2017 NF Conference in Washington, DC

Last month, nearly a dozen colleagues from UAB attended the 2017 NF Conference in Washington, DC.  This international conference, organized by the Children’s Tumor Foundation, began in the 1980s with the original purpose of promoting the sharing of data to assist in mapping and the ultimate identification of the NF genes.  When these goals were accomplished for NF1 and NF2, the meeting gradually evolved to an annual international research conference. The event now serves as the global flagship scientific forum where more than 300 participants from a range of scientific and clinical backgrounds gather annually to build consensus and foster collaboration for advancing basic, translational, and clinical research focused on improving outcomes for all forms of NF. The four-day conference features a series of poster presentations summarizing research, invited lectures, and platform presentations.  Many of the speakers are from outside the NF field, broadening the scientific input into the study of NF. 

While I’m not certain whether our UAB group was the largest contingent at the meeting, we were certainly among the largest groups in attendance. Several of us from UAB gave talks from the platform and most had poster presentations. A poster developed by Bob Kesterson, PhD, a professor of genetics and research scientist in our program, won the prize for best poster at the conference. Dr. Kesterson’s poster demonstrated how complementary DNA (cDNA) is now being used to provide a tool for assessing whether a mutation affects the function of the NF1 gene.  This approach will be useful in determining whether some variants of unknown significance in the NF1 gene are actually disease-causing.  It will also be used to determine whether skipping some part of the gene that contains a mutation will be tolerated (see last month’s blog on exon skipping).  Dr. Kesterson was invited to give a brief talk on his research, and his award and recognition was an honor for him and our program.  As I discussed in last month’s blog, there is an increasing focus within the NF scientific community on the development of genomic-guided therapies that will restore function to mutated genes. While this approach is already being used to develop potential treatments for other diseases such as cystic fibrosis and muscular dystrophy, it is receiving greater focus and attention from other scientific communities, including NF.  We at UAB are recognized as the pioneering group in genomic-guided therapeutics within the context of NF, and we look forward to continuing our role as a leader in developing initiatives that will advance this promising avenue of potential treatment for NF.

NF Clinical Trials Consortium and Commonly asked Questions

Every six months, the NF Clinical Trials Consortium Steering Committee meets to discuss plans for upcoming clinical trials.  Our most recent meeting was held in December in Baltimore with staff members from the Department of Defense (DoD) in attendance. This was the first steering committee meeting held since we learned of renewed funding, and we are preparing to launch the next round of clinical trials. Persons with NF often inquire about which clinical trials are available and if they can participate.  Sponsored by the US government, the Web site www.clinicaltrials.gov provides information about all clinical trials categorized by condition.  The federal government requires trials to be registered and to include detailed information on the site about eligibility criteria, site location, primary outcome measures, and other information.

In the past, clinical trials were not always forthcoming about outcome information, especially if the trial did not prove to be effective. Now it is mandated that outcome information be posted on the site for trials that have been completed.

We also receive occasional questions regarding the preliminary outcome of a clinical trial that is ongoing. We’re unable to provide any information about the preliminary findings of a clinical trial until the final data have been received. Typically, the investigators are not privy to the data because there is concern about possibly biasing the study. We therefore can’t answer the question of “What are you seeing so far?” A Data Safety Monitoring Board appointed to oversee a trial reviews the data for the ongoing study. In some cases, the trial is so effective that it is discontinued early. In other cases, the board may have data to indicate that the trial is not working or that side effects are too serious, and they will stop the trial.  Another frequent question from patients is whether they can participate in a trial at a distance, or even from outside the country, instead of at the site where the trial is being conducted. Depending on the trial design, sometimes this is possible, though most times challenges exist that may not make it possible. If a medication is part of a trial, it is required that participants receive the medication at the site of the trial. Also, there are often routine screening tests that must be performed on site. Because it is sometimes possible to participate in a clinical trial from another location, it’s best to contact the staff conducting a particular trial to learn about participation requirements.  Contact information is provided on clinicaltrials.gov.
Due in part to information featured in previous blog posts, I’ve received several e-mails recently from individuals interested in learning more about genome-guided therapeutics for NF. The UAB NF Program is actively engaged in research initiatives in genomic-guided therapy with a focus on identifying approaches that will allow function to be restored to a non-functional gene or gene product. This therapeutic approach would represent an individualized treatment that is tailored to the specific genetic variant responsible for causing NF in an individual.  In this month’s blog, I’d like to discuss the subsets of the most common NF1 mutations and the genomic therapies currently being developed with the goal of restoring at least partial function to the NF1 gene.  

Neurofibromatosis type 1 is caused by a change in the genetic sequence in the NF1 gene, a large and complicated gene that contains a code for making a protein called neurofibromin.  All individuals have two copies of this gene, one inherited from each parent. In people with NF1, one copy of the NF1 gene is altered due to either inheriting the altered gene from a parent, or acquiring a new genetic mutation that occurs in the egg or sperm prior to conception, or from a mutation that occurs early in embryonic development (this results in segmental NF). For someone to develop NF1, a random genetic mutation must occur to the second copy of the NF1 gene in the tissue that will become the neurofibroma, café-au-lait spot, or other lesion. This is referred to as the “second hit” mutation. All individuals – with or without NF1 -- probably have some acquired mutations, which are random errors, that result in a few cells containing an NF1 gene alteration. These cells will not become neurofibromas, however, if only one NF1 gene copy is altered.  The problem for individuals with NF1, however, is that this “backup copy” of the NF1 gene is already altered, which is why a neurofibroma will develop.   Genes function in the cell to direct the production of proteins.  The key question is whether we can find a way to restore function to an NF1 gene that has been damaged by mutation, or perhaps restore function to the abnormal neurofibromin that in some cases is produced.

Therapies Focused on Blocking the Ras/MAPK Signaling Pathway

The majority of therapeutics developed so far for NF1 has focused on blocking the Ras/MAPK signaling pathway that is hyperactive in cells in which both copies of the NF1 gene have been impaired.  Neurofibromin regulates the activity of the Ras/MAPK cellular signaling pathway that helps to control cell growth and division. This pathway is also implicated in other diseases, such as cancer.  Several drugs have been developed that have shown promise in inhibiting components of the Ras/MAPK signaling pathway implicated in NF1 and other diseases. For example, selumetinib is one of a family drugs that has been developed as an inhibitor of one of the components of the pathway and has been shown to have efficacy in reducing the size of plexiform neurofibromas. The development of therapies that inhibit the over-activated Ras/MAPK pathway and other Ras-connected pathways opens new opportunities for treatment for NF1, cancer, and other disorders that share a similar mechanism.

Development of Genome-Guided Therapies Based on Genetic Mutations

While the development of therapies that target Ras signaling is an important approach to developing potential treatments for NF, the possibility of restoring function to mutated genes using genome-guided therapies has gained increasing attention from the NF scientific community and represents an area of focus for the UAB NF Research Program.  An advantage of this approach is that restoring function to the mutated gene might result in fewer side effects than with drug treatments that block Ras signaling.  On the other hand, Ras signaling seems integral to the mechanism of disease in all patients with NF1, whereas genome-guided treatments are based on the specific type of genetic mutation causing an individual’s NF1, and therefore one treatment will not work for all patients. There are thousands of different mutations in different patients with NF1. These mutations are distributed across the gene with no specific mutation predominating. There are, however, subsets of mutations that can be identified through genetic testing, which enable the development of specific approaches to restore function to specific types of mutated genes. In this way, rather than require development of thousands of drugs, one for each mutation, it may be possible to develop a handful, each of which targets a specific type of mutation.

Mutation Subsets

The thousands of mutations can be classified into a number of types.  A deletion mutation results in the total loss, or deletion, of the entire gene and usually produces a severe form of NF. Approximately 3% - 5% of NF mutations are of this type. There are currently no effective methods for replacing large genes, such as the NF1 gene, although this capability may be developed at some future point.

Another type of mutation, called a truncating mutation, causes a blockage or interruption in the formation of a protein.  Neurofibromin is comprised of a chain of 3,818 amino acids strung together in a unique sequence.  One type of truncating mutation, called a premature stop mutation (or nonsense mutation), inserts a signal that tells the protein production machinery in the cell to cease production of neurofibromin before the complete protein is made. Drug therapies currently in development have shown potential effectiveness in overcoming the effects of premature stop mutations. The UAB NF Research Program is currently testing drug compounds that read through the premature stop signals caused by these mutations, with the goal of allowing cells to produce a full-length, functional protein.  

A frameshift mutation is caused by insertions or deletions of a number of nucleotides in a DNA sequence that is not divisible by three.  When DNA is used by the cell to produce protein, the genetic information is read out in groups of three DNA elements, called “bases.”  Hence a specific building block of a protein (an amino acid) is inserted into the protein because of the presence of a specific three-letter base sequence in the gene.  If there is a loss or gain of one or two bases in the DNA sequence for that gene, the reading of the three-letter “words” is confused.  This results in the sequence of amino acids being significantly altered, and at some point there will be a premature stop in the sequence. These types of mutations may be hard to correct, but we are exploring an approach that would jump over the segment of a gene that contains a frameshift when the gene is being processed for reading the sequence and producing the protein. 

Splice-site mutations also result in a meaningless sequence that causes the production of a nonfunctional protein. A gene is encoded in segments, called exons, which code for the amino acids of a protein, separated by introns, which are intervening sequences.  The genetic code in the DNA of a gene is first copied into a molecule called RNA, which is then read out to instruct the production of a protein.  Initially, both the exons and introns are copied into the RNA, but then the introns are cut out and the exons spliced together to make the final “messenger RNA.”  The process of splicing is precisely controlled by the base sequence of the gene, and some mutations occur at the sites that control this process, and therefore disrupt splicing. It may be possible to restore the normal splicing pattern using medications that interact with the splicing system.  This may restore function to a gene disrupted by a splicing mutation; it is also the same method that might be used to jump over a segment with a frameshift mentioned above – this is called “exon skipping.”

Lastly, missense mutations result in the production of a full protein, although one amino acid in the sequence is incorrect. With some sequences, this error won’t cause a problem; however, if the error is related to the production of a critical part of a protein it may disrupt function.  We’re currently working to develop compounds that that interact with protein to restore its function, at least partially. This has been a useful approach to therapeutics in the treatment of conditions such as cystic fibrosis.  The exon skipping approach also might be useful here.

Gene Editing or Replacement

A final possibility is to try to get into the cell and actually correct the gene mutation, or perhaps even to replace the mutated gene entirely.  There has been a lot of interest in these kinds of possibilities, especially recently with the advent of the CRISPR/Cas9 system.  This system was developed based on a natural mechanism discovered in bacteria that protects bacterial cells from infection by viruses.  It has been modified to permit editing of DNA sequences, including potentially correction of gene mutations.  Our lab, and many around the world, are using CRISPR/Cas9 as an approach to creation of model systems that require producing a specific mutation of interest.  Applying this to the treatment of a genetic disorder is much more complicated, especially one like NF1 that affects a very large number of cells in the body.  This is, however, a new area of research, and one where we may see significant progress in the years to come.

Conclusion

We are beginning to see benefits from small molecule treatments that target Ras signaling, but in the long run we are likely to need many parallel approaches to effectively treat NF1.  Our group, and many others, are pursuing such approaches, including the development of genome-guided therapeutics.   It is likely that the eventual treatments of NF1 will require combinations of different approaches that will synergize with one another to control the symptoms of the disorder.
Need for Effective Treatments

I’d like to focus this month’s blog post on a discussion of cutaneous neurofibromas, which are benign tumors that can grow on nerves throughout the body in some individuals with NF1. Typically beginning around the time of puberty, these tumors grow from small nerves either in or under the skin and appear as small bumps on the surface of the skin or as purplish spots when the tumors occur underneath the skin.  Although these tumors are sometimes also referred to as “dermal neurofibromas,” NF clinicians and scientists at a recent meeting of the Neurofibromatosis Therapeutic Acceleration Program (NATP) emphasized the need to move away from using this term in favor of the term “cutaneous neurofibromas.” The dermis is actually not the layer of the skin from which neurofibromas originate, while “cutaneous” is a general term referring to the skin and is therefore a more accurate term for these tumors.

In the past, we have found that obtaining funding for clinical trials of cutaneous neurofibromas has been somewhat difficult. Because these tumors are non-malignant and not life-threatening, the question often posed is:  Why is it necessary to treat cutaneous neurofibromas? Conversely, plexiform neurofibromas are much more serious and sometimes life-threatening due the risk of malignancy and the possibility of compression of the airway or the spine.  However, it is also true that cutaneous neurofibromas may be unfairly trivialized in their impact on the lives of individuals with NF. We receive numerous inquiries asking why cutaneous neurofibromas are not the subject of clinical trials.  Data indicate that quality of life for people with cutaneous neurofibromas can be significantly impaired. There are sometimes cosmetic concerns in a major sense, as these tumors may be quite disfiguring.  Also, the tumors may itch, can sometimes bleed, and even cause pain. 

Research Focused on Cutaneous Neurofibromas

A longitudinal study has been in progress at UAB for the past several years focused on understanding how cutaneous neurofibromas grow and change over time. As part of the study, 22 participants have had their neurofibromas counted and measured every three months. Our NF Program Genetics Counselor, Ashley Cannon, MS, PhD, CGC, assumed the principal investigative role in the study when she joined our program in 2015 and has now completed an analysis of eight years of quantitative data on many of the original study participants.  Dr. Cannon recently presented the study findings at the conference of the American College of Medical Genetics and Genomics (ACMG) in Phoenix and is preparing the results for upcoming publication. 

These findings will also serve as the basis of an upcoming clinical trial at UAB that will test the effectiveness of a systemic treatment for cutaneous neurofibromas administered in the form of a pill.  While development of a topical treatment was considered, it can be difficult to formulate a compound that permeates the skin layer. Also, for some people, cutaneous neurofibromas are too widespread on the body for a topical treatment to be effective.  Additional information about the trial and details about upcoming recruitment can be found at www.clinicaltrials.gov.

In other research for cutaneous neurofibromas, we are exploring other potential treatments for future clinical trials of cutaneous neurofibromas.  We’re also working to find ways to restore function to mutated genes or gene products, which could provide new ways of treating these tumors. Researchers at UAB are currently studying the more than 3,000 NF mutations contained in the library of the UAB Medical Genomics Laboratory to determine whether particular mutations increase the likelihood for cutaneous neurofibromas to occur. We know of two mutations that do not produce neurofibromas of any type. There are other mutations that don’t produce cutaneous neurofibromas but do produce neurofibromas deep inside the body (plexiform neurofibromas). We are currently developing animal models and other types of model systems to understand the characteristics of specific mutations with the goal of developing new treatments for cutaneous neurofibromas.