Diagnosing diseases of inborn errors of metabolism (IEM) has come a long way from the days of Sir Archibald Garrod who, in the late 1800s, relied on the darkening in the color of a person’s urine to diagnose the genetic IEM disease alkaptonuria. Today, researchers are combining genomics and metabolomics to identify genes that, when mutated, give rise to metabolic diseases in children.
By integrating whole exome sequencing (WES) with broad analysis of the chemical makeup of the blood, a team from the University of Texas Southwestern Medical Center was able to home in on the genetic changes that caused the previously undiagnosed disease of an 8-year-old patient who presented with developmental delay, seizures, and lactic acidemia.
Led by Ralph DeBerardinis, M.D., Ph.D., chief of the division of pediatric genetics and metabolism at the Children’s Medical Center Research Institute (CRI) at UT Southwestern Medical Center, the team found that the disease was caused by a genetic mutation in LIPT1, the lipoyltransferase required for 2-ketoacid dehydrogenase (2KDH) function.
The study that describes a new approach to understand the causes of rare genetic diseases is published in Cell Reports in a paper entitled “Functional Assessment of Lipoyltransferase-1 Deficiency in Cells, Mice, and Humans.”
“It’s a needle in a haystack problem” DeBerardinis told Clinical OMICs. The levels of some metabolites in patients’ blood are measured routinely. “The problem is that we only measure a few dozen of those compounds in the hospital. But, the chemical makeup of the blood is incredibly complex with thousands of metabolites. If you only test a subset, it’s easy to miss what you may need to find. So, we want to build a broader test. To do this, we combined the genetic and chemical information.”
The group’s ability to test the significance of the mutations in a wet lab is what makes their results so meaningful. DeBerardinis notes that sequencing routinely identifies genetic variants. But, the critical component of this study is their ability to determine whether those variants cause the phenotype. To do this, the team first identified metabolic abnormalities. After searching for sequence differences in the pathways that made sense with the metabolomics, they created the mutation in patient-derived fibroblasts and mice to analyze the resulting metabolic abnormalities. Although the mice died mid-gestation, the embryonic tissue could be used for metabolomic analysis. In both the mice and cells, metabolic abnormalities similar to those described in the patient were observed.
This study has provided incredibly important information to the patient and her family. Beyond that, DeBerardinis notes that “the next time there is a patient who gets WES without the metabolomic workup, and a mutation is found in the LIPT1 gene, it will be easy for the lab to say that this is the cause of the problem.”
“One of the most exciting parts of this study is that it allowed us to build a research platform using advanced genomics and metabolomics technologies together with experimental assays, to identify the disease cause of a rare IEM” noted Min Ni, Ph.D., assistant professor at the CRI and first author on the paper.
This is particularly important because, as Ni asserted, “efficient diagnosis of IEMs is always challenging.” There are more than 400 known IEMs that share the commonality of abnormal metabolism. Caused by having a mutation in an enzyme that catalyzes one of the steps in the biochemical network, some can be diagnosed by a phenotypic change caused by the shift in metabolites. But, for many others, a diagnosis requires sleuthing around in non-specific symptoms with limited means of molecular or biochemical testing. Therefore, many remain largely undiagnosed. However, if the underlying metabolic defect can be understood, a workaround of the metabolic block may be developed—fixing the broken step in the pathway.
Ni said she was “very surprised” that a single-point mutation in a gene, such as the one they found in LIPT1, could lead to the remarkable alterations of multiple metabolic pathways. Because LIPT1 activates multiple other enzymes, this patient actually has defects in multiple different enzymes in the Kreb’s Cycle. Although this complexity makes it more challenging to find a workaround, the results of the study have prompted the team to think about adding the dietary supplements to replenish those that have been depleted in the patient’s diet. DeBerardinis noted that “the generosity of this family to participate in this study means that the next time we encounter a patient with LIPT1 deficiency, we could potentially start diets that could be helpful to these patients earlier in life.”
Ni added that their hope is that this work reaches beyond LIPT1. She noted that “the workflow could be readily applied to study of many other IEMs.” DeBerardinis agrees, noting that “implementing metabolomics in a clinical setting is not impossible.” Mass spectrometry is already present in clinical labs, so “we hope to convince people that this is something that could be broadly implemented.”
For more on moving metabolomics into the clinic click here.