Abstract C087: Distinct gene expression and DNA methylation pattern associated with poor outcome of B-cell acute lymphoblastic leukemia in Hispanic/Latino children

Abstract

Abstract The risk of developing Acute Lymphoblastic Leukemia (B-ALL) in Hispanic/Latino (HL) children is 1.2-1.75 greater that Non-Hispanic whites (NHW) and after correcting for socioeconomic factors, mortality is 40% higher in HL children. H/L children have a higher incidence of high-risk genetic variations: a 2-fold greater rate of IKZF1 deletion (IKZF1-del) and a 4-fold greater rate of CRLF2 translocations. IKZF1-del is associated with chemotherapy resistance and CRLF2 translocations represent Ph-like status. These two genetic alterations are concomitant in H/L children. 94% of H/L patients with CRLF2 translocation had a coexisting IKZF1-del. Despite evidence of specific genomic alterations in B-ALL in H/L children, potential differences in gene expression in B-ALL from H/L vs. NHW children has not been studied. Here, we used transcriptomic and genomic approach to determine the role of specific mutations and genetic background in regulation of gene expression in B-ALL from H/L and NHW children and to gain insight into molecular mechanisms that regulate cellular proliferation and chemotherapy resistance. RNA-seq was performed on B-ALL from 42 H/L and 18 NHW children and differential gene expression patterns were compared between the two ethnic groups. Gene set enrichment analysis (GSEA), Gene ontology (GO), and Ingenuity pathway analysis (IPA) were performed. In addition, we performed separate analysis and compared both ethnic groups with wild-type status of IKZF1 (IKZF1-WT). We performed DNA methylation signature analysis using reduced representation bisulfite sequencing on 8 H/L and 8 NHW B-ALL samples. Results showed increased expression of the genes that regulate Immune and inflammatory response, interferon signaling, and JAK/STAT pathway in H/L compared to NHW B-ALL cells. These expression changes were more pronounced in IKZF1-del B-All cells. In contrast, H/L B-ALL cells have reduced expression of the genes that regulate genome stability, cell cycle checkpoint signaling, and specific amino acid synthesis pathways. IPA showed upregulated interferon, Tec Kinase, and CDK5 signaling in B-ALL cells of H/L compared to NHW children. Compared. DNA Methylation analysis showed distinct patterns associated with altered expression of several oncogenes in B-ALL from H/L, compared to NHW children. In conclusion, H/L B-ALL has a distinct expression of the genes that regulate signaling pathways that promote cellular proliferation and chemotherapy resistance that are different from B-ALL in NHW children. Results identified therapeutic targets and tumor vulnerabilities that can be used for precision medicine approach to reduce disparities in B-ALL outcome in H/L children. Citation Format: Sinisa Dovat, Joseph Schramm, Daniel Bogush, Dhimant Desai, Bing He, Dhimant Desai, Arati Sharma. Distinct gene expression and DNA methylation pattern associated with poor outcome of B-cell acute lymphoblastic leukemia in Hispanic/Latino children [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C087.