Cluster with high expression of CD83 and low expression of CXCR4, as well as positive for LMO2, which indicate that this cluster contains LZ-GCBC cells. Within this cluster, apart from the high expression of genes associated with the previously described LZ cluster, the cells start to express very specific genes such as MYC, MIR155HG or genes related to NF-kB pathway (i.e. NFKB1, NFKB2, NFKBIA, NFKBID, RELB). This transient expression of MYC and MYC targets (NME1) has been described in LZ cells re-entering into the DZ, to continue with additional rounds of affinity maturation (Dominguez-Sola et al., 2012). Additionally, as compared to the LZ cluster, this cluster shows higher expression of BATF, a gene known to be involved in regulating AIDCA (a DZ marker).
The annotation provided in this first version comprises 42 categories that provide a stable categories to classify single-cell transcriptomes of SLOs, useful for tools like Azimuth (see external URLs). In the next version, we will add a more detailed classification, encompassing all cell types and states identified in the tonsil atlas. A validation cohort was included to confirm the presence and accuracy of each annotation this latter level, using criteria such as cell neighborhood preservation, conservation of bona fide marker genes, and annotation confidence derived from the KNN classifier. For a full description and interpretation of this validation cohort, please refer to the final section of the manuscript.
