Chuan He, a CR-PSOC investigator, was one of three recipients of the 2017 Paul Marks Prize for Cancer Research. The award, given by Memorial Sloan Kettering (MSK), recognizes promising investigators aged 45 or younger at the time of nomination for their efforts in advancing cancer research. He will receive an award of $50,000 and give a scientific presentation at a symposium held at MSK.
Dr. He is the John T. Wilson Distinguished Service Professor in Chemistry, Biochemistry, and Molecular Biology at the University of Chicago; director of U of C’s Institute for Biophysical Dynamics; and a Howard Hughes Medical Institute (HHMI) investigator. He is also director of the Synthetic and Functional Biomolecules Center at Peking University in China.
He is an expert in the field of cancer epigenetics and RNA modification biology. Epigenetics involves variations in the way that genes are expressed that don’t affect the actual DNA sequence. “The human genome contains 3 billion base pairs but only roughly 20,000 genes,” he says. “We have tens of trillions of cells, and about 200 different tissue or cell types. Epigenetics facilitates cell differentiation into different identities, despite having the same genetic sequence in an individual human being.”
His major contribution to the field is that he was the first to put forward the idea that modifications to RNA are reversible and can control gene expression. Control of RNA, the molecule that carries DNA’s “message” to the protein-making machinery of the cell, is one of the major ways that affects the outcomes of gene expression.
“When I started this work back in 2008 and 2009, we knew that proteins called writers could install modifications to RNA molecules that altered their function, but no one knew that there were also proteins called erasers that could undo these changes,” Dr. He explains. His team went on to identify for the first time the eraser proteins, and in later work characterized a series of reader proteins that explain how RNA methylation functioned.
“This research laid down the mechanistic pathways for our current understanding of how these modifications impact biological outcomes, including those related to cancer,” he says. “Cancer and other diseases can hijack aberrant RNA methylation to gain a survival advantage, allowing cells to proliferate and grow out of control.”
These types of RNA changes are known to play a role in many types of cancer, including endometrial cancer, acute myelogenous leukemia, and glioblastoma. Dr. He’s work forms some of the foundations for developing potential future therapies that target RNA methylation effectors against human cancer.
For the first time, researchers control cells’ chromatin to prevent cancer from adapting to treatment
Chicago Region Physical Sciences Oncology Center investigator Vadim Backman has developed an effective new strategy for treating cancer, which has wiped out the disease to near completion in cellular cultures in the laboratory.
The treatment works by controlling chromatin, a group of macromolecules — including DNA, RNA, and proteins — that houses genetic information within cells and determines which genes get suppressed or expressed. In the case of cancer, chromatin has the ability to regulate the capacity of cancer cells to find ways to adapt to treatment by expressing genes that allow the cancer cells to become resistant to treatment.
Backman’s solution alters chromatin’s structure in a way that prevents cancer from evolving to withstand treatment, making the disease an easier target for existing drugs. If the cells cannot evolve to resist chemotherapy, for example, they die. After having shown great potential to fight cancer in cellular cultures, the treatment is now undergoing studies in an animal model.
“If you think of genetics as hardware, then chromatin is the software,” said Backman, the Walter Dill Scott Professor of Biomedical Engineering at Northwestern’s McCormick School of Engineering. “Complex diseases such as cancer do not depend on the behavior of individual genes, but on the complex interplay among tens of thousands of genes. By targeting chromatin, we can modulate global patterns in gene expression.”
Cancer has many distinctive features, but one trait underlies them all: its relentless ability to survive. Even as it is bombarded by the immune system and treatments such as chemotherapy, immunotherapy, and radiation, cancer might shrink or slow its proliferation, but it rarely disappears.
“How does cancer jump through so many hoops to survive? It’s a highly improbable event, if you think about it,” Backman said. “But there is one thing that all cancers do. They have a phenomenal ability to change, to adapt, to evolve in order to evade the treacherous conditions they frequently have to face during the process of their growth or in the face of treatment.”
Backman’s goal does not lie in discovering new drugs or treatment options. Instead his team aims to stop cancer’s adaptive behavior to boost the effectiveness of current treatments. The key is in the chromatin.
Found in cells, chromatin is a disordered chain polymer that is packed together at different densities throughout a cell’s nucleus. Through a combination of imaging, simulations, systems modeling, and in vivo experiments, Backman’s team discovered that this packing-density of chromatin in cancer cells produced predictable changes in gene expression. The more heterogeneous and disordered the packing density, the more likely cancer cells were to survive, even in the face of chemotherapy. The more ordered and conservative the packing density, however, the more likely the cells would die from cancer treatment.
“Just by looking at the cell’s chromatin structure, we could predict whether or not it would survive,” Backman said. “Cells with normal chromatin structures die because they can’t respond; they can’t explore their genome in search of resistance. They can’t develop resistance.”
The study leverages an imaging technique developed in Backman’s laboratory last year. Called Partial Wave Spectroscopic (PWS) microscopy, the technique allows researchers to examine chromatin in living cells in real time. More importantly, researchers can use PWS to peer inside of chromatin at the never-before-seen 20-200 nanometer length scale, which is exactly where chromatin undergoes a transformation when cancer is formed. Backman also worked with Szleifer, an expert on molecular dynamics simulations, to model how chromatin reacted to different stimuli.
A “macro” approach
When scientists finished decoding the human genome in 2003, many thought the findings would help them design smarter medicines by either knocking out or turning on genes.
“As significant as changing a gene is, it’s only one part of the story,” Backman said. “The second part is that the gene has to be expressed, amplified, or suppressed. We have about 20,000 genes, and the number of genomic states that a cell can have is absolutely astronomical.”
The large number of possible combinations of genes and genomic states is so high that knocking out one gene most likely cannot prevent or fully treat a complex disease such as cancer. His laboratory, instead, takes a “macrogenomics” approach. By altering chromatin packing densities, Backman’s team can control the overall behavior of biological systems.
“Think of the number of mutations that have been documented in cancer. We’re talking about thousands,” Backman said. “Just changing one gene is not going to give you cancer, and it’s not going to cure cancer either. But we can rewrite the software by using chromatin engineering to manipulate the genetic code.”
“This work helps establish how the physical environment within the cell nucleus shapes gene expression patterns for many genes simultaneously,” said Luay Almassalha, graduate student in Backman’s laboratory and a first author on the paper. “Analogous to how the organization of a city shapes the collective behavior of thousands of people, the physiochemical rules of chromatin that we uncovered govern the collective behavior of the genome.”
Finding a way to alter chromatin
Throughout the study, Backman and his team realized that they could control chromatin by changing the electrolytes present in the cell’s nucleus. His team screened multiple existing drug compounds to find promising candidates that could alter the physical environment inside cell nuclei in order to modulate the spatial arrangement of chromatin packing density.
Two of the drugs the team pinpointed, Celecoxib and Digoxin, are FDA-approved immunological agents already on the market. Physicians prescribe them for arthritis and heart conditions, respectively, but both have a side effect of altering chromatin packing density.
Backman combined these compounds, which he calls “chromatin protection therapeutics,” or CPT compounds, with chemotherapy to treat seven different types of cancer in cell cultures. Monitoring the cancer cells with PWS, Backman saw “something remarkable.”
“Within two or three days, nearly every single cancer cell died because they could not respond,” he said. “The CPT compounds don’t kill the cells; they restructure the chromatin. If you block the cells’ ability to evolve and to adapt, that’s their Achilles’ heel.”
A new tool to fight disease
Though the treatment is promising, much more testing is needed before it can be part of cancer treatment in humans.
“There is a big difference between cell cultures and humans,” Backman added. “You never know how the environment inside the human body will affect cancer’s behavior or if there will be unforeseen side effects. But, having said that, in seven different types of cancer, we see the same story unfold each and every time. That’s very promising.”
If Backman’s team can alter chromatin in cancer, they believe that the same technique could potentially work in other complex diseases, such as Alzheimer’s disease and atherosclerosis. Chromatin could also be controlled to have the opposite effect — to make normal cells more plastic and adaptable to behave like stem cells. By prolonging the lives of stem cells or turning normal cells into stem cells, researchers might have a new tool to repair brain and spinal cord damage. Although he does not yet have the data, Backman cannot help but wonder about how this discovery could change the future of medicine.
“Genetic changes are permanent, but this type of modulation is more like software,” Backman said. “By definition, it’s reversible. You could reprogram a neuron, and then remove the stimulus and allow it to go back to its normal state. If chromatin is software, then we are saying there is room to write new codes.”
In the paper “Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus”, recently published in the journal Molecular Biology of the Cell (http://www.molbiolcell.org/cgi/doi/10.1091/mbc.E16-09-0653), Dr. Andrew Stephens and collaborators from the Northwestern CR-PS-OC report experiments establishing differential roles played by the nuclear lamin proteins of the nuclear envelope and chromatin in the mechanics of the cell nucleus. By directly stretching nuclei of human cells, the team of researchers from the labs of Robert Goldman and John Marko at Northwestern University showed that chromatin – the chromosomes themselves – control the initial small-strain (< 30% lengthening) mechanics of the cell nucleus, with the lamin network coming into play for deformations of more than 30%. Dr. Ed Banigan showed that the experimental results are well-explained by a model in which the nuclear envelope is treated as a polymer “shell” and where the interior chromatin is modeled as a crosslinked polymer network.
The team also reports experiments showing that the state of the chromatin – whether it is more heterochromatic or euchromatic – affects nuclear stiffness. Given that the balance of heterochromatin and euchromatin, along with nuclear morphology and stability, are altered in many diseases, this new paper suggests that chromatin mechanics may play a much larger role in controlling nuclear stiffness and shape than has been previously appreciated.
Read the review from Nature Reviews Molecular Cell Biology below:
The positioning of nucleosomes along the DNA with regard to various genetic elements is thought to affect transcription by competing with transcription factors for binding DNA. Using a high-resolution chemical approach to map nucleosomes, Voong et al. provide new insights into the interplay between nucleosomes, transcription and splicing.
Looking to improve on the accuracy of the common nucleosome-mapping method MNase-seq, the authors developed a genome-wide nucleosome-mapping approach that determines nucleosome centre (dyad) positions at nucleotide resolution based on chemical cleavage of the DNA. The method requires substituting Ser47 of histone H4, which flanks the nucleosome centre with a Cys residue (H4S47C), which can be covalently bound by a copper-chelating compound. The copper ions direct cleavage of nucleosome DNA near the dyad by hydroxyl radicals, and the resulting DNA fragments are subjected to deep sequencing.
The authors substituted most of the endogenous H4 proteins in mouse embryonic stem (ES) cells with H4S47C. MNase-seq nucleosome maps generated in H4S47C and wild-type ES cells, as well as previously generated maps from different organisms, were generally in agreement. They showed the presence of nucleosome-depleted regions (NDRs) upstream of transcription start sites (TSSs) and at transcription termination sites (TTSs) in actively transcribed genes. By contrast, the chemical map revealed generally high nucleosome occupancy spanning the TSS, coding sequence and TTS of actively transcribed genes.
To investigate how nucleosome positioning correlates with RNA polymerase II (Pol II) elongation kinetics, the authors used an available global run-on and sequencing (GRO-seq) data set, from which sites of Pol II accumulation can be inferred. Alignment of Pol II accumulation at promoter-proximal sites with the chemically determined nucleosome positions revealed that occupancy of the +1 position relative to the TSS was positively associated with Pol II pausing.
The rate of transcription can influence co-transcriptional splicing. In contrast to recent studies, which found that nucleosomes have higher occupancy around exon centres, the chemical map revealed that nucleosomes are enriched at exon boundaries. Importantly, at all of the expressed genes (regardless of expression levels), Pol II accumulation correlated with nucleosome occupancy at exon boundaries, which is indicative of Pol II stalling at exon–intron junctions close to the nucleosome centre, where the strongest DNA–histone interactions occur.
It is still unclear whether pluripotency transcription factors can bind to their target sites when the DNA is bound by nucleosomes. The chemical map showed that the pluripotency factors OCT4, SOX2, Nanog and Krüppel-like factor 4 bind to their target sites within nucleosomes and modulate nucleosomes in the flanking regions. This suggests that they function as pioneer factors, which can induce chromatin opening and the formation of NDRs.
This study supports a dynamic function of nucleosome in gene regulation. At both promoter-proximal regions and exon–intron junctions, nucleosomes could function as transient barriers for Pol II progression, thereby regulating the kinetics of transcription elongation and splicing.
written by Eytan Zlotorynski | Published online 19 Dec 2016; doi:10.1038/nrm.2016.167
New nanoscale imaging technique allows researchers to study chromatin in live cells
When scientists finished decoding the human genome in 2003, they thought the findings would help us better understand diseases, discover genetic mutations linked to cancer, and lead to the design of smarter medicine. Now it’s 13 years later, and not all of these ideas have not yet come to fruition.
“We thought that understanding genes would answer all of our questions,” said Chicago-Region Physical Sciences Oncology Center investigator Vadim Backman. “But it’s not that simple.”It turns out that genes are just one piece of a much larger puzzle. To help put this puzzle together, Backman has developed a new way to image chromatin, a complex of macromolecules — including DNA, RNA, and proteins — within living cells that house genetic information and determines which genes get expressed.
Chromatin’s organization plays a major role in many molecular processes, including DNA transcription, replication, and repair. The structures within chromatin that regulate these processes span from nucleosomal (10 nanometers) to chromosomal (longer than 200 nanometers) length scales.
Backman’s imaging technique can capture nanoscopic information from dozens of nuclei within seconds, as seen here in cancer cells.
Little is known about chromatin’s dynamics between these length scales due to lack of imaging techniques. Because they require toxic fluorescent dyes to enhance contrast, previous techniques could not image chromatin in living cells without killing or perturbing the cells. Understanding this missing length scale is crucial, however, because it is the exact area where chromatin undergoes a transformation when cancer is formed.
“Changes in chromatin’s structure have been linked to the regulation in genes often implicated in cancer,” Backman said. “The organization of chromatin correlates both with the formation of tumors and their invasiveness. We want to understand how chromatin regulates these genes.”
Backman’s new imaging technique allows researchers to peer inside of chromatin at the missing, mysterious length scale (20-200 nanometers). Not only is the technique label-free, allowing researchers to study chromatin within unharmed, living cells, but it does so with high-throughput and at very low cost.
Supported by the National Science Foundation, National Institutes of Health, and Chicago Biomedical Consortium, the research is described online on October 4 in the Proceedings of the National Academy of Sciences. Luay Almassalha, Greta Bauer, John Chandler, and Scott Gladstein, all graduate students in Backman’s laboratory, served as co-first authors on the paper. Northwestern Engineering’s Igal Szleifer, the Christine Enroth-Cugell Professor of Biomedical Engineering, and Hariharan Subramanian, research assistant professor in biomedical engineering, also contributed to the work.
“Now we can look at live, healthy cells unperturbed and see their dynamic processes,” Almassalha said. “We can see how the chromatin is organized and how it responds to stimuli, such as drug treatments.”
Called live cell Partial Wave Spectroscopic (PWS) microscopy, the technique detects chromatin by using scattered light. Particles smaller than the diffraction limit of light cannot be visualized but their presence and organization can be sensed by analyzing the light they scatter. The approach can measure the nano-architecture in live cells within seconds, opening the door for large-scale screens. Researchers can run high-throughput screens on thousands of compounds and drugs, for example, and watch how they affect cells in real time.
“We know that chromatin is a major player in complex diseases,” Backman said. “We just haven’t had the techniques to study it. Now we can watch and record these dynamic processes as they unfold.”
Vadim Backman, a Chicago Region Physical Sciences Oncology Center Investigator and the Walter Dill Scott Professor of Biomedical Engineering at Northwestern University, was interviewed by the Amazing Things Podcast about his nanocytomics technology. Below is the re-print from the Amazing Things Podcast website. Link to full website here.
“What if you could detect cancer at its earliest stages – before there are any symptoms that would send you to a doctor? What if such a diagnostic tool existed and it was low-cost, minimally invasive and easy to use? The impact would be huge. Northwestern University professor of bioengineering and biophotonics Vadim Backman is closing in on this goal. By the end of 2017 he expects that the first of a series of cancer pre-screening tests will be available for use by physicians.
More than $100 billion is spent each year on cancer care in the United States.
Northwestern University professor of bioengineering and biophotonics Vadim Backman is closing in on this goal. By the end of 2017 he expects that the first of a series of cancer pre-screening tests will be available for use by physicians.”
The seven-year, $6.4 million grant supports leaders who have made significant contributions in cancer research and are pursuing areas with unusual potential to move the field forward. Chandel, whose work focuses on cellular organelles called mitochondria, will be exploring the mechanisms of mitochondrial metabolism that contribute to tumor formation and investigating related enzymes that may be targeted for future therapies.
“In the last five to ten years, the idea that the metabolism of cancer cells might be different than the metabolism of normal cells has emerged,” he said. “We believe that mitochondrial metabolism is central to tumorigenesis. If that’s true, we have to figure out how that works.”
Mitochondria are known for their ability to produce energy by making a molecule called adenosine triphosphate (ATP). Chandel’s lab has demonstrated that the organelles also have other important responsibilities, such as generating molecules called reactive oxygen species (ROS) that support cell proliferation and adaptation to hypoxia. Thus ROS can activate signaling inside cancer cells that leads to tumor growth, an interaction Chandel plans to study with the support of the new grant.
“We’re going to use CRISPR technology to conduct forward genetic screens in mammalian cells to explain mitochondrial biology in the context of cancer,” he explained.
In previous research, published in the journal eLife, Chandel’s group also showed that metformin, a widely used drug used to treat type II diabetes, can inhibit mitochondrial complex I and reduce human cancer cell growth in mouse models.
“We developed tools that uncovered that this drug can be repurposed as an anticancer agent,” Chandel said. “With the NCI’s award, we’ll continue these studies.”
Job Dekker (Project 2) and his colleagues, with support from the CR-PSOC, have just published an important paper in Science on activation of proto-oncogenes by disruption of chromosome neighborhoods. “Activation of proto-oncogenes by disruption of chromosome neighborhoods”. This finding ties to work from Vadim Backman (Project 3, Nanocytometry Core) showing an increase in nanoscale nuclear disorder during carcinogenesis.
On March 25th, Thomas V. O’Halloran (Chemistry) addressed the President’s Council of Advisors on Science and Technology (PCAST) on the “cancer moonshot” initiative described by President Obama in his State of the Union address. O’Halloran was asked to address the Council in his capacity as director of the Chicago Region Physical Science-Oncology Center. His talk focused on the need to integrate large scale teams of oncologists and cancer biologists with researchers in the physical sciences, complex systems, data mining and materials sciences. Current cancer research is concentrated upon molecular pathways involved in cancer and is driven by cancer researchers trained in the life sciences. He proposed the creation of a large scale national network of centers that will collaborate on early diagnosis and treatment of cancer using the tools and perspectives of the physical sciences.
This proposal has its genesis in the successes of Northwestern’s Chemistry of Life Processes Institute in large-scale team science built on collaboration among scientists and clinicians across a broad range of disciplines. A remarkable aspect of this capability is the Institute’s ability to “plug and play” diverse teams across a broad range of important biomedical topics.
A cell’s life is a noisy affair. These building blocks of life are constantly changing. They can spontaneously express different proteins and genes, change shape and size, die or resist dying, or become damaged and cancerous. Even within a population of the same type of cell, there is immense random variability between cells’ structures, levels of protein expression, and sizes.
“High dimensionality and noise are inherent properties of large intracellular networks,” said Adilson E. Motter, the Charles E. and Emma H. Morrison Professor of Physics and Astronomy at Northwestern University, and Chicago Region Physical Sciences Oncology Center Co-Investigator. “Both have long been regarded as obstacles to the rational control of cellular behavior.”
Motter and his collaborators at Northwestern have challenged and redefined this long-held belief. Using a newly-developed computational algorithm, they showed that this randomness within and among cells, called “noise,” can be manipulated to control the networks that govern the workings of living cells — promoting cellular health and potentially alleviating diseases such as cancer.
Supported by the National Cancer Institute Physical Science-Oncology Center at Northwestern and the National Science Foundation, the research is described in the September 16 issue of the journal Physical Review X. Motter and William L. Kath, professor of Engineering Sciences and Applied Mathematics, are coauthors of the paper. Daniel K.Wells, a graduate student in applied math, is the paper’s first author.
“Noise refers to the random aspects of cell behavior, especially gene regulation,” Wells said. “Gene regulation is not like a train station, where gene expression-regulating proteins are shipped in at regular intervals, turn a gene on or off, and then are shipped out. Instead, gene expression is constantly, and randomly, being modified.”
By leveraging noise, the team found that the high-dimensional gene regulatory dynamics could be controlled instead by controlling a much smaller and simpler network, termed a “network of state transitions.” In this network cells randomly transition from one phenotypic state to another — sometimes from states representing healthy cell phenotypes to unhealthy states where the conditions are potentially cancerous. The transition paths between these states can be predicted, as cells making the same transition will typically travel along similar paths in their gene expression.
The team compares this phenomenon to the formation of pathways at a university campus. If there is no paved path between a pair of buildings, people will usually taken the path that is the easiest to traverse, tromping down the grass to reveal the dirt beneath. Eventually, campus planners may see this pre-defined path and pave it.
Similarly, upon initially analyzing a gene regulatory network the team first used noise to define the most-likely transition pathway between different system states, and connected these paths into the network of state transitions. By doing so the researchers could then focus on just one path between any two states, distilling a multi-dimensional system to a series of one-dimensional interconnecting paths.
“Even in systems as complex and high-dimensional as a gene regulatory network, there’s typically only one best path that a noisy transition will follow from one state to the next,” Kath said. “You would think that many different paths are possible, but that’s not true: one path is much better than all of the others.”
The team then developed a computational approach that can identify optimal modifications of experimentally-adjustable parameters, such as protein activation rates, to encourage desired transitions between different states. The method is ideal for experimental implementations because it changes the system’s response to noise rather than changing the noise itself, which is nearly impossible to control.
“Noise is extremely important for systems,” Wells said. “Instead of directly controlling a cell to move from a bad state to a good state, which is hard, we just make it easier for noise to do this on its own. This is analogous to paving just one path departing a building and leaving all the others unpaved–people leaving the building are more likely to walk on the paved path, and will thus preferentially end up where that path goes.”
Though the current research is theoretical and focuses on biological networks, the team posits that this strategy could be used for other complex networks where noise is present, like in food webs and power grids, and could potentially be used to prevent sudden transitions in these systems, which lead to ecosystem collapses and power grid failures.