Monday, 18 August 2014

Suspect Gene Corrupts Neural Connections

'Diseases of synapses' demonstrated in a dish

Monday, 18 August 2014

Researchers have long suspected that major mental disorders are genetically-rooted diseases of synapses – the connections between neurons. Now, investigators supported in part by the National Institutes of Health have demonstrated in patients' cells how a rare mutation in a suspect gene disrupts the turning on and off of dozens of other genes underlying these connections.

Synapses – sites of intercellular communications
– are revealed in a mature iPSC cortex neuron
derived from a participant in the study. Immune-
based staining shows synapse markers (red,
green) and the cell's nucleus (blue). Credit:
Hongjun Song, Ph.D., Johns Hopkins University.
"Our results illustrate how genetic risk, abnormal brain development and synapse dysfunction can corrupt brain circuitry at the cellular level in complex psychiatric disorders," explained Hongjun Song, Ph.D., of Johns Hopkins University, Baltimore, a grantee of the NIH's National Institute of Mental Health (NIMH), a founder of the study.

Song and colleagues, from universities in the United States, China, and Japan, report on their discovery in the journal Nature, August 17, 2014.

"The approach used in this study serves as a model for linking genetic clues to brain development," said NIMH director Thomas R. Insel, M.D..

Most major mental disorders, such as schizophrenia, are thought to be caused by a complex interplay of multiple genes and environmental factors. However, studying rare cases of a single disease-linked gene that runs in a family can provide shortcuts to discovery. Decades ago, researchers traced a high prevalence of schizophrenia and other major mental disorders – which often overlap genetically – in a Scottish clan to mutations in the gene DISC1 (Disrupted In Schizophrenia-1). But until now, most of what's known about cellular effects of such DISC1 mutations has come from studies in the rodent brain.

To learn how human neurons are affected, Song's team used a disease-in-a-dish technology called induced pluripotent stem cells (iPSCs). A patient's skin cells are first induced to revert to stem cells. Stem cells play a critical role in development of the organism by transforming into the entire range of specialized cells which make up an adult. In this experiment, these particular "reverted" stem cells were coaxed to differentiate into neurons, which could be studied developing and interacting in a petri dish. This makes it possible to pinpoint, for example, how a particular patient's mutation might impair synapses. Song and colleagues studied iPSCs from four members of an American family affected by DISC1-linked schizophrenia and genetically related mental disorders.

Strikingly, iPSC-induced neurons, of a type found in front brain areas implicated in psychosis, expressed 80 percent less of the protein made by the DISC1 gene in family members with the mutation, compared to members without the mutation. These mutant neurons showed deficient cellular machinery for communicating with other neurons at synapses.

The researchers traced these deficits to errant expression of genes known to be involved in synaptic transmission, brain development, and key extensions of neurons where synapses are located. Among these abnormally expressed genes were 89 previously linked to schizophrenia, bipolar disorder, depression, and other major mental disorders. This was surprising, as DISC1's role as a hub that regulates expression of many genes implicated in mental disorders had not previously been appreciated, say the researchers.

The clincher came when researchers experimentally produced the synapse deficits by genetically engineering the DISC1 mutation into otherwise normal iPSC neurons – and, conversely, corrected the synapse deficits in DISC1 mutant iPSC neurons by genetically engineering a fully functional DISC1 gene into them. This established that the DISC1 mutation, was, indeed the cause of the deficits.

The results suggest a common disease mechanism in major mental illnesses that integrates genetic risk, aberrant neurodevelopment, and synapse dysfunction. The overall approach may hold promise for testing potential treatments to correct synaptic deficits, say the researchers.

Contact: Jules Asher

Reference:
Synaptic dysregulation in a human iPS cell model of major mental disorders 
Wen Z, Nguyen HN, Guo Z, Lalli MA, Wang X, Su Y, Kim N-S, Yoon K-J, Shin J, Zhang C, Makri G, Nauen D, Yu H, Guzman E, Chiang C-H, Yoritomo N, Kaibuchi K, Zou J, Christian KM, Cheng L, Ross CA, Margolis RL, Chen G, Kosik KS, Song H, Ming G
Nature, Aug. 17, 2014, doi:10.1038/nature13716
.........


For more on stem cells and cloning, go to CellNEWS at
http://cellnews-blog.blogspot.com/

Stem Cells Reveal How Schizophrenia-linked Genetic Variation Affects Neurons

Stem Cells Reveal How Schizophrenia-linked Genetic Variation Affects Neurons
Monday, 18 August 2014

A genetic variation linked to schizophrenia, bipolar disorder and severe depression wreaks havoc on connections among neurons in the developing brain, a team of researchers reports. The study, led by Guo-li Ming, M.D., Ph.D., and Hongjun Song, Ph.D., of the Johns Hopkins University School of Medicine and described online Aug. 17 in the journal Nature, used stem cells generated from people with and without mental illness to observe the effects of a rare and pernicious genetic variation on young brain cells. The results add to evidence that several major mental illnesses have common roots in faulty "wiring" during early brain development.

In this image, cell nuclei are shown in blue and
synapses in red and green. Credit: Zhexing Wen-
Johns Hopkins Medicine.
"This was the next best thing to going back in time to see what happened while a person was in the womb to later cause mental illness," says Ming.

"We found the most convincing evidence yet that the answer lies in the synapses that connect brain cells to one another."

Previous evidence for the relationship came from autopsies and from studies suggesting that some genetic variants that affect synapses also increase the chance of mental illness. But those studies could not show a direct cause-and-effect relationship, Ming says.

One difficulty in studying the genetics of common mental illnesses is that they are generally caused by environmental factors in combination with multiple gene variants, any one of which usually could not by itself cause disease. A rare exception is the gene known as disrupted in schizophrenia 1 (DISC1), in which some mutations have a strong effect. Two families have been found in which many members with the DISC1 mutations have mental illness.

Video of human neurons firing. Credit: Zhexing
Wen-Johns Hopkins Medicine.
To find out how a DISC1 variation with a few deleted DNA "letters" affects the developing brain, the research team collected skin cells from a mother and daughter in one of these families who have neither the variation nor mental illness, as well as the father, who has the variation and severe depression, and another daughter, who carries the variation and has schizophrenia. For comparison, they also collected samples from an unrelated healthy person. Postdoctoral fellow Zhexing Wen, Ph.D., coaxed the skin cells to form five lines of stem cells and to mature into very pure populations of synapse-forming neurons.

After growing the neurons in a dish for six weeks, collaborators at Pennsylvania State University measured their electrical activity and found that neurons with the DISC1 variation had about half the number of synapses as those without the variation. To make sure that the differences were really due to the DISC1 variation and not to other genetic differences, graduate student Ha Nam Nguyen spent two years making targeted genetic changes to three of the stem cell lines.

In one of the cell lines with the variation, he swapped out the DISC1 gene for a healthy version. He also inserted the disease-causing variation into one healthy cell line from a family member, as well as the cell line from the unrelated control. Sure enough, the researchers report, the cells without the variation now grew the normal amount of synapses, while those with the inserted mutation had half as many.

"We had our definitive answer to whether this DISC1 variation is responsible for the reduced synapse growth," Ming says.

To find out how DISC1 acts on synapses, the researchers also compared the activity levels of genes in the healthy neurons to those with the variation. To their surprise, the activities of more than 100 genes were different.

"This is the first indication that DISC1 regulates the activity of a large number of genes, many of which are related to synapses," Ming says.

The research team is now looking more closely at other genes that are linked to mental disorders. By better understanding the roots of mental illness, they hope to eventually develop better treatments for it, Ming says.

Contact: Shawna Williams

Reference:
Synaptic dysregulation in a human iPS cell model of major mental disorders 
Wen Z, Nguyen HN, Guo Z, Lalli MA, Wang X, Su Y, Kim N-S, Yoon K-J, Shin J, Zhang C, Makri G, Nauen D, Yu H, Guzman E, Chiang C-H, Yoritomo N, Kaibuchi K, Zou J, Christian KM, Cheng L, Ross CA, Margolis RL, Chen G, Kosik KS, Song H, Ming G
Nature, Aug. 17, 2014, doi:10.1038/nature13716
.........


For more on stem cells and cloning, go to CellNEWS at
http://cellnews-blog.blogspot.com/

Wednesday, 13 August 2014

New Material Could Enhance Fast and Accurate DNA Sequencing

New Material Could Enhance Fast and Accurate DNA Sequencing
Wednesday, 13 August 2014

Gene-based personalized medicine has many possibilities for diagnosis and targeted therapy, but one big bottleneck: the expensive and time-consuming DNA-sequencing process.

A DNA molecule passes through a nanopore in a
sheet of molybdenum disulphide, a material that
researchers have found to be better than
graphene at reading the DNA sequence. 
CreditNarayana Aluru, University of Illinois.
Now, researchers at the University of Illinois at Urbana-Champaign have found that nanopores in the material molybdenum disulphide (MoS2) could sequence DNA more accurately, quickly and inexpensively than anything yet available.

"One of the big areas in science is to sequence the human genome for under $1,000, the 'genome-at-home,'" said Narayana Aluru, a professor of mechanical science and engineering at the U. of I. who led the study.

"There is now a hunt to find the right material. We've used MoS2 for other problems, and we thought, why don't we try it and see how it does for DNA sequencing?"

As it turns out, MoS2 outperforms all other materials used for nanopore DNA sequencing – even graphene.

A nanopore is a very tiny hole drilled through a thin sheet of material. The pore is just big enough for a DNA molecule to thread through. An electric current drives the DNA through the nanopore, and the fluctuations in the current as the DNA passes through the pore tell the sequence of the DNA, since each of the four letters of the DNA alphabet – A, C, G and T – are slightly different in shape and size.

Illinois researchers found that the material
molybdenum disulphide could be the most
efficient yet found for DNA sequencing, making
personalized medicine more accessible. From
left: Amir Barati Farimani, Kyongmin Min and
Narayana Aluru. Credit: L. Brian Stauffer.
Most materials used for nanopore DNA sequencing have a sizable flaw: They are too thick. Even a thin sheet of most materials spans multiple links of the DNA chain, making it impossible to accurately determine the exact DNA sequence.

Graphene has become a popular alternative, since it is a sheet made of a single layer of carbon atoms – meaning only one base at a time goes through the nanopore. Unfortunately, graphene has its own set of problems, the biggest being that the DNA sticks to it. The DNA interacting with the graphene introduces a lot of noise that makes it hard to read the current, like a radio station marred by loud static.

MoS2 is also a single-layer sheet, thin enough that only one DNA letter at a time goes through the nanopore. In the study, the Illinois researchers found that DNA does not stick to MoS2, but threads through the pore cleanly and quickly. See an animation online.

"MoS2 is a competitor of graphene in terms of transistors, but we showed here a new functionality of this material by showing that it is capable of biosensing," said graduate student Amir Barati Farimani, the first author of the paper.

Most exciting for the researchers, the simulations yielded four distinct signals corresponding to the bases in a double-stranded DNA molecule. Other systems have yielded two at best – A/T and C/G – which then require extensive computational analysis to attempt to distinguish A from T and C from G.

The key to the success of the complex MoS2 simulation and analysis was the Blue Waters supercomputer, located at the National Center for Supercomputing Applications at the U. of Illinois.

"These are very detailed calculations," said Aluru, who is also a part of the Beckman Institute for Advanced Science and Technology at the U. of I.

"They really tell us the physics of the actual mechanisms, and why MoS2 is performing better than other materials. We have those insights now because of this work, which used Blue Waters extensively."

Now, the researchers are exploring whether they can achieve even greater performance by coupling MoS2 with another material to form a low-cost, fast and accurate DNA sequencing device.

"The ultimate goal of this research is to make some kind of home-based or personal DNA sequencing device," Barati Farimani said.

"We are on the path to get there, by finding the technologies that can quickly, cheaply and accurately identify the human genome. Having a map of your DNA can help to prevent or detect diseases in the earliest stages of development. If everybody can cheaply sequence so they can know the map of their genetics, they can be much more alert to what goes on in their bodies."

Contact: Liz Ahlberg

Reference:
DNA Base Detection Using a Single-Layer MoS2
Amir Barati Farimani, Kyoungmin Min, and Narayana R. Aluru 
ACS Nano, July 9, 2014, DOI: 10.1021/nn5029295
.........


For more on stem cells and cloning, go to CellNEWS at
http://cellnews-blog.blogspot.com/