Allosteric regulation of nitrate transporter NRT via the signaling protein PII.

Coordinated carbon and nitrogen metabolism is crucial for bacteria living in the fluctuating environments. Intracellular carbon and nitrogen homeostasis is maintained by a sophisticated network, in which the widespread signaling protein PII acts as a major regulatory hub. In cyanobacteria, PII was proposed to regulate the nitrate uptake by an ABC (ATP-binding cassette)-type nitrate transporter NrtABCD, in which the nucleotide-binding domain of NrtC is fused with a C-terminal regulatory domain (CRD). Here, we solved three cryoelectron microscopy structures of NrtBCD, bound to nitrate, ATP, and PII, respectively. Structural and biochemical analyses enable us to identify the key residues that form a hydrophobic and a hydrophilic cavity along the substrate translocation channel. The core structure of PII, but not the canonical T-loop, binds to NrtC and stabilizes the CRD, making it visible in the complex structure, narrows the substrate translocation channel in NrtB, and ultimately locks NrtBCD at an inhibited inward-facing conformation. Based on these results and previous reports, we propose a putative transport cycle driven by NrtABCD, which is allosterically inhibited by PII in response to the cellular level of 2-oxoglutarate. Our findings provide a distinct regulatory mechanism of ABC transporter via asymmetrically binding to a signaling protein.

Nucleic Acid Sensing by STING Induces an IFN-like Antiviral Response in a Marine Invertebrate.

The cytosolic detection of pathogen-derived nucleic acids has evolved as an essential strategy for host innate immune defense in mammals. One crucial component in this process is the stimulator of IFN genes (STING), which acts as a vital signaling adaptor, connecting the cytosolic detection of DNA by cyclic GMP-AMP (cGAMP) synthase (cGAS) to the downstream type I IFN signaling pathway. However, this process remains elusive in invertebrates. In this study, we present evidence demonstrating that STING, an ortholog found in a marine invertebrate (shrimp) called Litopenaeus vannamei, can directly detect DNA and initiate an IFN-like antiviral response. Unlike its homologs in other eukaryotic organisms, which exclusively function as sensors for cyclic dinucleotides, shrimp STING has the ability to bind to both double-stranded DNA and cyclic dinucleotides, including 2'3'-cGAMP. In vivo, shrimp STING can directly sense DNA nucleic acids from an infected virus, accelerate IFN regulatory factor dimerization and nuclear translocation, induce the expression of an IFN functional analog protein (Vago4), and finally establish an antiviral state. Taken together, our findings unveil a novel double-stranded DNA-STING-IKKε-IRF-Vago antiviral axis in an arthropod, providing valuable insights into the functional origins of DNA-sensing pathways in evolution.

The MIP-T3 from shrimp Litopenaeus vannamei restricts white spot syndrome virus infection via regulating NF-κB activation.

In vertebrate, MIP-T3 (microtubule-interacting protein associated with TRAF3) functions as a regulator of innate immune response that involves many cellular processes. However, the immune response regulated by shrimp (an arthropod) MIP-T3 remains unrevealed. In the present study, a MIP-T3 homolog from shrimp Litopenaeus vannamei (named as LvMIP-T3) was cloned and identified. LvMIP-T3 had a 2076 bp open reading frame (ORF), encoding a polypeptide of 691 amino acids that contained a classic coiled-coil domain in the C-terminal that showed a high degree of conservation to other homologs. LvMIP-T3 could interact with LvTRAF6, a member of the canonical NF-κB pathway, but not LvTRAF3, which implies that LvMIP-T3 is able to regulate NF-κB activity via its interaction with LvTRAF6. In addition, LvMIP-T3 was substantially inducted in response to white spot syndrome virus (WSSV) challenge, and we demonstrated that LvMIP-T3 facilitated the expression of NF-κB-mediated several Penaeidins (antimicrobial peptides, AMPs) to oppose infection. Taken together, we identified a MIP-T3 homolog from shrimp L. vannamei that played a positive role in the TRAF6/NF-κB/AMPs axis mediated defense response, which will contribute to better understand the regulator relationship among members of the canonical NF-κB pathway in shrimp, and provides some insights into disease resistance breeding.

Pancreatic fibroblast growth factor 21 protects against type 2 diabetes in mice by promoting insulin expression and secretion in a PI3K/Akt signaling-dependent manner.

Fibroblast growth factor 21 (FGF21) is important in glucose, lipid homeostasis and insulin sensitivity. However, it remains unknown whether FGF21 is involved in insulin expression and secretion that are dysregulated in type 2 diabetes mellitus (T2DM). In this study, we found that FGF21 was down-regulated in pancreatic islets of db/db mice, a mouse model of T2DM, along with decreased insulin expression, suggesting the possible involvement of FGF21 in maintaining insulin homeostasis and islet ß-cell function. Importantly, FGF21 knockout exacerbated palmitate-induced islet ß-cell failure and suppression of glucose-stimulated insulin secretion (GSIS). Pancreatic FGF21 overexpression significantly increased insulin expression, enhanced GSIS, improved islet morphology and reduced ß-cell apoptosis in db/db mice. Mechanistically, FGF21 promoted expression of insulin gene transcription factors and soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins, the major regulators of insulin secretion, as well as activating phosphatidylinositol 3-kinase (PI3K)/Akt signaling in islets of db/db mice. In addition, pharmaceutical inhibition of PI3K/Akt signaling effectively suppressed FGF21-induced expression of insulin gene transcription factors and SNARE proteins, suggesting an essential role of PI3K/Akt signaling in FGF21-induced insulin expression and secretion. Taken together, our results demonstrate a protective role of pancreatic FGF21 in T2DM mice through inducing PI3K/Akt signaling-dependent insulin expression and secretion.

Risk stratification of thymic epithelial tumors based on peritumor CT radiomics and semantic features.

OBJECTIVES: To develop and validate nomograms combining radiomics and semantic features to identify the invasiveness and histopathological risk stratification of thymic epithelial tumors (TET) using contrast-enhanced CT. METHODS: This retrospective multi-center study included 224 consecutive cases. For each case, 6764 intratumor and peritumor radiomics features and 31 semantic features were collected. Multi-feature selections and decision tree models were performed on radiomics features and semantic features separately to select the most important features for Masaoka-Koga staging and WHO classification. The selected features were then combined to create nomograms for the two systems. The performance of the radiomics model, semantic model, and combined model was evaluated using the area under the receiver operating characteristic curves (AUCs). RESULTS: One hundred eighty-seven cases (56.5 years ± 12.3, 101 men) were included, with 62 cases as the external test set. For Masaoka-Koga staging, the combined model, which incorporated five peritumor radiomics features and four semantic features, showed an AUC of 0.958 (95% CI: 0.912-1.000) in distinguishing between early-stage (stage I/II) and advanced-stage (III/IV) TET in the external test set. For WHO classification, the combined model incorporating five peritumor radiomics features and two semantic features showed an AUC of 0.857 (0.760-0.955) in differentiating low-risk (type A/AB/B1) and high-risk (B2/B3/C) TET. The combined models showed the most effective predictive performance, while the semantic models exhibited comparable performance to the radiomics models in both systems (p > 0.05). CONCLUSION: The nomograms combining peritumor radiomics features and semantic features could help in increasing the accuracy of grading invasiveness and risk stratification of TET. CRITICAL RELEVANCE STATEMENT: Peripheral invasion and histopathological type are major determinants of treatment and prognosis of TET. The integration of peritumoral radiomics features and semantic features into nomograms may enhance the accuracy of grading invasiveness and risk stratification of TET. KEY POINTS: Peritumor region of TET may suggest histopathological and invasive risk. Peritumor radiomic and semantic features allow classification by Masaoka-Koga staging (AUC: 0.958). Peritumor radiomic and semantic features enable the classification of histopathological risk (AUC: 0.857).

Overcoming artificial structures in resolution-enhanced Hi-C data by signal decomposition and multi-scale attention.

Computational enhancement is an important strategy for inferring high-resolution features from genome-wide chromosome conformation capture (Hi-C) data, which typically have limited resolution. Deep learning has been highly successful in this task but we show that it creates prevalent artificial structures in the enhanced data due to the need to divide the large contact matrix into small patches. In addition, previous deep learning methods largely focus on local patterns, which cannot fully capture the complexity of Hi-C data. Here we propose Smooth, High-resolution, and Accurate Reconstruction of Patterns (SHARP) for enhancing Hi-C data. It uses the novel approach of decomposing the data into three types of signals, due to one-dimensional proximity, contiguous domains, and other fine structures, and applies deep learning only to the third type of signals, such that enhancement of the first two is unaffected by the patches. For the deep learning part, SHARP uses both local and global attention mechanisms to capture multi-scale contextual information. We compare SHARP with state-of-the-art methods extensively, including application to data from new samples and another species, and show that SHARP has superior performance in terms of resolution enhancement accuracy, avoiding creation of artificial structures, identifying significant interactions, and enrichment in chromatin states.

Distribution, migration patterns, and food chain human health risks of endocrine-disrupting chemicals in water, sediments, and fish in the Xiangjiang River.

Exposure to endocrine-disrupting chemicals (EDCs) in freshwater systems has garnered increasing attention. A comprehensive analysis of the migration patterns, bioaccumulation, and consumer health risk of EDCs along the Xiangjiang River due to fish consumption from the river ecosystem was provided. Twenty natural and synthetic target EDCs were detected and analyzed from the water, sediments, and fish samples collected along the Xiangjiang River. There were significant correlations between the EDC concentrations in fish and the sediments. This revealed that EDCs in sediments play a dominant role in the uptake of EDCs by fish. The bioaccumulation factor and biota-sediment accumulation factor were calculated, with the highest values observed for nonylphenol. Pearson's correlation analysis showed that bisphenol A is the most reliable biological indicator of EDC contamination in fish. Furthermore, based on the threshold of toxicological concerns and the health risk with dietary intake, crucian carp and catfish from the Xiangjiang River pose a certain risk for children and pregnant women compared to grass carp. The Monte Carlo simulation results indicated a certain risk of cumulative ∑EDC exposure for local residents due to fish consumption.

Signaling events induced by lipopolysaccharide-activated Toll in response to bacterial infection in shrimp.

Toll-like receptors (TLR) play a crucial role in the detection of microbial infections in vertebrates and invertebrates. Mammalian TLRs directly recognize a variety of structurally conserved microbial components. However, invertebrates such as Drosophila indirectly recognize microbial products by binding to the cytokine-like ligand Spätzle, which activates signaling cascades that are not completely understood. In this study, we investigated the signaling events triggered by Toll in response to lipopolysaccharide (LPS), a cell wall component of gram-negative bacteria, and Vibrio parahaemolyticus infection in the arthropod shrimp Litopenaeus vannamei. We found that five of the nine Tolls from L. vannamei bound to LPS and the RNAi of LvToll1, LvToll2, LvToll3, LvToll5, and LvToll9 weakened LvDorsal-L phosphorylation induced by V. parahaemolyticus. All nine Tolls combined with MyD88 via the TIR domain, thereby conferring signals to the tumor necrosis factor receptor-associated factor 6 (TRAF6)-transforming growth factor-ß activated kinase 1 binding protein 2 (TAB2)-transforming growth factor-ß activated kinase 1 (TAK1) complex. Further examination revealed that the LvTRAF6-LvTAB2-LvTAK1 complex contributes to Dorsal-L phosphorylation and nuclear translocation during V. parahaemolyticus infection. Overall, shrimp Toll1/2/3/5/9-TRAF6/TAB2/TAK1-Dorsal cascades protect the host from V. parahaemolyticus infection, which provides a better understanding of how the innate immune system recognizes and responds to bacterial infections in invertebrates.

The combination of machine learning and transcriptomics reveals a novel megakaryopoiesis inducer, MO-A, that promotes thrombopoiesis by activating FGF1/FGFR1/PI3K/Akt/NF-κB signaling.

Radiation-induced thrombocytopenia (RIT) occurs widely and causes high mortality and morbidity in cancer patients who receive radiotherapy. However, specific drugs for treating RIT remain woefully inadequate. Here, we first developed a drug screening model using naive Bayes, a machine learning (ML) algorithm, to virtually screen the active compounds promoting megakaryopoiesis and thrombopoiesis. A natural product library was screened by the model, and methylophiopogonanone A (MO-A) was identified as the most active compound. The activity of MO-A was then validated in vitro and showed that MO-A could markedly induce megakaryocyte (MK) differentiation of K562 and Meg-01 cells in a concentration-dependent manner. Furthermore, the therapeutic action of MO-A on RIT was evaluated, and MO-A significantly accelerated platelet level recovery, platelet activation, megakaryopoiesis, MK differentiation in RIT mice. Moreover, RNA-sequencing (RNA-seq) indicated that the PI3K cascade was closely related to MK differentiation induced by MO-A. Finally, experimental verification demonstrated that MO-A obviously induced the expression of FGF1 and FGFR1, and increased the phosphorylation of PI3K, Akt and NF-κB. Blocking FGFR1 with its inhibitor dovitinib suppressed MO-A-induced MK differentiation, and PI3K, Akt and NF-κB phosphorylation. Similarly, inhibition of PI3K-Akt signal pathway by its inhibitor LY294002 suppressed MK differentiation, and PI3K, Akt and NF-κB phosphorylation induced by MO-A. Taken together, our study provides an efficient drug discovery strategy for hematological diseases, and demonstrates that MO-A is a novel countermeasure for treating RIT through activation of the FGF1/FGFR1/PI3K/Akt/NF-κB signaling pathway.

Stimulator of interferon genes defends against bacterial infection via IKKß-mediated Relish activation in shrimp.

Stimulator of interferon genes (STING) is crucial for the innate immune to defend against pathogenic infections. Our previous study showed that a STING homolog from Litopenaeus vannamei (LvSTING) was involved in antibacterial response via regulating antimicrobial peptides (AMPs). Nevertheless, how LvSTING induces AMPs expression to inhibit bacterial infection remains unknown. Herein, we revealed that the existence of a STING-IKKß-Relish-AMPs axis in shrimp that was essential for opposing to Vibrio parahaemolyticus invasion. We observed that LvRelish was essential for host defense against V. parahaemolyticus infection via inducing several AMPs, such as LvALF1, LvCRU1, LvLYZ1 and LvPEN4. Knockdown of LvSTING or LvIKKß in vivo led to the attenuated phosphorylation and diminished nuclear translocation of LvRelish, as well as the impaired expression levels of LvRelish-regulated AMPs. Accordingly, shrimps with knockdown of LvSTING or LvIKKß or both were vulnerable to V. parahaemolyticus infection. Finally, LvSTING could recruit LvRelish and LvIKKß to form a complex, which synergistically induced the promoter activity of several AMPs in vitro. Taken together, our results demonstrated that the shrimp STING-IKKß-Relish-AMPs axis played a critical role in the defense against bacterial infection, and provided some insights into the development of disease prevention strategies in shrimp culture.

SIRT1 Mediates Effects of FGF21 to Ameliorate Cisplatin-Induced Acute Kidney Injury.

Acute kidney injury (AKI) is a common complication in cancer patients. Kidney function is closely related to patients' quality of life and tumor prognosis. Cisplatin is a highly effective anti-tumor drug. However, the use of cisplatin is limited by its nephrotoxicity. It has been reported that FGF21 has a renal-protective function, but the mechanisms by which it does so remain unclear. In this study, we show that the expression of FGF21 is significantly upregulated in both in vitro and in vivo cisplatin-induced AKI models. Administration of recombinant FGF21 to cisplatin-induced AKI mice resulted in significantly decreased blood urea nitrogen (BUN) and serum creatinine levels, as well as significantly reduced protein levels of kidney injury molecule-1 (TIM-1), C-caspase 3, and Bax. H&E-stained kidney sections from cisplatin-induced AKI mice treated with recombinant FGF21 showed a relatively normal renal tissue structure, a reduced number of necrotic sites and vacuolar changes, and decreased casts, suggesting alleviated renal tubular injury. Experiments with an AKI cell model (cisplatin-treated HK-2 cells) yielded similar results as the mouse model; recombinant FGF21 significantly downregulated protein expression levels of TIM-1, C-caspase 3, and Bax. Furthermore, administration of recombinant FGF21 to cisplatin-treated AKI models significantly increased SIRT1 expression, and the beneficial effects of FGF21 on kidney injury were reversed by SIRT1 knockdown. Collectively, our results suggest that SIRT1 mediates the protective effect of FGF21 on cisplatin-induced kidney injury.