Friday, May 10, 2019

Organ bioprinting gets a breath of fresh air

Bioengineers have cleared a major hurdle on the path to 3D printing replacement organs with a breakthrough technique for bioprinting tissues.


Bioprinting research from the lab of Rice University bioengineer Jordan Miller featured a visually stunning proof-of-principle -- a scale-model of a lung-mimicking air sac with airways and blood vessels that never touch yet still provide oxygen to red blood cells.
Credit: Photo by Jordan Miller/Rice University


The new innovation allows scientists to create exquisitely entangled vascular networks that mimic the body's natural passageways for blood, air, lymph and other vital fluids.
The research is featured on the cover of this week's issue of Science. It includes a visually stunning proof-of-principle -- a hydrogel model of a lung-mimicking air sac in which airways deliver oxygen to surrounding blood vessels. Also reported are experiments to implant bioprinted constructs containing liver cells into mice.
The work was led by bioengineers Jordan Miller of Rice University and Kelly Stevens of the University of Washington (UW) and included 15 collaborators from Rice, UW, Duke University, Rowan University and Nervous System, a design firm in Somerville, Massachusetts.
"One of the biggest road blocks to generating functional tissue replacements has been our inability to print the complex vasculature that can supply nutrients to densely populated tissues," said Miller, assistant professor of bioengineering at Rice's Brown School of Engineering. "Further, our organs actually contain independent vascular networks -- like the airways and blood vessels of the lung or the bile ducts and blood vessels in the liver. These interpenetrating networks are physically and biochemically entangled, and the architecture itself is intimately related to tissue function. Ours is the first bioprinting technology that addresses the challenge of multivascularization in a direct and comprehensive way."
Stevens, assistant professor of bioengineering in the UW College of Engineering, assistant professor of pathology in the UW School of Medicine, and an investigator at the UW Medicine Institute for Stem Cell and Regenerative Medicine, said multivascularization is important because form and function often go hand in hand.
"Tissue engineering has struggled with this for a generation," Stevens said. "With this work we can now better ask, 'If we can print tissues that look and now even breathe more like the healthy tissues in our bodies, will they also then functionally behave more like those tissues?' This is an important question, because how well a bioprinted tissue functions will affect how successful it will be as a therapy."
The goal of bioprinting healthy, functional organs is driven by the need for organ transplants. More than 100,000 people are on transplant waiting lists in the United States alone, and those who do eventually receive donor organs still face a lifetime of immune-suppressing drugs to prevent organ rejection. Bioprinting has attracted intense interest over the past decade because it could theoretically address both problems by allowing doctors to print replacement organs from a patient's own cells. A ready supply of functional organs could one day be deployed to treat millions of patients worldwide.
"We envision bioprinting becoming a major component of medicine within the next two decades," Miller said.
"The liver is especially interesting because it performs a mind-boggling 500 functions, likely second only to the brain," Stevens said. "The liver's complexity means there is currently no machine or therapy that can replace all its functions when it fails. Bioprinted human organs might someday supply that therapy."
To address this challenge, the team created a new open-source bioprinting technology dubbed the "stereolithography apparatus for tissue engineering," or SLATE. The system uses additive manufacturing to make soft hydrogels one layer at a time.
Layers are printed from a liquid pre-hydrogel solution that becomes a solid when exposed to blue light. A digital light processing projector shines light from below, displaying sequential 2D slices of the structure at high resolution, with pixel sizes ranging from 10-50 microns. With each layer solidified in turn, an overhead arm raises the growing 3D gel just enough to expose liquid to the next image from the projector. The key insight by Miller and Bagrat Grigoryan, a Rice graduate student and lead co-author of the study, was the addition of food dyes that absorb blue light. These photoabsorbers confine the solidification to a very fine layer. In this way, the system can produce soft, water-based, biocompatible gels with intricate internal architecture in a matter of minutes.
Tests of the lung-mimicking structure showed that the tissues were sturdy enough to avoid bursting during blood flow and pulsatile "breathing," a rhythmic intake and outflow of air that simulated the pressures and frequencies of human breathing. Tests found that red blood cells could take up oxygen as they flowed through a network of blood vessels surrounding the "breathing" air sac. This movement of oxygen is similar to the gas exchange that occurs in the lung's alveolar air sacs.
To design the study's most complicated lung-mimicking structure, which is featured on the cover of Science, Miller collaborated with study co-authors Jessica Rosenkrantz and Jesse Louis-Rosenberg, co-founders of Nervous System.
"When we founded Nervous System it was with the goal of adapting algorithms from nature into new ways to design products," Rosenkrantz said. "We never imagined we'd have the opportunity to bring that back and design living tissues."
In the tests of therapeutic implants for liver disease, the team 3D printed tissues, loaded them with primary liver cells and implanted them into mice. The tissues had separate compartments for blood vessels and liver cells and were implanted in mice with chronic liver injury. Tests showed that the liver cells survived the implantation.
Miller said the new bioprinting system can also produce intravascular features, like bicuspid valves that allow fluid to flow in only one direction. In humans, intravascular valves are found in the heart, leg veins and complementary networks like the lymphatic system that have no pump to drive flow.
"With the addition of multivascular and intravascular structure, we're introducing an extensive set of design freedoms for engineering living tissue," Miller said. "We now have the freedom to build many of the intricate structures found in the body."
Miller and Grigoryan are commercializing key aspects of the research through a Houston-based startup company called Volumetric. The company, which Grigoryan has joined full time, is designing and manufacturing bioprinters and bioinks.
Miller, a longstanding champion of open-source 3D printing, said all source data from the experiments in the published Science study are freely available. In addition, all 3D printable files needed to build the stereolithography printing apparatus are available, as are the design files for printing each of the hydrogels used in the study.
"Making the hydrogel design files available will allow others to explore our efforts here, even if they utilize some future 3D printing technology that doesn't exist today," Miller said.
Miller said his lab is already using the new design and bioprinting techniques to explore even more complex structures.
"We are only at the beginning of our exploration of the architectures found in the human body," he said. "We still have so much more to learn."
Additional study co-authors include Rice's Samantha Paulsen, Daniel Sazer, Alexander Zaita, Paul Greenfield, Nicholas Calafat and Anderson Ta; UW's Daniel Corbett, Chelsea Fortin and Fredrik Johansson; Duke's John Gounley and Amanda Randles; and Rowan's Peter Galie.
The work was supported by the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation, the John H. Tietze Foundation, the National Science Foundation (1728239, 1450681 and 1250104), the National Institutes of Health (F31HL134295, DP2HL137188, T32EB001650, T32GM095421 and DP5OD019876) and the Gulf Coast Consortia.
VIDEO is available at:
https://youtu.be/GqJYMgAcc0Q

Journal Reference:
  1. Bagrat Grigoryan, Samantha J. Paulsen, Daniel C. Corbett, Daniel W. Sazer, Chelsea L. Fortin, Alexander J. Zaita, Paul T. Greenfield, Nicholas J. Calafat, John P. Gounley, Anderson H. Ta, Fredrik Johansson, Amanda Randles, Jessica E. Rosenkrantz, Jesse D. Louis-Rosenberg, Peter A. Galie, Kelly R. Stevens, Jordan S. Miller. Multivascular networks and functional intravascular topologies within biocompatible hydrogels. Science, 2019 DOI: 10.1126/science.aav9750 
Courtesy: ScienceDaily


Wednesday, May 8, 2019

A comprehensive map of how Alzheimer's affects the brain

In the Alzheimer’s affected brain, abnormal levels of the beta-amyloid protein clump together to form plaques (seen in brown) that collect between neurons and disrupt cell function. Abnormal collections of the tau protein accumulate and form tangles (seen in blue) within neurons, harming synaptic communication between nerve cells.
Credit: National Institute on Aging, NIH


MIT researchers have performed the first comprehensive analysis of the genes that are expressed in individual brain cells of patients with Alzheimer's disease. The results allowed the team to identify distinctive cellular pathways that are affected in neurons and other types of brain cells.
This analysis could offer many potential new drug targets for Alzheimer's, which afflicts more than 5 million people in the United States.
"This study provides, in my view, the very first map for going after all of the molecular processes that are altered in Alzheimer's disease in every single cell type that we can now reliably characterize," says Manolis Kellis, a professor of computer science and a member of MIT's Computer Science and Artificial Intelligence Laboratory and of the Broad Institute of MIT and Harvard. "It opens up a completely new era for understanding Alzheimer's."
The study revealed that a process called axon myelination is significantly disrupted in patients with Alzheimer's. The researchers also found that the brain cells of men and women vary significantly in how their genes respond to the disease.
Kellis and Li-Huei Tsai, director of MIT's Picower Institute for Learning and Memory, are the senior authors of the study, which appears in the May 1 online edition of Nature. MIT postdocs Hansruedi Mathys and Jose Davila-Velderrain are the lead authors of the paper.
Single-cell analysis
The researchers analyzed postmortem brain samples from 24 people who exhibited high levels of Alzheimer's disease pathology and 24 people of similar age who did not have these signs of disease. All of the subjects were part of the Religious Orders Study, a longitudinal study of aging and Alzheimer's disease. The researchers also had data on the subjects' performance on cognitive tests.
The MIT team performed single-cell RNA sequencing on about 80,000 cells from these subjects. Previous studies of gene expression in Alzheimer's patients have measured overall RNA levels from a section of brain tissue, but these studies don't distinguish between cell types, which can mask changes that occur in less abundant cell types, Tsai says.
"We wanted to know if we could distinguish whether each cell type has differential gene expression patterns between healthy and diseased brain tissue," she says. "This is the power of single-cell-level analysis: You have the resolution to really see the differences among all the different cell types in the brain."
Using the single-cell sequencing approach, the researchers were able to analyze not only the most abundant cell types, which include excitatory and inhibitory neurons, but also rarer, non-neuronal brain cells such as oligodendrocytes, astrocytes, and microglia. The researchers found that each of these cell types showed distinct gene expression differences in Alzheimer's patients.
Some of the most significant changes occurred in genes related to axon regeneration and myelination. Myelin is a fatty sheath that insulates axons, helping them to transmit electrical signals. The researchers found that in the individuals with Alzheimer's, genes related to myelination were affected in both neurons and oligodendrocytes, the cells that produce myelin.
Most of these cell-type-specific changes in gene expression occurred early in the development of the disease. In later stages, the researchers found that most cell types had very similar patterns of gene expression change. Specifically, most brain cells turned up genes related to stress response, programmed cell death, and the cellular machinery required to maintain protein integrity.
Sex differences
The researchers also discovered correlations between gene expression patterns and other measures of Alzheimer's severity such as the level of amyloid plaques and neurofibrillary tangles, as well as cognitive impairments. This allowed them to identify "modules" of genes that appear to be linked to different aspects of the disease.
"To identify these modules, we devised a novel strategy that involves the use of an artificial neural network and which allowed us to learn the sets of genes that are linked to the different aspects of Alzheimer's disease in a completely unbiased, data-driven fashion," Mathys says. "We anticipate that this strategy will be valuable to also identify gene modules associated with other brain disorders."
The most surprising finding, the researchers say, was the discovery of a dramatic difference between brain cells from male and female Alzheimer's patients. They found that excitatory neurons and other brain cells from male patients showed less pronounced gene expression changes in Alzheimer's than cells from female individuals, even though those patients did show similar symptoms, including amyloid plaques and cognitive impairments. By contrast, brain cells from female patients showed dramatically more severe gene-expression changes in Alzheimer's disease, and an expanded set of altered pathways.
"That's when we realized there's something very interesting going on. We were just shocked," Tsai says.
So far, it is unclear why this discrepancy exists. The sex difference was particularly stark in oligodendrocytes, which produce myelin, so the researchers performed an analysis of patients' white matter, which is mainly made up of myelinated axons. Using a set of MRI scans from 500 additional subjects from the Religious Orders Study group, the researchers found that female subjects with severe memory deficits had much more white matter damage than matched male subjects.
More study is needed to determine why men and women respond so differently to Alzheimer's disease, the researchers say, and the findings could have implications for developing and choosing treatments.
"There is mounting clinical and preclinical evidence of a sexual dimorphism in Alzheimer's predisposition, but no underlying mechanisms are known. Our work points to differential cellular processes involving non-neuronal myelinating cells as potentially having a role. It will be key to figure out whether these discrepancies protect or damage the brain cells only in one of the sexes -- and how to balance the response in the desired direction on the other," Davila-Velderrain says.
The researchers are now using mouse and human induced pluripotent stem cell models to further study some of the key cellular pathways that they identified as associated with Alzheimer's in this study, including those involved in myelination. They also plan to perform similar gene expression analyses for other forms of dementia that are related to Alzheimer's, as well as other brain disorders such as schizophrenia, bipolar disorder, psychosis, and diverse dementias.
The research was funded by the National Institutes of Health, the JBP Foundation, and the Swiss National Science Foundation.


Journal Reference:
  1. Hansruedi Mathys, Jose Davila-Velderrain, Zhuyu Peng, Fan Gao, Shahin Mohammadi, Jennie Z. Young, Madhvi Menon, Liang He, Fatema Abdurrob, Xueqiao Jiang, Anthony J. Martorell, Richard M. Ransohoff, Brian P. Hafler, David A. Bennett, Manolis Kellis & Li-Huei Tsai. Single-cell transcriptomic analysis of Alzheimer’s disease. Nature, 2019 DOI: 10.1038/s41586-019-1195-2
 Courtesy: ScienceDaily

Monday, May 6, 2019

Embryo stem cells created from skin cells

Researchers at the Hebrew University of Jerusalem (HU) have found a way to transform skin cells into the three major stem cell types that comprise early-stage embryos. The work (in mouse cells) has significant implications for modelling embryonic disease and placental dysfunctions, as well as paving the way to create whole embryos from skin cells.
As published in Cell Stem Cell, Dr. Yossi Buganim of HU's Department of Developmental Biology and Cancer Research and his team discovered a set of genes capable of transforming murine skin cells into all three of the cell types that comprise the early embryo: the embryo itself, the placenta and the extra-embryonic tissues, such as the umbilical cord. In the future, it may be possible to create entire human embryos out of human skin cells, without the need for sperm or eggs. This discovery also has vast implications for modelling embryonic defects and shedding light on placental dysfunctions, as well as solving certain infertility problems by creating human embryos in a petri dish.
Back in 2006, Japanese researchers discovered the capacity of skin cells to be "reprogrammed" into early embryonic cells that can generate an entire fetus, by expressing four central embryonic genes. These reprogrammed skin cells, termed "Induced Plutipotent Stem Cells" (iPSCs), are similar to cells that develop in the early days after fertilization and are essentially identical to their natural counterparts. These cells can develop into all fetal cell types, but not into extra-embryonic tissues, such as the placenta.
Now, the Hebrew University research team, headed by Dr. Yossi Buganim, Dr. Oren Ram from the HU's Institute of Life Science and Professor Tommy Kaplan from HU's School of Computer Science and Engineering, as well as doctoral students Hani Benchetrit and Mohammad Jaber, found a new combination of five genes that, when inserted into skin cells, reprogram the cells into each of three early embryonic cell types -- iPS cells which create fetuses, placental stem cells, and stem cells that develop into other extra-embryonic tissues, such as the umbilical cord. These transformations take about one month.
The HU team used new technology to scrutinize the molecular forces that govern cell fate decisions for skin cell reprogramming and the natural process of embryonic development. For example, the researchers discovered that the gene "Eomes" pushes the cell towards placental stem cell identity and placental development, while the "Esrrb" gene orchestrates fetus stem cells development through the temporary acquisition of an extrae-mbryonic stem cell identity.
To uncover the molecular mechanisms that are activated during the formation of these various cell types, the researchers analyzed changes to the genome structure and function inside the cells when the five genes are introduced into the cell. They discovered that during the first stage, skin cells lose their cellular identity and then slowly acquire a new identity of one of the three early embryonic cell types, and that this process is governed by the levels of two of the five genes.
Recently, attempts have been made to develop an entire mouse embryo without using sperm or egg cells. These attempts used the three early cell types isolated directly from a live, developing embryo. However, HU's study is the first attempt to create all three main cell lineages at once from skin cells. Further, these findings mean there may be no need to "sacrifice" a live embryo to create a test tube embryo.

Journal Reference:
  1. Hana Benchetrit, Mohammad Jaber, Valery Zayat, Shulamit Sebban, Avital Pushett, Kirill Makedonski, Zvi Zakheim, Ahmed Radwan, Noam Maoz, Rachel Lasry, Noa Renous, Michal Inbar, Oren Ram, Tommy Kaplan, Yosef Buganim. Direct Induction of the Three Pre-implantation Blastocyst Cell Types from Fibroblasts. Cell Stem Cell, 2019; DOI: 10.1016/j.stem.2019.03.018
 Courtesy: ScienceDaily