Biology subjects

Sheng, N.

Publications and source records attributed to Sheng, N..

8 recordsLinked to original sources

bioRxiv2025

Scalable single-cell metagenomic analysis with Bascet and Zorn

Single-cell metagenomic sequencing (scMetaG) can provide maximum-resolution insights into complex microbial communities. However, existing bioinformatic tools are not equipped to handle the massive amounts of data generated by novel high-throughput scMetaG methods. Here, we present a bioinformatic toolkit for complete, end-to-end scMetaG analysis: (i) Bascet, a command-line suite designed to scale to massive scMetaG datasets ([≥]1 million cells); (ii) Zorn, an R package/workflow manager that enables reproducible scMetaG data analysis, exploration, and visualization (http://zorn.henlab.org/). Enabled by recent advances in droplet microfluidics, we use Bascet and Zorn to develop and optimize a high-throughput scMetaG method on a ten-species mock community. To showcase their utility on a real-world sample, we use Bascet and Zorn to characterize a human saliva sample, generating single-amplified genomes (SAGs) from >10k prokaryotic cells. Overall, Bascet and Zorn enable reproducible scMetaG analysis, allowing users to query microbiomes at unprecedented resolution and scale.

microbiology↗

bioRxiv2024

Primate-specific BTN3A2 protects against SARS-CoV-2 infection by interacting with and reducing ACE2

BackgroundCoronavirus disease 2019 (COVID-19) is an immune-related disorder caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The complete pathogenesis of the virus remains to be determined. Unraveling the molecular mechanisms governing SARS-CoV-2 interactions with host cells is crucial for the formulation of effective prophylactic measures and the advancement of COVID-19 therapeutics. MethodsWe analyzed human lung single-cell RNA sequencing dataset to discern the association of butyrophilin subfamily 3 member A2 (BTN3A2) expression with COVID-19. The BTN3A2 gene edited cell lines and transgenic mice were infected by live SARS-CoV-2 in a biosafety level 3 (BSL-3) laboratory. Immunoprecipitation, flow cytometry, biolayer interferometry and competition ELISA assays were performed in BTN3A2 gene edited cells. We performed quantitative real-time PCR, histological and/or immunohistochemical analyses for tissue samples from mice with or without SARS-CoV-2 infection. FindingsThe BTN3A2 mRNA level was correlated with COVID-19 severity. BTN3A2 expression was predominantly identified in epithelial cells, elevated in pathological epithelial cells from COVID-19 patients and co-occurred with ACE2 expression in the same lung cell subtypes. BTN3A2 targeted the early stage of the viral life cycle by inhibiting SARS-CoV-2 attachment through interactions with the receptor-binding domain (RBD) of the Spike protein and ACE2. BTN3A2 inhibited ACE2-mediated SARS-CoV-2 infection by reducing ACE2 in vitro and in vivo. InterpretationThese results reveal a key role of BTN3A2 in the fight against COVID-19. Identifying potential monoclonal antibodies which mimic BTN3A2 may facilitate disruption of SARS-CoV-2 infection, providing a therapeutic avenue for COVID-19. FundingThis study was supported by the National Natural Science Foundation of China (32070569, U1902215, and 32371017), the CAS "Light of West China" Program, and Yunnan Province (202305AH340006). Research in contextO_ST_ABSEvidence before this studyC_ST_ABSOur understanding of the pathogenesis of COVID-19, especially key molecular events in the early stage of viral infection, remains incompletely albeit we witnessed many progresses. This knowledge gap hinders the finding for effective and specific antiviral agents against SARS-CoV-2. The entry of SARS-CoV-2 is mediated by the entry receptor angiotensin-converting enzyme 2 (ACE2) and is affected by host antiviral defenses. Targeting these universal host factors required for virus replication is the most promising approach for effective prevention and treatment of COVID-19. Added value of this studyOur study revealed that BTN3A2, a primate-specific gene, acts as a potent inhibitor of SARS-CoV-2 infection in vitro and in vivo. The up-regulation of BTN3A2 upon SARS-CoV-2 infection competed with the ACE2 receptor for binding to the Spike protein, subsequently reducing ACE2 expression and ACE2-mediated SARS-CoV-2 entry. Implications of all the available evidenceThese data highlighted that BTN3A2 as a novel host factor with protective effects against SARS-CoV-2 infection. The BTN3A2 holds considerable potential as a therapeutic drug for mitigating the impact of SARS-CoV-2 and its variants of concern (VOCs).

cell biology↗

bioRxiv2023

The E3 ubiquitin ligase RNF220 maintains hindbrain Hox expression patterns through regulation of WDR5 stability

The spatial and temporal linear expression of Hox genes establishes a regional Hox code, which is crucial for the antero-posterior (A-P) patterning, segmentation, and neuronal circuit development of the hindbrain. RNF220, an E3 ubiquitin ligase, is widely involved in neural development via targeting of multiple substrates. Here, we found that the expression of Hox genes in the pons was markedly up-regulated at the late developmental stage (post-embryonic day E15.5) in Rnf220-/- and Rnf220+/-mouse embryos. Single-nucleus RNA-seq analysis revealed different Hox de-repression profiles in different groups of neurons, including the pontine nuclei (PN). The Hox pattern was disrupted and the neural circuits were affected in the PN of Rnf220+/- mice. We showed that this phenomenon was mediated by WDR5, a key component of the TrxG complex, which can be polyubiquitinated and degraded by RNF220. Intrauterine injection of WDR5 inhibitor (WDR5-IN-4) and genetic ablation of Wdr5 in Rnf220+/- mice largely recovered the de-repressed Hox expression pattern in the hindbrain. In P19 embryonal carcinoma cells, the retinoic acid induced Hox expression was further stimulated by Rnf220 knockdown, which can also be rescued by Wdr5 knockdown. In short, our data suggest a new role of RNF220/WDR5 in Hox pattern maintenance and pons development in mice.

developmental biology↗

bioRxiv2023

Post-Transcriptional Methylation of Mitochondrial-tRNA Differentially Contributes to Mitochondrial Pathology

Human mitochondrial tRNAs (mt-tRNAs), critical for mitochondrial biogenesis, are frequently associated with pathogenic mutations. These mt-tRNAs have unusual sequence motifs and require post-transcriptional modifications to stabilize their fragile structures. However, whether a modification that stabilizes a wild-type (WT) mt-tRNA structure would also stabilize its pathogenic variants is unknown. Here we show that the N1-methylation of guanosine at position 9 (m1G9) of mt-Leu(UAA), while stabilizing the WT tRNA, has an opposite and destabilizing effect on variants associated with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes). This differential effect is further demonstrated by the observation that demethylation of m1G9, while damaging to the WT tRNA, is beneficial to the major pathogenic variant, improving its structure and activity. These results have new therapeutic implications, suggesting that the N1-methylation of mt-tRNAs at position 9 is a determinant of pathogenicity and that controlling the methylation level is an important modulator of mt-tRNA-associated diseases.

cell biology↗

bioRxiv2022

Initial niche condition determines the aging speed and regenerative activity of quiescent cells

Quiescent cell ages with decline in both the survivability and regenerative activity. While most cellular quiescence/ageing research have focused on the survivability and from the population level, the question how the regenerative activity change with the quiescence time (i.e., chronological age) has rarely been addressed quantitatively. In this work, we systematically measured both features in ageing quiescent fission yeast cells at single cell level. We found that the regenerative activity declines linearly before survivability decline and the cellular chronological ageing speed is predetermined by the initial niche condition. Moreover, this linear ageing behavior is robust under various niche conditions and follows a common ageing trajectory in terms of gene expression. Furthermore, initial calorie restriction was found to improve not only the survivability but also the later regenerative activity. Our results reveal a continuous diverse spectrum of quiescence depth and ageing plasticity.

cell biology↗

bioRxiv2021

Integrated analyses of the single-cell ATAC-seq and RNA-seq reveal the epigenetic landscape of human ovarian aging

Studying the molecular mechanisms of ovarian aging is crucial for understanding the age-related fertility issues in females. Recently, a single-cell transcriptomic roadmap of ovarian aging based on non-human primates revealed the molecular signatures of the oocytes at different developmental stages. Herein, we present the first epigenetic landscape of human ovarian aging, through an integrated analysis of the single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) and single-cell RNA-seq. We depicted the transcriptional profiles and chromatin accessibility of the ovarian tissues isolated from old (n=4) and young (n=2) donors. The unsupervised clustering of data revealed seven distinct cell populations in the ovarian tissues and six subtypes of oocytes, which could be distinguished by age difference. Further analysis of the scATAC-seq data from the young and old oocytes revealed that the interaction between the Notch signaling pathway and AP-1 family transcription factors may crucially determine oocyte aging. Finally, a machine-learning algorithm was applied to calculate the optimal model based on the single-cell dataset for predicting oocyte aging, which exhibited excellent accuracy with a cross-validated area under the receiver operating characteristics score of 0.99. In summary, this study provides a comprehensive understanding of human ovarian aging at both the transcriptomic and epigenetic levels, based on an integrated analysis of large-scale single-cell datasets. We believe our results will shed light on the discovery of potential therapeutic targets or diagnostic markers for age-related ovarian disorders.

genetics↗

bioRxiv2021

Maintenance of copy number variation at the human salivary agglutinin gene (DMBT1) by balancing selection driven by host-microbe interactions

Most genetic variation in humans occurs in a pattern consistent with neutral evolution, but a small subset is maintained by balancing selection. Identifying loci under balancing selection is important not only for understanding the processes explaining variation in the genome, but also to identify loci with alleles that affect response to the environment and disease. Several genome scans using genetic variation data have identified the 5 end of the DMBT1 gene as a region undergoing balancing selection. DMBT1 encodes the pattern-recognition glycoprotein DMBT1, also known as SALSA, gp340 or salivary agglutinin. It binds to a wide variety of pathogens through a tandemly-arranged scavenger receptor cysteine-rich (SRCR) domain, with the number of SRCR domains varying in humans. Here we use expression analysis, linkage in pedigrees, and long range single transcript sequencing, to show that the signal of balancing selection is driven by one haplotype usually carrying shorter SRCR repeats, and another usually carrying a longer SRCR repeat, within the coding region of DMBT1. The DMBT1 protein size isoform encoded by a shorter SRCR domain repeat allele showed complete loss of binding of a cariogenic and invasive Streptococcus mutans strain in contrast to the long SRCR allele. Taken together, our results suggest that balancing selection at DMBT1 is due to host-microbe interactions of encoded SRCR tandem repeat alleles.

genetics↗

bioRxiv2019

Dynamics, cariogenicity, and geographic distribution of Streptococcus mutans adhesin types suggest adaptation to individual hosts

Dental caries, the most common chronic infectious disease, involve Streptococcus mutans SpaP A/B/C and Cnm/Cbm adhesin types of different virulence. We have explored their stability and dynamics over 5 years, their geographic distribution, as well as the potentially increased cariogenicity of specific SpaP B subtypes. We performed qPCR and TaqMan typing using whole saliva and isolates from 452 Swedish adolescents followed from 12 to 17 years of age. Approximately 50% of the children were infected at baseline with a single dominant (44%) or mixed (6%) SpaP A, B, or C type, some of which were also Cnm (6%) or Cbm (1%) positive. Stability (+, +) was high for S. mutans infection (85%) and dominant SpaP A or C (80% and 67%) and Cnm or Cbm (85% and 100%) types, but low for SpaP B (51%) and mixed SpaP A/B/C types (26%). Only five children switched from one SpaP type to another, and none between Cnm and Cbm types. Mixed SpaP A/B/C types were typically lost or changed into dominant types. Moreover, children infected with Cnm (n=26) types were more frequent in the northern (Skellefte[a]) region (p = 0.0041), and those with Cbm types (n=7) in the southern (Ume[a]) region. Children infected with SpaP B-2 subtypes had a doubled caries experience (p = 0.009) and 5-year caries increment (p = 0.02) compared to those infected with SpaP A. In conclusion, the stable dominant but instable mixed adhesin types and geographic differentiation of Cnm and Cbm types suggest adaptation of low and high cariogenicity types to specific individuals.

microbiology↗