Global view of blood cell development reveals new and complex circuitry

Global view of blood cell development reveals new and complex circuitry

A small pool of stem cells replenishes the human body with about 200 billion new blood cells daily. But the elaborate circuitry that determines if a cell will develop into a T cell, red blood cell, or one of the nine or more other blood cell types remains largely unknown. A research team led by scientists from the Broad Institute and Brigham and Women's Hospital has taken a systematic approach to help decipher this circuitry, compiling a comprehensive catalog of the factors that determine a blood cell's fate. Their work appears in the January 21 issue of Cell.

The researchers found that blood cells are directed by a multitude of transcription factors, proteins that turn on and off genes. While many previous studies have focused on individual transcription factors or types of blood cells, this study examined the expression and regulation of all transcription factors throughout blood development. The findings point to densely, interconnected circuits that control this process, suggesting that the wiring for blood cell fate is far more complex than previously thought.

"One assumption in the field had been that there are a small number of transcription factors that orchestrate this process," said Aviv Regev, a Broad Institute core member and co-senior corresponding author of the study. "Some people have always thought there would be a lot of factors and that it would just take time to find them. It turns out there are more masters than we would have thought."

The researchers looked globally at how the expression of all 20,000 or so genes in the genome change as blood stem cells become specialized cell types (a process known as differentiation). They discovered that while a small fraction of genes are uniquely expressed in a single type of cell, other genes are more broadly expressed — present in a variety of cell types but at varying levels. Some of these genes are turned on in the blood stem cells and switched off at certain points in development while others are reused in several parallel developmental branches. The researchers found about 80 of these patterns of variable genes, called modules. Each kind of specialized cell has a unique profile, or combination, of these modules.

Looking at the genes modulated in the course of healthy cell development could give researchers clues about what events lead to blood cancers, such as leukemia, a disease where differentiation has gone wrong.

"When you look at leukemia cells beneath a microscope, they have a lack of differentiation and they look abnormal," said Broad associate member Ben Ebert, an associate physician of hematology at Brigham and Women's Hospital and a senior corresponding author of the study. "They've ended up in a place that doesn't exist in normal development." Now that the researchers have a clearer picture of the modules that normal cells exhibit, they can apply this knowledge to help identify the similarities and critical changes in leukemia cells' profiles.

"Leukemia cells have the same set of building blocks as normal blood cells – some, they keep the right way so a piece of the profile is right, and a piece of the profile is wrong," said Regev, who is also an assistant professor in the department of biology at MIT and an Early Career Scientist at Howard Hughes Medical Institute.

The research team included co-first author Noa Novershtern from the School of Computer Science at the Hebrew University of Jerusalem, co-first author Aravind Subramanian in Todd Golub's laboratory at the Broad, and Lee Lawton and other collaborators in Richard Young's laboratory at the Whitehead Institute. All of their results will be made publicly available online through a database known as the Differentiation Map Portal (or D-Map). Ebert, Regev and their colleagues intend for D-Map to be a starting point for other researchers, empowering their investigations into the biology of blood cells as well as leukemia and other human diseases.

"Already, many people are asking for the data. Other groups can now combine their data with ours to ask new questions," said Novershtern. "What's also exciting is that people can see the power of computational models, tools that can be used to find new biological insights from the data."

A pesky bacterial slime reveals its survival secrets

A pesky bacterial slime reveals its survival secrets

January 7, 2011

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Slimy bacterial coatings known as biofilms (Bacillus subtilis colony superimposed at center) exhibit an unmatched ability to repel a wide range of liquids and even vapors. An electron microscope image shows the biofilm surface's resilient meshwork made from proteins and polysaccharides and assembled into a multiscale, hierarchical structure. Credit: Courtesy of the laboratory of Joanna Aizenberg, Harvard School of Engineering and Applied Sciences.

By rethinking what happens on the surface of things, engineers at Harvard University have discovered that Bacillus subtilis biofilm colonies exhibit an unmatched ability to repel a wide range of liquids -- and even vapors.

Centimeters across yet only hundreds of microns thick, such slimy bacterial coatings cling to the surfaces of everything from pipes to teeth and are notoriously resistant to antimicrobial agents. The researchers now suspect they know the secret to a biofilm's resiliency.

Published in the January 5th early edition of the Proceedings of the National Academy of Sciences (PNAS), the study holds promise for both creating bio-inspired non-wetting materials and developing better ways to eliminate harmful biofilms that can clog pipes, contaminate food production and water supply systems, and lead to infections.

"By looking at biofilms from a materials perspective rather than a cellular or biochemical one, we discovered that they have a remarkable ability to resist wetting to an extent never seen before in nature," says lead author Alex Epstein, a graduate student at the Harvard School of Engineering and Applied Sciences (SEAS). "In fact the biofilm literally resisted our initial efforts to study it."

The finding came about serendipitously, as the original intention of the researchers was to study the structure of the biofilm. To image the interior of the biofilm, the team had to soak it with liquids such as ethanol and acetone, which normally spread and seep easily into a surface.

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Four drops of ethanol solution placed on a Bacillus subtilis biofilm colony, the light-colored film on top of the sectioned agar gel, bead up instead of readily wetting and seeping in. This macroscopic phenomenon reveals a critical clue to what may be responsible for biofilms' broad antimicrobial resistance. Credit: Courtesy of the laboratory of Joanna Aizenberg, Harvard School of Engineering and Applied Sciences

"But to our surprise, it was impossible. The liquids kept beading up on the surface and wouldn't infiltrate the colonies," says Epstein, who is a member of the laboratory of Joanna Aizenberg, Amy Smith Berylson Professor of Materials Science at SEAS; Susan S. and Kenneth L. Wallach Professor at the Radcliffe Institute; and a core member of the Wyss Institute for Biologically Inspired Engineering at Harvard.

As the Aizenberg lab studies materials and wetting, the engineers immediately recognized the significance of what they were observing. It turns out that biofilm has an unprecedented liquid-repellent surface, thereby revealing a critical clue to what may be responsible for its broad antimicrobial resistance.

Nature offers numerous examples of water-resistant surfaces, such as the lotus leaf, a longstanding inspiration for creating synthetic materials. Until now, however, no model natural systems have been found for broadly repellent materials.

While such surfaces can be manufactured, the top-down process is costly, labor intensive, and reliant on toxic chemicals and brittle structures. A biofilm, however, is living proof that only the simplest and most natural of components are required—namely, a resilient meshwork made from proteins and polysaccharides assembled into a multi-scale, hierarchical structure.

At the same time, the finding offers a completely new perspective on how biofilms are immune to so many different types of biocides. Even the most sophisticated biochemical strategy will be ineffective if a biocide cannot enter the slime to reach the bacteria. In short, the antimicrobial activity of alcohols and other solvents becomes compromised by the strongly non-wetting behavior at clinically relevant concentrations.

The team expects that their newfound knowledge will help alert researchers to the need to consider this requirement when designing ways to destroy harmful biofilms.

"Their notorious resistance to a broad range of biocide chemistries has remained a mysterious and pressing problem despite two decades of biofilm research," says Aizenberg, a pioneer in the field of biomimicry. "By looking at it as a macroscopic problem, we found an explanation that was just slightly out of view: antimicrobials can be ineffective simply by being a non-wetting liquid that cannot penetrate into the biofilm and access subsurface cells."

Aizenberg and her colleagues speculate that such strong liquid repellence may have evolved in response to the bacteria's natural soil environment where water can leach heavy metals and other toxins.

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A Bacillus subtilis biofilm, the light-colored, slimy, bacterial coating on top, displays unprecedented liquid repellency as it beads up a drop of ethanol solution that has been placed on it. This remarkable ability offers both a completely new perspective on how biofilms can protect themselves from a wide range of biocides and introduces the first model natural system for broadly non-wetting materials. Credit: Courtesy of the laboratory of Joanna Aizenberg, Harvard School of Engineering and Applied Sciences.

Moreover, the property may underlie the recent success of the use of biofilm as an eco-friendly form of biocontrol for agriculture, protecting plant roots from water-borne pathogens.

Looking ahead, the Harvard team plans to investigate precisely how the biochemical components of biofilms give rise to their exceptional resistance and to test the properties of other bacterial species.

"The applications are exciting, but we are equally thrilled that our findings have revealed a previously undocumented phenomenon about biofilms," says Aizenberg. "The research should be an inspiring reminder that we have only scratched the surface of how things really work."

Just as with biofilm, she adds, "It has been a challenge to get deep into the core of the problem."