Researcher Spotlight

Learn about notable advances in our single-cell science research with the Boston Children’s Hospital (BCH) community and beyond. We are committed to advancing single-cell science by making it accessible and empowering other scientists to dig deeper into their data, one cell at a time.

30.12.2025
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Getting To Know The CDN Leadership Team: Sangita Choudhury

From a small city in India to leading-edge cardiovascular genomics in Boston, Dr. Sangita Choudhury’s journey is one of persistence, curiosity, and vision. A microbiologist turned heart researcher, she leads a lab uncovering how our hearts change from birth to aging—mapping every cell, mutation, and molecular shift along the way. By combining single-cell and spatial genomics, her work explores why the human heart loses its ability to regenerate and how that knowledge could one day restore it. Guided by passion and intuition, Dr. Choudhury is not just studying the heart—she’s redefining what it means for it to heal.

Where are you from, and what inspired your journey into science?

Sangita Choudhury: I was born in a small city in India in the 1980s. My parents were both teachers, and while having a second daughter was not considered fortunate at the time, they believed deeply in education. They made the bold decision not to save money for a wedding, but to invest in my education instead. That choice changed everything for me.

As a teenager, I discovered microbiology almost by chance. I was fascinated by microbes under the microscope—watching them move, reproduce, and interact with each other. I could spend hours at the bench, and it never felt like work. This fascination drove me to study microbiology for five years. Later, I shifted to cancer biology during my master’s studies, where I realized that I wanted to pursue research with direct implications for health.

Eventually, I found myself drawn to cardiovascular research. What excited me was not just studying disease, but bringing together new technologies to answer biological questions that had never been addressed before. My path was not linear, but every step taught me something valuable.

At what age did you know you wanted to be a scientist?

Sangita Choudhury: By fourth grade, I knew that science was my future. The school library was my refuge—I read everything I could find, even if I didn’t fully understand it. Unlike other children who looked forward to trips or vacations, I often preferred staying behind with a stack of books.

In sixth grade, I carried out my first experiment at home: dissecting a frog. My mother encouraged me, even though my father thought it was outrageous. Seeing the organs inside the frog sparked a lifelong curiosity about how living systems work. That moment, more than any other, solidified my identity as a future scientist.

As I grew older, I fought hard to pursue education outside my hometown. My parents supported me despite limited finances, sending me to boarding school and then university in another state. Their sacrifices, especially my mother’s unwavering belief, laid the foundation for my career.

Who were your biggest influences along the way?

Sangita Choudhury: My mother has always been my greatest supporter. She was fearless and believed in me when others doubted. She encouraged me as a child when I wanted to explore science, and as an adult when I faced career crossroads. Even today, she travels to help me whenever I am overwhelmed by professional or family responsibilities.

Beyond family, I was fortunate to have incredible mentors. In Germany, my PhD advisor encouraged me to pursue innovative technologies, even when they seemed risky. In Boston, Bernard Kühn introduced me to single-cell approaches in cardiovascular research, and Chris Walsh welcomed me into his lab when I was transitioning to independence. Each mentor gave me not only technical guidance but also confidence in my own ideas. Their support taught me that science is never a solo journey—it is built on networks of encouragement and trust.

What values guide your work in science and life?

Sangita Choudhury: I am guided by passion, persistence, and intuition. Passion is essential because science is too demanding to succeed without it. Persistence is equally critical—experiments fail, grants are rejected, and papers can take years to publish. Without persistence, even brilliant ideas can fade away.

Intuition guides me in asking the right questions. Often, progress comes from trusting a hunch, even when others doubt it. But passion, persistence, and intuition are not enough on their own. Mentorship, family support, and luck are also vital. I have experienced moments when everything seemed to collapse, only to find that a mentor’s belief or a well-timed opportunity changed my path.

I also believe that no effort is wasted. A failed experiment today often becomes the foundation for tomorrow’s breakthrough. This perspective keeps me motivated even in the most challenging times.

Tell us about your current research focus.

Sangita Choudhury: My lab studies how the human heart changes at the genomic and transcriptomic level across development, aging, and disease. We combine cutting-edge technologies, whole genome and duplex sequencing, single-cell RNA sequencing and spatial transcriptomics to build comprehensive maps of heart cells to decipher how heart cells evolve over time. Using these high-resolution approaches, we examine how somatic genomic alterations change the genomic landscape in an organ- and cell-specific manner- and how these changes influence organ function and repair.
For example, how does a newborn heart differ from an aging one? What changes occur in cardiomyocytes during heart failure? By building these maps, we can begin to understand what makes a heart cell resilient—or vulnerable.

The ultimate goal is ambitious: to identify ways to preserve heart health for longer and to reactivate regenerative pathways that fade after childhood.

For a general audience, what does ‘polyploidy’ mean, and why does it matter for the heart?

Sangita Choudhury: Polyploidy refers to cells that contain more than two complete sets of chromosomes. Most cells in the human body are diploid, meaning they have two sets. Heart muscle cells, however, often have extra sets—four, six, or even more. Some also have multiple nuclei.

This unique feature of heart cells is one reason they behave differently from cells in other tissues. For example, zebrafish heart cells remain diploid, and zebrafish can regenerate their hearts after injury. Human heart cells, with their higher polyploidy, cannot.

Understanding why polyploidy develops in human hearts and what role it plays in limiting regeneration could hold the key to new therapies. It may even help explain why certain heart diseases progress the way they do.

What challenges come with studying polyploid cells?

Sangita Choudhury: Studying polyploid cells presents both conceptual and technical challenges.
Conceptually, polyploidy raises fascinating questions. Polyploid cells could be generated in many different ways, and different routes to polyploidization may result in different outcomes. Cancer cells, which often become polyploid, an indication of genome instability, continue to divide, while polyploid heart muscle cells cannot divide. Why does polyploidy seem to protect against certain stresses in some tissues but cause vulnerability in others?

These puzzles continue at technical level too, most genomic analysis tools assume that cells are diploid. When cells have four or more chromosome sets, these tools give misleading results. This means we must adapt methods or build new tools entirely.
The heart of our research. Solving them could lead not only to new treatments for heart disease but also to broader insights into cell biology.

What have you learned about how mutations accumulate in heart cells?

Sangita Choudhury: Even though cardiomyocytes stop dividing after early childhood, their DNA is constantly under pressure from metabolism and oxidative stress. This stress leads to mutations, which accumulate over time. Because these cells do not regenerate, they retain mutations permanently, acting almost like a diary of the cell’s life.

We have found that in diseases like ischemic heart failure, the mutation burden is significantly higher than in healthy hearts. This suggests that accumulated mutations may contribute to the disease processes. In the future, such patterns could help us predict risk, diagnose disease earlier, or develop therapies that protect against DNA damage.

How do you see your research translating to patient care?

Sangita Choudhury: Fundamental biology is the first step toward clinical impact. Without understanding how heart cells function at the most basic level, we cannot design effective treatments. By mapping genomic and transcriptomic changes in the heart, we hope to identify targets that could be used to preserve heart function or trigger regeneration.

In addition, our work with congenital heart disease patients provides direct clinical context. Seeing how malformations develop in children gives us clues about what goes wrong in development and how those processes might be corrected. It is a reminder that research is not an abstract exercise—it has direct implications for patients and families.

What scientific achievement are you most proud of?

Sangita Choudhury: I am especially proud of pioneering work that integrates cardiovascular biology, molecular techniques, and bioinformatics into a single framework. Early in my career, I helped develop ways to analyze individual heart cells at unprecedented resolution. These projects often took years to complete but demonstrated that it was possible to study the heart with the same granularity as cancer or neuroscience.

This integration has opened the door for new collaborations and inspired other labs to adopt similar approaches. To me, that is the mark of an impactful achievement—not just personal success, but influencing the direction of the field.

If you weren’t a scientist, what would you be?

Sangita Choudhury: If I were not a scientist, I would be a writer. Science and writing share a common thread: storytelling. Science builds narratives from data, while writing builds them from imagination. If I were not at the bench, I would still want to explore ideas and share them with others through words.

How can people follow your work?

Sangita Choudhury: The best place is our lab website, where we post updates on publications, projects, and opportunities. While I am not very active on social media, I recognize the importance of communicating science more broadly. We are working to make our website a place where colleagues and the public alike can learn what we are doing and why it matters.

11.11.2025
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Getting To Know The CDN Leadership Team: Jeff Moffitt

Jeff Moffitt’s path to biology began with lasers, not microscopes. Trained as a physicist, he was drawn to the beauty of building instruments that reveal the unseen. Today, as a professor at Boston Children’s Hospital, Moffitt leads a lab that merges engineering ingenuity with biological discovery. His team designs advanced imaging technologies that make it possible to see how cells and microbes organize in space—turning the invisible architecture of life into something measurable. By pairing this innovation with questions in mucosal immunology and the microbiome, Moffitt’s work is redefining how we understand the dynamic relationships that sustain health and drive disease.

Where are you from? What’s your professional background, and what set you on your current path?

Jeff Moffitt: Big question! I’m a physicist by training. I started out fully intending to do high-energy physics. As an undergrad I spent a lot of time in that world, then went to grad school planning to be an experimental accelerator physicist. I worked at CERN and at the Cornell accelerator, and when I arrived at UC Berkeley I expected to keep going down that road. But early in my PhD a few things shifted. I fell in love with biophysics and transitioned from high energy to biophysics, doing my PhD with Carlos Bustamante at Berkeley. Carlos pioneered optical methods to manipulate and monitor single molecules.

I began building optical tweezers—microscope systems that focus a laser to a diffraction-limited spot to trap small objects like polystyrene beads. You can attach those beads to single DNA molecules and use them as “handles.” As you move the beads with the laser, you can directly calculate the force on the beads—and therefore on the DNA.

My PhD focused on developing an assay to detect the motion of a molecular motor that translocates along DNA. The system was the double-stranded DNA bacteriophage φ29, which infects Bacillus subtilis. The phage forms a protein capsid first, then uses a powerful motor at one portal to pull its genome inside. The packing reaches crystalline densities, with internal pressures estimated at tens of atmospheres—energy later used for genome injection during infection.

That motor is a pentameric ring ATPase. When I started, there were open questions about how the five identical subunits coordinate. We wanted optical tweezers sensitive enough to resolve each increment of DNA translocated—the step size. Because the rise per base pair in B-form DNA is 3.4 Å, we needed angstrom-scale resolution in real time. We built a tweezers instrument that could do that, followed the packaging in real time, and worked out the mechanochemistry—how the motor uses ATP to drive compaction.

Why I gravitated to this? Biology’s complexity is beautiful. And, unlike high-energy physics, biophysics is a scale where one person can build the instrument, do the wet-lab work, and the theory to interpret the measurements.

When did you know you wanted to be a scientist? Was there a single moment?

Moffitt: No single moment. I’ve always been an engineer at heart—I like understanding how things work and building things. I enjoyed science through school and gravitated toward physics in college because it nicely merges math and mechanistic thinking. It felt natural to continue.

Many leaders we talk to come from MD or biology-heavy backgrounds. How does physics training shape how you frame biological questions and design experiments?

Moffitt: Biology is the science of complexity; you won’t reduce most of it from first principles. You still have to learn the biology. Where physics helped me most is in the experimental culture: define what you want to measure, then build the instrument. Molecular biology has been “kit-ified,” which is convenient, but it can limit imagination—you frame questions around what’s available. Physics trained me to say, “If it doesn’t exist, let’s build it,” and to iterate until it works. That mindset has guided my career, and it’s something I consciously instill in my lab.

There’s also a philosophical piece. Physics often deals with simple systems—an electron has charge, mass, spin. That is it. As such, this simplicity allows theory that can match experiment with astonishing precision. Growing up in that environment gives you a faith that things are understandable. In biology, even if some problems resist simple descriptions, that confidence helps you keep pushing.

Give us a two-to-three-minute elevator pitch: what does your lab do and what questions drive you?

Moffitt: We’re both a host–microbe/mucosal immunology lab and a microscopy technology development lab. Our niche is questions at mucosal surfaces where current technology can’t yet give good answers. Then we build the microscopy to make those answers possible.

We develop genome-scale microscopy: methods that retain the strengths of high-resolution imaging—cell morphology, architecture from nanometers to centimeters—while capturing the molecular complexity you associate with sequencing (transcriptomes, genomes). In short, we aim to do sequencing-scale readouts with a microscope. Most of our biology centers on what new insights are possible if we can measure more molecular complexity in situ at the host–microbe interface.

What does microscopy give you that dissociated single-cell or bulk sequencing doesn’t?

Moffitt: Several things:

Spatial context. Tissues aren’t well-mixed bags of cells; organization drives emergent behavior. We get cell type/state information and who neighbors whom, plus morphology—critical for explaining tissue function.
Avoidance of dissociation artifacts. Not all cells dissociate or survive prep equally, and some change their state. Imaging fixed tissue in situ avoids those issues and lets us capture populations that are hard to recover by dissociation (large, fragile, or adherent cells like stromal cells or megakaryocytes).
High detection efficiency. Sequencing workflows have losses at extraction, reverse transcription, etc. Our fluorescent, single-molecule readouts can achieve very high capture efficiency, which is crucial for low-abundance transcripts (certain receptors, transcription factors) where a few molecules matter.

Net: we reconstruct spatial organization, maintain morphology, avoid dissociation bias, and detect low-copy transcripts—often revealing cell states/types or spatial niches missed by other methods.

You’ve also emphasized intracellular spatial organization and the problem of signal crowding. How do you resolve dense RNA regions?

Moffitt: Intracellular localization is vital—many processes depend on where RNAs reside (development, stress responses, motility, synaptic plasticity). Our genome-scale readouts rely on optical barcodes created through repeated staining and imaging cycles; barcodes map to single RNA molecules, so we must resolve single-molecule spots. Optical resolution can limit that, especially in microbes where RNA densities are ~100× higher than in eukaryotes.

We addressed this using expansion microscopy (pioneered by Ed Boyden’s lab) to physically expand samples—diluting signals and overcoming crowding. We routinely expand tissue by ~1000× in volume, which lets us resolve densely packed RNAs, including in bacteria.

How many genes can you measure, and what are the trade-offs of ultra-high multiplexing?

Moffitt: Our probes are targeted oligos; barcodes can be arbitrarily long, so in principle we can target hundreds to hundreds of thousands of RNAs. Practically, as you target more RNAs, density increases and single-molecule resolution becomes harder—solvable with expansion, at the cost of throughput (fewer cells imaged per run).

Imaging can still be very high throughput—we routinely generate multi-million-cell datasets—so there’s room to balance multiplexing and cell count. In practice we often use thousands of genes, which lets us profile millions of cells, detect rare states, and interrogate spatial niches.

Because we’re targeted, we design panels around questions, not everything-omics by default. If we’re studying pathogenic E. coli in the gut, we load panels with cytokines, chemokines, receptors (~300 genes), matrix remodeling (collagens, proteases, inhibitors), morphogens (Wnts, BMPs, receptors), etc. Whole pathways go in. If we later have new questions, we build a new panel rather than trying to measure everything at once. As the field commercializes, learning to ask well-matched questions is key; these methods shine when you choose the right targets.

You generate a lot of custom data and still balance biology with technology development. How do you manage that?

Moffitt: My projects typically start with a biological question we can’t answer yet, then we build the technology, and finally we use it to answer the question. That arc keeps the technology anchored in biology—ensuring it at least gets used once—and it trains scientists across both tech-dev and application. Choices you make in tech-dev shape the biology you can do, and vice versa. It’s a rewarding feedback loop and, I think, a great training experience.

How do you get these technologies into other labs’ hands? Collaboration, open science, commercialization?

Moffitt: All of the above.

Collaboration. We work broadly beyond our core host–microbe focus, pairing with experts in other tissues. That spreads know-how—experimental design, analysis, and mindset. Some early collaborators now run spatial programs of their own.
Open sharing. We build our microscopes, fluidics, software, compute, storage—everything—and publish protocols, open-source software, and updates. Many labs have successfully replicated the methods.
Commercialization. Academia optimizes for “works and is novel,” not “robust and push-button.” A company can “sand off the edges,” engineer reliability, and build training pathways for users who can’t invest years building from scratch. I co-founded Vizgen with Xiaowei Zhuang to commercialize MERFISH. It’s gratifying to see MERFISH used across species and tissues—Arabidopsis, planaria, fish, and extensively in mouse brain and beyond. Collaboration and open tools scale only so far; commercialization brings true access at scale.

Pivoting to clinical impact: why focus on the host–microbe interface and mucosal immunology? Did this grow out of your earlier bacteriophage work?

Moffitt: In a way. As a physicist moving up in complexity, I went from molecules to cells; E. coli felt like biology’s “hydrogen atom.” My postdoc explored bacterial cytoplasmic structure and RNA organization, and some ideas that were used in MERFISH started there. I also worked with microfluidics and grew interested in microbial communities—most bacteria don’t live in test tubes.

Surrounded by early microbiome pioneers, I saw the opportunity. When I started my lab, the gut was a natural place: rich microbial communities, clear relevance to health and disease, and incredibly diverse host biology—development, nervous system, immunity, stroma. It let us push spatial transcriptomics on both microbes and host.

At Boston Children’s, we’ve been moving toward the clinic—mouse models and human samples in inflammatory bowel disease (IBD), for example—leveraging the clinical expertise here to make that translation. The amazing clinicians that are our colleagues have made this pivot to translational work possible.

What is the biggest challenge in moving from mouse to human gut tissue?

Moffitt: Two big ones:

Logistics. Human tissue collection is nontrivial. You need a deeply committed, well-coordinated clinical team. We’ve been fortunate to partner with Scott Snapper and colleagues—they’re phenomenal.
RNA preservation. MERFISH images RNA, which is fragile. Much of histology wasn’t designed for RNA integrity. Protocols that work in mouse under controlled conditions don’t necessarily translate to clinical workflows. We spent substantial effort optimizing fixation, processing, and sectioning for human samples, iterating closely with our clinical partners. That work was essential—and now we have robust solutions.

Microbiome identification is hard when references are incomplete. With targeted probes, how do you handle unknown diversity?

Moffitt: It depends on the question. We’ve leaned on two major community advances:

Defined, whole-genome–sequenced microbial consortia in germ-free mice. Many labs have built communities—from 8 to ~100 species—where every member is cultured and sequenced. These recover key host phenotypes and give exquisite experimental control. For targeted imaging these controlled communities are exceedingly powerful as you know exactly what’s there.
Metagenomic reconstruction. Powerful pipelines can assemble genomes from samples. For clinical translation, one can match biopsies to fecal samples, reconstruct the patient-specific microbiome, and then design targeted probe sets accordingly. Not a solved problem, but the foundation is strong—and that makes it an exciting technical frontier with clear biological payoff.

Looking ahead a few years, what big biological questions are you most excited to tackle?

Moffitt: A central one:
What spatial structures exist within commensal gut communities, how conserved are they, and how do they influence stability, dynamics, and interactions?

Even in the gut—with peristalsis and flow—there are sharp gradients of antimicrobials, oxygen, pH, and nutrients. We’ve had few tools to study how those gradients shape community structure and function. We’re building those tools now.

Inflammation physically remodels the environment, and there’s growing appreciation that pathogen “success” often involves exploiting host-created niches. Understanding the triad—commensals, pathogens, and host—in space is a major focus.

Fecal microbiota transplants (FMTs) can be lifesaving and have even shown cancer impacts. How might this reshape treatment, and where does spatial biology fit?

Moffitt: FMT highlights the potential but isn’t likely the endgame. Most envision designed, quality-controlled microbial consortia rather than donor stool. For that to work, we need to understand engraftment: which organisms can occupy which spatial niches and why. Spatial constraints will influence stability, competition, and co-occurrence. Our goal is to build the tools to quantify how space governs interactions and to inform the design of engraftable, therapeutic communities.

If you weren’t a scientist?

Moffitt: I’d be an engineer. I love building things.

Greatest scientific advance of the last decade?

Moffitt: The explosion of precise, efficient, rapid genome engineering—CRISPR and its many derivatives. Pairing defined perturbations with genome-scale spatial readouts is incredibly powerful. You can make exactly the change you want, in the cell type you want, and then ask how all surrounding cells respond in situ.

Any advice for young scientists interested in spatial optics/spatial biology?

Moffitt: Dive in. It’s still the wild west—plenty of room to make lasting contributions. Be bold, be brave, and roll up your sleeves. It’s not too late; it’s exactly the right time.

18.06.2025
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Getting to Know the CDN Research Community: Dr. Miao Cui

We are thrilled to feature Dr. Miao Cui, whose scientific journey bridges continents and disciplines—from evolutionary biology in China to cutting-edge heart regeneration research in the U.S.

Dr. Cui leads a lab focused on unlocking the regenerative potential of the heart, especially by studying how neonatal mice are able to recover from heart attacks—an ability lost in adulthood. Her team uses AAV-based gene therapy to understand and activate molecular pathways that promote tissue repair. One of her lab’s major discoveries includes identifying NRF1 as a key gene in neonatal heart regeneration, which regulates antioxidant defenses and protein homeostasis.

By combining tools like lineage tracing, CRISPR-Cas9, and spatial transcriptomics, Dr. Cui is uncovering how specific genes and cell states can be leveraged to heal the adult heart. Her current projects include high-throughput in vivo screening and mapping transcriptomic shifts across heart development, aging, and disease. Her ultimate goal? To translate these findings into therapies that help the human heart regenerate itself—no transplant required.

Outside the lab, Dr. Cui brings a creative eye to her work, inspired by a lifelong love of nature, math, and art. She even mused that if she weren’t a scientist, she’d be a painter or graphic designer—a nod to the beauty she sees in biology.

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We’d love to start with where you’re from! Please tell us about your background, and what lead you to a career in science?

Dr. Miao Cui: I grew up in China and moved quite a bit growing up. My family relocated between cities frequently, which gave me a broad exposure to different places and people. I did my undergraduate studies at Nanjing University, where I majored in zoology and evolutionary biology. Afterward, I pursued a master’s degree in evolutionary biology, also in China. In 2010, I came to the U.S. to begin my PhD in developmental biology at the California Institute of Technology. There, I studied gene regulatory networks in sea urchin embryonic development. Interestingly, that experience still influences how I think about gene regulation today.

That’s a big shift. What made you transition from sea urchins to heart research?

Dr. Miao Cui: Studying sea urchins was an excellent entry point into developmental biology. The system is clean, and you can learn a lot about fundamental mechanisms. But I increasingly felt the work was too far removed from human disease. What made the shift urgent and personal was the unexpected passing of my PhD advisor due to a heart attack during my final year at Caltech.

“The loss of my PhD advisor to a heart attack made me realize that I wanted to work on something that could have a more immediate impact on human health. That’s how I pivoted from sea urchins to the mammalian heart.”

That loss deeply impacted me and became a pivotal motivator in choosing a research path focused on cardiovascular biology. When I joined UT Southwestern for my postdoc, I started working on mechanisms that promote heart regeneration.

When did you know you wanted to become a scientist?

Dr. Miao Cui: It wasn’t a childhood dream—I wasn’t the kind of kid who declared, “I want to be a scientist!” I’ve always been curious, though. I loved nature, was drawn to math and logic puzzles, and I had a deep appreciation for the arts—especially painting.

“Science became the perfect blend of logic and creativity.”

Growing up in China, the college entrance exam system is incredibly competitive, and it shaped many decisions. I realized pursuing art professionally wouldn’t be practical. With encouragement from my parents and relatives—especially my mom, a math teacher—I chose biology. But my passion for research truly solidified during my graduate school years. It was a gradual process of discovery and affirmation.

What does your lab study, and how would you explain it to someone outside of science?

Dr. Miao Cui: At a high level, we study why newborn mammals can regenerate heart tissue and how we might reawaken that ability in adults. Specifically, our lab focuses on the regenerative potential of the neonatal heart.

“Nature has already solved the problem—we’re just trying to relearn the code.”

In mice, for instance, newborns can recover from severe heart injuries—like a heart attack—within a few weeks. That ability is lost as they age. We use genetic tools, especially AAV vectors, to explore the molecular and cellular mechanisms behind this phenomenon. Ultimately, we want to translate these discoveries into strategies that help adult hearts heal after injury.

Can you walk us through what happens during a heart injury experiment in your lab?

Dr. Miao Cui: We induce a myocardial infarction—essentially a simulated heart attack—by ligating the left anterior descending artery in neonatal mice. What’s amazing is that these mice can fully regenerate the damaged tissue within three weeks. Not only does the structure return to normal, but so does function—measured by metrics like ejection fraction. Adult mice, on the other hand, don’t recover in this way. They form permanent scar tissue, which leads to heart failure over time. Our mission is to understand why and figure out how to restore regenerative capacity.

Have you seen evidence of similar regeneration in human infants?

Dr. Miao Cui: Yes. There are rare but compelling clinical reports of human infants recovering from major heart injuries caused by congenital defects. These cases suggest that some regenerative potential exists in human newborns as well.

“We believe the key to healing adult hearts might be locked in the first few days of life.”

We’ve collaborated on studies analyzing single-cell RNA sequencing data from human neonatal hearts and found cardiomyocyte populations with similar molecular signatures to what we observe in mice. But these populations fade quickly with age, which parallels the loss of regenerative capacity.

What tools do you use to study this regenerative capacity?

Dr. Miao Cui: Our toolbox includes lineage tracing, spatial transcriptomics, and CRISPR-based barcoding. For instance, we use a system called the CARLIN mouse model, developed here at Boston Children’s Hospital, which allows us to label individual heart cells with a unique genetic barcode. That way, we can track which cells actually contribute to regeneration. Combined with transcriptomic data, we can see both the lineage and the gene expression profile of regenerating cells. This gives us a powerful view of how regeneration unfolds.

Can you talk about your work with the gene NRF1?

Dr. Miao Cui: NRF1 is a transcription factor that became a major focus for us because it’s highly expressed in the regenerative cardiomyocytes of neonatal mice. When we knocked out NRF1 in these cells, they lost the ability to regenerate. When we overexpressed it in adult hearts using AAV gene delivery, we saw improved recovery.

“NRF1 is like a personal trainer for stressed-out heart cells—getting them fit enough to divide and repair.”

Mechanistically, NRF1 regulates genes involved in oxidative stress response and protein homeostasis. It essentially helps cells stay healthy under stress, which is critical for them to proliferate and repair tissue.

What are the biggest hurdles to translating these findings to adult humans?

Dr. Miao Cui: Scalability and complexity. We’re generating large datasets from single-cell genomics that identify candidate genes but testing them one by one is inefficient.

“To fix adult hearts, we have to think big—and scale even bigger.”

That’s why we’re now building a high-throughput screening platform using barcoded AAV vectors. Each vector delivers a different gene to the heart, and we track which ones produce a beneficial effect. It’s a faster, more scalable way to move from discovery to therapy. We’re also studying how the heart’s transcriptome changes across the lifespan—from neonatal to aged—and asking whether we can reprogram aged or diseased hearts toward a more regenerative state.

Outside the lab, what are your interests?

Dr. Miao Cui: I still love painting. If I hadn’t become a scientist, I think I would’ve pursued visual arts or maybe even architecture. I find that engaging with art helps me think creatively in science too.

“Science and art are closer than people think. Both are about observing, interpreting, and imagining what’s possible.”

What scientific breakthroughs in the past decade have most inspired you?

Dr. Miao Cui: Single-cell genomics, hands down. It has completely transformed how we understand cellular diversity and gene regulation. I’m also excited by the potential of in vivo genomic screens. When combined, these technologies let us not only see what cells are doing but test how they respond to precise perturbations.

“Single-cell genomics is like giving biology a microscope for the soul.”

Where can people follow your work?

Dr. Miao Cui: We have a lab website where we share our publications and updates on ongoing projects. I used to be more active on Twitter but have shifted my attention elsewhere lately.

19.05.2025
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Getting To Know The CDN Leadership Team: Chris Walsh

In our latest CDN Leadership Team sit down, we welcome Dr. Chris Walsh, a pioneering physician-scientist whose work has fundamentally reshaped how we understand brain development, genetic disease, and human consciousness. As Chief of the Division of Genetics and Genomics at Boston Children’s Hospital and a professor at Harvard Medical School, Dr. Walsh has led groundbreaking research on somatic mosaicism, neurodevelopmental disorders, and the genomic intricacies of individual brain cells. In this conversation, he reflects on the personal and scientific journey that brought him to the forefront of neuroscience, shares surprising discoveries from his lab, and explores the ethical and philosophical questions raised by studying the brain at its most elemental level.

To start off, we usually ask our guests to share a bit about how they got to where they are—your background, where you’re from, and what sparked your interest in science.

Dr. Chris Walsh: I’m the seventh of eight kids. My mom was a teacher, my dad was a businessman. Science wasn’t really part of my upbringing. I went to college without a clear path. In my first semester, I took a psychology class and an organic chemistry course—both really clicked. I wasn’t sure whether to pursue medicine or science, but then I discovered MD-PhD programs, where you can do both. That was a turning point. I was fortunate to be accepted at the University of Chicago, where I did my PhD in developmental neurobiology, very much focused on neuroanatomy.

What fascinates me to this day is how the brain forms—how undifferentiated cells become this incredibly complex organ responsible for thought, creativity, and consciousness. It’s a kind of transformation that feels almost metaphysical.

That’s amazing. I feel like the field is evolving so fast. I’ve been reading Plant Sapiens, which proposes that plants are intelligent. What’s your take on that kind of broader definition of intelligence or consciousness?

Dr. Chris Walsh: I think intelligence exists in context. A plant might be the most intelligent “plant” it can be. Their genomes are huge, filled with enzymes to detoxify poisons—something we don’t need because we can walk away from toxins. Consciousness, on the other hand, likely requires internal sensation—feelings, emotions, and a body to experience them. Yuval Noah Harari made an interesting point: a conscious computer would need a body with sensory inputs. By that definition, many animals—and maybe more—could be considered conscious.

That idea has made me more cautious about animal research. We now do more work with post-mortem human brains.

That’s a powerful shift. Going back to your early inspirations—how has your motivation evolved since you started?

Dr. Chris Walsh: At first, I was drawn to the biology of behavior—conditions like schizophrenia. But at the time, decades ago, the science wasn’t very rigorous. So, I pivoted to something more foundational: understanding how neurons are formed and connected. That eventually led to studying human genetics—looking at what happens when things go wrong, so we can learn how they work. Interestingly, we’ve now returned to psychiatric disorders like schizophrenia, and we recently published two papers on it.

For me, disorders like autism and schizophrenia challenge our basic assumptions about reality. They might help us answer profound questions about consciousness and human potential.

An added result is that it makes us more compassionate along the way!

Dr. Chris Walsh: Absolutely.

You’ve studied many genetic mutations tied to neurodevelopmental disorders. What are some of the most exciting discoveries from your lab recently?

Dr. Chris Walsh: One of the biggest surprises is that neurons, despite being non-dividing, still accumulate genetic mutations over time—just like dividing cells do. We used to think neurons were stable because they don’t divide, which supposedly protected them so we could preserve memories. But when we sequenced the genomes of individual neurons, we found that they collect about 17 single-nucleotide variants per year. That’s as fast as some dividing stem cells.

This changes how we understand aging and neurodegeneration. Diseases like Alzheimer’s speed up that mutation accumulation. It’s as if the neurons in an Alzheimer’s patient reach the mutation load of a 100-year-old when they’re only 80.

That’s fascinating. Do glial cells show the same pattern of mutations?

Dr. Chris Walsh: They do—but it’s different. Oligodendrocytes, for instance, accumulate more single-nucleotide mutations than neurons, but those are often less damaging. Neurons, on the other hand, accumulate more insertions and deletions, which are more frequently damaging to protein structure. So, while glial cells accumulate more mutations overall, the ones in neurons are potentially more harmful. We’ve also developed techniques using 10x Genomics to measure mutation accumulation by cell type, and even found that different layers of cortical neurons mutate at different rates.

And this is all connected to transcription?

Dr. Chris Walsh: Exactly. When a gene is transcribed, the DNA has to unwind. That exposes it to damage—oxidation, deamination, and so on. It’s not that transcription itself is damaging, but the exposure makes those regions more vulnerable.

You’re also doing work with spatial transcriptomics, right?

Dr. Chris Walsh: Yes, our long-term goal is to combine gene expression and mutation data in 3D space. In Alzheimer’s, for instance, we found that microglia—the brain’s immune cells—accumulate cancer-like mutations as the disease progresses. They go from supportive to antagonistic. We want to see whether neurons near these mutated microglia are more affected. That’s the kind of spatial relationship we’re now exploring.

Another big topic in your lab is somatic mosaicism—the idea that different cells in the same brain can have different DNA. Can you explain this for readers who may not be familiar?

Dr. Chris Walsh: Sure. Somatic mosaicism means that as an embryo develops, some mutations arise in certain cells and get passed on only to that cell’s descendants. So not every cell in the body—or even the brain—has the same genome. These mutations don’t come from your parents; they arise during development or later in life.

What we’ve found is that many forms of epilepsy, particularly the ones that don’t respond to drugs, are caused by these somatic mutations. In kids, a tiny patch of neurons—just one or two percent of the cells in a small part of the brain—can carry a mutation that causes seizures. If that patch is found and surgically removed, the child can be cured. These are the same kinds of mutations we see in cancer, but because the cells are neurons, they can’t form tumors—they just behave abnormally.

And in adults?

Dr. Chris Walsh: In adults, the story’s similar. We found that the most common form of adult epilepsy—temporal lobe epilepsy—also involves cancer-like mutations. These mutations don’t cause epilepsy at birth but sometimes not until decades later, possibly because the temporal lobe still has stem cells into adulthood that undergo cell division, which might cause the cells with cancer-like mutations to become more common with time. Over time, enough cells acquire the mutation to cause symptoms. It’s like a slow-motion version of tumor growth—without the tumor.

This model might suggest perhaps that Alzheimer’s and other late-onset diseases may emerge the same way: through mutation accumulation in glia or stem-like cells over many years. Once a critical mass of altered cells builds up, the disease manifests.

Are these findings translating into real therapies?

Dr. Chris Walsh: Yes—and quickly. I’ll give you three examples:

Pediatric epilepsy: We found that many of these mutations affect the mTOR pathway. Drugs that inhibit mTOR, developed originally for cancer, are now being tested in kids with these epilepsies. They work—but they need to be reformulated to penetrate the brain better.
Adult epilepsy: The RAS pathway, another cancer-associated pathway, shows up in temporal lobe epilepsy. Companies are repurposing RAS inhibitors from oncology for these patients. Some of these drugs already cross the blood-brain barrier more effectively.
Alzheimer’s disease: We’ve identified cancer-like mutations in microglia, and these mutations overlap with those found in myeloid leukemias. Since microglia and blood myeloid cells share a lineage, this opens up the possibility of using leukemia-targeting drugs for Alzheimer’s.

So, the genetics are helping us trace a path from disease mechanism to potential treatment.

It’s amazing that cancer research is now helping to drive neurological therapy. What do you see as the biggest barriers?

Dr. Chris Walsh: The blood-brain barrier is a big one. Many effective drugs in cancer simply don’t get into the brain. In fact, they are often designed not to enter the brain, and so that has to be re-considered for these conditions. Another is modeling these conditions. mTOR and RAS mutations are easy to reproduce in mice—they cause seizures just like in humans. But Alzheimer’s is harder. Mice don’t live long enough, and their brains aren’t structured the same way. We may need better models—perhaps brain organoids or better post-mortem analyses.

Your lab spans genetics, neurodevelopment, disease modeling, and informatics. How do you manage such a diverse team and stay at the center of so many moving parts?

Dr. Chris Walsh: I’m trained primarily in anatomy and molecular biology, but I know I can’t do this work alone. Our research relies on collaborations with incredibly talented people. Some of our most important partnerships have been with Peter Park and Alice Lee, bioinformatics experts whose groups have developed computational tools to interpret the sequencing data from single neurons.

Sequencing a single neuron is relatively straightforward these days. The challenge is interpreting the data—distinguishing real mutations from amplification noise, figuring out what’s meaningful. That’s where Peter’s and Alice’s teams have been crucial.

We’ve also built internal expertise by bringing in and training computational scientists. Many of our best ideas have come from students and postdocs—people who saw something unexpected and followed it. Honestly, my job is to support them, guide them a little, and get out of the way.

That really speaks to the collaborative nature of modern science. You also touched on bioinformatics earlier. With the explosion of AI and neural networks, how do you see these tools impacting neuroscience research?

Dr. Chris Walsh: AI has a lot of promise, particularly in summarizing complex data or speeding up routine analyses. It’s helpful for writing, reviewing literature, even generating hypotheses. But I always come back to something Sydney Brenner said: “Progress in science depends on new techniques, new discoveries, and new ideas, probably in that order.”.

The kinds of breakthroughs we’ve had—like detecting somatic mutations in single neurons—were only possible because of advances in sequencing technology. That’s something AI can’t replicate by itself as far as I know. AI can help us analyze what we already know, but it won’t invent the tools that let us see what we’ve never seen before. That still takes human creativity, curiosity, and technical innovation.

You mentioned your medical background earlier. What perspective does being an MD bring to your work as a scientist?

Dr. Chris Walsh: It’s hard to overstate how motivating it is. I’ve cared for kids with developmental disorders, and seen how deeply their families fight for them. That stays with you. It puts a human face on the research.

It also gives me a mental library of what these conditions look like in real life. I don’t need to imagine what epilepsy or autism means—I’ve seen it. That makes it easier to prioritize what matters in the lab, and to focus on work that could lead to real improvements in patients’ lives.

Chris, this has been incredibly inspiring. Before we wrap up, we like to ask a few rapid-fire questions. First: what advice would you give to young scientists who want to study brain development and genetics?

Dr. Chris Walsh: The most important thing is to realize that we know almost nothing. It might feel like all the big discoveries have already been made, but that’s not true at all. In fact, I’d say it took me decades to appreciate just how little we understand.

And second, you don’t need to be the smartest person in the room. You just have to want to contribute. Be curious, work hard, and take advice. Most of all, be humble. If you’re not, science will humble you anyway—better to get ahead of it.

That humility really comes through. What would you say is your favorite scientific finding from your own career?

Dr. Chris Walsh: I feel like I am always most excited about something new. I mentioned already the surprising discovery that neurons—these non-dividing, “stable” cells—accumulate mutations over time. But just when we thought that the genomes of neurons were always getting more damaged with time, we find most recently that the human fetal brain has abundant neurons with very abnormal genomes, and then somehow purges these abnormal nondividing cells, probably by some sort of programmed cell death. This finding again has opened up whole new ways of thinking about development and degeneration.

If you weren’t a scientist or a doctor, what would you be doing?

Dr. Chris Walsh: Probably something with music—I played piano through college. I wasn’t good enough to be professional, but it was a real passion. I’ve also thought about writing. My grandfather was an MD-PhD with a PhD in theology. He spent his life trying to reconcile science and religion. People keep telling me his story deserves a book, so maybe I’d write that.

That would be a great read. Last question—how can people follow your work?

Dr. Chris Walsh: Our lab is based at Boston Children’s Hospital, and we also have a Center for Human Brain Evolution website. A lot of our preprints go up on bioRxiv. I used to be on Twitter, but I’ve stepped back from social media. I’ll probably join BlueSky or something eventually, but for now, the websites are your best bet.

Perfect—we’ll make sure to link those in the blog post. Chris, this was fantastic. Thank you so much for your time and for sharing your insights.

Dr. Chris Walsh: Thank you both. I really appreciate the chance to talk about our work and what makes it meaningful.

3.04.2025
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Getting To Know The CDN Leadership Team: Leslie Kean

In this Spotlight Interview, we feature CDN’s own Dr. Leslie Kean, Director of the Pediatric Bone Marrow Transplant Program at Boston Children’s Hospital and Dana-Farber Cancer Institute.

Before moving to Boston seven years ago, Dr. Kean worked at the Fred Hutchinson Cancer Research Center and Seattle Children’s, where she served as a transplanter and Associate Director of the Childhood Cancer Research Center. She shares her remarkable journey from early work in yeast genetics to leading-edge immunology, and the groundbreaking research her lab is doing to prevent graft-versus-host disease (GVHD). From her passion for pediatrics to her pioneering efforts with Abatacept, this conversation offers a compelling look at the science and purpose driving her work.

We know you’re also an MD by training. Can you share how having both a medical background and a strong scientific focus has shaped your work?

Dr. Keane: I began my scientific training by starting my PhD in biochemistry at Stanford, where I focused on yeast genetics. As an undergrad, I worked in bacterial genetics, and I really enjoyed conducting large screens and selections, working with big data in both organisms. When I moved to Atlanta for family reasons, I also realized that I had always wanted to be an MD, even though I initially resisted that idea because it felt like it would please too many people. I was so passionate about science. But eventually, I realized that being an MD would bring me joy as well.

I completed my PhD and medical training in Atlanta, and that shift really changed my perspective on my work. I view science as my art—something I do out of love and obsession with the questions it raises. But when I started my medical training, it became clear to me that I should be focusing on questions that are as close to the patient as possible. For me, combining my scientific training with medicine felt like the right approach. Instead of continuing with bacterial and yeast genetics, I shifted toward studying more complex organisms, particularly developing an interest in immunology. While my PhD is in biochemistry, my postdoctoral training and the rest of my career have been centered on immunology.

When would you say you transitioned into focusing more on pediatrics and bone marrow transplant? What was it about that area that really captured your interest?

Dr. Keane: I’ve always loved working with kids, so I knew from the beginning that pediatrics was the path for me. I was drawn to hematology and oncology, which led me to bone marrow transplant. The field really resonated with me because the science is so close to the patient and involves complex clinical scenarios. Many of these kids are critically ill, but their stories are full of hope and triumph. I love being able to support families and children on their journey, no matter where it leads.

While I was in Atlanta, I focused on bone marrow transplant for my clinical work, but I also wanted to explore transplant immunology further. The best transplant immunologist at Emory was Dr. Chris Larson, a physician-scientist studying the immunology of solid organ transplants. He had revolutionized the way we think about immune tolerance in transplants, and I joined his lab as a postdoc. He was also doing non-human primate research, which piqued my interest. I’ve always been drawn to complex systems, so the opportunity to learn non-human primate immunology was a perfect fit for me.

Until recently, genetic tools for non-human primates were very limited, so we had to rely on systems approaches to understand the immunology. This led me to systems immunology. I was working on solid organ transplant research and taking care of kids with graft-versus-host disease (GVHD), a complication that occurs after bone marrow transplant. I now spend most of my time studying GVHD, but I also work on autoimmune diseases. Since I was caring for kids with GVHD, I decided to create systems that would allow me to study it in non-human primates. That’s how I started my lab, over 20 years ago.

That’s a really important distinction you made between transplant rejection and graft-versus-host disease (GVHD). I think many people confuse the two because both seem like the body is rejecting something. However, in some cases, the transplant is perfectly accepted, and it’s incredible to see patients thrive and live their lives. Could you explain the difference between rejection and GVHD?

Dr. Keane: In contrast, bone marrow transplant is a different story. Solid organ transplants, such as kidneys, are among the most successful due to factors including the availability of kidney replacement therapy (dialysis), which allows patients to survive while waiting for a transplant. In addition, our kidneys are a paired organ, so living donor options are more feasible. However, for other organs like the liver, there is no replacement therapy, and liver failure can be fatal within days or weeks. Finding a living donor for liver or lung transplants is much more challenging than for kidneys.

Now, with bone marrow, we have quite the opposite scenario.. When you donate bone marrow, the donor’s body can regenerate that marrow within weeks, and this is why the National Marrow Donor Program exists, and why HLA matched BMT can come from unrelated donrs. Bone marrow transplants have a higher success rate of matching because HLA (human leukocyte antigen) matching is more available than in solid organ transplants. The donor’s marrow provides the recipient with a whole new immune system that’s trained and educated, producing the possibility for immune tolerance. In fact, a successful bone marrow transplant often involves plans to eventually stop immunosuppression.

However, just like solid organ transplants, bone marrow transplants have potential toxicities. The two main complications are rejection and graft-versus-host disease (GVHD). Rejection after bone marrow transplant is relatively rare, but GVHD is a major risk and can be deadly. With GVHD, instead of the recipient’s T cells attacking the new organ, the donor’s T cells attack the recipient’s tissues, treating them as foreign. This is the opposite of rejection. While patients are often on immunosuppressive drugs for GVHD, the ultimate goal is to reduce or stop these medications over time if possible.

Just to clarify, are bone marrow transplants typically given to patients with leukemia who need their immune systems depleted, or are there other conditions that also require this type of transplant?

Dr. Keane: Bone marrow transplants are used for both malignant conditions, like leukemia and lymphoma, as well as non-malignant hematologic diseases. Some examples of non-malignant conditions include sickle cell disease, thalassemia, bone marrow failure syndromes including aplastic anemia, and certain inborn errors of metabolism. So, there are a variety of reasons, especially in pediatric cases, that people might need a bone marrow transplant.

What are some of the strategies that you’ve seen be successful, or that you’ve personally worked on, to help treat patients with GVHD?

Dr. Kean: The history of transplant is relatively young, beginning in the 1970s. Initially, rejection was the main issue, not GVHD, as patients would reject their transplants before GVHD could even occur. To address rejection, doctors started using a single immunosuppressive agent, but they found that while it prevented rejection, it didn’t prevent GVHD. In the 1980s, a two-drug regimen was developed, typically using a calcineurin inhibitor (such as Tacrolimus or cyclosporine) and a proliferation inhibitor (such as low-dose methotrexate). This strategywas adopted for human use and remained the standard for decades.

However, in the last 10 years, there has been significant progress. New approaches include using cyclophosphamide post-transplant (called post-transplant cyclophosphamide or PTCy) to deplete T cells, which has demonstrated improved outcomes in comparison to the two-drug regimen. Additionally, my lab’s work on T cell signaling pathways, specifically co-stimulation pathways, led to the clinical studies that resulted in FDA approval of the first drug for GVHD prevention—Abatacept, a T cell co-stimulation blocker. There’s also been tremendous progress in GVHD treatment, with multiple targeted therapies emerging in the past 10 years.

Can you explain a bit more about how Abatacept works? You mentioned earlier that there were two agents used in combination, but now Abatacept targets a specific co-stimulatory molecule on T cells. Is there anything else involved in the process, or is it just targeting that one pathway?

Dr. Keane: Abatacept (CTLA4-Ig) is a drug that blocks signal 2 by inhibiting the co-stimulatory interaction between CD28 on T-cells and CD80/86 on APCs. In mouse models, if T-cells were activated via signal 1 but signal 2 was blocked, the T-cells would become tolerant to that antigen and wouldn’t respond again. While this doesn’t exactly apply to humans, it shows the potential of modulating co-stimulation.

Abatacept was initially approved for rheumatoid arthritis, but my work on bone marrow transplants led me to explore its use in GVHD prevention. We conducted studies in non-human primates and later in humans, showing that adding Abatacept to a standard transplant regimen—using a calcineurin inhibitor (like tacrolimus) and methotrexate—helped prevent acute GVHD, especially in patients with mismatched donors. This combination led to significantly better survival rates, and the research eventually resulted in Abatacept’s FDA approval. The pivotal trial for this approval was actually an investigator-initiated study funded through RO1 grants.

Diseases such as GVHD are orphan indications, affecting relatively few patients, which means that they are often not of particularly high interest to pharmaceutical companies. However, when we demonstrated that Abatacept could prevent GVHD, we were able to partner with Bristol Myers Squibb to push the treatment through for FDA approval. This wouldn’t have been possible without the NIH and foundation funding to support the research. The study we conducted became the pivotal trial for approval, and I was involved in the entire FDA approval process. Now, anyone who needs it can access Abatacept to help prevent acute GVHD, which is a major breakthrough.

Just to follow up on what you mentioned, in mice, the treatment induces tolerance. In humans, not so much. Does this mean that some patients don’t need to take Abatacept for life? Is it just a matter of taking it for a certain period to help their immune system become tolerant?

Dr. Kean: I don’t know for sure. With bone marrow transplants, tolerance can happen naturally, so it’s difficult to pinpoint if Abatacept is specifically helping some patients. My best guess is that there are certain patients who might otherwise die from acute GVHD, but with the help of Abatacept, they’re saved during that critical window and eventually become tolerant later on.

That’s really interesting. Earlier, you mentioned doing a lot of non-human primate work as well. How have these models helped you better understand the disease?

Dr. Leslie Kean: From my perspective the NHP work has been truly revolutionary. Mouse models are critical for investigating immune questions, but as you get closer to the clinic, there are some limitations. For one, mice are inbred, and we know that immune systems of wild-caught or “dirty” mice are much different. This has taught us how much more difficult it is to control the immune response in outbred, pathogen-exposed humans. Non-human primates are outbred and pathogen-exposed, so they more accurately replicate the immune system we see in humans.

Also, when testing a drug, some drugs created for humans won’t cross-react with their mouse counterparts, so you can’t test directly these agents in mice. However, in non-human primates, most drugs cross-react, which allows us to ask questions in a model system that’s more faithful to human immunology and test the drugs directly. That’s been key.

In addition, applying systems biology and single-cell techniques has enabled us to deeply dig into the mechanisms that control immunologic outcomes. Historically, non-human primate work has been limited by a lack of high-quality cellular and molecular immunology, but systems immunology approaches have allowed us to overcome that barrier.

On another front, Abatacept is a biological agent. If you were to explain the difference between a biological and non-biological drugs to someone who isn’t familiar with these terms, how would you explain it in simple terms?

Dr: Leslie Kean: So, when I think about it, especially in the context of our work, we treat patients with drugs such as post-transplant cyclophosphamide, which is a nitrogen mustard developed during World War I. It’s a biological agent in that it affects biological systems, but it’s not targeted in a precise way. It’s a very broad, non-specific drug. And honestly, I think we can do better. I believe the future lies in deeply understanding transplant biology and using more targeted agents. When I refer to a biologic agent, I really mean a targeted therapy—a drug, antibody, or even a cellular therapy—that’s been specifically designed to target something in the immune system. Abatacept is an example of this kind of approach. It’s targeted and purpose-built to block a specific molecule involved in immune activation. And with non-human primate models, we can conduct more controlled experiments to understand how these targeted therapies work, which leads to stronger inferences about their mechanisms of action and how they can benefit patients.

That’s super, right?? …when you’re targeting a specific pathway, it’s like tuning a fine instrument—you’re focusing in on exactly what needs to be changed without messing with the rest of the system. That’s the kind of strategy that holds a lot of potential for improving treatments while making them safer for patients.

Dr: Leslie Kean: Absolutely, and while agents like cyclophosphamide have been essential and play a key role, there are definitely limitations. The real goal is to evolve toward a future where all our treatments are more targeted, optimizing their effectiveness and minimizing unnecessary side effects.

How do you think the single-cell perspective of these complex systems provides deeper insights, and in which areas do you see it being most beneficial?

Dr. Leslie Kean: I think it’s indispensable. Let me give you an example. So, in the Abatacept clinical trial known as ‘ABA2, which was the trial that led to the FDA approval, we included real-time immunologic studies as well as a purpose-built biorepository. When I started this trial, single-cell techniques didn’t even exist—this was back in 2010. At that time, we sorted CD4 and CD8 cells and did bulk RNA sequencing on them. But we also created a cryopreserved, state-of-the-art PBMC biorepository to prepare for future studies.

When we performed RNA sequencing on the bulk samples, we found that patients who didn’t receive abatacept and developed GVHD had a significant proliferation signature, which was interesting. However, with bulk RNA sequencing, you can’t dive much deeper into those findings—everything gets averaged out. That’s where single-cell techniques come in. After adequately preparing the cryopreserved samples, we used single-cell RNA sequencing and TCR sequencing. This allowed us to focus our analysis on the proliferating cells, and we identified a candidate gene we believe is central to GVHD in the absence of abatacept.

We then analyzed samples from patients who received abatacept to see what happens to that gene, and we found that in those patients, the gene’s transcription was stabilized, which has been shown in other systems to suppress T cell activation. In contrast, in patients who didn’t receive abatacept, this transcription factor’s expression was significantly downregulated, which could explain the therapeutic effects of abatacept. This kind of insight wouldn’t be possible with bulk sequencing alone.

Single-cell techniques were absolutely necessary here. The bulk sequencing gave us initial clues, and then our biorepository allowed us to pull out cells and apply today’s technologies to dig deeper. By also doing single-cell TCR sequencing, we were able to explore multiple layers of immune responses. So, I’d say single-cell techniques were key to understanding the underlying mechanisms of the treatment’s success.

What do you think are the biggest challenges or unanswered questions in the field right now that you’re particularly excited for your lab to help address and tackle?

Dr. Leslie Kean: We think about this all the time. One thing that we’ve realized, especially with the work in the Abatacept study, is that while we were initially limited to sorting blood cells and doing bulk RNA sequencing, we were preparing ourselves for the next generation of technology. As I’ve mentioned, a lot of the current focus has been on blood, but the big leap for us now is into tissue-based immunology.

In the lab, we’ve started working with tissue samples, including gastrointestinal samples from patients with the autoimmune diseases Ulcerative Colitis and Crohn’s Disease. We have studied a unique cohort of patients, for whom we have performed the single cell analyses at their time of diagnosis—before they’ve been treated with any immunosuppressive therapies. In contrast, transplant patients, especially those with GVHD, have already been exposed to immunosuppressive medications, so analyzing the tissue samples from these patients can be trickier.

Now, with the foundation we’ve established with the UC and CD patients, we’re collecting biopsies from GVHD patients to investigate the tissue-specific mechanisms driving the disease and how those mechanisms can be linked back to what’s happening in the blood. This focus on tissue-based immunology is really at the cutting edge of the field right now, and we’re excited to explore these pathways more deeply in our work.

If you had to pick one scientific advancement from the past decade that stands out to you the most, whether it’s in your field or beyond, what would it be? What’s something that really caught your attention?

Dr. Leslie Keane: There’s so much to be excited about in science! I’m a huge fan of the history of scienceIf I had to pick something that stands out in the last decade, it would definitely be CRISPR and the subsequent advancements that have come from . When I started my career doing bacterial and yeast genetics, we had this saying, where we called out “the awesome power of yeast genetics.” I used to joke that I was trying to make primates like yeast, using systems-based approaches to apply the power of genetics to primates. And CRISPR has really made that possible. It’s allowed us to do genetic screens in mice, non-human primates, and human cells, which is remarkable. The pace of discovery is accelerating, and truly standing on the shoulders of giants. CRISPR and genetic screens in complex systems are driving forward advancements like never before. For example, gene therapies It’s an exciting time in science, for sure!

If you weren’t a scientist, would you what would you be doing?

Dr. Keane: Well, I’m not sure because I truly love being a scientist, but there are a couple of other things I really enjoy. First, I love working with kids. I have a deep connection with them—my family even jokes that I have the soul of an eight-year-old boy because I relate so well to children 🙂 That’s probably why I ended up in pediatrics. So, I think I might have become a teacher. But beyond that, I almost quit science in 1989. Before I truly understood that science was my art, I was also passionate about environmental activism. I worked for Greenpeace, and at the time, I took a year off after completing my master’s in Cambridge and was about to start graduate school at Stanford. I was feeling uncertain about what to do with my life and overwhelmed by the state of the world. I thought the planet was falling apart and science wasn’t important in comparison, so I threw myself into activism. But eventually, I realized that I could still be passionate about activism and care for the world, while also doing what I loved in science.

11.02.2025
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Expanding Horizons in Microbiology: The Breakthrough of Bacterial MERFISH

At CDN, we love diving into the science, but just as importantly, we love getting to know the scientists behind the discoveries. In this interview, we spoke with Jeff (PI) and Ari (Graduate Student) about their backgrounds, the journey that led them to their current research, and the recent paper on bacterial MERFISH—a groundbreaking technology expanding our ability to map bacterial RNA organization in single cells.

Meet the Scientists

Ari: A Journey from Switzerland to Boston

Ari grew up in Geneva, Switzerland, where he pursued his studies before making his way to Harvard Medical School for a fellowship during his master’s at EPFL. He joined Jeff’s lab, a lab deeply embedded in bacterial research, after the pandemic. This was about a year into his PhD program, following completion of his master’s project in a different lab.

What drives Ari? The thrill of discovery.

“We can’t discover new continents anymore—that’s been done. Maybe one day, we’ll explore other planets, but for now, biology is still an open frontier,” he says. “Problem-solving and troubleshooting can be frustrating, but they’re also what make this job so fun. When something doesn’t work, I get to ask: Why didn’t it work? How can I test it? How can I measure it?”

Jeff: From Physics to Biology

Jeff’s path took him from physics to biology. He earned his PhD at UC Berkeley, where he developed optical tweezers—biological “tractor beams” that allowed researchers to manipulate single molecules and study enzymes interacting with nucleic acids.

Wanting to explore the complexities of the cell, he transitioned to bacterial research during his postdoc. His work led to an exciting collaboration that helped pioneer spatial biology using a multiplexed RNA imaging method, MERFISH. “Our goal is to develop technologies that let us see things that were simply unobservable before,” Jeff explains.

Bacterial MERFISH: A New Window into Microbial Life

So how did this project come about?

MERFISH had already transformed how scientists study tissue biology, but Jeff wanted to apply it to bacteria. The problem? Bacteria are tiny, and their RNA is packed far more densely than in mammalian cells—about 1,000 times denser. This made it impossible to distinguish individual RNA molecules with traditional microscopy.

Ari and his collaborator, Dr. Yuanyou Wang, took on the challenge. “We had to solve a three-order-of-magnitude RNA density problem before we could even get started,” Jeff says.

Expanding Bacteria—Literally

To overcome this, the team turned to expansion microscopy, a technique that physically enlarges cells using hydrogels. Imagine a balloon: if you write on it and then inflate it, the text spreads out, becoming easier to read. Expansion microscopy works the same way, allowing researchers to visualize bacterial RNA organization at unprecedented resolution.

“Instead of making the microscope better, we make the sample bigger,” Ari explains. “We embed bacteria in a hydrogel, then let it expand. The molecules are pulled away from each other but are not themselves stretched that much, making them resolvable under a standard microscope.”

Mapping Bacterial RNA Organization

With this approach, Ari and his team were able to do something that had never been done before: map the spatial organization of over half of the E. coli transcriptome.

For years, scientists assumed bacteria had little RNA organization—after all, their small size and rapid molecular diffusion suggested otherwise. But Ari’s work contributed to a growing appreciation that bacterial transcriptomes are organized within the cell.

. “We found a surprising diversity of RNA spatial patterns,” Jeff says. “Some RNAs are evenly distributed, but many exhibit strikingly distinct localizations.”

These findings raise new questions: Why do bacteria organize their RNAs? How does this organization influence cellular function? The research has opened an entirely new avenue for studying bacterial cell biology.

Unexpected Insights into Bacterial Metabolism

One of the most surprising findings came when the team looked at how bacteria adapt to different nutrients. Bacteria don’t just switch to metabolizing a new sugar when their preferred one runs out. Instead, they go through an exploratory transcriptional phase, testing for alternative sugars—even ones that aren’t present in the environment.

“It’s like they’re sending out molecular feelers,” Ari explains. “They don’t immediately switch to the second-best sugar. Instead, they express genes for several different metabolic pathways before committing.”

Using their technology, the team was also able to uncover the molecular activities of subpopulations within identical bacterial cultures—some focused on amino acid synthesis, others on their functional machinery.

“This is a fundamental insight into bacterial gene regulation,” Jeff adds. “Even in minimal conditions, bacteria are exhibiting metabolic diversity.”

The Future of Bacterial MERFISH

Beyond understanding bacterial behavior in the lab, this technology has potential real-world applications. For the first time, researchers can apply MERFISH to bacteria inside living hosts, providing unprecedented insight into microbial interactions in their natural environments.

“We don’t just want to study bacteria in test tubes—we want to understand them in their real-world settings,” Ari says. “This technique gives us a way to do that.”

Closing Thoughts

Before wrapping up, we asked Jeff and Ari a few fun questions.

What’s the most impactful scientific advancement of the last decade?

For Jeff, it’s the explosion of spatial transcriptomics—merging genomics with microscopy to study biology at an unprecedented resolution. “The ability to map tens of thousands of RNAs while preserving spatial context is a game-changer,” he says.

Ari, on the other hand, struggles to pick just one. “AI is changing the way we process biological data. Gene therapy is becoming a reality. And cryo-electron microscopy has revolutionized how we visualize molecular structures. There’s too much to choose from!”

If you weren’t a scientist, what would you be doing?

Jeff: “I love discovery, but I also love mentorship and teaching. If I had to drop research, I’d probably still be a teacher.”

Ari: “I love the engineering side of research—building tools, optimizing processes. If I weren’t in science, I’d probably go into industrial design or automation.”

Final Takeaways

Jeff and Ari’s work is pushing the boundaries of bacterial research, making it possible to study microbial gene expression with an unprecedented level of detail.

Their study demonstrates that bacterial RNA isn’t randomly distributed—it’s spatially organized, and understanding this could transform how we think about bacterial physiology. By adapting MERFISH for bacteria, they’ve unlocked new opportunities to study bacterial adaptation, gene regulation, and cellular behavior in ways that were previously impossible.

The future of bacterial spatial transcriptomics is just beginning, and we can’t wait to see what comes next.