Biology subjects

Guo, W.

Publications and source records attributed to Guo, W..

At least 127 records · Page 7Linked to original sources

bioRxiv2023

uniLIVER: a Human Liver Cell Atlas for Data-Driven Cellular State Mapping

The liver performs several vital functions such as metabolism, toxin removal and glucose storage through the coordination of various cell types. The cell type compositions and cellular states undergo significant changes in abnormal conditions such as fatty liver, cirrhosis and liver cancer. As the recent breakthrough of the single-cell/single-nucleus RNA-seq (sc/snRNA-seq) techniques, there is a great opportunity to establish a reference cell map of liver at single cell resolution with transcriptome-wise features. In this study, we build a unified liver cell atlas uniLIVER by integrative analyzing a large-scale sc/snRNA-seq data collection of normal human liver with 331,125 cells and 79 samples from 6 datasets. Besides the hierarchical cell type annotations, uniLIVER also proposed a novel data-driven strategy to map any query dataset to the normal reference map by developing a machine learning based framework named LiverCT. Applying LiverCT on the datasets from multiple abnormal conditions (1,867,641 cells and 439 samples from 12 datasets), the alterations of cell type compositions and cellular states were systematically investigated in liver cancer.

bioinformatics↗

bioRxiv2023

Dynamics of Brain Lateralization and Genetic Underpinnings during Chinese Natural Speech Processing: Preferential Occurrence of Logic-Related Patterns in Males and Emotion-Related Patterns in Females

Though language is considered unique to humans with left dominant lateralization in the brain, the dynamic nature of the interplay between hemispheres during language processing remains largely unknown. Here, we investigated whole-brain functional dynamic lateralization patterns during Chinese language processing and potential sex disparities using functional MRI data of 20 subjects listening to narrative stories in a 7T MRI scanner. Our findings revealed two distinct dynamic lateralization states, with regions of the language system consistently showing the left lateralization but reversed lateralization for other regions. These two states, characterized by higher-level functioning regions exhibiting left- or right-lateralization, corresponded to the processing of rational and emotional contents, respectively. We observed pronounced inclinations towards the former state in males and the latter state in females, especially during the processing of rational contents. Finally, genetic analyses revealed that the sex differences in lateralization states were potentially influenced by sex hormones.

neuroscience↗

bioRxiv2023

Multi-task machine learning reveals the neuroanatomy fingerprint of mental processing

Mental processing delineates the functions of human mind encompassing a wide range of motor, sensory, emotional, and cognitive processes, each of which is underlain by the neuroanatomical substrates. Identifying accurate representation of functional neuroanatomy substrates of mental processing could inform understanding of its neural mechanism. The challenge is that it is unclear whether a specific mental process possesses a functional neuroanatomy fingerprint, i.e., a unique and reliable pattern of functional neuroanatomy that underlies the mental process. To address this question, we utilized a multi-task deep learning model to disentangle the functional neuroanatomy fingerprint of seven different and representative mental processes including Emotion, Gambling, Language, Motor, Relational, Social, and Working Memory. Results based on the functional magnetic resonance imaging data of two independent cohorts of 1235 subjects from the US and China consistently show that each of the seven mental processes possessed a functional neuroanatomy fingerprint, which is represented by a unique set of functional activity weights of whole-brain regions characterizing the degree of each region involved in the mental process. The functional neuroanatomy fingerprint of a specific mental process exhibits high discrimination ability (93% classification accuracy and AUC of 0.99) with those of the other mental processes, and is robust across different datasets and using different brain atlases. This study provides a solid functional neuroanatomy foundation for investigating the neural mechanism of mental processing. One-Sentence SummaryThere exists a functional neuroanatomy fingerprint to underlie the mental process.

bioinformatics↗

bioRxiv2023

Hippocampal Dipeptidyl Peptidase 9 Bilaterally Modulates Memory via its Enzymatic Activity

It has been reported that peripherally expressed subtypes of the dipeptidyl peptidase (DPP) family, such as DPP4, modulate memory. However, interestingly whether DPP9 which one of the central nervous systems (CNS) enriched isoforms, regulates memory has not been elucidated yet. Here, we report that DPP9, which is found almost exclusively in neurons, is highly expressed and has high enzyme activity in many brain regions, especially in the hippocampus. Hippocampal DPP9 expression increases after fear memory formation. Fear memory was weakened by DPP9 knockdown and enhanced by DPP9 protein overexpression in the hippocampus. According to subsequent hippocampal proteomics, multiple pathways were enriched by DPP9 expression changes, including the peptidase pathway, which can be bidirectionally regulated by DPP9, and pathways involved in the regulation of synaptic plasticity. DPP9 interacts with its enzymatic substrate neuropeptide Y (NPY) in neurons directly. Hippocampal long-term potentiation (LTP), a form of synaptic plasticity, further confirmed the key role of DPP9 in decreasing LTP through DPP9 knockdown and enhancing LTP through its overexpression. Moreover, inhibiting DPP9 enzyme activity impairs both plasticity and memory. Besides, Affinity purification mass spectrometry (AP-MS) revealed that DPP9-interacting proteins are involved in the functions of dendritic spines and axons. By combining AP-MS and proteomics, DPP9 was shown to play a role in regulating actin functions. Taken together, our findings reveal that DPP9 affects the CNS not only through enzymatic activity but also through protein-protein interactions. This study provides new insights into the molecular mechanisms of memory and DPP family functions.

neuroscience↗

bioRxiv2023

scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution

Single-cell RNA-seq (scRNA-seq) is a powerful technique for decoding the complex cellular compositions in the tumor microenvironment (TME). As previous studies have defined many meaningful cell subtypes in several tumor types, there is a great need to computationally transfer these labels to new datasets. Also, different studies used different approaches or criteria to define the cell subtypes for the same major cell lineages. The relationships between the cell subtypes defined in different studies should be carefully evaluated. In this updated package scCancer2, designed for integrative tumor scRNA-seq data analysis, we developed a supervised machine learning framework to annotate TME cells with annotated cell subtypes from 15 scRNA datasets with 594 samples in total. Based on the trained classifiers, we quantitatively constructed the similarity maps between the cell subtypes defined in different references by testing on all the 15 datasets. Secondly, to improve the identification of malignant cells, we designed a classifier by integrating large-scale pan-cancer TCGA bulk gene expression datasets and scRNA-seq datasets (10 cancer types, 159 samples, 652,160 cells). This classifier shows robust performances when no internal confidential reference cells are available. Thirdly, this package also integrated a module to process the seq-based spatial transcriptomic data and analyze the spatial features of TME. Software availability: http://lifeome.net/software/sccancer2/.

bioinformatics↗

bioRxiv2023

Ser149 is another potential 14-3-3 epsilon binding site of Cdc25B in the G2/M transition of mouse fertilized eggs

Cell cycle division 25B (CDC25B) belongs to the family of cell cycle regulatory proteins. It drives G2/M transition by activating cyclin-dependent protein kinases (CDK1), also known as CDC2, whose activity is directly related to its subcellular localization and phosphorylation state.14-3-3 (YHWA) regulates cell division cycle by binding to Cdc25B as a chaperone protein in mammals. Previously, we found that Cdc25B-Ser149 plays an important role in G2/M transition of mouse fertilized eggs, but the molecular mechanism of this transition remains unclear. In this study, we assessed the role of 14-3-3{varepsilon} (YHWAE) interaction with phosphorylated Cdc25B-Ser149 in G2/M transition of mouse fertilized eggs. Co-expression of Cdc25B-Ser149A and 14-3-3{varepsilon} could effectively activate maturation promoting factor (MPF) through direct dephosphorylation of Cdc2-Tyr15, and induce G2 fertilized eggs to enter mitosis rapidly. However, co-expression of the phosphomimic Cdc25B-Ser149D or Cdc25B-WT and 14-3-3{varepsilon} showed no significant difference in comparison with control groups. 14-3-3{varepsilon} binds to Cdc25B-WT, which is abolished when Ser149 is mutated to Ala. In addition, we found that 14-3-3{varepsilon} and Cdc25B were co-localized in the cytoplasm at the G1, S and early G2 phases. Cdc25B was translocated from the cytoplasm to the nucleus at the late G2 phase. However, when Ser149 is mutated to Ala, the cytoplasmic localization of Cdc25B is completely abolished. Our findings suggest that Cdc25B-Ser149 is another specific binding site for 14-3-3{varepsilon} in G2/M transition of one-cell fertilized mouse eggs, which plays essential roles in the regulation of early development of fertilized mouse eggs.

cell biology↗

bioRxiv2023

Highly conserved, positively charged tandem repeats mediate multimerization of ice nucleation proteins

In nature, frost can form at a few degrees below 0 {degrees}C. However, this process requires the assembly of tens of thousands of ice-like water molecules that align together to initiate freezing at these relatively high temperatures. Water ordering on this scale is mediated by the ice nucleation proteins of common environmental bacteria like Pseudomonas syringae and P. borealis. However, individually, these 100-kDa proteins are too small to organize enough water molecules for frost formation, and it is not known how giant, megadalton-sized multimers, which are crucial for ice nucleation at high sub-zero temperatures, form. The ability of multimers to self-assemble was suggested when the transfer of an ice nucleation protein gene into Escherichia coli led to efficient ice nucleation. Here we demonstrate that a positively-charged sub-domain at the C-terminal end of the central beta-solenoid of the ice nucleation protein is crucial for multimerization. Truncation, relocation, or change of the charge of this subdomain caused a catastrophic loss of ice nucleation ability. Cryo-electron tomography of the recombinant E. coli showed that the ice nucleation protein multimers form fibres that are [~] 5 nm across and up to 200 nm long. A model of these fibres as an overlapping series of antiparallel dimers can account for all their known properties and suggests a route to making cell-free ice nucleators for biotechnological applications.

biochemistry↗

bioRxiv2023

Pixel-wise programmability enables dynamic high-SNR cameras for high-speed microscopy

High-speed wide-field fluorescence microscopy has the potential to capture biological processes with exceptional spatiotemporal resolution. However, conventional cameras suffer from low signal-to-noise ratio at high frame rates, limiting their ability to detect faint fluorescent events. Here, we introduce an image sensor where each pixel has individually programmable sampling speed and phase, so that pixels can be arranged to simultaneously sample at high speed with a high signal-to-noise ratio. In high-speed voltage imaging experiments, our image sensor significantly increases the output signal-to-noise ratio compared to a low-noise scientific CMOS camera ([~]2-3 folds). This signal-to-noise ratio gain enables the detection of weak neuronal action potentials and subthreshold activities missed by the standard scientific CMOS cameras. Our camera with flexible pixel exposure configurations offers versatile sampling strategies to improve signal quality in various experimental conditions.

neuroscience↗

bioRxiv2023

HCCDB v2.0: Decompose the Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC

Large-scale transcriptomic data are crucial for understanding the molecular features of hepatocellular carcinoma (HCC). By integrating 15 transcriptomic datasets of HCC clinical samples, the first version of HCCDB was released in 2018. The meta-analysis of differentially expressed genes and prognosis-related genes across multiple datasets provides a systematic view of the altered biological processes and the inter-patient heterogeneities of HCC with high reproducibility and robustness. After four years, the database needs to integrate recently published datasets. Furthermore, the latest single-cell and spatial transcriptomics provided a great opportunity to decipher the complex gene expression variations at the cellular level with spatial architecture. Here, we present HCCDB v2.0, an updated version that combines bulk, single-cell, and spatial transcriptomic data of HCC clinical samples. It dramatically expands the bulk sample size, adding 1656 new samples of 11 datasets to the existing 3917 samples, thereby enhancing the reliability of transcriptomic meta-analysis. A total of 182,832 cells and 69,352 spatial spots are added to the single-cell and spatial transcriptomics sections, respectively. A novel single-cell level and 2-dimension (sc-2D) metric was proposed to summarize the cell type-specific and dysregulated gene expression patterns. Results are all graphically visualized in our online portal, allowing users to easily retrieve data through a user-friendly interface and navigate between different views. With extensive clinical phenotypes and transcriptomic data in the database, we show two applications for identifying prognosis-associated cells and tumor microenvironment. HCCDB v2.0 is available at http://lifeome.net/database/hccdb2.

cancer biology↗

bioRxiv2023

WBSCR16 Determines Metabolic Flexibility Via Regulating Mitochondrial 16S rRNA Maturation

Mitochondria play significant roles in energy homeostasis by dissipating excess calories. However, the key proteins in mitochondrial govern metabolically flexibility remain poorly understand. Herein, we generated adipose specific Wbscr16-/-mice and cells, both of which exhibited a preference for fat utilization and displayed dramatic mitochondrial changes. We demonstrated that WBSCR16 is essential for the specific cleavage of 16S rRNA-tRNALeu, leading to the production of maturated 16S rRNA, which in turn controls mitochondrial large ribosomal assembly. Importantly, WBSCR16 was identified as a 16S rRNA-binding protein that directly interacts with RNase P subunit MRPP3. Furthermore, evidence showed that WBSCR16 ablation promotes energy wasting via lipid cycling in BAT, leading to excess energy expenditure and resistance to obesity. Conversely, cells and mice with WBSCR16 overexpression preferred to glucose utilization. These findings suggest that WBSCR16 is the key mitochondrial switch protein between glucose and lipid metabolism, making it a promising target for the development of fat busting drug.

cell biology↗

bioRxiv2023

Design of multi-epitope vaccine candidate against Brucella type IV secretion system (T4SS)

Objective the dominant epitopes of T and B cells of VirB8 and VirB10 of Brucella type IV. Secretory systems were predicted and analyzed by bioinformatics, and then multi-epitope vaccines were constructed by reverse vaccination. Methods The amino acid sequences of VirB8 and VirB10 were obtained from the UniProt database, T and B cell dominant epitopes were selected and supplemented with adjuvants to construct a multi-epitope vaccine, SOPMA and RoseTTAFold were applied to predict secondary and tertiary structures respectively for immune simulations. Finally, molecular dynamics simulations of iMEV-TLR4 were then performed. Results one cytotoxic T lymphocyte (CTL) epitope, five helper T lymphocyte (HTL) epitopes, two linear B cell epitopes and three conformational B cell epitopes were obtained in VirB8. 1 cytotoxic T lymphocyte (CTL) epitope, 4 helper T lymphocyte (HTL) epitopes, 4 linear B cell epitopes, and 3 conformational B cell epitopes were obtained in VirB10. The resulting multiepitope vaccine is a protein with good antigenicity, hydrophilicity, and stability. Conclusion a novel brucella multiepitope vaccine was designed by reverse vaccination, and this study provides a theoretical basis for further research.

bioinformatics↗

bioRxiv2023

Intermediate basal cell population in prostate homeostasis and cancer initiation

Many glandular epithelia are mainly composed of basal cells and luminal cells, including the prostate gland. Adult prostate basal and luminal cells are independently self-sustained by unipotent stem cells that can reactivate multipotency under prostate inflammation and carcinogenesis contexts. However, the defined basal stem cell populations responsible for prostate regeneration and their cell fates in prostate homeostasis, inflammation and carcinogenesis remain unclear. Using a genetic proliferation tracer (ProTracer) system, we found that basal cells exhibited extensive cell loss and proliferation during androgen-mediated prostate regression and regeneration, respectively. A rare intermediate basal cell population that expresses luminal cell markers (Nkx3.1 and Pbsn) (termed Basal-B) and a large basal cell population (termed Basal-A) were identified in mouse prostates by single-cell RNA sequencing. Basal-B cells exhibited a greater capacity for organoid formation and luminal cell differentiation in vitro. Genetic lineage tracing using dual recombinases showed that prostate homeostasis and regeneration are not driven by specific basal cell types. Fate-mapping results showed that Basal-B cells had a greater tendency to generate luminal cells under bacteria-induced prostate inflammation. Deletion of Pten in basal cells resulted in Basal-A-to-Basal-B-to-luminal transition and prostatic intraepithelial neoplasia. Moreover, the human Basal-B-cell population was significantly increased in human benign prostate hyperplasia and prostatic intraepithelial neoplasia samples compared with normal prostate samples. This study identifies intermediate Basal-B cells as a potential stem cell population and provides genetic evidence of prostate basal cell lineage plasticity under physiological and pathological contexts.

developmental biology↗

bioRxiv2023

Translation in a Box: Orthogonal Evolution in the Saccharomyces cerevisiae Mitochondrion

The ability to re-engineer and creatively evolve the translation system (TS) would allow invention of new coded polymers by altering the amino acid sidechain inventory and by shifting the polypeptide backbone into new chemical spaces. Unfortunately, the TS is difficult to manipulate and is more constrained over evolution than any other biological system. An orthogonal TS, running in parallel to the primary TS within a given host cell, would release constraints and allow TS manipulation. A fully orthogonal TS requires dedicated rRNAs, rProteins, aminoacyl-tRNA synthetases, and initiation and termination factors, none of which interact with the primary TS. The S. cerevisiae mitochondrial TS is fully orthogonal to the cytosolic TS. Mito-rRNAs, mito- rProteins, mito-tRNAs, mito-aminoacyl tRNA synthetases, and mito-translation factors are distinct from, physically separated from, and functionally independent of their cytosolic counterparts. Here, the S. cerevisiae mitochondrial translation system was subjected to various stresses including antibiotics, mutagenesis and truncation of mito-rProteins, or wholesale replacement of mito-rProteins. Directed evolution of these stressed systems was facilitated by controlled transitions between fermentation and respiration, by changing the carbon source in the growth medium; the dependence of S. cerevisiae survival on mitochondrial translation can be toggled on and off. Specific recreation of the resulting mutations recapitulate the evolved phenotypes. The method developed here appears to be a general approach for discovering functional dependencies. Suppressor mutations reveal functional dependencies within the S. cerevisiae mitochondrial TS. For example proteins Rrg9 or Mrx1 interact with the mito-TS and have critical role in its function. The combined results indicate that the S. cerevisiae mitochondrial TS can be engineered and evolved in isolation of the cytosolic TS. SignificanceThe Central Dogma of Molecular Biology rules life on Earth. Information flows from DNA to mRNA to protein. In the last step of the Central Dogma, the translation system decodes mRNA and produces coded proteins by linking amino acids into polymers. Engineering and evolving the translation system could permits full technical control over this process and could lead to the generation of novel polymers. Here, we use the mitochondrial translation system in the budding yeast Saccharomyces cerevisiae for directed evolution of translation. We modify and evolve the translation system both directly and indirectly using antibiotics and gene editing tools and then measure resulting functionality. Our results show this secondary translation system inside S. cerevisiae mitochondria can be used as an approach for translation engineering.

synthetic biology↗

bioRxiv2023

REVEILLE2 Thermosensitive Splicing: A Molecular Basis for the Integration of Nocturnal Temperature Information by the Arabidopsis Circadian Clock

O_LICold stress is one of the major environmental factors that limit growth and yield of plants. However, it is still not fully understood how plants account for daily temperature fluctuations, nor how these temperature changes are integrated with other regulatory systems such as the circadian clock. C_LIO_LIWe demonstrate that REVEILLE2, a MYB-like transcription factor, exhibits a cold-induced alternative splicing switch from a non-translatable isoform at ambient temperature to a translatable isoform upon cold exposure. We explore the biological function of REVEILLE2 using a combination of molecular genetics, transcriptomics, and physiology. C_LIO_LIDisruption of the REVEILLE2 cooling switch alters regulatory gene expression, impairs circadian timing, and improves photosynthetic capacity. Changes in nuclear gene expression are particularly apparent in the initial hours following chilling, with chloroplast gene expression subsequently up-regulated. C_LIO_LIThe REVEILLE2 cold switch extends our understanding of plants immediate response to cooling. We propose that the circadian component REVEILLE2 restricts plants responses to nocturnal reductions in temperature, thereby enabling appropriate responses to daily environmental changes. C_LI Plain language summaryPlants need to respond appropriately to temperature, accounting for the expected daily patterns of reduced temperatures that occur every night relative to the day. Here, we show that a gene expressed at night fulfils this function.

plant biology↗

bioRxiv2023

Disruption of desmoplastic stroma overcomes restrictions to T cell extravasation, immune exclusion and immunosuppression in solid tumors

The desmoplastic stroma in solid tumors presents a formidable challenge to immunotherapies that rely on endogenous or adoptively transferred T cells, however, the mechanisms are poorly understood. To define mechanisms involved, we treat established desmoplastic pancreatic tumors with CAR T cells directed to fibroblast activation protein (FAP), an enzyme highly overexpressed on a subset of cancer-associated fibroblasts (CAFs). Depletion of FAP+CAFs results in loss of the structural integrity of desmoplastic matrix. This renders these highly treatment-resistant cancers susceptible to subsequent treatment with a tumor antigen (mesothelin)-targeted CAR and to anti-PD1 antibody therapy. Mechanisms include overcoming stroma-dependent restriction of T cell extravasation and/or perivascular invasion, reversing immune exclusion, relieving T cell suppression, and altering the immune landscape by reducing myeloid cell accumulation and increasing endogenous CD8+ T cell and NK cell infiltration. These data provide strong rationale for combining tumor stroma-and malignant cell-targeted therapies to be tested in clinical trials.

immunology↗

bioRxiv2023

Origin and early divergence of tandem duplicated sorbitol transporter genes in Rosaceae

Sorbitol is a critical photosynthate and storage substance in the Rosaceae family. Sorbitol transporters (SOTs) play a vital role in facilitating sorbitol allocation from source to sink organs and sugar accumulation in sink organs. Despite observing gene duplications in the SOT gene family, the origin and evolutionary process of these duplications are unclear, due to the complicated interplay of whole genome duplications and tandem duplications. Here, we investigated the synteny relationships of all detected Polyol/Monosaccharide Transporter (PLT) genes in 61 angiosperm genomes and SOT genes in major representative Rosaceae genomes. Combining phylogenetic analysis, we elucidated the lineage-specific expansion and syntenic conservation of PLTs and SOTs across different plant lineages. We found that Rosaceae SOTs, as PLT family members, originated from a pair of PLT tandem duplicating genes belonging to Class III-A. Additionally, lineage-specific and synergistic duplications in Amygdaloideae had contributed to the expansion of SOTs in Rosaceae plants. Overall, our findings provide insights into the genomic origins, duplication, and divergence of SOT gene family members, which are fundamental for further functional characterizations of each member.

genomics↗

bioRxiv2023

Rice Gene Index (RGI): a comprehensive pan-genome database for comparative and functional genomics of Asian rice

To integrate the genomic information of the rice pan-genome, we performed comparative analyses and established a user-friendly Rice Gene Index (RGI, https://riceome.hzau.edu.cn) platform with 16 platinum standard reference genomes and supplementary transcriptome data. To logically organize and scientifically the index of 744,233 genes among rice accessions, we detected 112,658 Ortholog Gene Indices, and provide GeneCard pages to query genomic, transcriptomic, and homology information for each gene. The RGI allows users to search for relationships and comprehensive information of genes in keyword-based, sequence-based, and relationship-based ways. Furthermore, users can visualize these relationships at local and global scales corresponding to Microcollinearity and Macrocollinearity modules.

genomics↗

bioRxiv2023

Top-down Proteomics of Myosin Light Chain Isoforms Define Chamber-Specific Expression in the Human Heart

Myosin functions as the "molecular motor" of the sarcomere and generates the contractile force necessary for cardiac muscle contraction. Myosin light chains 1 and 2 (MLC-1 and -2) play important functional roles in regulating the structure of the hexameric myosin molecule. Each of these light chains has an atrial and ventricular isoform, so called because they are believed to exhibit chamber-restricted expression in the heart. However, recently the chamber-specific expression of MLC isoforms in the human heart has been questioned. Herein, we analyzed the expression of MLC-1 and -2 atrial and ventricular isoforms in each of the four cardiac chambers in adult non-failing donor hearts using top-down mass spectrometry (MS)-based proteomics. Strikingly, we detected an isoform thought to be ventricular, MLC-2v, in the atria and confirmed the protein sequence using tandem MS (MS/MS). For the first time, a putative deamidation post-translation modification (PTM) located on MLC-2v in atrial tissue was localized to amino acid N13. MLC-1v and MLC-2a were the only MLC isoforms exhibiting chamber-restricted expression patterns across all donor hearts. Importantly, our results unambiguously show that MLC-1v, not MLC-2v, is ventricle-specific in adult human hearts. Overall, top-down proteomics allowed us an unbiased analysis of MLC isoform expression throughout the human heart, uncovering previously unexpected isoform expression patterns and PTMs.

systems biology↗