Associate Professor, Biomedical Engineering
Adjunct Associate Professor, Human Genetics
USTAR Associate Professor, Scientific Computing and Imaging (SCI) Institute Investigator
The University of Utah
Wednesday, June 5 | 4:00 pm Ryan 4003
Multi-Tensor Decompositions for Personalized Cancer Diagnostics and Prognostics
Professor Alter will describe the use of novel, multi-tensor generalizations of the singular value decomposition in the comparisons of brain, lung, ovarian, and uterine cancer and normal genomes, to uncover patterns of DNA copy-number alterations that predict survival and response to treatment, statistically better than, and independent of the best indicators in clinical use, and existing laboratory tests. Recurring alterations have been recognized as a hallmark of cancer for over a century, and observed in these cancers’ genomes for decades; however, copy-number subtypes predictive of patients’ outcomes were not identified before. The data had been publicly available, but the patterns remained unknown until the data were modeled by using the multi-tensor decompositions, illustrating the universal ability of these decompositions – generalizations of the frameworks that underlie the theoretical description of the physical world – to find what other methods miss.
Orly Alter is a USTAR associate professor of bioengineering and human genetics at the Scientific Computing and Imaging Institute and the Huntsman Cancer Institute at the University of Utah, and the principal investigator of an NCI Physical Sciences in Oncology U01 project grant. Inventor of the “eigengene,” she pioneered the matrix and tensor modeling of large-scale molecular biological data, which, as she demonstrated, can be used to correctly predict previously unknown physical, cellular, and evolutionary mechanisms. Alter received her Ph.D. in applied physics at Stanford University, and her B.Sc. magna cum laude in physics at Tel Aviv University. Her Ph.D. thesis on “Quantum Measurement of a Single System,” which was published by Wiley-Interscience as a book, is recognized today as crucial to the field of gravitational wave detection.
Sponsored by the Chicago Region Physical Sciences-Oncology Center NCI U54CA193419
Kyle P. Eagen, PhD
Feinberg Fellow, Northwestern University
Feinberg School of Medicine
Department of Biochemistry and Molecular Genetics
Simpson Querrey Center for Epigenetics
Wednesday, May 8| 4:00 pm Ryan 4003
Delineating how chromosomes fold at length scales beyond one megabase remains obscure relative to smaller-scale folding into self-associating domains (TADs), loops, and nucleosomes. We find that a fusion oncoprotein, which epigenetically re-writes large domains of chromatin, initiates distant interactions between loci separated by tens to hundreds of megabases, with notable effects on gene activity. These interactions occur both within and between chromosomes and are equivalent to TAD-TAD interactions. We find that genes within domains contacting other domains are more highly expressed than genes devoid of domain-domain interactions. In a patient-derived cell line, these interactions can be pharmacologically modulated with a small-molecule proteolysis targeting chimera (PROTAC) resulting in changes in gene expression that reflect loss or gain of domain-domain interactions. Our integrated structure-function approach thus reveals a link between megabase-scale chromosome folding, local chromatin composition, and gene regulation, and also indicates the potential of altering chromosome structure for the treatment of human disease.
Kyle Eagen was an undergraduate at Cornell University where he received his bachelor’s degree in Biological Sciences with a concentration in Biochemistry while studying the rapid chemical kinetics of neurotransmitter receptors in the lab of George Hess. He moved to California in 2008 for graduate studies at Stanford University. At Stanford, he worked with Roger Kornberg studying chromatin and chromosome structure. After completing his Ph.D. in Biophysics, Dr. Eagen began his independent career in 2017 as the inaugural Feinberg Fellow at the Northwestern University Feinberg School of Medicine within the Department of Biochemistry and Molecular Genetics.
The molecular basis of DNA folding within interphase nuclei and mitotic chromosomes is one of the great mysteries of biology and has fascinated scientists for over a century. An increasing number of human diseases, from congenital malformations to cancer, have been linked to DNA misfolding, hastening the need to resolve this mystery. We combine concepts and approaches from structural biology and biochemistry with methods and analytical tools from molecular biology and genomics to determine the…[Read full text]The molecular basis of DNA folding within interphase nuclei and mitotic chromosomes is one of the great mysteries of biology and has fascinated scientists for over a century. An increasing number of human diseases, from congenital malformations to cancer, have been linked to DNA misfolding, hastening the need to resolve this mystery. We combine concepts and approaches from structural biology and biochemistry with methods and analytical tools from molecular biology and genomics to determine the structural and biochemical basis of chromatin folding and chromosome condensation. Our long-term goal is to contribute fundamental knowledge about the nature of DNA folding and elucidate general principles of chromatin and chromosome organization that will enable insights into human disease processes and serve as a basis for developing targeted, precise therapeutics.
Sponsored by the Chicago Region Physical Sciences-Oncology Center NCI U54CA193419
There are 13 million people with cancer in the United States. It’s estimated that about 1.3 million of these cases are hereditary.
Despite advanced training in cancer genetics and years of practicing medicine, Dr. Theo Ross was never certain whether the history of cancers in her family was simple bad luck or a sign that they were carriers of a cancer-causing genetic mutation. Then she was diagnosed with melanoma, and for someone with a dark complexion, melanoma made no sense. It turned out there was a genetic factor at work.
Join us in welcoming oncologist and cancer gene hunter Theodora Ross, MD, PhD, for a talk about her fascinating novel, A Cancer in the Family.Using her own family’s story, the latest science of cancer genetics and her experience as a practicing physician, Dr. Ross will tell us how to spot the patterns of inherited cancer, how to get tested for cancer-causing genes and what to do if you have one.
Endorsed by Siddartha Mukherjee, prize winning author of The Emperor of All Maladies, Dr. Ross’s book is the first authoritative go-to for anyone facing inherited cancer.
Sponsored by the Chicago Region Physical Sciences-Oncology Center, National Cancer Institute U54CA193419
Image shown above DNA loops help to keep local regions of the genome together. (M. Imakaev/G. Fudenberg/N. Naumova/J. Dekker/L. Mirny)
Leonid Mirny swivels in his office chair and grabs the power cord for his laptop. He practically bounces in his seat as he threads the cable through his fingers, creating a doughnut-sized loop. “It’s a dynamic process of motors constantly extruding loops!” says Mirny, a biophysicist here at the Massachusetts Institute of Technology in Cambridge.
He argues that DNA is constantly being slipped through ring-like motor proteins to make loops. This process, called loop extrusion, helps to keep local regions of DNA together, disentangling them from other parts of the genome and even giving shape and structure to the chromosomes.
Scientists have bandied about similar hypotheses for decades, but Mirny’s model, and a similar one championed by Erez Lieberman Aiden, a geneticist at Baylor College of Medicine in Houston, Texas, add a new level of molecular detail at a time of explosive growth for research into the 3D structure of the genome. The models neatly explain the data flowing from high-profile projects on how different parts of the genome interact physically — which is why they’ve garnered so much attention.
But these simple explanations are not without controversy. Although it has become increasingly clear that genome looping regulates gene expression, possibly contributing to cell development and diseases such as cancer, the predictions of the models go beyond what anyone has ever seen experimentally.
For one thing, the identity of the molecular machine that forms the loops remains a mystery. If the leading protein candidate acted like a motor, as Mirny proposes, it would guzzle energy faster than it has ever been seen to do. “As a physicist friend of mine tells me, ‘This is kind of the Higgs boson of your field’,” says Mirny; it explains one of the deepest mysteries of genome biology, but could take years to prove.
And although Mirny’s model is extremely similar to Lieberman Aiden’s — and the differences esoteric — sorting out which is right is more than a matter of tying up loose ends. If Mirny is correct, “it’s a complete revolution in DNA enzymology”, says Kim Nasmyth, a leading chromosome researcher at the University of Oxford, UK. What’s actually powering the loop formation, he adds, “has got to be the biggest problem in genome biology right now”.
Geneticists have known for more than three decades that the genome forms loops, bringing regulatory elements into close proximity with genes that they control. But it was unclear how these loops formed.
Several researchers have independently put forward versions of loop extrusion over the years. The first was Arthur Riggs, a geneticist at the Beckman Research Institute of City of Hope in Duarte, California, who first proposed what he called “DNA reeling” in an overlooked 1990 report1. Yet it’s Nasmyth who is most commonly credited with originating the concept.
As he tells it, the idea came to him in 2000, after a day spent mountain climbing in the Italian Alps. He and his colleagues had recently discovered the ring-like shape of cohesin2, a protein complex best known for helping to separate copies of chromosomes during cell division. As Nasmyth fiddled with his climbing gear, it dawned on him that chromosomes might be actively threaded through cohesin, or the related complex condensin, in much the same way as the ropes looped through his carabiners. “It appeared to explain everything,” he says.
Nasmyth described the idea in a few paragraphs in a massive, 73-page review article3. “Nobody took notice whatsoever,” he says — not even John Marko, a biophysicist at Northwestern University in Evanston, Illinois, who more than a decade later developed a mathematical model that complemented Nasmyth’s verbal argument4.
Mirny joined this loop-modelling club around five years ago. He wanted to explain data sets compiled by biologist Job Dekker, a frequent collaborator at the University of Massachusetts Medical School in Worcester. Dekker had been looking at physical interactions between different spots on chromosomes using a technique called Hi-C, in which scientists sequence bits of DNA that are close to one another and produce a map of each chromosome, usually depicted as a fractal-like chessboard. The darkest squares along the main diagonal represent spots of closest interaction.
The Hi-C snapshots that Dekker and his collaborators had taken revealed distinct compartmentalized loops, with interactions happening in discrete blocks of DNA between 200,000 and 1 million letters long5.
These ‘topologically associating domains’, or TADs, are a bit like the carriages on a crowded train. People can move about and bump into each other in the same carriage, but they can’t interact with passengers in adjacent carriages unless they slip between the end doors. The human genome may be 3 billion nucleotides long, but most interactions happen locally, within TADs.
Mirny and his team had been labouring for more than a year to explain TAD formation using computer simulations. Then, as luck would have it, Mirny happened to attend a conference at which Marko spoke about his then-unpublished model of loop extrusion. (Marko coined the term, which remains in use today.) It was the missing piece of Mirny’s puzzle. The researchers gave loop extrusion a try, and it worked. The physical act of forming the loops kept the local domains well organized. The model reproduced many of the finer-scale features of the Hi-C maps.
When Mirny and his colleagues posted their finished manuscript on the bioRxiv preprint server in August 2015, they were careful to describe the model in terms of a generic “loop-extruding factor”. But the paper didn’t shy away from speculating as to its identity: cohesin was the driving force behind the looping process for cells not in the middle of dividing, when chromosomes are loosely packed6. Condensin, they argued in a later paper, served this role during cell division, when the chromosomes are tightly wound7.
A key clue was the protein CTCF, which was known to interact with cohesin at the base of each loop of uncondensed chromosomes. For a long time, researchers had assumed that loops form on DNA when these CTCF proteins bump into one another at random and lock together. But if any two CTCF proteins could pair, why did loops form only locally, and not between distant sites?
Mirny’s model assumes that CTCFs act as stop signs for cohesin. If cohesin stops extruding DNA only when it hits CTCFs on each side of a growing loop, it will naturally bring the proteins together.
But singling out cohesin was “a big leap of faith”, says biophysicist Geoff Fudenberg, who did his PhD in Mirny’s lab and is now at the University of California, San Francisco. “No one has seen these motors doing these things in living cells or even in vitro,” he says. “But we see all of these different features of the data that line up and can be unified under this principle.”
Experiments had shown, for example, that reducing the amount of cohesin in a cell results in the formation of fewer loops8. Overactive cohesin creates so many loops that chromosomes smush up into structures that resemble tiny worms9.
The authors of these studies had trouble making sense of their results. Then came Mirny’s paper on bioRxiv. It was “the first time that a preprint has really changed the way people were thinking about stuff in this field”, says Matthias Merkenschlager, a cell biologist at the MRC London Institute of Medical Sciences. (Mirny’s team eventually published the work in May 2016, in Cell Reports6.)
Lieberman Aiden says that the idea of loop extrusion first dawned on him during a conference call in March 2015. He and his former mentor, geneticist Eric Lander of the Broad Institute in Cambridge, Massachusetts, had published some of the most detailed, high-resolution Hi-C maps of the human genome available at the time10.
During his conference call, Lieberman Aiden was trying to explain a curious phenomenon in his data. Almost all the CTCF landing sites that anchored loops had the same orientation. What he realized was that CTCF, as a stop sign for extrusion, had inherent directionality. And just as motorists race through intersections with stop signs facing away from them, so a loop-extruding factor goes through CTCF sites unless the stop sign is facing the right way.
His lab tested the model by systematically deleting and flipping CTCF-binding sites, and remapping the chromosomes with Hi-C. Time and again, the data fitted the model. The team sent its paper for review in July 2015 and published the findings three months later11.
Mirny’s August 2015 bioRxiv paper didn’t have the same level of experimental validation, but it did include computer simulations to explain the directional bias of CTCF. In fact, both models make essentially the same predictions, leading some onlookers to speculate on whether Mirny seeded the idea. Lieberman Aiden insists that he came up with his model independently. “We submitted our paper before I ever saw their manuscript,” he says.
There are some tiny differences. The cartoons Mirny uses to describe his model seem to suggest that one cohesin ring does the extruding, whereas Lieberman Aiden’s contains two rings, connected like a pair of handcuffs (see ‘The taming of the tangles’). Suzana Hadjur, a cell biologist at University College London, calls this mechanistic nuance “absolutely fundamental” to determining cohesin’s role in the extrusion process.
Neither Lieberman Aiden nor Mirny say they have a strong opinion on whether the system uses one ring or two, but they do differ on cohesin’s central contribution to loop formation. Mirny maintains that the protein is the power source for looping, whereas Lieberman Aiden summarily dismisses this idea. Cohesin “is a big doughnut”, he says. It doesn’t do that much. “It can open and close, but we are very, very confident that cohesin itself is not a motor.”
Instead, he suspects that some other factor is pushing cohesin around, and many in the field agree. Claire Wyman, a molecular biophysicist at Erasmus University Medical Centre in Rotterdam, the Netherlands, points out that cohesin is only known to consume small amounts of energy for clasping and releasing DNA, so it’s a stretch to think of it motoring along the chromosome at the speeds required for Mirny’s model to work. “I’m willing to concede that it’s possible,” she says. “But the Magic 8-Ball would say that, ‘All signs point to no’.”
One group of proteins that might be doing the pushing is the RNA polymerases, the enzymes that create RNA from a DNA template. In a study online in Nature this week12, Jan-Michael Peters, a chromosome biologist at the Research Institute of Molecular Pathology in Vienna, and his colleagues show that RNA polymerases can move cohesin over long distances on the genome as they transcribe genes into RNA. “RNA polymerases are one type of motor that could contribute to loop extrusion,” Peters says. But, he adds, the data indicate that it cannot be the only force at play.
Frank Uhlmann, a biochemist at the Francis Crick Institute in London, offers an alternative that doesn’t require a motor protein at all. In his view, a cohesin complex might slide along DNA randomly until it hits a CTCF site and creates a loop. This model requires only nearby strands of DNA to interact randomly — which is much more probable, Uhlmann says. “We do not need to make any assumptions about activities that we don’t have experimental evidence for.”
Researchers are trying to gather experimental evidence for one model or another. At the Lawrence Livermore National Laboratory in California, for example, biophysicist Aleksandr Noy is attempting to watch loop extrusion in action in a test tube. He throws in just three ingredients: DNA, some ATP to provide energy, and the bacterial equivalent of cohesin and condensin, a protein complex known as SMC.
“We see evidence of DNA being compacted into these kinds of flowers with loops,” says Noy, who is collaborating with Mirny on the project. That suggests that SMC — and by extension cohesin — might have a motor function. But then again, it might not. “The truth is that we just don’t know at this point,” Noy says.
The experiment that perhaps comes the closest to showing cohesin acting as a motor was published in February13. David Rudner, a bacterial cell biologist at Harvard Medical School in Boston, Massachusetts, and his colleagues made time-lapse Hi-C maps of the bacterium Bacillus subtilis that reveal SMC zipping along the chromosome and creating a loop at a rate of more than 50,000 DNA letters per minute. This tempo is on par with what researchers estimate would be necessary for Mirny’s model to work in human cells as well.
Rudner hasn’t yet proved that SMC uses ATP to make that happen. But, he says, he’s close — and he would be “shocked” if cohesin worked differently in human cells.
For now, the debate rages about what cohesin is, or is not, doing inside the cell — and many researchers, including Doug Koshland, a cell biologist at the University of California, Berkeley, insist that a healthy dose of scepticism is still warranted when it comes to Mirny’s idea. “I am worried that the simplicity and elegance of the loop-extrusion model is already filling textbooks, coronated long before its time,” he says.
And although it may seem an academic dispute among specialists, Mirny notes that if it his model is correct, it will have real-world implications. In cancer, for instance, cohesin is frequently mutated and CTCF sites altered. Defective versions of cohesin have also been implicated in several rare human developmental disorders. If the loop-extruding process is to blame, says Mirny, then perhaps a better understanding of the motor could help fix the problem.
But his main interest remains more fundamental. He just wants to understand why DNA is configured in the way it is. And although his model assumes a lot of things about cohesin, Mirny says, “The problem is that I don’t know any other way to explain the formation of these loops.”
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.”