DOI: 10.25442/hku.30517886.v2
title: <b>Supporting data for "</b><b>Development and Characterization of Organoid-based Neutralization Platform for Predicting SARS-CoV-2 Antibody Efficacy</b><b>"</b>

description: The development of therapeutics against respiratory viruses, including neutralizing antibodies, is critically dependent on robust and physiologically relevant <i>in vitro</i> models for evaluation and screening for the most effective candidates. Yet commonly used cell lines cannot model the human respiratory epithelium, which is composed of multiple cell populations with distinct attributes and diverse physiological functions. We have developed a robust human respiratory organoid culture system, which enables us to derive organoids from nasal cells and primary lung tissues with high efficiency and generate mature nasal, airway, and alveolar organoids that emulate the native epithelium lining different segments of the entire human respiratory tract.Accumulating evidence suggests that standard cell-line-based neutralization assays presented a biased neutralization profile of SARS-CoV-2 monoclonal antibodies (mAbs), which notably differed from the real-life scenario of antibody effectiveness. For example, in contrast to the clinically verified effectiveness, VIR-7831, a class 3 mAb, showed diminished potency against Omicron variants in conventional cell-line-based assays, which ultimately led to its withdrawal from clinical use. Similarly, most S2 antibodies showed low neutralizing potency in conventional cell-line-based neutralization assays, despite the substantial protection in animal experiments. We hypothesized that organoid-based assays could provide an optimal <i>in vitro</i> correlate of protection and recapitulate real-world scenarios of antibody effectiveness.Based on the robust respiratory organoid culture system and the high biological relevance of nasal organoids, we developed organoid-based neutralization assays to measure the neutralizing potency of mAbs against SARS-CoV-2 and SARS-CoV-1, followed by detailed characterization to validate that the measurements are robust and reproducible. We found that most class 3 mAbs, especially those not blocking RBD-ACE2 binding, including VIR-7831, were substantially underestimated in conventional cell-line-based assays compared with organoid-based assays. Nasal organoids adequately recapitulated the real-world effectiveness of VIR-7831 due to low ACE2 expression, which is biologically relevant to the low ACE2 level in native human respiratory cells. Moreover, organoid-based neutralization assays uniquely reproduced the potent efficacy of S2-targeting mAbs demonstrated <i>in vivo</i>, due to the high TMPRSS2 expression, which is reminiscent of native human respiratory epithelial cells.We moved forward to evaluate an FDA-approved mAb Pemivibart using the validated organoid-based neutralization assays. Pemivibart displayed a significant reduction in its neutralizing potency against the rapidly spreading KP.3.1.1 variant, with an IC50 of approximately 3.3 µg/ml. In contrast, SA55, an mAb with the similar target site to Pemivibart, remained highly effective against all tested variants, including KP.3.1.1. Given the KP.3.1.1 variant's reliance on the TMPRSS2-mediated pathway for cellular entry, dual treatment with Pemivibart and S2 mAb produced a remarkable synergistic neutralization effect, indicating that combinational therapy, particularly those incorporating S2 antibodies, as a promising and robust approach to countering emerging variants such as KP.3.1.1.In summary, organoid-based neutralization assays provide a robust evaluation platform for recapitulating and predicting the clinical effectiveness of mAbs against SARS-CoV-2, outperforming the conventional cell-line-based neutralization assays. Human respiratory organoids bridge a critical gap between traditional cell line models and <i>in vivo</i> tissues and organs, providing an accurate projection of the real-world effectiveness of therapeutic antibodies against evolving viruses