Detailed DNA methylation characterisation of phyllodes tumours identifies a signature of malignancy and distinguishes phyllodes from metaplastic breast carcinoma

Braydon Meyer^#^{1

2}, Clare Stirzaker^#^{1

2}, Sonny Ramkomuth³, Kate Harvey³, Belinda Chan⁴, Cheok Soon Lee^{5

6

7}, Rooshdiya Karim^{5

8}, Niantao Deng³, Kelly A Avery-Kiejda^{9

10}, Rodney J Scott^{10

11}, Sunil Lakhani^{12

13}, Stephen Fox^{14

15}, Elizabeth Robbins⁵, Joo-Shik Shin⁵, Jane Beith^{16

17

18}, Anthony Gill^{19

20

21}, Loretta Sioson^{19

20

21}, Charles Chan^{22

23}, Mrudula Krishnaswamy^{22

23}, Caroline Cooper^{24

25}, Sanjay Warrier^{26

27

28}, Cindy Mak^{25

28}, John Ej Rasko^{25

29

30}, Charles G Bailey^{26

30

31}, Alexander Swarbrick^{2

3}, Susan J Clark^{1

2}, Sandra O'Toole^{3

5

8}, Ruth Pidsley^{1

2}

Affiliations

¹ Epigenetics Research Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
² St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia.
³ Tumour Progression Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
⁴ Department of Surgery, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia.
⁵ Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.
⁶ Department of Anatomical Pathology and Molecular Pathology Laboratory, Liverpool Hospital, Liverpool, New South Wales, Australia.
⁷ Discipline of Pathology, School of Medicine, Western Sydney University, Liverpool, New South Wales, Australia.
⁸ Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.
⁹ School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia.
¹⁰ Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia.
¹¹ Hunter Medical Research Institute, Newcastle, New South Wales, Australia.
¹² UQ Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia.
¹³ Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.
¹⁴ Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
¹⁵ Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
¹⁶ Psycho-Oncology Co-Operative Group (PoCoG), University of Sydney, Sydney, New South Wales, Australia.
¹⁷ Chris O'Brien Lifehouse, Sydney, New South Wales, Australia.
¹⁸ University of Sydney, Sydney, New South Wales, Australia.
¹⁹ Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, New South Wales, Australia.
²⁰ NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia.
²¹ Sydney Medical School, University of Sydney, St Leonards, New South Wales, Australia.
²² NSW Health Pathology, Department of Anatomical Pathology, Concord Repatriation General Hospital, Sydney, New South Wales, Australia.
²³ Concord Clinical School, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.
²⁴ Anatomical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia.
²⁵ Faculty of Medicine, The University of Queensland, St Lucia, Queensland, Australia.
²⁶ Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.
²⁷ Sydney Medical Program, The University of Sydney, Sydney, New South Wales, Australia.
²⁸ Department of Breast Surgery, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia.
²⁹ Department of Cell and Molecular Therapies, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia.
³⁰ Gene and Stem Cell Therapy Program, Centenary Institute, Sydney, New South Wales, Australia.
³¹ Cancer and Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, New South Wales, Australia.

^# Contributed equally.

PMID: 38300122
DOI: 10.1002/path.6250

Detailed DNA methylation characterisation of phyllodes tumours identifies a signature of malignancy and distinguishes phyllodes from metaplastic breast carcinoma

Braydon Meyer et al. J Pathol. 2024 Apr.

. 2024 Apr;262(4):480-494.

doi: 10.1002/path.6250. Epub 2024 Feb 1.

Authors

Affiliations

¹ Epigenetics Research Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
² St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia.
³ Tumour Progression Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
⁴ Department of Surgery, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia.
⁵ Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.
⁶ Department of Anatomical Pathology and Molecular Pathology Laboratory, Liverpool Hospital, Liverpool, New South Wales, Australia.
⁷ Discipline of Pathology, School of Medicine, Western Sydney University, Liverpool, New South Wales, Australia.
⁸ Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.
⁹ School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia.
¹⁰ Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia.
¹¹ Hunter Medical Research Institute, Newcastle, New South Wales, Australia.
¹² UQ Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia.
¹³ Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.
¹⁴ Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
¹⁵ Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
¹⁶ Psycho-Oncology Co-Operative Group (PoCoG), University of Sydney, Sydney, New South Wales, Australia.
¹⁷ Chris O'Brien Lifehouse, Sydney, New South Wales, Australia.
¹⁸ University of Sydney, Sydney, New South Wales, Australia.
¹⁹ Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, New South Wales, Australia.
²⁰ NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia.
²¹ Sydney Medical School, University of Sydney, St Leonards, New South Wales, Australia.
²² NSW Health Pathology, Department of Anatomical Pathology, Concord Repatriation General Hospital, Sydney, New South Wales, Australia.
²³ Concord Clinical School, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.
²⁴ Anatomical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia.
²⁵ Faculty of Medicine, The University of Queensland, St Lucia, Queensland, Australia.
²⁶ Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.
²⁷ Sydney Medical Program, The University of Sydney, Sydney, New South Wales, Australia.
²⁸ Department of Breast Surgery, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia.
²⁹ Department of Cell and Molecular Therapies, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia.
³⁰ Gene and Stem Cell Therapy Program, Centenary Institute, Sydney, New South Wales, Australia.
³¹ Cancer and Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, New South Wales, Australia.

^# Contributed equally.

PMID: 38300122
DOI: 10.1002/path.6250

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.

Keywords: DNA methylation; breast cancer; epigenetics; fibroadenoma; machine learning; phyllodes tumour; sarcoma.

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References

1. WHO Classification of Tumours Editorial Board. WHO Classification of Tumours: Breast Tumours (5th edn), 2019; 172-176.
1. Wiratkapun C, Piyapan P, Lertsithichai P, et al. Fibroadenoma versus phyllodes tumor: distinguishing factors in patients diagnosed with fibroepithelial lesions after a core needle biopsy. Diagn Interv Radiol 2014; 20: 27-33.
1. Tan PH, Thike AA, Tan WJ, et al. Predicting clinical behaviour of breast phyllodes tumours: a nomogram based on histological criteria and surgical margins. J Clin Pathol 2012; 65: 69-76.
1. Chng TW, Gudi M, Lim SH, et al. Validation of the Singapore nomogram for outcome prediction in breast phyllodes tumours in a large patient cohort. J Clin Pathol 2018; 71: 125-128.
1. Chng TW, Lee JY, Lee CS, et al. Validation of the Singapore nomogram for outcome prediction in breast phyllodes tumours: an Australian cohort. J Clin Pathol 2016; 69: 1124-1126.

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Detailed DNA methylation characterisation of phyllodes tumours identifies a signature of malignancy and distinguishes phyllodes from metaplastic breast carcinoma

Affiliations

Detailed DNA methylation characterisation of phyllodes tumours identifies a signature of malignancy and distinguishes phyllodes from metaplastic breast carcinoma

Authors

Affiliations

Abstract

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Medical

Molecular Biology Databases

Research Materials

Miscellaneous