Scientists funded by the National Institutes of Health (NIH) have identified genetic markers associated with eosinophilic oesophagitis (EoE), an inflammatory disease characterized by high levels of immune cells called eosinophils in the oesophagus. Their findings suggest that several genes are involved in the development of EoE, which can cause difficulty eating and often is associated with food allergies. The findings also may help explain why the disease specifically affects the oesophagus.
A team led by researchers at Cincinnati Children’s Hospital Medical Center searched the entire human genome for variations between 9,246 healthy people and 736 people with EoE. They confirmed previous results from a smaller study that linked variations in the region on chromosome 5 containing TSLP, a gene associated with allergic diseases, to a higher risk of developing EoE. They also identified variations in a region on chromosome 2 containing a gene called CAPN14, which produces an enzyme called calpain 14, that are associated with higher EoE risk. The researchers showed that CAPN14 is expressed, or “turned on,” primarily in the esophagus. CAPN14 expression and calpain activity rose when scientists treated cultured esophageal cells with a molecule that induces allergic inflammation, suggesting that the enzyme is part of an anti-inflammatory response. People with EoE who carry the variant form of the gene may be unable to mount this response as effectively.
Further research is needed to determine if these findings might lead to identification of biomarkers to detect a person’s risk of developing EoE. Understanding the factors underlying EoE may help guide development of new diagnostic and treatment strategies for the disease.
NIH
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Prostate cancer is a leading cause of cancer-related death in men in the United States. The development and progression of the disease depend on the actions of male sex hormones called androgens, which bind to the androgen receptor to activate signalling pathways involved in cell growth and survival. Therefore, there is a strong need to identify novel drug targets to alter androgen-receptor signalling and treat this often deadly disease.
Sanford-Burnham researchers have discovered that a protein called NWD1 affects androgen-receptor signalling to control the growth of prostate cancer cells. ‘A very limited number of proteins have been shown to specifically and exclusively affect androgen-receptor signalling, so our findings represent a major advance in the field,’ said lead study author Ricardo Correa, Ph.D., staff scientist at Sanford-Burnham. ‘NWD1 could represent a new biomarker for predicting patient prognosis as well as a therapeutic target for a novel class of prostate cancer drugs.’
High levels of androgens are critical for the growth of prostate cancer cells in early disease stages, and one major type of therapy focuses on inhibiting androgens. But over time, prostate cancer cells often respond to hormone therapy by expressing high levels of the androgen receptor, allowing these castration-resistant cells to grow even when androgen levels are low. Castration-resistant prostate cancer is an advanced form of the disease associated with poor survival rates. However, both early and advanced stages of prostate cancer depend on androgen-receptor signalling, highlighting the value of targeting this pathway for treating a broad range of patients.
While searching for novel modulators of androgen-receptor signalling, Correa and his team became interested in the nucleotide-binding domain and leucine-rich repeat (NLR) family of proteins. These proteins are involved in recognising pathogens and cell-injury signals and activating immune-defence pathways, but they have also been implicated in a variety of cancers. In particular, the researchers were intrigued by an NLR-related protein called NWD1, which was previously identified in zebrafish but had not yet been analyzed in humans.
In the new study, Correa and his colleagues found that the expression of the human NWD1 gene was very high in prostate tissue and other parts of the male reproductive system. Moreover, NWD1 expression was higher than normal in human prostate cancer cell lines, especially in castration-resistant and highly metastatic cell lines. Similarly, NWD1 protein levels were higher than normal in advanced-stage and castration-resistant prostate tumour tissue from patients.
Taken together, the findings suggest that NWD1 could be a potential prostate cancer biomarker because high levels of the protein are associated with malignant progression. ‘We believe that NWD1 could represent a promising biomarker because changes in NWD1 expression happen at stages where the levels of prostate-specific antigen (PSA), a protein that is widely used to screen men for prostate cancer, are not very accurate in the clinic,’ Correa said.
In addition to its potential use for predicting patient prognosis, NWD1 could represent a promising therapeutic target. When the researchers inhibited the activity of the NWD1 gene in prostate cancer cells, they noticed a drop in androgen-receptor levels as well as a decrease in cell growth and survival. On the other hand, an increase in NWD1 activity led to a rise in androgen-receptor levels in these cells.
Their experiments also shed light on the molecular mechanisms by which NWD1 affects androgen-receptor signalling. NWD1 silencing fed the activity of cancer-related genes such as PDEF (prostate-derived epithelial factor), which is known to bind to androgen receptors and belongs to a family of proteins that regulate cell growth and survival. Moreover, a protein called sex-determining region Y (SRY), which controls sex determination during fetal development, affected the activity of the NWD1 gene. Thus, the findings not only reveal a novel molecular pathway involved in prostate cancer, but also suggest that drugs targeting NWD1 could eventually become a new class of treatments for the disease.
Sanford-Burnham
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Stomach cancers fall into four distinct molecular subtypes researchers with The Cancer Genome Atlas (TCGA) Network have found. In the study, the scientists report that this discovery could change how researchers think about developing treatments for stomach cancer, also called gastric cancers or gastric adenocarcinomas.
Instead of considering gastric cancer as a single disease, as has been done in the past, researchers will now be able to explore therapies in defined sets of patients whose tumours have specific genomic abnormalities. Stomach cancers are a leading cause of cancer-related mortality worldwide, resulting in an estimated 723,000 deaths annually.
Previous attempts to examine the clinical characteristics of gastric cancer were hindered by how differently cancer cells can look under a microscope, even when from the same tumour. The researchers hope that the new classification system will serve as a valuable adjunct to the current pathology classification system, which has two categories: diffuse and intestinal.
“A key advance with this project is that we have identified and developed a much more useful classification system to find groups of gastric cancer that have distinct molecular features, and at the same time, we also identified key targets to pursue in different groups of patients,” said Adam Bass, M.D., Harvard Medical School, Dana-Farber Cancer Institute, the Broad Institute, Boston, and one of the lead investigators on the project. “This will provide a strong foundation for categorizing the disease and for doing so in a way in which we can develop clinical trials based on some of the critical molecular alterations that are driving different classes of cancers.”
The researchers identified the new subgroups through complex statistical analyses of molecular data from 295 tumours. They used six molecular analysis platforms including DNA sequencing, RNA sequencing, and protein arrays.
Tumours in the first group, which represented 9 percent of the tumours, were positive for Epstein-Barr virus (EBV) and had several other molecular commonalities. Tumours in a second subgroup (22 percent of the tumours) had high microsatellite instability (MSI), which is the tendency for mutations to accumulate in repeated sequences of DNA. The remaining subgroups differed in the level of somatic copy number alterations (SCNAs), which can result from duplication or deletion of sections of the genome. The tumours in the third subgroup, which comprised 20 percent of the tumours, were considered to have a low level of SCNAs and were called genomically stable. The remaining 50 percent of tumours were classified as chromosomally unstable, with a high level of SCNAs.
The EBV-positive subgroup of tumours was of particular interest. EBV is best known in the United States as the cause of infectious mononucleosis, which is characterized by fever, sore throat, and swollen lymph glands, especially in the neck. EBV is also suspected of causing certain cancers, including nasopharyngeal carcinoma and some types of lymphoma. Previous research had shown that EBV can be detected in a minority of gastric adenocarcinomas and that EBV genes are expressed in those tumours. However, this study found that the presence of EBV in gastric tumours is associated with a number of other molecular characteristics.
First, the researchers observed that EBV-positive tumours displayed a high frequency of mutations in the PIK3CA gene, which codes for a component of a protein, PI3-kinase, which is essential for cell growth and division and many other cellular activities that are important in cancer. Although 80 percent of EBV-positive tumours harboured a protein-changing alteration in PIK3CA, PIK3CA mutations were found in 3 percent to 42 percent of tumours of the other gastric cancer subtypes. The scientists suggested that EBV-positive tumours might respond to PI3-kinase inhibitors, some of which are in the early stages of testing in clinical trials but are not yet approved by the U.S. Food and Drug Administration for general use.
Some tumours in the EBV-positive subgroup also showed more gene copies being produced in a chromosomal region that contains the JAK2 gene. The JAK2 protein facilitates cell growth and division, and the increased expression of JAK2 may inappropriately activate cell growth. The amplified region also contains the genes for two proteins, PD-L1 and PD-L2, which suppress immune responses; their increased expression may help tumours escape destruction by the immune system. The investigators suggested that these findings support the evaluation of JAK2 inhibitors and PD-L1/2 antagonists for the treatment of EBV-positive gastric cancers.
And the EBV-positive subgroup showed a far higher prevalence of DNA hypermethylation than any other cancer subtype reported by TCGA researchers. Methylation is the process of adding methyl groups to DNA, which reduces gene expression. Hypermethylation occurs when this mechanism continues aberrantly, quieting genes that should be active. In the EBV-positive tumour subgroup, hypermethylation was most often observed in the promoter regions of genes, which would prevent the expression of the genes.
‘Gaining these insights into the connection between EBV and gastric cancer is the type of groundbreaking research that NIH is pleased to be a part of. We look forward to the potential clinical implications of this discovery,’ said NIH Director Francis S. Collins, M.D., Ph.D.
The Cancer Genome Atlas
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UCLA researchers led by Dr. Brigitte Gomperts have discovered the inner workings of the process thought to be the first stage in the development of lung cancer. Their study explains how factors that regulate the growth of adult stem cells that repair tissue in the lungs can lead to the formation of precancerous lesions.
Findings from the three-year study could eventually lead to new personalized treatments for lung cancer, which is responsible for an estimated 29 percent of U.S. cancer deaths, making it the deadliest form of the disease.
The study collaborated with Manash Paul and Bharti Bisht, postdoctoral scholars and co-lead authors of the study.
Adult stem cells in lung airways are present specifically to repair the airways after injury or disease caused by smoking, pollution, viruses or other factors. Gomperts and her team found that this reparative process is tightly regulated by molecules called reactive oxygen species, or ROS.
Recent research has shown that low levels of ROS are important for signalling the stem cells to perform important functions — such as repairing tissue damage — while high levels of ROS can cause stem cells to die. But the level of ROS needed for repair to be initiated has remained a subject of debate among researchers.
The UCLA study found that the dynamic flux of ROS from low to moderate levels in the airway stem cells is what drives the repair process, and that the increase in ROS levels in the repairing cell is quickly reduced to low levels to prevent excessive cell proliferation.
Gomperts’ lab found that disrupting this normal regulation of ROS back to low levels is equivalent to pulling the brakes off of the stem cells: They will continue to make too many of themselves, which causes the cells not to mature and instead become precancerous lesions. Subsequent progressive genetic changes to the cells in these lesions over time can eventually allow cancerous tumours to form.
‘Low ROS is what keeps stem cells primed so that your body is poised and ready to respond to injury and repair,’ said Gomperts, who also is an associate professor in the department of paediatrics at UCLA. ‘Loss of this ROS regulation leads to precancerous lesions. Now, with this precancerous model in place, we can begin looking for what we call ‘driver mutations,’ or those specific changes that take the precancerous lesions to full-blown cancer.’
Gomperts said that because many different factors — including cigarette smoke, smog and inflammation — could potentially trigger an increase in ROS in the airway stem cells, researchers might eventually be able to customize treatments based on the cause. ‘There are likely multiple ways for a person to get to a precancerous lesion, so the process could be different among different groups of people. Imagine a personalized way to identify what pathways have gone wrong in a patient, so that we could target a therapy to that individual.’
The research’s ultimate goal is to develop a targeted strategy to prevent pre-malignant lesions from forming by targeting the biology of these lesions and
University of California – Los Angeles
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Siemens Healthcare Diagnostics has become the first manufacturer to gain standardization of its ADVIA Centaur Vitamin D Total assay to the National Institute of Standards and Technology – Ghent University Reference Measurement Procedure based on isotope-dilution liquid chromatography-tandem mass spectrometry. The Vitamin D Standardization Programme (VDSP) was established in 2010 and stated that all manufacturers of Vitamin D assays need to demonstrate alignment. The Siemens ADVIA Centaur Vitamin D Total assay provides confidence in results through alignment with the VDSP, also offering an equimolar vitamin D response and minimal cross-reactivity with 3-epi-25-OH Vitamin D3 (1.1%). Results are available in 18 minutes.
SIEMENS HEALTHCARE DIAGNOSTICSwww.siemens.com
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Researchers at UT Southwestern Medical Center and the Gill Center for Cancer and Blood Disorders at Children’s Medical Center, Dallas, have made significant progress in defining new genetic causes of Wilms tumor, a type of kidney cancer found only in children.
Wilms tumour is the most common childhood genitourinary tract cancer and the third most common solid tumour of childhood.
“While most children with Wilms tumour are thankfully cured, those with more aggressive tumours do poorly, and we are increasingly concerned about the long-term adverse side effects of chemotherapy in Wilms tumour patients. We wanted to know – what are the genetic causes of Wilms tumour in children and what are the opportunities for targeted therapies? To answer these questions, you have to identify genes that are mutated in the cancer,” said Dr. James Amatruda, Associate Professor of Pediatrics, Molecular Biology, and Internal Medicine at UT Southwestern and senior author for the study.
Collaborating with Dr. Amatruda on the study were UT Southwestern faculty members Dr. Dinesh Rakheja, Associate Professor of Pathology and Pediatrics; Dr. Kenneth S. Chen, Assistant Instructor in Pediatrics; and Dr. Joshua T. Mendell, Professor of Molecular Biology. Dr. Jonathan Wickiser, Associate Professor in Pediatrics, and Dr. James Malter, Chair of Pathology, are also co-authors.
Previous research has identified one or two mutant genes in Wilms tumours, but only about one-third of Wilms tumors had these mutations.
“We wanted to know what genes were mutated in the other two-thirds. To accomplish this goal, we sequenced the DNA of 44 tumours and identified several new mutated genes,” said Dr. Amatruda, who holds the Nearburg Family Professorship in Pediatric Oncology Research and is an Attending Physician in the Pauline Allen Gill Center for Cancer and Blood Disorders at Children’s Medical Center. “The new genes had not been identified before. The most common, and in some ways the most biologically interesting, mutations were found in genes called DROSHA and DICER1. We found that these mutations affected the cell’s production of microRNAs, which are tiny RNA molecules that play big roles in controlling the growth of cells, and the primary effect was on a family of microRNAs called let-7.”
“Let-7 is an important microRNA that slows cell growth and in Wilms tumours in which DROSHA or DICER1 were mutated, let-7 RNA is missing, which causes the cells to grow abnormally fast,” Dr. Amatruda said.
These findings have implications for future treatment of Wilms tumour and several other childhood cancers, including neuroblastoma, germ cell tumour, and rhabdomyosarcoma.
“What’s exciting about these results is that we can begin to understand what drives the growth of different types of Wilms tumours. This is a critical first step in trying to treat the cancer based on its true molecular defect, rather than just what a tumour looks like under a microscope,” Dr. Amatruda said. “Most importantly, we begin to think in concrete terms about a therapy, which is an exciting translational goal of our work in the next few years.
UT Southwestern Medical Center
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A genetic screening test may help predict which patients with one of the most common childhood kidney diseases will respond to standard therapies. Using this test could help guide clinicians as they counsel and treat patients.
Sporadic nephrotic syndrome is one of the most common kidney diseases in children, and it can have a genetic cause.
Paola Romagnani, MD, PhD, Sabrina Giglio, MD, PhD (University of Florence and Meyer Children’s Hospital, in Florence, Italy), and their colleagues designed an innovative diagnostic approach that allows for a fast analysis of all genes involved in the disease. Using this method, the team analysed 46 different genes at the same time in 69 children with the disease, and they found that genetic mutations in the kidney’s filtration barrier were frequently linked with a lack of response to immunosuppressive treatments in patients. The genetic test was even more predictive than a kidney biopsy for identifying children who would not benefit from immunosuppressive therapies.
“Thus, this type of genetic analysis can improve the clinical approach to children with nephrotic syndrome by promoting better genetic counselling for the risk of recurrence of the disease in the family, and a better management of treatment and clinical follow up,” said Professor Romagnani.
The application of this new diagnostic approach also improved the speed of clinical diagnoses of the disease and reduced costs. “With a single test, we can help build a truly personalized therapy,” said Professor Giglio.
American Society of Nephrology
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Scientists have identified four biomarkers that may help resolve the difficult differential diagnosis between malignant pleural mesothelioma (MPM) and non-cancerous pleural tissue with reactive mesothelial proliferations (RMPs). This is a frequent differential diagnostic problem in pleural biopsy samples taken from patients with clinical suspicion of MPM. The ability to make more accurate diagnoses earlier may facilitate improved patient outcomes.
‘Our goal was to identify microRNAs (miRNAs) that can aid in the differential diagnosis of MPM from RMPs,’ says lead investigator Eric Santoni-Rugiu, MD, PhD, of the Laboratory of Molecular Pathology at the Department of Pathology of Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark. miRNAs, which are small, non-coding RNA strands composed of approximately 22 nucleotides, have been shown to be potential diagnostic, prognostic, and predictive markers in other cancers.
After screening 742 miRNAs, the investigators identified miR-126, miR-143, miR-145, and miR-652 as the best candidates to diagnose MPM. Using results from these four miRNAs, tissue samples from patients with known outcomes could be classified as MPM or non-cancerous with an accuracy of 0.94, sensitivity of 0.95, and specificity of 0.93. Further, an association between miRNA levels and patient survival could be made.
‘The International Mesothelioma Interest Group (IMIG) recommends that a diagnostic marker of MPM have sensitivity/specificity of >0.80, and these criteria are fulfilled by our miRNA classifier,’ comments Dr. Santoni-Rugiu. The authors suggest that diagnostic accuracy can be further improved by adding immunohistochemical testing of miRNA targets in biopsy tissue to their miRNA assay. This combined assay could enable analysis of samples with low tumour cell count.
MPM, which is linked to long-term asbestos exposure, is an aggressive cancer originating from the mesothelial cells that line the membrane surrounding each lung, known as the pleura. Distinguishing MPM from non-cancerous abnormalities, such as reactive mesothelial hyperplasia or fibrous pleurisy (organising pleuritis), can be challenging as there are no generally accepted diagnostic biomarkers for differentiating these two conditions. As a result, patients often present with the disease when they are already at an advanced stage, and less than 20% of patients can be successfully treated surgically.
The current study, however, suggests that miRNAs may provide new opportunities for improving the accuracy of the differential diagnosis between MPM and noncancerous pleural conditions. If further validated, the combination of ISH for miRNAs with immunohistocemical testing of miRNA targets may therefore have the potential to aid in the diagnosis, and thus outcome, of MPM.
EurekAlert
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A Finnish-Swedish research group at the Institute for Molecular Medicine Finland (FIMM), University of Helsinki, and Karolinska institutet, Stockholm, has developed a novel “man and machine” decision support system for diagnosing malaria infection. The method is based on computer vision algorithms similar to those used in facial recognition systems combined with visualization of only the diagnostically most relevant areas. Tablet computers can be utilized in viewing the images.
In this newly developed method, a thin layer of blood smeared on a microscope slide is first digitized. The algorithm analyses more than 50,000 red blood cells per sample and ranks them according to the probability of infection. Then the program creates a panel containing images of more than a hundred most likely infected cells and presents that panel to the user. The final diagnosis is done by a health-care professional based on the visualized images.
By utilizing a set of existing, already diagnosed samples, the researchers were able to show that the accuracy of this method was comparable to the quality criteria defined by the World Health Organization. In the test setting, more than 90% of the infected samples were accurately diagnosed based on the panel. The few problematic samples were of low quality and in a true diagnostic setting would have led to further analyses.
“We are not suggesting that the whole malaria diagnostic process could or should be automated. Rather, our aim is to develop methods that are significantly less labour intensive than the traditional ones and have a potential to considerably increase the throughput in malaria diagnostics”, said Research Director Johan Lundin (MD, PhD) from the Institute for Molecular Medicine Finland, FIMM.
“The equipment needed for digitization of the samples is a challenge in developed countries. In the next phase of our project we will test the system in combination with inexpensive mobile microscopy devices that our group has also developed”, told the shared first author of the article Nina Linder (MD, PhD) from FIMM.
The developed support system can be applied in various other fields of medicine. In addition to other infectious diseases such as tuberculosis, the research group is planning to test the system fro cancer diagnostics in tissue samples.
Institue for Molecular Medicine Finland
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Researchers from Dana-Farber Cancer Institute, the Broad Institute of MIT and Harvard, and other centres have identified novel mutations in a well-known cancer-causing pathway in lung adenocarcinoma, the most common subtype of lung cancer. Knowledge of these mutations could potentially identify a greater number of patients with treatable mutations because many potent cancer drugs that target these mutations already exist. In addition, these findings may expand the number of possible new therapeutic targets for this disease.
In this new study researchers from the Cancer Genome Atlas (TCGA) Research Network, led by Dana-Farber scientist Matthew Meyerson, MD, PhD, examined the genomes, RNA, and some protein from 230 lung adenocarcinoma samples. In three-quarters of the samples, the scientists ultimately identified mutations that put a cell-signalling pathway known as the RTK/RAS/RAF pathway into overdrive.
“Lung adenocarcinoma is the leading cause of human cancer death. This is because there are so many ways to develop the disease, and many different pathways are altered in this cancer,” said Meyerson, who is also a Broad senior associate member. “In recent years, we have made enormous progress in lung adenocarcinoma treatment by targeting EGFR, ALK, and other mutated proteins. Through this study, we are able to add to the range of such alterations and therefore gain potential new therapeutic targets.”
Mutations affecting the RTK/RAS/RAF pathway can cause it to become stuck in the “on” state. As a result, signals that promote cancer cell proliferation and survival are produced continuously. However, drugs are currently available that curb aberrant activity of this pathway and prompt therapeutic responses in patients.
“About 10% of patients have tumours with EGFR mutations, and these patients uniquely benefit from anti-EGFR therapy,” said Alice Berger, a post-doctoral fellow in the Meyerson lab and co-author of the study. “We were motivated to find genetic aberrations in patients that lack EGFR mutations and that might be similarly suitable for therapeutic targeting. Ultimately, we want to be able to provide every patient with an effective drug for their specific cancer.”
In the group’s initial scan of the tumour samples, researchers identified gene mutations that would increase RTK/RAS/RAF pathway activity in 62 percent of the samples. The affected genes are oncogenes, or genes that have the potential to cause cancer when mutated or expressed at high levels. Consequently, these tumour samples were classified as oncogene-positive. To identify additional alterations, the investigators looked at DNA copy number changes, or changes in gene number resulting from the deletion or amplification (multiplication) of sections of DNA in the genome. In doing so, they detected amplification of two oncogenes, ERBB2 and MET, which are part of the RTK/RAS/RAF pathway in the “oncogene negative” cancers. Gene amplification usually leads to increased expression of the encoded protein in cells.
Now that these amplifications have been identified in cancers without other activity of the RTK/RAS/RAF pathway, clinicians may be able to treat patients whose tumours have specific gene changes with drugs that are either currently available or under development.
“It is quite striking that we have now identified an actionable mutation in over 75 percent of patients with lung adenocarcinoma, a significant improvement from a decade ago,” said Meyerson.
Additional analysis identified other genes that may play important roles in lung cancer development. Mutations in one of these genes, NF1 — a known tumour suppressor gene that regulates the RTK/RAS/RAF pathway — had previously been reported in lung cancer. Mutations of NF1 also put that pathway into overdrive. Another mutated gene, RIT1, is also part of the RTK/RAS/RAF pathway, and this is the first study to associate mutation of this gene with lung cancer.
Dana-Farber Institute
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