Nakano, M.; Heo, L.; Yang, Y.-P.; Munoz, L. P.; Liu, Y.; Zhao, L.; Park, J.; Tsekitsidou, E.; Francois, A.; Liu, J.; Trotman-Grant, A. C.; Henao Echeverri, M. F.; Rada, C. C.; Tran, E.; Khokhar, A.; Yuki, K.; Bhattacharya, A.; Horn, H. T.; Polak, R.; Yenwongfai, L. N.; Li, Y.; Peach, M.; Nasajpour, E.; Pavlovitch-Bedzyk, A. J.; Chang, A. L.; Lim, M.; Petritsch, C. K.; Hayden Gephart, M.; Leppert, J. T.; Nair, R. V.; Davis, M. M.; Bassik, M. C.; Zhang, M.; Odegard, J.; Bates, J. G.; Leung, L. L.; Majeti, R.; Kuo, C. J.

Tumor-associated macrophages (TAM) exert essential functions during the immune response to cancer. However, investigations of TAM within a native human tumor microenvironment (TME) have been impeded by a lack of appropriate model systems. Here, patient-derived organoids (PDO) from air-liquid interface (ALI)-grown tumor fragments, containing a human TME that encompassed stroma and immune subsets, robustly preserved TAM that were maintained by endogenous CSF-1 and appropriately responded to polarization signals. Antibody blockade of the CD47 regulatory checkpoint in organoids stimulated phagocytosis and remodeled TAM cytokine secretion profiles that were confirmed in anti-CD47 phase I trial patients. Amongst PDO histologies screened, anti-CD47 tumor killing was notable in clear cell renal cell carcinoma (ccRCC) which was associated with increased TAM infiltration. PDO contained diverse previously described TAM subsets; however, anti-CD47 reprogrammed organoid TAM toward an immunosuppressive SPP1+ phenotype, highlighting a negative feedback mechanism. Our findings uncover a resistance circuit engaged by macrophage checkpoint blockade and position ALI PDO as a robust translational platform for dissecting human macrophage biology and informing precision immunotherapy.