Objective:To investigate the composition of immune cells and fibroblastic reticular cells (FRCs) in the lymph nodes (LNs) follicles of human immunodeficiency virus (HIV)-infected individuals with varying immune statuses, and their association with HIV replication.Methods:Neck LNs samples were collected from 4 treatment-naive, newly diagnosed HIV-infected individuals with diverse immune statuses. RNA in situ sequencing was employed, with imaging achieved via rolling circle amplification and fluorescence labeling. By integrating cell segmentation and nuclear staining, single-cell data from up to one hundred thousand cells were generated per paraffin tissue section. Using lymphoid follicles as the unit of analysis, compositional changes in immune cells and FRCs were characterized, and their correlations with viral replication were evaluated. Results:The peripheral blood CD4 + T cell counts of samples LN_1, LN_2, LN_3, and LN_4 exhibited a sequential decrease. A total of 31, 15, 16, and 18 structurally intact follicles were identified in each sample, respectively. In the follicles of LN_1, the proportion of HIV-replicating cells positively correlated with cDCs abundance ( R2=0.2, P=0.011), and HIV RNA signals were spatially colocalized with cDCs and FRCs. In the follicles of LN_2, HIV RNA molecules showed preferential enrichment within FRCs. In sample LN_3, HIV RNA enrichment was observed in both cDCs and CD4 + T cells. In sample LN_4, the proportion of cells with HIV replication was positively correlated with the proportions of the following cells: cDCs ( R2=0.38, P=0.006 4), CD4 + T cells ( R2=0.28, P=0.025), and FRCs ( R2=0.26, P=0.029), and HIV RNA molecules were detected in cDCs, CD4 + T cells, and FRCs. LN_1 and LN_2 samples showed a trend toward negative correlation between HIV-replicating cell proportion and CD8 + T cells proportion. LN_4 sample demonstrated a significant positive correlation between HIV-replicating cell proportion and CD8 + T cells proportion ( R2=0.23, P=0.046). Conclusions:RNA in situ sequencing technology reveals unique distribution patterns of immune cells and viral replication in LNs follicles of HIV-infected individuals. The follicular immune microenvironment exhibits distinct characteristics associated with peripheral blood CD4 + T cell counts, providing novel insights into the spatial dynamics of HIV persistence and immune cell interactions during infection.

Objective:To investigate the composition of immune cells and fibroblastic reticular cells (FRCs) in the lymph nodes (LNs) follicles of human immunodeficiency virus (HIV)-infected individuals with varying immune statuses, and their association with HIV replication.Methods:Neck LNs samples were collected from 4 treatment-naive, newly diagnosed HIV-infected individuals with diverse immune statuses. RNA in situ sequencing was employed, with imaging achieved via rolling circle amplification and fluorescence labeling. By integrating cell segmentation and nuclear staining, single-cell data from up to one hundred thousand cells were generated per paraffin tissue section. Using lymphoid follicles as the unit of analysis, compositional changes in immune cells and FRCs were characterized, and their correlations with viral replication were evaluated. Results:The peripheral blood CD4 + T cell counts of samples LN_1, LN_2, LN_3, and LN_4 exhibited a sequential decrease. A total of 31, 15, 16, and 18 structurally intact follicles were identified in each sample, respectively. In the follicles of LN_1, the proportion of HIV-replicating cells positively correlated with cDCs abundance ( R2=0.2, P=0.011), and HIV RNA signals were spatially colocalized with cDCs and FRCs. In the follicles of LN_2, HIV RNA molecules showed preferential enrichment within FRCs. In sample LN_3, HIV RNA enrichment was observed in both cDCs and CD4 + T cells. In sample LN_4, the proportion of cells with HIV replication was positively correlated with the proportions of the following cells: cDCs ( R2=0.38, P=0.006 4), CD4 + T cells ( R2=0.28, P=0.025), and FRCs ( R2=0.26, P=0.029), and HIV RNA molecules were detected in cDCs, CD4 + T cells, and FRCs. LN_1 and LN_2 samples showed a trend toward negative correlation between HIV-replicating cell proportion and CD8 + T cells proportion. LN_4 sample demonstrated a significant positive correlation between HIV-replicating cell proportion and CD8 + T cells proportion ( R2=0.23, P=0.046). Conclusions:RNA in situ sequencing technology reveals unique distribution patterns of immune cells and viral replication in LNs follicles of HIV-infected individuals. The follicular immune microenvironment exhibits distinct characteristics associated with peripheral blood CD4 + T cell counts, providing novel insights into the spatial dynamics of HIV persistence and immune cell interactions during infection.