CellCommuNet: an atlas of cell-cell communication networks from single-cell RNA sequencing of human and mouse tissues in normal and disease states.

Cell-cell communication, as a basic feature of multicellular organisms, is crucial for maintaining the biological functions and microenvironmental homeostasis of cells, organs, and whole organisms. Alterations in cell-cell communication contribute to many diseases, including cancers. Single-cell RNA sequencing (scRNA-seq) provides a powerful method for studying cell-cell communication by enabling the analysis of ligand-receptor interactions. Here, we introduce CellCommuNet (http://www.inbirg.com/cellcommunet/), a comprehensive data resource for exploring cell-cell communication networks in scRNA-seq data from human and mouse tissues in normal and disease states. CellCommuNet currently includes 376 single datasets from multiple sources, and 118 comparison datasets between disease and normal samples originating from the same study. CellCommuNet provides information on the strength of communication between cells and related signalling pathways and facilitates the exploration of differences in cell-cell communication between healthy and disease states. Users can also search for specific signalling pathways, ligand-receptor pairs, and cell types of interest. CellCommuNet provides interactive graphics illustrating cell-cell communication in different states, enabling differential analysis of communication strength between disease and control samples. This comprehensive database aims to be a valuable resource for biologists studying cell-cell communication networks.

DiSignAtlas: an atlas of human and mouse disease signatures based on bulk and single-cell transcriptomics.

Molecular signatures are usually sets of biomolecules that can serve as diagnostic, prognostic, predictive, or therapeutic markers for a specific disease. Omics data derived from various high-throughput molecular biology technologies offer global, unbiased and appropriately comparable data, which can be used to identify such molecular signatures. To address the need for comprehensive disease signatures, DiSignAtlas (http://www.inbirg.com/disignatlas/) was developed to provide transcriptomics-based signatures for a wide range of diseases. A total of 181 434 transcriptome profiles were manually curated from studies involving 1836 nonredundant disease types in humans and mice. Then, 10 306 comparison datasets comprising both disease and control samples, including 328 single-cell RNA sequencing datasets, were established. Furthermore, a total of 3 775 317 differentially expressed genes in humans and 1 723 674 in mice were identified as disease signatures by analysing transcriptome profiles using commonly used pipelines. In addition to providing multiple methods for the retrieval of disease signatures, DiSignAtlas provides downstream functional enrichment analysis, cell type analysis and signature correlation analysis between diseases or species when available. Moreover, multiple analytical and comparison tools for disease signatures are available. DiSignAtlas is expected to become a valuable resource for both bioscientists and bioinformaticians engaged in translational research.

Natural product P57 induces hypothermia through targeting pyridoxal kinase.

Induction of hypothermia during hibernation/torpor enables certain mammals to survive under extreme environmental conditions. However, pharmacological induction of hypothermia in most mammals remains a huge challenge. Here we show that a natural product P57 promptly induces hypothermia and decreases energy expenditure in mice. Mechanistically, P57 inhibits the kinase activity of pyridoxal kinase (PDXK), a key metabolic enzyme of vitamin B6 catalyzing phosphorylation of pyridoxal (PL), resulting in the accumulation of PL in hypothalamus to cause hypothermia. The hypothermia induced by P57 is significantly blunted in the mice with knockout of PDXK in the preoptic area (POA) of hypothalamus. We further found that P57 and PL have consistent effects on gene expression regulation in hypothalamus, and they may activate medial preoptic area (MPA) neurons in POA to induce hypothermia. Taken together, our findings demonstrate that P57 has a potential application in therapeutic hypothermia through regulation of vitamin B6 metabolism and PDXK serves as a previously unknown target of P57 in thermoregulation. In addition, P57 may serve as a chemical probe for exploring the neuron circuitry related to hypothermia state in mice.

OrganoidDB: a comprehensive organoid database for the multi-perspective exploration of bulk and single-cell transcriptomic profiles of organoids.

Organoids, three-dimensional in vitro tissue cultures derived from pluripotent (embryonic or induced) or adult stem cells, are promising models for the study of human processes and structures, disease onset and preclinical drug development. An increasing amount of omics data has been generated for organoid studies. Here, we introduce OrganoidDB (http://www.inbirg.com/organoid_db/), a comprehensive resource for the multi-perspective exploration of the transcriptomes of organoids. The current release of OrganoidDB includes curated bulk and single-cell transcriptome profiles of 16 218 organoid samples from both human and mouse. Other types of samples, such as primary tissue and cell line samples, are also integrated to enable comparisons with organoids. OrganoidDB enables queries of gene expression under different modes, e.g. across different organoid types, between different organoids from different sources or protocols, between organoids and other sample types, across different development stages, and via correlation analysis. Datasets and organoid samples can also be browsed for detailed information, including organoid information, differentially expressed genes, enriched pathways and single-cell clustering. OrganoidDB will facilitate a better understanding of organoids and help improve organoid culture protocols to yield organoids that are highly similar to living organs in terms of composition, architecture and function.

PertOrg 1.0: a comprehensive resource of multilevel alterations induced in model organisms by in vivo genetic perturbation.

Genetically modified organisms (GMOs) can be generated to model human genetic disease or plant disease resistance, and they have contributed to the exploration and understanding of gene function, physiology, disease onset and drug target discovery. Here, PertOrg (http://www.inbirg.com/pertorg/) was introduced to provide multilevel alterations in GMOs. Raw data of 58 707 transcriptome profiles and associated information, such as phenotypic alterations, were collected and curated from studies involving in vivo genetic perturbation (e.g. knockdown, knockout and overexpression) in eight model organisms, including mouse, rat and zebrafish. The transcriptome profiles from before and after perturbation were organized into 10 116 comparison datasets, including 122 single-cell RNA-seq datasets. The raw data were checked and analysed using widely accepted and standardized pipelines to identify differentially expressed genes (DEGs) in perturbed organisms. As a result, 8 644 148 DEGs were identified and deposited as signatures of gene perturbations. Downstream functional enrichment analysis, cell type analysis and phenotypic alterations were also provided when available. Multiple search methods and analytical tools were created and implemented. Furthermore, case studies were presented to demonstrate how users can utilize the database. PertOrg 1.0 will be a valuable resource aiding in the exploration of gene functions, biological processes and disease models.

Temporal-spatial low shear stress induces heterogenous distribution of hematopoietic stem cell budding in zebrafish.

Hematopoietic stem/progenitor cells (HSPCs) originate from endothelial cells (ECs) localized on the ventral side of the dorsal aorta (DA), and hemodynamic parameters may suffer sharp changes in DA at HSPCs development stage for intersegmental vessel formation. However, the temporal-spatial shear stress parameters and biomechanics mechanisms of HSPC budding remain unknown. Here, we found that the hematopoietic endothelium (HE) in the aorta-gonad-mesonephros was heterogeneous; that is, HEs were mainly distributed at the ventral side of the vascular bifurcation in zebrafish embryos, which was found to show low shear stress (LSS) through numerical simulation analysis. Furthermore, HSPCs localized in the posterior somite of aorta-gonad-mesonephros with slow velocity. On the temporal scale, there was a slow velocity and LSS during HE budding from 36 h post-fertilization and decreased shear stress with drug expanded HSPC numbers. Mechanistically, matrix metalloproteinase (MMP) expression and macrophage chemotaxis were significantly increased in HEs by RNA-seq. After treatment with an MMP13 inhibitor, HSPCs were significantly reduced in both the aorta-gonad-mesonephros and caudal hematopoietic tissue in embryos. Our results show that HSPC budding is heterogeneous, and the mechanism is that physiological LSS controls the emergence of HSPCs by promoting the accumulation of macrophages and subsequent MMP expression.

The clinical value of blood flow parameters of the umbilical artery and middle cerebral artery for assessing fetal distress.

OBJECTIVE: To explore the clinical value of blood flow parameters of the umbilical artery (UA) and middle cerebral artery (MCA) for gauging fetal distress. METHODS: This study was conducted among 256 pregnant women who presented for routine prenatal checkups and successfully gave birth in our hospital from January 2018 to February 2020. These pregnant women were examined with the Color Doppler Ultrasound, and the color Doppler flow imaging (CDFI) showed the blood flow of the UA and MCA. In accordance with the diagnostic criteria of fetal distress, they were divided into a fetal distress group (n=67) and a control group (n=189). The receiver operator characteristic (ROC) curve analysis was performed on the diagnostic value of the flow in the UA and MCA. According to their pregnancy outcomes, they were divided into a good pregnancy outcome group (n=209) and an adverse pregnancy outcome group (n=47), and their blood flow parameters of the UA and MCA were compared. RESULTS: The S/D, PI, and RI values of the UA in the fetal distress group exceeded those in the control group, and the S/D, PI, and RI values of the MCA were lower than those in the control group (P<0.05). The good pregnancy outcome group had lower S/D, PI, and RI values of the UA. The good pregnancy outcome group had higher S/D, PI, and RI values of the MCA (P<0.05). ROC curves revealed that the areas under curve of S/D, PI, and RI of the UA were 0.81, 0.76 and 0.74, respectively; the areas under curve of S/D, PI, and RI of the MCA were 0.82, 0.78 and 0.71, respectively. CONCLUSION: The hemodynamic indexes of the UA and MCA can be used as a basis for evaluating fetal distress, which shows important clinical indications for gauging pregnancy outcome.

Nanoparticles retard immune cells recruitment in vivo by inhibiting chemokine expression.

The large-scale utilization of nanotechnology depends on public and consumer confidence in the safety of this new technology. Studying the interaction of nanoparticles with immune cells plays a vital role in the safety assessment of nanomedicine. Although some researches have indicated that the immune cells undergo severe interfere after phagocytosis of nanoparticles, the impact on immune system of the whole body are still unclear. Here, we use immune cells labeled transgenic zebrafish to study the mechanisms of nanoparticles on zebrafish immune cells. We demonstrate that gold nanoparticles (Au NPs) phagocytized by immune cells can reduce and retard the sensitivity of immune response, resulting nanoparticle-induced bluntness in immune cell (NIBIC). RNA-seq and functional analysis reveal that NIBIC is mainly induced by the inhibiting expression of chemokine receptor 5 (CCR5). Furthermore, PVP-modified Au NPs can eliminate NIBIC by inhibiting the cell phagocytosis. Our results highlight the potential risk for Au NPs in vivo and further the understanding of the mechanism of the interaction between Au NPs and the immune response. We should consider this factor in future material design and pay more attention to the process of using nanomedicines on immune diseases.

SRGN, a new identified shear-stress-responsive gene in endothelial cells.

Endothelial cells (ECs) play an important role in the pathogenesis of cardiovascular disease, especially atherosclerosis (AS). The abnormal wall shear stress (WSS) which directly contacts with ECs is the key stimulating factor leading to AS. However, the underlying mechanism of ECs responding to WSS is still incompletely understood. This study aims to explore the novel mechano-sensitive genes and its potential mechanism in response to WSS in ECs by employing bioinformatics methods based on previously available high-throughput data from zebrafish embryos, both before and after blood flow formation. Six common differentially expressed genes (DEGs) (SRGN, SLC12A3, SLC25A4, PVALB1, ITGAE.2, zgc:198419) were selected out from two high-throughput datasets (GSE126617 and GSE20707) in the GEO database. Among them, SRGN was chosen for further verification through the in vitro shear stress loading experiments with human umbilical vein endothelial cells (HUVECs) and the in vivo partial ligation of carotid artery in mice. Our data indicated that low shear stress (LSS) could enhance the expression of SRGN via the PKA/CREB-dependent signaling pathway. The proportion of Ki67+ cells and the concentration of nitric oxide (NO) were high in SRGN high expression cells, suggesting that SRGN may be involved in the proliferation of HUVECs. Furthermore, in the partial ligation of the carotid artery mice model, we observed that the expression of SRGN was significantly increased in atherosclerotic plaques induced by abnormal shear stress. Taken together, this study demonstrated that SRGN is a key gene in the response of ECs to WSS and could be involved in AS.

Mussel adhesive protein fused with VE-cadherin domain specifically triggers endothelial cell adhesion.

Endothelium is the only known completely non-thrombogenic material. In the present study, a strategy to mimic the adhesive interactions of endothelial cells (ECs) to alter the vascular microenvironment was established and applied to directing the behaviour of cells. To facilitate the regeneration of a functional endothelium in vascular lesions, we designed a recombinant mussel foot protein (Mfp-5) fused with the VE-cadherin extracellular domain EC1-2, termed VE-M. Surface coating analysis showed that recombinant VE-M successfully formed a coating on substrate materials with uniform nanorods, low roughness, and sufficient hydrophilicity. We then evaluated the effects of VE-M on the adhesion of ECs and the capture of endothelial progenitor cells (EPCs). The result demonstrated that VE-M efficiently promoted the adhesion of ECs and EPCs. The number of ECs and EPCs on VE-M was 5.5- and 1.8-fold higher, respectively, than that on bare 316L SS under static conditions, whereas there was no significant difference in the number of captured smooth muscle cells (SMCs) between VE-M and other substrates. In addition, the number of EPCs captured by VE-M was approximately four times higher than that captured by 316L SS under dynamic conditions. In particular, the result of the neutralization test indicated that VE-M specifically triggered ECs' adhesion via the interaction of VE-cadherin EC1-2. Further investigation showed that VE-M significantly increased the levels of endogenous VE-cadherin in HUVECs as well as the endothelial eNOS content, with little or no endothelial inflammation. Our results showed that VE-M could be a promising biomimetic modification for accelerating endothelialization and vascularization in tissue engineering.

[Clinical and experimental studies on five cases of acute myeloid leukemia with translocation t(16;21)(p11;q22)].

OBJECTIVE: To report five cases of acute myeloid leukemia (AML) with t(16;21)(p11;q22) translocation and the result of chromosome painting analysis on one of them. METHODS: Chromosome specimens were prepared by short-term culture of bone marrow cells. Karyotype analysis was made by R-banding technique. Chromosome painting was performed using whole chromosome probes 16 and 21 in 1 case. RESULTS: Karyotype analysis showed identical translocation t(16;21)(p11;q22) in all five cases, accounting for 0.3% of 1448 cases of acute myeoid leukemia examined in the past fifteen years. Moreover, chromosome painting distinctly demonstrated t(16;21) in one of them. Leukemia blasts did not show hemophagocytosis in all of them. CONCLUSION: t(16;21) translocation is a rare and recurring chromosome rearrangement. It represents a specific type of AML. Chromosome painting technique is a more reliable means for detecting it, compared with the conventional karyotype analysis.