Whitehead scientists identify major flaw in standard approach to global gene expression analysis

Whitehead Institute researchers report that common assumptions employed in the generation and interpretation of data from global gene expression analyses can lead to seriously flawed conclusions about gene activity and cell behavior in a wide range of current biological research.

"Expression analysis is one of the most commonly used methods in ," says Whitehead Member Richard Young. "So we are concerned that flawed assumptions may affect the interpretation of many biological studies."

Much of today's interpretation of relies on the assumption that all cells being analyzed have similar total amounts of (mRNA), the roughly 10% of a cell's RNA that acts as a blueprint for . However, some cells, including cells, produce several times more mRNA than other cells. Traditional global gene expression analyses have typically ignored such differences.

"We've highlighted this common assumption in gene expression analysis that potentially affects many researchers," says Tony Lee, a scientist in Young's lab and a corresponding author of the article published in this week's issue of Cell. "We provided a concrete example of the problem and a solution that can be implemented by investigators."

Members of the Young lab recently uncovered the flaw while investigating genes expressed in cancer cells expressing high levels of c-Myc, a gene regulator known to be highly expressed in aggressive cancer cells. When comparing cells with high and low c-Myc levels, they were surprised to find very different results using different approaches to gene expression analysis. Further investigation revealed that there were striking differences in the total amounts of RNA from the high and low c-Myc -containing cells, yet these differences were masked by commonly used experimental and analytical methods.

"The different results we saw from different methods of gene expression analysis were shocking, and led us to reinvestigate the whole process on several platforms," says Jakob Lovén, postdoctoral reseacher in Young's lab and co-author of the Cell paper. "We then realized that the common assumption that cells contain similar levels of mRNA is badly flawed and can lead to serious misinterpretations, particularly with that can have very different amounts of RNA."

In addition to delineating this problem, the Whitehead scientists also describe a remedy. By using synthetically produced mRNAs, called RNA spike-ins, as standardized controls, researchers can compare experimental data and eliminate assumptions about total cell RNA amounts. The remedy applies to all three platforms they studied.

Although the researchers believe the use of RNA spike-ins should become the new standard for global gene expression analyses, questions are likely to persist about the interpretations of much prior research.

"There are over 750,000 expression datasets in public databases, and because they generally lack information about the cell numbers used in the analysis, it is unclear whether they can be re-examined in order to validate the original interpretation" says David Orlando, a scientist in the Young lab. "It may be necessary to reinvestigate some important concepts."

Related Stories

Major cancer protein amplifies global gene expression

Sep 27, 2012

Scientists may have discovered why a protein called MYC can provoke a variety of cancers. Like many proteins associated with cancer, MYC helps regulate cell growth. A study carried out by researchers at the National Institutes ...

In Brief: Guiding cancer cells to their fate

Nov 26, 2010

It is often said that the best way to spur change is to work within the system. Here, researchers create control devices based on RNA, which can be used to synthetically rewire cellular behavior, making the cells more sensitive ...

Circular RNAs more common than previously thought

Feb 01, 2012

In the classical model of gene expression, the genetic script encoded in our genomes is expressed in each cell in the form of RNA molecules, each consisting of a linear string of chemical "bases". It may be time to revise ...

Recommended for you

Scientists discover an on/off switch for aging cells

7 hours ago

(Medical Xpress)—Scientists at the Salk Institute have discovered an on-and-off "switch" in cells that may hold the key to healthy aging. This switch points to a way to encourage healthy cells to keep dividing ...

Gene variant that dramatically reduces 'bad' lipids

Sep 16, 2014

In the first study to emerge from the UK10K Project's cohort of samples from the general public, scientists have identified a rare genetic variant that dramatically reduces levels of certain types of lipids in the blood. ...

New diagnostic method identifies genetic diseases

Sep 16, 2014

People with genetic diseases often have to embark on an odyssey from one doctor to the next. Fewer than half of all patients who are suspected of having a genetic disease actually receive a satisfactory diagnosis. Scientists ...

User comments