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Archive for category: E-News

E-News

Protein implicated in osteosarcoma’s spread acts as air traffic controller

, 26 August 2020/in E-News /by 3wmedia

The investigation of a simple protein has uncovered its uniquely complicated role in the spread of the childhood cancer, osteosarcoma. It turns out the protein, called ezrin, acts like an air traffic controller, coordinating multiple functions within a cancer cell and allowing it to endure stress conditions encountered during metastasis.

It’s been known that ezrin is a key regulator of osteosarcoma’s spread to the lungs, but its mechanism was not known. Osteosarcoma is a tumour of bone that afflicts children, adolescents and young adults. In most cases, the tumour is localized in the extremities and can be completely removed by surgery or amputation.

“The main cause of death in osteosarcoma patients is not the tumour on their limbs, but the failure of their lungs when the cancer spreads there,” explains Aykut Üren, MD, professor of oncology at Georgetown Lombardi Comprehensive Cancer Center.

Üren and his colleagues have developed molecules that block ezrin’s function and prevent osteosarcoma spread in mouse models. In an attempt to explain the molecular mechanisms underlying ezrin-mediated cancer metastasis, the researchers discovered this previously unrecognized role for ezrin.

“Conventionally ezrin was believed to be functioning only on the inner surface of cancer cells,” Üren says, “but our new discovery indicates that ezrin may operate deeper in the core of the cell and regulate expression of critical genes that are important for cancer’s spread.”

The scientists say that ezrin functions in a new capacity that is unusual for its family of proteins. They found that ezrin’s unusual interaction with another protein called DDX3 results in modulation of genes that give cancer cells an edge in surviving harsh conditions.

“Knowing exactly how ezrin works will help our team develop the ezrin-targeting small molecules as potential new drugs to prevent the spread of cancer cells to lungs in osteosarcoma patients,” Uren says.

“Implications of our findings go beyond cancer research,” says the study’s first author Haydar Çelik, PhD. “Because this work suggests a new molecular mechanism on how ezrin is involved in the regulation of mRNA translation, these observations may provide important clues for scientists investigating how viruses enter and replicate in human cells too.” Georgetown Lombardi Comprehensive Cancer Center

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Ovarian cancer-specific markers set the stage for early diagnosis, personalized treatments

, 26 August 2020/in E-News /by 3wmedia

Ovarian cancer is notoriously difficult to diagnose and treat, making it an especially fatal disease. Researchers at University of California, San Diego School of Medicine and Moores Cancer Center have now identified six mRNA isoforms (bits of genetic material) produced by ovarian cancer cells but not normal cells, opening up the possibility that they could be used to diagnose early-stage ovarian cancer. What’s more, several of the mRNA isoforms code for unique proteins that could be targeted with new therapeutics.

“We were inspired by many studies aimed at using DNA to detect cancer,” said first author Christian Barrett, PhD, bioinformatics expert and project scientist in the UC San Diego School of Medicine Institute for Genomic Medicine. “But we wondered if we could instead develop an ovarian cancer detection test based on tumour-specific mRNA that has disseminated from cancer cells to the cervix and can be collected during a routine Pap test.”

While DNA carries all the instructions necessary for life, its actual sequence contains much more than just the genes that code for proteins. In contrast, mRNAs are complementary copies of just the genes. They carry the recipe for every protein that the cell will produce from the nucleus to the cytoplasm, where cellular machinery can read the recipe and build the corresponding proteins. According to the authors of this study, the advantage of using cancer mRNA for diagnosis rather than DNA is sheer number — a cancer cell might harbour just one or a few copies of a DNA mutation, but mRNA variants can occur in hundreds to thousands of copies per cell.

To determine if mRNAs can be used to distinguish ovarian cancer cells from normal cells, the team developed a custom bioinformatics algorithm and used it to mine two large public databases of genetic information — The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) program, both sponsored by the National Institutes of Health. TCGA is a catalog of RNA and DNA from 500 tumors covering many cancer types, while GTEx is a database of RNA and DNA from normal tissue samples. From these, the researchers were able to analyze mRNA sequence data from 296 ovarian cancers and 1,839 normal tissue samples.

Using this bioinformatics approach, the researchers identified six mRNA isoform molecules that have the tumour specificity required for an early detection diagnostic of ovarian cancer. They also validated their digital results in the real world using RT-quantitative PCR, a gene amplifying technique, to detect the same ovarian cancer-specific mRNA molecules in lab-grown cells.
Beyond their diagnostic potential, some of the mRNA isoforms identified in this study could also act as new therapeutic targets. These mRNA isoforms are predicted to encode proteins with unique amino acid sequences, which might allow them to be specifically targeted with certain therapeutics, such as monoclonal antibodies or T-cell-based vaccines. What’s more, the ovarian cancer-specific mRNA isoforms themselves could also be targeted with new therapeutic drugs.

“Our experimental findings were made in a laboratory and were performed on ovarian cancer cells from cell lines,” said study co-author Cheryl Saenz, MD, a clinical professor of reproductive medicine who specializes in treating gynaecologic cancers. “Clinical trials will need to be conducted on women to confirm the presence of these markers in women that we know have cancer, as well as to document the absence of the markers in women that do not have ovarian cancer.” University of California – San Diego Health System

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Sound separates cancer cells from blood samples

, 26 August 2020/in E-News /by 3wmedia

Separating circulating cancer cells from blood cells for diagnostic, prognostic and treatment purposes may become much easier using an acoustic separation method and an inexpensive, disposable chip, according to a team of engineers.

‘Looking for circulating tumour cells in a blood sample is like looking for a needle in a haystack,’ said Tony Jun Huang, professor of engineering science and mechanics.  ‘Typically, the CTCs are about one in every one billion blood cells in the sample.’

Existing methods of separation use tumour-specific antibodies to bind with the cancer cells and isolate them, but require that the appropriate antibodies be known in advance.  Other methods rely on size, deformability or electrical properties.  Unlike conventional separation methods that centrifuge for 10 minutes at 3000 revolutions per minute, surface acoustic waves can separate cells in a much gentler way with a simple, low-cost device.

Acoustic-based separations are potentially important because they are non-invasive and do not alter or damage cells.  However, in order to be effective for clinical use, they also need to be rapidly and easily applicable.

‘In order to significantly increase the throughput for capturing those rare CTCs, device design has to be optimized for much higher flow rates and longer acoustic working length,’ said Ming Dao, principal research scientist, materials science and engineering, Massachusetts Institute of Technology.  ‘With an integrated experimental/modelling approach, the new generation of the device has improved cell sorting throughput more than 20 times higher than previously achieved and made it possible for us to work with patient samples.’

The researchers worked both experimentally and with models to optimize the separation of CTCs from blood.   They used an acoustic-based microfluidic device so that the stream of blood could continuously pass through the device for separation.  Using the differential size and weight of the different cells they chose appropriate acoustic pressures that would push the CTCs out of the fluid stream and into a separate channel for collection.

Tilted-angle standing surface acoustic waves can separate cells using very small amounts of energy. The power intensity and frequency used in this study are similar to those used in ultrasonic imaging, which has proven to be extremely safe, even for fetuses. Also, each cell experiences the acoustic wave for only a fraction of a second.  In addition, cells do not require labelling or surface modification.  All these features make the acoustic separation method, termed acoustic tweezers, extremely biocompatible and maximize the potential of CTCs to maintain their functions and native states.

If two sound sources are placed opposite each other and each emits the same wavelength of sound, there will be a location where the opposing sounds cancel each other. Because sound waves have pressure, they can push very small objects, so a cell or nanoparticle will move with the sound wave until it reaches the location where there is no longer lateral movement, in this case, into the fluid stream that moves the separated cells along.

The researchers used two types of human cancer cells to optimize the acoustic separation — HELA cells and MCF7 cells.  These cells are similar in size.  They then ran an experiment separating these cells and had a separation rate of more than 83 percent.  They then did the separation on other cancer cells, ones for which the device had not been optimized, and again had a separation rate of more than 83 percent.

‘Because these devices are intended for use with human blood, they need to be disposable,’ said Huang.  ‘We are currently figuring out manufacturing and mass production possibilities.’

Physicians could use the devices to monitor how patients reacted to chemotherapy, for initial diagnosis and for determining treatment and prognosis. Penn State University

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ACMG releases new scope of practice document

, 26 August 2020/in E-News /by 3wmedia

The field of medical genetics is swiftly evolving. It’s a period of rapid scientific discovery, new technologies and subsequent translation into medical practice, public policy and public health. But what role should the Medical Genetics specialist have since genetics impacts all patients and specialties in some way? In an effort to clearly define the changing role of the specialty of Medical Genetics and the distinction between Medical Geneticists and other genetics healthcare professionals, the American College of Medical Genetics and Genomics (ACMG) has released a new ‘Scope of Practice of the Specialty of Medical Genetics’ document, revising its earlier 2008 Policy Statement. The ACMG is the specialty society for the American Board of Medical Genetics and Genomics diplomates and others, providing leadership and resources to facilitate the delivery of clinical and laboratory medical genetics services.

ACMG President Gerald Feldman, MD, PhD, FACMG said, ‘We wanted to clearly define the value that board-certified Clinical Geneticists and Clinical Laboratory Geneticists provide, from their roles performing genetic testing interpretation in the diagnostic laboratory to the medical genetics consultation. The ACMG Scope of Practice document also establishes how our specialty interacts with other members of the medical genetics healthcare team and where we find common ground with other medical specialists.’

Feldman explained the genesis of the new document, ‘The ACMG Board of Directors felt that it was critical to revise the original 2008 document to answer the who, what, where, when, why and how in the current era of genomic medicine, which involves other genetics health professionals, such as genetic counsellors, genetic nurses, and other lab professionals performing genetic and genomic testing.’
The Scope of Practice document is available at
www.acmg.net/docs/ACMG_SOP_GIM_AOP_072315.pdf. A Commentary from Dr.

The ‘ACMG Scope of Practice of the Specialty of Medical Genetics’ Policy Statement states that the specialty includes:
-Genetic consultations, in both inpatient and outpatient settings
-Genetic counselling
-Treatment of genetic diseases, involvement in clinical trials and natural history
studies leading to approval and use of new, orphan and other drugs
-Early detection and prevention of genetic diseases or their complications
-Performing genetic and genomic testing, interpreting such results and providing
these results to physicians to facilitate diagnosis, management and treatment
-Activities outside of direct patient care, including public health administration, health professional education and research. American College of Medical Genetics and Genomics

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New biomarker identified in women with mental illness

, 26 August 2020/in E-News /by 3wmedia

Psychiatric disorders can be difficult to diagnose because clinicians must rely upon interpreted clues, such as a patient’s behaviours and feelings. For the first time, researchers at University of California, San Diego School of Medicine report identifying a biological marker: the over-production of specific genes that could be a diagnostic indicator of mental illness in female psychiatric patients.

Researchers found that the gene XIST, which is responsible for inactivating one of the two copies of the X chromosome in cells that store genetic material, works overtime in female patients with mental illnesses, such as bipolar disorder, major depression and schizophrenia.
The study suggests that over-production of XIST and genes from the inactive X chromosome are common denominators in the development of psychiatric disorders in patients with rare chromosome disorders, such as Klinefelter syndrome and Triple X syndrome, and in the general population of female psychiatric patients.

“There has been an utmost urgency to identify biomarkers for mental illness that could significantly impact research and drug development,” said Xianjin Zhou, PhD, assistant professor in the Department of Psychiatry at UC San Diego School of Medicine and lead author.

The study was conducted on 60 lymphoblastoid cell lines from female patients, most of whom had a family history of mental illness. Approximately 50 percent of the female patients exhibited abnormally higher levels of XIST and other genes related to the X chromosome.

Zhou and his team said reversing the abnormal activity of the inactive X chromosome in patients suffering from mental illness may offer a potential new strategy for treating psychiatric disorders. UC San Diego

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Fracture’ prints, not fingerprints, help solve child abuse cases

, 26 August 2020/in E-News /by 3wmedia

Much like a finger leaves its own unique print to help identify a person, researchers are now discovering that skull fractures leave certain signatures that can help investigators better determine what caused the injury.

Implications from the Michigan State University research could help with the determination of truth in child abuse cases, potentially resulting in very different outcomes.

Until now, multiple skull fractures meant several points of impact to the head and often were thought to suggest child abuse.

Roger Haut, a University Distinguished Professor in biomechanics, and Todd Fenton, a forensic anthropologist, have now proven this theory false. They’ve found that a single blow to the head not only causes one fracture, but may also cause several, unconnected fractures in the skull. Additionally, they’ve discovered that not all fractures start at the point of impact – some actually may begin in a remote location and travel back toward the impact site.

“It’s a bit like smashing raw hamburger into a patty on the grill,” Haut said. “When you press down on the meat to flatten it, all the edges crack. That’s what can happen when a head injury occurs.”

Because piglet skulls have similar mechanical properties as infant human skulls – meaning they bend and break in similar ways – Haut and Fenton used the already deceased specimens in their research and found they were able to classify the different fracture patterns with a high degree of accuracy.

“Our impact scenarios on the piglet skulls gave us about an 82 percent accuracy rate, while on the older skulls, it improved to about 95 percent,” Fenton said.

To help them get to this level of accuracy, both researchers teamed up with Anil Jain, a University Distinguished Professor in computer science and engineering at MSU, to develop a mathematical algorithm to help classify the fractures.

“A major issue in child death cases is you never really know what happened,” Haut said. “The prosecutor may have one idea, the medical examiner another, and the defendant a completely different scenario.”

Fenton and Haut’s close relationship with medical examiners often results in them being called upon in certain, hard-to-determine cases. They’ve used this new knowledge to help solve these cases, but both are also looking to use Jain’s algorithm in an online resource that will provide even more assistance to investigators.

The team is currently developing a database, or Fracture Printing Interface, that will allow forensic anthropologists and investigators to upload human fracture patterns from different abuse cases and help them determine what most likely caused an injury.

Michigan State University
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Discovered: A cause of mental retardation and autism

, 26 August 2020/in E-News /by 3wmedia

The term intellectual disability covers a large number of clinical entities, some with known cause and others of uncertain origin. For example Down syndrome is due to an extra copy of chromosome 21 and Rett syndrome is in part caused by a mutation in the control switch gene called MeCP2.

In other cases the mechanisms by which they are produced are not clearly identified. It is the case of most of those disorders classified under the large umbrella of autism. An study by Manel Esteller, director of the Program Epigenetics and Cancer Biology (PEBC) of the Bellvitge Biomedical Research Institute (IDIBELL), ICREA researcher and Professor of Genetics at the University of Barcelona , has discovered a mechanism that identifies a cause of intellectual disabilities in these puzzling cases.

‘We have analysed the genome of 215 patients with mental retardation, autism or Rett syndrome, in which they had not found any genetic alteration in the genes classically associated with these clinical conditions, to see if we could find a molecular cause. And this process has allowed us to detect a new mutated gene that could be causing these disorders. ‘He explained Manel Esteller.

‘Specifically, the identified gene is called JMJD1C (Jumonji Domain Containing 1C) and is an epigenetic gene which its normal function is to control the activity of other genes. Only a small percentage of mental retardation of unknown origin is due to mutation of this gene. This finding suggests that many genes with low frequency disturbance are responsible for cases with unknown cause. They have demonstrated that this gene joins the MeCP2 gene so it could also contribute to cases of atypical Rett Syndrome ‘says Esteller. IDIBELL

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An immune system marker for therapy-resistant prostate cancer

, 26 August 2020/in E-News /by 3wmedia

You are a patient who has just been treated for a serious illness but neither you nor your doctor knows how likely it is that you – in comparison with other patients — will actually be helped by the treatment. This is often the situation with prostate cancer, one of the deadliest and most highly prevalent cancers. While hormone therapy can help, patient responses vary widely, and it’s still unclear why some types of prostate cancer seem to be resistant to the therapy.

A team led by Associate Professor Lloyd Trotman at Cold Spring Harbor Laboratory (CSHL) shows how signalling by an immune system component called interleukin-6 (IL-6) appears to play an important role in driving particularly aggressive and therapy-resistant prostate cancer.

“Our research suggests that IL-6 could be a marker for when the disease switches to a more dangerous state that is ultimately hormone therapy-resistant,” says Trotman.

The results could have important implications for human prostate cancer. “The gain could be immense, because today’s problem is that the variability in response of humans to hormone therapy is amazing,” Trotman says. “For one man this therapy might be great, might reduce disease burden dramatically for many, many, years, and be an extreme benefit,” he says. “For others there’s almost no response, and it’s still not clear to clinicians who is who.”

Being able to predict which patients would benefit from hormone therapy “would be amazing,” Trotman says. “We are really hopeful that translating the IL-6 discovery into the clinics could help us stratify patients into good responders and bad responders. For any hospital this would be a major breakthrough.”

Trotman and his team, which included Dawid Nowak, Ph.D., a postdoctoral investigator who is the paper’s first author, looked for cellular signals that led to metastasis and hormone therapy resistance in a genetically engineered mouse model for metastatic prostate cancer. They found that the combined loss of two genes, PTEN and p53 — closely associated with prostate cancer metastasis — led to the secretion of IL-6. Signalling by IL-6 was then responsible for activating a powerful cancer gene called MYC, which drives cell proliferation and disease progression.

“It suggested immediately that cell-cell communication is very, very important to make the cells resistant to therapy and very aggressive,” says Trotman.

The involvement of the MYC pathway suggests that it could potentially serve as a target of drugs against prostate cancer, Trotman says. The team’s next step is to study IL-6 signalling in humans. “IL-6 detection in blood has been developed to a high art,” Trotman says. “There are very good tools, which have been tested in the hospital setting.”  Cold Spring Harbor Laboratory 

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Circulating tumour DNA in blood a valid option for EGFR testing in patients who do not have accessible tumour tissue

, 26 August 2020/in E-News /by 3wmedia

Cancer DNA circulating in the bloodstream of lung cancer patients can provide doctors with vital mutation information that can help optimise treatment when tumour tissue is not available, an international group of researchers has reported at the European Lung Cancer Conference (ELCC) in Geneva, Switzerland.

The results have important implications for the use of cancer therapies that target specific cancer mutations, explains Dr Martin Reck from the Department of Thoracic Oncology at Lung Clinic Grosshansdorf, Germany, who presented the findings at the conference.

Testing for the presence of these mutations in the tumour itself is not always possible, however studies have suggested that DNA from the tumour that circulates in the bloodstream of patients may provide similar information.

The large international ASSESS study aimed to compare the ability of blood testing to detect EGFR mutations with the more standard method of testing the tumour itself.

“We were really asking a question on behalf of patients,” Reck said: “Is there a valid test that can identify an EGFR mutation and give me the opportunity for superior treatment, even if my lung tumour is not accessible for bronchoscopy or CT-guided biopsy? And, are the results of this blood test in agreement with the results of the ‘gold-standard’ tissue test?”

Overall, the study included 1162 matched tissue and blood samples. Comparison of the outcomes of EGFR testing in the two techniques showed an 89% rate of agreement between the blood test and tissue test. Plasma testing identified about half of the patients with EGFR mutations, compared to tissue testing (a sensitivity of 46%).

The tests in this study were not performed in specially selected central labs, but in local labs that are used for daily clinical routine. “This is important, because it does reflect the clinical reality and not a ‘virtual’ trial reality,” Reck said.

“The results mean that for patients who do not have accessible tumour tissue, plasma testing for EGFR mutation turns out to be an attractive option to offer these patients adequate targeted treatment,” Reck added.

Commenting on the study, Dr Rafael Rosell, from the Catalan Institute of Oncology, Barcelona, Spain, expert on the ESMO Faculty on Lung cancer, said: “Cell-free DNA detected in the bloodstream of cancer patients represents an excellent tool to examine genetic alterations that are usually  found through tumour tissue testing. This represents one of the most astonishing phenomena in biology.”

“The results of this study validate that the presence of EGFR mutations in circulating DNA from plasma or serum (fractions obtained from whole blood) can be detected in around half of the patients.”

Already, since this study was performed, improvement of techniques have seen the sensitivity of tests for EGFR mutations in circulating tumour DNA increase further, Rosell noted.

“This work paves the way for further studies and expands the routine use of examining mutations such as EGFR mutations as part of cancer patient care,” Rosell said. European Society for Medical Oncology

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Clinical Mass Spectrometry Congress Hosted by MSACL to Present Recent Advances

, 26 August 2020/in E-News /by 3wmedia

This September 8-11, the Association for Mass Spectrometry: Applications to the Clinical Lab (MSACL) will be hosting the 2nd European Congress at the Salzburg Congress Center in Austria. The congress will be prefaced by two days of Short Courses covering the topics of Getting Started with Quantitative LC-MS/MS in the Diagnostic Laboratory, Development and Validation of Quantitative LC-MS/MS Assays for Use in Clinical Diagnostics, Whole-Cell Pathogen Detection by MALDI-TOF MS and Advanced Proteomics Approaches, and A Newbie’s Introduction to the R Statistical Programming Language. The congress will open with an Exhibitor and Poster reception on Wednesday evening to kick-off the main scientific program presented over the following two days, including 36 research-based Podium presentations and Plenary presentations from Linda Thienpont, Douglas Kell, Andy Hoofnagle, Wiebke Arlt and Donald Hunt. Notably, the scientific program will also include a Newbies / Fundamentals track covering introductory topics such as the basic mass spectrometry, compound-specific tuning, developing MRM transitions, LC method development, and sample preparation basics. 

From inception, it has been MSACL’s mission to educate with the aim of developing an understanding of the value of mass spectrometry in the clinic, as well as technical aspects of use, while supporting the growth and attendance of young scientists who are shaping the field. To this end, MSACL provides an expansive Travel Grant program to recruit the attendance of Young Investigators, Trainees and Lab Directors. This year, MSACL is providing 144 grants for the 2015 US conference and 68 for the upcoming 2015 EU congress – approximately 15% of attendees. This investment in the future is supported by the generosity and foresight of Thermo Scientific, Waters, Shimadzu and Cambridge Isotope Labs, companies committed towards driving education, in order to accelerate the implementation of mass spectrometry in the clinic.

View the MSACL 2015 EU Preliminary Program at https://www.msacl.org/2015_EU_program.

Poster abstracts are being accepted for consideration through July 15.

If you are interested in attending the US version of MSACL, Travel Grant applications as well as Podium and Poster Abstracts may be submitted for the MSACL 2016 US conference to be held in Palm Springs, California from February 21-25, 2016.

MSACL is a non-profit educational association dedicated to the advancement of mass spectrometry in the clinical laboratory. More information is available at http://www.msacl.org

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