Biology

Subterms

    Latest story

    50 Shares129 Views

    Exploring the cellular neighborhood

    by

    Cells rely on complex molecular machines composed of protein assemblies to perform essential functions such as energy production, gene expression, and protein synthesis. To better understand how these machines work, scientists capture snapshots of them by isolating proteins from cells and using various methods to determine their structures. However, isolating proteins from cells also removes them from the context of their native environment, including protein interaction partners and cellular location.

    Recently, cryogenic electron tomography (cryo-ET) has emerged as a way to observe proteins in their native environment by imaging frozen cells at different angles to obtain three-dimensional structural information. This approach is exciting because it allows researchers to directly observe how and where proteins associate with each other, revealing the cellular neighborhood of those interactions within the cell.

    With the technology available to image proteins in their native environment, MIT graduate student Barrett Powell wondered if he could take it one step further: What if molecular machines could be observed in action? In a paper published March 8 in Nature Methods, Powell describes the method he developed, called tomoDRGN, for modeling structural differences of proteins in cryo-ET data that arise from protein motions or proteins binding to different interaction partners. These variations are known as structural heterogeneity. 

    Although Powell had joined the lab of MIT associate professor of biology Joey Davis as an experimental scientist, he recognized the potential impact of computational approaches in understanding structural heterogeneity within a cell. Previously, the Davis Lab developed a related methodology named cryoDRGN to understand structural heterogeneity in purified samples. As Powell and Davis saw cryo-ET rising in prominence in the field, Powell took on the challenge of re-imagining this framework to work in cells.

    When solving structures with purified samples, each particle is imaged only once. By contrast, cryo-ET data is collected by imaging each particle more than 40 times from different angles. That meant tomoDRGN needed to be able to merge the information from more than 40 images, which was where the project hit a roadblock: the amount of data led to an information overload.

    To address this, Powell successfully rebuilt the cryoDRGN model to prioritize only the highest-quality data. When imaging the same particle multiple times, radiation damage occurs. The images acquired earlier, therefore, tend to be of higher quality because the particles are less damaged.

    “By excluding some of the lower-quality data, the results were actually better than using all of the data — and the computational performance was substantially faster,” Powell says.

    Just as Powell was beginning work on testing his model, he had a stroke of luck: The authors of a groundbreaking new study that visualized, for the first time, ribosomes inside cells at near-atomic resolution, shared their raw data on the Electric Microscopy Public Image Archive (EMPIAR). This dataset was an exemplary test case for Powell, through which he demonstrated that tomoDRGN could uncover structural heterogeneity within cryo-ET data. 

    According to Powell, one exciting result is what tomoDRGN found surrounding a subset of ribosomes in the EMPIAR dataset. Some of the ribosomal particles were associated with a bacterial cell membrane and engaged in a process called cotranslational translocation. This occurs when a protein is being simultaneously synthesized and transported across a membrane. Researchers can use this result to make new hypotheses about how the ribosome functions with other protein machinery integral to transporting proteins outside of the cell, now guided by a structure of the complex in its native environment. 

    After seeing that tomoDRGN could resolve structural heterogeneity from a structurally diverse dataset, Powell was curious: How small of a population could tomoDRGN identify? For that test, he chose a protein named apoferritin, which is a commonly used benchmark for cryo-ET and is often treated as structurally homogeneous. Ferritin is a protein used for iron storage and is referred to as apoferritin when it lacks iron.

    Surprisingly, in addition to the expected particles, tomoDRGN revealed a minor population of ferritin particles — with iron bound — making up just 2 percent of the dataset, that was not previously reported. This result further demonstrated tomoDRGN’s ability to identify structural states that occur so infrequently that they would be averaged out of a 3D reconstruction. 

    Powell and other members of the Davis Lab are excited to see how tomoDRGN can be applied to further ribosomal studies and to other systems. Davis works on understanding how cells assemble, regulate, and degrade molecular machines, so the next steps include exploring ribosome biogenesis within cells in greater detail using this new tool.

    “What are the possible states that we may be losing during purification?” Davis asks. “Perhaps more excitingly, we can look at how they localize within the cell and what partners and protein complexes they may be interacting with.” More

    More stories

    • 138 Shares159 Views

      in Data Management & Statistics

      Creating new skills and new connections with MIT’s Quantitative Methods Workshop

      by

      Starting on New Year’s Day, when many people were still clinging to holiday revelry, scores of students and faculty members from about a dozen partner universities instead flipped open their laptops for MIT’s Quantitative Methods Workshop, a jam-packed, weeklong introduction to how computational and mathematical techniques can be applied to neuroscience and biology research. But don’t think of QMW as a “crash course.” Instead the program’s purpose is to help elevate each participant’s scientific outlook, both through the skills and concepts it imparts and the community it creates.

      “It broadens their horizons, it shows them significant applications they’ve never thought of, and introduces them to people whom as researchers they will come to know and perhaps collaborate with one day,” says Susan L. Epstein, a Hunter College computer science professor and education coordinator of MIT’s Center for Brains, Minds, and Machines, which hosts the program with the departments of Biology and Brain and Cognitive Sciences and The Picower Institute for Learning and Memory. “It is a model of interdisciplinary scholarship.”

      This year 83 undergraduates and faculty members from institutions that primarily serve groups underrepresented in STEM fields took part in the QMW, says organizer Mandana Sassanfar, senior lecturer and director of diversity and science outreach across the four hosting MIT entities. Since the workshop launched in 2010, it has engaged more than 1,000 participants, of whom more than 170 have gone on to participate in MIT Summer Research Programs (such as MSRP-BIO), and 39 have come to MIT for graduate school.

      Individual goals, shared experience

      Undergraduates and faculty in various STEM disciplines often come to QMW to gain an understanding of, or expand their expertise in, computational and mathematical data analysis. Computer science- and statistics-minded participants come to learn more about how such techniques can be applied in life sciences fields. In lectures; in hands-on labs where they used the computer programming language Python to process, analyze, and visualize data; and in less formal settings such as tours and lunches with MIT faculty, participants worked and learned together, and informed each other’s perspectives.

      Brain and Cognitive Sciences Professor Nancy Kanwisher delivers a lecture in MIT’s Building 46 on functional brain imaging to QMW participants.

      Photo: Mandana Sassanfar

      Previous item
      Next item

      And regardless of their field of study, participants made connections with each other and with the MIT students and faculty who taught and spoke over the course of the week.

      Hunter College computer science sophomore Vlad Vostrikov says that while he has already worked with machine learning and other programming concepts, he was interested to “branch out” by seeing how they are used to analyze scientific datasets. He also valued the chance to learn the experiences of the graduate students who teach QMW’s hands-on labs.

      “This was a good way to explore computational biology and neuroscience,” Vostrikov says. “I also really enjoy hearing from the people who teach us. It’s interesting to hear where they come from and what they are doing.”

      Jariatu Kargbo, a biology and chemistry sophomore at University of Maryland Baltimore County, says when she first learned of the QMW she wasn’t sure it was for her. It seemed very computation-focused. But her advisor Holly Willoughby encouraged Kargbo to attend to learn about how programming could be useful in future research — currently she is taking part in research on the retina at UMBC. More than that, Kargbo also realized it would be a good opportunity to make connections at MIT in advance of perhaps applying for MSRP this summer.

      “I thought this would be a great way to meet up with faculty and see what the environment is like here because I’ve never been to MIT before,” Kargbo says. “It’s always good to meet other people in your field and grow your network.”

      QMW is not just for students. It’s also for their professors, who said they can gain valuable professional education for their research and teaching.

      Fayuan Wen, an assistant professor of biology at Howard University, is no stranger to computational biology, having performed big data genetic analyses of sickle cell disease (SCD). But she’s mostly worked with the R programming language and QMW’s focus is on Python. As she looks ahead to projects in which she wants analyze genomic data to help predict disease outcomes in SCD and HIV, she says a QMW session delivered by biology graduate student Hannah Jacobs was perfectly on point.

      “This workshop has the skills I want to have,” Wen says.

      Moreover, Wen says she is looking to start a machine-learning class in the Howard biology department and was inspired by some of the teaching materials she encountered at QMW — for example, online curriculum modules developed by Taylor Baum, an MIT graduate student in electrical engineering and computer science and Picower Institute labs, and Paloma Sánchez-Jáuregui, a coordinator who works with Sassanfar.

      Tiziana Ligorio, a Hunter College computer science doctoral lecturer who together with Epstein teaches a deep machine-learning class at the City University of New York campus, felt similarly. Rather than require a bunch of prerequisites that might drive students away from the class, Ligorio was looking to QMW’s intense but introductory curriculum as a resource for designing a more inclusive way of getting students ready for the class.

      Instructive interactions

      Each day runs from 9 a.m. to 5 p.m., including morning and afternoon lectures and hands-on sessions. Class topics ranged from statistical data analysis and machine learning to brain-computer interfaces, brain imaging, signal processing of neural activity data, and cryogenic electron microscopy.

      “This workshop could not happen without dedicated instructors — grad students, postdocs, and faculty — who volunteer to give lectures, design and teach hands-on computer labs, and meet with students during the very first week of January,” Saassanfar says.

      MIT assistant professor of biology Brady Weissbourd (center) converses with QMW student participants during a lunch break.

      Photo: Mandana Sassanfar

      Previous item
      Next item

      The sessions surround student lunches with MIT faculty members. For example, at midday Jan. 2, assistant professor of biology Brady Weissbourd, an investigator in the Picower Institute, sat down with seven students in one of Building 46’s curved sofas to field questions about his neuroscience research in jellyfish and how he uses quantitative techniques as part of that work. He also described what it’s like to be a professor, and other topics that came to the students’ minds.

      Then the participants all crossed Vassar Street to Building 26’s Room 152, where they formed different but similarly sized groups for the hands-on lab “Machine learning applications to studying the brain,” taught by Baum. She guided the class through Python exercises she developed illustrating “supervised” and “unsupervised” forms of machine learning, including how the latter method can be used to discern what a person is seeing based on magnetic readings of brain activity.

      As students worked through the exercises, tablemates helped each other by supplementing Baum’s instruction. Ligorio, Vostrikov, and Kayla Blincow, assistant professor of biology at the University of the Virgin Islands, for instance, all leapt to their feet to help at their tables.

      Hunter College lecturer of computer science Tiziana Ligorio (standing) explains a Python programming concept to students at her table during a workshop session.

      Photo: David Orenstein

      Previous item
      Next item

      At the end of the class, when Baum asked students what they had learned, they offered a litany of new knowledge. Survey data that Sassanfar and Sánchez-Jáuregui use to anonymously track QMW outcomes, revealed many more such attestations of the value of the sessions. With a prompt asking how one might apply what they’ve learned, one respondent wrote: “Pursue a research career or endeavor in which I apply the concepts of computer science and neuroscience together.”

      Enduring connections

      While some new QMW attendees might only be able to speculate about how they’ll apply their new skills and relationships, Luis Miguel de Jesús Astacio could testify to how attending QMW as an undergraduate back in 2014 figured into a career where he is now a faculty member in physics at the University of Puerto Rico Rio Piedras Campus. After QMW, he returned to MIT that summer as a student in the lab of neuroscientist and Picower Professor Susumu Tonegawa. He came back again in 2016 to the lab of physicist and Francis Friedman Professor Mehran Kardar. What’s endured for the decade has been his connection to Sassanfar. So while he was once a student at QMW, this year he was back with a cohort of undergraduates as a faculty member.

      Michael Aldarondo-Jeffries, director of academic advancement programs at the University of Central Florida, seconded the value of the networking that takes place at QMW. He has brought students for a decade, including four this year. What he’s observed is that as students come together in settings like QMW or UCF’s McNair program, which helps to prepare students for graduate school, they become inspired about a potential future as researchers.

      “The thing that stands out is just the community that’s formed,” he says. “For many of the students, it’s the first time that they’re in a group that understands what they’re moving toward. They don’t have to explain why they’re excited to read papers on a Friday night.”

      Or why they are excited to spend a week including New Year’s Day at MIT learning how to apply quantitative methods to life sciences data. More

    • 125 Shares199 Views

      in Data Management & Statistics

      Search algorithm reveals nearly 200 new kinds of CRISPR systems

      by

      Microbial sequence databases contain a wealth of information about enzymes and other molecules that could be adapted for biotechnology. But these databases have grown so large in recent years that they’ve become difficult to search efficiently for enzymes of interest.

      Now, scientists at the McGovern Institute for Brain Research at MIT, the Broad Institute of MIT and Harvard, and the National Center for Biotechnology Information (NCBI) at the National Institutes of Health have developed a new search algorithm that has identified 188 kinds of new rare CRISPR systems in bacterial genomes, encompassing thousands of individual systems. The work appears today in Science.

      The algorithm, which comes from the lab of pioneering CRISPR researcher Professor Feng Zhang, uses big-data clustering approaches to rapidly search massive amounts of genomic data. The team used their algorithm, called Fast Locality-Sensitive Hashing-based clustering (FLSHclust) to mine three major public databases that contain data from a wide range of unusual bacteria, including ones found in coal mines, breweries, Antarctic lakes, and dog saliva. The scientists found a surprising number and diversity of CRISPR systems, including ones that could make edits to DNA in human cells, others that can target RNA, and many with a variety of other functions.

      The new systems could potentially be harnessed to edit mammalian cells with fewer off-target effects than current Cas9 systems. They could also one day be used as diagnostics or serve as molecular records of activity inside cells.

      The researchers say their search highlights an unprecedented level of diversity and flexibility of CRISPR and that there are likely many more rare systems yet to be discovered as databases continue to grow.

      “Biodiversity is such a treasure trove, and as we continue to sequence more genomes and metagenomic samples, there is a growing need for better tools, like FLSHclust, to search that sequence space to find the molecular gems,” says Zhang, a co-senior author on the study and the James and Patricia Poitras Professor of Neuroscience at MIT with joint appointments in the departments of Brain and Cognitive Sciences and Biological Engineering. Zhang is also an investigator at the McGovern Institute for Brain Research at MIT, a core institute member at the Broad, and an investigator at the Howard Hughes Medical Institute. Eugene Koonin, a distinguished investigator at the NCBI, is co-senior author on the study as well.

      Searching for CRISPR

      CRISPR, which stands for clustered regularly interspaced short palindromic repeats, is a bacterial defense system that has been engineered into many tools for genome editing and diagnostics.

      To mine databases of protein and nucleic acid sequences for novel CRISPR systems, the researchers developed an algorithm based on an approach borrowed from the big data community. This technique, called locality-sensitive hashing, clusters together objects that are similar but not exactly identical. Using this approach allowed the team to probe billions of protein and DNA sequences — from the NCBI, its Whole Genome Shotgun database, and the Joint Genome Institute — in weeks, whereas previous methods that look for identical objects would have taken months. They designed their algorithm to look for genes associated with CRISPR.

      “This new algorithm allows us to parse through data in a time frame that’s short enough that we can actually recover results and make biological hypotheses,” says Soumya Kannan PhD ’23, who is a co-first author on the study. Kannan was a graduate student in Zhang’s lab when the study began and is currently a postdoc and Junior Fellow at Harvard University. Han Altae-Tran PhD ’23, a graduate student in Zhang’s lab during the study and currently a postdoc at the University of Washington, was the study’s other co-first author.

      “This is a testament to what you can do when you improve on the methods for exploration and use as much data as possible,” says Altae-Tran. “It’s really exciting to be able to improve the scale at which we search.”

      New systems

      In their analysis, Altae-Tran, Kannan, and their colleagues noticed that the thousands of CRISPR systems they found fell into a few existing and many new categories. They studied several of the new systems in greater detail in the lab.

      They found several new variants of known Type I CRISPR systems, which use a guide RNA that is 32 base pairs long rather than the 20-nucleotide guide of Cas9. Because of their longer guide RNAs, these Type I systems could potentially be used to develop more precise gene-editing technology that is less prone to off-target editing. Zhang’s team showed that two of these systems could make short edits in the DNA of human cells. And because these Type I systems are similar in size to CRISPR-Cas9, they could likely be delivered to cells in animals or humans using the same gene-delivery technologies being used today for CRISPR.

      One of the Type I systems also showed “collateral activity” — broad degradation of nucleic acids after the CRISPR protein binds its target. Scientists have used similar systems to make infectious disease diagnostics such as SHERLOCK, a tool capable of rapidly sensing a single molecule of DNA or RNA. Zhang’s team thinks the new systems could be adapted for diagnostic technologies as well.

      The researchers also uncovered new mechanisms of action for some Type IV CRISPR systems, and a Type VII system that precisely targets RNA, which could potentially be used in RNA editing. Other systems could potentially be used as recording tools — a molecular document of when a gene was expressed — or as sensors of specific activity in a living cell.

      Mining data

      The scientists say their algorithm could aid in the search for other biochemical systems. “This search algorithm could be used by anyone who wants to work with these large databases for studying how proteins evolve or discovering new genes,” Altae-Tran says.

      The researchers add that their findings illustrate not only how diverse CRISPR systems are, but also that most are rare and only found in unusual bacteria. “Some of these microbial systems were exclusively found in water from coal mines,” Kannan says. “If someone hadn’t been interested in that, we may never have seen those systems. Broadening our sampling diversity is really important to continue expanding the diversity of what we can discover.”

      This work was supported by the Howard Hughes Medical Institute; the K. Lisa Yang and Hock E. Tan Molecular Therapeutics Center at MIT; Broad Institute Programmable Therapeutics Gift Donors; The Pershing Square Foundation, William Ackman and Neri Oxman; James and Patricia Poitras; BT Charitable Foundation; Asness Family Foundation; Kenneth C. Griffin; the Phillips family; David Cheng; and Robert Metcalfe. More

    • 100 Shares119 Views

      in Data Management & Statistics

      Summer research offers a springboard to advanced studies

      by

      Doctoral studies at MIT aren’t a calling for everyone, but they can be for anyone who has had opportunities to discover that science and technology research is their passion and to build the experience and skills to succeed. For Taylor Baum, Josefina Correa Menéndez, and Karla Alejandra Montejo, three graduate students in just one lab of The Picower Institute for Learning and Memory, a pivotal opportunity came via the MIT Summer Research Program in Biology and Neuroscience (MSRP-Bio). When a student finds MSRP-Bio, it helps them find their future in research. 

      In the program, undergraduate STEM majors from outside MIT spend the summer doing full-time research in the departments of Biology, Brain and Cognitive Sciences (BCS), or the Center for Brains, Minds and Machines (CBMM). They gain lab skills, mentoring, preparation for graduate school, and connections that might last a lifetime. Over the last two decades, a total of 215 students from underrepresented minority groups, who are from economically disadvantaged backgrounds, first-generation or nontraditional college students, or students with disabilities have participated in research in BCS or CBMM labs.  

      Like Baum, Correa Menéndez, and Montejo, the vast majority go on to pursue graduate studies, says Diversity and Outreach Coordinator Mandana Sassanfar, who runs the program. For instance, among 91 students who have worked in Picower Institute labs, 81 have completed their undergraduate studies. Of those, 46 enrolled in PhD programs at MIT or other schools such as Cornell, Yale, Stanford, and Princeton universities, and the University of California System. Another 12 have gone to medical school, another seven are in MD/PhD programs, and three have earned master’s degrees. The rest are studying as post-baccalaureates or went straight into the workforce after earning their bachelor’s degree. 

      After participating in the program, Baum, Correa Menéndez, and Montejo each became graduate students in the research group of Emery N. Brown, the Edward Hood Taplin Professor of Computational Neuroscience and Medical Engineering in The Picower Institute and the Institute for Medical Engineering and Science. The lab combines statistical, computational, and experimental neuroscience methods to study how general anesthesia affects the central nervous system to ultimately improve patient care and advance understanding of the brain. Brown says the students have each been doing “off-the-scale” work, in keeping with the excellence he’s seen from MSRP BIO students over the years. For example, on Aug. 10 Baum and Correa Menéndez were honored with MathWorks Fellowships.

      “I think MSRP is fantastic. Mandana does this amazing job of getting students who are quite talented to come to MIT to realize that they can move their game to the next level. They have the capacity to do it. They just need the opportunities,” Brown says. “These students live up to the expectations that you have of them. And now as graduate students, they’re taking on hard problems and they’re solving them.” 

      Paths to PhD studies 

      Pursuing a PhD is hardly a given. Many young students have never considered graduate school or specific fields of study like neuroscience or electrical engineering. But Sassanfar engages students across the country to introduce them to the opportunity MSRP-Bio provides to gain exposure, experience, and mentoring in advanced fields. Every fall, after the program’s students have returned to their undergraduate institutions, she visits schools in places as far flung as Florida, Maryland, Puerto Rico, and Texas and goes to conferences for diverse science communities such as ABRCMS and SACNAS to spread the word. 

      Taylor Baum

      Photo courtesy of Taylor Baum.

      Previous item
      Next item

      When Baum first connected with the program in 2017, she was finding her way at Penn State University. She had been majoring in biology and music composition but had just switched the latter to engineering following a conversation over coffee exposing her to brain-computer interfacing technology, in which detecting brain signals of people with full-body paralysis could improve their quality of life by enabling control of computers or wheelchairs. Baum became enthusiastic about the potential to build similar systems, but as a new engineering student, she struggled to find summer internships and research opportunities. 

      “I got rejected from every single progam except the MIT Center for Brains, Minds and Machines MSRP,” she recalls with a chuckle. 

      Baum thrived in MSRP-Bio, working in Brown’s lab for three successive summers. At each stage, she said, she gained more research skills, experience, and independence. When she graduated, she was sure she wanted to go to graduate school and applied to four of her dream schools. She accepted MIT’s offer to join the Department of Electrical Engineering and Computer Science, where she is co-advised by faculty members there and by Brown. She is now working to develop a system grounded in cardiovascular physiology that can improve blood pressure management. A tool for practicing anesthesiologists, the system automates the dosing of drugs to maintain a patient’s blood pressure at safe levels in the operating room or intensive care unit. 

      More than that, Baum not only is leading an organization advancing STEM education in Puerto Rico, but also is helping to mentor a current MSRP-Bio student in the Brown lab. 

      “MSRP definitely bonds everyone who has participated in it,” Baum says. “If I see anyone who I know participated in MSRP, we could have an immediate conversation. I know that most of us, if we needed help, we’d feel comfortable asking for help from someone from MSRP. With that shared experience, we have a sense of camaraderie, and community.” 

      In fact, a few years ago when a former MSRP-Bio student named Karla Montejo was applying to MIT, Baum provided essential advice and feedback about the application process, Montejo says. Now, as a graduate student, Montejo has become a mentor for the program in her own right, Sassanfar notes. For instance, Montejo serves on program alumni panels that advise new MSRP-Bio students. 

      Karla Alejandra Montejo

      Photo courtesy of Karla Alejandra Montejo.

      Previous item
      Next item

      Montejo’s family immigrated to Miami from Cuba when she was a child. The magnet high school she attended was so new that students were encouraged to help establish the school’s programs. She forged a path into research. 

      “I didn’t even know what research was,” she says. “I wanted to be a doctor, and I thought maybe it would help me on my resume. I thought it would be kind of like shadowing, but no, it was really different. So I got really captured by research when I was in high school.” 

      Despite continuing to pursue research in college at Florida International University, Montejo didn’t get into graduate school on her first attempt because she hadn’t yet learned how to focus her application. But Sassanfar had visited FIU to recruit students and through that relationship Montejo had already gone through MIT’s related Quantitative Methods Workshop (QMW). So Montejo enrolled in MSRP-Bio, working in the CBMM-affiliated lab of Gabriel Kreiman at Boston Children’s Hospital. 

      “I feel like Mandana really helped me out, gave me a break, and the MSRP experience pretty much solidified that I really wanted to come to MIT,” Montejo says. 

      In the QMW, Montejo learned she really liked computational neuroscience, and in Kreiman’s lab she got to try her hand at computational modeling of the cognition involved in making perceptual sense of complex scenes. Montejo realized she wanted to work on more biologically based neuroscience problems. When the summer ended, because she was off the normal graduate school cycle for now, she found a two-year post-baccalaurate program at Mayo Clinic studying the role a brain cell type called astrocytes might have in the Parkinson’s disease treatment deep brain stimulation. 

      When it came time to reapply to graduate schools (with the help of Baum and others in the BCS Application Assistance Program) Montejo applied to MIT and got in, joining the Brown lab. Now she’s working on modeling the role of  metabolic processes in the changing of brain rhythms under anesthesia, taking advantage of how general anesthesia predictably changes brain states. The effects anesthetic drugs have on cell metabolism and the way that ultimately affects levels of consciousness reveals important aspects of how metabolism affects brain circuits and systems. Earlier this month, for instance, Montejo co-led a paper the lab published in The Proceedings of the National Academy of Sciences detailing the neuroscience of a patient’s transition into an especially deep state of unconsciousness called “burst suppression.” 

      Josefina Correa Menendez

      Photo: David Orenstein

      Previous item
      Next item

      A signature of the Brown lab’s work is rigorous statistical analysis and methods, for instance to discern brain arousal states from EEG measures of brain rhythms. A PhD candidate in MIT’s Interdisciplinary Doctoral Program in Statistics, Correa Menéndez is advancing the use of Bayesian hierarchical models for neural data analysis. These statistical models offer a principled way of pooling information across datasets. One of her models can help scientists better understand the way neurons can “spike” with electrical activity when the brain is presented with a stimulus. The other’s power is in discerning critical features such as arousal states of the brain under general anesthesia from electrophysiological recordings. 

      Though she now works with complex equations and computations as a PhD candidate in neuroscience and statistics, Correa Menéndez was mostly interested in music art as a high school student at Academia María Reina in San Juan and then architecture in college at the University of Puerto Rico at Río Piedras. It was discussions at the intersection of epistemology and art during an art theory class that inspired Correa Menéndez to switch her major to biology and to take computer science classes, too. 

      When Sassanfar visited Puerto Rico in 2017, a computer science professor (Patricia Ordóñez) suggested that Correa Menéndez apply for a chance to attend the QMW. She did, and that led her to also participate in MSRP-Bio in the lab of Sherman Fairchild Professor Matt Wilson (a faculty member in BCS, CBMM, and the Picower Institute). She joined in the lab’s studies of how spatial memories are represented in the hippocampus and how the brain makes use of those memories to help understand the world around it. With mentoring from then-postdoc Carmen Varela (now a faculty member at Florida State University), the experience not only exposed her to neuroscience, but also helped her gain skills and experience with lab experiments, building research tools, and conducting statistical analyses. She ended up working in the Wilson lab as a research scholar for a year and began her graduate studies in September 2018.  

      Classes she took with Brown as a research scholar inspired her to join his lab as a graduate student. 

      “Taking the classes with Emery and also doing experiments made me aware of the role of statistics in the scientific process: from the interpretation of results to the analysis and the design of experiments,” she says. “More often than not, in science, statistics becomes this sort of afterthought — this ‘annoying’ thing that people need to do to get their paper published. But statistics as a field is actually a lot more than that. It’s a way of thinking about data. Particularly, Bayesian modeling provides a principled inference framework for combining prior knowledge into a hypothesis that you can test with data.” 

      To be sure, no one starts out with such inspiration about scientific scholarship, but MSRP-Bio helps students find that passion for research and the paths that opens up.   More

    • 63 Shares169 Views

      in Data Management & Statistics

      Making sense of cell fate

      by

      Despite the proliferation of novel therapies such as immunotherapy or targeted therapies, radiation and chemotherapy remain the frontline treatment for cancer patients. About half of all patients still receive radiation and 60-80 percent receive chemotherapy.

      Both radiation and chemotherapy work by damaging DNA, taking advantage of a vulnerability specific to cancer cells. Healthy cells are more likely to survive radiation and chemotherapy since their mechanisms for identifying and repairing DNA damage are intact. In cancer cells, these repair mechanisms are compromised by mutations. When cancer cells cannot adequately respond to the DNA damage caused by radiation and chemotherapy, ideally, they undergo apoptosis or die by other means.

      However, there is another fate for cells after DNA damage: senescence — a state where cells survive, but stop dividing. Senescent cells’ DNA has not been damaged enough to induce apoptosis but is too damaged to support cell division. While senescent cancer cells themselves are unable to proliferate and spread, they are bad actors in the fight against cancer because they seem to enable other cancer cells to develop more aggressively. Although a cancer cell’s fate is not apparent until a few days after treatment, the decision to survive, die, or enter senescence is made much earlier. But, precisely when and how that decision is made has not been well understood.

      In an open-access study of ovarian and osteosarcoma cancer cells appearing July 19 in Cell Systems, MIT researchers show that cell signaling proteins commonly associated with cell proliferation and apoptosis instead commit cancer cells to senescence within 12 hours of treatment with low doses of certain kinds of chemotherapy.

      “When it comes to treating cancer, this study underscores that it’s important not to think too linearly about cell signaling,” says Michael Yaffe, who is a David H. Koch Professor of Science at MIT, the director of the MIT Center for Precision Cancer Medicine, a member of MIT’s Koch Institute for Integrative Cancer Research, and the senior author of the study. “If you assume that a particular treatment will always affect cancer cell signaling in the same way — you may be setting yourself up for many surprises, and treating cancers with the wrong combination of drugs.”

      Using a combination of experiments with cancer cells and computational modeling, the team investigated the cell signaling mechanisms that prompt cancer cells to enter senescence after treatment with a commonly used anti-cancer agent. Their efforts singled out two protein kinases and a component of the AP-1 transcription factor complex as highly associated with the induction of senescence after DNA damage, despite the well-established roles for all of these molecules in promoting cell proliferation in cancer.

      The researchers treated cancer cells with low and high doses of doxorubicin, a chemotherapy that interferes with the function with topoisomerase II, an enzyme that breaks and then repairs DNA strands during replication to fix tangles and other topological problems.

      By measuring the effects of DNA damage on single cells at several time points ranging from six hours to four days after the initial exposure, the team created two datasets. In one dataset, the researchers tracked cell fate over time. For the second set, researchers measured relative cell signaling activity levels across a variety of proteins associated with responses to DNA damage or cellular stress, determination of cell fate, and progress through cell growth and division.

      The two datasets were used to build a computational model that identifies correlations between time, dosage, signal, and cell fate. The model identified the activities of the MAP kinases Erk and JNK, and the transcription factor c-Jun as key components of the AP-1 protein likewise understood to involved in the induction of senescence. The researchers then validated these computational findings by showing that inhibition of JNK and Erk after DNA damage successfully prevented cells from entering senescence.

      The researchers leveraged JNK and Erk inhibition to pinpoint exactly when cells made the decision to enter senescence. Surprisingly, they found that the decision to enter senescence was made within 12 hours of DNA damage, even though it took days to actually see the senescent cells accumulate. The team also found that with the passage of more time, these MAP kinases took on a different function: promoting the secretion of proinflammatory proteins called cytokines that are responsible for making other cancer cells proliferate and develop resistance to chemotherapy.

      “Proteins like cytokines encourage ‘bad behavior’ in neighboring tumor cells that lead to more aggressive cancer progression,” says Tatiana Netterfield, a graduate student in the Yaffe lab and the lead author of the study. “Because of this, it is thought that senescent cells that stay near the tumor for long periods of time are detrimental to treating cancer.”

      This study’s findings apply to cancer cells treated with a commonly used type of chemotherapy that stalls DNA replication after repair. But more broadly, the study emphasizes that “when treating cancer, it’s extremely important to understand the molecular characteristics of cancer cells and the contextual factors such as time and dosing that determine cell fate,” explains Netterfield.

      The study, however, has more immediate implications for treatments that are already in use. One class of Erk inhibitors, MEK inhibitors, are used in the clinic with the expectation that they will curb cancer growth.

      “We must be cautious about administering MEK inhibitors together with chemotherapies,” says Yaffe. “The combination may have the unintended effect of driving cells into proliferation, rather than senescence.”

      In future work, the team will perform studies to understand how and why individual cells choose to proliferate instead of enter senescence. Additionally, the team is employing next-generation sequencing to understand which genes c-Jun is regulating in order to push cells toward senescence.

      This study was funded, in part, by the Charles and Marjorie Holloway Foundation and the MIT Center for Precision Cancer Medicine. More

    • 138 Shares199 Views

      in Data Management & Statistics

      Bringing the social and ethical responsibilities of computing to the forefront

      by

      There has been a remarkable surge in the use of algorithms and artificial intelligence to address a wide range of problems and challenges. While their adoption, particularly with the rise of AI, is reshaping nearly every industry sector, discipline, and area of research, such innovations often expose unexpected consequences that involve new norms, new expectations, and new rules and laws.

      To facilitate deeper understanding, the Social and Ethical Responsibilities of Computing (SERC), a cross-cutting initiative in the MIT Schwarzman College of Computing, recently brought together social scientists and humanists with computer scientists, engineers, and other computing faculty for an exploration of the ways in which the broad applicability of algorithms and AI has presented both opportunities and challenges in many aspects of society.

      “The very nature of our reality is changing. AI has the ability to do things that until recently were solely the realm of human intelligence — things that can challenge our understanding of what it means to be human,” remarked Daniel Huttenlocher, dean of the MIT Schwarzman College of Computing, in his opening address at the inaugural SERC Symposium. “This poses philosophical, conceptual, and practical questions on a scale not experienced since the start of the Enlightenment. In the face of such profound change, we need new conceptual maps for navigating the change.”

      The symposium offered a glimpse into the vision and activities of SERC in both research and education. “We believe our responsibility with SERC is to educate and equip our students and enable our faculty to contribute to responsible technology development and deployment,” said Georgia Perakis, the William F. Pounds Professor of Management in the MIT Sloan School of Management, co-associate dean of SERC, and the lead organizer of the symposium. “We’re drawing from the many strengths and diversity of disciplines across MIT and beyond and bringing them together to gain multiple viewpoints.”

      Through a succession of panels and sessions, the symposium delved into a variety of topics related to the societal and ethical dimensions of computing. In addition, 37 undergraduate and graduate students from a range of majors, including urban studies and planning, political science, mathematics, biology, electrical engineering and computer science, and brain and cognitive sciences, participated in a poster session to exhibit their research in this space, covering such topics as quantum ethics, AI collusion in storage markets, computing waste, and empowering users on social platforms for better content credibility.

      Showcasing a diversity of work

      In three sessions devoted to themes of beneficent and fair computing, equitable and personalized health, and algorithms and humans, the SERC Symposium showcased work by 12 faculty members across these domains.

      One such project from a multidisciplinary team of archaeologists, architects, digital artists, and computational social scientists aimed to preserve endangered heritage sites in Afghanistan with digital twins. The project team produced highly detailed interrogable 3D models of the heritage sites, in addition to extended reality and virtual reality experiences, as learning resources for audiences that cannot access these sites.

      In a project for the United Network for Organ Sharing, researchers showed how they used applied analytics to optimize various facets of an organ allocation system in the United States that is currently undergoing a major overhaul in order to make it more efficient, equitable, and inclusive for different racial, age, and gender groups, among others.

      Another talk discussed an area that has not yet received adequate public attention: the broader implications for equity that biased sensor data holds for the next generation of models in computing and health care.

      A talk on bias in algorithms considered both human bias and algorithmic bias, and the potential for improving results by taking into account differences in the nature of the two kinds of bias.

      Other highlighted research included the interaction between online platforms and human psychology; a study on whether decision-makers make systemic prediction mistakes on the available information; and an illustration of how advanced analytics and computation can be leveraged to inform supply chain management, operations, and regulatory work in the food and pharmaceutical industries.

      Improving the algorithms of tomorrow

      “Algorithms are, without question, impacting every aspect of our lives,” said Asu Ozdaglar, deputy dean of academics for the MIT Schwarzman College of Computing and head of the Department of Electrical Engineering and Computer Science, in kicking off a panel she moderated on the implications of data and algorithms.

      “Whether it’s in the context of social media, online commerce, automated tasks, and now a much wider range of creative interactions with the advent of generative AI tools and large language models, there’s little doubt that much more is to come,” Ozdaglar said. “While the promise is evident to all of us, there’s a lot to be concerned as well. This is very much time for imaginative thinking and careful deliberation to improve the algorithms of tomorrow.”

      Turning to the panel, Ozdaglar asked experts from computing, social science, and data science for insights on how to understand what is to come and shape it to enrich outcomes for the majority of humanity.

      Sarah Williams, associate professor of technology and urban planning at MIT, emphasized the critical importance of comprehending the process of how datasets are assembled, as data are the foundation for all models. She also stressed the need for research to address the potential implication of biases in algorithms that often find their way in through their creators and the data used in their development. “It’s up to us to think about our own ethical solutions to these problems,” she said. “Just as it’s important to progress with the technology, we need to start the field of looking at these questions of what biases are in the algorithms? What biases are in the data, or in that data’s journey?”

      Shifting focus to generative models and whether the development and use of these technologies should be regulated, the panelists — which also included MIT’s Srini Devadas, professor of electrical engineering and computer science, John Horton, professor of information technology, and Simon Johnson, professor of entrepreneurship — all concurred that regulating open-source algorithms, which are publicly accessible, would be difficult given that regulators are still catching up and struggling to even set guardrails for technology that is now 20 years old.

      Returning to the question of how to effectively regulate the use of these technologies, Johnson proposed a progressive corporate tax system as a potential solution. He recommends basing companies’ tax payments on their profits, especially for large corporations whose massive earnings go largely untaxed due to offshore banking. By doing so, Johnson said that this approach can serve as a regulatory mechanism that discourages companies from trying to “own the entire world” by imposing disincentives.

      The role of ethics in computing education

      As computing continues to advance with no signs of slowing down, it is critical to educate students to be intentional in the social impact of the technologies they will be developing and deploying into the world. But can one actually be taught such things? If so, how?

      Caspar Hare, professor of philosophy at MIT and co-associate dean of SERC, posed this looming question to faculty on a panel he moderated on the role of ethics in computing education. All experienced in teaching ethics and thinking about the social implications of computing, each panelist shared their perspective and approach.

      A strong advocate for the importance of learning from history, Eden Medina, associate professor of science, technology, and society at MIT, said that “often the way we frame computing is that everything is new. One of the things that I do in my teaching is look at how people have confronted these issues in the past and try to draw from them as a way to think about possible ways forward.” Medina regularly uses case studies in her classes and referred to a paper written by Yale University science historian Joanna Radin on the Pima Indian Diabetes Dataset that raised ethical issues on the history of that particular collection of data that many don’t consider as an example of how decisions around technology and data can grow out of very specific contexts.

      Milo Phillips-Brown, associate professor of philosophy at Oxford University, talked about the Ethical Computing Protocol that he co-created while he was a SERC postdoc at MIT. The protocol, a four-step approach to building technology responsibly, is designed to train computer science students to think in a better and more accurate way about the social implications of technology by breaking the process down into more manageable steps. “The basic approach that we take very much draws on the fields of value-sensitive design, responsible research and innovation, participatory design as guiding insights, and then is also fundamentally interdisciplinary,” he said.

      Fields such as biomedicine and law have an ethics ecosystem that distributes the function of ethical reasoning in these areas. Oversight and regulation are provided to guide front-line stakeholders and decision-makers when issues arise, as are training programs and access to interdisciplinary expertise that they can draw from. “In this space, we have none of that,” said John Basl, associate professor of philosophy at Northeastern University. “For current generations of computer scientists and other decision-makers, we’re actually making them do the ethical reasoning on their own.” Basl commented further that teaching core ethical reasoning skills across the curriculum, not just in philosophy classes, is essential, and that the goal shouldn’t be for every computer scientist be a professional ethicist, but for them to know enough of the landscape to be able to ask the right questions and seek out the relevant expertise and resources that exists.

      After the final session, interdisciplinary groups of faculty, students, and researchers engaged in animated discussions related to the issues covered throughout the day during a reception that marked the conclusion of the symposium. More

    • 125 Shares109 Views

      in Data Management & Statistics

      Four from MIT receive NIH New Innovator Awards for 2022

      by

      The National Institutes of Health (NIH) has awarded grants to four MIT faculty members as part of its High-Risk, High-Reward Research program.

      The program supports unconventional approaches to challenges in biomedical, behavioral, and social sciences. Each year, NIH Director’s Awards are granted to program applicants who propose high-risk, high-impact research in areas relevant to the NIH’s mission. In doing so, the NIH encourages innovative proposals that, due to their inherent risk, might struggle in the traditional peer-review process.

      This year, Lindsay Case, Siniša Hrvatin, Deblina Sarkar, and Caroline Uhler have been chosen to receive the New Innovator Award, which funds exceptionally creative research from early-career investigators. The award, which was established in 2007, supports researchers who are within 10 years of their final degree or clinical residency and have not yet received a research project grant or equivalent NIH grant.

      Lindsay Case, the Irwin and Helen Sizer Department of Biology Career Development Professor and an extramural member of the Koch Institute for Integrative Cancer Research, uses biochemistry and cell biology to study the spatial organization of signal transduction. Her work focuses on understanding how signaling molecules assemble into compartments with unique biochemical and biophysical properties to enable cells to sense and respond to information in their environment. Earlier this year, Case was one of two MIT assistant professors named as Searle Scholars.

      Siniša Hrvatin, who joined the School of Science faculty this past winter, is an assistant professor in the Department of Biology and a core member at the Whitehead Institute for Biomedical Research. He studies how animals and cells enter, regulate, and survive states of dormancy such as torpor and hibernation, aiming to harness the potential of these states therapeutically.

      Deblina Sarkar is an assistant professor and AT&T Career Development Chair Professor at the MIT Media Lab​. Her research combines the interdisciplinary fields of nanoelectronics, applied physics, and biology to invent disruptive technologies for energy-efficient nanoelectronics and merge such next-generation technologies with living matter to create a new paradigm for life-machine symbiosis. Her high-risk, high-reward proposal received the rare perfect impact score of 10, which is the highest score awarded by NIH.

      Caroline Uhler is a professor in the Department of Electrical Engineering and Computer Science and the Institute for Data, Systems, and Society. In addition, she is a core institute member at the Broad Institute of MIT and Harvard, where she co-directs the Eric and Wendy Schmidt Center. By combining machine learning, statistics, and genomics, she develops representation learning and causal inference methods to elucidate gene regulation in health and disease.

      The High-Risk, High-Reward Research program is supported by the NIH Common Fund, which oversees programs that pursue major opportunities and gaps in biomedical research that require collaboration across NIH Institutes and Centers. In addition to the New Innovator Award, the NIH also issues three other awards each year: the Pioneer Award, which supports bold and innovative research projects with unusually broad scientific impact; the Transformative Research Award, which supports risky and untested projects with transformative potential; and the Early Independence Award, which allows especially impressive junior scientists to skip the traditional postdoctoral training program to launch independent research careers.

      This year, the High-Risk, High-Reward Research program is awarding 103 awards, including eight Pioneer Awards, 72 New Innovator Awards, nine Transformative Research Awards, and 14 Early Independence Awards. These 103 awards total approximately $285 million in support from the institutes, centers, and offices across NIH over five years. “The science advanced by these researchers is poised to blaze new paths of discovery in human health,” says Lawrence A. Tabak DDS, PhD, who is performing the duties of the director of NIH. “This unique cohort of scientists will transform what is known in the biological and behavioral world. We are privileged to support this innovative science.” More

    • 100 Shares189 Views

      in Data Management & Statistics

      New leadership at MIT’s Center for Biomedical Innovation

      by

      As it continues in its mission to improve global health through the development and implementation of biomedical innovation, the MIT Center for Biomedical Innovation (CBI) today announced changes to its leadership team: Stacy Springs has been named executive director, and Professor Richard Braatz has joined as the center’s new associate faculty director.

      The change in leadership comes at a time of rapid development in new therapeutic modalities, growing concern over global access to biologic medicines and healthy food, and widespread interest in applying computational tools and multi-disciplinary approaches to address long-standing biomedical challenges.

      “This marks an exciting new chapter for the CBI,” says faculty director Anthony J. Sinskey, professor of biology, who cofounded CBI in 2005. “As I look back at almost 20 years of CBI history, I see an exponential growth in our activities, educational offerings, and impact.”

      The center’s collaborative research model accelerates innovation in biotechnology and biomedical research, drawing on the expertise of faculty and researchers in MIT’s schools of Engineering and Science, the MIT Schwarzman College of Computing, and the MIT Sloan School of Management.

      Springs steps into the role of executive director having previously served as senior director of programs for CBI and as executive director of CBI’s Biomanufacturing Program and its Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB). She succeeds Gigi Hirsch, who founded the NEW Drug Development ParadIGmS (NEWDIGS) Initiative at CBI in 2009. Hirsch and NEWDIGS have now moved to Tufts Medical Center, establishing a headquarters at the new Center for Biomedical System Design within the Institute for Clinical Research and Health Policy Studies there.

      Braatz, a chemical engineer whose work is informed by mathematical modeling and computational techniques, conducts research in process data analytics, design, and control of advanced manufacturing systems.

      “It’s been great to interact with faculty from across the Institute who have complementary expertise,” says Braatz, the Edwin R. Gilliland Professor in the Department of Chemical Engineering. “Participating in CBI’s workshops has led to fruitful partnerships with companies in tackling industry-wide challenges.”

      CBI is housed under the Institute for Data Systems and Society and, specifically, the Sociotechnical Systems Research Center in the MIT Schwarzman College of Computing. CBI is home to two biomanufacturing consortia: the CAACB and the Biomanufacturing Consortium (BioMAN). Through these precompetitive collaborations, CBI researchers work with biomanufacturers and regulators to advance shared interests in biomanufacturing.

      In addition, CBI researchers are engaged in several sponsored research programs focused on integrated continuous biomanufacturing capabilities for monoclonal antibodies and vaccines, analytical technologies to measure quality and safety attributes of a variety of biologics, including gene and cell therapies, and rapid-cycle development of virus-like particle vaccines for SARS-CoV-2.

      In another significant initiative, CBI researchers are applying data analytics strategies to biomanufacturing problems. “In our smart data analytics project, we are creating new decision support tools and algorithms for biomanufacturing process control and plant-level decision-making. Further, we are leveraging machine learning and natural language processing to improve post-market surveillance studies,” says Springs.

      CBI is also working on advanced manufacturing for cell and gene therapies, among other new modalities, and is a part of the Singapore-MIT Alliance for Research and Technology – Critical Analytics for Manufacturing Personalized-Medicine (SMART CAMP). SMART CAMP is an international research effort focused on developing the analytical tools and biological understanding of critical quality attributes that will enable the manufacture and delivery of improved cell therapies to patients.

      “This is a crucial time for biomanufacturing and for innovation across the health-care value chain. The collaborative efforts of MIT researchers and consortia members will drive fundamental discovery and inform much-needed progress in industry,” says MIT Vice President for Research Maria Zuber.

      “CBI has a track record of engaging with health-care ecosystem challenges. I am confident that under the new leadership, it will continue to inspire MIT, the United States, and the entire world to improve the health of all people,” adds Daniel Huttenlocher, dean of the MIT Schwarzman College of Computing. More

    • 125 Shares189 Views

      in Data Management & Statistics

      New CRISPR-based map ties every human gene to its function

      by

      The Human Genome Project was an ambitious initiative to sequence every piece of human DNA. The project drew together collaborators from research institutions around the world, including MIT’s Whitehead Institute for Biomedical Research, and was finally completed in 2003. Now, over two decades later, MIT Professor Jonathan Weissman and colleagues have gone beyond the sequence to present the first comprehensive functional map of genes that are expressed in human cells. The data from this project, published online June 9 in Cell, ties each gene to its job in the cell, and is the culmination of years of collaboration on the single-cell sequencing method Perturb-seq.

      The data are available for other scientists to use. “It’s a big resource in the way the human genome is a big resource, in that you can go in and do discovery-based research,” says Weissman, who is also a member of the Whitehead Institute and an investigator with the Howard Hughes Medical Institute. “Rather than defining ahead of time what biology you’re going to be looking at, you have this map of the genotype-phenotype relationships and you can go in and screen the database without having to do any experiments.”

      The screen allowed the researchers to delve into diverse biological questions. They used it to explore the cellular effects of genes with unknown functions, to investigate the response of mitochondria to stress, and to screen for genes that cause chromosomes to be lost or gained, a phenotype that has proved difficult to study in the past. “I think this dataset is going to enable all sorts of analyses that we haven’t even thought up yet by people who come from other parts of biology, and suddenly they just have this available to draw on,” says former Weissman Lab postdoc Tom Norman, a co-senior author of the paper.

      Pioneering Perturb-seq

      The project takes advantage of the Perturb-seq approach that makes it possible to follow the impact of turning on or off genes with unprecedented depth. This method was first published in 2016 by a group of researchers including Weissman and fellow MIT professor Aviv Regev, but could only be used on small sets of genes and at great expense.

      The massive Perturb-seq map was made possible by foundational work from Joseph Replogle, an MD-PhD student in Weissman’s lab and co-first author of the present paper. Replogle, in collaboration with Norman, who now leads a lab at Memorial Sloan Kettering Cancer Center; Britt Adamson, an assistant professor in the Department of Molecular Biology at Princeton University; and a group at 10x Genomics, set out to create a new version of Perturb-seq that could be scaled up. The researchers published a proof-of-concept paper in Nature Biotechnology in 2020. 

      The Perturb-seq method uses CRISPR-Cas9 genome editing to introduce genetic changes into cells, and then uses single-cell RNA sequencing to capture information about the RNAs that are expressed resulting from a given genetic change. Because RNAs control all aspects of how cells behave, this method can help decode the many cellular effects of genetic changes.

      Since their initial proof-of-concept paper, Weissman, Regev, and others have used this sequencing method on smaller scales. For example, the researchers used Perturb-seq in 2021 to explore how human and viral genes interact over the course of an infection with HCMV, a common herpesvirus.

      In the new study, Replogle and collaborators including Reuben Saunders, a graduate student in Weissman’s lab and co-first author of the paper, scaled up the method to the entire genome. Using human blood cancer cell lines as well noncancerous cells derived from the retina, he performed Perturb-seq across more than 2.5 million cells, and used the data to build a comprehensive map tying genotypes to phenotypes.

      Delving into the data

      Upon completing the screen, the researchers decided to put their new dataset to use and examine a few biological questions. “The advantage of Perturb-seq is it lets you get a big dataset in an unbiased way,” says Tom Norman. “No one knows entirely what the limits are of what you can get out of that kind of dataset. Now, the question is, what do you actually do with it?”

      The first, most obvious application was to look into genes with unknown functions. Because the screen also read out phenotypes of many known genes, the researchers could use the data to compare unknown genes to known ones and look for similar transcriptional outcomes, which could suggest the gene products worked together as part of a larger complex.

      The mutation of one gene called C7orf26 in particular stood out. Researchers noticed that genes whose removal led to a similar phenotype were part of a protein complex called Integrator that played a role in creating small nuclear RNAs. The Integrator complex is made up of many smaller subunits — previous studies had suggested 14 individual proteins — and the researchers were able to confirm that C7orf26 made up a 15th component of the complex.

      They also discovered that the 15 subunits worked together in smaller modules to perform specific functions within the Integrator complex. “Absent this thousand-foot-high view of the situation, it was not so clear that these different modules were so functionally distinct,” says Saunders.

      Another perk of Perturb-seq is that because the assay focuses on single cells, the researchers could use the data to look at more complex phenotypes that become muddied when they are studied together with data from other cells. “We often take all the cells where ‘gene X’ is knocked down and average them together to look at how they changed,” Weissman says. “But sometimes when you knock down a gene, different cells that are losing that same gene behave differently, and that behavior may be missed by the average.”

      The researchers found that a subset of genes whose removal led to different outcomes from cell to cell were responsible for chromosome segregation. Their removal was causing cells to lose a chromosome or pick up an extra one, a condition known as aneuploidy. “You couldn’t predict what the transcriptional response to losing this gene was because it depended on the secondary effect of what chromosome you gained or lost,” Weissman says. “We realized we could then turn this around and create this composite phenotype looking for signatures of chromosomes being gained and lost. In this way, we’ve done the first genome-wide screen for factors that are required for the correct segregation of DNA.”

      “I think the aneuploidy study is the most interesting application of this data so far,” Norman says. “It captures a phenotype that you can only get using a single-cell readout. You can’t go after it any other way.”

      The researchers also used their dataset to study how mitochondria responded to stress. Mitochondria, which evolved from free-living bacteria, carry 13 genes in their genomes. Within the nuclear DNA, around 1,000 genes are somehow related to mitochondrial function. “People have been interested for a long time in how nuclear and mitochondrial DNA are coordinated and regulated in different cellular conditions, especially when a cell is stressed,” Replogle says.

      The researchers found that when they perturbed different mitochondria-related genes, the nuclear genome responded similarly to many different genetic changes. However, the mitochondrial genome responses were much more variable. 

      “There’s still an open question of why mitochondria still have their own DNA,” said Replogle. “A big-picture takeaway from our work is that one benefit of having a separate mitochondrial genome might be having localized or very specific genetic regulation in response to different stressors.”

      “If you have one mitochondria that’s broken, and another one that is broken in a different way, those mitochondria could be responding differentially,” Weissman says.

      In the future, the researchers hope to use Perturb-seq on different types of cells besides the cancer cell line they started in. They also hope to continue to explore their map of gene functions, and hope others will do the same. “This really is the culmination of many years of work by the authors and other collaborators, and I’m really pleased to see it continue to succeed and expand,” says Norman. More