TRA/D Rearrangements As a New Potential Alternative Prognostic Biomarker in Pediatric B-Cell Acute Lymphoblastic Leukemia
Authors: Zheng Jiajia , Bian Xinni , Lu Jun , Xiao Peifang , He Hailong , Wang Yi , Li Jie , Fan Junjie , Yao Yanhua , Ling Jing , Wang Yiting , Chen Nan , Lang Xingping , Feng Jingjing , Chen Xiaojun , Chen Huafei , Xiao Sheng , Xiao Sheng , Hu Shaoyan 
Published: December 2024

Introduction B-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer. Despite the significant advances in risk classification and improved treatment, recurrence still occurs in 15%-20% of cases. Therefore, identifying new biomarkers capable of predicting the risk of BCP-ALL is crucial for improving outcomes. Rearrangements of the T-cell receptor alpha-delta locus (TRA/D) and immunoglobulin (IG) loci are well-established diagnostic markers for T-cell acute lymphoblastic leukemia (T-ALL) and B-cell acute lymphoblastic leukemia (B-ALL), respectively. Chromosomal translocations involving the TRA/D at the 14q11.2 are found in around 17% of T-ALL but are rare in B-ALL. Herein, we use next-generation sequencing to detect TRA/D rearrangements and describe the clinical and biological characteristics of patients with B-cell ALL and TRA/D rearrangements.
Methods We conducted a retrospective study in a single institution involving 97 pediatric B-ALL patients diagnosed between June 2023 and January 2024 to identify TRA/D rearrangements using a targeted DNA next-generation sequencing (NGS) which highly sensitive to detect translocations at the genomic level and use this approach emploings probes spanning the entire IG/TR gene regions. Bone marrow aspirate, immunophenotyping, G-banding karyotype, fluorescent in situ hybridization (FISH), whole-transcriptome RNA sequencing (RNA-seq) and whole-genome sequencing (WGS) were performed for all 97 patients. The involvement of the TRA/D locus was confirmed by FISH and Sanger sequencing. The relative partner gene expression levels (fragments per kilobase of transcript per million mapped reads, FPKM) were estimated based on supporting reads retrieved from the transcriptome RNA-seq datasets and were compared to those with B-ALL without TRA/D rearrangements. We further characterized the expression of hematopoietic stem cells (HSCs)-related genes in this type of TRA/D rearrangements by gene set enrichment analysis (GSEA).
Results
Surprisingly, we revealed that 6/97 (6.18%) cases of B-cell ALL harbored TRA/D rearrangements. These rearrangements were associated with various partner genes including TCL1A/B, CEBPA, and CDKN2A. Patients with TRA/D rearrangements exhibited a gene expression profile enriched in hematopoietic stem cell features and, in some cases, had additional activating mutations in RAS signaling pathway genes. These tumors often expressed mixed lineage antigens. Compared with patients without TRA/D rearrangements, patients with TRA/D rearrangement were significantly more likely to be classified as intermediate risk (P = 0.047), havinghigher frequency of ZNF384/362 rearrangements (P &lt; 0.001), and s measurable residual disease (MRD) levels above 1% at day 19 (P = 0.034).
Conclusions
Our observations indicate that TRA/D rearranged may represent a distinct subgroup of pediatric B-ALL, characterized by unique gene expression profiles, immunophenotypes, and prognostic features which have prognostic implications for patients classified as intermediate risk.