Specific genetic errors that trigger congenital heart disease (CHD) in humans can be reproduced reliably in Drosophila melanogaster – the common fruit fly – an initial step toward personalized therapies for patients in the future.
“Studying CHD in fruit flies provides a fast and simple first step in understanding the roles that individual genes play in disease progression,” says Zhe Han, Ph.D., a principal investigator and associate professor in the Center for Cancer & Immunology Research at Children’s National Health System and senior author of the paper. “Our research team is the first to describe a high-throughput in vivo validation system to screen candidate disease genes identified from patients. This approach has the potential to facilitate development of precision medicine approaches for CHD and other diseases associated with genetic factors,” Han says.
Some 134 genes have been implicated in causing CHD, a birth defect that affects 8 in 1,000 newborns, according to the National Institutes of Health. The research team led by Han used high-throughput techniques to alter the activity of dozens of genes in flies’ hearts simultaneously in order to validate genes that cause heart disease.
“Our team was able to characterize the effect of these specific genetic alterations on heart development, structure and activity,” Han adds. “The development of the human heart is a complicated process in which a number of different cell types need to mature and differentiate to create all of the structures in this essential organ. The precise timing of those cellular activities is critical to normal heart development, with disruptions in the structure of proteins called histones linked to later heart problems.”.
Of 134 genes studied by the research team, 70 caused heart defects in fruit flies, and several of the altered genes are involved in modifying the structure of histones. Quantitative analyses of multiple cardiac phenotypes demonstrated essential structural, functional and developmental roles for these genes, including a subgroup encoding histone H3K4 modifying proteins. The scientists then corroborated their work by reliably reproducing in flies the effect of specific genetic errors identified in humans with CHD.
“This may allow researchers to replicate individual cases of CHD, study them closely in the laboratory and fashion treatments personalized to that patient specifically,” he adds. “Precise gene-editing techniques could be used to tailor-make flies that express a patient’s specific genetic mutation. Treating CHD at the level of DNA offers the potential of interrupting the current cycle of passing along genetic mutations to each successive generation.”
Children’s National Health System childrensnational.org/news-and-events/childrens-newsroom/2017/studying-chd-in-fruit-flies
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Engineers at the University of California San Diego have developed a desktop diagnosis tool that detects the presence of harmful bacteria in a blood sample in a matter of hours instead of days. The breakthrough was made possible by a combination of proprietary chemistry, innovative electrical engineering and high-end imaging and analysis techniques powered by machine learning.
To identify low levels of harmful bacteria among a large number of human blood cells, researchers for the first time melted bacterial DNA in 20,000 extremely small simultaneous reactions. Each reaction contained only 20 picoliters—a scale that is hard to picture: one drop of rain contains hundreds of thousands of picoliters.
Each type of DNA has a specific signature as it comes apart during melting. As the melting process is imaged and analysed, researchers can use machine learning to determine which types of DNA appear in blood samples. During experiments, the system accurately identified, 99 percent of the time, DNA sequences from bacteria causing food-borne illnesses and pneumonia—in less than four hours.
“Analysing this many reactions at the same time at this small a scale had never been attempted before,” said Stephanie Fraley, a professor of bioengineering at the Jacobs School of Engineering at UC San Diego and the paper’s lead author. “Most molecular tests look at DNA on a much larger scale and look for just one type of bacteria at a time. We analyse all the bacteria in a sample. This is a much more holistic approach.”
Current methods used to detect and identify bacteria rely on cultures, which can take days. That is too long to provide physicians with an effective and timely diagnosis tool—as anyone who has been prescribed antibiotics while waiting for test results knows.
It all starts with one milliliter of blood, which researchers inoculated with Listeria monocytogenes, a food-borne bacterium that causes about 260 deaths a year in the United States, and Streptococcus pneumoniae, which causes everything from sinus infections, to pneumonia, to meningitis.
Researchers isolated all DNA from the blood sample. The DNA was then placed on a digital chip that allowed each piece to independently multiply in its own small reaction. For the process to work at such small scales—each well containing DNA in the chip was only 20 picoliters in volume—researchers used a proprietary mix of chemicals subject to a provisional patent.
The chip with the amplified DNA was placed in an innovative high-throughput microscope that Fraley and her team designed. The DNA was then heated in increments of 0.2 degrees Celsius, causing it to melt at temperatures between 50 to 90 degrees Celsius –about 120 to 190 degrees Fahrenheit.
As the DNA double-helix melts, the bonds holding together the DNA strands break. Depending on the DNA’s sequence, the bonds have different strengths and that changes the way the strands unwind from each other. This creates a unique sequence-dependent fingerprint, which researchers can detect using a special dye. The dye causes the unwinding process to give off fluorescent light, creating what researchers call a melting curve—a unique signature for each type of bacteria.
When engineers imaged the melting process with the high-throughput microscope, they were able to capture the bacteria’s melting curves. They then analysed the curves with a machine learning algorithm they developed.
In previous work, the algorithm was trained on 37 different types of bacteria undergoing different reactions in different conditions. The researchers showed that it was able to identify bacteria strains with 99 percent accuracy.
University of California – San Diegoucsdnews.ucsd.edu/pressrelease/new_method_to_identify_bacteria_in_blood_samples_works_in_hours_instead_of
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A single blood test and basic information about a patient’s medical status can indicate which patients with myelodysplastic syndrome (MDS) are likely to benefit from a stem cell transplant, and the intensity of pre-transplant chemotherapy and/or radiation therapy that is likely to produce the best results, according to new research by scientists at Dana-Farber Cancer Institute and Brigham and Women’s Hospital.
In a study, the investigators report that genetically profiling a patient’s blood cells, while factoring in a patient’s age and other factors, can predict the patient’s response to a stem cell transplant and help doctors select the most effective combination of pre-transplant therapies. The findings are based on an analysis of blood samples from 1,514 patients with MDS, ranging in age from six months to more than 70 years, performed in collaboration with investigators from the Center for Blood and Marrow Transplant Research.
MDS is a family of diseases in which the bone marrow produces an insufficient supply of healthy blood cells. Treatments vary depending on the specific type of MDS a patient has; donor stem cell transplants are generally used for patients with a high risk of mortality with standard treatments.
“Although donor stem cell transplantation is the only curative therapy for MDS, many patients die after transplantation, largely due to relapse of the disease or complications relating to the transplant itself,” said the study’s lead author, R. Coleman Lindsley, MD, PhD, of Dana-Farber. “As physicians, one of our major challenges is to be able to predict which patients are most likely to benefit from a transplant. Improving our ability to identify patients who are most likely to have a relapse or to experience life-threatening complications from a transplant could lead to better pre-transplant therapies and strategies for preventing relapse.”
Researchers have long known that the specific genetic mutations within MDS patients’ blood cells are closely related to the course the disease takes. The current study sought to discover whether mutations also can be used to predict how patients will fare following a donor stem cell transplant.
Analysis of the data showed that the single most important characteristic of a patient’s MDS was whether their blood cells carried a mutation in the gene TP53. These patients tended to survive for a shorter time after a transplant, and also relapse more quickly, than patients whose cells lacked that mutation. This was true whether patients received standard “conditioning” therapy (which includes chemo- and/or radiation therapy) prior to transplant or received reduced-intensity conditioning, which uses lower doses of these therapies. Based on these results, doctors at Dana-Farber are now working on new strategies to overcome the challenges posed by TP53 mutations in MDS.
In patients 40 years old and over whose MDS didn’t carry TP53 mutations, those with mutations in RAS pathway genes or the JAK2 gene tended to have a shorter survival than those without RAS or JAK2 mutations. In contrast to TP53 mutations, the adverse effect of RAS mutations on survival and risk of relapse was evident only in reduced-intensity conditioning. This suggests that these patients may benefit from higher intensity conditioning regimens, the researchers indicated.
The study also yielded key insights about the biology of MDS in specific groups of patients. Surprisingly, one in 25 patients with MDS between the ages of 18 and 40 were found to have mutations associated with Shwachman-Diamond syndrome (a rare inherited disorder that often affects the bone marrow, pancreas, and skeletal system), but most of them had not previously been diagnosed with it. In each case, the patients’ blood cells had acquired a TP53 mutation, suggesting not only how MDS develops in patients with Schwachman-Diamond syndrome but also what underlies their poor prognosis after transplantation.
Dana Farber Cancer Institutewww.dana-farber.org/Newsroom/News-Releases/genetic-profiling-can-guide-stem-cell-transplantation-for-patients-with-myelodysplastic-syndrome-study-finds.aspx
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Each year, about 1.38 million women worldwide are diagnosed with breast cancer. Advances in diagnosis and treatment have facilitated a 90-percent, five-year survival rate, among those treated. However, with the increased rate and length of survival following breast cancer, patients face a lifetime risk of developing lymphedema, one of the most distressing and feared late onset breast cancer-related effects.
Lymphedema is an abnormal accumulation of lymph fluid in the ipsilateral body area, or upper limb. This remains an on-going major health problem affecting more than 40 percent of 3.1 million breast cancer survivors in the U.S. Lymphedema following breast cancer surgery is typically considered to be primarily due to the mechanical injury from surgery. However, recent research has found that inflammation-infection and higher body mass index are also main predictors of lymphedema.
Researchers from New York University Rory Meyers College of Nursing (NYU Meyers), led by Dr. Mei R. Fu, PhD, RN, FAAN, conducted a study, “Precision assessment of heterogeneity of lymphedema phenotype, genotypes and risk prediction,” to address this phenomenon and prospectively examine phenotype of arm lymphedema by limb volume and lymphedema symptoms in relation to inflammatory genes in women treated for breast cancer.
The study is the first of its kind in exploring associations between genetic susceptibility targeting identified phenotypic risk factors of inflammation and heterogeneous phenotypes of lymphedema.
“It remains puzzling that up to 23% of survivors who only had lumpectomy with sentinel lymph node biopsy of 1 or 2 lymph nodes removed have developed lymphedema, while some survivors who had mastectomy with more than 10 lymph nodes removed have not,” said Dr. Fu. “There is a critical need to understand heterogeneity of lymphedema phenotype in relation to assessment of lymphedema phenotype and related biological mechanism.”
The study consisted of 136 women with a mean age of 52 with a first time diagnosis of breast cancer (Stage I-III), and were scheduled for surgical treatment of lumpectomy or mastectomy. The researchers measured data at 4-8 weeks post-surgery and 12 months post-surgery to monitor development of lymphedema during this period. They used lymphedema phenotyping to measure more symptoms than the typical method of observing swelling and limb volume. The symptom phenotyping was important in indicating early stage lymphedema where limb volume cannot be assessed yet.
The researchers found that using symptom phenotyping, prior to surgery, only one participant had more than 8 symptoms and only 18 had 1-7 symptoms. At 4-8 weeks post-surgery all participants had at least one symptom, 53% had 1-7 symptoms, and 46% had more than 8 symptoms, whereas only 16% had arm lymphedema defined by limb volume increase. At 12 months post-surgery 26.5% had more than 8 symptoms and 63% reported 1-7 symptoms, whereas only 22.8% had arm lymphedema as defined by limb volume. Additionally, prior to surgery, identification of symptom phenotypes was not feasible, as 86% of participants were symptom-free. However, at 4-8 weeks post-surgery 58.1% of participants were classified as the phenotype of impaired limb mobility, with 86% discomfort, and 55.9% fluid accumulation. At 12 months 55.2% of participants were classified as the phenotype of impaired limb mobility with 38.2% pain/discomfort, and 44.1% fluid accumulation.
This data found significant associations between genotypes related to several lymphatic and inflammatory genes and symptom phenotypes of impaired limb mobility, fluid accumulation, and pain/discomfort. The data further provides support for heterogeneity of lymphedema phenotypes, especially phenotype of symptom clusters based on biological mechanisms.
Dr. Fu notes that the sample size and only 12-month period of observation does put limitations on the study.
New York Universitywww.nyu.edu/about/news-publications/news/2017/february/nyu-researchers-study-patients-genetic-and-susceptibility-risk-f.html
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Most of us would be lost without Google maps or similar route-guidance technologies. And when those mapping tools include additional data about traffic or weather, we can navigate even more effectively. For scientists who navigate the mammalian genome to better understand genetic causes of disease, combining various types of data sets makes finding their way easier, too.
A team at the Salk Institute has developed a computational algorithm that integrates two different data types to make locating key regions within the genome more precise and accurate than other tools. The method could help researchers conduct vastly more targeted searches for disease-causing genetic variants in the human genome, such as ones that promote cancer or cause metabolic disorders.
“Most of the variation between individuals is in noncoding regions of the genome,” says senior author Joseph Ecker, a Howard Hughes Medical Institute investigator and director of Salk’s Genomic Analysis Laboratory. “These regions don’t code for proteins, but they still contain genetic variants that cause disease. We just haven’t had very effective tools to locate these areas in a variety of tissues and cell types—until now.”
Only about two percent of our DNA is made up of genes, which code for proteins that keep us healthy and functional. For many years, the other 98 percent was thought to be extraneous “junk.” But, as science has developed ever more sophisticated tools to probe the genome, it has become clear that much of that so-called junk has vital regulatory roles. For example, sections of DNA called “enhancers” dictate where and when the gene information is read out.
Increasingly, mutations or disruption in enhancers have been tied to major causes of human disease, but enhancers have been hard to locate within the genome. Clues about them can be found in certain types of experimental data, such as in the binding of proteins that regulate gene activity, chemical modifications of proteins (called histones) that DNA wraps around, or in the presence of chemical compounds called methyl groups in DNA that turn genes on or off (an epigenetic factor called DNA methylation). Typically, computational methods for finding enhancers have relied on histone modification data. But Ecker’s new system, called REPTILE (for “regulatory-element prediction based on tissue-specific local epigenomic signatures”), combines histone modification and methylation data to predict which regions of the genome contain enhancers. In the team’s experiments, REPTILE proved more accurate at finding enhancers than algorithms that rely on histone modification alone.
“The novelty of this method is that it uses DNA methylation to really narrow down the candidate regulatory sequences suggested by histone modification data,” says Yupeng He, a Salk graduate student and first author of the paper. “We were then able to test REPTILE’S predictions in the lab and validate them with experimental data, which gave us a high degree of confidence in the algorithm’s ability to find enhancers.”
Salk Institute
www.salk.edu/news-release/finding-way-around-dna/
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Casting one of the largest genomic nets to date for the rare tumours of the autonomic nervous system known as pheochromocytoma and paraganglioma (PCC/PGL) captured several new mutations driving the disease that could serve as potential drug targets, researchers from Penn Medicine and other institutions report.
Analysing genetic data of 173 patients from The Cancer Genome Atlas, researchers, including senior author Katherine Nathanson, MD, a professor in the division of Translational Medicine and Human Genetics at the Perelman School of Medicine at the University of Pennsylvania and associate director for Population Science at Penn’s Abramson Cancer Center, identified CSDE1 and fusion genes in MAML3 as drivers of the disease, both a first for any cancer type. The researchers also classified PCC/PGL into four distinct subtypes, each driven by mutations in distinct biological pathways, two of which are novel.
“What’s interesting about these tumours is that while they are astonishingly diverse genetically, with both inherited and somatic drivers influencing tumorigenesis, each has a single driver mutation, not multiple mutations,” Nathanson said. “This characteristic makes these tumours ideal candidates for targeted therapy.” Other cancer types typically contain anywhere from two to eight of these driver mutations.
The discovery of these single drivers in PCC/PGL provides more opportunities for molecular diagnosis and prognosis in these patients, particularly those with more aggressive cancers, the authors said.
PGLs are rare tumours of nerve ganglia in the body, whereas PCCs form in the centre of the adrenal gland, which is responsible for producing adrenaline. The tumour causes the glands to overproduce adrenaline, leading to elevated blood pressure, severe headaches, and heart palpitations. Both are found in about two out of every million people each year. An even smaller percentage of those tumours become malignant – and become very aggressive. For that group, the five-year survival rate is about 50 percent.
Matthew D. Wilkerson, MD, the Bioinformatics Director at the Collaborative Health Initiative Research Program at the Uniformed Services University, is the paper’s co-senior author.
To identify and characterize the genetic missteps, researchers analysed tumour specimens using whole-exome sequencing, mRNA and microRNA sequencing, DNA-methylation arrays, and reverse-phase protein arrays. The four molecularly defined subgroups included: a kinase-signalling subtype, a pseudohypoxia subtype, a cortical admixture subtype, and a Wnt-altered subtype. The last two have been newly classified.
The results also provided clinically actionable information by confirming and identifying several molecular markers associated with an increased risk of aggressive and metastatic disease, including germline mutations in SDBH, somatic mutations in ATRX (previously established in a Penn Medicine study), and new gene fusions – a genetic hybrid, of sorts – in MAML3.
Because the MAML3 fusion gene activates the Wnt-altered subtype, the authors said, existing targeted therapies that inhibit the beta-catenin and STAT3 pathways may also prove effective in certain PCC/PGL tumours.
Penn Medicine
www.pennmedicine.org/news/news-releases/2017/february/in-depth-gene-search-reveals-new-mutations-drug-targets-in-rare-adrenal-tumors
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A genetic ‘switch’ has been discovered by MRC researchers at the University of Leicester that could help to prevent or delay the symptoms of Parkinson’s disease.
In a paper, the team discovered that a gene called ATF4 plays a key role in Parkinson’s disease, acting as a ‘switch’ for genes that control mitochondrial metabolism for neuron health.
Dr Miguel Martins from the MRC Toxicology Unit at the University of Leicester, who led the research, explained: “When the expression of ATF4 is reduced in flies, expression of these mitochondrial genes drops. This drop results in dramatic locomotor defects, decreased lifespan, and dysfunctional mitochondria in the brain.
“Interestingly, when we overexpressed these mitochondrial genes in fly models of Parkinson’s, mitochondrial function was re-established, and neuron loss was avoided.”
By discovering the gene networks that orchestrate this process, the researchers have singled out new therapeutic targets that could prevent neuron loss.
Some forms of Parkinson’s are caused by mutations in the genes PINK1 and PARKIN, which are instrumental in mitochondrial quality control.
Fruit flies with mutations in these genes accumulate defective mitochondria and exhibit Parkinson’s-like changes, including loss of neurons.
The researchers used PINK1 and PARKIN mutant flies to search for other critical Parkinson’s genes – and using a bioinformatics approach discovered that the ATF4 gene plays a key role.
Dr Martins added: “Studying the roles of these genes in human neurons could lead to tailored interventions that could one day prevent or delay the neuronal loss seen in Parkinson’s.”
The findings build upon recent research by the University of Leicester team, which recently discovered several genes that protect neurons in Parkinson’s disease, creating possibilities for new treatment options.
University of Leicester
www2.le.ac.uk/offices/press/press-releases/2017/february/discovery-of-genetic-2018switch2019-could-help-to-prevent-symptoms-of-parkinson2019s-disease
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Genomic testing of biopsies from patients with deadly, treatment-resistant cancerous blood syndromes called histiocytoses allowed doctors to identify genes fuelling the ailments and use targeted molecular drugs to successfully treat them.
Researchers from the Cincinnati Children’s Cancer and Blood Diseases Institute have recently report their data. They recommend the regular use of comprehensive genomic profiling at diagnosis to positively impact clinical care, as well as rigorous clinical trials to verify and extend the diagnostic and treatment conclusions in their study.
Histiocytoses are a group of disorders in which abnormal accumulations of white blood cells form tumours on vital organs, leading to systemic organ damage or death. About half of the patients can be treated successfully with chemotherapy, but others are treatment resistant.
Study authors conducted genomic profiling of biopsies from 72 child and adult patients with a variety of treatment-resistant histiocytoses, including the most common one in children, Langerhans cell histiocytosis (LCH), according to the lead investigator, Ashish Kumar, MD, PhD.
Twenty-six patients with treatment-resistant disease had gene mutations involving either BRAF or MAP2K1 that directly activate the MAP-kinase cancer pathway. Researchers determined such patients would benefit from the targeted molecular therapies dabrafenib or trametinib, which block the MAP kinase pathway. The approved cancer drugs were prescribed off label to the histiocytosis patients.
‘In the last year, three patients we treated were infants with disease that was resistant to several rounds of intense chemotherapy. In the past, these children either would have suffered serious complications including death or would have had to endure more intensive treatments and the ensuing toxicities, including the risk of death,” Kumar said. “All three are thriving now on one oral medication that put their disease into remission.”
In one case a 22-month-old child was referred to Cincinnati Children’s for treatment-resistant LCH that was complicated by a secondary diagnosis of HLH (hemophagocytic lymphohistiocytosis). HLH is a difficult-to-treat and often-fatal autoimmune disorder in which an overheated immune system causes uncontrolled inflammation and organ damage. The little girl, whose condition was worsening with organ failure, had a mutation in the BRAF gene.
Two days after starting targeted treatment with oral dabrafenib (which blocks the MAP-kinase pathway) the little girl’s fever disappeared and a week later her organ function returned to normal, according to study authors.
Previous studies, future directions
For their JCI Insight research project, in addition to their own laboratory tests, study authors drew from data in previous research papers by a number of institutions, which examined genetic and molecular processes affecting white blood cell expansion in different types of histiocytosis.
As Kumar and his colleagues continue their research, they plan to test methodologies that could expand the use of genomic profiling of patient biopsies and targeted molecular therapies in more patients with recurrent, treatment-resistant disease.
A new study shows how errors in a specific gene can cause growth defects associated with a rare type of dwarfism.
During the study, an international team of scientists led by the University of Birmingham looked at genetic information from more than 250 people around the world with primordial dwarfism, a group of disorders characterised by short stature and an abnormally small head.
They found that 29 of the individuals had a defective version of a gene called DONSON.
Tests on cells growing in the laboratory revealed that this gene plays a crucial role in ensuring DNA is copied correctly when cells divide and grow.
Cells from patients with mutations in the DONSON gene had difficulty in efficiently replicating their DNA and protecting it from uncontrolled damage, ultimately leading to the growth defects typical of primordial dwarfism.
Most children with primordial dwarfism are not diagnosed until they are around three years old, and doctors are often unable to pinpoint the causes. This research raises the potential of more accurate diagnoses for patients with genetic microcephaly, in addition to providing an insight into how similar rare hereditary diseases are caused.
Professor Grant Stewart, from the Institute of Cancer and Genomic Sciences at the University of Birmingham, says: ‘Despite DNA replication being a process that is fundamental to life, there is still a lot we don’t know. This research sheds new light on the mechanisms underlying DNA replication, and the effect on human health when this process goes wrong.’
Professor Andrew Jackson, of the University of Edinburgh’s Institute for Genetics and Molecular Medicine, says: ‘Identification of DONSON as a new microcephaly gene has given us new insights into how the genome is protected during DNA replication, and has only been possible through the close collaboration and contributions of clinicians and scientists from many countries around the world.’
Professor Christopher Mathew, from the National Institute for Health Research (NIHR) Biomedical Research Centre at Guy’s and St Thomas’ and King’s College London, adds: ‘This is a good example of how unravelling the genetics of rare human disorders can provide profound insight into basic biological processes.’
NIHR Medical Research Institute
www.guysandstthomasbrc.nihr.ac.uk/2017/02/14/research-gene-find-sheds-light-on-growth-defects-linked-to-dwarfism/
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Massachusetts General Hospital (MGH) researchers have identified a mechanism that controls the expression of genes regulating the growth of the most aggressive form of medulloblastoma, the most common paediatric brain tumour. The team also identifies potential targets for future treatments.
“We set out to find the most important regulators of gene expression programs in medulloblastoma,” says senior author Miguel Rivera, MD, of the MGH Department of Pathology and the Center for Cancer Research. “To do that we used a powerful genomic technology called chromatin profiling to map all the genomic elements contributing to transcription regulation in Group 3 medulloblastoma – the most aggressive subtype. This goes beyond measuring gene expression because it tells you how genes are turned on and off.”
Medulloblastoma is a fast-growing tumour that arises in the developing brain and most commonly affects children under the age of 10. Four molecular variants, each with different patterns of DNA alteration and gene expression, have been identified. Subtypes WNT and SSH are the best understood; the other two – Group 3 and Group 4 – are poorly understood and account for 60 percent of tumours.
Cells regulate whether specific genes are transcribed into RNA through the action of transcription factors, proteins that bind to DNA and either stimulate or suppress the expression of their target genes. Rivera’s team used advanced genomic technologies to identify key DNA elements called enhancers that were active in primary Group 3 medulloblastoma samples and cell lines. The transcription factor OTX2, which plays a role in normal brain development and is known to be highly expressed in Group 3 medulloblastomas, was present at the majority of active enhancer sites in tumours, suggesting it may have a role in promoting the expression of tumour-associated genes.
Subsequent experiments revealed that OTX2 can function as a “pioneer factor,” opening up chromatin – which consists of DNA wound around proteins called histones – to activate enhancers and that its function is amplified by a second transcription factor called NEUROD1. The investigators then identified a set of genes the expression of which was significantly reduced when OTX2 was suppressed. Among these genes, they found that expression of the kinase NEK2 responded to OTX2 levels and that its depletion or pharmacologic inhibition strongly reduced the growth and survival of medulloblastoma cells.
“Overall, our findings show that OTX2 is a critical factor in regulating gene expression programs in Group 3 medulloblastoma and possibly in the WNT and Group 4 subtypes, where it is also expressed,” says Rivera, who is an assistant professor of Pathology at Harvard Medical School. “This work points to OTX2 itself and its target genes – including NEK2 – as potential therapeutic targets. Disruption of the relationship between OTX2 and NEUROD1 may also be a potential treatment strategy.
Massachusetts General Hospitalwww.massgeneral.org/about/pressrelease.aspx?id=2063
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Personalized therapies for the most common birth defect among newborns
, /in E-News /by 3wmediaSpecific genetic errors that trigger congenital heart disease (CHD) in humans can be reproduced reliably in Drosophila melanogaster – the common fruit fly – an initial step toward personalized therapies for patients in the future.
“Studying CHD in fruit flies provides a fast and simple first step in understanding the roles that individual genes play in disease progression,” says Zhe Han, Ph.D., a principal investigator and associate professor in the Center for Cancer & Immunology Research at Children’s National Health System and senior author of the paper. “Our research team is the first to describe a high-throughput in vivo validation system to screen candidate disease genes identified from patients. This approach has the potential to facilitate development of precision medicine approaches for CHD and other diseases associated with genetic factors,” Han says.
Some 134 genes have been implicated in causing CHD, a birth defect that affects 8 in 1,000 newborns, according to the National Institutes of Health. The research team led by Han used high-throughput techniques to alter the activity of dozens of genes in flies’ hearts simultaneously in order to validate genes that cause heart disease.
“Our team was able to characterize the effect of these specific genetic alterations on heart development, structure and activity,” Han adds. “The development of the human heart is a complicated process in which a number of different cell types need to mature and differentiate to create all of the structures in this essential organ. The precise timing of those cellular activities is critical to normal heart development, with disruptions in the structure of proteins called histones linked to later heart problems.”.
Of 134 genes studied by the research team, 70 caused heart defects in fruit flies, and several of the altered genes are involved in modifying the structure of histones. Quantitative analyses of multiple cardiac phenotypes demonstrated essential structural, functional and developmental roles for these genes, including a subgroup encoding histone H3K4 modifying proteins. The scientists then corroborated their work by reliably reproducing in flies the effect of specific genetic errors identified in humans with CHD.
“This may allow researchers to replicate individual cases of CHD, study them closely in the laboratory and fashion treatments personalized to that patient specifically,” he adds. “Precise gene-editing techniques could be used to tailor-make flies that express a patient’s specific genetic mutation. Treating CHD at the level of DNA offers the potential of interrupting the current cycle of passing along genetic mutations to each successive generation.”
Children’s National Health System childrensnational.org/news-and-events/childrens-newsroom/2017/studying-chd-in-fruit-flies
New method to identify bacteria in blood samples works in hours instead of days
, /in E-News /by 3wmediaEngineers at the University of California San Diego have developed a desktop diagnosis tool that detects the presence of harmful bacteria in a blood sample in a matter of hours instead of days. The breakthrough was made possible by a combination of proprietary chemistry, innovative electrical engineering and high-end imaging and analysis techniques powered by machine learning.
To identify low levels of harmful bacteria among a large number of human blood cells, researchers for the first time melted bacterial DNA in 20,000 extremely small simultaneous reactions. Each reaction contained only 20 picoliters—a scale that is hard to picture: one drop of rain contains hundreds of thousands of picoliters.
Each type of DNA has a specific signature as it comes apart during melting. As the melting process is imaged and analysed, researchers can use machine learning to determine which types of DNA appear in blood samples. During experiments, the system accurately identified, 99 percent of the time, DNA sequences from bacteria causing food-borne illnesses and pneumonia—in less than four hours.
“Analysing this many reactions at the same time at this small a scale had never been attempted before,” said Stephanie Fraley, a professor of bioengineering at the Jacobs School of Engineering at UC San Diego and the paper’s lead author. “Most molecular tests look at DNA on a much larger scale and look for just one type of bacteria at a time. We analyse all the bacteria in a sample. This is a much more holistic approach.”
Current methods used to detect and identify bacteria rely on cultures, which can take days. That is too long to provide physicians with an effective and timely diagnosis tool—as anyone who has been prescribed antibiotics while waiting for test results knows.
It all starts with one milliliter of blood, which researchers inoculated with Listeria monocytogenes, a food-borne bacterium that causes about 260 deaths a year in the United States, and Streptococcus pneumoniae, which causes everything from sinus infections, to pneumonia, to meningitis.
Researchers isolated all DNA from the blood sample. The DNA was then placed on a digital chip that allowed each piece to independently multiply in its own small reaction. For the process to work at such small scales—each well containing DNA in the chip was only 20 picoliters in volume—researchers used a proprietary mix of chemicals subject to a provisional patent.
The chip with the amplified DNA was placed in an innovative high-throughput microscope that Fraley and her team designed. The DNA was then heated in increments of 0.2 degrees Celsius, causing it to melt at temperatures between 50 to 90 degrees Celsius –about 120 to 190 degrees Fahrenheit.
As the DNA double-helix melts, the bonds holding together the DNA strands break. Depending on the DNA’s sequence, the bonds have different strengths and that changes the way the strands unwind from each other. This creates a unique sequence-dependent fingerprint, which researchers can detect using a special dye. The dye causes the unwinding process to give off fluorescent light, creating what researchers call a melting curve—a unique signature for each type of bacteria.
When engineers imaged the melting process with the high-throughput microscope, they were able to capture the bacteria’s melting curves. They then analysed the curves with a machine learning algorithm they developed.
In previous work, the algorithm was trained on 37 different types of bacteria undergoing different reactions in different conditions. The researchers showed that it was able to identify bacteria strains with 99 percent accuracy.
University of California – San Diegoucsdnews.ucsd.edu/pressrelease/new_method_to_identify_bacteria_in_blood_samples_works_in_hours_instead_of
Genetic profiling can guide stem cell transplantation for patients with myelodysplastic syndrome
, /in E-News /by 3wmediaA single blood test and basic information about a patient’s medical status can indicate which patients with myelodysplastic syndrome (MDS) are likely to benefit from a stem cell transplant, and the intensity of pre-transplant chemotherapy and/or radiation therapy that is likely to produce the best results, according to new research by scientists at Dana-Farber Cancer Institute and Brigham and Women’s Hospital.
In a study, the investigators report that genetically profiling a patient’s blood cells, while factoring in a patient’s age and other factors, can predict the patient’s response to a stem cell transplant and help doctors select the most effective combination of pre-transplant therapies. The findings are based on an analysis of blood samples from 1,514 patients with MDS, ranging in age from six months to more than 70 years, performed in collaboration with investigators from the Center for Blood and Marrow Transplant Research.
MDS is a family of diseases in which the bone marrow produces an insufficient supply of healthy blood cells. Treatments vary depending on the specific type of MDS a patient has; donor stem cell transplants are generally used for patients with a high risk of mortality with standard treatments.
“Although donor stem cell transplantation is the only curative therapy for MDS, many patients die after transplantation, largely due to relapse of the disease or complications relating to the transplant itself,” said the study’s lead author, R. Coleman Lindsley, MD, PhD, of Dana-Farber. “As physicians, one of our major challenges is to be able to predict which patients are most likely to benefit from a transplant. Improving our ability to identify patients who are most likely to have a relapse or to experience life-threatening complications from a transplant could lead to better pre-transplant therapies and strategies for preventing relapse.”
Researchers have long known that the specific genetic mutations within MDS patients’ blood cells are closely related to the course the disease takes. The current study sought to discover whether mutations also can be used to predict how patients will fare following a donor stem cell transplant.
Analysis of the data showed that the single most important characteristic of a patient’s MDS was whether their blood cells carried a mutation in the gene TP53. These patients tended to survive for a shorter time after a transplant, and also relapse more quickly, than patients whose cells lacked that mutation. This was true whether patients received standard “conditioning” therapy (which includes chemo- and/or radiation therapy) prior to transplant or received reduced-intensity conditioning, which uses lower doses of these therapies. Based on these results, doctors at Dana-Farber are now working on new strategies to overcome the challenges posed by TP53 mutations in MDS.
In patients 40 years old and over whose MDS didn’t carry TP53 mutations, those with mutations in RAS pathway genes or the JAK2 gene tended to have a shorter survival than those without RAS or JAK2 mutations. In contrast to TP53 mutations, the adverse effect of RAS mutations on survival and risk of relapse was evident only in reduced-intensity conditioning. This suggests that these patients may benefit from higher intensity conditioning regimens, the researchers indicated.
The study also yielded key insights about the biology of MDS in specific groups of patients. Surprisingly, one in 25 patients with MDS between the ages of 18 and 40 were found to have mutations associated with Shwachman-Diamond syndrome (a rare inherited disorder that often affects the bone marrow, pancreas, and skeletal system), but most of them had not previously been diagnosed with it. In each case, the patients’ blood cells had acquired a TP53 mutation, suggesting not only how MDS develops in patients with Schwachman-Diamond syndrome but also what underlies their poor prognosis after transplantation.
Dana Farber Cancer Institutewww.dana-farber.org/Newsroom/News-Releases/genetic-profiling-can-guide-stem-cell-transplantation-for-patients-with-myelodysplastic-syndrome-study-finds.aspx
Researchers study patients’ genetic and susceptibility risk factors in hopes of finding the path to cure lymphedema
, /in E-News /by 3wmediaEach year, about 1.38 million women worldwide are diagnosed with breast cancer. Advances in diagnosis and treatment have facilitated a 90-percent, five-year survival rate, among those treated. However, with the increased rate and length of survival following breast cancer, patients face a lifetime risk of developing lymphedema, one of the most distressing and feared late onset breast cancer-related effects.
Lymphedema is an abnormal accumulation of lymph fluid in the ipsilateral body area, or upper limb. This remains an on-going major health problem affecting more than 40 percent of 3.1 million breast cancer survivors in the U.S. Lymphedema following breast cancer surgery is typically considered to be primarily due to the mechanical injury from surgery. However, recent research has found that inflammation-infection and higher body mass index are also main predictors of lymphedema.
Researchers from New York University Rory Meyers College of Nursing (NYU Meyers), led by Dr. Mei R. Fu, PhD, RN, FAAN, conducted a study, “Precision assessment of heterogeneity of lymphedema phenotype, genotypes and risk prediction,” to address this phenomenon and prospectively examine phenotype of arm lymphedema by limb volume and lymphedema symptoms in relation to inflammatory genes in women treated for breast cancer.
The study is the first of its kind in exploring associations between genetic susceptibility targeting identified phenotypic risk factors of inflammation and heterogeneous phenotypes of lymphedema.
“It remains puzzling that up to 23% of survivors who only had lumpectomy with sentinel lymph node biopsy of 1 or 2 lymph nodes removed have developed lymphedema, while some survivors who had mastectomy with more than 10 lymph nodes removed have not,” said Dr. Fu. “There is a critical need to understand heterogeneity of lymphedema phenotype in relation to assessment of lymphedema phenotype and related biological mechanism.”
The study consisted of 136 women with a mean age of 52 with a first time diagnosis of breast cancer (Stage I-III), and were scheduled for surgical treatment of lumpectomy or mastectomy. The researchers measured data at 4-8 weeks post-surgery and 12 months post-surgery to monitor development of lymphedema during this period. They used lymphedema phenotyping to measure more symptoms than the typical method of observing swelling and limb volume. The symptom phenotyping was important in indicating early stage lymphedema where limb volume cannot be assessed yet.
The researchers found that using symptom phenotyping, prior to surgery, only one participant had more than 8 symptoms and only 18 had 1-7 symptoms. At 4-8 weeks post-surgery all participants had at least one symptom, 53% had 1-7 symptoms, and 46% had more than 8 symptoms, whereas only 16% had arm lymphedema defined by limb volume increase. At 12 months post-surgery 26.5% had more than 8 symptoms and 63% reported 1-7 symptoms, whereas only 22.8% had arm lymphedema as defined by limb volume.
Additionally, prior to surgery, identification of symptom phenotypes was not feasible, as 86% of participants were symptom-free. However, at 4-8 weeks post-surgery 58.1% of participants were classified as the phenotype of impaired limb mobility, with 86% discomfort, and 55.9% fluid accumulation. At 12 months 55.2% of participants were classified as the phenotype of impaired limb mobility with 38.2% pain/discomfort, and 44.1% fluid accumulation.
This data found significant associations between genotypes related to several lymphatic and inflammatory genes and symptom phenotypes of impaired limb mobility, fluid accumulation, and pain/discomfort. The data further provides support for heterogeneity of lymphedema phenotypes, especially phenotype of symptom clusters based on biological mechanisms.
Dr. Fu notes that the sample size and only 12-month period of observation does put limitations on the study.
New York Universitywww.nyu.edu/about/news-publications/news/2017/february/nyu-researchers-study-patients-genetic-and-susceptibility-risk-f.html
Finding our way around DNA
, /in E-News /by 3wmediaMost of us would be lost without Google maps or similar route-guidance technologies. And when those mapping tools include additional data about traffic or weather, we can navigate even more effectively. For scientists who navigate the mammalian genome to better understand genetic causes of disease, combining various types of data sets makes finding their way easier, too.
A team at the Salk Institute has developed a computational algorithm that integrates two different data types to make locating key regions within the genome more precise and accurate than other tools. The method could help researchers conduct vastly more targeted searches for disease-causing genetic variants in the human genome, such as ones that promote cancer or cause metabolic disorders.
“Most of the variation between individuals is in noncoding regions of the genome,” says senior author Joseph Ecker, a Howard Hughes Medical Institute investigator and director of Salk’s Genomic Analysis Laboratory. “These regions don’t code for proteins, but they still contain genetic variants that cause disease. We just haven’t had very effective tools to locate these areas in a variety of tissues and cell types—until now.”
Only about two percent of our DNA is made up of genes, which code for proteins that keep us healthy and functional. For many years, the other 98 percent was thought to be extraneous “junk.” But, as science has developed ever more sophisticated tools to probe the genome, it has become clear that much of that so-called junk has vital regulatory roles. For example, sections of DNA called “enhancers” dictate where and when the gene information is read out.
Increasingly, mutations or disruption in enhancers have been tied to major causes of human disease, but enhancers have been hard to locate within the genome. Clues about them can be found in certain types of experimental data, such as in the binding of proteins that regulate gene activity, chemical modifications of proteins (called histones) that DNA wraps around, or in the presence of chemical compounds called methyl groups in DNA that turn genes on or off (an epigenetic factor called DNA methylation). Typically, computational methods for finding enhancers have relied on histone modification data. But Ecker’s new system, called REPTILE (for “regulatory-element prediction based on tissue-specific local epigenomic signatures”), combines histone modification and methylation data to predict which regions of the genome contain enhancers. In the team’s experiments, REPTILE proved more accurate at finding enhancers than algorithms that rely on histone modification alone.
“The novelty of this method is that it uses DNA methylation to really narrow down the candidate regulatory sequences suggested by histone modification data,” says Yupeng He, a Salk graduate student and first author of the paper. “We were then able to test REPTILE’S predictions in the lab and validate them with experimental data, which gave us a high degree of confidence in the algorithm’s ability to find enhancers.”
Salk Institute www.salk.edu/news-release/finding-way-around-dna/
New mutations, drug targets in rare adrenal tumours
, /in E-News /by 3wmediaCasting one of the largest genomic nets to date for the rare tumours of the autonomic nervous system known as pheochromocytoma and paraganglioma (PCC/PGL) captured several new mutations driving the disease that could serve as potential drug targets, researchers from Penn Medicine and other institutions report.
Analysing genetic data of 173 patients from The Cancer Genome Atlas, researchers, including senior author Katherine Nathanson, MD, a professor in the division of Translational Medicine and Human Genetics at the Perelman School of Medicine at the University of Pennsylvania and associate director for Population Science at Penn’s Abramson Cancer Center, identified CSDE1 and fusion genes in MAML3 as drivers of the disease, both a first for any cancer type. The researchers also classified PCC/PGL into four distinct subtypes, each driven by mutations in distinct biological pathways, two of which are novel.
“What’s interesting about these tumours is that while they are astonishingly diverse genetically, with both inherited and somatic drivers influencing tumorigenesis, each has a single driver mutation, not multiple mutations,” Nathanson said. “This characteristic makes these tumours ideal candidates for targeted therapy.” Other cancer types typically contain anywhere from two to eight of these driver mutations.
The discovery of these single drivers in PCC/PGL provides more opportunities for molecular diagnosis and prognosis in these patients, particularly those with more aggressive cancers, the authors said.
PGLs are rare tumours of nerve ganglia in the body, whereas PCCs form in the centre of the adrenal gland, which is responsible for producing adrenaline. The tumour causes the glands to overproduce adrenaline, leading to elevated blood pressure, severe headaches, and heart palpitations. Both are found in about two out of every million people each year. An even smaller percentage of those tumours become malignant – and become very aggressive. For that group, the five-year survival rate is about 50 percent.
Matthew D. Wilkerson, MD, the Bioinformatics Director at the Collaborative Health Initiative Research Program at the Uniformed Services University, is the paper’s co-senior author.
To identify and characterize the genetic missteps, researchers analysed tumour specimens using whole-exome sequencing, mRNA and microRNA sequencing, DNA-methylation arrays, and reverse-phase protein arrays. The four molecularly defined subgroups included: a kinase-signalling subtype, a pseudohypoxia subtype, a cortical admixture subtype, and a Wnt-altered subtype. The last two have been newly classified.
The results also provided clinically actionable information by confirming and identifying several molecular markers associated with an increased risk of aggressive and metastatic disease, including germline mutations in SDBH, somatic mutations in ATRX (previously established in a Penn Medicine study), and new gene fusions – a genetic hybrid, of sorts – in MAML3.
Because the MAML3 fusion gene activates the Wnt-altered subtype, the authors said, existing targeted therapies that inhibit the beta-catenin and STAT3 pathways may also prove effective in certain PCC/PGL tumours.
Penn Medicine www.pennmedicine.org/news/news-releases/2017/february/in-depth-gene-search-reveals-new-mutations-drug-targets-in-rare-adrenal-tumors
Genetic ‘switch’ could help to prevent symptoms of Parkinson’s disease
, /in E-News /by 3wmediaA genetic ‘switch’ has been discovered by MRC researchers at the University of Leicester that could help to prevent or delay the symptoms of Parkinson’s disease.
In a paper, the team discovered that a gene called ATF4 plays a key role in Parkinson’s disease, acting as a ‘switch’ for genes that control mitochondrial metabolism for neuron health.
Dr Miguel Martins from the MRC Toxicology Unit at the University of Leicester, who led the research, explained: “When the expression of ATF4 is reduced in flies, expression of these mitochondrial genes drops. This drop results in dramatic locomotor defects, decreased lifespan, and dysfunctional mitochondria in the brain.
“Interestingly, when we overexpressed these mitochondrial genes in fly models of Parkinson’s, mitochondrial function was re-established, and neuron loss was avoided.”
By discovering the gene networks that orchestrate this process, the researchers have singled out new therapeutic targets that could prevent neuron loss.
Some forms of Parkinson’s are caused by mutations in the genes PINK1 and PARKIN, which are instrumental in mitochondrial quality control.
Fruit flies with mutations in these genes accumulate defective mitochondria and exhibit Parkinson’s-like changes, including loss of neurons.
The researchers used PINK1 and PARKIN mutant flies to search for other critical Parkinson’s genes – and using a bioinformatics approach discovered that the ATF4 gene plays a key role.
Dr Martins added: “Studying the roles of these genes in human neurons could lead to tailored interventions that could one day prevent or delay the neuronal loss seen in Parkinson’s.”
The findings build upon recent research by the University of Leicester team, which recently discovered several genes that protect neurons in Parkinson’s disease, creating possibilities for new treatment options.
University of Leicester www2.le.ac.uk/offices/press/press-releases/2017/february/discovery-of-genetic-2018switch2019-could-help-to-prevent-symptoms-of-parkinson2019s-disease
Treating deadly cancerous disorders with gene-guided, targeted therapy
, /in E-News /by 3wmediaGenomic testing of biopsies from patients with deadly, treatment-resistant cancerous blood syndromes called histiocytoses allowed doctors to identify genes fuelling the ailments and use targeted molecular drugs to successfully treat them.
Researchers from the Cincinnati Children’s Cancer and Blood Diseases Institute have recently report their data. They recommend the regular use of comprehensive genomic profiling at diagnosis to positively impact clinical care, as well as rigorous clinical trials to verify and extend the diagnostic and treatment conclusions in their study.
Histiocytoses are a group of disorders in which abnormal accumulations of white blood cells form tumours on vital organs, leading to systemic organ damage or death. About half of the patients can be treated successfully with chemotherapy, but others are treatment resistant.
Study authors conducted genomic profiling of biopsies from 72 child and adult patients with a variety of treatment-resistant histiocytoses, including the most common one in children, Langerhans cell histiocytosis (LCH), according to the lead investigator, Ashish Kumar, MD, PhD.
Twenty-six patients with treatment-resistant disease had gene mutations involving either BRAF or MAP2K1 that directly activate the MAP-kinase cancer pathway. Researchers determined such patients would benefit from the targeted molecular therapies dabrafenib or trametinib, which block the MAP kinase pathway. The approved cancer drugs were prescribed off label to the histiocytosis patients.
‘In the last year, three patients we treated were infants with disease that was resistant to several rounds of intense chemotherapy. In the past, these children either would have suffered serious complications including death or would have had to endure more intensive treatments and the ensuing toxicities, including the risk of death,” Kumar said. “All three are thriving now on one oral medication that put their disease into remission.”
In one case a 22-month-old child was referred to Cincinnati Children’s for treatment-resistant LCH that was complicated by a secondary diagnosis of HLH (hemophagocytic lymphohistiocytosis). HLH is a difficult-to-treat and often-fatal autoimmune disorder in which an overheated immune system causes uncontrolled inflammation and organ damage. The little girl, whose condition was worsening with organ failure, had a mutation in the BRAF gene.
Two days after starting targeted treatment with oral dabrafenib (which blocks the MAP-kinase pathway) the little girl’s fever disappeared and a week later her organ function returned to normal, according to study authors.
Previous studies, future directions
For their JCI Insight research project, in addition to their own laboratory tests, study authors drew from data in previous research papers by a number of institutions, which examined genetic and molecular processes affecting white blood cell expansion in different types of histiocytosis.
As Kumar and his colleagues continue their research, they plan to test methodologies that could expand the use of genomic profiling of patient biopsies and targeted molecular therapies in more patients with recurrent, treatment-resistant disease.
Cincinnati Children’s www.cincinnatichildrens.org/news/release/2017/treating-deadly-disorders
Gene find sheds light on growth defects linked to dwarfism
, /in E-News /by 3wmediaA new study shows how errors in a specific gene can cause growth defects associated with a rare type of dwarfism.
During the study, an international team of scientists led by the University of Birmingham looked at genetic information from more than 250 people around the world with primordial dwarfism, a group of disorders characterised by short stature and an abnormally small head.
They found that 29 of the individuals had a defective version of a gene called DONSON.
Tests on cells growing in the laboratory revealed that this gene plays a crucial role in ensuring DNA is copied correctly when cells divide and grow.
Cells from patients with mutations in the DONSON gene had difficulty in efficiently replicating their DNA and protecting it from uncontrolled damage, ultimately leading to the growth defects typical of primordial dwarfism.
Most children with primordial dwarfism are not diagnosed until they are around three years old, and doctors are often unable to pinpoint the causes. This research raises the potential of more accurate diagnoses for patients with genetic microcephaly, in addition to providing an insight into how similar rare hereditary diseases are caused.
Professor Grant Stewart, from the Institute of Cancer and Genomic Sciences at the University of Birmingham, says: ‘Despite DNA replication being a process that is fundamental to life, there is still a lot we don’t know. This research sheds new light on the mechanisms underlying DNA replication, and the effect on human health when this process goes wrong.’
Professor Andrew Jackson, of the University of Edinburgh’s Institute for Genetics and Molecular Medicine, says: ‘Identification of DONSON as a new microcephaly gene has given us new insights into how the genome is protected during DNA replication, and has only been possible through the close collaboration and contributions of clinicians and scientists from many countries around the world.’
Professor Christopher Mathew, from the National Institute for Health Research (NIHR) Biomedical Research Centre at Guy’s and St Thomas’ and King’s College London, adds: ‘This is a good example of how unravelling the genetics of rare human disorders can provide profound insight into basic biological processes.’
NIHR Medical Research Institute www.guysandstthomasbrc.nihr.ac.uk/2017/02/14/research-gene-find-sheds-light-on-growth-defects-linked-to-dwarfism/
Molecular ‘on switch’ could point to treatments for paediatric brain tumour
, /in E-News /by 3wmediaMassachusetts General Hospital (MGH) researchers have identified a mechanism that controls the expression of genes regulating the growth of the most aggressive form of medulloblastoma, the most common paediatric brain tumour. The team also identifies potential targets for future treatments.
“We set out to find the most important regulators of gene expression programs in medulloblastoma,” says senior author Miguel Rivera, MD, of the MGH Department of Pathology and the Center for Cancer Research. “To do that we used a powerful genomic technology called chromatin profiling to map all the genomic elements contributing to transcription regulation in Group 3 medulloblastoma – the most aggressive subtype. This goes beyond measuring gene expression because it tells you how genes are turned on and off.”
Medulloblastoma is a fast-growing tumour that arises in the developing brain and most commonly affects children under the age of 10. Four molecular variants, each with different patterns of DNA alteration and gene expression, have been identified. Subtypes WNT and SSH are the best understood; the other two – Group 3 and Group 4 – are poorly understood and account for 60 percent of tumours.
Cells regulate whether specific genes are transcribed into RNA through the action of transcription factors, proteins that bind to DNA and either stimulate or suppress the expression of their target genes. Rivera’s team used advanced genomic technologies to identify key DNA elements called enhancers that were active in primary Group 3 medulloblastoma samples and cell lines. The transcription factor OTX2, which plays a role in normal brain development and is known to be highly expressed in Group 3 medulloblastomas, was present at the majority of active enhancer sites in tumours, suggesting it may have a role in promoting the expression of tumour-associated genes.
Subsequent experiments revealed that OTX2 can function as a “pioneer factor,” opening up chromatin – which consists of DNA wound around proteins called histones – to activate enhancers and that its function is amplified by a second transcription factor called NEUROD1. The investigators then identified a set of genes the expression of which was significantly reduced when OTX2 was suppressed. Among these genes, they found that expression of the kinase NEK2 responded to OTX2 levels and that its depletion or pharmacologic inhibition strongly reduced the growth and survival of medulloblastoma cells.
“Overall, our findings show that OTX2 is a critical factor in regulating gene expression programs in Group 3 medulloblastoma and possibly in the WNT and Group 4 subtypes, where it is also expressed,” says Rivera, who is an assistant professor of Pathology at Harvard Medical School. “This work points to OTX2 itself and its target genes – including NEK2 – as potential therapeutic targets. Disruption of the relationship between OTX2 and NEUROD1 may also be a potential treatment strategy.
Massachusetts General Hospitalwww.massgeneral.org/about/pressrelease.aspx?id=2063