Research Area: Stem Cell and Developmental Biology

Mary Gehring: Using flowering plants to explore epigenetic inheritance

Biologist’s studies illuminate a control system that influences how traits are passed along to new generations.

Anne Trafton | MIT News Office
December 16, 2019

Genes passed down from generation to generation play a significant role in determining the traits of every organism. In recent decades, scientists have discovered that another layer of control, known as epigenetics, is also critically important in shaping those characteristics.

Those added controls often work through chemical modifications of genes or other sections of DNA, which influence how easily those genes can be expressed by a cell. Many of those modifications are similar across species, allowing scientists to use plants as an experimental model to uncover how epigenetic processes work.

“Many of the epigenetic phenomena we know about were first discovered in plants, and in terms of understanding the molecular mechanisms, work on plants has also led the way,” says Mary Gehring, an associate professor of biology and a member of MIT’s Whitehead Institute for Biomedical Research.

Gehring’s studies of the small flowering plant Arabidopsis thaliana have revealed many of the mechanisms that underlie epigenetic control, shedding light on how these modifications can be passed from generation to generation.

“We’re trying to understand how epigenetic information is used during plant growth and development, and looking at the dynamics of epigenetic information through development within a single generation, between generations, and on an evolutionary timescale,” she says.

Seeds of discovery

Gehring, who grew up in a rural area of northern Michigan, became interested in plant biology as a student at Williams College, where she had followed her older sister. During her junior year at Williams, she took a class in plant growth and development and ended up working in the lab of the professor who taught the course. There, she studied how development of Arabidopsis is influenced by plant hormones called auxins.

After graduation, Gehring went to work for an environmental consulting company near Washington, but she soon decided that she wanted to go to graduate school to continue studying plant biology. She enrolled at the University of California at Berkeley, where she joined a lab that was studying how different genetic mutations affect the development of seeds.

That lab, led by Robert Fischer, was one of the first to discover an epigenetic phenomenon called gene imprinting in plants. Gene imprinting occurs when an organism expresses only the maternal or paternal version of particular gene. This phenomenon has been seen in flowering plants and mammals.

Gehring’s task was to try to figure out the mechanism behind this phenomenon, focusing on an Arabidopsis imprinted gene called MEDEA. She found that this type of imprinting is achieved by DNA demethylation, a process of removing chemical modifications from the maternal version of the gene, effectively turning it on.

After finishing her PhD in 2005, she worked as a postdoc at the Fred Hutchinson Cancer Research Center, in the lab of Steven Henikoff. There, she began doing larger, genome-scale studies in which she could examine epigenetic markers for many genes at once, instead of one at a time.

During that time, she began studying some of the topics she continues to investigate now, including regulation of the enzymes that control DNA methylation, as well as regulation of “transposable elements.” Also known as “jumping genes,” these sequences of DNA can change their position within the genome, sometimes to promote their own expression at the expense of the organism. Cells often use methylation to silence these genes if they generate harmful mutations.

Patterns of inheritance

After her postdoc, Gehring was drawn to MIT by “how passionate people are about what they’re working on, whether that’s biology or another subject.”

“Boston, especially MIT and Whitehead, is a great environment for science,” she says. “It seemed like there were a lot of opportunities to get really smart and talented students in the lab and have interesting colleagues to talk with.”

When Gehring joined the Whitehead Institute in 2010, she was the only plant biologist on the faculty, but she has since been joined by Associate Professor Jing-Ke Weng.

Her lab now focuses primarily on questions such as how maternal and paternal parents contribute to reproduction, and how their differing interests can lead to genetic conflicts. Gene imprinting is one way that this conflict is played out. Gehring has also discovered that small noncoding RNA molecules play an important role in imprinting and other aspects of inheritance by directing epigenetic modifications such as DNA methylation.

“One thing we’ve found is that this noncoding RNA pathway seems to control the transcriptional dosage of seeds, that is, how many of the transcripts are from the maternally inherited genome and how many from the paternally inherited genome. Not just for imprinted genes, but also more broadly for genes that aren’t imprinted,” Gehring says.

She has also identified a genetic circuit that controls an enzyme that is required to help patterns of DNA methylation get passed from parent to offspring. When this circuit is disrupted, the methylation state changes and unusual traits can appear. In one case, she found that the plants’ leaves become curled after a few generations of disrupted methylation.

“You need this genetic circuit in order to maintain stable methylation patterns. If you don’t, then what you start to see is that the plants develop some phenotypes that get worse over generational time,” she says.

Many of the epigenetic phenomena that Gehring studies in plants are similar to those seen in animals, including humans. Because of those similarities, plant biology has made significant contributions to scientists’ understanding of epigenetics. The phenomenon of epigenomic imprinting was first discovered in plants, in the 1970s, and many other epigenetic phenomena first seen in plants have also been found in mammals, although the molecular details often vary.

“There are a lot of similarities among epigenetic control in flowering plants and mammals, and fungi as well,” Gehring says. “Some of the pathways are plant-specific, like the noncoding RNA pathway that we study, where small noncoding RNAs direct DNA methylation, but small RNAs directing silencing via chromatin is something that happens in many other systems as well.”

Committed to reproduction
Greta Friar | Whitehead Institute
November 21, 2019

Cambridge, MA – Early in mammalian embryonic development, long before the organism’s ultimate form has taken shape, a precious subset of its cells are set aside for future use in creating offspring. This task bestows on that subset of cells a special kind of immortality. While the majority of the embryo’s cells go on to construct the growing body, and their journey begins and ends in that body, the cells that are set aside, called primordial germ cells (PGCs), will eventually produce sperm and eggs, which will in turn produce a new body—and so the circle of life continues.

An embryo’s earliest cells are pluripotent, meaning they have the potential to develop into many different cell types—for example, heart, brain, blood—but the descendants of these cells eventually become committed to a specific identity, after which each can only produce one type of cell. Scientists have long believed that when PGCs are set aside, they are immediately committed to the path of producing egg and sperm cells. However, new research from Whitehead Institute Director David Page, also a professor of biology at the Massachusetts Institute of Technology (MIT) and a Howard Hughes Medical Institute investigator, and postdoctoral researcher Peter Nicholls, suggests that instead, the primordial germ cells’ fate remains flexible for much longer: until much closer to the end of embryonic development. In most species, PGCs are set aside long before the gonads—the testes or ovaries—form, and then later travel to these developing gonads where they will ultimately produce sex cells. Page and Nicholls have found evidence that the fate of these PGCs remains flexible until shortly after they reach the gonads. Their findings, which appear in the journal PNAS on November 21, deepen our understanding of the process of reproduction.

“A fundamental question in biology is how we get from one generation to the next,” Page says. “And the cells that are tasked with producing the next generation are an important part of that story.”

Establishing a new timeline for when PGCs become committed could also shed light on the origins of some reproductive tract cancers, including testicular cancer, the incidence of which is on the rise, and which is already the most commonly diagnosed cancer in young men.

Although PGCs are precursors of sperm and eggs, they also share many features with pluripotent cells, like embryonic stem cells. If migrating PGCs are isolated and cultured like embryonic stem cells, the PGCs show indicators of pluripotency, and are able to spontaneously form tumors containing multiple cell types—a trademark of pluripotent cells. Page and Nicholls found evidence confirming that shortly after the PGCs reach the gonads, they lose this capacity to produce pluripotent cell lines, and their ability for tumor formation. From that point on, the PGCs can only develop into eggs and sperm, no matter their environment.

The researchers then set out to identify the gene that prompts PGCs to become committed to produce only eggs or sperm. First, Nicholls identified a set of genes that are activated around the time that PGCs enter the gonads in mice and humans, and of those, focused on the genes that appeared to have equivalents involved in sex cell commitment across a variety of animals, not just in mammals. He then narrowed in on one of these genes, Dazl, as the single gene necessary for PGCs to become irrevocably committed to their path as sex cells. Nicholls found that when the Dazl gene is deleted from mice, PGCs travel to the gonads but don’t develop into committed precursors of egg and sperm, suggesting that Dazl is the key ingredient in the recipe for sex cell commitment.

In the absence of Dazl, PGCs remain uncommitted, and in some cases, will form gonadal tumors. The researchers argue, based on their findings, that testicular cancer and other gonadal cancers may develop from PGCs that have travelled to the gonads, but have not properly committed to becoming sex cells and so are prone to forming tumors. In Dazl-deficient mice, which had large amounts of uncommitted PGCs, more than one out of four males developed testicular tumors at a young age. The early onset of the tumors is consistent with that seen in children and men with testicular cancer, most of whom are under 45 years old.

The researchers also found that female Dazl-deficient mice developed gonadal tumors, though at a lower rate than males. Further research demonstrated that the testis environment is particularly favorable for tumor formation from uncommitted PGCs.

“Testicular cancer is on the rise for reasons not yet known, and our findings suggest that the cancer has embryonic origins,” Page says. “Understanding the nature of primordial germ cells will be important for investigating and addressing this disease.”

The researchers hope that, along with providing insights into gonadal cancers, their work could help improve the derivation of eggs and sperm from stem cells in the lab. Figuring out the specifics of the process for sex cell commitment should allow researchers recreate it in a dish. Nicholls is also excited about the evolutionary implications of the work: he found evidence that a similar process of sex cell commitment occurs across a wide variety of species. In particular, research with DAZL-deficient pigs—whose last common ancestor with mice and humans lived 95 million years ago—provides strong evidence that this DAZL-dependent process has been in play since the early days of modern mammals.

“This work completely shifts the timing for when sex cells become committed in mammals,” Nicholls says. “Furthermore, our data suggest that a common set of factors might operate in sex cell commitment not only in mammals, but perhaps across all vertebrates, regardless of how the primordial germ cells are first established.”

This work was supported by the Howard Hughes Medical Institute; a Hope Funds for Cancer Research Fellowship; an Early Career Fellowship; a DFG grant; a research grant from Biogen, Inc.; the National Natural Science Foundation of China; and a National Institutes of Health SBIR award.

Written by Greta Friar

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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.

***

Citation:

“Mammalian germ cells are determined after PGC colonization of the nascent gonad”

PNAS, online, Nov 21, 2019, DOI: 10.1073/pnas.1910733116

Peter K. Nicholls (1), Hubert Schorle (1,2),  Sahin Naqvi (1,3), Yueh-Chiang Hu (1,4), Fan Yuting (1,5), Michelle A. Carmell (1), Ina Dobrinski (6), Adrienne L. Watson (7), Daniel F. Carlson (7), Scott C. Fahrenkrug (7) and David C. Page (1,3,8)

1. Whitehead Institute, Cambridge, MA 02142, USA

2. Department of Developmental Pathology, Institute of Pathology, University of Bonn Medical

School, Bonn 53127, Germany

3. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

4. Divisions of Developmental Biology and Reproductive Sciences, Cincinnati Children’s

Hospital Medical Center, Cincinnati, OH 45229, USA

5. Reproductive Medicine Center, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou,

510655, China

6. Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary

Medicine, University of Calgary, Alberta, T2N 4N1, Canada

7. Recombinetics, Inc., Saint Paul, MN 55104, USA

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

Study links certain metabolites to stem cell function in the intestine

Molecules called ketone bodies may improve stem cells’ ability to regenerate new intestinal tissue.

Anne Trafton | MIT News Office
August 22, 2019

MIT biologists have discovered an unexpected effect of a ketogenic, or fat-rich, diet: They showed that high levels of ketone bodies, molecules produced by the breakdown of fat, help the intestine to maintain a large pool of adult stem cells, which are crucial for keeping the intestinal lining healthy.

The researchers also found that intestinal stem cells produce unusually high levels of ketone bodies even in the absence of a high-fat diet. These ketone bodies activate a well-known signaling pathway called Notch, which has previously been shown to help regulate stem cell differentiation.

“Ketone bodies are one of the first examples of how a metabolite instructs stem cell fate in the intestine,” says Omer Yilmaz, the Eisen and Chang Career Development Associate Professor of Biology and a member of MIT’s Koch Institute for Integrative Cancer Research. “These ketone bodies, which are normally thought to play a critical role in energy maintenance during times of nutritional stress, engage the Notch pathway to enhance stem cell function. Changes in ketone body levels in different nutritional states or diets enable stem cells to adapt to different physiologies.”

In a study of mice, the researchers found that a ketogenic diet gave intestinal stem cells a regenerative boost that made them better able to recover from damage to the intestinal lining, compared to the stem cells of mice on a regular diet.

Yilmaz is the senior author of the study, which appears in the Aug. 22 issue of Cell. MIT postdoc Chia-Wei Cheng is the paper’s lead author.

An unexpected role

Adult stem cells, which can differentiate into many different cell types, are found in tissues throughout the body. These stem cells are particularly important in the intestine because the intestinal lining is replaced every few days. Yilmaz’ lab has previously shown that fasting enhances stem cell function in aged mice, and that a high-fat diet can stimulate rapid growth of stem cell populations in the intestine.

In this study, the research team wanted to study the possible role of metabolism in the function of intestinal stem cells. By analyzing gene expression data, Cheng discovered that several enzymes involved in the production of ketone bodies are more abundant in intestinal stem cells than in other types of cells.

When a very high-fat diet is consumed, cells use these enzymes to break down fat into ketone bodies, which the body can use for fuel in the absence of carbohydrates. However, because these enzymes are so active in intestinal stem cells, these cells have unusually high ketone body levels even when a normal diet is consumed.

To their surprise, the researchers found that the ketones stimulate the Notch signaling pathway, which is known to be critical for regulating stem cell functions such as regenerating damaged tissue.

“Intestinal stem cells can generate ketone bodies by themselves, and use them to sustain their own stemness through fine-tuning a hardwired developmental pathway that controls cell lineage and fate,” Cheng says.

In mice, the researchers showed that a ketogenic diet enhanced this effect, and mice on such a diet were better able to regenerate new intestinal tissue. When the researchers fed the mice a high-sugar diet, they saw the opposite effect: Ketone production and stem cell function both declined.

Stem cell function

The study helps to answer some questions raised by Yilmaz’ previous work showing that both fasting and high-fat diets enhance intestinal stem cell function. The new findings suggest that stimulating ketogenesis through any kind of diet that limits carbohydrate intake helps promote stem cell proliferation.

“Ketone bodies become highly induced in the intestine during periods of food deprivation and play an important role in the process of preserving and enhancing stem cell activity,” Yilmaz says. “When food isn’t readily available, it might be that the intestine needs to preserve stem cell function so that when nutrients become replete, you have a pool of very active stem cells that can go on to repopulate the cells of the intestine.”

The findings suggest that a ketogenic diet, which would drive ketone body production in the intestine, might be helpful for repairing damage to the intestinal lining, which can occur in cancer patients receiving radiation or chemotherapy treatments, Yilmaz says.

The researchers now plan to study whether adult stem cells in other types of tissue use ketone bodies to regulate their function. Another key question is whether ketone-induced stem cell activity could be linked to cancer development, because there is evidence that some tumors in the intestines and other tissues arise from stem cells.

“If an intervention drives stem cell proliferation, a population of cells that serve as the origin of some tumors, could such an intervention possibly elevate cancer risk? That’s something we want to understand,” Yilmaz says. “What role do these ketone bodies play in the early steps of tumor formation, and can driving this pathway too much, either through diet or small molecule mimetics, impact cancer formation? We just don’t know the answer to those questions.”

The research was funded by the National Institutes of Health, a V Foundation V Scholar Award, a Sidney Kimmel Scholar Award, a Pew-Stewart Trust Scholar Award, the MIT Stem Cell Initiative, the Koch Institute Frontier Research Program through the Kathy and Curt Marble Cancer Research Fund, the Koch Institute Dana Farber/Harvard Cancer Center Bridge Project, and the American Federation of Aging Research.

Biologists and mathematicians team up to explore tissue folding

An algorithm developed to study the structure of galaxies helps explain a key feature of embryonic development.

Anne Trafton | MIT News Office
July 25, 2019

As embryos develop, they follow predetermined patterns of tissue folding, so that individuals of the same species end up with nearly identically shaped organs and very similar body shapes.

MIT scientists have now discovered a key feature of embryonic tissue that helps explain how this process is carried out so faithfully each time. In a study of fruit flies, they found that the reproducibility of tissue folding is generated by a network of proteins that connect like a fishing net, creating many alternative pathways that tissues can use to fold the right way.

“What we found is that there’s a lot of redundancy in the network,” says Adam Martin, an MIT associate professor of biology and the senior author of the study. “The cells are interacting and connecting with each other mechanically, but you don’t see individual cells taking on an all-important role. This means that if one cell gets damaged, other cells can still connect to disparate parts of the tissue.”

To uncover these network features, Martin worked with Jörn Dunkel, an MIT associate professor of physical applied mathematics and an author of the paper, to apply an algorithm normally used by astronomers to study the structure of galaxies.

Hannah Yevick, an MIT postdoc, is the lead author of the study, which appears today in Developmental Cell. Graduate student Pearson Miller is also an author of the paper.

A safety net

During embryonic development, tissues change their shape through a process known as morphogenesis. One important way tissues change shape is to fold, which allows flat sheets of embryonic cells to become tubes and other important shapes for organs and other body parts. Previous studies in fruit flies have shown that even when some of these embryonic cells are damaged, sheets can still fold into their correct shapes.

“This is a process that’s fairly reproducible, and so we wanted to know what makes it so robust,” Martin says.

In this study, the researchers focused on the process of gastrulation, during which the embryo is reorganized from a single-layered sphere to a more complex structure with multiple layers. This process, and other morphogenetic processes similar to fruit fly tissue folding, also occur in human embryos. The embryonic cells involved in gastrulation contain in their cytoplasm proteins called myosin and actin, which form cables and connect at junctions between cells to form a network across the tissue. Martin and Yevick had hypothesized that the network of cell connectivity might play a role in the robustness of the tissue folding, but until now, there was no good way to trace the connections of the network.

To achieve that, Martin’s lab joined forces with Dunkel, who studies the physics of soft surfaces and flowing matter — for example, wrinkle formation and patterns of bacterial streaming. For this study, Dunkel had the idea to apply a mathematical procedure that can identify topological features of a three-dimensional structure, analogous to ridges and valleys in a landscape. Astronomers use this algorithm to identify galaxies, and in this case, the researchers used it to trace the actomyosin networks across and between the cells in a sheet of tissue.

“Once you have the network, you can apply standard methods from network analysis — the same kind of analysis that you would apply to streets or other transport networks, or the blood circulation network, or any other form of network,” Dunkel says.

Among other things, this kind of analysis can reveal the structure of the network and how efficiently information flows along it. One important question is how well a network adapts if part of it gets damaged or blocked. The MIT team found that the actomyosin network contains a great deal of redundancy — that is, most of the “nodes” of the network are connected to many other nodes.

This built-in redundancy is analogous to a good public transit system, where if one bus or train line goes down, you can still get to your destination. Because cells can generate mechanical tension along many different pathways, they can fold the right way even if many of the cells in the network are damaged.

“If you and I are holding a single rope, and then we cut it in the middle, it would come apart. But if you have a net, and cut it in some places, it still stays globally connected and can transmit forces, as long as you don’t cut all of it,” Dunkel says.

Folding framework

The researchers also found that the connections between cells preferentially organize themselves to run in the same direction as the furrow that forms in the early stages of folding.

“We think this is setting up a frame around which the tissue will adopt its shape,” Martin says. “If you prevent the directionality of the connections, then what happens is you can still get folding but it will fold along the wrong axis.”

Although this study was done in fruit flies, similar folding occurs in vertebrates (including humans) during the formation of the neural tube, which is the precursor to the brain and spinal cord. Martin now plans to apply the techniques he used in fruit flies to see if the actomyosin network is organized the same way in the neural tube of mice. Defects in the closure of the neural tube can lead to birth defects such as spina bifida.

“We would like to understand how it goes wrong,” Martin says. “It’s still not clear whether it’s the sealing up of the tube that’s problematic or whether there are defects in the folding process.”

The research was funded by the National Institute of General Medical Sciences and the James S. McDonnell Foundation.

Pulin Li

Education

  • PhD, 2012, Chemical Biology, Harvard University
  • BS, 2006, Life Sciences, Peking University

Research Summary

We are curious about how circuits of interacting genes in individual cells enable multicellular functions, such as self-organizing into structured tissues. To address this question, we analyze genetic circuits in natural systems, combining quantitative measurements and mathematical modeling. In parallel, we test the sufficiency of the circuits and understand their design principles by multi-scale reconstitution, from genes to circuits to multicellular behavior, using synthetic biology and bioengineering tools. Together, we aim to provide both a quantitative understanding of embryonic development and new ways to engineer tissues.

Awards

  • New Innovator Award, National Institutes of Health Common Fund’s High-Risk, High-Reward Research Program, 2021
  • R.R. Bensley Award in Cell Biology, American Association for Anatomy, 2021
  • Santa Cruz Developmental Biology Young Investigator Award, 2016
  • NIH Pathway to Independence Award K99/R00 (NICHD), 2016
  • American Cancer Society Postdoctoral Fellowship, 2015
A new approach to targeting tumors and tracking their spread

Researchers develop nanosized antibodies that home in on the meshwork of proteins surrounding cancer cells.

Helen Knight | MIT News correspondent
May 6, 2019

The spread of malignant cells from an original tumor to other parts of the body, known as metastasis, is the main cause of cancer deaths worldwide.

Early detection of tumors and metastases could significantly improve cancer survival rates. However, predicting exactly when cancer cells will break away from the original tumor, and where in the body they will form new lesions, is extremely challenging.

There is therefore an urgent need to develop new methods to image, diagnose, and treat tumors, particularly early lesions and metastases.

In a paper published today in the Proceedings of the National Academy of Sciences, researchers at the Koch Institute for Integrative Cancer Research at MIT describe a new approach to targeting tumors and metastases.

Previous attempts to focus on the tumor cells themselves have typically proven unsuccessful, as the tendency of cancerous cells to mutate makes them unreliable targets.

Instead, the researchers decided to target structures surrounding the cells known as the extracellular matrix (ECM), according to Richard Hynes, the Daniel K. Ludwig Professor for Cancer Research at MIT. The research team also included lead author Noor Jailkhani, a postdoc in the Hynes Lab at the Koch Institute for Integrative Cancer Research.

The extracellular matrix, a meshwork of proteins surrounding both normal and cancer cells, is an important part of the microenvironment of tumor cells. By providing signals for their growth and survival, the matrix plays a significant role in tumor growth and progression.

When the researchers studied this microenvironment, they found certain proteins that are abundant in regions surrounding tumors and other disease sites, but absent from healthy tissues.

What’s more, unlike the tumor cells themselves, these ECM proteins do not mutate as the cancer progresses, Hynes says. “Targeting the ECM offers a better way to attack metastases than trying to prevent the tumor cells themselves from spreading in the first place, because they have usually already done that by the time the patient comes into the clinic,” Hynes says.

The researchers began developing a library of immune reagents designed to specifically target these ECM proteins, based on relatively tiny antibodies, or “nanobodies,” derived from alpacas. The idea was that if these nanobodies could be deployed in a cancer patient, they could potentially be imaged to reveal tumor cells’ locations, or even deliver payloads of drugs.

The researchers used nanobodies from alpacas because they are smaller than conventional antibodies. Specifically, unlike the antibodies produced by the immune systems of humans and other animals, which consist of two “heavy protein chains” and two “light chains,” antibodies from camelids such as alpacas contain just two copies of a single heavy chain.

Nanobodies derived from these heavy-chain-only antibodies comprise a single binding domain much smaller than conventional antibodies, Hynes says.

In this way nanobodies are able to penetrate more deeply into human tissue than conventional antibodies, and can be much more quickly cleared from the circulation following treatment.

To develop the nanobodies, the team first immunized alpacas with either a cocktail of ECM proteins, or ECM-enriched preparations from human patient samples of colorectal or breast cancer metastases.

They then extracted RNA from the alpacas’ blood cells, amplified the coding sequences of the nanobodies, and generated libraries from which they isolated specific anti-ECM nanobodies.

They demonstrated the effectiveness of the technique using a nanobody that targets a protein fragment called EIIIB, which is prevalent in many tumor ECMs.

When they injected nanobodies attached to radioisotopes into mice with cancer, and scanned the mice using noninvasive PET/CT imaging, a standard technique used clinically, they found that the tumors and metastases were clearly visible. In this way the nanobodies could be used to help image both tumors and metastases.

But the same technique could also be used to deliver therapeutic treatments to the tumor or metastasis, Hynes says. “We can couple almost anything we want to the nanobodies, including drugs, toxins or higher energy isotopes,” he says. “So, imaging is a proof of concept, and it is very useful, but more important is what it leads to, which is the ability to target tumors with therapeutics.”

The ECM also undergoes similar protein changes as a result of other diseases, including cardiovascular, inflammatory, and fibrotic disorders. As a result, the same technique could also be used to treat people with these diseases.

In a recent collaborative paper, also published in Proceedings of the National Academy of Sciences, the researchers demonstrated the effectiveness of the technique by using it to develop nanobody-based chimeric antigen receptor (CAR) T cells, designed to target solid tumors.

CAR T cell therapy has already proven successful in treating cancers of the blood, but it has been less effective in treating solid tumors.

By targeting the ECM of tumor cells, nanobody-based CAR T cells became concentrated in the microenvironment of tumors and successfully reduced their growth.

The ECM has been recognized to play crucial roles in cancer progression, but few diagnostic or therapeutic methods have been developed based on the special characteristics of cancer ECM, says Yibin Kang, a professor of molecular biology at Princeton University, who was not involved in the research.

“The work by Hynes and colleagues has broken new ground in this area and elegantly demonstrates the high sensitivity and specificity of a nanobody targeting a particular isoform of an ECM protein in cancer,” Kang says. “This discovery opens up the possibility for early detection of cancer and metastasis, sensitive monitoring of therapeutic response, and specific delivery of anticancer drugs to tumors.”

This work was supported by a Mazumdar-Shaw International Oncology Fellowship, fellowships for the Ludwig Center for Molecular Oncology Research at MIT, the Howard Hughes Medical Institute and a grant from the Department of Defence Breast Cancer Research Program, and imaged on instrumentation purchased with a gift from John S. ’61 and Cindy Reed.

The researchers are now planning to carry out further work to develop the nanobody technique for treating tumors and metastases.

A supportive role for planarians’ multifaceted muscle
Greta Friar | Whitehead Institute
April 5, 2019

CAMBRIDGE, MA  — Planarians are flatworms best known for their incredible ability to regenerate all their body parts: chop a planarian in two and soon you will have two perfectly formed planarians. As Whitehead Institute Member Peter Reddien, also a professor of biology at Massachusetts Institute of Technology and an investigator with the Howard Hughes Medical Institute, has investigated planarians over the years, he has become increasingly fascinated with the functions of their muscle. Not only do planarians use muscle to move, but Reddien’s research group previously discovered they rely on muscle tissue to provide a full body map with instructions that helps guide stem cells to the right locations during both regeneration and normal turnover of cells. Muscle tissue does this by secreting positional signals that help cells identify where they are — and where they should be.

New research from Reddien and graduate student Lauren Cote shows that muscle serves yet another crucial function in planarians. In a paper published in Nature Communications on April 8, they show that muscle operates as the planarian’s connective tissue, providing basic architectural support for the body. Connective tissue functions in large part by secreting molecules that make up the extracellular matrix (ECM), a network of molecules outside of the body’s cells that provides tissues with, among other things, scaffolding, protection, separation of tissues, and a means of inter-tissue connection and communication. In vertebrates, including humans, connective tissue is a distinct tissue type containing dedicated cells such as fibroblasts that secrete most of the animal’s ECM proteins. Reddien and Cote found no such fibroblast-like cell type in planarians; instead, multipurpose muscle does it all.

The researchers began to suspect that planarian muscle might function as connective tissue when they discovered that the gene encoding a major type of ECM molecule, fibrous protein collagen, was expressed only in muscle. The researchers then catalogued the total collection of proteins found in the planarian’s ECM, called the matrisome, and tracked where the genes that code for those proteins were expressed. They identified nineteen collagen genes, and all nineteen were highly specific to muscle. The vast majority of other ECM genes followed suit.

To further test muscle’s role as connective tissue, the researchers silenced the gene hemicentin-1, which produces another ECM molecule expressed specifically in muscle. They found that when the gene was not expressed, the planarian’s inner tissues did not remain properly separated from its outer skin. In other words, a muscle-specific gene is necessary in the planarians they studied for the core connective tissue task of keeping tissues discrete.

Although it might seem unusual that planarians would use muscle tissue for both ECM secretion and body pattern maintenance, Reddien and Cote say the combination makes a certain sense.

“To establish a map of the body, muscle secretes positional signals, and in its role as connective tissue it is simultaneously creating the extracellular environment the signals travel through,” Reddien says.

Cote agrees: “Producing the body’s physical architectural support and its biochemical architectural blueprint seem to go hand in hand.”

One possibility raised by this synchronicity is that a link between connective tissue and harboring positional information exists broadly across animal species. Studies elsewhere have found some positional role or positional memory in connective tissues in several species, including axolotls, vertebrates capable of limb regeneration. Based on these observations, Reddien says, it would be interesting to consider the positional role that connective tissue cells, like fibroblasts, might play in humans and might have in instructing regeneration broadly.

 

Written by Greta Friar

 

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Peter Reddien’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. The authors also acknowledge the Eleanor Schwartz Charitable Foundation for support.

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Full citation:

“Muscle functions as a connective tissue and source of extracellular matrix in planarians”

Nature Communications, online April 8, 2019. DOI: 10.1038/s41467-019-09539-6

Lauren E. Cote, Eric Simental, and Peter W. Reddien.