We constructed an integrated and computational multi-omics approach to identify DRlncs for diverse chemotherapeutic drugs in BRCA. Some DRlncs were identified with Adriamycin, Cytoxan, Tamoxifen, and all samples for BRCA patients. These DRlncs showed specific features regarding both expression and computational accuracies. The DRlnc-gene co-expression networks were constructed and analyzed. Key DRlncs, such as HOXA-AS2 (Ensembl: ENSG00000253552), in the drug Adriamycin were characterized. The experimental analysis also suggested that HOXA-AS2 (Ensembl: ENSG00000253552) was a key DRlnc in Adriamycin drug resistance in BRCA patients. Some DRlncs were associated with survival and some specific functions. A possible mechanism of DRlnc HOXA-AS2 (Ensembl: ENSG00000253552) in the Adriamycin drug response for BRCA resistance was inferred. In summary, this study provides a framework for lncRNA-based evaluation of clinical drug responses in BRCA. Understanding the underlying molecular mechanisms of drug responses will facilitate improved responses to chemotherapy and outcomes of BRCA treatment.http://www.sciencedirect.com/science/article/pii/S2162253120300810breast cancerdrug responselong non-coding RNAsmulti-omics integrationprognosis |
| spellingShingle | Hao Cui Hanqing Kong Fuhui Peng Chunjing Wang Dandan Zhang Jiawei Tian Lei Zhang Inferences of Individual Drug Response-Related Long Non-coding RNAs Based on Integrating Multi-omics Data in Breast Cancer Molecular Therapy: Nucleic Acids breast cancer drug response long non-coding RNAs multi-omics integration prognosis |
| title | Inferences of Individual Drug Response-Related Long Non-coding RNAs Based on Integrating Multi-omics Data in Breast Cancer |
| title_full | Inferences of Individual Drug Response-Related Long Non-coding RNAs Based on Integrating Multi-omics Data in Breast Cancer |
| title_fullStr | Inferences of Individual Drug Response-Related Long Non-coding RNAs Based on Integrating Multi-omics Data in Breast Cancer |
| title_full_unstemmed | Inferences of Individual Drug Response-Related Long Non-coding RNAs Based on Integrating Multi-omics Data in Breast Cancer |
| title_short | Inferences of Individual Drug Response-Related Long Non-coding RNAs Based on Integrating Multi-omics Data in Breast Cancer |
| title_sort | inferences of individual drug response related long non coding rnas based on integrating multi omics data in breast cancer |
| topic | breast cancer drug response long non-coding RNAs multi-omics integration prognosis |
| url | http://www.sciencedirect.com/science/article/pii/S2162253120300810 |
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