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The cartographer of cells

Aviv Regev helped pioneer single-cell genomics. Now she’s cochairing a massive effort to map the trillions of cells in the human body. Biology will never be the same.

Sam Apple | MIT Technology Review
August 23, 2018

Last October, Aviv Regev spoke to a gathering of international scientists at Israel’s Weizmann Institute of Science. For Regev, a computational and systems biologist at the Broad Institute of MIT and Harvard, the gathering was also a homecoming of sorts. Regev earned her PhD from nearby Tel Aviv University in 2002. Now, 15 years later, she was back to discuss one of the most ambitious projects in the history of biology.

The project, the Human Cell Atlas, aims to create a reference map that categorizes all the approximately 37 trillion cells that make up a human. The Human Cell Atlas is often compared to the Human Genome Project, the monumental scientific collaboration that gave us a complete readout of human DNA, or what might be considered the unabridged cookbook for human life. In a sense, the atlas is a continuation of that project’s work. But while the same DNA cookbook is found in every cell, each cell type reads only some of the recipes—that is, it expresses only certain genes, following their DNA instructions to produce the proteins that carry out a cell’s activities. The promise of the Human Cell Atlas is to reveal which specific genes are expressed in every cell type, and where the cells expressing those genes can be found.

Speaking to her colleagues at the meeting in Israel, Regev, who is cochairing the Human Cell Atlas Organizing Committee with Sarah Teichmann of the Wellcome Trust Sanger Institute, displayed the no-nonsense demeanor you might expect of someone at the helm of a massive scientific undertaking. The project had been under way for a year, and Regev, an MIT biology professor who is also chair of the faculty of the Broad and director of its Klarman Cell Observatory and Cell Circuits Program, was reviewing a newly published white paper detailing how the Human Cell Atlas is expected to change the way we diagnose, monitor, and treat disease.

As Regev made her way through the white paper, the possibilities began to seem almost endless. At the most basic level, as a reference map detailing the genes expressed by each different type of healthy cell, the Human Cell Atlas will make it easier to identify how gene expression and signaling go awry in the case of disease. The same map could also help drug developers avoid toxic side effects: researchers targeting a gene that’s harmful in one part of the body would know if the same gene is playing a vital role in another. And because the atlas is expected to reveal many new types of cells, it could also add much more sensitivity to a type of standard blood test, which simply counts different subsets of immune cells. Likewise, looking at individual intestinal cells might provide new insights into the specific cells responsible for inflammation and food allergies. And a better understanding of types of neurons could have far-reaching implications for brain science.

The final product, Regev says, will amount to nothing less than a “periodic table of our cells,” a tool that is designed not to answer one specific question but to make countless new discoveries possible. Eric Lander, the founding director and president of the Broad Institute and a member of the Human Cell Atlas Organizing Committee, likens it to genomics. “People thought at the beginning they might use genomics for this application or that application,” he says. “Nothing has failed to be transformed by genomics, and nothing will fail to be transformed by having a cell atlas.”

Cellular circuits

Regev’s interest in cells began at Tel Aviv University, where she was one of just 15 or so entering students in a highly selective program that gave them the freedom to take high-level courses in any subject. “You could go your first day as a freshman and decide to take a graduate class in political science,” she says.

Regev took a genetics class her first semester and got hooked on the computational challenge of finding order in the complex, interconnected networks of proteins and genes within each cell. She pursued that topic for her doctoral work, characterizing living systems in a mathematical language that had been designed to describe computer processes. As she finished her doctorate in 2002, she was accepted into a program at Harvard’s Bauer Center for Genomics Research that allowed her to start her own lab without first training as a postdoc.

Not long after, Lander, who’d begun his own career as a mathematician after studying algebraic coding theory and combinatorial mathematics at Oxford, was searching for star talent for the newly created Broad Institute, whose mission is to use genomics to study human disease and help advance its treatment. He first met Regev at a lunch at the Bauer Center during which the fellows took turns speaking about their research for five to 10 minutes. “By the time we got all the way around the table I had written down ‘Hire Aviv Regev,’” he recalls.

Convinced by Lander to join the Broad after “many cups of tea” at Cafe Algiers in Harvard Square, Regev continued to apply computational approaches to study the mind-bogglingly complicated machinery of the cell. A single cell is made up of millions of molecules that are in constant conversation as they work together to do all the things cells need to do: divide, grow, repair internal damage, and, in the case of immune cells, signal other cells about threats. Inside the nucleus, the DNA is transcribed into RNA. That in turn gives rise to proteins, the molecules that do the work inside a cell. Meanwhile, proteins on the surface of the cell are constantly receiving molecular messages from outside—glucose is available, an invader has arrived. These must be relayed back to proteins in the nucleus, which will respond by transcribing other DNA, giving rise to new proteins and still more signaling networks.

“It’s like a complex computer that is made of these many, many different parts that are interacting with each other and telling each other what to do,” says Regev. The protein signaling networks are like “circuits”—and you can think about the cell “almost like a wiring diagram,” she says. But using computational approaches to understand their activity first requires gathering an enormous amount of data, which Regev has long done through RNA sequencing. Unlike DNA sequencing, she says, it can tell her which genes are actually being expressed, so it offers a far more dynamic picture of a cell in action. But simply sequencing the RNA of the cells she’s studying can tell her only so much. To understand how the circuits change under different circumstances, Regev subjects cells to different stimuli, such as hormones or pathogens, to see how the resulting protein signals change.

Next comes what she calls “the modeling step”—creating algorithms that try to decipher the most likely sequence of molecular events following a stimulus. And just as someone might study a computer by cutting out circuits and seeing how that changes the machine’s operation, Regev tests her model by seeing if it can predict what will happen when she silences specific genes and then exposes the cells to the same stimulus.

In a 2009 study, Regev and her team examined how exposure to molecular components of pathogens like bacteria, viruses, or fungi affected the circuitry of the immune system’s dendritic cells. She turned to a technique known as RNA interference (she now uses CRISPR), which allowed her to systematically shut genes down. Then she looked at which genes were expressed to determine how the cells’ response changed in each case. Her team singled out 100 different genes that were involved in regulating the response to the pathogens—some of which weren’t previously known to be involved in immune function. The study, published in Science, generated headlines. But according to longtime colleague Dana Pe’er, now chair of computational and systems biology at the Sloan Kettering Institute at the Memorial Sloan Kettering Cancer Center and a member of the Human Cell Atlas Organizing Committee, what really sets Regev apart is the elegance of her work. Regev, says Pe’er, “has a rare, innate ability of seeing complex biology and simplifying it and formalizing it into beautiful, abstract, describable principles.”

From smoothies to fruit salad

There are lots of empty coffee mugs in Regev’s office at the Broad Institute, but very little in the way of decoration. She approaches her science with a businesslike efficiency. “There are many brilliant people,” says Lander. “She’s a brilliant person who can get things done.”

In the fast-changing arena of genomics (“2015 in my field is considered ancient history,” she says), she is known for making the most of the latest innovations—and for helping to spur the next ones. For years, she and others in the field struggled with a dirty secret of RNA sequencing: though its promise has always been precision—the power of knowing the exact code—the techniques produced results that were unspecific. Every cell has only a minuscule amount of RNA. For sequencing purposes, the RNA from millions of cells had to be pooled together. Bulk RNA sequencing left researchers with what she likens to a smoothie. Once it’s blended together, there’s no way to distinguish all the fruits—or in this case, the RNA from individual cells—that went into it. What researchers needed was something more like a fruit salad, a way to separate all the blueberries, raspberries, and blackberries.

In 2011, working with Broad Institute colleague Joshua Levin, PhD ’92, and postdocs Alex Shalek, now at MIT’s Institute for Medical Engineering and Science, and Rahul Satija, now at the New York Genome Center, Regev managed to obtain enough RNA from a single cell to sequence it. To test the method, they sequenced 18 individual dendritic cells from the bone marrow of a mouse. The cells were all obtained in the same way and were expected to be the same type. But to the researchers’ amazement, they were expressing different genes and could be classified into two distinct subtypes. It was like finding out the smoothie you’d been drinking for years had ingredients you’d never known about.

Regev and her colleagues weren’t the only ones figuring out how to sequence a single cell with such sensitivity, nor were they the very first to succeed. Other labs were making similar advances at approximately the same time, each using its own technology and algorithms. And they all faced the same problem: isolating and extracting enough RNA from individual cells was time consuming and expensive. Regev and her colleagues had spent many thousands of dollars to sequence only 18 cells. If the body was full of rare, undiscovered cells, it was going to take an extraordinarily long time to find them.

Skip ahead seven years and the cost of single-cell RNA sequencing is down to only pennies per cell. A critical breakthrough was Drop-Seq, a new technology developed by researchers at Harvard and the Broad Institute, including Regev and members of her lab. The device embeds individual cells into distinct oil droplets with a tiny “bar-coded” bead. When the cell is broken apart for sequencing, some of its RNA attaches to the bead in its droplet. This allows researchers to analyze thousands at once without getting their genetic material mixed up.

Cell theory 2.0

When cell theory was first proposed by German scientists some 180 years ago, it was hard to fathom that our tissues are built from “individual elementary units,” as Theodor Schwann, one of the two scientists credited with the theory, described cells. But it soon became a central tenet of biology, and over the decades and centuries, cells began to give up their secrets. Microscopes improved; new staining and sorting techniques became available. With each advance, new distinctions became possible. Muscle cells could be distinguished from neurons, and then categorized again as smooth or skeletal muscle cells. Cells, it became clear, were all fundamentally similar but came in different forms that had different properties.

By the 21st century, 200 to 300 major cell types had been identified. And while biologists have long recognized that the true number of cell types must be higher, the extent of their diversity is only now coming into full focus, thanks in large part to single-cell RNA sequencing. Regev says that the immune system alone can now be divided into more than 200 cell types and that even our retinas have 100 or more distinct types of neurons. She and her colleagues have discovered several of them.

The idea that knowing so much more about our cells could lead to medical breakthroughs is no longer hypothetical. By sequencing the RNA of individual cancer cells in recent years—“Every cell is an experiment now,” she says—she has found remarkable differences between the cells of a single tumor, even when they have the same mutations. (Last year that work led to Memorial Sloan Kettering’s Paul Marks Prize for Cancer Research.) She found that while some cancers are thought to develop resistance to therapy, a subset of melanoma cells were resistant from the start. And she discovered that two types of brain cancer, oligodendroglioma and astrocytoma, harbor the same cancer stem cells, which could have important implications for how they’re treated.

The excitement in the field has become tangible as more new cell types have been found. And yet Regev realized that if the aim was comprehensive knowledge, the approach needed to be coordinated. If each lab were to rely on its own techniques, it would be hard to standardize the computational tools and the resulting data. The new studies were producing “very nice glimmers of light,” Regev says—“a thing here, a thing there.” But she wanted to make sure those findings could be connected.Regev has also been busily mapping cells from the immune system, brain, gut, and elsewhere. She is not alone. Other labs have started their own mapping projects, each tackling a different part of the body. Last year researchers at the University of Washington attempted to classify every cell type in the microscopic worm C. elegans. “Every single field in biology is saying, ‘Of course we have to look at single-cell resolution,’” says Lander. “How did we ever imagine we were going to solve a problem without single-cell resolution?”

Regev began to advocate creating something more unified: a map that would allow researchers to chart gene expression and cell types across the entire body. Sarah Teichmann had been thinking along the same lines. When she reached out to Regev in late 2015 about the possibility of joining forces, Regev immediately said yes.

A Google Maps for our cells

The Human Cell Atlas is a collaboration among hundreds of biologists, technologists, and software engineers across the globe. Results from single-cell RNA sequencing will be combined with other data points to provide a comprehensive catalogue of all human cells.

But the many researchers involved won’t simply be compiling spreadsheets listing different cell types. The atlas will also reveal where the cells are located in the body, how many there are, what forms they can take, even the developmental history of different cell types as they differentiated from stem cells. And all of this will be made accessible through a data coordination platform and a rich visual interface that Regev compares to Google Maps. It will allow users to zoom in to the molecular level of our cells, but zooming out to the level of tissues and organs will be important too. As a 2017 overview of the Human Cell Atlas by the project’s organizing committee noted, an atlas “is a map that aims to show the relationships among its elements.” Just as corresponding coastlines seen in an atlas of Earth offer visual evidence of continental drift, compiling all the data about our cells in one place could reveal relationships among cells, tissues, and organs, including some that are entirely unexpected. And just as the periodic table made it possible to predict the existence of elements yet to be observed, the Human Cell Atlas, Regev says, could help us predict the existence of cells that haven’t been found.

The plan is not to sequence all 37 trillion cells but to sample from every part of the body. As Regev talks about the project, her enthusiasm evident, she digs up a slide to demonstrate how effective sampling can be. The slide, first only an empty frame of white, begins to fill in, pixel by pixel, with specks of blue and yellow. Soon, even though many of the pixels haven’t yet been filled, the image on the screen is unmistakable: it is Van Gogh’s Starry Night. Likewise, Regev explains, the Human Cell Atlas can give a complete picture even if not every single cell has been sequenced.

To do the sequencing, Regev and Teichmann have welcomed and recruited experts in each different tissue type. Though expected to take years, the project is moving ahead rapidly with such backers as NIH, the EU, the Wellcome Trust, the Manton Foundation, and the Chan Zuckerberg Initiative, which pledged to spend $3 billion to battle disease over the next decade; this year alone it will fund 85 Human Cell Atlas grants. Early results are already pouring in. In March, Swedish researchers working on cells related to human development announced they had sequenced 250,000 individual cells. In May, a team at the Broad made a data set of more than 500,000 immune cells available on a preview site. The goal, Regev says, is for researchers everywhere to be able to use the open-source platform of the Human Cell Atlas to perform joint analyses.

Plenty of challenges remain before the atlas can become a reality. New visualization software must be developed. Sequencing and computational approaches will need to be standardized across a huge number of labs. Conceptual issues, such as what distinguishes one cell type from another, have to be worked through. But the community behind the Human Cell Atlas—including more than 800 individuals as of June—has no shortage of motivation.

One of Regev’s own recent studies, published in August in Nature, is perhaps the best example of how the project could change biology. In mapping cells of the lungs, Regev and Jay Rajagopal’s lab at Massachusetts General Hospital found a new, very rare cell type that primarily expresses a gene linked to cystic fibrosis. Regev now thinks that these rare cells probably play a key role in the disease. More surprising yet, researchers had previously thought that a different cell type was expressing the gene.

“Imagine if somebody wanted to do gene therapy,” Regev says. “You have to fix the gene, but you have to fix it in the right cell.” The Human Cell Atlas could help researchers identify the right cell and understand how the gene in question is regulated by that cell’s extraordinarily complicated molecular networks.

For Regev, the importance of the Human Cell Atlas goes beyond its promise to revolutionize biology and medicine. As she once put it, without an atlas of our cells, “we don’t really know what we’re made of.”

Antidepressant restores youthful flexibility to aging inhibitory neurons

Neural plasticity and arbor growth decline with age, study in mice shows.

David Orenstein | Picower Institute for Learning and Memory
August 20, 2018

A new study provides fresh evidence that the decline in the capacity of brain cells to change (called “plasticity”), rather than a decline in total cell number, may underlie some of the sensory and cognitive declines associated with normal brain aging. Scientists at MIT’s Picower Institute for Learning and memory show that inhibitory interneurons in the visual cortex of mice remain just as abundant during aging, but their arbors become simplified and they become much less structurally dynamic and flexible.

In their experiments published online in the Journal of Neuroscience they also show that they could restore a significant degree of lost plasticity to the cells by treating mice with the commonly used antidepressant medication fluoxetine, also known as Prozac.

“Despite common belief, loss of neurons due to cell death is quite limited during normal aging and unlikely to account for age-related functional impairments,” write the scientists, including lead author Ronen Eavri, a postdoc at the Picower Institute, and corresponding author Elly Nedivi, a professor of biology and brain and cognitive sciences. “Rather it seems that structural alterations in neuronal morphology and synaptic connections are features most consistently correlated with brain age, and may be considered as the potential physical basis for the age-related decline.”

Nedivi and co-author Mark Bear, the Picower Professor of Neuroscience, are affiliated with MIT’s Aging Brain Initiative, a multidisciplinary effort to understand how aging affects the brain and sometimes makes the brain vulnerable to disease and decline.

In the study the researchers focused on the aging of inhibitory interneurons which is less well-understood than that of excitatory neurons, but potentially more crucial to plasticity. Plasticity, in turn, is key to enabling learning and memory and in maintaining sensory acuity. In this study, while they focused on the visual cortex, the plasticity they measured is believed to be important elsewhere in the brain as well.

The team counted and chronically tracked the structure of inhibitory interneurons in dozens of mice aged to 3, 6, 9, 12 and 18 months. (Mice are mature by 3 months and live for about 2 years, and 18-month-old mice are already considered quite old.) In previous work, Nedivi’s lab has shown that inhibitory interneurons retain the ability to dynamically remodel into adulthood. But in the new paper, the team shows that new growth and plasticity reaches a limit and progressively declines starting at about 6 months.

But the study also shows that as mice age there is no significant change in the number or variety of inhibitory cells in the brain.

Retraction and inflexibility with age

Instead the changes the team observed were in the growth and performance of the interneurons. For example, under the two-photon microscope the team tracked the growth of dendrites, which are the tree-like structures on which a neuron receives input from other neurons. At 3 months of age mice showed a balance of growth and retraction, consistent with dynamic remodeling. But between 3 and 18 months they saw that dendrites progressively simplified, exhibiting fewer branches, suggesting that new growth was rare while retraction was common.

In addition, they saw a precipitous drop in an index of dynamism. At 3 months virtually all interneurons were above a crucial index value of 0.35, but by 6 months only half were, by 9 months barely any were, and by 18 months none were.

Bear’s lab tested a specific form of plasticity that underlies visual recognition memory in the visual cortex, where neurons respond more potently to stimuli they were exposed to previously. Their measurements showed that in 3-month-old mice “stimulus-selective response potentiation” (SRP) was indeed robust, but its decline went hand in hand with the decline in structural plasticity, so that it was was significantly lessened by 6 months and barely evident by 9 months.

Fountain of fluoxetine

While the decline of dynamic remodeling and plasticity appeared to be natural consequences of aging, they were not immutable, the researchers showed. In prior work Nedivi’s lab had shown that fluoxetine promotes interneuron branch remodeling in young mice, so they decided to see whether it could do so for older mice and restore plasticity as well.

To test this, they put the drug in the drinking water of mice at various ages for various amounts of time. Three-month-old mice treated for three months showed little change in dendrite growth compared to untreated controls, but 25 percent of cells in 6-month-old mice treated for three months showed significant new growth (at the age of 9 months). But among 3-month-old mice treated for six months, 67 percent of cells showed new growth by the age of 9 months, showing that treatment starting early and lasting for six months had the strongest effect.

The researchers also saw similar effects on SRP. Here, too, the effects ran parallel to the structural plasticity decline. Treating mice for just three months did not restore SRP, but treating mice for six months did so significantly.

“Here we show that fluoxetine can also ameliorate the age-related decline in structural and functional plasticity of visual cortex neurons,” the researchers write. The study, they noted, adds to prior research in humans showing a potential cognitive benefit for the drug.

“Our finding that fluoxetine treatment in aging mice can attenuate the concurrent age-related declines in interneuron structural and visual cortex functional plasticity suggests it could provide an important therapeutic approach towards mitigation of sensory and cognitive deficits associated with aging, provided it is initiated before severe network deterioration,” they continued.

In addition to Eavri, Nedivi and Bear, the paper’s other authors are Jason Shepherd, Christina Welsh, and Genevieve Flanders.

The National Institutes of Health, the American Federation for Aging Research, the Ellison Medical Fondation, and the Machiah Foundation supported the research.

Ankur Jain

Education

  • PhD, 2013, University of Illinois, Urbana-Champaign
  • BTech, 2007,  Biotechnology and Biochemical Engineering, Indian Institute of Technology Kharagpur

Research Summary

We study how biomolecules in a cell self-organize. In particular, we are interested in understanding how membrane-free cellular compartments such as RNA granules form and function. Our lab develops new biochemical and biophysical techniques to investigate these compartments and to understand their dysfunction in human disease.

Awards

  • Young Alumni Achiever’s Award, Indian Institute of Technology Kharagpur, 2019
  • NIH K99/R00 Pathway to Independence Award, 2017
  • Pew Scholar in the Biomedical Sciences, 2022
Altering Neuronal Activity at Will

Graduate student Nicole Aponte Santiago uses fruit flies to probe the relationship between the many nerve cells passing signals from the brain to the muscles.

Raleigh McElvery
August 16, 2018

As fifth year graduate student Nicole Aponte Santiago puts it, she has the power to alter nerve cell activity in fruit flies at will. She’ll also tell you point-blank that flies are her favorite model organism, although that wasn’t always the case. They have many well-cited advantages — they procreate often, have short lifespans, and many of their genes overlap with humans while being easy to manipulate. But Aponte suggests an additional reason for her change of heart. She suspects “looking them straight in the eye” so frequently ultimately convinced her, using their physical features to deduce their genetic makeup, and from there investigate the relationship between the many nerve cells (neurons) passing signals from the brain to the muscles.

Aponte credits her initial interest in science to her father, a dentist who used to take her for long walks on the beaches of Puerto Rico where she grew up. Together the two would examine the minute details of the coastal world around them, discussing various phenomena. Where does sand come from? How do the tides form? What types of shelled critters reside at the sea’s edge?

She first set foot on MIT’s campus in January of 2011 while a sophomore at the University of Puerto Rico, Río Piedras, attending the weeklong Quantitative Methods Workshop to learn various quantitative tools and programming languages. In June of that same year she returned, this time for 10 weeks as an MIT Summer Research Program (MSRP) student. Aponte joined Hazel Sive’s lab at the Whitehead Institute for Biomedical Research, gathering preliminary data for a paper that was eventually published in Fluids and Barriers of the CNS.

“I was introduced to basic science through both programs,” Aponte says. “Discovery-based research lays the foundation for translational research later on, and it allows you to address questions that no one has answered before. If you’re lucky enough to witness those discoveries, for a few moments you’re the only person in the world with that knowledge, and I find that prospect incredibly exciting.”

As a first-year graduate student in 2013, she tested out several different labs and ultimately chose Troy Littleton’s lab located in the Picower Institute for Learning and Memory. She was drawn to the friendly and collaborative atmosphere, as well as the breadth of potential projects — from those related to the central nervous system and Huntington’s disease to the connections between nerve cells.

Aponte investigates how nerve cells interface with one another and neighboring muscles, focusing on the tiny gap between neurons and muscles, known as neuromuscular junctions. Multiple neurons can form connections with the same neuron or muscle cell, but which connections remain depends on competition between the nerve cells and how often those connections are used. New ones are constantly being shaped as we learn new things and acquire new experiences, while less frequently used connections get trimmed away. Aponte wants to understand how neurons that talk to the same muscle cell interact with each other, determining which lines of communication will be strengthened and which will be pruned away.

When Aponte first began in the Littleton lab five years ago, she screened scores of unique drivers — segments of DNA that “drive” gene expression in specific cells during a specific time in development. She hoped to find drivers that could trigger the expression of a green fluorescent protein (GFP) at the neuromuscular junction, and ultimately identified two different drivers which caused GFP expression in two separate neurons targeting the same muscle near the back of the fly. These drivers would allow her to control the expression of not just GFP, but also other genes that she connected to the drivers, including genes that can increase or decrease the activity of the neurons, or even kill them.

“It’s really from there that my entire project was born,” Aponte recalls.

Each morning, she heads to the fly room to collect virgin flies and determine which ones to breed in order to generate progeny with her desired genetic makeup. She can infer something about the flies’ chromosomes based on their physical characteristics, which allow her to keep track of their genes and create offspring with the GFP marker in her neurons of interest. As is true for most things these days, there’s an app for that. As we chat, she takes out her phone and begins to scroll through images that illustrate which genetic markers engender which physical characteristics. The Tubby mutation makes the flies rather fat, whereas Bar makes their eyes noticeably skinnier.

“In the same way that I can express GFP in just one of the two motor neurons to distinguish between them and monitor their shape,” she says, “I can also express genes that increase or decrease activity of one of the neurons, or even kill one of the neurons. In this way, I create an input imbalance by increasing or decreasing the activity in either neuron to see how that affects the activity of its partner neuron.”

In the afternoons, sometimes she uses molecular fluorophores to highlight the changes in structure of these neurons. She also assesses the activity in the muscles by poking them with electrodes and observing what happens when the muscle receives more or less input from one of the motor neurons. Additionally, she explores what happens to surrounding muscles when these inputs are modified

Recently, she’s stumbled upon a rather baffling phenomenon. When she kills one of the two neurons (let’s call it “Neuron A”) the other one, Neuron B, remains relatively unchanged. Yet, when she kills Neuron B, Neuron A shrinks. This suggests Neuron B may be sending a “permissive” signal to Neuron A, telling it to contact the muscle. She is monitoring the neuromuscular junction over time to determine if Neuron A will ever reach the muscle, and if the muscle will change over time in response.

“This has never been seen before, so right now I’m trying to identify the smaller neuron to see if it is functional,” she says. “I’m going to look at it during different stages of development to see if it starts and stops communicating with the muscle at some point.”

This endeavor will constitute her main focus over the next few months. After she graduates, Aponte intends to pursue an academic postdoc studying flies, despite developing an allergy to her subjects over the past year. (She’s since acquired a face mask that keeps dust and fly particles away.) “I’m just excited to see where the research will take me,” she says. Now that’s dedication.

Photo credit: Raleigh McElvery
Study suggests glaucoma may be an autoimmune disease

Unexpected findings show that the body’s own immune system destroys retinal cells.

Anne Trafton | MIT News Office
August 11, 2018

Glaucoma, a disease that afflicts nearly 70 million people worldwide, is something of a mystery despite its prevalence. Little is known about the origins of the disease, which damages the retina and optic nerve and can lead to blindness.

A new study from MIT and Massachusetts Eye and Ear has found that glaucoma may in fact be an autoimmune disorder. In a study of mice, the researchers showed that the body’s own T cells are responsible for the progressive retinal degeneration seen in glaucoma. Furthermore, these T cells appear to be primed to attack retinal neurons as the result of previous interactions with bacteria that normally live in our body.

The discovery suggests that it could be possible to develop new treatments for glaucoma by blocking this autoimmune activity, the researchers say.

“This opens a new approach to prevent and treat glaucoma,” says Jianzhu Chen, an MIT professor of biology, a member of MIT’s Koch Institute for Integrative Cancer Research, and one of the senior authors of the study, which appears in Nature Communications on Aug. 10.

Dong Feng Chen, an associate professor of ophthalmology at Harvard Medical School and the Schepens Eye Research Institute of Massachusetts Eye and Ear, is also a senior author of the study. The paper’s lead authors are Massachusetts Eye and Ear researchers Huihui Chen, Kin-Sang Cho, and T.H. Khanh Vu.

Genesis of glaucoma

One of the biggest risk factors for glaucoma is elevated pressure in the eye, which often occurs as people age and the ducts that allow fluid to drain from the eye become blocked. The disease often goes undetected at first; patients may not realize they have the disease until half of their retinal ganglion cells have been lost.

Most treatments focus on lowering pressure in the eye (also known as intraocular pressure). However, in many patients, the disease worsens even after intraocular pressure returns to normal. In studies in mice, Dong Feng Chen found the same effect.

“That led us to the thought that this pressure change must be triggering something progressive, and the first thing that came to mind is that it has to be an immune response,” she says.

To test that hypothesis, the researchers looked for immune cells in the retinas of these mice and found that indeed, T cells were there. This is unusual because T cells are normally blocked from entering the retina, by a tight layer of cells called the blood-retina barrier, to suppress inflammation of the eye. The researchers found that when intraocular pressure goes up, T cells are somehow able to get through this barrier and into the retina.

The Mass Eye and Ear team then enlisted Jianzhu Chen, an immunologist, to further investigate what role these T cells might be playing in glaucoma. The researchers generated high intraocular pressure in mice that lack T cells and found that while this pressure induced only a small amount of damage to the retina, the disease did not progress any further after eye pressure returned to normal.

Further studies revealed that the glaucoma-linked T cells target proteins called heat shock proteins, which help cells respond to stress or injury. Normally, T cells should not target proteins produced by the host, but the researchers suspected that these T cells had been previously exposed to bacterial heat shock proteins. Because heat shock proteins from different species are very similar, the resulting T cells can cross-react with mouse and human heat shock proteins.

To test this hypothesis, the team brought in James Fox, a professor in MIT’s Department of Biological Engineering and Division of Comparative Medicine, whose team maintains mice with no bacteria. The researchers found that when they tried to induce glaucoma in these germ-free mice, the mice did not develop the disease.

Human connection

The researchers then turned to human patients with glaucoma and found that these patients had five times the normal level of T cells specific to heat shock proteins, suggesting that the same phenomenon may also contribute to the disease in humans. The researchers’ studies thus far suggest that the effect is not specific to a particular strain of bacteria; rather, exposure to a combination of bacteria can generate T cells that target heat shock proteins.

One question the researchers plan to study further is whether other components of the immune system may be involved in the autoimmune process that gives rise to glaucoma. They are also investigating the possibility that this phenomenon may underlie other neurodegenerative disorders, and looking for ways to treat such disorders by blocking the autoimmune response.

“What we learn from the eye can be applied to the brain diseases, and may eventually help develop new methods of treatment and diagnosis,” Dong Feng Chen says.

The research was funded by the National Institutes of Health, the Lion’s Foundation, the Miriam and Sheldon Adelson Medical Research Foundation, the National Nature Science Foundation of China, the Ivan R. Cottrell Professorship and Research Fund, the Koch Institute Support (core) Grant from the National Cancer Institute, and the National Eye Institute Core Grant for Vision Research.

The Y chromosome: Holding steadfast in a sea of change
Nicole Davis
August 2, 2018

The human Y chromosome is, in many ways, a study in contrasts. For decades, scientists have struggled to dissect its evolution in part because it does not have a genetic partner (or homolog), as all of the other human chromosomes do. That solitary existence means the Y chromosome is subject to some unusual evolutionary pressures. For example, it does not swap genetic material with a homologous chromosome — a practice known as recombination that other chromosomes follow — along the lion’s share of its length. However, its lack of recombination presents a unique opportunity: Because so much of its own genetic material stays put, scientists can trace the history of individual human Y chromosomes much further back in time than other chromosomes — in fact, they can go as far back as the data will allow.

That is precisely the approach taken by a team of Whitehead Institute researchers, led by Whitehead Institute Director David Page, who is also a professor of biology at the Massachusetts Institute of Technology and a Howard Hughes Medical Institute investigator. Their work is published in the August 2nd online issue of the American Journal of Human Genetics. Page and his colleagues, including graduate student and first author Levi Teitz, set out to examine a series of regions on the Y chromosome called amplicons — vast stretches of DNA, from tens of thousands to millions of nucleotides in length, which are present in two or more copies per chromosome. While the DNA contained in amplicons is often highly repetitive, it also houses biologically important genes. Although the precise functions of many of these genes remains to be determined, some have been found to play important roles in the development of sperm cells and testicular cancer. However, the amplicons vary drastically among species, so scientists cannot look to other organisms such as mice or chimpanzees to help reconstruct their past.

Page’s team zeroed in on these amplicons. Specifically, they looked at how the number of amplicon copies varies from one person’s Y chromosome to another. The researchers developed sophisticated computational tools to analyze DNA sequencing data collected from more than 1,200 males as part of the 1000 Genomes Project. What they discovered was quite surprising. Although the amplicons are quite variable, they found that overall, the configuration of amplicon copies on the Y chromosome has been painstakingly maintained over the last 300,000 years of human evolution. That means that despite the high level of mutation the chromosome experiences, evolutionary forces work to counteract this change and preserve its ancestral structure.

More work is needed to determine which aspects of the amplicons’ structure are important for chromosome biology, and in turn proper male development and fertility. However, the efforts of Teitz, Page, and their colleagues shed new light on the unusual tricks the solo chromosome uses to maintain its genomic integrity.

This research is supported by the National Institutes of Health and the Howard Hughes Medical Institute.

 

Written by Nicole Davis

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David Page’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also a Howard Hughes Medical Institute Investigator and a Professor of Biology at the Massachusetts Institute of Technology.

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Full citation:

“Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages”

American Journal of Human Genetics, online August 2, 2018.

Levi S. Teitz (1,2), Tatyana Pyntikova (1), Helen Skaletsky (1,3), and David C. Page (1,2,3).

1. Whitehead Institute, Cambridge, MA 02142, USA

2. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA

3. Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA

School of Science appoints eight faculty members to named professorships
School of Science
July 23, 2018

The School of Science announced that eight of its faculty members have been appointed to named professorships. These positions afford the faculty members additional support to pursue their research and develop their careers.

Eliezer Calo, assistant professor in the Department of Biology, has been named the Irwin W. and Helen Sizer Career Development Professor. He focuses on the coordination of RNA metabolism using a combination of genetic, biochemical, and functional genomic approaches. The core of Calo’s research program is to understand how ribosome biogenesis is controlled by specific RNA binding proteins, particularly RNA helicases of the “DEAD box” family, and how disregulation of ribosome biogenesis contributes to various diseases, including cancer. He proposes initially to characterize the functions of specific genes of interest, including the DDX21 RNA helicase and the TCOF1 factor involved in RNA Pol I transcription and rRNA processing, using biochemical, molecular and genome-wide approaches in mouse, Xenopus and Zebrafish models.

Steven Flavell, assistant professor in the Department of Brain and Cognitive Sciences, has been named the Lister Brothers Career Development Professor. He uses Caenorhabditis elegans to examine how neuromodulators coordinate activity in neural circuits to generate locomotion behaviors linked to the feeding or satiety states of an animal. His long-term goal is to understand how neural circuits generate sustained behavioral states, and how physiological and environmental information is integrated into these circuits. Gaining a mechanistic understanding of how these circuits function will be essential to decipher the neural bases of sleep and mood disorders.

Pablo Jarillo-Herrero, the Cecil and Ida Green Professor of Physics, explores quantum transport in novel condensed-matter systems such as graphene, transition metal dichalcogenides and topological insulators. In recent work, he has demonstrated the presence of a bandgap in graphene-based van der Waals heterostructures, novel quantum spin Hall and photothermoelectric effects in graphene, as well as light-emitting diodes, photodetectors and solar cells in the atomically thin tungsten diselenide system. He has also made advances in characterizing and manipulating the properties of other ultrathin materials such as ultrathin graphite and molybdenum disulphide, which lack graphene’s ultrarelativistic properties, but possess other unusual electronic properties.

Becky Lamason, assistant professor in the Department of Biology, has been named the Robert A. Swanson (1969) Career Development Professor of Life Sciences. She investigates how intracellular bacterial pathogens hijack host cell processes to promote infection. In particular, she studies how Rickettsia parkeri and Listeria monocytogenes move through tissues via a process called cell-to-cell spread. She utilizes cellular, molecular, genetic, biochemical, and biophysical approaches to elucidate the mechanisms of spread in order to reveal key aspects of pathogenesis and host cell biology.

Rebecca Saxe, the inaugural John W. Jarve (1978) Professor in Brain and Cognitive Sciences, is best known for her discovery of a brain region that is specialized for “theory of mind,” people’s ability to think about the thoughts, beliefs, plans, hopes and emotions of other people. Saxe continues to study this region and its role in social cognition, and is exploring the theory-of-mind system as a promising candidate for understanding the biological basis of autism. She also studies brain development in human babies, including her own.

Omer Yilmaz, assistant professor in the Department of Biology, has been named the Eisen and Chang Career Development Professor. He studies how the adult intestine is maintained by stem cells that require a cellular neighborhood, or niche, consisting in part of Paneth cells. Specifically, he investigates the molecular mechanisms of how intestinal stem cells and their Paneth cell niche respond to diverse diets to coordinate intestinal regeneration with organismal physiology and its impact on the formation and growth of intestinal cancers. By better understanding how intestinal stem cells adapt to diverse diets, he hopes to identify and develop new strategies that prevent and reduce the growth of cancers involving the intestinal tract that includes the small intestine, colon, and rectum.

Yufei Zhao, assistant professor in the Department of Mathematics, has been named the Class of 1956 Career Development Professor. He has made significant contributions in combinatorics with applications to computer science. Recently, Zhao and three undergraduates solved an open problem concerning the number of independent sets in an irregular graph, a conjecture first proposed in 2001. Understanding the number of independent sets — subsets of vertices where no two vertices are adjacent — is important to solving many other combinatorial problems. In other research accomplishments, Zhao co-authored a proof with Jacob Fox and David Conlon that contributed to a better understanding of the celebrated Green-Tao theorem that states prime numbers contain arbitrarily long arithmetic progressions. Their work improves our understanding of pseudorandom structures — non-random objects with random-like properties — and has other applications in mathematics and computer science.

Martin Zwierlein, the inaugural Thomas A. Frank (1977) Professor of Physics, studies ultracold gases of atoms and molecules. These gases host novel states of matter and serve as pristine model systems for other systems in nature, such as neutron stars or high-temperature superconductors. In contrast to bulk materials, in experiments with cold gases one can freely tune the interaction between atoms and make it as strong as quantum mechanics allows. This enabled the observation of a novel robust form of superfluidity: Scaled to the density of electrons in solids, superfluidity would in fact occur far above room temperature. Under a novel quantum gas microscope with single-atom resolution, the team recently studied charge and spin correlations and transport in a Fermi-Hubbard lattice gas. This system is believed to hold the key to high-temperature superconductivity in cuprate materials. Using ultracold molecules, Zwierlein’s group also demonstrated coherence times on the order of seconds, spurring hopes for the future use of such molecules in quantum information applications.

A tale of two projects

Graduate student Julie Monda has spent five years investigating two divergent aspects of cell division, revealing some unexpected results and new research questions.

Raleigh McElvery
July 23, 2018

To sixth year graduate student Julie Monda, dividing cells are among the most beautiful things she’s ever seen. Watching the tiny, delicate spheres split into identical versions of themselves also provides her with a visual readout for her experiments — will the process continue if she removes a certain piece of a certain protein? Will the genetic material still distribute equally between the two cells? Which molecules are crucial for cell division, and how are they regulated?

Our cells are constantly dividing in order to grow and repair themselves, although some (like skin cells) do so more often than others, say, in the brain. This process, known as mitosis, is the primary focus of Iain Cheeseman’s lab, situated in the Whitehead Institute for Biomedical Research. Most of the research in the Cheeseman lab involves the kinetochore, a group of proteins located on the chromosome where the arms join. During mitosis, long, fibrous structures, known as microtubules, attach to the kinetochore to pull apart the duplicated chromosomes as the parent cell splits in half, ensuring each daughter cell receives an exact copy of the parent’s genetic blueprint.

Before she arrived at MIT Biology in the fall of 2012, Monda worked as a research technician at St. Jude Children’s Research Hospital in Memphis, Tennessee in the lab of Brenda Schulman PhD ’96 . As she recalls, she always “preferred performing hands-on research techniques at the lab bench over being in a classroom.” So she surprised even herself when she chose MIT’s graduate program in biology precisely because it requires all first-year students to take a full course load their fall semester before beginning lab rotations.

“That structure seemed useful given that I studied biochemistry as an undergraduate at the University of Tulsa, and the degree requirements were weighted more towards chemistry than biology,” she says. “Plus, when you’re only taking classes, you spend more time interacting with your classmates. It creates a close-knit community that extends throughout your entire graduate career and beyond.”

Monda ultimately selected the Cheeseman lab because it married her interests in biochemistry and cell biology.

“The research in this lab focuses on various elements of kinetochore function and cell division, but everyone is generally working on their own distinct questions,” she explains. “I knew I would have an area that was mine to explore. It’s both exciting and challenging because no one else is thinking about your projects to the extent that you are.”

Monda’s story is a tale of two projects: one focused on the interface between the kinetochore and the array of microtubules known as the mitotic “spindle,” and another project that ended up taking both her and the lab in a slightly new direction.

The first, concerning kinetochore-microtubule interactions, represented a collaboration with former lab technician Ian Whitney. For this endeavor, Monda investigated a protein complex called Ska1, found at the outer kinetochore.

The Ska1 complex is located where the kinetochore and microtubule meet. Ska1’s role, Monda explains, is to allow the kinetochores to remain attached to the spindle during chromosome segregation, even as the microtubules that compose the spindle begin to disassemble (as they must do).

“We wanted to know how the kinetochore hangs onto this polymer that is essentially falling apart,” Monda explains. “Long story short, we ended up defining specific surfaces within the Ska1 complex that are important for holding on to the microtubule as it shrinks, and — as we were surprised to note — also as it grows”

Although Ska1 only requires a single point of contact to bind a microtubule, Monda and Whitney pinpointed multiple surfaces on Ska1 that are required to allow it to remain associated with the microtubules as they disassemble and reassemble themselves.

While her Ska1 project was very much in line with the types of questions that the Cheeseman lab traditionally pursues, Monda also worked on another endeavor that “began as a side project and slowly evolved into a more full-time effort.” This project involves a motor protein called dynein, which helps to align the chromosomes and position the spindle during mitosis.

Dynein piqued Monda’s interest because of its role in mitosis, as well as its importance throughout the entire cell cycle. Motor proteins are molecules powered by the release of chemical energy that move along surfaces, sometimes transporting cargo, sometimes performing other essential tasks. Dynein is a motor protein that walks in one direction along microtubules, even when the microtubules latch onto the kinetochore to yank apart the chromosomes during mitosis.

But dynein doesn’t act alone. There are a number of additional proteins that also play a key role in coordinating its activity and localization. Monda is studying two of these accessory regulatory proteins, Nde1 and NdeL1, which bind to dynein and help promote some of its functions. She wanted to understand how Nde1 and NdeL1 interact with dynein to activate it. Although Nde1 and NdeL1 are nearly identical in function, Monda discovered that Nde1 (but not NdeL1) binds to another complex: the 26S proteasome.

The proteasome degrades proteins within the cell, influencing virtually all aspects of cellular function, including DNA synthesis and repair, transcription, translation, and cell signaling. Given its ubiquity, it has remained a point of interest among the scientific community for years. And yet, before Monda’s research, the interaction between Nde1 and the proteasome had apparently gone unnoticed. Researchers have long studied Nde1 in relation to dynein, but it’s possible that the interaction between Nde1 and the proteasome represents a new function for Nde1 unrelated to dynein regulation. In fact, Monda’s finding may have implications for understanding the development of the human brain.

“It’s clear that patients with mutations in Nde1 have much more severe neurodevelopmental defects than scientists would have predicted,” Monda says, “so it’s possible that this new interaction between Nde1 and the proteasome could help to explain why Nde1 is so important in the brain.”

Her most recent results have been published in Molecular Biology of the Cell.

“I’ve found some exciting results over the past few years,” Monda says, “and even though a lot of my research has gone in a direction that’s not strictly mitosis-related, Iain has been great about allowing me to follow the science wherever it leads. We want to know what these proteins are actually doing, both in terms of this new interaction and also more broadly within the cell.”

Monda intends to submit and defend her thesis this summer, and assume a postdoctoral position at the University California, San Diego in the fall. Although she’s been watching cells divide for years now, the process still retains its grandeur.

“Often times biologists investigate questions at scales where we can’t really see what we’re studying as we study it,” she says. “But having this visual readout makes it more tangible; I feel like I can better appreciate what exactly it is that I’m trying to understand, as well as the beauty and complexity of the processes that sustain life.”

Sharpening the edges of cancer chemotherapy
Nicole Davis | Whitehead Institute
July 11, 2018

Cambridge, MA — Tackling unsolved problems is a cornerstone of scientific research, propelled by the power and promise of new technologies. Indeed, one of the shiniest tools in the biomedical toolkit these days is the genome editing system known as CRISPR/Cas9. Whitehead Institute Member David Sabatini and his colleagues pioneered the use of this tool as a foundation for large-scale genetic screens in human cells, turning up a treasure trove of new insights into cellular metabolism, in both normal cells and cancer cells.

When Naama Kanarek, a postdoc in Sabatini’s laboratory, pondered how to apply these state-of-the-art CRISPR/Cas9 screens to her own research, her thoughts turned to a classic cancer chemotherapy drug, methotrexate, which has been in clinical use for nearly seven decades. Often used to treat a form of pediatric leukemia, known as acute lymphoblastic leukemia (ALL), the drug, when deployed as part of a multifaceted treatment plan, can be highly effective. But its power comes at a cost. Because methotrexate can damage not only cancer cells but also healthy tissues, it must be administered with great care. For children who receive high doses of the drug, a mainstay of ALL treatment, that can mean several days spent in the hospital with rigorous clinical monitoring.

In other forms of cancer, methotrexate’s efficacy is more uncertain. For example, in pediatric osteosarcoma, only 65 percent of patients respond. Unfortunately, there is currently no way for doctors to pinpoint who will and who will not.

“From a scientific standpoint, methotrexate is quite special because it was the first metabolic drug to be developed, but much of its biology remains to be discovered — particularly what drives these different responses in patients,” Kanarek says. “So, this is really one of these old, classic questions that has been lingering in the field for some time. We thought we could learn something new.”

And they did. In the July 11 online issue of the journal Nature, Kanarek, Sabatini, and their colleagues report the findings of a CRISPR/Cas9 screen for factors involved in methotrexate sensitivity. The team’s work yielded a surprising set of discoveries that point to the breakdown of histidine — one of several amino acids used by the body to construct proteins — as a critical gatekeeper of cancer cells’ vulnerability to methotrexate. The researchers’ findings not only help illuminate the biology of a well-known cancer chemotherapy, but also suggest a simple dietary supplement that could help broaden its therapeutic window and reduce its toxicity.

 “This study is an example of the power of modern genomic tools to shine a bright light on longstanding questions in human biology,” says senior author David Sabatini, a Member of Whitehead Institute, a professor of biology at Massachusetts Institute of Technology and investigator with the Howard Hughes Medical Institute (HHMI). “While cancer chemotherapies can be quite effective, their biological effects are often poorly understood. By laying bare their biology, we may be able to devise ways to utilize them more wisely.”

ATTACK THE CANCER, NOT THE PATIENT

The history of methotrexate stretches back to the 1940s, a time when strikingly little was known about the origins of cancer much less how best to treat it. The birth of methotrexate as a chemotherapeutic agent was sparked by the astute observations of Sidney Farber, a pediatric pathologist at Boston Children’s Hospital who cared for children with a variety of maladies, including ALL. In the course of caring for patients with ALL, Farber recognized that cancer cells depended on the nutrient folic acid for their own proliferation. That gave him the idea of using folate antagonists to treat ALL. Methotrexate was developed in 1949 precisely for this purpose and was subsequently shown to induce remission in children with ALL. Fast forward to today, and the drug has evolved into a significant tool in oncologists’ toolkit.

“Methotrexate is a major part of the backbone of chemotherapy treatment across many human cancers,” says Loren Walensky, a pediatric hematologist/oncologist at the Dana-Farber Cancer Institute who is not a study co-author but served as an early adviser on the project and will also play a deeper role in planning future follow-up studies. “It is also used outside of the cancer field for the treatment of several autoimmune diseases.”

He added, “But as with all chemotherapy, the critical issue is how to best use it to inflict maximal damage on the cancer without irreparably harming the patient.”

Kanarek explains how new genetic tools are allowing insights into the sensitivity of cancer cells to methotrexate.

The basic mechanics of methotrexate are fairly well known. The drug inhibits dihydrofolate reductase (DHFR), an enzyme that generates the functional form of folate, known as tetrahydrofolate (THF). THF is essential for preparing the raw materials needed to make nucleic acids, such as DNA, which carries cells’ genetic information, and RNA, a close chemical relative involved in making proteins. “Proliferating cells must duplicate their DNA, so they need a lot of THF,” Kanarek explains. “But even cells that are not dividing need to make RNA, and that requires THF, too.”

The results of Kanarek’s CRISPR/Cas9 screen now bring greater clarity to this molecular picture. She and her colleagues uncovered another enzyme, called FTCD, which is involved in the breakdown of histidine. Interestingly, FTCD also requires THF for its function — though not nearly as much as the main target of methotrexate, DHFR. Despite the differential demands of the two enzymes, they both draw from the same, shared pool of THF.

“Under normal conditions, this pool is sufficiently full, so there is no competition for resources, even in rapidly dividing cells,” Kanarek says.

But when the amount of THF becomes limiting — as it does in cells that are treated with methotrexate — the story is quite different, the Whitehead Institute team discovered. In that case, the activity of FTCD poses serious problems, because there isn’t enough THF in the pool to support both cell proliferation and histidine breakdown. When that happens, the cells die.

That got Kanarek thinking more about histidine: Could the nutrient provide a way to tinker with FTCD activity and, by virtue of the cancer cells’ own metabolism, make them more vulnerable to methotrexate?

To explore this question, the researchers used mouse models of leukemia, engineered by transplanting human leukemia cells under the skin of immunocompromised mice. A subset of the mice received injections of methotrexate together with histidine. This one-two punch, Kanarek hypothesized, should ramp up the function of FTCD and more rapidly drain the THF pool, thereby making the cells more sensitive to the cancer-killing effects of methotrexate.

That is precisely what the team observed. Notably, these experiments involved lower than normal doses of methotrexate, suggesting the cells had indeed been made more sensitive to the cancer drug. Moreover, the studies included a human leukemia cell line, called SEM, which harbors a specific genetic mutation that is associated with a particularly poor prognosis in patients — further underscoring the power of the histidine degradation pathway to weaken cells’ defenses.

Now, Kanarek and her colleagues are working to extend these initial findings with additional preclinical studies and, together with Walensky, determine how to best evaluate the potential benefits of histidine supplementation in cancer patients. Their ultimate goal: to pursue clinical trials that will assess histidine’s ability to improve the effectiveness of methotrexate in humans.

In addition to making cancer cells more vulnerable to methotrexate, the Whitehead Institute team’s research also holds promise for another therapeutic challenge: identifying which patients will or will not respond to the drug.

Two other enzymes cooperate with FTCD in breaking down histidine. The levels of one of the enzymes, known as HAL, appears to correlate with cells’ sensitivity to methotrexate: That is, cancer cells with high levels of HAL tend to be more sensitive to the drug. More work is needed to determine whether this correlation extends to a broader swath of patient samples and if it has predictive value in the clinic. Nevertheless, Kanarek and her colleagues are already beginning work on this front. Together with Abner Louissaint, Jr., a hematopathologist at Massachusetts General Hospital who also served as an early adviser on the Nature study, the Whitehead Institute team will launch a second clinical study to examine whether HAL levels can predict methotrexate response in patients with lymphoma.

“Being able to understand who is going to respond to methotrexate and who is not, and how to achieve a therapeutic benefit while mitigating the drug’s potential side effects, could have a profound impact on patient care,” Walensky says. “The insights from this study bring an entirely new dimension to our understanding of a decades-old and critically important cancer medicine. And as a physician and a scientist, that’s truly exciting.”

Written by Nicole Davis

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David Sabatini’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also a Howard Hughes Medical Institute investigator and a professor of biology at Massachusetts Institute of Technology.

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Full citation:

“Histidine catabolism is a major determinant of methotrexate sensitivity”

Nature, online on July 11, 2018.

Naama Kanarek (1,2,3,4), Heather R. Keys (1), Jason R. Cantor (1,2,3,4), Caroline A. Lewis (1), Sze Ham Chan (1), Tenzin Kunchok (1), Monther Abu-Remaileh (1,2,3,4), Elizaveta Freinkman (1), Lawrence D. Schweitzer (4), and David M. Sabatini (1,2,3,4).

  1. Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 455 main Street, Cambridge, Massachusetts 02142, USA
  2. Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
  3. Koch Institute for Integrative Cancer Research and Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
  4. Broad Institute of Harvard and Massachusetts Institute of Technology, 415 main Street, Cambridge, Massachusetts 02142, USA