Coagulation FXIII-A Protein Expression Defines Three Novel Sub-populations in Pediatric B-Cell Progenitor Acute Lymphoblastic Leukemia Characterized by Distinct Gene Expression Signatures

Abstract

Background: Leukemic B-cell precursor (BCP) lymphoblasts were identified as a novel expression site for coagulation factor XIII subunit A (FXIII-A). Flow cytometry (FC) revealed three distinct expression patterns, i.e., FXIII-A negative, FXIII-A dim, and FXIII-A bright subgroups. The FXIII-A negative subgroup was significantly associated with the “B-other” genetic category and had an unfavorable disease outcome.Methods: RNA was extracted from bone marrow lymphoblasts of 42 pediatric patients with BCP-acute lymphoblastic leukemia (ALL). FXIII-A expression was determined by multiparameter FC. Genetic diagnosis was based on conventional cytogenetic method and fluorescence in situ hybridization. Affymetrix GeneChip Human Primeview array was used to analyze global expression pattern of 28,869 well-annotated genes. Microarray data were analyzed by Genespring GX14.9.1 software. Gene Ontology analysis was performed using Cytoscape 3.4.0 software with ClueGO application. Selected differentially expressed genes were validated by RT-Q-PCR.Results: We demonstrated, for the first time, the general expression of F13A1 gene in pediatric BCP-ALL samples. The intensity of F13A1 expression corresponded to the FXIII-A protein expression subgroups which defined three characteristic and distinct gene expression signatures detected by Affymetrix oligonucleotide microarrays. Relative gene expression intensity of ANGPTL2, EHMT1 FOXO1, HAP1, NUCKS1, NUP43, PIK3CG, RAPGEF5, SEMA6A, SPIN1, TRH, and WASF2 followed the pattern of change in the intensity of the expression of the F13A1 gene. Common enhancer elements of these genes revealed by in silico analysis suggest that common transcription factors may regulate the expression of these genes in a similar fashion. PLAC8 was downregulated in the FXIII-A bright subgroup. Gene expression signature of the FXIII-A negative subgroup showed an overlap with the signature of “B-other” samples. DFFA, GIGYF1, GIGYF2, and INTS3 were upregulated and CD3G was downregulated in the “B-other” subgroup. Validated genes proved biologically and clinically relevant. We described differential expression of genes not shown previously to be associated with pediatric BCP-ALL.Conclusions: Gene expression signature according to FXIII-A protein expression status defined three novel subgroups of pediatric BCP-ALL. Multiparameter FC appears to be an easy-to-use and affordable method to help in selecting FXIII-A negative patients who require a more elaborate and expensive molecular genetic investigation to design precision treatment.

Global expression profiling of CD10 + /CD19 + pre-B lymphoblasts from Hispanic B-ALL patients correlates with comparative TARGET database analysis

“…Likewise, Ma et al observed PIK3CA and PIK3R1 as the most frequent mutations in the PI3K and RAS pathways in leukemias. In contrast, Gyurina et al reported the relative expression of PIK3CG in bone marrow pre-B lymphoblasts from ALL and pointed out that the PIK3/AKT pathway plays a key regulatory role in BCP-ALL [33,40]. AIDA was also downregulated in the expression profile analyzed in this study.…”

Expression Patterns of Coagulation Factor XIII Subunit A on Leukemic Lymphoblasts Correlate with Clinical Outcome and Genetic Subtypes in Childhood B-cell Progenitor Acute Lymphoblastic Leukemia

“…Moreover, gene expression profile of FXIII-A-negative samples exhibited an almost complete overlap with that of samples classified as belonging to the 'B-other' genetic category. These data suggested that the three different FXIII-A expression profiles defined by FC might characterize novel subgroups of pediatric BCP-ALL [32]. Similar associations between expression intensity of biomarkers both at the mRNA and protein levels and clinical relevance have been observed to exist in T-ALL and in AML [33,34].…”

“…The inferior survival chances of the FXIII-A negative subgroup were explained by the significantly higher prevalence of patients with intermediate genetic risk group, and, within this group, patients belonging to the "B-other" category, compared with the FXIII-A positive group. Patients with "B-other" BCP-ALL were shown to have a higher risk for relapse [7,32]. We also demonstrated the significant prognostic value of the "B-other" genetic category on EFS and OS of patients with negative vs. dim FXIII-A expression by the multivariable Cox regression analysis [37].…”

“…The three groups had unique gene expression signatures according to FXIII-A expression pattern. The gene expression pattern of the FXIII-A negative subgroup overlapped with the gene expression profile of the "B-other" genetic subgroup [32].…”

Multifaced roles of PLAC8 in cancer

“…When referred to cancer immunity, PLAC8 is found to be most intensively expressed in the FXIII-A dim subgroup and helps to define three novel subpopulations in pediatric B-cell progenitor acute lymphoblastic leukemia [107]. And RNA sequencing data of clear cell renal cell carcinoma has shown that PLAC8 is mainly involved in immunity-related pathways [94].…”