Histone lysine demethylases in breast cancer

Abstract

Histone lysine demethylases (KDMs) have been recently discovered in mammals and have been nicknamed “erasers” for their ability to remove methyl groups from histone substrates. In cancer cells, KDMs can activate or repress gene transcription, behaving as oncogenes or tumor suppressors depending upon the cellular context. In order to investigate the potential role of KDMs in Breast Cancer (BC), we queried the Oncomine database and determined that the expression of KDMs correlates with BC prognosis. High expression of KDM3B and KDM5A is associated with a better prognosis (no recurrence after mastectomy p = 0.005 and response to docetaxel p = 0.005); conversely, KDM6A is overexpressed in BC patients with an unfavorable prognosis (mortality at 1 year, p = 8.65E−7). Our findings suggest that KDMs could be potential targets for BC therapy. Further, altering the interactions between KDMs and Polycomb Group genes (PcG) may provide novel avenues for therapy that specifically targets these genes in BC.

Introduction

Breast cancer (BC) is a major cause of morbidity and mortality worldwide. BC accounts for 23% of all cancer cases in the United States and continues to be the main cause of cancer-related deaths among females [1]. Many studies have demonstrated that breast carcinogenesis is driven by genetic and epigenetic alterations. Recent studies have shown that epigenetic regulation could have a potential therapeutic and prognostic role in BC. In particular, emerging evidence suggests that expression of histone lysine demethylases (KDMs) is elevated in BC. Moreover, through the action of lysine demethylation, KDMs play a functional role in cellular proliferation [2]. Recently, amplification/mutations of KDMs have been linked to histone methyl modifications and to many types of cancer. Mutations and amplification of KDMs were detected in both hematological and solid neoplasms, including prostate cancer, esophageal squamous cell carcinoma, desmoplastic medulloblastoma, metastatic lung sarcomatoid carcinoma, mucosa-associated lymphoid tissue (MALT) lymphoma, and breast cancer. How KDMs work in cancer biology remains to be explored.

KDMs are composed by two families, the FAD-dependent KDMs and the Jumonji C KDMs (JHDMs). KDMs are a novel family of histone modifiers that specifically remove mono-, di- or tri- methyl groups from lysines on histones (H3K4me3/2/1, H3K9me3/2/1, H3K36me3/2/1 and H3K27me3/2) [3]. The first KDM protein discovered in mammals was lysine-specific demethylase 1 (KDM1A). In BC, KDM1A (aliases: LSD1, BHC110, AOF2) is overexpressed and involved in many biological processes. In particular, it is strongly up-regulated in estrogen receptor negative (ER−) BC and could be a predictive biomarker for aggressive tumor biology in BC [4]. KDM1A activates gene transcription through H3K9 demethylation, while it is able to repress gene transcription through H3K4 demethylation. Therefore, KDM1A may display either an oncogenic or oncosuppressive role. The second KDM1 to be identified is the lysine-specific demethylase 2 (KDM1B). KDM1B (also known as LSD2, AOF1) specifically demethylates H3K4me2/1, resulting in repression of gene transcription [5].

KDM1, through the demethylation of H3K4, may influence the expression of multiple genes critical in early-stage breast carcinogenesis. Pargyline (KDM1 inhibitor) cooperates with vorinostat (HDAC inhibitor) to increase histone methylation and acetylation in BC [2], [6]. In BC, KDM1 is involved in many biological processes and is strongly up-regulated in ER− BC. It contributes to cell proliferation through the inhibition of p21 and the induction of cyclin A2 (CCNA2) and v-erb-b2 erythroblastic leukemia viral oncogene homolog 2 (ERBB2) [4].

KDM1 belongs to the family of flavin adenine dinucleotide (FAD)-dependent KDMs. They can demethylate histones in a FAD-dependent oxidative reaction. In this reaction, FAD oxidizes the methyl-lysine to lysine and formaldehyde [7]. Compared to FAD-dependent KDMs, the JHDMs family is larger. Indeed, these members are able to tri-demethylate lysines, because they have enough space in their active sites for three methyl groups [8], which is not the case for KDM1. The demethylase reaction of JHDMs family requires Fe²⁺ and α-ketoglutarate as cofactors in the presence of oxygen, resulting in the conversion of methyl groups to hydroxymethyl groups releasing formaldehyde [7].

The first JHDM identified was KDM2A (alias: JHDM1A, FBXL10) with H3K36 demethylation activity [9]. This discovery was followed by the identification of a long series of other KDM members (KDM3, KDM4, KDM5 and KDM6), their homologues (KDM3A, 3B, 3C; KDM4A, 4B, 4C; KDM5A, 5B, 5C, 5D and KDM6A, 6B) with specific demethylation activities and different roles in BC. Of these genes, KDM3C expression is reduced in BC tumors, indicating a putative tumor suppressor role [10]. Li et al. showed that silencing KDM4A results in inhibition of proliferation in several human BC cell lines [11]. KDM4B and KDM5B are highly expressed in human ER+ BC [12], [13].

Despite this seminal evidence, no study has systematically investigated the role of KDMs in BC. Due to their role in cancer biology, we decided to query the Oncomine database to identify correlations between KDMs expression and clinical outcome in BC patients. In order to further confirm the association between KDM expression and prognosis, we analyzed this relationship using the GOBO database [14].