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VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder

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Genomics, Proteomics & bioinformatics 2018年第5期16卷 320-331页

作者： Dongfang Wang Jin Gu MOE Key Laboratory of bioinformatics BNRIST Bioinformatics Division & Center for Synthetic and Systems BiologyDepartment of Automation Tsinghua University

Single-cell RNA sequencing(scRNA-seq) is a powerful technique to analyze the transcriptomic heterogeneities at the single cell level. It is an important step for studying cell subpopulations and lineages, with an effective low-dimensional representation and visualization of the original scRNA-Seq data. At the single cell level, the transcriptional fluctuations are much larger than the average of a cell population, and the low amount of RNA transcripts will increase the rate of technical dropout events. Therefore, scRNA-seq data are much noisier than traditional bulk RNA-seq data. In this study, we proposed the deep variational autoencoder for scRNA-seq data(VASC), a deep multi-layer generative model, for the unsupervised dimension reduction and visualization of scRNA-seq data. VASC can explicitly model the dropout events and find the nonlinear hierarchical feature representations of the original data. Tested on over 20 datasets, VASC shows superior performances in most cases and exhibits broader dataset compatibility compared to four state-of-the-art dimension reduction and visualization methods. In addition, VASC provides better representations for very rare cell populations in the 2D visualization. As a case study, VASC successfully re-establishes the cell dynamics in pre-implantation embryos and identifies several candidate marker genes associated with early embryo development. Moreover, VASC also performs well on a 10× Genomics dataset with more cells and higher dropout rate.

关键词： Single cell RNA sequencing Deep variational autoencoder Dimension reduction Visualization Dropout

The emerging role of mesenchymal stem cell-derived extracellular vesicles to ameliorate hippocampal NLRP3 inflammation induced by binge-like ethanol treatment in adolescence

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Neural Regeneration Research 2025年第4期20卷 1153-1163页

作者： Susana Mellado María JoséMorillo-Bargues Carla Perpiñá-Clérigues Francisco García-García Victoria Moreno-Manzano Consuelo Guerri María Pascual Department of Physiology School of Medicine and DentistryUniversity of ValenciaValenciaSpain bioinformatics and Biostatistics Unit Príncipe Felipe Research CenterValenciaSpain Neuronal and Tissue Regeneration Laboratory Príncipe Felipe Research CenterValenciaSpain

Our previous studies have reported that activation of the NLRP3(NOD-,LRR-and pyrin domain-containing protein 3)-inflammasome complex in ethanol-treated astrocytes and chronic alcohol-fed mice could be associated with neuroinflammation and brain *** stem cell-derived extracellular vesicles(MSC-EVs)have been shown to restore the neuroinflammatory response,along with myelin and synaptic structural alterations in the prefrontal cortex,and alleviate cognitive and memory dysfunctions induced by binge-like ethanol treatment in adolescent *** the therapeutic role of the molecules contained in mesenchymal stem cell-derived extracellular vesicles,the present study analyzed whether the administration of mesenchymal stem cell-derived extracellular vesicles isolated from adipose tissue,which inhibited the activation of the NLRP3 inflammasome,was capable of reducing hippocampal neuroinflammation in adolescent mice treated with binge *** demonstrated that the administration of mesenchymal stem cell-derived extracellular vesicles ameliorated the activation of the hippocampal NLRP3 inflammasome complex and other NLRs inflammasomes(e.g.,pyrin domain-containing 1,caspase recruitment domain-containing 4,and absent in melanoma 2,as well as the alterations in inflammatory genes(interleukin-1β,interleukin-18,inducible nitric oxide synthase,nuclear factor-kappa B,monocyte chemoattractant protein-1,and C–X3–C motif chemokine ligand 1)and miRNAs(miR-21a-5p,miR-146a-5p,and miR-141-5p)induced by binge-like ethanol treatment in adolescent *** analysis further revealed the involvement of miR-21a-5p and miR-146a-5p with inflammatory target genes and NOD-like receptor signaling *** together,these findings provide novel evidence of the therapeutic potential of MSC-derived EVs to ameliorate the hippocampal neuroinflammatory response associated with NLRP3 inflammasome activation induced by binge drinking in adolescence.

关键词： adolescence binge-like ethanol treatment extracellular vesicles hippocampus mesenchymal stem cells neuroinflammation NOD-,LRR-and pyrin domain-containing protein 3(NLRP3)

A multilevel pan-cancer map links gene mutations to cancer hallmarks

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Chinese Journal of Cancer 2015年第10期34卷 439-449页

作者： Theo A.Knijnenburg Tycho Bismeijer Lodewyk F.A.Wessels llya Shmulevich Institute for Systems biology bioinformatics and Statistics Division of Molecular CarcinogenesisNetherlands Cancer Institute

Background:A central challenge in cancer research is to create models that bridge the gap between the molecular level on which interventions can be designed and the cellular and tissue levels on which the disease phenotypes are *** study was undertaken to construct such a model from functional annotations and explore its use when integrated with large-scale cancer genomics ***:We created a map that connects genes to cancer hallmarks via signaling *** projected gene mutation and focal copy number data from various cancer types onto this *** performed statistical analyses to uncover mutually exclusive and co-occurring oncogenic aberrations within this ***:Our analysis showed that although the genetic fingerprint of tumor types could be very different,there were less variations at the level of hallmarks,consistent with the idea that different genetic alterations have similar functional ***,we showed how the multilevel map could help to clarify the role of infrequently mutated genes,and we demonstrated that mutually exclusive gene mutations were more prevalent in pathways,whereas many co-occurring gene mutations were associated with hallmark ***:Overlaying this map with gene mutation and focal copy number data from various cancer types makes it possible to investigate the similarities and differences between tumor samples systematically at the levels of not only genes but also pathways and hallmarks.

关键词： Cancer systems biology, Cancer hallmarks, Gene mutations, Multilevel model

Pathophysiological responses from human gut microbiome

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World Journal of Translational Medicine 2014年第3期3卷 133-140页

作者： Anindya Roy Chowdhury Utpal Bakshi structural biology and bioinformatics division CSIR-Indian Institute of Chemical Biology

The human gastrointestinal tract harbors a vast collection of symbiotic microorganisms-collectively termed as "gut microbiome". This microbiota has important effect in immune system and other host activities. Recent studies have suggested that alterations of the normal gut microbiota are associated with various human diseases and psychological disorders. The underlying cause, once proven, may provide novel insights into the importance of gut flora in human health. In this review, we give an attempt to describe how the alteration in the microbial community causes the development of certain widespread pathophysiological disorders; focusing on inflammatory bowel disease, colorectal cancer, obesity and autism. Proper knowledge about the hostmicrobiota interaction and linkage could be essential for the development of future personalized strategies of therapeutics.

关键词： Human gut microbiome Inflammatory bowel disease Colorectal cancer Obesity Autism

Negative PO3-implanted bionic ion transport channels for promoting Li-S battery

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Science China Chemistry 2025年

作者： Wenhuan Huang Shun Wang Xuehan Hou Yanan Zhang Xingxing Zhang Yaoxiao Zhao Xilang Jin Huabin Zhang Fei Wang Jian Zhang Key Laboratory of Chemical Additives for China National Light Industry College of Chemistry and Chemical EngineeringShaanxi University of Science and Technology School of Materials and Chemical Engineering Xi'an Technological University Chemistry Program Physical Science and Engineering Division King Abdullah University of Science and Technology State Key Laboratory of structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences

Lithium-sulfur （Li-S） battery,as a promising next-generation high-energy-density battery,suffers from lithium polysulfides（LPSs） shuttle and Li dendrites *** crystalline framework-based membranes as separator can effectively absorb and restrain LPSs but without precise structural design principal exploration and mechanism ***,bio-inspired 1D oriented lithium-ion transport channels with molecular negatively charged PO3（-1） have been developed in hybrid tetrazole frameworks for promoting the transmission of Li+*** theoretical calculations and in situ spectroscopy demonstrated the higher binding energy and inhibited diffusion of LPSs in *** assembled PP@PO3Janus separator in Li-S coin cell delivered a high initial capacity of 1410.9 mAh g-1at 0.1 C and a low attenuation rate of 0.038%per cycle over 500 cycles at 5 ***,the high capacities of 862,542 and 409 mAh g-1based on high-sulfur-loading cathodes of 2.6,3.8 and 5.0 mg cm-2at0.5 C were achieved,***,the punch battery of PO3@PP separator with S-cathode of 1.2 mg cm-2has been developed for demonstrating its potentials commercial application,which displays impressive capacity of 873.4 mAh g-1with the retention of～78.9%over 50 cycles.

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Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae

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Science China(Life Sciences) 2014年第1期57卷 52-58页

作者： LI YingXue LIU XueNing WANG XiaoWo ZHANG XueGong MOE Key Laboratory of bioinformatics Bioinformatics Division and Center for Synthetic and Systems Biology TNLIST/Department of Automation Tsinghua University School of Life Sciences Tsinghua University

Recent studies have found many antisense non-coding transcripts at the opposite strand of some protein-coding *** yeast,it was reported that such antisense transcripts play regulatory roles for their partner genes by forming a feedback loop with the protein-coding *** not all coding genes have accompanying antisense transcripts,it would be interesting to know whether there are sequence signatures in a coding gene that are decisive or associated with the existence of such antisense *** collected all the annotated antisense transcripts in the yeast Saccharomyces cerevisiae,analyzed sequence motifs around the genes with antisense partners,and classified genes with and without accompanying antisense transcripts by using machine learning *** weak but statistically significant sequence features are detected,which indicates that there are sequence signatures around the protein-coding genes that may be decisive or indicative for the existence of accompanying antisense transcripts.

关键词： antisense transcript pattern recognition motif finding yeast

Growth inhibition mediated by PSP94 or CRISP-3 is prostate cancer cell line specific

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Asian Journal of Andrology 2010年第5期12卷 677-689页

作者： Bhakti R. Pathak Ananya A. Breed Vaishali H. Nakhawa Dhanashree D. Jagtap Smita D. Mahale division of structural biology National Institute for Research in Reproductive Health Indian Council of Medical ResearchMumbai 400012 India

The prostate secretory protein of 94 amino acids （PSP94） has been shown to interact with cysteine-rich secretory protein 3 （CRISP-3） in human seminal plasma. Interestingly, PSP94 expression is redaced or lost in the majority of the prostate tumours, whereas CRISP-3 expression is upregulated in prostate cancer compared with normal prostate tissue. To obtain a better understanding of the individual roles these proteins have in prostate tumourigenesis and the functional relevance of their interaction, we ectopically expressed either PSP94 or CRISP-3 alone or PSP94 along with CRISP-3 in three prostate cell lines （PC3, WPE1-NB26 and LNCaP） and performed growth inhibition assays. Reverse transcription-polymerase chain reaction and Western blot analysis were used to screen prostate cell lines for PSP94 and CRISP-3 expression. Mammalian expression constructs for human PSP94 and CRISP-3 were also generated and the expression, localization and secretion of recombinant protein were assayed by transfection followed by Western blot analysis and immunofluorescence assay. The effect that ectopic expression of PSP94 or CRISP-3 had on cell growth was studied by clonogenic survival assay follokving transfection. To evaluate the effects of coexpression of the two proteins, stable clones of PC3 that expressed PSP94 were generated. They were subsequently transfected with a CRISP-3 expression construct and subjected to clonogenic survival assay. Our results showed that PSP94 and CRISP-3 could each induce growth inhibition in a cell line specific manner. Although the growth of CRISP-3-positive cell lines was inhibited by PSP94, growth inhibition mediated by CRISP-3 was not affected by the presence or absence of PSP94. This suggests that CRISP-3 may participate in PSP94-independent activities during prostate tumourigenesis.

关键词： β-microseminoprotein CRISP-3 clonogenic survival assay LNCaP PC3 WPE1-NB26

DIProT:A deep learning based interactive toolkit for efficient and effective Protein design

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Synthetic and Systems Biotechnology 2024年第2期9卷 217-222页

作者： Jieling He Wenxu Wu Xiaowo Wang Ministry of Education Key Laboratory of bioinformatics Center for Synthetic and Systems BiologyBioinformatics DivisionBeijing National Research Center for Information Science and TechnologyDepartment of AutomationTsinghua UniversityBeijingChina

The protein inverse folding problem,designing amino acid sequences that fold into desired protein structures,is a critical challenge in biological *** numerous data-driven and knowledge-driven methods,there remains a need for a user-friendly toolkit that effectively integrates these approaches for in-silico protein *** this paper,we present DIProT,an interactive protein design *** leverages a non-autoregressive deep generative model to solve the inverse folding problem,combined with a protein structure prediction *** integration allows users to incorporate prior knowledge into the design process,evaluate designs in silico,and form a virtual design loop with human *** inverse folding model demonstrates competitive performance in terms of effectiveness and efficiency on TS50 and CATH4.2 datasets,with promising sequence recovery and inference *** studies further illustrate how DIProT can facilitate user-guided protein design.

关键词： Computational Protein design Interactive design toolkit Protein inverse folding Non-autoregressive decoding

Single-cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction

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Genomics, Proteomics & bioinformatics 2021年第3期19卷 394-407页

作者： Tao Hu Lei Wei Shuailin Li Tianrun Cheng Xuegong Zhang Xiaowo Wang Ministry of Education Key Laboratory of bioinformatics Center for Synthetic and Systems BiologyBioinformatics DivisionBeijing National Research Center for Information Science and TechnologyDepartment of AutomationTsinghua UniversityBeijing 100084China

Isogenic cells growing in identical environments show cell-to-cell variations because of the stochasticity in gene *** levels of variation or noise can disrupt robust gene expression and result in tremendous consequences for cell *** this work,we showed evidence from single-cell RNA sequencing data analysis that microRNAs(miRNAs)can reduce gene expression noise at the mRNA level in mouse *** identified that the miRNA expression level,number of targets,target pool abundance,and miRNA-target interaction strength are the key features contributing to noise *** tend to work together in cooperative subnetworks to repress target noise synergistically in a cell type-specific *** building a physical model of post-transcriptional regulation and observing in synthetic gene circuits,we demonstrated that accelerated degradation with elevated transcriptional activation of the miRNA target provides resistance to extrinsic ***,through the integrated analysis of single-cell RNA and miRNA expression profiles,we demonstrated that miRNAs are important post-transcriptional regulators for reducing gene expression noise and conferring robustness to biological processes.

关键词： MicroRNA regulation Gene expression noise Competing RNA microRNA regulation network Singlecell RNA sequencing