Follicular Bcl6 expression is associated with a unique immune landscape and spatial transcriptomic in COVID-19.

This study investigated the immune architecture of lymphoid tissues in the context of SARS-CoV-2 infection using multiplex immunofluorescence (mIF). All tissue samples were formalin-fixed, paraffin-embedded (FFPE) and processed through a fully automated staining protocol. High-resolution imaging generated multiplex QPTIFF files, which are multi-channel fluorescence images created through tyramide signal amplification (TSA), allowing the spatial mapping of multiple immune markers within a single tissue section.

A total of 35 human lymph node (LN) tissues were analyzed, comprising:

·         COVID-19 deceased donors (n = 31):

o    Aged RF-Bcl6no/low: 12 samples

o    Aged RF-Bcl6int: 5 samples

o    Aged RF-Bcl6high: 6 samples

o    Young RF-Bcl6no/low: 4 samples

o    Young RF-Bcl6int: 3 samples

o    Young RF-Bcl6high: 1 sample

·         Non–COVID-19-infected control donors (n = 4):

o    Healthy lung-draining lymph nodes (HLNs)

Lymph nodes were sampled from a range of anatomical sites, including hilar, subdiaphragmatic, mediastinal, para-esophageal, para-aortic, para-tracheal, and axillary locations. Importantly, the dataset also includes 7 matched subdiaphragmatic lymph nodes, each paired with hilar nodes from the same donors, enabling comparative spatial analyses across anatomical compartments within individuals.

The resulting QPTIFF images offer detailed insights into immune cell distributions, follicular organization, and spatial relationships within the lymphoid microenvironment, both in COVID-19 and in healthy control conditions.