The Long Game

How John Daley leverages mass cytometry in his 36-year career fighting against cancer

One day in 1979, a young biochemistry graduate answered an ad in the Boston Globe:

“For those of you who want clinical relevance in the work you’re doing, we have an immediate opening available for a graduate biophysics background or relevant experience to operate a Becton Dickinson FACS 1 for cell sorting in immunological and cancer research.”

John Daley reads aloud from the ad he clipped more than 36 years ago, placed by the Sidney Farber Cancer Center and now kept in his office at the Dana-Farber Cancer Institute, where he is senior director of flow cytometry in the Dana-Farber core lab.

In 1979 fluorescence-activated cell sorting, the basis for the BD FACS™ instrument, was an emerging technology just beginning to find applications in immunology. “When I first saw a flow cytometer and a cell sorter and the guy explained to me that you could sort out cells at many thousand per second and look at very fine things, I said there’s no way that can do that,” Daley recalls. Once he saw it in action, he was hooked.

Today mass cytometry is the nascent technology, embodied in Helios™, a Fluidigm CyTOF® (cytometry by time-of-flight) system. Once again, Daley is in the thick of it. Dana-Farber has been an early adopter—then of flow and now of mass cytometry, with two CyTOF systems in its core lab. With the ability to tag hundreds of thousands of individual cells and measure dozens of parameters at once, CyTOF also seemed too good to be true.

“When I first saw the CyTOF, I did a little pilot experiment,” he explains. “And you could just feel that it was real science. Just feeling the machine and looking at the raw data output, I knew it was the real deal.”

Daley is joined at Dana-Farber by Nicole Paul, a young research scientist and CyTOF specialist who operates the mass cytometers. Paul previously worked to identify cell populations in acute myeloid leukemia (AML) to see how different treatments were contributing to apoptosis in patients. “People wanted to look at this marker and this one and this one, and the number of markers we got to would have made the whole experiment impossible,” Paul says. “That’s where my interest in CyTOF stemmed from.”

Like Daley, Paul found a home at Dana-Farber, where they are now in their third year of mass cytometry experiments. Daley notes that the lab location was Sidney Farber’s office way back when. It’s the oldest building on the campus but perhaps the most fitting home for the newest technology: the office of an original pioneer in cancer research.

The interplay of old and new underscores a lot in this lab, including the professional pairing of Daley and Paul. Though from different backgrounds and generations, they enjoy the kind of supportive relationship where they lunch together regularly and sometimes finish each other’s sentences. Their working style is easy and even, focused equally on task and goal, and operated with a seemingly unwavering belief that answers will be found.

Over the years Daley has seen countless advancements toward curing cancer and other diseases. He’s also developed a nuanced and balanced understanding of the potential and the limits of any technology, novel or proven. He is “fascinated” by mass cytometry and its ability to go deeper than flow in providing researchers with an understanding of cell populations and signaling pathways.

“The CyTOF to me feels more toward the chemistry level of precision, as opposed to the biological subjectiveness,” he says. “When I analyze the data when we use 17 or 18 markers simultaneously in a well-defined set, it comes just like what I would expect if I was doing five or six colors on three different panels. But here I get everything at once.”

“In my realm, spectral overlap compensation is more than just an additive effect,” Daley says. “It’s almost like a logarithmic effect as you start getting more and more markers.”

Paul notes the value of the sheer volume of data collected in mass cytometry in helping the research community learn more about biological systems. “CyTOF really has allowed us to open up and use more of the unsupervised analysis to see things we didn’t necessarily know were there before, because we can look at so many markers at once,” she says.

As a core lab, Dana-Farber makes the CyTOF systems available to outside researchers. Its location in the Longwood Medical Area and partnerships with Harvard Cancer Center, Brigham and Women’s Cancer Center and other institutions keep them busy, which is good not only for Dana-Farber but also for the technology and anyone else working on CyTOF. “The more pieces of data we put in these programs that they use, the better it works,” Daley says. “And CyTOF allows that to happen because you can do so many parameters simultaneously on hundreds of thousands of cells.”

As researchers work more and more with CyTOF systems like Helios, everyone learns more about the capabilities of mass cytometry, best practices for running protocols, efficient experimental design and more. “There’s a lot of interaction of people with this type of technology,” says Daley. “That is probably the most important ingredient to make it work at the capacity it has the potential for.”

“I’ve been at this since 1978 in cytometry, and I’ve always seen a sort of pendulum effect,” he says. “We have a piece of technology or equipment that we don’t know what to do with. But then as more people get exposed to it, they start to look at it from different perspectives.”

“We’re getting more and more different labs and different projects involved,” adds Paul. “Labs might have smaller projects, but they’re branching into more novel applications of the instrument that we haven’t seen before, and I think that is going to be interesting now that the technology is more established.”

Daley notes that there is no perfect system, saying that technology is always emerging and advancing. It’s the very use of the technology that improves it. The promise of mass cytometry is being defined and expanded with every experiment run on Helios.

“It’s like a glimmer of hope that’s getting stronger as we get more powerful probes and reagents, and the instrumentation becomes better-developed,” he says.

Daley speaks with the confidence of nearly four decades spent using and exploring cytometry. A light Boston brogue characterizes the poetic way he explains the benefits of the technology and his hopes for its future. It’s personal for him, as it is for many researchers, and as it only can be for someone who has dedicated an entire career to a single focus. And for such a technical endeavor, it seems like John Daley relies a lot on instinct.

“I feel there is a soul in the machine,” he says. “I can tell if something’s for real or not. There’s something when you’re around a lot of high-quality equipment, and there’s been a lot of energy involved in developing it.”

He ticks off developments and advancements over the years, saying that FACS, mass spectrometry and mass cytometry have the benefits of everything that came before, each ultimately greater than the sums of its parts. He imagines that discoveries in mass cytometry could be applied to advance flow cytometry, and back and forth until we arrive at the next step.

“You could say it’s like a gut feeling, but really: I see the output of the data.”

The data is the point, after all. It’s what originally enticed both Daley and Paul about mass cytometry, and it’s what furthers the mission to explore, understand and ultimately cure human disease, and specifically cancer. In their role of facilitating others’ research, the team is focused above all on ensuring top-quality data with every CyTOF run.

At Dana-Farber, Daley has always been in the forefront of what’s new and what’s possible. The legacy of Dana-Farber is also its mission—better understanding and treatment of cancer—and as its resident cytometry expert of 36 years, Daley can’t help but be defined by that.

“It does make me think a lot in the morning,” he says. “I call it ‘thoughts while shaving.’ I try to figure out where we’re going with the technology.”

To be sure, wherever cytometry goes, John Daley will be there too.

This spotlight was written for Fluidigm Corporation, a biotechnology and life sciences firm based in San Francisco. View the original here.