Mechanism study of ubiquitination in T cell development and autoimmune disease.

T cells play critical role in multiple immune processes including antigen response, tumor immunity, inflammation, self-tolerance maintenance and autoimmune diseases et. Fetal liver or bone marrow-derived thymus-seeding progenitors (TSPs) settle in thymus and undergo T cell-lineage commitment, proliferation, T cell receptor (TCR) rearrangement, and thymic selections driven by microenvironment composed of thymic epithelial cells (TEC), dendritic cells (DC), macrophage and B cells, thus generating T cells with diverse TCR repertoire immunocompetent but not self-reactive. Additionally, some self-reactive thymocytes give rise to Treg with the help of TEC and DC, serving for immune tolerance. The sequential proliferation, cell fate decision, and selection during T cell development and self-tolerance establishment are tightly regulated to ensure the proper immune response without autoimmune reaction. There are remarkable progresses in understanding of the regulatory mechanisms regarding ubiquitination in T cell development and the establishment of self-tolerance in the past few years, which holds great potential for further therapeutic interventions in immune-related diseases.

Identification of EMT-associated prognostic features among grade II/III gliomas.

Grade II/III gliomas have a highly heterogeneous clinical course. Identifying prognostic biomarkers in grade II/III gliomas is essential to guide clinical management. We explored epithelial-mesenchymal transition (EMT)-related genes to uncover prognostic features in grade II/III gliomas. Consensus cluster analysis of 200 EMT-related genes classified 512 grade II/III glioma samples into two molecular subtypes, C1 and C2. The C1 subtype had significantly worse overall survival compared to the C2 subtype. Pathway analysis revealed C1 tumors were highly associated with tumor progression pathways and demonstrated higher immune cell infiltration scores. Differential expression analysis identified four genes (ACTN1, AQP1, LAMC3, NRM) that discriminated the two subtypes. Validation in external datasets confirmed that high expression of this four-gene signature predicted poor prognosis in grade II/III gliomas. Cellular experiments showed ACTN1, AQP1 and NRM promoted glioma cell proliferation, migration and invasion. We examined correlations of the signature genes with T cell exhaustion markers and found ACTN1 expression had the strongest association. Immunohistochemistry analysis further demonstrated that ACTN1 protein expression in grade II/III gliomas was negatively correlated with patient overall survival. In summary, our study identified a concise four-gene signature that robustly predicts grade II/III gliomas prognosis across multiple datasets. The signature provides clinical relevance in distinguishing more aggressive grade II/III glioma tumors. Targeting the ACTN1, AQP1 and NRM genes may offer new therapeutic opportunities to improve grade II/III gliomas patient outcomes.

Comment on "An Injectable Hydrogel to Modulate T Cells for Cancer Immunotherapy".

Recent clinical successes of immune checkpoint blockade (ICB) therapies represents a milestone as a novel anti-tumor strategy beyond surgery, radiotherapy, chemotherapy, and targeted therapy in cancer therapy. T cells, especially CD8+ T cells, play crucial roles in anti-tumor immune responses. However, most T cells in the tumor microenvironment express high inhibitory receptors, such as PD-1, TIM-3, and LAG-3, and decreased T cell response in response to stimuli. Applying ICB therapies, such as anti-PD-1, promotes T cell activation and increases cytotoxic T lymphocyte (CTL) response, leading to the enhanced anti-tumor immune response in patients with malignancy. Therefore, studies aimed to define novel targets that can restrain T cell terminal exhaustion are urgently required to provide new strategies for patients resistant to immunotherapy. The previously published study by Zhang et al. (An Injectable Hydrogel to Modulate T Cells for Cancer Immunotherapy, https://doi.org/10.1002/smll.202202663) introduces a new type of injectable hydrogel that can regulate the function of T cells, thereby improving their effectiveness in cancer immunotherapy. However, it remains to be discussed for its conclusion, as the flow cell assay of this article may not be proper.

TRIM55 promotes noncanonical NF-κB signaling and B cell-mediated immune responses by coordinating p100 ubiquitination and processing.

The ubiquitination-dependent processing of NF-κB2 (also known as p100) is a critical step in the activation of the noncanonical NF-κB pathway. We investigated the molecular mechanisms regulating this process and showed that TRIM55 was the E3 ubiquitin ligase that mediated the ubiquitination of p100 and coordinated its processing. TRIM55 deficiency impaired noncanonical NF-κB activation and B cell function. Mice with a B cell-specific Trim55 deficiency exhibited reduced germinal center formation and antibody production. These mice showed less severe symptoms than those of control mice upon the induction of a systemic lupus-like disease, suggesting B cell-intrinsic functions of TRIM55 in humoral immune responses and autoimmunity. Mechanistically, the ubiquitination of p100 mediated by TRIM55 was crucial for p100 processing by VCP, an ATPase that mediates ubiquitin-dependent protein degradation by the proteasome. Furthermore, we found that TRIM55 facilitated the interaction between TRIM21 and VCP as well as TRIM21-mediated K63-ubiquitination of VCP, both of which were indispensable for the formation of the VCP-UFD1-NPL4 complex and p100 processing. Together, our results reveal a mechanism by which TRIM55 fine-tunes p100 processing and regulates B cell-dependent immune responses in vivo, highlighting TRIM55 as a potential therapeutic target for lupus-like disease.

Transcriptomic Profiling of Shoot Apical Meristem Aberrations in the Multi-Main-Stem Mutant (ms) of Brassica napus L.

Rapeseed (Brassica napus L.) is a globally important oilseed crop with various uses, including the consumption of its succulent stems as a seasonal vegetable, but its uniaxial branching habit limits the stem yield. Therefore, developing a multi-stem rapeseed variety has become increasingly crucial. In this study, a natural mutant of the wild type (ZY511, Zhongyou511) with stable inheritance of the multi-stem trait (ms) was obtained, and it showed abnormal shoot apical meristem (SAM) development and an increased main stem number compared to the WT. Histological and scanning electron microscopy analyses revealed multiple SAMs in the ms mutant, whereas only a single SAM was found in the WT. Transcriptome analyses showed significant alterations in the expression of genes involved in cytokinin (CK) biosynthesis and metabolism pathways in the ms mutant. These findings provide insight into the mechanism of multi-main-stem formation in Brassica napus L. and lay a theoretical foundation for breeding multi-main-stem rapeseed vegetable varieties.

"Turn-on" fluorescent sensor for oleanolic acid based on o-phenyl-bridged bis-tetraphenylimidazole.

Fluorescent sensors had been extensively applied on sensing various biomolecules effectively, but no fluorescent sensor for oleanolic acid was presented up to now. In this work, the first fluorescent sensor for oleanolic acid was designed and synthesized based on o-phenyl-bridged bis-tetraphenylimidazole (PTPI). PTPI was prepared by bridging two tetraphenylimidazole units and o-phenylenediamine via Schiff-base condensation in yield of 86%. PTPI showed high sensing selectivity for oleanolic acid among 26 biomolecules and ions. The blue fluorescence at 482 nm was enhanced by 4.5 times after sensing oleanolic acid in aqueous media. The fluorescence sensing ability of PTPI for oleanolic acid maintained stable in pH = 5-9. The detecting limitation was as low as 0.032 µM. The detecting mechanism was clarified as 1:1 binding stoichiometry by fluorescence Job's plot, mass spectrometry, 1H nuclear magnetic resonance and fourier transform infrared spectroscopy. The detecting ability of PTPI for oleanolic acid was successfully used for paper test and real samples of grapes and Kuding tea with recoveries in the range of 96.0%-106.0%, indicating the good application potential for on-site detecting oleanolic acid in real samples of fruits and food.

Effects of Low Nighttime Temperature on Fatty Acid Content in Developing Seeds from Brassica napus L. Based on RNA-Seq and Metabolome.

Brassica napus L. is a vital plant oil resource worldwide. The fatty acid biosynthesis and oil accumulation in its seeds are controlled by several genetic and environmental factors, including daytime and nighttime temperatures. We analyzed changes in oleic and erucic acid content in two double haploid (DH) lines, DH0729, a weakly temperature-sensitive line, and DH0815, a strongly temperature-sensitive line, derived from B. napus plants grown at different altitudes (1600, 1800, 2000, 2200, and 2400 m a.s.l., 28.85° N, 112.35° E) and nighttime temperatures (20/18, 20/16, 20/13 and 20/10 °C, daytime/nighttime temperature). Based on medium- and long-chain fatty acid metabolites, the total oleic acid content 35 and 43 days after flowering was significantly lower in low nighttime temperature (LNT, 20/13 °C) plants than in high nighttime temperature (HNT, 20/18 °C) plants (HNT: 58-62%; LNT: 49-54%; an average decrease of 9%), and the total erucic acid content was significantly lower in HNT than in LNT plants (HNT: 1-2%; LNT: 8-13%; an average increase of 10%). An RNA-seq analysis showed that the expression levels of SAD (LOC106366808), ECR (LOC106396280), KCS (LOC106419344), KAR (LOC106367337), HB1(LOC106430193), and DOF5 (LOC111211868) in STSL seeds increased under LNT conditions. In STSL seeds, a base mutation in the cis-acting element involved in low-temperature responsiveness (LTR), the HB1 and KCS promoter caused loss of sensitivity to low temperatures, whereas that of the KCS promoter caused increased sensitivity to low temperatures.

Targeting NF-κB pathway for the therapy of diseases: mechanism and clinical study.

NF-κB pathway consists of canonical and non-canonical pathways. The canonical NF-κB is activated by various stimuli, transducing a quick but transient transcriptional activity, to regulate the expression of various proinflammatory genes and also serve as the critical mediator for inflammatory response. Meanwhile, the activation of the non-canonical NF-κB pathway occurs through a handful of TNF receptor superfamily members. Since the activation of this pathway involves protein synthesis, the kinetics of non-canonical NF-κB activation is slow but persistent, in concordance with its biological functions in the development of immune cell and lymphoid organ, immune homeostasis and immune response. The activation of the canonical and non-canonical NF-κB pathway is tightly controlled, highlighting the vital roles of ubiquitination in these pathways. Emerging studies indicate that dysregulated NF-κB activity causes inflammation-related diseases as well as cancers, and NF-κB has been long proposed as the potential target for therapy of diseases. This review attempts to summarize our current knowledge and updates on the mechanisms of NF-κB pathway regulation and the potential therapeutic application of inhibition of NF-κB signaling in cancer and inflammatory diseases.

Tertiary Lymphoid Organs in Cancer Immunology: Mechanisms and the New Strategy for Immunotherapy.

The immune system plays pivotal roles in the occurrence and progression of cancers. As blockade of immune-checkpoint has been proven effective at improving anti-tumor immune response in multiple tumor types, the tumor immunotherapy still faces many challenges. Emerging evidence indicates lymphoid organ-like structures, also called tertiary lymphoid organs (TLOs) or ectopic lymphoid organs (ELOs), have been identified in cancers, as the result of lymphoid neoorganogenesis. The prognostic value of TLOs in cancer patients has been evaluated with debates, however, such well-organized lymphoid structures in the site of cancer indicate TLOs are the important modulators of cancer immunological microenvironment. TLOs have attracted remarkable efforts to investigate their neoorganogenesis and function in immune responses, aiming to develop new strategies for cancer immunotherapy. In this review, we summarize the current understandings about the molecular and cellular mechanisms governing the formation and function of TLOs in immune responses against cancer.

Comparative Transcriptome Analysis in Oilseed Rape (Brassica napus) Reveals Distinct Gene Expression Details between Nitrate and Ammonium Nutrition.

Nitrate (NO3-) and ammonium (NH4+) are the main inorganic nitrogen (N) sources absorbed by oilseed rape, a plant that exhibits genotypic differences in N efficiency. In our previous study, the biomass, N accumulation, and root architecture of two oilseed rape cultivars, Xiangyou 15 (high N efficiency, denoted "15") and 814 (low N efficiency, denoted "814"), were inhibited under NH4+ nutrition, though both cultivars grew normally under NO3- nutrition. To gain insight into the underlying molecular mechanisms, transcriptomic changes were investigated in the roots of 15 and 814 plants subjected to nitrogen-free (control, CK), NO3- (NT), and NH4+ (AT) treatments at the seedling stage. A total of 14,355 differentially expressed genes (DEGs) were identified. Among the enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway categories of these DEGs, carbohydrate metabolism, lipid metabolism, protein metabolism, and cell wall biogenesis were inhibited by AT treatment. Interestingly, DEGs such as N transporters, genes involved in N assimilation and CESA genes related to cellulose synthase were also mostly downregulated in the AT treatment group. This downregulation of genes related to crucial metabolic pathways resulted in inhibition of oilseed rape growth after AT treatment.

Erratum: Author Correction to: TRIM29 negatively controls antiviral immune response through targeting STING for degradation.

[This corrects the article DOI: 10.1038/s41421-018-0010-9.].

TRIM29 negatively controls antiviral immune response through targeting STING for degradation.

Innate immune system is armed by several lines of pattern recognition receptors to sense various viral infection and to initiate antiviral immune response. This process is under a tight control and the negative feedback induced by infection and/or inflammation is critical to maintain immune homoeostasis and to prevent autoimmune disorders, however, the molecular mechanism is not fully understood. Here we report TRIM29, a ubiquitin E3 ligase, functions as an inducible negative regulator of innate immune response triggered by DNA virus and cytosolic DNA. DNA virus and cytosolic DNA stimulation induce TRIM29 expression robustly in macrophages and dendritic cells, although the basal level of TRIM29 is undetectable in those cells. TRIM29 deficiency elevates IFN-I and proinflammatory cytokine production upon viral DNA and cytosolic dsDNA stimulation. Consistently, in vivo experiments show that TRIM29-deficient mice are more resistant to HSV-1 infection than WT controls, indicated by better survival rate and reduced viral load in organs. Mechanism studies suggest that STING-TBK1-IRF3 signaling pathway in TRIM29 KO cells is significantly enhanced and the degradation of STING is impaired. Furthermore, we identify that TRIM29 targets STING for K48 ubiquitination and degradation. This study reveals TRIM29 as a crucial negative regulator in immune response to DNA virus and cytosolic DNA, preventing potential damage caused by overcommitted immune responses.

Diphenylacrylonitrile-connected BODIPY dyes: fluorescence enhancement based on dark and AIE resonance energy transfer.

This study focuses on the construction of novel diphenylacrylonitrile-connected BODIPY dyes with high fluorescence in both solution and an aggregated state by combining DRET and FRET processes in a single donor-acceptor system. The first BODIPY derivatives with one, two, or three AIE-active diphenylacrylonitrile groups were designed and synthesized in moderate yields. Strong fluorescence emissions were observed in the THF solution under excitation at the absorption wavelength of non-emissive diphenylacrylonitrile chromophores, implying the existence of the DRET process between the dark diphenylacrylonitrile donor and the emissive BODIPY acceptor. In the THF/H2O solution, the fluorescence intensity of the novel BODIPY derivatives gradually increased under excitation at the absorption wavelength of diphenylacrylonitrile chromophores, suggesting a FRET process between diphenylacrylonitrile and BODIPY moieties. A greater number of diphenylacrylonitrile units led to higher energy-transfer efficiencies. The pseudo-Stokes shift for both DRET and FRET processes was as large as 190 nm.

[Somatic hybridization between Brassica napus and Eruca sativa mill].

In order to expand gene resources and improve Brassica napus cultivars, protoplasts isolated from hypocotyls of Brassica napus cv. Huayou No. 3 and Eruca sativa were fused by PEG-high Ca2+-high pH. Fusion frequency was up to 18.2% when fusion system contained 5 x 10(5) protoplasts/mL, and when PEG concentration of fusion agents were 35% and when fusion time was 25 min. Then the fused protoplasts were cultured by the method of thin liquid layer at the density of 1 x 10(5) protoplasts/mL in improved KM8p medium supplemented with 1.0 mg/L 2,4-D, 0.5 mg/L NAA, 0.5 mg/L 6-BA, 200 mg/L inositol, 300 mg/L protein hydrolysate, and the combinations of 0.1 mol/L sucrose and 0.2 mol/L glucose and 0.2 mol/L mannitol for osmotic regulator, the frequency of callus regeneration was up to 6.8%. When the micro-calli transferred to the proliferation medium that contained B5 salts, 0.087 mol/L sucrose, 0.2 mg/L 2,4-D, 0.5 mg/L NAA, 0.2 mg/L 6-BA and 0.5% Agar, pH 5.8, have grown up to 3-5 mm of diameter, the calli were transferred to the differentiation medium that contained MS salts, 0.087 mol/L sucrose, 0.1 mg/L IAA, 0.8 mg/L 6-BA, 0.8% Agar, pH5.8, the shoots were regenerated in 4 weeks and its frequency was up to 32.8%. Then 2-3 cm shoots were transferred to 1/2 MS medium with 0.5 mg/L IBA+0.2mg/L 6-BA, plantlets were obtained in 14 days and the plantlet frequency was up to 88%. When the protoplasts of Eruca sativa were treated with UV radiation for 2 minutes calli and plantlets have been regenerated, treated for 4 min only calli have been regenerated, and treated for more than 5 min calli have not been regenerated. The callus regeneration and callus proliferation and plant regeneration from symmetric fusion were more than from asymmetric fusion. 16 hybrid plantlets have been regenerated on 21 piece of hybrid calli identified by cytology method.