Construction of a Human Cell Landscape of COVID-19 Infection at Single-cell Level

Coupling of static ultramicromagnetic field with elastic micropillar-structured substrate for cell response

Micropillars have emerged as promising tools for a wide range of biological applications, while the influence of magnetic fields on cell behavior regulation has been increasingly recognized. However, the combined effect of micropillars and magnetic fields on cell behaviors remains poorly understood. In this study, we investigated the responses of H9c2 cells to ultramicromagnetic micropillar arrays using NdFeB as the tuned magnetic particles. We conducted a comparative analysis between PDMS micropillars and NdFeB/PDMS micropillars to assess their impact on cell function. Our results revealed that H9c2 cells exhibited significantly enhanced proliferation and notable cytoskeletal rearrangements on the ultramicromagnetic micropillars, surpassing the effects observed with pure PDMS micropillars. Immunostaining further indicated that cells cultured on ultramicromagnetic micropillars displayed heightened contractility compared to those on PDMS micropillars. Remarkably, the ultramicromagnetic micropillars also demonstrated the ability to decrease reactive oxygen species (ROS) levels, thereby preventing F-actin degeneration. Consequently, this study introduces ultramicromagnetic micropillars as a novel tool for the regulation and detection of cell behaviors, thus paving the way for advanced investigations in tissue engineering, single-cell analysis, and the development of flexible sensors for cellular-level studies.

Ginsenosides, potential TMPRSS2 inhibitors, a trade-off between the therapeutic combination for anti-PD-1 immunotherapy and the treatment of COVID-19 infection of LUAD patients

Background: Acting as a viral entry for coronavirus to invade human cells, TMPRSS2 has become a target for the prevention and treatment of COVID-19 infection. Before this, TMPRSS2 has presented biological functions in cancer, but the roles remain controversial and the mechanism remains unelucidated. Some chemicals have been reported to be inhibitors of TMPRSS2 and also demonstrated other pharmacological properties. At this stage, it is important to discover more new compounds targeting TMPRSS2, especially from natural products, for the prevention and treatment of COVID-19 infection.

Methods: We analyzed the correlation between TMPRSS2 expression, methylation level, overall survival rate, clinical parameters, biological process, and determined the correlation between TMPRSS2 and tumor-infiltrating lymphocytes in the tumor and adjacent normal tissue of adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) respectively by using various types of bioinformatics approaches. Moreover, we determined the correlation between TMPRSS2 protein level and the prognosis of LUAD and LUSC cohorts by immunohistochemistry assay. Furthermore, the cancer immunome atlas (TCIA) database was used to predict the relationship between the expression of TMPRSS2 and response to programmed cell death protein 1 (PD-1) blocker immunotherapy in lung cancer patients. Finally, the putative binding site of ginsenosides bound to TMPRSS2 protein was built from homology modeling to screen high-potency TMPRSS2 inhibitors.

Results: We found that TMPRSS2 recruits various types of immunocytes, including CD8+, CD4+ T cells, B cells and DCs both in LUAD and LUSC patients, and the correlation between TMPRSS2 expression and CD8+ and CD4+ T cells are stronger in LUAD rather than in LUSC, but excludes macrophages and neutrophils in LUAD patient cohorts. These might be the reason that higher mRNA and protein levels of TMPRSS2 are associated with better prognosis in LUAD cohorts rather than in LUSC cohorts. Furthermore, we found that TMPRSS2 was positively correlated with the prognosis in patient nonresponse to anti-PD-1 therapy. Therefore, we made an inference that increasing the expression level of TMPRSS2 may improve the anti-PD-1 immunotherapy efficacy. Finally, five ginsenosides candidates with high inhibition potency were screened from the natural chemical library to be used as TMPRSS2 inhibitors.

Conclusion: All these may imply that TMPRSS2 might be a novel prognostic biomarker and serve as a potential immunomodulator target of immunotherapy combination therapies in LUAD patients nonresponse to anti-PD-1 therapy. Also, these findings may suggest we should pay more attention to LUAD patients, especially those infected with COVID-19, who should avoid medicating TMPRSS2 inhibitors, such as ginsenosides to gain prophylactic and therapeutic benefits against COVID-19.

Resveratrol analog, triacetylresveratrol, a potential immunomodulator of lung adenocarcinoma immunotherapy combination therapies

Introduction

Resveratrol, an activator for longevity regulatory genes-sirtuin family (SIRTs) and Sirtuin 2 (SIRT2) is an important factor of SIRTs which demonstrated biological function in cancers, but the underlying mechanism is unrevealed.

Methods

We investigated the mRNA and protein levels of SIRT2 in a variety of cancers and the potential role for clinical prognosis, as well as analysed the association between the gene and immune infiltration in various cancers. And an analysis of two types of lung cancer was conducted to construct a systematic prognostic landscape. Finally, putative binding site of the triacetylresveratrol bound to SIRT2 was built from homology modeling.

Results and discussion

We concluded that higher mRNA and protein levels of SIRT2 affected prognosis in various types of cancers, especially in LUAD cohorts. In addition, SIRT2 is linked with a better overall survival (OS) in LUAD patients. Further research suggested a possible explanation for this phenotype might be that SIRT2 mRNA levels are positively correlated with infiltrating status of multiple immunocytes in LU-AD but not LUSC, i.e. SIRT2 expression may contribute to the recruitment of CD8+T cell, CD4+ T cell, T cell CD4+ memory resting, Tregs, T cell NK and positively correlated to the expression of PD-1, also excluding neutrophil, T cell CD8+ naïve and B cell plasma cells in LUAD. We found that triacetyl-resveratrol demonstrated the most potent agonist efficiency to SIRT2 and the EC 50 as low as 142.79 nM. As a result, SIRT2 appears to be a promising novel biomarker for prognosis prediction in patients with LUAD and triacetylresveratrol might be a potential immunomodulator of LUAD to anti-PD-1 based immunotherapy combination therapies.

Chronic alcohol intake regulates expression of SARS-CoV2 infection-relevant genes in an organ-specific manner

BACKGROUND

Chronic alcohol consumption and alcohol use disorder have a tremendous impact on the patient's psychological and physiological health. There is evidence that chronic alcohol consumption influences SARS-CoV2 infection risk, but so far, the molecular mechanism underlying such an effect is unknown.

METHODS

We generated the expression data of SARS-CoV2 infection-relevant genes (Ace2, Tmprss2, and Mas) in different organs in rat models of chronic alcohol exposure and alcohol dependence. Ace2 and Tmprss2 represent the virus entry point, whereas Mas activates the anti-inflammatory response once the cells are infected.

RESULTS

Across three different chronic alcohol test conditions, we found a consistent upregulation of Ace2 gene expression in the lung, which has been shown to be the most affected organ in COVID-19 patients. Other organs such as liver, ileum, kidney, heart, and brain also showed upregulation of Ace2 and Mas gene expression but less consistently across the different animal models, while Tmprss2 expression was unaffected in all conditions.

CONCLUSIONS

We conclude that alcohol-induced upregulation of Ace2 gene expression can lead to an elevated stochastic probability of virus entry into cells and may thus confer a molecular risk for SARS-CoV2 infection.

Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomics

BACKGROUND

Quality control (QC) of cells, a critical first step in single-cell RNA sequencing data analysis, has largely relied on arbitrarily fixed data-agnostic thresholds applied to QC metrics such as gene complexity and fraction of reads mapping to mitochondrial genes. The few existing data-driven approaches perform QC at the level of samples or studies without accounting for biological variation.

RESULTS

We first demonstrate that QC metrics vary with both tissue and cell types across technologies, study conditions, and species. We then propose data-driven QC (ddqc), an unsupervised adaptive QC framework to perform flexible and data-driven QC at the level of cell types while retaining critical biological insights and improved power for downstream analysis. ddqc applies an adaptive threshold based on the median absolute deviation on four QC metrics (gene and UMI complexity, fraction of reads mapping to mitochondrial and ribosomal genes). ddqc retains over a third more cells when compared to conventional data-agnostic QC filters. Finally, we show that ddqc recovers biologically meaningful trends in gradation of gene complexity among cell types that can help answer questions of biological interest such as which cell types express the least and most number of transcripts overall, and ribosomal transcripts specifically.

CONCLUSIONS

ddqc retains cell types such as metabolically active parenchymal cells and specialized cells such as neutrophils which are often lost by conventional QC. Taken together, our work proposes a revised paradigm to quality filtering best practices-iterative QC, providing a data-driven QC framework compatible with observed biological diversity.

Single‐cell RNA sequencing in oral science: Current awareness and perspectives

The emergence of single‐cell RNA sequencing enables simultaneous sequencing of thousands of cells, making the analysis of cell population heterogeneity more efficient. In recent years, single‐cell RNA sequencing has been used in the investigation of heterogeneous cell populations, cellular developmental trajectories, stochastic gene transcriptional kinetics, and gene regulatory networks, providing strong support in life science research. However, the application of single‐cell RNA sequencing in the field of oral science has not been reviewed comprehensively yet. Therefore, this paper reviews the development and application of single‐cell RNA sequencing in oral science, including fields of tissue development, teeth and jaws diseases, maxillofacial tumors, infections, etc., providing reference and prospects for using single‐cell RNA sequencing in studying the oral diseases, tissue development, and regeneration.