Identifying Regulatory Pathways of SYK Expression in Human Basophils

Abstract Background Expression levels of SYK, a critical signaling tyrosine kinase in basophils, are uniquely low relative to all other circulating leukocytes and levels are highly variable in the population. Hypothesis Transcriptional regulation of SYK through unique silencing of the SYK gene determines its basophil-specific expression patterns. Methods Basophils (CD34B) were derived from cultures of CD34+ progenitor cells by two methods (G1 or G3). Peripheral blood basophils (PBB, relative SYK protein level = 1), B-cell (SYK = 8), CD34B G1 (SYK = 11) and G3 (SYK = 5) were examined by ATACseq methods and the transcriptomes of 6 cell types, PBB, eosinophils (PBE, SYK = 11), dendritic cells (PDC, SYK = 30), CD34+ progenitors (SYK = 11), CD34B G1 and G3 were analyzed for patterns that matched patterns of SYK expression in these cells, with a focus on transcription factors. Results ATACseq showed that PBB have multiple open regions in the SYK gene suggesting a non-silenced state with: 1 region unique to PBB (low SYK expression), one region unique to both PBB (low SYK expression) and G1/G3 CD34B (high and moderate SYK expression, respectively) and 5 regions unique to B-cells (high SYK expression). SYK expression across the 6 cell types explored showed a unique pattern that was matched to the expression patterns of 3 transcription factors, KLF5, ZNF608, and c-MAF. Conclusions Two new potential regulatory pathways for SYK expression were identified. One appears independent of transcriptional regulation and one appears to be dependent on transcriptional control in the SYK gene.