DNA methylation map of mouse and human brain identifies target genes in Alzheimer’s disease

The central nervous system has a pattern of gene expression that is closely regulated with respect to functional and anatomical regions. DNA methylation is a major regulator of transcriptional activity, and aberrations in the distribution of this epigenetic mark may be involved in many neurological disorders, such as Alzheimer’s disease. Herein, we have analysed 12 distinct mouse brain regions according to their CpG 5’-end gene methylation patterns and observed their unique epigenetic landscapes. The DNA methylomes obtained from the cerebral cortex were used to identify aberrant DNA methylation changes that occurred in two mouse models of Alzheimer’s disease. We were able to translate these findings to patients with Alzheimer’s disease, identifying DNA methylation-associated silencing of three targets genes: thromboxane A2 receptor (TBXA2R), sorbin and SH3 domain containing 3 (SORBS3) and spectrin beta 4 (SPTBN4). These hypermethylation targets indicate that the cyclic AMP response element-binding protein (CREB) activation pathway and the axon initial segment could contribute to the disease.

Baby owls sleep like baby humans

Researchers at the Max Planck Institute for Ornithology and the University of Lausanne have discovered that the sleeping patterns of baby birds are similar to that of baby mammals. What is more, the sleep of baby birds appears to change in the same way as it does in humans. Studying barn owls in the wild, the researchers discovered that this change in sleep is strongly correlated with the expression of a gene involved in producing dark, melanic feather spots, a trait known to covary with behavioral and physiological traits in adult owls. These findings raise the intriguing possibility that sleep-related developmental processes in the brain contribute to the link between melanism and other traits observed in adult barn owls and other animals.

Sleep in mammals and birds consists of two phases, REM sleep (“Rapid Eye Movement Sleep”) and non-REM sleep. We experience our most vivid dreams during REM sleep, a paradoxical state characterized by awake-like brain activity. Despite extensive research, REM sleep’s purpose remains a mystery. One of the most salient features of REM sleep is its preponderance early in life. A variety of mammals spend far more time in REM sleep during early life than when they are adults. For example, as newborns, half of our time asleep is spent in REM sleep, whereas last night REM sleep probably encompassed only 20-25% percent of your time snoozing.Although birds are the only non-mammalian group known to clearly engage in REM sleep, it has been unclear whether sleep develops in the same manner in baby birds. Consequently, Niels Rattenborg of the MPIO, Alexandre Roulin of Unil, and their PhD student Madeleine Scriba, reexamined this question in a population of wild barn owls. They used an electroencephalogram (EEG) and movement data logger in conjunction with minimally invasive EEG sensors designed for use in humans, to record sleep in 66 owlets of varying age. During the recordings, the owlets remained in their nest box and were fed normally by their parents. After having their sleep patterns recorded for up to five days, the logger was removed. All of the owlets subsequently fledged and returned at normal rates to breed in the following year, indicating that there were no long-term adverse effects of eves-dropping on their sleeping brains.

Despite lacking significant eye movements (a trait common to owls), the owlets spent large amounts of time in REM sleep. “During this sleep phase, the owlets’ EEG showed awake-like activity, their eyes remained closed, and their heads nodded slowly”, reports Madeleine Scriba from the University of Lausanne (see video). Importantly, the researchers discovered that just as in baby humans, the time spent in REM sleep declined as the owlets aged.

In addition, the team examined the relationship between sleep and the expression of a gene in the feather follicles involved in producing dark, melanic feather spots. “As in several other avian and mammalian species, we have found that melanic spotting in owls covaries with a variety of behavioral and physiological traits, many of which also have links to sleep, such as immune system function and energy regulation”, notes Alexander Roulin from the University of Lausanne. Indeed, the team found that owlets expressing higher levels of the gene involved in melanism had less REM sleep than expected for their age, suggesting that their brains were developing faster than in owlets expressing lower levels of this gene. In line with this interpretation, the enzyme encoded by this gene also plays a role in producing hormones (thyroid and insulin) involved in brain development.

Although additional research is needed to determine exactly how sleep, brain development, and pigmentation are interrelated, these findings nonetheless raise several intriguing questions. Does variation in sleep during brain development influence adult brain organization? If so, does this contribute to the link between behavioral and physiological traits and melanism observed in adult owls? Do sleep and pigmentation covary in adult owls, and if so how does this influence their behavior and physiology? Finally, Niels Rattenborg from the Max Planck Institute for Ornithology in Seewiesen hopes that “this naturally occurring variation in REM sleep during a period of brain development can be used to reveal exactly what REM sleep does for the developing brain in baby owls, as well as humans.”

Gene switches make prairie voles fall in love

Epigenetic changes affect neurotransmitters that lead to pair-bond formation.

Love really does change your brain — at least, if you’re a prairie vole. Researchers have shown for the first time that the act of mating induces permanent chemical modifications in the chromosomes, affecting the expression of genes that regulate sexual and monogamous behaviour. The study is published today in Nature Neuroscience.

Prairie voles (Microtus ochrogaster) have long been of interest to neuroscientists and endocrinologists who study the social behaviour of animals, in part because this species forms monogamous pair bonds — essentially mating for life. The voles’ pair bonding, sharing of parental roles and egalitarian nest building in couples makes them a good model for understanding the biology of monogamy and mating in humans.

Previous studies have shown that the neurotransmitters oxytocin and vasopressin play a major part in inducing and regulating the formation of the pair bond. Monogamous prairie voles are known to have higher levels of receptors for these neurotransmitters than do voles who have yet to mate; and when otherwise promiscuous montane voles (M. montanus) are dosed with oxytocin and vasopressin, they adopt the monogamous behaviour of their prairie cousins.

Because behaviour seemed to play an active part in changing the neurobiology of the animals, scientists suspected that epigenetic factors were involved. These are chemical modifications to the chromosomes that affect how genes are transcribed or suppressed, as opposed to changes in the gene sequences themselves.

Love potion

To look for clues of epigenetic agents at play in monogamous behaviour, neuroscientist Mohamed Kabbaj and his team at Florida State University in Tallahassee took voles which had been housed together for 6 hours but had not mated. The researchers injected drugs into the voles’ brains near a region called the nucleus accumbens, which is closely associated with the reinforcement of reward and pleasure. The drugs blocked the activity of an enzyme that normally keeps DNA tightly wound up and thus prevents the expression of genes.

The team found that the genes for the vasopressin and oxytocin receptors had been transcribed, and as a result the nucleus accumbens of the animals bore high levels of these receptors. Animals that had been permitted to mate also had high levels of vasopressin and oxytocin receptors, confirming the link between bond formation and gene activity.

“Mating activates this brain area which leads to partner preference — we can induce this same change in the brain with this drug,” Kabbaj explains.

Interestingly, the injection alone cannot induce the partner preference. “The drug by itself won’t do all these molecular changes — you need the context: it’s the drug plus the six hours of cohabitation,” says Kabbaj.

“This is a study I myself wanted to do years ago,” says Thomas Insel, who heads the US National Institute of Mental Health in Bethesda, Maryland. “If mating causes the release of the neuropeptide, how does this kick into a higher gear for the rest of the animal’s life? This study for me really is the first experimental demonstration that the epigenetic change would be necessary for the long-term change in behaviour.”

“This paper really shows that there is an epigenetic mechanism underlying pair bonds — we ourselves have looked for that and not found it,” says Alaine Keebaugh of Emory University in Atlanta, Georgia, who also studies the neuroscience of prairie voles.

Kabbaj says he hopes that the work could ultimately lead to an enhanced understanding of how epigenetic factors affect social behaviour in humans — not only in monogamy and pair bonding, but also in conditions such as autism and schizophrenia, which affect social interactions.

Changes in brain chemistry sustain obesity

With obesity reaching epidemic levels in some parts of the world, scientists have only begun to understand why it is such a persistent condition. A study in the Journal of Biological Chemistry adds substantially to the story by reporting the discovery of a molecular chain of events in the brains of obese rats that undermined their ability to suppress appetite and to increase calorie burning.

It’s a vicious cycle, involving a breakdown in how brain cells process key proteins, that allows obesity to beget further obesity. But in a finding that might prove encouraging in the long term, the researchers at Brown University and Lifespan also found that they could intervene to break that cycle by fixing the core protein-processing problem.

Before the study, scientists knew that one mechanism in which obesity perpetuates itself was by causing resistance to leptin, a hormone that signals the brain about the status of fat in the body. But years ago senior author Eduardo A. Nillni, professor of medicine at Brown University and a researcher at Rhode Island Hospital, observed that after meals obese rats had a dearth of another key hormone — alpha-MSH — compared to rats of normal weight.

Alpha-MSH has two jobs in parts of the hypothalamus region of the brain. One is to suppress the activity of food-seeking brain cells. The second is to signal other brain cells to produce the hormone TRH, which prompts the thyroid gland to spur calorie burning activity in the body.

In the obese rats alpha-MSH was low, despite an abundance of leptin and despite normal levels of gene expression both for its biochemical precursor protein called pro-opiomelanocortin (POMC) and for a key enzyme called PC2 that processes POMC in brain cells. There had to be more to the story than just leptin, and it wasn’t a problem with expressing the needed genes.

Nillni and his co-authors, including lead authors Isin Cakir and Nicole Cyr, conducted the new study to find out where the alpha-MSH deficit was coming from. Nillni said he suspected that the problem might lie in the brain cells’ mechanism for processing the POMC protein to make alpha-MSH.

Protein processing problems

To do their work, the team fed some rats a high-calorie diet and fed others a normal diet for 12 weeks. The overfed rats developed the condition of “diet-induced obesity.” The team then studied the hormone levels and brain cell physiology of the rats. They also tested their findings by experimenting with the biochemistry of key individual cells on the lab bench.

They found that in the obese rats, a key “machine” in the brain cells’ assembly line of protein-making, called the endoplasmic reticulum (ER), becomes stressed and overwhelmed. The overloaded ER apparently fumbles the proper handling of PC2, perhaps discarding it because it can’t be folded up properly. The PC2 levels they measured in obese rats, for example, were 53 percent lower than in normal rats. Alpha-MSH peptides were also barely more than half as abundant in obese rats as they were in healthy rats.

“In our study we showed that what actually prevents the production of more alpha-MSH peptide is that ER stress was decreasing the biosynthesis of POMC by affecting one key enzyme that is essential for the formation of alpha-MSH,” Nillni said. “This is so novel. Nobody ever looked at that.”

Novel as it was, the story — a stressed ER mishandles PC2, which leaves POMC unfolded, which impedes alpha-MSH production — needed experimental confirmation.

The team provided that confirmation in several ways: In obese rats they measured elevated levels of known markers of ER stress. They also purposely induced ER stress in cells using pharmacological agents and saw that both PC2 and Alpha-MSH levels dropped.

Next they conducted an experiment to see if fixing ER stress would improve alpha-MSH production. They treated lean and obese rats for two days with a chemical called TUDCA, which is known to alleviate ER stress. If ER stress is responsible for alpha-MSH production problems, the researchers would see alpha-MSH recover in obese rats treated with TUDCA. Sure enough, while TUDCA didn’t increase alpha-MSH production in normal rats, it increased it markedly in the obese rats.

Similarly on the benchtop they took mouse neurons that produce PC2 and POMC and pretreated some with a similar chemical called PBA that prevents ER stress. They left others untreated. Then they induced ER stress in all the cells. Under that ER stress, those that had been pretreated with PBA produced about twice as much PC2 as those that had not.

Nillni cautioned that although his team found ways to restore PC2 and alpha-MSH by treating ER stress in living rats and individual cells, the agents used in the study are not readily applicable as medicines for treating obesity in humans. There could well be unknown and unwanted side effects, for example, and TUDCA is not approved for human use by the U.S. Food and Drug Administration.

But by laying out the exact mechanism responsible for why the brains of the obese rats failed to curb appetite or spur greater calorie burning, Nillni said, the study points drug makers to several opportunities where they can intervene to break this new, vicious cycle that helps obesity to perpetuate itself.

“Understanding the central control of energy-regulating neuropeptides during diet-induced obesity is important for the identification of therapeutic targets to prevent and or mitigate obesity pathology,” the authors wrote.

Boosting ‘cellular garbage disposal’ can delay the aging process

UCLA life scientists have identified a gene previously implicated in Parkinson’s disease that can delay the onset of aging and extend the healthy life span of fruit flies. The research, they say, could have important implications for aging and disease in humans.

The gene, called parkin, serves at least two vital functions: It marks damaged proteins so that cells can discard them before they become toxic, and it is believed to play a key role in the removal of damaged mitochondria from cells.

"Aging is a major risk factor for the development and progression of many neurodegenerative diseases," said David Walker, an associate professor of integrative biology and physiology at UCLA and senior author of the research. "We think that our findings shed light on the molecular mechanisms that connect these processes."

In the research, published today in the early online edition of the journal Proceedings of the National Academy of Sciences, Walker and his colleagues show that parkin can modulate the aging process in fruit flies, which typically live less than two months. The researchers increased parkin levels in the cells of the flies and found that this extended their life span by more than 25 percent, compared with a control group that did not receive additional parkin.

"In the control group, the flies are all dead by Day 50," Walker said. "In the group with parkin overexpressed, almost half of the population is still alive after 50 days. We have manipulated only one of their roughly 15,000 genes, and yet the consequences for the organism are profound."

"Just by increasing the levels of parkin, they live substantially longer while remaining healthy, active and fertile," said Anil Rana, a postdoctoral scholar in Walker’s laboratory and lead author of the research. "That is what we want to achieve in aging research — not only to increase their life span but to increase their health span as well."

Treatments to increase parkin expression may delay the onset and progression of Parkinson’s disease and other age-related diseases, the biologists believe. (If parkin sounds related to Parkinson’s, it is. While the vast majority of people with the disease get it in older age, some who are born with a mutation in the parkin gene develop early-onset, Parkinson’s-like symptoms.)

"Our research may be telling us that parkin could be an important therapeutic target for neurodegenerative diseases and perhaps other diseases of aging," Walker said. "Instead of studying the diseases of aging one by one — Parkinson’s disease, Alzheimer’s disease, cancer, stroke, cardiovascular disease, diabetes — we believe it may be possible to intervene in the aging process and delay the onset of many of these diseases. We are not there yet, and it can, of course, take many years, but that is our goal."

'The garbage men in our cells go on strike'

To function properly, proteins must fold correctly, and they fold in complex ways. As we age, our cells accumulate damaged or misfolded proteins. When proteins fold incorrectly, the cellular machinery can sometimes repair them. When it cannot, parkin enables cells to discard the damaged proteins, said Walker, a member of UCLA’s Molecular Biology Institute.

"If a protein is damaged beyond repair, the cell can recognize that and eliminate the protein before it becomes toxic," he said. "Think of it like a cellular garbage disposal. Parkin helps to mark damaged proteins for disposal. It’s like parkin places a sticker on the damaged protein that says ‘Degrade Me,’ and then the cell gets rid of this protein. That process seems to decline with age. As we get older, the garbage men in our cells go on strike. Overexpressed parkin seems to tell them to get back to work."

Rana focused on the effects of increased parkin activity at the cellular and tissue levels. Do flies with increased parkin show fewer damaged proteins at an advanced age? “The remarkable finding is yes, indeed,” Walker said.

Parkin has recently been shown to perform a similarly important function with regard to mitochondria, the tiny power generators in cells that control cell growth and tell cells when to live and die. Mitochandria become less efficient and less active as we age, and the loss of mitochondrial activity has been implicated in Alzheimer’s, Parkinson’s and other neurodegenerative diseases, as well as in the aging process, Walker said.

Parkin appears to degrade the damaged mitochondria, perhaps by marking or changing their outer membrane structure, in effect telling the cell, “This is damaged and potentially toxic. Get rid of it.”

If parkin is good, is more parkin even better?

While the researchers found that increased parkin can extend the life of fruit flies, Rana also discovered that too much parkin can have the opposite effect — it becomes toxic to the flies. When he quadrupled the normal amount of parkin, the fruit flies lived substantially longer, but when he increased the amount by a factor of 30, the flies died sooner.

"If you bombard the cell with too much parkin, it could start eliminating healthy proteins," Rana said.

In the lower doses, however, the scientists found no adverse effects. Walker believes the fruit fly is a good model for studying aging in humans — who also have the parkin gene — because scientists know all of the fruit fly’s genes and can switch individual genes on and off.

Previous research has shown that fruit flies die sooner when you remove parkin, Walker noted.

Walker and Rana do not know what the optimal amount of parkin would be in humans.

While the biologists increased parkin activity in every cell in the fruit fly, Rana also conducted an experiment in which he increased parkin expression only in the nervous system. That, too, was sufficient to make the flies live longer.

"This tells us that parkin is neuroprotective during aging," Walker said. "However, the beneficial effects of parkin are greater — twice as large — when we increased its expression everywhere."

"We were excited about this research from the beginning but did not know then that the life span increase would be this impressive," Rana said.

The image that accompanies this news release shows clumps or aggregates of damaged proteins in an aged brain from a normal fly (left panel) and an age-matched brain with increased neuronal parkin levels (right panel). As can be seen, increasing parkin levels in the aging brain reduces the accumulation of aggregated proteins.

Scientists have found that this kind of protein aggregation occurs in mammals as well, including humans, Rana said.

"Imagine the damage the accumulation of protein trash is doing to the cell," Walker said. "With increased Parkin, the trash has been collected. Without it, the garbage that should be discarded is accumulating in the cells."

Pathway Competition Affects Early Differentiation of Higher Brain Structures

Sand-dwelling and rock-dwelling cichlids living in East Africa’s Lake Malawi share a nearly identical genome, but have very different personalities. The territorial rock-dwellers live in communities where social interactions are important, while the sand-dwellers are itinerant and less aggressive.

Those behavioral differences likely arise from a complex region of the brain known as the telencephalon, which governs communication, emotion, movement and memory in vertebrates – including humans, where a major portion of the telencephalon is known as the cerebral cortex. A study published this week in the journal Nature Communications shows how the strength and timing of competing molecular signals during brain development has generated natural and presumably adaptive differences in the telencephalon much earlier than scientists had previously believed.

In the study, researchers first identified key differences in gene expression between rock- and sand-dweller brains during development, and then used small molecules to manipulate developmental pathways to mimic natural diversity.

“We have shown that the evolutionary changes in the brains of these fishes occur really early in development,” said Todd Streelman, an associate professor in the School of Biology and the Petit Institute for Bioengineering and Biosciences at the Georgia Institute of Technology. “It’s generally been thought that early development of the brain must be strongly buffered against change. Our data suggest that rock-dweller brains differ from sand-dweller brains – before there is a brain.”

For humans, the research could lead scientists to look for subtle changes in brain structures earlier in the development process. This could provide a better understanding of how disorders such as autism and schizophrenia could arise during very early brain development.

The research was supported by the National Science Foundation and published online April 23 by the journal.

“We want to understand how the telencephalon evolves by looking at genetics and developmental pathways in closely-related species from natural populations,” said Jonathan Sylvester, a postdoctoral researcher in the Georgia Tech School of Biology and lead author of the paper. “Adult cichlids have a tremendous amount of variation within the telencephalon, and we investigated the timing and cause of these differences. Unlike many previous studies in laboratory model organisms that focus on large, qualitative effects from knocking out single genes, we demonstrated that brain diversity evolves through quantitative tuning of multiple pathways.”

In examining the fish from embryos to adulthood, the researchers found that the mbuna, or rock-dwellers, tended to exhibit a larger ventral portion of the telencephalon, called the subpallium – while the sand-dwellers tended to have a larger version of the dorsal structure known as the pallium. These structures seem to have evolved differently over time to meet the behavioral and ecological needs of the fishes. The team showed that early variation in the activity of developmental signals expressed as complementary dorsal-ventral gradients, known technically as “Wingless” and “Hedgehog,” are involved in creating those differences during the neural plate stage, as a single sheet of neural tissue folds to form the neural tube.

To specifically manipulate those two pathways, Sylvester removed clutches of between 20 and 40 eggs from brooding female cichlids, which normally incubate fertilized eggs in their mouths. At about 36 to 48 hours after fertilization, groups of eggs were exposed to small-molecule chemicals that either strengthened or weakened the Hedgehog signal, or strengthened or weakened the Wingless signal. The chemical treatment came while the structures that would become the brain were little more than a sheet of cells. After treatment, water containing the chemicals was replaced with fresh water, and the embryos were allowed to continue their development.

“We were able to artificially manipulate these pathways in a way that we think evolution might have worked to shift the process of rock-dweller telencephalon development to sand-dweller development, and vice-versa. Treatment with small molecules allows us incredible temporal and dose precision in manipulating natural development,” Sylvester explained. “We then followed the development of the embryos until we were able to measure the anatomical structures – the size of the pallium and subpallium – to see that we had transformed one to the other.”

The two different brain regions, the dorsal pallium and ventral subpallium, give rise to excitatory and inhibitory neurons in the forebrain. Altering the relative sizes of these regions might change the balance between these neuronal types, ultimately producing behavioral changes in the adult fish.

“Evolution has fine-tuned some of these developmental mechanisms to produce diversity,” Streelman said. “In this study, we have figured out which ones.”

The researchers studied six different species of East African cichlids, and also worked with collaborators at King’s College in London to apply similar techniques in the zebrafish.

As a next step, the researchers would like to follow the embryos through to adulthood to see if the changes seen in embryonic and juvenile brain structures actually do change behavior of adults. It’s possible, said Streelman, that later developmental events could compensate for the early differences.

The results could be of interest to scientists investigating human neurological disorders that result from an imbalance between excitatory and inhibitory neurons. Those disorders include autism and schizophrenia. “We think it is particularly interesting that there may be some adaptive variation in the natural proportions of excitatory versus inhibitory neurons in the species we study, correlated with their natural behavioral differences,” said Streelman.

Do drugs for bipolar disorder “normalize” brain gene function?

Every day, millions of people with bipolar disorder take medicines that help keep them from swinging into manic or depressed moods. But just how these drugs produce their effects is still a mystery.

Now, a new University of Michigan Medical School study of brain tissue helps reveal what might actually be happening. And further research using stem cells programmed to act like brain cells is already underway.

Using genetic analysis, the new study suggests that certain medications may help “normalize” the activity of a number of genes involved in communication between brain cells. It is published in the current issue of Bipolar Disorders.

The study involved brain tissue from deceased people with and without bipolar disorder, which the U-M team analyzed to see how often certain genes were activated, or expressed. Funding support came from the National Institutes of Health and the Heinz C. Prechter Bipolar Research Fund.

“We found there are hundreds of genes whose activity is adjusted in individuals taking medication – consistent with the fact that there are a number of genes that are potentially amiss in people with bipolar,” says senior author Melvin McInnis, M.D., the U-M psychiatrist, U-M Depression Center member and principal investigator of the Prechter Fund Projects who helped lead the study. “Taking the medications, specifically ones in a class called antipsychotics, seemed to normalize the gene expression pattern in these individuals so that it approached that of a person without bipolar.”

Digging deeper into bipolar genetics

Scientists already know that bipolar disorder’s roots lie in genetic differences in the brain — though they are still searching for the specific gene combinations involved.  

McInnis and his colleagues have now embarked on research developing several a lines of induced pluripotent stem cells derived (iPSC) from volunteers with and without bipolar disorder, which will allow even more in-depth study of the development and genetics of bipolar disorder.

The newly published study looked at the expression, or activity levels, of 2,191 different genes in the brains of 14 people with bipolar disorder, and 12 with no mental health conditions. The brains were all part of a privately funded nonprofit brain bank that collected and stored donated brains, and recorded what medications the individuals were taking at the time of death.

Seven of the brains were from people with bipolar disorder who had been taking one or more antipsychotics when they died. These drugs include clozapine, risperidone, and haloperidol, and are often used to treat bipolar disorder. Most of the 14 brain donors with bipolar disorder were also taking other medications, such as antidepressants, at the time of death.

When the researchers compared the gene activity patterns among the brains of bipolar disorder patients who had been exposed to antipsychotics with patterns among those who weren’t, they saw striking differences.

Then, when they compared the activity patterns of patients who had been taking antipsychotics with those of people without bipolar disorder, they found similar patterns.

The similarities were strongest in the expression of genes involved in the transmission of signals across synapses – the gaps between brain cells that allow cells to ‘talk’ to one another. There were also similarities in the organization of nodes of Ranvier – locations along nerve cells where signals can travel faster.

McInnis, who is the Thomas B. and Nancy Upjohn Woodworth Professor of Bipolar Disorder and Depression in the U-M Department of Psychiatry, worked with U-M scientists Haiming Chen, M.D. and K. Sue O’Shea, Ph.D., of the U-M Department of Cell and Developmental Biology. They also teamed with Johns Hopkins University researcher Christopher Ross, M.D., Ph.D. on the new research; U-M and Johns Hopkins have a long history of collaboration on bipolar disorder research.

The research used brain tissue samples from the Stanley Brain Collection of the Stanley Medical Research Institute in Maryland.

Using “gene chip” analysis to measure the presence of messenger RNA molecules that indicate gene activity, and sophisticated data analysis, they were able to map the expression patterns from the brains and break the results down by bipolar status and medication use. The bipolar and control (non-bipolar) brains were matched by age, gender and other factors.

“In bipolar disorder, it’s not just one gene that’s involved – it’s a whole symphony of them,” says McInnis, who has helped lead U-M’s bipolar genetics research for nearly a decade. “Medications appear to nudge them in a direction that aligns more with the normal expression pattern.”

Among those that were “nudged” were genes that have already been shown to be linked to bipolar disorder, including glycogen synthase kinase 3 beta (GSK3β), FK506 binding protein 5 (FKBP5), and Ankyrin 3 (ANK3).

Going forward, says McInnis, cell culture studies will be critical to studying how medications for bipolar disorder work, and to screen new molecules as potential new medications.

Comparing mouse and human immune systems

It is a familiar note struck when authors conclude their reports on experiments conducted in mouse models: They suggest caution when translating their findings from mouse to human. A variation of this refrain can be heard when a small molecule that works in mice fails in human clinical trials.

There may be myriad reasons why results differ, and some challenges to the relevance of mouse models to human disease and therapy may be more anecdotal than evidence-driven, scientists say. But the need for better understanding the differences and similarities between human and mouse is clear. Genomic tools and analysis have opened the door to making comprehensive comparisons at a basic level that can inform future research in both mice and humans.

Scientists studying cell differentiation and function in the immune system set out to chart how the mouse and human compare in this area. Tal Shay, a postdoctoral associate in Aviv Regev’s lab at the Broad Institute of Harvard and MIT, led a team from Harvard Medical School, the Broad and Stanford University who compared two large compendia containing transcriptional profiles—how genes are expressed—in human and mouse immune cell types.

The researchers found remarkable consistency between gene expression profiles in the mouse and human immune systems but also some instances of divergence. The majority of gene expression patterns—conservatively estimated at 80 percent—were the same in mouse and human. In addition, they suggest a role for transcriptional regulators that may guide some of the similarities.

Shay and her colleagues reported their findings in PNAS and also deposited their data and analysis in a web portal, which they hope will serve as a reference map for other investigators. Their work is part of the ImmGen Consortium, a collaboration of immunologists and computational biologists generating a complete compendium of gene expression and its regulation in the mouse immune system.

“We wanted to pinpoint where immune system genes and gene expression are different and where you should be very suspicious if something is found in mouse and likely to be translated to human,” said Shay, who is a lead author of the paper. “We thought we might be able to map those places where the comparison is less robust, but we had a very hard time pinpointing convincing differences.”

The researchers had to take extraordinary pains to make sure they were comparing only what was comparable—apples to apples. Not all mouse genes had a corresponding gene in the human data set, or they had more than one: There might be one gene in humans versus five in mice for smell receptors, for example. Sometimes differences were a matter of timing: Genes were activated earlier or later, depending on the species, said David Puyraimond-Zemmour, an HMS graduate student in immunology in the lab of Christophe Benoist and Diane Mathis and a co-author of the PNAS paper.

In all, they found several dozen genes in seven immune cell types that have different expression in 80 human and 137 mouse samples. Their conclusions are based on comparing data from the Differentiation Map—which measures gene expression in about 40 human cell types—and data from ImmGen, which does the same for about 200 mouse cell types. They did further analyses of gene expression when cells were activated in different states, such as responding to infection, based on a data set produced by Ei Wakamatsu and Ting Feng, postdoctoral fellows in the Benoist-Mathis lab. Shay also worked with the Differentiation Map data from the lab of Benjamin Ebert, HMS associate professor of medicine at Brigham and Women’s Hospital and Dana-Farber Cancer Institute and an associate member of the Broad Institute, as well as from the ImmGen Project.

“What we assume most people will be interested in knowing is, if they are working on gene X, whether gene X has the same expression pattern in human and mouse immune systems,” Shay said. “Most lineages have the same expression signature but some genes behave differently and we think it’s important for why some things work in mice but not humans and the other way around.”

Benoist, Morton Grove-Rasmussen Professor of Immunohematology at Harvard Medical School, said the continuing debate about the usefulness of mouse models in understanding humans “is often at the level of the emotional and not necessarily very informed.” Wildly different experimental conditions—hugely varying doses or duration in clinical trials—make comparisons suspect, he said.

Having clear data that scientists can freely access will be useful, said Benoist, who is also a co-author of the PNAS paper.

“The value here is putting up signposts, signaling when the function of a gene in mice may not be relevant to humans,” he said, referring to data and analysis from the work published in PNAS. “Because the differentiation and function of human and mouse lineages are highly related, there is the expectation of conservation, so it is important to know when inter-species inferences may be an issue. Mouse models are far too valuable to be jettisoned for pre-clinical exploration, but it is important to know when caution is needed.”