New links between epigenetic processes and glucose metabolism in breast cancer progression

12 Oct 2017

New links between epigenetic processes and glucose metabolism in breast cancer progression


By Dr Sanjeev Shukla, Intermediate Fellow 

IISER Bhopal

We have identified a novel epigenetic mechanism of cancer-specific gene modification, which contributes to the growth of breast cancer cells by promoting the Warburg effect, increased glucose metabolism in cancer cells which helps them survive. This new information will help us develop better and more specific therapeutics to treat breast cancer.

In the recent times, cancer epigenetics has gained a lot of attention due to the involvement of epigenetic modifications in the initiation and progression of cancer. These epigenetic changes regulate how cells read the genes but do not affect the DNA sequence and is also considered to be reversible. Deregulation of these epigenetic processes have been shown to result in many diseases, including cancer. Following processes are considered as epigenetic modifications: DNA methylation, histone modification and non-coding RNA (ncRNA)-associated gene silencing. Since epigenetic modifications are reversible, they are an attractive target for cancer therapy.

Though epigenetic modifications are associated with changes in gene expression, their role in the regulation of alternative splicing in the cancer cells is not well understood.

Alternative splicing is a process by which one gene can generate multiple mRNA or protein isoforms. These alternatively spliced isoforms may differ in their structure and function and may play an important role in cancer-formation or tumorigenesis. Identification of epigenetic regulators of cancer-specific splicing will enable us to therapeutically target aberrant splicing and provide a new approach to cancer therapy.

In our recent report in Proceedings of the National Academy of Sciences (PNAS), we have demonstrated a new mechanism of DNA methylation-mediated regulation of alternative splicing by BORIS (Brother Of The Regulator Of Imprinted Sites), which can contribute to breast cancer tumorigenesis by favoring the Warburg effect. BORIS is a cancer-testis gene which is expressed in germ cells but not in the somatic cells. Interestingly, BORIS gets overexpressed in cancer cells making it an important target for cancer treatment.

The cancer cells thrive on glucose by converting it to lactate at the end of glycolysis. The phenomenon is known as aerobic glycolysis or Warburg effect and promotes the growth of the cancer cells. The alternative spliced protein isoform Pyruvate kinase M2 (PKM2) contributes to the Warburg effect by promoting aerobic glycolysis whereas PKM1 isoform promotes oxidative phosphorylation, which is a part of normal glucose metabolism. The PKM gene contains two mutually exclusive exons, exon 9 and 10 which are alternatively included in the final transcript to give rise to PKM1 and PKM2 isoform respectively. In this study, we demonstrate the increased PKM2 isoform expression in breast cancer, which correlates with higher DNA methylation at PKM exon 10 in breast cancer cells as compared to the normal cells.

The alternative splicing and DNA methylation are both known to be altered in the cancer cells but whether and how they are connected is not clear. Here, we describe for the first time that the differential intragenic DNA methylation in breast cancer cells is associated with cancer-specific mRNA splicing. This study provides a novel functional link between epigenetics, alternative splicing, Warburg effect and growth of breast cancer cells.

Interestingly, we show that how BORIS/DNA methylation contributes to the Warburg effect by regulating alternative splicing and inhibiting DNA methylation or down-regulation of BORIS leads to reversal of Warburg effect and growth inhibition of breast cancer cells. Importantly, our results show that in addition to PKM splicing, BORIS also regulates alternative splicing of several genes in a DNA methylation-dependent manner. Collectively, we have described a new mechanism based on BORIS binding to explain the alternative splicing events regulated by DNA methylation in breast cancer.

Furthermore, this study provides the mechanism to switch the PKM splicing from cancer-specific to normal isoform by controlling the upstream DNA methylation or BORIS, which may provide a route for therapeutic management of breast cancer in future.


Intragenic DNA methylation and BORIS mediated cancer-specific splicing contributes to Warburg effect. Singh S, Narayanan SP, Biswas S, Gupta A, Ahuja A, Yadav S, Panday RK, Samaiya A, Sharan SK, Shukla S*. Proceedings of the National Academy of Sciences (PNAS). October 2018

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Banner image credit -  Khuloud T. Al-Jamal, David McCarthy & Izzat Suffian, Wellcome Images.  False-coloured scanning electron micrograph of a 3-day old breast tumour spheroid (cluster of cells).