In June I had the chance to sit down and talk with Professors Jim Eberwine (University of Pennsylvania) and Cynthia McMurray (University of California, Berkeley/Lawrence Berkeley National Laboratory) about the Single Cell Analysis course they co-direct, held here at Cold Spring Harbor Laboratory (CSHL). The course, currently in only its second year, was a natural branch from a meeting and concurrent workshop on Single Cell Analyses. I wanted to know what made this nascent course so special. Jim and Cynthia enthusiastically recounted how the course got started, where it is going, and just what makes this area of science and the course they have put together so unique.
Scientists have studied cells since Robert Hooke first observed them under a crude microscope in 1665. You may remember looking down the microscope at high school and seeing the various esoterically named parts of the cell: the Golgi body; the endoplasmic reticulum; the mitochondria; the nucleus.
Today we have progressed to a point where scientists can gather astonishing kinds of information from a single cell, taking us deeply into its workings and providing insights about diseases, including cancer. The Single Cell Analysis course run by Jim Eberwine and Cynthia McMurray teaches researchers how to do just this kind of analysis.
When you consider that there is over 6 feet of DNA tightly coiled into the nucleus of a human cell, as well as the resulting multitude of genes being expressed, proteins made, and reactions taking place, you come to realize that there is a lot of ground to cover, even in looking at just one cell.
“We take a holistic approach to single-cell biology,” says Eberwine. “The idea is to understand every aspect of the cell in a quantitative manner.”
That’s the key to what makes this course unique. There are other courses where you can do single-cell analysis on one or two aspects of the cell. But, Eberwine emphasizes, “This is the only course that tries to do everything possible with the single cell.”
Such a comprehensive analysis includes not only reading the “letters” of the full DNA genome, i.e., DNA sequencing, but also sequencing the RNA “messages” copied from DNA (transcriptomics); analyzing many of the proteins present in the cell, their structure and biochemical functions (proteomics); studying the metabolic reactions within the cell (metabolomics); characterizing the global patterns and mechanisms that turn genes on and off; and determining where all these things happen in the cell, as well as how and in what manner the cell is moving relative to other cells.
Students go through each step, from stimulating and manipulating the cells, isolating single cells from their environment and the cells surrounding them, to analyzing the compartment of the cell they are interested in, under the tuition and watchful eyes of experts in each field.
CSHL provides a specific FTP site to host the “tons and tons” of sequencing and image data produced during the course. Eberwine and McMurray have also made sure to invite data analysis experts as instructors to teach students how to store and analyze all that data, using publicly available software, including learning programming languages such as R.
For those who come to the course with the idea of learning one particular technique, this approach broadens their horizons. “The students realize they can do all these other great things, that they can apply many other methodologies to their research,” says Eberwine.
Importantly those taking the course not only have considerable success in gathering and analyzing data, resulting in a number of breakthroughs and “firsts,” but they are also better placed to troubleshoot their work when they bring the techniques back to their respective labs.
This year, one of those “firsts” was some groundbreaking research using Planaria, a worm that Charles Darwin himself described as “an immortal organism.” Students were able to isolate single neoblasts, which are regenerative cells, and introduce some foreign DNA encoding a fluorescent protein. As a consequence the cells glow green, which helps investigators see them when they move.
The students then grew these cells and determined their DNA sequence. Studying regenerative cells in the worm could have dramatic implications for the understanding of stem cells in humans. “It’s exciting to ask age-old questions, in this case: what makes these Planaria cells immortal? We are able to start finding answers right here on this course!” says McMurray.
In addition, the course allows students to bring in their own cells and research to work on after the coursework has been completed. Cells brought in from the instructors’ labs provide known, repeatable results and the students then apply what they’ve learned to their own research in the same controlled environment. “This can jumpstart their own research and it keeps them excited and interested in what they are doing, both on the course and back at their lab,” says Eberwine.
Where do the students go from here? Jim Eberwine has asked the same question and has some suggestions. “The amazing part is that we are now able to measure variability in all these aspects of the cell at the single-cell level. So the next question is why? Why does each cell vary in its protein expression or RNA expression? What does that mean functionally? How do all these cells work together in a system with these differences? Its an exciting area to work in at the moment.”
This is what is happening with the work done on Planaria during the course as well as in research at CSHL. The Wigler and Hicks labs for example are concentrating on finding the differences in the genomes of single cancer cells sampled from different places in the same tumor. By doing this they hope to answer the question; How does a tumor evolve?
But the techniques involved in single-cell analysis are being used across disciplines, not just on important health-related issues such as these. “Almost any research that involves cellular analysis can make use of single-cell analysis,” says Eberwine.
A student from Woods Hole Oceanographic Institute (WHOI), for example, brought blue-green algae cells to study on the course. Blue-green algae are important as biogenerators, so understanding single-cell diversity within a blue-green algal bloom or colony could be exploited for bioenergy.
To do these studies requires some pretty special technology, but at the rate technology is advancing it won’t be long before analyzing single cells will become de rigueur. “The key to absolutely everything a scientist does is data capture — how do you get your data? You can ask any scientific question you want, but the ability to address it depends on technology development,” says Eberwine.
“It’s technology that drives the speed of the rate of change,” adds McMurray. Students on the single-cell analysis course have access to cutting-edge, some would say bleeding-edge technology, and become very familiar with it. That exposure can inspire people to become inventive and develop their own technologies, refining and redefining their own field of research.
All of these aspects contribute to a wonderfully vibrant and dynamic course and word is getting out. Participants have come from near and far, from the US to South Korea and Saudi Arabi and in between. For a course that is only in its second year this is exceptional, according to Dr. David Stewart, the executive director of CSHL’s Meetings & Courses program. It is clear from the enthusiasm of Jim Eberwine, Cynthia McMurray and the others involved, that this course will continue to go from strength to strength.