Context:
To understand HIV persistence, it’s crucial to visualize the tissue microenvironments where the virus resides. Current methods often require removing cells from their native context. Detecting low-abundance nucleic acids and proteins in situ is essential for studying viral infections.
Method:
The authors introduce PANINI (protein and nucleic acid in situ imaging), which includes:
Using FFPE cell pellets and lymphoid tissues from SIV-infected and uninfected rhesus macaques, PANINI-MIBI can simultaneously detect single-integration events of SIV DNA, RNA transcripts, and protein epitopes on the same tissue section.
Results:
The researchers confirmed retroviral infection markers, including CD4+ T cell depletion, heightened NK and CD8+ T cell responses, and lack of immune infiltration in B cell follicles. Integrating CN information with markers allowed us to differentiate infection status using LDA.
They discovered a B cell response to SIV infection through IL-10 secretion, attracting and immunosuppressing macrophages via an M2-phenotypic switch. This environment, with increased IL-10, FoxO1, and HLA-DR expression around infected cells, may explain viral transcription status. Increased IL-10 protein expression and transcriptomic signatures during chronic and ART-treated infections support this.
Implication/Impact:
The PANINI platform, with a 33-marker panel for FFPE tissues, spatial analytical workflow, and multimodal analysis framework, enables reexamination of previous observations and new model development. Antibody-based multiplexed imaging offers robust readouts and molecular pathway assessment. Recent resources show high concordance between single-plex immunohistochemistry and MIBI-TOF imaging and provide a guide for selecting and validating antibodies for high-dimensional imaging.
