Inflammatory responses revealed through HIV infection of microglia-containing cerebral organoids

Cerebral organoids (COs) are valuable tools for studying the intricate interplay between glial cells and neurons in brain development and disease, including HIV-associated neuroinflammation. We developed a novel approach to generate microglia containing COs (CO-iMs) by coculturing hematopoietic progenitors and inducing pluripotent stem cells from the same line. This approach allowed for the differentiation of microglia within the organoids concomitantly with the neuronal progenitors. Compared with conventional COs, CO-iMs were more efficient at generating CD45+/CD11b+/Iba-1+ microglia and presented a physiologically relevant proportion of microglia (~7%). CO-iMs presented substantially increased expression of microglial homeostatic and sensome markers as well as markers for the complement cascade. CO-iMs are susceptible to HIV infection, resulting in a significant increase in several pro-inflammatory cytokines/chemokines and compromised neuronal functions, which are abrogated by the addition of antiretrovirals. Thus, CO-iM is a robust model for deciphering neuropathogenesis, neurological disorders, and viral infections of brain cells in a 3D culture system. Overall design: Develop a new approach to model the interaction of human microglia with their neuronal environment in order to unmask the role of microglia and their specific genes in HIV-related inflammation, their role in viral persistence under cART, and the biological consequences of infection for CNS inflammation and neuronal health. We generated a novel 3D culture cerebral organoid model offering a platform where physiological proportions of microglia with or without HIV-1 infection can crosstalk with other glial and neuronal cell types in a human-brain-like environment. Assessed the differences between COs and CO-iMs with respect to microglia phenotype and genotype and the response of microglia to HIV-1 infection. Further, and to assessed the effectiveness of antiretrovirals in infected CO-iMs. We compared and characterized the global transcriptome profile bwetween COs and CO-iMs, and between uninfected CO-iMs, infected CO-iMs and infected+cART treated CO-iMs via bulk RNA-seq analysis.Performed RNA-seq analysis for 12 iPSC-Ru line derived organoids (~65 day old) divided into 4 groups: COs uninfected (CO 8, CO 9, and CO 10; n=3), CO-iMs uninfected (CO-iM 4, CO-iM 5, and CO-iM 6; n=3), CO-iM HIV-1 BAL infected (n = 3; CO-iM 12, CO-iM 19, and CO-iM 21), and CO-iM HIV-1 BAL infected + cART treated (CO-iM 15, CO-iM 24, and CO-iM 25; n = 3).