Scientists are using a new approach to pinpoint the causes of rare genetic diseases in children and identify treatment options faster than with traditional methods. The new approach combines DNA sequencing and a chemical analysis called metabolomics to identify mutant genes that cause defective metabolic pathways in patients.

We hope our new technique will increase the speed with which we can pinpoint the defective gene in patients evaluated in our clinics at Children's Health," said the senior author. "Pinpointing the mutation allows us to provide useful information to the family about the disease and its risk to other family members. In some cases, the information either points to an existing therapy or helps us to devise new ones," the author added.

Diseases with a genetic basis account for a large number of illnesses and mortality in children and result in about 25 percent of pediatric hospital admissions. The largest subset of these genetic diseases are known as inborn errors of metabolism (IEMs). Although individually these diseases are rare, collectively they affect a disproportionate number of children, the senior author said. IEMs are caused by defects in genes that help the body metabolize or break down the sugars, proteins, and fats in food. Defective metabolism can lead to chemical imbalances that can cause death or permanent disability in children, unless identified and treated at a young age.

Encouragingly, many IEMs are treatable through dietary modifications and medical therapy once the genetic basis of the disease has been identified. A handful of IEMs are diagnosed through newborn screening, but the majority are diagnosed only after a child becomes ill. Because these diseases are so rare, it can take months or even years to establish the correct diagnosis, and the process often involves invasive procedures like muscle or liver biopsies.

"IEMs are traditionally hard to identify," the senior author said. "Many of these diseases have overlapping symptoms, so even if you suspect an IEM, it is often difficult to pinpoint the problem. There are over 400 known IEMs and several thousand genes involved in human metabolism. Identifying the mutated gene in a child with an IEM - particularly a new or recently discovered disease - is like hunting for a needle in a haystack."

In the study, published in Cell Reports, researchers identified the gene responsible for a rare IEM causing abnormal brain development, seizures, and severe metabolic acidosis. To find the gene, they used a combination of DNA sequencing and metabolomics, a technique that can detect hundreds of small chemical compounds in the blood.

Researchers compared the level of each metabolite found in the patients to healthy subjects using a technique called untargeted metabolomic profiling. This technique allowed researchers to detect 20 times as many metabolites in the blood as would a conventional metabolic screen. This approach provided researchers with a granular view of the metabolic alterations in the patient.

Researchers then used advanced DNA sequencing techniques to look for mutations among the nearly 20,000 human genes. Next, they combined the list of metabolic alterations and the list of mutated genes to determine which mutation could explain the metabolic differences present in the patient.

The proband is a compound heterozygote for variants in LIPT1, which encodes the lipoyltransferase required for 2-ketoacid dehydrogenase (2KDH) function. Metabolomics reveals abnormalities in lipids, amino acids, and 2-hydroxyglutarate consistent with loss of multiple 2KDHs.

Homozygous knockin of a LIPT1 mutation reduces 2KDH lipoylation in utero and results in embryonic demise. In patient fibroblasts, defective 2KDH lipoylation and function are corrected by wild-type, but not mutant, LIPT1 alleles. The data extend the role of LIPT1 in metabolic regulation and demonstrate how integrating genomics and metabolomics can uncover broader aspects of IEM pathophysiology.

"Performing metabolomics in parallel with DNA studies makes it possible to pinpoint disease-causing mutations much faster than the DNA studies alone," said the, lead author of the study. "In this case, it helped us determine that the patient had a genetic defect in one enzyme known as LIPT1. We were able to confirm our new screening technique worked by using cultured cells from the patient and a mouse model to show that the mutation we identified in the patient caused the metabolic disturbances and prevented normal development."

https://www.cell.com/cell-reports/fulltext/S2211-1247(19)30460-7

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