COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas.

A dysfunctional immune response in coronavirus disease 2019 (COVID-19) patients is a recurrent theme impacting symptoms and mortality, yet a detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 196 COVID-19 patients and controls and created a comprehensive immune landscape with 1.46 million cells. The large dataset enabled us to identify that different peripheral immune subtype changes are associated with distinct clinical features, including age, sex, severity, and disease stages of COVID-19. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was found in diverse epithelial and immune cell types, accompanied by dramatic transcriptomic changes within virus-positive cells. Systemic upregulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis of and developing effective therapeutic strategies for COVID-19.

Comparative single-cell RNA sequencing analysis of immune response to inactivated vaccine and natural SARS-CoV-2 infection.

Uncovering the immune response to an inactivated SARS-CoV-2 vaccine (In-Vac) and natural infection is crucial for comprehending COVID-19 immunology. Here we conducted an integrated analysis of single-cell RNA sequencing (scRNA-seq) data from serial peripheral blood mononuclear cell (PBMC) samples derived from 12 individuals receiving In-Vac compared with those from COVID-19 patients. Our study reveals that In-Vac induces subtle immunological changes in PBMC, including cell proportions and transcriptomes, compared with profound changes for natural infection. In-Vac modestly upregulates IFN-α but downregulates NF-κB pathways, while natural infection triggers hyperactive IFN-α and NF-κB pathways. Both In-Vac and natural infection alter T/B cell receptor repertoires, but COVID-19 has more significant change in preferential VJ gene, indicating a vigorous immune response. Our study reveals distinct patterns of cellular communications, including a selective activation of IL-15RA/IL-15 receptor pathway after In-Vac boost, suggesting its potential role in enhancing In-Vac-induced immunity. Collectively, our study illuminates multifaceted immune responses to In-Vac and natural infection, providing insights for optimizing SARS-CoV-2 vaccine efficacy.

Development of predictive models for pathological response status in breast cancer after neoadjuvant therapy based on peripheral blood inflammatory indexes.

BACKGROUND: Achieving a pathological complete response (pCR) after neoadjuvant therapy (NAT) is considered to be a critical factor for a favourable prognosis in breast cancer. However, discordant pathological complete response (DpCR), characterised by isolated responses in the breast or axillary, represents an intermediate pathological response category between no response and complete response. This study aims to investigate predictive factors and develop models based on peripheral blood inflammatory indexes to more accurately predict NAT outcomes. METHOD: A total of 789 eligible patients were enrolled in this retrospective study. The patients were randomized into training and validation cohort according to a 7:3 ratio. Lasso and uni/multivariable logistic regression analysis were applied to identify the predictor variables. Two Nomograms combining clinico-pathologic features and peripheral blood inflammatory indexes were developed. RESULT: Molecular Subtype, HALP, P53, and FAR were used to construct the predictive models for traditional non pCR (T-NpCR) and total-pCR (TpCR). The T-NpCR group was divided into DpCR and non pCR (NpCR) subgroups to construct a new model to more accurately predict NAT outcomes. cN, HALP, FAR, Molecular Subtype, and RMC were used to construct the predictive models for NpCR and DpCR. The receiver operating characteristic (ROC) curves indicate that the model exhibits robust predictive capacity. Clinical Impact Curves (CIC) and Decision Curve Analysis (DCA) indicate that the models present a superior clinical utility. CONCLUSION: HALP and FAR were identified as peripheral blood inflammatory index predictors for accurately predicting NAT outcomes.

Population genomics reveals moderate genetic differentiation between populations of endangered Forest Musk Deer located in Shaanxi and Sichuan.

BACKGROUND: Many endangered species exist in small, genetically depauperate, or inbred populations, hence promoting genetic differentiation and reducing long-term population viability. Forest Musk Deer (Moschus berezovskii) has been subject to illegal hunting for hundreds of years due to the medical and commercial values of musk, resulting in a significant decline in population size. However, it is still unclear to what extent the genetic exchange and inbreeding levels are between geographically isolated populations. By using whole-genome data, we reconstructed the demographic history, evaluated genetic diversity, and characterized the population genetic structure of Forest Musk Deer from one wild population in Sichuan Province and two captive populations from two ex-situ centers in Shaanxi Province. RESULTS: SNP calling by GATK resulted in a total of 44,008,662 SNPs. Principal component analysis (PCA), phylogenetic tree (NJ tree), ancestral component analysis (ADMIXTURE) and the ABBA-BABA test separated Sichuan and Shaanxi Forest Musk Deer as two genetic clusters, but no obvious genetic differentiation was observed between the two captive populations. The average pairwise FST value between the populations in Sichuan and Shaanxi ranged from 0.05-0.07, suggesting a low to moderate genetic differentiation. The mean heterozygous SNPs rate was 0.14% (0.11%-0.15%) for Forest Musk Deer at the genomic scale, and varied significantly among three populations (Chi-square = 1.22, p < 0.05, Kruskal-Wallis Test), with the Sichuan population having the lowest (0.11%). The nucleotide diversity of three populations varied significantly (p < 0.05, Kruskal-Wallis Test), with the Sichuan population having the lowest genetic θπ (1.69 × 10-3). CONCLUSIONS: Genetic diversity of Forest Musk Deer was moderate at the genomic scale compared with other endangered species. Genetic differentiation between populations in Sichuan and Shaanxi may not only result from historical biogeographical factors but also be associated with contemporary human disturbances. Our findings provide scientific aid for the conservation and management of Forest Musk Deer. They can extend the proposed measures at the genomic level to apply to other musk deer species worldwide.

Factors associated with treatment response to CD19 CAR-T therapy among a large cohort of B cell acute lymphoblastic leukemia.

CD19-targeted chimeric antigen receptor (CAR) T cell therapy has demonstrated striking responses among B cell acute lymphoblastic leukemia (B-ALL), but analyses of potential factors associated with poor response and relapse are lacking. Here, we summarize the long-term follow-up of 254 B-ALL treated with CD19 CAR-T cells from 5 clinical trials (NCT03173417, NCT02546739, and NCT03671460 retrospectively registered on May 23, 2017, March 1, 2018, and September 7, 2018, respectively, at www.clinicaltrials.gov ; ChiCTR-ONC-17012829, and ChiCTR1800016541 retrospectively registered on September 28, 2017, and June 7, 2018, at www.chictr.org.cn ). Our data showed that TP53 mutation, bone marrow blasts > 20%, prior CAR-T/blinatumomab treatment, and severe cytokine release syndrome (CRS) were associated with a lower complete remission (CR) rate while age, extramedullary disease, complex cytogenetics, history of prior transplant, prior courses of chemotherapy, CAR-T cell dose, and manufacturing source of the cellular product did not affect patients' CR rate. Risk factors related to leukemia-free survival (LFS) and overall survival (OS) were history of prior transplant, complex cytogenetics, TP53 mutation, severe CRS, neurotoxicity, and CAR-T therapy without consolidative allogeneic hematopoietic stem cell transplantation (allo-HSCT). Age and CAR-T cell dose did not influence LFS and OS. Patients with consolidative allo-HSCT after CAR-T therapy had a superior OS and LFS compared to those who did not. This benefit was also observed in both pediatric and adult patients as well as in patients either in high- or low-risk groups. This large study to identify risk factors of CR, LFS, and OS may help to maximize clinical outcomes of CAR-T therapy. Précis TP53 mutation and BM blasts > 20% are two independent factors associated with the CR rate. Patients with high tumor burden as well as those with bone marrow blasts < 5% can benefit from consolidative allo-HSCT post-CAR-T therapy.

Regulatory Roles of Peroxisomal Metabolic Pathways Involved in Musk Secretion in Muskrats.

In this study, we analyzed the main components of muskrat musk by gas chromatography-mass spectrometry, the results showed that muskrat musk contained fatty acids (29.32%), esters (31.89%), cholesterol (4.38%), cyclic ketones (16.31%), alcohols (6.42%) and other compounds, among which 9-octadecenoic acid accounted for 4.89%. We also analyzed the genes of the metabolic pathway in the scent gland at the transcriptomic level during musk-secreting and non-secreting seasons by RNA-seq (RNA sequencing). We detected 21 genes in the peroxisomal metabolic pathways, including PEX14(peroxin-14) and ACOX3(acyl-CoA oxidase), which exhibited significant differential expression between the musk-secreting season and the non-secreting season (p < 0.05). The RNA-seq results for these genes were validated by reverse transcription PCR(RT-PCR) for both seasons. In addition, we examined changes in the composition of muskrat musk from the glandular cells of scent glands cultured in vitro after RNA interference-mediated silencing of 2 differentially expressed genes, ACOX3 and HSD17B4(D-bifunctional protein, DBP). The 9-Octadecenoic acid content in muskrat musk decreased significantly following the silencing of ACOX3 and HSD17B4(D-bifunctional protein, DBP). These results suggest that peroxisomal metabolic pathways play important roles in the regulation of musk secretion in scent glands in the muskrat.

Sex hormones play roles in determining musk composition during the early stages of musk secretion by musk deer (Moschus berezovskii).

Musk is a secreted external hormone or information compound that is stored in musk scent glands of the males of species within the family Moschidae, such as Moschus berezovskii. The secretion of musk changes periodically during the courtship and reproduction periods, with the early stage of secretion occurring from May to July, and the maturation stage occurring from August to April of the following year. In this study, we analyzed the dynamic changes in musk components from June to April of the following year. The result showed that musk morphological character, water content, total ion chromatographic pattern, and composition undergo seasonal change. Luminescence immunoassay and radioimmunoassay analyses were performed to determine corresponding fecal hormone levels. The results showed that testosterone, estrogen, and cortisol levels in feces change on a seasonal basis, and are significantly higher in June than in other months (p < 0.01). Correlation analysis showed that the contents of four examined musk components (muscone, cyclopentadecanone, cholesterol, and cholestenol) from June to August were significantly highly negatively correlated with fecal testosterone and estradiol levels (p < 0.01). In contrast, the correlation coefficients were low or not significant from August to April of the following year. These results indicate that testosterone and estradiol may play a major role in determining musk composition during the early stage of musk secretion but not during the course of musk maturation, which suggests that musk secretion may be promoted by increases in sex hormones in June.

Musk gland seasonal development and musk secretion are regulated by the testis in muskrat (Ondatra zibethicus).

BACKGROUND: The muskrat is a seasonal breeder. Males secrete musk to attract females during the breeding season. The testosterone binding to the androgen receptor (AR) in musk glands of muskrat may play an important role conducting the musk secretion process. METHODS: The musk gland, testis and blood samples of musk rats are collected in both breeding and non-breeding seasons. Some part of the samples are kept in liquid nitrogen for transcriptome analysis and Western blotting test. Some part of the samples are kept in 70% alcohol for histology experiment, blood samples are kept at -20 °C for the serum testosterone measurement experiment. RESULTS: This study demonstrates that the quantity of secreted musk, the volume of the musk glands, the diameter of the gland cells and AR expression are all higher during the breeding season than at other times (p < 0.01). StAR, P450scc and 3ß-HSD expression in the Leydig cells of the testis were also higher during this season, as was serum testosterone. AR was also observed in the gland cells of two other musk-secreting animals, the musk deer and small Indian civet, in their musk glands. These results suggest that the testes and musk glands co-develop seasonally. CONCLUSION: The musk glands' seasonal development and musk secretion are regulated by the testes, and testosterone plays an important role in the seasonal development of musk glands.

Adiponectin plays a role in energy metabolism for musk secretion in scent glands of muskrats (Ondatra zibethicus).

Adult male muskrats (Ondatra zibethicus) secret musk from their scent glands to attract females for seasonal mating. The goal of the present study was to investigate whether the changes in energy metabolism related to musk secretion during the breeding and non-breeding seasons are mediated by adiponectin. We found that the secretion of musk during the breeding season was markedly greater than that during the non-breeding season. The serum adiponectin concentration measured using an ELISA kit was higher during the breeding season than during the non-breeding season. Glandular cells, interstitial cells, epithelial cells and glandular cavities were detected in scent glands using histological methods. Immunohistochemical methods were used to show that AMP-activated protein kinase-gamma-1 (AMPKG1), and glucose transporter 1 (GLUT1) were more strongly expressed in glandular cells during the breeding season than the non-breeding season, whereas the immunoreactivity for acetyl-CoA carboxylase 1 (ACC1) was stronger during the non-breeding season. Consistent with these qualitative results, RNA-Seq analysis indicated that the expression of AdipoR1 mRNA was not significantly different during the two seasons. However, AMPKG1 and GLUT1 mRNA levels were higher in scent glands during the breeding season than during the non-breeding season, whereas ACC1 mRNA levels notably decreased during the breeding season. These results suggest that greater musk secretion requires additional energy, which may be provided by an adiponectin-mediated increase in ß-oxidation and glucose absorption.

Pinelliae rhizoma, a toxic chinese herb, can significantly inhibit CYP3A activity in rats.

Raw Pinelliae Rhizoma (RPR) is a representative toxic herb that is widely used for eliminating phlegm or treating cough and vomiting. Given its irritant toxicity, its processed products, including Pinelliae Rhizoma Praeparatum (PRP) and Pinelliae Rhizoma Praeparatum cum Zingibere et Alumine (PRPZA), are more commonly applied and administered concomitantly with other chemical drugs, such as cough medications. This study aimed to investigate the effects of RPR, PRP, and PRPZA on CYP3A activity. Testosterone (Tes) and buspirone (BP) were used as specific probe substrates ex vivo and in vivo, respectively. CYP3A activity was determined by the metabolite formation ratios from the substrates. Ex vivo results show that the metabolite formation ratios from Tes significantly decreased, indicating that RPR, PRP, and PRPZA could inhibit CYP3A activity in rats. CYP3A protein and mRNA levels were determined to explore the underlying mechanism. These levels showed marked and consistent down-regulation with CYP3A activity. A significant decrease in metabolite formation ratios from BP was also found in PRPZA group in vivo, implying that PRPZA could inhibit CYP3A activity. Conclusively, co-administration of PR with other CYP3A-metabolizing drugs may cause drug-drug interactions. Clinical use of PR-related formulae should be monitored carefully to avoid adverse interactions.

Seasonal expression of androgen receptor in scented gland of muskrat (Ondatra zibethicus).

Muskrat is a seasonal breeder, males of which secret musk from paired perineal scented glands found beneath the skin at the ventral base of the tail for attracting female during the breeding season. The aim of this study was to investigate the seasonal changes of expression of androgen receptor (AR) in the scented gland of muskrat during the breeding and nonbreeding seasons. Histologically, glandular cells, interstitial cells and excretory tubules were identified in scented glands in both seasons, whereas epithelial cells were sparse in the nonbreeding season. AR was observed in glandular cells of scented glands during the breeding and nonbreeding seasons with stronger immunostaining during the breeding season compared to the nonbreeding season. Consistent with the immunohistochemical results, AR protein level was higher in the scented glands of the breeding season, and then decreased to a relatively low level in the nonbreeding season. The mean mRNA level of Ar was significantly higher in the breeding season than in the nonbreeding season. In addition, plasma gonadotropins and testosterone concentrations were remarkably higher in the breeding season than those in the nonbreeding season. These results suggested that muskrat scented gland was the direct target organ of androgen, and stronger expression of AR in scented glands during the breeding season suggested that androgens may directly influence scented glandular function of the muskrats and also courtship behavior as we inferred.

Effects of crowding and sex on fecal cortisol levels of captive forest musk deer.

BACKGROUND: Restricted space and close contact with conspecifics in captivity may be stressful for musk deer, as they are highly territorial and solitary in the wild. So we tested the effects of crowding on stress of forest musk deer (Moschus berezovskii) in heterosexual groups, using fecal cortisol analysis as a non-invasive method. 32 healthy adults during non-breeding seasons were chose as our experimental objects. Group 1 was defined as higher crowding condition, with 10-15 m2/deer (6 enclosures, 10♀ and 6♂); group 2 was defined as lower crowding condition, with 23-33 m2/deer (6 enclosures, 10♀ and 6♂). Every enclosure contained 1 male and 3 female. These patterns had been existed for years. RESULTS: The results showed that females in lower crowding condition (217.1 ± 9.5 ug/g) had significantly higher fecal cortisol levels than those in higher crowding condition (177.2 ± 12.1 ug/g). Interestingly, crowding seemed have no effect on male fecal cortisol levels (148.1 ± 9.1 ug/g and 140.5 ± 13.3 ug/g, respectively). At both groups, cortisol was significantly lower in males than in females. CONCLUSIONS: These results showed that chronic crowding may affect stress status of captive forest musk deer. The captive environment should consider the space need for musk deer.

Transcription Factor Forkhead Box Protein 3 (FOXP3) as a Prognostic Indicator for Postoperative Outcomes in Patients with Breast Cancer: Establishment of a Prognostic Nomogram.

Purpose: The current investigation is to assess FOXP3 expression in breast cancer patients and evaluate the predictive significance of FOXP3. Patients and Methods: A cohort of 313 cases between January 2015 and November 2015 were enrolled this research. Immunohistochemistry (IHC) assay was utilized to detect the expression levels of FOXP3 in primary breast carcinoma specimens. These patients were separated into two groups by semiquantitative scoring approach. Chi-square test and Fisher's exact test were conducted to investigate the correlations between FOXP3 expression in tumors and clinicopathological variables. Kaplan-Meier method and Log rank test were utilized to generate survival curves for disease-free survival (DFS) and overall survival (OS). The independent factors were examined using Cox regression analysis. Nomogram models were created for assessing DFS and OS rates. Results: Depending on the levels of FOXP3 expression in tumors, these patients were categorized into two groups: low FOXP3 expression (174 cases) and high FOXP3 expression (139 cases). The patients exhibiting low levels of FOXP3 expression in tumors demonstrated a longer survival duration contrasted with those with high expression (DFS: 88.75 vs 65.87 months, χ2=36.1100, P<0.0001; OS: 89.70 vs 78.37 months, χ2=32.4900, P<0.0001). Multivariate analysis revealed that FOXP3 was a significant prognostic factor [DFS: hazard ratio (HR): 2.822, 95% CI: 1.595-4.992, P<0.0001; OS: HR: 3.232, 95% CI: 1.812-5.763, P<0.0001]. The good predictive clinical utility of FOXP3-based nomograms within the threshold probability range for different survival rates was demonstrated by calibration curve and decision curve analyses. Conclusion: FOXP3 expression serves as a crucial prognostic indicator in breast cancer patients, and may aid preoperative evaluation in clinical practice.

A positive feedback loop between PLD1 and NF-κB signaling promotes tumorigenesis of nasopharyngeal carcinoma.

Phospholipase D (PLD) lipid-signaling enzyme superfamily has been widely implicated in various human malignancies, but its role and underlying mechanism remain unclear in nasopharyngeal carcinoma (NPC). Here, we analyze the expressions of 6 PLD family members between 87 NPC and 10 control samples through transcriptome analysis. Our findings reveal a notable upregulation of PLD1 in both NPC tumors and cell lines, correlating with worse disease-free and overall survival in NPC patients. Functional assays further elucidate the oncogenic role of PLD1, demonstrating its pivotal promotion of critical tumorigenic processes such as cell proliferation and migration in vitro, as well as tumor growth in vivo. Notably, our study uncovers a positive feedback loop between PLD1 and the NF-κB signaling pathway to render NPC progression. Specifically, PLD1 enhances NF-κB activity by facilitating the phosphorylation and nuclear translocation of RELA, which in turn binds to the promoter of PLD1, augmenting its expression. Moreover, RELA overexpression markedly rescues the inhibitory effects in PLD1-depleted NPC cells. Importantly, the application of the PLD1 inhibitor, VU0155069, substantially inhibits NPC tumorigenesis in a patient-derived xenograft model. Together, our findings identify PLD1/NF-κB signaling as a positive feedback loop with promising therapeutic and prognostic potential in NPC.

Analysis and comparison of blood metabolome of forest musk deer in musk secretion and non-secretion periods.

Musk is an important animal product, but the musk secretion mechanism of forest musk deer (Moschus berezovskii) is still unclear. The musk synthesis process in forest musk deer is extremely complex, and many raw materials are directly or indirectly derived from forest musk deer blood. In this study, metabolomics was used to analyze the blood of forest musk deer in secretory and non-secretory phases for the first time, aim at explaining the secretion mechanism from the perspective of blood metabolism. We found that P450-related, choline-related, axonal regeneration and other pathways and related metabolites were significantly enriched during the musk secretion of forest musk deer. These pathways and metabolites related to P450 and choline in blood may have important implications for the mechanism of musk secretion in forest musk deer, because blood components were closely related to musk components and could provide raw materials for musk synthesis in musk gland cells.

Icariside II reduces testosterone production by inducing necrosis in rat Leydig cells.

The present study demonstrates that Icariside II (10, 20, and 40 µM) reduced Leydig cell testosterone production and cell viability in a concentration- and time-dependent manner. Hoechst 33342/propidium iodide staining indicated that no morphological changes in Leydig cell nuclear chromatin occurred, caspase-3 expression also showed no significant change, but cell death was caused by the 10-µM Icariside II treatment. Furthermore, a significant reduction in NAD(+) levels was observed following Icariside II exposure (10, 20, and 40 µM). Cell death was avoided when Icariside II treated cells were incubated with extracellular NAD(+) (5 and 10 mM). Moreover, the addition of NAD(+) (5 and 10 mM) could restore ATP production and prevent cell death. The results suggest that Icariside II can reduce testosterone production by inducing necrosis, but not apoptosis, in rat Leydig cells. This mechanism may also account for the Icariside II induced depletion of NAD(+) and ATP levels.

Acute stress show great influences on liver function and the expression of hepatic genes associated with lipid metabolism in rats.

BACKGROUND: The theory of Chinese medicine believes rage harms normal liver function, namely 'raged impairing liver' in short. The purpose of this study is to investigate the impact of acute stress on liver lipid metabolism in rats. METHODS AND RESULTS: Comparison of liver function indicators, serum lipid level of rats under acute stress and normal rats, as well as detection of liver tissue in the SR - BI, ABCG5 and ABCG8 protein and gene expression changes. Acute stressed rats had shown a lower serum levels of albumin (P<0.01), HDL- cholesterol (P<0.01) than normal rats, with higher serum levels of globulin (P<0.01) and LDL-cholesterol (P<0.05). Acute stressed rat's liver tissue exhibited a lower protein expression of ABCG5 (P<0.05), ABCG8 (P<0.01) and a higher level of SR-BI (P<0.05), compared with to normal rats. Furthermore, liver gene expression of ABCG5 (P<0.01) and ABCG8 (P<0.05) were lower in acute stressed rats than in normal rats, while SR-BI was higher in acute stressed rats than in normal rats (P<0.01). CONCLUSIONS: Acute stress had a direct influence on rat's liver lipid metabolism.

A Scalable Balz-Schiemann Reaction Protocol in a Continuous Flow Reactor.

The demand for aromatic fluorides is steadily increasing in the pharmaceutical and fine chemical industries. The Balz-Schiemann reaction is a straightforward strategy for preparing aryl fluorides from aryl amines, via the preparation and conversion of diazonium tetrafluoroborate intermediates. However, significant safety risks exist in handling the aryl diazonium salts when scaling up. In order to minimize the hazard, we present a continuous flow protocol that has been successfully performed at a kilogram scale that eliminates the isolation of aryl diazonium salts while facilitating efficient fluorination. The diazotization process was performed at 10 °C with a residence time of 10 min, followed by a fluorination process at 60 °C with a residence time of 5.4 s with about 70% yield. The reaction time has been dramatically reduced by introducing this multi-step continuous flow system.

Roles and Molecular Mechanisms of Biomarkers in Hepatocellular Carcinoma with Microvascular Invasion: A Review.

Hepatocellular carcinoma (HCC) being a leading cause of cancer-related death, has high associated mortality and recurrence rates. It has been of great necessity and urgency to find effective HCC diagnosis and treatment measures. Studies have shown that microvascular invasion (MVI) is an independent risk factor for poor prognosis after hepatectomy. The abnormal expression of biomacromolecules such as circ-RNAs, lncRNAs, STIP1, and PD-L1 in HCC patients is strongly correlated with MVI. Deregulation of several markers mentioned in this review affects the proliferation, invasion, metastasis, EMT, and anti-apoptotic processes of HCC cells through multiple complex mechanisms. Therefore, these biomarkers may have an important clinical role and serve as promising interventional targets for HCC. In this review, we provide a comprehensive overview on the functions and regulatory mechanisms of MVI-related biomarkers in HCC.