News Feed Item

Tissue development 'roadmap' created to guide stem cell medicine

Computer algorithm also provides 'quality assurance' for lab-created cells

BOSTON, Aug. 14, 2014 /PRNewswire-USNewswire/ -- In a boon to stem cell research and regenerative medicine, scientists at Boston Children's Hospital, the Wyss Institute for Biologically Inspired Engineering at Harvard University and Boston University have created a computer algorithm called CellNet as a "roadmap" for cell and tissue engineering, to ensure that cells engineered in the lab have the same favorable properties as cells in our own bodies. CellNet and its application to stem cell engineering are described in two back-to-back papers in the August 14 issue of the journal Cell.

Scientists around the world are engaged in culturing pluripotent stem cells (capable of forming all the body's tissues) and transforming them into specialized cell types for use in research and regenerative medicine. Available as an Internet resource for any scientist to use, CellNet provides a much needed "quality assurance" measure for this work.

The two papers also clarify uncertainty around which methods are best for stem cell engineering, and should advance the use of cells derived from patient tissues to model disease, test potential drugs and use as treatments. For example, using CellNet, one of the studies unexpectedly found that skin cells can be converted into intestinal cells that were able to reverse colitis in a mouse model.

"To date, there has been no systematic means of assessing the fidelity of cellular engineering—to determine how closely cells made in a petri dish approximate natural tissues in the body," says George Q. Daley, MD, PhD, Director of the Stem Cell Transplantation Program at Boston Children's and senior investigator on both studies. "CellNet was developed to assess the quality of engineered cells and to identify ways to improve their performance."

Gene signatures

CellNet applies network biology to discover the complex network of genes that are turned on or off in an engineered cell, known as the cell's Gene Regulatory Network or GRN. It then compares that network to the cell's real-life counterpart in the body, as determined from public genome databases. Through this comparison, researchers can rigorously and reliably assess:

  • the quality of induced pluripotent stem cells (iPS cells) made by reprogramming blood cells or skin cells
  • the quality of specialized cells—such as liver, heart, muscle, brain or blood cells—made from either iPS cells or embryonic stem cells
  • the quality of specialized cells made from other specialized cells (such as liver cells made directly from skin cells)
  • what specific improvements need to be made to the engineering process.

"CellNet will also be a powerful tool to advance synthetic biology—to engineer cells for specific medical applications," says James Collins, PhD, Core Faculty member at the Wyss Institute and the William F. Warren Distinguished Professor at Boston University, co-senior investigator on one of the studies.

Putting CellNet to the test

The researchers—including co-first authors Patrick Cahan, PhD and Samantha Morris, PhD, of Boston Children's, and Hu Li, PhD, of the Mayo Clinic, first used CellNet to assess the quality of eight kinds of cells created in 56 published studies.

In a second study, they applied CellNet's teachings to a recurring question in stem cell biology: Is it feasible to directly convert one specialized cell type to another, bypassing the laborious process of first creating an iPS cell? This study looked at two kinds of directly converted cells: liver cells made from skin cells, and macrophages made from B cells.

"Most attempts to directly convert one specialized cell type to another have depended on a trial and error approach," notes Cahan, principle architect of CellNet and a post-doctoral scientist in the Daley lab. "Until now, quality control metrics for engineered cells have not gotten to the core defining features of a cell type."

In both test cases, CellNet showed that the engineered cells hadn't completely converted, retaining some characteristics of their cells of origin—but pointed to specific genetic tweaks that could be done in the lab to fix the problem.

CellNet also pointed out some useful properties that weren't apparent before. "We found that liver-like cells made from mouse skin were actually more like intestinal cells," says Morris. "In fact, the converted skin cells could engraft into mice with inflammatory bowel disease—Crohn's or ulcerative colitis. After a short time, the cells became highly similar to native colon cells and assisted healing of the damaged tissue, a finding that surprised and excited us."

Guidance for stem cell engineering

Together, the two studies establish some general principles for stem cell science:

1) The GRN of iPS cells created by reprogramming a mature cell is nearly identical to that of stem cells made from embryos, confirming that iPS cells are a good raw material for creating specialized cells.

2) Once engineered cells are engrafted into laboratory mice, their GRN becomes even closer to that of the true target tissue, indicating that the body's own tissues contribute signals to enhance the performance of transplanted cells.

3) Differentiating pluripotent stem cells into specific tissues is currently more effective than attempting to convert one specialized cell directly to another, creating cells whose GRNs are much like those of cells in the body.

4) Most specialized cells made from other specialized cells retain some "memory" of their cell of origin, making them less than ideal for certain uses but better for others.

Supporters of the studies include the National Institutes of Health (grant #s R24DK092760, UO1-HL100001, P50HG005550, 1K01DK096013, 2T32HL06698, 5T32HL007623 and R01DK082889), the National Institute of Diabetes and Digestive and Kidney Diseases (K01DK096013), the National Heart, Lung, and Blood Institute (T32HL066987 and T32HL007623), the Children's Hospital Stem Cell Program, the Howard Hughes Medical Institute, Alex's Lemonade Stand Foundation, the Mayo Clinic, the Ellison Medical Foundation and the Doris Duke Medical Foundation.

Boston Children's Hospital is home to the world's largest research enterprise based at a pediatric medical center, where its discoveries have benefited both children and adults since 1869. More than 1,100 scientists, including seven members of the National Academy of Sciences, 14 members of the Institute of Medicine and 14 members of the Howard Hughes Medical Institute comprise Boston Children's research community. Founded as a 20-bed hospital for children, Boston Children's today is a 395-bed comprehensive center for pediatric and adolescent health care. Boston Children's is also the primary pediatric teaching affiliate of Harvard Medical School.

For more information about research and clinical innovation at BCH visit: http://vectorblog.org
Join the social discussion and tweet us @BostonChildrens
Follow BCH on Facebook: http://on.bchil.org/1mJ9fxf
Follow BCH on Youtube: http://on.bchil.org/1oJib5B  

The Wyss Institute for Biologically Inspired Engineering at Harvard University (http://wyss.harvard.edu) uses Nature's design principles to develop bioinspired materials and devices that will transform medicine and create a more sustainable world. Working as an alliance among all of Harvard's Schools, and in partnership with Beth Israel Deaconess Medical Center, Brigham and Women's Hospital, Boston Children's Hospital, Dana Farber Cancer Institute, Massachusetts General Hospital, the University of Massachusetts Medical School, Spaulding Rehabilitation Hospital, Boston University, Tufts University, and Charité - Universitätsmedizin Berlin, and the University of Zurich, the Institute crosses disciplinary and institutional barriers to engage in high-risk research that leads to transformative technological breakthroughs. By emulating Nature's principles for self-organizing and self-regulating, Wyss researchers are developing innovative new engineering solutions for healthcare, energy, architecture, robotics, and manufacturing. These technologies are translated into commercial products and therapies through collaborations with clinical investigators, corporate alliances, and new start-ups.

The Boston University College of Engineering offers a wide range of undergraduate, graduate and professional degrees in foundational and emerging engineering disciplines. Underlying the College's educational efforts is its commitment to creating Societal Engineers who have an appreciation for how the engineer's unique skills can be used to improve our quality of life. Ranked among the nation's best engineering research institutions, the College's faculty attracts more than $50 million in external research support annually.

Kristen Dattoli
Boston Children's Hospital
[email protected]

Kristen Kusek
Wyss Institute for Biologically Inspired Engineering
[email protected]

SOURCE Boston Children's Hospital

More Stories By PR Newswire

Copyright © 2007 PR Newswire. All rights reserved. Republication or redistribution of PRNewswire content is expressly prohibited without the prior written consent of PRNewswire. PRNewswire shall not be liable for any errors or delays in the content, or for any actions taken in reliance thereon.

Latest Stories
SYS-CON Events announced today that Cemware will exhibit at the 19th International Cloud Expo, which will take place on November 1–3, 2016, at the Santa Clara Convention Center in Santa Clara, CA. Use MATLAB functions by just visiting website mathfreeon.com. MATLAB compatible, freely usable, online platform services. As of October 2016, 80,000 users from 180 countries are enjoying our platform service.
Data is the fuel that drives the machine learning algorithmic engines and ultimately provides the business value. In his session at Cloud Expo, Ed Featherston, a director and senior enterprise architect at Collaborative Consulting, will discuss the key considerations around quality, volume, timeliness, and pedigree that must be dealt with in order to properly fuel that engine.
SYS-CON Events announced today that MathFreeOn will exhibit at the 19th International Cloud Expo, which will take place on November 1–3, 2016, at the Santa Clara Convention Center in Santa Clara, CA. MathFreeOn is Software as a Service (SaaS) used in Engineering and Math education. Write scripts and solve math problems online. MathFreeOn provides online courses for beginners or amateurs who have difficulties in writing scripts. In accordance with various mathematical topics, there are more tha...
Digitization is driving a fundamental change in society that is transforming the way businesses work with their customers, their supply chains and their people. Digital transformation leverages DevOps best practices, such as Agile Parallel Development, Continuous Delivery and Agile Operations to capitalize on opportunities and create competitive differentiation in the application economy. However, information security has been notably absent from the DevOps movement. Speed doesn’t have to negat...
SYS-CON Events announced today that eCube Systems, the leading provider of modern development tools and best practices for Continuous Integration on OpenVMS, will exhibit at SYS-CON's @DevOpsSummit at Cloud Expo New York, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. eCube Systems offers a family of middleware products and development tools that maximize return on technology investment by leveraging existing technical equity to meet evolving business needs. ...
In an era of historic innovation fueled by unprecedented access to data and technology, the low cost and risk of entering new markets has leveled the playing field for business. Today, any ambitious innovator can easily introduce a new application or product that can reinvent business models and transform the client experience. In their Day 2 Keynote at 19th Cloud Expo, Mercer Rowe, IBM Vice President of Strategic Alliances, and Raejeanne Skillern, Intel Vice President of Data Center Group and ...
The best way to leverage your Cloud Expo presence as a sponsor and exhibitor is to plan your news announcements around our events. The press covering Cloud Expo and @ThingsExpo will have access to these releases and will amplify your news announcements. More than two dozen Cloud companies either set deals at our shows or have announced their mergers and acquisitions at Cloud Expo. Product announcements during our show provide your company with the most reach through our targeted audiences.
@ThingsExpo has been named the Top 5 Most Influential Internet of Things Brand by Onalytica in the ‘The Internet of Things Landscape 2015: Top 100 Individuals and Brands.' Onalytica analyzed Twitter conversations around the #IoT debate to uncover the most influential brands and individuals driving the conversation. Onalytica captured data from 56,224 users. The PageRank based methodology they use to extract influencers on a particular topic (tweets mentioning #InternetofThings or #IoT in this ...
In the 21st century, security on the Internet has become one of the most important issues. We hear more and more about cyber-attacks on the websites of large corporations, banks and even small businesses. When online we’re concerned not only for our own safety but also our privacy. We have to know that hackers usually start their preparation by investigating the private information of admins – the habits, interests, visited websites and so on. On the other hand, our own security is in danger bec...
"We've discovered that after shows 80% if leads that people get, 80% of the conversations end up on the show floor, meaning people forget about it, people forget who they talk to, people forget that there are actual business opportunities to be had here so we try to help out and keep the conversations going," explained Jeff Mesnik, Founder and President of ContentMX, in this SYS-CON.tv interview at 18th Cloud Expo, held June 7-9, 2016, at the Javits Center in New York City, NY.
There is growing need for data-driven applications and the need for digital platforms to build these apps. In his session at 19th Cloud Expo, Muddu Sudhakar, VP and GM of Security & IoT at Splunk, will cover different PaaS solutions and Big Data platforms that are available to build applications. In addition, AI and machine learning are creating new requirements that developers need in the building of next-gen apps. The next-generation digital platforms have some of the past platform needs a...
Join Impiger for their featured webinar: ‘Cloud Computing: A Roadmap to Modern Software Delivery’ on November 10, 2016, at 12:00 pm CST. Very few companies have not experienced some impact to their IT delivery due to the evolution of cloud computing. This webinar is not about deciding whether you should entertain moving some or all of your IT to the cloud, but rather, a detailed look under the hood to help IT professionals understand how cloud adoption has evolved and what trends will impact th...
The Internet of Things (IoT) promises to simplify and streamline our lives by automating routine tasks that distract us from our goals. This promise is based on the ubiquitous deployment of smart, connected devices that link everything from industrial control systems to automobiles to refrigerators. Unfortunately, comparatively few of the devices currently deployed have been developed with an eye toward security, and as the DDoS attacks of late October 2016 have demonstrated, this oversight can ...
Enterprises have been using both Big Data and virtualization for years. Until recently, however, most enterprises have not combined the two. Big Data's demands for higher levels of performance, the ability to control quality-of-service (QoS), and the ability to adhere to SLAs have kept it on bare metal, apart from the modern data center cloud. With recent technology innovations, we've seen the advantages of bare metal erode to such a degree that the enhanced flexibility and reduced costs that cl...
Intelligent machines are here. Robots, self-driving cars, drones, bots and many IoT devices are becoming smarter with Machine Learning. In her session at @ThingsExpo, Sudha Jamthe, CEO of IoTDisruptions.com, will discuss the next wave of business disruption at the junction of IoT and AI, impacting many industries and set to change our lives, work and world as we know it.