CR-PSOC researchers define role of chromatin mechanics in nuclear stiffness

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 (, 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.

The chemical brothers: nucleosomes and transcription

New research from the pilot project Dynamic Nucleosome Landscape During Epithelial-Mesenchymal Transition was published in Cell on December 1, 2016.  Click here to read the publication, Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping


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

Understanding Chromatin’s Cancer Connection

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.
Vadim Backman

Vadim Backman

“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.

“If you think of cellular systems as computers, then genes are the hardware, and chromatin is the software,” said Backman, the Walter Dill Scott Professor of Engineering at Northwestern’s McCormick School of Engineering, member of the Robert H. Lurie Comprehensive Cancer Center of Northwestern, and leader of the Lurie Cancer Center’s Cancer and Physical Sciences Research Program.

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.

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.”

Podcast with Vadim Backman: Detecting Cancer at its Earliest Stages

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.

Listen to podcast by clicking 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.”

Chandel Awarded NCI Outstanding Investigator Award

Navdeep Chandel, PhD, David W. Cugell Professor of Medicine in the Division of Pulmonary and Critical Care Medicine and co-investigator for the Chicago Region Physical Sciences-Oncology Center, has received the National Cancer Institute’s Outstanding Investigator Award.

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.”

Chandel is also leader of the Membranes, Organelles and Metabolism Program in the Robert H. Lurie Comprehensive Cancer Center of Northwestern University.

Original article written by Nora Dunne and posted at the Feinberg News Center.

Groundbreaking Work from Dekker Lab

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.

See also this link for commentary:

CR-PSOC Leader Advises on President’s Cancer Moonshot 2020

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.

View video of Director O’Halloran’s address at the following web address. His talk starts at the 22 minute mark.

Computational Approach Shows “Noise” Can Influence Intracellular Networks

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.

The above post is reprinted from materials provided by Northwestern University. The original item was written by Amanda Morris.

Peng Ji Receives 2015 Young Physician-Scientist Award

Peng Ji, recipient of a PS-OC Outreach Pilot Project Award, received the 2015 Young Physician-Scientist Award from the American Society for Clinical Investigation.

Peng Ji, MD, PhD, ’13 GME, assistant professor in Pathology, was recently honored with one of the American Society of Clinical Investigation’s (ASCI) 2015 Young Physician-Scientist Awards. He is one of only 40 investigators nationwide to receive the honor this year.

“I feel very honored to receive this award and to be recognized among a prestigious group of young investigators,” Dr. Ji said.

Dr. Ji has made significant contributions in the fields of pathology and hematology. In a recent paper published in Blood, Dr. Ji and his colleagues discovered several genetic mutations associated with the development of Myelodysplastic syndromes (MDS), a group of diseases that affect bone marrow and lead to ineffective production of stem cells that become blood cells.

His lab discovered that the disease was associated with the loss of parts of chromosome 5, which in turn led to abnormal overexpression of the CD14 gene and contributed to the development of MDS.

Dr. Ji said that working on research both in a lab and clinical setting allows him to better treat his patients and recognize disease patterns in his research.

“When I started my post-doc training, I started to see there was a disconnect between basic science and clinical medicine,” Dr. Ji said. “I knew I needed to use my clinical training and knowledge to guide my basic science research.”

In addition to receiving the award, he is also finishing a clinical residency in pathology and pursuing research in his lab. He has been awarded The American Society of Hematology Scholar Award, The Chicago Biomedical Research Consortium Catalyst Award, the Department of Defense Career Development Award and recently an NIH R01 grant award for his study in terminal erythropoiesis.

The Young Physician Scientists Award is given to faculty who are supported by any NIH K award or equivalent, are early in their first faculty appointment and have made notable achievements in their research. Recipients were presented with their awards at a celebratory dinner in April.

Written by Amber Bemis and originally posted by the Northwestern University Feinberg School of Medicine News Center.

National Cancer Institute awards Northwestern nearly $10 million for cancer research

EVANSTON, Ill. — Northwestern University has received a five-year, $9.6 million grant from the National Cancer Institute (NCI) for a new Physical Science-Oncology Center that unites physical scientists and cancer researchers from Northwestern, the University of Chicago and University of Illinois at Chicago.

The Chicago Region Physical Science-Oncology Center (CR-PSOC) is part of a larger coalition assembled by the NCI to bring breakthroughs in the physical sciences to bear on the complex problem of cancer. Only four such centers have been funded across the nation this year.

“Cancer patients expect us to increase the speed with which we apply discoveries in the basic sciences to prevention, detection and treatment,” said Northwestern’s Thomas V. O’Halloran, the CR-PSOC’s principal investigator. “The center’s mission is to advance our understanding of cancer by examining the role of physical and chemical forces involved in transforming a normal cell into a cancer-causing cell.”

This is the second PS-OC at Northwestern. The first center, under the leadership of the late Jonathan Widom and Dr. Jonathan D. Licht, was funded in 2009 for five years. That innovative work led to the CR-PSOC’s expanded research scope and interdisciplinary collaborations with researchers across Chicago and the country.

“The National Cancer Institute expects these centers to stimulate the flow of new ideas, diagnostic methods and therapeutic approaches between the physical science and cancer research communities,” said O’Halloran, the Morrison Professor of Chemistry in the Weinberg College of Arts and Sciences.

O’Halloran, a physical scientist, and Licht, a cancer researcher and the Dobe Professor of Hematology-Oncology at Northwestern University Feinberg School of Medicine, will lead the CR-PSOC. Both are members of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University.

“What we’re trying to do is understand the fundamental rules of misbehavior of cancer cells with a particular class of mutations,” Licht said. “The center is reaching beyond genomics into the rapidly growing areas of epigenetics and metallomics.”

Scientists have long known that the transformation of healthy cells to cancer cells involves more than just mutations in our genetic DNA sequence. The CR-PSOC team will develop new ways to interrogate changes in the “epigenome” (the chemical markers that influence the folding and condensation of DNA within the nucleus) and changes in the “metallome” (the metal ion content of the cell) that support the development of cancer.

The “packaging” of DNA influences the local environment of genes and their regulation, O’Halloran explained. DNA is packaged together with proteins, RNA and metal ions into a structure known as chromatin, which is responsible for DNA folding and plays a vital role in gene expression.

CR-PSOC investigators will deploy a series of physical science approaches and novel imaging methods to determine whether changes in chromatin folding result in aberrant patterns of gene expression that drive cancer progression. Then, the researchers will translate these advances into a deeper understanding of cancer biology and, eventually, into novel cancer therapy.

The core Chicago-area team is composed of 12 physical scientists and eight cancer researchers from fields including physics, chemistry, biomedical engineering, biophysics, biochemistry, pharmacology and hematology-oncology from Northwestern, UChicago and UIC.

CR-PSOC project leaders have recruited additional experts in the physical sciences and chromatin fields from outside Chicago, namely from Massachusetts Institute of Technology, Memorial-Sloan Kettering Cancer Center and the University of Massachusetts Medical School.

“Thought leaders in the physical sciences and oncology fields have joined forces to share emergent ideas and cutting-edge methods and use them to understand molecular changes that allow cancer cells to grow out of control,” O’Halloran said. “By combining interdisciplinary strengths, this team hopes to make significant progress in the diagnosis and treatment of several types of cancer.”

Designed around the theme of “Spatio-Temporal Organization of Chromatin and Information Transfer in Cancer,” the center consists of three interrelated project areas, each focused on different aspects of chromatin structure and function, plus two core facilities and pilot project, education and outreach programs.

The center will be a knowledge hub for training the next generations of scholars to make breakthroughs at the convergence of physical sciences and oncology. Center programming will include an extensive series of workshops, student forums, symposia and journal clubs.  An institutional commitment by Northwestern to support the training of graduate students and postdoctoral fellows engaged in CR-PSOC research will further extend the center’s educational reach.

The CR-PSOC is supported by the resources and expertise of Northwestern’s foremost engines for transdisciplinary research, the Chemistry of Life Processes Institute and the Lurie Cancer Center, as well as by resources of UChicago and UIC.

In addition, a Chicago Biomedical Consortium (CBC) Lever Award of $1.5 million will support the center and its acquisition of new instrumentation and shared resources. These research capabilities also will be available to researchers across the region.

A full list of CR-PSOC investigators can be found on the center’s website.

Read full story as written by Megan Fellman on Northwestern News.

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