Scientists develop new strategy that rapidly quantifies transmissibility of COVID-19 variants

A team of researchers has developed a new nanomechanical technique for fast, one-step, immune-affinity tests, which can quantify the immune response induced by different COVID-19 variants in serum. Their technique provides a new tool for tracking infection immunity over time and for analysing new vaccine candidates.
Led by Professor Martin Hegner, Principal Investigator in the Trinity Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN) and Trinity College Dublin’s School of Physics, the team’s specific quantitative assay enables direct classification of variant-binding properties for screening emerging variants.
The major advantage of the newly developed technique with respect to (existing, commonly used) ELISA tests is that while it is equally sensitive — with added single amino-acid resolution — and able to directly detect multiple variants by in situ differential analysis, it can also do so in a mere fraction of the time.
Professor Hegner and his co-workers focused on COVID-19 variants of concern and their generated humoral immune response. Humoral immunity is an antibody-mediated response that occurs when foreign material is detected in the body. Given that the COVID-19 virus has developed substantial mutations in the spike protein this can undermine the efficacy of current vaccines and monoclonal antibody therapies.
The technology developed by Professor Hegner and his team can assist vaccine development studies in phase 1-3, with focus on comparing protection patterns and analysing novel vaccine candidates.
The team’s findings have been published in the interdisciplinary journal Nanoscale Advances, which is a high-impact, peer-reviewed journal of the Royal Society of Chemistry.
Professor Hegner said:
“Our measurements match the statistical analysis of, for example, the transmissibility of the alpha-variant that can otherwise only be gained by analysing the development of the disease proliferation within a population over weeks. We believe that this new technology can improve and speed up the public health guidance process.
“The direct technique greatly simplifies the preparation protocol that in ELISA includes many washings and waiting steps, hence reducing the amount of consumables needed and thus the relative cost. It will therefore be well suited to use in emergency situations.”
Story Source:
Materials provided by Trinity College Dublin. Note: Content may be edited for style and length.

Read more →

Fluorescent spray lights up tumors for easy detection during surgery

The prognosis for a cancer patient who undergoes surgery is better if the surgeon removes all of the tumor, but it can be hard to tell where a tumor ends and healthy tissue begins. Now, scientists report in ACS Sensors that they have developed a fluorescent spray that specifically lights up cancerous tissue so it can be identified readily and removed during surgery.
Surgeons often use sight and touch to identify cancerous tissue, but this approach can miss small tumors, as well as diseased cells at the margins between a tumor and healthy tissue. Fluorescence-guided surgery is an emerging technology that could enhance this difference. The method relies on fluorescent probes that target cancerous tissue and heighten its visibility. But some of these compounds must be administered many hours or days before surgery — sometimes necessitating a long hospital stay — and they might not reveal tiny tumors. In addition, these compounds can require a large dose if they’re injected, or a washing step to get rid of excess dye if they’re applied to the tumor site. So Ching-Hsuan Tung and colleagues set out to develop a fluorescent probe to rapidly visualize diseased tissue, even on a small scale, when sprayed on a surgical site or injected.
The researchers started with a compound they had previously designed that remains nearly invisible at the neutral pH of healthy tissue, but fluoresces brightly in the near-infrared range in the acidic environment of tumors. That initial compound linked a pH-sensitive amino group with a cyanine fluorophore. It worked when injected, but didn’t produce a signal when applied as a spray, so the team replaced some of its methyl groups with isopropyl groups. That made the new compound more responsive to the acidic tumor environment. When sprayed, it delineated tumor edges in mice within minutes, without the need for washing. And when injected in the abdomen of mice, it illuminated ovarian tumors as small as 1 mm in diameter in an hour. The researchers say the compound could enhance a surgeon’s ability to visualize and remove cancerous tissue.
The authors acknowledge funding from the National Institutes of Health. Tung and other authors are co-inventors of a patent application for the fluorescent spray. Two of the authors are employees of Molecular Targeting Technologies Inc.
Story Source:
Materials provided by American Chemical Society. Note: Content may be edited for style and length.

Read more →

Heartburn drugs may have unexpected benefits on gum disease

The use of heartburn medication is associated with decreased severity of gum disease, according to a recent University at Buffalo study.
The research found that patients who used proton pump inhibitors (PPIs) — a class of drugs commonly prescribed to treat heartburn, acid reflux and ulcers — were more likely to have smaller probing depths in the gums (the gap between teeth and gums). When gums are healthy, they fit snuggly against the teeth. However, in the presence of harmful bacteria, the gap deepens, leading to inflammation, bone loss and periodontitis, also known as gum disease.
The findings, published last month in Clinical and Experimental Dental Research, may be linked to the side effects of PPIs, which include changes in bone metabolism and in the gut microbiome, says lead investigator Lisa M. Yerke, DDS, clinical assistant professor in the Department of Periodontics and Endodontics at the UB School of Dental Medicine.
“PPIs could potentially be used in combination with other periodontal treatments; however, additional studies are first needed to understand the underlying mechanisms behind the role PPIs play in reducing the severity of periodontitis,” says Yerke.
Additional investigators include first author and UB alumnus Bhavneet Chawla, and Robert E. Cohen, DDS, PhD, professor of periodontics and endodontics in the UB School of Dental Medicine.
The study sought to determine whether a relationship exists between PPI use and gum disease. The researchers analyzed clinical data from more than 1,000 periodontitis patients either using or not using PPIs. Probing depths were used as an indicator of periodontitis severity.
Only 14% of teeth from patients who used PPIs had probing depths of 6 millimeters or more, compared to 24% of teeth from patients who did not use the medication. And 27% of teeth from patients using PPIs had probing depths of 5 millimeters or more, compared to 40% of teeth from non-PPI users, according to the study.
The researchers theorized that PPIs’ ability to alter bone metabolism or the gut microbiome, as well as potentially impact periodontal microorganisms, may help lessen the severity of gum disease.
Additional studies are under development to determine if this relationship can be found in other populations of patients with gum disease, and to learn to what extent the relationship can be directly attributed to PPIs, says Yerke.
Story Source:
Materials provided by University at Buffalo. Original written by Marcene Robinson. Note: Content may be edited for style and length.

Read more →

Minutes matter: Policies to improve care for deadliest heart attacks

The time it takes from the moment a heart attack starts to the delivery of definitive treatment is a determining factor in a patient’s ability to survive. The American Heart Association, the leading voluntary health organization devoted to a world of longer, healthier lives for all, today issued public policy guidance to address systems changes for patients with the most severe type of heart attack.
The policy statement, “Systems of Care for ST-Segment-Elevation Myocardial Infarction (STEMI),” published today in the Association’s flagship journal Circulation, sets forth recommendations for how the ideal cardiac system of care should be designed and implemented to ensure that patients with STEMI receive the best evidence-based care at each stage in their illness.
Improvements in cardiac systems of care are necessary to ensure scientific advances in the treatment and care of patients to improve patient outcomes. The policy statement comes as STEMI systems of care have seen significant improvement resulting from the American Heart Association’s Mission: Lifeline program, a national initiative to advance systems of care for patients with STEMI and other acute disease states. Since Mission: Lifeline was established in 2007, it has significantly increased timely access to percutaneous coronary intervention for patients with STEMI, resulting in declining morbidity and mortality rates and increased research that has improved understanding of effective STEMI systems of care.
However, significant barriers and opportunities remain that require changes and improvements in public policy.
“We can save more lives from the most serious heart attacks, and we know the policy changes that will allow us to do so,” said Alice Jacobs, M.D., FAHA, the statement’s lead author and vice chair for clinical affairs in the Department of Medicine at Boston University Medical Center. “From ensuring patients suffering a heart attack can access 9-1-1 emergency services, to guaranteeing they receive needed services including EMS triage and post-acute care, policy solutions can improve the efficiency of care protocols and save time at critical junctures to ensure every STEMI patient has the best chance of survival.”
Fully 85% of the U.S. population lives within reach of a STEMI system of care.[1] However, 40% of patients do not call 9-1-1 and instead go to their local emergency department.[2],[3] This can delay life-saving medical intervention by more than 30 minutes on average, decreasing the ability of coordinated response and care across all intervention teams and increasing the likelihood of acute heart failure or cardiac arrest.[4] Studies show that although 41% of patients arriving at the emergency room with chest pain/angina-equivalent symptoms receive an echocardiogram (ECG) within 10 minutes, women experience significant delays (nearly 20 minutes longer than for men). Regional STEMI systems perform better at decreasing sex and age disparities.[5],[6],[7]
“It takes our health care system an average of nearly 20 minutes longer to provide women the same emergency cardiac care they provide men. This is unacceptable, at a life-or-death moment,” said Jessica Zègre-Hemsey, Ph.D., R.N. statement co-author and associate professor of nursing at the University of North Carolina at Chapel Hill. “Taking the best care of patients requires a strategic policy playbook that ensures everyone on the care delivery team knows how to maximize a patient’s chances of survival and reduce health inequities.”
The statement’s specific policy recommendations include: Public Awareness and Community Education: Increase culturally diverse community education programs and mass communications on signs and symptoms of heart attacks, the need to immediately call 9-1-1 and the importance of bystander CPR. Entry Points and Transport: State protocols for EMS transport should include destination practices and training for STEMI support and EMS agencies should be engaged in quality improvement and be represented at regional quality improvement meetings. Direct to Cath Lab: Improve plans for both referring and receiving hospitals as well as transport between hospitals to collaboratively perform evidence-based, lifesaving protocols to activate the cardiac catheterization lab, prior to arrival when appropriate. Transitions in Care: Opportunities exist for improvement at each juncture of a patient’s care, from pre-hospital care to discharge to cardiac rehab plans and systems changes will save lives. Post-Heart Attack Care: Recovery care and prevention of additional heart attacks should be standard practice within all health care systems and in accordance with guidelines for accountability and quality improvement. Health insurance plans and other third-party payers should provide incentives for participation in cardiac rehabilitation. Special Considerations for Telemedicine and Rural Health: To best reach the 15% of people in America who are not within reach of a STEMI system of care, particularly in rural areas, telemedicine protocols can expedite appropriate care. Rural hospitals should collaborate with regional STEMI receiving centers for access to expertise and support, develop prehospital response and triage protocols and should establish rapid interfacility transport mechanisms for higher levels of acute care. Financial Considerations: There should be support for the global reimbursement of the system of care for the patients with STEMI with recognition of each of the components, including referring hospital, receiving center, EMS transport and transfer and ancillary services.This policy statement was prepared by the American Heart Association Advocacy Coordinating Committee.
Co-authors are Alice K. Jacobs, MD, FAHA, Chair; Murtuza J. Ali, MD; Patricia J. Best, MD; Mark C. Bieniarz, MD; Vincent J. Bufalino, MD, FAHA; William J. French, MD; Timothy D. Henry, MD; Lori Hollowell, MHIT, BSN, RN; Edward C. Jauch, MD, MS, FAHA; Michael C. Kurz, MD, MS, FAHA; Michael Levy, MD; Puja Patel, MS, MBA; Travis Spier, RN, MSN, NR-Paramedic, FP-C; R. Harper Stone, MD; Katie L. Tataris, MD, MPH; Randal J. Thomas, MD; and Jessica K. Zègre-Hemsey, PhD, RN. Authors’ disclosures are listed in the manuscript.

Read more →

Tackling the collateral damage from antibiotics

Antibiotics help us to treat bacterial infections and save millions of lives each year. But they can also harm the helpful microbes residing in our gut, weakening one of our body’s first lines of defence against pathogens and compromising the multiple beneficial effects our microbiota has for our health. Common side effects of this collateral damage of antibiotics are gastrointestinal problems and recurrent Clostridioides difficile infections. They also include long-term health problems, such as the development of allergic, metabolic, immunological or inflammatory diseases.
Researchers from the Typas group at EMBL Heidelberg, the Maier lab at the Cluster of Excellence ‘Controlling Microbes to Fight Infections’ at the University of Tübingen, and collaborators have analysed the effects of 144 antibiotics on our most common gut microbes. The study published in the journal Nature substantially improves our understanding of antibiotics’ effects on gut microbes. It also suggests a new approach to mitigating the adverse effects of antibiotics therapy on the gut microbiome.
The human gut harbours an intricate community of different microbial species as well as many viruses, collectively referred to as the gut microbiome. Together, they enable us to use nutrients more efficiently and hinder pathogenic bacteria from settling in our gut. However, when we treat a bacterial infection with antibiotics, there’s a risk of damaging the gut microbiome.
“Many antibiotics inhibit the growth of various pathogenic bacteria. This broad activity spectrum is useful when treating infections, but it increases the risk that the microbes in our gut are targeted as well,” explained Lisa Maier, DFG Emmy Noether group leader at the University of Tübingen. Maier is an alumna of the Typas lab and one of the two lead authors of the study.
If certain gut bacteria are harmed more than others, antibiotics therapy can lead to an imbalance in our microbiota composition, commonly referred to as dysbiosis. Diarrhea is a common short-term effect, while allergic conditions such as asthma or food allergies and obesity are possible long-term consequences. The fact that antibiotics are also active against gut microbes has been known for a long time, but their effects on the large diversity of microbes we carry in our gut had not yet been studied systematically, mostly due to technical challenges.
“So far, our knowledge of the effects of different antibiotics on individual members of our gut microbial communities has been patchy. Our study fills major gaps in our understanding of which type of antibiotic affects which types of bacteria, and in what way,” said Nassos Typas, Senior Scientist and Group Leader at EMBL Heidelberg.

Read more →

Stem cell transplant: How skin-derived T cells can damage other organs

More than 40,000 allogeneic hematopoietic stem cell transplants are carried out worldwide every year, mostly for patients suffering from leukemia or other diseases of the hematopoietic system. Very often, the so-called graft-versus-host reaction occurs, an inflammatory disease that can affect different organs and is caused by an unwanted defense reaction of the donor cells and the body’s own T cells. Scientists at CeMM, Medical University of Vienna and LBI-RUD, led by Georg Stary, now show how these endogenous, tissue-derived T cells enter other organs, such as the intestine, via the blood and contribute to inflammation there. The study provides important approaches to better therapy in stem cell transplantation and new diagnostic options. It was published in the Journal of Experimental Medicine.
Stem cell transplants are an important, essential treatment method, especially for leukemia patients. According to the Transplant Annual Report 2020, 630 of these transplants were performed in Austria alone in 2019. In this process, all blood cells of the affected patient are first killed by chemotherapy and radiation, and then replaced by healthy bone marrow or blood stem cells from a donor. About half of the patients develop inflammatory skin diseases with serious consequences after the transplantation. T-cell-mediated rejection is one of the main causes of death after hematopoietic stem cell transplantation. In a previous study, a team of researchers led by dermatologist Georg Stary at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, the Medical University of Vienna and the Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases was able to identify a mechanism that triggers this graft-versus-host reaction (graft-versus-host disease, GVHD). In skin samples taken from patients before and after transplantation, Stary and study author Johanna Strobl (MedUni) were able to show that host-derived T cells in the skin tissue are responsible for the inflammatory reactions.
Tissue-resident T cells of the skin migrate into the blood
In their current study, using the new model, Strobl and co-author Laura Marie Gail (CeMM/LBI-RUD) show that these tissue-resident T cells of the skin can be found in the blood of stem cell transplant patients. “The migration of the inflammatory, tissue-derived skin T cells into the bloodstream poses a risk of the skin inflammation being passed on to other organs. Especially in the intestine, which is often affected by GVHD, we found an astonishing number of cells that originally came from the skin,” say the study authors.
Deactivation of T cells as possible approach to improving therapy
For their study, Strobl, Gail and Stary investigated circulating T cells in the blood using samples from stem cell transplant patients. Using a special tracking method, the scientists were able to distinguish exactly which T cells were from the donor and which were from the patient. Research group leader Stary explains: “After all blood cells had already been killed by chemotherapy, we were able to conclude that the detected T cells could only come from the tissue. With the help of various markers, they could be traced back to the skin.”
Blood sample instead of biopsy
The study also provides indications for an additional important diagnostic aspect. The study authors were able to observe that more circulating T cells in stem cell transplant patients are detectable in the blood, depending on the clinical picture. Accordingly, it is quite conceivable that in the case of skin or tissue diseases, a blood analysis could be carried out and the phenotype of the skin-derived T cells in the blood evaluated instead of the time-consuming and often unpleasant sampling of the affected area. “This procedure would be a kind of ‘liquid biopsy’ in the case of inflammatory reactions in the tissue,” say the study authors.

Read more →

Increases in extreme humid-heat disproportionately affect populated regions

The world is not only getting hotter but also more humid and new research by Washington State University scientists shows people living in areas where humid-heat extremes are already a significant hazard are bearing the brunt of the impact.
Their study, published earlier this month in the journal Geophysical Research Letters, presents the timing, frequency, and severity of extreme humid-heat and dry-heat events and recent trends using hourly data at a spatial resolution of ~ 25 km or 15.5 mi.
“We identify a greater increase in population exposure to humid-heat as compared to dry-heat, emphasizing the importance of understanding humidity changes in a warming world,” said study lead author Cassandra Rogers, a postdoctoral research associate in the WSU Vancouver School of the Environment.
Most of Europe, northern South America, Africa, the Arabian Peninsula and the island chains between the Indian and Pacific Oceans, as well as the Northern Hemisphere oceans, have experienced statistically significant increases in both dry and humid-heat extremes, according to the researchers’ analysis.
However, a few regions of the planet showed trends that are particularly worrisome.
“For example, increases in the occurrence of humid-heat were strongest over highly populous regions in South and Southeast Asia and southeastern U.S. where changes in dry-heat frequency, as measured by temperature alone, are small or non-significant,” said study coauthor Deepti Singh, an assistant professor in the WSU Vancouver School of the Environment.

Read more →

Cervical myelopathy screening focusing on finger motion using noncontact sensor

Cervical myelopathy (CM)(1) results from compression of the spinal cord in the neck and causes difficulty moving the fingers and unsteady gait. As patients with early-stage CM have minimal subjective symptoms and are difficult for non-specialists to diagnose properly, the symptoms can be aggravated before patients are diagnosed with CM by a specialist. Therefore, the development of screening tools is required to realize the early diagnosis and treatment of CM.
A research team led by Drs. Koji Fujita, a lecturer at Tokyo Medical and Dental University, and Yuta Sugiura, an associate professor at Keio University, combined a finger motion analysis technique using a non-contact sensor and machine learning (2) to develop a simple screening tool for CM.
In this study, the team focused on changes in finger motion caused by CM. In the 10-second grip and release test, which is a conventional diagnostic test for CM, a subject repeats grip and release actions as many times as possible in 10 seconds. The test simply measures the number of grip and release actions and does not focus on changes in finger movements characteristic for patients with CM, such as wrist movements to compensate for difficulty moving the finger. Leap Motion (Ultraleap Ltd.), a sensor capable of real-time measurement of finger movements, can be used to extract such movements more precisely. The researchers expected that CM can be predicted using machine learning combined with the Leap Motion sensor. A subject sitting in front of Leap Motion connected to a laptop computer with arms extended was instructed to grip and release the fingers 20 times as rapidly as possible. Finger movements during this test were captured by the Leap Motion sensor, displayed on its screen in real time, and recorded as data. They recruited 50 patients with CM and 28 subjects who did not have CM. Time-series data on their finger movements acquired by Leap Motion were converted into frequency domains, which were subjected to machine learning using a support vector machine. Finally, the accuracy of the results was high as indicated by a sensitivity (3) of 84.0%, a specificity (4) of 60.7%, and an area under the curve (5) of 0.85. This level of accuracy is equivalent or superior to that of CM diagnosis by specialists based on physical findings.
The tool developed by the team allows for non-specialists to screen people for the possibility of having CM. The screening test results can be used to encourage those with suspected CM to seek specialist’s attention for early diagnosis and early treatment initiation. A goal of this research is to prevent disease aggravation which can cause decline in the physical functioning and social loss.
This research has been conducted under the JST Strategic Basic Research programs, AIP Accelerated PRISM research and Precursory Research for Embryonic Science and Technology (PRSTO).
(1) Cervical myelopathy (CM): CM is a disease resulted from compression of the spinal cord in the neck. CM patients are formally diagnosed with cervical spondylotic myelopathy or cervical ossification of the posterior longitudinal ligament depending on the cause.
(2) Machine learning: A mechanism through which computers learn about a given task and automatically calculate the results.
(3) Sensitivity: The proportion of subjects with a disease who test positive for the disease.
(4) Specificity: The proportion of subjects without a disease who test negative for the disease.
(5) Area Under Curve (AUC): A measure for evaluation of test methods, ranging from 0 to 1. An AUC closer to 1 means that the test method has high accuracy.
Story Source:
Materials provided by Japan Science and Technology Agency. Note: Content may be edited for style and length.

Read more →

New technique combines single-cell and metagenomic analyses to characterize microbes

The microbial inhabitants of the human body, collectively known as the “human microbiome,” play an integral role in maintaining the health of the body. These microbes often reside in harmony, while also aiding normal physiological processes. However, any imbalance in their populations can trigger various pathological conditions. Understanding these host-microbe relationships in health and disease is therefore crucial.
Metagenomics, an advanced DNA sequencing technique, enables the direct extraction and in silico (or computer-simulated) characterization of genetic material from mixed microbial populations at once, while bypassing the cumbersome task of isolating and culturing different bacterial species from the mixture. While this technique is useful in getting a broader picture regarding the microbiome, finer details across closely related species can be missed, thereby contributing to bias and inaccuracy.
Single-cell (sc) genomics is a promising alternative approach that enables the recovery of genomes from individual cells. In the larger picture, however, this approach can result in incompleteness of the assembled genomes given the smaller DNA fragment sizes, compared to the conventional metagenomics approach.
In a pioneering collaborative study between Waseda University, Japan, and bitBiome, a startup initiative from Waseda University, a team of researchers including Associate Professor Masahito Hosokawa tested a hybrid approach combining conventional metagenomics with sc-metagenomics that can bridge the gaps in both the techniques. “Bacterial genomes reconstructed from metagenomic analyses alone are imperfect and contain errors. We have developed a novel single cell metagenomics integration framework, termed SMAGLinker, which determines the genome sequence of each cell individually. Using this method, we aim to obtain accurate bacterial genomes comprehensively, which has been a challenge in the past,” explains Hosokawa, who is also the founder of bitBiome.
They first generated single-cell amplified genomes (SAG) using microfluidic technology (an advanced DNA amplification technique), for the human gut and skin microbiota, as well as for a “mock” microbial community containing known bacteria for validation purposes. Next, they analyzed and clustered the sequences, using a method called “contig binning.” They integrated this analysis with metagenome-assembled genomes (MAG) to improve the overall coverage and binning accuracy.
On comparing the integrated approach with the conventional metagenomics approach, they found that the former showed higher accuracy and precise binning along with a notably higher genome recovery rate (including rRNA, tRNA and plasmids), compared to the conventional approach.
Using SMAGLinker, the researchers could construct a large number of high-quality genomes from the gut and skin microbiota. Moreover, genomes obtained using this integrated approach spanned a larger number of bacterial genera compared to the conventional approach, indicating better coverage of bacterial diversity.
Diving deeper, the researchers also obtained better resolution of intra-species diversity using SMAGLinker. While the conventional metagenomic approach revealed only one genome of the bacterium Staphylococcus hominis, contaminated with other Staphylococcus species genomes, the integrated approach revealed two independent strains harboring distinct plasmids from the same skin microbiota sample. They were also able to successfully validate their findings using the mock microbial sample.
In summary, SMAGLinker is a powerful tool that can improve the accuracy and quality of genome recovery and resolution of closely related genomes in complex microbial mixtures. The authors are excited about the potential ramifications of their findings. “Human commensal bacteria are deeply related to human health and understanding host-microbe interactions is important for designing novel medical treatments as well as for industrial and environmental applications. We are hopeful that this technology can be extended across diverse research disciplines for accurate microbial characterization,” concludes Hosokawa.
Story Source:
Materials provided by Waseda University. Note: Content may be edited for style and length.

Read more →

Most commonly mutated gene in all cancers revealed

For the past fifteen years, cancer researchers have been using DNA sequencing technology to identify the gene mutations that cause the different forms of cancer. Now, Salk Assistant Professor Edward Stites and his team of computational scientists have combined gene mutation information with cancer prevalence data to reveal the genetic basis of cancer in the entire population of cancer patients in the United States.
The study, published in Nature Communications on October 13, 2021, reveals how common each gene in the genome is mutated within the cancer patient population. The findings could help guide genetic research to develop more effective treatments than presently available.
“The paper answers a very basic question: what are the most commonly mutated genes in human cancer?” says Stites, who is also a physician as well as holder of the Hearst Foundation Developmental Chair. “Surprisingly, this question had not been answered.”
Genetic mutations play a fundamental role in the development and growth of cancers. They can also be targeted for effective treatment. However, while many studies have identified the mutations involved in certain cancers, like breast cancer or lymphoma, no one had ever managed to combine the data in a way that could reveal which mutations are most common in the entire cancer patient population. Every cancer is different, and this makes it challenging to determine which cancer-causing genes and which drug targets should be prioritized for further study.
In the new study, Stites’ team combined data sets from genomic and epidemiological cancer studies to determine what percentage of all cancer patients will have any gene mutated. Although this task initially seemed straightforward, they soon discovered why the question had not been answered before: genomic and epidemiological studies do not use a common naming system for the various cancers. For example, some researchers classified cancers by location on the body while others grouped them by tumor type, and many used a combination of the two. This made it difficult to align the data sets, which was critical for determining how common the different mutations were.
To overcome the challenge, the scientists carefully analyzed more than 200 studies and individually reviewed and reclassified each cancer according to a consistent naming system. They then compared the data sets, taking into account the fact that some cancers are more common than others. When they analyzed the data, they found that some widespread beliefs were incorrect. For example, KRAS is an important cancer-promoting gene that was believed to be mutated in 25% of all cancers; rather, it was found to be involved in only about 11% of all cancers. This was part of a trend where individual genetic mutations were found to be less common than previously thought.
“These findings speak to a need to reevaluate where people have been focusing their time, attention and resources,” says Stites. “We should be balancing research efforts more evenly across the different genetic causes of cancer, and we should be balancing the development of new cancer treatments more evenly across the different major treatment strategies, because the concept of targeting specific mutations will be less impactful than has been assumed.”
Other authors on the study include Gaurav Mendiratta, Meraj Aziz, David Liarakos and Melinda Tong of Salk and Eugene Ke of the University of Virginia.
The research was supported by the Pioneer Fund, the National Institutes of Health and the Melanoma Research Alliance.
Story Source:
Materials provided by Salk Institute. Note: Content may be edited for style and length.

Read more →