Long-read single-cell isoform sequencing for cell type-specific detection of genomic rearrangement-dependent and -independent fusion transcripts

作者：Wencke Walter, Wolfgang Kern, Anna Stengel · 发表于：Blood · 年份：2025 · DOI：10.1182/blood-2025-6117 · 被引用次数：2 · 研究领域：Acute Lymphoblastic Leukemia research、Acute Myeloid Leukemia Research、Chronic Myeloid Leukemia Treatments

Abstract Background: Fusion transcripts are formed by combining exons from two different genes, often due to structural rearrangements such as deletions, inversions or translocations (genomic rearrangement-dependent, GRD) or through aberrant splicing (genomic rearrangement-independent, GRI). In hematological malignancies, many fusion transcripts act as driver events, playing crucial roles in leukemogenesis and serving as diagnostic markers, such as BCR::ABL1. However, the role and diagnostic significance of other fusion transcripts, like P2RY8::CD99—which has been found in both healthy samples and B-ALL patients—are less clear. Similarly, the clinical relevance of other GRI fusion transcripts, such as SEMA6A::FEM1C, often remains uncertain. Single-cell analysis is a promising approach to detect these fusion transcripts within individual cells and cell populations, shedding light on the subclonal architecture and cells of origin. Aim: Evaluating the feasibility of integrating long-read sequencing with single-cell library preparation to detect and characterize GRD and GRI fusion transcripts. Patients and Methods: Our cohort consisted of 10 samples diagnosed with B-ALL, featuring various fusion transcripts: BCR::ABL1 (n = 6, GRD), SEMA6A::FEM1C (n = 10, GRI), EBF1::PDGFRB (n = 1, GRD), and P2RY8::CD99 (n = 1, GRI), as identified through bulk whole transcriptome analysis. Cryopreserved cells were processed using the GEM-X Universal 3' Expression Library Prep Kit (10x Genomics) an...