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Identifying Epigenetic Signature of Breast Cancer with Machine Learning

The research reported in this paper identifies the epigenetic biomarker (methylation beta pattern) of breast cancer. Many cancers are triggered by abnormal gene expression levels caused by aberrant methylation of CpG sites in the DNA. In order to develop early diagnostics of cancer-causing methylations and to develop a treatment, it is necessary to identify a few dozen key cancer-related CpG methylation sites out of the millions of locations in the DNA. This research used public TCGA dataset to train a TensorFlow machine learning model to classify breast cancer versus non-breast-cancer tissue samples, based on over 300,000 methylation beta values in each sample. L1 regularization was applied to identify the CpG methylation sites most important for accurate classification. It was hypothesized that CpG sites with the highest learned model weights correspond to DNA locations most relevant to breast cancer. A reduced model trained on methylation betas of just the 25 CpG sites having the highest weights in the full model (trained on methylation betas at over 300,000 CpG sites) has achieved over 94% accuracy on evaluation data, confirming that the identified 25 CpG sites are indeed a biomarker of breast cancer.


Introduction
Methylation is the addition of methyl groups to nucleotides in the DNA molecule. The effects of methylation are particularly important at CpG sites, which are regions of DNA where a cytosine nucleotide is followed by a guanine nucleotide. When a cytosine nucleotide at a CpG site in a promoter region of DNA is methylated, the resulting effect is downregulation of the expression of the respective gene. Methylation can occur at millions of CpG sites throughout the DNA. The CpG sites can be both overmethylated and undermethylated compared to normal levels 1, 2 . Abnormalities in DNA methylation are important causes of development and progression of cancer [1][2][3][4][5][6] . Indeed, aberrations in methylation levels often appear well before the cancer develops, even while the cells still look completely normal under the microscope 6,7 .
In cancers, it is common that CpG sites are over-methylated at genes that make proteins promoting tumor suppressor genes 3,6,8,9 , DNA repair genes 7,10 , and genes that control cell cycle, differentiation, and apoptosis 11 . This results in silencing of tumor suppression and DNA repair, which contributes to development of cancer via an increased occurrence of unrepaired gene mutations and runaway cancer cells 2 . The silencing of tumor suppressor genes by abnormal over-methylation is in fact much more frequent than their inactivation by DNA mutations 12 .
At the same time, CpG sites in cancer are often under-methylated at oncogenes, which can cause tumors when overexpressed 6 . Genome-wide average methylation levels are also significantly lower in tumors than in healthy cells, and are still lower in metastatic cancer cells 3,8,9 .
The presence of both hypo-and hyper-methylation in cancer cells means that effective pharmaceutical treatments will have to be able to correct dangerous methylation levels in both directions: decrease methylation at CpG sites where abnormally high methylation is harmful, and increase at sites where abnormally low methylation is harmful. Methylation abnormalities are reversible 3 , and there are indeed pharmaceuticals approved by the FDA that can be used to reduce methylation levels genome-wide 4,6,[13][14][15] . They are used to treat precancerous conditions and certain cancers caused by over-methylation of tumor suppressor genes. However, those medications have side effects and may cause other cancers by increasing expression of oncogenes and genes that promote cell invasiveness, and by causing general instability of the genome via broad upregulation of gene expressions 14,16 .
Several years ago, CRISPR technology was developed to correct genetic abnormalities at precise locations in the DNA 17 . It is plausible that in another several years a technology will be developed to correct epigenetic abnormalities at precisely specified CpG methylation sites. In order to be able to apply this technology for prevention and treatment of cancer, it will be necessary to know exactly which CpG methylation sites to correct, and in which direction to change the methylation, out of the hundreds of thousands of CpG sites in the DNA whose methylation can be measured with currently available sequencing technologies.
This research identifies the key CpG sites in the DNA whose methylation levels comprise the biomarker (epigenetic signature) of breast cancer, and which can be used to identify, with high accuracy, breast cancer tissue samples among tissue samples of various other types of cancer.

Results and Discussion
This research has identified 25 CpG locations in the DNA whose methylation beta patterns are sufficient to classify breast cancer vs. non-breast-cancer solid tissue samples with a 94.6% accuracy using a machine learning classification model trained on methylation beta values at those 25 locations (Figure 4).
This represents only a modest drop from the 98.6% accuracy on evaluation data in the breast cancer vs. non-breast-cancer classification model trained on the full set of 323,179 CpG sites ( Figure 3). The retention of most of the accuracy indicates that the methylation beta patterns at the identified 25 CpG sites are, indeed, a biomarker of breast cancer and can be used to distinguish it from other types of cancer with high accuracy.
Nine of the genes containing the identified 25 CpG sites ( TAF3, SFRP4, SBDS, PPP2R2A, RASSF4, MTA2, ZNF135, CDHR2, PACS2) turn out to be directly involved in the cell cycle and to regulate cell growth, differentiation, division, apoptosis, and tumor suppression ( Table 1). These findings further confirm the significance of the CpG methylation sites identified by this research as an epigenetic biomarker of breast cancer.
Several of the genes containing the identified 25 CpG sites have unknown functions as of yet, and could turn out to regulate tumor-related activities as well. Their role in breast cancer is yet to be determined, and presents a direction for future research.
The mean methylation beta values for the 25 CpG sites, for the breast-cancer and non-breast-cancer solid tissue samples, are shown in Table 2.
The methodology applied in this research can be extended to identify epigenetic biomarkers for types of cancer other than breast cancer (the BRCA study in TCGA). Another direction for future research is to learn epigenetic biomarkers shared by multiple cancer types, by training a machine learning model to classify cancerous vs. normal tissues.
The knowledge of the epigenetic signature of breast cancer identified in this research is valuable in several ways: it can enable development of medications to correct abnormal methylation at precisely the CpG sites that control expression of genes involved in the development and progression of cancer, and it can also be used for early diagnostics and prevention of breast cancer, at the stage where analysis of tissue cells under the microscope (in biopsies) doesn't show any abnormalities, yet the epigenetic signature of cancer is already present.

Materials and Methods
The research reported in this paper was performed using data in the public DNA methylation betas dataset 18 produced by The Cancer Genome Atlas Program 19 , containing tissue samples from 32 different types of cancer. The data has been retrieved from the public dataset isb-cgc:TCGA_hg38_data_v0, hosted by the Institute for Systems Biology -Cancer Genomics Cloud (ISB-CGC) 20 project on Google Cloud 21 . The data has been accessed via Google BigQuery 22 . Methylation betas for more than 400,000 CpG sites in 8,703 solid cancer tissue samples (identified by unique aliquot barcodes) were retrieved from the TCGA_hg38_data_v0. DNA_Methylation table. A subset of samples and CpG probes were selected for use in the project, such that each included sample would contain methylation betas for the same set of CpG probes. This step reduced the size of the research dataset to 8,126 aliquots, with the same 323,179 probes included with each aliquot. In

Data Availability
The Cancer Genome Atlas data analysed during the current study is available in the public BigQuery dataset repository isb-cgc:TCGA_hg38_data_v0 in Google Cloud, at https://bigquery.cloud.google.com/dataset/isb-cgc: TCGA_hg38_data_v0.