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Tag: Sarma

Wistar Scientists Start New Conference on Foundational RNA Research

Written by The Wistar Institute on . Posted in Featured News.

Back from hosting the first-ever Genome Regulation through RNA Conference in Cancun, Mexico, Wistar faculty members Alessandro Gardini, Ph.D., and Kavitha Sarma, Ph.D., give us the inside scoop on what it was like to host a scientific meeting from scratch.

What made you want to create a new conference?

Alessandro Gardini: Hundreds of biomedical research conferences happen every year. They are hallmark meetings — featuring a great lineup of presenters and topics — but sometimes you want a fresh perspective. Kavitha and I were interested in a distinct conference focus, and thought, “why not create something together?”

With our friend and collaborator Dr. Roberto Bonasio, associate professor at University of Pennsylvania, we developed a new concept. Once we had a pitch, we created a “wish list” of top people in our field whom we’d want to invite, and in which topics we’d want to coalesce talks and panels.

What is a successful conference?

AG: If you want people to attend your conference, you need prestigious scientists. Researchers who’ve made big waves in the field can entice people to attend.

KS: Attending conferences is critical to being a scientist, but you only have a certain amount of travel per year, so you want to attend the most impactful meetings.

AG: We had 90 people – a great turnout for a first-time event.

You named your meeting the “Genome Regulation through RNA Conference.” Can you describe the scientific niche you were aiming to fill?

AG: Plenty of conferences are entirely RNA-focused, but we created this conference at the intersection of RNA and epigenetics – where we do most of our work.

KS: This meeting focused on the most foundational, basic levels of RNA-driven genome regulation: which genomic functions do RNAs perform, how are DNA-RNA hybrid structures implicated in gene expression. We didn’t even delve into the therapeutics side because we were focused on the fundamentals. This gathering of like-minded people presented abstracts centered on the mechanistic aspects of RNA within the human genome.

AG: That RNA focus – for the mere sake of understanding its genomic effects – led to some very interesting discussions. For example, the mitochondria in our cells have their own genomes, which we tend not to think about too much. But by having their own genomes, they naturally have genomic regulatory mechanisms, too, which involve certain mitochondrial RNAs. Those are the ideas and research topics that I love encountering at conferences. My research, on its own, may not have taken me there.

Why are conferences so important to scientists?

AG: In biological terms, it’s the “lymph” of our work—it enhances our research. Conferences are extremely important for fostering collaboration. Yes, there’s a body of literature, and our job is to stay current on published papers in our field. But that’s a small snapshot of knowledge compared to the free flow of information at conferences.

All science, but especially biomedical research, is highly specialized now. We’re a long way from the days of eccentrics conducting experiments in castles. Today, researchers can spend their entire lives analyzing something as minute and specific as the mitochondria.

Conferences give scientists much-needed exposure to other areas of research. We learn how to conduct science better, how to incorporate new ideas. And that keeps scientific passion alive. Seeing all the exciting work that others are doing refreshes my sense of enthusiasm and gives me ideas that I can begin to pursue.

KS: They’re also indispensable for collaboration. I can’t tell you how many times at a conference, a conversation leads to two people publishing on the same paper as co-authors. Without that conference, they may never have met.

You can never know how your work might be applicable in other fields because those areas aren’t your areas of expertise. Conferences open researchers’ eyes to opportunities to improve each other’s work, and everyone wins. By being there, talking and meeting new people, going to networking dinners, that turns into new ideas, new papers, and better science.

Genomic Origami: Wistar Scientist Dr. Kavitha Sarma Studies How the Shape of Our Genes Impacts Disease

Written by The Wistar Institute on . Posted in Featured News.

A Q&A with Dr. Kavitha Sarma

Dr. Kavitha Sarma runs an independent lab focused on nucleic acid structures called R-loops that contain both DNA and RNA and assist in gene expression. Dr. Sarma, associate professor in Wistar’s Gene Expression and Regulation Program, recently published a paper in Molecular Cell about genomic structures — specifically, G-quadruplexes and R-loops.

R-loops are bubble-like structures that can form in our DNA, and they can affect how genes are expressed — whether genes are turned on or off. G-quadruplexes form on the single-strand DNA of R-loops and can stabilize R-loops. In her research, Dr. Sarma found that R-loops and G-quadruplexes can influence the binding of a protein called CTCF, which helps fold and organize our DNA. This folding process is important for gene expression. If the genome is folded correctly, that allows genes to be expressed the way they should be. But if the genome is folded incorrectly, it can cause faulty patterns of gene expression, which can potentially lead to disease and cancer. R-loops and G-quadruplexes can play a role in cancer and disease by recruiting CTCF in a way that promotes faulty gene expression.

IN YOUR PAPER, YOU FOUND THAT R-LOOPS AND G4S HAD AN INTERESTING RELATIONSHIP WITH A CERTAIN MOLECULE. COULD YOU EXPLAIN THAT FINDING?

In every cell nucleus in your body, you have something like two meters of DNA, if you were to unravel it completely into one long double helix. Just to make genetic information physically fit in your body, the genome has to be compacted, and that needs to happen in every single cell, too.

There are many proteins that function in genome folding. We found that R-loops and G4s can influence the binding of one of these proteins – CTCF, which has a very important role in how the genome is folded.

This folding process, which also serves as a kind of information organization process, is important for how cells develop and specialize in our body. For example, the way a neuron’s genome is folded and expressed will be different from the genome folding and gene expression of a pancreatic cell because the two cell types fulfill different purposes. Epigenetic regulation from factors like genome folding allows for a diversity of gene expression — which, in turn, allows for a diversity of cell types and functions.

So, if a genome is folded correctly in the nucleus and the right regions are next to each other, that has a positive effect, and genes are expressed the way they should be. But if CTCF folds the genome incorrectly — for example, if R-loops and G4s form and facilitate CTCF binding to regions where it isn’t supposed to bind — we might see incorrect patterns of gene expression and the kinds of dysregulation you’d find in cancer and disease.

WHAT ARE THE PATHOGENIC IMPLICATIONS OF CTCF RECRUITMENT?

This finding, that G4s affect CTCF, tells us that the genome misfolding in disease can be at least partially due to the formation of R-loop structures. In addition to developmental disorders, R-loop and G4 structures can play problematic roles in cancer because they’re what we call co-transcriptional. When transcription happens, these structures tend to accumulate — they tend to become stabilized. Hypertranscription that occurs in many cancers can contribute to genome misfolding through R-loop and G4 formation, which can further reinforce faulty gene expression patterns by essentially rewiring the genome.

WHAT DOES THIS REWIRING CYCLE TELL US ABOUT THE EPIGENETICS OF CANCER AND DISEASE?

I think that this research gives us a good roadmap for looking for therapeutics down the line, because a better understanding of epigenetic regulation gives us deeper insight into how disease states work at a very localized level.

We know that R-loops and G4s can alter CTCF binding and change genome folding. Going forward, we can identify pathogenic contacts that occur because of these genomic structures and try to correct them. This is how foundational research — understanding processes that weren’t understood before — can lead to advances in the science of human health.

Learning How to Read the Book of Life

Written by The Wistar Institute on . Posted in Featured News.

Research in the Gene Expression & Regulation Program at Wistar continues to reveal new knowledge on RNA and its functions to regulate how our genes are expressed and how that can go awry.

The advent of mRNA vaccines for COVID-19 — touted as the next-generation tool in vaccinology — brought RNA to the fore, giving popularity to this once less-publicized cousin of DNA.

In high school biology, we learned that our genes are the repositories of the blueprint to make all of our proteins. Our genes carry out most of the functions in our cells. RNA is the carrier of information from DNA to ribosomes — the machines that manufacture proteins.

The process of reading and executing the instruction book of life involves strict oversight and multiple levels of regulation to allow a relatively small number of genes to orchestrate all the functions of our body. Control of gene expression plays a critical role in determining what proteins are present in a cell and in what amounts at any given time.

It is becoming abundantly clear that this control process happens both during and after RNA transcription.

Wistar scientists have pioneered the study of RNA biology, discovering new RNA types and unraveling some of the mechanisms that modify RNA to regulate its functions for gene expression. Following along that path, labs in the Gene Expression and Regulation Program continue to delve deep into the RNA world and make exciting discoveries related to RNA structure and functions.

R-LOOPS: Friend-Foes

Dr. Kavitha Sarma, assistant professor, focuses on particular nucleic acid structures called R-loops that contain both DNA and RNA and form during transcription, the first step of gene expression.

In our DNA book, consider genes as the individual words and nucleotides as the letters that make up those words. When a DNA template is “transcribed” into messenger RNA (mRNA), the sequence of letters that form each gene gets “read” and copied into an RNA molecule that will leave the nucleus and travel to the cytoplasm, where words will be read by ribosomes to provide instructions for making proteins.

Sometimes during transcription, the newly synthesized RNA molecule sticks to its template DNA strand, forming a stable DNA/RNA hybrid that appears like a loop when visualized by electron microscopy, hence the name R-loop.

This is a normal occurrence — R-loops are constantly formed and removed throughout the genome and their presence can be beneficial for transcriptional regulation. However, accumulation of R-loops can cause DNA damage, chromosome rearrangements and genomic instability and underlie a host of diseases from cancer to neurodegenerative disorders and possibly autism.

The Sarma lab is interested in R-loops for their potential in causing disease and in serving as new therapeutic targets. They have been busy developing new, improved techniques to detect R-loops to study the contributions of these structures in gene regulation and the consequences of their accumulation in the cell1.

Thanks to these technological advances, Dr. Sarma and her colleagues were able to identify new factors that regulate R-loops and are now closing in on their function in glioblastoma and colon cancer.

The lab received funding from the W.W. Smith Charitable Trust to study the role of R-loops in brain cancer and with support from the Basser Center for BRCA and the Margaret Q. Landenberger Research Foundation they are dissecting the correlation between R-loop formation and BRCA1/2 gene mutations in breast and ovarian cancer to eventually use R-loops for novel diagnostic and therapeutic applications. The Simons Foundation supports the lab’s work elucidating the consequences of unregulated R-loops in autism spectrum disorders.

EDITING RNA TO RESOLVE R-LOOPS

Dr. Kazuko Nishikura, professor, has published a new function of R-loops2 in preserving the integrity of our chromosome ends — the telomeres.

Dr. Nishikura has been a pillar of Wistar science for almost four decades with a career overlapping with the rise and expansion of the RNA biology field. She was one of the first to characterize a process called RNA editing and its multiple functions in the cell, and to discover the enzyme ADAR1 that is responsible for it.

RNA editing changes one or more letters in RNA “words,” allowing cells to make discrete modifications to an RNA molecule. RNA editing is a good example of how our cells make the most of their genes and create different protein products from a single gene by slightly modifying the RNA sequence.

With support from grants from the National Institutes of Health and Emerson Collective, the Nishikura lab recently showed that ADAR1 helps the cells resolve R-loops formed at the chromosome ends and prevents their accumulation by facilitating degradation of the RNA strand.

Nishikura and colleagues found that depletion of a particular form of the ADAR1 protein leads to extensive telomeric DNA damage and arrested proliferation specifically in cancer cells, indicating this process as a new target for cancer therapy.

ALTERNATIVE POLYADENYLATION: Tell Me What Your APA Is and I Will Tell You Where to Go

An important level of mRNA regulation involves modifying its structure, especially at the tail end of the sequence, termed 3’ end. A process called polyadenylation adds a stretch of specific nucleotides to protein-coding mRNAs to regulate their stability, transportation from nucleus to cytoplasm and translation into proteins.

Dr. Bin Tian, professor, and his lab study this process to understand regulatory mechanisms and to identify new drug targets. They have contributed important knowledge on polyadenylation in normal and diseased conditions, including the discovery that alternative polyadenylation (APA) is widespread across genes.

This is a dynamic mechanism of gene regulation that generates different 3′ ends in mRNA molecules, resulting in multiple mRNAs from the same gene, which scientists call isoforms.

The lab’s latest research is uncovering the role APA plays in facilitating protein production in certain sites within the cell where those proteins are most needed.

When mRNAs leave the nucleus and move to the cytoplasm, they need to be properly directed to reach the ribosomes and be translated into proteins. Although too small to be seen with the naked eye, a cell is a huge space for something as tiny as an mRNA molecule that has to find its way. Imagine finding yourself in a baseball stadium and not knowing how to get to your seat.

The Tian lab discovered that some mRNAs possess specific properties in their sequence and structure that enable them to associate with the endoplasmic reticulum (ER), a network of tubes that build, package and transport proteins and where a large fraction of ribosomes in the cell are located3.

These mRNAs tend to encode for proteins involved in cell signaling, the process that allows the cells to communicate with neighboring cells by sending, receiving and processing signals to respond to changes in their environment.

Dr. Tian and his team hypothesize that association with the ER anchors certain mRNA isoforms in specific cellular locations where important signaling events happen, making the whole process more efficient. According to this model, the ER would serve a new function as a scaffold to keep proteins at hand where they are needed, representing a platform that provides venues for signaling events to happen quickly and effectively.

The lab also creates computer-based data mining tools to analyze APA using large data sets, such as those from The Cancer Genome Atlas (TCGA) program.

The extraordinary biological complexity of human life is a reflection of the many sophisticated ways in which gene expression can be fine-tuned.

The cutting-edge science underway at Wistar pushes the limits of RNA research to advance our understanding of how the human genome is decoded, how the messengers of genetic information are guided, and how accidental mistakes that happen while reading and interpreting the DNA book can be fixed, all of which may enable researchers to develop novel and more precise ways to treat diseases.

1 A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide, Elife 2021
2 ADAR1 RNA editing enzyme regulates R-loop formation and genome stability at telomeres in cancer cells, Nature Communications 2021
3 Alternative 3’UTRs play a widespread role in translation-independent mRNA association with endoplasmic reticulum, Cell Reports 2021

A New Generation of Cancer Researchers at Wistar

Written by The Wistar Institute on . Posted in Featured News.

Expanding the faculty and enhancing its multidisciplinary nature are focal points in Wistar’s Cancer Center under the leadership of Dario Altieri, M.D., president and CEO, director of The Wistar Institute Cancer Center, and Robert and Penny Fox Distinguished Professor.

The recent recruitment efforts, supported by partners such as The Pew Charitable Trusts, were inspired by the idea that junior investigators—in their peak of scientific productivity and creativity—are most likely to generate cutting-edge research. Therefore, attracting the most brilliant scientists and persuading them to launch their laboratory at Wistar positions the Institute ahead of a trend that is becoming increasingly popular in many research institutions.

In the span of one year from 2015 to 2016, four assistant professors joined the Cancer Center, thereby enriching and complementing existing programs with new expertise and fresh perspectives:

Qing Chen, M.D., Ph.D., came to Wistar from Memorial Sloan-Kettering Cancer Center and started her lab researching the mechanisms of brain metastasis, a very challenging subject that is in urgent need of advancement.

Alessandro Gardini, Ph.D., an ‘old acquaintance’ of Wistar’s, began his postdoctoral training in a Wistar lab and completed it at the University of Miami. He studies genomics and epigenetics, or how our genome is decoded and how malfunctioning mechanisms can cause cancer.

Kavitha Sarma, Ph.D., came from Harvard Medical School. She is a biochemist and an epigenetics expert. Her current focus is in understanding how certain RNA molecules help shape the structure of chromatin, the combination of DNA and protein that makes up chromosomes, and elucidating the role of these mechanisms in cancer and other diseases.

Zachary Schug, Ph.D., a Philadelphia native who received his postdoctoral training across the ocean at the Beatson Institute in Glasgow, U.K., returned to Philadelphia to launch his research program at Wistar in cancer metabolism, looking at the mechanisms that support the high nutrient demands of tumor growth.

Four years after arriving, and well-settled at Wistar, these four assistant professors have made
significant progress establishing research programs, publishing their first papers as senior authors, and securing solid funding through federal grants and private foundations, such as the W. W. Smith Charitable Trusts, the American Cancer Society, Susan G. Komen, the V Foundation for Cancer Research, and The G. Harold & Leila Y. Mathers Foundation.

We brought the four scientists together to take stock of their experiences at Wistar.

A diverse and stimulating scientific environment

One of the common themes in the conversation was the intellectual and scientific support junior investigators receive at the Institute. “Wistar is a small place with exceptional scientific diversity,” said Gardini.

“Exposure to different expertise in a highly collaborative environment has created plenty of opportunities for me to expand my scientific horizon and skillset,” added Schug. “For example, because of the outstanding immunology community we have at the Institute and the frequent seminars they host, my knowledge of immunology has expanded dramatically, and that was an area in which I wanted to grow.”

“I kept myself distant from immunology until I joined Wistar; it wasn’t my favorite field,” joked Chen. “But no cancer biologist can stay away from immunology these days, especially if you study the tumor microenvironment like I do. Being at Wistar made that transition easier for me.”

Pursuing their projects and expanding their interests

When asked if they stayed their course and followed their original research plan, all four scientists said they are working on the overall ideas they proposed, but they’ve added new directions they can now pursue because of the expertise and support of other labs at the Institute.

“My drug development project was difficult to get off the ground,” said Schug. “At Wistar, though, through collaboration with Dr. Salvino, I took a different approach that was successful.”

When you are a basic research scientist, finding good model systems to test your hypothesis can really make a difference. “I felt safe exploring the ovarian cancer model because there is a lot of expertise in Dr. Zhang’s lab, in particular, and I can count on resources for future developments,”added Gardini.

“Even though my primary interest is breast cancer, I received a lot of mentorship from Dr. Weeraratna,” said Chen. “She brought me into melanoma—a great model to study brain metastasis because of its tendency to invade the brain. As a matter of fact, nearly 40% of melanoma patients develop brain metastasis.”

What about academic freedom, we asked. Everyone said they were given leeway to choose their scientific direction and explore their ideas.

Sometimes, access to funding can bring about involuntary restraints to the scientists’ ability to pursue their interests. “Access to funds for basic researchers can be a challenge because most of the money is diverted to applied research,” said Sarma.

“My work is clinically relevant, so I don’t necessarily face this issue,” added Chen. “Yet, I can’t wrap my head around the scarcity of funding for basic research, as it creates the foundations for clinical development.”

“I appreciate the Institute’s strategy for grant submission because we are not pushed to apply to every possible opportunity, but they encourage us to focus our efforts where we are stronger and have a better chance of success,” said Gardini. “In the long run, it’s an efficient approach and avoids putting too much pressure on the junior faculty members.”

A little weight off their shoulders

Technological and administrative support were also highly rated and considered crucial for growth and success.

“Wistar has a reputation for its core facilities, and they absolutely lived up to my expectations,” said Gardini. “Besides the quality of their work, their efficiency and fast turnaround help getting answers fast and moving the projects forward.”

“Dario kept his promise in terms of equipment and facilities,” said Schug. “Having a metabolomics core was a necessity for the research I wanted to pursue, and he and other professors worked with me to secure funding for new state-of-the-art instrumentation. Dario has been very supportive of me setting up new techniques at the Institute.”

Administrative support is very important for junior principal investigators who are starting to navigate grants and budget, and managing multiple projects and tasks at the same time. “The support we receive from the administrative departments is exceptional, it makes our lives easier so we can focus on the science as much as possible,” said Sarma.

Beyond Wistar

Expanding beyond Wistar’s walls and into the Philadelphia life sciences hub, there was consensus that, with so many academic research institutions and hospitals, most of which are expanding, Philadelphia is the place for biomedical scientists. “I have ongoing collaborations with nearly all the major cancer centers in Philadelphia at this point,” said Schug. “It’s as easy as going across the street or taking a walk downtown.”

“If my projects lead me in a new direction that I want to explore, there is a very high chance I’ll be able to find someone around who can help,” added Gardini.

The private biotech arena is also bourgeoning in Philly. “I’m not quite there yet,” said Schug. “Though I definitely see my research expanding in that direction. We are actively engaged in drug development and testing our compounds in preclinical models with the hope that in a year from now we may begin searching for a biotech or pharmaceutical company with which to partner. Fortunately, Wistar has a fantastic business development team that supports us throughout this process.”

“I’m not exposed to biotech now, maybe in the future, if my studies identify new therapeutic targets,” said Chen.

“Alessandro and I are a little less likely to benefit from it because of the basic nature of our science and the fact that the biotech industry in Philadelphia is geared towards drug development. Naturally, it can have a bigger impact on translational scientists,” said Sarma.

A home for basic research

Bringing basic investigators on board reflects Wistar’s everlasting commitment to fundamental research and the type of breakthroughs that can come from it. In addition to expanding the universal knowledge of biological mechanisms, basic discoveries point to new therapeutic targets that can be drugged, while bringing about technological advancement.

“Genomics is a very technology-driven field,” said Sarma. “I’m excited to witness and participate in this trend and always thrilled to see new technologies emerge that will allow us to explore biological phenomena and disease in greater depth.”

“We can now look at things in ways scientists have never before, we can do genomic analysis at the single-cell level, which is mind-blowing.” added Gardini. “Obviously, this also makes our work challenging, because we need to keep up with the fast pace of technology and stay abreast of new developments and incorporate them in our research in meaningful ways.”

A look at the future

“I am very excited about the developments of my research on how diet, metabolism, microbiome, and epigenetics talk to one another in cancer,” said Schug. “Speaking of new technologies, we have been advancing new tools to study the organism as a whole and I am eager to apply this new approach to my research at Wistar.”

“I’m happy that more labs are working on brain metastasis, and I look forward to more neurobiologists entering the field,” said Chen. “Looking at things just from the cancer angle is limiting, we can move forward much faster when we know the underlying physiology.”

“Cancer genomics studies in the past decade have highlighted that many transcriptional and chromatin modulators are mutated in cancer, and for the vast majority of these we don’t know what their role is,” said Gardini. “The field is getting more and more competitive, but I’m excited that there is so much room to explore and figure out new mechanisms, and with that also come growing funding opportunities.”

“I get excited about every new discovery, big and small,” said Sarma. “Having the first piece of data and looking at it for the first time is a lot of fun, and I look forward to more of these moments. I love figuring out how things work, solving puzzles, making sense of unexpected results. That’s the best part of my job.”

The gang

Maybe it’s because they arrived within a few months of each other, or maybe it’s because they are all first-time independent investigators launching their career in academia together, and it’s certainly because they get along well—but the fab four have formed a strong bond.

“Besides collaborating scientifically, I think we’ve created a support system for each other,” said Sarma. “We interact daily and make time to connect and discuss each other’s strategies and little bumps in the road.”

“They have dragged me out of my shell, and I’m glad they did that,” said Chen. “Someone will check if they haven’t seen me for a while.”

“I’ve received a lot of help on grants applications from these guys,” said Schug. “We exchange tips and learn from each other’s experiences.”

“We root for each other’s successes and celebrate each other’s accomplishments, which is not to be taken for granted,” said Gardini. “This reflects positively on the way I feel about Wistar.”

“We don’t just talk about science, though,” said Sarma. “We discuss work-life balance, vacations, and our lives and hobbies outside the lab.”

“I’m going to say that food is probably our most typical conversation subject,” interjected Gardini, and they all acknowledged that with a laugh.