The Penn researchers’ latest paper on the design of lipid nanoparticles was featured on the cover of the most recent edition of the journal Nano Letters.
From COVID vaccines to cancer immunotherapies to the potential for correcting developmental disorders in utero, mRNA-based approaches are a promising tool in the fight against a wide range of diseases. These treatments all depend on providing a patient’s cells with genetic instructions for custom proteins and other small molecules, meaning that getting those instructions inside the target cells is of critical importance.
The current delivery method of choice uses lipid nanoparticles (LNPs). Thanks to surfaces customized with binding and signaling molecules, they encapsulate mRNA sequences and smuggle them through the cell membrane. But with a practically unlimited number of variables in the makeup of those surfaces and molecules, figuring out how to design the most effective LNP is a fundamental challenge.
Now, in a study featured on the cover of the journal Nano Letters, researchers from the University of Pennsylvania’s School of Engineering and Applied Science and Perelman School of Medicine have now shown how to computationally optimize the design of these delivery vehicles.
Using an established methodology for comparing a wide range of variables known as “orthogonal design of experiments,” the researchers simultaneously tested 256 candidate LNPs. They found the frontrunner was three times better at delivering mRNA sequences into T cells than the current standard LNP formulation for mRNA delivery.
The study was led by Michael Mitchell, Skirkanich Assistant Professor of Innovation in the Department of Bioengineering in Penn’s School of Engineering and Applied Science, and Margaret Billingsley, a graduate student in his lab.
The antimicrobial peptides the researchers studied are “encrypted” in that they are contained within Apolipoprotein B, a blood plasma protein that is not directly involved in the immune response, but are not normally expressed on their own.
The rise of drug-resistant bacteria infections is one of the world’s most severe global health issues, estimated to cause 10 million deaths annually by the year 2050. Some of the most virulent and antibiotic-resistant bacterial pathogens are the leading cause of life-threatening, hospital-acquired infections, particularly dangerous for immunocompromised and critically ill patients. Traditional and continual synthesis of antibiotics will simply not be able to keep up with bacteria evolution.
To avoid the continual process of synthesizing new antibiotics to target bacteria as they evolve, Penn Engineers have looked at a new, natural resource for antibiotic molecules.
César de la Fuente, Ph.D.
A recent study on the search for encrypted peptides with antimicrobial properties in the human proteome has located naturally occurring antibiotics within our own bodies. By using an algorithm to pinpoint specific sequences in our protein code, a team of Penn researchers along with collaborators, led by César de la Fuente, Presidential Assistant Professor in Psychiatry, Bioengineering, Microbiology, and Chemical and Biomolecular Engineering, and Marcelo Torres, a post doc in de la Fuente’s lab, were able to locate novel peptides, or amino acid chains, that when cleaved, indicated their potential to fend off harmful bacteria.
Now, in a new study published in ACS Nano, the team along with Angela Cesaro, the lead author and post doc in de la Fuente’s lab, have identified three distinct antimicrobial peptides derived from a protein in human plasma and demonstrate their abilities in mouse models. Angela Cesaro performed a great part of the activities during her PhD under the supervision of corresponding author, Professor Angela Arciello, from the University of Naples Federico II. The collaborative study also includes Utrecht University in the Netherlands.
“We identified the cardiovascular system as a hot spot for potential antimicrobials using an algorithmic approach,” says de la Fuente. “Then we looked closer at a specific protein in the plasma.”
A scanning electron micrograph of a healthy human T cell. A better understanding the wide variety of antigen receptors that appear on the surfaces of these critical components of the immune system is necessary for improving a new class of therapies. (Credit: NIAID)
Our bodies are equipped with specialized white blood cells that protect us from foreign invaders, such as viruses and bacteria. These T cells identify threats using antigen receptors, proteins expressed on the surface of individual T cells that recognize specific amino acid sequences found in or on those invaders. Once a T cell’s antigen receptors bind to the corresponding antigen, it can directly kill infected cells or call for backup from the rest of the immune system.
We have hundreds of billions of T cells, each with unique receptors that recognize unique antigens, so profiling this T cell antigen specificity is essential in our understanding of the immune response. It is especially critical in developing targeted immunotherapies, which equip T cells with custom antigen receptors that recognize threats they would otherwise miss, such as the body’s own mutated cancer cells.
Jenny Jiang, Ph.D.
Jenny Jiang, Peter and Geri Skirkanich Associate Professor of Innovation in Bioengineering, along with lab members and colleagues at the University of Texas, Austin, recently published a study in Nature Immunology that describes their technology, which simultaneously provides information in four dimensions of T cell profiling. Ke-Yue Ma and Yu-Wan Guo, a former post doc and current graduate student in Jiang’s Penn Engineering lab, respectively, also contributed to this study.
This technology, called TetTCR-SeqHD, is the first to provide such detailed information about single T cells in a high-throughput manner, opening doors for personalized immune diagnostics and immunotherapy development.
There are many pieces of information needed to comprehensively understand the immune response of T cells, and gathering all of these measurements simultaneously has been a challenge in the field. Comprehensive profiling of T cells includes sequencing the antigen receptors, understanding how specific those receptors are in their recognition of invading antigens, and understanding T cell gene and protein expression. Current technologies only screen for one or two of these dimensions due to various constraints.
“Current technologies that measure T cell immune response all have limitations,” says Jiang. “Those that use cultured or engineered T cells cannot tell us about their original phenotype, because once you take a cell out of the body to culture, its gene and protein expression will change. The technologies that address T cell and antigen sequencing with mass spectrometry damage genetic information of the sample. And current technologies that do provide information on antigen specificity use a very expensive binding ligand that can cost more than a thousand dollars per antigen, so it is not feasible if we want to look at hundreds of antigens. There is clearly room for advancement here.”
The TetTCR-SeqHD technology combines Jiang’s previously developed T cell receptor sequencing tool, TetTCR-Seq, described in a Nature Biotechnology paper published in 2018, with the new ability of characterizing both gene and protein expression.
Michael Mitchell, Skirkanich Assistant Professor of Innovation in the Department of Bioengineering, has been awarded the 2022 Society for Biomaterials (SFB) Young Investigator Award for his “outstanding achievements in the field of biomaterials research.”
The Society for Biomaterials is a multidisciplinary society of academic, healthcare, governmental and business professionals dedicated to promoting advancements in all aspects of biomaterial science, education and professional standards to enhance human health and quality of life.
Mitchell, whose research lies at the interface of biomaterials science, drug delivery, and cellular and molecular bioengineering to fundamentally understand and therapeutically target biological barriers, is specifically being recognized for his development of the first nanoparticle RNAi therapy to treat multiple myeloma, an incurable hematologic cancer that colonizes in bone marrow.
“Before this, no one in the drug delivery field has developed an effective gene delivery system to target bone marrow,” said United States National Medal of Science recipient Robert S. Langer in Mitchell’s award citation. “Mike is a standout young investigator and leader that intimately understands the importance of research and collaboration at the interface of nanotechnology and medicine.”
Academic recipients of the SFB Young Investigator Award should not exceed the rank of Assistant Professor and must not be tenured at the time of nomination. The award includes a $1,000 endowment.
The brighter edges of the cells in the middle and upper right panels show the optogenetic proteins collecting at the membrane after light exposure. At higher temperatures, however, the proteins become rapidly inactivated and thus do not stay at the membrane, resulting in the duller edges seen in the bottom right panel.
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, Bomyi Lim, and Brian Chow
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.
Earlier this year, Penn President Amy Gutmann and Vijay Kumar, Nemirovsky Family Dean of Penn’s School of Engineering and Applied Science, announced a $100 million commitment to accelerate innovations in medical technologies. Called the Center for Precision Engineering for Health (CPE4H), the initiative aims to bring together researchers from a wide range of fields to develop customizable biomaterials and implantable devices that can be tailored for individualized diagnostics, treatments and therapies.
Now, Daniel A. Hammer, Alfred G. and Meta A. Ennis Professor in Penn Engineering’s Departments of Bioengineering and Chemical and Biomolecular Engineering, has been named CPE4H’s inaugural director.
“Penn is a unique environment where innovations in healthcare can emerge very rapidly, as we’ve seen with the development of CAR-T cancer immunotherapy, and the design and delivery of mRNA vaccines,” Hammer says. “Engineering plays a central role in making those technologies functional and maximizing their impact, and CPE4H is a golden opportunity to take these technologies to the next level in a way that actually helps people.”
Johnson, who has appointments in the Perelman School of Medicine and the School of Engineering and Applied Science, and a secondary appointment in the Annenberg School for Communication, will become the David L. Cohen University Professor.
Penn Integrates Knowledge Professor Kevin Johnson, a pediatrician who has pioneered the use of clinical information systems and artificial intelligence to improve medical research and patient care, has received a named University professorship.
“David Cohen’s extraordinary leadership at the University and Penn Medicine, and longtime dedication to Philadelphia, has without a doubt shaped the booming campus, health system, and city we so much enjoy today,” says Gutmann. “His dedication is mirrored by the extraordinarily influential, innovative, and committed Dr. Kevin Johnson, whose university professorship will now bear Ambassador Cohen’s name.”
Cohen has served for two decades on Penn’s Board of Trustees and recently concluded a 12-year term as chair. He was confirmed by the U.S. Senate last month as United States Ambassador to Canada, bringing to the role decades of experience as a senior executive at Comcast Corp., chair of the Ballard Spahr law firm, chief of staff to Philadelphia Mayor Ed Rendell, trustee chair at Penn, and major player in a number of other business, civic, political, and philanthropic venues.
In addition to serving as a Trustee, Cohen is a Penn alum, having graduated from what is now the University of Pennsylvania Carey School of Law in 1981. His wife and son also attended the Law School. Cohen’s leadership in the University has been credited with helping guide the growth and advancement of both the University and Health System, in close partnership with both President Gutmann and her predecessor, Judith Rodin.
“It’s an honor to hold a professorship named after Mr. Cohen,” Johnson says. “Throughout his career, he has provided inspired leadership across Penn and our city and region. He is a passionate believer in uniting the public, private, and nonprofit sectors to tackle complex challenges and strengthen communities. Those who know me know that I’ve played a similar role as a pediatrician who works with technology, and who uses digital media to communicate to lay audiences about both. His passion for this city and our University’s educational mission are inspiring.”
N.B.: Johnson also holds a secondary appointment in the Department of Bioengineering. Read his full appointment announcement here.
The impending danger of bacterial resistance to antibiotics is well-documented within the scientific community. Bacteria are the most efficient evolvers, and their ability to develop tolerance to drugs, in addition to antibiotic overuse and misuse, means that researchers have had to get particularly resourceful to ensure the future of modern medicine.
WIRED’s Max G. Levy recently spoke with de la Fuente and postdoctoral researcher and study collaborator Marcelo Torres about the urgency of the team’s work, and why developing these solutions is critical to the survival of civilization as we know it. The team’s algorithm, based on pattern recognition software used to analyze images, makes an otherwise insurmountable feat tangible.
De la Fuente’s lab specializes in using AI to discover and design new drugs. Rather than making some all-new peptide molecules that fit the bill, they hypothesized that an algorithm could use machine learning to winnow down the huge repository of natural peptide sequences in the human proteome into a select few candidates.
“We know those patterns—the multiple patterns—that we’re looking for,” says de la Fuente. “So that allows us to use the algorithm as a search function.”
Recently, Michael Birnbaum of the Washington Post spoke with Sizov about the hard work and flexibility it took to propel the company’s successful scaling endeavors: Strella is now monitoring 15 percent of all U.S. apples.
“Sizov, 24, wants to eliminate food waste one fruit at a time. In central Washington, it was an effort that required almost as much quick footwork as the épée squad she captained as a championship fencer in college. One moment, she was trying to beam the sensor’s WiFi signal through the reception black hole of millions of apples, which cause transmission issues because of their high water content. The next, she was sitting down with laconic apple growers with orchards planted generations ago, trying to convince them she could help them avoid wasted fruit. By day’s end, she might be folding her 6-foot frame into the passenger seat of a rental car, balancing her laptop on her knees and trying to win over Silicon Valley investors on Zoom calls using skills she had picked up partly by watching YouTube tutorials.”
Strella Biotechnology was founded by Penn alumna Katherine Sizov (Bio 2019) and was initially developed in the George H. Stephenson Foundation Educational Laboratory, the biomakerspace and primary teaching lab of the Department of Bioengineering. Sizov and Penn Bioengineering alumna Malika Shukurova (BSE 2019) won a President’s Innovation Prize in 2019. Read more BE blog stories featuring Strella Biotechnology.
Four of Penn’s 2021 iGEM team (left to right): Juliette Hooper, Grace Qian, Saachi Datta, and Gloria Lee.
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.
OptoReader
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.
