Penn Engineers have pioneered a new way to visualize the smallest protein clusters, skirting the physical limitations of light-powered microscopes and opening new avenues for detecting the proteins implicated in diseases like Alzheimer’s and testing new treatments.
In a paper in Cell Systems, Lukasz Bugaj, Assistant Professor in Bioengineering, describes the creation of CluMPS, or Clusters Magnified by Phase Separation, a molecular tool that activates by forming conspicuous blobs in the presence of target protein clusters as small as just a few nanometers. In essence, CluMPS functions like an on/off switch that responds to the presence of clusters of the protein it is programmed to detect.
Normally, says Bugaj, detecting such clusters requires laborious techniques. “With CluMPS, you don’t need anything beyond the standard lab microscope.” The tool fuses with the target protein to form condensates orders of magnitude larger than the protein clusters themselves that resemble the colorful blobs in a lava lamp. “We think the simplicity of the approach is one of its main benefits,” says Bugaj. “You don’t need specialized skills or equipment to quickly see whether there are small clusters in your cells.”
Congratulations to the 2022 University of Pennsylvania iGEM Team who took home a gold medal in the iGEM Grand Jamboree. This international competition of multidisciplinary teams of graduate and undergraduate students presenting original projects in synthetic biology culminated in the in-person Jamboree event held in Paris, France in October 2022. Over 370 judges awarded prizes and medals to the 350+ teams representing over 40 countries.
The 2022 Penn team was awarded a Gold Medal for their project “Photocreate,” a toolbox to control intercellular communication using optogenetics. Their plasmid constructs are designed to control protein secretion, display and shedding using a photocleavable protein, Phocl. The full abstract reads:
Intercellular communication is primarily studied using synthetic protein-level circuits. These circuits currently lack the spatial and temporal control necessary for targeted and time-sensitive applications. To address this gap, we developed Photocrete, a toolbox of protein constructs for light-inducible control of protein display, secretion, and shedding. We expanded upon RELEASE (Vlahos et al.), a modular and generalizable protein circuit which utilizes an ER retention motif and an exogenous protease to control protein secretion. We optogenetically modified RELEASE by replacing different components with the photocleavable protein PhoCl, allowing us to control the mammalian secretion pathway at distinct nodes with finely-tuned light administration regimens. Preliminary results indicate integration of Photocrete into the secretion pathway, but more research is necessary to determine optimal light administration settings. The potential for high spatial and temporal control of Photocrete could allow researchers to perform various signaling studies and develop therapeutics at a new level of precision.
The 2022 iGEM team includes undergraduates June Ahn (B.S. in Biochemistry, Physics and Nutrition), Adiva Daniar (B.S.E. in Bioengineering, minor in Engineering Entrepreneurship), Wangari Mbuthia (B.S.E. in Bioengineering), Cristina Perez (B.S.E. in Bioengineering, minor in Physics), Shreya Vallimanalan (B.S.E. in Bioengineering, minor in Computational Neuroscience), an d Moses Zeidan (B.S.E. in Bioengineering, minor in Chemistry and Spanish). They were mentored by graduate students David Gonzalez-Martinez, Gabrielle Ho, Zikang Huang, and Will Benman. Their faculty advisor is Lukasz Bugaj, Assistant Professor in Bioengineering.
Read the full results of the 2022 iGEM Competition here.
The Penn Center for Precision Engineering for Health (CPE4H) was established late last year to accelerate engineering solutions to significant problems in healthcare. The center is one of the signature initiatives for Penn’s School of Engineering and Applied Science and is supported by a $100 million commitment to hire faculty and support new research on innovative approaches to those problems.
Acting on that commitment, CPE4H solicited proposals during the spring of 2022 for seed grants of $80K per year for two years for research projects that address healthcare challenges in several key areas of strategic importance to Penn: synthetic biology and tissue engineering, diagnosis and drug delivery, and the development of innovative devices. While the primary investigators (PIs) for the proposed projects were required to have a primary faculty appointment within Penn Engineering, teams involving co-PIs and collaborators from other schools were eligible for support. The seed program is expected to continue for the next four years.
“It was a delight to read so many novel and creative proposals,” says Daniel A. Hammer, Alfred G. and Meta A. Ennis Professor in Bioengineering and the Inaugural Director of CPE4H. “It was very hard to make the final selection from a pool of such promising projects.”
Judged on technical innovation, potential to attract future resources, and ability to address a significant medical problem, the following research projects were selected to receive funding.
Evolving and Engineering Thermal Control of Mammalian Cells
Led by Lukasz Bugaj, Assistant Professor in Bioengineering, this project will engineer molecular switches that can be toggled on and off inside mammalian cells at near-physiological temperatures. Successful development of these switches will provide new ways to communicate with cells, an advance that could be used to make safer and more effective cellular therapies. The project will use directed evolution to generate and find candidate molecular tools with the desired properties. Separately, the research will also develop new technology for manipulating cellular temperature in a rapid and programmable way. Such devices will enhance the speed and sophistication of studies of biological temperature regulation.
A Quantum Sensing Platform for Rapid and Accurate Point-of-Care Detection of Respiratory Viral Infections
Combining microfluidics and quantum photonics, PI Liang Feng, Professor in Materials Science and Engineering and Electrical and Systems Engineering, Ritesh Agarwal, Professor in Materials Science Engineering, and Shu Yang, Joseph Bordogna Professor in Materials Science and Engineering and Chemical and Biomolecular Engineering, are teaming up with Ping Wang, Professor of Pathology and Laboratory Medicine in Penn’s Perelman School of Medicine, to design, build and test an ultrasensitive point-of-care detector for respiratory pathogens. In light of the COVID-19 pandemic, a generalizable platform for rapid and accurate detection of viral pathogenesis would be extremely important and timely.
Versatile Coacervating Peptides as Carriers and Synthetic Organelles for Cell Engineering
PI Amish Patel, Associate Professor in Chemical and Biomolecular Engineering, and Matthew C. Good, Associate Professor of Cell and Developmental Biology in the Perelman School of Medicine and in Bioengineering, will design and create small proteins that self-assemble into droplet-like structures known as coacervates, which can then pass through the membranes of biological cells. Upon cellular entry, these protein coacervates can disassemble to deliver cargo that modulates cell behavior or be maintained as synthetic membraneless organelles. The team will design new chemistries that will facilitate passage across cell membranes, and molecular switches to sequester and release protein therapeutics. If successful, this approach could be used to deliver a wide range of macromolecule drugs to cells.
Towards an Artificial Muscle Replacement for Facial Reanimation
Cynthia Sung, Gabel Family Term Assistant Professor in Mechanical Engineering and Applied Mechanics and Computer Information Science, will lead a research team including Flavia Vitale, Assistant Professor of Neurology and Bioengineering, and Niv Milbar, Assistant Instructor in Surgery in the Perelman School of Medicine. The team will develop and validate an electrically driven actuator to restore basic muscle responses in patients with partial facial paralysis, which can occur after a stroke or injury. The research will combine elements of robotics and biology, and aims to produce a device that can be clinically tested.
“These novel ideas are a great way to kick off the activities of the center,” says Hammer. “We look forward to soliciting other exciting seed proposals over the next several years.”
Therapies that use engineered cells to treat diseases, infections and chronic illnesses are opening doors to solutions for longstanding medical challenges. Lukasz Bugaj, Assistant Professor in Bioengineering, has been awarded a National Science Foundation CAREER Award for research that may be key to opening some of those doors.
Such cellular therapies take advantage of the complex molecular mechanisms that cells naturally use to interact with one another, enabling them to be more precise and less toxic than traditional pharmaceutical drugs, which are based on simpler small molecules. Cellular therapies that use engineered immune system cells, for example, have recently been shown to be highly successful in treating certain cancers and protecting against viral infections.
However, there is still a need to further fine-tune the behavior of cells in these targeted therapies. Bugaj and colleagues are addressing that need by developing new ways to communicate with engineered cells once they are in the body, such as turning molecular events on and off at specific times.
The research team recently discovered that both temperature and light can act as triggers of a specific fungal protein, dynamically controlling its location within a mammalian cell. By using light or temperature to instruct that protein to migrate toward or away from the cell’s membrane, Bugaj and his colleagues showed how it could serve as a key component in controlling the behavior of human cells.
Most organisms have proteins that react to light. Even creatures that don’t have eyes or other visual organs use these proteins to regulate many cellular processes, such as transcription, translation, cell growth and cell survival.
The field of optogenetics relies on such proteins to better understand and manipulate these processes. Using lasers and genetically engineered versions of these naturally occurring proteins, known as probes, researchers can precisely activate and deactivate a variety of cellular pathways, just like flipping a switch.
Now, Penn Engineering researchers have described a new type of optogenetic protein that can be controlled not only by light, but also by temperature, allowing for a higher degree of control in the manipulation of cellular pathways. The research will open new horizons for both basic science and translational research.
Lukasz Bugaj, Assistant Professor in Bioengineering (BE), Bomyi Lim, Assistant Professor in Chemical and Biomolecular Engineering, Brian Chow, Associate Professor in BE, and graduate students William Benman in Bugaj’s lab, Hao Deng in Lim’s lab, and Erin Berlew and Ivan Kuznetsov in Chow’s lab, published their study in Nature Chemical Biology. Arndt Siekmann, Associate Professor of Cell and Developmental Biology at the Perelman School of Medicine, and Caitlyn Parker, a research technician in his lab, also contributed to this research.
The team’s original aim was to develop a single-component probe that would be able to manipulate specific cellular pathways more efficiently. The model for their probe was a protein called BcLOV4, and through further investigation of this protein’s function, they made a fortuitous discovery: that the protein is controlled by both light and temperature.
Penn Health-Tech’s Nemirovsky Engineering and Medicine Opportunity (NEMO) Prize awards $80,000 to support early-stage ideas joining engineering and medicine. The goal of the prize is to encourage collaboration between the University of Pennsylvania’s Perelman School of Medicine and the School of Engineering and Applied Science by supporting innovative ideas that might not receive funding from traditional sources.
This year, the NEMO Prize has been awarded to a team of researchers from Penn Engineering’s Department of Bioengineering. Their project aims to develop a technology that can detect multiple cancer biomarkers in single cells from tumor biopsy samples.
As cancer cells grow in the body, one of the characteristics that influences tumor growth and response to treatment is cancer cell state heterogeneity, or differences in cell states. Methods that rapidly catalogue cell heterogeneity may be able to detect rare cells responsible for tumor growth and drug resistance.
Single-cell transcriptomics (scRNA-seq) is the standard method for studying cell states; by amplifying and analyzing the cell’s complement of RNA sequences at a given time, researchers can get a snapshot of what proteins the cell is in the process of making. However, this method does not fully capture the function of the cell. The field of proteomics, which captures the actual protein content of cells along with post-translational modifications, provides a better picture of the cell’s function, but single-cell proteomic methods with the same sensitivity as scRNA-seq do not currently exist.
This collaborative project, which joins Assistant Professors Alex Hughes and Lukasz Bugaj, as well as Professor Andrew Tsourkas, aims to change that by developing multiplexed, sensitive and highly specific single-cell proteomics technologies to advance our understanding of cancer, its detection and its treatment.
This new technology, called scProteome-seq, builds from Hughes’s previous work.
“My specific expertise here is as an inventor of single-cell western blotting, which is the core technology that our team is building on,” says Hughes. “Single-cell proteomics technologies of this type have a track-record of commercial translation for applications in basic science and clinical automation, so our approach has a high potential for real-world impact.”
The current technology from Hughes’ lab separates proteins in cells by their molecular weight and “blots” them on a piece of paper. Improvements to this technology included in this project will remove the limitation of using light-emitting dyes to detect different proteins and instead use DNA barcodes to differentiate them.
The University of Pennsylvania’s 2021 iGEM team has been awarded several distinctions in this year’s highly competitive iGEM Competition. The International Genetically Engineered Machine Competition is the largest synthetic biology community and the premiere synthetic biology competition for both university and high school level students from around the world. Each year, hundreds of interdisciplinary teams of students combine molecular biology techniques and engineering concepts to create novel biological systems and compete for prizes and awards through oral presentations and poster sessions.
The Penn team’s project, “OptoReader,” is a combined light-simulation device and plate reader, which makes optogenetic experiments more powerful and accessible. The abstract reads:
“Metabolic engineering has the potential to change the world, and optogenetic tools can make metabolic engineering research easier by providing spatiotemporal control over cells. However, current optogenetic experiments are low-throughput, expensive, and laborious, which makes them inaccessible to many. To tackle this problem, we combined a light-stimulation device with a plate reader, creating our OptoReader. This device allows us to automate ~100 complex optogenetic experiments at the same time. Because it is open source and inexpensive, our device would make optogenetic experiments more efficient and available to all.”
This year’s Penn team was mentored by Lukasz Bugaj, Assistant Professor in Bioengineering. In addition, the team was supported by Brian Chow, Associate Professor in Bioengineering. Chow has supported previous undergraduate iGEM teams at Penn, and was involved in the creation of the iGEM program during his time as a graduate student at MIT.
OptoReader took home the top prizes in three of the four categories in which it was nominated. These prizes include:
Best Foundational Advance (best in track)
Best Hardware (best from all undergraduate teams)
Best Presentation (best from all undergraduate teams)
They were also awarded a Gold Medal Distinction and were included in the Top 10 Overall (from all undergraduate teams, and the only team from the United States to make the top 10) and Top 10 Websites (from all undergraduate teams).
The awards were announced during iGEM’s online Jamboree Award Ceremony on November 14, 2021 (watch the full award ceremony here).
In addition to the outstanding awards recognition, OptoReader was also selected for an iGEM Impact Grant which awards teams $2,500 to continue development of their projects. This new initiative from the iGEM Foundation was announced earlier this year, and with the support of the Frederick Gardner Cottrell Foundation, is distributing a total of $225,000 in grant funds to 90 iGEM teams during the 2021 competition season. Learn more about the Impact Grant and read the full list of winning teams here.
Penn’s 2021 iGEM team was made up of an interdisciplinary group of women undergraduates from the School of Engineering and Applied Science (SEAS) and the School of Arts and Sciences (SAS):
Saachi Datta (B.A. in Biology and Religious Studies 2021)
Juliette Hooper (B.S.E. and M.S.E. in Bioengineering 2022)
Gabrielle Leavitt (B.S.E. in Bioengineering 2021 and current Master’s student in Bioengineering)
Gloria Lee (B.A. in Physics and B.S.E. in Bioengineering 2023)
Grace Qian (B.S.E. in Bioengineering 2023)
Lana Salloum (B.A. in Neuroscience 2022)
They were mentored by three doctoral students in Bioengineering: Will Benman (Bugaj Lab), David Gonzalez Martinez (Bugaj Lab), Gabrielle Ho (Chow Lab). Saurabh Malani, a graduate student in the Avalos Lab at Prince University, was also very involved in mentoring the team.
The graduate mentors were instrumental in quickly bringing the undergraduates up to speed on a diverse array of skills needed to accomplish this project including circuit design, optics, optogenetics, programming, and additive manufacturing. They then coached the team through building and testing prototypes, as well as accomplishing other objectives required for success at iGEM. These other objectives included establishing collaborations with other iGEM teams, performing outreach, and effectively communicating their project through a website and online presentations.
“This team and their work is outstanding,” said William Benman. “Not only did they sweep several awards, but they did it all with a small team and while working with technology they had no prior experience with. They created a device that not only increases accessibility to optogenetics but also allows optogenetic systems to interface directly with computer programs, allowing for completely new research avenues within the field. They are truly a remarkable group.”
Due to the COVID pandemic, the team operated virtually through the summer of 2020, and then continued in person in the summer of 2021 as the project progressed and more students returned to Penn’s campus. Upon return to campus, the work was conducted in both the Bugaj lab in the Stephenson Foundation Educational Laboratory & Bio-MakerSpace, the primary teaching laboratory in Penn Bioengineering and an interdisciplinary makerspace open to anyone at Penn. The team also collaborated with the Avalos Lab at Princeton University, which conducts research in the application of optogenetics to optimize production of valuable chemicals in microbes.
“I’m beyond excited about this phenomenal showing from team Penn at the iGEM Jamboree awards ceremony,” said faculty mentor Lukasz Bugaj. “This is truly outstanding recognition for what the team has accomplished, and it wouldn’t have happened without essential contributions from everyone on the team.”
Brian Chow added that this achievement is “no small feat,” especially for a hardware project. “The iGEM competition leans toward genetic strain engineering, but the advances in the field made by these incredible students were undeniable,” he said.
Going forward, the team plans to publish a scientific article and file a patent application describing their device. “It’s clear that there is excitement in the scientific community for what our students created, and we’re excited to share the details and designs of their work,” said Bugaj.
Congratulations to all the team members and mentors of OptoReader on this incredible achievement! Check out the OptoReader project website and Instagram to learn more about their project.
Advances in cell and molecular technologies are revolutionizing the treatment of cancer, with faster detection, targeted therapies and, in some cases, the ability to permanently retrain a patient’s own immune system to destroy malignant cells.
However, there are fundamental forces and associated challenges that determine how cancer grows and spreads. The pathological genes that give rise to tumors are regulated in part by a cell’s microenvironment, meaning that the physical push and pull of neighboring cells play a role alongside the chemical signals passed within and between them.
The Penn Anti-Cancer Engineering Center (PACE) will bring diverse research groups from the School of Engineering and Applied Science together with labs in the School of Arts & Sciences and the Perelman School of Medicine to understand these physical forces, leveraging their insights to develop new types of treatments and preventative therapies.
The Center’s founding members are Dennis Discher, Robert D. Bent Professor with appointments in the Departments of Chemical and Biomolecular Engineering (CBE), Bioengineering (BE) and Mechanical Engineering and Applied Mechanics (MEAM), and Ravi Radhakrishnan, Professor and chair of BE with an appointment in CBE.
Discher, an expert in mechanobiology and in delivery of cells and nanoparticles to solid tumors, and Radhakrishnan, an expert on modeling physical forces that influence binding events, have long collaborated within the Physical Sciences in Oncology Network. This large network of physical scientists and engineers focuses on cancer mechanisms and develops new tools and trainee opportunities shared across the U.S. and around the world.
Among the PACE Center’s initial research efforts are studies of the genetic and immune mechanisms associated with whether a tumor is solid or liquid and investigations into how physical stresses influence cell signaling.
We are very pleased to announce that ten current and future graduate students in the Department of Bioengineering have received 2021 National Science Foundation Graduate Research Fellowship Program (NSF GRFP) fellowships. The prestigious NSF GRFP program recognizes and supports outstanding graduate students in NSF-supported fields. Further information about the program can be found on the NSF website. BE is thrilled to congratulate our excellent students on these well-deserved accolades! Continue reading below for a list of 2021 recipients and descriptions of their research.
Puneeth Guruprasad is a Ph.D. student in the lab of Marco Ruella, Assistant Professor of Medicine in the Division of Hematology/Oncology and the Center for Cellular Immunotherapies at the Perelman School of Medicine. His work applies next generation sequencing methods to characterize tumors and study the genetic basis of resistance to cancer immunotherapy, namely chimeric antigen receptor (CAR) T cell therapy.
Gabrielle (Gabby) Ho is a Ph.D. student in the lab of Brian Chow, Associate Professor in Bioengineering. She works on design strategies for engineering near-infrared fluorescent proteins and tools.
Abbas Idris is a Master’s student in the lab of Lukasz Bugaj, Assistant Professor in Bioengineering. His work focuses on using optogenetic tools to develop controllable protein assemblies for the study of cell signaling behaviors.
Additionally, seven NSF GRFP honorees from other institutions will be joining our department as Ph.D. students in the fall of 2021. We congratulate them as well and look forward to welcoming them to Penn:
While the majority of courses remained online this spring, a small number of lab-based undergraduate courses were able to resume limited in-person instruction. One course was BE 310, the second semester of the Bioengineering Modeling, Analysis, and Design lab sequence. Better known as BE-MAD, this junior-year bioengineering course was able to bring students back to the teaching lab safely this spring while adapting its curriculum to keep remote learners engaged with hands-on lab modules at home.
An Essential Step Towards Becoming a Bioengineer
After learning the basics of chemistry, physics, biology, and math during freshman year and studying bioengineering fundamentals throughout sophomore year, BE-MAD is designed to provide essential hands-on experience to bioengineering majors during their junior years. In BE-MAD, students integrate what they’ve learned so far in the classroom to addressing complex, real-world problems by breaking down the silos that exist across different STEM fields.
“Usually what we hear from students is that this BE 309/310 sequence is when they really feel like they are engineers,” says Brian Chow, one of the BE 310 instructors. “They can put what they learn in classes to work in some practical setting and applied context.”
BE-MAD is also an important course to prepare students for senior design and is designed to be a “safe space to fail,” allowing students to build confidence through trial and error within a supportive environment, explains Sevile G. Mannickarottu, director of the educational laboratories. “We’re trying to build skills needed for senior year as well as teaching students how to think critically about problems by pulling together the materials they’ve learned all in one place,” he says. “By senior year, we want them to, when presented with a problem, not be afraid.”
Adapting BE-MAD for Both Remote and Hybrid Instruction
Traditionally, the BE-MAD lab is taught in the George H. Stephenson Foundation Educational Laboratory & Bio-MakerSpace, the primary bioengineering teaching lab, and includes modules on dialysis, drug delivery, insect limb control, microfluidics, cell-cell communication, ECG analysis, and spectroscopy. In the fall, the first lab in the series (BE-309) pivoted to remote learning using video tutorials of lab experiments and providing real data to students for analysis.
This spring, with more aspects of on-campus life able to reopen, the Educational Laboratory staff and BE-MAD instructors developed protocols in collaboration with David Meaney, Penn Engineering senior associate dean and an instructor for BE 309, and Penn’s Environmental Health and Radiation Safety office to safely reopen the teaching lab and Bio-MakerSpace for both BE-310 and for bioengineering senior design students.
To continue to meet the needs of remote students, BE 310 instructor Lukasz Bugaj says that the curriculum was adapted to be two parallel courses—one that could be done entirely at home and the other in-person. The challenge was to adjust the content so that it could be completed either in-person or virtually, and could be switched from in-person to virtual at a moment’s notice because of COVID precautions, all while maximizing the hands-on experience, says Bugaj. “That’s a real credit to the lab staff of Sevile and Michael Patterson, who put a lot of work into revamping this entire class.”