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Microbes are parasitic in various human body organs and play significant roles in a wide range of diseases. Identifying microbe-disease associations is conducive to the identification of potential drug targets. Considering the high cost and risk of biological experiments, developing computational approaches to explore the relationship between microbes and diseases is an alternative choice. However, most existing methods are based on unreliable or noisy similarity, and the prediction accuracy could be affected. Besides, it is still a great challenge for most previous methods to make predictions for the large-scale dataset. In this work, we develop a multi-component Graph Attention Network (GAT) based framework, termed MGATMDA, for predicting microbe-disease associations. MGATMDA is built on a bipartite graph of microbes and diseases. It contains three essential parts: decomposer, combiner, and predictor. The decomposer first decomposes the edges in the bipartite graph to identify the latent components by node-level attention mechanism. The combiner then recombines these latent components automatically to obtain unified embedding for prediction by component-level attention mechanism. Finally, a fully connected network is used to predict unknown microbes-disease associations. Experimental results showed that our proposed method outperformed eight state-of-the-art methods. Case studies for two common diseases further demonstrated the effectiveness of MGATMDA in predicting potential microbe-disease associations. The codes are available at Github https://github.com/dayunliu/MGATMDA.

Photostable and bright organic dyes emitting in the near-infrared region are highly desirable for long-term dynamic bioimaging. Herein, we report a synthetic approach to build novel methoxy modified Si-rhodamine (SiRMO) dyes by introducing the methoxybenzene on the xanthene moiety. The brightness of SiRMO increased from 2300 M–1cm–1(SiRMO-0) to 49000 M–1cm–1(SiRMO-2) when the substituent 2,5-dimethoxybenzene was replaced with 2,6-dimethoxybenzene. Moreover, the stability of SiRMO-2 was significantly improved due to the steric hindrance protection of the two methoxy groups on the ninth carbon atom of the xanthene. After fast cellular uptake, the SiRMO dyes selectively stained the mitochondria with a low background in live cultured cells and primary neurons. The high brightness and stability of SiRMO-2 significantly improved the capability of monitoring mitochondria dynamic processes in living cells under super-resolution conditions. Moreover, with the fluorescence nanoscopy techniques, we observed the structure of mitochondrial cristae and mitochondria fission, fusion, and apoptosis with a high temporal resolution. Under two-photon illumination, SiRMO-2 showed also enhanced two-photon brightness and stability, which are important for imaging in thick tissue.

Transmembrane protein 268 (TMEM268) encodes a novel human protein of previously unknown function. This study analyzed the biological activities and molecular mechanisms of TMEM268 in vivo and in vitro. We found that TMEM268deletion decreases cell viability, proliferation, and cell adhesion as well as causing S-phase cell cycle arrest and disrupts cytoskeleton remolding. Xenograft tumor mouse model studies showed that TMEM268deletion inhibits the tumorigenesis of BGC823 gastric cancer cells. In addition, TMEM268-deleted BGC823 cells failed to colonize the lungs after intravenous injection and to form metastatic engraftment in the peritoneum. Molecular mechanism studies showed a C-terminal interaction between TMEM268 and integrin subunit β4 (ITGB4). TMEM268knockout promotes ITGB4 ubiquitin-mediated degradation, increasing the instability of ITGB4 and filamin A (FLNA). The reduced ITGB4 protein levels result in the disassociation of the ITGB4/PLEC complex and cytoskeleton remodeling. This study for the first time demonstrates that TMEM268 plays a positive role in the regulation of ITGB4 homeostasis. The above results may provide a new perspective that targeting the TMEM268/ITGB4 signaling axis for the treatment of gastric cancer, which deserves further investigation in the future.

ABSTRACTMARCH2 (membrane-associated RING-CH protein 2), an E3 ubiquitin ligase, is mainly associated with the vesicle trafficking. In the present study, for the first time, we demonstrated that MARCH2 negatively regulates autophagy. Our data indicated that overexpression of MARCH2 impaired autophagy, as evidenced by attenuated levels of LC3B-II and impaired degradation of endogenous and exogenous autophagic substrates. By contrast, loss of MARCH2expression had the opposite effects. In vivo experiments demonstrate that MARCH2knockout mediated autophagy results in an inhibition of tumorigenicity. Further investigation revealed that the induction of autophagy by MARCH2deficiency was mediated through the PIK3CA-AKT-MTOR signaling pathway. Additionally, we found that MARCH2 interacts with CFTR (cystic fibrosis transmembrane conductance regulator), promotes the ubiquitination and degradation of CFTR, and inhibits CFTR-mediated autophagy in tumor cells. The functional PDZ domain of MARCH2 is required for the association with CFTR. Thus, our study identified a novel negative regulator of autophagy and suggested that the physical and functional connection between the MARCH2 and CFTR in different conditions will be elucidated in the further experiments.

Autophagy is a multistep process that involves the degradation and digestion of intracellular components by the lysosome. It has been proved that many core autophagy-related molecules participate in this event. However, new component proteins that regulate autophagy are still being discovered. At present, we report PHF23 (PHD finger protein 23) with a PHD-like zinc finger domain that can negatively regulate autophagy. Data from experiments indicated that the overexpression of PHF23 impaired autophagy, as characterized by decreased levels of LC3B-II and weakened degradation of endogenous and exogenous autophagic substrates. Conversely, knockdown of PHF23resulted in opposite effects. Molecular mechanism studies suggested that PHF23 interacts with LRSAM1, which is an E3 ligase key for ubiquitin-dependent autophagy against invading bacteria. PHF23 promotes the ubiquitination and proteasome degradation of LRSAM1. We also show that the PHD finger of PHF23 is a functional domain needed for the interaction with LRSAM1. Altogether, our results indicate that PHF23 is a negative regulator associated in autophagy via the LRSAM1 signaling pathway. The physical and functional connection between the PHF23 and LRSAM1 needs further investigation.

Human embryonic germ cells (hEGCs) are a valuable and underutilized source of pluripotent stem cells. Unlike embryonic stem cells, which have been extensively studied, little is known about the factors that regulate hEGC derivation and maintenance. This study demonstrates for the first time a central role for selective activation of PDGFR signaling in the derivation and maintenance of pluripotency in hEGCs. In the study, hEGCs were found to express PDGF receptor α at high levels compared to human embryonic stem cells (hESCs). PDGF significantly improved formation of alkaline phosphatase (AP) positive hEGC colonies. We subsequently determined that PDGF activates the phosphatidylinositol-3-kinase (PI3K) pathway as phosphorylation of AKT was up-regulated in response to PDGF. Furthermore, inhibition of PI3K signaling using small molecular inhibitor LY294002 led to significantly decreased AP positive hEGC colony formation whereas inhibition of MAPK pathway using U0126 had a negligible effect. We established a primary mechanism for PDGF mediated derivation and maintenance of hEGCs by demonstrating that OCT4 was upregulated and PTEN was suppressed in a dose dependent manner in response to PDGF.

Thymus transplantation has great clinical potential for treating immunological disorders, but the shortage of transplant donors limits the progress of this therapy. Human embryonic stem cells (hESCs) are promising cell sources for generating thymic epithelial cells. Here, we report a stepwise protocol to direct the differentiation of hESCs into thymic epithelial progenitor-like cells (TEPLCs) by mimicking thymus organogenesis with sequential regulation of Activin, retinoic acid, BMP, and WNT signals. The hESC-derived TEPLCs expressed the key thymic marker gene FOXN1 and could further develop in vivo into thymic epithelium expressing the functional thymic markers MHC II and AIRE upon transplantation. Moreover, the TEPLC-derived thymic epithelium could support mouse thymopoiesis in T-cell-deficient mice and promote human T cell generation in NOD/SCID mice engrafted with human hematopoietic stem cells (hHSCs). These findings could facilitate hESC-based replacement therapy and provide a valuable in vitro platform for studying human thymus organogenesis and regeneration.

Chemotherapy is an important method for the treatment of lung cancer, but multidrug resistance (MDR) greatly reduces the efficacy. The superfamily of ATP-binding cassette (ABC) transport proteins is related to MDR. As a subfamily of ABC proteins, ABCG2/BCRP (breast cancer resistance protein, BCRP) is considered a major player in the development of cancer MDR. For the stratification of chemotherapeutic choices, we constructed Cy5.5- or 89Zr-labeled ABCG2-targeted monoclonal antibody (mAb) ABCG2-PKU1 for noninvasive evaluation of ABCG2 expression in lung cancer xenograft models. ABCG2 expression was screened in H460/MX (mitoxantrone resistant), H460, and H1299 human lung cancer cell lines using Western blotting. ELISA, flow cytometry, and cell immunofluorescent staining were used to evaluate the binding ability of ABCG2-PKU1 to ABCG2 antigen. Lung cancer murine xenograft models were built for in vivoexperiments. ABCG2-PKU1 was labeled with Cy5.5 (Cy5.5-ABCG2) for fluorescent imaging and radiolabeled with 89Zr (89Zr-DFO-ABCG2) for immunoPET imaging following the conjugation with p-SCN-deferoxamine (DFO). In vivoimaging was performed in lung cancer models at 2, 24, 48, 72, 96, 120, 144, and 168 h postinjection. Ex vivobiodistribution was conducted after the terminal time point of imaging. Finally, tissue immunohistochemical staining was used to evaluate the tumor expression of ABCG2. Western blotting showed that the H460/MX cells had a high ABCG2 expression level whereas H460 and H1299 had moderate and low levels. ELISA, flow cytometry, and cell immunofluorescent staining results validated the good binding affinity between ABCG2-PKU1 and ABCG2. The H460/MX and H460 cells were used to build positive lung cancer models, and H1299 cells were used to build negative models. The fluorescent imaging showed that the tumor average radiant efficiency of Cy5.5-ABCG2 reached the maximum at 72 and 120 h in H460/MX and H460 respectively (n= 3, P< 0.01). The tumor uptake of Cy5.5-ABCG2 in H1299 (n= 3) was significantly lower than H460/MX and H460 (P< 0.01). ImmunoPET imaging showed that the tumor uptake of 89Zr-DFO-ABCG2 in H460/MX was significantly higher than H460, with a maximum of 4.15 ± 0.41 %ID/g and 2.81 ± 0.24 %ID/g at 168 and 144 h, respectively (n= 5, P< 0.01). The H1299 tumors showed significantly lower uptake than H460/MX and H460 (n= 5, P< 0.01). The radioactive uptake of 89Zr-DFO-ABCG2 among three groups in the heart, liver, and kidney gradually decreased over time. Ex vivobiodistribution verified the differential tumor uptake among the three groups (P< 0.01). Immunohistochemical staining revealed that the H460/MX tumor had the highest expression of ABCG2, whereas H460 and H1299 had the moderate and lowest expression, respectively. Therefore, in this study, fluorescent and immunoPET imaging of lung cancer MDR models using Cy5.5-ABCG2 and 89Zr-DFO-ABCG2 noninvasively evaluated the differential expression of ABCG2, which are expected to be used for the diagnosis and the selection for clinical treatment options for lung cancer MDR patients in future applications.

This study describes -imaging of the secondary tumors from the transplanted human fetal striatum neural stem cells-derived primary tumor cells in nude mice. The subcutaneous primary tumors were detected to express integrin v3, and the corresponding cells were isolated and enriched in vitro, then transplanted to the nude mice. The technetium-99m-labeled Arg-Gly-Asp peptide, with high affinity to integrin v3, was prepared for biodistribution and -imaging. The secondary tumors were readily visualized at 1-h postinjection, and the tumor uptake of radiotracer was similar to that of positive control animals transplanted with U87MG human glioma cells. The tumor specificity of radiotracer was demonstrated by blocking experiment. We concluded that -imaging is a promising approach in imaging the tumorigenesis of transplanted stem cells in vivo.

Ciliary neurotrophic factor (CNTF) is primarily known for its important cellular effects within the nervous system. However, recent studies indicate that its receptor can be highly expressed in denervated skeletal muscle. Here, we investigated the direct effect of CNTF on skeletal myoblasts of adult human. Surprisingly, we found that CNTF induced the myogenic lineage-committed myoblasts at a clonal level to dedifferentiate into multipotent progenitor cells—they not only could proliferate for over 20 passages with the expression absence of myogenic specific factors Myf5 and MyoD, but they were also capable of differentiating into new phenotypes, mainly neurons, glial cells, smooth muscle cells, and adipocytes. These “progenitor cells” retained their myogenic memory and were capable of redifferentiating into myotubes. Furthermore, CNTF could activate the p44/p42 MAPK and down-regulate the expression of myogenic regulatory factors (MRFs). Finally, PD98059, a specific inhibitor of p44/p42 MAPK pathway, was able to abolish the effects of CNTF on both myoblast fate and MRF expression. Our results demonstrate the myogenic lineage-committed human myoblasts can dedifferentiate at a clonal level and CNTF is a novel regulator of skeletal myoblast dedifferentiation via p44/p42 MAPK pathway.

Microglia are believed to participate in the mediation of neurodegeneration through producing a variety of cytotoxic factors upon activation. Pharmacological intervention in microglial activation may therefore exert a neuroprotective effect. In exploring pharmacological agents that can affect microglial activation, we found in this study that triptolide possesses a powerful inhibitory influence over microglia. Pretreatment with triptolide was able to dosedependently reduce the lipopolysaccharide LPSinduced nitrite accumulation and tumor necrosis factor and interleukin1 release from LPSactivated microglia as revealed by Griess reaction and ELISA, respectively. Triptolide reduced LPSstimulated mRNA expression of all three inflammatory factors. The results obtained from this study demonstrate that triptolide can inhibit inflammatory responses of microglia to inflammatory stimulation via a mechanism involving the inhibition of the synthesis and release of inflammatory factors.