Gene study compiles catalog of biomarkers for multiple cancers

Genetic alterations in different types of cell around the body give rise to hundreds of different forms of cancer. Scientists are starting to compile catalogs of these genetic alterations, or biomarkers, so they can be used to diagnose and stage several cancers from just a blood sample. However, few of these biomarkers are common to many different types of cancer.
Colorful DNA
Using two different gene databases, the researchers found over 120 pan-cancer biomarkers.

Now, a new study conducted in Japan and Australia and published in Cancer Research has identified a large number of genes that are “upregulated” in many different types of cancer. The hope is this will lead to biomarker tests for early detection – and, therefore, prompt treatment – of cancer.

When a gene is “upregulated” in cancer it means that in the gene is more highly expressed in cancer cells than in healthy cells. A more highly expressed gene has a stronger effect – for example, if the gene codes for a protein or enzyme, then more of that protein or enzyme will be made.

The researchers believe the strength of their study comes from the fact they used two different technologies to find the “pan-cancer” biomarkers.

First, they used data derived using a technology called Cap Analysis of Gene Expression (CAGE) as part of the FANTOM project. Here, they searched for differences in gene expression in 225 cancer cell lines and 339 normal cells.

Then, they looked at sequencing data on 4,055 primary tumors and 563 healthy tissues from the Cancer Genome Atlas (TCGA) database and compared the two results to look for genetic changes common to both datasets.

Study identifies 128 pan-cancer biomarkers

First author Bogumil Kaczkowski, of the RIKEN Center for Life Science Technologies in Japan, explains how using the two different datasets allowed them to combine their strengths and compensate for their weaknesses:

“The TCGA data is complicated by the fact that tumor samples are composed of mixture of different cells, while the FANTOM5 CAGE data is from cells grown in cell culture where changes might arise from the culture process. By putting the two together and looking at changes found in both, we have been able to make a robust catalog.”

From the analysis the team identified 128 biomarkers common to both datasets that are present in a variety of tumor types.

Some of the biomarkers are already well known – such as TOP2A and MKI67.

But the study also identifies a number of new markers, including hundreds of promoters – parts of the genome that trigger gene expression. They also found that a little-known repetitive element called REP522 appears to be upregulated in many cancers.

Coauthor Piero Carninci, also of the RIKEN Center for Life Science Technologies and one of the leaders of the FANTOM5 consortium, concludes:

“We hope that researchers will use our findings to identify markers for the many cancer types that currently have no useful markers. It may also be possible to target the genes we have identified as potential drug targets. These targets could potentially help many cancer patients as they are upregulated in many different types of tumors.”

Meanwhile, Medical News Today recently learned that natural gut bacteria may have anti-cancer effects. A University of Chicago study published in Science shows adding certain bacteria into mice’s digestive tracts strengthens their immune attack on tumor cells.

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