In a study published online in Genome Research, researchers have developed a novel method of interpreting data from single-cell images to identify genetic interactions within biological networks, offering a glimpse into the future of high-throughput cell imaging analysis.
For years, scientists have been peering through a microscope at cells as they change appearance in response to different treatments, yet data collection is arduous, largely conducted qualitatively by eye. However, recent technological advances have led to the development of high-throughput image screening methods that can produce extensive datasets of hundreds of different morphological features.
With the ability to collect large imaging datasets, researchers from MIT and Harvard Medical School recognized an opportunity to explore the cellular networks that regulate cell morphology. "These images are an enormous source of data that is only beginning to be tapped," said MIT researcher Bonnie Berger, senior author of the work published today. "We realized we had enough data to go beyond classification and start to understand the mechanism behind the differences in shape."
To meet the challenge of interpreting cell image data, Berger and MIT graduate student Oaz Nir developed a novel computational model to identify genetic interactions using high-dimensional morphological data. Integrating prerequisite knowledge of a pathway, their model maps potential interactions within a network by looking for similar morphological features upon genetic perturbation.
The group demonstrated the method by analyzing the Rho-signaling network in fruit flies, a network that regulates cell adhesion and motility in eukaryotic organisms. In collaboration with Chris Bakal and Norbert Perrimon at Harvard Medical School, they "knocked-down" components of the Rho-signaling network using RNA interference and then imaged thousands of fly cells, gathering measurements of cell perimeter, nuclear area, and more than 150 other morphological features for each cell. The data was then passed through the computational framework to produce a set of high-confidence interactions, supported by confirmation of previously known interactions.
The group found that by making combinatorial knockdowns of Rho network components, their computational method was able to accurately infer Rho-signaling network interactions more precisely than when using only data from single knockdowns. Berger noted that this finding highlights the importance of combinatorial experiments for inferring complex networks, necessary to overcome natural redundancy in signaling pathways. As perturbation of the Rho pathway in humans has been implicated in cancer and other diseases, the authors believe that these predicted interactions will be excellent candidates for future study.
Berger expects that in combination with other sources of data, imaging as a new source of high-throughput data should appreciably increase the accuracy of known signaling networks. "This work provides a glimpse into the future," added Berger, "where looking under the microscope manually at cells one-by-one is replaced with automated high-throughput processing of many cellular images."
Scientists from the Massachusetts Institute of Technology (Cambridge, MA) and Harvard Medical School (Boston, MA) contributed to this study.
This work was supported by the Department of Energy, the Leukemia and Lymphoma Society, the National Institutes of Health, and the Howard Hughes Medical Institute.
Media contacts: The authors are available for more information by contacting Jennifer Hirsch at the MIT News Office (email@example.com; +1-617-253-1682).
Interested reporters may obtain copies of the manuscript from Peggy Calicchia, Editorial Secretary, Genome Research (firstname.lastname@example.org; +1-516-422-4012).
About the article: The manuscript will be published online ahead of print on February 9, 2010. Its full citation is as follows: Nir O, Bakal C, Perrimon N, Berger B. Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen. Genome Res doi:10.1101/gr.100248.109.
About Genome Research:
Launched in 1995, Genome Research (www.genome.org) is an international, continuously published, peer-reviewed journal that focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine. Among the topics considered by the journal are genome structure and function, comparative genomics, molecular evolution, genome-scale quantitative and population genetics, proteomics, epigenomics, and systems biology. The journal also features exciting gene discoveries and reports of cutting-edge computational biology and high-throughput methodologies.
About Cold Spring Harbor Laboratory Press:
Cold Spring Harbor Laboratory is a private, nonprofit institution in New York that conducts research in cancer and other life sciences and has a variety of educational programs. Its Press, originating in 1933, is the largest of the Laboratory's five education divisions and is a publisher of books, journals, and electronic media for scientists, students, and the general public.
Genome Research issues press releases to highlight significant research studies that are published in the journal.
Further reports about: > Genom > Genome Research > Laboratory > Medical Wellness > RNA interference > Rho-signaling > biological systems > cell imaging analysis > comparative genomics > genetic interactions > high-dimensional morphological data > molecular evolution > morphological data > morphological features > signaling pathway > spring
New photocatalyst speeds up the conversion of carbon dioxide into chemical resources
29.05.2017 | DGIST (Daegu Gyeongbuk Institute of Science and Technology)
Copper hydroxide nanoparticles provide protection against toxic oxygen radicals in cigarette smoke
29.05.2017 | Johannes Gutenberg-Universität Mainz
The world's highest gain high power laser amplifier - by many orders of magnitude - has been developed in research led at the University of Strathclyde.
The researchers demonstrated the feasibility of using plasma to amplify short laser pulses of picojoule-level energy up to 100 millijoules, which is a 'gain'...
Staphylococcus aureus is a feared pathogen (MRSA, multi-resistant S. aureus) due to frequent resistances against many antibiotics, especially in hospital infections. Researchers at the Paul-Ehrlich-Institut have identified immunological processes that prevent a successful immune response directed against the pathogenic agent. The delivery of bacterial proteins with RNA adjuvant or messenger RNA (mRNA) into immune cells allows the re-direction of the immune response towards an active defense against S. aureus. This could be of significant importance for the development of an effective vaccine. PLOS Pathogens has published these research results online on 25 May 2017.
Staphylococcus aureus (S. aureus) is a bacterium that colonizes by far more than half of the skin and the mucosa of adults, usually without causing infections....
Physicists from the University of Würzburg are capable of generating identical looking single light particles at the push of a button. Two new studies now demonstrate the potential this method holds.
The quantum computer has fuelled the imagination of scientists for decades: It is based on fundamentally different phenomena than a conventional computer....
An international team of physicists has monitored the scattering behaviour of electrons in a non-conducting material in real-time. Their insights could be beneficial for radiotherapy.
We can refer to electrons in non-conducting materials as ‘sluggish’. Typically, they remain fixed in a location, deep inside an atomic composite. It is hence...
Two-dimensional magnetic structures are regarded as a promising material for new types of data storage, since the magnetic properties of individual molecular building blocks can be investigated and modified. For the first time, researchers have now produced a wafer-thin ferrimagnet, in which molecules with different magnetic centers arrange themselves on a gold surface to form a checkerboard pattern. Scientists at the Swiss Nanoscience Institute at the University of Basel and the Paul Scherrer Institute published their findings in the journal Nature Communications.
Ferrimagnets are composed of two centers which are magnetized at different strengths and point in opposing directions. Two-dimensional, quasi-flat ferrimagnets...
24.05.2017 | Event News
23.05.2017 | Event News
22.05.2017 | Event News
29.05.2017 | Earth Sciences
29.05.2017 | Life Sciences
29.05.2017 | Physics and Astronomy