Scientists grow human esophagus in lab

This confocal microscopic image shows a two-month-old human esophageal organoid bioengineered by scientists from pluripotent stem cells. About 700 micrometers (0.027 inches) in size, the organoid is stained to visualize key structural proteins expressed in mature esophagus, such as involucrin (green) and cornulin (blue). Researchers report in the journal Cell Stem Cell the organoids enhance the study of esophageal disorders, personalized medical and the development of regenerative tissue therapies for people.

Credit: Cincinnati Children's

Scientists working to bioengineer the entire human gastrointestinal system in a laboratory now report using pluripotent stem cells to grow human esophageal organoids.

Published in the journal Cell Stem Cell the study is the latest advancement from researchers at the Cincinnati Children's Center for Stem Cell and Organoid Medicine (CuSTOM). The center is developing new ways to study birth defects and diseases that affect millions of people with gastrointestinal disorders, such as gastric reflux, cancer, etc. The work is leading to new personalized diagnostic methods and focused in part on developing regenerative tissue therapies to treat or cure GI disorders.

The newly published research is the first time scientists have been able to grow human esophageal tissue entirely from pluripotent stem cells (PSCs), which can form any tissue type in the body, according to the authors. Cincinnati Children's scientists and their multi-institutional collaborators already have used PSCs to bioengineer human intestine, stomach, colon and liver.

"Disorders of the esophagus and trachea are prevalent enough in people that organoid models of human esophagus could be greatly beneficial," said Jim Wells, PhD, chief scientific officer at CuSTOM and study lead investigator. "In addition to being a new model to study birth defects like esophageal atresia, the organoids can be used to study diseases like eosinophilic esophagitis and Barrett's metaplasia, or to bioengineer genetically matched esophageal tissue for individual patients."

The study involves collaboration from researchers in the divisions of Developmental Biology, Oncology, Allergy and Immunology, and Endocrinology at Cincinnati Children's and the Gladstone Institutes in San Francisco. This includes study first author Stephen Trisno, a graduate student and member of the Wells laboratory.

The Food Channel

The esophagus is a muscular tube that actively passes food from the mouth to the stomach. The organ can be affected by congenital diseases, such as esophageal atresia -- a narrowing or malformation of the esophagus caused by genetic mutations.

Additionally, there are several diseases that can afflict people later in life. Some include esophageal cancer, gastroesophageal reflux disease (GERD), or a rare ailment called achalasia -- a disease affecting the muscles of the lower esophagus that prevents contraction of the organ and the passage of food.

All of the conditions need better treatments, researchers note. This requires a more precise understanding of the genetic and biochemical mechanisms behind their cause -- a need filled by the ability to generate and study robust, functional, genetically matched models of human esophageal tissue that can be grown from a person's own cells.

Tracing Nature's Path

The scientists based their new method for using human PSCs to general esophageal organoids on precisely timed, step-by-step manipulations of genetic and biochemical signals that pattern and form embryonic endoderm and foregut tissues. They focused in part on the gene Sox2 and its associated protein -- which are already known to trigger esophageal conditions when their function is disrupted. -- The scientists used mice, frogs and human tissue cultures to identify other genes and molecular pathways regulated by Sox2 during esophagus formation.

The scientists report that during critical stages of embryonic development, the Sox2 gene blocks the programming and action of genetic pathways that direct cells to become respiratory instead of esophageal. In particular, the Sox2 protein inhibits the signaling of a molecule called Wnt and promotes the formation and survival of esophageal tissues.

In another test to help confirm the importance of Sox2 expression on esophageal formation, researchers studied the complete loss of Sox2 during the development process in mice. The absence of Sox2 resulted in esophageal agenesis -- a condition in which the esophagus terminates in a pouch and does not connect to the stomach.

After successfully generating fully formed human esophageal organoids -- which grew to a length of about 300-800 micrometers in about two months -- the bioengineered tissues were compared biochemically to esophageal tissues from patient biopsies. Those tests showed the bioengineered and biopsies tissues were strikingly similar in composition, according to the authors.

The research team is continuing its studies into the bioengineering process for esophageal organoids and identifying future projects to advance the technology's eventual therapeutic potential, according to Wells. This includes using the organoids to examine the progression of specific diseases and congenital defects affecting the esophagus.

Journal Reference:

1. Stephen L. Trisno, Katherine E.D. Philo, Kyle W. McCracken, Emily M. Catá, Sonya Ruiz-Torres, Scott A. Rankin, Lu Han, Talia Nasr, Praneet Chaturvedi, Marc E. Rothenberg, Mohammad A. Mandegar, Susanne I. Wells, Aaron M. Zorn, James M. Wells. Esophageal Organoids from Human Pluripotent Stem Cells Delineate Sox2 Functions during Esophageal Specification. Cell Stem Cell, 2018; DOI: 10.1016/j.stem.2018.08.008 

Courtesy: ScienceDaily

Proof-of-concept HIV immunotherapy study passes Phase 1 safety trial

Preliminary results from a phase I clinical trial have demonstrated the safety and tolerability of a cell therapy involving the ex vivo expansion of T cells and their subsequent infusion into HIV-infected individuals previously treated with antiretroviral therapy (ART). The study appears September 21st in the journal Molecular Therapy.

"This study is focused on finding a way to re-educate the body's immune system to better fight HIV infection," says co-senior study author David Margolis of the University of North Carolina (UNC) at Chapel Hill. "We found that this approach of re-educating the immune cells and reinfusing them was safe, which was the primary goal of the study. The data from this trial will continue to help us design improved immunotherapies against HIV."

A game changer for patients living with HIV, ART has turned what was once a death sentence into a chronically managed disease. But it is not a cure, and the virus continues to persist within a latent reservoir that remains hidden from the immune system. Approaches using pharmacological HIV-latency-reversal agents to induce latent virus to express viral protein could make this reservoir vulnerable to T cells. However, the existing HIV-specific immune response in ART-treated individuals is insufficient to clear persistent infection, even in the presence of latency-reversal agents that induce HIV expression.

One safe avenue for harnessing T cell responses to fight HIV is adoptive cellular therapy. This procedure involves collecting T cells from a patient, growing them in the laboratory to increase their numbers, and then giving them back to the patient to help the immune system fight disease. Earlier adoptive-T-cell-therapy approaches for HIV had limited efficacy as a result of multiple factors. Since these earlier attempts, the adoptive-T-cell-therapy field has made significant advances, largely in the oncology field, that could help to overcome some of the pitfalls encountered with earlier T-cell-therapy approaches for HIV. T cells generated by these sophisticated methods of expansion have been safe and well tolerated, as well as highly effective.

"Before we can combine this approach with treatments meant to bring HIV out from hiding so the improved immune response can clear it from the body, we need to first establish that this immunotherapy approach is safe on its own," says co-senior study author Catherine Bollard of the Children's National Health System. "We have long-standing experience treating patients with virus-specific T cells targeting latent viruses such as Epstein-Barr virus and cytomegalovirus. Therefore, we were extremely excited to work with the UNC team to adapt this virus-specific T-cell-therapy approach to the HIV setting."

In the small proof-of-concept study, Margolis, Bollard, and their collaborators produced ex vivo expanded HIV-specific T cells (HXTCs); their long-term goal was to use HXTCs as part of a strategy to clear persistent HIV infection. The researchers administered two infusions of HXTCs over a 2 week period to six HIV-infected participants whose viral load had been reduced to an undetectable level by ART.

This treatment was well tolerated and had few adverse events. Moreover, two patients exhibited a detectable increase in T-cell-mediated antiviral activity after the two infusions, although the clinical significance of this mild-to-modest impact is unknown. When evaluating participants in aggregate, the research team found no overall enhancement of the magnitude of the HIV-specific immune response. This could be due to the low dose of the two infusions and the lack of strategies to promote the expansion of the T cells once they are in the body.

There was also no decrease in the size of the latent reservoir, most likely because of the absence of therapies such as latency-reversal agents, which are designed to perturb the reservoir and induce recognizable expression of HIV proteins that trigger immune responses. In the future, a critical question will be whether HXTC therapy in combination with latency-reversal agents can deplete the HIV reservoir to an extent that is measurable by current gold-standard assays of HIV latency. A study of HXTC in combination with the latency-reversal agent vorinostat is currently undergoing evaluation in an ongoing clinical trial.

"This is a promising advancement for the field," says first author Julia Sung of UNC, although she also cautions people against over-interpreting the results. "The study did not cure HIV and should not be interpreted as doing so, but we also are very encouraged by the safety data, so it should not be considered discouraging either. This paves the way for the next step, which is to combine this immunotherapy approach with latency-reversal therapy in order to wake up the HIV out of its latent state, where it is invisible to the immune system, then clear it out with the immunotherapy."

Journal Reference:

1. Julia A. Sung, Shabnum Patel, Matthew L. Clohosey, Lauren Roesch, Tamara Tripic, JoAnn D. Kuruc, Nancie Archin, Patrick J. Hanley, C. Russell Cruz, Nilu Goonetilleke, Joseph J. Eron, Clio M. Rooney, Cynthia L. Gay, Catherine M. Bollard, David M. Margolis. HIV-Specific, Ex Vivo Expanded T Cell Therapy: Feasibility, Safety, and Efficacy in ART-Suppressed HIV-Infected Individuals. Molecular Therapy, 2018; DOI: 10.1016/j.ymthe.2018.08.015 

Courtesy: ScienceDaily

Possible molecular pathway for neurodegeneration in prion diseases

Prion diseases are a group of fatal neurological disorders that includes Creutzfeldt-Jakob disease and bovine spongiform encephalopathy ("mad cow disease"). They are caused by the spread of "prions," which are altered forms of normal cellular proteins. These abnormal molecules then interact with normal proteins to promote misfolding. While we understand that this process of converting normal to abnormal protein is what causes the symptoms of prion disease (including rapidly progressive dementia, seizures and personality changes), the exact mechanism of damage to the neuronal connections in the brain and spinal cord has been poorly understood.

Researchers from Boston University School of Medicine (BUSM) used a method they previously described for culturing nerve cells from the hippocampal region of the brain, and then exposing them to prions, to illustrate the damage to nerve cell connections usually seen in these diseases. They then added a number of different chemical compounds with known inhibitory effects on cellular responses to stressful stimuli, with the objective of identifying which pathways may be involved.

They found that inhibition of p38 MAPK? (an enzyme that typically responds to stress, such as ultraviolet radiation and heat shock) prevented injury to nerve connections and promoted recovery from the initial damage. Hippocampal nerve cells that had a mutation preventing normal function of p38 MAPK? were also protected, seeming to confirm the role the enzyme plays in this disease process.

David. A. Harris, MD, PhD, professor and chair of the Department of Biochemistry at Boston University School of Medicine and corresponding author of the study, sees these findings as a major breakthrough in trying to understand and treat these diseases. "Our results provide new insights into the pathogenesis of prion diseases, they uncover new drug targets for treating these diseases, and they allow us to compare prion diseases to other, more common neurodegenerative disorders like Alzheimer's disease."

These findings appear online in PLOS Pathogens.

Journal Reference:

1. Cheng Fang, Bei Wu, Nhat T. T. Le, Thibaut Imberdis, Robert C. C. Mercer, David A. Harris. Prions activate a p38 MAPK synaptotoxic signaling pathway. PLOS Pathogens, 2018; 14 (9): e1007283 DOI: 10.1371/journal.ppat.1007283 

Courtesy: ScienceDaily

Superbugs jumping frequently between humans and animals

The MRSA staphylococcus is an example of a pathogen, the likes of which are often called superbugs. These are resistant to most antibiotics and can cause serious infections.

"In the case of MRSA, these bacteria have also spread in hospitals almost world-wide," says Jukka Corander, professor at the University of Helsinki, who was a member of the international research team that mapped several millennia of the evolution of the staphylococcus.
In their extensive study, the researchers sequenced whole genomes of the superbugs from a large sample from different animals as well as humans, and were able to study the DNA changes that helped the bacteria to adapt to new host organisms during thousands of years.
First, there were humans
Based on genome analysis, humans were most probably the original hosts to these superbugs, and judging from DNA changes, the ability to colonise domestic animals appeared in an age when the first animals were domesticated to become livestock on farms.
In the study, published recently in Nature Ecology & Evolution, the team discovered that cows are still the source for such strains of staphylococcus that are causing MRSA infections in humans around the world.
"Our observations give emphasis to the importance of detailed epidemiological monitoring, so that strains with the potential to cause epidemics can be discovered as early as possible," Jukka Corander says.
Detailed genomic analyses reveal that, when the bacteria move from one host species to another, it hijacks new genes to help it adapt and stay alive in the long term. In some cases, these genes give the bacteria resistance towards commonly used antibiotics, eventually rendering them so-called superbugs.
The research may promote the development of strategies to minimize the risk of new strains transferring into the human population, and help slow down the occurrence and spreading of resistance to antibiotics.
 

Journal Reference:

1. Emily J. Richardson, Rodrigo Bacigalupe, Ewan M. Harrison, Lucy A. Weinert, Samantha Lycett, Manouk Vrieling, Kirsty Robb, Paul A. Hoskisson, Matthew T. G. Holden, Edward J. Feil, Gavin K. Paterson, Steven Y. C. Tong, Adebayo Shittu, Willem van Wamel, David M. Aanensen, Julian Parkhill, Sharon J. Peacock, Jukka Corander, Mark Holmes, J. Ross Fitzgerald. Gene exchange drives the ecological success of a multi-host bacterial pathogen. Nature Ecology & Evolution, 2018; 2 (9): 1468 DOI: 10.1038/s41559-018-0617-0 

Courtesy: ScienceDaily
 

Building a better brain-in-a-dish, faster and cheaper

This is a false color image of a slice of human brain organoid from a patient with autism spectrum disorder.

Credit: Alysson Muotri, UC San Diego Health

Writing in the current online issue of the journal Stem Cells and Development, researchers at University of California San Diego School of Medicine describe development of a rapid, cost-effective method to create human cortical organoids directly from primary cells.

Experimental studies of developing human brain function are limited. Research involving live embryonic subjects is constrained by ethical concerns and the fragile nature of the brain itself. Animal models only partially mimic or recapitulate human biology and cognitive function. Single cell studies do not capture the complexity of neural networks.
In recent years, the development of in vitro human organoids -- three-dimensional, miniaturized, simplified versions of an organ produced from reprogrammed stem cells -- have allowed scientists to study biological functions, diseases and treatments more realistically and in greater detail.
"And that includes the brain," said Alysson R. Muotri, PhD, professor in the UC San Diego School of Medicine departments of Pediatrics and Cellular and Molecular Medicine, director of the UC San Diego Stem Cell Program and a member of the Sanford Consortium for Regenerative Medicine. "Cerebral organoids can form a variety of brain regions. They exhibit neurons that are functional and capable of electrical excitation. They resemble human cortical development at the gene expression levels."
Muotri is among the leaders in the field, having used the "brain-in-a-dish" approach to provide the first direct experimental proof that the Zika virus can cause severe birth defects, to repurpose existing HIV drugs on a rare, inherited neurological disorder and to create Neanderthalized "mini-brains."
But human brain organoids are difficult, time-consuming and expensive to produce, requiring sophisticated tools and know-how to first generate human induced pluripotent stem cells (iPSCs) capable of becoming almost any kind of cell from skin cells, called fibroblasts, then directing those iPSCs to differentiate into the variety of interconnected cell types that comprise an organ like the brain.
In the new paper, senior author Muotri and colleagues describe a new, rapid and cost-effective method to reprogram individual somatic cells directly into cortical organoids from hundreds of individuals simultaneously. To do so, they compressed and optimized several steps of the process so that somatic cells are reprogrammed, expanded and stimulated to form cortical cells almost simultaneously. The result is a cortical organoid that fully develops from somatic cells with only minor manipulation, Muotri said.
"What we've done is establish a proof-of-principle protocol for a systematic, automated process to generate large numbers of brain organoids," said Muotri. "The potential uses are vast, including creating large brain organoid repositories and the discovery of causal genetic variants to human neurological conditions associated with several mutations of unknown significance, such as autism spectrum disorder. If we want to understand the variability in human cognition, this is the first step."
Co-authors of the study include: Monique Schukking, Helen Miranda, Cleber A. Trujillo, and Priscilla D. Negraes, all at UC San Diego.
 

Journal Reference:

1. Monique Schukking, Helen Cristina Miranda, Cleber A Trujillo, Priscilla Davidson Negraes, Alysson Renato Muotri. Direct generation of human cortical organoids from primary cells. Stem Cells and Development, 2018; DOI: 10.1089/scd.2018.0112 

Courtesy: ScienceDaily
 

Genes are key to academic success, study suggests

Child working at school (stock image).

Credit: © Nikki / Fotolia

Parents always worry about whether their children will do well in school, but their kids probably were born with much of what they will need to succeed. A new study published in npj Science of Learning by researchers from The University of Texas at Austin and King's College London explains the substantial influence genes have on academic success, from the start of elementary school to the last day of high school.

For many years, research has linked educational achievement to life trajectories, such as occupational status, health or happiness. But if performing well in school predicts better life outcomes, what predicts how well someone will do throughout school?

"Around two-thirds of individual differences in school achievement are explained by differences in children's DNA," said Margherita Malanchini, a psychology postdoctoral fellow at the Population Research Center at UT Austin. "But less is known about how these factors contribute to an individual's academic success overtime."

Malanchini and Kaili Rimfeld, a postdoctoral researcher at the Institute of Psychiatry, Psychology and Neuroscience at King's College London, analyzed test scores from primary through the end of compulsory education of more than 6,000 pairs of twins.

Researchers found educational achievement to be highly stable throughout schooling, meaning that most students who started off well in primary school continued to do well until graduation. Genetic factors explained about 70 percent of this stability, while the twins shared environment contributed to about 25 percent, and their nonshared environment, such as different friends or teachers, contributed to the remaining 5 percent.

That's not to say that an individual was simply born smart, researchers explained. Even after accounting for intelligence, genes still explained about 60 percent of the continuity of academic achievement.

"Academic achievement is driven by a range of cognitive and noncognitive traits," Malanchini said. "Previously, studies have linked it to personality, behavioral problems, motivation, health and many other factors that are partly heritable."

However, at times grades did change, such as a drop in grades between primary and secondary school. Those changes, researchers said, can be explained largely by nonshared environmental factors.

"Our findings should provide additional motivation to identify children in need of interventions as early as possible, as the problems are likely to remain throughout the school years," said Rimfeld.

Journal Reference:

1. Kaili Rimfeld, Margherita Malanchini, Eva Krapohl, Laurie J. Hannigan, Philip S. Dale, Robert Plomin. The stability of educational achievement across school years is largely explained by genetic factors. npj Science of Learning, 2018; 3 (1) DOI: 10.1038/s41539-018-0030-0 

Courtesy: ScienceDaily

8,000 new antibiotic combinations are surprisingly effective

 

"We shouldn't limit ourselves to just single drugs or two-drug combinations in our medical toolbox," said Pamela Yeh (left), with Elif Tekin.

Credit: Reed Hutchinson/UCLA

Scientists have traditionally believed that combining more than two drugs to fight harmful bacteria would yield diminishing returns. The prevailing theory is that that the incremental benefits of combining three or more drugs would be too small to matter, or that the interactions among the drugs would cause their benefits to cancel one another out.

Now, a team of UCLA biologists has discovered thousands of four- and five-drug combinations of antibiotics that are more effective at killing harmful bacteria than the prevailing views suggested. Their findings, reported today in the journal npj Systems Biology and Applications, could be a major step toward protecting public health at a time when pathogens and common infections are increasingly becoming resistant to antibiotics.

"There is a tradition of using just one drug, maybe two," said Pamela Yeh, one of the study's senior authors and a UCLA assistant professor of ecology and evolutionary biology. "We're offering an alternative that looks very promising. We shouldn't limit ourselves to just single drugs or two-drug combinations in our medical toolbox. We expect several of these combinations, or more, will work much better than existing antibiotics."

Working with eight antibiotics, the researchers analyzed how every possible four- and five-drug combination, including many with varying dosages -- a total of 18,278 combinations in all -- worked against E. coli. They expected that some of the combinations would be very effective at killing the bacteria, but they were startled by how many potent combinations they discovered.

For every combination they tested, the researchers first predicted how effective they thought it would be in stopping the growth of E. coli. Among the four-drug combinations, there were 1,676 groupings that performed better than they expected. Among the five-drug combinations, 6,443 groupings were more effective than expected.

"I was blown away by how many effective combinations there are as we increased the number of drugs," said Van Savage, the study's other senior author and a UCLA professor of ecology and evolutionary biology and of biomathematics. "People may think they know how drug combinations will interact, but they really don't."

On the other hand, 2,331 four-drug combinations and 5,199 five-drug combinations were less effective than the researchers expected they would be, said Elif Tekin, the study's lead author, who was a UCLA postdoctoral scholar during the research.

Some of the four- and five-drug combinations were effective at least partly because individual medications have different mechanisms for targeting E. coli. The eight tested by the UCLA researchers work in six unique ways.

"Some drugs attack the cell walls, others attack the DNA inside," Savage said. "It's like attacking a castle or fortress. Combining different methods of attacking may be more effective than just a single approach."

Said Yeh: "A whole can be much more, or much less, than the sum of its parts, as we often see with a baseball or basketball team." (As an example, she cited the decisive upset victory in the 2004 NBA championship of the Detroit Pistons -- a cohesive team with no superstars -- over a Los Angeles Lakers team with future Hall of Famers Kobe Bryant, Shaquille O'Neal, Karl Malone and Gary Payton.)

Yeh added that although the results are very promising, the drug combinations have been tested in only a laboratory setting and likely are at least years away from being evaluated as possible treatments for people.

"With the specter of antibiotic resistance threatening to turn back health care to the pre-antibiotic era, the ability to more judiciously use combinations of existing antibiotics that singly are losing potency is welcome," said Michael Kurilla, director of the Division of Clinical Innovation at the National Institutes of Health/National Center for Advancing Translational Sciences. "This work will accelerate the testing in humans of promising antibiotic combinations for bacterial infections that we are ill-equipped to deal with today."

The researchers are creating open-access software based on their work that they plan to make available to other scientists next year. The software will enable other researchers to analyze the different combinations of antibiotics studied by the UCLA biologists, and to input data from their own tests of drug combinations.

Using a MAGIC framework

One component of the software is a mathematical formula for analyzing how multiple factors interact, which the UCLA scientists developed as part of their research. They call the framework "mathematical analysis for general interactions of components," or MAGIC.

"We think MAGIC is a generalizable tool that can be applied to other diseases -- including cancers -- and in many other areas with three or more interacting components, to better understand how a complex system works," Tekin said.

Savage said he plans to use concepts from that framework in his ongoing research on how temperature, rain, light and other factors affect the Amazon rainforests.

He, Yeh and Mirta Galesic, a professor of human social dynamics at the Santa Fe Institute, also are using MAGIC in a study of how people's formation of ideas is influenced by their parents, friends, schools, media and other institutions -- and how those factors interact.

"It fits in perfectly with our interest in interacting components," Yeh said.

Other co-authors of the new study are Cynthia White, a UCLA graduate who was a research technician while working on the project; Tina Kang, a UCLA doctoral student; Nina Singh, a student at the University of Southern California; Mauricio Cruz-Loya, a UCLA doctoral student; and Robert Damoiseaux, professor of molecular and medical pharmacology, and director of UCLA's Molecular Screening Shared Resource, a facility with advanced robotics technology where Tekin, White, and Kang conducted much of the research.

The research team reported in 2016 that combinations of three antibiotics can often overcome bacteria's resistance to antibiotics, even when none of the three antibiotics on its own -- or even two of the three together -- is effective. The biologists reported in 2017 two combinations of drugs that are unexpectedly successful in reducing the growth of E. coli bacteria.

Journal Reference:

1. Elif Tekin, Cynthia White, Tina Manzhu Kang, Nina Singh, Mauricio Cruz-Loya, Robert Damoiseaux, Van M. Savage, Pamela J. Yeh. Prevalence and patterns of higher-order drug interactions in Escherichia coli. npj Systems Biology and Applications, 2018; 4 (1) DOI: 10.1038/s41540-018-0069-9 

Courtesy: ScienceDaily