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Tuesday, December 17th, 2019
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| 12:00a |
Screen could offer better safety tests for new chemicals It’s estimated that there are approximately 80,000 industrial chemicals currently in use, in products such as clothing, cleaning solutions, carpets, and furniture. For the vast majority of these chemicals, scientists have little or no information about their potential to cause cancer.
The detection of DNA damage in cells can predict whether cancer will develop, but tests for this kind of damage have limited sensitivity. A team of MIT biological engineers has now come up with a new screening method that they believe could make such testing much faster, easier, and more accurate.
The National Toxicology Program, a government research agency that identifies potentially hazardous substances, is now working on adopting the MIT test to evaluate new compounds.
“My hope is that they use it to identify potential carcinogens and we get them out of our environment, and prevent them from being produced in massive quantities,” says Bevin Engelward, a professor of biological engineering at MIT and the senior author of the study. “It can take decades between the time you’re exposed to a carcinogen and the time you get cancer, so we really need predictive tests. We need to prevent cancer in the first place.”
Engelward’s lab is now working on further validating the test, which makes use of human liver-like cells that metabolize chemicals very similarly to real human liver cells and produce a distinctive signal when DNA damage occurs.
Le Ngo, a former MIT graduate student and postdoc, is the lead author of the paper, which appears today in the journal Nucleic Acids Research. Other MIT authors of the paper include postdoc Norah Owiti, graduate student Yang Su, former graduate student Jing Ge, Singapore-MIT Alliance for Research and Technology graduate student Aoli Xiong, professor of electrical engineering and computer science Jongyoon Han, and professor emerita of biological engineering Leona Samson.
Carol Swartz, John Winters, and Leslie Recio of Integrated Laboratory Systems are also authors of the paper.
Detecting DNA damage
Currently, tests for the cancer-causing potential of chemicals involve exposing mice to the chemical and then waiting to see whether they develop cancer, which takes about two years.
Engelward has spent much of her career developing ways to detect DNA damage in cells, which can eventually lead to cancer. One of these devices, the CometChip, reveals DNA damage by placing the DNA in an array of microwells on a slab of polymer gel and then exposing it to an electric field. DNA strands that have been broken travel farther, producing a comet-shaped tail.
While the CometChip is good at detecting breaks in DNA, as well as DNA damage that is readily converted into breaks, it can’t pick up another type of damage known as a bulky lesion. These lesions form when chemicals stick to a strand of DNA and distort the double helix structure, interfering with gene expression and cell division. Chemicals that cause this kind of damage include aflatoxin, which is produced by fungi and can contaminate peanuts and other crops, and benzo[a]pyrene, which can form when food is cooked at high temperatures.
Engelward and her students decided to try to adapt the CometChip so that it could pick up this type of DNA damage. To do that, they took advantage of cells’ DNA repair pathways to generate strand breaks. Typically, when a cell discovers a bulky lesion, it will try to repair it by cutting out the lesion and then replacing it with a new piece of DNA.
“If there’s something glommed onto the DNA, you have to rip out that stretch of DNA and then replace it with fresh DNA. In that ripping process, you’re creating a strand break,” Engelward says.
To capture those broken strands, the researchers treated cells with two compounds that prevent them from synthesizing new DNA. This halts the repair process and generates unrepaired single-stranded DNA that the Comet test can detect.
The researchers also wanted to make sure that their test, which is called HepaCometChip, would detect chemicals that only become hazardous after being modified in the liver through a process called bioactivation.
“A lot of chemicals actually are inert until they get metabolized by the liver,” Ngo says. “In the liver you have a lot of metabolizing enzymes, which modify the chemicals so that they become more easily excreted by the body. But this process sometimes produces intermediates that can turn out to be more toxic than the original chemical.”
To detect those chemicals, the researchers had to perform their test in liver cells. Human liver cells are notoriously difficult to grow outside the body, but the MIT team was able to incorporate a type of liver-like cell called HepaRG, developed by a company in France, into the new test. These cells produce many of the same metabolic enzymes found in normal human liver cells, and like human liver cells, they can generate potentially harmful intermediates that create bulky lesions.
Enhanced sensitivity
To test their new system, the researchers first exposed the liver-like cells to UV light, which is known to produce bulky lesions. After verifying that they could detect such lesions, they tested the system with nine chemicals, seven of which are known to lead to single-stranded DNA breaks or bulky lesions, and found that the test could accurately detect all of them.
“Our new method enhances the sensitivity, because it should be able to detect any damage a normal Comet test would detect, and also adds on the layer of the bulky lesions,” Ngo says.
The whole process takes between two days and a week, offering a significantly faster turnaround than studies in mice.
The researchers are now working on further validating the test by comparing its performance with historical data from mouse carcinogenicity studies, with funding from the National Institutes of Health.
They are also working with Integrated Laboratory Systems, a company that performs toxicology testing, to potentially commercialize the technology. Engelward says the HepaCometChip could be useful not only for manufacturers of new chemical products, but also for drug companies, which are required to test new drugs for cancer-causing potential. The new test could offer a much easier and faster way to perform those screens.
“Once it’s validated, we hope it will become a recommended test by the FDA,” she says.
The research was funded by the National Institute of Environmental Health Sciences, including the NIEHS Superfund Basic Research Program, and the MIT Center for Environmental Health Sciences. | | 12:00a |
A closer look at the diabetes disaster In Belize, where diabetes is rampant, patients need insulin every day to maintain proper blood sugar levels. But if people lack electricity or a refrigerator, they cannot store insulin at home. Medical advice pamphlets encourage such patients to keep their insulin in the refrigerators at small corner grocery stores instead. And so, in some cases, there the insulin sits — right next to soft drinks which, in good measure, have helped cause the growing diabetes epidemic in the first place.
“That one image, of soda bottles and the insulin side by side, has stuck with me,” says Amy Moran-Thomas, an MIT professor and cultural anthropologist who has spent over 10 years researching and writing about the global diabetes epidemic. “It’s emblematic of the larger problem, a robust infrastructure even in rural areas to deliver foods that are contributing to diabetes, and the huge gaps in global infrastructure for treating the same conditions.”
The International Diabetes Foundation estimates that 425 million people currently have diabetes, and that number is expected to increase to more than 600 million within a generation. (By the foundation’s count, annual diabetes deaths now outnumber those from HIV/AIDS and breast cancer, combined.) U.N. Secretary General Ban Ki-moon has called chronic illnesses such as diabetes a “public health emergency in slow motion.”
Now Moran-Thomas has chronicled that emergency in a new book, “Traveling with Sugar: Chronicles of a Global Epidemic,” published this month by the University of California Press. In it, Moran-Thomas examines the havoc diabetes has caused in Belize, a Central American country with resource limitations — annual per capita income is under $5,000 — and one that is heavily reliant on cheap, high-glucose foods made with white rice, white flour, and white sugar.
“Before I started getting to know people, I had this idea that infectious diseases were the primary health crisis in a lot of Central America,” says Moran-Thomas, who as a graduate student initially considered studying the problems of parasitic infections. Instead, she discovered, “Everyone was talking about diabetes.”
Looking at the scope of the problem as well as its causes, Moran-Thomas says she came to regard the situation in Belize as a case study in how lives are rearranged by the spread of diabetes globally: “I felt this was part of something bigger that was happening in the world.”
Vanishing from the photo album
Diabetes is a disease with many possible consequences. Patients often feel excessively thirsty or hungry, although those are just early symptoms; complications and effects over time can lead to heart failure, stroke, kidney failure, blindness, and amputation of limbs, among other things. Diabetes is so strongly associated with managing blood sugar levels that the word “sugar” has become a virtual synonym for the illness in many places; in Belize “traveling with sugar” is a common expression for living with diabetes.
Moran-Thomas conducted her ethnographic research in collaboration with people in Belize, getting to know many families and community caregivers. She also conducted years of archival research about the social context, reconstructing the history of colonialism and commerce that has left Belize largely impoverished and dependent on outside sources for food and income.
Grappling with matters that resonate across the Caribbean, Latin America, and beyond, “Traveling with Sugar” closely examines how sugar-heavy diets became so common. This includes issues such as the legacy of plantation landscapes on contemporary agriculture, and the ways diabetes risks are compounded by toxic pollution, climate change, stressful social environments, and interruptions of therapy.
The human consequences are stark. Among the stories Moran-Thomas chronicles in the book, one involves an older man lovingly paging through a family photo album showing how his late wife, a teacher, had endured multiple amputations — first a foot, then both legs below the knees — which became woven into the family’s larger story of caring for each other. In the family photo album, Moran-Thomas writes, “we watched her disappear a piece at a time from the pictures, until she was absent altogether.”
As people’s bodies have changed, Moran-Thomas observes, the local landscape has too. The first place where she conducted an interview in Belize is now under water, due to coastal erosion and sea-level rise. Such cases will become more common in Belize and around the world, Moran-Thomas thinks, if the global economy promoting the growth of “carbohydrates and hydrocarbons” continues unaltered.
“There is so much profit being made from the products that contribute to the condition, and there is also money to be made for treating its harmful effects,” she notes. “So it’s difficult to think about interrupting this engine, when money’s being made on both sides, of causing and treating a problem.”
Belize’s status as a resort area also leads to some incongruous scenes in the book. Oxygen-rich hyperbaric chambers can help prevent diabetic amputations, and do exist in Belize — but primarily for tourists, such as divers with the bends. Many Belizean citizens have barely heard of such devices, let alone used them for diabetes care.
“There is a segregation of infrastructures,” Moran-Thomas says. “The hyperbaric chambers exemplify that — Caribbean residents dying from amputations without being able to access the chambers in their own countries.”
Grassroots initiatives and equitable design
The research behind “Traveling with Sugar” has already been the basis of interdisciplinary work at MIT, where Moran-Thomas has collaborated with Jose Gomez-Marquez and other members of the Little Devices Lab to create a new MIT course, 21A.311 (Social Lives of Medical Objects). One focal point of the class involves bringing together readings with lab exercises to examine what the sociologist Ruha Benjamin has called “discriminatory design” — the outcome of which is that objects and devices can be impossible for many people to use effectively.
“Discrimination doesn’t have to be intentional in order to produce a pattern of exclusion that really impacts people,” Moran-Thomas says.
For instance, she adds, “Glucose meters can’t really be repaired by the people who need them most to thrive. This makes life so much harder for people who need those meters to safely manage drugs like insulin. I think that’s an additional entry point for thinking about the delivery of health care — the assumptions built into objects has a huge impact on delivery working. At places like MIT, co-created design ideas can be put into practice. [The students] did some amazing final projects for that class, trying to reimagine what equitable objects could look like.”
Beyond medical technologies, and alongside large-scale national or international action, Moran-Thomas suggests, the ongoing work many communities are doing to reverse the diabetes epidemic from the ground up deserves more recognition and resources.
“The grassroots level is where I saw the most committed work for real change,” says Moran-Thomas, citing projects like a diabetic foot care group working to prevent amputations and a local farming cooperative building a healthy-cereal program.
“I don’t know how to reorganize a global trade system — though more policies trying to address those things are absolutely crucial,” she adds. “But there are so many tiny, vital steps that people are already working on at the level of their own neighborhoods and communities. I focused on those stories in the book to show how a future approach to diabetes response can build from that grassroots scale.” | | 3:40p |
Study probing visual memory and amblyopia unveils many-layered mystery
In decades of studying how neural circuits in the brain’s visual cortex adapt to experience, MIT Professor Mark Bear’s lab has followed the science wherever it has led. This approach has yielded the discovery of cellular mechanisms serving visual recognition memory, in which the brain learns what sights are familiar so it can focus on what’s new, as well as a potential therapy for amblyopia, a disorder where children born with disrupted vision in one eye can lose visual acuity there permanently without intervention. But this time, his lab’s latest investigation has yielded surprising new layers of mystery.
Heading into the experiments described in a new paper in Cerebral Cortex, Bear and his team expected to confirm that key proteins called NMDA receptors act specifically in neurons in layer 4 of the visual cortex to make the circuit connection changes, or “plasticity,” necessary for both visual recognition memory and amblyopia. Instead, the study has produced unexpectedly divergent results.
“There are two stories here,” says Bear, who is a co-senior author and the Picower Professor of Neuroscience in the Picower Institute for Learning and Memory. “One is that we have further pinpointed where to look for the root causes of amblyopia. The other is that we have now completely blown up what we thought was happening in stimulus-selective response potentiation, or SRP, the synaptic change believed to give rise to visual recognition memory.”
The cortex is built like a stack of pancakes, with distinct layers of cells serving different functions. Layer 4 is considered to be the primary “input layer” that receives relatively unprocessed information from each eye. Plasticity that is restricted to one eye has been assumed to occur at this early stage of cortical processing, before the information from the two eyes becomes mixed. However, while the evidence demonstrates that NMDA receptors in layer 4 neurons are indeed necessary for the degradation of vision in a deprived eye, they apparently play no role in how neural connections, or synapses, serving the uncompromised eye strengthen to compensate, and similarly don’t matter for the development of SRP. That’s even though NMDA receptors in visual cortex neurons have directly been shown to matter in these phenomena before, and layer 4 neurons are known to participate in these circuits via telltale changes in electrical activity.
“These findings reveal two key things,” says Samuel Cooke, co-senior author and a former member of the Bear Lab who now has his own at King’s College London. “First, that the neocortical circuits modified to enhance cortical responses to sensory inputs during deprivation, or to stimuli that have become familiar, reside elsewhere in neocortex, revealing a complexity that we had not previously appreciated. Second, the results show that effects can be clearly manifest in a region of the brain that are actually echoes of plasticity occurring elsewhere, thereby illustrating the importance of not only observing biological phenomena, but also understanding their origins by locally disrupting known underlying mechanisms.”
To perform the study, Bear Lab postdoc and lead author Ming-fai Fong used a genetic technique to specifically knock out NMDA receptors in excitatory neurons in layer 4 of the visual cortex of mice. Armed with that tool, she could then investigate the consequences for visual recognition memory and “monocular deprivation,” a lab model for amblyopia in which one eye is temporarily closed early in life. The hypothesis was that knocking out the NMDA receptor in these cells in layer 4 would prevent SRP from taking hold amid repeated presentations of the same stimulus, and would prevent the degradation of vision in a deprived eye, as well as the commensurate strengthening of the unaffected eye.
“We were gratified to note that the amblyopia-like effect of losing cortical vision as a result of closing an eye for several days in early life was completely prevented,” Cooke says. “However, we were stunned to find that the two enhancing forms of plasticity remained completely intact.”
Fong says that with continued work, the lab hopes to pinpoint where in the circuit NMDA receptors are triggering SRP, and the compensatory increase in strength in a non-deprived eye, after monocular deprivation. Doing so, she says, could have clinical implications.
“Our study identified a crucial component in the visual cortical circuit that mediates the plasticity underlying amblyopia,” she says. “This study also highlights the ongoing need to identify the distinct components in the visual cortical circuit that mediate visual enhancement, which could be important both in developing treatments for visual disability as well as developing biomarkers for neurodevelopmental disorders. These efforts are ongoing in the lab.”
The search now moves to other layers, Bear said, including layer 6, which also receives unprocessed input from each eye.
“Clearly, this is not the end of the story,” Bear says.
In addition to Fong, Bear, and Cooke, the paper’s other authors are Peter Finnie, Taekeun Kim, Aurore Thomazeau, and Eitan Kaplan.
The National Eye Institute and the JPB Foundation funded the study.
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