October 4, 2016 § Leave a comment
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.
August 25, 2016 § Leave a comment
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.
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 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.”
May 31, 2016 § Leave a comment
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.”
May 6, 2016 § Leave a comment
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.”
March 17, 2016 § Leave a comment
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.”
March 14, 2016 § 1 Comment
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.”
January 20, 2016 § 2 Comments
Many of us can attest to the rejuvenating effects of a manicure or a pedicure. The same applies to mice, as recently determined by Stanford University School of Medicine researchers. The investigators report that a simple pedicure can treat ulcerative dermatitis, a ubiquitous and often fatal condition among laboratory mice.
UD affects up to 21 percent of lab mice. Its specific cause remains unknown, although strong evidence suggests that it is behavior-related. Deep, itchy lesions often appear first on the neck. These lesions spread as the mouse scratches itself. UD is currently the most common cause of unplanned euthanasia among lab mice.
In a PLoS ONE paper, Sean Adams’ group described nail trimming as an alternative to the laborious and ineffective application of daily ointment to treat UD. This method was the first of several anecdotally-reported strategies that the researchers planned to explore. A pedicure, they found, reduces animal suffering, saves time and money, and boosts the integrity of mouse studies by reducing the need for medical intervention. Fewer euthanized mice means fewer mice needed per study.
The investigators then carried out a study. In one 14-day trial, 93.3 percent of mice were cured of UD with a pedicure compared with 25.4 percent of mice treated with daily ointment. The nail-trimmed mice received a one-time dose of topical treatment to prevent bacterial growth and soothe inflammation. These mice resisted scratching even after their nails grew back. “By intervening in the itch-scratch cycle, we are giving the animals the time that they need to recover, and also perhaps for that behavior to ramp down,” says Joseph Garner at Stanford University, a coauthor on the study.
The researchers later devised a plastic restraint, a modified conical tube, to keep the mice still while their nails are trimmed. With training, this process can take as little as 30 seconds. The researchers have been distributing these tubes when they present their findings at conferences, hoping to encourage more labs to adopt this humane and economical practice.
“There was a lot of serendipity and luck involved,” says Garner. “We never expected that we would find a solution that works in such a high percentage of mice, that it would be so simple, or that we would find it on the first try.”
Alexandra Taylor (firstname.lastname@example.org) is a staff science writer at ASBMB and a master’s candidate in science and medical writing at Johns Hopkins University.
January 11, 2016 § 2 Comments
Mammals, there’s a new enzyme in town. In a paper just published in the Proceedings of the National Academy of Sciences, scientists report the discovery of a new enzyme called glycerol-3-phosphate phosphatase. The enzyme plays a critical role in metabolism by overseeing the levels of different fuels in the body.
Metabolism has been a heavily trodden field of study ever since the dawn of molecular biology. These days, “it is extremely rare that a novel enzyme is discovered at the heart of intermediary metabolism in all mammalian tissues,” says S.R. Murthy Madiraju at the Montreal Diabetes Research Center, one of the corresponding authors on the paper.
Madiraju, along with Marc Prentki at the Montreal Diabetes Research Center and others, found the enzyme while grappling with a puzzle. They were studying pancreatic beta cells that produce insulin to control blood glucose levels. These cells get stressed when barraged with metabolic fuel from the diet, such as glucose and fatty acids. When that happens, the cells make and get rid of glycerol as a way of dealing with the excessive fuel supply.
Initially researchers thought the glycerol came from the breakdown of fats. But when Madiraju, Prentki and colleagues inhibited fat breakdown, the cells kept making glycerol. This suggested there was another glycerol source.
Microorganisms, plants and some fish have an enzyme that turns a molecule called glycerol-3-phosphate into glycerol. Mammals were thought not to have the enzyme.
But the investigators set out to check if mammals really and truly didn’t have a glycerol-3-phosphate phosphatase. It turns out they do. Madiraju, Prentki and colleagues confirmed the presence of the enzyme both in cell and animal models.
In discovering a mammalian glycerol-3-phosphate phosphatase, “we have to re-adjust our thinking that fat breakdown is not the only way by which mammalian cells generate glycerol, as has been believed so far!” says Prentki.
Glycerol-3-phosphate, the molecule on which the enzyme works, is made from glucose and gets incorporated into fats. It lies at the heart of glucose and lipid metabolism. With the discovery of an enzyme that can directly break down glycerol-3-phosphate, researchers now have a new player to contend with in understanding how the body maintains energy levels under normal circumstances and what goes wrong in different metabolic diseases.
The investigators say that they believe that, because of its critical metabolic role, glycerol-3-phosphate phosphatase will be a new target for treating chronic conditions such as obesity and type 2 diabetes as well as some cancers.
December 14, 2015 § Leave a comment
Much like Legos, proteins can come together in a number of ways to create complex structures. The various ways make it hard to organize protein complexes into categories.
But now, in a paper just out in Science, researchers describe an approach to classify protein complexes that creates a periodic table, like the periodic table that’s used in chemistry to organize elements. “We’re bringing a lot of order into the messy world of protein complexes,” explained Sebastian Ahnert at the University of Cambridge who is the first author on the paper in a press release.
Many proteins spend much of their time interacting with other proteins and assembling into complexes in order to carry out their functions. But the interactions and functions are specific, much like in the way different Lego bricks can latch onto each other only in certain ways. The underlying principles of protein interactions and assembly are not yet fully understood. But by organizing the different ways protein comes together into a table, Ahnert, along with Sarah Teichmann at the European Molecular Biology Laboratory–European Bioinformatics Institute, Joseph Marsh at the University of Edinburgh and others, wanted to see if some of the fundamental steps in protein complex evolution would become apparent.
They did. The investigators organized complexes based on simple rules so that they could find the most basic structures. “In the end, we discovered that three possible steps of interface evolution, combined in very specific ways, give rise to almost all known structures of protein complexes,” says Ahnert.
The investigators say that the fact that almost all known protein complexes could be arranged into a periodic table is revealing and will help understand how protein complexes come about. “Most heteromeric protein complexes—ones with more than one protein type—consist of identical repeated units of several protein types,” says Ahnert. “Because of this, heteromeric protein complexes can, in fact, be viewed as simpler, homomeric protein complexes—ones that only consist of a single type of protein—if we think of these repeated units as larger ‘single proteins.’”
(For an interactive version of the periodic table for proteins, go here)