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Pariyar M, Thorne RF, Scott RJ, Avery-Kiejda KA. Verification and Validation of a Four-Gene Panel as a Prognostic Indicator in Triple Negative Breast Cancer. Front Oncol 2022; 12:821334. [PMID: 35387118 PMCID: PMC8977600 DOI: 10.3389/fonc.2022.821334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/25/2022] [Indexed: 11/15/2022] Open
Abstract
Triple negative breast cancer (TNBC) is a highly aggressive subtype with a high rate of metastasis, early distant recurrence and resistance to therapy leading to worse survival than other breast cancer subtypes. There are no well-established biomarkers that can determine women who will do better and those who are likely to have poorer outcomes with TNBC, nor are there targeted therapies. Thus, the identification of prognostic and/or predictive biomarkers will enable tailored therapies based on their likelihood of disease outcomes and may prevent over- and under-diagnosis. Previous studies from our laboratory have identified four genes (ANP32E, DSC2, ANKRD30A and IL6ST/gp130) that are specific to TNBC and were associated with lymph node metastasis (LNmets), the earliest indicator of tumor progression via distal spread. This study aimed to validate these findings using absolute quantitation by digital droplet PCR (ddPCR) and to determine relationships with clinicopathological features and survival. Our analysis confirmed all four genes displayed significant expression differences between TNBC cases and non-TNBC cases. Moreover, low IL6ST expression was significantly associated with grade 3 disease, hormone receptor negativity and earlier age at diagnosis; low ANKRD30A expression was associated with tumor size; and high ANP32E expression was significantly associated with grade and the number of positive lymph nodes. Individually, three of the four genes were associated with relapse-free survival in TNBC and in combination, all four genes were significantly associated with TNBC survival, but not in hormone receptor-positive cases. Collectively our results suggest that the four genes may have utility in TNBC prognostication.
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Affiliation(s)
- Mamta Pariyar
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Rick F Thorne
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.,Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.,NSW Health Pathology, John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - Kelly A Avery-Kiejda
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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Pariyar M, Johns A, Thorne RF, Scott RJ, Avery-Kiejda KA. Copy number variation in triple negative breast cancer samples associated with lymph node metastasis. Neoplasia 2021; 23:743-753. [PMID: 34225099 PMCID: PMC8259224 DOI: 10.1016/j.neo.2021.05.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/31/2021] [Indexed: 12/24/2022] Open
Abstract
Triple negative breast cancer (TNBC) is a highly metastatic and aggressive subtype of breast cancer and cases presenting with lymph node involvement have worse outcomes. This study aimed to determine the regions of copy number variation (CNV) associated with lymph node metastasis in TNBC patients. CNV analyses were performed in a study cohort of 23 invasive ductal carcinomas (IDCs), 12 lymph node metastases (LNmets), and 7 normal adjacent tissues (NATs); as well as in an independent cohort containing 70 TNBC IDCs and the same 7 NATs. CNV-associated genes were analyzed using GO-enrichment and Pathway analysis. The prognostic role for genes showing CNV-based changes in messenger RNA expression was determined using the Kaplan-Meier plotter database. For the IDCs, there were a number of variations that were common in both the study and independent cohorts in the amplified regions of 1q, 8q, 19 (p and q), 2p, 5p and the deleted regions in 8p followed by 5q, and 19p. The most frequently amplified regions in the LNmets of the study cohort were 4q28.3, 2p, 3q24, 1q21.2, 10p, 12p11.1, 8q, 20p11.22-20p11.21, 21q22.13, 6p22.1 and the most frequently deleted regions were in 1p36.23, 4q21.1 and 5q. A total of 686 (441 amplified and 245 deleted) genes were associated with LNmets. The LNmet-associated genes were highly enriched for “regulation of complement activation,” “regulation of protein activation cascade,” “regulation of humoral immune response,” “oxytocin signalling pathway,” and “TRAIL binding” pathways. Moreover, 6/686 LNmet-associated genes showed CNV-based changes in their mRNA expression of which, high expression of ASPM and KIF14 was significantly associated with worse relapse-free survival. This study has identified several CNV regions in TNBC that could play a major role in metastasis to the lymph node.
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Affiliation(s)
- Mamta Pariyar
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Andrea Johns
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Rick F Thorne
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia; NSW Health Pathology, John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - Kelly A Avery-Kiejda
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.
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Pariyar M, Mathe A, Scott R, Avery-Kiejda K. Abstract P6-10-26: Identification of copy number variation associated with lymph node metastasis in triple negative breast cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p6-10-26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Triple negative breast cancer (TNBC) is a highly metastatic and aggressive subtype of breast cancer which lacks receptors for-estrogen, progesterone and human epidermal growth factor 2. It accounts for approximately 10-20% of all breast cancer cases. It is commonly diagnosed in younger African-American women less than 40 years. There are no targeted therapies for this breast cancer subtype, therefore, chemotherapy and surgery remain the only options for treatment. However, there is a high chance of recurrence within three years of diagnosis and the majority of deaths occurs within the five years of diagnosis. High genomic aberration is a common event in this cancer where the differentially expressed genes in TNBC could be due to the variations in copy number of those genes. The dissemination of primary cancer cells to the lymphatic system represents one of the first signs of meta-static spread. In TNBC, any LN involvement is associated with worse disease-free and overall survival. Therefore, identification of copy number variations (CNVs) within LN metastases in this highly aggressive breast cancer subtype may serve as an indicator of prognosis. Objectives: The aim of the current study was to define regions of copy number gain or loss that are associated with metastasis to the lymph node in TNBC and their association with gene expression. Methods: Partek Genomic Suite was used to analyse the copy number variations in the study cohort containing 23 invasive ductal carcinoma (IDC), 12 lymph node metastasis (LNmets) and 3 normal adjacent tissues (NAT); as well as in validation cohort containing 70 IDC samples (Avery-Kiejda KA, Genom Data.2017;14:1-4).All the breast cancer samples were TNBC. The genomic segmentation algorithm was used for copy number detection. Moreover, their association with gene expression was also analysed using previous gene expression datasets (Accession No.GSE78758). Additionally, GO-enrichment and pathway analysis was performed to identify functional groups and pathways affected by copy number changes. Results: More CNV regions were amplified compared to loss in both the study and the validation cohort. The whole genome copy number profile was similar between IDC and lymph node metastases with 81% (263 in total) of amplified CNVs present in LNmets also present in matched IDCs, implying that many of the alterations in the primary tumour were carried over in metastasis. Very few genes were deleted and of those that were, only 2 were common to IDCs and LNmets. No significant CNVs were observed in NAT. Frequent amplification was mainly observed in chromosome 1q, 8q and 10p whereas the deletion in 4q, 5q and 14q was common in both IDC and metastasis samples. In total, 95 genes (66 gains and 29 losses) were only present in LNmet and not in IDCs from either the study or validation cohorts. According to GO-enrichment analysis, these LNmet associated genes were mainly enriched for DNA-binding transcription activity, cell fate specification and negative regulation of EGFR signalling pathway. Conclusion: This study has identified several regions of CNV in a well-defined TNBC cohort that could play major role in metastasis to lymph node.
Citation Format: Mamta Pariyar, Andrea Mathe, Rodney Scott, Kelly Avery-Kiejda. Identification of copy number variation associated with lymph node metastasis in triple negative breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-10-26.
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Affiliation(s)
- Mamta Pariyar
- Priority Research Centre for Cancer Research, Innovation and Translation, School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Andrea Mathe
- Priority Research Centre for Cancer Research, Innovation and Translation, School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Rodney Scott
- Priority Research Centre for Cancer Research, Innovation and Translation, School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Kelly Avery-Kiejda
- Priority Research Centre for Cancer Research, Innovation and Translation, School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Hunter Medical Research Institute, New Lambton Heights, Australia
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