Five Northwestern University professors — chemist Danna Freedman, computer scientist Han Liu, economist Mar Reguant, neuroscientist Joel Voss and surgeon Jason Wertheim — have been awarded the Presidential Early Career Award for Scientists and Engineers (PECASE)....
For years, drug developers have tried, but failed, to build the perfect biological Trojan horse. Now, a new approach that disguises chemotherapeutic drugs as fat stands to outsmart, penetrate and destroy tumors. For the first time, a team of Northwestern researchers, led by Chemistry of Life Processes Institute member Nathan Gianneschi, and collaborators from the University of California, San Diego have developed a highly effective method that delivers a powerful new anticancer drug, hidden inside human serum albumin (HSA), one of the most abundant proteins found in the blood, directly into tumors. Once inside, the drug activates and suppresses tumor growth with very low toxicity to normal tissues at much higher concentrations than two leading approved chemotherapy drugs.
The results, which elucidate the design, synthesis and efficacy of this new carrier strategy for small molecule drugs, is based on exploiting the natural interactions between long-chain fatty acids (LCFAs) and HSA. The study was published today (July 18) in the Journal of the American Chemical Society (JACS).
One of the key functions of HSA is to carry molecules, such as fats, to different parts of the body. LCFAs consist of a molecular chain with a hydrophilic head and a long hydrophobic tail. The heart-shaped HSA protein contains several channels where chains of water-hating fatty acids can attach and hide with their hydrophilic heads buried inside. Like a magnet, the channels with hydrophobic walls and hydrophilic bottoms, attract and store the fats, enabling safe transport throughout the circulatory system and into tissues.
The body’s cellular receptors recognize the fats and proteins supplied by HSA and allow them inside. Fast-growing cancer cells ravenously consume nutrients much faster than normal cells.
Several years ago, Gianneschi, the Jacob and Rosaline Cohn Professor of Chemistry in Northwestern’s Weinberg College of Arts and Sciences and professor of biomedical engineering and materials science and engineering in the McCormick School of Engineering and a former Northwestern classmate Paul Bertin, Research Group Leader of Innovation at Elevance Renewable Sciences, hatched an idea.
“Paul called me one day and said, ‘ERS had developed a new type of lipid, a normal fatty acid, but with two carboxylates on either end,’” said Gianneschi. The researchers believed the lipid’s bi-functional structure offered an intriguing new platform for developing a lipidated drug.
“Imagine you have an arm with a hand on it that is able to grab onto the drug,” said Gianneschi. “The chain is like the fat with a hand on both ends: one can grab onto the drug and one can grab onto proteins. The idea is to disguise drugs as fats so that they get into cells and the body is happy to transport them around.”
Researchers have tried for years to attach chemotherapeutic drugs to the single hydrophilic head of traditional LCFAs, but presence of the drug on the head altered the chemistry of the fatty chain making it too unstable to engage securely inside the HSA channel fatty acid binding channels. Instead of putting the drug on the single hydrophilic head of a fat chain, Gianneschi and Cassandra Callmann, a graduate student in Gianneschi’s lab at the time of the study and first author of the paper, developed a new way to attach a taxane anticancer drug to the tail end of the new type of lipid. The technique preserves the head of the LCFA, ensuring a good fit inside the HSA channel enabling the drug to be securely transported without detection into cancer cells.
The experiments showed that the fatty acid with the drug attached to the tail binds HSA in the same places as normal natural fatty acids and that it also preserves the structure of the HSA so it still looks natural to the tumor tissue.
The researchers found five ideal HSA binding sites and tested the new, purified compound they called VTX (the ‘V’ for the Roman numeral five, ‘TX’ for taxane, the drug of choice here) which consisted of the drug/LCFA combination and HSA. They performed extensive in vivo studies at both UC San Diego and with the assistance of Irawati Kandela, Assistant Director, Research Assistant Professor, Chemistry of Life Processes Institute’s Developmental Therapeutics Core, at Northwestern testing VTX against two FDA-approved paclitaxel formulations over a range of conditions.
What they found astonished them: the new drug eliminated tumors in three different types of cancer: fibrosarcoma, pancreatic cancer and colon cancer.
“It’s like a Trojan horse that looks like a nice little fatty acid, so the receptors see it and invite them in. Then, the drug starts getting metabolized and kills the tumor cells,” said Gianneschi.
Remarkably, the researchers found they could deliver 20 times the dose of paclitaxel with their system, compared to two other paclitaxel-based drugs. But even at such a high quantity, the drug in Gianneschi’s system was still 17 times safer.
Together with ERS, Gianneschi formed Vybyl Biopharma to commercialize the technology and develop new applications to treat a variety of different cancers.
”Commonly used small molecule drugs get into tumors — and other cells,” said Gianneschi. “They are toxic to tumors, but also to humans. Hence, in general, these drugs have horrible side effects. Our goal is to increase the amount that gets into a tumor versus into other cells and tissues. That allows us to dose at much higher quantities without side effects which kills the tumors faster.”
In addition to Gianneshi, Callmann, and Bertin, other authors of the paper include Clare LeGuyader, Spencer Burton, Matthew Thompson, Robert Hennis, Christopher Barback, Niel Henriksen, Warren Chan, Matt Jaremko, Jin Yang, Arnold Garcia, Michael Burkart, Michael Gilson and Jeremiah Momper. The work was supported by ERS, the ARCS Foundation and the Inamori Foundation.
by Lisa La Vallee
Feature image: A modified chemotherapy drug hitches a ride through the bloodstream on human serum albumin.
Nathan Gianneshi is a member of the Chemistry of Life Processes Institute.
Congratulations to NU scientists Richard B. Silverman and Neil L. Kelleher on their recent publication in the Journal of the American Chemical Society, titled
“Mechanism of Inactivation of Ornithine Aminotransferase by (1 S,3 S)-3-Amino-4-(hexafluoropropan-2-ylidenyl)cyclopentane-1-carboxylic Acid.”
The paper addresses new efforts towards developing drugs for hepatocellular carcinoma (HCC) — the most common form of liver cancer for which there is currently no effective treatment. The inhibition / inactivation of an enzyme called ornithine aminotransferase (OAT) has been implicated as a potential therapeutic pathway for HCC and the authors of the current study have previously identified several inhibitors of OAT. Here, they proceed to characterize the mechanism(s) of OAT inactivation and report that a two-step modification resulting in an addition of a trifluoromethyl group appears to be key to the process. This discovery provides an important start-point towards further development and optimization of potential HCC therapeutics.
Rick Silverman, the Patrick G. Ryan/Aon Professor of Chemistry at NU, is senior author on the publication. Rick is an active CBC
community member and in 2018, he won an inaugural CBC Accelerator Award for the project: “Novel Drug for Hepatocellular Carcinoma.” Neil Kelleher, one of co-authors on the paper is a CBC Senior Investigator, who was hired in 2010 by NU with help from a generous CBC Recruitment Funds Award. Additional CBC connections of both researchers are listed below.
PUBLICATION LINKED TO CBC FUNDING*:
Moschitto MJ, Doubleday PF, Catlin DS, Kelleher NL, Liu D, Silverman RB. Mechanism of Inactivation of Ornithine Aminotransferase by (1 S,3 S)-3-Amino-4-
(hexafluoropropan-2-ylidenyl)cyclopentane-1-carboxylic Acid. J Am Chem Soc. 2019 Jun 28. [Epub ahead of print] (PubMed)
The inhibition of ornithine aminotransferase (OAT), a pyridoxal 5′-phosphate-dependent enzyme, has been implicated as a treatment for hepatocellular carcinoma (HCC), the most common form of liver cancer, for which there is no effective treatment. From a previous evaluation of our aminotransferase inhibitors, (1 S,3 S)-3-amino-4-(perfluoropropan-2-ylidene)cyclopentane-1-carboxylic acid hydrochloride (1) was found to be a selective and potent inactivator of human OAT ( hOAT), which inhibited the growth of HCC in athymic mice implanted with human-derived HCC, even at a dose of 0.1 mg/kg. Currently, investigational new drug (IND)-enabling studies with 1 are underway. The inactivation mechanism of 1, however, has proved to be elusive. Here we propose three possible mechanisms, based on mechanisms of known aminotransferase inactivators: Michael addition, enamine addition, and fluoride ion elimination followed by conjugate addition. On the basis of crystallography and intact protein mass spectrometry, it was determined that 1 inactivates hOAT through fluoride ion elimination to an activated 1,1′-difluoroolefin, followed by conjugate addition and hydrolysis. This result was confirmed with additional studies, including the detection of the cofactor structure by mass spectrometry and through the identification of turnover metabolites. On the basis of this inactivation mechanism and to provide further evidence for the mechanism, analogues of 1 (19, 20) were designed, synthesized, and demonstrated to have the predicted selective inactivation mechanism. These analogues highlight the importance of the trifluoromethyl group and provide a basis for future inactivator design.
Graphical abstract. (Source: dx.doi.org)
The original story was published by the Chicago Biomedical Consortium on July 8, 2019.
Rick Silverman and Neil Kelleher are both members of the Chemistry of Life Processes Institute.
A pair of recent papers helps clear up a longstanding mystery about the enzyme particulate methane monooxygenase (pMMO). The enzyme sits in the membranes of bacteria that consume methane as their main food source, and catalyzes the conversion of methane to methanol.
“Everyone in the field agrees that it’s a copper-dependent enzyme,” says Amy C. Rosenzweig, a biochemist at Northwestern University who led both studies. What researchers don’t agree on is what the copper active site might look like. Decades of conflicting studies have left the active site shrouded in mystery. Various crystal structures have shown zinc, copper, or no metal at all in the potential binding sites.
In a study published in May, Rosenzweig, Brian M. Hoffman, and their coworkers used multiple electron paramagnetic resonance (EPR) spectroscopic techniques to reveal that pMMO purified from bacterial membranes contains two metal binding sites, each of which binds a single copper ion (Science 2019, DOI: 10.1126/science.aav2572). Rosenzweig points out that the team had previously proposed that one of the sites had a dicopper center.
For one of the two sites, the researchers couldn’t isolate its EPR signal, preventing them from characterizing the site. All they could tell was how far its copper ion was from the other site’s copper ion—about 2 nm. Previous crystal structures were no help because those data had shown that the mystery site was in a chronically disordered region of the protein.
So Rosenzweig turned to Neil L. Kelleher, another Northwestern chemistry professor, for help. Kelleher used top-down native mass spectrometry to analyze the protein. In that technique, researchers reconstitute the protein in a lipid nanodisc under conditions that cause it to remain in its native state.
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Members of Kelleher’s team were able to determine the number of coppers in each of pMMO’s three subunits, named PmoA, PmoB, and PmoC (Nat. Commun. 2019, DOI: 10.1038/s41467-019-10590-6). They found a single copper binding site in each of PmoB (the one that was visible with EPR) and PmoC (the one that was obscured).
The mass spec experiment told the team something else about the enzyme. While the researchers prepared the enzyme samples for native top-down mass spectrometry, the protein lost some of its copper. By adding copper during the preparation, the researchers could help the enzyme recover the metal, particularly in PmoC. The added copper also increased the enzyme’s activity, suggesting that the PmoC site is important for enzyme activity. But questions remain about what the active site looks like.
“The fact that copper is located in subunit PmoC and correlates with activity is something of a surprise and could indicate the location of the active site,” says Thomas J. Smith, an expert on pMMO at Sheffield Hallam University. “There is still such a large amount of conflicting evidence about the location of the active center that I think additional evidence is still needed.”
by Celia Henry Arnaud
The original story was published in Chemical and Engineering News on June 26, 2019. Feature image: This methane monooxygenase’s copper binding sites are located in the PmoB (purple) and PmoC (blue) subunits. PmoA is shown in pink. Credit: Nat. Commun.
Amy C. Rosenzweig and Neil L. Kelleher are both members of the Chemistry of Life Processes Institute.
It’s not an electron. But it sure does act like one.
Northwestern University researchers have made a strange and startling discovery that nanoparticles engineered with DNA in colloidal crystals — when extremely small — behave just like electrons. Not only has this finding upended the current, accepted notion of matter, it also opens the door for new possibilities in materials design.
“We have never seen anything like this before,” said Northwestern’s Monica Olvera de la Cruz, who made the initial observation through computational work. “In our simulations, the particles look just like orbiting electrons.”
With this discovery, the researchers introduced a new term called “metallicity,” which refers to the mobility of electrons in a metal. In colloidal crystals, tiny nanoparticles roam similarly to electrons and act as a glue that holds the material together.
“This is going to get people to think about matter in a new way,” said Northwestern’s Chad Mirkin, who led the experimental work. “It’s going to lead to all sorts of materials that have potentially spectacular properties that have never been observed before. Properties that could lead to a variety of new technologies in the fields of optics, electronics and even catalysis.”
The paper will publish Friday, June 21 in the journal Science.
Olvera de la Cruz is the Lawyer Taylor Professor of Materials Science and Engineering in Northwestern’s McCormick School of Engineering. Mirkin is the George B. Rathmann Professor of Chemistry in Northwestern’s Weinberg College of Arts and Sciences.
Mirkin’s group previously invented the chemistry for engineering colloidal crystals with DNA, which has forged new possibilities for materials design. In these structures, DNA strands act as a sort of smart glue to link together nanoparticles in a lattice pattern.
“Over the past two decades, we have figured out how to make all sorts of crystalline structures where the DNA effectively takes the particles and places them exactly where they are supposed to go in a lattice,” said Mirkin, founding director of the International Institute for Nanotechnology.
In these previous studies, the particles’ diameters are on the tens of nanometers length scale. Particles in these structures are static, fixed in place by DNA. In the current study, however, Mirkin and Olvera de la Cruz shrunk the particles down to 1.4 nanometers in diameter in computational simulations. This is where the magic happened.
“The bigger particles have hundreds of DNA strands linking them together,” said Olvera de la Cruz. “The small ones only have four to eight linkers. When those links break, the particles roll and migrate through the lattice holding together the crystal of bigger particles.”
When Mirkin’s team performed the experiments to image the small particles, they found that Olvera de la Cruz’s team’s computational observations proved true. Because this behavior is reminiscent to how electrons behave in metals, the researchers call it “metallicity.”
“A sea of electrons migrates throughout metals, acting as a glue, holding everything together,” Mirkin explained. “That’s what these nanoparticles become. The tiny particles become the mobile glue that holds everything together.”
Olvera de la Cruz and Mirkin next plan to explore how to exploit these electron-like particles in order to design new materials with useful properties. Although their research used gold nanoparticles, Olvera de la Cruz said “metallicity” applies to other classes of particles in colloidal crystals.
“In science, it’s really rare to discover a new property, but that’s what happened here,” Mirkin said. “It challenges the whole way we think about building matter. It’s a foundational piece of work that will have a lasting impact.”
The research, “Particle analogs of electrons in colloidal crystals,” was supported by the Center for Bio-Inspired Science, an Energy Frontier Research Center funded by the U.S. Department of Energy (award number DE-SC0000989); the Air Force Office of Scientific Research (award number FA9550-17-1-0348); the Office of Naval Research (award number 00014-15-1-0043) and the Sherman Fairchild Foundation. Martin Girard, a PhD graduate from Olvera de la Cruz’s laboratory and current postdoctoral scholar at the Max Planck Institute for Polymer Research in Germany, is the paper’s first author.
The original story appeared in Northwestern Now on June 20, 2019.
Monica Olvera de la Cruz is a member of the Chemistry of Life Processes Institute.
Training and inspiring the next generation of interdisciplinary scientists is central to the mission of the Chemistry of Life Processes Institute at Northwestern. This year, four aspiring scientists will join a growing list of students who have received funding through the Institute’s Executive Advisory Board members to receive hands-on experience and training at the intersection of multiple scientific disciplines.
Emma Schultz, a rising junior chemistry major, received the Institute’s most prestigious undergraduate award: the Lambert Fellowship. She will be working in the laboratory of Thomas O’Halloran (chemistry), inaugural director, CLP.
“I am so grateful for the Lambert Fellowship and the opportunity to receive mentorship, learn to think in depth about research, and develop greater presentation skills,” says Schultz.
Established in 2010 by Dr. Andrew Chan, CLP Executive Advisory Board Chair, the Lambert Fellows Program provides multi-year funding for rising sophomores and juniors majoring in chemistry to conduct laboratory research under the mentorship of CLP faculty members. Awardees receive a summer stipend as well as funding that covers research supplies and conference travel. Fellows work closely with an Institute faculty member to develop their research proposals and budget allocations. Graduate student and postdoctoral associate mentors also work closely with the students. The program aims to mentor and produce a cadre of enthusiastic, well-trained undergraduates with an entrepreneurial mindset. Fellowships begin in early summer and continue throughout the academic year for a minimum period of two years.
Emma Herzog, a rising senior chemistry major, Tyler Kramlich, a rising fifth year double major in Chemical Engineering and Music Composition, and Olivia Pura, a rising senior double major in Biology and Slavic Literatures & Languages, were the recipients of the Institute’s Summer Scholars research awards. Each will receive a stipend to spend the summer quarter working in CLP faculty laboratories. Working in collaboration with CLP researchers, students will learn the most innovative approaches to problem solving using methods developed by chemists, biologists, engineers, physicists, mathematicians and clinicians.
Since the programs’ inception, more than 60 undergraduates have participated in both summer and year-round programs, including the Chicago Area Undergraduate Research Symposium Award, awarded in the fall to support academic year research. Eighty-three percent of CLP-funded graduates have pursued PhDs at top graduate schools, enrolled in Medical Scientist Training programs, or attended medical school. One former student is attending law school and another is in veterinary school. In addition, CLP undergrads have co-authored more than 45 papers based on their work.
by Lisa La Vallee
Feature image: Summer scholars Emma Herzog and Tyler Kramlich.
With more than 30 years in the pharmaceutical industry, preceded by a decade as an independent researcher in academia, Chemistry of Life Processes Institute’s Entrepreneur-in-Residence William Sargent shared his perspective and advice about potential science career opportunities in industry with the most recent crop of CLP graduate student trainees.
At a recent ‘Lunch and Learn,’ Sargent described his industry career trajectory as a series of upward movements that started with working in the field with sales reps and quickly progressed to senior-level positions at Hoechst-Roussel Pharmaceuticals, Lorex Pharmaceuticals, Searle, Pharmacia and Pfizer. As president and general manager of Lorex, he oversaw FDA approval for direct to consumer advertising for their lead product Ambien®. He also led the international launch of Sutent® for renal cell carcinoma and gastrointestinal stromal cancer while senior medical director and team leader for the anti-angiogenic portfolio at Pfizer.
Sargent outlined a number of job opportunities within the pharmaceutical industry. Regulatory affairs, for instance, a field once dominated by lawyers, is now primarily the domain of scientists who need to speak and understand the language of scientific reviewers at the US Food and Drug Administration (FDA).
“Regulatory affairs is the conduit from the pharmaceutical industry to the people at FDA who are conducting the drug reviews. The kind of people you run into at FDA generally are very, very good scientists. It’s a lot of fun if you like working on project teams.”
Scientists (MDs, PhDs and PharmDs) are also in high demand for the clinical phase of drug development. “They’re the people who look at the FDA-required end points, design drug trials and write the clinical protocols.”
In addition, Medical Affairs groups in pharmaceutical companies are staffed by scientists who negotiate between marketing and clinical development and discuss clinical trial realities with marketing. The objective is to enhance information provided to marketing about the drug that will better inform physicians about the appropriate use of the drug.
“The pharmaceutical industry really does expand not only your vision of drug development, but it also expands your knowledge of patient and physician needs due to the extensive travel you have to put into it.” Sargent estimates he spent about 40 percent of his time spent outside of the office.
After spending 10 years with Pfizer traveling across the globe, a London-based medical communications company recruited him. In this role, Sargent conducted many group conversations with practicing physicians to decipher how to triage patients into different therapeutic regimens. His company would present a patient history and then listen to the doctors’ thoughts about how to treat the patient.
“The engines of the medical communications industry are medical writers. If you like to write, it’s a perfect place for you. We’d take a contract to write a manuscript and the medical writer would then go to the literature, get caught up on that particular aspect of medicine, and then interact with the authors to plan out the paper.”
In addition to a scientific background, a good medical writer is task-oriented as well as creative, says Sargent. Skilled medical writers can look at things differently and explain very complex subjects to an audience that may not be as well versed in that specific aspect of medical treatment.
Medical writing is also a good choice for people who like the freedom of working from home.
“I had one medical writer in Colorado,” says Sargent. “He would go skiing in the morning and write for eight hours after he went skiing. That was during the winter. During the summer, he played golf in the morning and wrote in the afternoon and evening. It’s a very nice lifestyle.”
Earlier in his career, Sargent noted that most scientific career opportunities were within the pharmaceutical industry, but that is no longer the case.
Government Funding Agencies, Investment Firms and Reimbursement Agencies
“Anybody who comes into your labs selling something is from an industry that you potentially could work in,” says Sargent. “Anybody who touches a lab, or a research facility, or a pharmaceutical company needs scientists at some point to develop products, represent them and to talk to customers.”
Other examples of industries that hire scientists include:
- National funding agencies like the National Institutes for Health, National Science Foundation and the Department of Defense.
- Patient support organizations, such as JDRF (The Juvenile Diabetes Research Foundation) with about 25 MD/PhDs in their New York office alone who support more than $100 million in basic science and clinical research
- Venture capital firms and investment banks that depend on scientists to evaluate the science for a particular drug before investing
- Reimbursement agencies like United Health Care that need scientists to determine which drugs to include in their formulary for reimbursements
“Today, there are numerous and varied careers for basic science PhDs. Your first job is the entry point from which you can get in the stream of things, shoot off and away you go.”
by Lisa La Vallee
This year, three teams of Chemistry of Life Processes Institute investigators received $90,000, collectively, in CLP-Cornew Innovation Awards to pursue potentially transformative proof-of-concept studies to better detect, diagnose and treat disease. The awardees included Neha Kamat (biomedical engineering) and Julius Lucks (chemical & biological engineering) for development of a next generation biosensor; Tom Meade (chemistry) and Keith Tyo (chemical & biological engineering) to develop a more accurate, portable diagnostic kit; and Nathan Gianneschi (chemistry) and Bin Zhang (Medicine) for a proof-of-concept study for a new immunotherapy.
A next generation biosensor
From detecting pathogens in water to attacking toxins in the blood stream, an enormous need exists for biosensors in a variety of health and environmental fields. Clinicians currently must draw blood to detect the presence of molecules that signal trouble in humans, but this method can miss critical information. For instance, a molecule located near the site of a cancerous tumor can become diluted by the time it reaches the side of extraction rendering it undetectable.
Collaborators Neha Kamat and Julius Lucks want to build a radically different biosensor— one that acts as a “molecular taste bud” that can travel through the body in a carefully designed container, detect its target, record what it sees and even act as a kind of therapeutic.
One of the biggest challenges is designing a compartment that will allow the sensor to move through the body.
“What is needed is a sensor that moves through those environments, see something it’s been designed to see, and then records that event,” says Kamat. “It basically generates a memory that it saw a toxin or a low ph, or a molecule, so that when we do collect it, the sensor tells us what it saw.”
Taking a cue from the basic structure of a cell, the collaborators will use an RNA-based sensor that takes the sensing capability outside of the cell. This genetic polymer has the unique ability to detect very specific biological analytes of interest and report detection of a molecule.
“This little RNA switch is thought to be one of the more ancient ways that cells have evolved to sense their environments,” says Lucks.
The tool promises a wide range of potential diagnostic and therapeutic applications. In countries, such as India and Bangladesh, it could be a game changer. The overabundance of fluoride in the ground water in certain areas has led to a widespread health condition known as skeletal fluorosis, a painful and deforming bone disease.
Ultimately, the team hopes to build a modular tool that can diagnose a wide range of conditions, but for this project, they will focus on fluoride.
“You could make a therapeutic product that binds fluoride and pulls it out of circulation. You could make a fluorescent protein just to tell you that it’s there, which opens up the door to a huge range of responses that would expand what the biosensor does,” says Lucks.
A more accurate portable diagnostic test
CLP members Thomas Meade and Keith Tyo are developing a more accurate portable diagnostic tool that will enable patients and doctors to make better on the spot health decisions.
Currently, there are limitations to the accuracy of certain kinds of portable diagnostic tests. The hepatitis C test, for example, can accurately detect antibodies, but it can’t distinguish whether the patient was infected years ago or is experiencing an active infection.
“Typically if an antibody-based test comes back positive, they then will have to do a second round of tests that are based on a PCR and molecular diagnostics— things that are very, very lab heavy, require a lot of infrastructure and require a lot of training and personnel. It’s just not useful for a point-of-care (POC) testing,” says Catherine Majors, a postdoctoral scholar in Tyo’s lab involved in the project.
Another problem with POC diagnostic tests is that a lack of sensitivity can lead to a weak positive or false negative result. In home pregnancy testing, for example, if only a small amount of the analyte for pregnancy is detected, the test will barely register a signal, and the person reading the test may be unable to read the signal.
“What we’re trying to do is make something that’s analogous to the molecular mousetrap. There’s no such thing as a weak positive for a mouse trap,” says Tyo. “There’s no pushing halfway down on the trigger and the trap slowly turning over. It’s either snapped or it’s not fired yet.”
The first order of business is getting the molecular switch to work. Once the switch is working, the researchers will look upstream to see if they can get their test input, a hepatitis C antigen, to flip the switch. In future, they hope to use the new mechanism to detect a variety of conditions. The approach is a plug-and-play system that could easily be adapted for other tests. The team will leverage a proprietary technology developed by Meade to convert the molecular information into an electrical signal that will enable them to develop a new digital tool for reporting and analyzing test results.
“CLP allows for this intersection of interdisciplinary scientists,” says Tyo. “It is extremely enabling to combine my synthetic biology expertise with Meade’s chemistry and surface science expertise. That wouldn’t be possible otherwise. If we’re successful with our proof of concept, CLP has lots of infrastructure to help us move this forward to an actual application in the field. That’s really exciting.”
A more effective cancer immunotherapy
“The common theme is how do I deliver material? How do I deliver your drug to the bloodstream, or in the mouth, or rub it on your skin, and get it where you need it to be to have the desired effect?” says Gianneschi. “We’re trying to solve both.”
The investigators’ approach targets the signals associated with inflammation, which are found in a number of diseases like cancer and heart disease. The goal of the project is to develop a new kind of injectable immunotherapeutic designed to circulate throughout the body and localize in tumor cells while avoiding normal tissue. Over time, the material will accumulate in the tumor in just the right concentration until its signal triggers the immune system to recognize and attack not just the material, but the surrounding tumor tissue as well.
“It’s absolutely necessary that you localize the materials, but you don’t always know exactly where you want to put the drugs,” says Gianneschi. “You need to be able to do a delivery to the whole body where the drug is activated and localized only at the tumor. This is a massive global challenge with many different types of drugs that fall under the general category of targeted therapeutics.”
When Gianneschi first moved to Northwestern, he knew from experience that collaboration was essential for his kind of work. As a member of CLP, he found Zhang, a highly skilled immunology expert, and Irawati (Angki) Kandela, Assistant Director of the Developmental Therapeutics Core, who helped test and evaluate promising therapeutic agents. The researchers also utilized the imaging technology and expertise of the Center for Advanced Molecular Imaging. Both CDT and CAMI are CLP-affiliated cores.
The team hopes the Cornew Award will enable them to generate enough seed data to provide the basis for an NIH grant.
“We’ve done a lot of studies in the run up to this in CLP core facilities. This is such complicated research that involves imaging, animal dosing and the right animal models,” says Gianneschi. “It’s more than just technicians at CLP; these people are fully engaged. We’ve worked in the past with technicians who have said, ‘I did your injection— it didn’t work’ and then you’re stuck. I’d have to have half my group trying to do it. This is a totally different game here.”
The CLP-Cornew Innovation Awards
Currently in its ninth year, the CLP-Cornew Innovation Awards, are made possible by the generosity of Chemistry of Life Processes Institute Executive Advisory Board members, support promising interdisciplinary teams of CLP researchers in early stage development of high-risk, high-reward research projects with the potential to make significant impact.
Since the program’s inception in 2010, the CLP Board has awarded more than $900,00 to faculty collaborators in pilot funding. Cornew Awards have resulted in 39 publications, nine patents, and more than $18 million in new external funding to advance these projects opening up critical areas of transdisciplinary research and resulting in discoveries that impact human health and disease.
by Lisa La Vallee
Featured image: (left to right) CLP-Cornew Awardees Julius Lucks, Neha Kamat, Keith Tyo and Thomas Meade.
A major dilemma faced by many people undergoing chemotherapy for cancer is whether the drugs will cause more harm than good.
“Chemotherapeutic drugs can have serious side effects. Some of the adverse events in chemotherapy, such as heart failure, can even take as long as 10 years to manifest in people down the road,” says Steven E. Johnson, ’16 PhD, former postdoctoral fellow in Chemistry of Life Processes Institute member Ming Zhao’s laboratory.
Johnson and Ming Zhao, PhD, Associate Professor of Medicine in the Division of Cardiology, developed an innovative new imaging technology, published in Clinical Cancer Research, that surveys the entire body’s response to potentially toxic drugs in real time by assessing a marker for cell death.
Pathologically elevated cell death is an unambiguous marker for tissue injury. The collaborators’ initial proof of concept studies began with observation of cellular changes in response to cytotoxic treatments. The scientists took notice of a phenomenon called aminophospholipid externalization, in which a type of phospholipid that resides inside viable cells becomes available for binding of select imaging agents when the cell is dead or dying.
“The technique works by detecting a molecular signature of cell death, which enables the near-real time monitoring of toxic side-effects in target and susceptible tissues,” says Zhao.
The “aha” moment came when the researchers realized that they could apply this technology in a whole-body and dynamic fashion as a survey for drug toxicity by imaging the location of tissue damage in real time throughout the subject.
Excited about the translational possibilities of their research, the pair patented their new technology and started Durametrix to develop its commercial potential. They are working with Northwestern to obtain the license for the invention. Zhao and Johnson applied to NIH for a Small Business Technology Transfer (STTR) grant to test potential applications. Initially, the company would like to roll out the product to pharma industry collaborators and other researchers involved in drug discovery and development. Down the road, they hope to develop it for clinical use.
“When you want to create a new drug, you don’t start with just one molecular entity,” says Johnson, CEO of the new startup. “You start with many different compounds and narrow it down to 4-5 candidates that all look like they could be the drug that you’re going to give somebody eventually. When you test how safe and effective these candidates are, you need to go through hundreds of subjects. These studies are time-consuming, labor-intensive, and very expensive. The average time is about 2-3 years for a good drug discovery company to get to the point where they’ll say, this is what we want to actually push forward into clinical development.
“Our technology could really help drug companies make educated decisions in an expeditious and effective manner saving valuable time and money,” says Johnson.
Throughout the project, Chemistry of Life Processes Institute faculty, technical staff and administrators provided valuable assistance and guidance. Andrew Mazar, Center for Developmental Therapeutics, partnered with the researchers in developing the cytotoxicity paradigm; Chad Haney, managing director, Center for Advanced Molecular Imaging, collaborated on the imaging studies; and Jody Hirsh, senior read more…
Northwestern University graduate student and Chemistry of Life Processes Institute trainee Jennifer Rachel Ferrer will finish her PhD tomorrow as a joint student of Drs. Chad Mirkin (chemistry), and Jason Wertheim (surgery). She will present her research on how spherical nucleic acids, which are being investigated as new drug delivery systems, localize in the body. Her findings will inform design of SNAs to target specific tissues and cells for potential therapies. The daughter of immigrant parents and the first in her family to receive a doctorate, Ferrer’s thesis defense marks the culmination of years of bench work. Her graduate school years have also included advocating for women in STEM, rock climbing, and finding her community on campus.
Jen had already begun to set up dual mentorship in chemistry and biology before learning about the dual mentor requirement of the NIH-funded CLP T32 Predoctoral Training Program. She had joined a lab in Evanston focusing on chemistry, and one on the Chicago campus that emphasized tissue engineering and biology.
“The CLP Training Program was exactly what I had wanted for myself in grad school, as I was already thinking along that chemistry-biology interface,” said Ferrer. “It was great to see that there was a program here that emphasizes the transdisciplinary nature of the research we do here at Northwestern that leads to the development of different therapeutics and diagnostic tools that might one day help and treat patients.”
In addition to lab work and her participation in the CLP Training Program, Ferrer wanted to work to empower other women and was a fellow at the Center for Leadership. She created a project at the end of her fellowship, alongside three other women who were members of her leadership trainee cohort, to revive Northwestern’s chapter of the American Association of University Women (AAUW), which was no longer in existence.
The newly revived AAUW chapter at Northwestern empowers women to pursue their education through AAUW fellowships, provides interactive workshops on salary negotiation, as well as leadership training. She says that her time as a graduate student has bled into normal life, and that now, everything becomes a scientific question for which she creates hypotheses.
“I’ve noticed at conferences and in interactions at career panels, there isn’t a lot of representation at the top. There aren’t a lot of women, or people of color. Everything becomes a hypothesis, or an experiment to me now, so I ask the question why is that? How do I get there? Once I have those answers, how do I translate that back to the next generation?”
As she worked to empower other women and on her research, Ferrer says her rock-climbing hobby helped her find balance within her life, and that she became a stronger student and found community in climbing gyms.
“Grad school was a new place and a totally new environment. You’re expected to be autonomous and come up with an interesting research question on your own and you’re not yet an expert, but by the end of it, well, you are,” said Ferrer. “There are going to be ups and downs all along the way, and I think that rock climbing has helped me become more resilient in school and that all the grad school failures have helped me become a more resilient climber and person.”
Ferrer has accepted a position as a research analyst with drug development startup Monopar Therapeutics, an opportunity that arose through an interaction with CLP Executive Advisory Board member Chandler Robinson, CEO of the biotech company. While she will no longer be working at the bench, “I’m excited to expand my knowledge of the drug-development space, but still very much be connected to the science part of it,” said Ferrer.
When reflecting on her time at Northwestern, Ferrer focuses primarily on the communities she has found across campus.
“When I was writing the acknowledgements section of my thesis, it just kept going and going. On one hand, I thought this is long, but on the other, it would be a disservice if I didn’t thank all of these people because they have all been integral to my development as a scientist and a more mature person.”
Jennifer defended her thesis on June 19, 2019.
Check out her rock climbing instagram: @coconutandcantaloupe
by Lydia Rivers
Guillermo A. Ameer, professor of biomedical engineering and surgery, has been named the 18th recipient of the Martin E. and Gertrude G. Walder Award for Research Excellence. A pioneer in the emerging field of regenerative engineering, Ameer is known for his creative approach to designing biodegradable materials that promote tissue regeneration and prevent scarring.
The award, established in 2002 by alumnus Dr. Joseph A. Walder and given annually by the University provost, recognizes excellence in research at Northwestern.
“Through his pioneering work with biomaterials and leadership of the Center for Advanced Regenerative Engineering, Guillermo Ameer exemplifies innovation and excellence in research at Northwestern,” said Provost Jonathan Holloway.
“I’m honored to receive this prestigious award in recognition of our work in regenerative engineering,” Ameer said.
With appointments in the McCormick School of Engineering and Feinberg School of Medicine, Ameer is the Daniel Hale Williams Professor of Biomedical Engineering and Surgery. He also is the founding director of the Center for Advanced Regenerative Engineering (CARE), which aims to develop a range of biomedical solutions to promote growth and healing in damaged organs and tissues.
Ameer’s laboratory has pioneered the development and medical applications of antioxidant citrate-based biomaterials that can be used as a liquid or solid scaffold to regenerate new tissue. The biomaterials then break down and absorb into the body without side effects. The material’s main component — citric acid — accelerates healing due to its inherently antioxidant nature. Hundreds of researchers around the world have adopted the material for various bioengineering applications in their laboratories.
Ameer has used his citrate-based biomaterials in a range of applications to address a host of issues, including cardiovascular disease, broken bones, torn ligaments and bladder disease. To help patients with diabetes, for example, Ameer’s team used the biomaterials to develop a “regenerative bandage” for chronic, non-healing diabetic foot ulcers. His bandage heals wounds four times faster than a standard bandage without any side effects.
Named as a top 100 young innovator by Technology Review in 2013, Ameer is a fellow of the American Institute of Medical and Biological Engineering, Biomedical Engineering Society, American Institute of Chemical Engineers and the American Association for the Advancement of Science. A native of Panama, he received a key to the city of Panama City by the Panamanian government in 2018 for his contributions to science and society. He also has received the American Heart Association Established Investigator Award, the National Science Foundation CAREER Award, the Walter H. Coulter Early Career Translational Research Award and an American Immigration Law Foundation Immigrant Achievement Award.
He has authored more than 250 scientific papers, which have been published in high impact journals, including Nature Materials and the Proceedings of the National Academy of Sciences. He also has more than 50 patents issued or pending in nine countries.
Through his leadership, CARE has successfully competed for more than $10 million in extramural funding to carry out several regenerative engineering projects, sponsored by several government agencies. Ameer also is a faculty affiliate of Northwestern’s Simpson Querrey Institute, Chemistry of Life Processes Institute and International Institute of Nanotechnology.
Joseph Walder earned his doctoral and medical degrees from Northwestern, then founded a company that supplies synthetic DNA for research and clinical applications. A complete list of award recipients can be found on the Office of the Provost website.
By Amanda Morris
The original story was published on June 4 in Northwestern Now.
Northwestern University faculty members William Dichtel, Michael Jewett and Emily Weiss have been named finalists for the 2019 Blavatnik National Awards for Young Scientists. They are among 31 scientists and engineers being recognized nationally this year.
The finalists are considered to be some of America’s most important young scientific researchers aged 42 years or younger, driving the next generation of innovation by addressing today’s most complex and intriguing scientific questions. They now will compete for the largest unrestricted awards of their kind for early career scientists and engineers.
There are 10 finalists in each of three categories: life sciences, chemistry and physical sciences and engineering. The 2019 Blavatnik National Laureates, one from each category, will be announced on June 26. Each laureate will receive a cash prize of $250,000.
The annual Blavatnik Awards were established in 2007 by the Blavatnik Family Foundation and are administered by the New York Academy of Sciences.
Dichtel, the Robert L. Letsinger Professor of Chemistry at the Weinberg College of Arts and Sciences, is a finalist in chemistry. He was also a Blavatnik finalist in 2017. Dichtel works at the frontiers of organic, polymer and materials chemistry. He has pioneered efforts to understand a new frontier in polymerization — the formation of 2D grids and 3D scaffolds. These materials, as well as other disordered structures that also contain tiny pores, possess extremely high surface areas and have applications in water purification and energy storage.
Dichtel is a member of Northwestern’s International Institute of Nanotechnology.
Jewett, the Charles Deering McCormick Professor of Teaching Excellence, a professor of chemical and biological engineering in the McCormick School of Engineering and co-director of Northwestern’s Center for Synthetic Biology, is a finalist in life sciences. His work focuses bio-manufacturing therapeutics, materials and chemicals. Jewett invented cell-free techniques that harness biological systems without intact cells, creating new routes toward on-demand synthesis of medicines, expanding the chemistry of life, portable molecular diagnostics and education kits.
Jewett is a member of the Robert H. Lurie Comprehensive Cancer Center at Northwestern University, Simpson Querrey Institute and the Chemistry of Life Processes Institute.
Weiss, the Mark and Nancy Ratner Professor of Chemistry at Weinberg, is a finalist in chemistry. She was also a Blavatnik finalist in 2018. Weiss’s transformative, cross-disciplinary work focuses on light-driven chemical reactions, high-time resolution biological imaging, chemical systems out of equilibrium and new mechanisms of charge transport in nominally insulating materials. Much of her lab’s research uses nanoscale semiconductor particles, called quantum dots, to transduce visible and near-infrared light energy to chemical and electrical energy, and for fundamental studies of processes at interfaces.
Weiss is a member of Northwestern’s International Institute of Nanotechnology.
by Amanda Morris
Original story published by Northwestern Now on May 29, 2019.
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.
Researchers improved the tool by combining existing sSMLM with a two-mirror system, allowing it to image molecules in 3-D at much larger depths. This new tool could help molecular biologists understand complex processes inside cells.
“Our design is relatively easy to implement, and will allow us to study molecular interactions much better than before,” said Hao Zhang, professor of biomedical engineering and coauthor of the research. “Now we can not only see where molecules are, but also what they are.” Zhang developed the technology with Cheng Sun, associate professor of mechanical engineering.
The results were published May 21 in the journal Optica. Coauthors included Ki-HeeSong, a Ph.D. candidate, and Yang Zhan, a postdoctoral fellow, both of Northwestern’s Biomedical Engineering department.
Imaging in 3-D
In recent years, scientists and engineers have used sSMLM to better understand molecular interactions and cellular dynamics. The system provides information on the location of molecules and how those molecules interact with light, which tells scientists what type of molecule they see.
But the system only works in two dimensions, giving just a partial view of molecules and their interactions.
Zhang and Sun wanted to extend imaging to 3-D and originally developed a way to do this by adding an additional lens, but found that a pair of mirrors can achieve the same effect in a much more elegant way.
The mirrors work by introducing an optical path length difference in the system that improves the way the system uses photons. Unlike lenses, most mirrors do not attenuate light that is reflected, meaning more photons can be used for nanoscopic localization to create a sharper picture and extends imaging into 3-D-depth range.
With 3-D nanoscale imaging capability, researchers can see more interactions happening within the intracellular volume without being overshadowed by the surface. For example, Zhang, Sun, and their collaborators are using the system to study the intercellular distribution of molecules, looking at how RNA is transported and interacts with cell organelles before being translated into proteins.
“This system could have profound implications in molecular biology,” Zhang said.
Though previous molecular imaging systems used optical filters to detect different types of molecules based on their well-separated emission colors, the new system can detect minute differences in molecular emissions from every different molecule and analyze the spectrum to differentiate them.
“We can now color code every single molecule,” Sun said. “That is a key strength.”
Understanding nanoscale processes
Next, the researchers hope to continue to refine the technology, as well as use it in molecular biology studies.
They are working with collaborators to study the pore structure of the nucleus and how it is involved in stem cell differentiation, and are also studying the depolarization of the mitochondrial membrane, an event associated with many diseases, including vision loss in diabetic patients. They also hope that their technology helps others in the field.
“It is a very elegant design,” Sun said. “The system can be very easily implemented in other labs, and it has a beautiful performance.”
by Emily Ayshford, Northwestern University
The original story was published in Physics.org on May, 22, 2019.
Hao Zhang and Cheng Sun are both members of the Chemistry of Life Processes Institute.
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.