Author: mantulin

New study reveals how cleft lip and cleft palate can arise

MIT biologists have found that defects in some transfer RNA molecules can lead to the formation of these common conditions.

Anne Trafton | MIT News
April 17, 2025

Cleft lip and cleft palate are among the most common birth defects, occurring in about one in 1,050 births in the United States. These defects, which appear when the tissues that form the lip or the roof of the mouth do not join completely, are believed to be caused by a mix of genetic and environmental factors.

In a new study, MIT biologists have discovered how a genetic variant often found in people with these facial malformations leads to the development of cleft lip and cleft palate.

Their findings suggest that the variant diminishes cells’ supply of transfer RNA, a molecule that is critical for assembling proteins. When this happens, embryonic face cells are unable to fuse to form the lip and roof of the mouth.

“Until now, no one had made the connection that we made. This particular gene was known to be part of the complex involved in the splicing of transfer RNA, but it wasn’t clear that it played such a crucial role for this process and for facial development. Without the gene, known as DDX1, certain transfer RNA can no longer bring amino acids to the ribosome to make new proteins. If the cells can’t process these tRNAs properly, then the ribosomes can’t make protein anymore,” says Michaela Bartusel, an MIT research scientist and the lead author of the study.

Eliezer Calo, an associate professor of biology at MIT, is the senior author of the paper, which appears today in the American Journal of Human Genetics.

Genetic variants

Cleft lip and cleft palate, also known as orofacial clefts, can be caused by genetic mutations, but in many cases, there is no known genetic cause.

“The mechanism for the development of these orofacial clefts is unclear, mostly because they are known to be impacted by both genetic and environmental factors,” Calo says. “Trying to pinpoint what might be affected has been very challenging in this context.”

To discover genetic factors that influence a particular disease, scientists often perform genome-wide association studies (GWAS), which can reveal variants that are found more often in people who have a particular disease than in people who don’t.

For orofacial clefts, some of the genetic variants that have regularly turned up in GWAS appeared to be in a region of DNA that doesn’t code for proteins. In this study, the MIT team set out to figure out how variants in this region might influence the development of facial malformations.

Their studies revealed that these variants are located in an enhancer region called e2p24.2. Enhancers are segments of DNA that interact with protein-coding genes, helping to activate them by binding to transcription factors that turn on gene expression.

The researchers found that this region is in close proximity to three genes, suggesting that it may control the expression of those genes. One of those genes had already been ruled out as contributing to facial malformations, and another had already been shown to have a connection. In this study, the researchers focused on the third gene, which is known as DDX1.

DDX1, it turned out, is necessary for splicing transfer RNA (tRNA) molecules, which play a critical role in protein synthesis. Each transfer RNA molecule transports a specific amino acid to the ribosome — a cell structure that strings amino acids together to form proteins, based on the instructions carried by messenger RNA.

While there are about 400 different tRNAs found in the human genome, only a fraction of those tRNAs require splicing, and those are the tRNAs most affected by the loss of DDX1. These tRNAs transport four different amino acids, and the researchers hypothesize that these four amino acids may be particularly abundant in proteins that embryonic cells that form the face need to develop properly.

When the ribosomes need one of those four amino acids, but none of them are available, the ribosome can stall, and the protein doesn’t get made.

The researchers are now exploring which proteins might be most affected by the loss of those amino acids. They also plan to investigate what happens inside cells when the ribosomes stall, in hopes of identifying a stress signal that could potentially be blocked and help cells survive.

Malfunctioning tRNA

While this is the first study to link tRNA to craniofacial malformations, previous studies have shown that mutations that impair ribosome formation can also lead to similar defects. Studies have also shown that disruptions of tRNA synthesis — caused by mutations in the enzymes that attach amino acids to tRNA, or in proteins involved in an earlier step in tRNA splicing — can lead to neurodevelopmental disorders.

“Defects in other components of the tRNA pathway have been shown to be associated with neurodevelopmental disease,” Calo says. “One interesting parallel between these two is that the cells that form the face are coming from the same place as the cells that form the neurons, so it seems that these particular cells are very susceptible to tRNA defects.”

The researchers now hope to explore whether environmental factors linked to orofacial birth defects also influence tRNA function. Some of their preliminary work has found that oxidative stress — a buildup of harmful free radicals — can lead to fragmentation of tRNA molecules. Oxidative stress can occur in embryonic cells upon exposure to ethanol, as in fetal alcohol syndrome, or if the mother develops gestational diabetes.

“I think it is worth looking for mutations that might be causing this on the genetic side of things, but then also in the future, we would expand this into which environmental factors have the same effects on tRNA function, and then see which precautions might be able to prevent any effects on tRNAs,” Bartusel says.

The research was funded by the National Science Foundation Graduate Research Program, the National Cancer Institute, the National Institute of General Medical Sciences, and the Pew Charitable Trusts.

Restoring healthy gene expression with programmable therapeutics

CAMP4 Therapeutics is targeting regulatory RNA, whose role in gene expression was first described by co-founder and MIT Professor Richard Young.

Zach Winn | MIT News
April 16, 2025

Many diseases are caused by dysfunctional gene expression that leads to too much or too little of a given protein. Efforts to cure those diseases include everything from editing genes to inserting new genetic snippets into cells to injecting the missing proteins directly into patients.

CAMP4 is taking a different approach. The company is targeting a lesser-known player in the regulation of gene expression known as regulatory RNA. CAMP4 co-founder and MIT Professor Richard Young has shown that by interacting with molecules called transcription factors, regulatory RNA plays an important role in controlling how genes are expressed. CAMP4’s therapeutics target regulatory RNA to increase the production of proteins and put patients’ levels back into healthy ranges.

The company’s approach holds promise for treating diseases caused by defects in gene expression, such as metabolic diseases, heart conditions, and neurological disorders. Targeting regulatory RNAs as opposed to genes could also offer more precise treatments than existing approaches.

“If I just want to fix a single gene’s defective protein output, I don’t want to introduce something that makes that protein at high, uncontrolled amounts,” says Young, who is also a core member of the Whitehead Institute. “That’s a huge advantage of our approach: It’s more like a correction than sledgehammer.”

CAMP4’s lead drug candidate targets urea cycle disorders (UCDs), a class of chronic conditions caused by a genetic defect that limits the body’s ability to metabolize and excrete ammonia. A phase 1 clinical trial has shown CAMP4’s treatment is safe and tolerable for humans, and in preclinical studies the company has shown its approach can be used to target specific regulatory RNA in the cells of humans with UCDs to restore gene expression to healthy levels.

“This has the potential to treat very severe symptoms associated with UCDs,” says Young, who co-founded CAMP4 with cancer genetics expert Leonard Zon, a professor at Harvard Medical School. “These diseases can be very damaging to tissues and causes a lot of pain and distress. Even a small effect in gene expression could have a huge benefit to patients, who are generally young.”

Mapping out new therapeutics

Young, who has been a professor at MIT since 1984, has spent decades studying how genes are regulated. It’s long been known that molecules called transcription factors, which orchestrate gene expression, bind to DNA and proteins. Research published in Young’s lab uncovered a previously unknown way in which transcription factors can also bind to RNA. The finding indicated RNA plays an underappreciated role in controlling gene expression.

CAMP4 was founded in 2016 with the initial idea of mapping out the signaling pathways that govern the expression of genes linked to various diseases. But as Young’s lab discovered and then began to characterize the role of regulatory RNA in gene expression around 2020, the company pivoted to focus on targeting regulatory RNA using therapeutic molecules known as antisense oligonucleotides (ASOs), which have been used for years to target specific messenger RNA sequences.

CAMP4 began mapping the active regulatory RNAs associated with the expression of every protein-coding gene and built a database, which it calls its RAP Platform, that helps it quickly identify regulatory RNAs to target  specific diseases and select ASOs that will most effectively bind to those RNAs.

Today, CAMP4 is using its platform to develop therapeutic candidates it believes can restore healthy protein levels to patients.

“The company has always been focused on modulating gene expression,” says CAMP4 Chief Financial Officer Kelly Gold MBA ’09. “At the simplest level, the foundation of many diseases is too much or too little of something being produced by the body. That is what our approach aims to correct.”

Accelerating impact

CAMP4 is starting by going after diseases of the liver and the central nervous system, where the safety and efficacy of ASOs has already been proven. Young believes correcting genetic expression without modulating the genes themselves will be a powerful approach to treating a range of complex diseases.

“Genetics is a powerful indicator of where a deficiency lies and how you might reverse that problem,” Young says. “There are many syndromes where we don’t have a complete understanding of the underlying mechanism of disease. But when a mutation clearly affects the output of a gene, you can now make a drug that can treat the disease without that complete understanding.”

As the company continues mapping the regulatory RNAs associated with every gene, Gold hopes CAMP4 can eventually minimize its reliance on wet-lab work and lean more heavily on machine learning to leverage its growing database and quickly identify regRNA targets for every disease it wants to treat.

In addition to its trials in urea cycle disorders, the company plans to launch key preclinical safety studies for a candidate targeting seizure disorders with a genetic basis, this year. And as the company continues exploring drug development efforts around the thousands of genetic diseases where increasing protein levels are can have a meaningful impact, it’s also considering collaborating with others to accelerate its impact.

“I can conceive of companies using a platform like this to go after many targets, where partners fund the clinical trials and use CAMP4 as an engine to target any disease where there’s a suspicion that gene upregulation or downregulation is the way to go,” Young says.

At the core of problem-solving

Stuart Levine ’97, director of MIT’s BioMicro Center, keeps departmental researchers at the forefront of systems biology.

Samantha Edelen | Department of Biology
March 19, 2025

As director of the MIT BioMicro Center (BMC), Stuart Levine ’97 wholeheartedly embraces the variety of challenges he tackles each day. One of over 50 core facilities providing shared resources across the Institute, the BMC supplies integrated high-throughput genomics, single-cell and spatial transcriptomic analysis, bioinformatics support, and data management to researchers across MIT.

“Every day is a different day,” Levine says, “there are always new problems, new challenges, and the technology is continuing to move at an incredible pace.” After more than 15 years in the role, Levine is grateful that the breadth of his work allows him to seek solutions for so many scientific problems.

By combining bioinformatics expertise with biotech relationships and a focus on maximizing the impact of the center’s work, Levine brings the broad range of skills required to match the diversity of questions asked by researchers in MIT’s Department of Biology.

Expansive expertise

Biology first appealed to Levine as an MIT undergraduate taking class 7.012 (Introduction to Biology), thanks to the charisma of instructors Professor Eric Lander and Amgen Professor Emerita Nancy Hopkins. After earning his PhD in biochemistry from Harvard University and Massachusetts General Hospital, Levine returned to MIT for postdoctoral work with Professor Richard Young, core member at the Whitehead Institute for Biomedical Research.

In the Young Lab, Levine found his calling as an informaticist and ultimately decided to stay at MIT. Here, his work has a wide-ranging impact: the BMC serves over 100 labs annually, from the the Computer Science and Artificial Intelligence Laboratory and the departments of Brain and Cognitive Sciences; Earth, Atmospheric and Planetary Sciences; Chemical Engineering; Mechanical Engineering; and, of course, Biology.

“It’s a fun way to think about science,” Levine says, noting that he applies his knowledge and streamlines workflows across these many disciplines by “truly and deeply understanding the instrumentation complexities.”

This depth of understanding and experience allows Levine to lead what longtime colleague Professor Laurie Boyer describes as “a state-of-the-art core that has served so many faculty and provides key training opportunities for all.” He and his team work with cutting-edge, finely tuned scientific instruments that generate vast amounts of bioinformatics data, then use powerful computational tools to store, organize, and visualize the data collected, contributing to research on topics ranging from host-parasite interactions to proposed tools for NASA’s planetary protection policy.

Staying ahead of the curve

With a scientist directing the core, the BMC aims to enable researchers to “take the best advantage of systems biology methods,” says Levine. These methods use advanced research technologies to do things like prepare large sets of DNA and RNA for sequencing, read DNA and RNA sequences from single cells, and localize gene expression to specific tissues.

Levine presents a lightweight, clear rectangle about the width of a cell phone and the length of a VHS cassette.

“This is a flow cell that can do 20 human genomes to clinical significance in two days — 8 billion reads,” he says. “There are newer instruments with several times that capacity available as well.”

The vast majority of research labs do not need that kind of power, but the Institute, and its researchers as a whole, certainly do. Levine emphasizes that “the ROI [return on investment] for supporting shared resources is extremely high because whatever support we receive impacts not just one lab, but all of the labs we support. Keeping MIT’s shared resources at the bleeding edge of science is critical to our ability to make a difference in the world.”

To stay at the edge of research technology, Levine maintains company relationships, while his scientific understanding allows him to educate researchers on what is possible in the space of modern systems biology. Altogether, these attributes enable Levine to help his researcher clients “push the limits of what is achievable.”

The man behind the machines

Each core facility operates like a small business, offering specialized services to a diverse client base across academic and industry research, according to Amy Keating, Jay A. Stein (1968) Professor of Biology and head of the Department of Biology. She explains that “the PhD-level education and scientific and technological expertise of MIT’s core directors are critical to the success of life science research at MIT and beyond.”

While Levine clearly has the education and expertise, the success of the BMC “business” is also in part due to his tenacity and focus on results for the core’s users.

He was recognized by the Institute with the MIT Infinite Mile Award in 2015 and the MIT Excellence Award in 2017, for which one nominator wrote, “What makes Stuart’s leadership of the BMC truly invaluable to the MIT community is his unwavering dedication to producing high-quality data and his steadfast persistence in tackling any type of troubleshooting needed for a project. These attributes, fostered by Stuart, permeate the entire culture of the BMC.”

“He puts researchers and their research first, whether providing education, technical services, general tech support, or networking to collaborators outside of MIT,” says Noelani Kamelamela, lab manager of the BMC. “It’s all in service to users and their projects.”

Tucked into the far back corner of the BMC lab space, Levine’s office is a fitting symbol of his humility. While his guidance and knowledge sit at the center of what elevates the BMC beyond technical support, he himself sits away from the spotlight, resolutely supporting others to advance science.

“Stuart has always been the person, often behind the scenes, that pushes great science, ideas, and people forward,” Boyer says. “His knowledge and advice have truly allowed us to be at the leading edge in our work.”

Helping the immune system attack tumors

Stefani Spranger is working to discover why some cancers don’t respond to immunotherapy, in hopes of making them more vulnerable to it.

Anne Trafton | MIT News
February 26, 2025

In addition to patrolling the body for foreign invaders, the immune system also hunts down and destroys cells that have become cancerous or precancerous. However, some cancer cells end up evading this surveillance and growing into tumors.

Once established, tumor cells often send out immunosuppressive signals, which leads T cells to become “exhausted” and unable to attack the tumor. In recent years, some cancer immunotherapy drugs have shown great success in rejuvenating those T cells so they can begin attacking tumors again.

While this approach has proven effective against cancers such as melanoma, it doesn’t work as well for others, including lung and ovarian cancer. MIT Associate Professor Stefani Spranger is trying to figure out how those tumors are able to suppress immune responses, in hopes of finding new ways to galvanize T cells into attacking them.

“We really want to understand why our immune system fails to recognize cancer,” Spranger says. “And I’m most excited about the really hard-to-treat cancers because I think that’s where we can make the biggest leaps.”

Her work has led to a better understanding of the factors that control T-cell responses to tumors, and raised the possibility of improving those responses through vaccination or treatment with immune-stimulating molecules called cytokines.

“We’re working on understanding what exactly the problem is, and then collaborating with engineers to find a good solution,” she says.

Jumpstarting T cells

As a student in Germany, where students often have to choose their college major while still in high school, Spranger envisioned going into the pharmaceutical industry and chose to major in biology. At Ludwig Maximilian University in Munich, her course of study began with classical biology subjects such as botany and zoology, and she began to doubt her choice. But, once she began taking courses in cell biology and immunology, her interest was revived and she continued into a biology graduate program at the university.

During a paper discussion class early in her graduate school program, Spranger was assigned to a Science paper on a promising new immunotherapy treatment for melanoma. This strategy involves isolating tumor-infiltrating T-cells during surgery, growing them into large numbers, and then returning them to the patient. For more than 50 percent of those patients, the tumors were completely eliminated.

“To me, that changed the world,” Spranger recalls. “You can take the patient’s own immune system, not really do all that much to it, and then the cancer goes away.”

Spranger completed her PhD studies in a lab that worked on further developing that approach, known as adoptive T-cell transfer therapy. At that point, she still was leaning toward going into pharma, but after finishing her PhD in 2011, her husband, also a biologist, convinced her that they should both apply for postdoc positions in the United States.

They ended up at the University of Chicago, where Spranger worked in a lab that studies how the immune system responds to tumors. There, she discovered that while melanoma is usually very responsive to immunotherapy, there is a small fraction of melanoma patients whose T cells don’t respond to the therapy at all. That got her interested in trying to figure out why the immune system doesn’t always respond to cancer the way that it should, and in finding ways to jumpstart it.

During her postdoc, Spranger also discovered that she enjoyed mentoring students, which she hadn’t done as a graduate student in Germany. That experience drew her away from going into the pharmaceutical industry, in favor of a career in academia.

“I had my first mentoring teaching experience having an undergrad in the lab, and seeing that person grow as a scientist, from barely asking questions to running full experiments and coming up with hypotheses, changed how I approached science and my view of what academia should be for,” she says.

Modeling the immune system

When applying for faculty jobs, Spranger was drawn to MIT by the collaborative environment of MIT and its Koch Institute for Integrative Cancer Research, which offered the chance to collaborate with a large community of engineers who work in the field of immunology.

“That community is so vibrant, and it’s amazing to be a part of it,” she says.

Building on the research she had done as a postdoc, Spranger wanted to explore why some tumors respond well to immunotherapy, while others do not. For many of her early studies, she used a mouse model of non-small-cell lung cancer. In human patients, the majority of these tumors do not respond well to immunotherapy.

“We build model systems that resemble each of the different subsets of non-responsive non-small cell lung cancer, and we’re trying to really drill down to the mechanism of why the immune system is not appropriately responding,” she says.

As part of that work, she has investigated why the immune system behaves differently in different types of tissue. While immunotherapy drugs called checkpoint inhibitors can stimulate a strong T-cell response in the skin, they don’t do nearly as much in the lung. However, Spranger has shown that T cell responses in the lung can be improved when immune molecules called cytokines are also given along with the checkpoint inhibitor.

Those cytokines work, in part, by activating dendritic cells — a class of immune cells that help to initiate immune responses, including activation of T cells.

“Dendritic cells are the conductor for the orchestra of all the T cells, although they’re a very sparse cell population,” Spranger says. “They can communicate which type of danger they sense from stressed cells and then instruct the T cells on what they have to do and where they have to go.”

Spranger’s lab is now beginning to study other types of tumors that don’t respond at all to immunotherapy, including ovarian cancer and glioblastoma. Both the brain and the peritoneal cavity appear to suppress T-cell responses to tumors, and Spranger hopes to figure out how to overcome that immunosuppression.

“We’re specifically focusing on ovarian cancer and glioblastoma, because nothing’s working right now for those cancers,” she says. “We want to understand what we have to do in those sites to induce a really good anti-tumor immune response.”

Professor Anthony Sinskey, biologist, inventor, entrepreneur, and Center for Biomedical Innovation co-founder, dies at 84

Colleagues remember the longtime MIT professor as a supportive, energetic collaborator who seemed to know everyone at the Institute.

Zach Winn | MIT News
February 20, 2025

Longtime MIT Professor Anthony “Tony” Sinskey ScD ’67, who was also the co-founder and faculty director of the Center for Biomedical Innovation (CBI), passed away on Feb. 12 at his home in New Hampshire. He was 84.

Deeply engaged with MIT, Sinskey left his mark on the Institute as much through the relationships he built as the research he conducted. Colleagues say that throughout his decades on the faculty, Sinskey’s door was always open.

“He was incredibly generous in so many ways,” says Graham Walker, an American Cancer Society Professor at MIT. “He was so willing to support people, and he did it out of sheer love and commitment. If you could just watch Tony in action, there was so much that was charming about the way he lived. I’ve said for years that after they made Tony, they broke the mold. He was truly one of a kind.”

Sinskey’s lab at MIT explored methods for metabolic engineering and the production of biomolecules. Over the course of his research career, he published more than 350 papers in leading peer-reviewed journals for biology, metabolic engineering, and biopolymer engineering, and filed more than 50 patents. Well-known in the biopharmaceutical industry, Sinskey contributed to the founding of multiple companies, including Metabolix, Tepha, Merrimack Pharmaceuticals, and Genzyme Corporation. Sinskey’s work with CBI also led to impactful research papers, manufacturing initiatives, and educational content since its founding in 2005.

Across all of his work, Sinskey built a reputation as a supportive, collaborative, and highly entertaining friend who seemed to have a story for everything.

“Tony would always ask for my opinions — what did I think?” says Barbara Imperiali, MIT’s Class of 1922 Professor of Biology and Chemistry, who first met Sinskey as a graduate student. “Even though I was younger, he viewed me as an equal. It was exciting to be able to share my academic journey with him. Even later, he was continually opening doors for me, mentoring, connecting. He felt it was his job to get people into a room together to make new connections.”

Sinskey grew up in the small town of Collinsville, Illinois, and spent nights after school working on a farm. For his undergraduate degree, he attended the University of Illinois, where he got a job washing dishes at the dining hall. One day, as he recalled in a 2020 conversation, he complained to his advisor about the dishwashing job, so the advisor offered him a job washing equipment in his microbiology lab.

In a development that would repeat itself throughout Sinskey’s career, he befriended the researchers in the lab and started learning about their work. Soon he was showing up on weekends and helping out. The experience inspired Sinskey to go to graduate school, and he only applied to one place.

Sinskey earned his ScD from MIT in nutrition and food science in 1967. He joined MIT’s faculty a few years later and never left.

“He loved MIT and its excellence in research and education, which were incredibly important to him,” Walker says. “I don’t know of another institution this interdisciplinary — there’s barely a speed bump between departments — so you can collaborate with anybody. He loved that. He also loved the spirit of entrepreneurship, which he thrived on. If you heard somebody wanted to get a project done, you could run around, get 10 people, and put it together. He just loved doing stuff like that.”

Working across departments would become a signature of Sinskey’s research. His original office was on the first floor of MIT’s Building 56, right next to the parking lot, so he’d leave his door open in the mornings and afternoons and colleagues would stop in and chat.

“One of my favorite things to do was to drop in on Tony when I saw that his office door was open,” says Chris Kaiser, MIT’s Amgen Professor of Biology. “We had a whole range of things we liked to catch up on, but they always included his perspectives looking back on his long history at MIT. It also always included hopes for the future, including tracking trajectories of MIT students, whom he doted on.”

Long before the internet, colleagues describe Sinskey as a kind of internet unto himself, constantly leveraging his vast web of relationships to make connections and stay on top of the latest science news.

“He was an incredibly gracious person — and he knew everyone,” Imperiali says. “It was as if his Rolodex had no end. You would sit there and he would say, ‘Call this person.’ or ‘Call that person.’ And ‘Did you read this new article?’ He had a wonderful view of science and collaboration, and he always made that a cornerstone of what he did. Whenever I’d see his door open, I’d grab a cup of tea and just sit there and talk to him.”

When the first recombinant DNA molecules were produced in the 1970s, it became a hot area of research. Sinskey wanted to learn more about recombinant DNA, so he hosted a large symposium on the topic at MIT that brought in experts from around the world.

“He got his name associated with recombinant DNA for years because of that,” Walker recalls. “People started seeing him as Mr. Recombinant DNA. That kind of thing happened all the time with Tony.”

Sinskey’s research contributions extended beyond recombinant DNA into other microbial techniques to produce amino acids and biodegradable plastics. He co-founded CBI in 2005 to improve global health through the development and dispersion of biomedical innovations. The center adopted Sinskey’s collaborative approach in order to accelerate innovation in biotechnology and biomedical research, bringing together experts from across MIT’s schools.

“Tony was at the forefront of advancing cell culture engineering principles so that making biomedicines could become a reality. He knew early on that biomanufacturing was an important step on the critical path from discovering a drug to delivering it to a patient,” says Stacy Springs, the executive director of CBI. “Tony was not only my boss and mentor, but one of my closest friends. He was always working to help everyone reach their potential, whether that was a colleague, a former or current researcher, or a student. He had a gentle way of encouraging you to do your best.”

“MIT is one of the greatest places to be because you can do anything you want here as long as it’s not a crime,” Sinskey joked in 2020. “You can do science, you can teach, you can interact with people — and the faculty at MIT are spectacular to interact with.”

Sinskey shared his affection for MIT with his family. His wife, the late ChoKyun Rha ’62, SM ’64, SM ’66, ScD ’67, was a professor at MIT for more than four decades and the first woman of Asian descent to receive tenure at MIT. His two sons also attended MIT — Tong-ik Lee Sinskey ’79, SM ’80 and Taeminn Song MBA ’95, who is the director of strategy and strategic initiatives for MIT Information Systems and Technology (IS&T).

Song recalls: “He was driven by same goal my mother had: to advance knowledge in science and technology by exploring new ideas and pushing everyone around them to be better.”

Around 10 years ago, Sinskey began teaching a class with Walker, Course 7.21/7.62 (Microbial Physiology). Walker says their approach was to treat the students as equals and learn as much from them as they taught. The lessons extended beyond the inner workings of microbes to what it takes to be a good scientist and how to be creative. Sinskey and Rha even started inviting the class over to their home for Thanksgiving dinner each year.

“At some point, we realized the class was turning into a close community,” Walker says. “Tony had this endless supply of stories. It didn’t seem like there was a topic in biology that Tony didn’t have a story about either starting a company or working with somebody who started a company.”

Over the last few years, Walker wasn’t sure they were going to continue teaching the class, but Sinskey remarked it was one of the things that gave his life meaning after his wife’s passing in 2021. That decided it.

After finishing up this past semester with a class-wide lunch at Legal Sea Foods, Sinskey and Walker agreed it was one of the best semesters they’d ever taught.

In addition to his two sons, Sinskey is survived by his daughter-in-law Hyunmee Elaine Song, five grandchildren, and two great grandsons. He has two brothers, Terry Sinskey (deceased in 1975) and Timothy Sinskey, and a sister, Christine Sinskey Braudis.

Gifts in Sinskey’s memory can be made to the ChoKyun Rha (1962) and Anthony J Sinskey (1967) Fund.

MIT biologists discover a new type of control over RNA splicing

They identified proteins that influence splicing of about half of all human introns, allowing for more complex types of gene regulation.

Anne Trafton | MIT News
February 20, 2025

RNA splicing is a cellular process that is critical for gene expression. After genes are copied from DNA into messenger RNA, portions of the RNA that don’t code for proteins, called introns, are cut out and the coding portions are spliced back together.

This process is controlled by a large protein-RNA complex called the spliceosome. MIT biologists have now discovered a new layer of regulation that helps to determine which sites on the messenger RNA molecule the spliceosome will target.

The research team discovered that this type of regulation, which appears to influence the expression of about half of all human genes, is found throughout the animal kingdom, as well as in plants. The findings suggest that the control of RNA splicing, a process that is fundamental to gene expression, is more complex than previously known.

“Splicing in more complex organisms, like humans, is more complicated than it is in some model organisms like yeast, even though it’s a very conserved molecular process. There are bells and whistles on the human spliceosome that allow it to process specific introns more efficiently. One of the advantages of a system like this may be that it allows more complex types of gene regulation,” says Connor Kenny, an MIT graduate student and the lead author of the study.

Christopher Burge, the Uncas and Helen Whitaker Professor of Biology at MIT, is the senior author of the study, which appears today in Nature Communications.

Building proteins

RNA splicing, a process discovered in the late 1970s, allows cells to precisely control the content of the mRNA transcripts that carry the instructions for building proteins.

Each mRNA transcript contains coding regions, known as exons, and noncoding regions, known as introns. They also include sites that act as signals for where splicing should occur, allowing the cell to assemble the correct sequence for a desired protein. This process enables a single gene to produce multiple proteins; over evolutionary timescales, splicing can also change the size and content of genes and proteins, when different exons become included or excluded.

The spliceosome, which forms on introns, is composed of proteins and noncoding RNAs called small nuclear RNAs (snRNAs). In the first step of spliceosome assembly, an snRNA molecule known as U1 snRNA binds to the 5’ splice site at the beginning of the intron. Until now, it had been thought that the binding strength between the 5’ splice site and the U1 snRNA was the most important determinant of whether an intron would be spliced out of the mRNA transcript.

In the new study, the MIT team discovered that a family of proteins called LUC7 also helps to determine whether splicing will occur, but only for a subset of introns — in human cells, up to 50 percent.

Before this study, it was known that LUC7 proteins associate with U1 snRNA, but the exact function wasn’t clear. There are three different LUC7 proteins in human cells, and Kenny’s experiments revealed that two of these proteins interact specifically with one type of 5’ splice site, which the researchers called “right-handed.” A third human LUC7 protein interacts with a different type, which the researchers call “left-handed.”

The researchers found that about half of human introns contain a right- or left-handed site, while the other half do not appear to be controlled by interaction with LUC7 proteins. This type of control appears to add another layer of regulation that helps remove specific introns more efficiently, the researchers say.

“The paper shows that these two different 5’ splice site subclasses exist and can be regulated independently of one another,” Kenny says. “Some of these core splicing processes are actually more complex than we previously appreciated, which warrants more careful examination of what we believe to be true about these highly conserved molecular processes.”

“Complex splicing machinery”

Previous work has shown that mutation or deletion of one of the LUC7 proteins that bind to right-handed splice sites is linked to blood cancers, including about 10 percent of acute myeloid leukemias (AMLs). In this study, the researchers found that AMLs that lost a copy of the LUC7L2 gene have inefficient splicing of right-handed splice sites. These cancers also developed the same type of altered metabolism seen in earlier work.

“Understanding how the loss of this LUC7 protein in some AMLs alters splicing could help in the design of therapies that exploit these splicing differences to treat AML,” Burge says. “There are also small molecule drugs for other diseases such as spinal muscular atrophy that stabilize the interaction between U1 snRNA and specific 5’ splice sites. So the knowledge that particular LUC7 proteins influence these interactions at specific splice sites could aid in improving the specificity of this class of small molecules.”

Working with a lab led by Sascha Laubinger, a professor at Martin Luther University Halle-Wittenberg, the researchers found that introns in plants also have right- and left-handed 5’ splice sites that are regulated by Luc7 proteins.

The researchers’ analysis suggests that this type of splicing arose in a common ancestor of plants, animals, and fungi, but it was lost from fungi soon after they diverged from plants and animals.

“A lot what we know about how splicing works and what are the core components actually comes from relatively old yeast genetics work,” Kenny says. “What we see is that humans and plants tend to have more complex splicing machinery, with additional components that can regulate different introns independently.”

The researchers now plan to further analyze the structures formed by the interactions of Luc7 proteins with mRNA and the rest of the spliceosome, which could help them figure out in more detail how different forms of Luc7 bind to different 5’ splice sites.

The research was funded by the U.S. National Institutes of Health and the German Research Foundation.

AI model deciphers the code in proteins that tells them where to go

Whitehead Institute and CSAIL researchers created a machine-learning model to predict and generate protein localization, with implications for understanding and remedying disease.

Greta Friar | Whitehead Institute
February 13, 2025

Proteins are the workhorses that keep our cells running, and there are many thousands of types of proteins in our cells, each performing a specialized function. Researchers have long known that the structure of a protein determines what it can do. More recently, researchers are coming to appreciate that a protein’s localization is also critical for its function. Cells are full of compartments that help to organize their many denizens. Along with the well-known organelles that adorn the pages of biology textbooks, these spaces also include a variety of dynamic, membrane-less compartments that concentrate certain molecules together to perform shared functions. Knowing where a given protein localizes, and who it co-localizes with, can therefore be useful for better understanding that protein and its role in the healthy or diseased cell, but researchers have lacked a systematic way to predict this information.

Meanwhile, protein structure has been studied for over half-a-century, culminating in the artificial intelligence tool AlphaFold, which can predict protein structure from a protein’s amino acid code, the linear string of building blocks within it that folds to create its structure. AlphaFold and models like it have become widely used tools in research.

Proteins also contain regions of amino acids that do not fold into a fixed structure, but are instead important for helping proteins join dynamic compartments in the cell. MIT Professor Richard Young and colleagues wondered whether the code in those regions could be used to predict protein localization in the same way that other regions are used to predict structure. Other researchers have discovered some protein sequences that code for protein localization, and some have begun developing predictive models for protein localization. However, researchers did not know whether a protein’s localization to any dynamic compartment could be predicted based on its sequence, nor did they have a comparable tool to AlphaFold for predicting localization.

Now, Young, also member of the Whitehead Institute for Biological Research; Young lab postdoc Henry Kilgore; Regina Barzilay, the School of Engineering Distinguished Professor for AI and Health at MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL); and colleagues have built such a model, which they call ProtGPS. In a paper published on Feb. 6 in the journal Science, with first authors Kilgore and Barzilay lab graduate students Itamar Chinn, Peter Mikhael, and Ilan Mitnikov, the cross-disciplinary team debuts their model. The researchers show that ProtGPS can predict to which of 12 known types of compartments a protein will localize, as well as whether a disease-associated mutation will change that localization. Additionally, the research team developed a generative algorithm that can design novel proteins to localize to specific compartments.

“My hope is that this is a first step towards a powerful platform that enables people studying proteins to do their research,” Young says, “and that it helps us understand how humans develop into the complex organisms that they are, how mutations disrupt those natural processes, and how to generate therapeutic hypotheses and design drugs to treat dysfunction in a cell.”

The researchers also validated many of the model’s predictions with experimental tests in cells.

“It really excited me to be able to go from computational design all the way to trying these things in the lab,” Barzilay says. “There are a lot of exciting papers in this area of AI, but 99.9 percent of those never get tested in real systems. Thanks to our collaboration with the Young lab, we were able to test, and really learn how well our algorithm is doing.”

Developing the model

The researchers trained and tested ProtGPS on two batches of proteins with known localizations. They found that it could correctly predict where proteins end up with high accuracy. The researchers also tested how well ProtGPS could predict changes in protein localization based on disease-associated mutations within a protein. Many mutations — changes to the sequence for a gene and its corresponding protein — have been found to contribute to or cause disease based on association studies, but the ways in which the mutations lead to disease symptoms remain unknown.

Figuring out the mechanism for how a mutation contributes to disease is important because then researchers can develop therapies to fix that mechanism, preventing or treating the disease. Young and colleagues suspected that many disease-associated mutations might contribute to disease by changing protein localization. For example, a mutation could make a protein unable to join a compartment containing essential partners.

They tested this hypothesis by feeding ProtGOS more than 200,000 proteins with disease-associated mutations, and then asking it to both predict where those mutated proteins would localize and measure how much its prediction changed for a given protein from the normal to the mutated version. A large shift in the prediction indicates a likely change in localization.

The researchers found many cases in which a disease-associated mutation appeared to change a protein’s localization. They tested 20 examples in cells, using fluorescence to compare where in the cell a normal protein and the mutated version of it ended up. The experiments confirmed ProtGPS’s predictions. Altogether, the findings support the researchers’ suspicion that mis-localization may be an underappreciated mechanism of disease, and demonstrate the value of ProtGPS as a tool for understanding disease and identifying new therapeutic avenues.

“The cell is such a complicated system, with so many components and complex networks of interactions,” Mitnikov says. “It’s super interesting to think that with this approach, we can perturb the system, see the outcome of that, and so drive discovery of mechanisms in the cell, or even develop therapeutics based on that.”

The researchers hope that others begin using ProtGPS in the same way that they use predictive structural models like AlphaFold, advancing various projects on protein function, dysfunction, and disease.

Moving beyond prediction to novel generation

The researchers were excited about the possible uses of their prediction model, but they also wanted their model to go beyond predicting localizations of existing proteins, and allow them to design completely new proteins. The goal was for the model to make up entirely new amino acid sequences that, when formed in a cell, would localize to a desired location. Generating a novel protein that can actually accomplish a function — in this case, the function of localizing to a specific cellular compartment — is incredibly difficult. In order to improve their model’s chances of success, the researchers constrained their algorithm to only design proteins like those found in nature. This is an approach commonly used in drug design, for logical reasons; nature has had billions of years to figure out which protein sequences work well and which do not.

Because of the collaboration with the Young lab, the machine learning team was able to test whether their protein generator worked. The model had good results. In one round, it generated 10 proteins intended to localize to the nucleolus. When the researchers tested these proteins in the cell, they found that four of them strongly localized to the nucleolus, and others may have had slight biases toward that location as well.

“The collaboration between our labs has been so generative for all of us,” Mikhael says. “We’ve learned how to speak each other’s languages, in our case learned a lot about how cells work, and by having the chance to experimentally test our model, we’ve been able to figure out what we need to do to actually make the model work, and then make it work better.”

Being able to generate functional proteins in this way could improve researchers’ ability to develop therapies. For example, if a drug must interact with a target that localizes within a certain compartment, then researchers could use this model to design a drug to also localize there. This should make the drug more effective and decrease side effects, since the drug will spend more time engaging with its target and less time interacting with other molecules, causing off-target effects.

The machine learning team members are enthused about the prospect of using what they have learned from this collaboration to design novel proteins with other functions beyond localization, which would expand the possibilities for therapeutic design and other applications.

“A lot of papers show they can design a protein that can be expressed in a cell, but not that the protein has a particular function,” Chinn says. “We actually had functional protein design, and a relatively huge success rate compared to other generative models. That’s really exciting to us, and something we would like to build on.”

All of the researchers involved see ProtGPS as an exciting beginning. They anticipate that their tool will be used to learn more about the roles of localization in protein function and mis-localization in disease. In addition, they are interested in expanding the model’s localization predictions to include more types of compartments, testing more therapeutic hypotheses, and designing increasingly functional proteins for therapies or other applications.

“Now that we know that this protein code for localization exists, and that machine learning models can make sense of that code and even create functional proteins using its logic, that opens up the door for so many potential studies and applications,” Kilgore says.

Kingdoms collide as bacteria and cells form captivating connections

Studying the pathogen R. parkeri, researchers discovered the first evidence of extensive and stable interkingdom contacts between a pathogen and a eukaryotic organelle.

Lillian Eden | Department of Biology
January 24, 2025

In biology textbooks, the endoplasmic reticulum is often portrayed as a distinct, compact organelle near the nucleus, and is commonly known to be responsible for protein trafficking and secretion. In reality, the ER is vast and dynamic, spread throughout the cell and able to establish contact and communication with and between other organelles. These membrane contacts regulate processes as diverse as fat metabolism, sugar metabolism, and immune responses.

Exploring how pathogens manipulate and hijack essential processes to promote their own life cycles can reveal much about fundamental cellular functions and provide insight into viable treatment options for understudied pathogens.

New research from the Lamason Lab in the Department of Biology at MIT recently published in the Journal of Cell Biology has shown that Rickettsia parkeri, a bacterial pathogen that lives freely in the cytosol, can interact in an extensive and stable way with the rough endoplasmic reticulum, forming previously unseen contacts with the organelle.

It’s the first known example of a direct interkingdom contact site between an intracellular bacterial pathogen and a eukaryotic membrane.

The Lamason Lab studies R. parkeri as a model for infection of the more virulent Rickettsia rickettsii. R. rickettsii, carried and transmitted by ticks, causes Rocky Mountain Spotted Fever. Left untreated, the infection can cause symptoms as severe as organ failure and death.

Rickettsia is difficult to study because it is an obligate pathogen, meaning it can only live and reproduce inside living cells, much like a virus. Researchers must get creative to parse out fundamental questions and molecular players in the R. parkeri life cycle, and much remains unclear about how R. parkeri spreads.

Detour to the junction

First author Yamilex Acevedo-Sánchez, a BSG-MSRP-Bio program alum and a graduate student at the time, stumbled across the ER and R. parkeri interactions while trying to observe Rickettsia reaching a cell junction.

The current model for Rickettsia infection involves R. parkeri spreading cell to cell by traveling to the specialized contact sites between cells and being engulfed by the neighboring cell in order to spread. Listeria monocytogenes, which the Lamason Lab also studies, uses actin tails to forcefully propel itself into a neighboring cell. By contrast, R. parkeri can form an actin tail, but loses it before reaching the cell junction. Somehow, R. parkeri is still able to spread to neighboring cells.

After an MIT seminar about the ER’s lesser-known functions, Acevedo-Sánchez developed a cell line to observe whether Rickettsia might be spreading to neighboring cells by hitching a ride on the ER to reach the cell junction.

Instead, she saw an unexpectedly high percentage of R. parkeri surrounded and enveloped by the ER, at a distance of about 55 nanometers. This distance is significant because membrane contacts for interorganelle communication in eukaryotic cells form connections from 10-80 nanometers wide. The researchers ruled out that what they saw was not an immune response, and the sections of the ER interacting with the R. parkeri were still connected to the wider network of the ER.

“I’m of the mind that if you want to learn new biology, just look at cells,” Acevedo-Sánchez says. “Manipulating the organelle that establishes contact with other organelles could be a great way for a pathogen to gain control during infection.”

The stable connections were unexpected because the ER is constantly breaking and reforming connections, lasting seconds or minutes. It was surprising to see the ER stably associating around the bacteria. As a cytosolic pathogen that exists freely in the cytosol of the cells it infects, it was also unexpected to see R. parkeri surrounded by a membrane at all.

Small margins

Acevedo-Sánchez collaborated with the Center for Nanoscale Systems at Harvard University to view her initial observations at higher resolution using focused ion beam scanning electron microscopy. FIB-SEM involves taking a sample of cells and blasting them with a focused ion beam in order to shave off a section of the block of cells. With each layer, a high-resolution image is taken. The result of this process is a stack of images.

From there, Acevedo-Sánchez marked what different areas of the images were — such as the mitochondria, Rickettsia, or the ER — and a program called ORS Dragonfly, a machine learning program, sorted through the thousand or so images to identify those categories. That information was then used to create 3D models of the samples.

Acevedo-Sánchez noted that less than 5 percent of R. parkeri formed connections with the ER — but small quantities of certain characteristics are known to be critical for R. parkeri infection. R. parkeri can exist in two states: motile, with an actin tail, and nonmotile, without it. In mutants unable to form actin tails, R. parkeri are unable to progress to adjacent cells — but in nonmutants, the percentage of R. parkeri that have tails starts at about 2 percent in early infection and never exceeds 15 percent at the height of it.

The ER only interacts with nonmotile R. parkeri, and those interactions increased 25-fold in mutants that couldn’t form tails.

Creating connections

Co-authors Acevedo-Sánchez, Patrick Woida, and Caroline Anderson also investigated possible ways the connections with the ER are mediated. VAP proteins, which mediate ER interactions with other organelles, are known to be co-opted by other pathogens during infection.

During infection by R. parkeri, VAP proteins were recruited to the bacteria; when VAP proteins were knocked out, the frequency of interactions between R. parkeri and the ER decreased, indicating R. parkeri may be taking advantage of these cellular mechanisms for its own purposes during infection.

Although Acevedo-Sánchez now works as a senior scientist at AbbVie, the Lamason Lab is continuing the work of exploring the molecular players that may be involved, how these interactions are mediated, and whether the contacts affect the host or bacteria’s life cycle.

Senior author and associate professor of biology Rebecca Lamason noted that these potential interactions are particularly interesting because bacteria and mitochondria are thought to have evolved from a common ancestor. The Lamason Lab has been exploring whether R. parkeri could form the same membrane contacts that mitochondria do, although they haven’t proven that yet. So far, R. parkeri is the only cytosolic pathogen that has been observed behaving this way.

“It’s not just bacteria accidentally bumping into the ER. These interactions are extremely stable. The ER is clearly extensively wrapping around the bacterium, and is still connected to the ER network,” Lamason says. “It seems like it has a purpose — what that purpose is remains a mystery.”

An abundant phytoplankton feeds a global network of marine microbes

New findings illuminate how Prochlorococcus’ nightly “cross-feeding” plays a role in regulating the ocean’s capacity to cycle and store carbon.

Jennifer Chu | MIT News
January 3, 2025

One of the hardest-working organisms in the ocean is the tiny, emerald-tinged Prochlorococcus marinus. These single-celled “picoplankton,” which are smaller than a human red blood cell, can be found in staggering numbers throughout the ocean’s surface waters, making Prochlorococcus the most abundant photosynthesizing organism on the planet. (Collectively, Prochlorococcus fix as much carbon as all the crops on land.) Scientists continue to find new ways that the little green microbe is involved in the ocean’s cycling and storage of carbon.

Now, MIT scientists have discovered a new ocean-regulating ability in the small but mighty microbes: cross-feeding of DNA building blocks. In a study appearing today in Science Advances, the team reports that Prochlorococcus shed these extra compounds into their surroundings, where they are then “cross-fed,” or taken up by other ocean organisms, either as nutrients, energy, or for regulating metabolism. Prochlorococcus’ rejects, then, are other microbes’ resources.

What’s more, this cross-feeding occurs on a regular cycle: Prochlorococcus tend to shed their molecular baggage at night, when enterprising microbes quickly consume the cast-offs. For a microbe called SAR11, the most abundant bacteria in the ocean, the researchers found that the nighttime snack acts as a relaxant of sorts, forcing the bacteria to slow down their metabolism and effectively recharge for the next day.

Through this cross-feeding interaction, Prochlorococcus could be helping many microbial communities to grow sustainably, simply by giving away what it doesn’t need. And they’re doing so in a way that could set the daily rhythms of microbes around the world.

“The relationship between the two most abundant groups of microbes in ocean ecosystems has intrigued oceanographers for years,” says co-author and MIT Institute Professor Sallie “Penny” Chisholm, who played a role in the discovery of Prochlorococcus in 1986. “Now we have a glimpse of the finely tuned choreography that contributes to their growth and stability across vast regions of the oceans.”

Given that Prochlorococcus and SAR11 suffuse the surface oceans, the team suspects that the exchange of molecules from one to the other could amount to one of the major cross-feeding relationships in the ocean, making it an important regulator of the ocean carbon cycle.

“By looking at the details and diversity of cross-feeding processes, we can start to unearth important forces that are shaping the carbon cycle,” says the study’s lead author, Rogier Braakman, a research scientist in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS).

Other MIT co-authors include Brandon Satinsky, Tyler O’Keefe, Shane Hogle, Jamie Becker, Robert Li, Keven Dooley, and Aldo Arellano, along with Krista Longnecker, Melissa Soule, and Elizabeth Kujawinski of Woods Hole Oceanographic Institution (WHOI).

Spotting castaways

Cross-feeding occurs throughout the microbial world, though the process has mainly been studied in close-knit communities. In the human gut, for instance, microbes are in close proximity and can easily exchange and benefit from shared resources.

By comparison, Prochlorococcus are free-floating microbes that are regularly tossed and mixed through the ocean’s surface layers. While scientists assume that the plankton are involved in some amount of cross-feeding, exactly how this occurs, and who would benefit, have historically been challenging to probe; any stuff that Prochlorococcus cast away would have vanishingly low concentrations,and be exceedingly difficult to measure.

But in work published in 2023, Braakman teamed up with scientists at WHOI, who pioneered ways to measure small organic compounds in seawater. In the lab, they grew various strains of Prochlorococcus under different conditions and characterized what the microbes released. They found that among the major “exudants,” or released molecules, were purines and pyridines, which are molecular building blocks of DNA. The molecules also happen to be nitrogen-rich — a fact that puzzled the team. Prochlorococcus are mainly found in ocean regions that are low in nitrogen, so it was assumed they’d want to retain any and all nitrogen-containing compounds they can. Why, then, were they instead throwing such compounds away?

Global symphony

In their new study, the researchers took a deep dive into the details of Prochlorococcus’ cross-feeding and how it influences various types of ocean microbes.

They set out to study how Prochlorococcus use purine and pyridine in the first place, before expelling the compounds into their surroundings. They compared published genomes of the microbes, looking for genes that encode purine and pyridine metabolism. Tracing the genes forward through the genomes, the team found that once the compounds are produced, they are used to make DNA and replicate the microbes’ genome. Any leftover purine and pyridine is recycled and used again, though a fraction of the stuff is ultimately released into the environment. Prochlorococcus appear to make the most of the compounds, then cast off what they can’t.

The team also looked to gene expression data and found that genes involved in recycling purine and pyrimidine peak several hours after the recognized peak in genome replication that occurs at dusk. The question then was: What could be benefiting from this nightly shedding?

For this, the team looked at the genomes of more than 300 heterotrophic microbes — organisms that consume organic carbon rather than making it themselves through photosynthesis. They suspected that such carbon-feeders could be likely consumers of Prochlorococcus’ organic rejects. They found most of the heterotrophs contained genes that take up either purine or pyridine, or in some cases, both, suggesting microbes have evolved along different paths in terms of how they cross-feed.

The group zeroed in on one purine-preferring microbe, SAR11, as it is the most abundant heterotrophic microbe in the ocean. When they then compared the genes across different strains of SAR11, they found that various types use purines for different purposes, from simply taking them up and using them intact to breaking them down for their energy, carbon, or nitrogen. What could explain the diversity in how the microbes were using Prochlorococcus’ cast-offs?

It turns out the local environment plays a big role. Braakman and his collaborators performed a metagenome analysis in which they compared the collectively sequenced genomes of all microbes in over 600 seawater samples from around the world, focusing on SAR11 bacteria. Metagenome sequences were collected alongside measurements of various environmental conditions and geographic locations in which they are found. This analysis showed that the bacteria gobble up purine for its nitrogen when the nitrogen in seawater is low, and for its carbon or energy when nitrogen is in surplus — revealing the selective pressures shaping these communities in different ocean regimes.

“The work here suggests that microbes in the ocean have developed relationships that advance their growth potential in ways we don’t expect,” says co-author Kujawinski.

Finally, the team carried out a simple experiment in the lab, to see if they could directly observe a mechanism by which purine acts on SAR11. They grew the bacteria in cultures, exposed them to various concentrations of purine, and unexpectedly found it causes them to slow down their normal metabolic activities and even growth. However, when the researchers put these same cells under environmentally stressful conditions, they continued growing strong and healthy cells, as if the metabolic pausing by purines helped prime them for growth, thereby avoiding the effects of the stress.

“When you think about the ocean, where you see this daily pulse of purines being released by Prochlorococcus, this provides a daily inhibition signal that could be causing a pause in SAR11 metabolism, so that the next day when the sun comes out, they are primed and ready,” Braakman says. “So we think Prochlorococcus is acting as a conductor in the daily symphony of ocean metabolism, and cross-feeding is creating a global synchronization among all these microbial cells.”

This work was supported, in part, by the Simons Foundation and the National Science Foundation.

A blueprint for better cancer immunotherapies

By examining antigen architectures, MIT researchers built a therapeutic cancer vaccine that may improve tumor response to immune checkpoint blockade treatments.

Bendta Schroeder | Koch Institute
November 25, 2024

Immune checkpoint blockade (ICB) therapies can be very effective against some cancers by helping the immune system recognize cancer cells that are masquerading as healthy cells.

T cells are built to recognize specific pathogens or cancer cells, which they identify from the short fragments of proteins presented on their surface. These fragments are often referred to as antigens. Healthy cells will will not have the same short fragments or antigens on their surface, and thus will be spared from attack.

Even with cancer-associated antigens studding their surfaces, tumor cells can still escape attack by presenting a checkpoint protein, which is built to turn off the T cell. Immune checkpoint blockade therapies bind to these “off-switch” proteins and allow the T cell to attack.

Researchers have established that how cancer-associated antigens are distributed throughout a tumor determines how it will respond to checkpoint therapies. Tumors with the same antigen signal across most of its cells respond well, but heterogeneous tumors with subpopulations of cells that each have different antigens, do not. The overwhelming majority of tumors fall into the latter category and are characterized by heterogenous antigen expression. Because the mechanisms behind antigen distribution and tumor response are poorly understood, efforts to improve ICB therapy response in heterogenous tumors have been hindered.

In a new study, MIT researchers analyzed antigen expression patterns and associated T cell responses to better understand why patients with heterogenous tumors respond poorly to ICB therapies. In addition to identifying specific antigen architectures that determine how immune systems respond to tumors, the team developed an RNA-based vaccine that, when combined with ICB therapies, was effective at controlling tumors in mouse models of lung cancer.

Stefani Spranger, associate professor of biology and member of MIT’s Koch Institute for Integrative Cancer Research, is the senior author of the study, appearing recently in the Journal for Immunotherapy of Cancer. Other contributors include Koch Institute colleague Forest White, the Ned C. (1949) and Janet Bemis Rice Professor and professor of biological engineering at MIT, and Darrell Irvine, professor of immunology and microbiology at Scripps Research Institute and a former member of the Koch Institute.

While RNA vaccines are being evaluated in clinical trials, current practice of antigen selection is based on the predicted stability of antigens on the surface of tumor cells.

“It’s not so black-and-white,” says Spranger. “Even antigens that don’t make the numerical cut-off could be really valuable targets. Instead of just focusing on the numbers, we need to look inside the complex interplays between antigen hierarchies to uncover new and important therapeutic strategies.”

Spranger and her team created mouse models of lung cancer with a number of different and well-defined expression patterns of cancer-associated antigens in order to analyze how each antigen impacts T cell response. They created both “clonal” tumors, with the same antigen expression pattern across cells, and “subclonal” tumors that represent a heterogenous mix of tumor cell subpopulations expressing different antigens. In each type of tumor, they tested different combinations of antigens with strong or weak binding affinity to MHC.

The researchers found that the keys to immune response were how widespread an antigen is expressed across a tumor, what other antigens are expressed at the same time, and the relative binding strength and other characteristics of antigens expressed by multiple cell populations in the tumor

As expected, mouse models with clonal tumors were able to mount an immune response sufficient to control tumor growth when treated with ICB therapy, no matter which combinations of weak or strong antigens were present. However, the team discovered that the relative strength of antigens present resulted in dynamics of competition and synergy between T cell populations, mediated by immune recognition specialists called cross-presenting dendritic cells in tumor-draining lymph nodes. In pairings of two weak or two strong antigens, one resulting T cell population would be reduced through competition. In pairings of weak and strong antigens, overall T cell response was enhanced.

In subclonal tumors, with different cell populations emitting different antigen signals, competition rather than synergy was the rule, regardless of antigen combination. Tumors with a subclonal cell population expressing a strong antigen would be well-controlled under ICB treatment at first, but eventually parts of the tumor lacking the strong antigen began to grow and developed the ability evade immune attack and resist ICB therapy.

Incorporating these insights, the researchers then designed an RNA-based vaccine to be delivered in combination with ICB treatment with the goal of strengthening immune responses suppressed by antigen-driven dynamics. Strikingly, they found that no matter the binding affinity or other characteristics of the antigen targeted, the vaccine-ICB therapy combination was able to control tumors in mouse models. The widespread availability of an antigen across tumor cells determined the vaccine’s success, even if that antigen was associated with weak immune response.

Analysis of clinical data across tumor types showed that the vaccine-ICB therapy combination may be an effective strategy for treating patients with tumors with high heterogeneity. Patterns of antigen architectures in patient tumors correlated with T cell synergy or competition in mice models and determined responsiveness to ICB in cancer patients. In future work with the Irvine laboratory at the Scripps Research Institute, the Spranger laboratory will further optimize the vaccine with the aim of testing the therapy strategy in the clinic.