Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19.

Inferring how gene expression in a cell is influenced by cellular microenvironment is of great importance yet challenging. In this study, we present a single-cell RNA-sequencing data based multilayer network method (scMLnet) that models not only functional intercellular communications but also intracellular gene regulatory networks (https://github.com/SunXQlab/scMLnet). scMLnet was applied to a scRNA-seq dataset of COVID-19 patients to decipher the microenvironmental regulation of expression of SARS-CoV-2 receptor ACE2 that has been reported to be correlated with inflammatory cytokines and COVID-19 severity. The predicted elevation of ACE2 by extracellular cytokines EGF, IFN-γ or TNF-α were experimentally validated in human lung cells and the related signaling pathway were verified to be significantly activated during SARS-COV-2 infection. Our study provided a new approach to uncover inter-/intra-cellular signaling mechanisms of gene expression and revealed microenvironmental regulators of ACE2 expression, which may facilitate designing anti-cytokine therapies or targeted therapies for controlling COVID-19 infection. In addition, we summarized and compared different methods of scRNA-seq based inter-/intra-cellular signaling network inference for facilitating new methodology development and applications.

CO2 Absorption Mechanism by the Deep Eutectic Solvents Formed by Monoethanolamine-Based Protic Ionic Liquid and Ethylene Glycol.

Deep eutectic solvents (DESs) have been widely used to capture CO2 in recent years. Understanding CO2 mechanisms by DESs is crucial to the design of efficient DESs for carbon capture. In this work, we studied the CO2 absorption mechanism by DESs based on ethylene glycol (EG) and protic ionic liquid ([MEAH][Im]), formed by monoethanolamine (MEA) with imidazole (Im). The interactions between CO2 and DESs [MEAH][Im]-EG (1:3) are investigated thoroughly by applying 1H and 13 C nuclear magnetic resonance (NMR), 2-D NMR, and Fourier-transform infrared (FTIR) techniques. Surprisingly, the results indicate that CO2 not only binds to the amine group of MEA but also reacts with the deprotonated EG, yielding carbamate and carbonate species, respectively. The reaction mechanism between CO2 and DESs is proposed, which includes two pathways. One pathway is the deprotonation of the [MEAH]+ cation by the [Im]- anion, resulting in the formation of neutral molecule MEA, which then reacts with CO2 to form a carbamate species. In the other pathway, EG is deprotonated by the [Im]-, and then the deprotonated EG, HO-CH2-CH2-O-, binds with CO2 to form a carbonate species. The absorption mechanism found by this work is different from those of other DESs formed by protic ionic liquids and EG, and we believe the new insights into the interactions between CO2 and DESs will be beneficial to the design and applications of DESs for carbon capture in the future.

[Highly efficient production of L-valine by multiplex metabolic engineering of Corynebacterium glutamicum].

As a branched chain amino acid, L-valine is widely used in the medicine and feed sectors. In this study, a microbial cell factory for efficient production of L-valine was constructed by combining various metabolic engineering strategies. First, precursor supply for L-valine biosynthesis was enhanced by strengthening the glycolysis pathway and weakening the metabolic pathway of by-products. Subsequently, the key enzyme in the L-valine synthesis pathway, acetylhydroxylate synthase, was engineered by site-directed mutation to relieve the feedback inhibition of the engineered strain. Moreover, promoter engineering was used to optimize the gene expression level of key enzymes in L-valine biosynthetic pathway. Furthermore, cofactor engineering was adopted to change the cofactor preference of acetohydroxyacid isomeroreductase and branched-chain amino acid aminotransferase from NADPH to NADH. The engineered strain C. glutamicum K020 showed a significant increase in L-valine titer, yield and productivity in 5 L fed-batch bioreactor, up to 110 g/L, 0.51 g/g and 2.29 g/(L‧h), respectively.

Interrogating glioma-M2 macrophage interactions identifies Gal-9/Tim-3 as a viable target against PTEN-null glioblastoma.

Genomic alteration can reshape tumor microenvironment to drive tumor malignancy. However, how PTEN deficiency influences microenvironment-mediated cell-cell interactions in glioblastoma (GBM) remains unclear. Here, we show that PTEN deficiency induces a symbiotic glioma-M2 macrophage interaction to support glioma progression. Mechanistically, PTEN-deficient GBM cells secrete high levels of galectin-9 (Gal-9) via the AKT-GSK3ß-IRF1 pathway. The secreted Gal-9 drives macrophage M2 polarization by activating its receptor Tim-3 and downstream pathways in macrophages. These macrophages, in turn, secrete VEGFA to stimulate angiogenesis and support glioma growth. Furthermore, enhanced Gal-9/Tim-3 expression predicts poor outcome in glioma patients. In GBM models, blockade of Gal-9/Tim-3 signaling inhibits macrophage M2 polarization and suppresses tumor growth. Moreover, α-lactose attenuates glioma angiogenesis by down-regulating macrophage-derived VEGFA, providing a novel antivascularization strategy. Therefore, our study suggests that blockade of Gal-9/Tim-3 signaling is effective to impair glioma progression by inhibiting macrophage M2 polarization, specifically for PTEN-null GBM.