Genetic Study Finds Novel CMT-linked Mutations
New genetic analysis tools identified previously unknown genetic mutations in people diagnosed with various types and subtypes of Charcot-Marie-Tooth (CMT) disease, a study reveals.
The new techniques used to discern different genes and rare variants may enable researchers to improve detection rates of this neuropathic disorder.
The study, “Cohort Analysis of 67 Charcot-Marie-Tooth Italian Patients: Identification of New Mutations and Broadening of Phenotype Expression Produced by Rare Variants,” was published in the journal Frontiers in Genetics.
CMT is a group of inherited diseases caused by mutations in genes that affect the function of peripheral nerves, which are found outside the brain and spinal cord and control movement and sensory functions.
While the most common disease-causing genetic alteration is a duplication of the PMP22 gene, about 100 different genes have been associated with a wide variety of disease characteristics.
As such, there are various types and subtypes of CMT that are classified based on specific defective genes, how they are inherited, the age of disease onset, disease severity, and the speed of electrical impulses along nerve fibers.
Despite the availability of genetic analysis, not all genes associated with CMT have been identified.
New technologies, such as next-generation sequencing (NGS), can analyze hundreds of genes in a single experiment and help identify new genes and mutations (variants) associated with CMT. Another technique known as multiple ligation-dependent probe amplification (MLPA) can detect variations in the number of gene copies, such as PMP22 duplication.
In this observational study (NCT03084224), a team of researchers from Italy applied these genetic analysis techniques to a group of 67 unrelated CMT patients to identify genetic features associated with their condition.
CMT diagnosis was based on progressive nerve damage, or neuropathy, with or without family history after excluding other acquired causes of neuropathy. Subtypes were diagnosed on whether motor or sensory nerves (or both) were affected, as was the speed of nerve impulses. Blood samples were collected, and genomic DNA from isolated immune cells was extracted and analyzed.
The MLPA experiments found variations in the number of PMP22 gene copies in 26 of the 67 participants (38.8%). Of these, 20 participants had whole PMP22 gene duplications in one of the two gene copies inherited from their parents (heterozygous). These results confirmed a diagnosis of CMT type 1A (CMT1A), the most common subtype of CMT1, which is characterized by damage to the myelin sheath that surrounds nerve fibers.
Another CMT1A-diagnosed patient carried an extra copy of PMP22 due to mosaic duplication, characterized by extra genetic material. In five patients, the PMP22 gene was missing, which confirmed the alternate diagnosis of hereditary neuropathy with pressure palsies (HNPP), a similar condition that also affects peripheral nerves.
NGS tested the remaining 41 participants against a panel of 49 genes shown to be associated with CMT. The results identified eight pathogenic (disease-causing) or likely pathogenic mutations in the 41 cases (19.5%) or nearly 12% of the 67 patients.
“Thus, NGS improved the detection rate to 50.8% (38.8% MLPA + 12% NGS),” the team wrote.
The age of disease onset in all those with an identified genetic defect ranged from 7 to 57 years, with clinical features consistent with known disease characteristics.
The eight genes with CMT-related mutations included MFN2, MPZ, GDAP1, SH3TC2, HSPB1, KIF5A, MTMR2, and KIF1A. Five of these gene defects impact myelin, while the other three are associated with damage to nerve fibers directly (axonal) or to nerve fibers and myelin. Three variants had been reported previously; five were unknown.
Families of six of the eight participants that carry these genetic defects were available for further analysis. The mutations were classified as sporadic in three of the eight cases, and familiar in five.
Of the sporadic cases, based on a lack of mutations or disease in parents, one occurred in a 45-year-old woman due to a mutation in the MFN2 gene, which was responsible for diagnosing axonal CMT2A. A man of 45 years carried an MPZ gene mutation that caused CMT dominant intermediate D disease, a rare form of CMT with axonal and demyelinating neuropathy.
The third case was a 76-year-old woman who had a mutation in the HSPB1 gene, previously associated with the familial form of the neurological condition amyotrophic lateral sclerosis (ALS). Her mutation caused axonal CMT type 2F.
Of the five cases caused by familial CMT, one was a 67-year-old man with a previously unknown KIF1A variant, which was considered likely pathogenic due to an affected brother. This variant caused CMT2C, a rare form of CMT, which also is caused by mutations in the TRPV4 gene. A 69-year-old man with axonal neuropathy was found via a new mutation in the GADP1 gene, which was responsible for CMT2K. His sister had a similar condition, but she was not tested.
The third familiar patient was a 45-year-old man with demyelinating disease and known mutations in both SH3TC2 gene copies, which caused CMT4C. Both parents were healthy carriers of these variants. A 60-year-old man was the fourth case due to a previously unknown mutation in KIF5A, which also is associated with ALS. He was diagnosed with a similar condition called spastic paraplegia, and this variant was present in his affected sister but absent in a healthy sister.
The fifth familiar patient was a 30-year-old woman with axonal neuropathy caused by a novel mutation in the two MTMR2 gene copies. It was classified as likely disease-causing due to her affected brother, who also carried this defect, and caused CMT4B1. Her parents were carriers.
Finally, seven variants of uncertain significance (VoUS), whose function is still unknown, were found in six of the 67 participants. In these cases, there was not enough evidence these mutations were associated with their CMT, or family members were not available for testing.
“This cohort [group] analysis demonstrates the importance of combining different molecular approaches to identify the causative variant in CMT patients,” the scientists concluded. “The use of NGS target panel consisting of 49 genes identified the causative variants in eight patients, improving the detection rate to 50.8%.”
“Therefore, these approaches allow the identification of new genes and rare variants, thus improving the genetic detection rate,” they added.