Prostate cancer is the and, for men in the United States, it’s the second leading cause of death.

Some prostate cancers might be slow-growing and can be monitored over time whereas others need to be treated right away. To determine how aggressive someone’s cancer is, doctors look for abnormalities in slices of biopsied tissue on a slide. But this 2D method makes it hard to properly diagnose borderline cases.

Now a team led by the 91̽�� has developed a new, non-destructive method that images entire 3D biopsies instead of just a slice. In a proof-of-principle experiment, the researchers imaged 300 3D biopsies taken from 50 patients — six biopsies per patient — and had a computer use 3D and 2D results to predict the likelihood that a patient had aggressive cancer. The 3D features made it easier for the computer to identify the cases that were more likely to recur within five years.

The team Dec. 1 in Cancer Research.

“We show for the first time that compared to traditional pathology — where a small fraction of each biopsy is examined in 2D on microscope slides — the ability to examine 100% of a biopsy in 3D is more informative and accurate,” said senior author , a 91̽��professor of mechanical engineering and of bioengineering. “This is exciting because it is the first of hopefully many clinical studies that will demonstrate the value of non-destructive 3D pathology for clinical decision-making, such as determining which patients require aggressive treatments or which subsets of patients would respond best to certain drugs.”

The researchers used prostate specimens from patients who underwent surgery more than 10 years ago, so the team knew each patient’s outcome and could use that information to train a computer to predict those outcomes. In this study, half of the samples contained a more aggressive cancer.

To create 3D samples, the researchers extracted “biopsy cores” — cylindrically shaped plugs of tissue — from surgically removed prostates and then stained the biopsy cores to mimic the typical staining used in the 2D method. Then the team imaged each entire biopsy core using an open-top light-sheet microscope, which uses a sheet of light to optically “slice” through and image a tissue sample without destroying it.

The 3D images provided more information than a 2D image — specifically, details about the complex tree-like structure of the glands throughout the tissue. These additional features increased the likelihood that the computer would correctly predict a cancer’s aggressiveness.

Shown here is a video of a volume rendering of glands in two 3D biopsy samples from prostates (yellow: the outer walls of the gland; red: the fluid-filled space inside the gland; purple: what researchers called the “gland skeleton,” a stick-like model of the fluid-filled spaces inside the glands). The cancer sample (top) shows smaller and more densely packed glands compared to the benign tissue sample (bottom). Credit: Xie et al./Cancer Research

The researchers used new AI methods, including deep-learning image transformation techniques, to help manage and interpret the large datasets this project generated.

“Over the past decade or so, our lab has focused primarily on building optical imaging devices, including microscopes, for various clinical applications. However, we started to encounter the next big challenge toward clinical adoption: how to manage and interpret the massive datasets that we were acquiring from patient specimens,” Liu said. “This paper represents the first study in our lab to develop a novel computational pipeline to analyze our feature-rich datasets. As we continue to refine our imaging technologies and computational analysis methods, and as we perform larger clinical studies, we hope we can help transform the field of pathology to benefit many types of patients.”

The lead author on this paper is , a 91̽��mechanical engineering doctoral student. Other co-authors on this paper are , , and , all 91̽��mechanical engineering doctoral students; , a 91̽��bioengineering doctoral student; , a clinical instructor in the laboratory medicine and pathology department in the 91̽��School of Medicine; Hongyi Huang, 91̽��research staff in mechanical engineering; , a 91̽��doctoral student in the chemistry department; , a research scientist in the laboratory medicine and pathology department in the 91̽��School of Medicine; , a 91̽��assistant teaching professor in the mechanical engineering department; Qinghua Han, a 91̽��undergraduate student studying bioengineering; Jonathan Wright, a professor in the urology department in the 91̽��School of Medicine; and , both professors in the laboratory medicine and pathology department in the 91̽��School of Medicine; , a 91̽��associate professor of chemistry; , a senior scientist at the Allen Institute who completed this research as a 91̽��mechanical engineering postdoctoral researcher; , , and , all at Case Western Reserve University; at Genentech, who completed this research as a doctoral student at Case Western Reserve University; and Sarah Hawley at the Canary Foundation.

This research was funded by the Department of Defense Prostate Cancer Research Program; the National Cancer Institute; the National Heart, Lung and Blood Institute; the National Institute of Biomedical Imaging and Bioengineering; the National Institute of Mental Health; the VA Merit Review Award; the National Science Foundation; the Nancy and Buster Alvord Endowment; and the Prostate Cancer Foundation Young Investigator Award.

Nicholas Reder, Adam Glaser, Lawrence True and Jonathan Liu are co-founders and shareholders of the 91̽��spinout This company has licensed the technology used in this paper.

For more information, contact Liu at jonliu@uw.edu.

Grant numbers: W81XWH-18-10358, W81XWH-19-1-0589, W81XWH-15-1-0558, W81XWH-20-1-0851, K99 CA24068, R01CA244170, U24CA199374, R01CA249992, R01CA202752, R01CA208236, R01CA216579, R01CA220581, R01CA257612, U01CA239055, U01CA248226, U54CA254566, R01HL151277, R01EB031002, R43EB028736, R01MH115767, IBX004121A, 1934292 HDR: I-DIRSE-FW, DGE-1762114, DGE-1762114

Karin Bornfeldt receives Outstanding Investigator Award from National Heart, Lung, and Blood Institute

, a professor of medicine and pathology, has received an from the National Heart, Lung, and Blood Institute, part of the National Institutes of Health. The award will total more than $7.2 million for up to seven years, with about $1 million in the first year.

The award is under the institute’s R35 Program, which promotes scientific productivity by giving principal investigators with multiple projects the freedom to conduct research that breaks new ground or extend previous discoveries in heart, lung, blood and sleep research.

Bornfeldt’s research project is titled “Identifying New Strategies for Prevention of Cardiovascular Complications of Diabetes.”

Bornfeldt is director of the , deputy director of the and associate director for research of the . She serves as associate editor of the journals Circulation Research, Diabetes, and the Journal of Lipid Research.

Read more at the Department of Medicine .

* * *

Guntis Šmidchens of Scandinavian studies honored by Republic of Lithuania

, 91̽��associate professor of Scandinavian studies and Baltic studies, has received a state decoration from the Republic of Lithuania.

Lithuanian President Gitanas Nausėda presented Šmidchens the in a celebration on Feb. 16, which since 1918 has been Lithuanian Independence Day. The award notes Šmidchens’ “active promotion of Lithuanian language, history and culture in the United States.”

Šmidchens is the UW’s Kazickas Family Endowed Professor of Baltic Studies. He is the author of the 2014 book “The Power of Song: Nonviolent National Culture in the Baltic Singing Revolution,” about a nonviolent resistance movement in the Baltic nations of Latvia, Lithuania and Estonia in the late 1980s and early 1990s.

Order for Merits to Lithuania is one of four types of orders bestowed, and the Cross of the Knight one of five of Insignia of the Orders.

* * *
10 91̽��engineering professors receive Google Faculty Research Awards

Ten 91̽��College of Engineering faculty have been named recipients of . The grants, among Google recently , support world-class technical research in computer science, engineering and related fields. Each award provides funding to support one graduate student for a year.

The recipients are , , , , and of the Paul G. Allen School of Computer Science & Engineering; and of the Department of Human Centered Design & Engineering; of the Department of Civil & Environmental Engineering; and of both the Department of Electrical & Computer Engineering and the Department of Bioengineering.

The is “to identify and strengthen long-term collaborative relationships with faculty working on problems that will impact how future generations use technology,” according to Google.

91̽��Notebook is a section of the 91̽��News site dedicated to telling stories of the good work done by faculty and staff at the 91̽��. Read all posts here.

The six 91̽��faculty members who have been named as fellows are:

, professor emeritus in the School of Oceanography, is honored for his continuing work on the ecology of the plankton, the very small algae and animals that float with the currents. His career has focused on how plankton interact with light, temperature, oxygen, bound nitrogen, iron and other nutrients. At sea, Banse worked in the Baltic, the North Sea and Puget Sound, but especially the Arabian Sea. In other work, using an early color global satellite, he investigated the offshore seasonality of phytoplankton chlorophyll. With former students he also studied bottom-living polychaetous annelid worms and published identification keys for the nearly 500 species of these worms found between Oregon and southeast Alaska, between the shore and about 200 meters depth. Banse joined the 91̽��faculty in 1960. The 90-year-old researcher became emeritus in 1995 and remains scientifically active.

, a professor of health metrics sciences and director of the at the Institute for Health Metrics and Evaluation, was selected for his research resolving infectious diseases in space and time in order to expose inequalities in health metrics and improve intervention strategies. He currently leads an international collaboration of researchers from a wide variety of academic disciplines to create even better maps of infectious disease. He has published over 400 peer-reviewed articles and other contributions, including two major, in-depth research papers published independently. His published works are cited more than 18,000 times each year, leading to more than 82,000 lifetime citations. With the support of the Bill & Melinda Gates Foundation, Hay has embarked on a project to expand this research to a much wider range of diseases to ultimately harmonize this mapping with the Global Burden of Disease Study, IHME’s signature project.

, a professor of microbiology, studies Kaposi’s Sarcoma Herpesvirus, a virus that alters the cells lining blood and lymphatic vessels. Those changes can cause Kaposi’s Sarcoma, a form of cancer that commonly affects AIDS patients worldwide and people in parts of central Africa. Lagunoff’s lab has studied how the Kaposi’s Sarcoma Herpesvirus interferes with endothelial cell signaling, gene expression and metabolism to promote the formation of tumors containing numerous blood vessels. His lab used RNA-sequencing, metabolomics, proteomics and other techniques to determine global changes in host-cell gene expression and signaling. This information has helped to identify key cellular pathways induced by the virus. His team is studying how the virus alters the host cell metabolism to mimic cancer cell metabolism, and is searching for novel therapeutic targets for Kaposi’s Sarcoma.

, a professor of pathology and genome sciences and an investigator at the , studies DNA damage and repair mechanisms, genome instability, and its role in cancer and other conditions. He is noted for his work on Werner, Bloom and Rothman-Thomson syndromes. These inherited disorders cause distinctive physical characteristics, such as premature aging in Werner’s, and predispose to cancer. Monnat’s team explores how the loss of key proteins important to DNA metabolism may underlie these rare syndromes. Aberrant expression of those proteins may be common in some adult cancers and affect response to chemotherapy. Monnat and his group use certain genome engineering techniques to try to correct disease-causing mutations in patient-derived stem cells. His lab has also identified “safe-harbor sites” in the human genome where new genetic elements might be inserted without disrupting the expression of nearby genes.

, professor in the School of Aquatic and Fishery Sciences and the Department of Biology, is elected for her work in marine ecology. Her research focuses on seabird ecology, marine conservation and public science. A committed advocate of citizen science, she founded and directs the , which for two decades has enlisted coastal residents from California to Alaska to monitor West Coast beaches for dead birds and marine debris. Parrish spoke at the White House in 2013 about public engagement in science and scientific literacy. She holds the Lowell A. and Frankie L. Wakefield endowed professorship, and is associate dean for academic affairs in the 91̽��College of the Environment.

, a professor of Earth and space sciences, is honored for his work in glaciology and climate science. Steig uses ice cores and other records to study climate variability over thousands of years. He works on the climate history and dynamics of polar ice sheets and mountain glaciers, and develops new tools to extract the chemical clues in samples of ice and other material. Steig was among the leaders of a project to drill the first deep ice core at South Pole, and was on the team that drilled a 2-mile-deep ice core in West Antarctica. His recent research has focused on the links between large-scale climate conditions and changes in West Antarctica, where glaciers are rapidly retreating. In addition to his research and teaching, he is committed to fostering greater public understanding of climate change, and is a founding contributor to RealClimate.org.

In addition, , an investigator at the Fred Hutchinson Cancer Research Center and an affiliate professor of genome sciences at the UW, was selected for his research on genetic conflict.

When women undergo lumpectomies to remove breast cancer, doctors try to remove all the cancerous tissue while conserving as much of the healthy breast tissue as possible.

But currently there’s no reliable way to determine during surgery whether the excised tissue is completely cancer-free at its margins — the proof that doctors need to be confident that they removed all of the tumor. It can take several days for pathologists using conventional methods to process and analyze the tissue.

That’s why between 20 and 40 percent of women have to undergo second, third or even fourth breast-conserving surgeries to remove cancerous cells that were missed during the initial procedure, according to

A new microscope invented by a team of 91̽�� mechanical engineers and pathologists could help solve this, and other, problems. It can rapidly and non-destructively image the margins of large fresh tissue specimens with the same level of detail as traditional pathology — in no more than 30 minutes.

“Surgeons are sort of flying blind during these breast-conserving surgeries,” said mechanical engineering professor . “Oftentimes they’ve left some tumor behind which they don’t know about until a few days later when the pathologist finds it.”

“If we can rapidly image the entire surface or margin of the excised tissue during the procedure, we can tell them if they still have tumor left in the body or not. And that would be a huge benefit to cancer patients,” Liu said.

The new light-sheet microscope — which is described in a published June 26 in — offers other advantages over existing processes and microscope technologies. It conserves valuable tissue for genetic testing and diagnosis, quickly and accurately images the irregular surfaces of large clinical specimens, and allows pathologists to zoom in and “see” biopsy samples in three dimensions.

“The tools we use in pathology have changed little over the past century,” said co-author , chief resident and clinical research fellow in 91̽��Medicine’s Department of Pathology. “This light-sheet microscope represents a major advance for pathology and cancer patients, allowing us to examine tissue in minutes rather than days and to view it in three dimensions instead of two — which will ultimately lead to improved clinical care.”

Current pathology techniques involve processing and staining tissue samples, embedding them in wax blocks, slicing them thinly, mounting them on slides, staining them, and then viewing these two-dimensional tissue sections with traditional microscopes — a process that can take days to yield results.

Another technique to provide real-time information during surgeries involves freezing and slicing the tissue for quick viewing. But the quality of those images is inconsistent, and certain fatty tissues, such as those from the breast, do not freeze well enough to reliably use the technique.

By contrast, the 91̽��open-top light-sheet microscope uses a sheet of light to optically “slice” through and image a tissue sample without destroying any of it. All of the tissue is conserved for potential downstream molecular testing, which can yield additional valuable information about the nature of the cancer and lead to more effective treatment decisions.

“Slide-based pathology is still an analog technique, much like radiology was several decades ago when X-rays were obtained on film. By imaging tissues in 3-D without having to mount thin tissue sections on glass slides, we are trying to transform pathology much like 3-D X-ray CT has transformed radiology,” Liu said.  “While it is possible to scan microscope slides for digital pathology, we digitally image the intact tissues and bypass the need to prepare slides, which is simpler, faster and potentially less expensive.”

“If we can do this without consuming any tissue, so much the better,” said co-author , professor of pathology at 91̽��Medicine. “We want to use that valuable tissue for purposes which are becoming ever more important for treating patients — such as sequencing the tumor cells and finding genetic abnormalities that we can target with specific drugs and other precision medicine techniques.”

The light-sheet microscope also offers advantages over other non-destructive optical- sectioning microscopes on the market today, which process images slowly and have difficulty maintaining the optimal focus when dealing with clinical specimens, which always have microscopic surface irregularities.

The 91̽��microscope can both image large tissue surfaces at high resolution and stitch together thousands of two-dimensional images per second to quickly create a 3-D image of a surgical or biopsy specimen. That additional data could one day allow pathologists to more accurately and consistently diagnose and grade tumors.

“Pathologists are currently very limited in how much they can look at on a glass slide,” said co-author , a postdoctoral fellow in the 91̽��. “If we can give them three-dimensional data, we can give them more information to help improve the accuracy of a patient’s diagnosis.”

The 91̽��team achieved these improvements by configuring various optical technologies in new ways and optimizing them for clinical use. Their open-top arrangement, which places all of the optics underneath a glass plate, allows them to image larger tissues than other microscopes.

The team is currently working on speeding up the optical-clearing process that allows light to penetrate biopsy samples more easily. Future areas of research include optimizing their 3-D immunostaining processes, as well as as continuing a collaboration formed during the 91̽��eScience Institute’s Winter Incubator program with Dr. Ariel Rokem to develop algorithms that can process the vast amounts of 3-D pathology data that their system generates, with the ultimate goal of helping pathologists zero in on suspicious areas of tissue.

The research was funded by the National Institutes of Health and the 91̽��.

Additional co-authors include Ye Chen, Chengbo Yin, Linpeng Wei and Yu Wang of the 91̽��Department of Mechanical Engineering and Erin F. McCarty of 91̽��Medicine’s Department of Pathology.

For more information on the light-sheet microscope, contact Jonathan Liu at jonliu@uw.edu. To reach Larry True or Nicholas Reder at 91̽��Medicine, contact Leila Gray at 206-685-0381 or leilag@uw.edu.

Humans make rational choices — though perhaps not all the time. But does the ability for rational decision-making extend to other members of the animal kingdom? If so, how far are they from the human lineage?

The answer, according to researchers from the 91̽��, is pretty far.

In published Jan. 17 in the journal , they report that fruit flies — perhaps the most widely studied insect in history — show signs of rational decision-making when choosing a mate. Through a complex series of behavioral experiments, the team shows that male fruit flies, when presented with a pair of females as potential mating partners, display a key component of rational choice: transitivity.

“Transitivity is a hallmark of rational decision-making,” said senior author , a 91̽��professor of pathology and biology. “Essentially, it is the process of establishing a rank order of preference, and then making behavioral decisions based on that hierarchy.”

Transitivity has been shown in other animals, such as some bird species, while searching for food. But Promislow’s team, led by first author and postdoctoral researcher , is among the first to see if rationality extends to mate choice.

The researchers showed that individual male fruit flies from one wild-derived strain, called Canton-S, displayed transitivity when presented with potential female mates from 10 different laboratory strains of fruit flies. In these tests, a researcher would place one Canton-S male in an arena with a pair of females, each from a different strain, and note if the male mated with either female.

“Before each test, we would mark each female with a yellow or red fluorescent powder,” said Arbuthnott, who is now a postdoctoral researcher at the University of British Columbia. “If the male attempted to mate with either female, we could determine the female’s identity based on her color.”

To account for all possible pairings of females from the 10 strains, they tested Canton-S males against 45 pairs of females. No fly, male or female, was tested more than once. After repeating these tests 10 to 20 times for each combination, the researchers discovered that Canton-S males displayed a consistent, ranked preference regarding which female to mate with.

“This is the pattern we would expect to see if males are making transitive decisions — a sign of rational choice,” said Arbuthnott.

Using the same assays, they showed that males from a second strain, Oregon-R, also display transitivity with females from the 10 laboratory strains. There were only a few small differences between the hierarchies displayed by Oregon-R males and Canton-S males, said Arbuthnott.

Though the researchers only tested mate choice in male flies, the decision to mate in this species is definitely a two-way street. But Arbuthnott focused on male mate choice in these experiments to help dispel a misconception about mating in many animal species.

“There is a classic theory that females are the ‘choosy’ sex and males aren’t choosy,” said Arbuthnott. “We wanted to show that males are definitely making choices too when interacting with the females.”

The males are likely responding to a combination of visual, chemical and behavioral cues from the females. The team conducted more experiments to learn about the “information” the males picked up from females. Blind males still displayed transitivity when choosing between females, as did mutant males who had no sense of taste and smell. But blind males with no sense of smell or taste did not display transitivity.

“The results from these sensory deprivation experiments indicate that there is some redundancy in the information provided by the female visual and chemical cues,” said Promislow.

They also analyzed one particular signal, a complex secretion of chemicals known as cuticular hydrocarbons, or CHCs.

“CHCs are essentially ‘contact pheromones,'” said Arbuthnott. “When they’re in close proximity, fruit flies can taste one another’s secretions and — we believe — learn information about a potential mate.”

By gas chromatography, which separates and identifies individual CHC molecules, they discovered that females from lines less likely to be chosen for mating secreted higher levels of two particular CHCs, which may act as “repellant” signals.

In addition, the researchers counted the number of offspring produced by females from each line, and discovered that males were more likely to mate with females with a greater capacity to produce the next generation.

Their results indicate that male fruit flies construct a hierarchy — a sign of transitivity and rational choice — and may be doing so by integrating diverse visual and chemical cues from females.

“They’re able to process the information they’re receiving in the most advantageous way,” said Arbuthnott. “Their decisions are transitive, which is indicative of rational choice.”

Co-authors are and with the University of Michigan. The research was funded by the National Institutes of Health.

###

For more information, contact Promislow at 206-616-6994 or promislo@uw.edu and Arbuthnott at 604-356-4714 or darbuth@zoology.ubc.ca.

: 10.1038/NCOMMS13953

Grant number: GM102279.

The 91̽��fellows are:

, professor of atmospheric sciences, was elected for his outstanding contributions to measuring and understanding how radiative heat is transferred through the Earth’s atmosphere, and how this relates to climate and climate change. Fu’s work interpreting satellite data established a key consistency in climate warming in recent decades between the atmosphere and the Earth’s surface. He discovered a shift toward the poles of subtropical jets in a warming climate, showing a widening of the tropics. His parameterization of optical properties of cirrus clouds has been widely used in global climate models. Fu is a fellow of the American Geophysical Union and a fellow of the American Meteorological Society, and holds an affiliate faculty position at China’s Lanzhou University. He earned his doctorate at the University of Utah in 1991 and joined the 91̽��in 2000.

, professor of anthropology, was chosen for her contributions at the interface of anthropology, demography and endocrinology, particularly in the areas of hormones and behavior and reproduction across the life span. O’Connor is the director of the UW’s Biological Anthropology and Biodemography Laboratory, which specializes in developing and optimizing collection methods and assays for population-level research in reproductive ecology. O’Connor’s research and teaching interests focus on variation in human fertility and mortality, as well as the biological, cultural and environmental factors that contribute to that variation. In her research on human fertility, O’Connor examines aged-related, population and individual-level variation in female productive function. Her latest research focuses on men’s health, with the goal of understanding the biological and behavioral factors that cause men to have higher mortality rates than women. O’Connor earned her doctorate from the State University of New York at Albany in 1995 and has been a member of the 91̽��faculty since 1999.

, professor of pathology, is noted for his work on the biology of longevity. In mammalian cells, he studies physiological and biochemical processes that contribute to a longer, healthier life. His research with transgenic mouse models has increased knowledge of cell signals that delay physical decline. For example, the Rabinovitch lab looks at pathways that might mitigate the aging effects of oxygen metabolism byproducts and of damage to mitochondria, the cell’s powerhouses. Certain chemicals and signaling pathways appear to protect against some debilitations of advancing age: enlargement of the heart, heart failure, loss of muscle tissue and certain cancers. Rabinovitch is the founding director of the 91̽��Nathan Shock Center for Excellence in the Basic Biology of Aging, one of five in the country funded by the National Institute on Aging of the National Institutes of Health. He also is a leader in training new scientists in his field. He has received a Senior Scholar in Aging grant from the Ellison Medical Foundation and a Breakthroughs in Gerontology grant from the American Federation for Aging Research. Rabinovitch earned both his doctoral and medical degrees at the UW, and joined the faculty in 1981.

, professor of pharmacology, is interested in the coordination, timing and precision of protein interactions. He studies a small protein called ubiquitin that is found in almost all living things, except primitive lifeforms. Cells use ubiquitin to control activities of many other proteins. This modification — called protein ubiquitination — regulates nearly all biological functions. Problems with protein ubiquitination have been linked to cancer, susceptibility to infection and neurological disorders. Zheng uses X-ray crystallography to visualize the atomic details of protein ubiquitination. His work has suggested new strategies for protecting cells’ antiviral pathways during virus attacks. He also studies how plant hormones and metabolic compounds manage the chemical transfer of ubiquitin onto proteins. His findings may open new avenues for developing drugs that enhance protein interactions. In addition, Zheng analyzes cell membrane proteins to discover potential drug-binding sites. Zheng is a Howard Hughes Medical Institute investigator and his projects are also supported by the National Institutes of Health, the Pew Scholar Program, the National Science Foundation and the Burroughs Wellcome Fund. He earned his doctorate at the University of Texas Southwestern Medical Center at Dallas and has been at the 91̽��since 2002.

The transplant anti-rejection drug rapamycin showed unexpected benefits in a mouse model of a fatal defect in the energy powerhouses of cells, the mitochondria. Children with the condition, Leigh syndrome, show progressive brain damage, muscle weakness, lack of coordination or muscle control, and weight loss, and usually succumb to respiratory failure.

Leigh syndrome is often diagnosed within the first year of life. Affected children rarely survive beyond 6 or 7 years. At present, the disorder, which can result from several different underlying causes, has no effective treatment.

Reporting this week in , 91̽��researchers said that they found that treatment with rapamycin “robustly enhances survival and attenuates disease progression in a mouse model of Leigh’s syndrome.” Given as a daily injection, the drug delayed the onset of neurological symptoms, reduced brain inflammation, and prevented brain lesions.

For most of their lives, the treated mice breathed normally, and did not clasp their legs against their bodies, a posture characteristic of this and related brain disorders in mice. Unlike the untreated mice, they could balance and run on a rotarod, a miniature log rolling exercise toy. Both the median and maximum lifespans within the group of treated mice were strikingly extended, the authors noted.

The median lifespan for this mouse condition is 50 days. In comparison, treated males lived a median of 114 days, and females 111 days. The longest survival in the treated group was 269 days, more than triple that of the untreated animals.

“We were excited at the findings because of the potential impact on treatment for kids with this or related mitochondrial diseases,” said the senior author of the study, Dr. Matt Kaeberlein, 91̽��associate professor of pathology. “Similar intervention strategies might also prove useful for a broad range of mitochondrial diseases or for other conditions resulting from mitochondrial dysfunction.”

Mitochondrial defects lessen the amount of energy available to cells. The depletion can damage or destroy vital tissues. Symptoms and severity of illness depends on which types of cells are affected, but in many cases several organ systems operate poorly as a consequence of malfunctioning mitochondria.

Beyond specific mitochondrial diseases, most of them genetic in origin, the decline or dysfunction of mitochondria contribute to many common health problems, including some forms of heart disease, cancer, and muscle, nerve or brain degeneration associated with aging.

Kaeberlein, who researches factors that lengthen life, has been studying the anti-aging effects of rapamycin for several years. The drug, like calorie-restricting diets, acts by inhibiting mTOR, an abbreviation for the eponymously named mechanistic target of rapamycin.

Kaeberlein said, “This study suggests that this drug’s inhibition of mTOR may have a major impact on mitochondria and energy production in cells. We know that rapamycin appears to slow aging. What we don’t know is whether the effects of rapamycin on mitochondria are a major part of the effects of rapamycin on normal aging and aging-related diseases.”

Alongside their work in aging and lifespan in normal mice, Kaeberlein and his lab decided to study rapamycin’s actions on mice with a severe mitochondrial defect. The mouse model for Leigh syndrome was created in the 91̽��laboratory of Dr. Richard Palmiter, a professor of biochemistry and Howard Hughes Medical Institute investigator who was one of the early originators of transgenic mouse models.

The research team included Dr. Philip G. Morgan and Dr. Margaret M. Sedensky, from the Department of Anesthesiology and Pain Medicine at Seattle Children’s Hospital, who study mitochondrial diseases in patients. The lead scientist was Simon C. Johnson from the 91̽��Department of Pathology.

After seeing unexpected benefits on health and survival, the research group looked closely at the effects on metabolism by examining the levels of more than 100 different metabolites – cellular building blocks and intermediates used to make energy – in the treated and untreated Leigh syndrome mice. The team observed that treated mice appear to burn more amino acids and fats as an energy source, rather than the sugar, glucose. This eliminated the accumulation of glucose breakdown byproducts, including lactate. These byproducts can be toxic and are seen at high levels in human Leigh syndrome patients.

“The drug did not substantially alter mitochondrial composition. Instead, the mice appear to bypass the deficiency in their mitochondria through a shift in their metabolic pattern,” Kaeberlein said. “However, we can’t yet explain exactly how this rescues the mice with Leigh syndrome.”

Because this was a mouse study, evidence of efficacy of rapamycin in Leigh syndrome patients will be a necessary next step. Rapamycin already has FDA approval for several uses, including preventing organ transplant rejection and for treating rare forms of cancer; however, the drug also has side-effects which might limit its utility in very young children. Kaeberlein is optimistic, however, that “even if rapamycin doesn’t turn out to be be useful as a treatment for Leigh Syndrome, the lessons learned here will pave the way to new therapies for this devastating disease.”

In addition to Kaeberlein, Palmiter, Morgan, Sedensky and Johnson, the researchers on the study were Melana E. Yanos, Ernst-Bernhard Kayser, Albert Quintana, Maya Sangesland, Anthony Castanza, Lauren Uhde, Jessica Hui, Valerie Z. Wall, Arni Gagnidze, Kelly Oh, Brian M. Wasko, Fresnida J. Ramos, and Peter S. Rabinovitch.

The study was funded by the 91̽��School of Medicine and the 91̽��Department of Pathology through the Healthy Aging and Longevity Research Institute. Some of the researchers were supported by NIH training grants T32AG000057 and T32ES007032, and an Amgen Scholar grant.

The gene, PAX5, has long been known to be involved in acute lymphoblastic leukemia.  The new study indicates a mutation in the gene alone is sufficient to eventually cause the disease, which affects nearly 3,000 children and teenagers in the United States each year.

The discovery should make it possible to screen for the gene in families with a history of the disease and suggests new strategies for treating the disease, said Dr. Marshall Horwitz, professor of pathology and of medicine at the 91̽��. He is a co-author of the new study.

He was joined in the study by researchers at St. Jude Children’s Research Hospital in Memphis, Tennessee led by Dr. Charles Mullighan; Memorial Sloan-Kettering Cancer Center in New York City led by Dr. Kenneth Offit, and others at the UW. The results were published Sept. 8 in the journal Nature Genetics.

The researchers looked at the genes from two unrelated families that had a high rate of acute lymphoblastic leukemia and identified the same mutation of the PAX5 gene that ran in both the families.

This variant does not cause leukemia as long as it is paired with a normal version of the PAX5 gene, said Horwitz, but if the normal copy of the gene is lost and only the abnormal variant remains, some blood cells fail to become normally functioning white blood cells and, instead, turn into leukemia cells.

In the case of the families in the study, all the children who developed leukemia had damage to a chromosome in the affected blood cells. The damage, in which part of chromosome 9 was lost, removed the normal copy of the PAX5 gene. This left the abnormal gene unopposed.

PAX5 codes for a kind of protein, called a transcription factor, that plays a key role not only in blood cell maturation, but also in embryonic development.

“It was not a surprise that PAX5 turned out to be involved. It’s  the most commonly mutated gene found in ALL cells,” said Horwitz. “But it has not been clear whether PAX5 mutations were just mutations that had to happen at some point in the transformation of a normal cell to a leukemic cell or whether PAX5 variants were driving the leukemia.”

He said the findings indicate that PAX5 variants alone are sufficient to eventually cause acute lymphoblastic leukemia.

The finding has another important implication, said Horwitz. The fact that PAX5 is sufficient to cause acute lymphoblastic leukemia supports the concept that mutations that affect differentiation of blood cells are the key drivers of leukemia. If that is the case, it may be possible to design treatments that block de-differentiation or induce leukemic cells to re-differentiate so that they would begin to behave like normal cells again.

Such treatments might be more effective and have far fewer side effects than chemotherapy, the current standard treatment for these cancers, said Horwitz.

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Morayma Reyes, professor of pathology and laboratory medicine, and Hannele Ruohola-Baker, professor of biochemistry and associate director of the Institute for Stem Cell and Regenerative Medicine, headed the 91̽�� team that made the discovery. The first authors of the paper were Nicholas Ieronimakis, 91̽��Department of Pathology; and Mario Pantoja, 91̽��Department of Biochemistry.

They explained that the mice in their study, like boys with the gender-linked inherited disorder, are missing the gene that produces dystrophin, a muscle-repair protein. Neither the mice nor the affected boys can replace enough of their routinely lost muscle cells. In people, muscle weakness begins when the boys are toddlers, and progresses until, as teens, they can no longer walk unaided.  During early adulthood, their heart and respiratory muscles weaken. Even with ventilators to assist breathing, death usually ensues before age 30. No cure or satisfactory treatment is available. Prednisone drugs relieve some symptoms, but at the cost of severe side effects.

The disabling, then lethal, nature of the rare disease in young men presses scientists to search for better therapeutic agents. Reyes and Ruohola-Baker are seeking ways to suppress the disorder’s characteristic functional and structural muscle defects.

Ruohola-Baker’s lab originally identified the sphingosine 1-phosphate (S1P) pathway as a critical player in ameliorating muscular dystrophy in flies. Her lab did this through a large genetic suppressor screen using the fruit fly, Drosophila melanogaster. Sphingosine 1-phosphate is found in the cells of most living beings from yeasts to mammals. Named after the enigmatic sphinx, this cell signal is important in many activities of living cells, from migration to proliferation. The multi-talented, bioactive lipid is essential, Reyes said, in turning stem cells into specific types of cells, in regenerating damaged tissue, and in inhibiting cell death. Without cell receptors for sphingosine 1-phosphate, an embryo would fail to develop.

Other scientists had observed that levels of sphingosine 1-phosphate are lower in the muscles of mice with the muscular dystrophy mutation, and that certain cell repair pathways involving this signal are impaired. However, sphingosine 1-phosphate couldn’t be administered as a drug because it is rapidly used up.

Instead, Reyes and Ruohola-Baker sought to prevent the sphingosine 1-phosphate occurring naturally in the body from degrading. A fruit fly model of Duchenne muscular dystrophy allowed Ruohola-Baker’s lab to rapidly score small molecule therapy candidates for raising the level of sphingosine 1-phosphate. Flies with the genetic defect act normally after they hatch and fly around, but in a few weeks, due to muscle degeneration, they are flightless. By using insect activity monitors, the scientists assessed the effects of drug and gene therapy candidates on the flies’ ability to move.

This screening tool led to the discovery that a small molecule with a long name, 2-acetyl4 (5)-tetrahydroxybutyl imidazole, or THI for short, blocks an enzyme that breaks down sphingosine 1-phosphate.

“It’s interesting to note that THI is a trace component of Caramel Color III, which the U.S. Food and Drug Administration categories as ‘generally recognized as safe’,” said Reyes. The substance is also found in very tiny amounts in burnt sugar, brown sugar, beer, cola and some candies.

The researchers added a purified, concentrated form of THI to the food of young flies with the muscular dystrophy-like mutation. They confirmed that the THI alleviated muscle wasting in the flies. A few other drugs, including a THI derivative and an unrelated drug now in clinical trials for rheumatoid arthritis, also showed beneficial effects in fruit flies.

The study of THI then switched from insects to mammals. Reyes lab began by treating old dystrophic mice with direct injection of THI. Later, the researchers simply added the compound to the drinking water in the habitats of young dystrophic mice. These mice were comparable in developmental stage to human teens who have muscular dystrophy genetic variation.

“We observed that treatment with THI significantly increased muscle fiber size and muscle-specific force in our affected mice,” Reyes said.  “We also saw that other hallmarks of impaired muscle regeneration – fat deposits and fibrosis [scar tissue] accumulation – were also lower in the THI-treated mice.”

The research team linked the desired regenerative effects in the mice to the response of muscle-forming cells and the subsequent regrowth of muscle fibers. A type of sphingosine 1-phosphate, and cell receptors for it, also were observed in the cells in the regenerating muscle fibers. The researchers proposed that sphingosine 1-phosphate turned up the dial on the regulators for the biochemical pathways that mediate skeletal muscle mass and muscle function.

Now that they have shown proof-of-concept, the researchers hope to conduct additional animal studies on THI and other compounds that protect the body’s supply of sphingosine 1-phosphate necessary for muscle cell regeneration. If THI continues to show promise as a nutraceutical or food-based drug, medical scientists will head into pre-clinical studies of effectiveness and safety before advancing to human trials.  In addition to muscular dystrophy treatment research, similar studies might also be conducted in the future on loss of muscle strength during normal or accelerated aging.

While excited about the preliminary findings, the scientists cautioned that they are still at the very earliest stages of research, and that much more work needs to be done before any conclusions can be drawn about the potential of THI as a muscular dystrophy treatment.

Other members of the research team were Aislinn L. Hays, 91̽��Pathology; Timothy L. Dose, Junli Qi, Karin A. Fischer, all of 91̽��Biochemistry and the 91̽��Institute for Stem Cell and Regenerative Medicine; Andrew N. Hoofnagle, 91̽��Laboratory Medicine; Martin Sadilek, 91̽��Chemistry; and Jeffrey S. Chamberlain of 91̽��Neurology and the UW’s Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center.

The researchers have filed a federal patent on sphingosine 1-phosphate-promoting therapies for muscular dystrophy. They have not received any benefits from any organization with a financial stake in the research and have no competing financial interests in analyzing and reporting their findings.

The work was supported by the 91̽�� Department of Pathology and Department of Laboratory Medicine, a Provost Bridge grant, a Nathan Shock Center of Excellence in the Basic Biology of Aging, Genetic Approaches to Aging Training Grant, and the American Recovery and Reinvestment Act of 2009 Challenge Grants 5RC1AR058520, R01GM083867, R01GM097372, and 1P01GM081619.

The scientists also received funding from the Washington Research Foundation, the Duchenne Alliance, RaceMD, and Ryan’s Quest.

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Exposure to diesel exhaust may render friendly, cholesterol-fighting molecules incapable of performing their important job. A new study suggests that the traffic air pollutant may prevent good cholesterol from battling the bad, artery-clogging cholesterol that promotes heart attack and stroke.

The study’s team included environmental health scientists led by Michael E. Rosenfeld at the 91̽��School of Public Health and heart disease specialist Jesus Araujo and his colleagues in the Division of Cardiology at the University of California, Los Angeles. Their , published in the June issue of Arteriosclerosis, Thrombosis, and Vascular Biology, is the first to report that exposure to traffic sources of air pollution — diesel exhaust from combustion engines — can alter the protective nature of normal high-density lipoprotein, or HDL, and set in motion biological mechanisms that lead to cardiovascular disease.

Best known for its ability to scavenge harmful “bad” cholesterol from blood vessels and excrete it from the body, HDL is also an antioxidant powerhouse. Set against bad cholesterol — low-density lipoprotein or LDL — HDL blocks oxidation, a process that induces inflammation in the blood vessels and leads to the hardening of arteries, explained Rosenfeld, professor of environmental and occupational health sciences. But that’s not all. An additional virtue of HDL’s “goodness” lies in its ability to prevent inflammation caused by white blood cell patrols honing in tissues antagonized by air pollution particulates.

All of this adds up. Scoring high levels of HDL in blood tests at the doctor’s office has generally been accepted as protective against cardiovascular disease. Higher levels of HDL mean less risk of heart attack and stroke. That is, until now.

Researchers found that exposure to diesel exhaust led to the loss of the anti-oxidant and anti-inflammatory properties of the HDL.

“It turned the good cop into a bad cop,” said study co-author Timothy Larson,   91̽��professor of environmental and occupational health sciences.

HDL normally performs protective functions, but if the molecules are exposed to pollution, they lose their protective quality.

In the arm of the study completed at the UW, mice were exposed to diesel exhaust over a two-week period at levels comparable to those we encounter everyday. The lab is one of the few in the country that can accurately simulate ambient air pollution exposures in a controlled environment. Results of the mice’s exposure were compared to a control group that received only clean filtered air. In a second experiment, a third group was exposed to diesel exhaust for two weeks and filtered air for an additional week. Researchers wanted to assess whether a week was sufficient time for the HDL to return to normal.

“What was really surprising: the one week of recovery time was not sufficient,” said Rosenfeld, who is also a 91̽��professor of pathology. “This has some pretty significant implications for how exposure to air pollution can impact development of cardiovascular disease. Even short-term exposures to pollution can have pretty long-term effects.”

The National Institute of Environmental Health Sciences, one of the National Institutes of Health, supported the research through grant number R01 ES016959/ES/NIEHS.