Revealing the Rules Behind Virus Scaffold Construction

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...

Promising young faculty receive prestigious career award

Promising young faculty receive prestigious career award

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.

Nicholas Diakopoulos

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.

Yevgenia Kozorovitskiy

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.

Sepehr Vakil

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.

New blueprint for understanding, predicting and optimizing complex nanoparticles

New blueprint for understanding, predicting and optimizing complex nanoparticles

Northwestern University researchers have developed a blueprint for understanding and predicting the properties and behavior of complex nanoparticles and optimizing their use for a broad range of scientific applications. These include catalysis, optoelectronics, transistors, bio-imaging, and energy storage and conversion.

Recent research findings have successfully enabled the synthesis, or creation, of a wide variety of polyelemental nanoparticles — structures with as many as eight different elements. However, there is still a limited understanding of how the arrangement of phases within these structures impact their properties and how specific interfaces (the common surface between bound structures, called heterostructures) can be optimally designed and synthesized.

“As the combinatorial space of mixtures is nearly infinite, with billions of possibilities, predicting and understanding how specific classes of interfaces can be established in a single particle is crucial for designing new and functional nanostructures and, ultimately, optimizing their properties for various scientific applications,” said Chad A. Mirkin, the George B. Rathmann Professor of Chemistry in the Weinberg College of Arts and Sciences and the director of the International Institute for Nanotechnology at Northwestern, who led the research.

In the study, the researchers utilized scanning probe block copolymer lithography (SPBCL), invented and developed at Northwestern by Mirkin, to construct a new library of polyelemental heterostructured nanoparticles containing up to seven different metals.

The research will be published in the March 1 issue of the journal Science.

“We used computational tools, such as density functional theory, to compute interfacial energies between phases, as well as surface energies, and combined these into an overall nanoparticle energy,” said Chris Wolverton, the Jerome B. Cohen Professor of Materials Science and Engineering in Northwestern’s McCormick School of Engineering. “What we found is that observed morphologies minimized calculated energies. As a result, we now have a tool to predict and understand these types of phase arrangements in nanoparticles.”

Wolverton is a co-author of the study.

“Our contribution enables the synthesis of numerous types of interfaces, providing a vast playground to explore their properties and phenomena — such as novel catalysts and light-emitting nanostructures — for useful purposes,” said co-author Vinayak Dravid. He is the Abraham Harris Professor of Materials Science and Engineering and the director of the Northwestern University Atomic and Nanoscale Characterization Experimental Center (NUANCE).

The Science paper is titled “Interface and heterostructure design in polyelemental nanoparticles.” Peng-Cheng Chen and Mohan Liu are the first authors of the study.

The research is supported by the Sherman Fairchild Foundation, the Air Force Office of Scientific Research (award FA9550-17-1-0348) and the Vannevar Bush Faculty Fellowship program, sponsored by the Basic Research Office of the Assistant Secretary of Defense for Research Engineering and funded by the Office of Naval Research (grant N00014-15-1-0043).

— By Sheryl Hislop Cash

Original story published by Northwestern Now on February 28, 2019

 Vinayak Dravid is a resident member of the Chemistry of Life Processes Institute.

New machine learning technique rapidly analyzes nanomedicines for cancer immunotherapy

New machine learning technique rapidly analyzes nanomedicines for cancer immunotherapy

With their ability to treat a wide a variety of diseases, spherical nucleic acids (SNAs) are poised to revolutionize medicine. But before these digitally designed nanostructures can reach their full potential, researchers need to optimize their various components.

A Northwestern University team led by nanotechnology pioneer Chad A. Mirkin has developed a direct route to optimize these challenging particles, bringing them one step closer to becoming a viable treatment option for many forms of cancer, genetic diseases, neurological disorders and more.

“Spherical nucleic acids represent an exciting new class of medicines that are already in five human clinical trials for treating diseases, including glioblastoma (the most common and deadly form of brain cancer) and psoriasis,” said Mirkin, the inventor of SNAs and the George B. Rathmann Professor of Chemistry in Northwestern’s Weinberg College of Arts and Sciences.

A new study published this week in Nature Biomedical Engineering details the optimization method, which uses a library approach and machine learning to rapidly synthesize, measure and analyze the activities and properties of SNA structures. The process, which screened more than 1,000 structures at a time, was aided by SAMDI-MS technology, developed by study co-author Milan Mrksich, Henry Wade Rogers Professor of Biomedical Engineering in Northwestern’s McCormick School of Engineering and director of the Center for Synthetic Biology.

Invented and developed at Northwestern, SNAs are nanostructures consisting of ball-like forms of DNA and RNA arranged on the surface of a nanoparticle. Researchers can digitally design SNAs to be precise, personalized treatments that shut off genes and cellular activity, and more recently, as vaccines that stimulate the body’s own immune system to treat diseases, including certain forms of cancer.

SNAs have been difficult to optimize because their structures — including particle size and composition, DNA sequence and inclusion of other molecular components — can vary in many ways, impacting or enhancing their efficacy in triggering an immune response. This approach revealed that variation in structure leads to biological activities showing non-obvious and interdependent contributions to the efficacy of SNAs. Because these relationships were not predicted, they likely would have gone unnoticed in a typical study of a small set of structures.

For example, the ability to stimulate an immune response can depend on nanoparticle size, composition and/or how DNA molecules are oriented on the nanoparticle surface.

“With this new information, researchers can rank the structural variables in order of importance and efficacy, and help establish design rules for SNA effectiveness,” said Andrew Lee, assistant professor of chemical and biological engineering in the McCormick School of Engineering and study co-author.

“This study shows that we can address the complexity of the SNA design space, allowing us to focus on and exploit the most promising structural features of SNAs, and ultimately, to develop powerful cancer treatments,” said Mirkin, who is also director of the International Institute for Nanotechnology.

The Nature Biomedical Engineering paper is titled “Addressing Nanomedicine Complexity with Novel High-Throughput Screening and Machine Learning.” Other coauthors are Neda Bagheri, Gokay Yamankurt, Eric J. Berns and Albert Xue, of Northwestern University.

The research was conducted as part of the Northwestern University Center for Cancer Nanotechnology Excellence (Northwestern CCNE), a partnership between the Robert H. Lurie Comprehensive Cancer Center and the IIN, that is solely focused on utilizing SNAs to develop next-generation cancer treatments. The program is funded through a grant from the National Cancer Institute (NCI).

— By Sheryl Hislop Cash

Original story appeared in Northwestern Now on 2/19/19.

Neda Bagheri is a member of the Chemistry of Life Processes Institute. Gkay Yamankurt is a former graduate trainee with the Institute.

A new approach to a deadly disease

A new approach to a deadly disease

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.”

Bucking convention

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. 

New technology gives unprecedented look inside capillaries

New technology gives unprecedented look inside capillaries

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.”

Vadim Backman

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.


In the Immune System’s Trenches, a New Discovery

In the Immune System’s Trenches, a New Discovery

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.

Northwestern graduate student Roli Mandhana was first author of a pathbreaking study of RNA viruses recently that was published in Scientific Reports.

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.

Pediatric leukemia ‘super drug’ could be developed in the coming years

Pediatric leukemia ‘super drug’ could be developed in the coming years

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. 

Click here to learn more about the resources and research capabilities of CMIDD.

Carla Rosenfeld appointed associate director of CLP’s Quantitative Bioelement Imaging Center

Carla Rosenfeld appointed associate director of CLP’s Quantitative Bioelement Imaging Center

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.

About QBIC

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

Full-Body Scan Could Improve Chemotherapy Effectiveness

Full-Body Scan Could Improve Chemotherapy Effectiveness

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.”

SPECT/CT fusion images of the femurs in control and methotrexate treated animals are presented. Significant signal elevation was detected in the bones. Hematoxylin and eosin-stained section of femoral bone demonstrates a depletion of hematopoietic cells in bone marrow of methotrexate-treated animals.

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.

Young black gay men have vastly higher HIV rates yet fewer partners

Young black gay men have vastly higher HIV rates yet fewer partners

Young black men who have sex with men (MSM) are 16 times more likely to have an HIV infection than their white peers despite more frequent testing for HIV and being less likely to have unsafe sex, reports a new Northwestern Medicine study.

The study was recently published in the Journal of Acquired Immunodeficiency Syndromes.

If these rates persist, one out of every two black MSM will become infected with HIV at some point in their lives, compared to one in five Hispanic MSM and one in 11 white MSM, reports the Centers for Disease Control and Prevention.

“We have known from prior studies that this paradox exists — black young MSM engage in fewer risk behaviors but have a much higher rate of HIV diagnosis,” said senior study author Brian Mustanski, professor of medical social sciences at Northwestern University Feinberg School of Medicine and director of the Northwestern Institute for Sexual and Gender Minority Health and Wellbeing. “Our study illuminates how HIV disparities emerge from complex social and sexual networks and inequalities in access to medical care for those who are HIV positive.”

“Their social and sexual networks are more dense and interconnected, which from an infectious disease standpoint makes infections transmitted more efficiently through the group,” Mustanski said. “That, coupled with the higher HIV prevalence in the population, means any sexual act has a higher chance of HIV transmission.”

The study is the largest and most comprehensive to assess why these disparities exist. It analyzed young black MSM’s social networks, such as past sexual partners, as well as measures of stress, past trauma and stigma. The authors used data from RADAR, a project funded by the National Institute on Drug Abuse, that identifies drivers of HIV infections on multiple levels, including sexual partner and relationship characteristics, network dynamics and community-level factors. The study collected data from 1,015 MSM between the ages of 16 and 29 living in the Chicago metropolitan area.

Among the study’s key findings about racial disparities in HIV infection:

  • Black MSM reported the lowest number of sexual partners overall.
  • Black MSM tested for HIV more frequently but were more likely to have a detectable HIV viral load if HIV positive.
  • Black MSM were more likely to report not having close relationships with their sexual partners.
  • Black MSM were more likely to report hazardous marijuana use, while white MSM were more likely to report high levels of alcohol problems.
  • Black MSM experienced greater levels of stigma, victimization, trauma and childhood sexual abuse.

The study’s findings suggest current HIV prevention efforts are effective in reducing risky sexual behaviors and promoting awareness about the importance of HIV testing among black MSM.

“Overall, young black MSM do not report higher rates of HIV risk behaviors like condomless sex,” said Ethan Morgan, a postdoctoral fellow at Northwestern’s Institute of Sexual and Gender Minority Health and Wellbeing and a co-author on the study. “But aspects of their social networks align with increased HIV risk. By learning more about young black MSM’s social networks, we can better understand what drives such persistent racial disparities in HIV — and close that gap.”

Other Northwestern authors include Richard D’Aquila, Michelle Birkett, Patrick Janulis and Michael Newcomb.

Study co-author Richard D’Aquila is a member of the Chemistry of Life Processes Institute.

Original story published in Northwestern Now on December 04, 2018 by Marla Paul

Altruism, curiosity drive CLP undergraduate awardee Viswajit Kandula

Altruism, curiosity drive CLP undergraduate awardee Viswajit Kandula

“As an undergrad, I finally thought I knew what I wanted to do, but I’ve been constantly swayed by new things that are creative and exciting,” says Viswajit Kandula, this year’s recipient of Chemistry of Life Processes Institute’s Chicago Area Undergraduate Research Symposium Award (CAURS) undergraduate award.

A third-year biomedical engineering undergraduate enrolled in Northwestern University’s McCormick School of Engineering and Honors Program in Medical Education, Kandula will earn his undergraduate degree in three years, then immediately begin training as a medical doctor at Feinberg School of Medicine.

Each year, one undergraduate student receives the award based on his or her academic achievements and scientific interests. Recipients receive $1,000 for interdisciplinary research with a CLP faculty member, purchase of scientific supplies and registration and travel costs to the Symposium in April 2019 where the recipient is required to present his/her research.  The CLP CAURS program was established and continues to be supported by a CLP alum and Executive Advisory Board member, Dr. Chandler Robinson.

“I wanted to have the experience of going to conferences and sharing my research because I think the work I’m doing is really innovative and has the potential to revolutionize medical therapies. Plus, being able to talk to like-minded individuals is something I’ve always enjoyed doing and found very rewarding,” Kandula says. “It also opens your mind to other types of research that addresses similar questions using different, unique approaches.”

After spending his first two years at Northwestern conducting basic science research in molecular biosciences, Kandula joined a new subgroup last summer led by Joseph Muldoon, a fifth year Interdisciplinary Biological Sciences (IBiS) Program graduate student in the lab of CLP member Josh Leonard, Associate Professor of Chemical and Biological Engineering. The subgroup’s aim is to develop a framework that will allow for the implementation of customizable therapeutic strategies. Currently, therapies such as CAR T-Cells will search for one antigen before invoking an immune response. Muldoon’s group aims to develop a platform that would enable cells to sense multiple cues and integrate this information to induce a more appropriate immunological response. This would greatly improve the specificity of cell-based devices to create safe, effective and long – lasting treatments.

“A big reason I decided to pursue research in a new field was because I wanted to do something that was more in line with medical therapeutics; I wanted to work on a project that I thought could scale to actual medical treatment,” says Kandula.

“Traditional labs have people who are primarily chemists or biologists, but I gravitated towards a CLP lab because these labs have individuals who integrate viewpoints and approaches from various fields to tackle problems in a more well informed manner,” he said.

For example, although the Leonard lab mostly focuses on developing cellular devices and biomolecular engineering, Kandula likes how the lab aims to solve medical challenges using a design driven research process. Before conducting experiments in the wet lab, the researchers first use computational models and statistical analyses to accurately predict experimental outcomes in order to develop platforms that look promising. The team also utilizes the High Throughput Analysis Lab, one of eight core facilities managed by CLP, to rapidly screen and characterize the behavior of their engineered mammalian cells.

Another passion that drives Kandula is the idea of practicing medicine, with a likely focus in neuro-oncology.

“Before I was born, my grandfather had a stroke that paralyzed him on one side of the body,” says Kandula.  “When I was in third grade, he had another stroke that paralyzed him on the other side, so while he was still able to comprehend and was aware of everything that was going on around him, he wasn’t able to respond, react, or communicate his thoughts in any way.”

The mystery behind his grandfather’s condition baffled the 10-year-old and motivated him to work with mostly elderly patients in a rehabilitation center while in high school. “Elderly patients always have a story to share and it was very enlightening to learn so many things from all these people who were from different cultures, backgrounds, and socio-economic status,” he says. “The experience as a whole was very, very rewarding and further cemented my desire to pursue medicine.”

Despite his busy schedule, Kandula also volunteers for NU Tutors, a campus organization that provides affordable tutoring and mentorship for Evanston high school students, and he is part of the school’s squash team which travels to the Northeast every winter to compete against teams from all over the country. His ideal career would encompass his love for teaching, biomedical research and collaborating with others.

“I’ve learned through talking to other physicians that you don’t have to limit yourself. You can still do everything you want to do as long as you’re focused, have a plan and are able to manage your time. Most of all, though, I hope to work with patients one-on-one because that’s kind of been the dream from day one.”


by Lisa La Vallee