Researcher: Feng Zhang

Bacterial injection system delivers proteins in mice and human cells

by Allessandra DiCorato, Broad Institute of MIT and Harvard |

Researchers at the McGovern Institute and the Broad Institute of MIT and Harvard have harnessed a natural bacterial system to develop a new protein delivery approach that works in human cells and animals. The technology, described today in Nature, can be programmed to deliver a variety of proteins, including ones for gene editing, to different cell types. The system could potentially be a safe and efficient way to deliver gene therapies and cancer therapies.

Led by McGovern Institute investigator and Broad Institute core member Feng Zhang, the team took advantage of a tiny syringe-like injection structure, produced by a bacterium, that naturally binds to insect cells and injects a protein payload into them. The researchers used the artificial intelligence tool AlphaFold to engineer these syringe structures to deliver a range of useful proteins to both human cells and cells in live mice.

“This is a really beautiful example of how protein engineering can alter the biological activity of a natural system,” said Joseph Kreitz, the study’s first author and a graduate student in Zhang’s lab. “I think it substantiates protein engineering as a useful tool in bioengineering and the development of new therapeutic systems.”

“Delivery of therapeutic molecules is a major bottleneck for medicine, and we will need a deep bench of options to get these powerful new therapies into the right cells in the body,” added Zhang. “By learning from how nature transports proteins, we were able to develop a new platform that can help address this gap.”

Zhang is senior author on the study and is also the James and Patricia Poitras Professor of Neuroscience at MIT and an investigator at the Howard Hughes Medical Institute.

Injection via contraction

Portrait of Joseph Kreitz.
Graduate student Joseph Kreitz holds a 3D printed bacteriophage. Photo: Steph Stevens

Symbiotic bacteria use the roughly 100-nanometer-long syringe-like machines to inject proteins into host cells to help adjust the biology of their surroundings and enhance their survival. These machines, called extracellular contractile injection systems (eCISs), consist of a rigid tube inside a sheath that contracts, driving a spike on the end of the tube through the cell membrane. This forces protein cargo inside the tube to enter the cell.

On the outside of one end of the eCIS are tail fibers that recognize specific receptors on the cell surface and latch on. Previous research has shown that eCISs can naturally target insect and mouse cells, but Kreitz thought it might be possible to modify them to deliver proteins to human cells by reengineering the tail fibers to bind to different receptors.

Using AlphaFold, which predicts a protein’s structure from its amino acid sequence, the researchers redesigned tail fibers of an eCIS produced by Photorhabdus bacteria to bind to human cells. By reengineering another part of the complex, the scientists tricked the syringe into delivering a protein of their choosing, in some cases with remarkably high efficiency.

The team made eCISs that targeted cancer cells expressing the EGF receptor and showed that they killed almost 100 percent of the cells, but did not affect cells without the receptor. Though efficiency depends in part on the receptor the system is designed to target, Kreitz says that the findings demonstrate the promise of the system with thoughtful engineering.

Photorhabdus virulence cassettes (green) binding to insect cells (blue) prior to injection of payload proteins. Image: Joseph Kreitz | McGovern Institute, Broad Institute

The researchers also used an eCIS to deliver proteins to the brain in live mice — where it didn’t provoke a detectable immune response, suggesting that eCISs could one day be used to safely deliver gene therapies to humans.

Packaging proteins

Kreitz says the eCIS system is versatile, and the team has already used it to deliver a range of cargos including base editor proteins (which can make single-letter changes to DNA), proteins that are toxic to cancer cells, and Cas9, a large DNA-cutting enzyme used in many gene editing systems.

Cancer cells killed by programmed Photorhabdus virulence cassettes (PVCs), imaged with a scanning electron microscope. Image: Joseph Kreitz | McGovern Institute, Broad Institute

In the future, Kreitz says researchers could engineer other components of the eCIS system to tune other properties, or to deliver other cargos such as DNA or RNA. He also wants to better understand the function of these systems in nature.

“We and others have shown that this type of system is incredibly diverse across the biosphere, but they are not very well characterized,” Kreitz said. “And we believe this type of system plays really important roles in biology that are yet to be explored.”

This work was supported in part by the National Institutes of Health, Howard Hughes Medical Institute, Poitras Center for Psychiatric Disorders Research at MIT, Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT, K. Lisa Yang and Hock E. Tan Molecular Therapeutics Center at MIT, K. Lisa Yang Brain-Body Center at MIT, Broad Institute Programmable Therapeutics Gift Donors, The Pershing Square Foundation, William Ackman, Neri Oxman, J. and P. Poitras, Kenneth C. Griffin, BT Charitable Foundation, the Asness Family Foundation, the Phillips family, D. Cheng, and R. Metcalfe.

MIT scientists discover new antiviral defense system in bacteria

by Leah Eisenstadt | Broad Institute |

Bacteria use a variety of defense strategies to fight off viral infection, and some of these systems have led to groundbreaking technologies, such as CRISPR-based gene-editing. Scientists predict there are many more antiviral weapons yet to be found in the microbial world.

A team led by researchers at the Broad Institute of MIT and Harvard and the McGovern Institute for Brain Research at MIT has discovered and characterized one of these unexplored microbial defense systems. They found that certain proteins in bacteria and archaea (together known as prokaryotes) detect viruses in surprisingly direct ways, recognizing key parts of the viruses and causing the single-celled organisms to commit suicide to quell the infection within a microbial community. The study is the first time this mechanism has been seen in prokaryotes and shows that organisms across all three domains of life — bacteria, archaea, and eukaryotes (which includes plants and animals) — use pattern recognition of conserved viral proteins to defend against pathogens.

The study appears in Science.

“This work demonstrates a remarkable unity in how pattern recognition occurs across very different organisms,” said senior author Feng Zhang, who is a core institute member at the Broad, the James and Patricia Poitras Professor of Neuroscience at MIT, a professor of brain and cognitive sciences and biological engineering at MIT, and an investigator at MIT’s McGovern Institute and the Howard Hughes Medical Institute. “It’s been very exciting to integrate genetics, bioinformatics, biochemistry, and structural biology approaches in one study to understand this fascinating molecular system.”

Microbial armory

In an earlier study, the researchers scanned data on the DNA sequences of hundreds of thousands of bacteria and archaea, which revealed several thousand genes harboring signatures of microbial defense. In the new study, they homed in on a handful of these genes encoding enzymes that are members of the STAND ATPase family of proteins, which in eukaryotes are involved in the innate immune response.

In humans and plants, the STAND ATPase proteins fight infection by recognizing patterns in a pathogen itself or in the cell’s response to infection. In the new study, the researchers wanted to know if the proteins work the same way in prokaryotes to defend against infection. The team chose a few STAND ATPase genes from the earlier study, delivered them to bacterial cells, and challenged those cells with bacteriophage viruses. The cells underwent a dramatic defensive response and survived.

The scientists next wondered which part of the bacteriophage triggers that response, so they delivered viral genes to the bacteria one at a time. Two viral proteins elicited an immune response: the portal, a part of the virus’s capsid shell, which contains viral DNA; and the terminase, the molecular motor that helps assemble the virus by pushing the viral DNA into the capsid. Each of these viral proteins activated a different STAND ATPase to protect the cell.

The finding was striking and unprecedented. Most known bacterial defense systems work by sensing viral DNA or RNA, or cellular stress due to the infection. These bacterial proteins were instead directly sensing key parts of the virus.

The team next showed that bacterial STAND ATPase proteins could recognize diverse portal and terminase proteins from different phages. “It’s surprising that bacteria have these highly versatile sensors that can recognize all sorts of different phage threats that they might encounter,” said co-first author Linyi Gao, a junior fellow in the Harvard Society of Fellows and a former graduate student in the Zhang lab.

Structural analysis

For a detailed look at how the microbial STAND ATPases detect the viral proteins, the researchers used cryo-electron microscopy to examine their molecular structure when bound to the viral proteins. “By analyzing the structure, we were able to precisely answer a lot of the questions about how these things actually work,” said co-first author Max Wilkinson, a postdoctoral researcher in the Zhang lab.

The team saw that the portal or terminase protein from the virus fits within a pocket in the STAND ATPase protein, with each STAND ATPase protein grasping one viral protein. The STAND ATPase proteins then group together in sets of four known as tetramers, which brings together key parts of the bacterial proteins called effector domains. This activates the proteins’ endonuclease function, shredding cellular DNA and killing the cell.

The tetramers bound viral proteins from other bacteriophages just as tightly, demonstrating that the STAND ATPases sense the viral proteins’ three-dimensional shape, rather than their sequence. This helps explain how one STAND ATPase can recognize dozens of different viral proteins. “Regardless of sequence, they all fit like a hand in a glove,” said Wilkinson.

STAND ATPases in humans and plants also work by forming multi-unit complexes that activate specific functions in the cell. “That’s the most exciting part of this work,” said Strecker. “To see this across the domains of life is unprecedented.”

The research was funded in part by the National Institutes of Health, the Howard Hughes Medical Institute, Open Philanthropy, the Edward Mallinckrodt, Jr. Foundation, the Poitras Center for Psychiatric Disorders Research, the Hock E. Tan and K. Lisa Yang Center for Autism Research, the K. Lisa Yang and Hock E. Tan Center for Molecular Therapeutics in Neuroscience, the Phillips family, J. and P. Poitras, and the BT Charitable Foundation.

New research center focused on brain-body relationship established at MIT

by Julie Pryor |

The inextricable link between our brains and our bodies has been gaining increasing recognition among researchers and clinicians over recent years. Studies have shown that the brain-body pathway is bidirectional — meaning that our mental state can influence our physical health and vice versa. But exactly how the two interact is less clear.

A new research center at MIT, funded by a $38 million gift to the McGovern Institute for Brain Research from philanthropist K. Lisa Yang, aims to unlock this mystery by creating and applying novel tools to explore the multidirectional, multilevel interplay between the brain and other body organ systems. This gift expands Yang’s exceptional philanthropic support of human health and basic science research at MIT over the past five years.

“Lisa Yang’s visionary gift enables MIT scientists and engineers to pioneer revolutionary technologies and undertake rigorous investigations into the brain’s complex relationship with other organ systems,” says MIT President L. Rafael Reif.  “Lisa’s tremendous generosity empowers MIT scientists to make pivotal breakthroughs in brain and biomedical research and, collectively, improve human health on a grand scale.”

The K. Lisa Yang Brain-Body Center will be directed by Polina Anikeeva, professor of materials science and engineering and brain and cognitive sciences at MIT and an associate investigator at the McGovern Institute. The center will harness the power of MIT’s collaborative, interdisciplinary life sciences research and engineering community to focus on complex conditions and diseases affecting both the body and brain, with a goal of unearthing knowledge of biological mechanisms that will lead to promising therapeutic options.

“Under Professor Anikeeva’s brilliant leadership, this wellspring of resources will encourage the very best work of MIT faculty, graduate fellows, and research — and ultimately make a real impact on the lives of many,” Reif adds.

microscope image of gut
Mouse small intestine stained to reveal cell nucleii (blue) and peripheral nerve fibers (red).
Image: Polina Anikeeva, Marie Manthey, Kareena Villalobos

Center goals  

Initial projects in the center will focus on four major lines of research:

  • Gut-Brain: Anikeeva’s group will expand a toolbox of new technologies and apply these tools to examine major neurobiological questions about gut-brain pathways and connections in the context of autism spectrum disorders, Parkinson’s disease, and affective disorders.
  • Aging: CRISPR pioneer Feng Zhang, the James and Patricia Poitras Professor of Neuroscience at MIT and investigator at the McGovern Institute, will lead a group in developing molecular tools for precision epigenomic editing and erasing accumulated “errors” of time, injury, or disease in various types of cells and tissues.
  • Pain: The lab of Fan Wang, investigator at the McGovern Institute and professor of brain and cognitive sciences, will design new tools and imaging methods to study autonomic responses, sympathetic-parasympathetic system balance, and brain-autonomic nervous system interactions, including how pain influences these interactions.
  • Acupuncture: Wang will also collaborate with Hilda (“Scooter”) Holcombe, a veterinarian in MIT’s Division of Comparative Medicine, to advance techniques for documenting changes in brain and peripheral tissues induced by acupuncture in mouse models. If successful, these techniques could lay the groundwork for deeper understandings of the mechanisms of acupuncture, specifically how the treatment stimulates the nervous system and restores function.

A key component of the K. Lisa Yang Brain-Body Center will be a focus on educating and training the brightest young minds who aspire to make true breakthroughs for individuals living with complex and often devastating diseases. A portion of center funding will endow the new K. Lisa Yang Brain-Body Fellows Program, which will support four annual fellowships for MIT graduate students and postdocs working to advance understanding of conditions that affect both the body and brain.

Mens sana in corpore sano

“A phrase I remember reading in secondary school has always stuck with me: ‘mens sana in corpore sano’ — ‘a healthy mind in a healthy body,’” says Lisa Yang, a former investment banker committed to advocacy for individuals with visible and invisible disabilities. “When we look at how stress, nutrition, pain, immunity, and other complex factors impact our health, we truly see how inextricably linked our brains and bodies are. I am eager to help MIT scientists and engineers decode these links and make real headway in creating therapeutic strategies that result in longer, healthier lives.”

“This center marks a once-in-a-lifetime opportunity for labs like mine to conduct bold and risky studies into the complexities of brain-body connections,” says Anikeeva, who works at the intersection of materials science, electronics, and neurobiology. “The K. Lisa Yang Brain-Body Center will offer a pathbreaking, holistic approach that bridges multiple fields of study. I have no doubt that the center will result in revolutionary strides in our understanding of the inextricable bonds between the brain and the body’s peripheral organ systems, and a bold new way of thinking in how we approach human health overall.”

Clinical trials bring first CRISPR-based therapies to patients

by Jennifer Michalowski |

Nearly ten years ago, Feng Zhang and other pioneering scientists developed CRISPR, a revolutionary technology that quickly became biologists’ preferred method of editing DNA. Biologists, computer scientists, and engineers in Zhang’s lab are continuing to explore natural CRISPR systems and expand researchers’ gene-editing toolkit. But for their long-term goal of using those tools to improve health, clinical collaboration is essential.

Clinical trials are rarely led by academic researchers; licensing agreements and partnerships with industry are usually essential to transform laboratory findings into advances that impact patients. Editas Medicine, a company co-founded by Zhang, aims to use CRISPR to correct disease-causing genetic errors inside patient cells—and two of Editas’s experimental CRISPR-based therapies have reached clinical trials.

One is a treatment for sickle cell anemia, a disorder in which a single genetic mutation disrupts the production of hemoglobin, creating misshapen red blood cells that can’t carry oxygen efficiently. With CRISPR, that mutation can be corrected in stem cells isolated from a patient’s blood. The CRISPR-modified cells are then returned to the patient, where they are expected to generate healthy red blood cells. The same strategy may also be effective for treating another inherited blood disorder, transfusion-dependent beta thalassemia.

Editas is pursuing a similar strategy to correct the mutation that causes Leber congenital amaurosis, an inherited form of blindness—but in that case, the CRISPR-based therapy is delivered directly to cells inside the body. The experimental treatment uses a viral vector to introduce CRISPR to the retina of the eye, where a gene mutation impairs the function of light-sensitive photoreceptors. Clinical trial participants received their first treatments in 2020, and in 2021, the company announced that some patients had experienced improvements to their vision.

Five with MIT ties elected to the National Academy of Medicine for 2021

by Julie Pryor |

The National Academy of Medicine (NAM) has announced the election of 100 new members for 2021, including two MIT faculty members and three additional Institute affiliates.

Faculty honorees include Linda G. Griffith, a professor in the MIT departments of Biological Engineering and Mechanical Engineering; and Feng Zhang, a professor in the MIT departments of Brain and Cognitive Sciences and Biological Engineering. Guillermo Antonio Ameer SCD ’99, a professor of biomedical engineering and surgery at Northwestern University; Darrell Gaskin SM ’87, a professor of health policy and management at Johns Hopkins University; and Vamsi Mootha, an institute member of the Broad Institute of MIT and Harvard and former student in the Harvard-MIT Program in Health Sciences and Technology, were also honored.

The new inductees were elected through a process that recognizes individuals who have made major contributions to the advancement of the medical sciences, health care, and public health. Election to the academy is considered one of the highest honors in the fields of health and medicine and recognizes individuals who have demonstrated outstanding professional achievement and commitment to service.

Griffith, the School of Engineering Professor of Teaching Innovation and director of the Center for Gynepathology Research at MIT, is credited for her longstanding leadership in research, education, and medical translation. Specifically, the NAM recognizes her pioneering work in tissue engineering, biomaterials, and systems biology, including the development of the first “liver chip” technology. Griffith is also recognized for inventing 3D biomaterials printing and organotypic models for systems gynopathology, and for the establishment of the biological engineering department at MIT.

The academy recognizes Zhang, the Patricia and James Poitras ’63 Professor in Neuroscience at MIT, for revolutionizing molecular biology and powering transformative leaps forward in our ability to study and treat human diseases. Zhang, who also is an investigator at the Howard Hughes Medical Institute and the McGovern Institute for Brain Research, and a core member of the Broad Institute of MIT and Harvard, is specifically credited for the discovery of novel microbial enzymes and their development as molecular technologies, including optogenetics and CRISPR-mediated genome editing. The academy also commends Zhang for his outstanding mentoring and professional services.

Ameer, the Daniel Hale Williams Professor of Biomedical Engineering and Surgery at the Northwestern University Feinberg School of Medicine, earned his Doctor of Science degree from the MIT Department of Chemical Engineering in 1999. A professor of biomedical engineering and of surgery who is also the director of the Center for Advanced Regenerative Engineering, he is cited by the NAM “For pioneering contributions to regenerative engineering and medicine through the development, dissemination, and translation of citrate-based biomaterials, a new class of biodegradable polymers that enabled the commercialization of innovative medical devices approved by the U.S. Food and Drug Administration for use in a variety of surgical procedures.”

Gaskin, the William C. and Nancy F. Richardson Professor in Health Policy and Management, Bloomberg School of Public Health at Johns Hopkins University, earned his Master of Science degree from the MIT Department of Economics in 1987. A health economist who advances community, neighborhood, and market-level policies and programs that reduce health disparities, he is cited by the NAM “For his work as a leading health economist and health services researcher who has advanced fundamental understanding of the role of place as a driver in racial and ethnic health disparities.”

Mootha, the founding co-director of the Broad Institute’s Metabolism Program, is a professor of systems biology and medicine at Harvard Medical School and a professor in the Department of Molecular Biology at Massachusetts General Hospital. An alumnus of the Harvard-MIT Program in Health Sciences and Technology and former postdoc with the Whitehead Institute for Biomedical Research, Mootha is an expert in the mitochondrion, the “powerhouse of the cell,” and its role in human disease. The NAM cites Mootha “For transforming the field of mitochondrial biology by creatively combining modern genomics with classical bioenergetics.”

Established in 1970 by the National Academy of Sciences, the NAM addresses critical issues in health, science, medicine, and related policy and inspires positive actions across sectors. NAM works alongside the National Academy of Sciences and National Academy of Engineering to provide independent, objective analysis and advice to the nation and conduct other activities to solve complex problems and inform public policy decisions. The National Academies of Sciences, Engineering, and Medicine also encourage education and research, recognize outstanding contributions to knowledge, and increase public understanding of STEMM. With their election, NAM members make a commitment to volunteer their service in National Academies activities.

New programmable gene editing proteins found outside of CRISPR systems

by Jennifer Michalowski |

Within the last decade, scientists have adapted CRISPR systems from microbes into gene editing technology, a precise and programmable system for modifying DNA. Now, scientists at MIT’s McGovern Institute and the Broad Institute of MIT and Harvard have discovered a new class of programmable DNA modifying systems called OMEGAs (Obligate Mobile Element Guided Activity), which may naturally be involved in shuffling small bits of DNA throughout bacterial genomes.

These ancient DNA-cutting enzymes are guided to their targets by small pieces of RNA. While they originated in bacteria, they have now  been engineered to work in human cells, suggesting they could be useful in the development of gene editing therapies, particularly as they are small (~30% the size of Cas9), making them easier to deliver to cells than bulkier enzymes. The discovery, reported September 9, 2021, in the journal Science, provides evidence that natural RNA-guided enzymes are among the most abundant proteins on earth, pointing toward a vast new area of biology that is poised to drive the next revolution in genome editing technology.

The research was led by McGovern Investigator Feng Zhang, who is the James and Patricia Poitras Professor of Neuroscience at MIT, a Howard Hughes Medical Institute investigator, and a Core Institute Member of the Broad Institute. Zhang’s team has been exploring natural diversity in search of new molecular systems that can be rationally programmed.

“We are super excited about the discovery of these widespread programmable enzymes, which have been hiding under our noses all along,” says Zhang. “These results suggest the tantalizing possibility that there are many more programmable systems that await discovery and development as useful technologies.”

Natural adaptation

Programmable enzymes, particularly those that use an RNA guide, can be rapidly adapted for different uses. For example, CRISPR enzymes naturally use an RNA guide to target viral invaders, but biologists can direct Cas9 to any target by generating their own RNA guide. “It’s so easy to just change a guide sequence and set a new target,” says graduate student and co-first author of the paper, Soumya Kannan. “So one of the broad questions that we’re interested in is trying to see if other natural systems use that same kind of mechanism.”

Zhang lab graduate student Han Altae-Tran, co-author of the Science paper with Soumya Kannan. Photo: Zhang lab

The first hints that OMEGA proteins might be directed by RNA came from the genes for proteins called IscBs. The IscBs are not involved in CRISPR immunity and were not known to associate with RNA, but they looked like small, DNA-cutting enzymes. The team discovered that each IscB had a small RNA encoded nearby and it directed IscB enzymes to cut specific DNA sequences. They named these RNAs “ωRNAs.”

The team’s experiments showed that two other classes of small proteins known as IsrBs and TnpBs, one of the most abundant genes in bacteria, also use ωRNAs that act as guides to direct the cleavage of DNA.

IscB, IsrB, and TnpB are found in mobile genetic elements called transposons. Graduate student Han Altae-Tran, co-first author on the paper, explains that each time these transposons move, they create a new guide RNA, allowing the enzyme they encode to cut somewhere else.

It’s not clear how bacteria benefit from this genomic shuffling—or whether they do at all.  Transposons are often thought of as selfish bits of DNA, concerned only with their own mobility and preservation, Kannan says. But if hosts can “co-opt” these systems and repurpose them, hosts may gain new abilities, as with CRISPR systems which confer adaptive immunity.

“A lot of the things that we have been thinking about may already exist naturally in some capacity,” says Altae-Tran.

IscBs and TnpBs appear to be predecessors of Cas9 and Cas12 CRISPR systems. The team suspects they, along with IsrB, likely gave rise to other RNA-guided enzymes, too—and they are eager to find them. They are curious about the range of functions that might be carried out in nature by RNA-guided enzymes, Kannan says, and suspect evolution likely already took advantage of OMEGA enzymes like IscBs and TnpBs to solve problems that biologists are keen to tackle.

Comparison of Ω (OMEGA) systems with other known RNA-guided systems. In contrast to CRISPR systems, which capture spacer sequences and store them in the locus within the CRISPR array, Ω systems may transpose their loci (or trans-acting loci) into target sequences, converting targets into ωRNA guides. Image courtesy of the researchers.

“A lot of the things that we have been thinking about may already exist naturally in some capacity,” says Altae-Tran. “Natural versions of these types of systems might be a good starting point to adapt for that particular task.”

The team is also interested in tracing the evolution of RNA-guided systems further into the past. “Finding all these new systems sheds light on how RNA-guided systems have evolved, but we don’t know where RNA-guided activity itself comes from,” Altae-Tran says. Understanding those origins, he says, could pave the way to developing even more classes of programmable tools.

This work was made possible with support from the Simons Center for the Social Brain at MIT; National Institutes of Health Intramural Research Program; National Institutes of Health grants 1R01-HG009761 and 1DP1-HL141201; Howard Hughes Medical Institute; Open Philanthropy; G. Harold and Leila Y. Mathers Charitable Foundation; Edward Mallinckrodt, Jr. Foundation; Poitras Center for Psychiatric Disorders Research at MIT; Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT; Yang-Tan Center for Molecular Therapeutics at MIT; Lisa Yang; Phillips family; R. Metcalfe; and J. and P. Poitras.

Scientists harness human protein to deliver molecular medicines to cells

by Broad Institute | McGovern Institute |

Researchers from MIT, the McGovern Institute for Brain Research at MIT, the Howard Hughes Medical Institute, and the Broad Institute of MIT and Harvard have developed a new way to deliver molecular therapies to cells. The system, called SEND, can be programmed to encapsulate and deliver different RNA cargoes. SEND harnesses natural proteins in the body that form virus-like particles and bind RNA, and it may provoke less of an immune response than other delivery approaches.

The new delivery platform works efficiently in cell models, and, with further development, could open up a new class of delivery methods for a wide range of molecular medicines — including those for gene editing and gene replacement. Existing delivery vehicles for these therapeutics can be inefficient and randomly integrate into the genome of cells, and some can stimulate unwanted immune reactions. SEND has the promise to overcome these limitations, which could open up new opportunities to deploy molecular medicine.

“The biomedical community has been developing powerful molecular therapeutics, but delivering them to cells in a precise and efficient way is challenging,” said CRISPR pioneer Feng Zhang, senior author on the study, core institute member at the Broad Institute, investigator at the McGovern Institute, and the James and Patricia Poitras Professor of Neuroscience at MIT. “SEND has the potential to overcome these challenges.” Zhang is also an investigator at the Howard Hughes Medical Institute and a professor in MIT’s Departments of Brain and Cognitive Sciences and Biological Engineering.

SEND packages are introduced to diseased cells to deliver therapeutic mRNA and restore health. Image: McGovern Institute

Reporting in Science, the team describes how SEND (Selective Endogenous eNcapsidation for cellular Delivery) takes advantage of molecules made by human cells. At the center of SEND is a protein called PEG10, which normally binds to its own mRNA and forms a spherical protective capsule around it. In their study, the team engineered PEG10 to selectively package and deliver other RNA. The scientists used SEND to deliver the CRISPR-Cas9 gene editing system to mouse and human cells to edit targeted genes.

First author Michael Segel, a postdoctoral researcher in Zhang’s lab, and Blake Lash, second author and a graduate student in the lab, said PEG10 is not unique in its ability to transfer RNA. “That’s what’s so exciting,” said Segel. “This study shows that there are probably other RNA transfer systems in the human body that can also be harnessed for therapeutic purposes. It also raises some really fascinating questions about what the natural roles of these proteins might be.”

Inspiration from within

The PEG10 protein exists naturally in humans and is derived from a “retrotransposon” — a virus-like genetic element — that integrated itself into the genome of human ancestors millions of years ago. Over time, PEG10 has been co-opted by the body to become part of the repertoire of proteins important for life.

Four years ago, researchers showed that another retrotransposon-derived protein, ARC, forms virus-like structures and is involved in transferring RNA between cells. Although these studies suggested that it might be possible to engineer retrotransposon proteins as a delivery platform, scientists had not successfully harnessed these proteins to package and deliver specific RNA cargoes in mammalian cells.

Knowing that some retrotransposon-derived proteins are able to bind and package molecular cargo, Zhang’s team turned to these proteins as possible delivery vehicles. They systematically searched through these proteins in the human genome for ones that could form protective capsules. In their initial analysis, the team found 48 human genes encoding proteins that might have that ability. Of these, 19 candidate proteins were present in both mice and humans. In the cell line the team studied, PEG10 stood out as an efficient shuttle; the cells released significantly more PEG10 particles than any other protein tested. The PEG10 particles also mostly contained their own mRNA, suggesting that PEG10 might be able to package specific RNA molecules.

Developing a modular system

To develop the SEND technology, the team identified the molecular sequences, or “signals,” in PEG10’s mRNA that PEG10 recognizes and uses to package its mRNA. The researchers then used these signals to engineer both PEG10 and other RNA cargo so that PEG10 could selectively package those RNAs. Next, the team decorated the PEG10 capsules with additional proteins, called “fusogens,” that are found on the surface of cells and help them fuse together.

By engineering the fusogens on the PEG10 capsules, researchers should be able to target the capsule to a particular kind of cell, tissue, or organ. As a first step towards this goal, the team used two different fusogens, including one found in the human body, to enable delivery of SEND cargo.

“By mixing and matching different components in the SEND system, we believe that it will provide a modular platform for developing therapeutics for different diseases,” said Zhang.

Advancing gene therapy

SEND is composed of proteins that are produced naturally in the body, which means it may not trigger an immune response. If this is demonstrated in further studies, the researchers say SEND could open up opportunities to deliver gene therapies repeatedly with minimal side effects. “The SEND technology will complement viral delivery vectors and lipid nanoparticles to further expand the toolbox of ways to deliver gene and editing therapies to cells,” said Lash.

Next, the team will test SEND in animals and further engineer the system to deliver cargo to a variety of tissues and cells. They will also continue to probe the natural diversity of these systems in the human body to identify other components that can be added to the SEND platform.

“We’re excited to keep pushing this approach forward,” said Zhang. “The realization that we can use PEG10, and most likely other proteins, to engineer a delivery pathway in the human body to package and deliver new RNA and other potential therapies is a really powerful concept.”

This work was made possible with support from the Simons Center for the Social Brain at MIT; National Institutes of Health Intramural Research Program; National Institutes of Health grants 1R01-HG009761 and 1DP1-HL141201; Howard Hughes Medical Institute; Open Philanthropy; G. Harold and Leila Y. Mathers Charitable Foundation; Edward Mallinckrodt, Jr. Foundation; Poitras Center for Psychiatric Disorders Research at MIT; Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT; Yang-Tan Center for Molecular Therapeutics at MIT; Lisa Yang; Phillips family; R. Metcalfe; and J. and P. Poitras.

Four MIT scientists honored with 2021 National Academy of Sciences awards

Anne Trafton |

Four MIT scientists are among the 20 recipients of the 2021 Academy Honors for major contributions to science, the National Academy of Sciences (NAS) announced at its annual meeting. The individuals are recognized for their “extraordinary scientific achievements in a wide range of fields spanning the physical, biological, social, and medical sciences.”

The awards recognize: Pablo Jarillo-Herrero, for contributions to the fields of nanoscience and nanotechnology through his discovery of correlated insulator behavior and unconventional superconductivity in magic-angle graphene superlattices; Aviv Regev, for using interdisciplinary information or techniques to solve a contemporary challenge; Susan Solomon, for contributions to understanding and communicating the causes of ozone depletion and climate change; and Feng Zhang, for pioneering achievements developing CRISPR tools with the potential to diagnose and treat disease.

Pablo Jarillo-Herrero: Award for Scientific Discovery

Pablo Jarillo-Herrero, a Cecil and Ida Green Professor of Physics, is the recipient of the NAS Award for Scientific Discovery for his pioneering developments in nanoscience and nanotechnology, which is presented to scientists in the fields of astronomy, materials science, or physics. His findings expand nanoscience by demonstrating for the first time that orientation can be used to dramatically control nanomaterial properties and to design new nanomaterials. This work lays the groundwork for developing a whole new family of 2D materials and has had a transformative impact on the field and on condensed-matter physics.

The biannual award recognizes “an accomplishment or discovery in basic research, achieved within the previous five years, that is expected to have a significant impact on one or more of the following fields: astronomy, biochemistry, biophysics, chemistry, materials science, or physics.”

In 2018, his research group discovered that by rotating two layers of graphene relative to each other by a magic angle, the bilayer material can be turned from a metal into an electrical insulator or even a superconductor. This discovery has fostered new theoretical and experimental research, inspiring the interest of technologists in nanoelectronics. The result is a new field in condensed-matter physics that has the potential to result in materials that conduct electricity without resistance at room temperature.

Aviv Regev: James Prize in Science and Technology Integration

Aviv Regev, who is a professor of biology, a core member of the Broad Institute of Harvard and MIT, a member of the Koch Institute, and a Howard Hughes Medical Institute investigator has been selected for the inaugural James Prize in Science and Technology Integration, along with Harvard Medical School Professor Allon Kelin, for “their concurrent development of now widely adopted massively parallel single-cell genomics to interrogate the gene expression profiles that define, at the level of individual cells, the distinct cell types in metazoan tissues, their developmental trajectories, and disease states, which integrated tools from molecular biology, engineering, statistics, and computer science.”

The prize recognizes individuals “who are able to adopt or adapt information or techniques from outside their fields” to “solve a major contemporary challenge not addressable from a single disciplinary perspective.”

Regev is credited with forging new ways to unite the disciplines of biology, computational science, and engineering as a pioneer in the field of single-cell biology, including developing some of its core experimental and analysis tools, and their application to discover cell types, states, programs, environmental responses, development, tissue locations, and regulatory circuits, and deploying these to assemble cellular atlases of the human body that illuminate mechanisms of disease with remarkable fidelity.

Susan Solomon: Award for Chemistry in Service to Society

Susan Solomon, the Lee and Geraldine Martin Professor of Environmental Studies in the Department of Earth, Atmospheric and Planetary Sciences who holds a secondary appointment in the Department of Chemistry, is the recipient of the Award for Chemistry in Service to Society for “influential and incisive application of atmospheric chemistry to understand our most critical environmental issues — ozone layer depletion and climate change — and for her effective communication of environmental science to leaders to facilitate policy changes.”

The award is given biannually for “contributions to chemistry, either in fundamental science or its application, that clearly satisfy a societal need.”

Solomon is globally recognized as a leader in atmospheric science, notably for her insights in explaining the cause of the Antarctic ozone “hole.” She and her colleagues have made important contributions to understanding chemistry-climate coupling, including pioneering research on the irreversibility of global warming linked to anthropogenic carbon dioxide emissions, and on the influence of the ozone hole on the climate of the southern hemisphere.

Her work has had an enormous effect on policy and society, including the transition away from ozone-depleting substances and to environmentally benign chemicals. The work set the stage for the Paris Agreement on climate, and she continues to educate policymakers, the public, and the next generation of scientists.

Feng Zhang: Richard Lounsbery Award

Feng Zhang, who is the James and Patricia Poitras Professor of Neuroscience at MIT, an investigator at the McGovern Institute for Brain Research and the Howard Hughes Medical Institute, a professor of brain and cognitive sciences and biological engineering at MIT, and a core member of the Broad Institute of MIT and Harvard, is the recipient of the Richard Lounsbery Award for pioneering CRISPR-mediated genome editing.

The award recognizes “extraordinary scientific achievement in biology and medicine” as well as stimulating research and encouraging reciprocal scientific exchanges between the United States and France.

Zhang continues to lead the field through the discovery of novel CRISPR systems and their development as molecular tools with the potential to diagnose and treat disease, such as disorders affecting the nervous system. His contributions in genome engineering, as well as his earlier work developing optogenetics, are enabling a deeper understanding of behavioral neural circuits and advances in gene therapy for treating disease.

In addition, Zhang has championed the open sharing of the technologies he has developed through extensive resource sharing. The tools from his lab are being used by thousands of scientists around the world to accelerate research in nearly every field of the life sciences. Even as biomedical researchers around the world adopt Zhang’s discoveries and his tools enter the clinic to treat genetic diseases, he continues to innovate and develop new technologies to advance science.

The National Academy of Sciences is a private, nonprofit society of distinguished scholars, established in 1863 by the U.S. Congress. The NAS is charged with providing independent, objective advice to the nation on matters related to science and technology as well as encouraging education and research, recognize outstanding contributions to knowledge, and increasing public understanding in matters of science, engineering, and medicine. Winners received their awards, which include a monetary prize, during a virtual ceremony at the 158th NAS Annual Meeting.

This story is a modified compilation from several National Academy of Sciences press releases.

A large-scale tool to investigate the function of autism spectrum disorder genes

by Harvard University |

Scientists at Harvard University, the Broad Institute of MIT and Harvard, and MIT have developed a technology to investigate the function of many different genes in many different cell types at once, in a living organism. They applied the large-scale method to study dozens of genes that are associated with autism spectrum disorder, identifying how specific cell types in the developing mouse brain are impacted by mutations.

The “Perturb-Seq” method, published in the journal Science, is an efficient way to identify potential biological mechanisms underlying autism spectrum disorder, which is an important first step toward developing treatments for the complex disease. The method is also broadly applicable to other organs, enabling scientists to better understand a wide range of disease and normal processes.

“For many years, genetic studies have identified a multitude of risk genes that are associated with the development of autism spectrum disorder. The challenge in the field has been to make the connection between knowing what the genes are, to understanding how the genes actually affect cells and ultimately behavior,” said co-senior author Paola Arlotta, the Golub Family Professor of Stem Cell and Regenerative Biology at Harvard. “We applied the Perturb-Seq technology to an intact developing organism for the first time, showing the potential of measuring gene function at scale to better understand a complex disorder.”

The study was also led by co-senior authors Aviv Regev, who was a core member of the Broad Institute during the study and is currently Executive Vice President of Genentech Research and Early Development, and Feng Zhang, a core member of the Broad Institute and an investigator at MIT’s McGovern Institute.

To investigate gene function at a large scale, the researchers combined two powerful genomic technologies. They used CRISPR-Cas9 genome editing to make precise changes, or perturbations, in 35 different genes linked to autism spectrum disorder risk. Then, they analyzed changes in the developing mouse brain using single-cell RNA sequencing, which allowed them to see how gene expression changed in over 40,000 individual cells.

By looking at the level of individual cells, the researchers could compare how the risk genes affected different cell types in the cortex — the part of the brain responsible for complex functions including cognition and sensation. They analyzed networks of risk genes together to find common effects.

“We found that both neurons and glia — the non-neuronal cells in the brain — are directly affected by different sets of these risk genes,” said Xin Jin, lead author of the study and a Junior Fellow of the Harvard Society of Fellows. “Genes and molecules don’t generate cognition per se — they need to impact specific cell types in the brain to do so. We are interested in understanding how these different cell types can contribute to the disorder.”

To get a sense of the model’s potential relevance to the disorder in humans, the researchers compared their results to data from post-mortem human brains. In general, they found that in the post-mortem human brains with autism spectrum disorder, some of the key genes with altered expression were also affected in the Perturb-seq data.

“We now have a really rich dataset that allows us to draw insights, and we’re still learning a lot about it every day,” Jin said. “As we move forward with studying disease mechanisms in more depth, we can focus on the cell types that may be really important.”

“The field has been limited by the sheer time and effort that it takes to make one model at a time to test the function of single genes. Now, we have shown the potential of studying gene function in a developing organism in a scalable way, which is an exciting first step to understanding the mechanisms that lead to autism spectrum disorder and other complex psychiatric conditions, and to eventually develop treatments for these devastating conditions,” said Arlotta, who is also an institute member of the Broad Institute and part of the Broad’s Stanley Center for Psychiatric Research. “Our work also paves the way for Perturb-Seq to be applied to organs beyond the brain, to enable scientists to better understand the development or function of different tissue types, as well as pathological conditions.”

“Through genome sequencing efforts, a very large number of genes have been identified that, when mutated, are associated with human diseases. Traditionally, understanding the role of these genes would involve in-depth studies of each gene individually. By developing Perturb-seq for in vivo applications, we can start to screen all of these genes in animal models in a much more efficient manner, enabling us to understand mechanistically how mutations in these genes can lead to disease,” said Zhang, who is also the James and Patricia Poitras Professor of Neuroscience at MIT and a professor of brain and cognitive sciences and biological engineering at MIT.

This study was funded by the Stanley Center for Psychiatric Research at the Broad Institute, the National Institutes of Health, the Brain and Behavior Research Foundation’s NARSAD Young Investigator Grant, Harvard University’s William F. Milton Fund, the Klarman Cell Observatory, the Howard Hughes Medical Institute, a Center for Cell Circuits grant from the National Human Genome Research Institute’s Centers of Excellence in Genomic Science, the New York Stem Cell Foundation, the Mathers Foundation, the Poitras Center for Psychiatric Disorders Research at MIT, the Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT, and J. and P. Poitras.

Rapid test for Covid-19 shows improved sensitivity

by Anne Trafton |

Since the start of the Covid-19 pandemic, researchers at MIT and the Broad Institute of MIT and Harvard, along with their collaborators at the University of Washington, Fred Hutchinson Cancer Research Center, Brigham and Women’s Hospital, and the Ragon Institute, have been working on a CRISPR-based diagnostic for Covid-19 that can produce results in 30 minutes to an hour, with similar accuracy as the standard PCR diagnostics now used.

The new test, known as STOPCovid, is still in the research stage but, in principle, could be made cheaply enough that people could test themselves every day. In a study appearing today in the New England Journal of Medicine, the researchers showed that on a set of patient samples, their test detected 93 percent of the positive cases as determined by PCR tests for Covid-19.

“We need rapid testing to become part of the fabric of this situation so that people can test themselves every day, which will slow down outbreak,” says Omar Abudayyeh, an MIT McGovern Fellow working on the diagnostic.

Abudayyah is one of the senior authors of the study, along with Jonathan Gootenberg, a McGovern Fellow, and Feng Zhang, a core member of the Broad Institute, investigator at the MIT McGovern Institute and Howard Hughes Medical Institute, and the James and Patricia Poitras ’63 Professor of Neuroscience at MIT. The first authors of the paper are MIT biological engineering graduate students Julia Joung and Alim Ladha in the Zhang lab.

A streamlined test

Zhang’s laboratory began collaborating with the Abudayyeh and Gootenberg laboratory to work on the Covid-19 diagnostic soon after the SARS-CoV-2 outbreak began. They focused on making an assay, called STOPCovid, that was simple to carry out and did not require any specialized laboratory equipment. Such a test, they hoped, would be amenable to future use in point-of-care settings, such as doctors’ offices, pharmacies, nursing homes, and schools.

“We developed STOPCovid so that everything could be done in a single step,” Joung says. “A single step means the test can be potentially performed by nonexperts outside of laboratory settings.”

In the new version of STOPCovid reported today, the researchers incorporated a process to concentrate the viral genetic material in a patient sample by adding magnetic beads that attract RNA, eliminating the need for expensive purification kits that are time-intensive and can be in short supply due to high demand. This concentration step boosted the test’s sensitivity so that it now approaches that of PCR.

“Once we got the viral genomes onto the beads, we found that that could get us to very high levels of sensitivity,” Gootenberg says.

Working with collaborators Keith Jerome at Fred Hutchinson Cancer Research Center and Alex Greninger at the University of Washington, the researchers tested STOPCovid on 402 patient samples — 202 positive and 200 negative — and found that the new test detected 93 percent of the positive cases as determined by the standard CDC PCR test.

“Seeing STOPCovid working on actual patient samples was really gratifying,” Ladha says.

They also showed, working with Ann Woolley and Deb Hung at Brigham and Women’s Hospital, that the STOPCovid test works on samples taken using the less invasive anterior nares swab. They are now testing it with saliva samples, which could make at-home tests even easier to perform. The researchers are continuing to develop the test with the hope of delivering it to end users to help fight the COVID-19 pandemic.

“The goal is to make this test easy to use and sensitive, so that we can tell whether or not someone is carrying the virus as early as possible,” Zhang says.

The research was funded by the National Institutes of Health, the Swiss National Science Foundation, the Patrick J. McGovern Foundation, the McGovern Institute for Brain Research, the Massachusetts Consortium on Pathogen Readiness Evergrande Covid-19 Response Fund, the Mathers Foundation, the Howard Hughes Medical Institute, the Open Philanthropy Project, J. and P. Poitras, and R. Metcalfe.

 

FULL PAPER AT NEJM