Fast and flexible profiling of chromatin accessibility and total RNA expression in single nuclei using Microwell-seq3.

Single cell chromatin accessibility profiling and transcriptome sequencing are the most widely used technologies for single-cell genomics. Here, we present Microwell-seq3, a high-throughput and facile platform for high-sensitivity single-nucleus chromatin accessibility or full-length transcriptome profiling. The method combines a preindexing strategy and a penetrable chip-in-a-tube for single nucleus loading and DNA amplification and therefore does not require specialized equipment. We used Microwell-seq3 to profile chromatin accessibility in more than 200,000 single nuclei and the full-length transcriptome in ~50,000 nuclei from multiple adult mouse tissues. Compared with the existing polyadenylated transcript capture methods, integrative analysis of cell type-specific regulatory elements and total RNA expression uncovered comprehensive cell type heterogeneity in the brain. Gene regulatory networks based on chromatin accessibility profiling provided an improved cell type communication model. Finally, we demonstrated that Microwell-seq3 can identify malignant cells and their specific regulons in spontaneous lung tumors of aged mice. We envision a broad application of Microwell-seq3 in many areas of research.

Reactive oxygen species (ROS) scavenging biomaterials for anti-inflammatory diseases: from mechanism to therapy.

Inflammation is a fundamental defensive response to harmful stimuli, but the overactivation of inflammatory responses is associated with most human diseases. Reactive oxygen species (ROS) are a class of chemicals that are generated after the incomplete reduction of molecular oxygen. At moderate levels, ROS function as critical signaling molecules in the modulation of various physiological functions, including inflammatory responses. However, at excessive levels, ROS exert toxic effects and directly oxidize biological macromolecules, such as proteins, nucleic acids and lipids, further exacerbating the development of inflammatory responses and causing various inflammatory diseases. Therefore, designing and manufacturing biomaterials that scavenge ROS has emerged an important approach for restoring ROS homeostasis, limiting inflammatory responses and protecting the host against damage. This review systematically outlines the dynamic balance of ROS production and clearance under physiological conditions. We focus on the mechanisms by which ROS regulate cell signaling proteins and how these cell signaling proteins further affect inflammation. Furthermore, we discuss the use of potential and currently available-biomaterials that scavenge ROS, including agents that were engineered to reduce ROS levels by blocking ROS generation, directly chemically reacting with ROS, or catalytically accelerating ROS clearance, in the treatment of inflammatory diseases. Finally, we evaluate the challenges and prospects for the controlled production and material design of ROS scavenging biomaterials.

Genome-wide analysis of WD40 protein family and functional characterization of BvWD40-82 in sugar beet.

Sugar beet is one of the most important sugar crops in the world. It contributes greatly to the global sugar production, but salt stress negatively affects the crop yield. WD40 proteins play important roles in plant growth and response to abiotic stresses through their involvement in a variety of biological processes, such as signal transduction, histone modification, ubiquitination, and RNA processing. The WD40 protein family has been well-studied in Arabidopsis thaliana, rice and other plants, but the systematic analysis of the sugar beet WD40 proteins has not been reported. In this study, a total of 177 BvWD40 proteins were identified from the sugar beet genome, and their evolutionary characteristics, protein structure, gene structure, protein interaction network and gene ontology were systematically analyzed to understand their evolution and function. Meanwhile, the expression patterns of BvWD40s under salt stress were characterized, and a BvWD40-82 gene was hypothesized as a salt-tolerant candidate gene. Its function was further characterized using molecular and genetic methods. The result showed that BvWD40-82 enhanced salt stress tolerance in transgenic Arabidopsis seedlings by increasing the contents of osmolytes and antioxidant enzyme activities, maintaining intracellular ion homeostasis and increasing the expression of genes related to SOS and ABA pathways. The result has laid a foundation for further mechanistic study of the BvWD40 genes in sugar beet tolerance to salt stress, and it may inform biotechnological applications in improving crop stress resilience.

Metabolic reprogramming in cancer: Mechanisms and therapeutics.

Cancer cells characterized by uncontrolled growth and proliferation require altered metabolic processes to maintain this characteristic. Metabolic reprogramming is a process mediated by various factors, including oncogenes, tumor suppressor genes, changes in growth factors, and tumor-host cell interactions, which help to meet the needs of cancer cell anabolism and promote tumor development. Metabolic reprogramming in tumor cells is dynamically variable, depending on the tumor type and microenvironment, and reprogramming involves multiple metabolic pathways. These metabolic pathways have complex mechanisms and involve the coordination of various signaling molecules, proteins, and enzymes, which increases the resistance of tumor cells to traditional antitumor therapies. With the development of cancer therapies, metabolic reprogramming has been recognized as a new therapeutic target for metabolic changes in tumor cells. Therefore, understanding how multiple metabolic pathways in cancer cells change can provide a reference for the development of new therapies for tumor treatment. Here, we systemically reviewed the metabolic changes and their alteration factors, together with the current tumor regulation treatments and other possible treatments that are still under investigation. Continuous efforts are needed to further explore the mechanism of cancer metabolism reprogramming and corresponding metabolic treatments.

Ellagic Acid-Cyclodextrin Inclusion Complex-Loaded Thiol-Ene Hydrogel with Antioxidant, Antibacterial, and Anti-inflammatory Properties for Wound Healing.

Hydrogel dressings not only have basic functions such as swelling, water retention, gas permeability, and good biocompatibility but also can be endowed with advanced functions such as antibacterial, antioxidant, adhesion, hemostasis, and anti-inflammation, which make hydrogels have great application potential in clinical trauma. However, the complexity of the wound healing process makes the development of multifunctional wound dressings a great challenge. In this work, based on the thiol-ene photoclickable PEG hydrogel, the inclusion complex of the hydrophobic drug ellagic acid (EA) with mono-(6-mercapto-6-deoxy)-ß-cyclodextrin (SH-ß-CD) participated in the formation of a hydrogel as a crosslinker. The drug EA with antioxidant, antibacterial, and anti-inflammatory activities was introduced into the hydrogel. This strategy increases the loading capacity of the hydrogel for EA and endows the hydrogel with multifunctional properties. Then, dithiothreitol was added to adjust the mechanical stiffness of the hydrogel to meet the requirements of the wound dressing. Our results demonstrated that this wound dressing has excellent cytocompatibility, antioxidant, antibacterial, and anti-inflammatory activities. Furthermore, the results of the infected wound healing model experiment in rats confirmed that the hydrogel has the ability to rapidly shrink the wound area, prevent wound infection, and promote angiogenesis and collagen deposition. All these results suggest that this hydrogel could be a candidate for the treatment of infected wounds and shed new light on the development of multifunctional wound dressings.

Changes in Maternal Serum Levels of C3 and C4 Complement Components in Different Delivery Methods and Postpartum Hemorrhage.

BACKGROUND: Activation of the complement system may play a role in the pathophysiology of human labor. Yet no unanimous conclusion has been drawn. OBJECTIVE: To compare the differences in maternal complement components C3 and C4 serum levels in cesarean section and the vaginal delivery at term and in the postpartum hemorrhage. METHODS: One hundred and sixty six women delivered at term were enrolled in this study. Maternal blood samples were obtained from 47 cases of elective cesarean section and 119 cases of the vaginal delivery. Serum complement levels were measured subsequently by immuno-scatter turbidimetry. RESULTS: The maternal complement levels declined significantly during delivery by both the cesarean section and the vaginal delivery (p＜0.01) in comparison with the baseline. A much larger drop of C3 serum level was found in the postpartum hemorrhage and in the vaginal delivery, and the incidence of the postpartum hemorrhage has a positive correlation with the complement decline rate. CONCLUSION: The complement system may be involved in the delivery process and represents a predictive value in postpartum hemorrhage.

Ketogenic diet may be a new approach to treatment stress urinary incontinence in obese elderly women: report of five cases.

BACKGROUND: Stress urinary incontinence (SUI) as a serious social problem restricted women's daily life and affect their quality of life, especially for obese women. The mechanism of stress urinary incontinence is unclear. Weight loss is the first line of treatment for stress incontinence in obese women. Ketogenic diet is a special diet with high fat, low carbohydrate and moderate protein, which can reduce body mass faster than the traditional diet. There exist no reports on the therapeutic effect of ketogenic diet on SUI in obese women. CASE PRESENTATION: Five postmenopausal obese women are diagnosed as mild to moderate stress urinary incontinence, which affected their quality of life for medical treatment. After 4 weeks ketogenic diet, we found that ketogenic diet can significantly improve urine leakage, reduce body weight, decrease visceral fat area, reduce body fat percentage, and reduce BMI. CONCLUSION: Reports in this case reveal that ketogenic diet may become one of the effective methods for the treatment of stress urinary incontinence in obese women in the future, providing a minimally invasive, highly profitable and highly compliant treatment for stress urinary incontinence in obese women.

Systematic identification of cell-fate regulatory programs using a single-cell atlas of mouse development.

Waddington's epigenetic landscape is a metaphor frequently used to illustrate cell differentiation. Recent advances in single-cell genomics are altering our understanding of the Waddington landscape, yet the molecular mechanisms of cell-fate decisions remain poorly understood. We constructed a cell landscape of mouse lineage differentiation during development at the single-cell level and described both lineage-common and lineage-specific regulatory programs during cell-type maturation. We also found lineage-common regulatory programs that are broadly active during the development of invertebrates and vertebrates. In particular, we identified Xbp1 as an evolutionarily conserved regulator of cell-fate determinations across different species. We demonstrated that Xbp1 transcriptional regulation is important for the stabilization of the gene-regulatory networks for a wide range of mouse cell types. Our results offer genetic and molecular insights into cellular gene-regulatory programs and will serve as a basis for further advancing the understanding of cell-fate decisions.

C. acnes qPCR-Based Antibiotics Resistance Assay (ACQUIRE) Reveals Widespread Macrolide Resistance in Acne Patients and Can Eliminate Macrolide Misuse in Acne Treatment.

Background: Macrolides have been widely used to treat moderate-to-severe acne for more than 50 years. However, the prevalent antibiotic resistance of Propionibacterium acnes, along with the absence of clinically available resistance tests, has made macrolide misuse a frequent occurrence around the globe, with serious consequences. Objective: We developed Cutibacterium acnes quantitative PCR (qPCR)-based antibiotics resistance assay (ACQUIRE) to enable fast and accurate detection of C. acnes macrolide resistance in clinical settings, representing an opportunity to administer antibiotics more wisely and improve the quality of care. Methods: A cross-sectional observational study (n = 915) was conducted to probe into the macrolide resistance of C. acnes in patients with acne. Results: The high sensitivity of ACQUIRE enabled us to reveal a much higher C. acnes 23S recombinant DNA (rDNA) point mutation rate (52%) and thus a higher macrolide resistance (75.5%) compared to previous reports. Carriage of ermX gene was discovered on 472 (53%) subjects, which concurs with previous studies. Conclusion: The macrolide resistance of C. acnes is much higher than previously reported. Integrating ACQUIRE into acne treatment modalities may eliminate macrolide misuse and achieve better clinical improvements.

Cys-SH based quantitative redox proteomics of salt induced response in sugar beet monosomic addition line M14.

BACKGROUND: Salt stress is a major abiotic stress that limits plant growth, development and productivity. Studying the molecular mechanisms of salt stress tolerance may help to enhance crop productivity. Sugar beet monosomic addition line M14 exhibits tolerance to salt stress. RESULTS: In this work, the changes in the BvM14 proteome and redox proteome induced by salt stress were analyzed using a multiplex iodoTMTRAQ double labeling quantitative proteomics approach. A total of 80 proteins were differentially expressed under salt stress. Interestingly, A total of 48 redoxed peptides were identified for 42 potential redox-regulated proteins showed differential redox change under salt stress. A large proportion of the redox proteins were involved in photosynthesis, ROS homeostasis and other pathways. For example, ribulose bisphosphate carboxylase/oxygenase activase changed in its redox state after salt treatments. In addition, three redox proteins involved in regulation of ROS homeostasis were also changed in redox states. Transcription levels of eighteen differential proteins and redox proteins were profiled. (The proteomics data generated in this study have been submitted to the ProteomeXchange and can be accessed via username: reviewer_pxd027550@ebi.ac.uk, password: q9YNM1Pe and proteomeXchange# PXD027550.) CONCLUSIONS: The results showed involvement of protein redox modifications in BvM14 salt stress response and revealed the short-term salt responsive mechanisms. The knowledge may inform marker-based breeding effort of sugar beet and other crops for stress resilience and high yield.

A single-cell survey of cellular hierarchy in acute myeloid leukemia.

BACKGROUND: Acute myeloid leukemia (AML) is a fatal hematopoietic malignancy and has a prognosis that varies with its genetic complexity. However, there has been no appropriate integrative analysis on the hierarchy of different AML subtypes. METHODS: Using Microwell-seq, a high-throughput single-cell mRNA sequencing platform, we analyzed the cellular hierarchy of bone marrow samples from 40 patients and 3 healthy donors. We also used single-cell single-molecule real-time (SMRT) sequencing to investigate the clonal heterogeneity of AML cells. RESULTS: From the integrative analysis of 191727 AML cells, we established a single-cell AML landscape and identified an AML progenitor cell cluster with novel AML markers. Patients with ribosomal protein high progenitor cells had a low remission rate. We deduced two types of AML with diverse clinical outcomes. We traced mitochondrial mutations in the AML landscape by combining Microwell-seq with SMRT sequencing. We propose the existence of a phenotypic "cancer attractor" that might help to define a common phenotype for AML progenitor cells. Finally, we explored the potential drug targets by making comparisons between the AML landscape and the Human Cell Landscape. CONCLUSIONS: We identified a key AML progenitor cell cluster. A high ribosomal protein gene level indicates the poor prognosis. We deduced two types of AML and explored the potential drug targets. Our results suggest the existence of a cancer attractor.

Effects of exposure to anionic surfactants (SDBS and SDS) on nitrogen removal of aerobic denitrifier.

In order to explain the effect of anionic surfactants on aerobic denitrification in the urban river, sodium dodecyl benzene sulfonate (SDBS) and sodium dodecyl sulfonate (SDS) were added in aerobic denitrifier and the efficiency of nitrogen removal, microbial mechanisms, and enzyme activity was investigated in this study. The results showed that the total nitrogen (TN) and the nitrate nitrogen ( NO 3 - - N ) removal efficiency decreased as an increase of SDBS concentration. In contrast, 59.70% of the TN and 75.12% of NO 3 - - N were removed as the SDBS was 0 mg/L (Control). When SDBS was 200 mg/L (SDBS-200), the removal efficiency of TN and NO 3 - - N was reduced to 4.92% and 4.00%, respectively. However, the denitrification efficiency was significantly accelerated when the concentration of SDS increased, except for 200 mg/L treatment (SDS-200). As the SDS increased from 0 to 100 mg/L (SDS-100), the removal efficiency of TN and NO 3 - - N raised from 59.70% to 70.8% and from 75.12% to 85.08%, respectively. The community structure of aerobic denitrifiers was significantly affected in the SDBS and SDS. While the Cupriavidus and Achromobacter were dominant genera in the group of Control (39.59%, and 42.45%) and SDS-100 (44.40% and 34.86%), the relative abundance of Cupriavidus increased to 84.06% and 59.45% in the group of SDBS-200 and SDS-200, respectively. Enzyme activity assays proved that the nitrite reductase (NiR) relative activity of aerobic denitrification was suppressed by both SDBS and SDS. The increase in the SDS concentrations (from 0 to 50 mg/L) resulted in sharp growth of the nitrate reductase (NR) relative activities (from 100% to 146.86%). These findings demonstrated that SDBS and SDS affected aerobic denitrification efficiency of the aerobic denitrifiers by changing its microbial community structure and enzyme activity. PRACTITIONER POINTS: SDS strengthened aerobic denitrification at low concentration, but the aerobic denitrifiers were inhibited in SDBS. The variation of community structure played a vital role in the aerobic denitrification system. The enzyme activity was seriously affected by SDBS and SDS. Microorganisms and enzyme activity were synergistically involved in the aerobic denitrification.

Construction of a human cell landscape at single-cell level.

Single-cell analysis is a valuable tool for dissecting cellular heterogeneity in complex systems1. However, a comprehensive single-cell atlas has not been achieved for humans. Here we use single-cell mRNA sequencing to determine the cell-type composition of all major human organs and construct a scheme for the human cell landscape (HCL). We have uncovered a single-cell hierarchy for many tissues that have not been well characterized. We established a 'single-cell HCL analysis' pipeline that helps to define human cell identity. Finally, we performed a single-cell comparative analysis of landscapes from human and mouse to identify conserved genetic networks. We found that stem and progenitor cells exhibit strong transcriptomic stochasticity, whereas differentiated cells are more distinct. Our results provide a useful resource for the study of human biology.

Maintenance of human haematopoietic stem and progenitor cells in vitro using a chemical cocktail.

Identification of effective culture conditions to maintain and possibly expand human HSPCs in vitro is an important goal. Recent advances highlight the efficacy of chemicals in maintaining and converting cell fates. We screened 186 chemicals and found that a combination of CHIR-99021, Forskolin and OAC1 (CFO) maintained human CD34-positive cells in vitro. Efficiency of the culture system was characterized using flow cytometry for CD34-positive cells, a colony-forming assay and xeno-transplants. We found that human CD34-positive cells treated with this combination had enhanced expression of human HSPC markers and increased haematopoietic re-populating ability in immune-deficient mice. Single-cell RNA-seq analyses showed that the in vitro cultured human CD34-positive cells were heterogeneous. We found that CFO supports maintenance of human CD34-positive cells by activating HOXA9, GATA2 and AKT-cAMP signaling pathway. These data have implications in therapies requiring maintenance and/or expansion of human HSPCs.

Effects of ovarian reserve and hormone therapy on hearing in premenopausal and postmenopausal women: A cross-sectional study.

OBJECTIVES: To observe the hearing function around menopause, to analyze the effects of ovarian reserve and hormone therapy on hearing, and to study factors related to hearing loss among women around menopause. STUDY DESIGN: In this cross-sectional study, we evaluated 109 women around menopause aged 45-55 years, including 40 women with ovarian failure, 48 with ovarian non-failure, and 21 receiving hormone therapy. All women underwent an audiologic evaluation, and hormone blood testing was performed. The general condition, reproductive history, medical history, lifestyle, and menopausal symptoms were collected through a questionnaire. MAIN OUTCOME MEASURE: The auditory threshold and anti-Mullerian hormone level. RESULTS: Women in the ovarian failure group presented with a decreased hearing level in all frequency bands compared with those in the ovarian non-failure group; the significant differences occurred at 8000 Hz, 10 000 Hz, 12 500 Hz, and 16 000 Hz in the right-ear air conduction. The auditory threshold was lower in the hormone therapy group than in the ovarian failure group, but the difference was statistically significant only in the right-ear air conduction at 10 000 Hz. There were two risk factors for hearing loss: an anti-Mullerian hormone level <0.01 ng/mL (odds ratio [OR] = 2.624) and frequent earphone use (OR = 3.846). CONCLUSIONS: A decline in ovarian function is associated with hearing loss in women, especially in relation to extended high-frequency air conduction of the right ear. Preserving ovarian function and reducing earphone use are important measures to protect women's hearing. However, the effect of hormone therapy on hearing requires further investigation.

CRL4 antagonizes SCFFbxo7-mediated turnover of cereblon and BK channel to regulate learning and memory.

Intellectual disability (ID), one of the most common human developmental disorders, can be caused by genetic mutations in Cullin 4B (Cul4B) and cereblon (CRBN). CRBN is a substrate receptor for the Cul4A/B-DDB1 ubiquitin ligase (CRL4) and can target voltage- and calcium-activated BK channel for ER retention. Here we report that ID-associated CRL4CRBN mutations abolish the interaction of the BK channel with CRL4, and redirect the BK channel to the SCFFbxo7 ubiquitin ligase for proteasomal degradation. Glioma cell lines harbouring CRBN mutations record density-dependent decrease of BK currents, which can be restored by blocking Cullin ubiquitin ligase activity. Importantly, mice with neuron-specific deletion of DDB1 or CRBN express reduced BK protein levels in the brain, and exhibit similar impairment in learning and memory, a deficit that can be partially rescued by activating the BK channel. Our results reveal a competitive targeting of the BK channel by two ubiquitin ligases to achieve exquisite control of its stability, and support changes in neuronal excitability as a common pathogenic mechanism underlying CRL4CRBN-associated ID.

CRL4DCAF8 Ubiquitin Ligase Targets Histone H3K79 and Promotes H3K9 Methylation in the Liver.

Transcription from chromosomes is regulated by posttranslational modifications to histones, such as methylation and ubiquitination. Monoubiquitination of histones H2A and H2B influences H3 methylation to reinforce the activation or repression of gene expression. Here, we provide evidence that H3 polyubiquitination represses transcription of fetal and cell-cycle genes in postnatal mouse liver by crosstalk with H3K9 methylation. We found that the CRL4 ubiquitin ligase targets H3 for polyubiquitination at K79 via the DCAF8 substrate receptor in hepatocytes. Genetic inactivation of DCAF8 and overexpression of an H3K79 mutant in cells or inducible deletion of CRL4 in mouse liver abrogates H3 ubiquitination, reactivates the expression of fetal liver and cell-cycle genes by interfering with methylated H3K9 occupancy, and leads to cell senescence. Restoring CRL4DCAF8 expression in cells with decreased H3 ubiquitination reinstates the epigenetic gene silencing. Our results suggest that progressive H3 ubiquitination plays an important role in postnatal liver maturation.