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Association of Variably Methylated Tumour DNA Regions with Overall Suman et al. Clin Epigenet (2021) 13:11 https://doi.org/10.1186/s13148-020-00975-6 RESEARCH Open Access Association of variably methylated tumour DNA regions with overall survival for invasive lobular breast cancer Medha Suman1,2, Pierre‑Antoine Dugué2,3,4, Ee Ming Wong1,2, JiHoon Eric Joo1, John L. Hopper3,4, Tu Nguyen‑Dumont1,2, Graham G. Giles2,3,4, Roger L. Milne2,3,4, Catriona McLean5 and Melissa C. Southey1,2,3* Abstract Background: Tumour DNA methylation profling has shown potential to refne disease subtyping and improve the diagnosis and prognosis prediction of breast cancer. However, limited data exist regarding invasive lobular breast cancer (ILBC). Here, we investigated the genome‑wide variability of DNA methylation levels across ILBC tumours and assessed the association between methylation levels at the variably methylated regions and overall survival in women with ILBC. Methods: Tumour‑enriched DNA was prepared by macrodissecting formalin‑fxed parafn embedded (FFPE) tumour tissue from 130 ILBCs diagnosed in the participants of the Melbourne Collaborative Cohort Study (MCCS). Genome‑ wide tumour DNA methylation was measured using the HumanMethylation 450K (HM450K) BeadChip array. Variably methylated regions (VMRs) were identifed using the DMRcate package in R. Cox proportional hazards regression models were used to assess the association between methylation levels at the ten most signifcant VMRs and overall survival. Gene set enrichment analyses were undertaken using the web‑based tool Metaspace. Replication of the VMR and survival analysis fndings was examined using data retrieved from The Cancer Genome Atlas (TCGA) for 168 ILBC cases. We also examined the correlation between methylation and gene expression for the ten VMRs of interest using TCGA data. 8 Results: We identifed 2771 VMRs (P < 10− ) in ILBC tumours. The ten most variably methylated clusters were pre‑ dominantly located in the promoter region of the genes: ISM1, APC, TMEM101, ASCL2, NKX6, HIST3H2A/HIST3H2BB, HCG4P3, HES5, CELF2 and EFCAB4B. Higher methylation level at several of these VMRs showed an association with reduced overall survival in the MCCS. In TCGA, all associations were in the same direction, however stronger than in the MCCS. The pooled analysis of the MCCS and TCGA data showed that methylation at four of the ten genes was associated with reduced overall survival, independently of age and tumour stage; APC: Hazard Ratio (95% Confdence interval) per one‑unit M‑value increase: 1.18 (1.02–1.36), TMEM101: 1.23 (1.02–1.48), HCG4P3: 1.37 (1.05–1.79) and CELF2: 1.21 (1.02–1.43). A negative correlation was observed between methylation and gene expression for CELF2 (R 0.25, P 0.001), but not for TMEM101 and APC. =− = Conclusions: Our study identifed regions showing greatest variability across the ILBC tumour genome and found methylation at several genes to potentially serve as a biomarker of survival for women with ILBC. Introduction *Correspondence: [email protected] Invasive lobular breast cancer (ILBC) is the second most 2 Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia common histological subtype of breast cancer account- Full list of author information is available at the end of the article ing for 10–15% of all cases [1–3]. ILBCs are typically © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/publi cdoma in/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Suman et al. Clin Epigenet (2021) 13:11 Page 2 of 16 oestrogen receptor (ER) and progesterone receptor (PR) to be more frequently methylated for other genes in the positive and human epidermal growth factor receptor 2 panel compared with IDBC [47]. (HER2) negative and are strongly associated with hor- In this study, we hypothesised that genome-wide vari- monal risk factors for breast cancer [4–7]. Te incidence ations in DNA methylation patterns within the ILBC of ILBC increased sharply in the late 1990s as a conse- group may guide or refect diferent tumour biologies quence of the increased use of hormone replacement leading to subgroups of tumours that difer in their clini- therapy (HRT) [8–13]. Awareness of the increased risk cal behaviour. Our aims were twofold: i) to investigate of breast cancer associated with HRT led to reduced the genome-wide DNA methylation variability within use and a decline in ILBC incidence [14], but it has been the ILBC group and ii) to assess associations between shown to increase again recently [15, 16]. tumour methylation at the most variable methylated ILBCs display an obscure growth pattern with small, regions and overall survival for women with ILBC. round and discohesive cells growing in a single fle with- out forming any distinct clusters [17]. Tis is likely to Results be related to a loss of E-cadherin protein which is com- Study participants mon in ILBC tumourigenesis and is a hallmark of this Te median age at breast cancer diagnosis in the MCCS subtype [18]. Compared with other breast cancer types, was 65 years with tumours being diagnosed at stage ILBCs are less likely to form a frm and distinct lump and 1A/1B (50%), 2A/2B (37%) and 3A/3C/4 (9%). Tere were often present as undefned palpable masses on mammog- 37 deaths observed during follow-up (median [IQR]: 13 raphy [19, 20]. Tis poses a signifcant challenge for its [9–18] years). Te tumours were mainly ER-positive, PR- early detection by routine mammographic screening [19, positive and HER2-negative (47%). In TCGA data, the 21–23]. Tis occult nature may explain the detection of median age at diagnosis was 62 years. In both datasets, ILBC cases at advanced stages [4, 24–26]. ILBCs display a older women (aged 60 years or older at diagnosis) formed unique metastatic behaviour and often metastasis to the the majority of the cases (65%, in the MCCS and 58%, in gastrointestinal tract [27, 28], colon [29], ovaries [30] and TCGA). Tere was a higher proportion of young women uterus [31], which is uncommon for other breast cancers at diagnosis (age less than 50 years: 21%) in TCGA com- types. pared with the MCCS (5%). Te proportion of later-stage ILBC is biologically and histologically heterogeneous tumours (3A/3B/3C/4) was also higher in TCGA (33%) with several histological subtypes described that show compared with the MCCS (9%). A total of 14 deaths were distinct clinical behaviour and outcomes [3, 17, 32–35]. recorded during the follow-up (median [IQR]: 2 [1.5–5] Aberrant tumour DNA methylation is a hallmark of can- years) in TCGA dataset. Te clinical and pathological fea- cer that occurs early in cancer development and is thus tures of the study participants in the MCCS and TCGA and a potentially valuable marker of tumour progression and a comparison of the two studies are summarised in Table 1. patient survival. Alterations in tumour DNA methylation have been investigated in detail for many types of cancer, Variably methylated regions in ILBC including breast cancer but ILBCs are largely underrep- We identified 2,771 regions across the genome resented in these studies [36, 37]. Studies focusing on that showed substantially variable methylation ILBC-specifc DNA methylation alterations have mainly (P < 10−8) across ILBCs in the MCCS (Additional used a candidate gene approach and have reported aber- file 2: Table S1). These VMRs corresponded to 2,208 rant promoter methylation status for specifc genes such genes and 563 intergenic regions. The most signifi- as CDH1 [38–41], RASSF1A, HIN-1, RAR-β, cyclin-D2, cant regions (P < 10−8) and the genes associated with TWIST [42], ADAM33 [43], SFRP1 [44] and DAPK1 [45]. these regions were chr20:13199787–13201844 (ISM1, Moelans et al. (2015) compared the methylation profles 29 CpGs), chr5:112073348–112074043 (APC, 16 of classic ILBC (n = 20), pleomorphic ILBC (n = 16) and CpGs), chr17:42091713–42093050 (TMEM101, 16 IDBC (n = 20) for 24 established and putative tumour CpGs), chr11:2290953–2293552 (ASCL2, 41 CpGs), suppressor genes and found lower TP73 and MLH1 pro- chr10:134598496–134602228 (NKX6, 39 CpGs) and moter methylation and higher RASSF1 promoter meth- chr1:22844750–228647248 (HIST3H2A/HIST3H2BB, ylation in pleomorphic compared with classic ILBC [46]. 28 CpGs). The average methylation level (beta-val- Bae et al. (2004) compared the methylation profles of ues) ranged between 0.09 and 0.63 at ISM1, 0.08 and ILBC (n = 19), IDBC (n = 60) and mucinous breast cancer 0.82 at APC, 0.15 and 0.83 at TMEM101, 0.15 and (n = 30) for a panel of 12 genes and found BRCA1 pro- 0.77 at ASCL2, 0.07 and 0.70 at NKX6, and 0.05 and moter hypermethylation in 92% of mucinous breast can- 0.58 at HIST3H2A/ HIST3H2BB (Fig.
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