Possible FDA Approval Could Spread Mass Spec Assay for Newborn Lysosomal Storage Disease Screening

pompe_vacuoles.jpg

Courtesy of Wikimedia Commons
Muscle biopsy showing large vacuoles in a case of pompe disease

NEW YORK (GenomeWeb) – A new mass spectrometry-based screening kit for newborns from PerkinElmer could find its way to the US Food and Drug Administration for approval as early as this year, according to Michael Gelb, a professor at the University of Washington who developed the method it's based on. 

If that happens, screening for rare, but deadly diseases could become more prevalent and more consistent across the country. The multiplex assay for lysosomal storage disorder (LSD) screening looks at enzyme activity to find inborn errors of metabolism, with a specificity that allows it to separate patients with enzymatic pseudo-deficiencies from those with bona fide LSDs, often fatal diseases that affect children around the world.

"The technology exists to give reliable screening with minimal false positives," Gelb said in an interview. His method, developed over the last decade with UW researchers Frantisek Turecek and Ron Scott, has helped push more states around the country to mandate LSD screening and has even helped push two LSDs — mucopolysaccharidosis type 1 (MPS I) and glycogen storage disease type II (Pompe disease) — onto the US Department of Health and Human Services' recommended uniform screening panel (RUSP) for newborns in the last two years. Many states are either live with tests for those diseases or are going live soon, he said, and some states have started doing additional LSDs, largely out of parent-led advocacy efforts.

Because the RUSP is only a recommendation, newborn screening for LSDs varies from state to state. Some state health departments, including New York State, have turned Gelb's tandem mass spec method, which uses dried blood spot samples, into laboratory-developed tests. But the PerkinElmer kit could have wider access and offers separate channels for six different LSDs, some on the RUSP and some not: MPS I and Fabry disease, Pompe disease, Krabbe disease, Gaucher disease, and Niemann Pick diseases type A and B.

According to Gelb, PerkinElmer plans to submit its kit this year to the FDA for potential approval. A PerkinElmer representative confirmed development of the mass spec-based LSD kit, but declined to provide further details.

"A few states are mandated to do all of those," said Gelb, who is a consultant to PerkinElmer. "Most are doing a subset but you can tell the mass spec [instrument] what to sniff for." For example, Illinois has a mandate to test for five LSDs, while Missouri test for four.

And the number of LSDs to screen for could increase over the next few years. Pharmaceutical firms Shire, Biomarin, and Ultragenyx are working on therapies for LSDs, and mass spec, rather than fluorometric or genome sequencing, is the best technology to find the kids who could benefit from them, Gelb said. He's working on pilot studies for assays for several more LSDs. "[Mass spec] just works better than any other method," he said, adding, "genomics is not the solution here."

LSDs are a collection of rare, inherited metabolism disorders that kill cells by allowing an enzymatic substrate to accumulate. "The lysosome starts to blow up and expand, fill up with trash, and the cell dies," Gelb explained.

Theoretically, one way to detect defective enzyme function is to measure the buildup of substrates, but that's not how Gelb's method works. "What we do is measure how fast the chemical reaction goes," he said. "We take the blood spot, which has the enzymes, we add substrate, let it incubate, and measure the amount of product." Factoring in for time yields the enzyme rate, which depends exactly on the amount of enzyme activity. 

Individually, LSDs are so rare that getting them on the RUSP can be a challenge. Mucopolysaccharidosis II (MPS II, aka Hunter syndrome) affects approximately 1 in 162,000 male births, according to Shire, which is working on a therapy for that disease. But taken together – there are about 50 – they're estimated to affect between 1 in 10,000 and 1 in 5,000 newborns, according to the National Organization for Rare Disorders.

South Carolina's Greenwood Genetic Center is one of several clinics that have created an LDT based on Gelb's method, screening for the same six diseases that the PerkinElmer kit will cover.

"Overall, these new MS/MS enzyme assays are user friendly, with great sensitivity and specificity for the diagnosis of lysosomal storage disorders," Laura Pollard, associate director of Greenwoods biochemical genetics laboratory, said in an email. "Sample processing is much quicker than that for previous MS/MS-based methods for enzyme analysis. The multiplex nature of the assay improves efficiency compared to using fluorometric enzyme assays, which must be set up in separate individual reactions." 

Mass spec-based enzyme activity assays have also been applied in drug development. This kind of assay can also be done fluorometrically or colorimetrically, but mass spec seems to be able to offer separation in several cases where those methods can't. "Newborn screening for Pompe disease with fluorescence is essentially impossible, but it seems to be working by mass spec" Gelb said.

Moreover, mass spec's analytical range is approximately 10 to 100 times higher than that of fluorometric assays, he said. For every enzyme activity assay, there's some level of signal even when there's no activity, what he called a "blank value." The ratio between the assay readout and the blank value is the analytical range. With his mass spec-based method, Gelb said he can tell the difference between 1 percent activity and 2 percent.

That's extremely important for LSDs, which can appear in screens as pseudo-deficiencies, caused by mutations that reduce enzyme activity, but not to the point that causes the disease.  "For many diseases, we're born with much more enzyme than we need, and it only becomes pathogenic when the enzyme activity gets really low," Gelb said. "That causes trouble in screening, because you're splitting hairs down at the low end."

At January's Mass Spectrometry: Applications to the Clinical Lab conference, Gelb presented data from Taiwan, where Pompe pseudo-deficiencies are fairly common. In a study cohort with more than 300 pseudo-deficiency patients and less than 30 bona fide Pompe disease patients, he showed that his assay could find 97 percent of the pseudo-deficiencies. "But with fluorescence, they don't separate at all," he said.

That's potentially a big time- and money-saver. In many places, including most states, first-line tests like Gelb's assay are followed up with sequencing. "When they get a hit, they will sequence the DNA for the relevant gene and maybe half the time, roughly, they can tell that the kid has the disease, and maybe half the time they don't know," he said. For a first-line test, that's unacceptable because "there would be too many unknowns."

That hasn't stopped several companies from pursuing genomic newborn screening for LSDs in the US. Children's Mercy Hospital researchers have been working on rapid whole-genome sequencing for newborn screening, including Krabbe disease. And Colorado-based Baby Genes has included many of the LSDs on its targeted next-generation sequencing panel.

As reported by GenomeWeb, the Children's Mercy test for Krabbe disease led to false positives, raising anxiety and contributing to unnecessary treatment for some patients.

"It's contentious, but in this case it's pretty clear that it's not going to be genomics early on," Gelb said.

Genomic technologies aren't the only contentious issue in newborn screening and LSDs are especially rife with controversy. Some parent-led advocacy groups have been aggressive in lobbying for screening and grassroots advocacy is unlikely to wane as more pharmaceutical companies develop promising treatments for LSDs. Shire's therapy for Hunter syndrome, Elaprasen, is getting reformulated for a different delivery method and received fast track designation from the FDA. Screening for Hunter is limited to a couple of states that mandate it.

Gelb said his lab is working on pilot studies to apply his method to this disease. He's also working on a screen for MPS VI, an even rarer disease — but one that has had an enzyme replacement therapy, Naglazyme (galsulfase) , available from Biomarin since 2005 — and MPS VII (Sly syndrome), for which Ultragenyx is conducting clinical trials for a therapy.

"There's both parent and biotech interest in these screens," Gelb said. "They want to know whether screening is possible.

"Shire would like to see newborn screening for MPS II, and Biomarin would like to see it for MPS-6," he said, noting it was somewhat of a conflict of interest for those companies. "They want to push screening to find patients for their drug, but they're not the bad guys."