RNA analysis more sensitive in detecting KIT mutation in SM diagnosis: study

RNA techniques could enable clinicians to identify SM earlier.

RNA-based testing methods were more sensitive in detecting genetic mutations necessary for diagnosing systemic mastocytosis (SM) than traditional DNA-based methods, according to a study published recently in Virchows Archiv, the official journal of the European Society of Pathology.

Results showed that RNA testing methods such as pyrosequencing of mRNA/cDNA successfully identified mutations in cases missed by DNA analysis, offering new diagnostic possibilities for patients. Detecting KIT mutations is key to diagnosing SM.

SM is usually caused by a sporadic mutation in the KIT gene, which codes for a protein called CD117 transmembrane tyrosine kinase. The protein is involved in the growth, survival and migration of mast cells. The most common KIT mutation associated with SM is the D816V mutation, which results in the amino acid aspartic acid being replaced by the amino acid valine in the protein chain.

“In our study, the success rate for DNA and RNA analysis of routinely processed bone marrow trephines was 100%,” study authors said.

Read more about SM testing and diagnosis

The implications extend beyond diagnosis. Patients with SM often face delayed or missed diagnoses because of inadequate testing sensitivity. By adopting RNA-based techniques, health care providers could better identify the disease, improving the accuracy of treatment plans and ultimately enhancing patient outcomes.

Prior research highlighted variability in success rates for DNA testing, with suboptimal methods resulting in incomplete or unreliable data. The new study confirmed that RNA-based approaches not only overcome these limitations but also enable precise correlation with morphological evaluations.

The study analyzed 101 samples of bone marrow, achieving a 100% success rate for extraction of both DNA and RNA. Among 80 samples with a confirmed KIT mutation, 11 were detected exclusively through digital PCR of genomic DNA, while seven were identified only through mRNA/cDNA pyrosequencing. Importantly, traditional DNA pyrosequencing failed to detect mutations in 44 samples that were positive by other methods, underscoring its lower sensitivity.

For patients, the findings showed that RNA-based testing can identify critical mutations earlier, especially in cases with low levels of the mutant allele. This could ensure that SM is diagnosed more reliably, even when biopsy samples are small or compromised. The use of mRNA from routinely processed decalcified bone marrow samples would also facilitate broader access to testing without requiring fresh tissue.

The ability to detect mutations in preserved bone marrow samples represents a major step forward in the diagnostic capabilities for mastocytosis.

“This study demonstrates that reliable and sensitive analyses of nucleic acids extracted from formalin-fixed, EDTA decalcified, and paraffin-embedded bone marrow trephines is possible under routine conditions and that the analysis of mRNA for mutation detection is a useful complement for the comprehensive diagnostic work-up in hematopathology,” the authors said.