Research Area: Human Disease

Reading and writing DNA

Department of Biology kicks off IAP seminar series with a lecture by synthetic-biology visionary George Church.

Raleigh McElvery | Department of Biology
January 31, 2018

Thanks to the invention of genome sequencing technology more than three decades ago, we can now read the genetic blueprint of virtually any organism. After the ability to read came the ability to edit — adding, subtracting, and eventually altering DNA wherever we saw fit. And yet, for George Church, a professor at Harvard Medical School, associate member of the Broad Institute, and founding core faculty and lead for synthetic biology at the Wyss Institute — who co-pioneered direct genome sequencing in 1984 — the ultimate goal is not just to read and edit, but also to write.

What if you could engineer a cell resistant to all viruses, even the ones it hadn’t yet encountered? What if you could grow your own liver in a pig to replace the faulty one you were born with? What if you could grow an entire brain in a dish? In his lecture on Jan. 24 — which opened the Department of Biology’s Independent Activities Period (IAP) seminar series, Biology at Transformative Frontiers — Church promised all this and more.

“We began by dividing the Biology IAP events into two tracks: one related to careers in academia and another equivalent track for industry,” says Jing-Ke Weng, assistant professor and IAP faculty coordinator for the department. “But then it became clear that George Church, Patrick Brown, and other speakers we hoped to invite blurred the boundaries between those two tracks. The Biology at Transformative Frontiers seminar series became about the interface of these trajectories, and how transferring technologies from lab bench to market is altering society as we know it.”

The seminar series is a staple in the Department of Biology’s IAP program, but during the past several years it has been oriented more toward quantitative biology. Weng recalls these talks as being relegated to the academic sphere, and wanted to show students that the lines between academia, industry, and scientific communication are actually quite porous.

“We chose George Church to kick off the series because he’s been in synthetic biology for a long time, and continues to have a successful academic career even while starting so many companies,” says Weng.

Church’s genomic sequencing methods inspired the Human Genome Project in 1984 and resulted in the first commercial genome sequence (the bacterium Helicobacter pylori) 10 years later. He also serves as the director of the Personal Genome Project, the “Wikipedia” of open-access human genomic data. Beyond these ventures, he’s known for his work on barcoding, DNA assembly from chips, genome editing, and stem cell engineering.

He’s also the same George Church who converted the book he co-authored with Ed Regis, “Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves,” into a four-letter code based on the four DNA nucleotides (A, T, C, and G), subsisted on nutrient broth from a lab vendor for an entire year, and dreams of eventually resurrecting woolly mammoths. He’s being featured in an upcoming Netflix Original documentary, so when he arrived at the Stata Center to give his lecture last week he was trailed by a camera crew.

According to Church, the transformative technologies that initially allowed us to read and edit DNA have grown exponentially in recent years with the invention of molecular multiplexing and CRISPR-Cas9 (think Moore’s Law but even more exaggerated). But there’s always room for improvement.

“There’s been a little obsession with CRISPR-Cas9s and other CRISPRs,” said Church. “Everybody is saying how great it is, but it’s important to say what’s wrong with it as well, because that tells us where we’re going next and how to improve on it.”

He outlined several of his own collaborations, including those aimed at devising more precise methods of genome editing, one resulting in 321 changes to the Escherichia coli genome — the largest change in any genome yet — rendering the bacterium resistant to all viruses, even those it had not yet come into contact with. The next step? Making similarly widespread changes in plants, animals, and eventually perhaps even human tissue. In fact, Church and his team have set their sights on combatting the global transplantation crisis with humanlike organs grown in animals.

“Since the dawn of transplantation as a medical practice, we’ve had to use either identical twins or rare matches that are very compatible immunologically, because we couldn’t engineer the donor or the recipient,” said Church.

Since it’s clearly unethical to engineer human donors, Church reasoned, why not engineer animals with compatible organs instead? Pigs, to be exact, since most of their organs are comparable in size and function to our own.

“This is an old dream; I didn’t originate it,” said Church. “It started about 20 years ago, and the pioneers of this field worked on it for a while, but dropped it largely because the number of changes to the genome were daunting, and there was a concern that the viruses all pigs make — retroviruses — would be released and infect the immunocompromised organ recipient.”

Church and his team successfully disrupted 62 of these retroviruses in pig cells back in 2015, and in 2017 they used these cells to generate living, healthy pigs. Today, the pigs are thriving and rearing piglets of their own. Church is also considering the prospect of growing augmented organs in pigs for human transplantation, perhaps designing pathogen-, cancer-, and age-resistant organs suitable for cryopreservation.

“Hopefully we’ll be doing nonhuman primate trials within a couple of years, and then almost immediately after that human trials,” he said.

Another possibility, rather than cultivating organs in animals for transplant, is to generate them in a dish. A subset of Church’s team is working on growing from scratch what is arguably the most complicated organ of all, the brain.

This requires differentiating multiple types of cells in the same dish so they can interact with each other to form the complex systems of communication characteristic of the human brain.

Early attempts at fashioning brain organoids often lacked capillaries to distribute oxygen and nutrients (roughly one capillary for each of the 86 billion neurons in the human brain). However, thanks to their new human transcription factor library, Church and colleagues have begun to generate the cell types necessary to create such capillaries, plus the scaffolding needed to promote the three-dimensional organization of these and additional brain structures. Church and his team have not only successfully integrated the structures with one another, but have also created an algorithm that spits out the list of molecular ingredients required to generate each cell type.

Church noted these de novo organoids are extremely useful in determining which genetic variants are responsible for certain diseases. For instance, you could sequence a patient’s genome and then create an entire organoid with the mutation in question to test whether it was the root cause of the condition.

“I’m still stunned by the breadth of projects and approaches that he’s running simultaneously,” says Emma Kowal, a second-year graduate student, member of Weng’s planning committee, and a former researcher in Church’s lab. “The seminar series is called Biology at Transformative Frontiers, and George is very much a visionary, so we thought it would be a great way to start things off.”

The four-part series also features Melissa Moore, chief scientific officer of the Moderna Therapeutics mRNA Research Platform, Jay Bradner, president of the Novartis Institutes for BioMedical Research, and Patrick Brown, CEO and founder of Impossible Foods.

How some facial malformations arise

Study explains why mutations that would seemingly affect all cells lead to face-specific birth defects.

Anne Trafton | MIT News Office
January 24, 2018

About 1 in 750 babies born in the United States has some kind of craniofacial malformation, accounting for about one-third of all birth defects.

Many of these craniofacial disorders arise from mutations of “housekeeping” genes, so called because they are required for basic functions such as building proteins or copying DNA. All cells in the body require these housekeeping genes, so scientists have long wondered why these mutations would produce defects specifically in facial tissues.

Researchers at MIT and Stanford University have now discovered how one such mutation leads to the facial malformations seen in Treacher-Collins Syndrome, a disorder that affects between 1 in 25,000 and 1 in 50,000 babies and produces underdeveloped facial bones, especially in the jaw and cheek.

The team found that embryonic cells that form the face are more sensitive to the mutation because they more readily activate a pathway that induces cell death in response to stress. This pathway is mediated by a protein called p53. The new findings mark the first time that scientists have determined how mutations in housekeeping genes can have tissue-specific effects during embryonic development.

“We were able to narrow down, at the molecular level, how issues with general regulators that are used to make ribosomes in all cells lead to defects in specific cell types,” says Eliezer Calo, an MIT assistant professor of biology and the lead author of the study.

Joanna Wysocka, a professor of chemical and systems biology at Stanford University, is the senior author of the study, which appears in the Jan. 24 online edition of Nature.

From mutation to disease

Treacher-Collins Syndrome is caused by mutations in genes that code for proteins required for the assembly and function of polymerases. These proteins, known as TCOF1, POLR1C, and POLR1D, are responsible for transcribing genes that make up cell organelles called ribosomes. Ribosomes are critical to all cells.

“The question we were trying to understand is, how is it that when all cells in the body need ribosomes to function, mutations in components that are required for making the ribosomes lead to craniofacial disorders? In these conditions, you would expect that all the cell types of the body would be equally affected, but that’s not the case,” Calo says.

During embryonic development, these mutations specifically affect a type of embryonic cells known as cranial neural crest cells, which form the face. The researchers already knew that the mutations disrupt the formation of ribosomes, but they didn’t know exactly how this happens. To investigate that process, the researchers engineered larvae of zebrafish and of an aquatic frog known as Xenopus to express proteins harboring those mutations.

Their experiments revealed that the mutations lead to impairment in the function of an enzyme called DDX21. When DDX21 dissociates from DNA, the genes that encode ribosomal proteins do not get transcribed, so ribosomes are missing key components and can’t function normally. However, this DDX21 loss only appears to happen in cells that are highly sensitive to p53 activation, including cranial neural crest cells. These cells then undergo programmed cell death, which leads to the facial malformations seen in Treacher-Collins Syndrome, Calo says.

Other embryonic cells, including other types of neural crest cells, which form nerves and other parts of the body such as connective tissue, are not affected by the loss of DDX21.

Role of DNA damage

The researchers also found that mutations of POLR1C and POLR1D also cause damage to stretches of DNA that encode some of the RNA molecules that make up ribosomes. The amount of DNA damage correlated closely with the severity of malformations seen in individual larvae, and mutations in POLR1C led to far more DNA damage than mutations in POLR1D. The researchers believe these differences in DNA damage may explain why the severity of Treacher-Collins Syndrome can vary widely among individuals.

Calo’s lab is now studying why affected cells experience greater levels of DNA damage in those particular sequences. The researchers are also looking for compounds that could potentially prevent craniofacial defects by making the cranial neural crest cells more resistant to p53-induced cell death. Such interventions could have a big impact but would have to be targeted very early in embryonic development, as the cranial neural crest cells begin forming the tissue layers that will become the face at about three weeks of development in human embryos.

The research was funded by the National Institutes of Health, Howard Hughes Medical Institute, and March of Dimes Foundation.

Biology by Numbers

Undergraduate Camilo Espinosa grew up with a love for math, before developing a second passion for immunology at MIT

Raleigh McElvery
November 10, 2017

Biology by Numbers

Person with short brown hair and green jacket stands in front of MIT pillars.

Undergraduate Camilo Espinosa grew up with a love for math, before developing a second passion for immunology at MIT

Raleigh McElvery

 

Undergraduate Camilo Espinosa, now in his senior year, tackles biological problems with the mindset of a mathematician. That’s because he initially approached the STEM fields (science, technology, engineering and mathematics) starting with the “M” and ending with the “S” — developing an appetite for math before realizing a second love for biology.

Every six months, beginning his first year of middle school, Espinosa would venture from his home on the north coast of Colombia to the nation’s capital. There, for several weeks, he would do nothing but math.

“These were math olympiads — basically a combination of math camp and competitions,” he explains. “That was the first real community I had outside my school.”

But he didn’t just glean formulas and analytical strategies from those competitions; it was his olympiad team that first introduced him to MIT. In Colombia, he explains, students must select a major almost immediately upon entering university, and are offered limited electives. MIT came to represent “academic freedom” for Espinosa, who, despite his avid and early love of math, intended to explore multiple academic avenues before limiting himself to just one.

Now, as a math and chemistry-biology double major with a concentration in philosophy, he says MIT has enabled him to pursue his many academic interests, as well as his non-academic ones. He has served as an active member of not one but four dance teams, as well as president of his fraternity. He also helped establish a channel of communication between the International Students Office and the Department of Biology, to streamline the work authorization process for international students.

He was drawn to biology, he explains, because he prefers learning processes over basic facts. “I don’t care much for memorization, but I do care about the underlying reasons for why and how things function,” he says. “I think that mindset stems from my dad.”

Espinosa’s father is an OB/GYN specializing in female oncology, who initially helped to popularize laparoscopic surgery techniques in Colombia. Often, he sees patients at a discounted price or for free if they could not afford his services.

“At the end of the day, he is just trying to help people,” Espinosa explains. “He taught me the way I think about the world. He’s the reason I do what I do, and why I’m so oriented towards the life sciences.”  

Espinosa’s siblings are studying to become doctors and veterinarians, and he himself is intrigued by the possibilities of using our body’s innate defense mechanisms to treat diseases like cancer.

His foray into the field of immunology began with antibodies — special ones taken from furry, gawky alpacas — so tiny and versatile that they can be employed for all manner of imaging, therapeutic, and diagnostic techniques. These “single domain” antibodies were a popular area of interest in Hidde Ploegh’s lab (formerly a Professor of Biology at the Whitehead Institute for Biomedical Research), where Espinosa began mid-way through October of his freshman year. Using these single-domain antibodies, the Ploegh lab had developed a treatment for melanoma in mice, and Espinosa worked to pinpoint antibodies directed against melanoma in humans.

The summer between his sophomore and junior years, Espinosa began a separate project that eventually evolved into his thesis. He honed in on one tiny antibody, known as A4, which binds to a particular protein expressed on the surface of red blood cells, and has the potential to thwart the immune response by activating a process known as “tolerance.”

Our body’s immune system is programmed to discern self from non-self, targeting foreign entities for destruction. It does so in two distinct steps. First, it creates an army of cells, that together express antibodies tailored to combat virtually every possible substance, both self and non-self. The immune system is then primed to spring into action whenever it senses something foreign, amplifying those cells that express antibodies against it. However, the body would also attack itself if not for the second step in this process: tolerance. The immune system essentially deletes the cells expressing antibodies against itself, and in doing so learns to “tolerate” its own proteins.

For example, when red blood cells die of old age (and many do every day), this triggers tolerance to the various protein components that constitute those cells — preventing related antibodies from being created.

Previous work has shown that binding a foreign protein to red blood cells triggers tolerance for that specific protein, despite being “non-self.” This could have implications for therapies to treat conditions like hemophilia, Espinosa explains, which require injections of proteins to reinstate the body’s blood-clotting abilities.

In a large proportion of patients, the immune system responds and attacks these proteins as foreign, rendering the treatment useless and barring the patients from receiving it again in the future. However, Espinosa proposes, if he could couple A4 to the treatment protein, then A4 would link the protein to the red blood cells and initiate tolerance to it. Since the body can no longer create antibodies against the treatment proteins, the therapy can run its course. In other words, the body would now see the injected proteins as self.

After months of methodical experiments, A4 didn’t appear to disguise proteins as self in the way Espinosa had initially hoped, although it did reduce the immune response triggered by the protein injection, if he staggered the protein and antibody infusions in the proper manner.

“So maybe A4 doesn’t work as a camouflage per se, but rather as a suppressor of certain immune responses,” he says. “So the results didn’t turn out exactly as we expected, but it is still a step in the right direction.”

He ultimately submitted his thesis to MIT’s Ilona Karmel Writing Prizes, earning second place in the technical writing category.  

Last summer, Espinosa explored a different side of basic research — the corporate side — during an internship at the biotechnology company Genentech. There, he investigated the pathways by which uncontrolled cell death leads to sepsis in patients.

As he wraps up his senior year and begins applying to graduate programs, Espinosa reflects on his transition from student to instructor, having served as a teaching assistant in a number of biology courses during the past three years. “As someone who arrived at MIT with a weak foundation in biology, almost everything I’ve learned since was because someone taught it to me, and taught it to me well,” he says. “I feel honored to be able to pass it on.”

Photo credit: Raleigh McElvery
Posted: 1.18.18
Combatting chemotherapy resistance

Graduate student Faye-Marie Vassel investigates a protein that helps cells tolerate DNA damage, sharing her expertise with budding scientists to further STEM education

Raleigh McElvery
December 8, 2017

Combatting chemotherapy resistance

Person with long, dark hair and lab coat stares into microscope.

Graduate student Faye-Marie Vassel investigates a protein that helps cells tolerate DNA damage, sharing her expertise with budding scientists to further STEM education

Raleigh McElvery

 

Faye-Marie Vassel has a protein. Well, as a living entity, technically she has many, but just one she affectionately refers to as her own. “My protein, REV7.” And it makes sense — if you were hard at work characterizing a single protein for all six years of your graduate career, you’d be pretty attached, too. Plus, the stakes are high. REV7, which aids in DNA damage repair, could ultimately provide insight into ways to combat chemotherapy resistance.

Although Vassel’s mother trained as an OB/GYN in Russia before moving to the U.S., serving as what Vassel describes as a “quiet” scientific role model, Vassel spent her early childhood emulating her father, a social worker, and engrossed in the social sciences. She intended to one day work in science policy — until high school when she joined an after-school program at the American Museum of Natural History in New York City, and discovered an additional interest.

Here, Vassel took a series of molecular biology classes and met her first female research mentor, a postdoctoral fellow at Rockefeller University, who encouraged her to participate in another, more advanced science program funded by the National Science Foundation.

“I initially had my doubts, but just having that support changed everything,” Vassel says. “That was my first time doing research of any kind, and I got a sense of the sheer diversity of potential research projects. That’s also when I heard there was something called biophysics.”

From that point on, Vassel was hooked. As an undergraduate at Stony Brook University, she initially declared a major in physics before switching to biochemistry. Later, when it came time to select a graduate school, she was split between MIT and the University of California, Berkeley. As she recalls, MIT’s graduate preview weekend made all the difference.

“I had the chance to stay with biology students and speak with professors,” she says. “The whole experience made the department seem personal, and demystified the graduate school process by making it more tangible.”

She proposed a joint position between two labs: Graham Walker’s lab, based in Building 68, and Michael Hemann’s lab situated in the Koch Institute for Integrative Cancer Research. Walker’s lab focuses on microbiology, DNA repair, and antibiotic resistance, while Hemann’s lab investigates chemotherapy resistance in hopes of improving cancer therapies. After stumbling upon one of their joint papers, Vassel decided she’d like to combine the two.

“It’s invaluable to have both perspectives,” she says. “Mike’s lab just celebrated its 10th anniversary, while Graham‘s just had its 35th. It’s been interesting seeing the different ways they approach their respective research questions, because they were trained in such different scientific eras.”

Although Vassel is currently the only student formally working in both labs, the collaboration between Walker and Hemann, aimed at combatting chemotherapy resistance, has been ongoing.

Frontline chemotherapies, including one anticancer agent called cisplatin, kill cancer cells by damaging their DNA and preventing them from synthesizing new genetic material. Just how sensitive cancer cells are to cisplatin — and therefore how effective the treatment is — depends on whether the cell can repair the damage and bypass DNA-damage induced cell death. In some cases, cells increase production of “translesion polymerases,” which are specialized DNA polymerases that can help cells tolerate certain kinds of DNA damage by synthesizing across from damaged DNA or DNA bound to a carcinogen.

Vassel’s protein, REV7, is a structural subunit of one key translesion polymerase, and its expression is deregulated in many different cancer cells. As Vassel suggests, if one aspect of these translesion polymerases — say, the REV7 subunit — could be altered to hinder repair, then perhaps cancer-ridden cells could regain drug sensitivity.

Thanks to recently-developed CRISPR-Cas9 gene editing techniques, Vassel has removed REV7 entirely from drug resistant lung cancer cells, and watched as cisplatin sensitivity was restored. She also conducted rescue experiments, adding REV7 back into cell lines lacking the protein to see whether those cells become resistant to the drug once again. Most recently, she has been working in murine models to see whether REV7 has similar effects in a living system.

If her hypothesis is correct, REV7 would be a powerful target for drug development. Treatments that inhibit REV7, she explains, could be used in tandem with frontline chemotherapies like cisplatin to prevent resistance.

Since her foray into biology at the American Museum of Natural History almost a decade ago, Vassel has maintained her passion for science outreach. During her time at MIT, she has served as a math tutor for middle schoolers in the Cambridge public school system. She also volunteered as a science and math mentor for high school students, as part of a dual athletic and academic program founded by MIT.

As Vassel wraps up her final year of graduate studies, she is torn between completing an academic postdoc and indulging her early interest in science education policy.

“Growing up in New York City, it was not lost on me that — despite the city’s wonderful diversity — people from historically underserved groups were still missing from many science-related positions,” Vassel says. “It got me thinking about the dire need for policymakers to improve curricula to make science more inclusive of all life experiences. There’s this idea that science is apolitical when it’s really not, and that mindset can have detrimental effects on equity and diversity in science.”

Photo credit: Raleigh McElvery
Biologists’ new peptide could fight many cancers

Drug that targets a key cancer protein could combat leukemia and other types of cancer.

Anne Trafton | MIT News Office
January 15, 2018

MIT biologists have designed a new peptide that can disrupt a key protein that many types of cancers, including some forms of lymphoma, leukemia, and breast cancer, need to survive.

The new peptide targets a protein called Mcl-1, which helps cancer cells avoid the cellular suicide that is usually induced by DNA damage. By blocking Mcl-1, the peptide can force cancer cells to undergo programmed cell death.

“Some cancer cells are very dependent on Mcl-1, which is the last line of defense keeping the cell from dying. It’s a very attractive target,” says Amy Keating, an MIT professor of biology and one of the senior authors of the study.

Peptides, or small protein fragments, are often too unstable to use as drugs, but in this study, the researchers also developed a way to stabilize the molecules and help them get into target cells.

Loren Walensky, a professor of pediatrics at Harvard Medical School and a physician at Dana-Farber Cancer Institute, is also a senior author of the study, which appears in the Proceedings of the National Academy of Sciences the week of Jan. 15. Researchers in the lab of Anthony Letai, an associate professor of medicine at Harvard Medical School and Dana-Farber, were also involved in the study, and the paper’s lead author is MIT postdoc Raheleh Rezaei Araghi.

A promising target

Mcl-1 belongs to a family of five proteins that play roles in controlling programmed cell death, or apoptosis. Each of these proteins has been found to be overactive in different types of cancer. These proteins form what is called an “apoptotic blockade,” meaning that cells cannot undergo apoptosis, even when they experience DNA damage that would normally trigger cell death. This allows cancer cells to survive and proliferate unchecked, and appears to be an important way that cells become resistant to chemotherapy drugs that damage DNA.

“Cancer cells have many strategies to stay alive, and Mcl-1 is an important factor for a lot of acute myeloid leukemias and lymphomas and some solid tissue cancers like breast cancers. Expression of Mcl-1 is upregulated in many cancers, and it was seen to be upregulated as a resistance factor to chemotherapies,” Keating says.

Many pharmaceutical companies have tried to develop drugs that target Mcl-1, but this has been difficult because the interaction between Mcl-1 and its target protein occurs in a long stretch of 20 to 25 amino acids, which is difficult to block with the small molecules typically used as drugs.

Peptide drugs, on the other hand, can be designed to bind tightly with Mcl-1, preventing it from interacting with its natural binding partner in the cell. Keating’s lab spent many years designing peptides that would bind to the section of Mcl-1 involved in this interaction — but not to other members of the protein family.

Once they came up with some promising candidates, they encountered another obstacle, which is the difficulty of getting peptides to enter cells.

“We were exploring ways of developing peptides that bind selectively, and we were very successful at that, but then we confronted the problem that our short, 23-residue peptides are not promising therapeutic candidates primarily because they cannot get into cells,” Keating says.

To try to overcome this, she teamed up with Walensky’s lab, which had previously shown that “stapling” these small peptides can make them more stable and help them get into cells. These staples, which consist of hydrocarbons that form crosslinks within the peptides, can induce normally floppy proteins to assume a more stable helical structure.

Keating and colleagues created about 40 variants of their Mcl-1-blocking peptides, with staples in different positions. By testing all of these, they identified one location in the peptide where putting a staple not only improves the molecule’s stability and helps it get into cells, but also makes it bind even more tightly to Mcl-1.

“The original goal of the staple was to get the peptide into the cell, but it turns out the staple can also enhance the binding and enhance the specificity,” Keating says. “We weren’t expecting that.”

Killing cancer cells

The researchers tested their top two Mcl-1 inhibitors in cancer cells that are dependent on Mcl-1 for survival. They found that the inhibitors were able to kill these cancer cells on their own, without any additional drugs. They also found that the Mcl-1 inhibitors were very selective and did not kill cells that rely on other members of the protein family.

Keating says that more testing is needed to determine how effective the drugs might be in combating specific cancers, whether the drugs would be most effective in combination with others or on their own, and whether they should be used as first-line drugs or when cancers become resistant to other drugs.

“Our goal has been to do enough proof-of-principle that people will accept that stapled peptides can get into cells and act on important targets. The question now is whether there might be any animal studies done with our peptide that would provide further validation,” she says.

Joshua Kritzer, an associate professor of chemistry at Tufts University, says the study offers evidence that the stapled peptide approach is worth pursuing and could lead to new drugs that interfere with specific protein interactions.

“There have been a lot of biologists and biochemists studying essential interactions of proteins, with the justification that with more understanding of them, we would be able to develop drugs that inhibit them. This work now shows a direct line from biochemical and biophysical understanding of protein interactions to an inhibitor,” says Kritzer, who was not involved in the research.

Keating’s lab is also designing peptides that could interfere with other relatives of Mcl-1, including one called Bfl-1, which has been less studied than the other members of the family but is also involved in blocking apoptosis.

The research was funded by the Koch Institute Dana-Farber Bridge Project and the National Institutes of Health.

Harnessing nature’s riches
December 19, 2017

Cambridge, MA – Researchers at Whitehead Institute have reconstructed the full suite of biochemical steps required to make salidroside, a plant-derived compound widely used in traditional medicine to combat depression and fatigue and boost immunity and memory. Their new study, which appears online this week in the journal Molecular Plant, resolves some long-standing questions about how this compound is manufactured by a type of high-altitude plant, known commonly as golden root. This work not only paves a path toward large-scale synthetic efforts—thereby protecting plants already in danger of extinction—but also provides a model for dissecting the biochemical synthesis of a host of natural products, which represent a treasure trove for modern medical discoveries.

“By cracking open the natural synthesis of this compound, known as salidroside, we have helped eliminate a major bottleneck in the broader development of plant-derived natural products into pharmaceuticals,” says Jing-Ke Weng, the senior author of the paper, a Member of Whitehead Institute, and an assistant professor of biology at Massachusetts Institute of Technology. “We simply can’t rely on the native plants as the sole sources of these biologically important molecules.”

Golden root, also called Tibetan ginseng, typically grows in high-altitude, arctic environments, such as Tibet. It is well known in Eastern cultures for its medicinal properties and produces a variety of chemical substances, particularly salidroside, which have garnered interest in the biomedical research community for their potential therapeutic effects.

“People have tried to farm golden root, but the medicinal value is much lower because the plants make much less salidroside when cultivated outside of their normal habitat,” says Weng.

That means collecting enough salidroside to fuel scientific studies is largely impossible, without risking the viability of these plants and their surroundings. So Weng and his team, including first author Michael Torrens-Spence, set out to find a better way. “If we can figure out how plants make these high-value natural products, then we can devise sustainable engineering approaches to recreate such molecules—we won’t have to destroy nature in order to harness its riches,” says Torrens-Spence, a postdoctoral researcher in Weng’s laboratory.

Torrens-Spence and his colleagues used a systematic multi-omics approach to characterize various tissues from a three-month-old, greenhouse-grown golden root plant. By correlating the active genes with the abundance of key metabolites between various tissue types, the researchers created a massive biochemical catalog of the plant’s tissues.

The researchers then mined these data and matched the likely biochemical precursors of salidroside with the candidate genes (and their corresponding enzymes) responsible for those compounds’ synthesis. This approach allowed Weng and his team to create a kind of draft blueprint of how salidroside is made in nature.

To test the validity of this draft blueprint—and the molecular players from the golden root plant that comprise it—the scientists turned to two well-studied laboratory organisms: the baker’s yeast Saccharomyces cerevisiae and the tobacco plant Nicotiana benthamiana. Normally, these organisms do not make salidroside. But if the researchers’ model was correct, by inserting the candidate genes involved in salidroside synthesis Weng and his colleagues should be able to bestow that special property upon them.

That is precisely what the researchers did. Using three key enzymes they identified through their “-omics” approach, including 4HPAAS (4-hydroxyphenylacetaldehyde synthase), 4HPAR (4-hydroxyphenylacetaldehyde reductase), and T8GT (tyrosol:UDP-glucose 8-O-glucosyltransferase), they engineered yeast and tobacco plants with the capacity to make salidroside. Notably, this biochemical pathway for synthesizing salidroside involves three enzymes, rather than four, as had previously been proposed.

“This is an exciting proof-of-principle for how we can systematically unlock the biochemistry behind a range of intriguing plant-derived natural products,” says Weng. “With this capability, we can accelerate biomedical studies of these unique compounds as well as their potential therapeutic development.”

Written by Nicole Davis
* * *
Jing-Ke Weng’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also an assistant professor of biology at Massachusetts Institute of Technology.
* * *
Full citation:
“Complete pathway elucidation and heterologous reconstitution of Rhodiola salidroside biosynthesis”
Molecular Plant, online December 19, 2017. DOI: 10.1016/j.molp.2017.12.007
Michael P. Torrens-Spence (1), Tomáš Pluskal (1), Fu-Shuang Li (1), Valentina Carballo (1) and Jing-Ke Weng (1,2).
1. Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
2. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
Jacqueline Lees

Education

  • PhD, 1990, University of London
  • BSc, 1986, Biochemistry, University of York

Research Summary

We identify the proteins and pathways involved in tumorigenicity — establishing their mechanism of action in both normal and tumor cells. To do so, we use a combination of molecular and cellular analyses, mutant mouse models and genetic screens in zebrafish.

Michael T. Hemann

Education

  • PhD, 2001, Johns Hopkins University
  • BS, 1993, Molecular Biology and Biochemistry, Wesleyan University

Research Summary

Many human cancers do not respond to chemotherapy, and often times those that initially respond eventually acquire drug resistance. Our lab uses high-throughput screening technology — combined with murine stem reconstitution and tumor transplantation systems — to investigate the genetic basis for this resistance. Our goal is to identify novel cancer drug targets, as well as strategies for tailoring existing cancer therapies to target the vulnerabilities associated with specific malignancies.

Rethinking transcription factors and gene expression

Study shows that, like proteins, genomes must fold appropriately to function properly and that some transcription factors provide the structural support.

Nicole Giese Rura | Whitehead Institute
December 7, 2017

Transcription — the reading of a segment of DNA into an RNA template for protein synthesis — is fundamental for nearly all cellular processes, including growth, responding to stimuli, and reproduction. Now, Whitehead Institute researchers have upended our understanding of how transcription is controlled and the role of transcription factors in the process.

The paradigm shift, described in an article online on Dec. 7 in the journal Cell, hinges on a small protein that plays a key role in genome structure and gives us new insights into how changes in the control of transcription and gene expression can lead to disease.

Transcription has several important players that must all be in the right place at the right time: the transcription machinery, transcription factors, promoters, and enhancers.  According to the existing model, transcription factors are proteins that bind to enhancer regions of the genome and recruit the transcription machinery to the promoter DNA regions, which then initiate the genes’ transcription.

“We’ve always assumed that the role of transcription factors was to recruit the transcription machinery to genes to turn them on or turn them off,” says Richard Young, a Whitehead Insistute member and professor of biology at MIT. “But we never imagined that the transcription factors we’ve studied for three decades actually contribute to the genome’s structure. And as a consequence, they regulate genes. So we now look at genomes like proteins: They have to fold up appropriately in order to control genes.”

Scientists have known that the genome’s structure — how it bends and folds — is essential for efficiently compressing two meters of DNA into each human cell, which is the equivalent of packing a strand ten football fields long into a space the size of a marble. Yet until recently, researchers have not had the tools necessary to appreciate this architecture’s importance in fine control of gene expression or study the genome’s structure at sites ready for transcription.

In 2014, Young and his lab determined that portions of the genome reside in loop-based structures, creating insulated neighborhoods that bring enhancers, promoters, and genes into close proximity. Each loop is tied at the top by a pair of molecules, called CTCF, that are bound together. This structure is essential for proper gene control: If the loop structure is broken, gene expression is altered, and cells can become diseased or die.

In the current research, Young along with co-first authors Abraham Weintraub and Charles Li took a closer look at a protein that is well known but not well understood: Yin Yang 1 (YY1). Hundreds of scientific papers have linked YY1 dysfunction to diseases such as viral infections, cancer, and arthritis, and yet the studies produced seemingly contradictory observations of YY1’s function.

According to Young and colleagues, YY1 is a unique transcription factor that occupies both enhancers and promoters, is essential for cell survival, and is found in almost every cell type in humans and mice. Like CTCF, YY1 can also pair with itself and bind to DNA to form loops that enhance DNA transcription.

“YY1 is expressed broadly, and it is necessary for establishing enhancer-promoter loops in multiple cell types,” says Weintraub. “That’s its job, not recruiting the transcription apparatus. When the structure created by YY1 is removed, the genome is no longer folded properly, gene control is lost and transcription of the affected genes is significantly diminished, which can cause dysfunction.”

This model of YY1’s function could account for its association with a number of disparate diseases. Earlier this year, scientists reported YY1 syndrome — a genetic syndrome causing cognitive disabilities in people with mutations in their YY1 gene.

According to Young, YY1 is probably not the only transcription factor with this loop-forming role, and his lab will be searching for additional factors with similar functions.

“YY1 is most likely just the first one, and there are probably a bunch of collaborators that have similar roles,” says Young. “Instead of the classic function that we thought these transcription factors had — interacting with the transcription apparatus and giving instructions on how much or how little of a gene’s transcript to produce — they are bringing together regulatory elements with the gene. The whole job of these transcription factors is just making structure. We are realizing that the things that form physical structures are much more important than we had appreciated.”

The researchers’ work was supported by the National Institutes of Health, the Ludwig Graduate Fellowship funds, the National Science Foundation, the American Cancer Society, a Margaret and Herman Sokol Postdoctoral Award, the Damon Runyon Cancer Research Foundation, and the Cancer Research Institute. The Whitehead Institute has filed a patent application based on this study.

Laurie A. Boyer

Education

  • PhD, 2001, University of Massachusetts Medical School
  • BS, 1990, Biomedical Science, Framingham State University

Research Summary

We investigate how complex circuits of genes are regulated to produce robust developmental outcomes particularly during heart development. A main focus is to determine how DNA is packaged into chromatin, and how ATP-dependent chromatin remodelers modify this packaging to control lineage commitment. We are now applying these principles to develop methods to stimulate repair of damaged cardiac tissue (e.g., regeneration). Our ability to combine genomic, genetic, biochemical, and cell biological approaches both in vitro and in vivo as well as ongoing efforts to use tissue engineering to model the 3D architecture of the heart will ultimately allow us to gain a systems level and quantitative understanding of the regulatory circuits that promote normal heart development and how faulty regulation can lead to disease.

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Awards

  • Medicine by Design Distinguished Lecture, 2017
  • Cardiovascular Rising Star Distinguished Lecture, 2017
  • American Heart Association Innovative Research Award, 2013
  • Irvin and Helen Sizer Career Development Award, 2012
  • Smith Family Award for Excellence in Biomedical Science, 2009
  • Massachusetts Life Sciences Center New Investigator Award, 2008
  • Pew Scholars Award in the Biomedical Sciences, 2008
  • Honorary Doctorate, Framingham State College, 2007
  • The Scientific American World’s 50 Top Leaders in Research, Business or Policy, 2006