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Author: The Wistar Institute

Wistar Scientists Identify Esophageal Cancer Biomarkers

Dr. Noam Auslander and authors trained a neural network to identify cancer risk from microbes.

PHILADELPHIA—(Dec. 5, 2023)—Wistar scientists have developed a new tool that can help identify cancer-associated microbes by using machine learning technology. Under the leadership of Dr. Noam Auslander — assistant professor in the Ellen and Ronald Caplan Cancer Center’s Molecular & Cellular Oncogenesis Program — the group has analyzed short read RNA-sequencing data to detect biomarkers for esophageal carcinoma, or ESCA. Their paper, “Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes,” was published in International Society for Microbial Ecology Communications.

Tumor microenvironments are often analyzed using RNA sequencing, or RNAseq, which identifies mRNA in a population of cells to find which genes are being expressed. Theoretically, RNAseq data can reveal the expression of microbial genes in cancerous tissue, which could help to identify microbiome shifts that might be playing a role in the cancer’s development. But RNAseq “reads” — the physical lengths of genetic data that correspond with gene expression — are often quite short, posing a challenge for classifying them into diverse microbial genetic origins. Assembling the short RNAseq reads into longer contiguous segments that can be associated with a vast array of potential origins — be they human, viral, or bacterial — to identify specific microbes whose expression correlates with ESCA is computationally challenging.

That’s where Dr. Auslander and her group decided to intervene by training a convolutional neural network, a type of machine-learning technology that can be taught to train itself to accurately assess large quantities of data. The team, using large publicly available datasets of characterized short-read data, trained the network to sort short-read RNAseq data by its likely origin: human, viral, or bacterial. Their model sought to pare down the number of short reads that would need to be assembled for identification, which would reduce the computational load of screening for microbial influences in cancer tissue.

Once the model was trained, its sorting capabilities allowed the group to selectively analyze ESCA tissue for reads of microbial origin and compare those data with apparently healthy esophageal tissue. Auslander’s team found several instances of microbial expression present in ESCA with significantly less incidence in apparently healthy esophageal tissue.

In particular, they found that nearly half of the microbial genes over-expressed in cancer originated from bacteriophages, which are viruses that infect bacteria; this finding may indicate that viruses infecting microorganisms within the tumor microenvironment facilitate ongoing cancerous gene expression.

The team also identified patient outcome predictors amid the data. Bacterial iron-sulfur proteins were found to impact human genes involved in ferroptosis — a type of cell death pathway that’s modulated by iron — which predicted poor prognosis in ESCA patients. Microbial genes involved in mitochondrial reprogramming were also found to predict ESCA patient prognosis.

“By building on our previous work, our team has successfully leveraged machine learning to dive deeper into what’s going on inside cancer,” said Dr. Auslander. “While it’s always important to remember that correlation does not equal causation, the associations we’ve been able to find between certain microbial genes and ESCA will allow scientists to further understand the mechanics of esophageal cancer — which is the first step in stopping it.”

Co-authors: Daniel E. Schäffer of Carnegie Mellon University, The Wistar Institute, and the Massachusetts Institute of Technology; Wenrui Li of The University of Pennsylvania; Abdurrahman Elbasir and Dario C. Altieri of The Wistar Institute; Qi Long of The University of Pennsylvania; and Noam Auslander of The Wistar Institute.

Work supported by: National Cancer Institute grant numbers R00CA252025 and P30-CA016520 and National Institute on Aging grant number RF1-AG063481.

Publication information: “Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes,” published in International Society for Microbial Ecology Communications.

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The Wistar Institute is the nation’s first independent nonprofit institution devoted exclusively to foundational biomedical research and training. Since 1972, the Institute has held National Cancer Institute (NCI)-designated Cancer Center status. Through a culture and commitment to biomedical collaboration and innovation, Wistar science leads to breakthrough early-stage discoveries and life science sector start-ups. Wistar scientists are dedicated to solving some of the world’s most challenging problems in the field of cancer and immunology, advancing human health through early-stage discovery and training the next generation of biomedical researchers. wistar.org

Wistar President Dario Altieri, M.D., recognized as one of Philadelphia’s Most Admired CEOs

PHILADELPHIA—(Dec. 4, 2023) — Dario C. Altieri, M.D.The Wistar Institute’s president and CEO, director of its Ellen and Ronald Caplan Cancer Center and the Robert & Penny Fox Distinguished Professor — is a recipient of the 2023 Most Admired CEO Awards recognized by the Philadelphia Business Journal for his leadership and service to Wistar.

The Most Admired CEO Award is given to recognize select leaders from the Greater Philadelphia area “who have earned respect from within and outside their companies and are leaving a mark on Greater Philadelphia and beyond.” Dr. Altieri and fellow awardees are being honored with a special December edition of the Philadelphia Business Journal commemorating their achievements and a celebration at the Switch House in Philadelphia.

“I’m honored and delighted to receive this award,” said Dr. Altieri. “I’ve had the privilege to lead The Wistar Institute for eight years now, and I continue to be inspired by all the people I have the privilege to work with at Wistar. To be recognized this way is truly a great personal and professional honor.”

Since 2015 Dr. Altieri has served as Wistar’s President and CEO while continuing to run both the NCI-designated Ellen and Ronald Caplan Cancer Center at Wistar and his research laboratory —which investigates the role of mitochondria in cancer and is recognized for having discovered the survivin gene, a fundamental cancer gene. Under his leadership, The Wistar Institute has continued to steadily grow for research impact and innovation, development of a diverse and well-trained workforce, and creation of an inclusive ecosystem for the life sciences in our region.

“Dario’s leadership has taken Wistar to new heights,” said Maureen Murphy, M.D., deputy director of the Ellen and Ronald Caplan Cancer Center and Ira Brind Professor and program leader of Wistar’s Molecular & Cellular Oncogenesis Program. “I speak for all the faculty here when I say that we’re lucky to have such a stellar leader.”

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The Wistar Institute, the first independent, nonprofit biomedical research institute in the United States, marshals the talents of an international team of outstanding scientists through a culture of biomedical collaboration and innovation. Wistar scientists are focused on solving some of the world’s most challenging and important problems in the field of cancer, infectious disease, and immunology. Wistar has been producing groundbreaking advances in world health for more than a century, consistent with its legacy of leadership in biomedical research and a track record of life-saving contributions in immunology and cell biology. wistar.org.

Dr. Cori Bargmann: A Q&A with the Winner of the 2023 Helen Dean King Award

Wistar researchers, staff and guests gathered to present the 2023 Helen Dean King Award to Dr. Cori Bargmann, Torsten N. Wiesel Professor and head of the Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior at The Rockefeller University. Dr. Bargmann was recognized for her work exploring the genetic and neural circuit mechanisms of behavior in pursuit of understanding how genes influence decisions.

The award, established in 2016 to honor women who have achieved distinction in biomedical research, is named after Dr. Helen Dean King, a well-respected geneticist and member of Wistar’s research staff from 1908 to 1950.

We sat down with Dr. Bargmann to learn more about the nature of her research and its applications.

The human brain has 86 billion neurons, but the worms you study have 302 neurons in their whole body. Just how similar are their neural functions to ours?

There’s no question that worms have much simpler capabilities and information processing than humans. Worms are never going to speak French or play the piano. There’s a limit to what their central nervous systems can do — and a limit to how far you can apply and understand many important processes in human psychology, cognition, neurology, and so on.

One of the big surprises, even to those of us who work in invertebrate biology, was the discovery that genes encoded in the genome and active in the nervous system are actually highly conserved among different species. So, 75% of the genes that are present in a human are present in other animals, including invertebrates. And that includes many of the genes that are implicated in human neurological, developmental, or psychiatric disorders.

I remember going to the first talk that uncovered some of the genetic risk factors for bipolar disorder. Ed Scolnick used large-scale human studies to identify two genes implicated in these diseases, and it turned out that they were the exact same two genes that my lab was studying in C. elegans at the time. That really confirmed that the machinery used to build complex brains is really the same as the machinery that’s being used to build simple brains. You can study it in a complex system or a simple system, but underneath it all, it’s the same machinery. Genes are like a vocabulary of biology, and our genes speak the same fundamental language for all animals.

Your work looks at how neurons can form circuits in response to genes and environmental cues. How rigid or flexible are these connections?

We certainly know that many animals — worms, mice, even people — can sometimes have an experience that they then remember for their entire life. These long-lasting changes in the brain stabilize and become very robust over time. But there are other forms of flexibility in the brain that are much more dynamic and transient; these functional connections can form and dissolve as needed. That kind of dynamism is also present in worms.

Learning and memory excite many researchers, but we’ve been less focused on cognition per se than studying how neurons can form reversible functional networks. When an animal is in a good environment, it will generate one set of behaviors, but when it moves to a stressful environment, it will just flip and generate a completely different set of behaviors with the same nervous system. In complex organisms like mice and people, even these kinds of basic nervous system reactions are incredibly elaborate because of the sheer number of neurons. But in the worm, you can really see how this exceptionally small system can give rise to completely different behaviors. There aren’t nearly enough neurons to accommodate a “one neuron, one function” design. So worms rewire their machinery somehow, actively and dynamically — and that’s something in which my lab is very interested.

I’m only looking at 302 neurons, so I can realize a more detailed sense of what’s causing a response than I could if I were to look at your brain. These worms are working with the same molecular machinery as you and me — and applying it to fewer neurons. You’ve heard of oxytocin, serotonin, and dopamine; all these molecules are present and fulfill similar roles in these tiny organisms as they do in our massive brains.

The worms’ simplicity allows us to better understand ourselves because the biology is the same all the way down, even to the simplest organisms. Brains are like computers. Now think about the history of computers. The circuitry in your laptop or even your cell phone is obviously much more advanced than the vacuum tubes from the 1950s — but a transistor is a transistor. In the same way, a neuron is a neuron.

How do you go from a small-scale understanding of neurobiology to understanding complex disorders and pathologies?

Because worms have very simple systems — we can uncover useful information about how neuronal systems work. And that can inform how other researchers might approach something like an anxiety disorder or autism.

We humans have complex interpersonal experiences and inner lives. While I know that we can sometimes look at something like a mother mouse defending her young and anthropomorphize because we recognize similar behaviors in ourselves, my research has taught me to instead zoo-morphize humans. Remember during the height of the pandemic, when we were locking down, when a lot of us were feeling on-edge and irritable? Well, it turns out that if you stick a mouse in isolation for two weeks, its brain produces a lot of certain neuropeptides called tachykinins, which cause it to be more aggressive and fearful. All this is to say that biology is biology. Studying neurobiology at the minute level can help us humans understand when that biology is working with us as well as when it’s working against us.

Congratulations on receiving the Dr. Helen Dean King award, whose story is quite an inspirational one. Was there any scientist whose work inspired you to become the researcher you are today?

My own love of the problems that I study in behavior was inspired by the work of classical neurobiologists in the 1930s. Studies like those of Konrad Lorenz, who studied parental behaviors and the bonding of mother and offspring — what’s called imprinting.

Then there’s Karl von Frisch, who studied the honeybee waggle dance. And, of course, Nikolaas Tinbergen, who studied innate aggressive behaviors. There’s a famous story about Tinbergen having a fish in a fishbowl on his windowsill. A red mail truck comes by, and the fish goes into a highly aggressive display because the fish is a red fish — he thinks the truck is another male. What those scientists in the 1930s were saying is, “Look, there are parts of behavior that are shared by every individual in a species and the behaviors are innate.” But they knew nothing of genes, or DNA, or how that might work.

Today, scientists like me look at these shared behaviors and say, “Hey, there must be something genetic underlying these patterns; each behavior must be encoded in a genetic template.” And then we ask questions: What is that template? What genes are involved, and how do they work? Those initial discoveries inspired me to think about these questions and how to answer them. That fish in the bowl, almost 100 years ago, was displaying exactly the same kind of behavior that my lab and many others are studying. Except now, we know which neuropeptides the red mail truck triggers in the fish.

Last question: favorite neurotransmitter?

Ah, that’s not fair, they’re all great! I’m not prepared to choose a favorite. That said, serotonin is very interesting in the way that it can achieve paradoxical effects. I’d say at any given time, I’m most attached to the neurotransmitter I don’t understand yet.

Wistar Trainee Research Symposium

Special Event
Friday, Feb. 23, 2024

The Wistar Institute Trainee Research Symposium is an annual all-day event showcasing academic research excellence and diversity in the Philadelphia area. Trainees who are interested in presenting their research are encouraged to submit an abstract for poster sessions. Wistar’s Trainee Association will select a few of the most exciting trainee abstract submissions to give brief talks at the Symposium. Prizes will be given to the best poster presentations by postdoctoral fellows, graduate, undergraduate, and open categories.

Keynote address
Dr. Erika Pearce, Immunology and Cellular Metabolism, Sidney Kimmel Comprehensive Cancer Center, School of Medicine and Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health.

Special presentation
Dr. Ami Patel, Assistant Professor in the Vaccine & Immunotherapy Center at The Wistar Institute.

Agenda
  • 8:00-9:00 am

    Registration/Breakfast

  • 9:00-9:05 am

    Welcome

  • 9:05-9:15 am

    Wistar’s Expanding Education and Training Programs
    Dr. Kristy Shuda McGuire

  • 9:15-10:00 am

    Session 1

    Sabina Hlavaty: ACSS1-dependent acetate utilization rewires mitochondrial metabolism to support AML and melanoma growth and metastasis

    SinoBiological: Sponsored Talk

    Patrick Exconde: The tetrapeptide sequence of IL-18 and IL-1b regulates their recruitment and activation by inflammatory caspases

  • 10:00-11:00 am

    Poster Session 1

  • 11:00-11:45 am

    Session 2

    Alessio Ugolini: Hypoxia-driven histone lactylation controls the function of immunosuppressive CD71+ Neutrophils in Glioblastoma

    Miltenyi Biotech: Sponsored Talk

    Genscript: Sponsored Talk

  • 11:45-12:30 pm

    Special Presentation
    Dr. Ami Patel

  • 12:30-1:30 pm

    Lunch

  • 1:30-2:15 pm

    Session 3

    Gauri Mirji: Boosting macrophage-specific BCAA oxidation enhances immune activation within the tumor microenvironment and diminishes tumor growth in pancreatic cancer

    Nikolas Kinney: Evaluating TDP-43 Dysregulated RNA Targets in Blood for Potential Biomarker Identification

    Diane Rafizadeh: Synthesis and design of macrocyclic collagen mimetic peptides for targeting the cancer-implicated DDR2 kinase

  • 2:15-3:15 pm

    Poster Session 2

  • 3:15-4:15 pm

    Keynote Address
    Dr. Erika Pearce

  • 4:15-6:00 pm

    Awards/Reception

The Wistar Institute
3601 Spruce Street
Philadelphia, PA 19144

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2023 Champion Run for Research Takes to the Streets to Support Wistar Trainees

A group of more than 35 Wistar trainees, researchers, staff, and family members donned their sneakers, stretched their hamstrings, and took to the sidewalks of University City on November 13 to participate in the annual Wistar Run for Research. Wistar’s Education and Training team was on hand with donuts, coffee, and water to keep everyone adequately fueled for the trek. 

Beginning at The Wistar Institute on 36th and Spruce St, participants in the two-mile fun run/walk snaked their way down Spruce St., across the South St. Bridge, and along the banks of the Schuylkill toward the finish line at the Philadelphia Art Museum.

Culminating at the foot of the iconic Rocky statue adjacent to the museum, participants gathered around the symbol of Philly’s grit and raised their arms in triumph. Several finishers even performed the traditional run up the art museum steps, emulating Sylvester Stallone’s famous scene from the 1976 movie. 

“We’re really excited by the turnout and the amount we were able to raise,” said Brennah Britten, co-president of the Wistar Trainee Association and a participant in the walk. “This is a great way for us to showcase the work that we do and help raise funds for the association at the same time.”

The event raised more than $5,000, eclipsing the trainee association’s goal by $1,000 and setting a new fundraising milestone for the annual event. Funds raised go toward training, education, and the development of our next generation of biomedical researchers.

Thank you to all that participated!  

How Does our Immune System Respond to Vaccines? 

A Q&A with Wistar’s Dr. Amelia Escolano

What got you interested in immunology?

My interest in immunology started in college. I took several immunology courses, and I was particularly attracted by antibody biology. One of these courses was Immunotechnology, and I remember being fascinated by the immense potential of antibodies for immunotherapy development. This interest further developed during my Ph.D. studies, which focused on macrophages, a type of immune cell. I investigated the role of calcineurin, a phosphatase enzyme, in macrophage polarization. In other words, I studied how calcineurin determined the specific pro- or anti-immune functions of macrophages and how this could impact the progression and outcomes of inflammatory processes.

The immune system is immensely complex. It is a very sophisticated and orchestrated network of immune mediators that interact and influence each other to provide protection against pathogenic threats. We have so much to learn about the many different immune cells and the cellular and molecular mechanisms involved in immune responses; the complexity and ingenious mechanisms of the immune system make it a very exciting area of study.

In addition to my interest in shedding light on some aspects of the immune response, the fact that the implications of immune system research are so clearly beneficial to human health makes this area of research very attractive to me and my team.

Now, in your lab, you investigate the mechanisms governing the immune responses to vaccines. Very broadly, can you tell us about that work?

Our research revolves around vaccine design; that’s the goal that informs our approach. We are interested in understanding how B cells and T cells respond to vaccination so that we can leverage this information to design better vaccines. In particular, we study the process of antibody affinity maturation.

Affinity maturation is the process by which antibodies are produced and refined to target a specific antigen, a component of a pathogen that activates the immune system. Antibody affinity maturation takes place in the germinal centers, which are anatomical sites where B cells work with a certain kind of T cell called T follicular helper (Tfh) cells to iteratively refine and test their B cell receptors — otherwise known as antibodies. This process allows the immune system to improve its antibody responses.

With this process in mind, we aim to understand how a vaccine should be designed so that the elicited antibody response can efficiently prevent infectious diseases for long periods of time.
In my lab, we study the immune response to sequential immunization in the context of HIV-1. Sequential immunization is a novel form of vaccination that requires multiple boost immunizations with different but related viral proteins. In the case of HIV-1, sequential immunization involves multiple boost immunizations with different versions of the envelope protein of HIV-1.

Sequential immunization takes advantage of the antibody affinity maturation process with the ultimate goal of getting the immune system to produce high-quality antibodies that can fight complex, highly variable viruses like HIV.

We analyze how B cell populations and their antibodies evolve in response to sequential immunization, and we’re testing strategies to make that antibody affinity maturation more efficient by focusing on both B cells and T follicular helper cells.

Why is sequential immunization necessary against HIV-1?

To vaccinate effectively against HIV, we need B cells to produce what we call a broadly neutralizing antibody, or bNAb. bNAbs are rare antibodies that can neutralize multiple different variants of HIV-1, and we expect a vaccine that elicits bNabs to protect effectively against HIV-1.

Our previous work showed that repeated immunization with the same HIV-1 envelope protein was not capable of inducing bNAbs. Instead, sequential immunization efficiently induced antibodies that potently neutralized a large number of different HIV-1 variants.

In a sequential immunization protocol, we start with an engineered HIV-1 envelope immunogen, which is a term that we use to describe an antigen we’re testing as a vaccine candidate. The role of this first immunogen is to activate a rare subset of B cells that have receptors with the capacity to be refined into bNAbs. These B cells respond to this first immunogen and increase their affinity for it.

That increase in affinity for the first immunogen is associated with an increase in affinity for a slightly more complex HIV-1 envelope immunogen, which is then used for a second immunization. Sequential immunization repeats this process multiple times as a way of gradually increasing the affinity of B cells for the unmodified wild-type, or naturally occurring, HIV-1 envelope protein. We nudge B cells along to make sure that they mature in a way where they get progressively better at reacting to different HIV-1 strains.

How are you able to tell that your sequential vaccination protocol has produced a broadly neutralizing antibody? What do you look for?

We test our sequential immunization protocols by looking at blood after vaccination and running what’s called a serum neutralization assay. This assay can determine whether the mix of antibodies in the blood, elicited upon vaccination, can neutralize different HIV-1 strains. The number of different HIV-1 strains that the serum antibodies can neutralize determines the breadth of these antibodies. This assay also informs us of the potency of the antibodies to neutralize each HIV-1 strain.

In addition to these neutralization assays, we analyze B cells from lymph node tissue to see which antibodies they’re expressing. We are then able to evaluate individual antibodies for their capacity to neutralize HIV-1. These evaluations help us refine our vaccine candidates and sequential immunization protocols by showing us what’s working and what isn’t.

For how long has this immunology work been your focus?

I’ve been working on this approach for HIV vaccine development since I started my postdoctoral studies in the Nussenzweig laboratory at The Rockefeller University in 2014. Now, at The Wistar Institute, where I established my independent lab two years ago in September of 2021, my lab is expanding this research.

I came to The Wistar Institute with a vision of what I wanted my science to be, and Wistar has helped make that vision a reality. Here, I have found great colleagues, I have established fantastic collaborations both at Wistar and UPenn and I have seen my program grow exponentially. I’ve also found great opportunities to explore other research areas that have strengthened my program’s approach.

I find it hard to believe that two years have gone by already; the time has been both positive and productive. The welcome and support I’ve had at Wistar make me feel like a real part of a community. I can tell that all my Wistar colleagues — across the labs, across the departments — have an investment in seeing our science succeed.

Biomedical Technician Training (BTT) Pre-apprenticeship Information Session

Special Event
Friday, Nov. 17, 2023

Join us to learn more about The Wistar Institute’s Biomedical Technician Training (BTT) Pre-apprenticeship Program for community college students at the Community College of Philadelphia (CCP), Montgomery County Community College (MCCC), Bucks County Community College (BCCC), and Delaware County Community College (DCCC) in PA as well as Camden County College (CCC) in NJ. Event will be online via Zoom.

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From Lab to Laptop: The Interdisciplinary World of Computational Biology 

Wistar’s Dr. Avi Srivastava seamlessly integrates elements of computer science and traditional biology into his new computational biology research lab. By combining wet and dry lab approaches — experimental biology and computational data — he can be innovative in research derived from both worlds. Here’s how he does it.

What is computational biology?

Computational biology is different for different people. For me, the fine line between bioinformatics and computational biology is a live question, but we can think about computational methods intersecting with biology in two basic ways.

The first element is existing methods. These are open-source tools that exist on the internet as downloadable, which can then be applied to data and generate something useful. When scientists talk about “mining” datasets, they’re using tools like this on a particular dataset. This large area of research takes a good deal of resources, and many scientists interact with computational elements of research on this level.

Let’s define open source. Open source is freely accessible. An example might be an algorithm that can analyze RNA data in bulk to look for a particular pattern associated with something, maybe a disease biomarker. Scientists can simply download that algorithm, execute it on the dataset they’re interested in, and interpret the results. So, using these existing methods to answer questions about biological data is the first component of computational biology.

The second component would be the actual development of those tools. Someone has to develop them, right? And I relish in developing new methods; that’s who I am. Every software method in the field of biology needs to be informed biologically, through experimentation. That’s how you make these tools better. It’s not just sitting in your room on your laptop coding for hours — it’s getting in the lab to understand how the biology behind the code works.

Once you understand the tools’ foundations and limitations, you can modify lab experiments and refine methods. This process complements itself through experimenting, collaborating, and refining. Computational biology loops from lab to code to lab — a virtuous circle that continues to improve, because the field moves so fast.

How long has computational biology existed and when did it emerge as a field?

I think that computational biology grew out of computer science. Now, computer science has been around for ages; we can go all the way back to Turing machines, or even further. But I think that the Human Genome Project in the 1990s really opened a lot of scientists’ eyes to the power of combining computer science with biological research.

The Human Genome Project developed enormous data sets, and back then, the sequencing technologies weren’t advanced enough to sequence long segments of DNA. So, scientists began to ask themselves how they could chop up the human genome into segments of DNA for sequencing and then reassemble the human genome from those chunks. To do that, they turned to computer methods.

Think of it like file compression, when you email a picture and it loses some image quality: that’s what scientists did to the human genome, and I believe that’s the time computational biology came into its own. Since then, the field has matured and tech has improved, and our ability to “see” more of the genome has improved too, because we can process more data.

Software and code can change very quickly. How do you stay up-to-date on all the new developments in the field?

Staying current in the field is one of the million-dollar questions in computational biology, and I don’t know that anyone has cracked it. Because with software and open-source code, things do move fast, and scientists want to use the best, latest methods to answer their research questions.

In my experience, you have to orient your lab around reading papers efficiently. Rather than spending an hour on every paper and discussing it in-depth, I like the setup of my previous boss where I have my lab discuss four papers in an hour when reviewing the literature. In general, we keep 15 minutes a paper to get a broader sense of the method, what’s new, and how we can learn from it — and then we selectively discuss relevant papers in-depth. It’s not a perfect solution, but it helps you get a broader perspective of the way the field is growing.

The pace of the science makes computational biology exciting, in part because the changing tech is a challenge in its own right, and scientists like me love a good challenge.

What do you see as the Srivastava Lab’s role in such a dynamic research landscape?

Computational biology methods should be adjustable and easy to use, but I think the field needs better tools and better support for those tools. When I say “support,” I mean that if I download software and it doesn’t work except in one specific circumstance, then that tool has very limited use for the broad scientific community. It’s a big problem when some papers can’t even be replicated using the same methods because of a lack of support from the developers. With well-supported tools, researchers can utilize the method effectively, which is necessary for reproducing and verifying results.

Yes, we need to make sure programs and tools work properly, but providing support when building them allows diverse applications by allowing scientists to adapt these tools to their own research questions. When programs are tweaked and iterated upon, scientists can get creative and research flourishes — but that can only happen if those tools are built in a way that lets scientists tweak them easily.

I will support those kinds of innovative alterations in the way I go about developing tools, but also by keeping the user in mind and providing tutorials, instructional PDFs, videos, etc. That takes time, but if you’re invested in your methods, providing that support can make them even more impactful.

What excites you about the field and your work in it?

We talked about this computational biology “loop” — code feeds into the wet lab, which feeds into the code, and so on. I’m very excited to be at Wistar working on both sides of that loop; many scientists focus on one or the other, but my lab is focused on bringing both the lab and the code to the fore simultaneously.

That’s an exciting space to be in because we have so much room for interdisciplinary discovery and collaboration. I can work with computer scientists who want to learn more about biology, and I can work with biologists who want to learn more about coding. My lab is interested in the epigenome — how the genome is modified — because it’s important for so many different processes and disease states across cell types. By focusing on the computational and the biological, I think we have a tremendous opportunity to build tools that will give us a more detailed understanding of the epigenome’s complexities.

Wistar Scientists Engineer New NK cell Engaging Immunotherapy Approaches to Target and potentially Treat recalcitrant Ovarian Cancer

PHILADELPHIA—(Nov. 1, 2023)— The Wistar Institute’s David B. Weiner, Ph.D., executive vice president, director of the Vaccine & Immunotherapy Center (VIC) and W.W. Smith Charitable Trust Distinguished Professor in Cancer Research, and collaborators, have engineered novel monoclonal antibodies that engage Natural Killer cells through a unique surface receptor that activates the immune system to fight against cancer.

In their publication titled, “Siglec-7 glyco-immune binding MAbs or NK cell engager biologics induce potent anti-tumor immunity against ovarian cancers,” published in Science Advances, the team demonstrates the preclinical feasibility of utilizing these new cancer immunotherapeutic approaches against diverse ovarian cancer types, including treatment-resistant and refractory ovarian cancers — alone or in combination with checkpoint inhibitor treatment.

The research started as a collaboration between Wistar’s Drs. Weiner and Mohamed Abdel-Mohsen, who were exploring the development of new glyco-signaling biologic tools that may be important in the fight against cancer.

Ovarian cancer (OC) is frequently diagnosed late in the disease process, and OC resistance to currently available treatments make it especially problematic; according to the NIH, the chances of someone diagnosed with OC and surviving for five years is around fifty-fifty. Ovarian cancer demonstrates a low response rate to standard-of-care treatments like chemotherapies, PARP inhibitors and the widely used checkpoint inhibitor, PD-1.

In the small proportion of ovarian cancer patients that do respond to these treatments, resistance becomes problematic over time — resulting in tumor escape and cancer progression. Genetic mutations, such as the well-known BRCA gene mutations, predispose women to a high risk of progressive OC. The CDC expects more than thirteen thousand women to die of ovarian cancer this year in the U.S. alone.

To combat ovarian cancer treatment resistance, the team hypothesized that they might be able to engage not only the traditional T cell immune arm of the immune system which PD-1 and known checkpoint inhibitors (CPI) activate, but also implement a strategy to activate Natural killer cells (NK cells), a subset of important anti-tumor immune cells, through a conserved glyco-immune marker found on the surface of most NK cells called Siglec-7 (Sialic acid-binding immunoglobulin-type lectin). NK cells have been recently described to express Siglec-7, so the team tested two new strategies to engage and activate NK cells against ovarian cancer through Siglec-7.

The first approach used human monoclonal antibodies (mAb) discovered and developed at Wistar and novel assays to visualize and demonstrate that certain anti-Siglec-7 mAbs could activate human NK cells — which, in the presence of the antibodies, responded against multiple human OC cell lines. These now-activated NK cells would kill OC but not non-cancer cells with the Siglec-7 mAb treatment.

The researchers demonstrated that multiple OC carrying mutations, including BRCA1 and BRCA2, could be targeted by Siglec-7 antibodies through activated NK cells. The group moved to study the treatment of OC in a humanized mouse model and observed that the Siglec-7 treatment could impact OC growth slowing the tumors and increasing the animals’ survival.

Having demonstrated the feasibility of utilizing a Siglec-7 mAb in OC models, the team thought there were additional ways to use the Siglec-7 mAb to further focus on OC disease. They hypothesized that directly fusing the Siglec-7 reactive binding site of the Siglec-7 mAb to a second mAb that uniquely binds late OC through a molecule named Follicle Stimulating Hormone receptor (FSHR), which they had previously developed, would create a targeted Siglec-7 bispecific antibody that could bind through two distinct targets creating a new class of NK cell engagers (NKCE).

The team sought to test whether this Siglec-7 NKCE approach would be effective through the direct linkage of potentially killer NK cells to a guided missile aimed specifically at OC, which would open up a new path to develop additional Siglec-7 based immunotherapeutic approaches. In both bench and humanized mouse challenge studies, the Siglec-7-NKCE was effective at targeting OC, activating NK cells in local proximity and efficiently killing multiple OC.

Both Siglec-7 technologies (mAbs and NKCEs) demonstrated an ability to recruit and activate the NK cell population, shrink tumors and prolong survival in the models studied. The observation of on-target specificity of the approaches suggests that cancer’s apparent Siglec vulnerability can be exploited therapeutically, perhaps with limited toxicity — a promising sign for the future of anti-cancer Siglec research, but the team cautions that more work in this regard is important.

In an additional set of preliminary studies, the team also found that this Siglec-7 approach could complement PD-1 checkpoint inhibitor (CPI) therapy. This is an important area of further study that could uncover more details of the mechanisms involved and possibly extend the utility of such CPI in OC and, potentially, other cancers. “These findings open the door to further exploration of how we can engineer Siglec-7 immunotherapies and perhaps other related molecules for ovarian cancer and perhaps a larger group of recalcitrant cancers,” stated Dr. David B. Weiner, adding, “Further studies may bring such approaches as described to represent new tools in our antitumor toolbelt.”

As always, more research is needed to refine these technologies further on the long journey from the lab bench to the clinic. But this paper offers a different avenue for attempting to exploit these unique interactions of immune surface molecules such as Siglec-7 and perhaps other Siglecs.

“We have observed not one but two methods that can target NK cells in an effort to control ovarian cancer in both Petri dishes and in vivo models,” said Dr. Devivasha Bordoloi, the first author on the paper. “This research shows a lot of promise, and I’m excited to move these studies to the next steps.”

Co-authors: Devivasha Bordoloi, Abhijeet J. Kulkarni, Opeyemi S. Adeniji, Pratik S. Bhojnagarwala, Shushu Zhao, Candice Ionescu, Alfredo Perales-Puchalt, Elizabeth M Parzych, Xizhou Zhu, Ali R. Ali, Joel Cassel, Rugang Zhang, Mohamed Abdel-Mohsen and David B. Weiner of The Wistar Institute; and M. Betina Pampena and Michael R. Betts of Perelman School of Medicine, University of Pennsylvania,

Work supported by: Department of Defense Ovarian Cancer Research Program award W81XWH-19-1-0189; the W.W. Smith Charitable Trust Professorship in Cancer Research; and the Wistar Science Accelerator Postdoctoral Fellowship.

Publication information: “Siglec-7 glyco-immune binding MAbs or NK cell engager biologics induce potent anti-tumor immunity against ovarian cancers,” from Science Advances.

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The Wistar Institute, the first independent, nonprofit biomedical research institute in the United States, marshals the talents of an international team of outstanding scientists through a culture of biomedical collaboration and innovation. Wistar scientists are focused on solving some of the world’s most challenging and important problems in the field of cancer, infectious disease, and immunology. Wistar has been producing groundbreaking advances in world health for more than a century, consistent with its legacy of leadership in biomedical research and a track record of life-saving contributions in immunology and cell biology. wistar.org.

Jesper Pallesen, MBA, Ph.D.

Assistant Professor, Vaccine & Immunotherapy Center

Pallesen received his Ph.D. degree from Aarhus University. He received his postdoctoral training at Columbia University and The Scripps Research Institute. Here, he specialized in cryo-electron microscopy of bio-molecular protein complexes relating to infectious disease and immunobiology. In parallel to his postdoctoral training, he has extensive experience as a technical consultant in IP law and he received his M.B.A. from Rady School of Management with specialization in statistics, finance and management. His group studies infectious disease and cancer and develops vaccines and immunotherapeutics from a structural biology guided approach.

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Selected Publications

  • DNA-delivered antibody cocktail exhibits improved pharmacokinetics and confers prophylactic protection against SARS-CoV-2.

    Parzych EM, Du J, Ali AR, Schultheis K, Frase D, Smith TRF, Cui J, Chokkalingam N, Tursi NJ, Warner BM, Gary EN, Li Y, Choi J, Eisenhauer J, Maricic I, Kulkarni A, Chu J, Villafana G, Rosenthal K, Ren K, Francica JR, Wootton S, Tebas P, Kobasa D, Broderick K, Boyer JD, Esser MT, Pallesen J, Kulp DW, Patel A, Weiner DB. “DNA-delivered antibody cocktail exhibits improved pharmacokinetics and confers prophylactic protection against SARS-CoV-2.” Nat. Commun. 2022 Oct 6;13(1):5886.

  • The Chimpanzee SIV Envelope Trimer: Structure and Deployment as an HIV Vaccine Template.

    Andrabi R*, Pallesen J*, Allen JD, Song G, Zhang J, de Val N, Gegg G, Porter K, Su CY, Pauthner M, Newman A, Bouton-Verville H, Garces F, Wilson IA, Crispin M, Hahn BH, Haynes BF, Verkoczy L, Ward AB, Burton DR. “The Chimpanzee SIV Envelope Trimer: Structure and Deployment as an HIV Vaccine Template.” Cell Rep. 2019 May 21;27(8):2426-2441.e6.

  • Immunogenicity and Structures of a Rationally Designed Prefusion MERS-CoV Spike Antigen.

    Pallesen J*, Wang N*, Corbett KS*, Wrapp D, Kirchdoerfer RN, Turner HL, Cottrell CA, Becker MM, Wang L, Shi W, Kong W, Kettenbach AN, Denison MR, Chappell JD, Graham BS, Ward AB, McLellan JS. “Immunogenicity and Structures of a Rationally Designed Prefusion MERS-CoV Spike Antigen.” Proc Natl Acad Sci USA. 2017 Aug 29;114(35):E7348-E7357.

  • Open and Closed Structures Reveal Allostery and Pliability in the HIV-1 Envelope Spike.

    Ozorowski G*, Pallesen J*, de Val N, Lyumkis D, Cottrell CA, Torres JL, Copps J, Stanfield RL, Cupo A, Pugach P, Moore JP, Wilson IA, Ward AB. “Open and Closed Structures Reveal Allostery and Pliability in the HIV-1 Envelope Spike.” Nature. 2017 Jul 20;547(7663):360-363.

  • Structures of Ebola Virus GP and sGP in Complex with Therapeutic Antibodies.

    Pallesen J*, Murin CD*, de Val N, Cottrell CA, Hastie KM, Turner HL, Fusco ML, Flyak AI, Zeitlin L, Crowe JE Jr, Saphire EO, Ward AB. “Structures of Ebola Virus GP and sGP in Complex with Therapeutic Antibodies.” Nat Microbiol. 2016;1 pii: 16128. Epub 2016 Aug 8.

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