Northwestern Engineering researchers have developed a new platform that can image single molecules in 3-D, allowing deeper probes into the inner workings of cells. The platform uses spectroscopic single-molecule localization microscopy (sSMLM), a tool that can...
Three pharmaceutical and life sciences industry leaders: Michael Boyne, PhD, Vice President, Product Development and Analytics, Cour Pharmaceutical Development Company, Inc.; Christopher J. O’Connell, Chairman and Chief Executive Officer, Waters Corporation; and Michael O’Shea, Founder, The O’Shea Firm, recently joined the Chemistry of Life Processes Institute’s Executive Advisory Board (EAB).
“We are very pleased to welcome these talented individuals to our board,” says Thomas O’Halloran, Founding Director, Chemistry of Life Processes Institute. “Their collective expertise in drug development and the biotech research industry will help aid and advance our mission to bring new discoveries to society.”
The EAB is integral to the growth and success of the Institute. Founded in 2005, the Board includes business leaders, entrepreneurs, researchers, physicians and tech experts providing CLP faculty members with a gateway to the world of transdisciplinary biomedical discovery, innovation and education. Board members contribute their individual strengths to the Institute in the form of business advice and assistance in commercializing innovations, insight into educational programs, feedback on operations, strategic plans, marketing, fundraising, and individual philanthropy.
Michael Boyne, PhD, Vice President, Product Development and Analytics, Cour Pharmaceutical Development Company, Inc.
Michael Boyne is the VP of Product Development and Analytics at Cour Pharmaceuticals. In this role, he oversees the overall pipeline and all aspects of CMC and R&D. Before joining Cour, he was a Senior Consultant at BioTechLogic where he advised pharmaceutical manufacturers on drug development and CMC strategy, including drafting, reviewing, and authoring Pharmaceutical Quality/CMC sections (Module 3) of the CTD for regulatory submissions.
Prior to consulting, Boyne was a Research Chemist in the Division of Pharmaceutical Analysis at the US Food and Drug Administration where he established a laboratory developing and applying modern analytical technologies for the evaluation and regulation of complex drug products. Boyne has authored over 40 peer-reviewed publications and is an internationally recognized speaker on the application of modern analytical technologies to drug development. He is the past chair of the 15th Symposium on the Practical Applications of Mass Spectrometry in the Biotechnology Industry and sits on the organizing committee for the CASSS meeting on Cell and Gene Therapies.
Boyne was a postdoctoral scholar at Washington University Medical School in Saint Louis where he was an American Cancer Society/Canary Foundation Fellow in Early Detection. He has a BA in Chemistry from Northwestern University, Evanston, IL and a PhD in Chemistry from the University of Illinois Urbana-Champaign.
Christopher J. O’Connell, Chairman and Chief Executive Officer, Waters Corporation
Christopher O’Connell was appointed Chairman of the Board of Directors for Waters Corporation in January 2018, in addition to his position as Chief Executive Officer, which he assumed upon joining Waters in September 2015. Waters (NYSE: WAT) develops, manufactures and distributes innovative analytical technologies for a broad range of life science, food, environmental and industrial customers globally. Waters is committed to advancing science to enable better medical therapies, safer food and a higher quality world.
Previously, O’Connell served at Medtronic plc for twenty-one years, most recently as Executive Vice President and President of its Restorative Therapies Group, and was a member of Medtronic’s Executive Committee for nine years. He started his career at Chemical Banking Corporation in New York. O’Connell earned a Bachelor’s degree from Northwestern University in 1989 and a Master’s degree in Business Administration from Harvard University in 1994.
Michael O’Shea, Founder, The O’Shea Firm
Before starting The O’Shea Firm in Washington D.C., Michael O’Shea worked for three major law firms: Clifford Chance, Akin Gump and Hunton & Williams. The O’Shea Firm specializes in patent monetization and patent litigation at the intersection of business and technology. O’Shea has litigated numerous patent cases in virtually every technology, from semiconductors to pharmaceuticals, automobiles to medical instrumentation, and software to specialty chemicals. He has also litigated in jurisdictions nationwide, including numerous district courts, the International Trade Commission, the Federal Circuit and the United States Supreme Court.
O’Shea earned his undergraduate degree from Northwestern University, and his JD from Fordham University School of Law. He is a member of the American Bar Association; the Federal Circuit Bar Association; and the Intellectual Property Owners.
About the Chemistry of Life Processes Institute
Chemistry of Life Processes Institute is where new cures and biomedical discoveries begin at Northwestern. Drawn by the lnstitute’s extraordinary expertise and facilities for innovation and translation, investigators from across the University converge at the Institute to apply path-breaking science and transdisciplinary approaches that define new fields and open up promising areas of inquiry. CLP lowers the barriers to success and hastens the development and delivery of new diagnostic tools and therapeutics to millions of people around the world living with cancer, neurological diseases, heart disease and other disorders.
CLP drives innovation and translation at Northwestern and transforms science and lives. Since its founding, the Institute has advanced 75 new drug candidates, medical devices and diagnostic tools towards clinical trials. CLP investigators have spun out 26 new companies that have attracted $1.5 billion in investment.
by Lisa La Vallee
How can high school students learn about a technology as complex and abstract as CRISPR? It’s simple: just add water.
A Northwestern University-led team has developed BioBits, a suite of hands-on educational kits that enable students to perform a range of biological experiments by adding water and simple reagents to freeze-dried cell-free reactions. The kits link complex biological concepts to visual, fluorescent readouts, so students know — after a few hours and with a single glance — the results of their experiments.
After launching BioBits last summer, the researchers are now expanding the kit to include modules for CRISPR and antibiotic resistance. A small group of Chicago-area teachers and high school students just completed the first pilot study for these new modules, which include interactive experiments and supplementary materials exploring ethics and strategies.
“After we unveiled the first kits, we next wanted to tackle current topics that are important for society,” said Northwestern’s Michael Jewett, principal investigator of the study. “That led us to two areas: antibiotic resistance and gene editing.”
Called BioBits Health, the new kits and pilot study are detailed in a paper published on May 7 in the journal ACS Synthetic Biology.
Jewett is a professor of chemical and biological engineering in Northwestern’s McCormick School of Engineering and co-director of Northwestern’s Center for Synthetic Biology. Jessica Stark, a graduate student in Jewett’s laboratory, led the study.
Test in a tube
Instead of using live cells, the BioBits team removed the essential cellular machinery from inside the cells and freeze-dried them for shelf stability. Keeping cells alive and contained for an extended period of time involves several complicated, time-consuming preparation and processing steps as well as expensive equipment. Freeze-dried cell-free reactions bypass those complications and costs.
“These are essentially test-tube biological reactions,” said Stark, a National Science Foundation graduate research fellow. “We break the cells open and use their guts, which still contain all of the necessary biological machinery to carry out a reaction. We no longer need living cells to demonstrate biology.”
This method to harness biological systems without intact, living cells became possible over the last two decades thanks to multiple innovations, including many in cell-free synthetic biology by Jewett’s lab. Not only are these experiments doable in the classroom, they also only cost pennies compared to standard high-tech experimental designs.
“I’m hopeful that students get excited about engineering biology and want to learn more,” Jewett said.
One of the biggest scientific breakthroughs of the past decade, CRISPR (pronounced “crisper”) stands for Clustered Regularly Interspaced Short Palindromic Repeats. The powerful gene-editing technology uses enzymes to cut DNA in precise locations to turn off or edit targeted genes. It could be used to halt genetic diseases, develop new medicines, make food more nutritious and much more.
BioBits Health uses three components required for CRISPR: an enzyme called the Cas9 protein, a target DNA sequence encoding a fluorescent protein and an RNA molecule that targets the fluorescent protein gene. When students add all three components — and water — to the freeze-dried cell-free system, it creates a reaction that edits, or cuts, the DNA for the fluorescent protein. If the DNA is cut, the system does not glow. If the DNA is not cut, the fluorescent protein is made, and the system glows fluorescent.
“We have linked this abstract, really advanced biological concept to the presence or absence of a fluorescent protein,” Stark said. “It’s something students can see, something they can visually understand.”
The curriculum also includes activities that challenge students to consider the ethical questions and dilemmas surrounding the use of gene-editing technologies.
“There is a lot of excitement about being able to edit genomes with these technologies,” Jewett said. “BioBits Health calls attention to a lot of important questions — not only about how CRISPR technology works but about ethics that society should be thinking about. We hope that this promotes a conversation and dialogue about such technologies.”
Jewett and Stark are both troubled by a prediction that, by the year 2050, drug-resistant bacterial infections could outpace cancer as a leading cause of death. This motivated them to help educate the future generation of scientists about how antibiotic resistance emerges and inspire them to take actions that could help limit the emergence of resistant bacteria.
In this module, students run two sets of reactions to produce a glowing fluorescent protein — one set with an antibiotic resistance gene and one set without. Students then add antibiotics. If the experiment glows, the fluorescent protein has been made, and the reaction has become resistant to antibiotics. If the experiment does not glow, then the antibiotic has worked.
“Because we’re using cell-free systems rather than organisms, we can demonstrate drug resistance in a way that doesn’t create drug-resistant bacteria,” Stark explained. “We can demonstrate these concepts without the risks.”
A supporting curriculum piece challenges students to brainstorm and research strategies for slowing the rate of emerging antibiotic resistant strains.
Part of something cool
After BioBits was launched in summer 2018, 330 schools from around the globe requested prototype kits for their science labs. The research team, which includes members from Northwestern and MIT, has received encouraging feedback from teachers, students and parents.
“The students felt like scientists and doctors by touching and using the laboratory materials provided during the demo,” one teacher said. “Even the students who didn’t seem engaged were secretly paying attention and wanted to take their turn pipetting. They knew they were part of something really cool, so we were able to connect with them in a way that was new to them.”
“My favorite part was using the equipment,” a student said. “It was a fun activity that immerses you into what top scientists are currently doing.”
Jewett is a member of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University as a part of its Cancer & Physical Sciences Program, the Simpson Querrey Institute and the Chemistry of Life Processes Institute.
The study, “BioBits Health: Classroom activities exploring engineering, biology and human health with fluorescent readouts,” was supported by the Army Research Office (award numbers W911NF-16-1-0372 and W911NF-18-1-0200), the National Science Foundation (grant numbers MCB-1413563 and MCB-1716766), the Air Force Research Laboratory Center of Excellence (grant number FA8650-15-2-5518), the Defense Threat Reduction Agency (grant number HDTRA1-15-10052/P00001), the Department of Energy (grant number DE-SC0018249), the Human Frontiers Science Program (grant number RGP0015/2017), the David and Lucile Packard Foundation, the Office of Energy Efficiency and Renewable Energy (grant number DE-EE008343) and the Camille Dreyfus Teacher-Scholar Program.
by Amanda Morris
The original story was published on May 7 by Northwestern Now.
Michael Jewett is a member of the Chemistry of Life Processes Institute.
Core facility experts, researchers gather to exchange best practices in preclinical imaging
From preclinical imaging best practices and career opportunities for facility managers, to core research and commercialization, the 2019 Pre-clinical Imaging Consortium (PIC) Annual Meeting held at Northwestern University, April 28-30, covered a lot of territory. More than 150 core facility experts, faculty and researchers from across the US attended the conference, hosted by Chemistry of Life Processes Institute’s Center for Advanced Molecular Imaging (CAMI) and sponsored by over twenty companies in partnership with the World Molecular Imaging Society.
Faculty and experts from Northwestern and several other academic institutions presented exciting new imaging facility research. The program also included ample time for networking, roundtables, power pitches by industry vendors and poster sessions led by scientists and facility managers from participating universities. The gala dinner was sponsored by Bruker BioSpin and the Robert H. Lurie Comprehensive Cancer Center.
“The mission of the PIC,” said the consortium’s co-founder Chad Haney, PhD, managing director, CAMI, “is to create a meeting place where knowledge of operating preclinical imaging facilities is shared openly.”
Advancing cutting-edge research
The fifth annual meeting kicked off with a talk by Heather Gray-Edwards, Assistant Professor, University of Massachusetts Medical School who is developing a new gene therapy to correct the enzyme deficiency found in people with Tay-Sachs and Sandhoff disease. Lysosomal storage diseases (there are more than 40 altogether) are often fatal pediatric diseases. A specific protein deficiency that breaks down waste products within the cell is the cause. For several of these diseases, gene therapy clinical trials are ongoing, or about to start, but a way to track therapeutic efficacy is lacking.
Together with the research lab of Thomas Meade, PhD, faculty director of the Chemistry of Life Processes Institute’s Center for Advanced Molecular Imaging, she developed a series of MRI-based contrast agents that non-invasively track the delivery of a therapeutic protein and its activation for the therapeutic effect. Using high field strength MR imaging (7 Tesla) they developed an entirely new way of non-invasively demonstrating that the gene of interest was active. The novel approach enables Gray-Edwards and collaborators from UMMS and Auburn University in Alabama to immediately assess the efficacy of gene therapy treatments.
Martha Vitaterna, PhD, research professor and deputy director of Northwestern’s Center for Sleep and Circadian Biology, provided an overview of a landmark study that she and fellow collaborator Fred Turek, PhD, Charles & Emma Morrison Professor, conducted in partnership with NASA’s Human Research Program. The goal of the research was to determine the effect of space flight on gut microbiota, the thousands of species of bacteria that live inside the stomach and intestines. The yearling investigation tested the gut bacteria of astronaut Scott Kelly during a space mission against his identical twin brother, retired astronaut Mark Kelly who served as the experiment’s baseline. The study found that two major categories of bacteria in Scott Kelly’s gut microbiome had shifted during spaceflight, but the diversity of bacteria in his microbiome remained unchanged. Northwestern’s CAMI facility was instrumental in producing the whole body fat measurements for the experiment. This was one of several studies by the team examining how spaceflight affects the human body, including changes in gene expression, bone density, immune system responses and telomere dynamics.
Career Paths for Facility Managers
A leading advocate for the professionalization of cores as a scientific field Philip Hockberger, PhD, associate vice president for research at Northwestern, discussed his efforts to create a new professional path for those looking to make a difference in managing core facilities.
According to Hockberger, the U.S. government invests approximately $30 billion per year in research (core) facilities.
“Maximizing that investment requires development of a professional workforce to operate and manage those facilities effectively,” said Hockenberger in a statement. “Effective management requires multiple skill sets including technical, writing, business and management skills. Northwestern’s Kellogg School of Management offers a five-day executive education course specifically for managers and administrators overseeing core facilities.”
At Northwestern, professional development of staff working in core facilities includes membership in regional and national organizations, presentations at conferences and colloquia, advanced technical training, and participation in mentorship programs, said Hockberger. Northwestern also has core-specific job families for staff working in core facilities as well as publication guidelines for users of core facilities.
Commercializing Core Discoveries
The program wrapped up with a no-holds-barred primer on commercialization given by veteran entrepreneur Thomas Meade, PhD, the Eileen M. Foell Professor of Cancer Research and Professor of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology. Meade cautioned attendees to consider the risks before diving in because the odds of a biotech startup actually making it to an exit strategy is low— about 1 in 103, he says.
“Don’t do it. It’s a black hole,” joked Meade. “It’s deeper than you’re ever going to see in. And once you’re in, you’re never going to get out.”
He also refuted some common misconceptions, such as believing the process will make academics rich, or an assumption that scientists understand business and marketing. Typically, the process doesn’t make people wealthy. He also strongly encouraged would-be entrepreneurs to listen to the experts and seek outside counsel from business people. Meade talked from experience having started five companies based on translational discoveries he made in the lab.
Some of his breakthroughs, such as an electronic DNA biosensor that instantly detects the presence of diseases like cystic fibrosis and also has broad applications for agriculture, succeeded brilliantly. Others, including one startup he spent more than 6,000 hours over 10 years developing, are unlikely ever to reap any benefits. Nevertheless, he admitted to being bit by the entrepreneurial bug and notes that several of his post docs and graduate students have become very wealthy from the process.
By Lisa La Vallee
Today, biology is easier than ever to observe but still incredibly difficult to understand. Powerful advancements in DNA sequencing and synthesis have inched scientists ever forward in their quest to “master” biology. But countless challenges still remain.
When engineering an organism, most labs synthesize genes, insert them into cells, and see if the desired effect occurs. There are many limitations to this approach; the process can be time-consuming and genes often do not “work” as expected. Many in the field, therefore, now see cell-free systems — an in vitro tool to study biology — as a readily accessible approach to prototype genes before they are inserted into a living cell. Cell-free systems possess some crucial advantages compared to living organisms, and they can either be made from whole cell extracts or from individually-purified components, such as the PURE system.
Cell-free systems can be used to produce toxins at high yields, unlike living cells, and components can typically be added or removed without consequence, whereas deletion of a protein in vivo might kill the cell. Importantly, several laboratories have also shown that measurements made using cell-free systems closely mirror in vivo results, meaning they can typically used as a rapid prototyping tool for characterizing genetic parts and devices.
But many are only now seeing cell-free systems for what they really are: an incredibly powerful approach to dissect complex biological problems that, today, is on the cusp of realizing its full potential. Synthetic biology labs around the world are now leveraging cell-free systems to produce proteins with unnatural chemistries, prototype entire metabolic pathways, and even detect biomolecules of clinical importance in a matter of minutes. And they are just getting started.
Protein Production 2.0: Unlocking Unnatural Chemistries
Cell-free systems have long been used to produce proteins, since preparing an extract only takes a couple of days and toxic proteins can be produced while the chemical environment is tightly controlled. But some laboratories are looking beyond natural proteins, opting instead to produce proteins riddled with unnatural amino acids.
In living organisms, unnatural amino acids are typically incorporated into proteins with a method called Stop Codon Suppression. This is where a stop codon, typically UAG, is recoded to another codon and its related machinery removed. In this way, an orthogonal tRNA that recognizes UAG can be expressed, but instead of signaling translation to stop, it incorporates an unnatural amino acid instead. Over 100 unnatural amino acids have been incorporated into proteins using this approach.
Yuan Lu, Assistant Professor in Chemical Engineering at Tsinghua University, aims to use cell-free systems, rather than living organisms, to build unnatural proteins. “Compared to living cells…cell-free systems have a higher tolerance for the toxicity caused by unnatural components, no cell membrane barrier limiting the transportation of unnatural amino acids, more flexible reaction control by adjusting the system composition freely, and higher incorporation efficiency of unnatural amino acids,” he says.
As cell-free systems improve and expand the diversity of proteins that can be assembled, Lu’s group at Tsinghua University aims to apply them for broad applications in human health and biocatalysis.
While synthetic biologists are adopting cell-free systems to produce proteins decorated with unnatural amino acids, others are eagerly applying newfound capabilities to probe dozens of interacting proteins simultaneously.
Beyond Protein Production: Cell-free Systems for Pathway Prototyping
Ashty Karim sees cell-free systems as more than a prototyping tool for standalone genetic parts. He envisions them as tools to test entire metabolic pathways. As a Research Fellow and the Assistant Scientific Director in Professor Michael Jewett’s lab at Northwestern University, he understands that, often, metabolic engineers want to convert a readily available molecule to a high-value product, but repeatedly testing metabolic pathways in vivo is detrimentally time-consuming.
To circumvent this laborious process, Karim has pioneered methods for high-throughput pathway prototyping using modified cell-free systems.
“Our in vitro prototyping approach utilizes crude E. coli lysates in which genomic DNA and cellular debris are removed, leaving metabolic enzymes and transcription and translation machinery present. The idea is that we can construct discrete enzymatic pathways through modular assembly of these lysates containing enzymes produced by cell-free protein synthesis rather than by living organisms. This reduces the overall time to build pathways from weeks, or even months, to a few days,” says Karim.
By creating many cell extracts, each with a single part of the pathway expressed, Karim is essentially making cell-free systems into a modular system that can be used to assemble any desired pathway in vitro. This clever approach, coupled with automation and machine learning, could dramatically expedite the way that scientists test combinations of metabolic pathways. Still, Karim is quick to acknowledge that there are fundamental limits in our ability to apply findings from cell-free systems to living organisms.
“One of our goals of being able to build pathways in the cell-free environment quickly is to use the data generated to inform cellular design,” says Karim. “In our most recent work, we are trying to develop cell-free to cell correlations that would allow us to test hundreds to thousands of pathway combinations–varying enzyme homologs and concentrations–in cell-free systems and then down-select a handful to test in cells.”
The abundance of data that Karim’s approach enables even extends beyond metabolic pathways; it could also prove useful for creating cell-free systems for clinical biosensing.
Cells sense their environment constantly, responding to signals and carefully actuating their responses. It naturally follows that the brilliant responsiveness and programmability of biology could then be leveraged to sense molecules of human clinical importance. Cell-free systems have made this possible.
Paul Freemont, a Professor of Medicine at Imperial College London and co-founder of Imperial’s Centre for Synthetic Biology, has pioneered cell-free systems for biosensing applications, aiming to develop tests that accurately diagnose diseases in minutes, rather than hours.
“Our biosensor work has focused on applying cell free systems to design genetically encoded biosensors that measure biomarkers in clinically relevant samples. While many biosensor designs have been shown to work in the lab, few have actually been tested on real clinical samples,” he says. “The exemplar we chose was sputum from cystic fibrosis patients and our biomarker target was quorum sensing molecules from Pseudomonas aeruginosa,” Freemont explains. “To our great surprise, our humble and very cheap cell-free biosensor producing a [green fluorescent protein] output showed remarkable correlation with the gold standard [diagnostic approach]…on the same sample.”
Not only did the team manage to create a simple, cell-free assay for measuring a specific biomolecule, the approach now offers a method for rapid, portable quantitation of these biomarkers.
“The reason that cell-free systems are preferable to living systems [as biosensors] in some contexts is because the assays are cheap, quick, quantitative, scalable to automation, and reproducible. They also offer advantages for biosensing in that they can be freeze dried onto surfaces like paper, are not GM organisms and thus are more acceptable for use in clinical environments and in the field,” says Freemont.
In the years to come, we will likely see cell-free systems used increasingly in clinical settings, especially in situations where a rapid preliminary test is desirable. But while unnatural chemistries, pathway prototyping, and on-demand biosensing are already being actively explored in labs around the world, what will cell-free systems be used for in 5 or 10 years?
A More Distant Cell-Free Future
An amalgamation of disciplines, everything from physics to electrical engineering and mathematics, is what made synthetic biology great. So too are diverse disciplines the recipe for unlocking the full potential of cell-free systems.
Yuan Lu, for example, envisions that cell-free systems will be used in fields other than biology. “To make this happen, the cell-free systems cannot just focus on biological transcription and translation,” he says. “To achieve breakthrough development, the cell-free systems need to be highly integrated with materials science, neuroscience, electronic engineering, 3D printing, artificial intelligence, and other next-generation technologies.”
Ashty Karim thinks that cell-free systems will increasingly be used for “direct-use” applications. “We will start seeing cell-free sensors as diagnostics in agriculture, defense, and medicine, and we will see biomanufacturing on-demand of therapeutics, vaccines, and commodities,” he says, emphasizing that these advancements are made possible by improvements in extract preparation and cell-free mixes, such as “cell-free systems that can glycosylate proteins and cell-free systems that contain orthogonal transcription factors.”
Perhaps the most ambitious application of cell-free systems, exemplified by the Build-a-Cell consortium, aims to construct a minimal, synthetic cell from scratch. According to Paul Freemont, a member of the consortium, this endeavor is not so straightforward, but will be facilitated by cell-free systems. “If we build a series of modules that mimic various aspects of living systems [in cell-free systems] like motility, sensing, and regulation, then the real challenge will be how to interface these various modules to produce a more complex synthetic cell,” he says.
Cell-free systems are rapidly expanding the potential of synthetic biology, ushering in a wave of powerful applications not yet realized in living organisms. So as scientists break apart cells to expand the genetic code, probe pathways, and detect biomarkers, others should pay close attention; cell-free systems are here to unlock biology.
Learn about the technologies used to go from DNA to protein without the cell and its finicky ways — and how cell-free biology will affect sectors from biopharma to food and beverages, at SynBioBeta 2019, October 1-3 in San Francisco.
by Niko McCarty
Original story published by synbiobeta on April 30, 2019
Studying the movement of tiny cells is no small task. For chromatin, the group of DNA, RNA, and protein macromolecules packed within our genome, motion is an integral part of its active role as a regulator of how our genes get expressed or repressed.
“Understanding macromolecular motion is critical, but scientists know very little about it,” said Vadim Backman, Walter Dill Scott Professor of Biomedical Engineering at Northwestern University and member of Chemistry of Life Processes Institute. “Part of the reason is because we lack instrumental techniques to observe those processes.”
Now, a research team at the McCormick School of Engineering led by Backman has developed a new optical technique to study the movement of cells without using labels or dyes to track them. The innovative method has also revealed an undiscovered phenomenon that may play a role in the earliest stages of cell death.
The team’s insights were published on April 10 in the journal Nature Communications. The paper is titled “Multimodal interference-based imaging of nanoscale structure and macromolecular motion uncovers UV induced cellular paroxysm.”
While scientists can currently track the movement of cells using molecular dyes or labels, the practice comes with limitations. Dyes are toxic and alter the behavior of cells before, eventually, killing them. Labels are attached to cells, can be toxic or result in photobleaching, and may alert the motion of the very molecules they label.
The new technique, called dual-PWS, is label-free and can image and measure macromolecular motion without using dyes. Building off of a quantitative imaging technique previously created by Backman called Partial Wave Spectroscopy (PWS), the platform uses the interference and pattern changes from backscattered light to monitor both the macromolecular structure of cells along with their dynamic movement.
“Critical processes like the transcription of a gene or the repair of damaged proteins requires the movement of many molecules simultaneously within a highly packed, complex environment,” said Scott Gladstein, a Ph.D. student in Backman’s lab and the study’s first author. “As an imaging platform with the capability to measure both intracellular structure and macromolecular dynamics in living cells with a sensitivity to structures as small as 20?nm with millisecond temporal resolution, the dual-PWS is uniquely suited to allow us to study these processes.”
The researchers applied dual-PWS by studying the nanoscale structural and dynamic changes of chromatin in eukaryotic cells in vitro. Using ultraviolet light to induce cellular death, the team measured how the movement of the cells’ chromatin was changed.
“It makes sense that as cells are about to die, their dynamics lessen,” Backman said. “The facilitative motion that exists in live cells to help express genes and change their expression in response to stimuli disappear. We expected that.”
What the researchers didn’t expect was to witness a biological phenomenon for the first time. A cell reaches a “point of no return” during decay, where even if the source of the cellular damage is stopped, the cell would be unable to repair itself to a functioning state, Backman said. Using dual-PWS, the researchers observed that just prior to this turning point, the cells‘ genomes burst with fast, instantaneous motion, with different parts of the cell moving seemingly at random.
“Every cell we tested that was destined to die experienced this paroxysmal jerk. None of them could return to a viable state after it took place,” said Backman, who leads Northwestern’s new Center for Physical Genomics and Engineering.
The team is unclear why or how the phenomenon, called cellular paroxysm, occurs. Backman originally wondered if the movement could be due to ions entering the cell, but such a process would have taken too long. The uncoordinated motions of the cellular structures occurred over milliseconds.
“There’s simply nothing in biology that moves that fast,” Backman said. He added that members of his lab were so surprised by the results, they joked that the phenomenon could be explained as “Midichlorians” leaving the cell, a reference to the chemical embodiment of “the Force” in the Star Wars films.
While cellular paroxysms remain a mystery for now, Backman believes the team’s findings highlight the importance of studying the macromolecular behavior of live cells. The more insights researchers can gain about chromatin, the more likely they can one day be able to regulate gene expression, which could change how people are treated for diseases like cancer and Alzheimer’s.
“Every single biological process you can imagine involves some sort of macromolecular rearrangement,” Backman said. “As we expand our research, I can’t help but wonder, ‘What will we find next?'”
by Alex Gerage
The original story was published by Physics.org on April 11, 2019.
- Scott Gladstein, Luay M. Almassalha, Lusik Cherkezyan, John E. Chandler, Adam Eshein, Aya Eid, Di Zhang, Wenli Wu, Greta M. Bauer, Andrew D. Stephens, Simona Morochnik, Hariharan Subramanian, John F. Marko, Guillermo A. Ameer, Igal Szleifer, Vadim Backman. Multimodal interference-based imaging of nanoscale structure and macromolecular motion uncovers UV induced cellular paroxysm. Nature Communications, 2019; 10 (1) DOI: 10.1038/s41467-019-09717-6
Three of the paper’s authors: Vadim Backman, Guillermo Ameer, and Igal Szleifer are members of the Chemistry of Life Processes Institute.
CLP’s Center for Advanced Molecular Imaging to Host the 5th Annual Preclinical Imaging Consortium
April 28 – 30, 2019
Norris University Center, 2nd Floor
1999 Campus Dr, Evanston, IL 60208
This week, the Chemistry of Life Processes Institute’s Center for Advanced Molecular Imaging (CAMI) will host the 5th Annual Preclinical Consortium (PIC) meeting at Northwestern University, Evanston, IL. The mission of PIC is to create a meeting place where knowledge of operating preclinical imaging facilities is shared openly.
PIC began five years ago as a small gathering of Midwestern preclinical imaging center directors. It has grown rapidly over the past five years and expanded its scope well beyond the Midwest. PIC brings together experts in preclinical imaging from both academia and industry with this year’s focus on research rigor and best practices. While other meetings focus on disease models or technical aspects of imaging modalities, one goal of this meeting is to educate imaging scientists about techniques they may be less familiar with. The casual setting of an intentionally small attendance facilitates candid dialog among imaging centers and industry representatives.
The meeting would not have taken place without the generous support of our numerous sponsors, including host sponsors Robert H. Lurie Comprehensive Cancer Center and World Molecular Imaging Society; Bruker, MR Solutions and others.
Click here or the image to the left to view the program.
Erik C. Andersen, a molecular geneticist at Northwestern University, has received a Human Frontier Science Program grant to study the evolution of behavior.
Andersen will lead an international team to study the repeatability of the genetic mechanisms underlying behavioral evolution. He will receive $350,000 per year for three years from the Human Frontier Science Program Organization to support these efforts.
“This support gives us a rare opportunity to study how evolution works, especially on behaviors,” said Andersen, an assistant professor of molecular biosciences in the Weinberg College of Arts and Sciences.
Andersen’s team will focus on the conundrum of why many completely different species seem to exhibit similar behaviors. Some related examples from nature include how different species of Hawaiian spiders that spin similar web architectures or diverse anoles lizard species that bob their heads with the same styles and speeds.
The researchers will study three species of the nematode genus Caenorhabditis. The transparent roundworms offers a unique experimental platform to connect behavioral differences to genetic differences. The team will use genotype data and imaging of behaviors to create a map to identify shared gene variants that are most important evolutionarily.
“Our results will provide the first systematic glimpse into the genomic ‘knobs’ that control behaviors at the single-variant level across species,” Andersen said. “We also will gain insights into the repeatability of the evolution of behaviors.”
Andersen’s collaborators on the project are Andre Brown of Imperial College London and Kathryn Hodgins of Monash University in Australia.
The original story was published by Northwestern Now on April 11, 2019.
Andersen is a member of the Chemistry of Life Processes Institute.
“Renewed hope for millions.” That was the promise on display when a team of world-renowned Northwestern faculty presented their pathbreaking research as part of the inaugural Oppenheimer Biotech Summit by the Lake.
Joined by partners and presenters from Oppenheimer & Co., AbbVie, Genentech, and other industry leaders, the daylong summit — held March 27 at the Kellogg Global Hub — offered a glimpse into new strategies to prevent, diagnose and treat cancer, ALS, infertility, and other hard-to-treat diseases.
“The Summit afforded the Chemistry of Life Sciences Institute and Northwestern University the opportunity to highlight for investors some of our most innovative research programs that are pushing the barriers of science,” said Thomas O’Halloran, director of the Chemistry of Life Processes (CLP) Institute. “At the same time, we introduced investors to cutting-edge biotechnology companies with Northwestern affiliations.”
Cohosted by the CLP Institute and Oppenheimer, summit programming included presentations from institute faculty innovators and Northwestern alumni who lead major public companies. Members of Oppenheimer & Co. moderated a lunchtime panel discussion.
“The basic and translational research at Northwestern and at CLP specifically has been nothing short of groundbreaking across so many fields,” said Sujal Shah, a CLP board member and president and CEO of clinical-stage biopharmaceutical company CymaBay.
“Our goal was to bring potential investors and potential collaborators from industry together with faculty and researchers at the institute. The summit was a great first step and we owe a tremendous amount of gratitude to Oppenheimer for sponsoring and running the event.”
The Chemistry of Life Processes Institute launched in 2005 as a catalyst for transdisciplinary biomedical research and drug discovery and development at Northwestern. The institute, housed in Silverman Hall on the Evanston campus, is composed of more than 60 investigators across multiple disciplines and includes more than 70 research faculty, administrative staff, technical staff, and research associates. CLP’s eight affiliated core facilities serve more than 500 faculty research programs across the University. The institute has contributed to launching successful therapeutics such as Lyrica™ — the most financially successful drug ever to have come from a US academic institution — and has advanced 75 new drug candidates and incubated 26 companies, which have attracted more than $1.5 billion in external funding.
Lyrica™ creator Richard Silverman, the Patrick G. Ryan/Aon Professor, and many other presenters at the Biotech Summit by the Lake are featured in a new CLP video highlighting the institute’s charge to accelerate the time required for new treatments to go from the lab and into the clinic. “Programs such as this summit really help solidify CLP’s reputation as a biotech incubator and ensure continued financial support from the investment community to drive future discovery and translational innovation at Northwestern,” said O’Halloran.
About Chemistry of Life Processes Institute
Chemistry of Life Processes Institute is where new cures and better diagnostics for life-threatening diseases begin at Northwestern. Drawn by the Institute’s extraordinary expertise and facilities for innovation and translation, researchers from across Northwestern converge to develop fresh insights and approaches for treating and diagnosing complex diseases such as cancer, epilepsy, heart disease, and Parkinson’s. CLP researchers accelerate the delivery of revolutionary science that improves lives and transforms human health.
About Oppenheimer & Co. Inc.
For more than 130 years, Oppenheimer & Co. Inc. has provided its clients with the financial expertise and insight to help achieve their goals. Oppenheimer has a proud tradition of providing innovative, customized solutions to its clients. Its partners believe in independent thinking that leads to innovative strategies tailored to client needs. Oppenheimer is proud of its reputation as a firm that helps individuals, families, corporate executives, foundations and endowments, charities, pension plans, businesses, and institutions. Biotech Summit by the Lake faculty presentations:
- Vadim Backman, Walter Dill Scott Professor of Biomedical Engineering “Developing Novel Strategies for Chromatin Regulation to Fight Resistance in Cancer Chemotherapy”
- Susan E. Quaggin, Charles H. Mayo, M.D., Professor of Medicine “A High ‘TEK’ Solution for Vascular Diseases”
- Evan Scott, Assistant Professor of Biomedical Engineering “A Scalable Platform for Enhanced Delivery and Efficacy of Diverse Therapeutic and Diagnostic Agents”
- Richard B. Silverman, Patrick G. Ryan/Aon Professor and inventor of Lyrica™ “Hepatocellular Carcinoma and ALS: Serious Unmet Medical Diseases Being Addressed in the Silverman Group”
- Douglas Vaughan, Irving S. Cutter Professor of Medicine “Targeting PAI-1: A Novel Approach to Delay the Multi-morbidity of Aging”
- Teresa Woodruff, Thomas J. Watkins Professor of Obstetrics and Gynecology “Oncofertility: From Bench to Bedside to Babies”
Corporate presenters and panelists:
- Brian Bernick, Co-Founder and Director, TherapeuticsMD
- Andrew Chan, SVP, Research Biology, Genentech
- Margarita Chavez, Managing Director, AbbVie Ventures
- Ankit Mahadevia, President and CEO, Spero Therapeutics
- Michael Margolis, Managing Director, Oppenheimer & Co.
- Chandler Robinson, Co-Founder and CEO, Monopar Therapeutics
- Sujal Shah, President and CEO, CymaBay
- Jim Sullivan, Venture Partner, OrbiMed
- S. Edward Torres, Founder and Managing Director, Lilly Ventures
- Silvan Tuerkcan, Director, Oppenheimer & Co.
by Roger Anderson
The original story was published on April 9, 2019 by Northwestern Research News.
Current methods for detecting crops with disease require expensive lab equipment located far from the field, but point-of-use diagnostics technology being developed by Northwestern Engineering will be able to help farmers test their crops for disease using nothing but their own body heat to activate the portable technology, called PLANT-Dx.
The aim of PLANT-Dx is to help low-income farmers around the world access a low-cost field test to improve methods for detecting viruses and bacteria in their crops.
“These farmers don’t really have an avenue to do crop testing,” said Julius Lucks, associate professor and associate chair of chemical and biological engineering at the McCormick School of Engineering. “They don’t have access to laboratory testing, or if they do, it’s too expensive.”
Members of The Lucks Lab published their first steps toward proof of concept for this technology in ACS Synthetic Biology. The research is supported by a $100,000 Grand Challenges Explorations grant, an initiative funded by the Bill & Melinda Gates Foundation that encourages research that can break the mold for solving persistent global health and development challenges.
All a farmer needs to do is take a sample of ground-up plant material and place it in a PLANT-Dx test tube that utilizes molecular sensors to produce a visible color if the plant is infected with a virus. Using body heat or ambient heat, the test tube will change colors within a few hours if bacteria or a virus is present.
“If your plant has a disease, then you see this yellow color. Knowing this, farmers can communicate the issue to their neighbors or a local pest management network,” said Lucks, a member of Northwestern’s Center for Synthetic Biology.
The next steps for PLANT-Dx, led by graduate student Matthew Verosloff and with researchers at Cornell University, involve further field testing and adjusting the technology to detect multiple viruses, producing different colors in the test tubes. Lucks and his researchers are also looking at ways to connect the technology to an electronic data collection infrastructure, as well as speeding up the technology.
“One of the philosophies of this research, which is fun especially here at McCormick, is this whole-brain engineering concept where we’re constantly trying to get out of the lab and in the field to talk to people about what they want and what would solve their problems — and then deliver that technology,” he added.
Going forward, the Lucks Lab is using PLANT-Dx as a launching pad to create synthetic biology solutions for point-of-use diagnostics technology for a variety of issues beyond crop surveillance, including water quality.
“We’re really trying to enable individuals to sense their environment and make decisions to help them be healthier,” Lucks said.
by ALEXANDRIA JACOBSON
Original story published on March 11, 2019 by Northwestern Engineering.
Julius Lucks is a member of the Chemistry of Life Processes Institute.
A team of researchers including Northwestern Engineering faculty has expanded the understanding of how virus shells self-assemble, an important step toward developing techniques that use viruses as vehicles to deliver targeted drugs and therapeutics throughout the body.
By performing multiple amino acid substitutions, the researchers discovered instances of epistasis, a phenomenon in which two changes produce a behavior different from the behavior that each change causes individually.
“We found occurrences where two separate single amino acid changes caused the virus shell to break or become really unstable, but making both changes together produced a stable structure that functioned better than ever,” said Danielle Tullman-Ercek, associate professor of chemical and biological engineering at the McCormick School of Engineering.
The paper titled “Experimental Evaluation of Coevolution in a Self-Assembling Particle,” was published March 19 in the journal Biochemistry. Tullman-Ercek served as the paper’s co-corresponding author along with collaborator Matthew Francis, professor of chemistry at the University of California at Berkeley.
The work builds on past research in which Tullman-Ercek and collaborators developed a new technique, called SyMAPS (Systematic Mutation and Assembled Particle Selection), to test variations of a protein used by a bacterial virus called the MS2 bacteriophage. By substituting amino acids one at a time along the MS2 protein chain, the team could study how the virus scaffold was impacted by the different combinations, including which changes preserved the shell’s structure or broke it apart.
The latest research builds on the team’s progress by using SyMAPS to analyze multiple amino acid changes within the MS2 particle, a requirement to effectively manipulate virus shells in the future, Tullman-Ercek said. Researchers studied every double amino acid combination along a polypeptide loop located within the MS2 scaffold and measured how the virus scaffold was affected.
One factor producing epistasis was balancing the amino acid charges that were substituted, said Tullman-Ercek, a member of Northwestern’s Center for Synthetic Biology. Swapping two positively charged amino acids, for instance, caused the particle to repel and break apart, but balancing a single positive amino acid change with a separate negative charge compensated the switch and preserved stability.
“It looked like an unpredictable effect, but if you look at the overall trends of the data, we learned that charge is really important to maintain balance,” Tullman-Ercek said. “We couldn’t see that based on the data we accumulated with the single changes, but we kept coming back to this charge balancing issue.”
The team plans to expand testing to determine if the behaviors found in the MS2 particle apply to similar viruses.
“It takes years to optimize each component of a virus scaffold,” Tullman-Ercek said. “We’re trying to reduce the time it takes to optimize the delivery vehicle by learning the rules of how it assembles so we can eventually build one from scratch.”
Depending on its purpose or final destination in the body, virus scaffolds require unique design properties. A virus deployed to the brain to treat a tumor, for example, may need greater stability in its shape than one sent to the lungs. The more general the rules governing design, the greater variety of particles can be constructed and deployed in the future.
“If we have to optimize the delivery vehicle for every individual case, it will take decades to make progress, so figuring out the underlying rules is important,” she said. “It’s a fundamental science project, but it has the potential to really impact the design of a lot of future therapies.”
The insights also prompted the team to question how their strategy can be coupled with what is already known — and unknown — about evolution.
“In evolution, changes build on each other one at a time,” Tullman-Ercek said. “We’re making these changes deliberately in our lab, which makes you wonder how nature reaches these epistatic states with combinations that would produce negative results on their own. We want to build this for drug delivery, but the results raise interesting questions about how changes are optimized in nature to begin with.”
by Alex Gerage
Danielle Tullman-Ercek is a member of the Chemistry of Life Processes Institute.
Original story published on March 19, 2019 by Northwestern Engineering.
Three Northwestern University assistant professors — Nicholas Diakopoulos, Yevgenia Kozorovitskiy and Sepehr Vakil — have received the prestigious Faculty Early Career Development (CAREER) Award from the National Science Foundation (NSF), the foundation’s most prestigious honor for junior faculty members.
Diakopoulos is an assistant professor of communication studies in the School of Communication and director of the Computational Journalism Lab. He will receive $549,562 over five years from NSF’s Division of Information and Intelligent Systems to develop tools to advance the practice of computational journalism.
Kozorovitskiy is an assistant professor of neurobiology in the Weinberg College of Arts and Sciences and a member of the Chemistry of Life Processes Institute. She will receive $824,670 over five years from NSF’s Division of Integrative Organismal Systems to map the proteomic landscape of neural systems, work that can be applied to a broad range of cells.
Vakil is an assistant professor of learning sciences in the School of Education and Social Policy. He will receive $672,379 over five years from NSF’s Division of Human Resource Development to design and study innovative learning contexts that engage contemporary issues of race, ethics and technology.
The CAREER Award is designed to support promising young faculty members who exemplify the role of teacher-scholar through the combination of outstanding research and education.
The goal of Diakopoulos’ project is to develop computational news-report discovery workflows and tools that weave together expert journalists, online crowd contributors and algorithms, with the intent of lowering the cost and increasing the efficiency, effectiveness and scale at which new news reports can be identified.
In an effort to better equip those who operate in an algorithm-driven media landscape, Diakopoulos says his work will help increase journalists’ data literacy and computational skills, as the research underscores the importance of understanding how computing can enhance the future of journalism.
The major focus of the Kozorovitskiy lab is to understand the function of neuromodulation and plasticity in the brain and, along the way, to develop and share new tools that advance this core mission.
The brain is composed of intricate circuits of neurons that communicate via electrical signals. The slower signals that function on the order of milliseconds to hours are known collectively as neuromodulation. Humans would be unable to pay attention, move, eat or sleep without these instructive signals, but relatively little is known about them compared to fast neurotransmission.
With her NSF support, Kozorovitskiy and her group will build and use a powerful suite of techniques for unlocking the proteome of any cell type in the brain or in the body — not only neurons. (The proteome is the entire complement of proteins expressed by a given cell.) The researchers will use their new platform to understand how particular cell types essential for motor behavior and reward processing develop after birth and reshape their proteomes in response to neuromodulation. The tools will help Kozorovitskiy’s group and other biologists target the precise groups of cells they want to study and capture the proteins within them.
Vakil’s NSF CAREER project aims to illuminate how undergraduate learning experiences within engineering and computer science are interconnected with identity development processes for historically underrepresented students of color. In particular, his project examines how opportunities to explore the ethics of new technologies shapes students’ political and civic as well as disciplinary identities.
Through a participatory community-engaged approach, Vakil and his research team will co-design and study a learning environment that brings together undergraduate students from Northwestern and local high school students from Evanston and Chicago to critically interrogate how new technologies (e.g., artificial intelligence) are shaping the experiences of communities of color in the city of Chicago and surrounding areas.
by Megan Fellman
The original story was published in Northwestern Now on March 08, 2019.
A New Approach to a Deadly Disease
A career spent bucking convention leads Bill Klein to new Alzheimer’s diagnostics and therapeutics
“When I was in graduate school, three papers per month were published on Alzheimer’s disease. Now, there are thousands every month.”
Neurobiology professor Bill Klein says the last 20 years have seen a revolution in the understanding of Alzheimer’s disease. That sea change, he says, has been focused on two key abnormalities in the Alzheimer’s brain: amyloid plaques and tau protein tangles.
“Alzheimer’s has been defined as dementia with plaques and tangles,” Klein says. Dementia is a broad term, and Alzheimer’s disease is the most common form among people over age 65. Determined to both improve diagnostic tools and develop more effective treatments, Klein has spent decades looking beyond plaques and tangles toward the tiny toxins he says are the true drivers of the disease.
Tiny toxins in the brain
Early in his career, Klein was focused on amyloid plaques, but a surprise finding led him down a vastly different path. He and his colleagues initially assumed that if they could halt the growth of these amyloid plaques, they could stop Alzheimer’s from damaging cell tissue. But even after they successfully stopped plaque growth, the damage continued, prompting the researchers to look at the brain before plaque formation. It was through this work that they identified Abeta oligomers, which would become the central focus of Klein’s research.
In a healthy brain, the molecule Abeta is created and cleared at an equal rate, like the brain regularly taking out the trash. But if the brain does not clear Abeta sufficiently, the molecules form tiny clusters — Abeta oligomers. These build up in the Alzheimer’s brain — like toxic mold building up in your home.
In a breakthrough 1998 paper, Klein’s team showed that Abeta oligomers attach to nerve synapses, where they impede signaling and destroy the delicate system that forms new memories. These oligomers cause changes in the nerve cell that eventually lead to the formation of tau protein tangles.
“First, there’s the effect on signaling, and then there’s a deterioration of the synapse,” Klein says. “Ultimately, the entire neuron deteriorates.”
Following Klein’s discovery, Eliezer Masliah, director of neuroscience at the National Institute on Aging, said that “progressive accumulation of Abeta oligomers has been identified as one of the central toxic events in Alzheimer’s disease.”
Despite Masliah’s proclamation, Klein says he’s swimming upstream, in that amyloid plaques — not Abeta oligomers — are still regarded by many as the hallmark of Alzheimer’s. But Klein says there is evidence to suggest the presence of plaques does not mean a person has Alzheimer’s, and the disease can occur without any plaques at all.
“We’ve worked with a team of scientists in Japan who have identified a family in the city of Osaka who develops Alzheimer’s disease because they have a mutation — the so-called Osaka mutation,” Klein says. “They get all of the pathology of Alzheimer’s disease, and they make lots of oligomers, but they don’t make plaques.”
In a related experiment, Klein’s team injected amyloid into the brains of some mice, and Abeta oligomers into the brains of others. “Amyloid was without effect, but the oligomers were incredibly potent at inhibiting the memory mechanism,” Klein says. “That was a very exciting result, and it caused a lot of pathologists to say ‘hold on’ with this amyloid theory.”
A diagnostic test
Klein’s team has developed MRI tools to identify oligomers in the Alzheimer’s brain, and Klein is now working with Northwestern urology professor Shad Thaxton to develop clinical tools to detect the toxins in blood plasma and spinal fluid. This collaboration builds on Klein’s earlier work with chemistry professors Chad Mirkin and Rick van Duyne, which showed people with Alzheimer’s disease in their spinal fluid had high levels of oligomers, while people who did not have Alzheimer’s disease had low levels of oligomers.
Klein’s lab has a broad goal — to develop a molecular basis for the cause, diagnosis and treatment of Alzheimer’s disease — and their work reflects that breadth.
“We have our fingers in lots of projects,” Klein says. “We would like to create a blood test to detect oligomers. We also continue to look at spinal fluid — and now — brain imaging as an approach for non-invasive studies.”
A (treatment) hope for the future
At least three companies are now testing therapeutics aimed at Abeta oligomers. One of these companies — Acumen Pharmaceuticals, which Klein co-founded in the 1970s, is testing an antibody vaccine licensed from Northwestern. This antibody binds to oligomers and renders them unable to damage nerve signaling.
Klein says the antibody vaccine works like an anti-venom treatment after a rattlesnake bite. In the same way the anti-venom drug neutralizes the toxin in the bite, the antibody neutralizes the oligomers in the brain.
Klein is hopeful that Acumen’s vaccine — and maybe other treatments — will be available in under a decade.
“Some people think an effective therapeutic could be out there by 2025,” he says. “I’m not thinking that that’s so crazy.”
By Clare Millikin
Original story published by Northwestern Now on January 23, 2019.
Bill Kein is a member of the Chemistry of Life Processes Institute. Scientists from both the Center for Advanced Molecular Imaging and the High Throughput Analysis Lab collaborated with Klein’s team to developed MRI tools to identify Abeta oligomers in the Alzheimer’s brain and found they were incredibly potent at inhibiting the memory mechanism.
More than 40 billion capillaries — tiny, hair-like blood vessels — are tasked with carrying oxygen and nutrients to the far reaches of the human body. But despite their sheer number and monumental importance to basic functions and metabolism, not much is known about their inner workings.
Now a Northwestern University team has developed a new tool that images blood flow through these tiny vessels, giving insight into this central portion of the human circulatory system. Called spectral contrast optical coherence tomography angiography (SC-OCTA), the 3D-imaging technique can detect subtle changes in capillary organization for early diagnosis of disease.
“There has been a progressive push to image smaller and smaller blood vessels and provide more comprehensive, functional information,” said Vadim Backman, who led the study. “Now we can see even the smallest capillaries and measure blood flow, oxygenation and metabolic rate.”
The paper was published last week in the journal Light: Science and Applications. Backman is the Walter Dill Scott Professor of Biomedical Engineering in Northwestern’s McCormick School of Engineering. He co-leads the Cancer and Physical Sciences Research Program at the Robert H. Lurie Comprehensive Cancer Center of Northwestern University.
Researchers and physicians have long been able to see inside major veins and arteries with Doppler ultrasound, which uses high-frequency sound waves to measure blood flow. But this insight does not give a full picture of the circulatory system. Unlike veins and arteries, capillaries are responsible for oxygen exchange, or delivering oxygen to organs and tissues throughout the body while shuttling carbon dioxide away. Low blood oxygen can cause mild problems such as headaches to severe issues such as heart failure.
“You can have great blood flow through arteries and still have absolutely no blood sending oxygen to tissues if you don’t have the right microvasculature,” Backman said. “Oxygen exchange is important to everything the body does. But many questions about what happens in microvasculature have gone unanswered because there was no tool to study them. Now we can tackle that.”
“SC-OCTA is a valuable diagnostic tool,” added James Winkelmann, a graduate student in Backman’s laboratory and the study’s first author. “We can now detect alterations to capillary organization, which is evident in a variety of conditions ranging from cancer to cardiovascular disease. Detecting these diseases earlier has the potential to save lives.”
Researchers have had difficulties peering inside capillaries because of the vessels’ microscopic size. A single capillary is a mere 5-10 microns in diameter — so small that red blood cells must flow through in single file.
SC-OCTA works by combining spectroscopy, which looks at the various visible light wavelengths, or color spectra, with conventional optical coherence tomography (OCT), which is similar to ultrasound except uses light waves instead of sound waves. Like a radar, OCT pinpoints the tissue of interest, and then spectroscopy characterizes it.
SC-OCTA has many advantages over traditional imaging: it does not rely on injected dyes for contrast or harmful radiation. Many types of imaging also only work if the area of interest is moving (for example, ultrasound can only image blood when it is flowing) or completely still. SC-OCTA can take a clear picture of both. This enables it to image stagnant blood or moving organs, such as a beating heart.
“It can measure blood flowing regardless of how fast it goes, so motion is not a problem,” Backman said.
“SC-OCTA’s unique ability to image non-flowing blood could also become a valuable tool for the booming field of organoids, which studies how organs develop and respond to disease,” Winkelmann said. “I am excited to start exploring all the applications.”
The new technology’s only limitation is that it cannot image deeper than 1 millimeter. This might seem shallow compared to ultrasound, which can see several centimeters below the surface. Backman said this can be remedied by putting the tool on the end of an endoscopic probe. By inserting it into the body, the tool can image organs up-close. That is something that his laboratory is working on now.
The title of the paper is “Spectral contrast optical coherence tomography angiography enables single-scan vessel imaging. The research was supported by the National Science Foundation and the National Institutes of Health (award numbers R01CA200064, R01CA183101, R01CA173745 and R01CA165309).
By Amanda Morris
Original story published by Northwestern Now on January 23, 2019
Vadmin Backman is a resident member of the Chemistry of Life Processes Institute.
Few everyday scenarios illicit as much trepidation as a nearby sneeze during flu season. Suddenly surrounded by tens of thousands of potentially virus-filled particles, a person’s evolving cellular reaction actually matters far more than the ability to shield one’s face.
“Most people know about the body’s immune system, but not as many understand that every cell has its own immune defenses,” says Curt Horvath, molecular biosciences, who studies the cellular recognition of and response to ribonucleic acid (RNA) viruses, as well as the manner in which viruses employ immune-evasion tactics. “The cell’s defense system acts as an initial barrier and is what prevents us from getting sick from every infectious particle we’re exposed to.”
Horvath and Northwestern graduate student Roli Mandhana recently published a pathbreaking study of RNA viruses in Scientific Reports, in which they identified hundreds of new such viruses induced by infection. RNAs are responsible for the signaling cascades — the innate immune response — that result in widespread changes to gene expression when a virus is recognized as foreign. RNAs also carry out many biological functions that keep humans healthy, including the coding, decoding, regulation, and expression of genes.
The most widely studied virus-inducible RNAs (viRNAs) encode proteins that mediate virus response; however, the completion of the Human Genome Project in 2003 and technological advances in genome-wide sequencing since have provided researchers with an opportunity to explore viral dynamics further.
“As we looked more closely, we found a lot of RNAs unable to encode proteins but whose levels change because of a response to infection,” says Horvath, a professor in the Weinberg College of Arts and Sciences. “As our lab and others identify more of these noncoding viRNAs, researchers are finding unexpected functions for them.”
The Horvath lab’s experiments most frequently involve infecting cell cultures with viruses and then monitoring the RNA response with the support of Northwestern’s NUSeq Core Facility, the High Throughput Analysis Laboratory within the Chemistry of Life Processes Institute (CLP), and the University’s Quest High Performance Computing Facility.
High throughput screening is a critical aspect of Horvath’s work because it greatly reduces the time it takes to scan large numbers of cell lines.
“We can now look at every gene in the cell simultaneously through these deep sequencing approaches,” he says. “At Northwestern, we are lucky to have the support of expert core facilities to enable us to easily pursue new and technologically advanced research directions. University investment in state-of-the-art support infrastructure pays dividends to every research area.”
Having identified the novel viRNAs — which the lab refers to as nviRNAs — Horvath set out to screen different viruses, including influenza A and herpes simplex virus 1. The goal was to cast a broad net and determine which nviRNAs were generalizable and which were virus specific.
The recent discoveries build upon prior research by former graduate student Jonathan Freaney, who investigated regulators of antiviral response and found widespread activity well beyond what researchers knew. The latest findings may someday help reveal why some viral infections — like HIV — are adept at evading immune response.
“We still don’t know what role these newly discovered noncoding RNAs play, but we now know that they exist and we can further explore if they are controlling the virus infection or helping the virus to replicate,” says Horvath. “Knowing those answers would introduce the possibility of targeting them for diagnostics or therapeutics.”
As a basic scientist, Horvath will rely on his lab’s latest discoveries to apply for new grants as he continues to help construct a more complete understanding of the total cellular response to virus infection.
“The ability to take these basic research findings and translate them into some diagnostic, therapeutic, or antiviral remedy really relies on our ability to take the next steps and connect our observation to some functional mechanistic consequence during the course of a virus infection,” he says. “We will continue to make these characterizations at the cellular level, but the long-term plan is to work with additional collaborators to explore what is happening in living models.”
By Roger Anderson
Curt Horvath is a member of the Chemistry of Life Processes Institute and faculty director of the Institute’s High Throughput Analysis Laboratory, an open resource for projects involving massively parallel experiments that open up unexpected frontiers in basic science and accelerate development of new medicines. Learn more about how the HTAL can advance your research.
Original story published by Northwestern Research on January 10, 2019.
Northwestern Medicine scientists have discovered two successful therapies that slowed the progression of pediatric leukemia in mice, according to three studies published over the last two years in the journal Cell, and the final paper published Dec. 20 in Genes & Development.
When a key protein responsible for leukemia, MLL, is stabilized, it slows the progression of the leukemia, the most recent study found. The next step will be to combine the treatments from the past two years of research into a pediatric leukemia “super drug” to test on humans in a clinical trial.
The survival rate is only 30 percent for children diagnosed with MLL-translocation leukemia, a cancer that affects the blood and bone marrow. Patients with leukemia have a very low percentage of red blood cells, making them anemic, and have approximately 80 times more white blood cells than people without cancer.
“These white blood cells infiltrate many of the tissues and organs of the affected individuals and is a major cause of death in leukemia patients,” said senior author Ali Shilatifard, the Robert Francis Furchgott Professor of Biochemistry and Molecular Genetics and Pediatrics, the chairman of biochemistry and molecular genetics and the director of Northwestern’s Simpson Querrey Center for Epigenetics. “This is a monster cancer that we’ve been dealing with for many years in children.”
There are several types of leukemia. This research focused on the two most common found in infants through teenagers: acute myeloid leukemia (AML) and acute lymphocytic leukemia (ALL).
For the past 25 years, Shilatifard’s laboratory has been studying the molecular function of MLL within its complex known as COMPASS (Complex Proteins Associated with Set1). Most recently, it was demonstrated that COMPASS components are one of the most frequently identified mutations in cancer. The next step of this work will be to bring the drug to a clinical trial setting, which Shilatifard said he hopes will happen in the next three to five years.
“I’ve been working on this translocation for more than two decades, and we’re finally at the point where in five to 10 years, we can get a drug in kids that can be effective,” Shilatifard said. “If we can bring that survival rate up to 85 percent, that’s a major accomplishment.”
Earlier work from Shilatifard’s laboratory published in Cell in 2018 identified compounds that could slow cancer growth by interrupting a gene transcription process known as “Super Elongation Complex” (SEC). It was the first compound in its class to do this.
This MLL stabilization process discovered in the most recent paper could potentially work in cancers with solid tumors, such as breast or prostate cancer, said first author Zibo Zhao, a postdoctoral research fellow in Shilatifard’s lab.
“This opens up a new therapeutic approach not only for leukemia, which is so important for the many children who are diagnosed with this terrible cancer, but also for other types of cancers that plague the population,” Zhao said.
“The publication of these four papers and the possibility of a future human clinical trial could not have happened if it weren’t for the cross-disciplinary collaboration at Northwestern,” Shilatifard said.
This collective research was made possible because of the interdisciplinary collaboration between Northwestern’s chemistry, biochemistry, biology and clinical departments, Shilatifard said.
Other Northwestern co-authors included Lu Wang, Andrew Volk, Noah Birch, Kristen Stoltz, Elizabeth Bartom, Stacy Marshall, Emily Rendleman, Carson Nestler, Joseph Shilati, Gary Schiltz and John Crispino. Shilatifard and Crispino are members of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University.
Funding for this research was provided in part by the National Institutes of Health grant T32 CA070085 and the National Cancer Institute Outstanding Investigator Award R35-CA197569.
By Kristin Samuelson.
Original story appeared in Northwestern Now on December 21, 2019.
Ali Shilatifard is a member of the Chemistry of Life Processes Institute. Kirsten Stoltz and Gary Schiltz work in Chemistry of Life Processes Institute’s Center for Molecular Innovation and Drug Discovery.
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The Chemistry of Life Processes Institute (CLP) has appointed Dr. Carla Rosenfeld associate director, Quantitative Bioelement Imaging Center (QBIC) at Northwestern University.
In this capacity, Rosenfeld will lead the facility into its next phase of growth and development as a national resource for bio-element imaging and analysis. Her responsibilities include operation and routine maintenance of facility instruments, training and supervising student users, supervision of technical staff, grant writing and advising faculty on experimental design and data analyses.
Previously, Rosenfeld held the position of visiting research associate in the Molecular Environmental Sciences Group, Biosciences Division, Argonne National Laboratory, where she focused on trace metal biogeochemistry and water quality. Rosenfeld completed her postdoctoral fellowship in environmental chemistry and microbiology at the Smithsonian Institution (Department of Mineral Sciences) and University of Minnesota (Department of Earth Sciences), where she held an NSF Postdoctoral Fellowship. She received her Ph.D. research in Soil Science and Biogeochemistry from Penn State University and B.S. degree in Chemistry from McGill University.
Rosenfeld’s expertise includes analysis of metals in numerous environmental and biological matrices and preparing solid samples for analysis and other analytical approaches including electron microscopy, chromatography, Fourier transform infrared (FTIR) spectroscopy, X-ray absorption spectroscopy (XAS), and X-ray diffraction (XRD), and X-ray fluorescence (XRF). An experienced manager and grant writer, she has also overseen multiple interdisciplinary environmental science projects, operated and maintained numerous analytical instruments, coordinated field and laboratory endeavors and trained and supervised students.
Located in Silverman Hall on Northwestern University’s Evanston campus, QBIC focuses on the development and application of novel tools, methods, and instrumentation for the analysis and mapping of inorganic elements in biological samples. Transitional metal atoms are found within all living cells and are conserved during evolutionary processes. Through a suite of high-resolution instruments capable of quantitatively imaging biologically essential elements in individual cells, QBIC’s instrumentation enables physical, life, and material scientists to analyze metal quotas at scales ranging from the subcellular level to entire ecosystems shaping global biogeochemical cycles. This work sheds light on the co-evolution of microbial and eukaryotic life within a broad range of challenging chemical environments.
A shared resource facility serving investigators within the Northwestern scientific community and beyond, QBIC provides researchers with access to state-of-the-art imaging and quantification instrumentation while supporting its use with an expert technical staff that offers a range of services, including instrument training, sample preparation and analysis, experiment design, and grant proposal assistance. The combination of both extremely high sensitivity elemental analysis and high resolution imaging enables QBIC customers to perform cutting edge experiments with expert staff support. Operating under the direction of Thomas O’Halloran, Charles E. and Emma H. Morrison Professor of Chemistry and founding director of CLP, QBIC is the only facility in the greater Chicago area with multiple inductively coupled plasma (ICP) systems dedicated to the analysis of inorganic elements in biological and materials samples. Additionally, QBIC offers the only laser ablation system dedicated to mapping biological samples in the Chicago area.
by Lisa La Vallee
A new full-body scan could help clinicians to better assess toxicity during cancer treatment, according to a Northwestern Medicine study published in Clinical Cancer Research.
The scan, which detects the presence of molecules exposed during tissue damage, could give a precise evaluation of patient toxicity during chemotherapy, said Ming Zhao, PhD, associate professor of Medicine in the Division of Cardiology and senior author of the study.
“After a single chemotherapy treatment, you already see changes,” said Zhao, who is also a member of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University. “This could give doctors the opportunity to intervene and reduce the dose or switch to another drug for example, hopefully preventing any further damage to the patient.”
Steven Johnson, ’18 PhD, postdoctoral fellow in the Zhao laboratory, was lead author of the study.
Chemotherapy works by targeting and killing actively dividing cells. While this fights cancer, casting such a wide therapeutic net damages healthy cells as well, resulting in potentially harmful side effects in patients.
While there are a range of clinical tools to measure cancer’s response to chemotherapy, tools that assess patient toxicity are limited, according to Zhao.
“While tumor kill is the main therapeutic goal in anticancer treatment, toxicity is equally important because it tends to dictate the patients’ tolerance ceiling for treatment,” Zhao said. “Current tools rely on patient symptoms and subsequent blood or serum tests, which can lag behind actual tissue damage. Instead, an imaging based method could be a quicker and more accurate way to ascertain patient toxicity.”
In the current study, scientists mapped tissue damage in rodent models using a novel whole-body imaging technique developed in collaboration with the Chemistry of Life Processes Institute’s Center for Advanced Molecular Imaging (CAMI). The technique detected a lipid molecule that is not accessible in normal cells, but becomes visible in dead and dying cells.
The lipid molecule, called phosphatidylethanolamine (PE), usually resides inside the cell. However, when a cell dies, it deactivates enzymes that maintain the asymmetrical structure of the cell membrane, redistributing PE to the cell surface.
“This provides a molecular marker for detecting cell death,” Zhao said.
The scientists compared the results of blood and serum tests to the imaging results, finding the signal changes in the scans correlated with the results of the conventional tests — with the scan providing earlier, broader and more dynamic information, according to Zhao.
“Damage to the skin can be highly local; if you take a biopsy, you might miss it,” he said. “With this test, you look at the entire organ; if there is a heterogeneous distribution of damaged tissue, you can tell where it went wrong.”
They also tested the scan in both male and female rodents, finding it detected damage in reproductive organs, a life-changing issue for some patients.
“Reproduction is a major issue in younger patients,” Zhao said. “This may help predict if this individual will have problems down the line.”
Further, the scan could also detect damage, or lack thereof, in the tumor itself, providing another data point to drive clinical decision making.
“A lack of PE on the tumor will tell you that the drug isn’t killing the tumor effectively, suggesting you should make the decision to switch to another treatment,” Zhao said. “This scan should help optimize cancer treatment to maximize tumor damage and minimize side effects.”
Now, Zhao and his collaborators are exploring the technology’s potential in humans.
“We’ve shown the proof of concept; this can be done,” Zhao said. “But for human translation, we need to make sure everything works well — and safely.”
Currently, the scientists are working on implementing a second-generation imaging agent, which could produce significantly greater data quality for clinical translation.
The study was an inter-departmental and interdisciplinary effort, involving authors from different areas of expertise. Co-authors included Chad Haney, PhD, research associate professor of Chemistry of Life Processes Institute, Biomedical Engineering, and of Radiology; Gennadiy Bondarenko, PhD, postdoctoral fellow; Emily Waters, research associate at the CAMI; Andy Tran, research assistant; Thomas O’Halloran, PhD, professor of Medicine in the Division of Endocrinology, Metabolism and Molecular Medicine. Former Feinberg faculty Raymond Bergan, MD; Andrew Mazar, PhD; Andrey Ugolkov, MD, PhD and Lin Li, MD, were also co-authors.
This work was funded by a “Provocative Questions” grant from the National Cancer Institute (NCI) R01 CA185214 awarded through the Chemistry of Life Processes Institute, 1S10OD016398 to fund acquisition of the SPECT/CT scanner in CAMI, and 5R01HL102085 and NCI CCSG P30
by Will Doss
Original story published in Northwestern Medicine on January 9.