Epigenetic regulation of Cancer Testis Antigens: candidate drivers of genomic instability in Triple Negative Breast Cancer

Abstract

Cancer Testis (CT) genes are restrictedly expressed in immune-privileged germ tissues and recognised as non-self antigens if aberrantly reactivated in tumours. Beyond their immunotherapeutic potential, certain CT genes have known oncogenic roles, reflecting highly specialised physiological functions in the germline. Meiosis-associated CT genes have been implicated as drivers of genomic instability, whose reactivation through epigenetic mechanisms could provide a selective advantage to an evolving tumour. In this study, promoter methylation and expression were analysed for a large set of putative CT genes in two Triple Negative Breast Cancer datasets, TCGA and SCAN-B. We aimed to establish whether epigenetic reactivation of CT genes may be linked to homologous recombination deficiency and genomic instability, and to characterise this event in the context of global epigenetic alterations, and the tumour immune response. Hypomethylation of CT genes was found to reflect global hypomethylation and epigenetic reactivation of the inactive X chromosome, representing a passenger of global epigenetic events which are themselves linked to chromosomal instability. Yet we demonstrate that tumour-specific epigenetic events, independent of global hypomethylation, can also permit expression of certain CT genes. 8 autosomal CT genes are here identified as potential “epi-drivers” of genomic instability, which by this mechanism are preferentially activated in tumours with high levels of genomic scars. Selected “epi-drivers'' are enriched for genes known to function in meiosis and DNA repair, and some seem to share transcriptional regulatory programs. We further provide evidence that increased expression of selected “epi-drivers” coincides with an immunomodulatory phenotype and a unique pattern of HLA gene expression - features not shared by the majority of CT genes nor with global epigenetic events. Characterising the mechanism of CT gene reactivation, and their potential driver roles may shed light on combination therapeutic strategies, whereby epigenetic modulation of CT genes could be exploited to enhance tumor immune visibility.

Popular Abstract

Hijacking the Germline

Gene expression in healthy tissues is under careful regulation by a collection of silencing and activating signals which decorate the genome. These simple chemical modifications can powerfully regulate the activity of nearby genes, deciding how and when a sequence is read without changing its content. Unlike the genome itself, which is constant across human tissues, this so-called “epigenome” is a highly dynamic layer, configured differently from tissue to tissue. This gives rise to functional diversity throughout the body and ensures that only essential gene products are created at the appropriate time and setting. In cancer, the orderly balance of epigenetic silencing and activation is often disturbed. Widespread loss of epigenetic silencing is a typical feature of aggressive cancers, in some cases causing inappropriate activation of genes that are silenced under most normal circumstances.

The so-called cancer testis (CT) genes are rarely expressed outside of the germline, where their activity is not necessary and could threaten normal cell function. Yet CT genes can be abnormally reactivated in tumours when epigenetic factors are disturbed. The testis is one of few body sites that is hidden from the immune system. This unique privilege means that if a testis-restricted gene appears unexpectedly somewhere else in the body, it could be recognised as a foreign or “non-self” entity and trigger an immune response. Such an attack at the site of a tumour would be favorable but is often circumvented in aggressive cancers which develop mechanisms to escape from immune detection. Owing to their immunogenicity and absence in healthy tissues, CT genes have been recognised as attractive targets for immunotherapies - drugs which aim to eradicate a growing tumour by amplifying the immune response mounted against it.

Beyond their immunogenic potential, certain CT genes have been pinned as drivers of tumour progression, which may be actively engaged to support tumour cell fitness or to satisfy some unmet need of an evolving tumour. The expression of a gene exclusively in testis reflects a highly specialised function, which if activated outside of its physiological context could have unusual consequences. Many CT genes are normally active in meiosis - a unique stage in the formation of a sperm or egg during which chromosomes are pieced apart, reshuffled and stitched back together. These events are somewhat similar to DNA repair mechanisms utilised by normally dividing cells. Yet the meiotic chromosome processing is distinct in certain ways, as it aims to maximise genetic diversity rather than minimise erroneous repair. Activation of such a program in tumours, if favored over normal high-fidelity DNA repair, is expected to compromise stability of the genome. Persistent expression of meiotic genes could therefore drive chromosomal alterations, potentially contributing to malignant transformation or progression.

Here we set out to investigate whether CT genes might drive chromosomal alterations when their epigenetic silencers are lost. We focused on the highly aggressive Triple Negative Breast Cancer (TNBC), so called for its lacking expression of three common therapeutic targets, which renders such tumours resistant to currently available therapies. Understanding the causes and functional consequences of CT gene expression could shed light on combination therapeutic strategies that could make TNBCs more visible to the host immune system.

From a large set of putative CT genes, a group of 8 were ultimately identified. The selected genes are epigenetically silenced in healthy breast tissues, but in aggressive breast tumours harbouring extremely altered genomes, this epigenetic silencer is often lost, permitting activation of the gene. This can happen even in tumours where the overall state of the epigenome appears to be normal, suggesting that their activation is not merely a passive byproduct of epigenetic disarray, but potentially a tumour driver event. The selected genes are often expressed in tumours with high levels of immune activity - a feature not shared by the majority of CT genes or with global epigenetic events that we have analysed. Some selected genes are known to function during meiosis and DNA repair, and some share binding sites for transcription factors that are known to mediate meiotic events. This gives us reason to speculate that their activation could favor the progression of tumours that have lost function in normal DNA repair pathways.

Master’s Degree Project in Bioinformatics 60 credits 2021
Department of Biology, Lund University

Advisors: Anita Grigoriadis 1, Jelmar Quist 1, Johan Staaf 2
1 King’s College London; 2 Division of Oncology, Department of Clinical Sciences Lund, Lund University

• author: Kelly, Katherine
• supervisor: Anita Grigoriadis; Jelmar Quist; Johan Staaf
• organization: Degree Projects in Bioinformatics
• course: BINP52 20201
• year: 2021
• type: H2 - Master's Degree (Two Years)
• subject: Biology and Life Sciences
• language: English
• id: 9043587
• date added to LUP: 2021-05-04 13:50:37
• date last changed: 2021-05-04 13:50:37