Neoadjuvant therapy for non-small cell lung cancer and esophageal cancer.

As the major malignant tumors in the chest, non-small cell lung cancer (NSCLC) and esophageal cancer (EC) bring huge health burden to human beings worldwide. Currently, surgery is still the mainstay for comprehensive treatment for NSCLC and EC, but the prognosis is still poor as the results of cancer recurrence and distant metastasis. Neoadjuvant therapy refers to a single or combined treatment before surgery, aiming to improve the therapeutic effects of the traditional therapies. Unfortunately, the clinical outcomes and effects of neoadjuvant therapy are still controversial due to its apparent advantages and disadvantages, and different patients may respond differentially to the same scheme of neoadjuvant therapy, which makes it urgent and necessary to develop personalized scheme of neoadjuvant therapy for different individuals. Therefore, this review summarizes the novel schemes and strategies of neoadjuvant therapy, which may help to significantly improve of life quality of patients suffering from chest-related malignancies.

Functional requirement of alternative splicing in epithelial-mesenchymal transition of pancreatic circulating tumor.

Circulating tumor cells (CTCs) that undergo epithelial-to-mesenchymal transition (EMT) can provide valuable information regarding metastasis and potential therapies. However, current studies on the EMT overlook alternative splicing. Here, we used single-cell full-length transcriptome data and mRNA sequencing of CTCs to identify stage-specific alternative splicing of partial EMT and mesenchymal states during pancreatic cancer metastasis. We classified definitive tumor and normal epithelial cells via genetic aberrations and demonstrated dynamic changes in the epithelial-mesenchymal continuum in both epithelial cancer cells and CTCs. We provide the landscape of alternative splicing in CTCs at different stages of EMT, uncovering cell-type-specific splicing patterns and splicing events in cell surface proteins suitable for therapies. We show that MBNL1 governs cell fate through alternative splicing independently of changes in gene expression and affects the splicing pattern during EMT. We found a high frequency of events that contained multiple premature termination codons and were enriched with C and G nucleotides in close proximity, which influence the likelihood of stop codon readthrough and expand the range of potential therapeutic targets. Our study provides insights into the EMT transcriptome's dynamic changes and identifies potential diagnostic and therapeutic targets in pancreatic cancer.

DeepCCI: a deep learning framework for identifying cell-cell interactions from single-cell RNA sequencing data.

MOTIVATION: Cell-cell interactions (CCIs) play critical roles in many biological processes such as cellular differentiation, tissue homeostasis, and immune response. With the rapid development of high throughput single-cell RNA sequencing (scRNA-seq) technologies, it is of high importance to identify CCIs from the ever-increasing scRNA-seq data. However, limited by the algorithmic constraints, current computational methods based on statistical strategies ignore some key latent information contained in scRNA-seq data with high sparsity and heterogeneity. RESULTS: Here, we developed a deep learning framework named DeepCCI to identify meaningful CCIs from scRNA-seq data. Applications of DeepCCI to a wide range of publicly available datasets from diverse technologies and platforms demonstrate its ability to predict significant CCIs accurately and effectively. Powered by the flexible and easy-to-use software, DeepCCI can provide the one-stop solution to discover meaningful intercellular interactions and build CCI networks from scRNA-seq data. AVAILABILITY AND IMPLEMENTATION: The source code of DeepCCI is available online at https://github.com/JiangBioLab/DeepCCI.

Equalization equal gain combining for a single-input to multiple-output underwater wireless optical communication system under a Gaussian beam.

In this study, we examined the performance of an underwater wireless optical communication (UWOC) system employing a single-input to multiple-output (SIMO) scheme and proposed an equalization equal gain combining (EEGC) algorithm for it under Gaussian beam conditions. Furthermore, based on a Yue spectrum with the instability of oceanic water stratification and a finite outer scale, we derived the closed analytical formulas for the scintillation index and spatial coherence radius in weak oceanic turbulence for a Gaussian beam, from which we could obtain the threshold of the detector spacing and the strength of oceanic turbulence. We then derived the closed-form formula for the upper bound average bit error rate of the EEGC SIMO system with ON-OFF keying modulation by using the hyperbolic tangent distribution function. Our simulations demonstrate two issues if oceanic water stratification is treated as a steady state: the performance of the diversity receiver system will be significantly underestimated in salinity-dominated weak oceanic turbulence channels and will be significantly overestimated in temperature-dominated weak oceanic turbulence channels. Additionally, the SIMO system performance improvement using the proposed EEGC algorithm was more evident with increasing detector spacing, and the EEGC algorithm reduced the impact of the layout of the avalanche photodiode arrays on the UWOC system performance, in contrast to the equal gain combining algorithm.

N-glycosylation at N57/100/110 affects CD44s localization, function and stability in hepatocellular carcinoma.

The glycosylation levels of proteins in cancer cells are closely related to cancer invasion and migration. CD44 is a transmembrane glycoprotein that is significantly overexpressed in a variety of tumor cells and has been proven to promote the migration and motility of cancer cells, but the effect of its N-glycosylation modification on CD44 protein function in tumors is less studied. Here, we investigated the effect of six N-glycan chains (N25/57/100/110/120/255) on CD44s localization, function and stability in hepatocarcinoma cells. When the six sites were mutated, we found that CD44s lost its membrane localization in Huh7 and MHCC-97H cells. On this basis, we identified three glycosylation sites on CD44s (N57, N100 and N110) that played key roles in intracellular localization. When N57, N100 and N110 were mutated together, CD44 localized to the cytoplasm, while another three-site mutant (N25/N120/N255) was still anchored to the membrane. In addition, the ability of CD44-N57Q/N100Q/N110Q to promote the metastasis and invasion of Huh7 and 97H cells was weakened compared with that of CD44-N25Q/N120Q/N255Q. Furthermore, CD44-N57Q/N100Q/N110Q accumulated abnormally in the ER, and a high level of the ER stress (ERS) marker BiP was detected at the same time compared with wild-type CD44. When the lysosome inhibitor CQ was added, the content of mutant protein that triggered ERS significantly increased, which indicated that the degradation mode of CD44-N57Q/N100Q/N110Q after ERS was mainly through the lysosomal pathway (ERLAD). The results revealed that the N-glycosylation sites N57, N100 and N110 mutated on CD44s affected its function and degraded it by lysosomes after triggering ERS. These findings provide data for new studies on ER-related degradation, further promote the study of the glycan chain function of CD44 and furnish new ideas for the treatment of liver cancer metastasis.

N-glycosylation by N-acetylglucosaminyltransferase IVa enhances the interaction of integrin ß1 with vimentin and promotes hepatocellular carcinoma cell motility.

N-glycosylation has been revealed to be tightly associated with cancer metastasis. As a key transferase that catalyzes the formation of ß1,4 N-acetylglucosamine (ß1,4GlcNAc) branches on the mannose core of N-glycans, N-acetylglucosaminyltransferase IVa (GnT-IVa) has been reported to be involved in hepatocellular carcinoma (HCC) metastasis by forming N-glycans; however, the underlying mechanisms are largely unknown. In the current study, we found that GnT-IVa was upregulated in HCC tissues and positively correlated with worse outcomes in HCC patients. We found that GnT-IVa could promote tumor growth in mice; notably, this effect was attenuated after mutating the enzymatic site (D445A) of GnT-IVa, suggesting that GnT-IVa regulated HCC progression by forming ß1,4GlcNAc branches. To mechanistically investigate the role of GnT-IVa in HCC, we conducted GSEA and GO functional analysis as well as in vitro experiments. The results showed that GnT-IVa could enhance HCC cell migration, invasion and adhesion ability and increase ß1,4GlcNAc branch glycans on integrin ß1 (ITGB1), a tumor-associated glycoprotein that is closely involved in cell motility by interacting with vimentin. Interruption of ß1,4GlcNAc branch glycan modification on ITGB1 could suppress the interaction of ITGB1 with vimentin and inhibit cell motility. These results revealed that GnT-IVa could promote HCC cell motility by affecting the biological functions of ITGB1 through N-glycosylation. In summary, our results revealed that GnT-IVa is highly expressed in HCC and can form ß1,4GlcNAc branches on ITGB1, which are essential for interactions with vimentin to promote HCC cell motility. These findings not only proposed a novel mechanism for GnT-IVa in HCC progression but also revealed the significance of N-glycosylation on ITGB1 during the process, which may provide a novel target for future HCC therapy.

A multifactorial analysis of FAP to regulate gastrointestinal cancers progression.

Background: Fibroblast activation protein (FAP) is a cell-surface serine protease that has both dipeptidyl peptidase as well as endopeptidase activities and could cleave substrates at post-proline bond. Previous findings showed that FAP was hard to be detected in normal tissues but significantly up-regulated in remodeling sites like fibrosis, atherosclerosis, arthritis and embryonic tissues. Though increasing evidence has demonstrated the importance of FAP in cancer progression, no multifactorial analysis has been developed to investigate its function in gastrointestinal cancers until now. Methods: By comprehensive use of datasets from The Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), scTIME Portal and Human Protein Atlas (HPA), we evaluated the carcinogenesis potential of FAP in gastrointestinal cancers, analyzing the correlation between FAP and poor outcomes, immunology in liver, colon, pancreas as well as stomach cancers. Then liver cancer was selected as example to experimentally validate the pro-tumor and immune regulative role of FAP in gastrointestinal cancers. Results: FAP was abundantly expressed in gastrointestinal cancers, such as LIHC, COAD, PAAD and STAD. Functional analysis indicated that the highly-expressed FAP in these cancers could affect extracellular matrix organization process and interacted with genes like COL1A1, COL1A2, COL3A1 and POSTN. In addition, it was also observed that FAP was positively correlated to M2 macrophages infiltration across these cancers. To verify these findings in vitro, we used LIHC as example and over-expressed FAP in human hepatic stellate LX2 cells, a main cell type that produce FAP in tumor tissues, and then investigate its role on LIHC cells as well as macrophages. Results showed that the medium from FAP-over-expressed LX2 cells could significantly promote the motility of MHCC97H and SK-Hep1 LIHC cells, increase the invasion of THP-1 macrophages and induce them into pro-tumor M2 phenotype. Conclusion: In summary, we employed bioinformatic tools and experiments to perform a comprehensive analysis about FAP. Up-regulation of FAP in gastrointestinal cancers was primarily expressed in fibroblasts and contributes to tumor cells motility, macrophages infiltration and M2 polarization, revealing the multifactorial role of FAP in gastrointestinal cancers progression.

Identification of shared characteristics in tumor-infiltrating T cells across 15 cancers.

Tumor-infiltrating T cells are essential players in tumor immunotherapy. Great progress has been achieved in the investigation of T cell heterogeneity. However, little is well known about the shared characteristics of tumor-infiltrating T cells across cancers. In this study, we conduct a pan-cancer analysis of 349,799 T cells across 15 cancers. The results show that the same T cell types had similar expression patterns regulated by specific transcription factor (TF) regulons across cancers. Multiple T cell type transition paths were consistent in cancers. We found that TF regulons associated with CD8+ T cells transitioned to terminally differentiated effector memory (Temra) or exhausted (Tex) states were associated with patient clinical classification. We also observed universal activated cell-cell interaction pathways of tumor-infiltrating T cells in all cancers, some of which specifically mediated crosstalk in certain cell types. Moreover, consistent characteristics of TCRs in the aspect of variable and joining region genes were found across cancers. Overall, our study reveals common features of tumor-infiltrating T cells in different cancers and suggests future avenues for rational, targeted immunotherapies.

Hepatocyte-targeted delivery using oleanolic acid-loaded liposomes for enhanced hepatocellular carcinoma therapy.

Drug-loaded liposomes have been shown to be effective in the treatment of hepatocellular carcinoma (HCC). However, the systemic non-specific distribution of drug-loaded liposomes in tumor patients is a critical therapeutic challenge. To address this issue, we developed galactosylated chitosan-modified liposomes (GC@Lipo) that could selectively bind to the asialoglycoprotein receptor (ASGPR), which is highly expressed on the membrane surface of HCC cells. Our study demonstrated that the GC@Lipo significantly enhanced the anti-tumor efficacy of oleanolic acid (OA) by enabling targeted drug delivery to hepatocytes. Remarkably, treatment with OA-loaded GC@Lipo inhibited the migration and proliferation of mouse Hepa1-6 cells by upregulating E-cadherin expression and downregulating N-cadherin, vimentin, and AXL expressions, compared to a free OA solution and OA-loaded liposomes. Furthermore, using an axillary tumor xenograft mouse model, we observed that OA-loaded GC@Lipo led to a significant reduction in tumor progression, accompanied by concentrated enrichment in hepatocytes. These findings strongly support the clinical translation of ASGPR-targeted liposomes for the treatment of HCC.

The regulation loop of MARVELD1 interacting with PARP1 in DNA damage response maintains genome stability and promotes therapy resistance of cancer cells.

The DNA damage response (DDR) plays crucial roles in cancer prevention and therapy. Poly(ADP-ribose) polymerase 1 (PARP1) mediates multiple signal transduction in the DDR as a master regulator. Uncovering the regulatory factors of PARP1 contributes to a more comprehensive view of tumorigenesis and treatment strategies. Here, we reveal that MARVELD1 acts as a mediator of DDR to perform early events and maintain genome stability. Mechanistically, PARP1 PARylates MARVELD1 at D102, D118 and D130, and in turn, MARVELD1 stabilizes PARP1 by enhancing NAA50-mediated acetylation, thus forming a positive feedback loop. MARVELD1 knockout mice and their embryo fibroblasts exhibit genomic instability and shorter half-life of PARP1. Moreover, MARVELD1 partnering with PARP1 facilitates resistance to genotoxic drugs and disrupts PARP inhibitor (PARPi) effect in PDX model of colorectal cancer (CRC). Overall, our results underline the link between MARVELD1 and PARP1 in therapeutic resistance based on DDR and provide new insights for clinical tumor therapy of PARPi.

Ambient nitrogen dioxide and cardiovascular diseases in rural regions: a time-series analyses using data from the new rural cooperative medical scheme in Fuyang, East China.

Most of studies relating ambient nitrogen dioxide (NO2) exposure to hospital admissions for cardiovascular diseases (CVDs) were conducted among urban population. Whether and to what extent these results could be generalizable to rural population remains unknown. We addressed this question using data from the New Rural Cooperative Medical Scheme (NRCMS) in Fuyang, Anhui, China. Daily hospital admissions for total CVDs, ischaemic heart disease, heart failure, heart rhythm disturbances, ischaemic stroke, and haemorrhagic stroke in rural regions of Fuyang, China, were extracted from NRCMS between January 2015 and June 2017. A two-stage time-series analysis method was used to assess the associations between NO2 and CVD hospital admissions and the disease burden fractions attributable to NO2. In our study period, the average number (standard deviation) of hospital admissions per day were 488.2 (117.1) for total CVDs, 179.8 (45.6) for ischaemic heart disease, 7.0 (3.3) for heart rhythm disturbances, 13.2 (7.2) for heart failure, 267.9 (67.7) for ischaemic stroke, and 20.2 (6.4) for haemorrhagic stroke. The 10-µg/m3 increase of NO2 was related to an elevated risk of 1.9% (RR: 1.019, 95% CI: 1.005 to 1.032) for hospital admissions of total CVDs at lag0-2 days, 2.1% (1.021, 1.006 to 1.036) for ischaemic heart disease, and 2.1% (1.021, 1.006 to 1.035) for ischaemic stroke, respectively, while no significant association was observed between NO2 and hospital admissions for heart rhythm disturbances, heart failure, and haemorrhagic stroke. The attributable fractions of total CVDs, ischaemic heart disease, and ischaemic stroke to NO2 were 6.52% (1.87 to 10.94%), 7.31% (2.19 to 12.17%), and 7.12% (2.14 to 11.85%), respectively. Our findings suggest that CVD burdens in rural population are also partly attributed to short-term exposure to NO2. More studies across rural regions are required to replicate our findings.

Understanding metabolic alterations after SARS-CoV-2 infection: insights from the patients' oral microenvironmental metabolites.

BACKGROUND: Coronavirus disease 2019 is a type of acute infectious pneumonia and frequently confused with influenza since the initial symptoms. When the virus colonized the patient's mouth, it will cause changes of the oral microenvironment. However, few studies on the alterations of metabolism of the oral microenvironment affected by SARS-CoV-2 infection have been reported. In this study, we explored metabolic alterations of oral microenvironment after SARS-CoV-2 infection. METHODS: Untargeted metabolomics (UPLC-MS) was used to investigate the metabolic changes between oral secretion samples of 25 COVID-19 and 30 control participants. To obtain the specific metabolic changes of COVID-19, we selected 25 influenza patients to exclude the metabolic changes caused by the stress response of the immune system to the virus. Multivariate analysis (PCA and PLS-DA plots) and univariate analysis (students' t-test) were used to compare the differences between COVID-19 patients and the controls. Online hiplot tool was used to perform heatmap analysis. Metabolic pathway analysis was conducted by using the MetaboAnalyst 5.0 web application. RESULTS: PLS-DA plots showed significant separation of COVID-19 patients and the controls. A total of 45 differential metabolites between COVID-19 and control group were identified. Among them, 35 metabolites were defined as SARS-CoV-2 specific differential metabolites. Especially, the levels of cis-5,8,11,14,17-eicosapentaenoic acid and hexanoic acid changed dramatically based on the FC values. Pathway enrichment found the most significant pathways were tyrosine-related metabolism. Further, we found 10 differential metabolites caused by the virus indicating the body's metabolism changes after viral stimulation. Moreover, adenine and adenosine were defined as influenza virus-specific differential metabolites. CONCLUSIONS: This study revealed that 35 metabolites and tyrosine-related metabolism pathways were significantly changed after SARS-CoV-2 infection. The metabolic alterations of oral microenvironment in COVID-19 provided new insights into its molecular mechanisms for research and prognostic treatment.

Selenium attenuates the association of co-exposure to arsenic, cadmium, and lead with cognitive function among Chinese community-dwelling older adults.

The effects of interactions between the toxic and essential metal mixtures on cognitive function are poorly understood. This study aims to identify the joint association of arsenic (As), cadmium (Cd), and lead (Pb) with cognitive function in older adults and the moderating role of selenium (Se), zinc (Zn), and copper (Cu) in this association. This study included 1000 community-dwelling older adults. Cognitive function was assessed by the Mini-Mental State Examination (MMSE). Blood concentrations of As, Cd, Pb, Se, Zn, and Cu were measured using inductively coupled plasma mass spectrometry. Linear regression and Bayesian kernel machine regression (BKMR) models were applied to assess the individual and joint associations of As, Cd, and Pb with cognitive function and to examine whether Se, Zn, and Cu (individually and as a mixture) modified these associations. In the adjusted single-metal models, both Cd (ß = - 0.37, 95% CI: - 0.73 to - 0.01) and Pb (ß = - 0.44, 95% CI: - 0.86 to - 0.02) were associated with MMSE scores, while Se (ß = 0.71, 95% CI: 0.30 to 1.13) exhibited a positive relationship with MMSE scores. Univariate exposure-response functions from BKMR models showed similar results. Moreover, the toxic metal mixture (As, Cd, and Pb) exhibited a significant negative association with MMSE scores in a dose-response pattern, with Pb being the greatest contributor within the mixture. The negative association of Pb alone or the toxic metal mixture with MMSE scores became weaker at higher concentrations of Se within its normal range, especially when Se levels were greater than the median (89.18 µg/L). Our findings support that Se can attenuate the negative associations of exposure to single Pb or the As, Cd, and Pb mixtures with cognitive function. Future prospective studies are needed to replicate our findings.

Characteristics and factors associated with morbidity of migrant workers with pneumoconiosis: a cross-sectional study.

OBJECTIVES: To better understand the characteristics of migrant workers with pneumoconiosis in China, and the factors that contribute to their morbidity. DESIGN: A cross-sectional study. SETTING: This study was conducted in Shanghai, Nanning and Shenzhen, China, between December 2020 and December 2021. PARTICIPANTS: There were 601 questionnaires that were analysed involving 198 migrant workers with pneumoconiosis, 205 workers with pneumoconiosis in state-owned enterprises (SOEs) and 198 other migrant workers with non-pulmonary occupational diseases. OUTCOME MEASURES: Epidemiological characteristics of pneumoconiosis among migrant workers were determined. Using logistic regression, we examined the factors related to the morbidity of pneumoconiosis in migrant workers. RESULTS: The response rate was 93.27%. In comparison with pneumoconiosis among SOE workers, the number of migrant workers with pneumoconiosis who first encountered dust exposure between the ages of 30 and 44 years and had an accumulated dust exposure of 1-10 years was proportionately greater. Migrant workers who developed pneumoconiosis between 18 and 32 years and those who had stage III pneumoconiosis were proportionately greater (p<0.05). Compared with migrant workers with non-pulmonary occupational diseases, six factors were associated with the morbidity of pneumoconiosis in migrant workers. Risk factors were dust exposure (OR=499.25, 95% CI: 68.33 to 3647.59) and someone smoking in the workplace (OR=5.67, 95% CI: 2.18 to 14.78). Protective factors were regular sleeping hours per night, (OR=0.23, 95% CI: 0.09 to 0.60), excellent ventilation (OR=0.09, 95% CI: 0.01 to 0.65), rules and regulations (OR=0.22, 95% CI: 0.07 to 0.66) and post-departure medical examinations (OR=0.24, 95% CI: 0.09 to 0.63). CONCLUSIONS: Compared with SOE workers with pneumoconiosis, migrant workers are exposed to dust at an earlier age, but for shorter duration, display morbidity at an earlier age and have a higher proportion of tertiary pneumoconiosis. They are predominantly male and have inadequate employment stability and medical insurance. Occupational health check-ups and management systems are inadequate.

Network analysis between neuron dysfunction and neuroimmune response based on neural single-cell transcriptome of COVID-19 patients.

Despite global vaccination efforts, COVID-19 breakthrough infections caused by variant virus continue to occur frequently, long-term sequelae of COVID-19 infection like neuronal dysfunction emerge as a noteworthy issue. Neuroimmune disorder induced by Inflammatory factor storm was considered as a possible reason, however, little was known about the functional factors affecting neuroimmune response to this virus. Here, using medial prefrontal cortex single cell data of COVID-19 patients, expression pattern analysis indicated that some immune-related pathway genes expressed specifically, including genes associated with T cell receptor, TNF signaling in microglia and Cytokine-cytokine receptor interaction and HIF-1 signaling pathway genes in astrocytes. Besides the well-known immune-related cell type microglia, we also observed immune-related factors like IL17D, TNFRSF1A and TLR4 expressed in Astrocytes. Based on the ligand-receptor relationship of immune-related factors, crosstalk landscape among cell clusters were analyzed. The findings indicated that astrocytes collaborated with microglia and affect excitatory neurons, participating in the process of immune response and neuronal dysfunction. Moreover, subset of astrocytes specific immune factors (hinged neuroimmune genes) were proved to correlate with Covid-19 infection and ventilator-associated pneumonia using multi-tissue RNA-seq and scRNA-seq data. Function characterization clarified that hinged neuroimmune genes were involved in activation of inflammation and hypoxia signaling pathways, which could lead to hyper-responses related neurological sequelae. Finally, a risk model was constructed and testified in RNA-seq and scRNA data of peripheral blood.

The association between essential trace element mixture and atherosclerotic cardiovascular disease risk among Chinese community-dwelling older adults.

The evidence about the association of the essential trace element (ETE) mixture with atherosclerotic cardiovascular disease (ASCVD) amongst older adults is limited. This study aims to evaluate the associations of single ETEs and the ETE mixture with the 10-year ASCVD risks and its predicting factors in Chinese community-dwelling older adults. A total of 607 community-dwelling older adults were included in this study. Blood levels of vanadium (V), chromium (Cr), manganese (Mn), cobalt (Co), nickel (Ni), and selenium (Se) were assessed by inductively coupled plasma mass spectrometry. The predicted 10-year ASCVD risk was calculated using the Prediction for ASCVD Risk in China (China-PAR) equations. Traditional linear regressions and Bayesian kernel machine regression (BKMR) were used to assess the associations of single ETEs and the ETE mixture with the 10-year ASCVD risks and its predicting factors such as systolic blood pressure (SBP), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), diabetes, and waist circumference (WC). In linear regression models, blood Cr levels were negatively associated with the 10-year ASCVD risks after adjustment for covariates (ß = - 0.07, 95% CI = - 0.11 ~ - 0.03); The 3th quartile (Q3) of Se levels was also associated with a lower 10-year ASCVD risks when compared with the lowest quartile (Q1) of Se levels (ßQ3 vs. Q1: - 0.12, 95% CI = - 0.22 ~ - 0.02). In BKMR models, the negative associations of Cr and Se with the 10-year ASCVD risks were observed. Higher blood levels of ETE mixture were associated with decreased 10-year ASCVD risks in a dose-response pattern, with Cr having the highest value of the posterior inclusion probability (PIP) within the mixture. Furthermore, a positive association between Cr and HDL-C and a negative association between Se and SBP were found in both linear regression and BKMR models. Cr and Se were negatively associated with the 10-year ASCVD risks, individually and as a mixture. ETE mixture showed a linear dose-response association with decreased 10-year ASCVD risks, with Cr being the most important component within the mixture. The negative association of the ETE mixture with the 10-year ASCVD risks may be attributed to Cr and Se, mainly mediated by HDL-C and SBP, respectively. Further cohort studies are needed to clarify this association.

PGE2-EP2/EP4 signaling elicits immunosuppression by driving the mregDC-Treg axis in inflammatory tumor microenvironment.

Active inflammation generally promotes immune activation. However, in the tumor microenvironment (TME), active inflammation occurs in parallel with immunosuppression, and both contribute to tumor growth. Why inflammation does not lead to immune activation in TME remains unclear. In this study, using the immune checkpoint inhibitor-insensitive mouse cancer model and single-cell RNA sequencing, we show that PGE2-EP2/EP4 signaling simultaneously promotes active inflammation by inducing expression of the NF-κB genes in myeloid cells and elicits immunosuppression by driving the mregDC (mature DC enriched in immunoregulatory molecules)-Treg (regulatory T cell) axis for Treg recruitment and activation in the tumor. Importantly, the EP2/EP4 expression level is strongly correlated with the gene signatures of both active inflammation and the mregDC-Treg axis and has significant prognosis value in various human cancers. Thus, PGE2-EP2/EP4 signaling functions as the key regulatory node linking active inflammation and immunosuppression in TME, which can be targeted by EP2 and EP4 antagonists for cancer therapeutics.

[Exploration of multi-faceted model in plant biology teaching].

Plant biology is a basic course for students majoring in biological science. Under the guidance of developmental biology, we have constructed a comprehensive, systematic and dynamic new curriculum system for plant biology. There are still some problems existing in the current curriculum teaching mode, e.g. the students do not listen carefully to the lecture due to single classroom teaching mode, the mismatch between theoretical and experimental courses in terms of content and timing, the incomplete understanding on plants and the difficulty of integrating learning and practicing due to insufficient field practices. In view of these problems, a series of new teaching strategies for bioscience major of Harbin Institute of Technology were proposed and implemented. The combination of lectures and high quality massive open online courses (MOOC) were used for theoretical study, to which the flipped classroom was added. In addition, the theoretical study and the experiment work were combined. Moreover, the plant cognitive practices were carried out in the campus and the botanical garden in early spring, late spring and summer, respectively. Satisfactory results were achieved after two rounds of teaching practice, which fulfilled the education requirements and laid foundations for students to continue follow-up basic and professional courses.

MutCov: A pipeline for evaluating the effect of mutations in spike protein on infectivity and antigenicity of SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing an outbreak of coronavirus disease 2019 (COVID-19), is a major threat to public health worldwide. Previous studies have shown that the spike protein of SARS-CoV-2 determines viral infectivity and major antigenicity. However, the spike protein has been undergoing various mutations, which bring a great challenge to the prevention and treatment of COVID-19. Here we present the MutCov, a pipeline for evaluating the effect of mutations in spike protein on infectivity and antigenicity of SARS-CoV-2 by calculating the binding free energy between spike protein and angiotensin-converting enzyme 2 (ACE2) or neutralizing monoclonal antibody (mAb). The predicted infectivity and antigenicity were highly consistent with biologically experimental results, and demonstrated that the MutCov achieved good prediction performance. In conclusion, the MutCov is of high importance for systematically evaluating the effect of novel mutations and improving the prevention and treatment of COVID-19. The source code and installation instruction of MutCov are freely available at http://jianglab.org.cn/MutCov.

Global Characterization of Peripheral B Cells in Parkinson's Disease by Single-Cell RNA and BCR Sequencing.

Immune system plays important roles in the pathogenesis of Parkinson's disease (PD). However, the role of B cells in this complex disease are still not fully understood. B cells produce antibodies but can also regulate immune responses. In order to decode the relative contribution of peripheral B cell subtypes to the etiology of PD, we performed single cell RNA and BCR sequencing for 10,466 B cells from 8 PD patients and 6 age-matched healthy controls. We observed significant increased memory B cells and significant decreased naïve B cells in PD patients compared to healthy controls. Notably, we also discovered increased IgG and IgA isotypes and more frequent class switch recombination events in PD patients. Moreover, we identified preferential V and J gene segments of B cell receptors in PD patients as the evidence of convergent selection in PD. Finally, we found a marked clonal expanded memory B cell population in PD patients, up-regulating both MHC II genes (HLA-DRB5, HLA-DQA2 and HLA-DPB1) and transcription factor activator protein 1 (AP-1), suggesting that the antigen presentation capacity of B cells was enhanced and B cells were activated in PD patients. Overall, this study conducted a comprehensive analysis of peripheral B cell characteristics of PD patients, which provided novel insights into the humoral immune response in the pathogenesis of PD.