Scientists from Sydney’s Garvan Institute of Medical Research have published a paper, online in Nature Cell Biology,
describing gene expression in a prostate cancer cell: more sweeping,
more targeted and more complex than we could ever have imagined, even
five years ago.
The study shows that changes within the prostate cancer cell
‘epigenome’ (biochemical processes that target DNA and affect gene
expression) alter the expression of many genes, silencing their
expression within large regions of DNA — nearly 3% of the cell’s
Epigenetic ‘events’ include ‘DNA methylation’ and ‘chromatin
modification’. Methylation occurs when a methyl group — one carbon
atom and three hydrogen atoms — attaches to a gene, determining the
extent to which it is ‘switched on’ or ‘switched off’. Chromatin,
responsible for the physical coiling or structuring of DNA, can
determine whether or not a gene is accessible for interaction with
other molecules inside a cell.
Project leader Professor Susan Clark describes the typical cancer
cell as a ‘lean mean machine’. "Epigenetic changes reduce the available
genome to a point where only the genes that promote cell proliferation
are accessible in the cancer cell," she said.
"We can see that the epigenome is remodelled in a very consistent
and precise way, effectively swamping the expression of any gene that
goes against the cancer cell’s interests."
"The swamping encompasses tumour suppressor genes, and all the
neighbouring genes around them, as well as non-coding RNA, intergenic
regions and microRNAs. Only those genes essential for growth activation
are allowed to be active, while all the genes and regions that apply
brakes are inactivated."
"We now have an epigenomic map of the prostate cancer cell — which
we didn’t have before. That has taken three years to develop, including
the technology and methods to interpret our tissue samples."
"The map tells us that the tumour cell is very different from the
healthy cell. It also tells us that it works in a programmed rather
than a random way, and that it targets a significant part of the
genome, rather than just single genes."
"It tells us that treating cancer will be far more complex than we
imagined, as it will first involve understanding and reversing
The findings are timely in that they coincide with very recent
events and publications that have brought the concepts of the
‘epigenome’ and ‘epigenetics’ into world focus. In January 2010 the
International Human Epigenome Consortium (IHEC) was launched in Paris
(with Professor Clark on the interim steering Committee). Time magazine
ran a feature on epigenetics in January, and Nature published two
articles on the subject this month: one addressing the importance of
IHEC and the urgency of pooling international mind power and resources;
the other describing the infinite complexity of the project — orders
of magnitude more challenging than the Human Genome Project.
The ultimate aim of IHEC is to produce a map of the human epigenome.
The initial intention is to map 1,000 epigenomes within a decade. This
will provide a healthy tissue base against which to compare the
epigenomes of diseased tissue.
The Human Genome Project, completed in March 2000, found that the
human genome contains around 25,000 genes. It took 3 billion US dollars
to map them.
We do not yet know how many variations the human epigenome is likely
to contain — certainly millions — as a single person could have many
epigenomes in a lifetime, or even in a day. The technological advances
and computational power necessary to map the epigenome, therefore,
The project at Garvan involved an initial bioinformatics phase; a comparative tissue analysis phase; and a data analysis phase.
The bioinformatics phase analysed publicly available microarray
datasets (glass slides containing fragments of every gene across the
genome) that had been done on prostate cancer.
Dr Warren Kaplan, Bioinformatics Analyst at Garvan’s Peter Wills
Bioinformatics Centre, developed new techniques to analyse the
microarray data. "We designed a computer program which used a ‘sliding
window’ — a window that computationally moves along the genome, noting
the number of genes inside that window and how many of them are
downregulated," he said.
"Some of the microarrays we used only measured mRNA — or the level
of gene expression. Others measured the overall methylation status of
the genes in that same region. It was an opportunity for us to examine
the genome in a multi-layered way."
Once Kaplan had provided an initial map, Drs Marcel Coolen and Clare
Stirzaker and Jenny Song from Professor Clark’s lab found a way to
treat and analyse prostate cancer cells, allowing their comparative DNA
methylation and chromatin states analysis against the microarray data.
Bioinformaticians within the Clark lab, Aaron Statham and Dr Mark
Robinson, then developed novel methodologies to interpret resulting
data — essentially tens of millions of numbers. "It was like cracking
a code," said Aaron. "At first the data made no sense."
Professor Clark emphasises the importance of developing the new
genome technology and knowhow that allows analysis of epigenetic
"There is so much we still don’t know," she said. "Already we have
an idea of the complexity and how it might impact on the specific drug
combinations that you will have to use to reactivate genes, non-coding
RNAs and microRNAs within these cancer-affected regions."
"Now that we have a prostate cancer epigenome map, our next step
will be to understand the mechanism that’s driving the chromatin
reduction, or genome reduction within these ‘lean mean machines’. In
other words, what’s the link between the genetics and the epigenetics?"
Source : Garvan Institute of Medical Research