November 21, 2011 (Montreal, Quebec, Canada) — A novel heritable deletion of exon 2 of the TMLHE (trimethyllysine hydroxylase epsilon) gene on the X chromosome has been identified in a number of males with autism, according to results from a comparative genomic hybridization (CGH) multicenter study.

Results were presented here at the 12th International Congress of Human Genetics (ICHG)/61st Annual Meeting of the American Society of Human Genetics (ASHG).

Because TMLHE encodes for the first enzyme in the biosynthesis of carnitine, researchers are suggesting that neuronal carnitine deficiency may be a risk factor for autism, at least in males, and that autism associated with TMLHE or nutritional carnitine deficiency may be preventable or partially reversible with dietary supplementation.

"Our goal was to discover novel genes mutated in autism and we used array CGH with genome-wide, exon by exon coverage, to screen 100 simplex families from the Simons Simplex Collection (SSC)," Patricia Celestino-Soper, PhD, Baylor College of Medicine, Houston, Texas, and colleagues from other centers told delegates here.

A simplex family is characterized as having 1 affected offspring, and a multiplex family has 2. Dr. Celestino-Soper reported that 1 male in the first 100 trios and then numerous other males with autism were found to have inherited deletions involving exon 2 of the TMLHE gene.

This deletion leads to a novel inborn error of metabolism in carnitine biosynthesis. As Dr. Celestino-Soper observed, carnitine is used in the transport of fatty acids into the mitochondria, which are broken down for energy production. Along the way, trimethyllysine (TML) is converted to 3-hydroxy-TML via the mitochondrial enzyme, trimethyllysine dioxygenase (TMLD).

TMLHE deficiency in turn is characterized by an increase in TML and a decrease in hydroxyl-TML, as well as a decrease in gamma-butyrobetaine in plasma, urine, and the brain.

Independent Autism Probands

For the study, researchers used an array CGH for 8 independent autism probands, all of whom had deletions involving exon 2 of the TMLHE gene. Another 24 unrelated individuals who had similar deletions were used as controls. "The first question we asked is, do TMLHE exon 2 deletions cause loss of function?" Dr. Celestino-Soper observed.

To study this, researchers evaluated TMLD activity in individuals hemizygous for TMLHE exon 2 deletions. Results showed loss of TMLD enzyme activity in autism probands and unaffected controls, "suggesting that the TMLHE exon 2 deletion does cause loss of enzyme activity," she added. The researchers also asked whether TMLHE deficiency causes metabolic abnormalities.

To answer this, the team evaluated 2 autistic brothers with exon 2 deletions, as well as 5 other unrelated autistic individuals with the same deletion. They observed an increase in TML and a decrease in hydroxyl-TML, as well as a decrease in gamma-butyrobetaine in both plasma and urine. As Dr. Celestino-Soper noted, an investigation of plasma carnitine levels in the 2 brothers at the ages of 15 to 17 showed they had normal levels of free carnitine.

However, she pointed out, "this is likely due to dietary intake of carnitine, and we don’t know what carnitine levels are in the brains of these 2 boys [or]…what their carnitine levels were when they were young infants."

The researchers also sought to determine whether TMLD deficiency was a common cause of autism. The answer turns out to be no — when they assessed TMLD activity in lymphoblastoid cell lines of autistic individuals and controls, they found no widespread TMLD deficiency.

Finally, the investigators asked whether TMLHE deficiency could be a risk factor for autism. When they compared simplex probands with controls, they found no differences in the frequency of exon 2 deletions between cases and controls. They also observed that the TMLHE exon 2 deletion was common in unaffected males, occurring in approximately 1 out of every 350 males.

On the other hand, when they compared multiplex autistic cases with controls, they "found that the frequency of exon 2 deletions was 3 times higher in multiplex probands compared with controls and this increase was significant," Dr. Celestino-Soper said. Looking at 7 multiplex probands with the TMLHE deletion, she and her colleagues then asked whether the same deletion might have been transmitted from the mother, who was also autistic, to her sons.

"What we found is that 6 out of 7 of these autistic siblings also had a deletion, with a P value of .029, which is again significant," she added. After considering that multiplex probands had a significant increase in the frequency of exon 2 deletions and that 6 of the 7 autistic siblings had the same deletion, researchers concluded that TMLHE deficiency is a risk factor for autism (P = .0014).

Penetrance of TMLHE Deficiency

Finally, the researchers calculated the penetrance of TMLHE deficiency for autism. They made several assumptions to arrive at this calculation: that autism spectrum disorders have a prevalence of 1 in 100; that there is a 4:1 male to female ratio in these disorders; and that 1 in 150 to 1 in 250 individuals with autism have the TMLHE exon 2 deletion, as do 1 in approximately 350 unaffected males.

On the basis of these assumptions, "we get a penetrance of 2.2% to 3.7%, which is pretty low," Dr. Celestino-Soper said, "but we hypothesize that perhaps in a population that has a lower dietary carnitine intake, such as vegetarians, that penetrance could be higher."

Session moderator Tjitske Kleefstra, PhD, UMC, St. Radboud, the Netherlands, told Medscape Medical News that to find a number of cases with the same genetic defect in an X-linked cohort is quite exceptional.

Nevertheless, "the difficulty is that this deletion is also present in healthy controls," she noted, which clearly confounds the investigators' findings. Dr. Kleefstra also would have liked to have seen findings from not only probands or single cases but larger family clusters of autism spectrum disorders with several generations of affected family members.

"Their observations are interesting," she added, "but we need further follow-up before we draw any conclusions from these findings. But if this deficiency is important in clinical practice, we need to find out."

The 12th International Congress of Human Genetics (ICHG)/61st Annual Meeting of the American Society of Human Genetics (ASHG). Abstract #83. Presented October 13, 2011.


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