[Transcriptome sequencing-based classification and quantification of IKZF1 transcript isoforms in B-cell acute...

Area of Science:

• Hematology
• Molecular Biology
• Bioinformatics

Background:

• IKZF1 (Ikaros family zinc finger 1) gene alterations are crucial in B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis.
• Accurate classification and quantification of IKZF1 mutant transcripts are essential for understanding B-ALL.
• RNA sequencing (RNA-seq) offers a powerful tool for transcriptomic analysis.

Purpose of the Study:

• To classify and quantify IKZF1 mutant transcripts in B-ALL using RNA-seq and bioinformatics.
• To evaluate the diagnostic performance of RNA-seq compared to RT-PCR for IKZF1 mutations.
• To investigate the correlation of IKZF1 mutations with specific B-ALL subtypes and molecular pathways.

Main Methods:

• RNA sequencing (RNA-seq) was performed on 263 B-ALL patient samples.
• An integrated bioinformatics pipeline was developed for IKZF1 transcript classification and quantification.
• Results were validated against qualitative reverse transcription PCR (RT-PCR) and Sanger sequencing.

Main Results:

• RNA-seq identified IKZF1 mutant transcripts in 51 B-ALL patients, with high concordance (94.3% sensitivity, 99.5% specificity) to RT-PCR.
• IK6 and IK10 were the predominant mutant transcripts, accounting for 67.9% and 28.3% respectively.
• Mutant IKZF1 expression clustered into two distinct groups, and mutations were frequently observed in Ph+ and Ph-like B-ALL, often with PAX5 translocations and JAK-STAT pathway abnormalities.

Conclusions:

• Optimized RNA-seq and bioinformatics analysis provide a reliable method for classifying and quantifying IKZF1 transcripts in B-ALL.
• The study identified two distinct expression patterns of mutant IKZF1 transcripts.
• IKZF1 mutations are associated with specific B-ALL subtypes, including those with PAX5 translocations and altered JAK-STAT signaling.