German research advances in cancer and blood disorders reported in human gene therapy

Virotherapy capable of destroying tumor cells and activating anti-tumor immune reactions, and the use of engineered hematopoietic stem cells (HSCs) to deliver replacement genes that have the potential to cure blood diseases are among the key areas of gene therapy being advanced by German researchers and highlighted in a special issue of Human Gene Therapy, a peer-reviewed journal from Mary Ann Liebert, Inc., publishers. The issue is available free on the Human Gene Therapy website.

The special focus issue entitled “German Gene Therapy Research — Part 1 ,” was developed by Guest Editors Christof von Kalle, MD, Boris Fehse, PhD, and Hildegard Büning, PhD. Dr. Büning, Hannover Medical School, is Editor of Human Gene Therapy Methods and serves as Chair of the 25th Anniversary ESGCT Congress, October 17-20, in Berlin.

In the special issue, Guy Ungerechts and Christine Engeland led a team of colleagues from Germany and Luxembourg in coauthoring the review article entitled “Virotherapy Research in Germany: From Engineering to Translation.” The researchers present the latest preclinical and clinical research activities to engineer oncolytic viruses, which selectively infect tumor cells, for use in tumor-targeted gene therapy. They discuss the different types of virus platforms being investigated–including adenovirus, arenavirus, measles vaccine virus, parvovirus, and vaccinia virus — and the potential to take advantage of the immunotherapeutic properties of oncolytic viruses and of their use in combination with other types of pharmaco-, radio-, and immunotherapy.

In the review article “Promises and Challenges in Hematopoietic Stem Cell Gene Therapy,” Saskia Kohlscheen, Halvard Bonig, and Ute Modlich, Paul-Ehrlich-Institute (Langen), Goethe University (Frankfurt), German Red Cross Blood Service Baden-Württemberg-Hessen (Frankfurt), Germany, and University of Washington, Seattle, describe the state-of-the-art in HSC-directed gene therapy, including viral vector delivery systems, transduction of HSCs, and protocols prior to HSC transplantation. The researchers discuss the main targets for this innovative approach, focusing on immunodeficiencies and inborn errors of metabolism, what has been learned to date from the limiting clinical studies performed, and how best to move forward to overcome the challenges the field still faces.

“The rapid pace of innovation among gene and cell therapy researchers in Germany is striking and significant,” says Editor-in-Chief Terence R. Flotte, MD, Celia and Isaac Haidak Professor of Medical Education and Dean, Provost, and Executive Deputy Chancellor, University of Massachusetts Medical School, Worcester, MA. “We are very proud to reflect the impact of German gene therapy science in this special issue of Human Gene Therapy.”

Immunotherapy treatment option for selected breast cancer patients, genetic study suggests

Immunotherapy drugs could help some breast cancer patients based on the genetic changes in their tumours, researchers at the Wellcome Trust Sanger Institute and their collaborators find. Published today (13 September) in Cancer Research, scientists identify particular genetic changes in a DNA repair mechanism in breast cancer.

The results open up the possibility to another therapy option for around 1,000 breast cancer patients in the UK, who could benefit from existing drugs.

Breast cancer is the most common cancer in the UK, affecting nearly 55,000 women a year. Globally it accounts for nearly 1.7 million cancer cases.

In the study, scientists found that a particular group of breast cancer patients have genetic changes, or mutations, that occur because of an abnormality of a DNA repair mechanism known as mismatch repair*. These mutations are found in other cancers, such as colorectal cancer, but are rarely looked for in breast cancer.

Colorectal cancers with deficient mismatch repair have recently been treated with immunotherapies called checkpoint inhibitors in the US**, including the drug pembrolizumab. Immunotherapies exploit the fact that, under the influence of check point inhibitors, highly mutated tumour cells can be recognised as ‘foreign’ by the patient’s immune system.

The results of this new study suggest that these immunotherapies could also be effective for some breast cancer patients based on the same mutation patterns seen in their tumours. Therefore clinical trials are required to determine if immunotherapies could help selected breast cancer patients.

In the study, the team analysed the whole genome sequences of 640 breast cancer tumours. They looked for patterns in the mutations, known as mutational signatures, which indicated abnormalities in the mismatch repair mechanism. From the mutational signatures, the team identified 11 tumours that had the mismatch repair defects causing the breast cancer.

Dr Serena Nik-Zainal, lead author from the Wellcome Trust Sanger Institute, said: “We’ve unequivocally found mismatch repair deficient breast cancers. As these tumours have the same mutational signatures as those of other cancers, like colorectal cancer, they should in theory respond to the same immunotherapy drugs. Our results suggest expanding the cohort of cancer patients that could possibly be treated with checkpoint inhibitors to include these mismatch repair deficient breast cancer patients.”

Dr Helen Davies, first author from the Wellcome Trust Sanger Institute, said: “Using whole genome sequencing we can start to stratify breast cancer patients into different categories based on their mutational signatures. Current clinical criteria means these tumours would not have been detected as being deficient in the mismatch repair pathway. We have shown that there is in fact another category of breast cancers – those with defective mismatch repair.”

Professor Karen Vousden, Cancer Research UK’s chief scientist, said: “Immunotherapies have shown promise for some cancer patients, but the challenge for doctors has been predicting which patients they are likely to help. This study, using a technique called whole genome sequencing, reveals more about the genetic patterns that could show which women with breast cancer are more likely to respond to immunotherapy treatments. The next step will be to test this approach in clinical trials to find out if identifying these patterns and using them to tailor breast cancer treatments helps to improve survival.”

Using DNA to predict schizophrenia and autism

Huntington’s disease, cystic fibrosis, and muscular dystrophy are all diseases that can be traced to a single mutation. Diagnosis in asymptomatic patient for these diseases is relatively easy – You have the mutation? Then you are at risk. Complex diseases, on the other hand, do not have a clear mutational footprint. A new multi-institutional study by Japanese researchers shows a potential rare gene mutation that could act as a predictor for two neurodevelopmental disorders, schizophrenia and autism.

“Aberrant synapse formation is important in the pathogenesis of schizophrenia and autism,” says Osaka University Professor Toshihide Yamashita, one of the authors of the study. “Microglia contribute to the structure and function of synapse connectivities.”

Microglia are the only cells in the brain that express the receptor CX3CR1. Mutations in this receptor are known to affect synapse connectivity and cause abnormal social behavior in mice. They have also been associated with neuroinflammatory diseases such as multiple sclerosis, but no study has shown a role in neurodevelopment disorders.

Working with this hypothesis, the researchers conducted a statistical analysis of the CX3CR1 gene in over 7000 schizophrenia and autism patients and healthy subjects, finding one mutant candidate, a single amino acid switch from alanine to threonine, as a candidate marker for prediction.

“Rare variants alter gene function but occur at low frequency in a population. They are of high interest for the study of complex diseases that have no clear mutational cause,” said Yamashita, who added the alanine threonine substitution was a rare variant.

The structure of CX3CR1 includes a domain known as Helix 8, which is important for initiating a signaling cascade. Computer models showed that one amino acid change is enough to compromise the signaling.

“The variant changes the region from hydrophobic to hydrophilic and destabilize Helix 8. We overexpressed the mutation in cells and found Akt signaling was disrupted,” explains Yamashita.

According to Yamashita, the findings are the first to connect a genetic variation in microglia with neurodevelopment disorders. Moreover, he hopes that the discovery could become a basis for predictive diagnostics.

“There is no reliable way to diagnose schizophrenia or autism in asymptomatic patients. Deeper understanding of the genetic risk factors will help us develop preventative measures.”

Stabilizing TREM2 — a potential strategy to combat Alzheimer’s disease

A gene called triggering receptor expressed on myeloid cells 2, or TREM2, has been associated with numerous neurodegenerative diseases, such as Alzheimer’s disease, Frontotemporal lobar degeneration, Parkinson’s disease, and Nasu-Hakola disease. Recently, a rare mutation in the gene has been shown to increase the risk for developing Alzheimer’s disease.

Independently from each other, two research groups have now revealed the molecular mechanism behind this mutation. Their research, published today in EMBO Molecular Medicine, sheds light on the role of TREM2 in normal brain function and suggests a new therapeutic target in Alzheimer’s disease treatment.

Alzheimer’s disease, just like other neurodegenerative diseases, is characterized by the accumulation of specific protein aggregates in the brain. Specialized brain immune cells called microglia strive to counter this process by engulfing the toxic buildup. But as the brain ages, microglia eventually lose out and fail to rid all the damaging material.

TREM2 is active on microglia and enables them to carry out their protective function. The protein spans the microglia cell membrane and uses its external region to detect dying cells or lipids associated with toxic protein aggregates. Subsequently, TREM2 is cut in two. The external part is shed from the protein and released, while the remaining part still present in the cell membrane is degraded. To better understand TREM2 function, the two research groups took a closer look at its cleavage. They were led by Christian Haass at the German Center for Neurodegenerative Diseases at the Ludwig-Maximilians-University in Munich, Germany, and Damian Crowther of AstraZeneca’s IMED Neuroscience group in Cambridge, UK together with colleagues at the Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto and the Cambridge Institute for Medical Research, University of Cambridge, UK.

Using different technological approaches, both groups first determined the exact site of protein shedding and found it to be at amino acid 157. Amino acid 157 was no unknown. Only recently, researchers from China had uncovered that a mutation at this exact position, referred to as p.H157Y, increased the risk of Alzheimer’s disease. Together, these observations indicate that protein cleavage is perturbed in the p.H157 mutant and that this alteration promotes disease development.

As a next step, Haass and Crowther’s groups investigated the biochemical properties of the p.H157Y mutant protein more closely. They found that the mutant was cleaved more rapidly than a healthy version of the protein. “Our results provide a detailed molecular mechanism for how this rare mutation alters the function of TREM2 and hence facilitates the progression of Alzheimer’s disease,” said Crowther.

While most TREM2 mutations affect protein production, the mechanism behind p.H157Y is somewhat different. The p.H157Y mutation allows the protein to be correctly manufactured and transported to the microglia cell surface, but then it is cleaved too quickly. “The end result is the same. In both cases, there is too little full-length TREM protein on microglia,” said Haass. “This suggests that stabilizing TREM2, by making it less susceptible to cleavage, may be a viable therapeutic strategy.”

Wistar scientists develop novel immunotherapy technology for prostate cancer

A study led by scientists at The Wistar Institute describes a novel immunotherapeutic strategy for the treatment of cancer based on the use of synthetic DNA to directly encode protective antibodies against a cancer specific protein. This is the first application of the new technology, called DNA-encoded monoclonal antibody (DMAb), for cancer immunotherapy. The study was published online in Cancer Immunology, Immunotherapy.

Prostate cancer is the second most common cancer in men worldwide. Traditional treatments are invasive and can impair the quality of life of patients, underscoring the need for alternative therapeutic strategies, including immunotherapy. One of the immunotherapeutic approaches that has been explored thus far relies on the use of monoclonal antibodies that specifically target a protein present on the surface of prostate cancer cells called prostate specific membrane antigen (PSMA) to elicit an anti-tumor immune response and control the cancer. Although promising, this strategy is limited by the production cost required to make these therapeutic antibodies. Additionally, multiple infusions are often required to achieve efficacy.

Wistar researchers devised a novel DNA-based approach in which an engineered DNA plasmid is constructed and used to deliver the instructions to make the desired anti-PSMA antibody so that the therapy can be generated in the patient’s body in a sustained manner. This research has important implications for the use of DNA-encoded monoclonal antibody technology as a platform for delivering the next generation of immunotherapies for cancer and many human diseases.

“This is an important demonstration of the possibilities opened up for immunotherapy by DMAb technology to direct in vivo production of antibodies of major relevance to human cancer,” said David B. Weiner, Ph.D., executive vice president of The Wistar Institute, director of The Wistar Institute Vaccine & Immunotherapy Center, W.W. Smith Charitable Trust Professor in Cancer Research, and senior author of the study. “There is a great need for such new approaches for prostate disease as well as many other cancers. As recent data suggest, PSMA is an important cancer antigen expressed on many human prostate, bladder, renal as well as ovarian cancers, so additional study of the possible benefits of this therapy are important.”

The new technology was tested in mice for the ability to generate antibodies in their blood stream that would target human PSMA as well as target PSMA-positive tumors. Results showed that antibodies were able to bind to the cancer cells and recruited specific immune cells called natural killer cells, resulting in shrinkage of the tumor, significantly improving survival.

“Our data provide proof of concept that DMAb engineered DNA plasmids can be successfully used to target important cancers,” said Kar Muthumani, M.Sc., Ph.D., assistant professor in the Translational Tumor Immunology Program at Wistar, member of the Vaccine & Immunotherapy Center and lead author of the study. “The unique features of our synthetic DNA-based system make it a promising novel approach for cancer therapy, alone or in combination with other treatments.”

Skewing the aim of targeted cancer therapies

Headlines, of late, have touted the successes of targeted gene-based cancer therapies, such as immunotherapies, but, unfortunately, also their failures.

Broad inadequacies in a widespread biological concept that affects cancer research could be significantly deflecting the aim of such targeted drugs, according to a new study. A team exploring genetic mechanisms in cancer at the Georgia Institute of Technology has found evidence that a prevailing concept about how cells produce protein molecules, particularly when applied to cancer, could be erroneous as much as two-thirds of the time.

Prior studies by other researchers have also critiqued this concept about the pathway leading from genetic code to proteins, but this new study, led by cancer researcher John McDonald, has employed rare analytical technology to explore it in unparalleled detail. The study also turned up novel evidence for regulating mechanisms that could account for the prevailing concept’s apparent shortcomings.

RNA concept incomplete

The concept stems from common knowledge about the assembly line inside cells that starts with code in DNA, is transcribed to messenger RNA, then translated into protein molecules, the cell’s building blocks.

That model seems to have left the impression that cellular protein production works analogously to an old-style factory production line: That the amount of a messenger RNA encoded by DNA on the front end translates directly into the amount of a corresponding protein produced on the back end. That idea is at the core of how gene-based cancer drug developers choose their targets.

To put that assumed congruence between RNA production and protein production to the test, the researchers examined — in ovarian cancer cells donated by a patient — 4,436 genes, their subsequently transcribed messenger RNA, and the resulting proteins. The assumption, that proverbial factory orders passed down the DNA-RNA line determine in a straightforward manner the amount of a protein being produced, proved incorrect 62 percent of the time.

RNA skews drug cues

“The messenger RNA-protein connection is important because proteins are usually the targets of gene-based cancer therapies,” McDonald said. “And drug developers typically measure messenger RNA levels thinking they will tell them what the protein levels are.” But the significant variations in ratios of messenger RNA to protein that the researchers found make the common method of targeting proteins via RNA seem much less than optimal.

McDonald, Mengnan Zhang and Ronghu Wu published their results on August 15, 2017 in the journal Scientific Reports. The work was funded by the Ovarian Cancer Institute, The Deborah Nash Endowment, Atlanta’s Northside Hospital and the National Science Foundation. The spectrophotometric technology needed to closely identify a high number of proteins is rare and costly but is available in Wu’s lab at Georgia Tech.

Whereas many studies look at normal tissue versus cancerous tissue, this new study focused on cancer progression, or metastasis, which is what usually makes cancer deadly. The researchers looked at primary tumor tissue and also metastatic tissue.

Hiding drug targets

“The idea that any change in RNA level in cancerous development flows all the way up to the protein level could be leading to drug targeting errors,” said McDonald, who heads Georgia Tech’s Integrated Cancer Research Center. Drug developers often look for oddly high messenger RNA levels in a cancer then go after what they believe must be the resulting oddly high levels of a corresponding protein.

Taking messenger RNA as a protein level indicator could actually work some of the time. In the McDonald team’s latest experiment, in 38 percent of the cases, the rise of RNA levels in cancerous cells did indeed reflect a comparable rise of protein levels. But in the rest of cases, they did not.

“So, there are going to be many instances where if you’re predicting what to give therapeutically to a patient based on RNA, your prescription could easily be incorrect,” McDonald said. “Drug developers could be aiming at targets that aren’t there and also not shooting for targets that are there.”

RNA muted or magnified

The analogy of a factory producing building materials can help illustrate what goes wrong in a cancerous cell, and also help describe the study’s new insights into protein production. To complete the metaphor: The materials produced are used in the construction of the factory’s own building, that is, the cell’s own structures.

In cancer cells, a mutation makes protein production go awry usually not by deforming proteins but by overproducing them. “A lot of mutations in cancer are mutations in production levels. The proteins are being overexpressed,” said McDonald, who is also a professor in Georgia Tech’s School of Biological Sciences.

A bad factory order can lead to the production of too much of a good material and then force it into the structures of the cell, distorting it. The question is: Where in the production line do bad factory orders appear?

According to the new study, the answer is less straightforward than perhaps previously thought.

Micro RNA managing

The orders don’t all appear on the front end of the assembly line with DNA over-transcribing messenger RNA. Additionally, some mutations that do over-transcribe messenger RNA on the front end are tamped down or canceled by regulating mechanisms further down the line, and may never end up boosting protein levels on the back end.

Regulating mechanisms also appear to be making other messenger RNA, transcribed in normal amounts, unexpectedly crank out inordinate levels of proteins.

At the heart of those regulating systems, another RNA called micro RNA may be micromanaging how much, or little, of a protein is actually produced in the end.

“We have evidence that micro RNAs may be responsible for the non-correlation between the proteins and the RNA, and that’s completely novel,” McDonald said. “It’s an emerging area of research.”

Micro RNA, or miRNA, is an extremely short strand of RNA.

No one at fault

McDonald would like to see tissues from more cancer patients undergo similar testing. “Right now, with just one patient, the data is limited, but I also really think it shows that the phenomenon is real,” McDonald said.

“Many past studies have looked at one particular protein and a particular gene, or a particular handful. We looked at more than 4,000,” McDonald said. “What that brings up is that the phenomenon is probably not isolated but instead genome-wide.”

The study’s authors would also like to see rarely accessible, advanced protein detecting technology become more widely available to biomolecular researchers, especially in the field of cancer drug development. “Targeted gene therapy is a good idea, but you need the full knowledge of whether it’s affecting the protein level,” McDonald said.

He pointed out that no one is at fault for the possible incompleteness of commonly held concepts about protein production.

As science progresses, it naturally illuminates new details, and formerly useful ideas need updating. With the existence of new technologies, it may be time to flesh out this particular concept for the sake of cancer research progress.

Spider peptides battle superbugs and cancer

As antibiotic resistance rises and fears over superbugs grow, scientists are looking for new treatment options. One area of focus is antimicrobial peptides (AMPs), which could someday be an alternative to currently prescribed antibiotics, many of which are becoming increasingly useless against some bacteria. Now, a team reports in ACS Chemical Biology that they have improved the antimicrobial — and anticancer — properties of an AMP from a spider.

According to the U.S. Centers for Disease Control and Prevention, 2 million people become infected with antibiotic-resistant bacteria in the U.S. each year. Because no known antibiotics work against these bacteria, patients simply have to hope that their natural defenses eventually overcome the infection. But some patients experience severe symptoms, landing them in a hospital, and in extreme cases, they could die. Researchers are trying to find alternatives to traditional antibiotics, and one such possibility is a group of peptides called AMPs. These peptides are found in all plants and animals as a type of immune response and have been shown to be potent antibiotics in the laboratory. Gomesin, an AMP from the Brazilian spider Acanthoscurria gomesiana can function as an antibiotic, but it also has anticancer activity. When gomesin was synthesized as a circle instead of as a linear structure, these characteristics were enhanced. Sónia Troeira Henriques and colleagues wanted to further boost the peptide’s traits.

The team made several variations of the cyclic gomesin peptide and found that some of these were 10 times better at killing most bacteria than the previously reported cyclic form. In other experiments, the new AMPs specifically killed melanoma and leukemia cells, but not breast, gastric, cervical or epithelial cancer cells. The researchers determined that the modified peptides killed bacteria and cancer cells in a similar way — by disrupting the cells’ membranes. The group also notes that the modified AMPs were non-toxic to healthy blood cells.

Study identifies molecules that could help to prevent the development of brain tumors

Researchers from the University of Portsmouth’s Brain Tumour Research Centre of Excellence have identified molecules which are responsible for metastatic lung cancer cells binding to blood vessels in the brain.

In order for a cancer cell to enter the brain, it must first bind to the cells which line the structure separating the blood from the brain which is called the blood-brain barrier (BBB). Such information about the factors associated with this process may provide a way of preventing the cancer cells binding to the BBB and crossing over into the brain.

Twenty to 40 percent of patients with non-small cell lung cancer (NSCLC) develop brain metastasis.

The study, funded by the charity Brain Tumour Research and conducted by researchers at their UK Centre of Excellence at the University of Portsmouth, examined the factors present on the surface of NSCLC cells. These cells have different factors on their surfaces which determines how “sticky” the cells are and whether they are responsible for mediating the cancer cells binding to the blood vessel walls.

One of these factors is a molecule called CD15s. While it is present on a number of different types of cells in the body, it is expressed at higher levels on metastatic tumour cells, including those which have spread from the lung. It is only present at low levels in lung cancer cells which are not metastatic and remain within the lung.

The scientists examined what CD15s binds to on the blood vessel wall and identified another factor called CD62E. The researchers then used a specific tool to block the CD15s on the surface of the tumour cells, and this prevented the NSCLC cells from attaching to the blood vessels. They also used a model which simulated the cancer cells flowing through the blood vessels, and got the same result. So, blocking the adhesive properties of CD15s may provide a tool to prevent the establishment of secondary cancers.

Professor Geoff Pilkington, study co-author and Head of the Brain Tumour Research Centre, said: “Although this work is still at an early stage, we have demonstrated key elements that are associated with tumour cell binding to blood vessels and this may provide a target for future drug development to prevent the development of secondary tumours in the brain. Increasing our understanding of the adhesive properties of tumours may also help to develop new treatments to halt the development and spread of primary brain tumours.”

The adhesive properties of cancer cells play a key role in the formation and development of a tumour. While cells in a low-grade tumour bind very tightly together, the cells become less adhesive as the tumour becomes malignant. This is very important for the tumour cells which then spread into the surrounding nervous tissue.

Understanding more about the factors which mediate cell adhesion is key for the potential identification of new therapies.

Dr Kieran Breen, Director of Research at Brain Tumour Research, said: “Brain tumours kill more children and adults under the age of 40 than any other cancer, yet just 1 per cent of the national spend on cancer research has been allocated to this devastating disease. We are funding vital research in the UK to address this situation and are encouraged by Professor Pilkington’s findings.”

In addition to primary tumours which start in the brain, the secondary or ‘metastatic’ tumours which originate elsewhere and which migrate to the brain have been the focus of this new study. Secondary brain tumours are most likely to originate in the breast, lung or skin (melanoma). When they enter the brain, they generally form multiple tumours and can be extremely difficult to treat. Usually, treatment would require whole-brain radiation which is extremely toxic and the average survival time is just 3-6 months from diagnosis, with fewer than 20 per cent of patients surviving more than one year. If the people whose tumours are more likely to spread to the brain could be identified, researchers may be able to prevent this from happening.

Cell mechanism discovery could lead to ‘fundamental’ change in leukaemia treatment

Researchers have identified a new cell mechanism that could lead to a fundamental change in the diagnosis and treatment of leukaemia.

A team in the University of Kent’s pharmacy school conducted a study that discovered that leukaemia cells release a protein, known as galctin-9, that prevents a patient’s own immune system from killing cancerous blood cells.

Acute Myeloid Leukaemia (AML) — a type of blood cancer that affects over 250,000 people every year worldwide — progresses rapidly because its cells are capable of avoiding the patient’s immune surveillance. It does this by inactivating the body’s immune cells, cytotoxic T lymphocytes and natural killer (NK) cells.

Existing treatment strategies consist of aggressive chemotherapy and stem cell transplantation, which often do not result in effective remission of the disease. This is because of a lack of understanding of the molecular mechanisms that allow malignant cells to escape attack by the body’s immune cells.

Now the researchers at the Medway School of Pharmacy, led by Dr Vadim Sumbayev, Dr Bernhard Gibbs and Professor Yuri Ushkaryov, have found that leukaemia cells — but not healthy blood cells — express a receptor called latrophilin 1 (LPHN1). Stimulation of this receptor causes these cancer cells to release galectin-9, which then prevents the patient’s immune system from fighting the cancer cells.

The discovery of this cell mechanism paves the way for new ‘biomarkers’ for AML diagnosis, as well as potential targets for AML immune therapy, say the researchers.

‘Targeting this pathway will crucially enhance patients own immune defences, helping them to eliminate leukaemia cells’, said Dr Sumbayev. He added that the discovery has the potential to also be beneficial in the treatment of other cancers.

Largest study of malaria gene function reveals many potential drug targets

The malaria parasite’s success is owed to the stripping down of its genome to the bare essential genes, scientists at the Wellcome Trust Sanger Institute and their collaborators have found. In the first ever large-scale study of malaria gene function, scientists analysed more than half of the genes in the parasite’s genome and found that two thirds of these genes were essential for survival — the largest proportion of essential genes found in any organism studied to date.

The results, published today (13 July) in Cell, identify many potential targets for new antimalarial drug development, which is an important finding for this poorly understood parasite where drug resistance is a significant problem.

Nearly half of the world’s population is at risk of malaria and more than 200 million people are infected each year. The disease caused the deaths of almost half a million people globally in 2015*.

The genetics of the parasite that causes malaria, Plasmodium, have been tricky to decipher. Plasmodium parasites are ancient organisms and around half their genes have no similar genes — homologs — in any other organism, making it difficult for scientists to find clues to their function. This study provides the first ever experimental evidence of function for most of the genes.

Scientists studied the genes in one species of malaria, Plasmodium berghei, which were expressed in a single blood stage of its complicated, multi-stage life cycle. In the study, scientists designed a new method to decipher the function of the malaria parasite’s genes. The team switched off, or knocked out, 2,578 genes — more than half of the genome — and gave each knockout a unique DNA barcode**.

The team then used next generation genome sequencing technology to count those barcodes, and hence measure the growth of each genetically modified malaria parasite. If the switched-off gene was not essential, the parasite numbers shot up, but if the knocked out gene was essential, the parasite disappeared.

Dr Oliver Billker, joint lead author from the Wellcome Trust Sanger Institute, said: “This work was made possible by a new method that enabled us to investigate more than 2,500 genes in a single study — more than the entire research community has studied over the past two decades. We believe that this method can be used to build a deep understanding of many unknown aspects of malaria biology, and radically speed up our understanding of gene function and prioritisation of drug targets.”

The team systematically showed that the malaria parasite can easily dispose of the genes which produce proteins that give away its presence to the host’s immune system. This poses problems for the development of malaria vaccines as the parasite can quickly alter its appearance to the human immune system, and as a result the parasite can build resistance to the vaccine.

Dr Julian Rayner, joint lead author from the Wellcome Trust Sanger Institute, said: “We knew from previous work that on its surface the malaria parasite has many dispensable parts. Our study found that below the surface the parasite is more of a Formula 1 race car than a clunky people carrier. The parasite is fine-tuned and retains the absolute essential genes needed for growth. This is both good and bad: the bad news is it can easily get rid of the genes behind the targets we are trying to design vaccines for, but the flip side is there are many more essential gene targets for new drugs than we previously thought.”

Dr Francisco Javier Gamo, Director of the Malaria Unit at GlaxoSmithKline, said: “This study of unprecedented scale has resulted in many more, unique drug targets for malaria. The Holy Grail would be to discover genes that are essential across all of the parasite lifecycle stages, and if we could target those with drugs it would leave malaria with nowhere to hide. The technology that the Sanger Institute has developed gives us the potential to ask those questions systematically for the first time.”

How dragon blood could save your life (video)

Chemists have found potential drugs and other really useful compounds in some truly bizarre places in nature. For example, a natural immune defense in the blood of komodo dragons, a sponge armed with resistance to bacterial infection or a 400-million-year-old medical workhorse just might save your life someday.

The American Chemical Society, the world’s largest scientific society, is a not-for-profit organization chartered by the U.S. Congress. ACS is a global leader in providing access to chemistry-related information and research through its multiple databases, peer-reviewed journals and scientific conferences. ACS does not conduct research, but publishes and publicizes peer-reviewed scientific studies. Its main offices are in Washington, D.C., and Columbus, Ohio.

New inhibitor drug shows promise in relapsed leukemia

A new drug shows promise in its ability to target one of the most common and sinister mutations of acute myeloid leukemia (AML), according to researchers at the Perelman School of Medicine at the University of Pennsylvania and Penn’s Abramson Cancer Center. The Fms-like tyrosine kinase 3 (FLT3) gene mutation is a known predictor of AML relapse and is associated with short survival. In a first-in-human study, researchers treated relapsed patients with gilteritinib, an FLT3 inhibitor, and found it was a well-tolerated drug that led to frequent and more-sustained-than-expected clinical responses, almost exclusively in patients with this mutation. They published their findings today in The Lancet Oncology.

FLT3 is one of the most commonly mutated genes in AML patients. FLT3 mutations are found in about 30 percent of patients’ leukemia cells. Clinically, these mutations are associated with aggressive disease that often leads to rapid relapse, after which the overall survival is an average of about four months with current therapies. To avoid relapse, oncologists often recommend the most aggressive chemotherapy approaches for patients with FLT3 internal tandem duplication (FLT3-ITD), including marrow transplantation. But even that cannot always stave off the disease.

The FLT3 gene is present in normal bone marrow cells and regulates the orderly growth of blood cells in response to daily demands. When the gene is mutated in a leukemia cell, however, the mutated cells grow in an uncontrolled manner unless the function of FLT3 is turned off.

“Other drugs have tried to target these mutations, and while the approach works very well in the laboratory, it has proven very challenging to develop FLT3 inhibitors in the clinic for several reasons,” said Alexander Perl, MD, MS, an assistant professor of Hematology Oncology in Penn’s Abramson Cancer Center and the study’s lead author. “First, we’ve learned it takes unusually potent inhibition of the FLT3 target to generate clinical responses. Second, many of these drugs are not selective in their activity against FLT3. When they target multiple kinases, it can lead to more side-effects. That limits whether you can treat a patient with enough drug to inhibit FLT3 at all. Finally, with some FLT3 inhibitors, the leukemia adapts quickly after response and cells can develop new mutations in FLT3 that don’t respond to the drugs at all. So ideally, you want a very potent, very selective, and very smartly designed drug. That’s hard to do.”

For this phase 1/2 clinical trial, Perl and his team evaluated the drug gilteritinib – also known as ASP2215 – at increasing doses in patients whose AML had relapsed or was no longer responding to chemotherapy. The team focused on dose levels at 80mg and above, which were associated with more potent inhibition of the FLT3 mutation and higher response rates. They found these doses were also associated with longer survival. Of the 252 patients on this study, 67 were on a 120mg dose and 100 were on a 200mg dose. Seventy-six percent (191) of the patients on the trial had a FLT3 mutation. Overall, 49 percent of patients with FLT3 mutations showed a response. Just 12 percent of patients who didn’t have the mutation responded to the drug.

“The fact that the response rate tracked with the degree of FLT3 inhibition and was so much lower among patients who did not have an FLT3 mutation gives us confidence that this drug is hitting its target,” Perl said.

In leukemia cells, FLT3 itself can mutate again to a form called a D835 mutation that is resistant to several FLT3 inhibitors treatments. Gilteritinib, however, remains active against D835 mutations in laboratory models of leukemia. Clinical response rates from the trial appeared to be the same, whether patients had a FLT3-ITD alone or both a FLT3-ITD and a D835 mutation. The response rates also were similar in patients in whom gilteritinib was their first FLT3 inhibitor and those who previously were treated with other FLT3 inhibitors.

The drug was also generally well-tolerated. The three most common side effects attributed to the drug were diarrhea in 41 patients (16 percent), fatigue in 37 (15 percent), and abnormal liver enzyme tests in 33 (13 percent). These generally were mild in severity and discontinuation of gilteritinib for side effects was uncommon (25 patients, 10 percent).

“These look like data you want to see for a drug to eventually become a standard therapy,” Perl said, though he noted more research will be necessary.

A new multicenter trial, which compares gilteritinib to standard chemotherapy in patients with FLT3 mutations who relapsed or did not respond to initial therapy, is now underway, and Penn’s Abramson Cancer Center is one of the sites.

There are also studies underway that give the drug in combination with frontline chemotherapy and as an adjunct to bone marrow transplantation in hopes of preventing relapse altogether.

Penn study details impact of antibiotics, antiseptics on skin microbiomes

The use of topical antibiotics can dramatically alter communities of bacteria that live on the skin, while the use of antiseptics has a much smaller, less durable impact. The study, conducted in mice in the laboratory of Elizabeth Grice, PhD, an assistant professor of Dermatology in the Perelman School of Medicine at the University of Pennsylvania, is the first to show the long-term effects of antimicrobial drugs on the skin microbiome. Researchers published their findings today in the journal Antimicrobial Agents and Chemotherapy.

The skin, much like the gut, is colonized by a diverse multitude of microorganisms which generally coexist as a stable ecosystem — many of which are harmless or even beneficial to the host. However, when that ecosystem is disturbed or destabilized, colonization and/or infection by more dangerous microbes can occur. Antiseptics, such as ethanol or iodine, are commonly used to disinfect the skin prior to surgical procedures or following exposure to contaminated surfaces or objects. Topical antibiotics may be used to decolonize skin of specific types of bacteria or for rashes, wounds, or other common conditions.

In the gut, research shows medication that alters microbial communities can lead to complications like Clostridium difficile, or C. diff — which causes diarrhea and is the most common hospital-acquired infection. But when it comes to the skin, the impact of these medications on bacteria strains like Staphylococcus aureus, or S. aureus — the most common cause of skin infections — is still largely unstudied.

“We know antibiotics and antiseptics can be effective in stopping the growth of certain bacteria, but we wanted to know about the larger impact these treatments can have on the resident microbial communities on the skin,” said the study’s lead author, Adam J. SanMiguel, PhD, a researcher in the Grice Laboratory at Penn.

Researchers treated the skin of hairless mice with a variety of antibiotics, including a narrowly targeted mupirocin ointment and a broadly applicable triple-antibiotic ointment (TAO) containing bacitracin, neomycin, and polymyxin B. All of the antibiotics changed the makeup of the microbial communities, and, in a key finding of the study, the impact of that change lasted for days after treatment stopped.

“The problem in this case isn’t antibiotic resistance, but instead, how long the disruption of the skin microbiomes continues,” SanMiguel said. “That disruption opens the door for colonization by an unwanted strain.”

The researchers similarly evaluated antiseptics, using alcohol or povidone-iodine and comparing those treatments with two control groups – mice treated with water and mice entirely untreated. They found neither antiseptic caused responses similar enough to cluster the mice together into groups based on their microbiomes. They also found no clear difference between the treatment groups and the control groups when comparing the relative number of individual bacteria strains.

“We thought antiseptics would be even more disruptive to microbial communities than antibiotics since they are less targeted, but it turns out the opposite is true,” SanMiguel said. “It shows how stable the skin microbiome can be in the face of stress.”

However, both antibiotic and antiseptic treatments removed skin resident bacteria that compete against the pathogenic S. aureus to colonize the skin. Colonization with S. aureus is a risk factor for developing a skin infection.

“This gives us a better understanding of how topical antimicrobials affect the skin microbiome and what kind of impact their disturbance can have in the context of pathogenic colonization,” said Grice, the study’s senior author. “This helps us anticipate their potential effects.”

The researchers say this work can provide the foundation for greater understanding of how the skin defends against infection. They have already begun similar testing in humans.

Better treatment for kidney cancer thanks to new mouse model

Roughly 2-3 percent of all people suffering from cancer have kidney cancer. The most common form of this disease is called clear cell renal cell carcinoma (ccRCC). In roughly half of all patients with this disease, the tumor develops metastases and generally cannot be cured.

New Mouse Model for Investigating Kidney Cancer

The research of different types of cancer and the testing of new treatments depends on accurate mouse models. This is because the tumors in mice mirror the genetics as well as the molecular and cellular properties of tumors in humans. Despite decades of effort, however, researchers were unable to develop a mouse model of renal cell carcinoma – until now. Scientists conducting a long-term research project at the University of Zurich were able to develop a mouse model. The study was led by Sabine Harlander and her colleagues at the Institute of Physiology of the University of Zurich in the lab of Professor Ian Frew, who has recently joined the University of Freiburg in Germany. The researchers began by identifying the genes that often mutate in human renal cell carcinomas. They then mutated three of these genes simultaneously in renal cells of mice, which then developed renal cancer.

Gene Mutations Promote Uncontrolled Cell Division

The progression from gene mutation in the renal cells to the development of a tumor took eight to twelve months. This lengthy period of time, compared to a mouse’s lifetime, indicates that additional factors play a role in tumor development. The researchers therefore decided to take a closer look at the protein-encoding genes in the mouse tumors. They discovered that in all of the tumors at least one of the many genes responsible for the correct functioning of the primary cilium had mutated. The primary cilium is a hair-like structure found on the cell’s surface and is responsible for coordinating cell signaling, among other things.

Based on this finding, the researchers found that similar mutations also occur in renal cell carcinomas in humans. The scientists now believe that the loss of normal function in the primary cilium leads to the uncontrollable division of renal epithelial cells, which contributes to the formation of ccRCC. “This research project is a prime example of how mouse models can help us to better understand cancer diseases in human beings,” says Sabine Harlander.

Mouse Model Enables Development of Better Treatments

The new mouse model will make it possible to develop better therapies for renal cancer. For example, in the case of patients with renal carcinoma metastasis who are given different medications, some patients respond to the medications, while others do not. The same phenomenon can be observed when mice with renal cancer are treated with the same drugs as the humans. Some tumors shrink, while others do not. Now researchers can investigate the factors that contribute to why certain tumours respond to certain medications and not to others. “We hope that our mouse model, which allows us to combine drug testing and genetic analysis, will provide a deeper understanding of why tumors are sensitive or resistant to drugs,” states Ian Frew. Such vital information could be used to better adjust treatments to the characteristics of each patient.

The mouse model could also contribute to the further development of immunotherapies – a method in which the body’s immune system is stimulated, so that it intensifies its fight against tumor cells. In the last few years, much progress has been made in this field of cancer research, also for the treatment of renal cell carcinomas. Now, thanks to the new mouse model, it will be possible to study how renal tumors are able to develop in an environment with a normal immune system, and how cancer cells manage to evade the immune system’s attacks. Ultimately, the researchers’ goal is to use these new findings to improve the effectiveness of immunomodulatory treatments.

Scientists confirm correlation between malignant hyperthermia and exertional heat stroke

New research published online in The FASEB Journal may ultimately help athletes and trainers better understand who may be more at risk for heat stroke. In the report, scientists use animals to show that there is a link between the susceptibility to malignant hyperthermia (MH) and exertional heat stroke.

“Global warming and increasing frequency of heat waves, which are particularly dangerous in large urban areas, in future years will represent a reason of concern for human health,” said Feliciano Protasi, Ph.D., a researcher involved in the work at the Department of Neuroscience, Imaging and Clinical Sciences, University G. d’Annunzio, Chieti, Italy. “However, in spite of the increased incidence, severity and life-threatening nature of heat stroke, there are currently no safe and effective drug interventions to protect or reverse this deadly syndrome. We hope that our study will contribute to develop preventive measures and/or acute treatments for heat stroke caused by environmental heat and physical exertion.”

Scientists used three groups of mice to reach their conclusion. The first two groups (RYR1Y522S/WT and CASQ1-null mice) had altered genes that made them susceptible to lethal hyperthermic crises when exposed to anesthetics, while the third group was normal (wild-type mice). When the three sets of mice were exposed to a protocol of exertional stress (incremental running at 34 degrees Celsius and 40 percent humidity) the MH-susceptible mice (but not the normal mice) suffered lethal overheating episodes.

“This work addresses a dangerous, often lethal, physiological maladjustment that animals and humans can undergo,” said Thoru Pederson, Ph.D., Editor-in-Chief of The FASEB Journal. “The door now stands open to finding effective preventative drugs.”

Maternal High-Fat Diet May Increase Offspring Risk for Liver Disease

Research could uncover who is most at risk for nonalcoholic fatty liver disease and lead to new treatments for this increasingly common condition

Nonalcoholic fatty liver disease, a condition where fat builds up in the liver, is now the most common chronic liver disease diagnosed in adults and children. Although the disease is linked with obesity, scientists don’t fully understand why some people develop it and others don’t. Findings from a new mouse study suggest that exposure to a high-fat diet in the womb and immediately after birth may change the liver in a way that promotes more rapid progression of nonalcoholic fatty liver disease later in life.

Michael Thompson, MD, PhD, pediatric endocrinology fellow at Nationwide Children’s Hospital, will present the new research at the American Society for Investigative Pathology annual meeting during the Experimental Biology 2017 meeting, to be held April 22–26 in Chicago.

“Complications of obesity are a significant cost burden for the medical system, especially given the prevalence of obesity,” said Thompson. “Understanding how maternal exposures impact obesity-related disease such as nonalcoholic fatty liver disease will allow us to develop lower cost preventative therapies to utilize up front rather than awaiting complications down the road.”

In the new study, the researchers found that the offspring of pregnant mice that consumed a high-fat diet developed liver fibrosis, a type of tissue scarring that is a sign that more serious disease will develop. The offspring weaned to a low-fat diet after maternal high-fat diet exposure developed fibrosis in adulthood. The livers of these mice also had signs of fat accumulation and inflammation.

The findings showed that developmental exposure to a high-fat diet can produce changes in the liver that last into adulthood, even with consumption of a low-fat diet after birth. These findings could have implications for people who are not obese themselves but who had obese mothers.

Additional analysis showed that bile acid levels and genes involved in bile-acid regulation were changed in the offspring exposed to the maternal high-fat diet. This finding suggests that the offspring may have a liver disease called cholestasis, which occurs when the normal flow of bile is impaired.

“If human offspring from obese mothers have a similar risk for developing fibrosis as we see in mice, we may be able to predict who is going to develop more serious disease,” said Thompson.  “Knowing who is most at risk for more serious disease will guide us on which patients should be treated more aggressively. Furthermore, understanding the biological mechanisms involved in this increased risk could lead to preventative therapies.”

The researchers are now working to further understand the mechanisms involved in the risk for disease progression. They also plan to use their mouse model of developmental high-fat diet exposure to evaluate preventative therapies that could be administered during pregnancy or to the offspring.

Lysosomes in Healthy Neurons and in Neurons with Juvenile Batten Disease

Researchers at Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital and King’s College London have discovered a treatment that improves the neurological symptoms in a mouse model of juvenile Batten disease. This discovery brings hope to patients and families affected by the disease that a treatment might be available in the future. The study appears in Nature Communications.

“Patients with juvenile Batten disease are born healthy and reach the expected developmental milestones of the first 4 to 6 years of age,” said senior author Dr. Marco Sardiello, assistant professor of molecular and human genetics at Baylor. “Then, these children progressively regress their developmental achievements; they gradually lose their vision and develop intellectual and motor disabilities, changes in behavior and speech difficulties. Most people with this condition live into their 20s or 30s. This inherited, rare disease has no cure or treatment other than palliative care.”

“As we started this project, patients and families affected by this condition visited us in the laboratory,” said first author Dr. Michela Palmieri, who was a postdoctoral fellow in the Sardiello lab during this project and currently is at the San Raffaele Scientific Institute in Milan, Italy. “We were deeply affected by our interactions with the patients and their families and this further motivated us to pursue this research with the hope that maybe one day it will lead to a treatment that will improve the lives of people affected by this condition.”

Juvenile Batten disease, a problem with cellular waste management

Like a large dynamic city, a cell carries out many activities that generate waste. Waste needs to be disposed of properly in order for the city to continue its activities without interruption. If waste management fails, waste progressively accumulates and eventually leads to interruption and paralysis of the activities of the city. Something similar happens in cells when cellular waste is not discarded.

The lysosomes are the structures in charge of clearing the waste produced by the cell’s regular functions. Lysosomes are sacs inside all cells containing enzymes that degrade cellular waste into its constituent components, which the cell can recycle or discard. When lysosomes fail and cellular waste accumulates, disease follows. Although all types of cells can be affected by defects in lysosomal waste processing and cellular waste accumulation, brain cells – neurons – are particularly susceptible.

“In juvenile Batten disease, one of nearly 50 human lysosomal storage disorders, the function of brain cells is progressively affected by the accumulation of cellular waste,” Sardiello said. “This accumulation leads to perturbation of many cellular processes, cell death and progressive regression of motor, physical and intellectual abilities.”

A novel approach to finding a treatment

“A few years back we discovered a protein in cells called TFEB, a master transcription factor that stimulates the cell to produce more lysosomes and degrade cellular waste more effectively,” said Sardiello. “So we thought about counteracting the accumulation of cellular waste in Batten disease by acting on TFEB.”

“We and others had found that enhancing the activity of TFEB genetically can help counter the accumulation of cellular waste in different diseases,” Sardiello said. “What was missing was a way to activate TFEB with a drug that in the future could be put in a pill to treat the condition. We focused on investigating how to activate TFEB pharmacologically.”

“We discovered that TFEB is under the control of another molecule called Akt, which is a kinase, a protein that can modify other proteins,” said Palmieri. “Akt has been studied in detail. There are drugs available that can modulate the activity of Akt.”

The researchers discovered that Akt modifies TFEB by adding a chemical group, a phosphate, to it. This chemical modification inactivates TFEB.

“We wanted to inhibit Akt to keep TFEB more active,” said Palmieri. “We discovered that the sugar trehalose is able to do this job.”

Testing a treatment for juvenile Batten disease in a mouse model of the condition

The scientists tested the effect of trehalose in a mouse model of juvenile Batten disease.

“We dissolved trehalose in drinking water and gave it to mice that model juvenile Batten disease,” said Sardiello. “Then, over time we examined the mice’s brain cells under the microscope. We found that the continuous administration of trehalose inhibits Akt and activates TFEB in the brains of the mice. More active TFEB meant more lysosomes in the brain and increased lysosomal activity, followed by decreased accumulation of the storage material and reduced tissue inflammation, which is one of the main features of this disease in people, and reduced neurodegeneration. These changes resulted in the mice living significantly longer. This is a good start toward finding a treatment for people with this disease.”

“We are very excited that these findings put research a step closer to understanding the mechanisms that underlie human lysosomal storage diseases,” said Palmieri. “We hope that our research will help us design treatments to counteract this and other human diseases with a pathological storage component, such as Alzheimer’s, Huntington’s and Parkinson’s diseases, and hopefully ameliorate the symptoms or reduce the progression of the disease for those affected.”

Naturally Occurring Mechanism of Cancer Drug-Resistance May Itself Be a Treatment Target

The use of proteasome inhibitors to treat cancer has been greatly limited by the ability of cancer cells to develop resistance to these drugs. But Whitehead Institute researchers have found a mechanism underlying this resistance—a mechanism that naturally occurs in many diverse cancer types and that may expose vulnerabilities to drugs that spur the natural cell-death process.

This finding—which also identifies a biomarker that can be used to gain a deeper understanding of the proteasome inhibitor-resistant state— is reported in the Proceedings of the National Academy of Sciences (PNAS) in an article entitled, Suppression of 19S proteasome subunits marks emergence of an altered cell state in diverse cancers.

Proteasomes are large protein complexes that mediate protein degradation and play a crucial role in maintaining protein equilibrium within the cell. When cells become cancerous, tremendous stresses are placed on the cellular machinery responsible for maintaining protein equilibrium—and that machinery is the target of anti-cancer drugs called proteasome inhibitors. Although proteasome inhibitors are very efficient in selective killing of cancer tumor cells grown in a dish (in-vitro), their success in the clinic has largely been undermined by the development of resistance—mechanisms of which are poorly understood.

“However, recently, we discovered a counterintuitive mechanism by which cells can acquire resistance to proteasome inhibitors in vitro,” explains Peter Tsvetkov, lead author of the PNAS article and a post-doctoral researcher at Whitehead Institute. “Now, in this report, we show that this mechanism is at work in many human cancers. Moreover, we have determined that the mechanism is symptomatic of a broadly altered state in the cell, with a unique gene signature and newly exposed vulnerabilities that can be targeted with existing drugs.” Notably, the mechanism was clearly associated with poor outcome in patients with the blood cancer myeloma, where proteasome inhibitors are a mainstay of treatment.

Analyzing data from thousands of cancer lines and tumors, the researchers found that those demonstrating resistance to proteasome inhibitor drugs were marked by suppressed expression of one or more of the cells’ proteasome cap subunits (which are a subsets of the larger proteasome). Suppressing the expression of even one of the many subunits making up the cap will impair the assembly of the whole cap, resulting in a proteasome-inhibitor resistant state. “This fact reinforces just how complex the mechanisms of resistance to chemotherapy can be,” says Luke Whitesell, a senior author of the PNAS paper and senior scientist at Whitehead Institute

Nevertheless, this new report reveals a strategy to address such resistance which may have broad utility. The researchers found that, beyond conferring resistance to proteasome inhibitors, the suppressed expression of proteasome subunits reflects a broad remodeling of the cell’s gene signature. Furthermore, this can also serve as a biomarker to stratify patients for treatment. “That signature marks a heritably altered and therapeutically relevant state in diverse cancers—a state that may expose vulnerability to specific drugs that are already in use in the clinic,” Tsvetkov observes. “Cancers can achieve this resistance by multiple mechanisms, genetic or epigenetic. But these findings point us to new strategies and novel compounds that can be developed as treatments that will be more effective for an array of cancer types because they are less susceptible to the emergence of resistance.”

Engineers design a new weapon against bacteria

Over the past few decades, many bacteria have become resistant to existing antibiotics, and few new drugs have emerged. A recent study from a U.K. commission on antimicrobial resistance estimated that by 2050, antibiotic-resistant bacterial infections will kill 10 million people per year, if no new drugs are developed.

To help rebuild the arsenal against infectious diseases, many scientists are turning toward naturally occurring proteins known as antimicrobial peptides, which can kill not only bacteria but other microbes such as viruses and fungi. A team of researchers at MIT, the University of Brasilia, and the University of British Columbia has now engineered an antimicrobial peptide that can destroy many types of bacteria, including some that are resistant to most antibiotics.

“One of our main goals is to provide solutions to try to combat antibiotic resistance,” says MIT postdoc Cesar de la Fuente. “This peptide is exciting in the sense that it provides a new alternative for treating these infections, which are predicted to kill more people annually than any other cause of death in our society, including cancer.”

De la Fuente is the corresponding author of the new study, and one of its lead authors along with Osmar Silva, a postdoc at the University of Brasilia, and Evan Haney, a postdoc at the University of British Columbia. Timothy Lu, an MIT associate professor of electrical engineering and computer science, and of biological engineering, is also an author of the paper, which appears in the Nov. 2 issue of Scientific Reports.

Improving on nature

Antimicrobial peptides, produced by all living organisms as part of their immune defenses, kill microbes in several different ways. First, they poke holes in the invaders’ cell membranes. Once inside, they can disrupt several cellular targets, including DNA, RNA, and proteins.

These peptides also have another critical ability that sets them apart from traditional antibiotics: They can recruit the host’s immune system, summoning cells called leukocytes that secrete chemicals that help kill the invading microbes.

Scientists have been working for several years to try to adapt these peptides as alternatives to antibiotics, as bacteria become resistant to existing drugs. Naturally occurring peptides can be composed of 20 different amino acids, so there is a great deal of possible variation in their sequences.

“You can tailor their sequences in such a way that you can tune them for specific functions,” de la Fuente says. “We have the computational power to try to generate therapeutics that can make it to the clinic and have an impact on society.”

In this study, the researchers began with a naturally occurring antimicrobial peptide called clavanin-A, which was originally isolated from a marine animal known as a tunicate. The original form of the peptide kills many types of bacteria, but the researchers decided to try to engineer it to make it even more effective.

Antimicrobial peptides have a positively charged region that allows them to poke through bacterial cell membranes, and a hydrophobic stretch that enables interaction with and translocation into membranes. The researchers decided to add a sequence of five amino acids that would make the peptides even more hydrophobic, in hopes that it would improve their killing ability.

This new peptide, which they called clavanin-MO, was very potent against many bacterial strains. In tests in mice, the researchers found that it could kill strains of Escherichia coli and Staphylococcus aureus that are resistant to most antibiotics.

Suppressing sepsis

Another key advantage of these peptides is that while they recruit immune cells to combat the infection, they also suppress the overactive inflammatory response that can cause sepsis, a life threatening condition.

“In this single molecule, you have a synthetic peptide that can kill microbes — both susceptible and drug-resistant — and at the same time can act as an anti-inflammatory mediator and enhance protective immunity,” de la Fuente says.

The researchers also found that these peptides can destroy certain biofilms, which are thin layers of bacterial cells that form on surfaces. That raises the possibility of using them to treat infections caused by biofilms, such as the Pseudomonas aeruginosa infections that often affect the lungs of cystic fibrosis patients. Or, they could be embedded into surfaces such as tabletops to make them resistant to microbial growth.

Other possible applications for these peptides include antimicrobial coatings for catheters, or ointments that could be used to treat skin infections caused by Staphylococcus aureus or other bacteria.

If these peptides are developed for therapeutic use, the researchers anticipate that they could be used either in stand-alone therapy or together with traditional antibiotics, which would make it more difficult for bacteria to evolve drug resistance. The researchers are now investigating what makes the engineered peptides more effective than the naturally occurring ones, with hopes of making them even better.

Heart disease, leukemia linked to dysfunction in nucleus

We put things into a container to keep them organized and safe. In cells, the nucleus has a similar role: keeping DNA protected and intact within an enveloping membrane. But a new study by Salk Institute scientists, detailed in the November 2 issue of Genes & Development, reveals that this cellular container acts on its contents to influence gene expression.

“Our research shows that, far from being a passive enclosure as many biologists have thought, the nuclear membrane is an active regulatory structure,” says Salk Professor Martin Hetzer, who is also holder of the Jesse and Caryl Philips Foundation chair. “Not only does it interact with portions of the genome to drive gene expression, but it can also contribute to disease processes when components are faulty.”

Using a suite of molecular biology technologies, the Salk team discovered that two proteins, which sit in the nuclear envelope, together with the membrane-spanning complexes they form, actively associate with stretches of DNA to trigger expression of key genes. Better understanding these higher-level functions could provide insight into diseases that appear to be related to dysfunctional nuclear membrane components, such as leukemia, heart disease and aging disorders.

Historically, the nuclear membrane’s main purpose was thought to be keeping the contents of the nucleus physically separated from the rest of the cell. Complexes of at least thirty different proteins, called nucleoporins, form gateways (pores) in the membrane, controlling what goes in or out. But as the Hetzer lab’s work on nucleoporins shows, these nuclear pore complexes (NPCs), beyond being mere gateways into the nucleus, have surprising regulatory effects on the DNA inside.

“Discovering that key regulatory regions of the genome are actually positioned at nuclear pores was very unexpected,” says Arkaitz Ibarra, a Salk staff scientist and first author of the paper. “And even more importantly, nuclear pore proteins are critical for the function of those genomic sites.”

Curious about all the regions of DNA with which nucleoporins potentially interact, the team turned to a human bone cancer cell line. The scientists used a molecular biology technique called DamID to pinpoint where two nucleoporins, Nup153 and Nup93, came into contact with the genome. Then they used several other sequencing techniques to understand which genes were being affected in those regions, and how.

The Salk team discovered that Nup153 and Nup93 interacted with stretches of the genome called super-enhancers, which are known to help determine cell identity. Since every cell in our body has the same DNA, what makes a muscle cell different from a liver cell or a nerve cell is which particular genes are turned on, or expressed, within that cell. In the Salk study, the presence of Nup153 and Nup93 was found to regulate expression of super-enhancer driven genes and experiments that silenced either protein resulted in abnormal gene expression from these regions. Further experiments in a lung cancer cell line validated the bone cancer line results: Nucleoporins in the NPC were found to interact with multiple super-enhancer regions to drive gene expression, while experiments that altered the NPC proteins made related gene expression faulty, even though the proteins still performed their primary role as gatekeepers in the cell membrane.

“It was incredible to find that we could perturb the proteins without affecting their gateway role, but still have nearby gene expression go awry,” says Ibarra.

The results bolster other work indicating that problems with the nuclear membrane play a role in heart disease, leukemia and progeria, a rare premature aging syndrome.

“People have thought the nuclear membrane is just a protective barrier, which is maybe the reason why it evolved in the first place. But there are many more regulatory levels that we don’t understand. And it’s such an important area because so far, every membrane protein that has been studied and found to be mutated or mis-localized, seems to cause a human disease,” says Hetzer.