MIT researchers have invented a new method to accurately measure the growth of multiple individual cells at the same time.
This invention provides a better understanding into the variation in the growth of individual cells in larger populations. It could potentially lead to faster drug tests and help to observe the growth of cells to environmental changes.
The details of the research have been reported in Nature Biotechnology. The study used suspended microchannel resonators (SMR), which is a microfluidic device that calculates the mass of single cells when they flow through tiny channels.
The novel design has increased the device’s throughput by almost two orders of magnitude while maintaining precision. MIT professor Scott Manalis, the senior author of the paper, and his teammates have been focusing on the development of SMRs for almost 10 years.
The researchers employed the device in their research to study the effect of antimicrobial peptides and antibiotics on bacteria. They also used the device to discover growth variations in individual cells within populations, which has significant clinical implications. For example, bacteria that grows slowly could have more resistance to antibiotics and may result in recurrent infections.
The device provides new insights into how cells grow and respond to drugs.
Scott Manalis, Professor, MIT
Malalis is the Andrew (1956) and Erna Viterbi Professor in the MIT departments of Biological Engineering and Mechanical Engineering and a member of the Koch Institute for Integrative Cancer Research.
The paper’s lead authors are Nathan Cermak, a recent PhD graduate from MIT’s Computational and Systems Biology Program, and Selim Olcum, a research scientist at the Koch Institute. There are 13 other co-authors on the paper, from the Koch Institute, MIT’s Microsystems Technology Laboratory, the Dana-Farber Cancer Institute, Innovative Micro Technology, and CEA LETI in France.
Array of Hope
The SMR was first developed in 2007 by Manalis and his colleagues. Since its introduction the researchers have introduced many innovations for various purposes, such as observing individual cell growth over time, weighing cell-secreted nanovesicles, and measuring cell density. The most recent innovation was to measure the cells’ short-term growth response to changing nutrient conditions.
These methods have all been based on an important scheme. This scheme involves etching a fluid-filled microchannel in a small vibrating silicon cantilever sensor in a vacuum cavity. The sensor’s vibration frequency is altered minutely when a cell enters the cantilever.
The cell weight can be measured using this signal. The researchers could measure the growth of an individual cell by passing it back and forth through the channel for a period of 20 minutes. The cell can gain mass during this time, which can be measured by SMR.
Although SMR can measure cells with 10 to 100% more accuracy over other devices, it is limited to measuring one cell at a time. As a result it can take many hours or even days at a time to measure enough cells.
Designing and controlling a series of 10 to 12 cantilever sensors that serve as weigh stations and recording a cell’s mass as it passes through the postage-stamp-sized device was the key to the new method.
Winding “delay channels” five centimeters in length between the sensors allowed the cells to grow while they passed through them from one sensor to the next. The device’s throughput can be maximized by passing a cell into the sensor right after the previous one exits it. The outcomes display the mass of all the cells at each sensor while showing the extent to which a cell has shrunk or grown.
The researchers were able to measure 150 bacterial and 60 mammalian cells per hour, as compared to a few cells that could have been measured by single SMRs in the same time.
Being able to rapidly measure the full distribution of growth rates shows us both how typical cells are behaving, and also lets us detect outliers — which was previously very difficult with limited throughput or precision.
Nathan Cermak, PhD Gradute, MIT
Quantitative phase microscopy (QPM) is another method that can be compared with the new technique to measure numerous single cells simultaneously. QPM measures the optical thickness of cells and thereby calculates their dry mass.
This technique can be employed to measure cells that grow adhered to surfaces, unlike the SMR-based method. The accuracy of the SMR based approach is, however, higher.
“We can reliably resolve changes of less than one-tenth of a percent of a cancer cell’s mass in about 20 minutes. This precision is proving to be essential for many of the clinical applications that we’re pursuing,” Olcum says.
New Drug-Testing Capabilities
The team observed the effects of kanamycin, an antibiotic on E.coli during one of their experiments. Kanamycin prevents the synthesis of protein in bacteria and thereby stops their growth and kills the cells.
A culture of bacteria needs to be grown to conduct conventional antibiotic tests and this takes a day or more. The new device enables the researchers to observe a change in the rate at which mass accumulates in the cells within an hour.
The reduction in recording time is significant in testing anti-bacterial infection drugs, says Manalis. He adds, “In some cases, having a rapid test for selecting an antibiotic can make an important difference in the survival of a patient.”
The researchers also used the device to track the effects of CM15, an antimicrobial peptide, which is a new protein-based candidate to fight bacteria. These candidates are highly important because bacteria strains develop resistance to common antibiotics.
CM15 drills microscopic holes in the cells wall, draining the cell of its content and eventually killing it. But, the effects can be overlooked by conventional methods as there is no change in its size but only in its mass.
The team did observe a rapid loss of mass in the E.coli cells after they were exposed to CM15. Manalis says that the results can validate the peptide and other novel drugs that provide a better understanding of the mechanism.
The team are currently collaborating with the Dana Farber Cancer Institute, through the Koch Institute and Dana Farber/Harvard Cancer Center Bridge Project, to figure out if the device can be employed to anticipate patient response to therapy by measuring the weight of tumor cells in the presence of anticancer cells.
Professor and chair of the Department of Systems Biology at Harvard Medical School, Marc Kirschner, who was not a part of the study, stated that the new microfluidics device will create new paths for exploring the “physiology and pharmacology of cell growth. … Since growth is related to proliferation and to the stress a cell is under, it is a natural feature to study, but it has been difficult before this method.”
The technical problems to get this working were significant and it is still incredible for me to think that they pulled this off. I expect that when it is … into biology labs it will be useful for many problems in cancer, metabolism, cell death, and cell stress.
Marc Kirschner, Professor, Harvard Medical School
The study was partly funded by the Koch Institute and Dana Farber/Harvard Cancer Center Bridge Project, the U.S. Army Research Office, the National Cancer Institute and the National Science Foundation.