Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Scientists Identify Major Flaw in Standard Approach to Global Gene Expression Analysis

29.10.2012
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 modern biology,” 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 gene expression data relies on the assumption that all cells being analyzed have similar total amounts of messenger RNA (mRNA), the roughly 10% of a cell’s RNA that acts as a blueprint for protein synthesis. However, some cells, including aggressive cancer 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 cancer cells 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 gene expression analysis 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.”

This work was supported by National Institutes of Health (NIH) grants HG002668 and CA146445, the American Cancer Society, and the Swedish Research Council.

Written by Nicole Giese Rura

Richard Young's primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also a professor of biology at Massachusetts Institute of Technology.

Full Citation:

“Revisiting Global Gene Expression Analysis”

Cell, in print October 26, 2012.

Jakob Lovén (1,5), David A. Orlando (1,5), Alla A. Sigova (1), Charles Y. Lin (1,2), Peter B. Rahl (1), Christopher B. Burge (3), David L. Levens (4), Tong Ihn Lee (1,5,*) and Richard A. Young (1,3,5)

1. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
2. Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
3. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
4. Gene Regulation Section, Laboratory of Pathology, National Cancer Institute, Center for Cancer Research, Bethesda, MD, 20892, USA

5. These authors contributed equally.

Nicole Giese Rura | Newswise Science News
Further information:
http://www.wi.mit.edu

More articles from Life Sciences:

nachricht Tag it EASI – a new method for accurate protein analysis
20.06.2018 | Max-Planck-Institut für Biochemie

nachricht How to track and trace a protein: Nanosensors monitor intracellular deliveries
19.06.2018 | Universität Basel

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Temperature-controlled fiber-optic light source with liquid core

In a recent publication in the renowned journal Optica, scientists of Leibniz-Institute of Photonic Technology (Leibniz IPHT) in Jena showed that they can accurately control the optical properties of liquid-core fiber lasers and therefore their spectral band width by temperature and pressure tuning.

Already last year, the researchers provided experimental proof of a new dynamic of hybrid solitons– temporally and spectrally stationary light waves resulting...

Im Focus: Overdosing on Calcium

Nano crystals impact stem cell fate during bone formation

Scientists from the University of Freiburg and the University of Basel identified a master regulator for bone regeneration. Prasad Shastri, Professor of...

Im Focus: AchemAsia 2019 will take place in Shanghai

Moving into its fourth decade, AchemAsia is setting out for new horizons: The International Expo and Innovation Forum for Sustainable Chemical Production will take place from 21-23 May 2019 in Shanghai, China. With an updated event profile, the eleventh edition focusses on topics that are especially relevant for the Chinese process industry, putting a strong emphasis on sustainability and innovation.

Founded in 1989 as a spin-off of ACHEMA to cater to the needs of China’s then developing industry, AchemAsia has since grown into a platform where the latest...

Im Focus: First real-time test of Li-Fi utilization for the industrial Internet of Things

The BMBF-funded OWICELLS project was successfully completed with a final presentation at the BMW plant in Munich. The presentation demonstrated a Li-Fi communication with a mobile robot, while the robot carried out usual production processes (welding, moving and testing parts) in a 5x5m² production cell. The robust, optical wireless transmission is based on spatial diversity; in other words, data is sent and received simultaneously by several LEDs and several photodiodes. The system can transmit data at more than 100 Mbit/s and five milliseconds latency.

Modern production technologies in the automobile industry must become more flexible in order to fulfil individual customer requirements.

Im Focus: Sharp images with flexible fibers

An international team of scientists has discovered a new way to transfer image information through multimodal fibers with almost no distortion - even if the fiber is bent. The results of the study, to which scientist from the Leibniz-Institute of Photonic Technology Jena (Leibniz IPHT) contributed, were published on 6thJune in the highly-cited journal Physical Review Letters.

Endoscopes allow doctors to see into a patient’s body like through a keyhole. Typically, the images are transmitted via a bundle of several hundreds of optical...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Munich conference on asteroid detection, tracking and defense

13.06.2018 | Event News

2nd International Baltic Earth Conference in Denmark: “The Baltic Sea region in Transition”

08.06.2018 | Event News

ISEKI_Food 2018: Conference with Holistic View of Food Production

05.06.2018 | Event News

 
Latest News

Could this material enable autonomous vehicles to come to market sooner?

20.06.2018 | Materials Sciences

Innovative autonomous system for identifying schools of fish

20.06.2018 | Information Technology

Controlling robots with brainwaves and hand gestures

20.06.2018 | Information Technology

VideoLinks
Science & Research
Overview of more VideoLinks >>>