Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development
Invasive ductal carcinoma (IDC) is a major histo-morphologic type of breast cancer. Histological grading (HG) of IDC is widely adopted by oncologists as a prognostic factor. However, HG evaluation is highly subjective with only 50%–85% inter-observer agreements. Specifically, the subjectivity in the...
| Principais autores: | , , , , , |
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| Formato: | Journal Article |
| Idioma: | English |
| Publicado em: |
2015
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| Acesso em linha: | https://hdl.handle.net/10356/81038 http://hdl.handle.net/10220/39116 |
| _version_ | 1826121537176993792 |
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| author | Aswad, Luay Yenamandra, Surya Pavan Ow, Ghim Siong Grinchuk, Oleg Ivshina, Anna V. Kuznetsov, Vladimir A. |
| author2 | School of Computer Engineering |
| author_facet | School of Computer Engineering Aswad, Luay Yenamandra, Surya Pavan Ow, Ghim Siong Grinchuk, Oleg Ivshina, Anna V. Kuznetsov, Vladimir A. |
| author_sort | Aswad, Luay |
| collection | NTU |
| description | Invasive ductal carcinoma (IDC) is a major histo-morphologic type of breast cancer. Histological grading (HG) of IDC is widely adopted by oncologists as a prognostic factor. However, HG evaluation is highly subjective with only 50%–85% inter-observer agreements. Specifically, the subjectivity in the assignment of the intermediate grade (histologic grade 2, HG2) breast cancers (comprising ~50% of IDC cases) results in uncertain disease outcome prediction and sub-optimal systemic therapy. Despite several attempts to identify the mechanisms underlying the HG classification, their molecular bases are poorly understood. We performed integrative bioinformatics analysis of TCGA and several other cohorts (total 1246 patients). We identified a 22-gene tumor aggressiveness grading classifier (22g-TAG) that reflects global bifurcation in the IDC transcriptomes and reclassified patients with HG2 tumors into two genetically and clinically distinct subclasses: histological grade 1-like (HG1-like) and histological grade 3-like (HG3-like). The expression profiles and clinical outcomes of these subclasses were similar to the HG1 and HG3 tumors, respectively. We further reclassified IDC into low genetic grade (LGG = HG1+HG1-like) and high genetic grade (HGG = HG3-like+HG3) subclasses. For the HG1-like and HG3-like IDCs we found subclass-specific DNA alterations, somatic mutations, oncogenic pathways, cell cycle/mitosis and stem cell-like expression signatures that discriminate between these tumors. We found similar molecular patterns in the LGG and HGG tumor classes respectively. Our results suggest the existence of two genetically-predefined IDC classes, LGG and HGG, driven by distinct oncogenic pathways. They provide novel prognostic and therapeutic biomarkers and could open unique opportunities for personalized systemic therapies of IDC patients. |
| first_indexed | 2024-10-01T05:33:51Z |
| format | Journal Article |
| id | ntu-10356/81038 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:33:51Z |
| publishDate | 2015 |
| record_format | dspace |
| spelling | ntu-10356/810382022-02-16T16:26:39Z Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development Aswad, Luay Yenamandra, Surya Pavan Ow, Ghim Siong Grinchuk, Oleg Ivshina, Anna V. Kuznetsov, Vladimir A. School of Computer Engineering Invasive ductal carcinoma Low and high genetic grades Genome and transcriptome alterations Mutations Oncogenic pathway Invasive ductal carcinoma (IDC) is a major histo-morphologic type of breast cancer. Histological grading (HG) of IDC is widely adopted by oncologists as a prognostic factor. However, HG evaluation is highly subjective with only 50%–85% inter-observer agreements. Specifically, the subjectivity in the assignment of the intermediate grade (histologic grade 2, HG2) breast cancers (comprising ~50% of IDC cases) results in uncertain disease outcome prediction and sub-optimal systemic therapy. Despite several attempts to identify the mechanisms underlying the HG classification, their molecular bases are poorly understood. We performed integrative bioinformatics analysis of TCGA and several other cohorts (total 1246 patients). We identified a 22-gene tumor aggressiveness grading classifier (22g-TAG) that reflects global bifurcation in the IDC transcriptomes and reclassified patients with HG2 tumors into two genetically and clinically distinct subclasses: histological grade 1-like (HG1-like) and histological grade 3-like (HG3-like). The expression profiles and clinical outcomes of these subclasses were similar to the HG1 and HG3 tumors, respectively. We further reclassified IDC into low genetic grade (LGG = HG1+HG1-like) and high genetic grade (HGG = HG3-like+HG3) subclasses. For the HG1-like and HG3-like IDCs we found subclass-specific DNA alterations, somatic mutations, oncogenic pathways, cell cycle/mitosis and stem cell-like expression signatures that discriminate between these tumors. We found similar molecular patterns in the LGG and HGG tumor classes respectively. Our results suggest the existence of two genetically-predefined IDC classes, LGG and HGG, driven by distinct oncogenic pathways. They provide novel prognostic and therapeutic biomarkers and could open unique opportunities for personalized systemic therapies of IDC patients. ASTAR (Agency for Sci., Tech. and Research, S’pore) Published version 2015-12-17T02:43:06Z 2019-12-06T14:20:05Z 2015-12-17T02:43:06Z 2019-12-06T14:20:05Z 2015 Journal Article Aswad, L., Yenamandra, S. P., Ow, G. S., Grinchuk, O., Ivshina, A. V., & Kuznetsov V. A. (2015). Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development. Oncotarget, 6(34), 36652-. https://hdl.handle.net/10356/81038 http://hdl.handle.net/10220/39116 10.18632/oncotarget.5543 26474389 en Oncotarget All site content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 License. 23 p. application/pdf |
| spellingShingle | Invasive ductal carcinoma Low and high genetic grades Genome and transcriptome alterations Mutations Oncogenic pathway Aswad, Luay Yenamandra, Surya Pavan Ow, Ghim Siong Grinchuk, Oleg Ivshina, Anna V. Kuznetsov, Vladimir A. Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development |
| title | Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development |
| title_full | Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development |
| title_fullStr | Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development |
| title_full_unstemmed | Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development |
| title_short | Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development |
| title_sort | genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development |
| topic | Invasive ductal carcinoma Low and high genetic grades Genome and transcriptome alterations Mutations Oncogenic pathway |
| url | https://hdl.handle.net/10356/81038 http://hdl.handle.net/10220/39116 |
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