A new piece of the typhoid ‘puzzle’

In October 2016, researchers at the Aga Khan University’s microbiology laboratory spotted a number of unusual organisms in blood samples from Hyderabad. Blood culture tests from the city contained a novel strain of typhoid that had developed resistance to an unprecedented range of antibiotics.
Over the next few months, several similar cases were detected from the city pointing to an outbreak of a form of the disease that would be especially difficult to treat. 
The research team, led by Pofessor Rumina Hasan, acted quickly to alert local government, the National Institutes of Health and the World Health Organization to this development. They also contacted the UK-based Wellcome Sanger Institute to explore the genetic cause behind the emergence of this extensively drug-resistant (XDR) typhoid strain.
“This was the world’s first outbreak of XDR typhoid,” said Professor Zahra Hasan of the department of pathology and laboratory medicine. “Understanding this new threat required high-level genome sequencing which would enable us to analyse the molecular blueprint of this new form of typhoid.”
Over the next six months, the research team collaborated with experts at the Wellcome Sanger Institute to jointly analyse over 100 DNA samples which resulted in a striking finding. The typhoid bacteria had acquired a DNA molecule through a plasmid from a bacterium commonly found in contaminated water and food, making it resistant to the majority of available medications .  
“We used to think that we had a complete picture of the typhoid ‘puzzle’,” said Dr Sadia Shakoor, assistant professor in pathology and laboratory medicine at AKU. “Together with our partners, we’ve found a missing piece that affects how we diagnose and treat the most complex strains of the disease.”   
Since patients with XDR typhoid do not respond to commonly prescribed antibiotics, blood culture tests have become an even more important tool for physicians, according to Dr Shakoor. Not only do these tests enable early detection but they also highlight the type of typhoid being tackled that affects the choice of antibiotic.
“There are currently three antibiotics available to treat XDR typhoid,” Dr Shakoor stated. “These drugs are expensive and we must only prescribe them when needed. Otherwise, bacteria could develop resistance to the only medications we have left.”
Beyond resistance, researchers also warn of the risk of the disease spreading since every patient is a potential ‘disease carrier’. The likelihood of the proliferation of the disease is especially high in developing countries where poor sanitation facilities result in the contamination of drinking water with sewage containing the typhoid bacteria.
Aga Khan Universitywww.aku.edu/news/Pages/News_Details.aspx?nid=NEWS-001521

Medical laboratory professionals set to benefit from 15 CME-accredited conferences at MEDLAB Asia Pacific Exhibition & Congress

More than 100 industry experts to highlight the latest medical laboratory and diagnostics trends and innovation
The 5th edition of MEDLAB Asia Pacific Exhibition & Congress, leading B2B business and educational platform in the field of laboratory and diagnostics for the Asia Pacific region, will offer visitors the opportunity to attend a series of scientific conferences that will cover advancement in science, technology and application of various laboratory techniques to strengthen cooperation between lab and clinic interface.
Supported by The Academy of Medicine, Singapore and accredited by Singapore Medical Council, the 15 CME-certified conferences will empower delegates with the knowledge and skills to guarantee the fastest, safest and most accurate laboratory results in improving patient service and care.
During the three-day congress, which takes place from 2 – 4 April 2018 at Suntec Singapore Convention & Exhibition Centre in Singapore, a variety of carefully-designed sessions, panel discussions, demonstrations and interactive activities will enable delegates to network and share best practices with more than 100 regional and international experts who are champions of laboratory medicine in the Asia Pacific.
The congress will host 11 dedicated laboratory tracks: Laboratory Management, ­Clinical Chemistry, Haematology & Blood Transfusion, Infectious Diseases, Point of Care Testing, Cytology, Molecular Diagnostics, Laboratory Informatics, Cardiac Markers, ­ Lab Testing: Obs Gyne & Women’s Health and Lab Testing & Management: Diabetes.
During these sessions, delegates will able schooled in a wide variety of key topics including the role of the laboratory director, 4th generation sequencing, updates in assays to improve skills in test accuracy, digital pathology, and the evaluation of current and future biomarkers, to name a few.
Due to the expanding role of laboratory medicine, the meeting is combined with other clinical specialties that will underscore the overarching influence of the laboratory in medical decision-making and treatment. New conferences in the MEDLAB Asia Pacific Congress portfolio are: Obs Gyne & Women’s Health, Gynae-Oncology, Diabetes Management and Antimicrobial Resistance.
“The advent of groundbreaking diagnostic solutions is gaining pace across the region. By introducing new medical tracks from key specialties that interact with the laboratory, the 2018 MEDLAB Asia Pacific Congress will provide the latest evidence-based research into diagnosis and treatment as well as enhance cooperation between laboratory professionals and clinicians to enable the best possible patient outcomes.” said Rejoy Penacerrada, Senior Conference Producer, MEDLAB Asia.
MEDLAB Asia Pacific 2018  is supported by a large number of key healthcare federations and associations across the region including The Royal College of Pathologists of Australasia, Singapore Society of Pathology, College of Pathologists, Academy of Medicine of Malaysia, Indonesian Association of Clinical Pathologist and Laboratory Medicine, Singapore Society of Haematology, College of American Pathologists, Philippine Society of Pathologists, Inc., Philippine Society of Biochemistry and Molecular Biology, Philippine Society of Microbiology, Indonesian Association of Clinical Chemistry, Society of Infectious Disease Singapore, and Society of Cytology Singapore and Diabetes Singapore.
Held alongside the congress is the MEDLAB Asia Pacific exhibition – a platform for leading companies from across the globe to showcase current technologies and innovations in the field of laboratory and diagnostics to an expected 4,000 visitors.
MEDLAB Asia Pacific is also co-located with Asia Health, a trade exhibition for medical equipment, products, services and technologies hosting more than 250 international companies and bringing together the world of medical laboratory and healthcare under one roof.
Registration for the MEDLAB Asia Pacific Congress is now open via www.medlabasia.com.

Genomics tool for more accurate identification of rare mutations in cancer cells

A new computational method developed by researchers at the New York Genome Center (NYGC) allows scientists to identify rare gene mutations in cancer cells with greater accuracy and sensitivity than currently available approaches.
The technique is called Lancet and represents a major advance in the identification of tumour cell mutations, a process known as somatic variant calling.
"With its unique ability to jointly analyse the whole genome of tumour and matched normal cells, Lancet provides a useful tool for researchers to conduct more accurate genome-wide somatic variant calling," notes first author Giuseppe Narzisi, PhD, Senior Bioinformatics Scientist, NYGC.
To identify gene mutations in cancer cells, researchers sequence the genomes of tumour cells and normal cells. Current computational methods then involve comparing both tumour and normal to a reference genome and looking for differences unique to the tumour. Lancet instead uses an approach called micro-assembly to reconstruct the complete sequences of small regions of the genome without relying on a reference. Because the approach does not rely on a reference to identify variants, it also works well in regions of the genome where comparing reads to a reference is challenging for technical reasons. By using a data structure called a coloured de Bruijn graph, Lancet jointly analyses the tumour and normal DNA, providing greater sensitivity to find rare variants unique to the tumour while also providing greater accuracy of differentiating tumour variants from those present in healthy tissue in that individual. Using Lancet to combine the sequencing data from the normal and tumour cells represents a more powerful way of identifying mutations, Dr. Narzisi said, since users are no longer dependent on analysing sequence data from tumour and normal cells separately.
In the study, through extensive experimental comparison on synthetic and real whole-genome sequencing datasets, the researchers demonstrated that Lancet performed better and had higher accuracy and better sensitivity to detect somatic variants compared to the most widely-used somatic variant callers.
"In our study, we show that existing tools are not that precise in scoring mutations, so that some candidate variants which were highly scored by some tools ended up being false positives," Dr. Narzisi said. "That becomes a problem when you want to prioritize which variants to validate using other technologies or you want to move forward with a clinical study. You may end up focusing on variants that do not exist."
EurekAlertwww.eurekalert.org/pub_releases/2018-03/nygc-ngt032218.php

Gene-based test for urine detects, monitors bladder cancer

Researchers at The Johns Hopkins Kimmel Cancer Center have developed a test for urine, gathered during a routine procedure, to detect DNA mutations identified with urothelial cancers.
UroSEEK uses urine samples to seek out mutations in 11 genes or the presence of abnormal numbers of chromosomes that would indicate the presence of DNA associated with bladder cancer or upper tract urothelial cancer (UTUC).
The researchers said the test, when combined with cytology, the gold standard non-invasive test currently used for detection, significantly enhanced early detection for patients who are considered at risk for bladder cancer and surveillance of patients who had already been treated for bladder cancer.
“There were nearly 80,000 new cases of bladder cancer and more than 18,000 deaths in 2017,” said George Netto, M.D., a senior author on the UroSEEK paper, formerly at The Johns Hopkins University and currently chair of pathology at the University of Alabama-Birmingham. “This is about using the urine to detect the cancer. UroSEEK is a method of detection that many people have tried to find that is non-invasive.”
Most cancers are curable if they are detected early, and the researchers are exploring ways to use cancer gene discoveries to develop cancer screening tests to improve cancer survival. They announced the development of CancerSEEK, a single blood test that screens for eight cancer types, and PapSEEK, a test that uses cervical fluid samples to screen for endometrial and ovarian cancers.
UroSEEK is aimed toward early detection of bladder cancer in at-risk patients, those who may have blood in their urine or people who smoke, as well as patients who have already gone through a procedure to treat bladder cancer and need to be monitored for any recurrence of the disease.
“In almost one-third of patients, bladder cancer detection is late. The cancer has already gotten into the surrounding muscle,” Netto said. “Even in those detected at an earlier stage, the tumours frequently recur. Patients are committed to a lifelong surveillance that requires invasive cystoscopy procedures and biopsies and is costly.”
Saying current non-invasive approaches for detection of urothelial cancer are suboptimal, researchers wanted to develop a test for bladder and UTUC cancer that would allow it to be found sooner and cheaper than current methods using cytology, which is not particularly sensitive and does not do well in detecting low-grade bladder cancer or UTUC.
Researchers studied 570 patients who were considered at risk for bladder cancer and found UroSEEK was 83 percent positive in those who developed cancer. When combined with cytology, the sensitivity increased to 95 percent of patients who developed the disease.
“When you combine them, you get better results,” said Nickolas Papadopoulos, Ph.D., a senior author and an investigator at the Ludwig Center at Johns Hopkins. “Side by side, UroSEEK has better sensitivity. There are some cases when cytology detects when UroSEEK doesn’t. Combining them produces the best results.”
John Hopkins Kimmel Cancer Centerwww.hopkinsmedicine.org/news/media/releases/gene_based_test_for_urine_detects_monitors_bladder_cancer

Pap test fluids used in gene-based screening test for two Gyn cancers

Cervical fluid samples gathered during routine Papanicolaou (Pap) tests are the basis of a new screening test for endometrial and ovarian cancers developed by researchers at the Johns Hopkins Kimmel Cancer Center.
PapSEEK detects mutations in DNA that have been identified for specific cancers sooner. Earlier detection of cancer could lead to earlier treatment and potentially better outcomes for patients.
The test uses cervical fluid samples to look for mutations in 18 genes, which are highly or commonly mutated in endometrial or ovarian cancers, and aneuploidy, the presence of abnormal numbers of chromosomes in cells. The researchers said their results showed the potential for mutation-based diagnostics to detect endometrial and ovarian cancers earlier.
“More than 86,000 U.S. cases of endometrial and ovarian cancer were diagnosed in 2017. Treatment often involves surgery and, in some cases, chemotherapy or radiation,” said Amanda Nickles Fader, M.D., director of the Johns Hopkins Kelly Gynecological Oncology Service, Department of Gynecology and Obstetrics, and a corresponding author on this study.
“Additionally for young women who are diagnosed, loss of fertility is common. If we could detect the cancer earlier using a test like PapSEEK, the potential to achieve more cures and preserve fertility in select women could be realized.”
Most cancers are curable if they are detected early, and the researchers are exploring ways to use cancer gene discoveries to develop cancer screening tests to improve cancer survival. They announced the development of CancerSEEK, a single blood test that screens for eight cancer types, and UroSEEK, a test that uses urine to detect for bladder and upper tract urothelial cancer.
PapSEEK targets the most common and most lethal gynaecological cancers, endometrial and ovarian cancer. There is currently no screening test for endometrial cancer and, due to the obesity epidemic, it is on the rise, particularly in younger women.
“Gynaecological cancers are responsible for approximately 25,000 deaths per year and are the third leading cause of cancer-related mortality,” said Nickolas Papadopoulos, Ph.D., a senior author and an investigator at the Ludwig Center at Johns Hopkins. “Most of the deaths are caused by tumours that metastasize prior to the onset of symptoms. With PapSEEK, we are aiming to detect these cancers early when they are most curable.”
Since fluid from the Pap test occasionally contains cells from the endometrium or ovaries, researchers found they could detect cancer cells from these organs that are present in the fluid.
John Hopkins Kimmel Cancer Centerwww.hopkinsmedicine.org/news/media/releases/pap_test_fluids_used_in_gene_based_screening_test_for_two_gyn_cancers

Parkinson’s gene initiates disease outside of the brain

Until very recently, Parkinson’s had been thought a disease that starts in the brain, destroying motion centres and resulting in the tremors and loss of movement. New research shows the most common Parkinson’s gene mutation may change how immune cells react to generic infections like colds, which in turn trigger the inflammatory reaction in the brain that causes Parkinson’s. The research offers a new understanding of Parkinson’s disease.                                                     
“We know that brain cells called microglia cause the inflammation that ultimately destroys the area of the brain responsible for movement in Parkinson’s,” said Richard Smeyne, PhD, Director of the Jefferson Comprehensive Parkinson’s Disease and Movement Disorder Center at the Vickie and Jack Farber Institute for Neuroscience. “But it wasn’t clear how a common inherited mutation was involved in that process, and whether the mutation altered microglia.”
Together with Dr. Smeyne, first author Elena Kozina, PhD, looked at the mutant version of the LRRK2 gene (pronounced ‘lark’). Mutations in the LRRK2 gene are the most common cause of inherited Parkinson’s disease and are found in 40 percent of people of North African Arab descent and 18 percent of people of Ashkenazi Jewish descent with Parkinson’s. However there’s been controversy around the exact function of the LRRK2 gene in the brain.
“We know that gene mutation is not enough to cause the disease,” said Dr. Kozina, Post-Doctoral student at Jefferson.“We know that twins who both carry the mutation, won’t both necessarily develop Parkinson’s. A second ‘hit’ or initiating event is needed.”
Based on his earlier work showing that the flu might increase risk of Parkinson’s disease, Dr. Smeyne decided to investigate whether that second hit came from an infection. Suspecting that the LRRK2 mutations might be acting outside of the brain, the researchers used an agent — the outer shell of bacteria, called lippopolysaccharide (LPS) – that causes an immune reaction. LPS itself does not pass into the brain, nor do the immune cells it activates, which made it ideal for testing whether this second hit was acting directly in the brain.
When the researchers gave the bacterial fragments to the mice carrying the two most common LRRK2 gene mutations, the immune reaction became a “cytokine storm,” with inflammatory mediators rising to levels that 3-5 times higher than a normal reaction to LPS. These inflammatory mediators were produced by T and B immune cells expressing the LRRK2 mutation.
Despite the fact that LPS did not cross the blood-brain barrier, the researchers showed that the elevated cytokines were able to enter the brain, creating an environment that caused the microglia to activate pathologically and destroy the brain region involved in movement.
“Although more tests are needed to prove the link, as well as testing whether the same is true in humans, these findings give us a new way to think about how these mutations could cause Parkinson’s,” said Dr. Smeyne. “Although we can’t treat people with immunosuppressants their whole lives to prevent the disease, if this mechanism is confirmed, it’s possible that other interventions could be effective at reducing the chance of developing the disease.”
Thomas Jefferson Universitywww.jefferson.edu/university/news/2018/03/21/Parkinsons_gene_triggers_the_disease_from_outside_brain.html

Proteins reveal new mechanisms in prostate cancer

A study by the University of Tampere in Finland used protein profiling to find new prostate cancer mechanisms that are not shown by aberrations at the genomic level. Several new potential biomarkers of prostate cancer were also found.
Genes that affect prostate cancer evolution have been studied for a long time. However, changes in the protein levels are not well known.
The Center for Prostate Cancer Research and the Center for Proteomics and Personalized Medicine at the University of Tampere cooperated to profile the protein expression of prostate cancer by using mass spectrometry for the first time. The researchers compared protein expression to genomic and messenger RNAs in the same samples.
The result was that the changes in gene copy numbers and DNA methylation largely explain messenger RNA expression but not the changes on the protein level. The association between messenger RNA expression and protein levels was also weak. The study thus uncovered such mechanisms of prostate cancer that are not indicated by the alterations at the genomic level.
“In particular, changes in the citric acid cycle emerged in our analyses,” Adjunct Professor Leena Latonen says.
“The results enable exploring the significance of these changes," Latonen continues.
In addition to the disease mechanisms, protein profiling revealed several potential new biomarkers.
According to Professor Tapio Visakorpi, biomarkers able to recognize the aggressive forms of prostate cancer would be especially useful. That is one of the aspects on which the researchers will focus next.
“Discovering these protein biomarkers was enabled by the long-term interdisciplinary work of the research groups on the Kauppi campus of the University of Tampere,” says Professor Hannu Uusitalo, Director of the Center for Proteomics and Personalized Medicine.
University of Tamperewww.uta.fi/en/news/story/proteins-reveal-new-mechanisms-prostate-cancer

Mutations of the bassoon gene causing new brain disorder

Newly discovered gene mutations may help explain the cause of a disease that drastically impairs walking and thinking.
Mutations have been found in the bassoon (BSN) gene, which is involved with the central nervous system, in patients with symptoms similar to, but different from, a rare brain disorder called progressive supranuclear palsy (PSP).
PSP, a form of Parkinson’s disease, is often difficult to diagnose because it can affect people in different ways. Serious problems often include difficulty with walking and balance in addition to a decline in cognitive abilities such as frontal lobe dysfunction.
A team of Japanese researchers investigated patients whose symptoms resembled not only PSP but also Alzheimer’s disease. Despite similarities in the symptoms, detailed pathological analyses showed no resemblance to either disease, which prompted the team to further research the new disease’s underlying mechanism.
They first analysed the genomes of a Japanese family with several members displaying PSP-like symptoms. They identified a mutation in the BSN gene only in family members with symptoms. These individuals did not have mutations in the 52 other genes associated with PSP and other neurological disorders such as Alzheimer’s and Parkinson’s. This was the first time BSN gene is associated with a neurological disorder.
The researchers also detected three other mutations in the BSN gene in four out of 41 other patients displaying sporadic, or non-familial, PSP-like symptoms. None of the BSN mutations were detected in a random sample of 100 healthy individuals, underscoring the strong involvement of BSN mutations in the disease.
An autopsy done on one of the family members with the BSN mutation showed an accumulation of a protein called tau in the brain, which is not seen in a normal brain. The researchers believe that the BSN mutation is involved in the tau accumulation, which could cause the development of PSP-like symptoms. An experiment introducing a mutated rat BSN gene to cultured cells also suggested that the mutation causes the accumulation of tau. Communication between nerve fibres could also be affected, as BSN protein play a role in it.
ScienceDailywww.sciencedaily.com/releases/2018/03/180323093731.htm

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A new blood test useful to detect people at risk of developing Alzheimer’s disease

There is as yet no cure for Alzheimer’s disease. It is often argued that progress in drug research has been hampered by the fact that the disease can only be diagnosed when it is too late for an effective intervention. Alzheimer’s disease is thought to begin long before patients show typical symptoms like memory loss. Scientists have now developed a blood test for Alzheimer’s disease and found that it can detect early indicators of the disease long before the first symptoms appear in patients. The blood test would thus offer an opportunity to identify those at risk and may thereby open the door to new avenues in drug discovery.
One of the hallmarks of Alzheimer’s disease is the accumulation of amyloid-β plaques in the patient’s brain. The blood test, developed by Klaus Gerwert and his team at Ruhr University Bochum, Germany, works by measuring the relative amounts of a pathological and a healthy form of amyloid-β in the blood. The pathological form is a misfolded version of this molecule and known to initiate the formation of toxic plaques in the brain. Toxic amyloid-β molecules start accumulating in the patients’ body 15-20 years before disease onset. In the present study, Gerwert and colleagues from Germany and Sweden addressed whether the blood test would be able to pick up indications of pathological amyloid-β in very early phases of the disease.
The researchers first focused on patients in the early, so called prodromal stages of the disease from the Swedish BioFINDER cohort conducted by Oskar Hanson. They found that the test reliably detected amyloid-β alterations in the blood of participants with mild cognitive impairment that also showed abnormal amyloid deposits in brain scans.
In a next step, Gerwert and colleagues investigated if their assay was able to detect blood changes well ahead of disease onset. They used data from the ESTHER cohort study, which Hermann Brenner started in 2000 at DKFZ, comparing blood samples of 65 participants that were later in the follow-up studies diagnosed with Alzheimer’s disease with 809 controls. The assay was able to detect signs of the disease on average eight years before diagnosis in individuals without clinical symptoms. It correctly identified those with the disease in almost 70% of the cases, while about 9% of true negative subjects would wrongly be detected as positive. The overall diagnostic accuracy was 86%.
Currently available diagnostic tools for Alzheimer’s disease either involve expensive positron emission tomography (PET) brain scans, or analyse samples of cerebrospinal fluid that are extracted via lumbar puncture. The researchers suggest that their blood test serves as a cheap and simple option to pre-select individuals from the general population for further testing by these more invasive and costly methods to exclude the falsely positive subjects.
EMBOwww.embo.org/news/press-releases/2018/a-new-blood-test-useful-to-detect-people-at-risk-of-developing-alzheimer-s-disease