Changes in the transcriptome and long non-coding RNAs but not the methylome occur in human cells exposed to Borrelia burgdorferi

Lyme disease, caused by infection with members of the Lyme borreliosis group of Borrelia spirochete bacteria, is increasing in frequency and distribution worldwide. This spread is driven by the expansion of ticks, vectors of these pathogens. Epigenetics may be involved in the interaction between mammalian host, tick, and bacterial pathogen, but is still poorly understood. Next-generation sequencing (NGS) allows the study of host response at the transcriptomic and methylomic scale. We tested the effect of the Borrelia burgdorferi strain B31 on a human primary cell line (HUVEC) and an immortalized cell line (HEK-293) for 72 h, a time consistent with the duration of tick feeding and host cell exposure to B. burgdorferi. RNA and DNA were extracted from cells and used for RNA-seq and Enzymatic-Methyl-seq (EM-seq). Differential expression and Reactome pathway enrichment analysis were performed. More significantly differentially expressed genes (a total of 69) were found in HUVECs compared to HEK-293 (a total of 8). Borrelia burgdorferi exposure significantly induced genes in the interferon, cytokine, and other immune response signaling in HUVECs. In HEK-293, pre-NOTCH processing in Golgi was identified as a significant pathway. Other significant genes suggest extracellular matrix binding and interaction in HEK-293. Data comparison with other transcriptomic studies of human cells exposed to B. burgdorferi revealed a small overlap in genes identified in HUVEC, but no overlap for HEK-293. No significant methylation changes were detected in HUVECs or HEK-293 exposed to B. burgdorferi. However, two long non-coding RNAs and a pseudogene were deregulated in response to B. burgdorferi in HUVEC suggesting that other epigenetic mechanisms may be initiated by infection. This is the first study examining the transcriptome and methylome of human cells exposed to B. burgdorferi for 72 h and so contributes to the description of early-stage B. burgdorferi infection at the cellular level.