Case report and novel treatment of an autosomal recessive Leigh syndrome caused by short-chain enoyl-CoA hydratase deficiency

Abstract

Short chain enoyl-CoA hydratase (SCEH) deficiency leads to a severe form of autosomal recessive Leigh syndrome with inevitable neurological decline and early mortality. SCEH is most notably involved in valine catabolism, a deficiency of which results in various metabolic alterations, including increased levels of the highly reactive metabolite 2-methacrylyl-CoA. With no proven treatments available to date, it has been speculated that patients may respond to a valine restricted diet and/or N-acetylcysteine supplementation, as suggested by early studies of a very similar inborn error of metabolism, 3-hydroxyisobutyryl-CoA hydrolase deficiency. We describe a patient with typical Leigh syndrome clinical findings and identified compound heterozygous variants in ECSH1. Valine-restricted diet was initiated at 6 months of age and N-acetylcysteine supplementation at 9 months with subsequent improvement in growth and slow progress in developmental milestones. However, at 15 months, the patient aspirated during a breakthrough seizure from which he did not recover and died soon after from related complications. This report highlights some of the challenges that remain in the management and treatment of SCEH deficiency, while demonstrating that a valine restricted diet and N-acetylcysteine can be safely administered with the potential for clinical improvement.

1 |. INTRODUCTION

Leigh syndrome is a severe neurological disorder that may be the initial manifestation of several different metabolic genetic diseases. Clinically, Leigh syndrome is characterized by decompensation during intercurrent illnesses with psychomotor regression, followed by periods of transient stabilization or slight improvement. With few exceptions, effective treatments for the majority of causes remain elusive and inevitable neurological decline is the norm with a median age of mortality at 2.4 years (Sofou et al., 2014). Various vitamin and cofactor supplements have been proposed as therapeutic approaches; however, their efficacy is usually dependent on the underlying molecular defect and for the most part have not proven to alter the natural history of the disorder (Soler-Alfonso et al., 2015).

Short-chain enoyl-CoA hydratase (SCEH) deficiency, also known as crotonase deficiency, is one particularly rare cause of autosomal recessive Leigh syndrome. It was first described by Peters et al. (2014) and found to be caused by pathogenic variants in the ECHS1 gene. The gene itself is approximately 11 kb in length, composed of eight exons with the first and last containing 5′- and 3′-untranslated regions, and is located on chromosome 10 (Janssen, Davis, Le Beau, & Stoffel, 1997). Reduced SCEH activity caused by biallelic pathogenic variants in ECHS1 clinically results in a typical Leigh syndrome presentation with early onset of hypotonia, failure to thrive, developmental delay, cardiomyopathy, and sensorineural hearing loss. The pathophysiological mechanism at this time is poorly understood as SCEH plays a complex and multidimensional role in times of prolonged fasting or metabolic stress. SCEH has wide substrate specificity in different metabolic pathways including valine catabolism, propionate metabolism, and fatty acid oxidation.

SCEH most notably is involved in the distal part of the valine degradation pathway, mediating the enzymatic hydration of methylacrylyl-CoA to 3-OH-isobutyryl-CoA. Insufficient SCEH enzyme activity results in the abnormal accumulation of the highly reactive metabolite 2-methacrylyl-CoA, which reacts with sulfhydryl-containing molecules including the cysteine residues of various cellular proteins and enzymes (Peters et al., 2015). This in turn causes reduced activity of such cysteine containing enzymes including pyruvate dehydrogenase and respiratory chain enzymes, leading to further cellular disruption (Ali, Roche, & Patel, 1993; Burwell, Nadtochiy, Tompkins, Young, & Brookes, 2006; Cooperstein, 1963; Khailova, Korochkina, & Severin, 1989; Schwartz & Reed, 1970). Additionally, 2-methacrylyl-CoA reacts with cysteine containing thiol groups of antioxidants like glutathione and thioredoxin, resulting in antioxidant depletion and the potential for further oxidative damage to the cell (Ferdinandusse, 2015; Perry, Godin, & Hansen, 1982; Salmi, Leonard, & Lapatto, 2012). Characterization of biochemical profiles in patients affected with SCEH deficiency has shown elevations of S-(2-carboxypropyl)cysteine, S-(2-carboxypropyl)cysteamine, S-(2-carboxyethyl)cysteine, S-(2-carboxyethyl)cysteamine, 3-methylglutaconate, and 2,3-dihydroxy-2-methylbutyrate in urine, with current debate regarding the potential use of such metabolites for diagnostic purposes and in monitoring treatment efficacy (Fitzsimons et al., 2018; Peters et al., 2014).

The remaining enzymatic functions of SCEH are less understood, but in general thought to have little to no clinical significance in deficient patients. For example, SCEH plays a role in the degradation of leucine and isoleucine via the hydration of 3-methylcrotonyl-CoA and tiglyl-CoA; however, accumulation of reflective metabolites 3-methylcrotonyl-glycine and N-tiglylglycine has not been observed in affected patients (Ferdinandusse et al., 2015; Yamada et al., 2015). Further downstream, SCEH also catalyzes the hydration of acryloyl-CoA, derived from propionyl-CoA, into 3-hydroxypropionyl-CoA. In SCEH deficient patients, subsequent build-up of acryloyl-CoA metabolites has been observed with elevations in 2,3-dihydroxy-2-methylbutyric (23DH2MB) and N-acetyl-S-(2-carboxyethyl)cysteine (Peters et al., 2015). Acryloyl-CoA, a homologous compound to methacrylyl-CoA, also contains a highly reactive double bond that is capable of spontaneously reacting with sulfhydryl groups and may contribute to some of the metabolic derangement of affected patients (Peters et al., 2015).

Despite all that has been learned about the pathophysiological mechanism of SCEH deficiency, very little progress has been made in the discovery of therapeutic approaches. Because SCEH deficiency is a relatively newly described metabolic disease, most of the current treatment approaches have been based on the prior experience with 3-hydroxyisobutyryl-CoA hydrolase deficiency (HIBCH). HIBCH is responsible for the next step in the valine degradation pathway, immediately after SCEH, and catalyzes the hydrolysis of 3-hydroxyisobutyryl-CoA to 3-hydroxybutyrate. Similar to SCEH deficiency, HIBCH deficiency also presents as Leigh syndrome and the mechanism of the disease is thought to be related to the toxic effects of methacrylyl-CoA and acryloyl-CoA metabolite build-up.

Soler-Alfonso et al. (2015) took a different therapeutic approach and first attempted to treat a single HIBCH deficient patient with a valine restricted diet. Valine restriction was utilized in their patient for 1 year with reported clinical improvement of muscle tone, energy level, and nystagmus. Given the clinical and metabolic similarities of these two diseases, it has been speculated that SCEH deficient patients may also respond to a valine restricted diet; however, there are no reports of this proposed treatment being used in the current literature. Therefore, we present our experience in treating an SCEH deficient patient with a valine restricted diet and N-acetylcysteine to determine the safety and efficacy of such a treatment in a disease with an otherwise very poor prognosis.

2 |. PATIENT AND METHODS

2.1 |. Patient presentation

Appropriate consent for publication and photography was obtained from the proband’s parents. The proband was a male born from an uncomplicated pregnancy and vaginal delivery at 39 weeks gestation to a non-consanguineous 24 year old mixed German/Czech father and 21 year old G3P1 mixed Russian/Irish/English mother. At birth, the patient was well appearing with a normal birth weight and length. No phenotypic abnormalities or dysmorphic features were observed within the first few days of life. However, at 2.5 months of age, he was found to have profound hypotonia, projectile vomiting, diarrhea, and failure to thrive.

The patient was first evaluated by the inpatient Genetics Consult Service at Texas Children’s Hospital at 4 months due to new onset episodic opisthotonic posturing and continued weight loss. At this time, the patient’s growth parameters were a weight of 5.0 kg (Z-score −3.36), length of 61 cm (Z-score −2.02), and head circumference of 39.8 cm (Z-score −2.04). Developmentally, he could smile, coo, and make eye contact, but he did not have appropriate head control. A subsequent brain MRI revealed restricted diffusion in the bilateral internal capsule and putamen, confirming the diagnosis of Leigh syndrome.

Biochemical studies at presentation were significant for a normal plasma ammonia level of 44 μmol/L (normal 15–47 μmol/L) and elevated plasma lactate of 5.7 mmol/L (normal 0.2–2.0 mmol/L). Additional investigations did not reveal abnormalities in the patient’s plasma amino acids, acylcarnitine profile, and urine organic acid analysis. Subsequent evaluation of pyruvate dehydrogenase complex activity in blood was normal. Untargeted plasma metabolomic analysis was obtained after the patient was medically stabilized and resuscitated but before the implementation of specific dietary changes. Untargeted plasma metabolomics analysis showed multiple perturbations including beta-hydroxyisovalerate (Z-score 2.81), 1-lignoceroyl-GPC (24:0) (Z-score 2.64), 3-hydroxy-3-methylglutarate (Z-score 2.61), and laurate (12:0) (Z-score 2.51). This non-specific metabolomics pattern was not in support of a specific inborn error of metabolism, although beta-hydroxyisovalerate had been reported to be elevated in another case of SCEH deficiency (Fitzsimons et al., 2018). A limitation of this study was that it did not measure the previously described biochemical indicators of SCEH deficiency such as S-(2-carboxypropyl)cysteine, S-(2-carboxypropyl)cysteamine, S-(2-carboxyethyl)cysteamine, and 2-methyl-2,3-dihydroxybutyric acid (Peters et al., 2014). Cultured fibroblasts from the patient revealed markedly reduced SCEH activity level of <31 nmol/min mg protein (normal 179–816 nmol/min mg protein), confirming the diagnosis.

The patient developed feeding difficulties with weight loss and evidence of aspiration on a swallow study, necessitating G-tube placement at 9 months of age. The clinical course was complicated by infantile spasms and seizures. Electroencephalography revealed diffuse delta background slowing indicative of a moderate degree of diffuse encephalopathy and intermittent hypsarrhythmia. Infantile spasms were increasingly difficult to control, but ultimately responsive to vigabatrin. At 15 months, the patient had unexpectedly stopped taking his vigabatrin and aspirated during a breakthrough seizure from which he did not recover and passed away soon after from related complications.

2.2 |. Genetic testing

A chromosomal microarray analysis (Oligo V8.1.1) was performed by Baylor Genetics in Houston, TX. No copy number changes associated with known microdeletions or microduplications disorders were identified. Additionally, no copy number variants of the mitochondrial genome were detected. Mitochondrial sequencing via NGS detected a likely pathogenic variant in MT-TV, m.1642G>A. This variant has been associated with MELAS syndrome; however, a heteroplasmic level of 1.9% is far less than has been described in affected patients and was not considered clinically significant (de Coo et al., 1998; Taylor et al., 1996).

Whole exome sequencing (WES) was performed by Baylor Genetics. Interpretation was limited to variants determined to be pathogenic, likely pathogenic, and variants of unknown significance (VUS) according to the American College of Medical Genetics guidelines (Richards et al., 2015). The WES identified compound heterozygous variants in ECHS1 including the previously reported pathogenic variant c.538A>G p.T180A in exon 5, inherited from the mother and a novel variant classified as a VUS c.444G>T p.M148I in exon 4, inherited from the father. The VUS had previously been seen in two alleles of European descent according to gnomAD database, and SIFT and PolyPhen-2 predicted this VUS to be damaging/possibly damaging. The compromised methionine in this VUS at position 148 is a highly conserved amino acid, extending as far back as C. elegans.

2.3 |. Treatment regimen

Appropriate consent for dietary intervention from the proband’s parents was obtained after detailed discussion of available data on valine restriction in 3-hydroxyisobutryl-CoA hydrolase deficiency, a similar condition also involved in the catabolism of valine which also presents with Leigh syndrome and neurological deterioration during times of metabolic stress (Soler-Alfonso et al., 2015). A valine restricted diet was initiated at 6 months of age with a 26 kcal/oz formula preparation of branched-chain amino acid free formula (standard maple syrup urine disease formula), natural protein (standard infant formula), and an energy module to supplement calories to provide the patient with 98 kcal/kg/day, 1.5 g total protein/kg/day, valine 45 mg/kg/day, isoleucine 41 mg/kg/day, and leucine 76 mg/kg/day. This diet prescription was created to restrict valine while meeting the recommended Dietary Reference Intake for the patient’s weight and age. Baseline amino acids levels including valine, leucine, and isoleucine were all within the reference range prior to initiation of the prescribed diet. Follow-up levels showed a reduction of all three, but they remained in the reference range or borderline low, so adjustments were only made to accommodate changes in weight (Table 1). Additionally, natural protein intake provided sufficient leucine and isoleucine based on these levels, thus supplementation was not prescribed. At 9 months, N-acetylcysteine supplementation with 70 mg/kg/day 10% oral solution divided into three doses per day was initiated for the purpose of providing extra cysteine pool to replenish reduced glutathione stores. Around the same time, the patient’s growth hit a nadir with a weight of 5.625 kg (Z-score −4.17) due to progressive feeding difficulties that improved with the initiation of G-tube feedings with the valine restricted diet. At 15 months of age, the patient’s growth had continued to improve to a weight of 9 kg (Z-score −1.32). Prior to his breakthrough seizure and aspiration, he had made developmental progress as well; at 15 months he was able to roll from supine to prone and had better head control, but was still not tracking or reaching for objects and remained noticeably hypotonic.

TABLE 1.

Branched chain amino acid levels measured prior to and after initiation of a valine restricted diet

Age	Valine (reference range 50–242 mmol/L)	Isoleucine (reference range 10–86 mmol/L)	Leucine (reference range 30–142 mmol/L)
4 months	124	42	65
6 months	Initiation of valine restricted diet
8 months	47	18	25
9 months	69	24	25
10 months	84	34	52

3 |. DISCUSSION

SCEH deficiency is a complex inborn error of metabolism involving multiple metabolic pathways. However, its pivotal role as the fourth step in valine degradation, is thought to be responsible for the major clinical and biochemical features of the disease. This is owed to the fact that the presentation is remarkably similar to that of Leigh syndrome caused by a deficiency in the enzyme responsible for the fifth step in valine degradation, HIBCH. In both SCEH and HIBCH deficiencies, accumulation of the toxic compound 2-methacrylyl-CoA and its effect on cysteine residues is suspected to be the underlying disease mechanism. Elevated levels of 2-methyl-2,3-dihydroxybutyrate is also a common biochemical feature that is currently being evaluated as a possible screening test for these two conditions.

Support for the use of N-acetylcysteine is based on the increased N-acetyl-S-(2-carboxypropyl)cysteine levels observed in SCEH and HIBCH patients, suggesting glutathione metabolism may be responsible for the sulfur-containing groups of such metabolites in urine (Peters et al., 2015). Conjugation of glutathione via glutathione S-transferases is a well-established mechanism for the body to detoxify xenobiotic substrates for excretion in the urine (Wang & Ballatori, 1998). As such, it has been suggested that N-acetylcysteine supplementation may be beneficial by increasing reduced glutathione levels for the removal of the toxic metabolites, the clinical efficacy of which remains to be determined.

Recently, Soler-Alfonso et al. (2015) demonstrated that HIBCH deficiency patients may respond to the introduction of a valine restricted diet, utilizing medical food products without branched chain amino acids intended for patients with maple syrup urine disease and supplementing isoleucine and leucine (Soler-Alfonso et al., 2015). In their study, the patient showed clinical response to the treatment regimen with marked improvement in muscle tone, energy level, and nystagmus. While a specific biochemical marker cannot be used to verify the effects of the treatment in their case, it was hypothesized to be the result of the synergistic effects of valine restriction along with vitamin/cofactor supplementation. The compassionate use of EPI-743 in their patient may have also contributed to patient’s clinical improvement, although the efficacy of this medication in mitochondrial diseases is still being studied.

Suspecting a similar disease mechanism, we hypothesized our SCEH deficient patient should have a similar positive response to a valine restricted diet and N-acetylcysteine treatment. Before his death, the proband had some clinical improvement with catch-up weight gain and slow progress in developmental milestones, although this is confounded by the overall improved nutrition following G-tube placement. Limitations in the availability of a reliable biomarker to assess response to treatment make it difficult to make a conclusive statement regarding the efficacy of these therapeutic approaches. This report highlights the need for the identification of a metabolite that could be used for diagnostic purposes and to monitor the efficacy of potential treatments. Nonetheless, we have demonstrated that as exemplified in the case of our patient, the combined approach of N-acetylcysteine supplementation and a valine restricted diet can be safely utilized in SCEH deficient patients. Furthermore, when the clinical course is not complicated by intercurrent illnesses, such patients may also have improved growth and development as our patient did.

Despite the similarities between SCEH and HIBCH deficiency, there are some notable differences between the two. For example, SCEH deficient patients are much less likely to have evidence of impaired oxidative phosphorylation compared to HIBCH deficient patients. Interestingly, patients with SCEH deficiency that do have detectable oxidative phosphorylation impairment tend to be more severely affected with death typically occurring in infancy or early childhood (Haack et al., 2015). The role of SCEH in the other metabolic pathways including propionate metabolism, bioenergetics, and fatty acid oxidation are less well understood, thought to overall be less clinically significant. Thus, more research is needed to understand the biological role of all SCEH enzymatic activities, to further characterize the disease, and to create a more specific and targeted treatment regimen.

4 |. CONCLUSION

Leigh syndrome is a generally devastating diagnosis with a very poor prognosis. Treatment options are limited to very few specific underlying causes. More recently, HIBCH deficiency has been suspected to be one treatable type via a valine restricted diet. Given the similarities, SCEH deficiency may be amenable to treatment with a similar dietary approach as well.

We have shown in this study that a valine restricted diet can be tolerated in a patient with SCEH deficiency and in conjunction with N-acetylcysteine, has the potential to improve clinical outcomes. However, this is a very difficult disorder to treat as children may still succumb to intercurrent illnesses. Nonetheless, more remains to be learned about SCEH deficiency to better understand the disease mechanism and create a more specific and targeted treatment regimen.