Discovery of tumor-reactive T cell receptors by massively parallel library synthesis and screening.

T cell receptor (TCR) gene therapy is a potent form of cellular immunotherapy in which patient T cells are genetically engineered to express TCRs with defined tumor reactivity. However, the isolation of therapeutic TCRs is complicated by both the general scarcity of tumor-specific T cells among patient T cell repertoires and the patient-specific nature of T cell epitopes expressed on tumors. Here we describe a high-throughput, personalized TCR discovery pipeline that enables the assembly of complex synthetic TCR libraries in a one-pot reaction, followed by pooled expression in reporter T cells and functional genetic screening against patient-derived tumor or antigen-presenting cells. We applied the method to screen thousands of tumor-infiltrating lymphocyte (TIL)-derived TCRs from multiple patients and identified dozens of CD4+ and CD8+ T-cell-derived TCRs with potent tumor reactivity, including TCRs that recognized patient-specific neoantigens.

USP3 plays a critical role in the induction of innate immune tolerance.

Microbial products, such as lipopolysaccharide (LPS), can elicit efficient innate immune responses against invading pathogens. However, priming with LPS can induce a form of innate immune memory, termed innate immune "tolerance", which blunts subsequent NF-κB signaling. Although epigenetic and transcriptional reprogramming has been shown to play a role in innate immune memory, the involvement of post-translational regulation remains unclear. Here, we report that ubiquitin-specific protease 3 (USP3) participates in establishing "tolerance" innate immune memory through non-transcriptional feedback. Upon NF-κB signaling activation, USP3 is stabilized and exits the nucleus. The cytoplasmic USP3 specifically removes the K63-linked polyubiquitin chains on MyD88, thus negatively regulating TLR/IL1ß-induced inflammatory signaling activation. Importantly, cytoplasmic translocation is a prerequisite step for USP3 to deubiquitinate MyD88. Additionally, LPS priming could induce cytoplasmic retention and faster and stronger cytoplasmic translocation of USP3, enabling it to quickly shut down NF-κB signaling upon the second LPS challenge. This work identifies a previously unrecognized post-translational feedback loop in the MyD88-USP3 axis, which is critical for inducing normal "tolerance" innate immune memory.

Next Generation Sequencing-Based Identification of T-Cell Receptors for Immunotherapy Against Hepatocellular Carcinoma.

Hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) remains a global health concern, and HBV proteins may be ideal targets for T cell-based immunotherapy for HCC. There is a need for fast and efficient identification of HBV-specific T cell receptors (TCRs) for the development of TCR-transduced T (TCR-T) cell-based immunotherapy. Two widely employed TCR identification approaches, T cell clonal expansion and single-cell sequencing, involve a TCR singularization process for the direct identification of Vα and Vß pairs of TCR chains. Clonal expansion of T cells is well known to have tedious time and effort requirements due to the use of T cell cultures, whereas single-cell sequencing is limited by the requirements of cell sorting and the preparation of a single-cell immune-transcriptome library as well as the massive cost of the whole procedure. Here, we present a next-generation sequencing (NGS)-based HBV-specific TCR identification that does not require the TCR singularization process. Conclusion: Two pairing strategies, ranking-based strategy and α-ß chain mixture-based strategy, have proved to be useful for NGS-based TCR identification, particularly for polyclonal T cells purified by a peptide-major histocompatibility complex (pMHC) multimer-based approach. Functional evaluation confirmed the specificity and avidity of two identified HBV-specific TCRs, which may potentially be used to produce TCR-T cells to treat patients with HBV-related HCC.

High-throughput screening of functional deubiquitinating enzymes in autophagy.

Macroautophagy/autophagy, a eukaryotic homeostatic process that sequesters cytoplasmic constituents for lysosomal degradation, is orchestrated by a number of autophagy-related (ATG) proteins tightly controlled by post-translational modifications. However, the involvement of reversible ubiquitination in the regulation of autophagy remains largely unclear. Here, we performed a single-guide RNA-based screening assay to investigate the functions of deubiquitinating enzymes (DUBs) in regulating autophagy. We identified previously unrecognized roles of several DUBs in modulating autophagy at multiple levels by targeting various ATG proteins. Mechanistically, we demonstrated that STAMBP/AMSH (STAM-binding protein) promotes the stabilization of ULK1 by removing its lysine 48 (K48)-linked ubiquitination, whereas OTUD7B mediates the degradation of PIK3 C3 by enhancing its K48-linked ubiquitination, thus positively or negatively affects autophagy flux, respectively. Together, our study elaborated on the broad involvement of DUBs in regulating autophagy and uncovered the critical roles of the reversible ubiquitination in the modification of ATG proteins.Abbreviations: ATG: autophagy-related; Baf A1: bafilomycin A1; DUB: deubiquitinating enzyme; EBSS: Earle's balanced salt solution; KO: knockout; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; OTUD7B: OTU domain-containing protein 7B; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; sgRNA: single-guide RNA; SQSTM1/p62: sequestosome 1; STAMBP/AMSH: STAM-binding protein; ULK1: unc-51 like autophagy activating kinase 1; USP: ubiquitin specific peptidase.

Phenotypic analysis of tumor-infiltrating lymphocytes from non-small cell lung cancer and their potential application for adoptive cell therapy.

AIM: Adoptive cell therapy (ACT) of tumor-infiltrating lymphocytes (TILs) has demonstrated clinical benefits in metastatic melanoma treatment. However, the clinical application of TILs produced by a widely used standard protocol from non-small cell lung cancer (NSCLC) can be quite challenging because of the limited clinical benefits. A comprehensive phenotypic knowledge of TILs obtained from NSCLC is important for the development and improvement of personalized TIL therapy for NSCLC patients. METHODS: In this study, we successfully expanded TILs from 141 NSCLC tissues which can be used in clinical ACT after expansion by a rapid expansion protocol (REP). RESULTS: Our study indicates that the clinicopathological characteristics of patients have considerable impacts on the phenotype of in vitro TIL culture products. Different culture conditions are necessary for patients with different clinical features. Specific manipulations before REP expansion are required depending on the different phenotypes of TIL cultures (e.g. depletion of immune-suppressive γδT cells). With these optimizations, next-generation TIL therapy may become a treatment alternative for NSCLC patients in the future.

A Novel Order Analysis and Stacked Sparse Auto-Encoder Feature Learning Method for Milling Tool Wear Condition Monitoring.

Milling is a main processing mode of the modern manufacturing industry, which seriously affects the quality and precision of the machined workpiece. However, it is difficult to monitor the tool wear condition in the continuous cutting process, especially under a variable speed condition. The existing tool wear condition monitoring methods only carry out analysis with a constant engine speed. Different from the general monitoring methods, this paper put forward a milling cutter wear condition monitoring method based on order analysis (OA) and stacked sparse autoencoder (SSAE). The methodology in the research include signals feature extraction and tool wear state monitoring and were designed to analyze the three-phase spindle current signals instead of the traditional force signals and vibration signals. The variable speed signals were transformed into angle domain stationary signals by order analysis, and the SSAE neural network was used to monitor the tool wear state. The proposed method was verified on the laboratory signals and the results showed a better performance than the other methods and a better applicability in actual industrial manufacturing.

Targeted photoresponsive carbazole-coumarin and drug conjugates for efficient combination therapy in leukemia cancer cells.

Phototriggered drug delivery systems (PTDDSs) facilitate controlled delivery of drugs loaded on photoactive platform to the target region under light stimulation. The present study investigated the synthesis and efficacy of carbazole-coumarin (CC)-fused heterocycles as a PTDDS platform for the photocontrolled release of a chemotherapeutic agent, chlorambucil, in an in vitro model of human breast and leukemia cancer cells. CC-fused heterocycles were constructed using 4-hydroxycarbazole as the starting material, and further modification of these heterocycles yielded two CC derivatives. CC-7 with an additional - COOH group and CC-8 with the triphenylphosphonium (TPP) group, a mitochondria-targeting ligand introduced in the carbazole ring, dissolved in polar solvents and exhibited emission bands at 360 and 450 nm, respectively. The results indicate that visible light of 405 nm triggers the photolysis of the CC-drug conjugate and efficiently delivers the drug in both in vitro cancer cell models. Cytotoxicity evaluation indicates the suppression of proliferation of both types of cells treated with CC-8 under synergy effect combining drug potency and photosensitization. Further, the lower IC50 of CC-8 toward leukemia cells suggests the efficacy of the TPP ligand in increasing the bioavailability of CC-drug conjugates in leukemia treatment. Studies on mitochondria-targeting drug delivery systems are required for improving the performance of anticancer drugs.

A Reliable Prognosis Approach for Degradation Evaluation of Rolling Bearing Using MCLSTM.

Prognostics and health management technology (PHM), a measure to ensure the reliability and safety of the operation of industrial machinery, has attracted attention and application adequately. However, how to use the monitored information to evaluate the degradation of rolling bearings is a significant issue for its predictive maintenance and autonomic logistics. This work presents a reliable health prognosis approach to estimate the health indicator (HI) and remaining useful life (RUL) of rolling bearings. Firstly, to accurately capture the degradation process, a novel health index (HI) is constructed based on correlation kurtosis for different iteration periods and a Gaussian process latency variable model (GPLVM). Then, a multiple convolutional long short-term memory (MCLSTM) network is proposed to predict HI values and RUL values. Finally, we perform experimental datasets of rolling bearings, demonstrating that the presented method surpasses other state-of-the-art prognosis approaches. The results also confirm the feasibility of the presented method in industrial machinery.

LRRC62 attenuates Toll-like receptor signaling by deubiquitinating TAK1 via CYLD.

TGF-ß-activated kinase 1 (TAK1) plays a pivotal role in Toll-like receptor (TLR) signaling pathway. However, the mechanisms controlling its activity remain poorly understood. Here, we show that leucine-rich repeat containing 62 (LRRC62), a previously uncharacterized protein, negatively regulates TLR signaling by targeting TAK1. Expression of LRRC62 inhibits the TLRs-induced production of pro-inflammatory cytokine, whereas deficiency in LRRC62 enhances the activation of NF-κB and MAPK signaling and increases the production of pro-inflammatory cytokines. Mechanically, LRRC62 functions as an adaptor to recruit deubiquitinase CYLD to TAK1, thus inhibits the K63-linked poly-ubiquitination and activation of TAK1. Together, our findings uncover an unrecognized mechanism by which LRRC62 antagonizes the activation of TAK1 in a CYLD-mediated deubiquitination-dependent manner, thereby balancing Toll-like receptor signaling to avert overzealous inflammation.

Photodegradable coumarin-derived amphiphilic dendrons for DNA binding: Self-assembly and phototriggered disassembly in water and air-water interface.

In this article, we demonstrate the self-assembly and photoresponive behavior of a novel coumarin-based amphiphilic dendron in both aqueous solution and air-water interface. The dendritic structure, namely C-IG1, was composed of a lipophilic cholesterol and hydrophilic poly(amido amine) (PAMAM) dendron, and the amphiphilic counterpart is interconnected by a photolabile coumarin carbonate ester, enabling the photoinduced degradation of the amphiphiles in protic solvents via SN1-like mechanism. A Nile red solubilization fluorescence assay suggests a low critical aggregation concentration for the micelle formation of C-IG1 in aqueous solutions (3.9 × 10-5 M); the Langmuir analysis further indicates that C-IG1 possesses significant compressibility in air-water interface, eventually forming homogeneous monolayers with a final molecular area (A0) of 36 Å2. Notably, the micelles and Langmuir monolayer are quite stable until photo-triggered dissociation based on the photocleavage of C-IG1 amphiphile activated by 365-nm incident light. Moreover, the transition in interfacial morphology of the Langmuir monolayer during the assembly and photodegradation processes also can be visually analyzed by incorporating Nile red probes with in situ monitoring through fluorescence microscopy. The thin film deposited on a glass substrate by the Langmuir-Blodgett technique also shows a photoresponsive behavior based on the change in the contact angles of a water droplet on the surface upon light stimulation. The binding affinity of C-IG1 and cyclic DNA determined by the fluorescence quenching analysis of the coumarin reporter suggests a ground-state macromolecular complexation process occurring through polyvalent interactions between the pseudodendrimers and biomacromolecules. The ethidium bromide displacement assay further indicates thus dendriplex formation at low nitrogen-to-phosphorous value (N/P < 1) and confirms that the decomplexation accompanied by DNA release can be achieved through an active phototriggered route under spatiotemporal control.

NLRP11 attenuates Toll-like receptor signalling by targeting TRAF6 for degradation via the ubiquitin ligase RNF19A.

The adaptor protein TRAF6 has a central function in Toll-like receptor (TLR) signalling, yet the molecular mechanisms controlling its activity and stability are unclear. Here we show that NLRP11, a primate specific gene, inhibits TLR signalling by targeting TRAF6 for degradation. NLRP11 recruits the ubiquitin ligase RNF19A to catalyze K48-linked ubiquitination of TRAF6 at multiple sites, thereby leading to the degradation of TRAF6. Furthermore, deficiency in either NLRP11 or RNF19A abrogates K48-linked ubiquitination and degradation of TRAF6, which promotes activation of NF-κB and MAPK signalling and increases the production of proinflammatory cytokines. Therefore, our findings identify NLRP11 as a conserved negative regulator of TLR signalling in primate cells and reveal a mechanism by which the NLRP11-RNF19A axis targets TRAF6 for degradation.

TRIM45 functions as a tumor suppressor in the brain via its E3 ligase activity by stabilizing p53 through K63-linked ubiquitination.

Tripartite motif-containing protein 45 (TRIM45) belongs to a large family of RING-finger-containing E3 ligases, which are highly expressed in the brain. However, little is known regarding the role of TRIM45 in cancer biology, especially in human glioma. Here, we report that TRIM45 expression is significantly reduced in glioma tissue samples. Overexpression of TRIM45 suppresses proliferation and tumorigenicity in glioblastoma cells in vitro and in vivo. In addition, CRISPR/Cas9-mediated knockout of TRIM45 promotes proliferation and inhibits apoptosis in glioblastoma cells. Further mechanistic analyses show that TRIM45 interacts with and stabilizes p53. TRIM45 conjugates K63-linked polyubiquitin chain to the C-terminal six lysine residues of p53, thereby inhibiting the availability of these residues to the K48-linked polyubiquitination that targets p53 for degradation. These findings suggest that TRIM45 is a novel tumor suppressor that stabilizes and activates p53 in glioma.

The F-box protein FBXL18 promotes glioma progression by promoting K63-linked ubiquitination of Akt.

F-box proteins play pivotal roles in multiple cellular processes; however, little is known about their functions in glioma progression. In this study, we found that expression of the F-box and leucine-rich repeat protein 18 (FBXL18) is significantly upregulated in glioma tissues. Depletion of FBXL18 in glioma cells suppresses proliferation and anchorage-independent cell growth, and promotes apoptosis. We also demonstrate that depletion of FBXL18 significantly inhibits Akt activity and the phosphorylation of FOXO3a, which leads to upregulation of BCL2L11. Further mechanistic analyses indicate that FBXL18 promotes the K63-linked ubiquitination of Akt, which is required for its activation. Taken together, our results suggest that FBXL18 plays an oncogenic role through promoting K63-linked ubiquitination of Akt in glioma.

LRRC14 attenuates Toll-like receptor-mediated NF-κB signaling through disruption of IKK complex.

Activation of NF-κB signaling plays pivotal roles in innate immune responses against pathogens. It requires strict control to avert inflammatory diseases. However, the mechanisms underlying this tight regulation are not completely understood. Here, we identified LRRC14, a novel member of LRR (leucine-rich repeat) protein family, as a negative regulator in TLR signaling. Expression of LRRC14 resulted in decreased activation of NF-κB, whereas knockdown of LRRC14 enhanced NF-κB activation as well as the production of inflammatory cytokines. Mechanistically, LRRC14 bound to HLH domain of IKKß to block its interaction with NEMO and thereby inhibiting the phosphorylation of IKKß and NF-κB activation. In addition, our data showed that TLR signaling led to lower expression of LRRC14. Together, LRRC14 may function as a checkpoint to prevent overzealous inflammation.