Xu Zhang

Proximity labeling has emerged as a powerful strategy for interrogating cell-cell interactions. However, the nanometer-scale labeling radius impedes the use of current methods for indirect cell communications and makes recording cell spatial organization in tissue samples difficult. Here, we develop quinone methide–assisted identification of cell spatial organization (QMID), a chemical strategy with the labeling radius matching the cell dimension. The activating enzyme is installed on the surface of bait cells, which produces QM electrophiles that can diffuse across micrometers and label proximal prey cells independent of cell-cell contacts. In cell coculture, QMID reveals gene expression of macrophages that are regulated by spatial proximity to tumor cells. Furthermore, QMID enables labeling and isolation of proximal cells of CD4 ⁺ and CD8 ⁺ T cells in the mouse spleen, and subsequent single-cell RNA sequencing uncovers distinctive cell populations and gene expression patterns within the immune niches of specific T cell subtypes. QMID should facilitate dissecting cell spatial organization in various tissues.

Single‐cell RNA sequencing (scRNA‐seq) has emerged as a powerful tool for profiling gene expression of distinct cell populations at the single‐cell level. However, the information of the positions of cells within the multicellular samples is missing in scRNA‐seq datasets. To overcome this limitation, we herein develop OpTAG (optical cell tagging) as a new chemical platform for attaching functional tags onto cell surfaces in a spatially resolved manner. With OpTAG, we establish OpTAG‐seq, which enables spatially resolved scRNA‐seq. We apply OpTAG‐seq to investigate the spatially defined transcriptional program in migrating cancer cells and identified a list of genes that are potential regulators for cancer cell migration and invasion. OpTAG‐seq provides a convenient method for mapping cellular heterogeneity with spatial information within multicellular biological systems.

Single‐cell RNA sequencing (scRNA‐seq) has emerged as a powerful tool for profiling gene expression of distinct cell populations at the single‐cell level. However, the information of the positions of cells within the multicellular samples is missing in scRNA‐seq datasets. To overcome this limitation, we herein develop OpTAG (optical cell tagging) as a new chemical platform for attaching functional tags onto cell surfaces in a spatially resolved manner. With OpTAG, we establish OpTAG‐seq, which enables spatially resolved scRNA‐seq. We apply OpTAG‐seq to investigate the spatially defined transcriptional program in migrating cancer cells and identified a list of genes that are potential regulators for cancer cell migration and invasion. OpTAG‐seq provides a convenient method for mapping cellular heterogeneity with spatial information within multicellular biological systems.

Wenzhou virus (WENV), a newly discovered mammarenavirus in rodents, is associated with fever and respiratory symptoms in humans. This study was aimed to detect and characterize the emerging virus in rodents in Guangzhou, China. A total of 100 small mammals, including 70 Rattus norvegicus, 22 Suncus murinus, 4 Bandicota indica, 3 Rattus flavipectus, and 1 Rattus losea, were captured in Guangzhou, and their brain tissues were collected and pooled for metagenomic analysis, which generated several contigs targeting the genome of WENV. Two R. norvegicus (2.9%) were further confirmed to be infected with WENV by RT-PCR. The complete genome (RnGZ37-2018 and RnGZ40-2018) shared 85.1–88.9% nt and 83.2–96.3% aa sequence identities to the Cambodian strains that have been shown to be associated with human disease. Phylogenetic analysis showed that all identified WENV could be grouped into four different lineages, and the two Guangzhou strains formed an independent clade. We also analyzed the potential recombinant events occurring in WENV strains. Our study showed a high genetic diversity of WENV strains in China, emphasizing the relevance of surveillance of this emerging mammarenavirus in both natural reservoirs and humans.

Nepal is an endemic area for hepatitis E virus (HEV) epidemics. The research on viral hepatitis in Nepal is limited. Serum samples from 170 patients presenting with symptoms of hepatitis were collected from April to May 2014 in Biratnagar, Nepal, and then transported to Xiamen, China, for further evaluation. All samples were tested for HEV RNA, HEV antigen, anti-HEV IgM, anti-HEV IgG and anti-HBc IgM, anti-HCV IgG, and anti-HAV IgM. Sixteen patients were identified as acute hepatitis E with the presence of ≥ 2 HEV acute phase markers (antigen, RNA, and anti-HEV IgM). HEV infection was the major cause of potential active viral hepatitis (59.2%, 16 of 27), followed by HBV (25.9%, 7 of 27, anti-HBc IgM positive), HAV (18.5%, 5 of 27, anti-HAV IgM positive), and HCV (3.7%, 1 of 27, anti-HCV antibodies). All 16 confirmed HE cases were positive for HEV antigen, while 5 cases were HEV RNA positive, as well as 15 anti-HEV IgM positive. The low positive rate of RNA might be related to the collection and/or the transportation of these samples. This study showed that HEV is a major cause of acute hepatitis in developing countries and regions. Application of immunoassay diagnostic kits, especially the HEV antigen tests, showed great potential for HE detection in these countries and regions.