The gut-based tango of microbial and host genes

December 5, 2016 § Leave a comment

When you think ‘oscillations in your gut,’ you might think of motion sickness or food poisoning. But there is another type of oscillations in both the gut and other organs. These oscillations are an interplay of genetic switches for protein expression that turn on and off throughout the day as we transition through eating, working, exercising and sleeping. In a paper published in Cell on Dec. 1, researchers in Israel have investigated the links between the day-and-night circadian rhythm in mice and the microbes that thrive in their gastrointestinal tracts. They’ve found that the daily fluctuations that occur between the two systems are more intimately linked than previously expected.

The diurnal oscillations of microbial localization and metabolite production extend far beyond the gastrointestinal tract the microbes inhabit. Credit: Thaiss et al/Cell 2016

The diurnal oscillations of microbial localization and metabolite production extend far beyond the gastrointestinal tract the microbes inhabit.
Credit: Thaiss et al/Cell 2016

The systems close to one another but tightly coordinated, like a “tango between two partners,” says Eran Elinav at the Weizmann Institute of Science in Rehovot, Israel. Elinav and colleagues had previously linked shifts in our day-and-night circadian rhythm, such as jet lag, to disruptions of microbial gut communities in humans and mice that can lead to metabolic conditions, such as obesity and diabetes.

 

In their Cell paper, Elinav and colleagues, including Eran Segal from the same institute, homed in on the microbes that adhere to the epithelial cells of the gastrointestinal tract in mice with imaging and sequencing. They targeted the microbes’ entire genome. The targeting allowed the researchers to determine both the composition and function of the microbes.

They found that the bacteria residing in close proximity to the host lining epithelial cells displayed highly circadian behavior, with composition, function and microbial numbers differing at throughout a 24-hour cycle. Moreover, the thickness of the mucosal layer separating the gut bacteria from the mice’s epithelial layers fluctuated with the mice’s circadian rhythm and feeding patterns.

“Our findings also add to the increasing body of evidence that strongly suggests that disruption of proper circadian activity, such as that present in shift workers and frequent travelers, may drive metabolic derangements through a mechanism that is partly mediated by disruption of proper diurnal microbiome activity,” says Segal.

The investigators then wiped out these microbial communities with antibiotics to see how the mice’s transcriptome, the aggregate of genes being expressed via messenger RNA, adapted to the loss.

“There were a few hundred genes — the genes encoding the host clock itself — which did not care about the disruption to the microbiome,” says Elinav. “But there was another group of genes which normally oscillate in the host. Once we disrupted the gut microbes, these oscillations were completely lost.”

The investigators also noted that a subset of mouse genes that normally operate independently of the mice’s circadian oscillations began to follow the oscillations after the microbial communities were wiped out. These genes were picking up functions that had previously been performed by genes expressed by the microbiome.  “This brings the option that this “superorganism” shifts the tasks from one partner to the other once it is disrupted,” says Elinav.

The researchers were most shocked when they checked up on the mice’s livers. Despite the liver’s relative distance from the gastrointestinal tract, about 15 to 20 percent of its genes displayed circadian activity. “Surprisingly, when we disrupted the gut microbiome, the genetic program in the liver was severely disrupted,” says Elinav.

The researchers found that the metabolites, small molecules that are extensively modified by the microbiome and make up 80 percent of all the small molecules in peripheral blood, also displayed strong circadian activity. These molecules allow the gut microbiome to regulate the circadian activity in the liver.

When this was brought into the context of drug metabolism, the researchers found that liver toxicity induced by administration of high doses of the painkiller acetaminophen also displayed circadian activity. Interestingly, the researchers found that disrupting the gut microbiome reduced the toxicity of acetaminophen and stabilized it throughout a 24-hour period.

Elinav and colleagues are currently planning to continue investigating the intimacy of the gut microbiota and the effects of its diurnal activity in humans in order to elucidate potential systemic effects of antibiotics. They want to develop rational and safe intervention methods in the microbiome, potentially impacting human disease and drug metabolism.

This post was written by John Arnst, ASBMB Today’s science writer. 

Lifestyle chemistries of phones

November 22, 2016 § Leave a comment

Swabbing a phone for chemical signatures. Credit: Amina Bouslimani and Neha Garg, UCSD

Swabbing a phone for chemical signatures.
Credit: Amina Bouslimani and Neha Garg, UCSD

It used to be that the most troubling information you could get from swabbing someone’s phone case was an abundance of E. coli indicating his or her lack of good hygiene. In a paper published in Proceedings of the National Academies of Sciences on Nov. 14, researchers at the University of California, San Diego, expanded the scope of interrogation to include a number of trace chemical signatures. The signatures can give a picture of someone’s lifestyle.

“The number of molecules detected on every object will vary depending on the surface of the object and the lifestyle of these people,” says Amina Bouslimani at UCSD. Bouslimani is a postdoctoral researcher in the laboratory of Pieter Dorrestein and the first author on the PNAS study, which was funded by the National Institute of Justice, the research arm of the U. S. Department of Justice. “For every phone, we were able to detect between hundreds and thousands of molecules or compounds,” she continues.

Bouslimani and colleagues swabbed the phones and hands of 39 volunteers. They then paired mass spectrometry with a visualization process known as molecular networking. This allowed the researchers to group similar molecules and identify unknown molecules absent from a reference database based on their similarity to known compounds.

The researchers detected a 69 percent overlap between the samples taken from participants’ hands and the backs of their phones, which demonstrated a high transferability of chemicals between the two surfaces. Among many other food items, pharmaceuticals and hygiene products, the compounds detected corresponded to citrus fruits, caffeine, antidepressants, antifungal creams, hair-loss treatments, sunscreen and mosquito-repelling DEET.

The researchers also evaluated each participant’s potential exposure to flame-retardant plasticizing agents. They posited that this analysis could be used to monitor exposure to additional environmental hazards.

While the approach is not a replacement for DNA or fingerprint analyses, Bouslimani and colleagues hope that it might fill in gaps when DNA samples are contaminated or fingerprints recovered are only partials or not in a database.

“This work is exciting and very thought-provoking,” says Glen Jackson at West Virginia University, an expert in forensic analyses by mass spectrometry.

Jackson is cautious, however, about the accuracy of linking predicted activities with mass spectrometry-confirmed exposure to chemicals.

For example, while the presence of DEET based on data analysis may be very reliable information, he says, “proving that the lifestyle, or activity level, of the suspect is camping versus gardening is a different proposition altogether.” He added that there’s more work to be done to make sure that the results of such testing aren’t misconstrued.

The strength of the approach, according to Bouslimani, is the aggregate of the individual chemical signatures. “Our work flow doesn’t just detect one unique compound on this phone,” she says. “It is the combination of many such lifestyle chemistries that will help us to understand the personal habit and lifestyle.”

Bouslimani and colleagues hope to expand the breadth of their database, which would require the efforts of outside collaborators. “It has to be now a community effort,” she says. “We really hope that other people will start to apply this technology, to take this kind of development to the next level in forensic application.”

In the meantime, Bouslimani and colleagues plan to expand the study to include 80 people and each subjects’ keys, computers and wallets.

This post was written by John Arnst, ASBMB Today’s science writer. 

Metals help sniff out offensive odors

October 4, 2016 § Leave a comment

Sketch by Hanyi Zhuang

Sketch by Hanyi Zhuang

What do skunks, decomposing cadavers and garlic have in common? Their odors contain sulfur. Humans are very sensitive to those odors. We’re able to pick up mere whiffs of them.

A team of researchers now report that they have found the olfactory receptor that gives us this exquisite sensitivity to sulfur-containing compounds. The receptor, known as OR2T11, requires metals for its activation. The finding, published in the Journal of the American Chemical Society, is the first to report the activation of a human olfactory receptor solely by metals.

Genetically speaking, olfactory receptors come in large numbers. There are about 400 genes for olfactory receptors in humans and 1,200 in mice. Figuring out which olfactory receptor picks up which scent is a challenge.

Finding OR2T11 demanded a multifaceted team. Victor Batista at Yale University, Lucky Ahmed and their group brought computational modeling expertise to the project. Eric Block at the University at Albany, State University of New York, is a chemist interested in organosulfur compounds and their smells. Jessica Burger at the National Institute of Standards and Technology in Boulder, Colorado, is a specialist in nuclear magnetic resonance spectroscopy. Hanyi Zhuang at the Shanghai Jiaotong University School of Medicine in China and colleagues are neuroscientists with expertise in olfactory receptors.

Zhuang’s laboratory has a cell-based system that can effectively express olfactory receptors. She says, “In this study, this platform enabled high-throughput screening of a human odorant receptor library and led to the discovery of the highly responsive thiol receptor OR2T11.”

The investigators discovered that OR2T11 was particularly sensitive to picking up tertiary-butyl mercaptan, also named 2-methyl-2-propanethiol, as well as ethanethiol. These two compounds are interesting because they are used in the fuel industry. With fuels, a very serious problem, called odor masking, occasionally arises. “Fuels sometimes cannot be smelled because of a combination of intermolecular and physiological interactions,” says Burger. “Utilities purchase fuel gas but, upon delivery, sometimes notice that there is little detectable or recognizable odor.”

Tertiary-butyl mercaptan is the main odorizing agent added to highly flammable natural gas, which is itself odorless. Ethanethiol gets added to liquified petroleum gas, which is also odorless and flammable. Both compounds give humans a warning smell if the fuels escape from containers.

The investigators also discovered that the receptor is activated by copper or silver. Although Zhuang says that the possible involvement of metal in olfaction has been proposed by chemists even before the cloning of the odorant receptors, Block adds, “there was only very limited experimental evidence for the role of metals in olfaction.”

The Batista group’s computations backed up the investigators’ experimental findings. The computations, Batista says, “enabled us to build a fully atomistic molecular model of the human odorant receptor with copper or silver binding sites for organosulfur compounds” that were consistent with experimental observations.

The investigators also were struck by how OR2T11 responds only to low-molecular-weight thiols — those with five or fewer carbon atoms — even though thiols with six or more carbons also have strong odors. Block says the finding indicates that size matters when dealing with particular classes of odorants interacting with their most responsive olfactory receptors.

Given that ionic and nanoparticulate silver can activate the receptor and enhance its sensitivity to sulfur-based compounds, Block notes there can be environmental issues. The finding “is a potentially important observation given that there are concerns about nanoparticulate metals in the environment, for example in bodies of water, which could impact olfaction in fish,” he says.

 

 

 

Treating congenital adrenal hyperplasia with an underestimated hormone

August 25, 2016 § Leave a comment

Image of adipocytes with lipids labelled in red and corticosterone in green.

 

In healthy people, the adrenal glands putter away atop the kidneys, releasing hormones as needed. For most people with congenital adrenal hyperplasia, the adrenal glands produce the glucocorticoid class of hormones, such as cortisol and corticosterone, in greatly diminished quantities.

The standard treatment for the disorder is hormone replacement therapy with hydrocortisone, the pharmaceutical version of cortisol. However, this tends to cause unpleasant side effects, such as obesity, hypertension and cardiovascular disease. In a paper just out in the journal Science Translational Medicine, researchers at the University of Edinburgh have found that using corticosterone can be just as effective as standard hydrocortisone, with fewer side effects.

Congenital adrenal hyperplasia affects about 1 out of every 10,000 people. When left unchecked, it can manifest as adrenal insufficiency, which can cause fatigue, depression, vomiting, severe abdominal pains and mood disorders. It can also lead to increased synthesis of adrenal androgens because adrenal androgens and glucocorticoids share precursor building blocks, which can have adverse effects on the development of primary or secondary sex characteristics in women.

Most cases of congenital adrenal hyperplasia are the result of a deficiency in 21-hydroxylase, which participates in the pathways that produce cortisol. Under stressful conditions, the anterior pituitary gland releases a molecule called adrenocorticotropic hormone, or ACTH. The ACTH travels to the kidney’s adrenal glands and stimulates the production of 17-hydroxyprogesterone, which is modified by 21-hydroxylase to ultimately become the stress-response hormone cortisol.

When glucocorticoid production is insufficient, as it is in congenital adrenal hyperplasia, 17-hydroxyprogesterone starts to accumulate and is diverted to the synthesis of adrenal androgens, such as testosterone. This also causes a buildup of ACTH, a precursor to the adrenal androgen, and also can cause unnatural darkening of the skin.

Treatment for these glucocorticoid deficiencies involves capsules of hydrocortisone, the pharmaceutical version of cortisol. But the treatment treads a fine line with cortisol cytotoxicity, according to Brian Walker, a professor at the University of Edinburgh and the primary investigator on the Science Translational Medicine paper.

The best way to suppress the overproduction of androgens “is to suppress this ACTH, but if you suppress the ACTH you almost always end up giving a dose that produces adverse side effects,” says Walker.

Because those side effects are mediated in the adipose tissue, the researchers decided to scrutinize the presence of cortisol and corticosterone in human adipocytes, the cells that store energy as fat.

After examining the adipocytes’ expression of the ATP-binding cassette transporters ABCB1 and ABCC1, which were known to export cortisol and corticosterone respectively, the researchers found that ABCC1 was dominant in the adipocytes. The transporter clears the cells of corticosterone. This suggested corticosterone, not cortisol, would be the better choice for replacement therapy; corticosterone wouldn’t stimulate activity in the cells and cause side effects.

To test this, Walker and his colleagues recruited two groups of six individuals with Addison’s disease, a disease similar to congenital adrenal hyperplasia. The investigators chose Addison’s disease patients over those with congenital adrenal hyperplasia to avoid any confounding effects of high androgen concentrations in the adipose tissues. They gave the patients either cortisol or corticosterone via short-term infusions.

Walker and colleagues found that while corticosterone treatments weren’t any more effective at suppressing circulating ACTH than cortisol treatments, they did reduce the presence of biomarkers for pathways in adipose tissues that lead to fat accumulation and hypertension.

Based on these results, Walker says, “We think it would be worth developing a treatment using corticosterone rather than cortisol or hydrocortisone. We are anticipating that that would have fewer side effects mediated in the adipose tissue for a dose that is equally efficacious in other tissues.”

At present, the researchers are working on developing such a therapy, Walker says, “because it doesn’t exist at present. We only have hydrocortisone tablets.”

 

This post was written by John Arnst, ASBMB Today’s science writer. 

 

The most complete catalog of proteins in king cobra venom yet

June 30, 2016 § Leave a comment

King cobra at Kaeng Krachan National Park. Photo by Thai National Parks. Photo obtained from https://commons.wikimedia.org/wiki/File:Ophiophagus-hannah-king_cobra-kaeng-krachan-national-park.jpg

King cobra at Kaeng Krachan National Park. Photo by Thai National Parks. Photo obtained from https://commons.wikimedia.org/wiki/File:Ophiophagus-hannah-king_cobra-kaeng-krachan-national-park.jpg

Seven milliliters of a king cobra’s venom can kill 20 people. But what exactly is in the snake’s venom? Researchers have pursued that question for decades.

 

Now, in a paper published in the journal Molecular & Cellular Proteomics, a team of researchers reveals a detailed account of the proteins in the venom of king cobras. “I believe this study to be one of the most complete and precise catalogues of proteins in a venom yet obtained,” states Neil Kelleher at Northwestern University, one of the study’s senior investigators.

 

Snake venoms always have intrigued scientists, because they “have a rich diversity of biological activities,” says Kelleher’s collaborator Gilberto Domont at Universidade Federal do Rio de Janeiro in Brazil.  Among other things, venoms contain various proteases, lipases, nerve growth factors and enzyme inhibitors. Besides understanding how venoms function, researchers want to develop better antidotes to snake venom and identify molecules from venom that can be exploited as drugs, such as painkillers, anticlotting medications and blood pressure treatments. Domont points to captopril, a drug now commonly used to treat high blood pressure and heart failure. It was derived from a molecule found in the venom of a poisonous Brazilian viper.

 

Although the venom of the king cobra, the largest venomous snake in the world, which can stretch up to 13 feet, has been analyzed previously, questions persist about the venom. How do the sequences of the toxins evolutionarily vary? How do some post-translational modifications on proteins make the venom lethal? But to answer these questions, researchers need a proper count of the proteins in king cobra venom.

 

The advent of proteomics has allowed scientists to survey the rich diversity of proteins in a given sample. There are different approaches that rely on mass spectrometry to carry out proteomic analyses. One approach is called top-down proteomics. It allows researchers to look at proteins as whole, intact entities. In the more conventional approach, called bottom-up proteomics, proteins are cut into bite-sized fragments for analysis.

 

In bottom-up proteomics, researchers have to use computer algorithms to stitch back together protein fragments identified by mass spectrometry. Top-down proteomics avoids this problem. Its biggest advantage is that it can capture variations within the proteins as well as post-translational modifications.

 

Kelleher’s group is one of the leaders in developing top-down proteomics, so that’s what the investigators decided to use to analyze king cobra venom. Domont, Kelleher, Domont’s graduate student Rafael Melani and colleagues obtained venom from two Malaysian king cobras held at the Kentucky Reptile Zoo. They analyzed the venom by top-down proteomics in two modes, denatured and native. In the denatured mode, the protein complexes were taken apart; in the native mode, the venom was kept as is so the protein complexes remained intact.

 

The investigators identified 113 proteins in king cobra venom as well as their post-translational modifications. To date, only 17 proteins had been known in king cobra venom.

Taking a holistic view of ovarian cancer

June 29, 2016 § 1 Comment

 

The American Cancer Society estimates about 22,280 women this year will receive a first-time diagnosis of ovarian cancer. The cancer, which has various forms, is the most lethal disease of the female reproductive system.

 

In a paper just out in the journal Cell, researchers present one of the largest studies ever done of the most malignant type of ovarian cancer. The scientists carried out proteomic analyses of highly malignant tumors and integrated their data with genetic and clinical information. The detailed view of the tumors gave the researchers a better understanding of what makes these tumors so aggressive.

 

In 2011, The Cancer Genome Atlas, a project undertaken by the National Cancer Institute, provided a list of genetic mutations in ovarian cancers. “The Cancer Genome Atlas did a fantastic job of cataloging the genomic aberrations associated with many different cancer types, including the most lethal form of ovarian cancer, high-grade serous carcinoma,” says Karin Rodland at the Pacific Northwest National Laboratory who co-led the study in Cell with Daniel W. Chan at Johns Hopkins University.

 

The researchers, who came from nine institutions across the U.S. and were funded by NCI, were interested in how genetic defects affected proteins, which are one of the workhorses in the cell. “We were also interested in protein phosphorylation as a marker of information flow in the cancer cell and as a way of telling which signaling pathways were most activated in HGSC,” says Rodland.

 

Rodland adds that the researchers wanted to compare those cases of HGSC that had the worst outcome, where the women died in less than three years, with patients who lived for five years or longer. The hope was to see if the comparison gave scientists fresh clues about the disease.

 

The illustration hints at the complexity of the development of ovarian cancer. Here, more than two dozen proteins are affected by PDGFR, or platelet-derived growth factor receptor. The team showed that this molecule and its pathways are much more active in the tumors of patients with ovarian cancer who had short survival compared to other patients who lived longer than five years. Image from Zhang et al./Cell, 2016

The illustration hints at the complexity of the development of ovarian cancer. Here, more than two dozen proteins are affected by PDGFR, or platelet-derived growth factor receptor. The team showed that this molecule and its pathways are much more active in the tumors of patients with ovarian cancer who had short survival compared to other patients who lived longer than five years. Image from Zhang et al./Cell, 2016

The team examined 169 tumor samples and identified 9,600 proteins from all the samples. They focused on 3,586 proteins common to all the samples and combined their analyses with genetic and clinical data. The team found that a critical malfunction in HGSC involved changes in DNA where parts either were deleted or copied more than once.

 

Duplications of sections in chromosomes 2, 7, 20 and 22 caused 200 proteins to be produced in greater numbers. When they looked more closely at those 200 proteins, the researchers found “the affected proteins were highly enriched for functions related to cell motility, invasion and immunity,” says Rodland. These functions help make a cancer more aggressive.

 

Proteins undergo post-translational modifications, which influence their functions. By looking at the copies of proteins produced as well as their post-translational modifications, the investigators were “able to derive a signature from the pattern of affected proteins that could discriminate between patients with short and long overall survival with a highly significant probability,” says Rodland. This signature was much better at predicting survival outcomes of the women with ovarian cancer than other prognostic signatures.

 

Moreover, Chan explains that the Hopkins group of researchers selected 122 of the 196 samples based on a deficiency in homologous recombination, a process that is supposed to repair damaged DNA. Ovarian cancer patients with the deficiency usually get treated with a particular drug.

 

Chan notes that the study revealed several protein post-translational modifications that were associated with the deficiency that “might help explain why not every patient with the homologous recombination deficiency responds to the same drug treatment,” he says. “This finding could help select patients for the right therapy.”

 

The researchers now are working to validate their observations using a completely different set of patients, but Rodland says that the current study unequivocally shows the importance of a holistic view. “You have to look at the whole flow of information, from genome to transcriptome to proteome and phosphoproteome in order to get a complete picture of cancer biology,” she says. Rodland points out that the protein phosphorylation data helped the team identify activated pathways that provided “an additional level of information about cancer biology that cannot be derived from genomic data alone.”

Analyzing zits: Researchers study fats in sebum

May 31, 2016 § Leave a comment

Researchers analyzed some of fat molecules in acne.

Researchers analyzed some of fat molecules in acne. Photo by Thirteen Of Clubs and used by the Creative Commons license.

One of the many insults of adolescence is pimple-speckled skin. Sebum, an oily skin secretion, plays a major role in causing zits. But “the knowledge of what exactly in sebum is responsible for the occurrence of acne is rather limited,” says Emanuela Camera at the San Gallicano Dermatologic Institute in Italy.

 

In a paper recently published in the Journal of Lipid Research, Camera and colleagues described their analysis of the lipids in sebum and report a clue as to how sebum composition might correlate with the severity of acne.

 

The lipids in sebum “are highly complex and unique,” notes Camera. The lipids in human sebum are so diverse that some aren’t found in other oily substances in the body or even in other species. The complexity of sebum lipids make them hard to analyze. Researchers are unsure of what they are and how they contribute to skin disorders, such as acne.

 

For their study, Camera and colleagues, with the help of dermatologists, recruited 61 teenagers. They grouped adolescents, who were almost evenly split between male and female, into those who had acne and those who didn’t. The acne group was further subdivided into mild, moderate and severe groups. They asked all the teenagers to stick a special tape onto their foreheads to absorb sebum.

 

Camera and colleagues then took those tapes and analyzed them by mass spectrometry to see what lipids collected on them. To avoid going on a wild fishing expedition, the investigators focused on the neutral lipids in sebum. Their data suggested that diacylglycerols were the predominant species among the lipids in acne sebum. There also were fatty acyls, sterols and prenols. Notably, the investigators discovered that higher amounts of diacylglycerols correlated with the more acute cases of acne.

 

Given that more severe forms of acne can be disfiguring, it’s important to understand what causes the skin disorder. Acne can look different from person to person, such as in “white and black heads, papules, pustules, or as a miscellany of them.” Camera says that the different ways acne can manifest itself and its varying severity “calls for a personalized approach. Thus, biomarkers of acne and acne severity can be instrumental in the definition of acne pathogenic mechanisms and indicate novel drug targets.”

 

 

A new test for diagnosing Niemann-Pick disease

May 6, 2016 § Leave a comment

The new test can use already collected dried blood spots from heel sticks to diagnose NPC. Image credit: US Air Force

Niemann–Pick disease is a rare genetic disease with devastating effects. For one type of the disease, known as type C, defects in lysosomal storage within the cell lead to impaired neurological function. In infants, these symptoms can be especially difficult to recognize. They often include subtle changes in children’s behavior, such as failure to meet expected cognitive milestones or inability to control balance.

Until recently, the first-line diagnostic test for NPC disease has involved a skin biopsy and filipin staining, which is invasive, cumbersome and expensive. Patients with NPC typically often go up to five years without a diagnosis, drastically limiting the possibility of early interventions.

In a paper just published in the journal Science Translational Medicine, Daniel Ory of Washington University School of Medicine in St. Louis and colleagues lay the groundwork for a promising new diagnostic test for NPC. Importantly, the new noninvasive assay produces results within a day instead of months.

Here’s how it came to be.

The team used mass spectrometry to analyze dried blood spots, collected at various times after birth, from patients known to have NPC. They found three bile acids biomarkers that could clearly distinguish NPC patients from people without the disease.

The scientists then determined the structures of the bile acids. Ory and colleagues identified one bile acid as a trihydroxycholanic acid and another as its glycine conjugate.

As the second bile acid helped the team distinguish NPC patients from non-NPC patients more consistently, the researchers decided to use it to develop a new diagnostic test.

As a diagnostic test, Ory says, the assay already is being used at Washington University. He expects other centers to follow suit.

For its use in newborn screening, Ory said, researchers will need to put the assay to the test in the undiagnosed newborn population to ensure its usefulness in recognizing NPC in that age group, a process Ory believes will take several years.

Although the U.S. Food and Drug Administration hasn’t yet approved treatments for NPC, a promising drug called cyclodextrin is rapidly moving through clinical trials. The most effective treatment strategies will need to intervene early in the disease process, which is something the new test could accomplish. “We’re really trying to make an impact in this NPC community by being able to develop the therapies and being able to diagnose early,” says Ory. The approach “we’ve taken over the last 10 years, I feel like, it’s getting close to bearing fruit.”

Bree Yanagisawa, the guest author of this blog post, is a science writing intern at ASBMB Today. You can follow her on Twitter @BreeTalksSci.

Bree Yanagisawa, the guest author of this blog post, is a science writing intern at ASBMB Today. You can follow her on Twitter @BreeTalksSci.

Fat mice lead researchers to finding a new pathway in brain involved in feeding control

March 17, 2016 § Leave a comment

Littermates were injected with either a control virus or a virus that knocked out OGT in a part of the brain. The mouse missing OGT (left) ate twice as much as its normal sibling (right). This photo was taken about five weeks after virus injection. Image Credit: Olof Lagerlof

Littermates were injected with either a control virus or a virus that knocked out OGT in a part of the brain. The mouse missing OGT (left) ate twice as much as its normal sibling (right). This photo was taken about five weeks after virus injection. Image credit: Olof Lagerlof

When their lab mice unexpectedly packed on weight, Richard Huganir at the Johns Hopkins School of Medicine and his colleagues had to figure out why the mice suddenly turned obese. In a paper just out in the journal Science, the investigators describe their discovery of a protein-modification pathway in the brain that plays a surprising role in feeding control and satiety.

“This was a serendipitous discovery,” says Huganir, a neuroscientist. “We had to learn a whole new area of biology — feeding control, metabolism and obesity. Luckily, we had great collaborators at Hopkins who had the expertise to help us figure out what was going on. We eventually found out that the mice had impaired satiety and ate larger meals.”

The investigators originally were working on deciphering the role of an enzyme called O-GlcNac transferase, known as OGT, in regulating synaptic transmission and plasticity in the brain as well as its potential role in learning and memory. OGT catalyzes the attachment of a short sugar molecule to proteins; the sugar molecule then influences the function of the proteins.

As part of their project, Huganir and colleagues genetically modified the brains of mice so that the researchers could turn off the expression of OGT in the forebrain and hippocampus. These two regions of the brain are important for learning and memory.

“Much to our surprise, a couple of weeks after we knocked out OGT, the mice got very, very fat,” says Huganir. “We stopped studying learning and started studying feeding control.”

The parts of the brain the investigators had targeted in their mice are not usually associated with feeding control. But the hypothalamus is.

When the investigators looked at the hypothalamus, they discovered that they had inadvertently removed OGT in specific cells in a region of the hypothalamus called the paraventricular nucleus.

To make sure that OGT in the paraventricular nucleus cells was what was influencing the feeding and satiety of the mice, Huganir and colleagues created another set of genetically modified mice. These mice had OGT missing only in the paraventricular nucleus cells. “Knocking out OGT in only these cells inhibited their activity and produced the same overeating phenotype,” says Huganir.

The investigators now know that OGT plays an important role in the paraventricular nucleus cells in feeding control, but the molecular details are still unknown. For one, the investigators don’t know what substrates OGT acts on in the paraventricular nucleus cells to regulate their activity.

And, as with any work done on mice, the implications for humans have to be worked out. “This work in mice does suggest similar mechanisms are important in human satiety,” says Huganir. “However, much more work is needed to identify potential therapeutic targets to modify this pathway in humans to regulate food intake.”

Predicting preeclampsia

March 14, 2016 § 1 Comment

Researchers are developing new ways to predict preeclampsia using serum lipid profiles. Photo credit: Wikimedia Commons

Preeclampsia affects roughly three percent of pregnant women in the U.S., bringing on a host of complications that include premature births and even death. Unfortunately, there is no effective diagnostic test to predict the onset of disease.

In a recent paper published in the Journal of Lipid Research, Steven Graves of Brigham Young University and colleagues described a set of biomarkers that could help in the early detection of preeclampsia.

In spite of efforts to identify the mechanisms surrounding the disease, researchers haven’t been able to pinpoint a causative factor. When attempting to develop predictive assays for prenatal complications, scientists place the safety of the mothers’ and their unborn babies first. While a sampling of the placenta may provide critical information about preeclamptic processes, the placenta sampling procedure is risky. Scientists interested in developing prenatal diagnostic tests need to consider methods that are both informative and reasonable to use in a clinical setting.

Graves and colleagues decided to look at lipids although proteins tend to be the more conventional class of biomarker. Graves says the team focused on lipids in the blood because lipids tend to be more forgiving than their protein counterparts. Lipids, “are not particularly heat-sensitive compared to a protein or peptide and they’re not degraded rapidly by proteolytic enzymes which exist in the serum,” explains Graves. Additionally, serum samples can be collected in the clinic relatively easily with blood draws, keeping the risk to patients low.

The researchers took samples collected for another trial that was studying the early events of Down’s syndrome. Of the serum samples available, they used those collected at the earliest available time point which was 12–14 weeks into the pregnancy.

Using mass spectrometry data, the team compared the serum lipid profiles of women who went on to develop preeclampsia and those who did not. After an initial analysis and a second confirmatory run in another sample set, the team identified a set of 23 biomarkers in the form of mass spectral profiles that were able to predict those women who would go on to have a preeclamptic event.

Any biomarker on its own can’t provide sufficient predictive value, but combining the markers together into sets increased predictability. For their sample population, the investigators found that using six biomarkers helped with predicting preeclampsia; combining more than six markers failed to show an increase in predictive value. When the lipid test becomes publically available, Graves advises using all 23 biomarkers together to better account for individual patient factors.

Though the lipid biomarkers are intriguing, Graves is careful to point out these biomarkers aren’t ready for the clinic just yet. “What should happen now is one should establish a clear hypothesis that this set of markers would be useful and then carry out studies” focused on these markers. A lipid-based test will only be available after it passes through all the necessary studies and approval of a clinical test by the U.S. Food and Drug Administration.

Currently, the true advantage of this research isn’t in its immediate clinical value but the potential use of the biomarkers for streamlining the research process. Because the disease is so rare, one of the biggest issues with prospective studies for preeclampisa is the sheer number of women that need to be enrolled in order to have adequate numbers of preeclamptic cases. However, if researchers first can narrow down the population, using a set of predictive biomarkers such as the one proposed in the paper, fewer women would need to be enrolled. Graves proposes, “It could save time and allow for more things to be tested more efficiently.”

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Bree Yanagisawa, the guest author of this blog post, is a science writing intern at ASBMB Today. You can follow her on Twitter @BreeTalksSci .