ID1 and ID3 functions in the modulation of the tumor immune microenvironment in Adult Patients with B-Cell Acute Lymphoblastic Leukemia
The diagnosis of B-Cell acute lymphoblastic leukemia (B-ALL) in adults often carries a poor prognosis. ID1 and ID3 genes have been identified as predictors of poor response in Colombian adult B-ALL patients, playing roles in cancer development. In different cancer models, these genes have been associated with immune regulator populations within the tumor immune microenvironment (TIME). B-ALL development alters the immune cell composition and the bone marrow (BM) tumor microenvironment, affecting disease progression and response to therapy. This study analyzes gene expression levels of ID1 and ID3 in relation to TIME and immune evasion. This exploratory study analyzed BM samples from 10 B-ALL adult patients diagnosed at the National Cancer Institute of Colombia. First, RT-qPCR was used to assess ID1 and ID3 expression in BM tumor cells. Flow cytometry characterized immune populations in the TIME. RNA-seq evaluated immune genes associated with B-ALL immune response, while xCell and cytosig analyzed TIME cell profiles and cytokines. Pathway analysis, gene ontology, and differential gene expression (DEGs) were examined, with functional enrichment analysis performed using KEGG ontology. Patients were divided into two groups based on ID1 and ID3 expression, namely basal and overexpression. A total of 94 differentially expressed genes were identified between these groups, with top overexpressed genes associated with neutrophil pathways. Gene set enrichment analysis revealed increased expression of genes associated with neutrophil degranulation, immune response-related neutrophil activation, and neutrophil-mediated immunity. These findings correlated with xCell data. Overexpression group showed significant differences in neutrophils (p=0.0008), monocytes (<0.0001) and CD4+ naive T cells (p=0.0240) compared to basal group patients. Microenvironment and immune scores were also significantly different (p=0.0016 and p=0.0017, respectively), consistent with the flow cytometry results. Elevated cytokine levels associated with neutrophil activation supported these findings. Validation was performed using the TARGET and MILE B-ALL cohorts. Our results show important differences between the expression level of ID1 and ID3 in cancer cells and the populations of TIME, suggesting a role in evading the immune response of ID1 and ID3 in B-ALL, mainly related to neutrophil pathways. Overall design: We use RT-qPCR to evaluate the expression levels of ID1 and ID3 in BM tumor cells. Immune populations within the tumor immune microenvironment (TIME) were characterized through flow cytometry. RNA sequencing (RNA-seq) was employed to investigate immune-related genes associated with the B-ALL immune response. Additionally, the xCell and cytosig tools were utilized to analyze the cellular profiles and cytokine patterns within the TIME. The study also included pathway analysis, gene ontology, and differential gene expression (DEG) analysis, with functional enrichment carried out using KEGG ontology. Based on the expression levels of ID1 and ID3, patients were categorized into basal and overexpression groups.