Integrated RNA-seq and RT-qPCR Workflow Identifies Non-IGH Fusion Transcripts as Individualized Molecular Markers for...

Area of Science:

• Hematology
• Genomics
• Molecular Biology

Background:

• Multiple myeloma (MM) is a plasma cell malignancy with complex genomic rearrangements.
• Immunoglobulin heavy chain (IGH) translocations are common, but routine molecular monitoring is challenging, especially in non-secretory MM (NSMM).
• Existing minimal residual disease (MRD) monitoring tools are limited in NSMM due to the absence of serologic markers.

Purpose of the Study:

• To develop and validate fusion gene-based molecular markers for MRD surveillance in MM.
• To establish a clinically practical pipeline integrating RNA sequencing (RNA-seq) and reverse transcription quantitative polymerase chain reaction (RT-qPCR).
• To enable earlier relapse detection and personalized treatment strategies for MM patients.

Main Methods:

• Integrated RNA-seq and RT-qPCR pipeline applied to bone marrow samples from 22 newly diagnosed MM patients.
• Identification and characterization of global fusion landscape, focusing on non-immunoglobulin fusions.
• Validation of selected fusion transcripts using RT-PCR and Sanger sequencing for specificity and quantitative assessment.

Main Results:

• Identified 362 fusion events, with 190 non-immunoglobulin fusions characterized; five recurrent fusions detected in nine patients.
• Recurrent breakpoints found on chromosomes 1 and 19, involving genes in RNA splicing, cancer pathways, and focal adhesion.
• Quantitative assessment of fusion transcripts enabled earlier relapse detection than flow cytometry, proving effective even in NSMM.

Conclusions:

• Individualized fusion transcripts are robust molecular markers for MRD surveillance in MM.
• The RNA-seq-RT-qPCR pipeline offers a practical strategy for precision diagnosis and personalized MM treatment.
• This approach enhances MRD monitoring capabilities, particularly for challenging cases like NSMM.