Spencer Haws Receives Druckenmiller Fellowship

Spencer Haws, Ph.D.

Spencer Haws, Postdoctoral Research Fellow in the laboratory of Jennifer E. Phillips-Cremins, Associate Professor and Dean’s Faculty Fellow in Bioengineering and in Genetics, was awarded a 2022 Druckenmiller Fellowship from the New York Stem Cell Foundation Research Institute (NYSCF). This prestigious program is the largest dedicated stem cell fellowship program inn the world and was developed to train and support young scientists working on groundbreaking research in the field of stem cell research. Haws is one of only five inductees into the 2022 class of fellows.

Haws earned his Ph.D. in Nutritional Sciences in 2021 from the University of Wisconsin-Madison, where he studied metabolism-chromatin connections under the mentorship of John Denu, Professor in Biomolecular Chemistry at the University of Wisconsin-Madison. As a NYSCF – Druckenmiller Fellow in the Cremins Laboratory for Genome Architecture and Spatial Neurobiology, Haws is using this previously developed expertise to frame his investigations into the underlying mechanisms driving the neurodegenerative disorder fragile X syndrome (FXS). “Ultimately, I hope that this work will help guide the development of future FXS-specific therapeutics of which none currently exist,” says Haws.

Read the full list of 2022 Druckenmiller Fellows and view introductory videos on the NYSCF website.

Taimoor Qazi Appointed Assistant Professor at Purdue University

Taimoor H. Qazi, Ph.D.

The Department of Bioengineering is proud to congratulate Taimoor H. Qazi, Ph.D. on his appointment as Assistant Professor in the Weldon School of Biomedical Engineering at Purdue University. Qazi’s appointment will begin in Fall 2022.

Qazi obtained his Ph.D. at the Technical University of Berlin and the Charité Hospital in Berlin, Germany working on translational approaches for musculoskeletal tissue repair using biomaterials and stem cells under the co-advisement of Georg Duda, Director of the Berlin Institute of Health and David Mooney, Mercator Fellow at Charité – Universitätsmedizin Berlin. After arriving at Penn in 2019, Qazi performed research on microscale granular hydrogels in the Polymeric Biomaterials Laboratory of Jason Burdick, Adjunct Professor in Bioengineering at Penn and Bowman Endowed Professor in Chemical and Biological Engineering at the University of Colorado, Boulder. While conducting postdoctoral research, Qazi also collaborated with the groups of David Issadore, Associate Professor in Bioengineering and in Electrical and Systems Engineering, and Daeyeon Lee, Professor and Evan C. Thompson Term Chair for Excellence in Teaching in Chemical and Biomolecular Engineering and member of the Penn Bioengineering Graduate Group. Qazi’s postdoctoral research was supported through a fellowship from the German Research Foundation, and resulted in several publications in high-profile journals, including Advanced Materials, Cell Stem Cell, Small, and ACS Biomaterials Science and Engineering.

“Taimoor has done really fantastic research as a postdoctoral fellow in the group,” says Burdick. “Purdue has a long history of excellence in biomaterials research and will be a great place for him to build a strong research program.”

Qazi’s future research program will engineer biomaterials to make fundamental and translational advances in musculoskeletal tissue engineering, including the study of how rare tissue-resident cells respond to spatiotemporal signals and participate in tissue repair, and developing modular hydrogels that permit minimally invasive delivery for tissue regeneration. The ultimate goal is to create scalable, translational, and biologically inspired healthcare solutions that benefit a patient population that is expected to grow manifold in the coming years.

Qazi is looking to build a strong and inclusive team of scientists and engineers with diverse backgrounds interested in tackling problems at the interface of translational medicine, materials science, bioengineering, and cell biology, and will be recruiting graduate students immediately. Interested students can contact him directly at thqazi@seas.upenn.edu.

“I am excited to launch my independent research career at a prestigious institution like Purdue,” says Qazi. “Being at Penn and particularly in the Department of Bioengineering greatly helped me prepare for the journey ahead. I am grateful for Jason’s mentorship over the years and the access to resources provided by Jason, Dave Issadore, Ravi, Dave Meany and other faculty which support the training and professional development of postdoctoral fellows in Penn Bioengineering.”

Congratulations to Dr. Qazi from everyone at Penn Bioengineering!

Penn Engineers Develop a New Method that Could Enable a Patient’s Own Antibodies to Eliminate Their Tumors

Tsourkas
Andrew Tsourkas, Ph.D.

One of the reasons that cancer is notoriously difficult to treat is that it can look very different for each patient. As a result, most targeted therapies only work for a fraction of cancer patients. In many cases, patients will have tumors with no known markers that can be targeted, creating an incredible challenge in identifying effective treatments. A new study seeks to address this problem with the development of a simple methodology to help differentiate tumors from healthy, normal tissues.

This new study, published in Science Advances, was led by Andrew Tsourkas, Professor in Bioengineering and Co-Director of the Center for Targeted Therapeutics and Translational Nanomedicine (CT3N), who had what he describes as a “crazy idea” to use a patient’s antibodies to find and treat their own tumors, taking advantage of the immune system’s innate ability to identify tumors as foreign. This study, spearheaded by Burcin Altun, a former postdoctoral researcher in Tsourkas’s lab, and continued and completed by Fabiana Zappala, a former graduate student in Penn Bioengineering, details their new method for site-specifically labeling “off-the-shelf” and native serum autoantibodies with T cell–redirecting domains.

Researchers have known for some time that cancer patients will generate an antibody response to their own tumors. These anti-tumor antibodies are quite sophisticated in their ability to specifically identify cancer cells; however, they are not sufficiently potent to confer a therapeutic effect. In this study, Tsourkas’s team converted these antibodies into bispecific antibodies, thereby increasing their potency. T cell-redirecting bispecific antibodies are a new form of targeted therapeutic that forms a bridge between tumor cells and T cells which have been found to be as much as a thousand-times more potent than antibodies alone. By combining the specificity of a patient’s own antibodies with the potency of bispecific antibodies, researchers can effectively create a truly personalized therapeutic that is effective against tumors.

In order to test out this new targeted therapeutic approach, the Tsourkas lab had to develop an entirely new technology, allowing them to precisely label antibodies with T cell targeting domains, creating a highly homogeneous product.  Previously it has not been possible to convert native antibodies into bispecific antibodies, but Tsourkas’s Targeted Imaging Therapeutics and Nanomedicine or TITAN lab specializes in the creation of novel targeted imaging and therapeutic agents for detection and treatment of various diseases. “Much is yet to be done before this could be considered a practical clinical approach,” says Tsourkas. “But I hope at the very least this works stimulates new ideas in the way we think about personalized medicine.”

In their next phase, Tsourkas’s team will be working to separate anti-tumor antibodies from other antibodies found in patients’ serum (which could potentially redirect the bispecific antibodies to other locations in the body), as well as examining possible adverse reactions or unintended effects and immunogenicity caused by the treatment. However, this study is just the beginning of a promising new targeted therapeutic approach to cancer treatment.

This work was supported by Emerson Collective and the National Institutes of Health, National Cancer Institute (R01 CA241661).

Moving Away From ‘Average,’ Toward the Individual

by Michele W. Berger

In a course from Annenberg’s David Lydon-Staley, seven graduate students conducted single-participant experiments. This approach, what’s known as an “n of 1,” may better capture the nuances of a diverse population than randomized control trials can.

David Lydon-Staley is an assistant professor of communication and principal investigator of the Addiction, Health, & Adolescence Lab in the Annenberg School for Communication.

To prep for an upcoming course he was teaching, Penn researcher David Lydon-Staley decided to conduct an experiment: Might melatonin gummies—supplements touted to improve sleep—help him, as an individual, fall asleep faster?

For two weeks, he took two gummies on intervention nights and none on control nights. The point, however, wasn’t really to find out whether the gummies worked for him (which they didn’t), but rather to see how an experiment with a single participant played out, what’s known as an “n of 1.”

Randomized control experiments typically include hundreds or thousands of participants. Their aim is to show, on average, how the intervention being studied affects people in the treatment group. But often “there’s a failure to include women and members of minoritized racial and ethnic groups in those clinical trials,” says Lydon-Staley, an assistant professor in the Annenberg School for Communication. “The single-case approach says, instead of randomizing a lot of people, we’re going to take one person at a time and measure them intensively.”

In Lydon-Staley’s spring semester class, Diversity and the End of Average, seven graduate students conducted their own n-of-1 experiments—on themselves—testing whether dynamic stretching might improve basketball performance or whether yoga might decrease stress. One wanted to understand the effect of journaling on emotional clarity. They also learned about representation in science, plus which analytical approaches might best capture the nuance of a diverse population and individuals with many intersecting identities.

“It’s not just an ‘n of 1’ trying to do what the big studies are doing. It’s a different perspective,” says Lydon-Staley. “Though it’s just one person, you’re getting a much more thorough characterization of how they’re changing from moment to moment.”

Read the full story in Penn Today.

David Lydon-Staley is an Assistant Professor of communication and principal investigator of the Addiction, Health, & Adolescence Lab in the Annenberg School for Communication at the University of Pennsylvania. Lydon-Staley is a former postdoctoral research in the Complex Systems Lab of Dani S. Bassett, J. Peter Skirkanich Professor in Bioengineering and in Electrical and Systems Engineering.

Newly Discovered ‘Encrypted Peptides’ Found in Human Plasma Exhibit Antibiotic Properties

by Melissa Pappas

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.”

Read the full story in Penn Engineering Today.

César de La Fuente Uses AI to Discover Germ-fighting Peptides

César de la Fuente, PhD

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.  

Presidential Assistant Professor in Bioengineering, Microbiology, Psychiatry, and Chemical and Biomolecular Engineering César de la Fuente and his team are using an algorithm to search the human genome for microbe-fighting peptides. So far, the team has synthesized roughly 55 peptides that, when tested against popular drug-resistant microbes such as the germ responsible for staph infections, have proven to prevent bacteria from replicating.  

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.”

Read Max G. Levy’s An AI Finds Superbug-Killing Potential in Human Proteins” at WIRED. 

This story previously appeared in Penn Engineering Today.

Yogesh Goyal Selected as 2021 STAT Wunderkind

Yogesh Goyal, Ph.D.

Yogesh Goyal, Ph.D.,  a postdoctoral researcher in Genetics and Bioengineering, has been selected as a 2021 STAT Wunderkind, which honors the “next generation of scientific superstars.” Goyal’s research is centered around developing novel mathematical and experimental frameworks to study how a rare subpopulation of cancer cells are able to survive drug therapy and develop resistance, resulting in relapse in patients. In particular, his work provides a view of different paths that single cancer cells take when becoming resistant, at unprecedented resolution and scale. This research aims to help devise novel therapeutic strategies to combat the challenge of drug resistance in cancer.

Goyal is a Jane Coffin Childs Postdoctoral Fellow in the systems biology lab of Arjun Raj, Professor in Bioengineering and Genetics at Penn. He will begin an appointment as Assistant Professor in the Department of Cell and Developmental Biology (CDB) in the Feinberg School of Medicine at Northwestern University in spring 2022.

Read the announcement in Penn Medicine News.

BE Seminar: “Phage and Robotics-Assisted Biomolecular Evolution” (Emma Chory)

Emma Chory, Ph.D.

Speaker: Emma Chory, Ph.D.
Postdoctoral Fellow
Sculpting Evolution Laboratory
Massachusetts Institute of Technology

Date: Thursday, October 21, 2021
Time: 3:30-4:30 PM EDT
Zoom – check email for link or contact ksas@seas.upenn.edu
Room: Moore 216

Abstract: Evolution occurs when selective pressures from the environment shape inherited variation over time. Within the laboratory, evolution is commonly used to engineer proteins and RNA, but experimental constraints have limited our ability to reproducibly and reliably explore key factors such as population diversity, the timing of environmental changes, and chance. We developed a high-throughput system for the analytical exploration of molecular evolution using phage-based mutagenesis to evolve many distinct classes of biomolecules simultaneously. In this talk, I will describe the development of our open-source python:robot integration platform which enables us to adjust the stringency of selection in response to real-time evolving activity measurements and to dissect the historical, environmental, and random factors governing biomolecular evolution. Finally, I will talk about our many on-going projects which utilize this system to evolve previously intractable biomolecules using novel small-molecule substrates to target the undruggable proteome.

Emma Chory Bio: Emma Chory is a postdoctoral fellow in the Sculpting Evolution Group at MIT, advised by Kevin Esvelt and Jim Collins. Emma’s research utilizes directed evolution, robotics, and chemical biology to evolve biosynthetic pathways for the synthesis of novel peptide-based therapeutics. Emma obtained her PhD in Chemical Engineering in the laboratory of Gerald Crabtree at Stanford University. She is the recipient of the NSF Graduate Research Fellowship and a pre- and postdoctoral NIH NRSA Fellowship.

Reimagining Scientific Discovery Through the Lens of an Artist

by Erica K. Brockmeier

Rebecca Kamen, Penn artist-in-residence and visiting scholar, has a new exhibition titled “Reveal: The Art of Reimagining Scientific Discovery” at American University Museum at the Katzen Arts Center that explores curiosity and the creative process across art and science. (Image: Greg Staley)

Rebecca Kamen, Penn artist-in-residence and visiting scholar, has long been interested in science and the natural world. As a Philadelphia native and an artist with a 40-plus-year career, her intersectional work sheds light on the process of scientific discovery and its connections to art, with previous exhibitions that celebrate Apollo 11’s “spirit of exploration and discovery” to new representations of the periodic table of elements.

Now, in her latest exhibition, Kamen has created a series of pieces that highlight how the creative processes in art and science are interconnected. In “Reveal: The Art of Reimagining Scientific Discovery,” Kamen chronicles her own artistic process while providing a space for self-reflection that enables viewers to see the relationship between science, art, and their own creativity.

The exhibit, on display at the Katzen Art Center at American University, was inspired by the work of Penn professor Dani Bassett and American University professor Perry Zurn, the exhibit’s faculty sponsor. The culmination of three years of work, “Reveal” features collaborations with a wide range of scientists, including philosophers at American University, microscopists at the National Institutes of Health studying SARS-CoV-2 , and researchers in Penn’s Complex Systems Lab and the Addiction, Health, and Adolescence (AHA!) Lab.

Continue reading at Penn Today.

Dani S. Bassett is the J. Peter Skirkanich Professor in the departments of Bioengineering and Electrical and Systems Engineering in the School of Engineering and Applied Science at the University of Pennsylvania. She also has appointments in the Department of Physics and Astronomy in Penn’s School of Arts & Sciences and the departments of Neurology and Psychiatry in the Perelman School of Medicine at Penn.

Rebecca Kamen is a visiting scholar and artist-in-residence in the Department of Physics & Astronomy in Penn’s School of Arts & Sciences.

David Lydon-Staley is an assistant professor in the Annenberg School for Communication at Penn and was formerly a postdoc in the Bassett lab.

Dale Zhou is a Ph.D. candidate in Penn’s Neuroscience Graduate Group.

“Reveal: The Art of Reimagining Scientific Discovery,” presented by the Alper Initiative for Washington Art and curated by Sarah Tanguy, is on display at the American University Museum in Washington, D.C., until Dec. 12.

The exhbition catalog, which includes an essay on “Radicle Curiosity” by Perry Zurn and Dani S. Bassett, can be viewed online.

Yogesh Goyal Appointed Assistant Professor at Northwestern University

Yogesh Goyal, Ph.D.

The Department of Bioengineering is proud to congratulate Yogesh Goyal on his appointment as Assistant Professor in the Department of Cell and Developmental Biology (CDB) in the Feinberg School of Medicine at Northwestern University. His lab will be housed within the Center for Synthetic Biology. His appointment will begin in Spring 2022.

Yogesh grew up in Chopra Bazar, a small rural settlement in Jammu and Kashmir, India. He received his undergraduate degree in Chemical Engineering from the Indian Institute of Technology Gandhinagar. Yogesh joined Princeton University for his Ph.D. in Chemical and Biological Engineering, jointly mentored by Professors Stanislav Shvartsman and Gertrud Schüpbach. Yogesh is currently a Jane Coffin Childs Postdoctoral Fellow in the lab of Arjun Raj, Professor in Bioengineering and Genetics at Penn.

“I am so excited for Yogesh beginning his faculty career,” Raj says. “He is a wonderful scientist with a sense of aesthetics. His work is simultaneously significant and elegant, a powerful combination.”

With a unique background in engineering, developmental biology, biophysical modeling, and single-cell biology, Yogesh develops quantitative approaches to problems in developmental biology and cancer drug resistance. As a postdoc, Yogesh developed theoretical and experimental lineage tracing approaches to study how non-genetic fluctuations may arise within genetically identical cancer cells and how these fluctuations affect the outcomes upon exposure to targeted therapy drugs. The Goyal Lab at Northwestern will “combine novel experimental, computational, and theoretical frameworks to monitor, perturb, model, and ultimately control single-cell variabilities and emergent fate choices in development and disease, including cancer and developmental disorders.”

“I am excited to start a new chapter in my academic career at Northwestern University,” Goyal says. “I am grateful for my time at Penn Bioengineering, and I thank my mentor Arjun Raj and the rest of the lab members for making this time intellectually and personally stimulating.”

Congratulations to Dr. Goyal from everyone at Penn Bioengineering!