An immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors.

Analysis of the human hematopoietic progenitor compartment is being transformed by single-cell multimodal approaches. Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) enables coupled surface protein and transcriptome profiling, thereby revealing genomic programs underlying progenitor states. To perform CITE-seq systematically on primary human bone marrow cells, we used titrations with 266 CITE-seq antibodies (antibody-derived tags) and machine learning to optimize a panel of 132 antibodies. Multimodal analysis resolved >80 stem, progenitor, immune, stromal and transitional cells defined by distinctive surface markers and transcriptomes. This dataset enables flow cytometry solutions for in silico-predicted cell states and identifies dozens of cell surface markers consistently detected across donors spanning race and sex. Finally, aligning annotations from this atlas, we nominate normal marrow equivalents for acute myeloid leukemia stem cell populations that differ in clinical response. This atlas serves as an advanced digital resource for hematopoietic progenitor analyses in human health and disease.

CellDrift: inferring perturbation responses in temporally sampled single-cell data.

Cells and tissues respond to perturbations in multiple ways that can be sensitively reflected in the alterations of gene expression. Current approaches to finding and quantifying the effects of perturbations on cell-level responses over time disregard the temporal consistency of identifiable gene programs. To leverage the occurrence of these patterns for perturbation analyses, we developed CellDrift (https://github.com/KANG-BIOINFO/CellDrift), a generalized linear model-based functional data analysis method that is capable of identifying covarying temporal patterns of various cell types in response to perturbations. As compared to several other approaches, CellDrift demonstrated superior performance in the identification of temporally varied perturbation patterns and the ability to impute missing time points. We applied CellDrift to multiple longitudinal datasets, including COVID-19 disease progression and gastrointestinal tract development, and demonstrated its ability to identify specific gene programs associated with sequential biological processes, trajectories and outcomes.

Genotype of dengue virus serotype 1 in relation to severe dengue in Guangzhou, China.

Guangzhou has been the city most affected by the dengue virus (DENV) in China, with a predominance of DENV serotype 1 (DENV-1). Viral factors such as dengue serotype and genotype are associated with severe dengue (SD). However, none of the studies have investigated the relationship between DENV-1 genotypes and SD. To understand the association between DENV-1 genotypes and SD, the clinical manifestations of patients infected with different genotypes were investigated. A total of 122 patients with confirmed DENV-1 genotype infection were recruited for this study. The clinical manifestations, laboratory tests, and levels of inflammatory mediator factors were statistically analyzed to investigate the characteristics of clinical manifestations and immune response on the DENV-1 genotype. In the case of DENV-1 infection, the incidence of SD with genotype V infection was significantly higher than that with genotype I infection. Meanwhile, patients infected with genotype V were more common in ostealgia and bleeding significantly. In addition, levels of inflammatory mediator factors including IFN-γ, TNF-α, IL-10, and soluble vascular cell adhesion molecule 1 were higher in patients with SD infected with genotype V. Meanwhile, the concentrations of regulated upon activation normal T-cell expressed and secreted and growth-related gene alpha were lower in patients with SD infected with genotype V. The higher incidence of SD in patients infected with DENV-1 genotype V may be attributed to elevated cytokines and adhesion molecules, along with decreased chemokines.

Robust Chemical Synthesis of "Difficult Peptides" via 2-Hydroxyphenol-pseudoproline (ψ2-hydroxyphenolpro) Modifications.

The challenging preparation of "difficult peptides" has always hindered the development of peptide-active pharmaceutical ingredients. Pseudoproline (ψpro) building blocks have been proven effective and powerful tools for the synthesis of "difficult peptides". In this paper, we efficiently prepared a set of novel 2-(oxazolidin-2-yl)phenol compounds as proline surrogates (2-hydroxyphenol-pseudoprolines, ψ2-hydroxyphenolpro) and applied it in the synthesis of many well-known "difficult peptides", including human thymosin α1, amylin, and ß-amyloid (1-42) (Aß42).

Synthesis and antimicrobial studies of cadasides analogues via on-resin esterification.

A series of cadasides analogues have been prepared via a combination of solid-phase peptide synthesis and solution-phase cyclization. Primary structure-activity relationship studies of cadasides have also been established and revealed the critical roles of unnatural amino acid residues, which will facilitate the further development of cadasides analogues with improved antimicrobial activities.

N6-methyladenosine (m6A) depletion regulates pluripotency exit by activating signaling pathways in embryonic stem cells.

N6-methyladenosine (m6A) deposition on messenger RNA (mRNA) controls embryonic stem cell (ESC) fate by regulating the mRNA stabilities of pluripotency and lineage transcription factors (TFs) [P. J. Batista et al., Cell Stem Cell 15, 707-719 (2014); Y. Wang et al., Nat. Cell Biol. 16, 191-198 (2014); and S. Geula et al., Science 347, 1002-1006 (2015)]. If the mRNAs of these two TF groups become stabilized, it remains unclear how the pluripotency or lineage commitment decision is implemented. We performed noninvasive quantification of Nanog and Oct4 TF protein levels in reporter ESCs to define cell-state dynamics at single-cell resolution. Long-term single-cell tracking shows that immediate m6A depletion by Mettl3 knock-down in serum/leukemia inhibitory factor supports both pluripotency maintenance and its departure. This is mediated by differential and opposing signaling pathways. Increased FGF5 mRNA stability activates pErk, leading to Nanog down-regulation. FGF5-mediated coactivation of pAkt reenforces Nanog expression. In formative stem cells poised toward differentiation, m6A depletion activates both pErk and pAkt, increasing the propensity for mesendodermal lineage induction. Stable m6A depletion by Mettl3 knock-out also promotes pErk activation. Higher pErk counteracts the pluripotency exit delay exhibited by stably m6A-depleted cells upon differentiation. At single-cell resolution, we illustrate that decreasing m6A abundances activates pErk and pAkt-signaling, regulating pluripotency departure.

Cross-platform validation of neurotransmitter release impairments in schizophrenia patient-derived NRXN1-mutant neurons.

Heterozygous NRXN1 deletions constitute the most prevalent currently known single-gene mutation associated with schizophrenia, and additionally predispose to multiple other neurodevelopmental disorders. Engineered heterozygous NRXN1 deletions impaired neurotransmitter release in human neurons, suggesting a synaptic pathophysiological mechanism. Utilizing this observation for drug discovery, however, requires confidence in its robustness and validity. Here, we describe a multicenter effort to test the generality of this pivotal observation, using independent analyses at two laboratories of patient-derived and newly engineered human neurons with heterozygous NRXN1 deletions. Using neurons transdifferentiated from induced pluripotent stem cells that were derived from schizophrenia patients carrying heterozygous NRXN1 deletions, we observed the same synaptic impairment as in engineered NRXN1-deficient neurons. This impairment manifested as a large decrease in spontaneous synaptic events, in evoked synaptic responses, and in synaptic paired-pulse depression. Nrxn1-deficient mouse neurons generated from embryonic stem cells by the same method as human neurons did not exhibit impaired neurotransmitter release, suggesting a human-specific phenotype. Human NRXN1 deletions produced a reproducible increase in the levels of CASK, an intracellular NRXN1-binding protein, and were associated with characteristic gene-expression changes. Thus, heterozygous NRXN1 deletions robustly impair synaptic function in human neurons regardless of genetic background, enabling future drug discovery efforts.

Function and structure of bradykinin receptor 2 for drug discovery.

Type 2 bradykinin receptor (B2R) is an essential G protein-coupled receptor (GPCR) that regulates the cardiovascular system as a vasodepressor. Dysfunction of B2R is also closely related to cancers and hereditary angioedema (HAE). Although several B2R agonists and antagonists have been developed, icatibant is the only B2R antagonist clinically used for treating HAE. The recently determined structures of B2R have provided molecular insights into the functions and regulation of B2R, which shed light on structure-based drug design for the treatment of B2R-related diseases. In this review, we summarize the structure and function of B2R in relation to drug discovery and discuss future research directions to elucidate the remaining unknown functions of B2R dimerization.

Spatiotemporal variability and environmental effects of greenhouse gases, nutrients, and dissolved carbons in an ice-covered reservoir.

Ice cover restructures the distribution of substances in ice and underlying water and poses non-negligible environmental effects. This study aimed to clarify the spatiotemporal variability and environmental effects of methane (CH4), nitrous oxide (N2O), total nitrogen (TN), total phosphorus (TP), dissolved organic carbon (DOC), and dissolved inorganic carbon (DIC) in ice and water columns during different ice-covered periods. We surveyed the ice-growth, ice-stability, and ice-melt periods in an ice-covered reservoir located in Northeast China. The results showed that underlying water (CH4: 1218.9 ± 2678.9 nmol L-1 and N2O: 19.3 ± 7.3 nmol L-1) and ice (CH4: 535.2 ± 2373.1 nmol L-1 and N2O: 9.9 ± 1.5 nmol L-1) were sources of atmospheric greenhouse gases. N2O concentrations were the highest in the bottom water of the reservoir while CH4 accumulated the most below the ice in the riverine zone. These can be attributed to differences in the solubilities and relative molecular masses of the two gases. Higher concentrations of N2O, TN, TP, DOC, and DIC were recorded in the underlying water than those in the ice due to the preferential redistribution of these substances in the aqueous phase during ice formation. Additionally, we distinguished between bubble and no-bubble areas in the riverine zone and found that the higher CH4 concentrations in the underlying water than those in the ice were due to CH4 bubbles. In addition, we reviewed various substances in ice-water systems and found that the substances in ice-water systems can be divided into solute exclusion and particle entrapment, which are attributed to differences between dissolved and particulate states. These findings are important for a comprehensive understanding of substances dynamics during ice-covered periods.

Objective Assessment of Visual Field Defects Caused by Optic Chiasm and Its Posterior Visual Pathway Injury.

OBJECTIVES: To investigate the characteristics and objective assessment method of visual field defects caused by optic chiasm and its posterior visual pathway injury. METHODS: Typical cases of visual field defects caused by injuries to the optic chiasm, optic tracts, optic radiations, and visual cortex were selected. Visual field examinations, visual evoked potential (VEP) and multifocal visual evolved potential (mfVEP) measurements, craniocerebral CT/MRI, and retinal optical coherence tomography (OCT) were performed, respectively, and the aforementioned visual electrophysiological and neuroimaging indicators were analyzed comprehensively. RESULTS: The electrophysiological manifestations of visual field defects caused by optic chiasm injuries were bitemporal hemianopsia mfVEP abnormalities. The visual field defects caused by optic tract, optic radiation, and visual cortex injuries were all manifested homonymous hemianopsia mfVEP abnormalities contralateral to the lesion. Mild relative afferent pupil disorder (RAPD) and characteristic optic nerve atrophy were observed in hemianopsia patients with optic tract injuries, but not in patients with optic radiation or visual cortex injuries. Neuroimaging could provide morphological evidence of damages to the optic chiasm and its posterior visual pathway. CONCLUSIONS: Visual field defects caused by optic chiasm, optic tract, optic radiation, and visual cortex injuries have their respective characteristics. The combined application of mfVEP and static visual field measurements, in combination with neuroimaging, can maximize the assessment of the location and degree of visual pathway damage, providing an effective scheme for the identification of such injuries.

LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung.

An improved understanding of the human lung necessitates advanced systems models informed by an ever-increasing repertoire of molecular omics, cellular, imaging, and pathological datasets. To centralize and standardize information across broad lung research efforts we expanded the LungMAP.net website into a new gateway portal. This portal connects a broad spectrum of research networks, bulk and single-cell multi-omics data and a diverse collection of image data that span mammalian lung development, and disease. The data are standardized across species and technologies using harmonized data and metadata models that leverage recent advances including those from the Human Cell Atlas, diverse ontologies, and the LungMAP CellCards initiative. To cultivate future discoveries, we have aggregated a diverse collection of single-cell atlases for multiple species (human, rhesus, mouse), to enable consistent queries across technologies, cohorts, age, disease, and drug treatment. These atlases are provided as independent and integrated queryable datasets, with an emphasis on dynamic visualization, figure generation, re-analysis, cell-type curation, and automated reference-based classification of user-provided single-cell genomics datasets (Azimuth). As this resource grows, we intend to increase the breadth of available interactive interfaces, supported data types, data portals and datasets from LungMAP and external research efforts.

Research and Prospect of Visual Event-Related Potential in Traumatic Brain Injury and Visual Function Evaluation.

Visual event-related potential (ERP) is an electrophysiological technique that objectively reflects the cognitive processing of stimulus from the perspective of detecting and recording neural electrophysiology responses using different paradigms of visual stimuli. Its endogenous components are closely related to advanced psychological activities. This article introduces the characteristics of main endogenous components including visual mismatch negativity (vMMN), N200 and P300, reviews the research progress of visual ERP in the sequelae of brain injury and objective evaluation of visual function, and prospects the application prospect of visual ERP in the field of forensic medicine.

Oleanolic acid regulates the Treg/Th17 imbalance in gastric cancer by targeting IL-6 with miR-98-5p.

BACKGROUND: Gastric cancer (GC) was a type of malignant tumor with a very high fatality rate. Oleanolic acid (OA) was a class of pentacyclic triterpenes which was proved to have anti-cancer activity. While the specific molecular mechanism of OA's role in inhibiting GC was not fully understood. This study aimed to explore how OA played an anti-cancer role in GC. METHODS: Expression of miR-98-5p was examined using qPCR, and expression levels of Treg/Th17-related factors were evaluated using qPCR and western blot. Flow cytometry was conducted to assess the proportion of Treg cells and Th17 cells. Besides, dual luciferase reporter assay was performed to verify that IL-6 was a target of miR-98-5p. RESULTS: Downregulation of miR-98-5p and upregulation of Treg/Th17-related factors were observed in GC tissues. What's more, the Treg/Th17 imbalance was found in PBMCs of GC patients. Overexpression of miR-98-5p promoted balance of Treg/Th17 cells via directly targeting IL-6 to downregulate expression of IL-6. Finally, OA could promote balance of Treg/Th17 cells by upregulating expression of miR-98-5p. DISCUSSION: All our results proved that OA could promote balance of Treg/Th17 cells in GC by targeting IL-6 with miR-98-5p, indicating a potential drug for treatment of GC.

A gold mine for drug discovery: Strategies to develop cyclic peptides into therapies.

As a versatile therapeutic modality, peptides attract much attention because of their great binding affinity, low toxicity, and the capability of targeting traditionally "undruggable" protein surfaces. However, the deficiency of cell permeability and metabolic stability always limits the success of in vitro bioactive peptides as drug candidates. Peptide macrocyclization is one of the most established strategies to overcome these limitations. Over the past decades, more than 40 cyclic peptide drugs have been clinically approved, the vast majority of which are derived from natural products. The de novo discovered cyclic peptides on the basis of rational design and in vitro evolution, have also enabled the binding with targets for which nature provides no solutions. The current review summarizes different classes of cyclic peptides with diverse biological activities, and presents an overview of various approaches to develop cyclic peptide-based drug candidates, drawing upon series of examples to illustrate each strategy.

Identification of Vaccinia-H1 Related Phosphatase as an Anticancer Target for 1,2,3,4,6-O-Pentagalloylglucose.

Protein tyrosine phosphatases are involved in diverse human diseases, including cancer, diabetes and inflammatory disorders. Loss of Vaccinia-H1 related phosphatase (VHR) has been shown to arrest at the G1-S and G2-M transitions of the cell cycle, and to increases cell death of prostate cancer cells through JNK activation, suggesting that VHR can be considered as an anticancer target. In this study, 658 natural products were screened through in vitro enzyme assay to identify VHR inhibitor. Among the VHR-inhibitory compounds, 1,2,3,4,6-O-pentagalloylglucose (PGG) was selected for further study as it has been reported to show antitumor effects against tumor model mice, but its direct target has not been identified. PGG inhibited the catalytic activity of VHR (Ki =53 nm) in vitro. Furthermore, the incubation of HeLa cervical cancer cells with PGG dramatically decreased cell viability and markedly increased the protein levels of the cleaved PARP, a hallmark of apoptosis. In addition, treatment of HeLa cells with PGG significantly reduced the protein levels of cyclin D1, Bcl-2 and STAT3 phosphorylation. Taken together, these results suggest that PGG could be a potential therapeutic candidate for the treatment of cervical cancer through VHR inhibition.

Genome-Wide Identification of the Expansin Gene Family and Its Potential Association with Drought Stress in Moso Bamboo.

Expansins, a group of cell wall-loosening proteins, are involved in cell-wall loosening and cell enlargement in a pH-dependent manner. According to previous study, they were involved in plant growth and abiotic stress responses. However, information on the biological function of the expansin gene in moso bamboo is still limited. In this study, we identified a total of 82 expansin genes in moso bamboo, clustered into four subfamilies (α-expansin (EXPA), ß-expansin (EXPB), expansin-like A (EXLA) and expansin-like B (EXPB)). Subsequently, the molecular structure, chromosomal location and phylogenetic relationship of the expansin genes of Phyllostachys edulis (PeEXs) were further characterized. A total of 14 pairs of tandem duplication genes and 31 pairs of segmented duplication genes were also identified, which may promote the expansion of the expansin gene family. Promoter analysis found many cis-acting elements related to growth and development and stress response, especially abscisic acid response element (ABRE). Expression pattern revealed that most PeEXs have tissue expression specificity. Meanwhile, the expression of some selected PeEXs was significantly upregulated mostly under abscisic acid (ABA) and polyethylene glycol (PEG) treatment, which implied that these genes actively respond to expression under abiotic stress. This study provided new insights into the structure, evolution and function prediction of the expansin gene family in moso bamboo.

Cysteine/Penicillamine Ligation Independent of Terminal Steric Demands for Chemical Protein Synthesis.

The chemical ligation of two unprotected peptides to generate a natural peptidic linkage specifically at the C- and N-termini is a desirable goal in chemical protein synthesis but is challenging because it demands high reactivity and selectivity (chemo-, regio-, and stereoselectivity). We report an operationally simple and highly effective chemical peptide ligation involving the ligation of peptides with C-terminal salicylaldehyde esters to peptides with N-terminal cysteine/penicillamine. The notable features of this method include its tolerance of steric hinderance from the side groups on either ligating terminus, thereby allowing flexible disconnection at sites that are otherwise difficult to functionalize. In addition, this method can be expanded to selective desulfurization and one-pot ligation-desulfurization reactions. The effectiveness of this method was demonstrated by the synthesis of VISTA (216-311), PD-1 (192-288) and Eglin C.

Predicted Arabidopsis Interactome Resource and Gene Set Linkage Analysis: A Transcriptomic Analysis Resource.

An advanced functional understanding of omics data is important for elucidating the design logic of physiological processes in plants and effectively controlling desired traits in plants. We present the latest versions of the Predicted Arabidopsis Interactome Resource (PAIR) and of the gene set linkage analysis (GSLA) tool, which enable the interpretation of an observed transcriptomic change (differentially expressed genes [DEGs]) in Arabidopsis (Arabidopsis thaliana) with respect to its functional impact for biological processes. PAIR version 5.0 integrates functional association data between genes in multiple forms and infers 335,301 putative functional interactions. GSLA relies on this high-confidence inferred functional association network to expand our perception of the functional impacts of an observed transcriptomic change. GSLA then interprets the biological significance of the observed DEGs using established biological concepts (annotation terms), describing not only the DEGs themselves but also their potential functional impacts. This unique analytical capability can help researchers gain deeper insights into their experimental results and highlight prospective directions for further investigation. We demonstrate the utility of GSLA with two case studies in which GSLA uncovered how molecular events may have caused physiological changes through their collective functional influence on biological processes. Furthermore, we showed that typical annotation-enrichment tools were unable to produce similar insights to PAIR/GSLA. The PAIR version 5.0-inferred interactome and GSLA Web tool both can be accessed at http://public.synergylab.cn/pair/.

Advances in Native Chemical Ligation-Desulfurization: A Powerful Strategy for Peptide and Protein Synthesis.

Cysteine-based native chemical ligation (NCL) has been a very powerful approach for convergent synthesis of peptides and proteins. However, owing to the low abundance of cysteine (Cys) in proteins, applications of NCL in protein chemical synthesis are limited. To expand the peptide ligation toolbox, NCL followed by desulfurization has been developed to enable peptide ligation at Xaa-Ala conjunctions, that is, formal "alanine ligation". In this regard, effective peptide desulfurization methods are critical. This Concept article summarizes the development of different desulfurization strategies for peptide and protein chemical synthesis.