Translational Research


Puzzling It Out

Symposium examines cluster randomized trials

Suppose you’d like to determine if a new hand sanitization product is a better choice for hospitals than the product in standard use. A randomized trial is in order. But what is the best way to randomize the interventions?

Randomizing the patients—those whose outcomes will be measured to see if, say, infection rates fall because of the new product—are not a good choice; they won’t be using the products.

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The hospital staff members who will be using it seem a better choice, but there is no practical way to be sure they use the appropriate sanitizer as they move around the hospital.

Enter the cluster randomized trial (CRT), a study design that randomizes clusters of individuals to receive one intervention or another. In this case, a CRT could randomize hospitals to use one or the other product.

The simplicity ends there, said Barbara Bierer, Harvard Medical School professor of medicine (pediatrics) at Brigham and Women’s Hospital who spoke at a symposium examining the issues on Nov. 3 called “Cluster Randomized Trials: Ethics, Regulations, Statistics and Design.”

Held at the Joseph B. Martin Conference Center, the event brought together experts to discuss the complexities of CRTs with an audience equally split between investigators, statisticians and institutional review board (IRB) members.

The event, sponsored by Harvard Catalyst | The Harvard Clinical and Translational Science Center, kicked off what Bierer described as an ongoing conversation.

“We’re here to figure out the issues and spend time together now and in the future addressing them,” Bierer said.

Subject Matters

Among the big questions were concerns about ethics, particularly regarding questions around who can be a research subject and who must give consent to participate in a cluster randomized trial. Take the hand sanitizer example, said Holly Fernandez Lynch, executive director of the Petrie-Flom Center for Health Law Policy, Biotechnology and Bioethics at Harvard Law School.

“Do hospital staff members need to consent? Are patients involved in the research?” she asked.

Answers to these questions vary depending on the individuals in the cluster, the intervention in question and how the two intersect. It may not be necessary to obtain consent from patients who are visiting doctors participating in hand sanitation research, for example. In contrast, an intervention in an emergency room that directly affects every patient who visits that ER would require patient consent.

But ER patients cannot give consent in advance, since anyone can walk through the doors of an ER. Nor can they consent if they are incapacitated by a medical emergency. In this case, consent should be obtained as early as possible.

“If you’re doing something to someone that you wouldn’t do but for the research, you get consent,” — Holly Fernandez Lynch

“It’s important to consider the public trust in research,” said Michele Russell-Einhorn, vice president of oncology services for the Central Oncology Review division of Schulman IRB.

“When you’re randomizing health professionals or facilities and patients don’t know they’re involved, you run into concerns: ‘No one told me; you used my data without permission.’ It’s important to think about this in advance,” she said.

Both Lynch and Russell-Einhorn referred to the “but for” test as a way to determine who needs to be asked for consent.

“If you’re doing something to someone that you wouldn’t do but for the research, you get consent,” said Lynch. “We really have to home in on who counts as a subject because this is who we have to get consent from.”

Lynch and Russell-Einhorn also directed researchers to recent recommendations that have come from advisory groups interested in the ethics and regulations related to CRTs: The Ottawa Statement on the Ethical Design and Conduct of Cluster Randomized Trials was developed by bioethicists funded by the Canadian government and lists 15 principles of CRTs.

The U.S. Department of Health and Human Services Secretary’s Advisory Committee on Human Research Protections (SACHRP) also recently published recommendations regarding CRTs.

Calculating Concerns

The design of a CRT also raises important and complicated questions about statistical analysis. In one example, Michael Hughes, professor of biostatistics at the Harvard T. H. Chan School of Public Health, presented the design of a cluster randomized tuberculosis prevention trial called PHOENIx (protecting households on exposure to newly diagnosed Index multidrug-resistant tuberculosis patients). In the trial, individuals at high risk of contracting tuberculosis, and sharing a household with an individual with multi-drug resistant TB, were given one of two preventive drugs. In this trial, each household forms a cluster because study subjects in the same household receive the same drug.

One design challenge Hughes grappled with was intra-cluster correlation — the idea that people within a cluster tend to be more similar to one another than those in different clusters.

This is possible in any cluster, but in this trial, the similarities stem from the fact that people in the same household will be frequently exposed to the same pathogen, which could be more or less virulent than in other clusters.

They are also exposed to the same household conditions, which could be more or less conducive to infection. In addition, household members could influence one another to take the drug or to skip it.

The likelihood that outcomes will be more similar within a cluster must be factored into statistical analyses and in study design.

“With intra-cluster correlation, you have less information compared to a trial with randomized individuals, so you need more clusters to get the same power as an individually randomized clinical trail,” said Hughes. “There is an inflation factor.”

Such considerations add time to the design process.

“PHOENIx took five years to develop, with cluster issues contributing to a significant amount of the complexity,” said Hughes. “My idea of fun is getting the study designed nicely so that the data is super simple. It’s important to get statisticians involved early.”

“From the beginning,” added Rebecca Betensky, professor of biostatistics at the Harvard Chan School and a symposium moderator. “It’s better science to involve statisticians from the beginning to help with design.”

Investigators must also worry about clusters interfering with one another, a phenomenon called cross-contamination.

For instance, Rui Wang, HMS assistant professor of medicine at Brigham and Women’s, presented a community randomized HIV prevention trial in Botswana in which she randomized villages to receive either an HIV prevention intervention or standard care. She found out, however, that sexual networks crossed between villages and, therefore, between her clusters.

“The randomized effect shrinks when participants have partners outside the cluster,” she said.

Wang, who is also assistant professor in the Department of Biostatistics at Harvard Chan School, addressed this by increasing the number of clusters and also by analyzing sexual networks of individuals in the study to get a better sense of their statistical impact.

These examples demonstrate the power of CRTs to enable research interventions that cannot be directed to singularly selected individuals. Yet they also illustrate the complexities involved in conducting such trials ethically and with certainty that they will produce reliable, statistically powerful results.

Even with guidelines and regulations, each study will come with its own puzzles.

“We’re trying to design these studies—and our statisticians are trying to figure out how to analyze them—on the fly,” said Bierer. “It’s an evolution.”


Sweet Math

Scientists devise a more accurate way to gauge blood sugar averages in people with diabetes

Combining the power of advanced math with tests commonly used to measure blood sugar, scientists from Harvard Medical School and Massachusetts General Hospital have created a new model that more accurately accounts for long-term blood sugar fluctuations in people with diabetes. The disease affects more than 422 million people worldwide, according to the World Health Organization and more than 29 million Americans, according to the Centers for Disease Control and Prevention.

By factoring in the age of each patient’s red blood cells, the new method offers a more precise, individualized gauge of three-month blood sugar averages and reduces in half the error rate of the most commonly used — but sometimes inaccurate — test known as A1C. Findings of the study are described Oct. 5 in Science Translational Medicine.

“What we currently deem the gold standard for estimating average blood glucose is nowhere as precise as it should be,” said senior investigator John Higgins, an associate professor of systems biology at HMS and a clinical pathologist at Massachusetts General Hospital. “Our study not only pinpoints the root of the inaccuracy but also offers a way to get around it.”

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The A1C test led to notable off-target estimates in about a third of more than 200 patients whose test results were analyzed as part of the research. The team found these inaccuracies stemmed entirely from individual variations in the life span of a person’s red blood cells.


In a final step, the scientists calculated new, age-adjusted estimates and tested their predictive accuracy by comparing them to actual blood sugar levels measured directly via continuous glucose monitors — wearable devices that read a person’s blood sugar every five minutes. 

Incorporating the new model into existing tests, the researchers said, could lead to more precise diagnosis, monitoring and better-tailored treatments.

Estimating a person’s three-month blood sugar average is the best indicator of disease control and the most accurate predictor of looming complications, according to experts. Persistently elevated blood sugar can, over time, damage the heart, brain, kidneys, eyes, nerves and other organs.

Because blood sugar varies by the hour and even by the minute, capturing “an average” to account for fluctuations over an extended period is a far better indicator of disease status than taking a “snapshot” measurement at one time.

To estimate blood sugar averages, physicians use the A1C test as a proxy. The A1C measures so-called glycated hemoglobin — the amount of sugar soaked up by red blood cells over an extended period of time.

“Like a water-soaked sponge that’s been sitting on the kitchen sink for days, older red blood cells tend to have absorbed more glucose, while newly produced red blood cells have less because they haven’t been around as long,” --John Higgins​

The test, however, is somewhat imprecise. As little as 15 milligrams of glucose per deciliter of blood could signal the difference between high normal values in a person without diabetes and low abnormal values in someone with the disease. The A1C test can lead to identical readings for people with average blood sugar levels that differ by as much as 60 mg/dl. At the same time, people with similar blood sugar levels can end up having widely divergent results. Researchers are not sure what fuels this discrepancy, but the age of red blood cells has recently emerged as a prime suspect.

“Like a water-soaked sponge that’s been sitting on the kitchen sink for days, older red blood cells tend to have absorbed more glucose, while newly produced red blood cells have less because they haven’t been around as long,” Higgins said.

Thus, the researchers said, two people with the same amount of sugar in their blood but could end up with different results on their A1C test depending on the average lifespan of their red blood cells.

To eliminate the influence of age-related variation, the HMS team developed a formula that factors in the life span of a person’s red blood cells. The formula is based on several values, including directly measured glucose levels, and, crucially, on earlier findings by Higgins’ team showing that in each person, the lifespan of red blood cells is tightly regulated, within 1 percent or so. Next, researchers compared the age-adjusted blood sugar estimates to estimates derived from the standard A1C test and then to readouts of glucose levels measured directly by continuous glucose monitors.

The standard A1C test provided values that were significantly off target — by 15 mg/dl or more — in one out of three patients. By factoring in red blood cell age, however, the scientists reduced the error rate to 1 in 10.

For example, using the standard A1c test, one patient’s glycated hemoglobin levels measured at 8.1 percent, leading to an estimated blood sugar level of 186 mg/dl. When the researchers factored in the person’s red blood cell age — 45 days — the estimate went up to 209 mg/dl. Compared with the actual glucose levels measured by a continuous glucose monitor — 210mg/dl — the age-adjusted estimate was off by a mere point. By contrast, the standard estimate was off by 24 points.

Incorporating the age-adjusted formula into current A1C testing approaches would significantly boost the accuracy of glucose estimates, the researchers said. Under the new model, patients could wear a glucose monitor for a few weeks to have their blood sugar tracked as a baseline, also allowing physicians to calculate the average age of a person’s red blood cells before having the monitor removed.

“Physicians treating recently diagnosed patients would immediately know what a patient’s red blood cell age is,” Higgins said. “The patient’s test results can then be adjusted to factor in the red blood cell age and get a result that more accurately reflects the actual levels of blood sugar, allowing them to tailor treatment accordingly.” 


Kaelin Honored with Lasker Award

HMS scientist awarded for pivotal discovery in cells' response to oxygen deprivation

Harvard Medical School Professor of Medicine William G. Kaelin Jr. has been named a recipient of the 2016 Lasker Award for Basic Medical Research from the Albert and Mary Lasker Foundation.  The Lasker is one of the world's most prestigious biomedical research awards.

William Kaelin Jr.  Image: Courtesy Dana-Farber Cancer Institute

Kaelin, based at Dana-Farber Cancer Institute, was cited along with Peter J. Ratcliffe of the University of Oxford/Francis Crick Institute and Gregg L. Semenza of the Johns Hopkins University School of Medicine, for the discovery of the pathway by which cells from humans and most animals sense and adapt to changes in oxygen availability—a process essential for survival.

"Dr. Kaelin is an outstanding physician, scientist and educator," said Barbara J. McNeil, acting dean of Harvard Medical School.  We are very proud of Bill's achievements. I am delighted that his extraordinary dedication, his years of hard work and his remarkable discoveries have been recognized by the Lasker Foundation." 

"Bill Kaelin is an extraordinary researcher and highly deserving of this honor. His work has guided and inspired cancer researchers and caregivers all over the world in understanding the mysteries of cancer," said Edward J. Benz Jr., president and CEO of Dana-Farber.

Kaelin's research explores why mutations in genes known as tumor-suppressor genes can lead to cancer. His study of a tumor-suppressor gene called VHL provided key insights into the body's response to changes in oxygen levels.

Kaelin discovered that VHL helps control the levels of a protein known as HIF, which ratchets up or down the response to low oxygen, such as in the production of red blood cells and new blood vessels.

His subsequent discovery of a molecular switch that renders HIF oxygen-sensitive was critical to the understanding of how cells react to variations in oxygen level.

"The work of this year's honorees epitomizes the power and impact of dedication to rigorous and innovative medical research,” said Claire Pomeroy, president of the Lasker Foundation. “These outstanding advances have illuminated fundamental aspects of life, developed a cure for a deadly disease, and raised public engagement with science."

Kaelin received his medical degree from Duke University in 1982 and was a house officer and chief resident in internal medicine at Johns Hopkins Hospital. He became a medical oncology clinical fellow at Dana-Farber and a postdoctoral fellow in the laboratory of Dr. David Livingston, where he began his studies of tumor suppressor proteins. Kaelin was named an independent investigator at Dana-Farber in 1992 and a Howard Hughes Medical Institute Investigator in 2002.

"The 2016 Lasker winners combined exceptional insight, creativity and perseverance in pursuing crucial questions in medical science," said Joseph L. Goldstein of the University of Texas Southwestern Medical Center and chair of the Lasker Medical Research Awards Jury. Goldstein is a recipient of the 1985 Lasker Award for Basic Medical Research and the Nobel Prize in Physiology or Medicine.

For 71 years, the Lasker Awards, America's most prestigious biomedical research awards, have recognized the contributions of scientists, clinicians and public citizens who have made major advances in the understanding, diagnosis, treatment, cure or prevention of human disease.

Eighty-seven Lasker laureates have received a Nobel Prize, including 41 over the past three decades. The Lasker Awards carry an honorarium of $250,000 for each category. This year’s awards will be presented on Friday, Sept. 23, in New York City.

More details on the Lasker Award recipients, the full citations for each award category, video interviews and photos of the awardees and additional information on the Foundation are available at


Keeping Up with HIV Mutations

New model technology offers nimble AIDS vaccine testing

AIDS vaccines able to fight any HIV strain have thus far eluded science. HIV frequently mutates its coat protein, dodging vaccine makers’ efforts to elicit sufficiently broadly neutralizing antibodies.

Sometimes HIV-infected people can produce such antibodies on their own. But this usually requires years of exposure to the virus, allowing the immune system to modify its antibodies over time to keep up with HIV mutations, and generally occurs too late to prevent infection.

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“Only a small fraction of patients are able to develop broadly neutralizing antibodies, and by the time they do, the virus has already integrated into the genomes of their T-cells,” said Ming Tian, lecturer on genetics at Harvard Medical School and a research associate in the Program in Cellular and Molecular Medicine (PCMM) at Boston Children’s Hospital.

Tian is part of a group led by HMS Professor of Genetics and PCMM Director Frederick Alt that has developed a technology to greatly speed up HIV development.

Described Sept. 8 in Cell, the group’s method generates mouse models with built-in human immune systems. The models recapitulate what the human immune system does, only much more rapidly, enabling researchers to continuously test and tweak potential HIV vaccines.

A souped-up human immune system

People exposed to HIV (or any pathogen) first make precursor antibodies, which then mature via mutation and natural selection—an evolution-like process that makes the antibodies more protective over time.

“This is a long-term process involving many intermediate antibodies, making it very challenging to design HIV vaccines to protect uninfected individuals,” said Alt, who is also the Charles A. Janeway Professor of Pediatrics at Boston Children’s and co-senior author on the paper.

“To facilitate this effort, we wanted to design a new type of humanized mouse model that would be more physiological and allow us to very quickly test new vaccination strategies,” he said.

How do broadly neutralizing antibodies to HIV naturally arise? The team began with the basic components of the known human antibody response to HIV.

Building a diverse immune repertoire

Our immune system’s B lymphocytes assemble antibody genes from building blocks known as V (variable), D (diversity) and J (joining) segments. Through various V-D-J combinations, our B lymphocytes are able to produce enormous numbers of different antibodies—enough to recognize almost any invader.

After a B cell recognizes a pathogen, it further mutates the V-D-J sequence, often in successive steps, enabling its progeny B cells to produce even stronger antibodies.

Prior work had revealed the structure of broadly neutralizing antibodies against HIV and deduced the V-D-J combinations that constituted their precursors. The team inserted the corresponding DNA into mouse embryonic stem cells.

The researchers then used the modified embryonic stem cells to rapidly generate mice whose B cells were primed to assemble a highly diverse set of HIV antibody precursors—combining the human precursor broadly neutralizing antibody V segment with various D or J segments.

An iterative process

The mice began by making immature “ancestor” antibodies. Collaborators at the National Institute of Allergy and Infectious Diseases’ Vaccine Research Center, together with colleagues at the Duke Human Vaccine Institute, the Scripps Research Institute, the Fred Hutchinson Cancer Research Center and other institutes, then sequentially exposed the Alt lab’s test mice to a series of specially designed HIV antigens.

Through this sequential exposure, the animals’ B cells “learned” to produce ever more diverse and effective humanized antibodies that eventually were able to neutralize some HIV viral strains.

“Rather than go through generations of mouse breeding to make models, our approach allows us to quickly delete and replace genomic elements to create changes in B cells,” explained Alt.

“Thus, we can rapidly reprogram this mouse model with the intermediate antibody genes selected from the first successful immunizations and expose them to new antigens,” said Alt. “Over time, we hope this process will lead to the generation of broadly neutralizing HIV antibodies.”

As the engineered antigens engaged the system, upping the ante each time, the researchers could watch the antibodies acquire mutations.

“You move the B cells in a direction and find out what works and the potential hang ups,” said Alt. “You then work to figure out how to next adapt the mouse model and the immunogens to eventually get to a broadly neutralizing antibody stage.”

Speeding up AIDS vaccine development

There’s still a long way to go, but Alt believes the technology could hasten the search for a truly effective HIV vaccine, as well as vaccines against other viruses.

It may also allow researchers to generate highly specific therapeutic antibodies.

“We’re hoping it will be broadly useful,” Alt said.

John Mascola, director of the NIAID Vaccine Research Center, was co-first author of the study. Tian and Hwei-Ling Cheng of the Alt lab and Cheng Cheng, Xuejun Chen and Hongying Duan of the Vaccine Research Center were co-first authors.

The study was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (R01AI077595, AI020047, P01AI094419, U19AI109632), the NIH Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (AI100645, 5UM1AI100645, 1UM1AI100663), the International AIDS Vaccine Initiative Neutralizing Antibody Consortium, the Collaboration for AIDS Vaccine Discovery, the NIAID Vaccine Research Center, the Howard Hughes Medical Institute and the Ragon Institute of MGH, MIT and Harvard.

Adapted from a post on Vector, the clinical and research innovation blog at Boston Children’s.


An Agent of Demise

Scientists identify spark plug that ignites nerve cell damage in Lou Gehrig’s disease

Scientists from Harvard Medical School have identified a key instigator of nerve cell damage in people with amyotrophic lateral sclerosis, or ALS, a progressive and incurable neurodegenerative disorder. 

Researchers say the findings of their study, published Aug. 5 in the journal Science, may lead to new therapies to halt the progression of the uniformly fatal disease that affects more than 30,000 Americans. One such treatment is already under development for testing in humans after the current study showed it stopped nerve cell damage in mice with ALS. 

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The onset of ALS, also known as Lou Gehrig’s disease, is marked by the gradual degradation and eventual death of neuronal axons, the slender projections on nerve cells that transmit signals from one cell to the next. The HMS study reveals that the aberrant behavior of an enzyme called RIPK1 damages neuronal axons by disrupting the production of myelin, the soft gel-like substance enveloping axons to insulate them from injury.

“Our study not only elucidates the mechanism of axonal injury and death but also identifies a possible protective strategy to counter it by inhibiting the activity of RIPK1,” said the study’s senior investigator Junying Yuan, the Elizabeth D. Hay Professor of Cell Biology at HMS.

The new findings come on the heels of a series of pivotal discoveries made by Yuan and colleagues over the last decade revealing RIPK1 as a key regulator of inflammation and cell death. But up until now, scientists were unaware of its role in axonal demise and ALS. Experiments conducted in mice and in human ALS cells reveal that when RIPK1 is out of control, it can spark axonal damage by setting off a chemical chain reaction that culminates in stripping the protective myelin off of axons and triggering axonal degeneration—the hallmark of ALS. RIPK1, the researchers found, inflicts damage by directly attacking the body’s myelin production plants—nerve cells known as oligodendrocytes, which secrete the soft substance, rich in fat and protein that wraps around axons to support their function and shield them from damage. Building on previous work from Yuan’s lab showing that the activity of RIPK1 could be blocked by a chemical called necrostatin-1, the research team tested how ALS cells in lab dishes would respond to the same treatment. Indeed, necrostatin-1 tamed the activity of RIPK1 in cells of mice genetically altered to develop ALS. 

In a final set of experiments, the researchers used necrostatin-1 to treat mice with axonal damage and hind leg weakness, a telltale sign of axonal demise similar to the muscle weakness that occurs in the early stages of ALS in humans. Necrostatin-1 not only restored the myelin sheath and stopped axonal damage but also prevented limb weakness in animals treated with it.

“It was as if we saw the chemical footprints of cell death left behind by RIPK1 and its recruits,” - Junying Yuan

Connecting the Dots

At the outset of their experiments, investigators homed in on a gene called optineurin  (OPTN). Past research had revealed the presence of OPTN defects in people with both inherited and sporadic forms of ALS, but scientists were not sure whether and how OPTN was involved in the development of the disease. To find out, researchers created mice genetically altered to lack OPTN. Examining spinal cord cells under a microscope, the scientists noticed that the axons of mice missing the OPTN gene were swollen, inflamed and far fewer in number, compared with spinal cord cells obtained from mice with the OPTN gene. These axons also bore signs of myelin degradation. Strikingly, the researchers noticed the same signs of axonal demise in spinal cord cells obtained from human patients with ALS. Mice with OPTN deficiency also exhibited loss of strength in their hind legs. Further experiments revealed that lack of OPTN was particularly harmful to myelin-secreting cells. Thus, the researchers concluded, OPTN deficiency was directly incapacitating the nervous system’s myelin factories. But one question remained: How did the absence of OPTN damage these cells?

A Smoking Gun

Looking for the presence of chemicals commonly seen during inflammation and cell death, the researchers noticed abnormally high levels of RIPK1—a known promoter of cell death—in spinal cord cells from mice lacking OPTN. Moreover, the scientists observed traces of other damaging chemicals often recruited by RIPK1 to kill cells.

“It was as if we saw the chemical footprints of cell death left behind by RIPK1 and its recruits,” --Junying Yuan

That observation, Yuan added, was the smoking gun linking RIPK1’s misbehavior to OPTN deficiency. In other words, researchers said, when functioning properly, the OPTN gene appears to regulate the behavior of RIPK1 by ensuring its levels are kept in check, that it is broken down fast and that it is cleared out of cells in a timely fashion. In the absence of such oversight, however, RIPK1 appears to get out of control and cause mischief.

In a closing set of experiments, the researchers examined neurons obtained from mice with the most common inherited form of ALS, one caused by mutations in a gene called SOD1. Indeed, RIPK1 levels were elevated in those cells too. Thus, the investigators said, OPTN may not be the sole gene regulating RIPK1’s behavior. Instead, RIPK1 appears to fuel axonal damage across various forms of inherited and acquired forms of ALS. The findings suggest that RIPK1 may be involved in a range of other neurodegenerative diseases marked by axonal damage, including multiple sclerosis, certain forms of spinal muscular atrophy and even Alzheimer’s disease.

The Harvard Office of Technology Development (OTD) and collaborating institutions have developed a patent portfolio for RIPK1 modulating compounds. Harvard OTD has licensed the patent to a biotechnology company.

The work was supported in part by grants from the National Institute of Neurological Disorders and Stroke (1R01NS082257) and the National Institute on Aging (1R01AG047231), by the National Science and Technology Major Project of China (2014ZX09102001-002) and the State Key Program of the National Natural Science Foundation of China (31530041).



Cracking the Wall

Scientists discover new bacterial cell wall builders—and a target for antibiotic development

Harvard Medical School scientists have identified a new family of proteins that virtually all bacteria use to build and maintain their cell walls.

The discovery of a second set of cell wall synthesizers can help pave the way for much-needed therapies that target the cell wall as a way to kill harmful bacteria, said study leaders David Rudner and Thomas Bernhardt.

Findings of the research are published Aug. 15 in Nature.

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“We know these proteins are a great target because they are enzymes we can inhibit from the outside of the cell,” said Rudner, senior author of the paper and HMS professor of microbiology and immunobiology.

“Now we have a better handle on what these proteins do and how a potential drug might affect their activity,” said Bernhardt, the paper’s co-author and HMS professor of microbiology and immunobiology.

The cell wall plays a critical role in maintaining a bacterium’s structural integrity, dictating its shape and warding off external assaults from toxins, drugs and viruses.  The cell wall is made of chains of sugars linked together by short peptides.

For half a century, penicillin-binding proteins—molecules named for the drug that disables them—were thought to be the major, perhaps only, cell wall synthesizers.

“Now we have a better handle on what these proteins do and how a potential drug might affect their activity.” — Thomas Bernhardt. 

Penicillin was discovered in 1928 and first used to treat bacterial infections in 1942, but it wasn’t until 1957 that scientists understood how penicillin blocked the proteins that build the cell walls of bacteria. Research in the 1970s and 1980s on the bacterium Escherichia coli fleshed out the mechanism by which penicillin-binding proteins build the cell wall.

Clues that other players may be involved in cell wall biogenesis emerged later. A crucial discovery, made in 2003, was overlooked by many in the field: The bacterium Bacillus subtilis was capable of growing and synthesizing its cell wall even in the absence of penicillin-binding proteins. Some researchers were tantalized by the “missing polymerase,” sometimes called the “moonlighting enzyme.”

Tsuyoshi Uehara, former HMS research fellow in the Bernhardt lab and co-author of the paper, was one of those scientists. He thought a family of proteins responsible for a cell’s shape, elongation, division and spore formation, or SEDS proteins in scientific shorthand, might be prime suspects for the missing enzyme. SEDS proteins move around the circumference of the bacterial cell in a manner suggesting they might be involved in synthesizing the wall, and, if inactivated, perturb cell wall synthesis.

Testing the hypothesis

To test the hypothesis that SEDS proteins may be involved in cell wall synthesis, Alexander Meeske, HMS graduate student in the Rudner lab and the paper’s first author, deleted all the known penicillin-binding proteins involved in polymerizing the cell wall. Yet, SEDS proteins continued to move in much the same way as they always had. The observation made SEDS proteins look like the missing enzymes and more like major players than mere moonlighters.

Later experiments, both genetic and biochemical, confirmed that SEDS proteins are indeed a completely new family of cell wall synthesizers.

The scientists also showed that the two families of cell wall synthesizers could work in tandem: While SEDS proteins circumnavigate the cell wall making hoop-like structures, penicillin-binding proteins move diffusely, making smaller strands that, together with the hoop-like strands, build the cell wall.

Earlier studies showing that bacteria died when the penicillin-binding proteins were blocked obscured the importance of SEDS proteins, the researchers said.

In the current paper, the scientists found that SEDS proteins are more common in bacteria than are the penicillin-binding proteins, raising hopes that a potential antibiotic targeting SEDS proteins could be effective against a broad spectrum of bacteria.

“That’s what makes this so exciting. In this modern era of sequenced genomes, we’re still discovering new enzymes that work in this pathway.”— David Rudner

“For a long time in the field, it was thought that one set of enzymes worked in one set of complexes to build a wall. Now we have two sets of enzymes appearing to work in different systems,” Bernhardt said. “Somehow they have to coordinate to build this netlike structure that maintains integrity and expands as the cells grow and divide.”

How the two families of proteins work together is just one of many questions raised by the new work.

“Even though the history goes all the way back to the 1920s with penicillin, there’s plenty to learn,” Bernhardt said.

“That’s what makes this so exciting,” Rudner said. “In this modern era of sequenced genomes, we’re still discovering new enzymes that work in this pathway.”

This work was supported by the National Institutes of Health grants GM073831, RC2 GM092616, AI083365 and AI099144; and CETR grant U19AI109764.

Co-investigators included Eammon Riley, William Robins, John Mekalanos, Daniel Kahne, Suzanne Walker and Andrew Kruse. All six Harvard labs are participants in a Centers of Excellence for Translational Research (CETR) grant.


Obesity, Insulin Resistance Focus of 2015 Dunham Lectures

Cambridge Professor Sir Stephen O’Rahilly to be guest speaker 

Obesity and its associated health risks are a major health care concern in the U.S.  More than 78 million American adults are considered obese, with a growing number of American children affected as well, according to the National Heart, Lung, and Blood Institute.

In 2013, NHLBI statistics indicated that about 17 percent of U.S. children and adolescents between the ages of 2 and 19 were obese—one in six. Obesity can lead to increased rates of heart disease, type 2 diabetes, high blood pressure and certain cancers.

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Sir Stephen O’Rahilly, professor of clinical biochemistry and medicine at the University of Cambridge and an authority on human obesity and insulin resistance, will be a guest lecturer at the 2015 Dunham Lecture Series at Harvard Medical School on April 6 and 7.

Sir Stephen O'Rahilly will be the guest speaker at the 2015 Dunham Lectures at HMS.  Image: Academy of Medical Sciences

O’Rahilly is director of the University of Cambridge Metabolic Research Laboratories, co-director of the Institute of Metabolic Science and director of the MRC Metabolic Diseases unit. 

A member of the Academy of Medical Sciences and the Royal Society, O’Rahilly is one of the United Kingdom’s most renowned clinical researchers. He is widely known for combining research into the causes of obesity and insulin resistance with clinical practice.

“I have a long-standing interest in the aetiology and pathophysiology of human metabolic and endocrine disease and how such information might be used to improve diagnosis, prognostication, therapy and prevention,” O’Rahilly says on his Cambridge lab website.

According to his nomination to the Royal Society in 2003, O’Rahilly’s “work first established that mutations in a single gene could result in severe human obesity and that these defects largely acted through disruption of central satiety mechanisms.”  He was knighted in 2013 for his service to medical research.

O’Rahilly’s 60-minute lecture on Monday, April 6, is entitled “Human Obesity as a Neurobehavioral Disorder: Lessons from Human Genetics.”  The lecture will take place in the Joseph B. Martin Conference Center from 4 to 5 p.m. with a reception to follow.

The hour-long Tuesday, April 7, lecture is entitled “Mechanisms of Human Insulin Resistance,” and it will take place from noon to 1 p.m. in the Martin Conference Center at 77 Avenue Louis Pasteur.

Both lectures are free and open to students, faculty and staff of HMS and Harvard University, as well as other interested professionals. Seats are available on a first-come, first-served basis. 

Those planning to attend may RSVP to by April 1, indicating which lectures they will attend.

The prestigious Dunham Lecture Series was inaugurated at HMS in 1923, established by Mary Dows Dunham in honor of her late husband, Edward Kellogg Dunham (Harvard 1886), to strengthen the bonds of fellowship and understanding among students, investigators and faculty within the medical and basic sciences, for the purpose of advancing medical science in the broadest sense.

Twenty-eight of the 78 biomedical researchers who have been honored with a Dunham lectureship have been Nobel laureates.






New Department of Biomedical Informatics

Power of big data leveraged for biomedical research 

Following a multiyear process of self-reflection and review, Jeffrey S. Flier, Dean of Harvard Medical School, has announced the establishment of a new Department of Biomedical Informatics (DBMI). It will officially become a Quad-based department on July 1, 2015.

Isaac “Zak” Kohane, co-director of the HMS Center for Biomedical Informatics, director of the Countway Library of Medicine and the HMS Lawrence J. Henderson Professor of Pediatrics at Boston Children’s Hospital, will be the department’s inaugural chair.

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“The field of biomedical informatics has its roots in a half century of academic development, in which Harvard has played a prominent role since its earliest days,” Flier said in a letter to the community.

“The field represents two converging communities: one involving health care-related data, and the other addressing the study of health and disease at a molecular and naturally occurring systems level, " he said, adding, "These two communities are jointly focused on new methods for the capture, representation, storage and analysis of big biomedical data and knowledge. Successful implementation of precise and individualized medical care will require the development of a new generation of informatics tools to guide clinicians in applying this rapidly growing base of biomedical knowledge.”

Isaac Kohane. Rose Lincoln/Harvard Staff PhotographerThe new department evolved out of the HMS Center for Biomedical Informatics (CBMI), which was founded in 2005. Led by Kohane and Alexa McCray, HMS associate professor of medicine at Beth Israel Deaconess Medical Center, CBMI has developed an international reputation.

In 2014, the center brought in an array of federal grants that have established large collaborations with researchers on the Quad, at affiliated hospitals and at the Harvard University Faculty of Arts and Sciences.

“Based on the increasing impact of the field and the tremendous success of CBMI, we have concluded that biomedical informatics is a field now ready for full academic recognition as a new appointing department at HMS,” Flier said.

The department will launch with five core faculty members now associated with CBMI, with recruits added over the upcoming years to achieve representation from across the field.

Kohane will also chair an executive committee, with membership drawn from leaders in biomedical informatics at HMS-affiliated institutions. The committee will eventually review and recommend primary and secondary appointments to the department across the faculty.

Mastering the surge in biomedical data streams goes beyond storage and computation. It includes developing and applying new methods for both research and clinical care.

Central to the department’s mission will be creating a way to address methodological, engineering and educational challenges. CBMI already has a strong history of education through its involvement in master’s- and doctoral-level programs. The new department will continue to expand this commitment to education.

“Biomedical informatics has the potential to transform biomedical research and human health in ways that we could not have imagined only a few years ago,” said Flier.

“I am excited to launch this new department, and I’m grateful to Provost Alan Garber, HMS preclinical department chairs, affiliated hospital leaders, and the external advisory group who worked with our HMS team, to evaluate how such a department could most effectively advance the ambitious research and clinical missions of our School,” Flier said.

Members of the Harvard Medical School Biomedical Informatics Advisory Group are Edward Frymoyer, president of Frymoyer Holdings, Inc.; Jeff Hammerbacher, founder and chief scientist of Cloudera; Gilbert Omenn, director of the center for computational medicine and  at the University of Michigan; Jim Reese, former chief operations engineer and “head neurosurgeon” at Google, Inc.; and Halle Tecco, cofounder and managing director of Rock Health. 



Bridging the Gap

TransMed course applies translational solutions to unmet medical needs

The music was so loud Eileen Sun could feel the drums thrumming in her chest. With a dozen fellow students, she was witnessing a traditional healing ceremony in rural South Africa, part of fieldwork for TransMed, a Harvard Medical School summer course on translational medicine offered through the HMS Office of Global Programs.

The healers danced, calling on spirits to help their patients. They presented scarves in vibrant colors to their guests before sharing a feast with them—one for which a cow had been sacrificed earlier in the week.

Sun saw firsthand how TransMed’s hosts at Edendale Hospital in KwaZulu-Natal were bridging the gap between Western medicine and traditional healing. In the countryside, the healers are the first choice for many people when they fall ill.

In a region where 37.4 percent of the population lives with HIV infection, these healers have been enlisted by a nonprofit program at the hospital, iTEACH (Integration of TB in Education and Care for HIV/AIDS), ), run by Krista Dong,  HMS lecturer on medicine at Massachusetts General Hospital, to refer people to physicians for testing and, if the results are positive, to encourage them to take antiretroviral medications.

It took respectful relationship building to bridge the gulf between traditional and modern medicine. Sun saw a similar spirit of collaboration in FRESH (Females Rising through Empowerment, Support, and Health). The program enrolls young women when they are at highest risk for HIV infection in a study that screens their blood samples for potential infection and in exchange offers them education and employment skills training. The project is a collaboration with the Ragon Institute of MGH, MIT and Harvard.

“Behind each sample, there’s a story,” said Sun, a doctoral student studying RNA viruses at Harvard’s Program in Virology and in the Leder Human Biology and Translational Medicine Program. “The trip opened up a whole new dimension to how I’ve viewed scientific research. We saw firsthand how weaving science with a social mission—women’s empowerment—can be life changing for both researchers and research participants. The trip was inspirational.”

TransMed students joined their hosts after a traditional healing ceremony in KwaZulu-Natal, South Africa.  Image: iTEACH

The students’ trip to South Africa followed two weeks of boot camp-style classes at HMS.

The mission of the course: to teach students how to assess unmet medical needs, follow the discovery process that uncovers the causes of disease, and examine how disease is detected, diagnosed and treated.

On the HMS Quad, students learned about the gap between basic discoveries and approved therapies. “The valley of death” is a term used in drug development for the abyss where promising drug leads can languish, never reaching the people they were intended to help.

The TransMed course brought in experts from the biotech and pharmaceutical industries who had traversed that chasm. They shared their stories in the inaugural session of a course that its director, Jagesh Shah, hopes will be repeated next summer.

It all started with identifying unmet medical needs.

“The basic scientists, the clinicians, the industry people and the regulatory people—every single one of these groups has a very different view of what an unmet medical need is,” said Shah, HMS associate professor of systems biology. “That was a design principle of the course.”

Compressed into three weeks, 24 students learned how disease mechanisms are discovered and how the drug discovery pipeline is primed to treat them. Students came not only from Harvard but also from China, South Africa and Zimbabwe.

On the Quad, the students rotated through four perspectives—basic scientist, clinician, industry professional or regulatory scientist—as they learned about three drugs (statins, Vioxx and Gleevec) and two diseases (Alzheimer’s and polycystic kidney disease).

The course also addressed how drug resistance, a well-known problem in infectious disease as well as cancer, plays out differently depending on where the patient lives.

Don Coen, HMS professor of biological chemistry and molecular pharmacology, led the discussion during a session in which HMS faculty presented cases on drug resistance, including one presented by Jonathan Li, HMS assistant professor of medicine at Brigham and Women’s Hospital, on drug-resistant mutations in the virus that causes AIDS. Certain of these mutant viruses are resistant to some older HIV drugs, but have decreased ability to replicate in the body.

The students from Africa pointed out that those older drugs are still used there because newer ones are not available for doctors to prescribe.

“Even though the viruses will evolve to be resistant to these drugs, the patient will be less ill than if you didn’t do anything, largely because of the decreased replication. In this country you would use newer combinations of drugs,” Coen said. “These drugs are clearly being used in the developing world setting. So in this course, we got the different perspectives of people on the ground in Africa, which was really enlightening.”

Felix Manyeruke, a physician from Zimbabwe who plans to specialize in respiratory medicine, sought out the course to explore translational medicine and the role of clinicians doing basic science and clinical research in developing countries.

“I learnt how we as clinicians should be involved in identifying clinical problems and how we can interact with researchers in basic sciences and engineering to be able to come up with a solution which can be used to benefit the patient,” he said in an email interview. “Patient advocacy was one new area which I was exposed to and I got to appreciate its value in driving drug development and drug regulation.”

Shah, the course director, said all the students are hungry to learn what they can do to advance drug discovery and diagnostic tool development to help patients wherever they live.

“We think about making more drugs that work, but actually if we didn’t make as many drugs that didn’t work, we would also save a lot of money,” said Shah, who favors borrowing “failure analysis,” a method widely used in engineering disciplines to learn from mistakes.

The TransMed course itself was an experiment.

“Strictly speaking, in three weeks, no one’s an expert,” Shah said. “But at the end, the students told us in their assessments that they had a better sense that the path for each drug is slightly different, but each study of how it works is an important scientific problem unto itself.”

Sun, who is in her sixth year as a doctoral student in virology, said TransMed is pushing her closer to translational research.

“Having participated in the TransMed class, I’m motivated more than ever to pursue research that will change people’s lives.”

The HMS TransMed program was supported by the Office of Global Programs and the Paul Dudley White Fund. The TransMed Global Component was facilitated by the Ragon Institute of MGH, MIT and Harvard and the HIV Pathogenesis Programme at Nelson R. Mandela School of Medicine at the University of Kwa-Zulu Natal (UKZN) in Durban, South Africa Co-Directors of Global Component are Filippos Porichis, instructor in medicine at Mass General, (Boston) and Victoria Kasprowicz, instructor in medicine at Mass General (Durban).


New Immunotherapy Breakthrough

Novel approach to battling cancer sees striking success in Hodgkin lymphoma patients

Image: iStock

A therapy that liberates the immune system to attack cancer cells drove Hodgkin lymphoma (HL) into complete or partial remission in fully 87 percent of patients with resistant forms of the disease who participated in an early-phase clinical trial, Harvard Medical School investigators at Dana-Farber Cancer Institute and partnering institutions report in a study published in the New England Journal of Medicine and also presented at the annual meeting of the American Society of Hematology (ASH) in San Francisco.

The results provide some of the most dramatic evidence to date of the potential of therapies that increase the ability of the immune system to kill cancer cells. While clinical trials of such immunotherapies in other cancers have shown them to be highly effective in a subgroup of patients, the new study stands out because nearly all patients benefited from the treatment.

The success of the agent, nivolumab, in this study has prompted the U.S. Food and Drug Administration to designate it a “breakthrough therapy” for treating relapsed HL, and a large, multinational Phase 2 trial is now under way.

“What makes these results especially encouraging is that they were achieved in patients who had exhausted other treatment options,” said the study’s co-senior author Margaret Shipp, HMS professor of medicine and chief of Division of Hematologic Neoplasia at Dana-Farber. “We’re also excited by the duration of responses to the drug: The majority of patients who had a response are still doing well more than a year after their treatment.”

The study involved 23 patients with relapsed or treatment-resistant HL, a cancer of white blood cells called lymphocytes. Although relatively uncommon—with fewer  than 10,000 new cases each year in the U.S.—it is one of the most frequent cancers in children and young adults. While the disease can often be treated successfully with current therapies, up to a quarter of all patients eventually have a relapse.

In the current study, almost 80 percent of the patients had undergone a previous stem cell transplant. More than a third had received at least six prior lines of therapy without lasting success.

The patients received biweekly infusions of nivolumab, which is an antibody that blocks a protein called PD-1 on the surface of immune system T cells. T cells are key actors in the body’s defenses, identifying foreign or diseased cells and leading an assault on them. But when PD-1 binds to proteins called PD-L1 and PD-L2 on the surface of certain cancer cells, the T cells essentially become paralyzed: The immune attack on cancer is called off. By blocking PD-1, nivolumab allows the attack to proceed.

“This is a treatment that, rather than targeting cancer cells themselves, targets the immune response, reactivating the T cells in the neighborhood of the tumor cells,” Shipp remarked.

Twenty of the 23 patients had a measurable response to the treatment, with four achieving a complete response—in which no detectable tumor was left – and 16 having a partial response—in which their tumors shrank to less than half their original size. Six months after completing therapy, 86 percent of the patients were alive with continued responses. Most patients continue to do well a year after their treatment.

Side effects mirrored those that have occurred in tests of nivolumab in patients with solid tumors. About 20 percent experienced a serious treatment-related adverse effect but none was life-threatening.

The approach to immunotherapy embodied in nivolumab is a legacy of work at that began in the 1980s. HMS associate professor of medicine at Dana-Farber Gordon Freeman and Arlene Sharpe, the HMS George Fabyan Professor of Comparative Pathology, did some of the original research that resulted in the identification of PD-1 on T cells, as well as the PD-L1 and -L2 protein “ligands” on tumor cells.

“Their work was critical to our understanding that the increased presence of PD-L1 and -L2 on some tumor cells may allow those cells to escape attack from the immune system,” Shipp said.

Freeman and Sharpe’s work dovetailed with Shipp and her colleague’s own research into the genetic features of HL. “We found that Hodgkin lymphoma tumor cells frequently have an extra region of a specific chromosome that causes an increased production of the two ligands—PD-L1 and PD-L2—in the PD pathway,” Shipp said. “This characteristic genetic alteration suggested that inhibiting the PD-1 pathway might be particularly effective in this disease.”

Shipp and her co-authors offer two possible explanations for the high response rate to nivolumab in this study. One has to do with the sparse nature of HL. “Hodgkin lymphoma is unusual among cancers in that it consists of a small number of tumor cells in a sea of inflammatory cells and immune system cells, including T cells that don’t work very effectively.” Shipp observed. “Activating those T cells may create a very strong response to a relatively small number of cancer cells.” Another related possibility is the genetic trait that causes HL cells to produce an abundance of PD-L1 and PD-L2 ligands makes the tumor particularly vulnerable to PD-1 blockade.

For the investigators involved in the research, the results, though obtained in a relatively small, phase 1 trial, are compelling. “For someone like myself, in this kind of work, this is the kind of result that you get to see once in your career,” said study co-senior author Philippe Armand, HMS associate professor of medicine and medical oncologist in the Hematologic Oncology Treatment Center at Dana-Farber.

The study was supported by Bristol Myers Squibb, National Institutes of Health grants R01CA161026, U54CA163125 and P01AI056299 and with support from the Miller Family Fund to the Shipp laboratory.

Adapted from a Dana-Farber news release.