Follicular Bcl6 reactivity is associated with a unique immune landscape and spatial transcriptome in COVID-19

Abstract

The regulation of follicular (F) and germinal center (GC) immune reactivity in human lymph nodes (LNs), particularly during the early stages of viral infections, remains poorly understood. We have analyzed lung-draining lymph nodes (LD-LNs) from COVID-19 autopsies using multiplex imaging and spatial transcriptomics to examine the immune landscape and with respect to the aging. We identified three subgroups of Reactive Follicles (RFs) based on Bcl6 prevalence, RF-Bcl6no/low, RF-Bcl6int and RF-Bcl6high. RF-Bcl6high tissues express a distinct B/TFH immune landscape associated with increased prevalence of proliferating B- and TFH-cell subsets. Comparison between LD-LNs and matched subdiaphragmatic LNs revealed a disconnected Bcl6 reactivity between the two anatomical sites. LD-LNs Bcl6 reactivity was associated with a distinct spatial transcriptomic profile. TH1-associated genes/pathways (e.g. CXCR3, STAT5, TNF signaling) were significantly upregulated in RF-Bcl6no/low tissues while the RF-Bcl6high tissues exhibited significant upregulation of GC-promoting genes/pathways (e.g. CXCL13, B cell receptor signaling). Despite the similar prevalence, the in-situ transcriptome profiling indicates a higher monocyte/macrophage functionality in "Aged" compared to "Young" follicles from donors with comparable Bcl6 reactivity. Our findings reveal a heterogeneous F/GC landscape in COVID-19 LD-LNs and highlight specific molecular targets and pathways that could regulate human F/GC immune dynamics during early viral infections.