When small cell differences have far-reaching implications

In certain tissues or organs, cells may appear very similar or even identical. But at the molecular level, these cells can have small differences that lead to wide variations in their function.

Alex K. Shalek, a professor of chemistry at MIT, loves the challenge of uncovering those tiny differences. In his lab, the researchers develop and deploy technologies such as single-cell RNA sequencing, which allows them to analyze differences in gene expression patterns and allows them to know how each cell contributes to tissue function.

“Single-cell RNA sequencing is a very powerful way to check what a cell is doing at any given moment. By looking at the associations among the different mRNAs that cells express, we can identify very important tissue features — such as what cells are present and what they are trying to do,” said Shalek, who is also a core member of the MIT Institute for Medical Engineering and Science. and an extramural member of the Koch Institute for Integrative Cancer Research, as well as a member of the Ragon Institute of MGH, MIT and Harvard and a member of the Broad Institute of Harvard and MIT.

While his work focuses on identifying small-scale differences, he hopes it will have large-scale implications, as he seeks to better understand globally important diseases such as HIV, tuberculosis, and cancer.

“Much of what we are doing now is global collaborative work that is really focused on understanding the cellular and molecular basis of human disease – partnering with people in more than 30 countries on six continents,” he said. “I love the fundamental work and precision possible in model systems, but I’ve always been very motivated to connect our science to human health, and to understand what happens to various diseases so that we can develop better prevention and treatment.”

Exploring the physical world

As a student at Columbia University, Shalek bounced between different majors before settling on chemical physics. He started in physics because he wanted to understand the basic laws of how the physical world works. However, as he went further, he realized that most of the available research opportunities involved the detection of high-energy particles, which did not interest him.

He then took several math courses but felt no real connection to matter, so he turned to chemistry, where he found a course that suited him: statistical mechanics, which involves using statistical methods to describe the behavior of large numbers of atoms or molecules.

“I like it because it helps me understand how all the rules I’m learning in physics about these microscopic particles actually translate to macroscopic things in the world around me,” Shalek said.

Confused about what he wants to do after graduating from college, he decides to go to graduate school. At Harvard University, where he earned his PhD in chemical physics, he ended up working with Hongkun Park, a professor of chemistry and physics. Park, who recently accepted a job title for measuring the optical and electronic properties of single molecules and nanomaterials, is building a new program to study the brain. In particular, he wanted to find a way to make high-precision electrical measurements of many neurons at once.

As the first person to join the new endeavor, Shalek found himself responsible for inventing computational models, building devices, writing software to control electronics, analyzing data, and many other things he didn’t know how to do, on top of studying neurobiology.

“It was challenging, to say the least. I got a crash course on how to do a lot of different things,” he recalls. “It was a very humbling experience, but I learned a lot. By begging to the various labs around town at Harvard and MIT, I was able to pick things up faster. I feel very comfortable taking up new subjects and overcoming difficult problems by leaning on others and learning from them.”

His efforts led to the development of several new technologies, including nanowire arrays that can be used to record neuronal activity as well as to inject molecules into individual cells without damaging them and to erase some cell contents. This proved very useful for studying immune cells, which normally resist other delivery methods such as viruses.

Individual approach

Shalek’s work in graduate school stimulated his interest in systems biology, which involves comprehensive measurements of many aspects of biological systems using genomics and other techniques, then building models that take the observed measurements into account, and finally testing models in living cells using perturbation techniques. However, to his frustration, he often finds that when he tries to test a model’s predictions, not all cells in the system will show the expected results.

“There’s a lot of variability,” he said. “I’d see differences in mRNA levels, or in protein expression or activity, or sometimes all my cells don’t differentiate into the same thing.”

He began to wonder whether it would be worthwhile to try to study each individual cell in a system, rather than the traditional approach of performing combined sequencing of their mRNA. During the postdoc, he worked with Park and Aviv Regev, an MIT biology professor and member of the Broad Institute, to develop technology to sequence all of the mRNA found in large sets of individual cells. This information can then be used to classify cells into different types and reveal their state at any given moment.

In his lab at MIT, Shalek is now using improvements he helped make to this approach to analyze many types of cells and tissues, and to study how their identities are shaped by their environment. His recent work includes studies of how the state of cancer cells affects responses to chemotherapy, the cellular targets of the SARS-CoV-2 virus, analysis of cell types involved in lactation, and identification of T cells that readily produce inflammation during an allergic response.

The overarching theme of this work is how cells maintain homeostasis, or a stable state of physical and chemical conditions in living organisms.

“We know how important homeostasis is because we know that imbalances can lead to autoimmune disease and immune deficiency, or cancer growth,” Shalek said. “We wanted to really define at the cellular level, what is balance, how do you maintain that balance, and how do various environmental factors like exposure to various infections or diet change that balance?”

Shalek says he appreciates the many opportunities he has to work with other researchers around MIT and the Boston area, in addition to his many international collaborators. As his lab tackles human disease issues, he makes sure to help nurture the next generation of scientists, in the same way he can receive training and mentoring as a graduate and postdoctoral student.

“If you gather the collective trust of this community, as well as partner with people around the world, you can do extraordinary things,” said Shalek. “My experience taught me the importance of supporting and empowering scientists and trying to uplift the community, which is my main focus. I realized that a lot of my success depended on people opening their labs and giving me time and supporting me, so I tried to pay for it.”

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