Gene Therapy- Are we reaching the beginning of an era? …. Wait a minute

Coming of Age

“We saw it coming in pharma”

It is a rare thing in life that one gets to be a spectator of events that shape the world, and that too from the front row. The approval of an Adeno Associated Virus therapy from Spark Therapeutics in October 2017 happened to be one such event for many people like me, who are dabbling with elegant cutting edge technologies. Apart from its impact as a therapy for an unmet need, the significance of the news cannot be stressed enough. We have finally reached a stage in the field of gene therapy where we now see a glimpse of hope for it to become a standard of care for several diseases. Deanna Peterson rightly stated in her blog last month in LifeSciVC “We saw it coming in pharma”.

Venture Capital funding since 2013 (2018 Roots Analysis)

Spinal Muscular Atrophy and Gene Therapy

I started to dig into some recent trials in the field of gene therapy inspired by Deanne’s blog. My interest in neuroscience led me to do some background reading on two studies about Spinal Muscular Atrophy that were published in the same issue of the New England Journal of Medicine (NEJM) . One of them was approved as a priority designation drug by the FDA.

Spinal Muscular Atrophy (SMA) (also called as Werdnig-Hoffman Syndrome), is characterized by the atrophy of motor neurons and their associated muscles. In 1891, Guido Werdnig (1844–1919) from the Department of Pathological Anatomy, at the University of Graz in Austria, described two brothers with the onset of weakness around ten months of age. One of them suffered from complicated pertussis (whooping cough) and hydrocephalus (build-up of fluid in the brain ventricles) and died three years later. The second child survived up to six years. When Werdnig did the autopsy on the child, he found degeneration of the anterior horn cells of the spinal cord. This would be the first report on SMA. In 1990, precisely after hundred more years, the cause of the disease was attributed to a disease-causing gene called the survival motor neuron (SMN) and the locus was identified in 1995. Normally, we have two genes SMN1 and 2. In SMA patients, SMN1 gene becomes nonfunctional due to mutations, gene deletion or a genetic rearrangement resulting from recombination of the DNA. The SMN2, however, remains to produce 10% of the SMN protein in those individuals. The inefficiency in the production of viable SMN protein is attributed to a molecular process called splicing (A process by which nascent RNA transcribed from the DNA is processed to release mature RNA ready for protein synthesis) of the Exon 7 of the SMN2.

SMA is considered as the second most common autosomal recessive genetic disorder after cystic fibrosis, and affects every 1 in 10000 live births with a carrier frequency of 1 in 54. The disease is divided into four subtypes (1 through 4) based on the age of onset and the milestones achieved. SMA type 1 (SMA1) is the most severe form of the disease and also the most common genetic cause of death among infants. Infants with SMN1 biallelic deletions (where both alleles or copies of the gene are deleted) or two copies of SMN2 have a 97% risk of SMA1. The disease is associated with a very high death rate. In patients with SMA type I, the median survival is seven months and the mortality rate is as high as 95% by 18 months. Almost all patients are known to require respiratory and feeding support at some point during their life time. The disease is devastating not only for the infants but for the entire family of the patient.

Provides an overview of the mechanism of disease (MOD) of spinal muscular atrophy (SMA) created for educational purposes only.

SMA Clinical Trials

Ever since the SMN gene was identified, the race to find a cure for the disease has resulted in numerous publications in neuroscience. But practically no therapy was developed for several years. In Nov 2017, Ionis Pharmaceuticals (erstwhile Isis) in collaboration with Biogen reported the first successful and historical phase 3 trial against the disease using their antisense RNA technology. This technology involves an antisense RNA called Nusinersen (Spinraza) that inhibits the Exon 7 splicing of SMN2. The FDA approved it as a treatment for SMA in December 2016 under the fast-track designation. This drug is administered using repeated intrathecal injections after four loading doses within the first two months of life. The trial was hailed for its efficient and rigorous clinical trial design and was referred as a model trial to develop future gene therapies for the treatment of serious or life-threatening diseases. A new Phase 3 study published in the NEJM in its February 15th issue of 2018, showed pretty amazingly that Spinraza (Nusinersen) meaningfully improves motor function and upper limb movement in patients with later-onset SMA. However, it should be noted, Spinraza is not classified as Gene Therapy by FDA. Rather it is classified among products that mediate their effects by transcription or translation of transferred genetic material, or by specifically altering host genetic sequences.

How Nusinersen works

A potential alternative to repeated intrathecal injection of spinraza is gene therapy where a single dose of the gene might be able to give a long-lasting therapeutic effect. This is precisely what Avexis, a clinical-stage gene therapy company is trying to do. On November 2, 2017 (Biogen’s clinical trial data was also published in the same issue), an yet another historic and seminal work in the field of gene therapy was published in the NEJM by Mendell et. al. The group used an intravenous injection of engineered Adeno Associated Virus (AAV) called non-replicating self-complementary Adeno-Associated Virus serotype 9 (ScAAV9) carrying the wild-type allele (normal copy) of the gene controlled by the chicken beta-actin promoter (switch), in patients with SMA. Fifteen patients received a single dose of intravenous Adeno-associated virus serotype 9 carrying SMN complementary DNA encoding the missing SMN protein. The trial included a high and a low dose of the virus (pretty common in gene therapy studies). The primary expectation from this trial was about safety outcomes. The secondary expectation was estimating the time until death or the need for permanent ventilatory assistance. The results were stunning. All of the 15 patients were alive and event-free at 20 months of age, as compared with an 8% rate of survival in a historical cohort. The report stated that of the 12 patients who had received the high dose, 11 sat unassisted, nine rolled over, 11 fed orally and could speak, and two walked independently. Elevated serum aminotransferase levels (a marker that shows how much damage might have occurred in the liver) occurred in 4 patients and were controlled by prednisolone (a type of steroid to bring down allergic/inflammatory reactions). In a layman’s language, the trial outcomes were very positive.

“Future is here”

These spectacular results in the last two years have rejuvenated the entire field of gene therapy. Media heralded “Future is here”. It looked as if finally, we have reached an era of gene therapy. But, probably not just yet.

Developing AAV

“The observation about AAV being present in the host genome formed the foundation of modern gene therapy.”

AAV is the most used choice of vectors in gene therapy. AAV was accidentally discovered in 1965, as a virus-like particle associated with Adenovirus cultures, by Bob Atchison, M David Hoggan and Wallace Rowe. Atchison named it as Adeno Associated Virus. However, the idea that these might be useful in gene therapy was not conceived until the early 80s when low numbers of the AAV genome were found to be integrated into the host chromosome. The viral genome is known to integrate into its host genome by the process of recombination. In fact, quite a chunk of the human genome originates from viruses that integrated into its genome over a million years of evolutionary time frame. The observation about AAV being present in the host genome formed the foundation of modern gene therapy. It is now possible to send corrected genes back into the patients via a virus that can integrate into the genome and drive the synthesis of a functional protein, which was absent in them originally.

It took another ten years to bring the virus to preclinical and clinical trials. For the virus to be targeted, tissue-specific promoters (that would allow the gene to express in the desired cells or tissues) were engineered into the viral vectors. The first in vivo expression/transduction of CFTR by Terry Flote showed that it is possible to express foreign genes in tissues infected with AAV. One challenge that needed to be solved was to design viruses that can avoid the body’s immune surveillance. The scAAV, that bypasses the need for double-strand synthesis, resulted in several fold increase in the transgene expression. The packaging efficiency (how much of DNA to be packaged) was tweaked too to increase the load of DNA that a virus can carry with it. From there it took another three decades since the discovery of AAV to produce GMP level yield of viruses that can be used for human consumption. However, one problem remained. In order to use these vectors for neurological diseases, the virus has to travel through the blood-brain barrier. The efficiency of these viruses to perform this task is poor, to say the least. The way researchers got around the issue was by injecting very high doses of the virus. This has been a holy grail for many scientists working in this field. That is how to keep the viral load low but still be able to get through the blood-brain barrier efficiently.

Adeno Associated Virus remains most preferred vector ( 2018 Roots Analysis)

Early Trials:

“we all got ourselves all hyped up”

Armored with a vast amount of preclinical data, validation, and standardization protocols the field was now ready to test the viruses in clinical settings. AAV2 was the first serotype that was used against a large number of diseases like hemophilia B, Cystic Fibrosis, Parkinson’s, and Rheumatoid Arthritis. The field rapidly engineered AAVs that can address issues such as biodistribution potential, toxicity, immune response, tissue specificity, etc. By early 90s researchers started to believe that one just had to put the repaired gene back as Jim Williams one of the pioneers and a historical figure in the field would remark several years later.

It was September 14th 1990, when gene therapy actually became a reality. At the National Institutes of Health in Maryland, USA, a 4-year old female suffering from a severe immunodeficiency, received engineered white blood cells that had several copies of the gene she lacked at birth. Soon after the trial, Dr. W. French Anderson who ran the experiment was christened as the father of gene therapy. Later in an interview with the New York Times, he said: “we all got ourselves all hyped up”. However, what followed was yet another 25 years of delay before the community again conjured up the courage to pursue gene therapy trials with renewed vigor.

The Gene Therapy press conference held on September 13, 1990. From left to right: R. Michael Blaese, M.D., W. French Anderson, M.D., and Kenneth Culver,. M.D.Source: NCI (Wikimedia Commons)

In 1999, Jesse Gelsinger, an 18-year-old from Tucson Arizona succumbed to multiple organ failure during a gene therapy trial that was being supervised by Jim Wilson at the University of Pennsylvania. The trial was targeted to test the efficacy of a therapy for transcarbamylase (OTC) deficiency, a rare disorder in which the liver lacks a functional copy of OTC, resulting in accumulation of toxic ammonia in the body. Penn scientist Mark Batshaw had engineered a weakened adenovirus to deliver a normal copy of the gene to the liver and, under Jim’s supervision, the virus was administered to Jesse to test the safety of the procedure. However, the tragic failure of the trial brought the entire field to a halt. Not only did it change the field, but also altered Jim’s perception of gene therapy. Since then, Jim dedicated his research on figuring out safety issues with viral-based gene therapy technology.

A word of caution:

So, when the clinical trial data from Mendell’s group showed promising results, Jim’s group set out to test the transduction of related viruses in different animal model systems. The results from Jim’s work were published in the journal “Human Gene Therapy”, in early February (I came to know about it in an article covered by Endpoint News, ironically just after the blog from LifeSciVC was published). The study showed that high systemic doses of certain AAV variants (similar to the one used in SMA trials) could result in variable and lethal effects in large animal models. When they injected non-human primates (NHP) and piglets with high doses of AAV, they found that the animals responded differently. Of the 3 NHPs, one developed severe liver toxicity and acute shock that prompted its euthanization. They also exhibited a degenerating dorsal root ganglion sensory neurons. Piglets, on the other hand, were found to have proprioceptive defects and ataxia, suggesting that systemic and sensory neuron toxicity may be associated with high doses of AAV vector delivery in animals. The study cautions that clinical trials involving high systemic doses of AAV should be designed based on thorough preclinical and early laboratory studies on non-human primates, evaluating systemic toxicity, liver damage, and sensory neuropathy.

There is little doubt that gene therapy is poised to have a significant impact on human health in the next few decades. The 2017 SMA study showed that a single dose therapy compared to Biogen’s multiple intrathecal injections can be a game changer for not only SMA patients but can be a reality for several other rare, genetic, disabling and life-threatening diseases. However, the field still needs careful scrutiny before such therapies become a routine to overcome human suffering.

PS:

As I was wrapping up this blog:

Abbvie announced their $69 million collaboration (pledging up to $155 million) with Voyager therapeutics to develop viral-based gene therapy against Alzheimer’s disease.
Researchers at the University of North Carolina School of Medicine, have engineered a strain of AAV called AAV1 utilizing 8 amino acids in the viral capsids, that allowed the virus to reach the brain efficiently. Easier access to the nervous system means lower vector doses and that can help reduce the toxicity associated with these viruses. The study, “Mapping the Structural Determinants Required for AAVrh.10 Transport across the Blood-Brain Barrier,” was published in the journal Molecular Therapy.
Gene therapy start up called Generation Bio, Atlas Venture backed biotech just closed a 100 million dollar second round of financing. They are developing therapies that use closed ended DNA rather than virus to deliver therapeutic proteins.

Gene Therapy: Boon or Bane? Manasi Pethe ©

References:

We Saw It Coming In Pharma: Now Gene Therapy Is Biotech 2.0 For Rare Diseases https://lifescivc.com/2018/02/saw-coming-pharma-now-gene-therapy-biotech-2-0-rare-diseases/

Ramblings in the history of spinal muscular atrophy https://www.sciencedirect.com/science/article/pii/S096089660800672X?via%3Dihub

Single-Dose Gene-Replacement Therapy for Spinal Muscular Atrophy http://www.nejm.org/doi/full/10.1056/NEJMoa1706198

Nusinersen versus Sham Control in Later-Onset Spinal Muscular Atrophy http://www.nejm.org/doi/full/10.1056/NEJMoa1710504

The Biotech Death of Jesse Gelsinger http://www.nytimes.com/1999/11/28/magazine/the-biotech-death-of-jesse-gelsinger.html

Gene therapy: trials and tribulations https://www.nature.com/articles/35038533

AbbVie and Voyager Therapeutics Announce Global Strategic Collaboration to Develop Potential New Treatments for Alzheimer’s Disease and Other Tau-Related Neurodegenerative Diseases https://goo.gl/NDvaox

More efficient gene therapy vectors found that may help disorders like FA https://goo.gl/387868

Author: Ananda Ghosh

Acknowledgments

Editor: Anshu Malhotra, PhD

Image: The Nightmare-Henry Fuseli Wikimedia Commons

Illustrations/Doodles: Manasi Pethe, Ph.D. San Diego

Obsession & Opinions Cartoons: Manasi Pethe, Ph.D. San Diego

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