Researchers from the Fraunhofer Institute have developed a new prototype lab-on-a-chip platform for the easy and versatile detection of molecular pathogens. Nuclear amplification testing is commonly used for pathogen detection; however, the process is currently manually intensive and complex, and requires dedicated equipment. This prevents its use in some settings, and pathogen detection in individual samples. In a bid to solve these issues, Natalia Sandetskaya and colleagues at the Fraunhofer Institute for Cell Therapy & Immunology (Leipzig, Germany) have developed a prototype lab-on-a-chip platform capable of automating the process in a single instrument. “We were motivated by the existing need for making the molecular analysis of complex samples much simpler for the users,” commented Sandetskaya. “Our particular applied interest is the detection of the pathogens in blood; for instance in sepsis, when only a few microorganisms must be rapidly found in a large volume of blood.” The chip utilizes microfluidics and integrates sample volume transition, lysis, nucleic acid isolation, amplification (PCR or LAMP), and real-time fluorescence detection. As a single instrument, it could enable diagnostics in situations not previously feasible. The researchers go on to demonstrate its proof-of-concept in the detection of E. coli and Salmonella bacterial species. “Although our current prototype of the platform will need further development for this application, we have already demonstrated a high level of integration of very diverse processes without making the system overly complex,” noted Sandetskaya. The team is now planning experiments to evaluate the platform in real-world samples and perfect its design.
Future Science OA www.future-science-group.com/new-lab-on-a-chip-platform-seeks-to-improve-pathogen-detection/
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National Human Genome Research Institute (NHGRI) researchers have identified new genes associated with the Erdheim-Chester disease (ECD) and some possible new therapies. This ultra-rare disease is found in approximately 600 people in the world. "The discovery of new genes associated with ECD provides hope for improving the diagnoses of a disease that affects so many parts of the body. We also hope it will help us identify new treatments," said Juvianee I. Estrada-Veras, M.D., clinical investigator and staff clinician in NHGRI’s Medical Biochemical Genetics Residency Program. "Our work on ECD builds on the institute’s goals to advance medical knowledge about rare diseases and to potentially provide insights into more common disorders." ECD is caused by the accumulation of specialized white blood cells called histiocytes in different organs. The resulting inflammation damages organs and tissues throughout the body, causing them to become thickened, dense and scarred. Histiocytes normally function to destroy foreign substances and protect the body from infection. ECD has no standard therapy, although consensus guidelines for clinical management were published in 2014. Between 2011 and 2015, researchers examined 60 adults with ECD at the NIH Clinical Center. Of 59 samples that were available for molecular testing, half had BRAF V600E gene mutations, which is sometimes seen in colon cancer, lung cancer, thyroid cancer, brain tumours and some blood cancers. Other patients had mutations in genes of the MAPK pathway, which controls cell growth and proliferation. These findings indicate that, despite the presence of inflammation and the absence of metastases (spread of cancer cells from the place where they first formed to another part of the body), ECD should be considered a type of cancer and treated by oncologists, researchers wrote. Until now, the most common treatment for ECD has been interferon, a drug that interferes with the division of cancer cells and slows tumour growth. Some patients with severe forms of disease can succumb to the illness even with treatment. The mortality rate for ECD has been estimated at 60 percent at 3 years from the time of diagnosis. Researchers suggested that therapies that stop the growth and proliferation of cells by blocking the MAPK pathway — vemurafenib, dabrafenib and trametinib — may provide new hope for treating and improving the survival of people with ECD. A therapeutic trial of dabrafenib and trametinib is now enrolling new ECD patients with BRAF V600E mutations.
National Human Genome Research Institute www.genome.gov/27568398/2017-news-feature-genes-associated-with-erdheimchester-disease-also-linked-to-cancer/
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Mutations in tumour suppressor genes mean that they can no longer keep tumours from growing. In developing cancer, often several mutations come into play. Using "jumping genes," scientists from the Technical University of Munich (TUM) and the German Cancer Consortium (DKTK) together with teams from Great Britain and Spain have identified a number of genes that can influence the growth of prostate and breast tumours. Prostate cancer is the most common cancer in men in Germany with around 63,000 patients diagnosed every year. About half of them have an altered Pten gene. This well-known tumour suppressor gene can help prevent cancer development in healthy people by inducing cell death in tumour cells. However, little is known about which other genes cooperate with Pten to prevent cancer. In order to find out more, the international team designed a new method. They converted the Pten-Gene in mice into a mobile DNA element known as a transposon. This transposon "jumps" from its original position and lands at a random position throughout the genome, damaging and thus deactivating genes into which it is inserted. The transposons "starting point", i.e. the Pten-Gene, is deactivated as well. In the experiment, cancers would grow when the transposon damaged a tumour suppressor gene that co-operated with Pten. "Using the new transposon-based approach, we were able to systematically search the genome for genes cooperating with Pten and influencing the development of prostate cancer, but also other forms of cancer like breast or brain cancer," says Dr Juan Cadiñanos, joint lead author from the Instituto de Medicina Oncologica y Molecular de Asturias and the Wellcome Trust Sanger Institute in Britain. "This approach could also be used to look into relations between other genes." The researchers analysed 278 prostate, breast and skin tumours and revealed hundreds of genes that could cooperate with Pten and act as further tumour suppressor genes. Human cell lines and data from human prostate tumours were then used to study the five most promising genes. "Coupled with Pten inactivation, a loss of function in these genes led to typical cancer pathways being activated," says Jorge de la Rosa, one of the study’s first authors. The researchers found that in human prostate tumours, the genes in question were considerably limited in their function. Transposon-based approaches are useful for looking into the molecular basics of the development of tumours. "They allow us to find genes connected to cancer that are hard to find using other methods," says Roland Rad, a DKTK-Professor for translational Oncology at TUM’s Klinikum rechts der Isar. "In order to understand the biology of tumour development, we must uncover the complex tumor suppressor networks. This is a prerequisite for developing new therapeutic strategies."
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Over a fourth of the eighty samples tested positive for new psychoactive substances. In the last decade hundreds of new psychoactive substances (NPS) have emerged in the drug market, taking advantage of the delay occurring between their introduction into the market and their legal ban. According to the Drug Enforcement Agency (DEA) NPS describes a recently emerged drug that may pose a public health threat. The DEA issues a quarterly Emerging Threat Report, which catalogues the newest identified NPS. NPS tend to mimic the psychotropic effects of traditional drugs of abuse, but their acute and chronic toxicity, and side-effects are largely unknown. While seizure data from the DEA is often used to indicate what new drugs are being sold in the US, there is a lack of research examining and confirming who has been using such drugs. Joseph J. Palamar, PhD, MPH, a New York University researcher, has been researching incidental and intentional use of NPS by young adults. His current line of inquiry has focused on survey methods, qualitative interviews, and hair sampling to ascertain frequency and type of NPS use by nightclub-goers–a demographic which traditionally has a relaxed view towards recreational drug experimentation and use. NPS are common adulterants in drugs such as ecstasy (MDMA), which has seen an increase in popularity since it became marketed as “Molly”. Ironically, “Molly” connotes a product that is pure MDMA. In a related study, Palamar and his team found that four out of ten nightclub/festival attendees who used ecstasy or “Molly” tested positive for “bath salts” despite reporting no use. In their current study, “Hair Testing for Drugs of Abuse and New Psychoactive Substances in a High-Risk Population,” Dr. Alberto Salomone, an affiliated researcher at the Centro Regionale Antidoping e di Tossicologia “A. Bertinaria”, Orbassano, Turin, Italy and Dr. Palamar, affiliated with NYU’s Center for Drug Use and HIV Research (CDUHR), collected hair samples from 80 young adults outside of New York City nightclubs and dance festivals, from July through September of 2015. Hair samples from high-risk nightclub and dance music attendees were tested for 82 drugs and metabolites (including NPS) using ultra-high performance liquid chromatography–tandem mass spectrometry. “Hair analysis represents a reliable and well-established means of clinical and forensic investigations to evaluate drug exposure, said Dr. Salomone. “Hair is the most helpful specimen when either long-time retrospective information on drug consumption is of interest.” “Most NPS can no longer be detected in urine, blood, or saliva within hours or days after consumption, but hair is particularly beneficial because many drugs can be detected months after use.” Of the eighty samples, twenty-six tested positive for at least one NPS—the most common being a “bath salt” (synthetic cathinone) called butylone (present in twenty-five samples). The “bath salts” methylone and even alpha-PVP (a.k.a.: “Flakka”) were also detected. The researchers find the presence of Flakka alarming as this drug has been associated with many episodes of erratic behaviour and even death in Florida. Other new drugs detected included new stimulants called 4-FA and 5/6-APB. “We found that many people in the nightclub and festival scene have been using new drugs and our previous research has found that many of these people have been using unknowingly,” said Dr. Palamar, also an assistant professor of Population Health at NYU Langone Medical Center (NYULMC). Hair analysis proved a powerful tool to Drs. Salomone and Palamar and their team, allowing them to gain objective biological drug-prevalence information, free from possible biases of unintentional or unknown intake and untruthful reporting of use.
NYU Langone Medical Center www.nyu.edu/about/news-publications/news/2017/march/hair-testing-shows-high-prevalence-of-new-psychoactive-substance.html
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Five simple medical tests together provide a broader and more accurate assessment of heart-disease risk than currently used methods, cardiologists at UT Southwestern Medical Center found. Combined, results from the five tests – an EKG, a limited CT scan, and three blood tests – better predict who will develop heart disease compared with standard strategies that focus on blood pressure, cholesterol, diabetes, and smoking history, researchers reported. “This set of tests is really powerful in identifying unexpected risk among individuals with few traditional risk factors. These are people who would not be aware that they are at risk for heart disease and might not be targeted for preventive therapies,” said Dr. James de Lemos, Professor of Internal Medicine. The five tests, and the information they provide:
A 12-lead EKG provides information about hypertrophy, or thickening of the heart muscle.
A coronary calcium scan, a low-radiation imaging test, identifies calcified plaque buildup in the arteries of the heart.
A blood test for C-reactive protein indicates inflammation.
A blood test for the hormone NT-proBNP indicates stress on the heart.
A blood test for high-sensitivity troponin T indicates damage to heart muscle. Troponin testing is regularly used by hospitals to diagnose heart attacks, but high-sensitivity troponin fine-tunes that measure, pointing to small amounts of damage that can be detected in individuals without any symptoms or warning signs.
Four of the five tests are currently readily available and the fifth – high-sensitivity troponin T – will be available soon. Researchers used data from two large population studies, including the Dallas Heart Study, that each followed a large group of healthy individuals for more than a decade. Their study was partly funded by NASA to develop strategies for predicting heart disease in astronauts. The new study focused on a broader spectrum of cardiovascular disease events rather than only those related to cholesterol plaque buildup, as traditional risk assessment does.
UT Southwestern Medical Center www.utsouthwestern.edu/newsroom/news-releases/year-2017/mar/risk-assessment-khera.html
Corneal diseases are among the most common causes of visual impairment and blindness, with Fuchs endothelial corneal dystrophy (FECD), a gradual swelling and clouding of the cornea, being the most common reason for eventual corneal transplants. The cornea is the transparent front part of the eye covering the iris, pupil and anterior chamber. In Fuchs endothelial corneal dystrophy, the innermost cell layer of the cornea begins to progressively deteriorate, eventually resulting in severe vision impairment and blindness. Researchers at University of California San Diego School of Medicine, with colleagues at Case Western University, Duke University, the National Institutes of Health and elsewhere, have identified three novel genomic loci — distinct stretches of genetic material on chromosomes — linked to FECD, which often clusters in families and is roughly 39 percent heritable. “Previously, there was one known FECD locus. We’ve expanded that number to four,” said the study’s first author Natalie A. Afshari, MD, professor of ophthalmology, Stuart Brown MD Chair in Ophthalmology in Memory of Donald Shiley and chief of cornea and refractive surgery at Shiley Eye Institute at UC San Diego Health. “These findings provide a deeper understanding of the pathology of FECD, which in turn will help us develop better therapies for treating or preventing this disabling disease.” FECD affects the innermost layer of cells in the cornea (the transparent front cover of the eye), called the endothelium. The endothelium is responsible for maintaining the proper amount of fluid in the cornea, keeping it clear. FECD is a progressive disorder in which the endothelium slowly degrades, with lost clarity, pain and severely impaired vision. It affects 4 percent of the U.S. population above age 40 and worsens with age. Women are two to four times more affected than men. While there is symptomatic treatment in early stages, surgery — often a corneal transplant — is the only remedy after significant vision loss occurs. The research team conducted a genome-wide association study, an analytical approach in which scientists look for genetic variants in individuals associated with a particular disease. This study involved 1,404 patients with FECD and 2,564 controls of European ancestry. The results confirmed the known role of the TCF4 gene, but also revealed associations with three other loci: KANK4, LAMC1 and LINC009970/ATPB1. Researchers also found some genomic markers that were more associated by gender, with LAMC1 increasing FECD risk in women while TCF4 increased risk in men. “While more work must be done to precisely elucidate what these proteins do,” said Afshari, “the results suggest they have essential roles in sustaining and maintaining the health of the corneal endothelium. This knowledge improves our understanding of the genetic risk factors for FECD and gives us new therapeutic targets.”
UCSD Center for Health health.ucsd.edu/news/releases/Pages/2017-03-30-new-genetic-links-underlying-progressive-eye-disease.aspx
Researchers affiliated with the University of Campinas (UNICAMP) in São Paulo State, Brazil, have shown that genetic information can be used to improve early prediction of the response to drugs in patients with mesial temporal lobe epilepsy (MTLE), one of the most severe forms of epilepsy. Patients who do not respond well to treatment with antiepileptic drugs are candidates for surgery. The research was conducted at the Brazilian Research Institute for Neuroscience and Neurotechnology (BRAINN) – one of the Research, Innovation and Dissemination Centers (RIDCs) funded by FAPESP – and led by Professor Iscia Lopes-Cendes. "According to estimates, at the world’s best centres, it takes between 15 and 20 years for patients with MTLE refractory to drug treatment to be referred for surgery," Lopes-Cendes said. "Meanwhile, they continue to suffer from uncontrolled seizures. If we can shorten this process, we can improve the lives of many patients, potentially making the difference between going or not going to university, having or not having a job and a normal life." MTLE, she explained, is caused by alterations in the functioning of neurons located in the deepest structures of the brain, such as the hippocampus and amygdala, which control important functions such as memory, attention, and anxiety, among others. Seizures due to abnormal electric discharges in a large group of neurons may or may not result in convulsions but do impair memory and other brain functions, often putting the patient at risk of accident and death. Although MTLE is not the most frequent form of epilepsy, accounting for only 30-40% of cases, it is considered the hardest to treat in adults. Up to 40% of patients with MTLE do not respond to any of the available drugs. In these cases, surgical removal of the brain area that originates the seizures is often recommended. The aim of the study, according to Lopes-Cendes, was to develop a methodology for distinguishing between the two groups by analysing their genetic material. To do this, the researchers selected a set of 11 genes that have been shown to be involved in antiepileptic drug absorption, metabolism, and transport in the scientific literature. For these 11 genes, they genotyped 119 different single nucleotide polymorphism (SNP) molecular markers to see which alleles were present. "We deployed a series of statistical procedures to develop the model with the best capacity to predict whether the patient would be responsive to drug treatment," Lopes-Cendes said. "In this model, we included and excluded variables to see which ones contributed most to the power of the predictors. Besides genetic polymorphisms, we also included clinical data such as the presence or absence of hippocampal atrophy, the age at and frequency of seizures at epilepsy onset, patient gender, and so on." When only the clinical variables were taken into account, the model’s predictions were about 45% accurate, which, according to Lopes-Cendes, is less than would be achieved by tossing a coin. However, the model’s accuracy increased to 80% when only SNP markers were used and to 82% when both clinical and genetic variables were used. As Lopes-Cendes explained, in order to be sure that the two groups of patients belonged to the same population from a genetic standpoint and hence were genuinely comparable, the researchers also genotyped 90 other SNPs in different genes located on the same chromosomes as in the previous analysis. "We call this testing technique ‘genome control’," she said. "Without it, we risk selecting patient and control groups from different populations, which would invalidate the results of the analysis." In light of the model’s high level of accuracy, Lopes-Cendes revealed that she and her team at BRAINN now plan to begin a multicentre study involving patients from several countries. "The idea is to genotype these SNPs at the start of treatment and to follow the patients for two years to see what happens. If the results corroborate our findings in this first study, we’ll have sufficient evidence to include the methodology in clinical practice," she said.
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A study of people from an isolated village in the Netherlands reveals a link between rare variants in the gene NKPD1 and depressive symptoms. The study, led by co-first authors Najaf Amin, PhD, of Erasmus University Medical Center in the Netherlands and Nadezhda Belonogova of the Russian Academy of Sciences in Novosibirsk, Russia, helps researchers understand the molecular pathology of the disease, which could eventually improve how depression is diagnosed and treated. Genetics play a strong role in risk for depression, but the identification of specific genes contributing to the disorder has eluded researchers. "By sequencing all of the DNA that codes for mRNA and ultimately, proteins, Dr. Amin and colleagues found a single gene that may account for as much as 4% of the heritable risk for depression," said Doctor John Krystal, Editor of Biological Psychiatry. To identify the gene, the researchers assessed data from the Erasmus Rucphen Family study, which was composed of a collection of families and their descendants living in social isolation until the past few decades. In a population like this, genetic isolation leads to an amplification of rarely occurring variants with little other genetic variation, providing a more powerful cohort for the discovery of rare variants. Nearly 2,000 people who had been assessed for depressive symptoms were included in the analysis. Using whole-exome sequencing to examine portions of DNA containing genetic code to produce proteins, Amin and colleagues found that several variants of NKPD1 were associated with higher depressive symptom scores. The association between depressive symptoms and NKPD1 were also replicated in an independent sample of people from the general population, although the replication sample highlighted different variants within NKPD1. "The involvement of NKPD1 in the synthesis of sphingolipids and eventually of ceramides is interesting," said Dr. Amin, referring to the predicted role of NKPD1 in the body. Altered sphingolipid levels in blood have been associated with depression and have been proposed as a therapeutic target for major depressive disorder. "We are the first to show a possible genetic connection in this respect," said Dr. Amin, adding that this implies that such a therapy might be beneficial for patients carrying risk variants in the NKPD1 gene. As with other psychiatric disorders, depression lacks genetic or biochemical markers to aid diagnosis and treatment of the disorder. According to Dr. Amin, moving depression treatment into the era of precision and personalized medicine will require a transition to objective and unbiased measurements where patients are stratified based on the molecular pathology of the disease. "NKPD1 may be one such molecular mechanism," she said.
For years, scientists have been trying to determine what effect a gene linked to the brain chemical serotonin may have on depression in people exposed to stress. But now, analysing information from more than 40,000 people who have been studied over more than a decade, researchers led by a team at Washington University School of Medicine in St. Louis have found no evidence that the gene alters the impact stress has on depression. New research findings often garner great attention. But when other scientists follow up and fail to replicate the findings? Not so much. In fact, a recent study published in PLOS One indicates that only about half of scientific discoveries will be replicated and stand the test of time. So perhaps it shouldn’t come as a surprise that new research led by Washington University School of Medicine in St. Louis shows that an influential 2003 study about the interaction of genes, environment and depression may have missed the mark. Since its publication in Science, that original paper has been cited by other researchers more than 4,000 times, and some 100 other studies have been published about links between a serotonin-related gene, stressful life events and depression risk. It indicated that people with a particular variant of the serotonin transporter gene were not as well-equipped to deal with stressful life events and, when encountering significant stress, were more likely to develop depression. Such conclusions were widely accepted, mainly because antidepressant drugs called selective serotonin reuptake inhibitors (SSRIs) help relieve depression for a significant percentage of clinically depressed individuals, so many researchers thought it logical that differences in a gene affecting serotonin might be linked to depression risk. But in this new study, the Washington University researchers looked again at data from the many studies that delved into the issue since the original publication in 2003, analysing information from more than 40,000 people, and found that the previously reported connection between the serotonin gene, depression and stress wasn’t evident. “Our goal was to get everyone who had gathered data about this relationship to come together and take another look, with each research team using the same tools to analyze data the same way,” said the study’s first author, Robert C. Culverhouse, PhD, an assistant professor of medicine and of biostatistics. “We all ran exactly the same statistical analyses, and after combining all the results, we found no evidence that this gene alters the impact stress has on depression.” Over the years, dozens of research groups had studied DNA and life experiences involving stress and depression in the more than 40,000 people revisited in this study. Some previous research indicated that those with the gene variant were more likely to develop depression when stressed, while others didn’t see a connection. So for almost two decades, scientists have debated the issue, and thousands of hours of research have been conducted. By getting all these groups to work together to reanalyze the data, this study should put the questions to rest, according to the researchers. “The idea that differences in the serotonin gene could make people more prone to depression when stressed was a very reasonable hypothesis,” said senior investigator Laura Jean Bierut, MD, the Alumni Endowed Professor of Psychiatry at Washington University. “But when all of the groups came together and looked at the data the same way, we came to a consensus. We still know that stress is related to depression, and we know that genetics is related to depression, but we now know that this particular gene is not.” Culverhouse noted that finally, when it comes to this gene and its connection to stress and depression, the scientific method has done its job.
Washington University School of Medicine medicine.wustl.edu/news/study-reverses-thinking-genetic-links-stress-depression/
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In overweight and obese children and adolescents, vitamin D deficiency is associated with early markers of cardiovascular disease, a new study reports. "Paediatric obesity affects 17 percent of infants, children, and adolescents ages 2 to 19 in the United States, and obesity is a risk factor for vitamin D deficiency. These findings suggest that vitamin D deficiency may have negative effects on specific lipid markers with an increase in cardiovascular risk among children and adolescents," said lead author Marisa Censani, M.D., pediatric endocrinologist and director of the Pediatric Obesity Program in the Division of Pediatric Endocrinology at New York Presbyterian Hospital/Weill Cornell Medicine in New York, N.Y. "This research is newsworthy because this is one of the first studies to assess the relationship of vitamin D deficiency to both lipoprotein ratios and non-high density lipoprotein (non-HDL) cholesterol, specific lipid markers impacting cardiovascular risk during childhood, in children and adolescents with obesity/overweight," Censani noted. Censani and her colleagues reviewed the medical records, including vitamin D levels, of children and adolescents between 6 and 17 years of age who were evaluated at the paediatric endocrinology outpatient clinics at Weill Cornell Medicine over a two-year period. Overall, 178 of 332 patients met criteria for overweight and obesity: Body Mass Index (BMI) above the 85th percentile; and 60 patients with BMI above the 85th percentile had fasting lipid test results available. Total cholesterol, triglycerides, HDL, low-density lipoprotein (LDL), and non-HDL cholesterol were collected; and total cholesterol/HDL and triglyceride/HDL ratios were calculated. Vitamin D deficiency was considered to be 25 hydroxyvitamin D (25OHD) below 20 ng/ml. Vitamin D deficiency was found to be significantly associated with an increase in atherogenic lipids and markers of early cardiovascular disease. Total cholesterol, triglycerides, LDL, non-HDL cholesterol, as well as total cholesterol/HDL and triglyceride/HDL ratios, were all higher in vitamin D-deficient patients compared to patients without vitamin D deficiency. "These results support screening children and adolescents with overweight and obesity for vitamin D deficiency and the potential benefits of improving vitamin D status to reduce cardiometabolic risk," Censani said.
The Endocrine Society www.endocrine.org/news-room/current-press-releases/vitamin-d-deficiency-may-indicate-cardiovascular-disease-in-overweight-and-obese-children
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New lab-on-a-chip platform seeks to improve pathogen detection
, /in E-News /by 3wmediaResearchers from the Fraunhofer Institute have developed a new prototype lab-on-a-chip platform for the easy and versatile detection of molecular pathogens.
Nuclear amplification testing is commonly used for pathogen detection; however, the process is currently manually intensive and complex, and requires dedicated equipment. This prevents its use in some settings, and pathogen detection in individual samples.
In a bid to solve these issues, Natalia Sandetskaya and colleagues at the Fraunhofer Institute for Cell Therapy & Immunology (Leipzig, Germany) have developed a prototype lab-on-a-chip platform capable of automating the process in a single instrument.
“We were motivated by the existing need for making the molecular analysis of complex samples much simpler for the users,” commented Sandetskaya. “Our particular applied interest is the detection of the pathogens in blood; for instance in sepsis, when only a few microorganisms must be rapidly found in a large volume of blood.”
The chip utilizes microfluidics and integrates sample volume transition, lysis, nucleic acid isolation, amplification (PCR or LAMP), and real-time fluorescence detection. As a single instrument, it could enable diagnostics in situations not previously feasible.
The researchers go on to demonstrate its proof-of-concept in the detection of E. coli and Salmonella bacterial species.
“Although our current prototype of the platform will need further development for this application, we have already demonstrated a high level of integration of very diverse processes without making the system overly complex,” noted Sandetskaya.
The team is now planning experiments to evaluate the platform in real-world samples and perfect its design.
Future Science OA
www.future-science-group.com/new-lab-on-a-chip-platform-seeks-to-improve-pathogen-detection/
Genes associated with Erdheim-Chester disease also linked to cancer
, /in E-News /by 3wmediaNational Human Genome Research Institute (NHGRI) researchers have identified new genes associated with the Erdheim-Chester disease (ECD) and some possible new therapies. This ultra-rare disease is found in approximately 600 people in the world.
"The discovery of new genes associated with ECD provides hope for improving the diagnoses of a disease that affects so many parts of the body. We also hope it will help us identify new treatments," said Juvianee I. Estrada-Veras, M.D., clinical investigator and staff clinician in NHGRI’s Medical Biochemical Genetics Residency Program. "Our work on ECD builds on the institute’s goals to advance medical knowledge about rare diseases and to potentially provide insights into more common disorders."
ECD is caused by the accumulation of specialized white blood cells called histiocytes in different organs. The resulting inflammation damages organs and tissues throughout the body, causing them to become thickened, dense and scarred. Histiocytes normally function to destroy foreign substances and protect the body from infection. ECD has no standard therapy, although consensus guidelines for clinical management were published in 2014.
Between 2011 and 2015, researchers examined 60 adults with ECD at the NIH Clinical Center. Of 59 samples that were available for molecular testing, half had BRAF V600E gene mutations, which is sometimes seen in colon cancer, lung cancer, thyroid cancer, brain tumours and some blood cancers. Other patients had mutations in genes of the MAPK pathway, which controls cell growth and proliferation. These findings indicate that, despite the presence of inflammation and the absence of metastases (spread of cancer cells from the place where they first formed to another part of the body), ECD should be considered a type of cancer and treated by oncologists, researchers wrote.
Until now, the most common treatment for ECD has been interferon, a drug that interferes with the division of cancer cells and slows tumour growth. Some patients with severe forms of disease can succumb to the illness even with treatment. The mortality rate for ECD has been estimated at 60 percent at 3 years from the time of diagnosis.
Researchers suggested that therapies that stop the growth and proliferation of cells by blocking the MAPK pathway — vemurafenib, dabrafenib and trametinib — may provide new hope for treating and improving the survival of people with ECD. A therapeutic trial of dabrafenib and trametinib is now enrolling new ECD patients with BRAF V600E mutations.
National Human Genome Research Institute
www.genome.gov/27568398/2017-news-feature-genes-associated-with-erdheimchester-disease-also-linked-to-cancer/
“Jumping gene” uncovers genetic networks involved in prostate and breast cancer
, /in E-News /by 3wmediaMutations in tumour suppressor genes mean that they can no longer keep tumours from growing. In developing cancer, often several mutations come into play. Using "jumping genes," scientists from the Technical University of Munich (TUM) and the German Cancer Consortium (DKTK) together with teams from Great Britain and Spain have identified a number of genes that can influence the growth of prostate and breast tumours.
Prostate cancer is the most common cancer in men in Germany with around 63,000 patients diagnosed every year. About half of them have an altered Pten gene. This well-known tumour suppressor gene can help prevent cancer development in healthy people by inducing cell death in tumour cells. However, little is known about which other genes cooperate with Pten to prevent cancer. In order to find out more, the international team designed a new method. They converted the Pten-Gene in mice into a mobile DNA element known as a transposon. This transposon "jumps" from its original position and lands at a random position throughout the genome, damaging and thus deactivating genes into which it is inserted. The transposons "starting point", i.e. the Pten-Gene, is deactivated as well. In the experiment, cancers would grow when the transposon damaged a tumour suppressor gene that co-operated with Pten.
"Using the new transposon-based approach, we were able to systematically search the genome for genes cooperating with Pten and influencing the development of prostate cancer, but also other forms of cancer like breast or brain cancer," says Dr Juan Cadiñanos, joint lead author from the Instituto de Medicina Oncologica y Molecular de Asturias and the Wellcome Trust Sanger Institute in Britain. "This approach could also be used to look into relations between other genes."
The researchers analysed 278 prostate, breast and skin tumours and revealed hundreds of genes that could cooperate with Pten and act as further tumour suppressor genes. Human cell lines and data from human prostate tumours were then used to study the five most promising genes. "Coupled with Pten inactivation, a loss of function in these genes led to typical cancer pathways being activated," says Jorge de la Rosa, one of the study’s first authors. The researchers found that in human prostate tumours, the genes in question were considerably limited in their function.
Transposon-based approaches are useful for looking into the molecular basics of the development of tumours. "They allow us to find genes connected to cancer that are hard to find using other methods," says Roland Rad, a DKTK-Professor for translational Oncology at TUM’s Klinikum rechts der Isar. "In order to understand the biology of tumour development, we must uncover the complex tumor suppressor networks. This is a prerequisite for developing new therapeutic strategies."
DKFZ
www.dkfz.de/en/presse/pressemitteilungen/2017/dkfz-pm-17-14b-Jumping-gene-uncovers-genetic-networks-involved-in-prostate-and-breast-cancer.php
Hair testing shows high prevalence of new psychoactive substance use
, /in E-News /by 3wmediaOver a fourth of the eighty samples tested positive for new psychoactive substances.
In the last decade hundreds of new psychoactive substances (NPS) have emerged in the drug market, taking advantage of the delay occurring between their introduction into the market and their legal ban. According to the Drug Enforcement Agency (DEA) NPS describes a recently emerged drug that may pose a public health threat. The DEA issues a quarterly Emerging Threat Report, which catalogues the newest identified NPS.
NPS tend to mimic the psychotropic effects of traditional drugs of abuse, but their acute and chronic toxicity, and side-effects are largely unknown. While seizure data from the DEA is often used to indicate what new drugs are being sold in the US, there is a lack of research examining and confirming who has been using such drugs.
Joseph J. Palamar, PhD, MPH, a New York University researcher, has been researching incidental and intentional use of NPS by young adults. His current line of inquiry has focused on survey methods, qualitative interviews, and hair sampling to ascertain frequency and type of NPS use by nightclub-goers–a demographic which traditionally has a relaxed view towards recreational drug experimentation and use.
NPS are common adulterants in drugs such as ecstasy (MDMA), which has seen an increase in popularity since it became marketed as “Molly”. Ironically, “Molly” connotes a product that is pure MDMA. In a related study, Palamar and his team found that four out of ten nightclub/festival attendees who used ecstasy or “Molly” tested positive for “bath salts” despite reporting no use.
In their current study, “Hair Testing for Drugs of Abuse and New Psychoactive Substances in a High-Risk Population,” Dr. Alberto Salomone, an affiliated researcher at the Centro Regionale Antidoping e di Tossicologia “A. Bertinaria”, Orbassano, Turin, Italy and Dr. Palamar, affiliated with NYU’s Center for Drug Use and HIV Research (CDUHR), collected hair samples from 80 young adults outside of New York City nightclubs and dance festivals, from July through September of 2015. Hair samples from high-risk nightclub and dance music attendees were tested for 82 drugs and metabolites (including NPS) using ultra-high performance liquid chromatography–tandem mass spectrometry.
“Hair analysis represents a reliable and well-established means of clinical and forensic investigations to evaluate drug exposure, said Dr. Salomone. “Hair is the most helpful specimen when either long-time retrospective information on drug consumption is of interest.” “Most NPS can no longer be detected in urine, blood, or saliva within hours or days after consumption, but hair is particularly beneficial because many drugs can be detected months after use.”
Of the eighty samples, twenty-six tested positive for at least one NPS—the most common being a “bath salt” (synthetic cathinone) called butylone (present in twenty-five samples). The “bath salts” methylone and even alpha-PVP (a.k.a.: “Flakka”) were also detected. The researchers find the presence of Flakka alarming as this drug has been associated with many episodes of erratic behaviour and even death in Florida. Other new drugs detected included new stimulants called 4-FA and 5/6-APB.
“We found that many people in the nightclub and festival scene have been using new drugs and our previous research has found that many of these people have been using unknowingly,” said Dr. Palamar, also an assistant professor of Population Health at NYU Langone Medical Center (NYULMC).
Hair analysis proved a powerful tool to Drs. Salomone and Palamar and their team, allowing them to gain objective biological drug-prevalence information, free from possible biases of unintentional or unknown intake and untruthful reporting of use.
NYU Langone Medical Center
www.nyu.edu/about/news-publications/news/2017/march/hair-testing-shows-high-prevalence-of-new-psychoactive-substance.html
These 5 tests better predict heart disease risk
, /in E-News /by 3wmediaFive simple medical tests together provide a broader and more accurate assessment of heart-disease risk than currently used methods, cardiologists at UT Southwestern Medical Center found.
Combined, results from the five tests – an EKG, a limited CT scan, and three blood tests – better predict who will develop heart disease compared with standard strategies that focus on blood pressure, cholesterol, diabetes, and smoking history, researchers reported.
“This set of tests is really powerful in identifying unexpected risk among individuals with few traditional risk factors. These are people who would not be aware that they are at risk for heart disease and might not be targeted for preventive therapies,” said Dr. James de Lemos, Professor of Internal Medicine.
The five tests, and the information they provide:
Four of the five tests are currently readily available and the fifth – high-sensitivity troponin T – will be available soon.
Researchers used data from two large population studies, including the Dallas Heart Study, that each followed a large group of healthy individuals for more than a decade. Their study was partly funded by NASA to develop strategies for predicting heart disease in astronauts.
The new study focused on a broader spectrum of cardiovascular disease events rather than only those related to cholesterol plaque buildup, as traditional risk assessment does.
UT Southwestern Medical Center
www.utsouthwestern.edu/newsroom/news-releases/year-2017/mar/risk-assessment-khera.html
Researchers find new genetic links underlying progressively blinding eye disease
, /in E-News /by 3wmediaCorneal diseases are among the most common causes of visual impairment and blindness, with Fuchs endothelial corneal dystrophy (FECD), a gradual swelling and clouding of the cornea, being the most common reason for eventual corneal transplants.
The cornea is the transparent front part of the eye covering the iris, pupil and anterior chamber. In Fuchs endothelial corneal dystrophy, the innermost cell layer of the cornea begins to progressively deteriorate, eventually resulting in severe vision impairment and blindness.
Researchers at University of California San Diego School of Medicine, with colleagues at Case Western University, Duke University, the National Institutes of Health and elsewhere, have identified three novel genomic loci — distinct stretches of genetic material on chromosomes — linked to FECD, which often clusters in families and is roughly 39 percent heritable.
“Previously, there was one known FECD locus. We’ve expanded that number to four,” said the study’s first author Natalie A. Afshari, MD, professor of ophthalmology, Stuart Brown MD Chair in Ophthalmology in Memory of Donald Shiley and chief of cornea and refractive surgery at Shiley Eye Institute at UC San Diego Health. “These findings provide a deeper understanding of the pathology of FECD, which in turn will help us develop better therapies for treating or preventing this disabling disease.”
FECD affects the innermost layer of cells in the cornea (the transparent front cover of the eye), called the endothelium. The endothelium is responsible for maintaining the proper amount of fluid in the cornea, keeping it clear. FECD is a progressive disorder in which the endothelium slowly degrades, with lost clarity, pain and severely impaired vision. It affects 4 percent of the U.S. population above age 40 and worsens with age. Women are two to four times more affected than men. While there is symptomatic treatment in early stages, surgery — often a corneal transplant — is the only remedy after significant vision loss occurs.
The research team conducted a genome-wide association study, an analytical approach in which scientists look for genetic variants in individuals associated with a particular disease. This study involved 1,404 patients with FECD and 2,564 controls of European ancestry.
The results confirmed the known role of the TCF4 gene, but also revealed associations with three other loci: KANK4, LAMC1 and LINC009970/ATPB1. Researchers also found some genomic markers that were more associated by gender, with LAMC1 increasing FECD risk in women while TCF4 increased risk in men.
“While more work must be done to precisely elucidate what these proteins do,” said Afshari, “the results suggest they have essential roles in sustaining and maintaining the health of the corneal endothelium. This knowledge improves our understanding of the genetic risk factors for FECD and gives us new therapeutic targets.”
UCSD Center for Health
health.ucsd.edu/news/releases/Pages/2017-03-30-new-genetic-links-underlying-progressive-eye-disease.aspx
Method identifies epileptic patients who can benefit from surgery
, /in E-News /by 3wmediaResearchers affiliated with the University of Campinas (UNICAMP) in São Paulo State, Brazil, have shown that genetic information can be used to improve early prediction of the response to drugs in patients with mesial temporal lobe epilepsy (MTLE), one of the most severe forms of epilepsy. Patients who do not respond well to treatment with antiepileptic drugs are candidates for surgery.
The research was conducted at the Brazilian Research Institute for Neuroscience and Neurotechnology (BRAINN) – one of the Research, Innovation and Dissemination Centers (RIDCs) funded by FAPESP – and led by Professor Iscia Lopes-Cendes.
"According to estimates, at the world’s best centres, it takes between 15 and 20 years for patients with MTLE refractory to drug treatment to be referred for surgery," Lopes-Cendes said. "Meanwhile, they continue to suffer from uncontrolled seizures. If we can shorten this process, we can improve the lives of many patients, potentially making the difference between going or not going to university, having or not having a job and a normal life."
MTLE, she explained, is caused by alterations in the functioning of neurons located in the deepest structures of the brain, such as the hippocampus and amygdala, which control important functions such as memory, attention, and anxiety, among others. Seizures due to abnormal electric discharges in a large group of neurons may or may not result in convulsions but do impair memory and other brain functions, often putting the patient at risk of accident and death.
Although MTLE is not the most frequent form of epilepsy, accounting for only 30-40% of cases, it is considered the hardest to treat in adults. Up to 40% of patients with MTLE do not respond to any of the available drugs. In these cases, surgical removal of the brain area that originates the seizures is often recommended.
The aim of the study, according to Lopes-Cendes, was to develop a methodology for distinguishing between the two groups by analysing their genetic material. To do this, the researchers selected a set of 11 genes that have been shown to be involved in antiepileptic drug absorption, metabolism, and transport in the scientific literature.
For these 11 genes, they genotyped 119 different single nucleotide polymorphism (SNP) molecular markers to see which alleles were present.
"We deployed a series of statistical procedures to develop the model with the best capacity to predict whether the patient would be responsive to drug treatment," Lopes-Cendes said. "In this model, we included and excluded variables to see which ones contributed most to the power of the predictors. Besides genetic polymorphisms, we also included clinical data such as the presence or absence of hippocampal atrophy, the age at and frequency of seizures at epilepsy onset, patient gender, and so on."
When only the clinical variables were taken into account, the model’s predictions were about 45% accurate, which, according to Lopes-Cendes, is less than would be achieved by tossing a coin.
However, the model’s accuracy increased to 80% when only SNP markers were used and to 82% when both clinical and genetic variables were used.
As Lopes-Cendes explained, in order to be sure that the two groups of patients belonged to the same population from a genetic standpoint and hence were genuinely comparable, the researchers also genotyped 90 other SNPs in different genes located on the same chromosomes as in the previous analysis.
"We call this testing technique ‘genome control’," she said. "Without it, we risk selecting patient and control groups from different populations, which would invalidate the results of the analysis."
In light of the model’s high level of accuracy, Lopes-Cendes revealed that she and her team at BRAINN now plan to begin a multicentre study involving patients from several countries.
"The idea is to genotype these SNPs at the start of treatment and to follow the patients for two years to see what happens. If the results corroborate our findings in this first study, we’ll have sufficient evidence to include the methodology in clinical practice," she said.
EurekAlert
www.eurekalert.org/pub_releases/2017-04/fda-mie040417.php
NKPD1 variant increases depression risk
, /in E-News /by 3wmediaA study of people from an isolated village in the Netherlands reveals a link between rare variants in the gene NKPD1 and depressive symptoms. The study, led by co-first authors Najaf Amin, PhD, of Erasmus University Medical Center in the Netherlands and Nadezhda Belonogova of the Russian Academy of Sciences in Novosibirsk, Russia, helps researchers understand the molecular pathology of the disease, which could eventually improve how depression is diagnosed and treated.
Genetics play a strong role in risk for depression, but the identification of specific genes contributing to the disorder has eluded researchers. "By sequencing all of the DNA that codes for mRNA and ultimately, proteins, Dr. Amin and colleagues found a single gene that may account for as much as 4% of the heritable risk for depression," said Doctor John Krystal, Editor of Biological Psychiatry.
To identify the gene, the researchers assessed data from the Erasmus Rucphen Family study, which was composed of a collection of families and their descendants living in social isolation until the past few decades. In a population like this, genetic isolation leads to an amplification of rarely occurring variants with little other genetic variation, providing a more powerful cohort for the discovery of rare variants. Nearly 2,000 people who had been assessed for depressive symptoms were included in the analysis.
Using whole-exome sequencing to examine portions of DNA containing genetic code to produce proteins, Amin and colleagues found that several variants of NKPD1 were associated with higher depressive symptom scores. The association between depressive symptoms and NKPD1 were also replicated in an independent sample of people from the general population, although the replication sample highlighted different variants within NKPD1.
"The involvement of NKPD1 in the synthesis of sphingolipids and eventually of ceramides is interesting," said Dr. Amin, referring to the predicted role of NKPD1 in the body. Altered sphingolipid levels in blood have been associated with depression and have been proposed as a therapeutic target for major depressive disorder.
"We are the first to show a possible genetic connection in this respect," said Dr. Amin, adding that this implies that such a therapy might be beneficial for patients carrying risk variants in the NKPD1 gene.
As with other psychiatric disorders, depression lacks genetic or biochemical markers to aid diagnosis and treatment of the disorder. According to Dr. Amin, moving depression treatment into the era of precision and personalized medicine will require a transition to objective and unbiased measurements where patients are stratified based on the molecular pathology of the disease. "NKPD1 may be one such molecular mechanism," she said.
ScienceDaily
www.sciencedaily.com/releases/2017/04/170404090027.htm
Study reverses thinking on genetic links to stress, depression
, /in E-News /by 3wmediaFor years, scientists have been trying to determine what effect a gene linked to the brain chemical serotonin may have on depression in people exposed to stress. But now, analysing information from more than 40,000 people who have been studied over more than a decade, researchers led by a team at Washington University School of Medicine in St. Louis have found no evidence that the gene alters the impact stress has on depression.
New research findings often garner great attention. But when other scientists follow up and fail to replicate the findings? Not so much.
In fact, a recent study published in PLOS One indicates that only about half of scientific discoveries will be replicated and stand the test of time. So perhaps it shouldn’t come as a surprise that new research led by Washington University School of Medicine in St. Louis shows that an influential 2003 study about the interaction of genes, environment and depression may have missed the mark.
Since its publication in Science, that original paper has been cited by other researchers more than 4,000 times, and some 100 other studies have been published about links between a serotonin-related gene, stressful life events and depression risk. It indicated that people with a particular variant of the serotonin transporter gene were not as well-equipped to deal with stressful life events and, when encountering significant stress, were more likely to develop depression.
Such conclusions were widely accepted, mainly because antidepressant drugs called selective serotonin reuptake inhibitors (SSRIs) help relieve depression for a significant percentage of clinically depressed individuals, so many researchers thought it logical that differences in a gene affecting serotonin might be linked to depression risk.
But in this new study, the Washington University researchers looked again at data from the many studies that delved into the issue since the original publication in 2003, analysing information from more than 40,000 people, and found that the previously reported connection between the serotonin gene, depression and stress wasn’t evident.
“Our goal was to get everyone who had gathered data about this relationship to come together and take another look, with each research team using the same tools to analyze data the same way,” said the study’s first author, Robert C. Culverhouse, PhD, an assistant professor of medicine and of biostatistics. “We all ran exactly the same statistical analyses, and after combining all the results, we found no evidence that this gene alters the impact stress has on depression.”
Over the years, dozens of research groups had studied DNA and life experiences involving stress and depression in the more than 40,000 people revisited in this study. Some previous research indicated that those with the gene variant were more likely to develop depression when stressed, while others didn’t see a connection. So for almost two decades, scientists have debated the issue, and thousands of hours of research have been conducted. By getting all these groups to work together to reanalyze the data, this study should put the questions to rest, according to the researchers.
“The idea that differences in the serotonin gene could make people more prone to depression when stressed was a very reasonable hypothesis,” said senior investigator Laura Jean Bierut, MD, the Alumni Endowed Professor of Psychiatry at Washington University. “But when all of the groups came together and looked at the data the same way, we came to a consensus. We still know that stress is related to depression, and we know that genetics is related to depression, but we now know that this particular gene is not.”
Culverhouse noted that finally, when it comes to this gene and its connection to stress and depression, the scientific method has done its job.
Washington University School of Medicine
medicine.wustl.edu/news/study-reverses-thinking-genetic-links-stress-depression/
Vitamin D deficiency may indicate cardiovascular disease in overweight and obese children
, /in E-News /by 3wmediaIn overweight and obese children and adolescents, vitamin D deficiency is associated with early markers of cardiovascular disease, a new study reports.
"Paediatric obesity affects 17 percent of infants, children, and adolescents ages 2 to 19 in the United States, and obesity is a risk factor for vitamin D deficiency. These findings suggest that vitamin D deficiency may have negative effects on specific lipid markers with an increase in cardiovascular risk among children and adolescents," said lead author Marisa Censani, M.D., pediatric endocrinologist and director of the Pediatric Obesity Program in the Division of Pediatric Endocrinology at New York Presbyterian Hospital/Weill Cornell Medicine in New York, N.Y.
"This research is newsworthy because this is one of the first studies to assess the relationship of vitamin D deficiency to both lipoprotein ratios and non-high density lipoprotein (non-HDL) cholesterol, specific lipid markers impacting cardiovascular risk during childhood, in children and adolescents with obesity/overweight," Censani noted.
Censani and her colleagues reviewed the medical records, including vitamin D levels, of children and adolescents between 6 and 17 years of age who were evaluated at the paediatric endocrinology outpatient clinics at Weill Cornell Medicine over a two-year period.
Overall, 178 of 332 patients met criteria for overweight and obesity: Body Mass Index (BMI) above the 85th percentile; and 60 patients with BMI above the 85th percentile had fasting lipid test results available.
Total cholesterol, triglycerides, HDL, low-density lipoprotein (LDL), and non-HDL cholesterol were collected; and total cholesterol/HDL and triglyceride/HDL ratios were calculated. Vitamin D deficiency was considered to be 25 hydroxyvitamin D (25OHD) below 20 ng/ml.
Vitamin D deficiency was found to be significantly associated with an increase in atherogenic lipids and markers of early cardiovascular disease. Total cholesterol, triglycerides, LDL, non-HDL cholesterol, as well as total cholesterol/HDL and triglyceride/HDL ratios, were all higher in vitamin D-deficient patients compared to patients without vitamin D deficiency.
"These results support screening children and adolescents with overweight and obesity for vitamin D deficiency and the potential benefits of improving vitamin D status to reduce cardiometabolic risk," Censani said.
The Endocrine Society
www.endocrine.org/news-room/current-press-releases/vitamin-d-deficiency-may-indicate-cardiovascular-disease-in-overweight-and-obese-children