Issue 2 • 2021
Genetic discovery and translation in neuromuscular diseases
At the 2021 RACP Congress, Dr Monkol Lek’s highly engaging virtual presentation explained how exome sequencing can drastically reduce the diagnostic ordeal of patients with neuromuscular diseases and bring in a new era of individualised therapeutics through the cutting-edge CRISPR technology.
Dr Lek has been at the forefront of a number of human genetics projects and is passionate about rare disease research. As a rare muscular disease patient himself, he has experienced, first-hand, the issues of the traditional diagnostic process.
Originally from Sydney, Australia, Dr Lek has three undergraduate degrees in Computer Engineering, Bioinformatics and Physiology from the University of New South Wales. He did his PhD at the University of Sydney with Professor Kathryn North before doing his post-doctoral research in Boston, joining a new group led by a fellow Aussie, and Professor North’s former student, Dr Daniel MacArthur.
The problem
In his presentation, Dr Lek highlights certain gaps in the traditional genetic diagnostic process:
  1. Delayed diagnostic journey of patients Prior to the introduction and wide adoption of exome sequencing, there were technological limitations of clinical diagnosis and non-disease genes could only be screened one at a time. This process was quite time-consuming, with patients having to wait several years to have a diagnosis so they could begin therapy. Additionally, when the disease is not diagnosed early enough, such as with late onset of neuromuscular diseases, treatment is further delayed.
  2. Limitations of data and lack of information on wider populations The existing data doesn’t cover various rare diseases or non-European population groups. Further, the diagnostic process doesn’t sufficiently address the genetic root cause of the disease. It highlights the biases that the diagnosis has to be correct, and only non-disease genes can be detected and screened. That means, if a patient had a rare sub-type of the disease that hasn’t been studied so far or was of non-European descent, the disease might even get missed in the genetic screening.
“With rare diseases, the genetic diagnostic journey can be quite an ordeal,” says Dr Lek who was diagnosed with muscular dystrophy at age 21, which was quite a late onset of the disease, but could receive genetic diagnosis and treatment only at age 32.
“I feel ten years is too long for someone to figure out what is the root of the problem to even begin treatment. I found that the eight-base pair duplication that causes my condition were not found in the carriers in the European population,” he adds. “This is found mostly in the general populations in East Asia but unfortunately, there isn’t much information available on non-European populations.” The solution
Dr Lek is hopeful that exome sequencing aided by CRISPR technology can usher in a new era of individualised medicine.
“So far, personalised medicine has been available to patients where they are profiled and provided with off the shelf drugs and treatments that are best suited to their requirement,” he says. “Individualised medicine is when a patient’s specific condition is diagnosed at the genetic level and a tailored treatment is provided by developing the therapeutic approach from scratch, specifically suited to their condition.”
With exome sequencing, the patient’s genomic DNA is sourced from the blood or saliva and fragmented. The DNA is then tested with probes which bind to millions of these DNA fragments, and sequenced as ‘short reads’, all at the same time. These reads are mapped and aligned back to the human genome reference to detect how the patient’s DNA differs from the human genome reference. That way, the genes that result in the disease are detected quickly. Moreover, exome sequencing discovers all protein coding variants which makes it easier to detect even the rarer forms of the disease that were previously going undetected due to the lack of information present.
Dr Lek’s contribution to human genetics projects
While at the Broad Institute of MIT and Harvard, Dr Lek had the good fortune of working on some ground-breaking human genetics projects. He played a lead role in the Exome Aggregation Consortium (ExAC) project and made an impact on patients with rare neuromuscular diseases across diverse populations. He also had an opportunity to use cutting-edge genomic technologies to improve the diagnosis rate of rare neuromuscular diseases using a cohort from Australia, and played a leadership role in the Broad Center of Mendelian Genomics.
During his post-doctoral training he was generously supported by the National Health and Medical Research Council (NHMRC) CJ Martin Fellowship, Sir Keith Murdoch Fellowship and the Muscular Dystrophy Association Development Grant. In 2018, he started his own lab in Yale as an Assistant Professor with the goal to also work on translating genetic discoveries into patient specific genetic therapies.
Dr Lek’s endeavours resonate with his mentor Dr MacArthur’s sentiment that ‘to make sense of one patient’s exome, studies need be done in the context of tens of thousands of exomes’.
Through his ExAC project, Dr Lek was able to extract approximately 60,000 exomes using samples from non-related, diverse population groups. This approach allowed him to explore a diverse range of variants and determine their role in the rarer forms of neuromuscular diseases.
“We have designed and validated a CRISPR based up-regulation of non-muscle DMD isoforms in cell lines and in the hDMD/mdxD2 mouse model,” explains Dr Lek. “This study highlights the importance of furthering our understanding of genetic mechanisms in known disease genes for translation into potential therapeutic approaches. As a rare disease patient myself, and as part of the genomic research community, I can say that exome sequencing and CRISPR technology have proven to be a powerful approach.”   Highlighted points
  • Exome sequencing is the solution to the long-drawn traditional genetic diagnostic process, as it has the potential to reduce the diagnostic wait time for patients with known and rare neuromuscular diseases from several years to a few months.
  • Prior to the introduction and wider adoption of exome sequencing, traditional genetic diagnostics was a time consuming process, screening only one gene at a time. Exome sequencing simultaneously screens all the genes and maps the patient’s DNA to the human genome reference to determine where the disease may exist more accurately.
  • Typically, the traditional genetic diagnostic process required patients to provide a sample through a painful biopsy, but exome sequencing is a considerably simpler, painless testing process using a mere blood or saliva sample from the patient.
  • Exome sequencing is now becoming more affordable and available than before. Plus, with a large number of variants from exomes and genomes now available, many rarer forms of neuromuscular diseases can be diagnosed across diverse population groups.
  • CRISPR technology allows genome editing and targeted gene programming so that only the problematic gene causing the disease can be edited or modified. It can therefore be leveraged to provide very specific, individualised therapeutic solutions that are tailored to the patient’s condition.
© 2021 The Royal Australasian College of Physicians