The Application of Organoids in the Study of Antiviral Innate Immunity.

Antiviral innate immunity plays a critical role in the defense against viral infections, yet its complex interactions with viruses have been challenging to study using traditional models. Organoids, three-dimensional (3D) tissue-like structures derived from stem cells, have emerged as powerful tools for modeling human tissues and studying the complex interactions between viruses and the host innate immune system. This chapter summarizes relevant applications of organoids in antiviral innate immunity studies and provides detailed information and experimental procedures for using organoids to study antiviral innate immunity.

Wu T ，Zheng C ，Zou X 《-》

Antiviral function and viral antagonism of the rapidly evolving dynein activating adaptor NINL.

Viruses interact with the intracellular transport machinery to promote viral replication. Such host-virus interactions can drive host gene adaptation, leaving signatures of pathogen-driven evolution in host genomes. Here, we leverage these genetic signatures to identify the dynein activating adaptor, ninein-like (NINL), as a critical component in the antiviral innate immune response and as a target of viral antagonism. Unique among genes encoding components of active dynein complexes, NINL has evolved under recurrent positive (diversifying) selection, particularly in its carboxy-terminal cargo-binding region. Consistent with a role for NINL in host immunity, we demonstrate that NINL knockout cells exhibit an impaired response to interferon, resulting in increased permissiveness to viral replication. Moreover, we show that proteases encoded by diverse picornaviruses and coronaviruses cleave and disrupt NINL function in a host- and virus-specific manner. Our work reveals the importance of NINL in the antiviral response and the utility of using signatures of host-virus genetic conflicts to uncover new components of antiviral immunity and targets of viral antagonism.

Stevens DA ，Beierschmitt C ，Mahesula S ，Corley MR ，Salogiannis J ，Tsu BV ，Cao B ，Ryan AP ，Hakozawki H ，Reck-Peterson SL ，Daugherty MD ... -  《eLife》

Exploring the host response in infected lung organoids using NanoString technology: A statistical analysis of gene expression data.

In this study, we used a three-dimensional airway "organ tissue equivalent" (OTE) model at an air-liquid interface (ALI) to mimic human airways. We investigated the effects of three viruses (Influenza A virus (IAV), Human metapneumovirus (MPV), and Parainfluenza virus type 3 (PIV3) on this model, incorporating various control conditions for data integrity. Our primary objective was to assess gene expression using the NanoString platform in OTE models infected with these viruses at 24- and 72-hour intervals, focusing on 773 specific genes. To enhance the comprehensiveness of our analysis, we introduced a novel algorithm, namely MAS (Magnitude-Altitude Score). This innovative approach uniquely combines biological significance, as indicated by fold changes in gene expression, with statistical rigor, as represented by adjusted p-values. By incorporating both dimensions, MAS ensures that the genes identified as differentially expressed are not mere statistical artifacts but hold genuine biological relevance, providing a more holistic understanding of the airway tissue response to viral infections. Our results unveiled distinct patterns of gene expression in response to viral infections. At 24 hours post-IAV infection, a robust interferon-stimulated gene (ISG) response was evident, marked by the upregulation of key genes including IFIT2, RSAD2, IFIT3, IFNL1, IFIT1, IFNB1, ISG15, OAS2, OASL, and MX1, collectively highlighting a formidable antiviral defense. MPV infection at the same time point displayed a dual innate and adaptive immune response, with highly expressed ISGs, immune cell recruitment signaled by CXCL10, and early adaptive immune engagement indicated by TXK and CD79A. In contrast, PIV3 infection at 24 hours triggered a transcriptional response dominated by ISGs, active immune cell recruitment through CXCL10, and inflammation modulation through OSM. The picture evolved at 72 hours post-infection. For IAV, ISGs and immune responses persisted, suggesting a sustained impact. MPV infection at this time point showed a shift towards IL17A and genes related to cellular signaling and immune responses, indicating adaptation to the viral challenge over time. In the case of PIV3, the transcriptional response remained interferon-centric, indicating a mature antiviral state. Our analysis underscored the pivotal role of ISGs across all infections and time points, emphasizing their universal significance in antiviral defense. Temporal shifts in gene expression indicative of adaptation and fine-tuning of the immune response. Additionally, the identification of shared and unique genes unveiled host-specific responses to specific pathogens. IAV exerted a sustained impact on genes from the initial 24 hours, while PIV3 displayed a delayed yet substantial genomic response, suggestive of a gradual and nuanced strategy.

Rezapour M ，Walker SJ ，Ornelles DA ，Niazi MKK ，McNutt PM ，Atala A ，Gurcan MN ... -  《PLoS One》

Immunity to viruses: learning from successful human vaccines.

For more than a century, immunologists and vaccinologists have existed in parallel universes. Immunologists have for long reveled in using 'model antigens', such as chicken egg ovalbumin or nitrophenyl haptens, to study immune responses in model organisms such as mice. Such studies have yielded many seminal insights about the mechanisms of immune regulation, but their relevance to humans has been questioned. In another universe, vaccinologists have relied on human clinical trials to assess vaccine efficacy, but have done little to take advantage of such trials for studying the nature of immune responses to vaccination. The human model provides a nexus between these two universes, and recent studies have begun to use this model to study the molecular profile of innate and adaptive responses to vaccination. Such 'systems vaccinology' studies are beginning to provide mechanistic insights about innate and adaptive immunity in humans. Here, we present an overview of such studies, with particular examples from studies with the yellow fever and the seasonal influenza vaccines. Vaccination with the yellow fever vaccine causes a systemic acute viral infection and thus provides an attractive model to study innate and adaptive responses to a primary viral challenge. Vaccination with the live attenuated influenza vaccine causes a localized acute viral infection in mucosal tissues and induces a recall response, since most vaccinees have had prior exposure to influenza, and thus provides a unique opportunity to study innate and antigen-specific memory responses in mucosal tissues and in the blood. Vaccination with the inactivated influenza vaccine offers a model to study immune responses to an inactivated immunogen. Studies with these and other vaccines are beginning to reunite the estranged fields of immunology and vaccinology, yielding unexpected insights about mechanisms of viral immunity. Vaccines that have been proven to be of immense benefit in saving lives offer us a new fringe benefit: lessons in viral immunology.

Pulendran B ，Oh JZ ，Nakaya HI ，Ravindran R ，Kazmin DA ... -  《-》

Emerging Roles of TRIM56 in Antiviral Innate Immunity.

Wang D ，Li K 《Viruses-Basel》