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Meyer B, Stirzaker C, Ramkomuth S, Harvey K, Chan B, Lee CS, Karim R, Deng N, Avery-Kiejda KA, Scott RJ, Lakhani S, Fox S, Robbins E, Shin JS, Beith J, Gill A, Sioson L, Chan C, Krishnaswamy M, Cooper C, Warrier S, Mak C, Rasko JE, Bailey CG, Swarbrick A, Clark SJ, O'Toole S, Pidsley R. Detailed DNA methylation characterisation of phyllodes tumours identifies a signature of malignancy and distinguishes phyllodes from metaplastic breast carcinoma. J Pathol 2024; 262:480-494. [PMID: 38300122 DOI: 10.1002/path.6250] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/03/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Phyllodes tumours (PTs) are rare fibroepithelial lesions of the breast that are classified as benign, borderline, or malignant. As little is known about the molecular underpinnings of PTs, current diagnosis relies on histological examination. However, accurate classification is often difficult, particularly for distinguishing borderline from malignant PTs. Furthermore, PTs can be misdiagnosed as other tumour types with shared histological features, such as fibroadenoma and metaplastic breast cancers. As DNA methylation is a recognised hallmark of many cancers, we hypothesised that DNA methylation could provide novel biomarkers for diagnosis and tumour stratification in PTs, whilst also allowing insight into the molecular aetiology of this otherwise understudied tumour. We generated whole-genome methylation data using the Illumina EPIC microarray in a novel PT cohort (n = 33) and curated methylation microarray data from published datasets including PTs and other potentially histopathologically similar tumours (total n = 817 samples). Analyses revealed that PTs have a unique methylome compared to normal breast tissue and to potentially histopathologically similar tumours (metaplastic breast cancer, fibroadenoma and sarcomas), with PT-specific methylation changes enriched in gene sets involved in KRAS signalling and epithelial-mesenchymal transition. Next, we identified 53 differentially methylated regions (DMRs) (false discovery rate < 0.05) that specifically delineated malignant from non-malignant PTs. The top DMR in both discovery and validation cohorts was hypermethylation at the HSD17B8 CpG island promoter. Matched PT single-cell expression data showed that HSD17B8 had minimal expression in fibroblast (putative tumour) cells. Finally, we created a methylation classifier to distinguish PTs from metaplastic breast cancer samples, where we revealed a likely misdiagnosis for two TCGA metaplastic breast cancer samples. In conclusion, DNA methylation alterations are associated with PT histopathology and hold the potential to improve our understanding of PT molecular aetiology, diagnostics, and risk stratification. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Braydon Meyer
- Epigenetics Research Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Sonny Ramkomuth
- Tumour Progression Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Kate Harvey
- Tumour Progression Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Belinda Chan
- Department of Surgery, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia
| | - Cheok Soon Lee
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Department of Anatomical Pathology and Molecular Pathology Laboratory, Liverpool Hospital, Liverpool, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Liverpool, New South Wales, Australia
| | - Rooshdiya Karim
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Niantao Deng
- Tumour Progression Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Kelly A Avery-Kiejda
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia
| | - Rodney J Scott
- Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Sunil Lakhani
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Stephen Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Elizabeth Robbins
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Joo-Shik Shin
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Jane Beith
- Psycho-Oncology Co-Operative Group (PoCoG), University of Sydney, Sydney, New South Wales, Australia
- Chris O'Brien Lifehouse, Sydney, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
| | - Anthony Gill
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Sydney Medical School, University of Sydney, St Leonards, New South Wales, Australia
| | - Loretta Sioson
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Sydney Medical School, University of Sydney, St Leonards, New South Wales, Australia
| | - Charles Chan
- NSW Health Pathology, Department of Anatomical Pathology, Concord Repatriation General Hospital, Sydney, New South Wales, Australia
- Concord Clinical School, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Mrudula Krishnaswamy
- NSW Health Pathology, Department of Anatomical Pathology, Concord Repatriation General Hospital, Sydney, New South Wales, Australia
- Concord Clinical School, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Caroline Cooper
- Anatomical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
- Faculty of Medicine, The University of Queensland, St Lucia, Queensland, Australia
| | - Sanjay Warrier
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Medical Program, The University of Sydney, Sydney, New South Wales, Australia
- Department of Breast Surgery, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia
| | - Cindy Mak
- Faculty of Medicine, The University of Queensland, St Lucia, Queensland, Australia
- Department of Breast Surgery, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia
| | - John Ej Rasko
- Faculty of Medicine, The University of Queensland, St Lucia, Queensland, Australia
- Department of Cell and Molecular Therapies, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
- Gene and Stem Cell Therapy Program, Centenary Institute, Sydney, New South Wales, Australia
| | - Charles G Bailey
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Gene and Stem Cell Therapy Program, Centenary Institute, Sydney, New South Wales, Australia
- Cancer and Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, New South Wales, Australia
| | - Alexander Swarbrick
- St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
- Tumour Progression Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Sandra O'Toole
- Tumour Progression Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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Watson CJG, Lawlor M, Sy J, Krishnaswamy M, Buckland ME, Brennan JW, Satgunaseelan L. Anaplasia and age of onset in desmoplastic infantile ganglioglioma: Case report and review of the literature. Pediatr Blood Cancer 2023; 70:e29808. [PMID: 35670752 DOI: 10.1002/pbc.29808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/10/2022] [Indexed: 12/25/2022]
Affiliation(s)
- Christopher J G Watson
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia.,Department of Ophthalmology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Mitchell Lawlor
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia.,Department of Ophthalmology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Joanne Sy
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Mrudula Krishnaswamy
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Michael E Buckland
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Jeffrey W Brennan
- Department of Neurosurgery, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Laveniya Satgunaseelan
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
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