Uncategorized

Promising new method for rapidly screening cancer drugs

Dr. Expert No Comments

As Rotello and his doctoral graduate student Le Ngoc, one of the lead authors, explain, to discover a new drug for any disease, researchers must screen billions of compounds, which can take months. One of the added keys to bringing a new drug to market, they add, is to identify how it works, its chemical mechanism. “Rapid determination of drug mechanism would greatly streamline the drug discovery process, opening the pipeline of new therapeutics,” Ngoc says.

She adds, “Drugs with different mechanisms cause changes in the surface of cells that can be read out using the new sensor system. We found that each drug mechanism generated a unique pattern, and we used these cell surface differences to quickly profile different drug mechanisms.” Details of this work appear in the current issue of Nature Nanotechnology.

To expedite drug screening, the research team, which in addition to the chemists includes a UMass Amherst cognitive scientist and a materials scientist from Imperial College, London, developed a new, signature-based approach using a gold nanoparticle sensor system and three differently labeled proteins by color: blue, green and red. Using an engineered nanoparticle and three fluorescent proteins provides “a three-channel sensor that can be trained to detect subtle changes in cell surface properties,” the authors note.

Drug-induced cell surface changes trigger different sets of fluorescent proteins to turn on together, offering patterns that identify specific cell death mechanisms. The new nanosensor is generalizable to different cell types and does not require processing steps before analysis. So, it offers a simple, effective way to expedite research in drug discovery, toxicology and cell-based sensing, the researchers add.

Some signature-based drug screening using traditional biomarkers exists today, but it requires multi-step cell processing and special equipment, limiting its usefulness the authors point out. With their three-channel, gold nanoparticle sensor platform, Rotello and colleagues solve those challenges and enhance accuracy. Further, they say, “the information-rich output allows the determination of a chemotherapeutic mechanism from a single measurement, providing answers far more quickly (in minutes) than current methods, using standard laboratory instrumentation.”

This invention could have a substantial potential impact on the drug discovery pipeline, says Ngoc. “The sensor is not only able to profile mechanisms for individual drugs but also determine the mechanisms of drug mixtures, that is, drug ‘cocktails’ that are an emerging tool with many therapies,” she adds.

Rotello emphasizes, “While we have decent knowledge of individual drugs, we still have a lot to learn about the mechanisms of combination therapies. In addition to drug screening, the simplicity and speed of this enabling technology holds the promise to greatly accelerate the search for effective cancer treatments, and provides a step forward in areas such as toxicology, where the safety of thousands of uncategorized chemicals needs to be assessed.

The researchers point out that their new sensor system offers “a potential way forward for toxicology, providing a viable method to classify the tens of thousands of commercial chemicals for which no data are available.”

source : http://www.sciencedaily.com/releases/2014/12/141215114238.htm

New, more accurate way of imaging lung cancer tumors

Dr. Brilliant No Comments

Their study appeared in the March issue of Pattern Recognition.

Lung cancer is the deadliest cancer in men and women. According to the National Institutes of Health, the five-year survival rate (16.3 percent) is worse than many other cancers, such as colon (65.2 percent), breast (90.0 percent) and prostate (99.9 percent). More accurate tumor imaging, in terms of tumor feature extraction, could improve diagnostic and predictive accuracy

“The new method we developed will improve diagnostic accuracy and make more individualized cancer care possible,” said study senior author Robert J. Gillies, Ph.D., chair of the Department of Cancer Imaging and Metabolism at Moffitt. “It will improve our ability to quantify changes in cancer and respond appropriately with therapy.”

Tumor segmentation was previously a difficult task because of the diverse composition of cancer lesions when compared to normal tissues. The new segmentation method marks a great improvement over a previously used manual method, said the researchers.

“A common approach to delineate lung cancer tumors is for the radiologist or radiation oncologist to manually draw the boundary of the tumor,” explained Gillies. “This method is variable and operator-dependent. A highly automatic, accurate and reproducible lung tumor delineation algorithm would offer a significant advance.”

Their development of SCES offers that advancement, and because the process is automated, it requires less time and effort.

“A big advantage with single click ensemble segmentation is that it only requires one human interaction – the manual seed input. This is when the radiologist or radiation oncologist places the seed points in the tumor area,” Gillies said. “With SCES, lesion delineation was accurate and consistent, and the lung segmentations workload was greatly reduced.”

The new algorithm uses the original by incorporating the original seed point to define an area within which multiple seed points are automatically generated. Ensemble segmentation can then be obtained from the multiple regions.

According to the researchers, the measurement can be used to determine if the tumor is increasing or decreasing in size, as well as describe features such as shape and texture.

“With this method, all the radiologist has to do is click their mouse on a tumor and the program will automatically perform an accurate measurement,” explained Hall. “We also demonstrated that this approach reduces inter-observer variability with significantly fewer operator interactions when compared with the original algorithm.”

The capabilities of the new algorithm were successfully tested on a large patient tumor imaging data set.

Their work was funded by National Institutes of Health Grant 1U01 CA 143062-01

source : http://www.sciencedaily.com/releases/2013/05/130502115527.htm

Focus on STD, not cancer prevention, to promote HPV vaccine use

Dr. Brilliant No Comments

These results go against the conventional wisdom that scaring women about the possibility of cancer is the best way to get them vaccinated.

The failure of that cancer-threat message may be one reason that fewer than 20 percent of adolescent girls in the United States have received the HPV vaccine, said Janice Krieger, lead author of the study and assistant professor of communication at The Ohio State University.

"Young women don’t respond strongly to the threat of cervical cancer," Krieger said.

"They seem to be more worried about getting an STD. That’s the way we should try to encourage them to get the HPV vaccine."

The vaccine — most commonly sold under the brand name Gardasil — prevents the types of HPV, or human papillomavirus, that cause most cases of cervical cancer and most cases of genital warts, a sexually transmitted disease.

Krieger conducted the study with Melanie Sarge of Texas Tech University. It appears in a recent issue of the journal Health Communication.

Many early studies of how to sell the benefits of the HPV vaccine found that the message that it prevents cancer was effective. But these studies often involved women of all ages, from adolescence to old age. The problem, though, is that the vaccine is targeted to women under the age of 26.

"Cancer is something people start to worry about later in life, not when they’re in high school and college. We decided to do a clean study that compared what message worked best with college-aged women versus what worked with their mothers," Krieger said.

Participants in the study included 188 female college students (average age of 22) and 115 of their mothers (average age of 50).

The mothers and students both received a packet of materials that included a questionnaire and a pro-vaccine message. The student message recommended talking to a doctor about the HPV vaccine, and the parent message recommended encouraging their daughter to talk to a doctor.

Two different messages were created. Half of the mothers and students received a message sheet about the vaccine with a large headline that read, "Prevent cervical cancer." The other half received a similar message, but with the headline declaring, "Prevent genital warts." A text box on the sheet also re-emphasized either the cancer or the genital warts message.

Participants then filled out the questionnaire, which asked a variety of questions that included how they felt about the threat of HPV and whether they felt they (or their daughter) could talk to a doctor about receiving the vaccine.

Results showed that the message emphasizing the vaccine’s effectiveness at preventing genital warts was a clear winner with the young women.

Compared to those who received the cancer prevention message, young women who read that the vaccine prevented genital warts were more likely to say they intended to talk to their doctor about the vaccine. They also said they felt more comfortable talking to their doctor about the vaccine.

"Preventing cancer was not a big motivator," Krieger said.

Overall, the findings showed that scaring young women into getting the vaccine doesn’t seem to be a good strategy.

Young women who perceived HPV as a bigger threat to their health than others, or who thought they were more likely to get the virus, were not consequently more likely to say they would get the vaccine or talk to their doctor.

"Our results suggest it is more important to get women to feel comfortable talking to their doctor about the vaccine," she said. "Fear doesn’t work. They need to feel it is not difficult or embarrassing to discuss the vaccine with their doctor. That’s the best way to encourage them to be vaccinated."

The researchers expected that the mothers in the study would be more likely to talk to their daughters about getting the HPV vaccine if they read the cancer prevention message rather than the STD prevention message.

Part of their reasoning was that the mothers, being older, were at a stage in their life when cancer was a bigger issue for them, Krieger said. But they also thought mothers would not feel comfortable about an STD message that assumes that their daughters were sexually active.

However, it turned out that the mothers weren’t affected by which of the messages they received.

"We believed that mothers would react negatively to the message about preventing genital warts, but that wasn’t supported. Mothers reacted similarly to the genital warts and cancer prevention messages. It suggests that if we focus on the prevention of genital warts in our messages to daughters, it may not mean we have lost the mothers."

Krieger said the results should encourage policymakers, doctors and others to shift their messages to young women concerning the HPV vaccine.

"Cancer may seem to be the more serious issue to some older adults, but it is not the top concern for young women," she said.

source : http://www.sciencedaily.com/releases/2013/05/130502120439.htm

Adult cells transformed into early-stage nerve cells, bypassing the pluripotent stem cell stage

Dr. Brilliant No Comments

Bypassing the ultra-flexible iPSC stage was a key advantage, says senior author Su-Chun Zhang, a professor of neuroscience and neurology. "IPSC cells can generate any cell type, which could be a problem for cell-based therapy to repair damage due to disease or injury in the nervous system."

In particular, the absence of iPSC cells rules out the formation of tumors by pluripotent cells in the recipient, a major concern involving stem cell therapy.

A second advance comes from the virus that delivers genes to reprogram the adult skin cells into a different and more flexible form. Unlike other viruses used for this process, the Sendai virus does not become part of the cell’s genes.

Jianfeng Lu, Zhang’s postdoctoral research associate at the UW-Madison Waisman Center, removed skin cells from monkeys and people, and exposed them to Sendai virus for 24 hours. Lu then warmed the culture dish to kill the virus without harming the transforming cells. Thirteen days later, Lu was able to harvest a stem cell called an induced neural progenitor. After the progenitor was implanted into newborn mice, neural cells seemed to grow normally, without forming obvious defects or tumors, Zhang says.

Other researchers have bypassed the pluripotent stem cell stage while turning skin cells into neurons and other specialized cells, Zhang acknowledges, but the new research, just published in Cell Reports, had a different goal. "Our idea was to turn skin cells to neural progenitors, cells that can produce cells relating to the neural tissue. These progenitors can be propagated in large numbers."

The research overcomes limitations of previous efforts, Zhang says. First, the Sendai virus, a kind of cold virus, is considered safe because it does not enter the cell’s DNA, and it is killed by heat within 24 hours. (This is quite similar to the fever that raises our temperature to remove cold virus.) Second, the neural progenitors have a greater ability to grow daughter cells for research or therapy. Third, the progenitor cells are already well along the path toward specialization, and cannot become, say, liver or muscle cells after implantation. Finally, the progenitors can produce many more specialized cells.

The neurons that grew from the progenitor had the markings of neurons found in the rear of the brain, and that specialization can also be helpful. "For therapeutic use, it is essential to use specific types of neural progenitors," says Zhang. "We need region-specific and function-specific neuronal types for specific neurological diseases."

Progenitor cells grown from the skin of ALS (Lou Gehrig’s disease) or spinal muscular atrophy patients can be transformed into various neural cells to model each disease and allow rapid drug screening, Zhang adds.

Eventually, the process could produce cells used to treat conditions like spinal cord injury and ALS.

"These transplantation experiments confirmed that the reprogrammed cells indeed belong to cells of the intended brain regions and the progenitors produced the three major classes of neural cells: neurons, astrocytes and oligodendrocytes," Zhang says. "This proof-of-principle study highlights the possibility to generate many specialized neural progenitors for specific neurological disorders."

source : http://www.sciencedaily.com/releases/2013/05/130502131713.htm

Making cancer less cancerous

Dr. Brilliant No Comments

"This master regulator is normally turned off in adult cells, but it is very active during embryonic development and in all highly aggressive tumors studied to date," says Linda Resar, M.D., an associate professor of medicine, oncology and pediatrics, and affiliate in the Institute for Cell Engineering at the Johns Hopkins University School of Medicine. "Our work shows for the first time that switching this gene off in aggressive cancer cells dramatically changes their appearance and behavior." A description of the experiments appears in the May 2 issue of the journal PLOS ONE.

Resar has been investigating genes in the master regulator’s family, known as high mobility group or HMG genes, for two decades. In addition to their role in cancer, these genes are essential for giving stem cells their special powers, and that’s no coincidence, she says. "Many investigators consider cancer cells to be the evil twin of stem cells, because like stem cells, cancer cells must acquire special properties to enable the tumor to grow and metastasize or spread to different sites," she explains.

In a previous study , she and her team devised techniques to block the HMGA1 gene in stem cells in order to study its role in those cells. In their prior work, they discovered that HMGA1 is essential for reprogramming adult cells, like blood or skin cells, into stem cells that share most, if not all, properties of embryonic stem cells.

In the newly reported study, the Resar team applied the same techniques to several strains of human breast cancer cells in the laboratory, including the so-called triple negative cells — those that lack hormone receptors or HER2 gene amplification. Triple-negative breast cancer cells tend to behave aggressively and do not respond to many of our most effective breast cancer therapies. The Resar team blocked HMGA1 expression in aggressive breast cancer cells and followed their appearance and growth patterns.

"The aggressive breast cancer cells grow rapidly and normally appear spindle-shaped or thin and elongated. Remarkably, within a few days of blocking HMGA1 expression, they appeared rounder and much more like normal breast cells growing in culture," says Resar. The team also found that the cells with suppressed HMGA1 grow very slowly and fail to migrate or invade new territory like their HMGA1-expressing cousins.

The team next implanted tumor cells into mice to see how the cells would behave. The tumors with HMGA1 grew and spread to other areas, such as the lungs, while those with blocked HMGA1 did not grow well in the breast tissue or spread to distant sites.

"From previous work, we know that HMGA1 turns on many different genes needed during very early development, but it’s normally turned off by the time we’re born," says postdoctoral fellow Sandeep Shah, Ph.D., who led the study. "Flipping that master regulator back on seems to be necessary for a cancer to become highly aggressive, and now we’ve seen that flipping HMGA1 off again can reverse that aggressive behavior."

The next step, Resar says, is to try to develop a therapy based on that principle. The team is working with other researchers at Johns Hopkins to see whether HMGA1-blocking molecules could be delivered to tumors inside nanoparticles. Another possible approach, she says, would be to block not HMGA1 itself, but one of the pathways or processes that it affects.

Other authors of the report were Leslie Cope, Weijie Poh, Amy Belton, Sujayita Roy, C. Conover Talbot, Jr., Saraswati Sukumar, and David L. Huso, all of The Johns Hopkins University School of Medicine.

This study was funded by the National Cancer Institute (grant number 5R21CA149550), the Maryland Stem Cell Research Fund, and the Safeway Breast Cancer Foundation.

source : http://www.sciencedaily.com/releases/2013/05/130502185252.htm

New target for personalized cancer therapy

Dr. Brilliant No Comments

The research team has pinpointed the cancer abnormality to a mutation in a gene called PIK3CA that results in a mutant protein, which may be an early cancer switch. By disrupting the mutated signaling pathway, the Case Western Reserve team, led by John Wang, PhD, inhibited the growth of cancer cells, opening the possibility to new cancer therapies.

Their findings, "Gain of interaction with IRS1 by p110 helical domain mutants is crucial for their oncogenic functions," was published on May 2 in the journal Cancer Cell.

Cancer arises from a single cell, which has mutated in a small number of genes because of random errors in the DNA replication process. These mutations play key roles in carcinogenesis.

"This discovery has a broad impact on the treatment of human cancer patients because so many cancers are affected by this particular mutation in the p110 protein, which is encoded by the PIK3CA gene," said Wang, an associate professor in the Department of Genetics and Case Comprehensive Cancer Center. "This is a significant advance because we can now disrupt this misdirected signaling pathway in cancer cells."

"If you turn on a light, you have to turn on a switch. But in the case of the mutation of this protein, p110 turns on by itself," Wang said. "The mutation rewires the circuit and is uncontrolled. This implies that if you break these wires, you can control the growth of cancer. Our current discovery may lead to finding less toxic drugs that can be used for personalized treatment for cancer patients in the future."

"This research will impact the field by focusing us on new targets for treating and preventing metastasis in patients in a many different types of human cancers," said Stanton Gerson, MD, Asa and Patricia Shiverick-Jane Shiverick (Tripp) Professor of Hematological Oncology, and director of Case Comprehensive Cancer Center and of Seidman Cancer Center at University Hospitals Case Medical Center.

Wang’s multidisciplinary team of Case Western Reserve researchers includes: Yujun Hao, Chao Wang, Bo Cao, Brett M. Hirsch, Jing Song, Sanford D. Markowitz, Rob M. Ewing, David Sedwick, Lili Liu and Weiping Zheng.

source : http://www.sciencedaily.com/releases/2013/05/130502185258.htm

Discovery helps show how breast cancer spreads

Dr. Brilliant No Comments

It has long been known that women with denser breasts are at higher risk for breast cancer. This greater density is caused by an excess of a structural protein called collagen.

"We have shown how increased collagen in the breasts could increase the chances of breast tumors spreading and becoming more invasive," says Gregory D. Longmore, MD, professor of medicine. "It doesn’t explain why women with dense breasts get cancer in the first place. But once they do, the pathway that we describe is relevant in causing their cancers to be more aggressive and more likely to spread."

The results appear online May 5 in Nature Cell Biology.

Working in mouse models of breast cancer and breast tumor samples from patients, Longmore and his colleagues showed that a protein that sits on the surface of tumor cells, called DDR2, binds to collagen and activates a multistep pathway that encourages tumor cells to spread.

"We had no idea DDR2 would do this," says Longmore, also professor of cell biology and physiology. "The functions of DDR2 are not well understood, and it has not been implicated in cancer — and certainly not in breast cancer — until now.

At the opposite end of the chain of events initiated by DDR2 is a protein called SNAIL1, which has long been associated with breast cancer metastasis. Longmore and his colleagues found that DDR2 is one factor helping to maintain high levels of SNAIL1 inside a tumor cell’s nucleus, a necessary state for a tumor cell to spread. Though they found it is not the only protein keeping SNAIL1 levels high, Longmore says DDR2 is perhaps the one with the most potential to be inhibited with drugs.

"It’s expressed only at the edge of the tumor," says Longmore, a physician at Siteman Cancer Center at Washington University and Barnes-Jewish Hospital and co-director of the Section of Molecular Oncology. "And it’s on the surface of the cells, which makes it very nice for developing drugs because it’s so much easier to target the outside of cells."

Longmore emphasizes that DDR2 does not initiate the high levels of SNAIL1. But it is required to keep them elevated. This mechanism that keeps tumor cells in a state that encourages metastasis requires constant signaling — meaning constant binding of DDR2 to collagen.

If that continuous signal is blocked, the cell remains cancerous, but it is no longer invasive. So a drug that blocks DDR2 from binding with collagen won’t destroy the tumor, but it could inhibit the invasion of these tumors into surrounding tissue and reduce metastasis.

One possible way DDR2 may govern metastasis is its influence on the alignment of collagen fibers. If fibers are aligned parallel to the tumor’s surface, the tumor is less likely to spread. While fibers aligned perpendicular to the surface of the tumor provide a path for the tumor cells to follow and encourage spreading. Tumors without DDR2 or SNAIL1 tend to show the parallel fiber alignment that is protective against spreading.

"This whole notion of fiber alignment and the tumor interface is a hot topic right now," Longmore says. "Our co-authors at the University of Wisconsin have developed a scoring method for collagen alignment that correlates with prognosis. And the bad prognosis disappears when you take away DDR2."

With the current emphasis on genetic mutations in cancer, Longmore is careful to point out that 70 percent of invasive ductal breast cancers show DDR2. But in 95 percent of these tumors the genes in this pathway — from DDR2 to SNAIL1 — are entirely normal, without mutations.

"If you did genomic sequencing, all of these particular genes would be normal," Longmore says. "You have to be careful not to just focus on mutations in cancer. This is an example of normal genes put together in an aberrant situation. The change in the environment — the tumor and its surroundings — causes the abnormal expression of these proteins. It is abnormal, but it’s not caused by a gene mutation."

In early drug development efforts, Longmore and his colleagues have done some preliminary work looking for small molecules that may inhibit DDR2 binding to collagen.

"Currently there are no DDR2 specific inhibitors," Longmore says. "But there is great interest and work being done here and elsewhere to develop them."

source : http://www.sciencedaily.com/releases/2013/05/130505145807.htm

Discovery may help prevent chemotherapy-induced anemia

Dr. Brilliant No Comments

Constantly regenerating and maturing, the hematopoietic (blood-producing) stem cells in our bone marrow produce billions of red blood cells (RBC) every day. Cancer chemotherapy is notorious for injuring the bone marrow, leading to anemia, or low RBC counts. But just how chemotherapy harms the bone marrow has not been clear.

Anemia can lead to numerous health problems including chronic fatigue, tachycardia (abnormally rapid heartbeat), cognitive impairment, shortness of breath, depression and dizziness. In addition, studies have shown that cancer patients who develop anemia have a 65 percent increased risk of death compared with cancer patients without anemia.

In an earlier study, senior author Paul Frenette, M.D., professor of medicine and of cell biology and director of the Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research at Einstein, found that sympathetic nerves within bone marrow direct the movement of hematopoietic stem cells. (The body’s sympathetic nervous system helps in controlling most internal organs — increasing heart rate and dilating the pupils of the eye, for example.)

"Since many chemotherapies used in cancer treatment are neurotoxic, we wondered whether they might also damage sympathetic nerves in bone marrow itself, impairing the ability of hematopoietic cells to regenerate and to manufacture RBCs," said Dr. Frenette. "This possibility hadn’t been examined before."

Dr. Frenette and his colleagues treated mice with seven cycles of cisplatin, a common chemotherapy drug with known neurotoxic effects. The cisplatin caused peripheral neuropathy problems similar to those seen in cancer patients. The mice were then given fresh bone marrow transplants to see how well their marrow would regenerate. Despite receiving fresh stem cells, the cisplatin-treated mice had delayed recovery of blood counts compared to controls — suggesting that the prior cisplatin treatments had affected the bone marrow and prevented hematopoietic stem cells from regenerating. By contrast, mice treated with carboplatin — a non-neurotoxic chemotherapy — recovered their ability to produce blood after bone marrow transplantation.

To confirm that healthy sympathetic nerves in the bone marrow are needed to regenerate hematopoietic stem cells and produce RBCs, the researchers selectively damaged sympathetic nerves in bone marrow using chemicals or genetic engineering. In both cases, the mice with the damaged sympathetic nerves were less able than control mice to recover after bone marrow transplant.

The researchers found that injury to these nerves could be reduced by giving mice nerve-protecting agents along with chemotherapy. Mice treated with seven cycles of cisplatin along with 4-methylcatechol (an experimental drug that reportedly protects sympathetic nerves) showed improved response to bone marrow transplantation, compared to controls.

Dr. Frenette and his colleagues now plan to look for compounds that can protect sympathetic nerves in the bone marrow without reducing the effectiveness of cancer chemotherapies.

source : http://www.sciencedaily.com/releases/2013/05/130505145810.htm

Protein complex may play role in preventing many forms of cancer

Dr. Brilliant No Comments

The broad reach of the effect of mutations in the complex, called BAF, rivals that of another well-known tumor suppressor called p53. It also furthers a growing notion that these so-called chromatin-regulatory complexes may function as much more than mere cellular housekeepers.

"Although we knew that this complex was likely to play a role in preventing cancer, we didn’t realize how extensive it would be," said postdoctoral scholar Cigall Kadoch, PhD. "It’s often been thought that these complexes play supportive, maintenance-like roles in the cell. But this is really changing now."

Kadoch shares lead authorship of the study with postdoctoral scholar Diana Hargreaves, PhD. Gerald Crabtree, MD, professor of developmental biology and of pathology, is the senior author of the study, published online May 5 in Nature Genetics.

Chromatin-regulatory complexes work to keep DNA tightly condensed, while also granting temporary access to certain portions for replication or to allow the expression of genes necessary for the growth or function of the cell.

Members of Crabtree’s laboratory have been interested in BAF complexes and their function for many years. Recently, they reported in the journal Nature that switching subunits within these complexes can convert human fibroblasts to neurons, which points to their instructive role in development and, possibly, cancer.

"Somehow these chromatin-regulatory complexes manage to compress nearly two yards of DNA into a nucleus about one one-thousandth the size of a pinhead," said Crabtree, who is also a member of the Stanford Cancer Institute and a Howard Hughes Medical Institute investigator. "And they do this without compromising the ability of the DNA to be replicated and selectively expressed in different tissues — all without tangling. In 1994 we reported that complexes of this type were likely to be tumor suppressors. Here we show that they are mutated in nearly 20 percent of all human malignancies thus far examined."

The researchers combined biochemical experiments with the data mining of 44 pre-existing studies to come to their conclusions, which would not have been possible without the advent of highly accurate, genome-wide DNA sequencing of individual human tumor samples. Interestingly, mutations to certain subunits, or particular combinations of mutations in the complex’s many subunits, seem to herald the development of specific types of cancer — favoring the development of ovarian versus colon cancer, for example.

The importance of the BAF complex as a tumor suppressor is further emphasized by the fact that, in some cases, a mutation in one subunit is sufficient to initiate cancer development.

"For example," said Kadoch, "a type of mutation called a chromosomal translocation in the gene encoding one of these newly identified subunits, SS18, is known to be the hallmark of a cancer called synovial sarcoma. It is clearly the driving oncogenic event and very often the sole genomic abnormality in these cancers." Kadoch and Crabtree published a study in March in Cell uncovering the mechanism and functional consequences of BAF complex perturbation in synovial sarcoma.

The startling prevalence of mutations in the BAF complex was discovered when Kadoch conducted a series of experiments to determine exactly which proteins in the cell were true subunits of the complex. (The exact protein composition of the large complex varies among cell types and species.) Kadoch used an antibody that recognized one core component to purify intact BAF complexes in various cell types, including embryonic stem cells and skin, nerve and other cells. She then analyzed the various proteins isolated by the technique.

Using this method, Kadoch identified seven proteins previously unknown to be BAF components. She and Hargreaves then turned to previously published studies in which the DNA from a variety of human tumors had been sequenced to determine how frequently any of the members of the complex were mutated.

The results, once the newly discovered members were included, were surprising: 19.6 percent of all human tumors displayed a mutation in at least one of the complex’s subunits. In addition, for some types of cancers (such as synovial sarcoma), every individual tumor sample examined had a mutation in a BAF subunit. The results suggest that the BAF complex, when unmutated, plays an important protective role against the development of cancer in many different tissues.

The researchers are now focused on learning how the mutations affect the tumor-suppressing activity of the BAF complex.

"We certainly want to further our understanding of the mechanism behind these findings," said Hargreaves. "Do they promote cancer development by inhibiting the proper progression of the cell cycle? Or perhaps they affect how the complex is positioned on the DNA. We’d like to determine how to recapitulate some of these mutations experimentally to see what types of defects they introduce into the complex."

Other Stanford authors of the study include postdoctoral scholar Courtney Hodges, PhD, and former lab members Laura Elias, PhD, and Lena Ho, PhD.

source : http://www.sciencedaily.com/releases/2013/05/130505150040.htm

Portable device provides rapid, accurate diagnosis of tuberculosis, other bacterial infections

Dr. Brilliant No Comments

"Rapidly identifying the pathogen responsible for an infection and testing for the presence of resistance are critical not only for diagnosis but also for deciding which antibiotics to give a patient," says Ralph Weissleder, MD, PhD, director of the MGH Center for Systems Biology (CSB) and co-senior author of both papers. "These described methods allow us to do this in two to three hours, a vast improvement over standard culturing practice, which can take as much as two weeks to provide a diagnosis."

Investigators at the MGH CSB previously developed portable devices capable of detecting cancer biomarkers in the blood or in very small tissue samples. Target cells or molecules are first labeled with magnetic nanoparticles, and the sample is then passed through a micro NMR system capable of detecting and quantifying levels of the target. But initial efforts to adapt the system to bacterial diagnosis had trouble finding antibodies — the detection method used in the earlier studies — that would accurately detect the specific bacteria. Instead the team switched to targeting specific nucleic acid sequences.

The system described in the Nature Communications paper, published on April 23, detects DNA from the tuberculosis bacteria in small sputum samples. After DNA is extracted from the sample, any of the target sequence that is present is amplified using a standard procedure, then captured by polymer beads containing complementary nucleic acid sequences and labeled with magnetic nanoparticles with sequences that bind to other portions of the target DNA. The miniature NMR coil incorporated into the device — which is about the size of a standard laboratory slide — detects any TB bacterial DNA present in the sample.

Tests of the device on samples from patients known to have TB and from healthy controls identified all positive samples with no false positives in less than three hours. Existing diagnostic procedures can take weeks to provide results and can miss up to 40 percent of infected patients. Results were even stronger for patients infected with both TB and HIV — probably because infection with both pathogens leads to high levels of the TB bacteria — and specialized nucleic acid probes developed by the research team were able to distinguish treatment-resistant bacterial strains.

The Nature Nanotechnology paper, being issued online today, describes a similar system using ribosomal RNA (rRNA) — already in use as a bacterial biomarker — as a target for nanoparticle labeling. The investigators developed both a universal nucleic acid probe that detects an rRNA region common to many bacterial species and a set of probes that target sequences specific to 13 clinically important pathogens, including Streptococcus pneumoniae, Escherichia coli and methicillin-resistant Staphylococcus aureus (MRSA).

The device was sensitive enough to detect as few as one or two bacteria in a 10 ml blood sample and to accurately estimate bacterial load. Testing the system on blood samples from patients with known infections accurately identified the particular bacterial species in less than two hours and also detected two species that had not been identified with standard culture techniques.

While both systems require further development to incorporate all steps into sealed, stand-alone devices, reducing the risk of contamination, Weissleder notes that the small size and ease of use of these devices make them ideal for use in developing countries. "The magnetic interactions that pathogen detection is based on are very reliable, regardless of the quality of the sample, meaning that extensive purification — which would be difficult in resource-limited setting — is not necessary. The ability to diagnose TB in a matter of hours could allow testing and treatment decisions within the same clinic visit, which can be crucial to controlling the spread of TB in developing countries."

Hakho Lee, PhD, of the MGH Center for Systems Biology. co-senior author of both papers, notes that the system will also have important applications in developed countries. "The capacity of the system not only to identify bacterial species but also to differentiate factors such as antibiotic resistance will help clinicians treat patients with the ‘right’ drugs from the start, which also helps reduce the emergence of treatment-resistant strains. The fact that this device requires only a tiny drop of the sample to be tested will be helpful in instances when specimens can be hard to obtain, such as treating children or seniors."

source : http://www.sciencedaily.com/releases/2013/05/130505150042.htm