Combination Strategy Could Hold Promise for Ovarian Cancer

 Johns Hopkins Kimmel Cancer Center researchers demonstrated that mice with ovarian cancer that received drugs to reactivate dormant genes along with other drugs that activate the immune system had a greater reduction of tumor burden and significantly longer survival than those that received any of the drugs alone.

The study already spurred a clinical trial in ovarian cancer patients. The investigators, led by graduate student Meredith Stone, Ph.D.; postdoctoral fellow Kate Chiappinelli, Ph.D.; and senior author Cynthia Zahnow, Ph.D., believe it could lead to a new way to attack ovarian cancer by strengthening the body’s natural immune response against these tumors. It was published in the Dec. 4, 2017, issue of the Proceedings of the National Academy of Sciences.

Ovarian cancer is currently the leading cause of death from gynecological malignancies in the U.S. “We’ve taken two types of therapies that aren’t very effective in ovarian cancer and put them together to make them better at revving up the immune system and attacking the tumor,” says Zahnow, associate professor of oncology at the Johns Hopkins Kimmel Cancer Center.

Zahnow says that a class of immunotherapy drugs known as checkpoint inhibitors, currently being studied at the Bloomberg~Kimmel Institute for Cancer Immunotherapy, helps the immune system recognize cancers and fight them off. The drugs have shown success in treating melanoma, nonsmall cell lung cancer and renal cell cancers, but they have had only modest effects on ovarian cancer.

Similarly, another class of drugs known as epigenetic therapies has been used to treat some types of cancer by turning on genes that have been silenced— either by the presence of chemical tags, known as methyl groups, or by being wound too tightly around protein spools, known as histones—but these drugs haven’t been effective against ovarian cancer either.

Zahnow and her colleagues became inspired to investigate a new way to treat ovarian cancer by two recent publications from their group that showed epigenetic drugs turn on immune signaling in ovarian, breast and colon cancer cells (Li et al., Oncotarget 2014). These immune genes are activated when epigenetic therapy turns on segments of ancient retroviruses that activate type 1 interferon signaling in the cells (Chiappinelli et al., Cell 2015).  Stone, Chiappinelli and Zahnow wanted to know if this increase in immune signaling could lead to the recruitment of tumor killing immune cells to the cancer.

Zahnow and her colleagues worked with a mouse model of the disease in which mouse ovarian cancer cells are injected into the animals’ abdomens to mimic human disease. These cells eventually develop into hundreds of small tumors, which cause fluid to collect within the abdomen, a condition known as ascites. Floating in this fluid is a milieu of both cancer and immune cells, offering a convenient way to keep tabs on both the tumor and the animals’ immune response.

The researchers started by pretreating the ovarian cancer cells outside of the animal in a culture dish with a DNA methyltransferase inhibitor (a drug that knocks methyl groups from DNA) called 5-azacytidine (AZA). After injecting these cells into mice, the researchers found that animals receiving the pretreated cells had significantly decreased ascites or tumor burden and significantly more cancer-fighting immune cells in the ascites fluid compared to those injected with untreated cells. These cells also had increased activity in a variety of genes related to immune response. Pretreating these cells with histone deacetylase inhibitors (HDACis), which help DNA uncoil from histones, didn’t affect the animals’ ascites or boost their immune response.

These early findings suggested that changes in gene activity induced by AZA cause the tumor cells themselves to summon immune cells to their location. In addition, when the researchers transplanted untreated cells into mice and treated the animals with both AZA and an HDACi, significantly more immune cells were in the ascites fluid, suggesting that the HDACi was acting on the animals’ immune systems. These mice also had decreased ascites, lower tumor burden and longer survival than mice that received just AZA.

When the researchers treated the mice with both AZA and an HDACi, along with an immune checkpoint inhibitor, they got the greatest response—the highest decreases in ascites and tumor burden, and the longest survival. Further experiments using immunocompromised mice showed that the immune system is pivotal to the action of these drugs, rather than the drugs themselves acting directly to kill tumor cells.

“We think that AZA and the HDACis are bringing the soldiers, or immune cells, to the battle. But the checkpoint inhibitor is giving them the weapons to fight,” says Zahnow, who also collaborated with epigenetics scientist Stephen Baylin, M.D., on this project.

The preclinical data generated through this study is already being used to help patients with ovarian cancer through an ongoing clinical trial to test the effectiveness of combining AZA and a checkpoint inhibitor. Future trials may add an HDACi to determine if it affects outcomes.

“Combining epigenetic therapy and a checkpoint blocker leads to the greatest reduction in tumor burden and increase in survival in our mouse model and may hold the greatest promise for our patients,” says Zahnow.

Deadly Lung Cancers Are Driven by Multiple Genetic Changes

Blood-Based Cancer Tests Reveal Complex Genomic Landscape of Non-Small Cell Lung Cancers

A new UC San Francisco–led study challenges the dogma in oncology that most cancers are caused by one dominant “driver” mutation that can be treated in isolation with a single targeted drug. Instead, the new research finds one of the world’s most deadly forms of lung cancer is driven by changes in multiple different genes, which appear to work together to drive cancer progression and to allow tumors to evade targeted therapy.

These findings — published online on November 6, 2017 in Nature Genetics — strongly suggest that new first-line combination therapies are needed that can treat the full array of mutations contributing to a patient’s cancer and prevent drug resistance from arising.

“Currently we treat patients as if different oncogene mutations are mutually exclusive. If you have an EGFR mutation we treat you with one class of drugs, and if you have a KRAS mutation we pick a different class of drugs. Now we see such mutations regularly coexist, and so we need to adapt our approach to treatment,” said Trever Bivona, MD, PhD, a UCSF Medical Center oncologist, associate professor in hematology and oncology, and member of the Helen Diller Family Comprehensive Cancer Center at UCSF.

Lung cancer is by far the leading cause of cancer death worldwide. Efforts to identify the genetic mutations that drive the disease have led to targeted treatments that improve life expectancy for many patients, but these drugs produce temporary remission at best — sooner or later, cancers inevitably develop drug resistance and return, deadlier than ever.

The new UCSF-led study — which analyzed tumor DNA from more than 2,000 patients in collaboration with Redwood City–based Guardant Health — is the first to extensively profile the genetic landscape of advanced-stage non–small cell (NSC) lung cancer, the most common form of the disease.

“The field has been so focused on treating the ‘driver’ mutation controlling a tumor’s growth that many assumed that drug-resistance had to evolve from new mutations in that same oncogene. Now we see that there are many different genetic routes a tumor can take to develop resistance to treatment,” said Bivona, who is also co-director of a new UCSF-Stanford Cancer Drug Resistance and Sensitivity Center funded by the National Cancer Institute. “This could also explain why many tumors are already drug-resistant when treatment is first applied.”

MDI Biological Laboratory study finds immune system is critical to regeneration

The answer to regenerative medicine’s most compelling question — why some organisms can regenerate major body parts such as hearts and limbs while others, such as humans, cannot — may lie with the body’s innate immune system, according to a new study of heart regeneration in the axolotl, or Mexican salamander, an organism that takes the prize as nature’s champion of regeneration.

The study, which was conducted by James Godwin, Ph.D., of the MDI Biological Laboratory in Bar Harbor, Maine, found that the formation of new heart muscle tissue in the adult axolotl after an artificially induced heart attack is dependent on the presence of macrophages, a type of white blood cell. When macrophages were depleted, the salamanders formed permanent scar tissue that blocked regeneration.

The study has significant implications for human health. Since salamanders and humans have evolved from a common ancestor, it’s possible that the ability to regenerate is also built into our genetic code.

Godwin’s research demonstrates that scar formation plays a critical role in blocking the program for regeneration. “The scar shoots down the program for regeneration,” he said. “No macrophages means no cardiac regeneration.”

Godwin’s goal is to activate regeneration in humans through the use of drug therapies derived from macrophages that would promote scar-free healing directly, or those that would trigger the genetic programs controlling the formation of macrophages, which in turn could promote scar-free healing. His team is already looking at molecular targets for drug therapies to influence these genetic programs.

“If humans could get over the fibrosis hurdle in the same way that salamanders do, the system that blocks regeneration in humans could potentially be broken,” Godwin explained. “We don’t know yet if it’s only scarring that prevents regeneration or if other factors are involved. But if we’re really lucky, we might find that the suppression of scarring is sufficient in and of itself to unlock our endogenous ability to regenerate.”

The prevailing view in regenerative biology has been that the major obstacle to heart regeneration in mammals is insufficient proliferation of cardiomyocytes, or heart muscle cells. But Godwin found that cardiomyocyte proliferation is not the only driver of effective heart regeneration. His findings suggest that research efforts should pay more attention to the genetic signals controlling scarring.

The extraordinary incidence of disability and death from heart disease, which is the world’s biggest killer, is directly attributable to scarring. When a human experiences a heart attack, scar tissue forms at the site of the injury. While the scar limits further tissue damage in the short term, over time its stiffness interferes with the heart’s ability to pump, leading to disability and ultimately to terminal heart failure.

In addition to regenerating heart tissue following a heart attack, the ability to unlock dormant capabilities for regeneration through the suppression of scarring also has potential applications for the regeneration of tissues and organs lost to traumatic injury, surgery and other diseases, Godwin said.

Godwin’s findings are a validation of the MDI Biological Laboratory’s unique research approach, which is focused on studying regeneration in a diverse range of animal models with the goal of gaining insight into how to trigger dormant genetic pathways for regeneration in humans. In the past year and a half, laboratory scientists have discovered three drug candidates with the potential to activate regeneration in humans.

“Our focus on the study of animals with amazing capabilities for regenerating lost and damaged body parts has made us a global leader in the field of regenerative medicine,” said Kevin Strange, Ph.D., MDI Biological Laboratory president. “James Godwin’s discovery of the role of macrophages in heart regeneration demonstrates the value of this approach: we won’t be able to develop rational and effective therapies to enhance regeneration in humans until we first understand regeneration works in animals like salamanders.”

Godwin, who is an immunologist, originally chose to look at the function of the immune system in regeneration because its role as the equivalent of a first responder at the site of an injury means that it is responsible for preparing the ground for tissue repairs. The recent study was a follow-up to an earlier study which found that macrophages also play a critical role in limb regeneration.

The next step is to study the function of macrophages in salamanders and compare them with their human and mouse counterparts. Ultimately, Godwin would like to understand why macrophages produced by adult mice and humans don’t suppress scarring in the same way as in axolotls and then identify molecules and pathways that could be exploited for human therapies.

Godwin holds a dual appointment with The Jackson Laboratory, also located in Bar Harbor, which is focused on the mouse as a model animal. The dual appointment allows him to conduct experiments that compare genetic programming in the highly regenerative animals used as models at the MDI Biological Laboratory with genetic programming in neonatal and adult mice.

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.”

Accelerating the Development of Next-Generation Cancer Therapies

To accelerate the development of next-generation cancer therapies, the Gene Editing Institute of the Helen F. Graham Cancer Center & Research Institute at Christiana Care Health System has agreed to provide genetically modified cell lines to Analytical Biological Services, Inc. (ABS) of Wilmington, Delaware.

Under a three-year agreement, the Gene Editing Institute will act as sole provider of gene editing services and genetically modified cell lines to ABS for replication, marketing and distribution to leading pharmaceutical and biomedical research companies worldwide.

“This agreement with ABS will speed the progress in the discovery of effective cancer therapies and accelerate the path to prevention, diagnosis and treatment of many forms of cancer,” said Nicholas J. Petrelli, M.D., the Bank of America endowed medical director of the Helen F. Graham Cancer Center & Research Institute at Christiana Care Health System.

“This partnership greatly enhances our capability to provide the highest quality genetically engineered cells for drug discovery,” said ABS President and CEO Charles Saller, Ph.D. “Our partners at the Gene Editing Institute are advancing molecular medicine, and their expertise adds a new dimension to our efforts to speed up drug discovery.”

“One goal of The Gene Editing Institute is to develop community partnerships that can advance translational cancer research,” said Eric Kmiec, Ph.D., founder and director of the Gene Editing Institute. “The Gene Editing Institute is driving innovation in gene engineering, and ABS has the know-how to grow and expand the cells in sufficient quantities, as well as to market them to pharmaceutical and biotechnology clients for drug screening and research.”

The Gene Editing Institute is a worldwide leader in the design of the tools that scientists need to manipulate and alter human genetic material easier and more efficiently than ever before. Scientists at the Gene Editing Institute have designed and customized an expanding tool-kit for gene editing, including the renowned CRISPR-Cas9 system, to permanently disrupt or knock out genes, add or knock in DNA fragments and create point mutations in genomic DNA. Last year, scientists at the Gene Editing Institute described in the journal Scientific Reports how they combined CRISPR and short strands of synthetic DNA to greatly enhance the precision and reliability of the CRISPR gene editing technique. Called Excision and Corrective Therapy, or EXACT, this new tool acts as both a Band-Aid and a template during gene mutation repairs.

Genetically modified cells can help advance cancer research. By inactivating a single gene, scientists can test if it affects tumor formation or somehow alters the response to cancer therapies. Similarly, inserting a gene into a cell can produce a gene product that is a target for potential new drugs.

“Gene editing and the CRISPR technology is having a major impact on anticancer drug development because it allows us to validate the target of the candidate drug,” said Dr. Kmiec. “Pharmaceutical companies want to use gene editing tools to identify new targets for anti-cancer drugs and to validate the targets they already have identified.”

The Delaware BioScience Association helped connect the Gene Editing Institute with ABS. “The collaborative agreement between the Gene Editing Institute and ABS exemplifies the power of building a strong biotech community, flourishing further innovation, and keeping businesses engaged and thriving in the state of Delaware,” said Helen Stimson, president and CEO of The Delaware BioScience Association. “The Delaware BioScience Association is committed to fostering meaningful relationships, such as this one, among its members, and establishing strategic partnerships that bolster the state’s innovation economy,” she said.

“This is one of those times when the forces of nature align to bring two perfectly matched skill sets together,” said Dr. Kmiec. “There is no question that our collaboration with ABS will accelerate the pace of drug discovery around the world.”

About The Gene Editing Institute

The Gene Editing Institute of Christiana Care Health System’s Helen F. Graham Cancer Center & Research Institute is unlocking the genetic mechanisms that drive cancer that can lead to new therapies and pharmaceuticals to revolutionize cancer treatment. Gene editing in lung cancer research has already begun setting the stage for clinical trials.

The Gene Editing Institute is integrated into the Molecular Screening Facility at The Wistar Institute in Philadelphia, PA, where its innovative gene-editing technologies are available to research projects at Wistar and to external users. Working with Wistar scientists, the Gene Editing Institute has begun research to conduct a clinical trial in melanoma. With funding from the National Institutes of Health, the Gene Editing Institute is partnering with A.I. duPont/Nemours to develop a gene editing strategy for the treatment of sickle cell anemia and leukemia. Under a grant from the U.S.–Israel Binational Industrial Research & Development Foundation, the Gene Editing Institute is working with Jerusalem-based NovellusDx to improve the efficiency and speed of cancer diagnostic screening tools. This work could lead to earlier identification of genetic mechanisms responsible for both the onset and progression of many types of cancers and the development of individualized therapeutics.

Gene Editing Institute scientists also provide instruction in the design and implementation of genetic tools. Partnerships with Bio-Rad Inc. and the Delaware Technical and Community College are producing gene editing curricula and teacher training workshops for both community colleges and secondary schools.

Study Unlocks How Changes in Gene Activity Early During Therapy Can Establish the Roots of Drug-Resistant Melanoma

FINDINGS
A UCLA-led study of changes in gene activity in BRAF-mutated melanoma suggests these epigenomic alterations are not random but can explain how tumors are already developing resistance as they shrink in response to treatment with a powerful class of drugs called MAP kinase (MAPK)-targeted inhibitors. The discovery marks a potential milestone in the understanding of treatment-resistant melanoma and provides scientists with powerful targets for drug development and new clinical studies.

BACKGROUND
Approximately 50 percent of advanced melanoma tumors are driven to grow by the presence of BRAF mutations. The use of BRAF inhibitors, both alone and in combination with another MAPK pathway inhibitor called MEK, have shown unprecedented responses as a treatment for these types of tumors, rapidly shrinking them. However, BRAF-mutated tumors frequently show early resistance to treatment and respond only partially to BRAF inhibitors, leaving behind cancer cells that may evolve to cause eventual tumor regrowth.

The findings build upon research by Dr. Roger Lo, professor of medicine (dermatology) and molecular and medical pharmacology at the David Geffen School of Medicine, and lead author of the new study. Previously, he discovered that epigenomic alterations (via a regulatory mechanism called CpG methylation) accounted for a wide range of altered gene activities and behaviors in BRAF-mutant therapy-resistant melanoma tumor cells. The loss of tumor-fighting immune or T-cells in drug-resistant tumors may lead to resistance to subsequent salvage immunotherapy, Lo said, and drug resistance can grow at the same time that anti-tumor immune cells diminish and weaken.

This means that in some patients the melanoma might develop resistance to both MAP kinase-targeted therapy and anti-PD-L1 antibodies, which capitalize on the abundance of immune cells inside the tumor to unleash their anti-cancer activities. Lo concluded that non-genomic, epigenomic, and immunologic evolution of melanoma explain why patients relapse on MAPK-targeted therapies.

Along with co-first authors, Drs. Chunying Song, Marco Piva and Lu Sun, Lo hypothesized that epigenomic and immunologic resistance evident during clinical relapse may be developing already during the first few weeks of therapy as the tumors shrink and clinical responses are viewed as successes. If this proves to be true, then scientists could potentially identify combination treatments that suppress the earliest resistance-promoting activities.

METHOD
Lo’s team utilized state-of-the-art technologies to comprehensively profile recurrent patterns of gene activity changes. They analyzed 46 samples of patients’ melanoma tumors, both before and early during MAPK therapy. They also replicated the process outside of the human body, modeling both non-genomic drug resistance by growing melanoma cell lines from patients’ tumors and immunologic resistance in mouse melanoma. Patient-derived cell lines and mouse melanoma tumors were treated with drugs that block the MAP kinase pathway and sampled at various times over the course of the study to track gene activity changes.

The researchers found that MAPK therapies fostered CpG methylation and gene activity reprogramming of tumors. This reduced the tumor cells’ dependence on the mutated BRAF protein, and switched their growth and survival strategies to rely on proteins called receptor-tyrosine kinases and PD-L2. In addition, PD-L2 gene activity was found to be turned on in immune cells surrounding the tumor cells. They also demonstrated that blocking PD-L2 with an antibody could prevent the loss of T-cells in the tumor’s immune microenvironment and suppressing therapy resistance.

Lo’s team continues to identify other adaptations during this early phase of therapy that could be targets of future combination treatment regiments.

IMPACT
More than 87,000 new cases of melanoma will be diagnosed this year in the United States alone, and more than 9,500 people are expected to die of the disease.

The findings can prompt drug development and new clinical studies based on epigenetic or gene expression and immune targets in combination with mutation-targeted therapies. As scientists learn what these mechanisms of tumor resistance are, they can combine inhibitor drugs that block multiple resistance routes and eventually make the tumors shrink for much longer or go away completely, Lo said.

JOURNAL
The research is published online in Cancer Discovery, the peer-reviewed journal of the American Association of Cancer Research.

AUTHORS
UCLA’s Dr. Roger Lo is senior author. The co-first authors are Drs. Chunying Song, Marco Piva and Lu Sun at the David Geffen School of Medicine at UCLA. Other authors are Drs. Aayoung Hong, Gatien Moriceau, Xiangju Kong, Hong Zhang, Shirley Lomeli, Jin Qian, Clarissa Yu, Robert Damoiseaux, Philip Scumpia, Antoni Ribas and Willy Hugo at UCLA; and Mark Kelley, Kimberly Dahlman, Jeffrey Sosman, Douglas Johnson at Vanderbilt University. Lo, Damoiseaux, Scumpia and Ribas are members of UCLA’s Jonsson Comprehensive Cancer Center.

FUNDING
The research was supported by the National Institutes of Health, the American Cancer Society, the Melanoma Research Alliance, the American Skin Association, the American Association for Cancer Research, the National Cancer Center, the Burroughs Wellcome Fund, the Ressler Family Foundation, the Ian Copeland Melanoma Fund, the SWOG/Hope Foundation, the Steven C. Gordon Family Foundation, the Department of Defense Horizon Award, the Dermatology Foundation, and the ASCO Conquer Cancer Career Development Award.

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.”

Genetically enhanced, cord-blood derived immune cells strike B-cell cancers

Immune cells with a general knack for recognizing and killing many types of infected or abnormal cells also can be engineered to hunt down cells with specific targets on them to treat cancer, researchers at The University of Texas MD Anderson Cancer Center report in the journal Leukemia.

The team’s preclinical research shows that natural killer cells derived from donated umbilical cords can be modified to seek and destroy some types of leukemia and lymphoma. Genetic engineering also boosts their persistence and embeds a suicide gene that allows the modified cells to be shut down if they cause a severe inflammatory response.

A first-in-human phase I/II clinical trial of these cord-blood-derived, chimeric antigen receptor-equipped natural killer cells opened at MD Anderson in June for patients with relapsed or resistant chronic lymphocytic leukemia (CLL), acute lymphocytic leukemia (ALL), or non-Hodgkin lymphoma. All are cancers of the B cells, another white blood cell involved in immune response.

“Natural killer cells are the immune system’s most potent killers, but they are short-lived and cancers manage to evade a patient’s own NK cells to progress,” said Katy Rezvani, M.D., Ph.D., professor of Stem Cell Transplantation and Cellular Therapy.

“Our cord-blood derived NK cells, genetically equipped with a receptor that focuses them on B-cell malignancies and with interleukin-15 to help them persist longer — potentially for months instead of two or three weeks — are designed to address these challenges,” Rezvani said.

Moon Shots Program funds project

The clinical trial is funded by MD Anderson’s Moon Shots Program™, designed to more rapidly develop life-saving advances based on scientific discoveries.

The chimeric antigen receptor (CAR), so-called because it’s added to the cells, targets CD19, a surface protein found on B cells.

In cell lines and mouse models of lymphoma and CLL, CD19-targeted NK cells killed cancer cells and extended survival of animals compared to simply giving NK cells alone. Addition of IL-15 to the CD19 receptor was crucial for the longer persistence and enhanced activity of the NK cells against tumor cells.

NK cells are a different breed of killer from their more famous immune system cousins, the T cells. Both are white blood cells, but T cells are highly specialized hunters that look for invaders or abnormal cells that bear a specific antigen target, kill them and then remember the antigen target forever.

Natural killers have an array of inhibitory and activating receptors that work together to allow them to detect a wider variety of infected, stressed or abnormal cells.

“By adding the CD19 CAR, we’re also turning them into guided missiles,” said Elizabeth Shpall, M.D., professor of Stem Cell Transplantation and Cell Therapy.

Using a viral vector, the researchers transduce NK cells taken from cord blood with the CD19 CAR, the IL-15 gene, and an inducible caspase-9-based suicide gene.

Cell line tests found the engineered NK cells to be more efficient killers of lymphoma and CLL cells, compared to unmodified NK cells, indicating the engineered cells’ killing was not related to non-specific natural killer cell cytotoxicity.

Another experiment showed the engineered cord blood NK cells killed CLL cells much more efficiently than NK cells taken from CLL patients and engineered, highlighting the need to transplant CAR-engineered NK cells from healthy cord blood rather than use a patient’s own cells.

Suicide gene to counter cytokine release syndrome

Mouse model lymphoma experiments using a single infusion of low dose NK cells resulted in prolongation of survival. At a higher, double dose, none of the mice treated with the CD19/IL-15 NK cells died of lymphoma, with half surviving for 100 days and beyond. All mice treated with other types of NK cells died by day 41.

A proportion of mice treated with the higher dose of engineered NK cells died of cytokine release syndrome, a severe inflammatory response that also occurs in people treated with CAR T cells.

To counteract this toxicity, the researchers incorporated a suicide gene (iC9) that can be activated to kill the NK cells by treatment with a small-molecule dimerizer. This combination worked to swiftly reduce the engineered NK cells in the mouse model.

Subsequent safety experiments were conducted in preparation for the clinical trial. Rezvani, the principal investigator of the clinical trial, says the protocol calls for vigilance for signs of cytokine release syndrome, treatment with steroids and tocilizumab for low-grade CRS with AP1903 added to activate the suicide gene for grade 3 or 4 CRS.

NK CARs available off the shelf

T cells modified with chimeric antigen receptors against CD19 have shown efficacy in clinical trials. In these therapies, a patient’s own T cells are modified, expanded, and given back to the patient, a process that takes weeks. Finding a matched donor for T cells would be a challenge, but would be necessary because unmatched T cells could attack the recipient’s normal tissue – graft vs. host disease.

Rezvani and Shpall have given patients cord-blood derived NK cells in a variety of clinical trials and found that they do not cause graft vs. host disease, therefore don’t have to be matched. NK cells can be an off-the-shelf product, prepared in advance with the necessary receptor and given promptly to patients.

“CAR NK cells are scalable in a way that CAR T cells are not,” Rezvani noted.

A strength of T cells is the development of memory cells that persist and repeatedly attack cells bearing the specific antigen that return. NK cells do not seem to have a memory function, but Rezvani says the experience of the longer-lived mice, which are now more than a year old, raises the possibility that a prolonged NK cell attack will suffice.

Shpall, Rezvani and colleagues are developing cord blood NK CARs for other targets in a variety of blood cancers and solid tumors.

MD Anderson and the researchers have intellectual property related to the engineered NK cells, which is being managed in accordance with the institution’s conflict-of-interest rules.

Shpall founded and directs MD Anderson’s Cord Blood Bank, originally established to provide umbilical cord blood stem cells for patients who need them but cannot get a precise donor match. Donated by mothers who deliver babies at seven Houston hospitals and two others from California and Michigan, the bank now has 26,000 cords stored. MD Anderson researchers pioneered the extraction and expansion of NK cells from umbilical cords.

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.

Genetic modifier for Huntington’s disease progression identified

A team led by UCL and Cardiff University researchers has developed a novel measure of disease progression for Huntington’s disease, which enabled them to identify a genetic modifier associated with how rapidly the disease progresses.

“We’ve identified a gene that could be a target for treating Huntington’s disease. While there’s currently no cure for the disease, we’re hopeful that our finding could be a step towards life-extending treatments,” said Dr Davina Hensman Moss (UCL Huntington’s Disease Centre, UCL Institute of Neurology), one of the lead authors of the Lancet Neurology study.

Huntington’s disease (HD) is a fatal neurological disease caused by a genetic mutation. Larger mutations are linked to rapidly progressing disease, but that does not account for all aspects of disease progression. Understanding factors which change the rate of disease progression can help direct drug development and therapies.

The research team used the high quality phenotypic data from the intensively studied TRACK-HD cohort of people with the HD gene mutation. They established that different symptoms of disease progress in parallel, so they were able to combine the data from 24 cognitive, motor and MRI brain imaging variables to generate their progression score for genetic analysis.

They then looked for areas of the genome associated with their progression measure, and found a significant result in their sample of 216 people, which they then validated in a larger sample of 1773 people from a separate cohort, the European Huntington’s Disease Network (EHDN) REGISTRY study.

The genetic signal is likely to be driven by the gene MSH3, a DNA repair gene which has been linked to changes in size of the HD mutation. The researchers identified that a variation in MSH3 encodes an amino acid change in the gene. MSH3 has previously been extensively implicated in the pathogenesis of HD in both mouse and cell studies. The group’s findings may also be relevant to other diseases caused by repeats in the DNA, including some spinocerebellar ataxias.

Dr Hensman Moss said: “The gene variant we pinpointed is a common variant that doesn’t cause problems in people without HD, so hopefully it could be targeted for HD treatments without causing other problems.”

Professor Lesley Jones (Cardiff University), who co-led the study, said: “The strength of our finding implies that the variant we identified has a very large effect on HD, or that the new progression measure we developed is a much better measure of the relevant aspects of the disease, or most likely, both.”

The researchers say their study demonstrates the value of getting high quality data about the people with a disease when doing genetic studies.

Professor Sarah Tabrizi (UCL Huntington’s Disease Centre), who co-led the study said: “This is an example of reverse translation: these novel findings we observed in people with HD support many years of basic laboratory work in cells and mice. Now we know that MSH3 is critical in the progression of HD in patients, we can focus our attention on it and how this finding may be harnessed to develop new therapies that slow disease progression.”

Altered virus may expand patient recruitment in human gene therapy trials

For many patients, participating in gene therapy clinical trials isn’t an option because their immune system recognizes and fights the helpful virus used for treatment. Now, University of Florida Health and University of North Carolina researchers have found a solution that may allow it to evade the body’s normal immune response.

The discovery, published May 29 in the Proceedings of the National Academy of Sciences, is a crucial step in averting the immune response that prevents many people from taking part in clinical trials for various disorders, said Mavis Agbandje-McKenna, Ph.D., a professor in the University of Florida College of Medicine department of biochemistry and molecular biology and director of the Center for Structural Biology.

During gene therapy, engineered viruses are used to deliver new genes to a patient’s cells. While the recombinant adeno-associated virus, or AAV, is effective at delivering its genetic cargo, prior natural exposure to AAV results in antibodies in some people. As many as 70 percent of patients have pre-existing immunity that makes them ineligible for gene therapy clinical trials, Agbandje-McKenna said.

The findings provide a road map for designing virus strains that can evade neutralizing antibodies, said Aravind Asokan, Ph.D., an associate professor in the department of genetics at the University of North Carolina, who led the study. At UF Health, the structural “footprints” where pre-existing antibodies interact with the virus were identified using cryo-electron microscope resources provided by the UF College of Medicine and the UF Office of Research’s Division of Sponsored Programs. The UNC researchers then evolved new viral protein shells. Using serum from mice, rhesus monkeys and humans, the researchers showed that the redesigned virus can slip past the immune system.

“This is the blueprint for producing AAV strains that could help more patients become eligible for human gene therapy. Now we know how to do it,” Agbandje-McKenna said.

While the findings prove that one variation of AAV can be evolved, further study in preclinical models is needed before the approach can be tested in humans. Next, the immune profile of one particularly promising virus variant will need to be evaluated in a larger number of human serum samples, and dose-finding studies are needed in certain animal models. Researchers may also need to study whether the same virus-manipulating technique can be used in a broader range of gene therapy viruses, Agbandje-McKenna said.

Although human gene therapy remains an emerging field and has yet to reach patients on a wide scale, researchers elsewhere have used AAV therapy to successfully treat hemophilia, a blood-clotting disorder, in a small trial. It has also been or is now being studied as a way to treat hereditary blindness, certain immune deficiencies, neurological and metabolic disorders, and certain cancers.

The latest findings are the result of more than 10 years of studying the interactions between viruses and antibodies and a long-standing collaboration with Asokan, who heads the synthetic virology group at the UNC Gene Therapy Center, according to Agbandje-McKenna.

Study reveals sweetened drinks during pregnancy puts infants at higher risk for obesity

A recent Danish study of children born to women with gestational diabetes, found that maternal daily consumption of artificially-sweetened beverages during pregnancy was associated with a higher body mass index score and increased risk of overweight/obesity at 7 years.

Artificial sweeteners are widely replacing caloric sweeteners, due to the health concern related to sugar-sweetened beverages (SSBs) within the general population. Artificially sweetened beverages have been considered as potential healthier alternatives, although this study suggests contrary. This study looks to investigate the long-term impact of ASBs consumption during pregnancy on offspring obesity risk in relation to offspring growth through age 7 years among children born to women with gestational diabetes .

In particular, children born to women with gestational diabetes –the most common pregnancy complication affecting approximately 16% of pregnancies worldwide–represent a high-risk phenotype, which may serve as a unique model to study the early origins of obesity. Further evidence has linked nutritional biological disruptions during pregnancy to fetal development and obesity risk in later life. Thus, the authors argue it is important to identify modifiable dietary factors that may prevent offspring obesity and maternal complications.

The study investigated 918 mother and child pairs from the Danish National Birth Cohort. Enrolled participants completed four telephone interviews at gestational weeks 12 and 30, and 6 and 18 months postpartum, which collected data on sociodemographic, perinatal, and clinical factors. In addition, maternal dietary intake was assessed by a food questionnaire during pregnancy. Offspring body mass index scores and overweight/obesity status were calculated using weight and length/height at birth, 5 and 12 months, and 7 years. When the children were 7 years old, a follow-up questionnaire about the child’s health and development was delivered to the parents.

Results showed that approximately half (45.4%) of women reported consuming artificially sweetened beverages during pregnancy. Whereas 68.7% reported consuming SSBs, artificially sweetened beverage consumption–compared to never consuming artificially sweetened beverages–by pregnant women with gestational diabetes was associated with a 1.57 increased risk of being overweight for gestational age babies and a 1.93-fold increase in overweight/obesity risk at 7 years after adjustment for major maternal and offspring risk factors.

Associations were more pronounced in male than female offspring. Substituting SSBs with artificially sweetened beverages was associated with an increased risk of offspring overweight/obesity at 7 years whereas substitution of artificially sweetened beverage with water was associated with a 17% reduced risk. The findings illustrated a positive association between uterus exposure to artificially sweetened beverages and birth size and risk of overweight/obesity at 7 years.

One gene closer to regenerative therapy for muscular disorders

A detour on the road to regenerative medicine for people with muscular disorders is figuring out how to coax muscle stem cells to fuse together and form functioning skeletal muscle tissues. A study published June 1 by Nature Communications reports scientists identify a new gene essential to this process, shedding new light on possible new therapeutic strategies.

Led by researchers at the Cincinnati Children’s Hospital Medical Center Heart Institute, the study demonstrates the gene Gm7325 and its protein – which the scientists named “myomerger” – prompt muscle stem cells to fuse and develop skeletal muscles the body needs to move and survive. They also show that myomerger works with another gene, Tmem8c, and its associated protein “myomaker” to fuse cells that normally would not.

In laboratory tests on embryonic mice engineered to not express myomerger in skeletal muscle, the animals did not develop enough muscle fiber to live.

“These findings stimulate new avenues for cell therapy approaches for regenerative medicine,” said Douglas Millay, PhD, study senior investigator and a scientist in the Division of Molecular Cardiovascular Biology at Cincinnati Children’s. “This includes the potential for cells expressing myomaker and myomerger to be loaded with therapeutic material and then fused to diseased tissue. An example would be muscular dystrophy, which is a devastating genetic muscle disease. The fusion technology possibly could be harnessed to provide muscle cells with a normal copy of the missing gene.”

Bio-Pioneering in Reverse

One of the molecular mysteries hindering development of regenerative therapy for muscles is uncovering the precise genetic and molecular processes that cause skeletal muscle stem cells (called myoblasts) to fuse and form the striated muscle fibers that allow movement. Millay and his colleagues are identifying, deconstructing and analyzing these processes to search for new therapeutic clues.

Genetic degenerative disorders of the muscle number in the dozens, but are rare in the overall population, according to the National Institutes of Health. The major categories of these devastating wasting diseases include: muscular dystrophy, congenital myopathy and metabolic myopathy. Muscular dystrophies are a group of more than 30 genetic diseases characterized by progressive weakness and degeneration of the skeletal muscles that control movement. The most common form is Duchenne MD.

Molecular Sleuthing

A previous study authored by Millay in 2014 identified myomaker and its gene through bioinformatic analysis. Myomaker is also required for myoblast stem cells to fuse. However, it was clear from that work that myomaker did not work alone and needed a partner to drive the fusion process. The current study indicates that myomerger is the missing link for fusion, and that both genes are absolutely required for fusion to occur, according to the researchers.

To find additional genes that regulate fusion, Millay’s team screened for those activated by expression of a protein called MyoD, which is the primary initiator of the all the genes that make muscle. The team focused on the top 100 genes induced by MyoD (including GM7325/myomerger) and designed a screen to test the factors that could function within and across cell membranes. They also looked for genes not previously studied for having a role in fusing muscle stem cells. These analyses eventually pointed to a previously uncharacterized gene listed in the database – Gm7325.

Researchers then tested cell cultures and mouse models by using a gene editing process called CRISPR-Cas9 to demonstrate how the presence or absence of myomaker and myomerger – both individually and in unison – affect cell fusion and muscle formation. These tests indicate that myomerger-deficient muscle cells called myocytes differentiate and form the contractile unit of muscle (sarcomeres), but they do not join together to form fully functioning muscle tissue.

Looking Ahead

The researchers are building on their current findings, which they say establishes a system for reconstituting cell fusion in mammalian cells, a feat not yet achieved by biomedical science.

For example, beyond the cell fusion effects of myomaker and myomerger, it isn’t known how myomaker or myomerger induce cell membrane fusion. Knowing these details would be crucial to developing potential therapeutic strategies in the future, according to Millay. This study identifies myomerger as a fundmentally required protein for muscle development using cell culture and laboratory mouse models.

The authors emphasize that extensive additional research will be required to determine if these results can be translated to a clinical setting.

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.

Genetic risk factor for equine eye cancer identified

Squamous cell carcinoma (SCC) is the most common cancer found in equine eyes and the second most common tumor of the horse overall. Thanks to a recent genetic study led by UC Davis, horse owners can now identify horses at risk for ocular SCC and make informed breeding decisions.

In the cover article for the International Journal of Cancer, scientists announced the discovery of a genetic mutation in horses that is hypothesized to impact the ability of damage specific DNA binding protein 2 (DDB2) to carry out its standard role. Normally, the protein conducts DNA surveillance, looking for UV damage and then calling in other proteins to help repair the harm.

“The mutation is predicted to alter the shape of the protein so it can’t recognize UV-damaged DNA,” said Dr. Rebecca Bellone, an equine geneticist at the Veterinary Genetics Laboratory and associate adjunct professor at UC Davis School of Veterinary Medicine. “We believe this is a risk factor because cells can’t repair the damage and accumulate mutations in the DNA that lead to cancer.”

Several equine breeds, including Haflingers, have a higher occurrence of limbal SCC, the form of the disease that originates in the junction between the cornea–the clear surface of the eyeball–and the conjunctiva that covers the white of the eye. A former study, conducted by Bellone and one of her research partners, Dr. Mary Lassaline, found that about 26 percent of SCC-affected horses in a retrospective study were Haflingers.

“The fact that we see this type of cancer in a relatively small breed with a narrow pedigree makes it a good model to study,” said Lassaline, associate professor of clinical equine ophthalmology at the UC Davis School of Veterinary Medicine.

Ocular SCC can lead to vision loss and even loss of the eye. In advanced cases, SCC can be locally invasive and spread to the orbit and eat away at bone and eventually the brain–leading to loss of life. These recent study results offer a huge application in identifying horses at risk for developing SCC on two fronts.

“One, it’s important for the individual horse with a known risk and we can be more vigilant about exams as well as protecting their eyes from UV exposure,” Lassaline said. “If detected early, we can remove the tumor and save the eye. Secondly, that knowledge is important for making informed breeding decisions.”

Scientists at the UC Davis Veterinary Genetics Laboratory were able to develop a genetic test for horses based on the research. The test determines if a horse carries the mutation or has two copies of the risk variant, putting it at highest risk for cancer.

In addition to improving the health of horses, this study may have implications for human health as well. The gene found to be associated with equine SCC is also linked in humans to xeroderma pigmentosum complementation group E–a disease characterized by sun sensitivity and increased risk of cutaneous SCC and melanoma.

“There is an interesting parallel in humans with mutation in this protein,” Bellone said. “Now we have the ability to understand why it’s affecting the eyes of horses as well as the skin of humans.”

Stalking the ‘Unknown Enemy’: Doctors Turn Scope On Rare Diseases


WHITTIER, Calif. — Lynn Whittaker stood in the hallway of her home looking at the framed photos on the wall. In one, her son, Andrew, is playing high school water polo. In another, he’s holding a trombone.

The images show no hint of his life today: the seizures that leave him temporarily paralyzed, the weakness that makes him fall over, his labored speech, his scrambled thoughts.

Andrew, 28, can no longer feed himself or walk on his own. The past nine years have been a blur of doctor appointments, hospital visits and medical tests that have failed to produce answers.

“You name it, he doesn’t have it,” his mother said.

Andrew has never had a clear diagnosis. He and his family are in a torturous state of suspense, hanging their hopes on every new exam and evaluation.

Recently, they have sought help from the Undiagnosed Diseases Network, a federally funded coalition of universities, clinicians, hospitals and researchers dedicated to solving the nation’s toughest medical mysteries. The doctors and scientists in the network harness advances in genetic science to identify rare, sometimes unknown, illnesses.

At UCLA, one of the network’s sites, Andrew’s medical team would later map his genetic makeup, then bring him in for a week of exams and consultations with specialists.

Writing A New Disease Encyclopedia

The Undiagnosed Diseases Network was founded in 2015 with a $43 million grant from the National Institutes of Health (NIH). Building on work already being done at NIH, the initiative expanded to include universities across the country: Duke, Columbia and Stanford are among the other sites. The goals are to provide answers for patients with mysterious diseases and to learn more about the disorders.

A proposal last month by President Donald Trump to cut the NIH budget by $5.8 billion could put the program in jeopardy.

Even with the best technology and the finest brains at work, progress is slow. Since its launch, the network has received nearly 1,400 applications on behalf of patients. It has accepted 545 for review so far. Just 74 of the cases have been diagnosed, including 11 at UCLA. Andrew Whittaker’s case is among many in progress.

It’s like battling “an unknown enemy,” said Euan Ashley, one of the principal investigators of the network’s Stanford University site. “That is a particular form of torment that other patients don’t have.”

A diagnosis can end families’ painful odyssey while helping physicians and scientists better understand rare diseases and human physiology, said Rachel Ramoni, former executive director of the network, which is based at Harvard University.

Researchers throughout the network use advanced medical technology. For example, to study patients’ gene expression and disease progression, they can make models using nearly transparent zebrafish, whose genetic structure is similar to that of humans. And scientists can conduct whole genome sequencing, which allows the medical team to read a patient’s DNA and identify changes that can reveal what may be causing a disease.

“We have powerful techniques to look at every gene that is being expressed as well as every gene that is inherited,” said Stanley Nelson, one of UCLA’s principal investigators and the lead doctor on Andrew’s case. “This is an example of true precision medicine.”

Nelson said the network can examine all known genes — not just the ones believed to have mutations that cause diseases. Doing that can lead to the discovery of new illnesses.

“Part of what we have to do is keep building that library, that encyclopedia of what gene and what gene mutations cause what symptoms,” Nelson said. “It’s just incomplete at this moment.”

Already the work is helping patients and their families come to terms with their illnesses. In one case, at Stanford, a toddler was diagnosed with two rare diseases, including a connective tissue disorder called Marfan Syndrome, after doctors conducted a form of sequencing that looks for changes in coded genetic segments known as exons.

Sometimes answers come from something decidedly lower-tech: collaboration among clinicians and researchers who share experiences, data and expertise.

“A lot of times your ability to be diagnosed depends on who is in the room,” Ramoni said. “And what we are doing with the network is we are expanding exponentially the number of people in the room.”

Doctors at one institution might think their patient is a unique case, only to learn that colleagues elsewhere have a patient with a similar illness. But even when diseases are diagnosed or gene mutations are discovered, treatments may still not be available.

A Life-Changing Mystery

Andrew Whittaker’s odyssey began one afternoon at age 19, when he started trembling and couldn’t speak. Doctors suspected he was suffering from anxiety and prescribed medication to control it. But Andrew said he continued to have “episodes,” during which everything just went blank.

“It’s like there’s not enough blood going to your brain,” he said. “You can’t think.”

Andrew also started losing his balance and falling off his bicycle. The family visited several hospitals. Doctors discovered that the receptors in his brain were malfunctioning and that he lacked sufficient dopamine, a chemical compound in the body responsible for transmitting signals between nerve cells. As a result, Andrew has some symptoms similar to those of Parkinson’s disease. Doctors also confirmed he was having seizures.

Still, Andrew’s symptoms didn’t add up to any known disease.

One afternoon last fall at precisely noon, as Andrew sat propped up on the living room couch, Lynn’s phone alarm sounded, signaling it was time for his medication. Lynn pried open Andrew’s hand, which was clenched into a fist, and dropped in the pills.

To keep Andrew from falling, the family has lowered his bed and removed carpet from the house. They also bought him a wheelchair. Their precautions don’t always work. One morning, Lynn was in the kitchen when she heard a crash. “I ran in there and he’s laid flat on his back,” she said.

Lynn gives Andrew his medicine. (Heidi de Marco/KHN)

Lynn says not knowing what is causing her son’s disease is devastating. “We don’t know what we are dealing with,” she says. “We just know it’s worsening … and it’s like somebody ripping your insides out.” (Heidi de Marco/KHN)

Andrew is close to his mom. But he also gets frustrated. He can’t shower or dress without her help. He’s had to give up the things he loved to do: printing T-shirts. Skateboarding. Shooting short films. He’s lost friends and can’t imagine dating anymore.

“Girlfriends? Forget about it,” he said, his face twitching as he talks. “They want a guy who can do stuff for them, not the other way around.”

Running The Medical Gauntlet

On a Monday morning in late January, Andrew and his parents were in an exam room at UCLA. Lynn teased her son, saying she was going to put him in a freezer until doctors figured out what was wrong.

“Then we’ll pull you back out again,” she said, smiling.

“I’ll never get pulled out,” Andrew responded.

“Yes, you will,” she said. “You will.”

 

Nelson, Andrew’s main doctor, walked into the room. He told Andrew he’d read through the medical records. “We’re going to try to figure you out.”

The work Nelson does is personal. His teenage son, Dylan, has Duchenne muscular dystrophy, a genetic disorder that causes muscle degeneration and weakness. Nelson knows his son’s disease will eventually take his life, but he said having a diagnosis makes all the difference.

“My heart very much goes out to the families that don’t even get an adequate diagnosis,” he said.

Nelson suspects that Andrew’s disease is genetic as well.

He asked the Whittakers to describe their son’s journey, then he conducted a short physical exam, asking Andrew to push against his hand and touch his own nose. Andrew trembled and his shoulders tensed, but he did it.

The rest of the week, Andrew underwent several other diagnostic tests, including a muscle biopsy, an EEG, MRI and a lumbar puncture. He remained upbeat, though running the medical gauntlet clearly wore him out. He also met with UCLA specialists in brain degeneration and muscle and nerve disorders.

At week’s end, Nelson sat down with the family to explain what he’d found. He had reviewed Andrew’s genome and compared it with that of both parents. Andrew had one copy of a defective gene that leads to Parkinson’s but the genome sequencing didn’t show a second copy, without which it could not be Parkinson’s.

He explained that Andrew’s illness was clearly progressive and that his brain was shrinking, making it harder for him to process language and information. Nelson said he still didn’t have a diagnosis — he believed it was a brand-new disease.

Nelson planned to continue poring over the test results, conducting additional exams and communicating with others in the network. He also is analyzing Andrew’s muscle tissue, skin and blood to see whether any mutated gene is expressed abnormally.

Even in the absence of a clear diagnosis, Nelson said, rare diseases like Andrew’s help educate scientists and may help other patients. “These are the people we as a society will owe a great debt of gratitude,” he said. “They are effectively donating their lives to this process.”

Lynn Whittaker was disappointed. “We are still left with just hope that they will come up with something,” she lamented. “What else do we have?”

Andrew said his relatives have asked if he’s scared the doctors will find something. “I’m more scared if they don’t,” he replied.

KHN’s coverage in California is funded in part by Blue Shield of California Foundation.

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.”

Personalized Cancer Therapy on the Horizon Thanks to New Genomic Cancer Research Partnership

Gene Editing Institute at Christiana Care Health System partners with NovellusDx in BIRD Foundation Grant

Wilmington, Del, Jan. 30, 2017 – For its enormous potential to accelerate the development of personalized cancer therapies, the Gene Editing Institute of Christiana Care Health System’s Helen F. Graham Cancer Center & Research Institute has been awarded a grant of $900,000 from the U.S.-Israel Binational Industrial Research and Development (BIRD) Foundation in partnership with the biotechnology company NovellusDx.

The BIRD Foundation promotes collaboration between U.S. and Israeli companies in a wide range of technology fields for the purpose of joint product development. Projects submitted to the BIRD Foundation undergo evaluation by the U.S. National Institute of Standards and Technology of the U.S. Department of Commerce and by the Israel Innovation Authority.

The grant allows the Gene Editing Institute to partner with Jerusalem-based NovellusDx on a new series of state-of-the-art gene editing technologies that help identify the genetic mechanism responsible for both the onset and progression of many types of cancer. The two organizations are collaborating on a licensing agreement to commercialize the gene editing technologies that result from the research.

“Thanks to this generous BIRD Foundation grant, this partnership promises to be a catalyst that will speed progress in personalized medicine for many forms of cancer, accelerating the path to prevention, diagnosis, treatment, and ultimately, to a cure of cancer,” said Nicholas J. Petrelli, M.D., the Bank of America endowed medical director of the Helen F. Graham Cancer Center & Research Institute at Christiana Care Health System.

“We are honored to partner with the exceptional team at NovellusDx to advance genomic cancer research and to discover new gene editing techniques,” said Eric Kmiec, Ph.D., director of the Gene Editing Institute. “Our partnership is not only based on the skills of both organizations, but on the unique opportunity to license our gene editing technology with a company capable of commercializing it. The due diligence and peer review process for this award are extensive. I’m enormously grateful to the Research Institute at the Philadelphia-Israeli Chamber of Commerce for its invaluable support of our application.”

NovellusDx has established a unique approach to identify unknown “driver” gene mutations that often accelerate or facilitate cancer progression. With clinical partners throughout the world, including at MD Anderson Cancer Center and Massachusetts General Hospital in the U.S., NovellusDx obtains DNA sequence information and creates a personal profile of the genetic mutations from individual patients. The Gene Editing Institute will use its expertise in gene editing to re-create these mutations that allows NovellusDx and its partners to identify, design and implement the most effective therapy for each patient.

Cancer genomics plays a critical role in pharmacogenomics, or the study of how genes impact a patient’s response to drugs. “With our joint research, we hope to develop gene editing technologies that help develop effective, safe medications and doses that can be tailored to a person’s genetic profile,” Dr. Kmiec said. “This will lead to precision and personalized cancer therapy at its very best.”

“We have been working closely with Dr. Kmiec and the Gene Editing Institute for the last nine months to generate preliminary data to support this ground-breaking idea and grant application,” said Haim Gil-Ad, CEO of NovellusDx. “We are excited that the BIRD Foundation with its stringent review process found our application worthy of the generous funding, which also provides external validation. This work has the potential to change the way functional genomics is done. Once the genetic makeup is known, we will be immediately able to test and monitor the effect of the patient mutations in live cells.”

The BIRD Foundation grant recognizes the Gene Editing Institute’s pioneering work to advance gene editing toward clinical applications in cancer research. The Gene Editing Institute is partnering with The Wistar Institute to develop translational genetic approaches to melanoma cancer research, and with Bio-Rad Inc. to advance a gene editing educational curriculum. In addition, with funding from the U.S. National Institutes of Health, the Gene Editing Institute is developing a gene editing strategy for the treatment of sickle cell anemia.

The BIRD Foundation supports projects without receiving any equity or intellectual property rights in the participating companies or in the projects themselves. BIRD funding is repaid as royalties from sales of products that were commercialized as a result of BIRD support. The Foundation shares the risk and does not require repayment if the project fails to reach the sales stage.

The Gene Editing Institute at the Graham Cancer Center is a worldwide leader in personalized genetic medicine. Founded and led by Dr. Kmiec, the Gene Editing Institute is unlocking the genetic mechanisms that drive cancer and that can lead to new therapies and pharmaceuticals to revolutionize cancer treatment. The Gene Editing Institute also provides instruction in the design and implementation of these precise new genetic tools.

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.

LJI Scientists Flip Molecular Switches To Distinguish Closely Related Immune Cell Populations

The cornerstone of genetics is the loss-of-function experiment. In short, this means that to figure out what exactly gene X is doing in a tissue of interest—be it developing brain cells or a pancreatic tumor—you somehow cut out, switch off or otherwise destroy gene X in that tissue and then watch what happens. That genetic litmus test has been applied since before people even knew the chemical DNA is what makes up genes. What has changed radically are the tools used by biologists to inactivate a gene.

Until now, scientists wishing to delete a gene in a model organism like a mouse did it by clipping out stretches of DNA encoding entire genes or very big chunks of them from the animal’s genome. This type of gene “knockout” is what La Jolla Institute for Allergy and Immunology (LJI) investigator Catherine C. Hedrick, Ph.D., used in 2011, when her lab discovered that mice without the gene Nr4a1 lack an anti-inflammatory subtype of white blood cells, nicknamed ‘patrolling monocytes’.

Now, the Hedrick group’s latest study reports a next-generation molecular manipulation aimed at inactivating Nr4a1 in a more precise manner. That study, published in the November 15, 2016, edition of Immunity, reports the loss of the same patrolling monocyte population following inactivation of a molecular switch that turns on Nr4a1. “This new work is exciting, because it shows that we can directly target genes within a specific cell type, which is important for targeted therapies,” says Hedrick, a Professor in the Division of Inflammation Biology.

The Hedrick laboratory’s previous demonstration that patrolling monocytes disappear following global Nr4a1 loss proved that the gene is necessary for development of that cell type. Later, her group reported that cancer cells injected into mice lacking Nr4a1 (therefore lacking patrolling monocytes) underwent unchecked metastasis, supporting the idea that patrolling monocytes play anti-cancer roles. But an important experimental question lingered: could the cancer metastasis seen in Nr4a1 knockout mice have anything to do with potential loss of Nr4a1 in a closely related group of cells called macrophages, which use Nr4a1 to control inflammation?

The new paper answers this question by silencing Nr4a1 only in patrolling monocytes. The Hedrick group accomplished this by applying good old-fashioned biochemistry to isolate stretches of DNA that flank the gene and define the on-switch for monocytes. Scientists call tissue-specific gene regulatory elements like this “enhancers.” They then showed that when activated, that DNA region, which they called “enhancer #2” (E2), was capable of switching on Nr4a1 expression only in patrolling monocytes, and not in related cells like macrophages.

The group proved the specificity of the enhancer by engineering mice whose genomes lacked only the E2 enhancer—not the gene itself—and indeed observed a lack of patrolling monocytes. “Until now, we did not have a way to delete a gene only in monocytes without also deleting it in macrophages,” says Graham Thomas, Ph.D., a postdoc in the Hedrick lab and the study’s first author. “Targeting the enhancer allows us to study particular cell types in a highly specific way,” says Thomas. “Also, eliminating enhancers teaches us what turns these genes on in the first place. That knowledge is essential if we are going to design rational targets to go after these cells.”

To confirm that macrophages throw an entirely different molecular switch to turn on Nr4a1, the group exposed mice missing the monocyte E2 switch to a noxious toxin found in bacterial membranes, as a way of seeing whether macrophages can still mount normal inflammatory responses. Indeed, the macrophage response was entirely normal in E2 mutants, unlike the global Nr4a1 “knockout”, showing that macrophages do not use the genetic E2 switch.

Finally, to make sure that E2 enhancer loss mimicked deletion of the entire gene in monocytes the group revisited a tumor model previously used to test Nr4a1’s anti-cancer effect. To do so, they injected melanoma cells into the bloodstream of normal or E2 mutant mice and monitored lung metastasis. Remarkably, outcomes following loss of the switch mirrored what the group had previously observed when they physically removed the gene itself: the lungs of mutant mice contained many more melanoma cells than did lungs of normal mice. This confirmed that the gene regulatory switch is highly specific to one cell type, monocytes and that tumor cell invasion in the absence of this population had nothing to do with deregulated macrophage activity.

Hedrick also thinks the new findings provide new understanding of just how important DNA enhancer regions can be. “Being able to selectively target specific cell types opens up a new world for understanding how to design therapies to treat disease,” she says.