Single-cell transcriptomic analysis of tumor heterogeneity and intercellular networks in human urothelial carcinoma

Background:Heterogeneity of tumor cells and the tumor microenvironment(TME)is significantly associated with clinical outcomes and treatment responses in patients with urothelial carcinoma(UC).Comprehensive profiling of the cellular diversity and interactions between malignant cells and TME may clarify the mechanisms underlying UC progression and guide the development of novel therapies.This study aimed to extend our understanding of intra-tumoral heterogeneity and the immunosuppressive TME in UC and provide basic support for the development of novel UC therapies.Methods:Seven patients with UC were included who underwent curative surgery at our hospital between July 2020 and October 2020.We performed single-cell RNA sequencing(scRNA-seq)analysis in seven tumors with six matched adjacent normal tissues and integrated the results with two public scRNA-seq datasets.The functional properties and intercellular interactions between single cells were characterized,and the results were validated using multiplex immunofluorescence staining,flow cytometry,and bulk transcriptomic datasets.All statistical analyses were performed using the R package with two-sided tests.Wilcoxon-rank test,log-rank test,one-way analysis of variance test,and Pearson correlation analysis were used properly.Results:Unsupervised t-distributed stochastic neighbor embedding clustering analysis identified ten main cellular subclusters in urothelial tissues.Of them,seven urothelial subtypes were noted,and malignant urothelial cells were characterized with enhanced cellular proliferation and reduced immunogenicity.CD8^(+)T cell subclusters exhibited enhanced cellular cytotoxicity activities along with increased exhaustion signature in UC tissues,and the recruitment of CD4^(+)T regulatory cells was also increased in tumor tissues.Regarding myeloid cells,coordinated reprogramming of infiltrated neutrophils,M2-type polarized macrophages,and LAMP3^(+)dendritic cells contribute to immunosuppressive TME in UC tissues.Tumor tissues demonstrated enhanced angiogenesis mediated by KDR^(+)endothelial cells and RGS5^(+)/ACTA2^(+)pericytes.Through deconvolution analysis,we identified multiple cellular subtypes may influence the programmed death-ligand 1(PD-L1)immunotherapy response in patients with UC.Conclusion:Our scRNA-seq analysis clarified intra-tumoral heterogeneity and delineated the pro-tumoral and immunosuppressive microenvironment in UC tissues,which may provide novel therapeutic targets.

抗SARS-CoV-2变异株的广谱mRNA疫苗RQ3013的临床前研究

全球SARS-CoV-2病毒的不同变异株导致已接种疫苗的人群中突破性感染的比例上升,迫切需要研发更为有效和广谱的COVID-19疫苗.本研究报告了一项mRNA疫苗RQ3013的临床前研究结果,旨在提供对SARS-CoV-2各种变异株(VOCs)的广谱保护.RQ3013疫苗包含经过假尿苷修饰的mRNA,制备成脂质纳米颗粒的形式.该mRNA编码了SARS-CoV-2的刺突(S)蛋白嵌合体,包含与免疫逃逸有关的重要突变位点.我们在多种动物模型中对RQ3013的免疫原性、保护效果和安全性进行了评估.RQ3013在小鼠、仓鼠和非人灵长类动物(NHP)中引发了显著的免疫反应.它能够诱导高滴度的抗体产生,具备对野生型、B.1.1.7、B.1.351、B.1.617.2和奥密克戎系列变异株的广泛中和能力.在小鼠和NHP中,两剂RQ3013疫苗能够有效保护上呼吸道和下呼吸道免受SARS-CoV-2及其变异株的感染.此外,在NHP中对RQ3013的安全性进行了评估,未观察到不良反应.这些结果为在临床试验中评估RQ3013提供了有力的支持,表明它可能成为对抗COVID-19及其变种的广泛保护的有希望的候选疫苗.

Unusual substructure conformations observed in crystal structures of a dicistrovirus RNA-dependent RNA polymerase suggest contribution of the N-terminal extension in proper folding

The Dicistroviridae is a virus family that includes many insect pathogens.These viruses contain a positive-sense RNA genome that is replicated by the virally encoded RNA-dependent RNA polymerase(RdRP)also named 3D^(pol).Compared with the Picornaviridae RdRPs such as poliovirus(PV)3D^(pol),the Dicistroviridae representative Israeli acute paralysis virus(IAPV)3D^(pol) has an additional N-terminal extension(NE)region that is about 40-residue in length.To date,both the structure and catalytic mechanism of the Dicistroviridae RdRP have remain elusive.Here we reported crystal structures of two truncated forms of IAPV 3D^(pol),namelyΔ85 andΔ40,both missing the NE region,and the 3D^(pol) protein in these structures exhibited three conformational states.The palm and thumb domains of these IAPV 3D^(pol) structures are largely consistent with those of the PV 3D^(pol) structures.However,in all structures,the RdRP fingers domain is partially disordered,while different conformations of RdRP substructures and interactions between them are also present.In particular,a large-scale conformational change occurred in the motif B-middle finger region in one protein chain of theΔ40 structure,while a previously documented alternative conformation of motif A was observed in all IAPV structures.These experimental data on one hand show intrinsic conformational variances of RdRP substructures,and on the other hand suggest possible contribution of the NE region in proper RdRP folding in IAPV.

Imbalanced fault diagnosis of rotating machinery using autoencoder-based SuperGraph feature learning

Existing fault diagnosis methods usually assume that there are balanced training data for every machine health state.However,the collection of fault signals is very difficult and expensive,resulting in the problem of imbalanced training dataset.It will degrade the performance of fault diagnosis methods significantly.To address this problem,an imbalanced fault diagnosis of rotating machinery using autoencoder-based SuperGraph feature learning is proposed in this paper.Unsupervised autoencoder is firstly used to compress every monitoring signal into a low-dimensional vector as the node attribute in the SuperGraph.And the edge connections in the graph depend on the relationship between signals.On the basis,graph convolution is performed on the constructed SuperGraph to achieve imbalanced training dataset fault diagnosis for rotating machinery.Comprehensive experiments are conducted on a benchmarking publicized dataset and a practical experimental platform,and the results show that the proposed method can effectively achieve rotating machinery fault diagnosis towards imbalanced training dataset through graph feature learning.