Tianying Zhang

Trimerization motifs play pivotal roles in structural biology and therapeutic protein engineering. Here, we describe a short trimerization motif (rFd1303) derived from the Reoviridae family reovirus σ1 protein. Compared with the widely used T4-Foldon, the rFd1303 increased recombinant protein yields. The rFd1303-fused immunogens of SARS-CoV-2 spike and influenza hemagglutinin elicited antibody responses comparable to T4-Foldon-fused controls in mice. Using this tag, we engineered a trimeric ACE2-Ig fusion protein (TriACE2-Ig) that remained stable after 30 days at room temperature and neutralized a broad range of ACE2-utilizing sarbecoviruses, including 19 SARS-CoV-2 variants, SARS-CoV, and pangolin coronaviruses GD and GX, with higher potency than monomeric ACE2-Ig. In the hamster model challenged with various SARS-CoV-2 variants, our data demonstrated that intranasal TriACE2-Ig administration markedly reduced viral loads, virus-induced body-weight loss, lung pathology, and decreased within-cage virus transmission. These findings highlight rFd1303 as a versatile trimerization platform for vaccine and therapeutic protein development.

The continued evolution of SARS-CoV-2 has reduced the protective effectiveness of first-generation vaccines and underscores the need for broadly reactive next-generation vaccine candidates. Here, we evaluated STFKB, an alum-adjuvanted bivalent recombinant protein vaccine composed of the monomeric Spike (STFK_prototype) and the engineered Spike (STFK_1628X). We assessed the immunogenicity, tolerability, and protective efficacy of STFKB in mice, rats, guinea pigs, rhesus macaques, and Syrian hamsters. STFKB induced robust STFK- and STFK_1628X-specific antibody responses and broadly reactive neutralizing antibodies against multiple SARS-CoV-2 variants in the tested animal models. In hamster challenge studies, STFKB vaccination protected animals from Omicron BA.1 and BA.5 challenge, as shown by reduced body-weight loss, lower viral RNA loads in respiratory tissues, and improved gross lung pathology. Across the tested preclinical models, STFKB was well tolerated, with no vaccine-related overt toxicity observed under the study conditions. These findings support the rationale and translational potential of the bivalent vaccine strategy proposed in this study.

Precisely identifying cancer drivers helps us to understand the molecular mechanisms of cancer, offering critical targets for early diagnosis. Despite the increasing application of graph neural networks in predicting cancer driver genes, existing approaches do not fully leverage the information from gene networks, and are unable to effectively extract node features from directed graphs. To this end, we propose MDIGNN, a novel deep learning model designed to identify cancer driver genes by integrating directed gene networks with multi-omics data. First, we construct a directed graph through the integration of existing gene networks from diverse databases and multi-omics data. Then, to encode the edge directionality, we develop a graph neural network based on the magnetic Laplacian, which relies on a complex Hermitian matrix for representing the directed graph structure. Next, we apply the channel attention and spatial attention mechanisms to improve the model’s feature representation ability. Finally, MDIGNN uses a fully connected layer to compute the cancer driver probability for each gene. In a comparative evaluation, MDIGNN outperforms existing state-of-the-art methods in the field, and it is capable of detecting potential cancer driver genes.

呼吸道病毒感染不仅造成全球性疾病负担，还是新发突发传染病大流行的主要风险源。现有疫苗技术对应对高变异病毒和未知病原体的广谱保护效力不足，暴露出抗原依赖性策略的固有局限。因此，解析呼吸道广谱保护性免疫的构成属性和效应机制，并发展新型干预策略，已成为当前亟需解决的命题。训练免疫（trained immunity）作为先天免疫的记忆形式，革新了传统免疫学认为只有适应性免疫具有记忆性的观点，其通过表观遗传重塑和代谢重编程等机制，赋予巨噬细胞、单核细胞、自然杀伤细胞及呼吸道组织结构细胞非特异免疫记忆功能，使其对二次异源感染产生增强应答，为广谱疫苗研发和疾病治疗提供了新思路。然而，训练免疫研究仍面临诸多挑战：（1）机制复杂性：训练免疫形成、维持和效应的机制及动态调控规律尚未明晰；（2）评价体系缺失：缺乏标准化的生物标志物和定量评估模型；（3）定向诱导策略未知：定向诱导特定的“有利”训练免疫印迹的策略有待探索。突破上述瓶颈需聚焦多组学整合分析、免疫力数字化解码以及精准调控技术。通过解析“抵抗性-耐受性”双重训练免疫的分子开关，设计可编程诱导剂（如工程化病毒载体、代谢激动剂等），或实现呼吸道感染的“一防多效”。本文系统探讨训练免疫在呼吸道抗病毒防御中的角色，旨在为下一代广谱疫苗和免疫治疗策略提供启示。

Trimerization motifs play pivotal roles in structural biology and therapeutic protein engineering. Here, we engineered a novel short trimerization motif (rFd1303) derived from the Reoviridae family reovirus σ1 protein. Compared with the widely used T4-Foldon, the rFd1303 enhanced thermal stability and increased recombinant protein yields. The rFd1303-fused immunogens of SARS-CoV-2 spike and influenza hemagglutinin elicited antibody responses comparable to T4-Foldon-fused controls in murine models. Leveraging the new tag, we engineered the trimeric ACE2-Ig (TriACE2-Ig), which exhibits exceptional stability (room-temperature storage for 30 days) and broad neutralization against multiple SARS-CoV-2 variants (average IC ₅₀ of 2.9 ng/mL), showing a 20.9-fold potency improvement over monomeric ACE2-Ig. In the hamster model challenged with various SARS-CoV-2 variants, our data demonstrated that intranasal TriACE2-Ig administration markedly reduced viral loads, virus-induced body-weight loss, lung pathology, and decreased within-cage virus transmission. These findings highlight rFd1303 as a versatile trimerization platform for vaccine and therapeutic protein development.

Recombinant vesicular stomatitis virus (rVSV) is a promising viral vaccine vector for addressing the COVID-19 pandemic. Inducing mucosal immunity via the intranasal route is an ideal strategy for rVSV-based vaccines, but it requires extremely stringent safety standards. In this study, we constructed two rVSV variants with amino acid mutations in their M protein: rVSV-M2 with M33A/M51R mutations and rVSV-M4 with M33A/M51R/V221F/S226R mutations, and developed COVID-19 vaccines based on these attenuated vectors. By comparing viral replication capacity, intranasal immunization, intracranial injection, and blood cell counts, we demonstrated that the M protein mutation variants exhibit significant attenuation effects both in vitro and in vivo. Moreover, preliminary investigations into the mechanisms of virus attenuation revealed that these attenuated viruses can induce a stronger type I interferon response while reducing inflammation compared to the wild-type rVSV. We developed three candidate vaccines against SARS-CoV-2 using the wildtype VSV backbone with either wild-type M (rVSV-JN.1) and two M mutant variants (rVSV-M2-JN.1 and rVSV-M4-JN.1). Our results confirmed that rVSV-M2-JN.1 and rVSV-M4-JN.1 retain strong immunogenicity while enhancing safety in hamsters. In summary, the rVSV variants with M protein mutations represent promising candidate vectors for mucosal vaccines and warrant further investigation.

Elderly individuals face heightened susceptibility to infectious diseases and diminished vaccine responses. Vaccine adjuvants offer a solution. Despite aluminum adjuvant’s long history, its limitations in inducing strong cellular immunity and protecting immunocompromised individuals restrict its application. Building upon our previous development of zinc salt particle-based risedronate (Zn-RS), we systematically investigated the immunoenhancing effects of Zn-RS in aged mice and thoroughly explored the underlying mechanisms responsible for these observations in this study. Compared to formulations using aluminum adjuvant, Zn-RS combined with either varicella-zoster virus glycoprotein E (gE) or SARS-CoV-2 monovalent STFK protein (STFK) elicited significantly higher IgG and neutralization titers, as well as superior long-term humoral immunity. Moreover, Zn-RS induced greater quantities of dendritic cells (DCs), antigen-presenting cells (APCs), follicular helper T (TFH) cells, Th1/Th2/Th9/Th17 type immune cells, germinal center B cells (GCBs) and plasma cells. These findings support Zn-RS as a promising adjuvant candidate for elderly populations, warranting further exploration of its mechanisms and potential applications.