All-352 exploring dux4-rearranged b-all in india: incidence, molecular pathways, and potential biomarkers

Abstract

Context DUX4-rearranged B-ALL (DUX4-r), characterized by cryptic DUX4-rearrangements, has not been investigated in Indian patients. Gaining an understanding of the clinical and molecular characteristics is crucial for targeted therapy development. Objective We aimed to determine the incidence, clinical characteristics, gene fusions, single nucleotide variants (SNVs), and copy number alterations (CNAs) in DUX4-r subtype. Gene set enrichment analysis (GSEA) and Qiagen Ingenuity Pathway Analysis (IPA) were employed, with external validation using a publicly available dataset. Design Total RNA sequencing identified DUX4-r subtype using Rtsne and FusionCatcher/Cicero. SNVs were identified using GATK HaplotypeCaller, and CNAs were assessed using MLPA. After differential gene expression analysis, GSEA was performed and pathways with P<0.05 and false discovery rate (FDR) <0.05 were considered significant. Core analysis and biomarker filtering were conducted using IPA. Patients We analyzed bone marrow/peripheral blood samples from 394 de-novo B-ALL patients (67.1% males, 32.9 females, median age, 15.2 years) at AIIMS, India (2018-2022). Sentinel aberrations were identified using multiplex reverse transcription polymerase chain reaction and fluorescence in situ hybridization. Results Twenty-nine cases (7.36%) were classified as DUX4-r ALL, with fusions including IGH::DUX4 (n=24, 82.75%), ERG::LINC01423 (n=3, 10.34%), and a novel fusion, DUX4::EML4 (n=1, 3.44%). ERG and IKZF1 alterations were observed in 25% and 20.83% of patients, respectively. Mutations were found in KRAS, FLT3, JAK3, PAX5, PTPN11 (n=8, 27.58%), and ZEB2:H1038R (n=2, 6.89%) in DUX4-r samples. The MYC pathway (NES=1.77) was enriched while the P53 pathway (NES=-2.18) was downregulated. Out of 25 gene networks, 1 was involved in hematological development, and 3 in cell death/survival processes. The merged network identified potential master regulators: CCR6, DLC1, ECM1, HMGA2, MMP2, and PAWR. Upstream functional analysis showed activation of COMMD3-BMI1, MTDH, GSTO1, TNFRSF1A, and SHH. S100 signaling and CREB signaling were downregulated (P<0.01). Fifteen potential biomarkers (BAK1, BAX, BCL2, MMP2, GP5, JAK3, COG2, DLC1, FAS, IFNG, IL-10, PCNA, WEE1, MCL1, H2AX) were identified. All networks and biomarkers were significant with P<0.01. Conclusions This study provides the first insights into the incidence of DUX4-r B-ALL, expression profile, dysregulated pathways, and clinical features among Indian patients. Further experimental validation is warranted.