Julianna LeMieux Ph.D. Senior Science Writer GEN

Armed with New Tools and Lower Cost Sequencing, Researchers Take an Omics Approach to Neuro Diseases

In the absence of a cure, the number of people who suffer from neurodegenerative diseases in the future will be staggering. Because these diseases primarily strike older people, and our aging population is increasing, it is estimated that more than 12 million Americans will be afflicted by neurodegeneration 30 years from now (roughly 1 in 5 Americans will be over the age of 65 by the year 2030).

Some progress has been made in developing treatments for neurodegenerative diseases, but far too slowly. One of the reasons for that is the lack of a full understanding of the basic biology of the diseases, something that researchers are trying to change.

Some of the most exciting research going on in the Parkinson’s disease (PD) and amyotrophic lateral sclerosis (ALS) fields takes an “omics” approach to better understand the biology behind these diseases, which will undoubtedly open doors to new therapeutics.

Seeking Answers in PD-Associated Genes

A team of researchers in the human genetics group at Genentech, led by Rob Graham, Ph.D., a senior scientist who has worked in the department for 11 years, works to identify new therapeutic targets and pathways associated with disease risk and progression.

Most recently, that work centered on identifying novel genes involved in PD. “We’re still trying to understand the basic biology of PD,” Graham said. “When we do that, we can more intelligently think about how to target the disease.” He added that despite significant effort and some progress in PD research, “things have moved more slowly than we would all like.”

More than 30 years ago, Robert Nussbaum’s, M.D., group at the National Institutes of Health (NIH) discovered that mutations in SNCA (which encodes alpha-synuclein) were common in several families with a high prevalence of Parkinson’s. The paper, “Mutation in the alpha-synuclein gene identified in families with Parkinson’s disease” was published in Science in 1997. Since then, two other genes, LRRK2 and GBA, have been associated with familial, early-onset PD.

For the more common, later onset form of the disease, there are dozens of genes associated with an increase in disease risk. In January of 2015, Genentech paid 23andMe $10 million (with up to $50 million more in further milestones) to access their database to find more. The resulting paper, “A meta-analysis of genome-wide association studies identifies 17 new Parkinson’s disease risk loci,” published in Nature in September of 2017 was the largest meta-analysis of PD.

When asked why searching for new genes was important, Graham answered that although there are known pathways that are important for PD, the pathways need to be rounded out. The way to do that is to identify more genes within them.

For example, the lysosomal pathway, with its well-known role in the degradation of protein aggregates and autophagy, and its role in targeting long-lived proteins and dysfunctional organelles for lysosomal degradation, plays a role in PD. However, the genes that are already known in those pathways may not make good drug targets. Therefore, hunting for new genes within those key pathways to find additional targets may result in novel drug targets.

In addition, the core pathways that lead to disease processes can be present a decade or longer before clinical PD symptoms, making if difficult to identify specific genes for drug targets. Graham’s work aims to find pathways that could be druggable when the patients present with their initial clinical symptoms. And, Graham thinks that their study made progress on all of these fronts.

Some of the genes his team identified fill in gaps within the well–accepted autophagy and lysosomal pathways, providing additional support for those while helping to pinpoint which genes play a specific role in PD. They also identified new pathways. One gene that they found, inositol 1,4,5-triphosphate kinase B (ITKPB), may open up new pathways to target.

What is Genentech’s plan with all of these new genes? Graham told Clinical OMICs that the neuroscience and genetics teams at Genentech are working to try to clarify the importance of the newly identified genes, determine how the networks interact and understand what new pathways may be important. Only after that, Graham said, can we think about therapeutic approaches to best target the disease.

Researcers at Genentech, led by Rob Graham, Ph.D., are searching for new genes associated with Parkinson’s disease with the aim finding pathways that could be druggable when the patients initially present with symptoms. [Tetra Images/Getty Images]

A Multi–Omics Approach to ALS

Enough people dumped buckets of ice on their heads four years ago to raise $115 million dollars for ALS research. But, with one failed drug candidate after another, researchers are taking a new approach to find a cure for the 30,000 people living with ALS.

One group, “Answer ALS,” which was launched in September of 2015, has a goal to “produce the largest and most comprehensive foundation of ALS data ever amassed.” And to “use that data to investigate the unique pathways of each variation of ALS and begin to develop the right cure for each patient.”

Started by Jeffrey D. Rothstein, M.D., Ph.D., director of the Robert Packard Center for ALS Research at Johns Hopkins Medicine, Answer ALS is using multi-omics analysis to comprehensively assess every aspect of motor neuron function in ALS patients. This includes genomics, transcriptomics, epigenomics, proteomics, metabolomics, and robotic imaging.

Patients are recruited at eight centers across the United States. Rothstein said that he chose the eight clinics that would enroll patients the fastest. Indeed, Answer ALS has been recruiting patients faster than any other trial—on target to recruit 1,000 patients over three years. The fact that Rothstein’s research program is moving quickly is not surprising, as even his speaking pace indicates that there is no time to be wasted.

What led Rothstein to start Answer ALS? He said that medical history taught him a valuable lesson having “seen one hundred drugs fail.” Although there is an ALS mouse model used widely in labs around the world, Rothstein noted that the mouse (although useful) is not equivalent to patients. He recognized that the ALS research world needs reagents that better match their patients. Although human tissue would be ideal, it is not possible to work on human brains. Rarely, a postmortem brain becomes available, but working on non–living tissue is not ideal, either. Generating induced pluripotent stem cells (iPSCs) from ALS patients was the best platform that Rothstein could imagine.

How do they do it? The pipeline starts in the clinic and ends with research. First, samples (whole blood, plasma, serum, and cerebrospinal fluid) are taken from enrolled participants. These are sent to the New York Genome Center where DNA is extracted and sequenced. The blood is then sent to Cedars Sinai Medical Center where cells are reprogrammed into iPSCs and then neurons. They already have 400 lines made and banked, all of which are available to any researcher, whether working in the commercial setting or academia.

The even bigger challenge than the sample collection is building an open-source platform of all of the biological and clinical data and making it available through a portal that anyone can use. To help overcome this, Answer ALS has given GNS Healthcare access to their data. Funded by the ALS Association, GNS will use its machine learning platform, REFS, to help create a comprehensive disease model. GNS states that they will “transform these petabytes of patient data into mechanistic models, connecting genetic, molecular, and biochemical variables to clinical outcomes that will allow in silico experiments to be performed at a rapid rate on the computer.”

Another focus of this omics-based work is to create subtypes of ALS patients, in order to personalize treatment and stratify clinical trials. This is one of the main goals of the Genomic Translation for ALS Clinical Care (GTAC) program, a collaboration between Biogen, the ALS Association, and Columbia University Medical Center (CUMC) launched three years ago.

GTAC is heavily focused on classifying ALS patients into subgroups based on similar RNA transcriptomic profiles. Once these data are made available, clinicians could offer more personalized and effective treatment after a simple blood test on a patient. In addition to new gene discovery and genotype–phenotype correlations, GTAC is also taking careful exposure and epidemiological data on their patients, noting environmental factors that have been rumored to play a role in ALS like chemical exposure, jobs, and living areas.

While it might seem this work would have been done long ago as a building block to better understand the disease, Matthew Harms, M.D., the director of GTAC and an associate professor of neurology at the Columbia University College of Physicians and Surgeons, told Clinical OMICs that, “we have always known that there are biologically relevant clusters of ALS patients that we haven’t had the tools to detect.” He credits new technology and the falling cost of sequencing as opening “a whole new wave of study.”

It is this new set of tools enabling renewed study of ALS that has Rosenstein energized and optimistic. Looking ahead to 2030, he said assuredly that “we’ll have drugs,” to treat the disease. 

Might CRISPR-Cas9 Gene Editing Cure Huntington’s Disease?

Research in the field of Huntington’s disease (HD) is light years ahead of the omics-based exploration being done in ALS or Parkinson’s disease. The reason lies in the deep understanding of the genetic mutations that are the cause of HD. In fact, it would be hard to complete an undergraduate genetics course without a good understanding of the genetics behind HD and the biology that underlies it.

HD falls into a class of diseases known as trinucleotide repeat diseases, which also encompass roughly a dozen other neurological diseases, including Fragile X syndrome and Myotonic dystrophy—a form of muscular dystrophy. These diseases are caused by an expansion of unstable trinucleotide repeats.

In the case of HD, three nucleotides, cytosine-adenine-guanine (CAG), are repeated in the huntingtin (HTT) gene. When there are too many repeats, the resulting protein is toxic, and HD is the result. Because HD is caused by a mutant form of the protein huntingtin, if the protein can be blocked, the disease could be halted. Since the mutations are known, and the expression is dominant, CRISPR-Cas9 gene editing may be a potential way to cure the disease.

Gary Dunbar, Ph.D., faculty in the Experimental Psychology and Neuroscience Program at Central Michigan University told Clinical OMICs that the most recent research is “looking at ways in which the CRISPR-Cas9 system can specifically target the mutated allele, blocking transcription of the mutated protein, and allowing the production of the normal protein.”

Jong-Min Lee, Ph.D., assistant professor of Neurology at Harvard Medical School and Center for Genomic Medicine noted that “mutant-specific CRISPR strategies are being actively developed for HD.” If the editing target is the CAG repeat, “one CRISPR strategy can be applied to all HD patients.” 

Lee added that it may not be so easy. One hurdle, he said, is that CRISPR strategies targeting CAG repeats may “suffer from significant off-targeting because there are many genes containing CAG repeats in the genome.” Because of this, researchers need to “capitalize on other genetic variations that selectively generate CRISPR [protospacer adjacent motif] sites [sequences required for Cas9 function] on the mutant HTT gene for allele-specific targeting.”

“Many independent CAG expansion mutations might have happened over time, generating mutant HTT gene on diverse haplotype backbones,” Lee said. “Therefore, mutant-specific
CRISPR strategies have to be designed after considering both mutant and normal haplotypes in a given patient, requiring fully customized approaches.”

Dunbar said there is also another hurdle. The biggest obstacle will be to “deliver the CRISPR-Cas9 effectively to cells that need it most. We are working on packaging the system in an AAV9 virus or by using nanoparticle (dendrimers) that cross the blood-brain-barrier as a potential means of delivery.”

Lee agreed that the “development of delivery methods and CRISPR systems that are efficient, specific, and safe [will] likely make CRISPR HD intervention trials possible.”

As to when this may become a reality, Lee said “It is hard to predict when, but technology development can be much faster than we anticipate.” 

Dunbar added another layer of optimism, noting that the technology may be even wider reaching than just HD. When asked if this technology could be applied to other neurodegenerative disorders, Dunbar is hopeful and said that he thinks “a tool like CRISPR will be adopted for polygenetic disorders, as CRISPR can be adapted to hit multiple targets.”

Huntington’s disease affects the basal ganglia region of the brain. [Tim Vernon / Science Photo Library / Getty Images]

This article was originally published in the September/October 2018 issue of Clinical OMICs. For more content like this and details on how to get a free subscription, go to www.clinicalomics.com.

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