In this study we aim to extensively investigate the anti-influenza virus immune responses in human pharyngeal epithelial cell line (Hep-2) and evaluate the protective role of Toll-like receptor (TLR) ligands in seasonal influenza A H1N1 (sH1N1) infections in vitro. We first investigated the expression of the TLRs and cytokines genes in resting and sH1N1 infected Hep-2 cells. Clear expressions of TLR3, TLR9, interleukin (IL)-6, tumour necrosis factor (TNF)-α and interferon (IFN)-β were detected in resting Hep-2 cells. After sH1N1 infection, a ten-fold of TLR3 and TLR9 were elicited. Concomitant with the TLRs activation, transcriptional expression of IL-6, TNF-α and IFN-β were significantly induced in sH1N1-infected cells. Pre-treatment of cells with poly I:C (an analog of viral double-stranded RNA) and CpG-ODN (a CpG-motif containing oligodeoxydinucleotide) resulted in a strong reduction of viral and cytokines mRNA expression. The results presented indicated the innate immune response activation in Hep-2 cells and affirm the antiviral role of Poly I:C and CpG-ODN in the protection against seasonal influenza A viruses.

Limited studies have focused on the association between the protein tyrosine phosphates non-receptor type 22 (PTPN22) genetic polymorphisms and Juvenile idiopathic arthritis (JIA) susceptibility in different populations, but the results were inconclusive. Therefore, this meta-analysis of PTPN22 polymorphism (1858 C>T) was performed to get a precise systematic estimation. The "rs" number of the PTPN22 polymorphism (1858 C>T) is 4.

EYA4, one of the four members of the EYA gene family, is associated with several human cancers. However, its biological functions and molecular mechanisms in the progression of cancer, particularly in esophageal squamous cell carcinoma (ESCC), remain unknown. In the present study, we found that EYA4 was underexpressed and hypermethylated in most of the ESCC cell lines tested (85.7%, 6/7). Treatment with 5-aza-dC and/or trichostatin A (TSA) restored EYA4 expression in ESCC cell lines, which indicates that EYA4 expression was epigenetically regulated. Similarly, EYA4 was aberrantly hypermethylated in ESCC tissues (78%, 39/50) and downregulation of EYA4 occurred in approximately 65% of primary ESCC at protein level where it was associated significantly with TNM stage and lymph node metastases. Knockdown of EYA4 in KYSE30 and KYSE70 ESCC cells using small hairpin RNA increased migration and invasive motility in vitro. Conversely, the overexpression of EYA4 in KYSE180 and KYSE450 promoted an epithelial phenotype, which consisted of decreased migration and invasion abilities and a decrease in TGF-β1-induced epithelial-mesenchymal transition. Mechanistically, EYA4 overexpression reduced the phosphorylation of Akt and glycogen synthase kinase (GSK) 3β, which led to the inactivation of slug. In addition, we found that TGF-β1 decreased EYA4 expression in both a dose-dependent and a time-dependent manner in KYSE30 cells, accompanied by an increase in the expression of DNA methyltransferases, especially DNMT3A. In summary, EYA4 is frequently hypermethylated in ESCC and may function as a tumor suppressor gene in the development of ESCC.

Immune checkpoint inhibitors against PD-1/PD-L1 yield improved survival rates of KRAS-mutant NSCLC patients, who conferred a poor prognosis without effective targeted therapy until now. Yet, the underlying association between KRAS mutations and immune responses remains unclear. We performed an integrated analysis of the data from publicly available repositories and from clinical center cohorts to explore the association between KRAS mutation status and tumor immunity-associated features, including PD-L1 expression, CD8+ tumor-infiltrating lymphocytes (TILs) and tumor mutational burden (TMB). Our results revealed that KRAS mutations are correlated with an inflammatory tumor microenvironment and tumor immunogenicity, resulting in superior patient response to PD-1/PD-L1 inhibitors. Meanwhile, three-pool analysis further confirmed that KRAS-mutant NSCLC patients show remarkable clinical benefit from anti-PD-1/PD-L1 immunotherapy. In addition, a KRAS-mutant lung adenocarcinoma mouse model was established to estimate the relative efficacy of anti-PD-L1 monoclonal antibody monotherapy or combination treatment with docetaxel versus docetaxel alone. Most surprisingly, we found that PD-L1 blockade combined with docetaxel did not promote an anti-tumor response. These findings uncover that PD-1/PD-L1 blockade monotherapy may be the optimal therapeutic schedule in NSCLC patients harboring KRAS mutations.

No clinically available biomarkers can predict pathological complete response (pCR) for esophageal squamous cell carcinomas (ESCCs) with neoadjuvant chemoradiotherapy (nCRT). Considering that antitumor immunity status is an important determinant for nCRT, we performed an integrative analysis of immune-related gene profiles from pretreatment biopsies and constructed the first individualized immune signature for pCR and outcome prediction of ESCCs through a multicenter analysis. During the discovery phase, 14 differentially expressed immune-related genes (DEIGs) with greater than a twofold change between pCRs and less than pCRs (

BGISEQ-500 is a new desktop sequencer developed by BGI. Using DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics™ sequencing technologies, it generates short reads at a large scale. Here, we present the first human whole-genome sequencing dataset of BGISEQ-500. The dataset was generated by sequencing the widely used cell line HG001 (NA12878) in two sequencing runs of paired-end 50 bp (PE50) and two sequencing runs of paired-end 100 bp (PE100). We also include examples of the raw images from the sequencer for reference. Finally, we identified variations using this dataset, estimated the accuracy of the variations, and compared to that of the variations identified from similar amounts of publicly available HiSeq2500 data. We found similar single nucleotide polymorphism (SNP) detection accuracy for the BGISEQ-500 PE100 data (false positive rate [FPR] = 0.00020%, sensitivity = 96.20%) compared to the PE150 HiSeq2500 data (FPR = 0.00017%, sensitivity = 96.60%) better SNP detection accuracy than the PE50 data (FPR = 0.0006%, sensitivity = 94.15%). But for insertions and deletions (indels), we found lower accuracy for BGISEQ-500 data (FPR = 0.00069% and 0.00067% for PE100 and PE50 respectively, sensitivity = 88.52% and 70.93%) than the HiSeq2500 data (FPR = 0.00032%, sensitivity = 96.28%). Our dataset can serve as the reference dataset, providing basic information not just for future development, but also for all research and applications based on the new sequencing platform.

The tumor mutational burden (TMB) is closely related to immunotherapy outcome. However, the cost of TMB detection is extremely high, which limits its use in clinical practice. A new indicator of genomic instability, the average copy number variation (CNVA), calculates the changes of 0.5-Mb chromosomal fragments and requires extremely low sequencing depth.

The prevalence of early-stage lung adenocarcinoma (LUAD) has increased alongside increased implementation of lung cancer screenings. Robust discrimination criteria are urgently needed to identify those patients who might benefit from additional systemic therapy. Here, to develop a reliable, individualized immune gene-set-based signature to predict recurrence in early-stage LUAD, a novel recurrence-associated immune signature was identified using a least absolute shrinkage and selection operator model, and a stepwise Cox proportional hazards regression model with a training set comprised of 338 early-stage LUAD samples form TCGA, which was subsequently validated in 226 cases from GSE31210 and an independent set of 68 frozen tumor samples with qRT-PCR data. This new classification system remained strongly predictive of prognoses across clinical subgroups and mutation status. Further analysis revealed that samples from high-risk cases were characterized by active interferon signal transduction, distinctive immune cell proportions and immune checkpoint profiles. Moreover, the signature was identified as an independent prognostic factor. In conclusion, the signature is highly predictive of recurrence in patients with early-stage LUAD, which may serve as a powerful prognostic tool to further optimize immunotherapies for cancer.

We aimed to verify the expression status and diagnostic significance of isocitrate dehydrogenase 1 (IDH1) in non-small-cell lung cancer (NSCLC), especially during early stages. Serum IDH1 levels were measured by ELISA. A total of 1223 participants (660 patients with NSCLC, 276 healthy controls [HCs], 95 patients with benign pulmonary conditions [BPCs], 135 patients with other cancers [OCs], and 57 samples with interfering factors) were divided into a training cohort and a validation cohort according to 3 testing centers. The IDH1 concentrations in the NSCLC group were obviously higher than those in the control groups (P < .001). Area under the receiver operating characteristic curves (AUCs) for discriminating NSCLC patients from controls (HC, BPC, and OC) were 0.870 and 0.745 (sensitivity, 63.3% and 55.0%; specificity, 86.8% and 86.3%) in the training cohort and validation cohort, respectively. The AUCs for discriminating stage 0-IA lung cancer patients from HCs were 0.907 and 0.788 (sensitivity, 58.6% and 59.1%; specificity, 92.9% and 89.3%) in 2 cohorts, respectively. Isocitrate dehydrogenase 1 showed specificity for NSCLC and had no diagnostic value for other common cancers. Furthermore, IDH1 was significantly reduced in postoperative serum. Isocitrate dehydrogenase 1 shows clinical utility as a serum protein biomarker for the early diagnosis of NSCLC.

The tumor microenvironment (TME) is a vital component of tumor tissue. Increasing evidence suggests their significance in predicting outcomes and guiding therapies. However, no studies have reported a systematic analysis of the clinicopathologic significance of TME in lung adenocarcinoma (LUAD). Here, we inferred tumor stromal cells in 1184 LUAD patients using computational algorithms based on bulk tumor expression data, and evaluated the clinicopathologic significance of stromal cells. We found LUAD patients showed heterogeneous abundance in stromal cells. Infiltration of stromal cells was influenced by clinicopathologic features, such as age, gender, smoking, and TNM stage. By clustering stromal cells, we identified 2 clinically and molecularly distinct LUAD subtypes with immune active and immune repressed features. The immune active subtype is characterized by repressed metabolism and repressed proliferation of tumor cells, while the immune repressed subtype is characterized by active metabolism and active proliferation of tumor cells. Differentially expressed gene analysis of the two LUAD subtypes identified an immune activation signature. To diagnose TME subtypes practically, we constructed a TME score using principal component analysis based on the immune activation signature. The TME score predicted TME subtypes effectively in 3 independent datasets with areas under the receiver operating characteristic curves of 0.960, 0.812, and 0.819, respectively. In conclusion, we proposed 2 clinically and molecularly distinct LUAD subtypes based on tumor microenvironment that could be valuable in predicting clinical outcome and guiding immunotherapy.

Alternative splicing (AS) and the regulation of AS by splicing factors play critical roles in cancer. Plant homeodomain (PHD)-finger domain protein PHF5A, a critical splicing factor involved in AS, has been demonstrated to play an oncogenic role in glioblastoma multiforme and breast cancer, but its biological function in lung cancer remains unclear. In the present study, we systematically analyzed the biological function and clinical relevance of PHF5A in non-small cell lung cancer (NSCLC). We found that PHF5A was significantly upregulated in NSCLC tumors compared with normal tissues in both TCGA data set and tissue microarrays. Upregulation of PHF5A was negatively correlated to the overall survival (OS) of lung adenocarcinoma (LUAD) patients. Loss-of-function and gain-of-function experiments confirmed that PHF5A functioned as an oncoprotein by promoting LUAD cell proliferation, migration and invasion, inducing G0/G1 cell cycle progression and inhibiting cisplatin-induced apoptosis. RNA-seq analysis identified many essential genes whose AS was dysregulated by PHF5A, including cell cycle-associated genes such as SKP2, CHEK2, ATR and apoptosis-associated genes such as API5 and BCL2L13. Additionally, pladienolide, a small molecular inhibitor of PHF5A, inhibited LUAD cell proliferation in a dose-dependent manner and induced AS changes similar to PHF5A knockdown. In conclusion, we validated that PHF5A played an oncogenic role via AS in LUAD and suggested that PHF5A might serve as a potential drug target with a promising anticancer therapeutic effect.

Whether to trust or distrust another individual is a complex interpersonal challenge, especially when such individuals behave inconsistently. It is still unclear as to how individuals learn and adapt to fluctuations in the trustworthiness of others and how this process changes from adolescence to adulthood. To address these issues, we implemented repeated rounds of a trust game within the context of a complicated and changeable interpersonal environment. Specifically, adolescents and adults played the role of trustors who had to decide whether to invest money in two anonymous partners carrying the risk of no reciprocation. Unbeknownst to participants, these two partners had different trustworthiness profiles: one partner initially yielded a higher initial return rate (70%) while the other initially yielded a lower initial return rate (30%). Crucially, over repeated rounds, these two partners gradually changed their responses to the point where, finally, return rates were both neutral (50%). Results indicated that all participants showed less updating in the negative direction in response to good-to-neutral partners while more updating in the positive direction in response to the bad-to-neutral partner. Compared to adults, this behavioral disparity in responses to good-to-neutral and bad-to-neutral partners was less pronounced in adolescents. Based on the computational modeling approach, the potential mechanisms underlying their behavioral patterns were revealed: the higher learning rate promoted flexible adaptions in participants to untrustworthy trustees as they changed to neutral. The less pronounced distinction between good-to-neutral and bad-to-neutral partners in adolescents was related to their lower learning rate. Overall, our study extends the understanding of trust behavior to a fluctuating social context and highlights the role of social learning in social emotion and interaction.

Cancer-associated fibroblasts (CAFs) plays an important role in the tumor microenvironment. The heterogeneity of CAFs affects the effect of CAFs on promoting or inhibiting tumors, which can be regulated by other cells in the tumor microenvironment through paracrine methods. The urokinase-type plasminogen activator (PLAU) system mediates cell proliferation, migration, adhesion, and other functions through the proteolytic system, intracellular signal transduction, and chemokine activation. PLAU promotes tumor progression in many tumors. We explored the function of PLAU in ESCC and the influence of PLAU secreted by tumor cells on the heterogeneity of CAFs. We found that PLAU is highly expressed in ESCC, which is related to poor prognosis and can be used as a prognostic marker for ESCC. Through loss-of function and gain-of function experiments, we found that PLAU promoted ESCC proliferation and clone formation via MAPK pathway, and promotes migration by upregulating Slug and MMP9, which can be reversed by the MEK 1/2 inhibitor U0126. At the same time, through sequencing, cytokine detection, and RT-qPCR verification, we found that tumor cells secreted PLAU promoted the conversion of fibroblasts to inflammatory CAFs, which upregulated expression and secretion of IL8 via the uPAR/Akt/NF-κB pathway. The IL8 secreted by CAFs in turn promotes the high expression of PLAU in tumor cells and further promoted the progression of ESCC. In summary, PLAU was not only a prognostic marker of ESCC, which promoted tumor cell proliferation and migration, but also promoted the formation of inflammatory CAFs by the PLAU secreted by tumor cells.

The proportion of patients with stage I lung adenocarcinoma (LUAD) has dramatically increased with the prevalence of low-dose computed tomography use for screening. Up to 30% of patients with stage I LUAD experience recurrence within 5 years after curative surgery. A robust risk stratification tool is urgently needed to identify patients who might benefit from adjuvant treatment.

The pathogenesis of post-traumatic stress disorder (PTSD) remains largely unclear. A large body of evidence suggests that the abnormal level of serotonin (5-HT) is closely related to the onset of PTSD. Several reports reveal that nitric oxide (NO) affects extracellular 5-HT levels in various brain regions, but no consistent direction of change was found and the underlying mechanisms remain unknown. The most of serotonergic neurons in dorsal raphe nucleus (DRN), a major source of serotonergic input to the forebrain, co-expresses neuronal nitric oxide synthase (nNOS), a synthase derived nitric oxide (NO) in the central nervous system. Here, we found that the excessive expression of nNOS and thereby the high concentration of NO followed by single-prolonged stress (SPS) caused suppression of the activity of DRN 5-HT neurons, inducing PTSD-like phenotype including increased anxiety-like behaviors, enhanced contextual fear memory, and fear generalization. Our study uncovered an important role of DRN nNOS-NO pathway in the pathology of PTSD, which may contribute to new understanding of the molecular mechanism of PTSD.

Background: Warfarin is a commonly used oral anticoagulant. It has a narrow therapeutic window and wide variation in individualized dosing, and is used clinically for the treatment of thromboembolic diseases. Due to the widespread use of traditional Chinese medicine (TCM) in China and the complex composition and diverse mechanisms of action of TCM, the combination of TCM and warfarin in patients has led to fluctuations in the international normalized ratio of warfarin or bleeding. To ensure rational clinical use, we summarize the TCMs with which warfarin interacts and the possible mechanisms, with a view to providing a clinical reference. Aim of the study: To summarize the mechanisms by which Chinese herbal medicines affect the enhancement or weakening of the anticoagulant effect of warfarin, to provide theoretical references for clinicians and pharmacists to use warfarin safely and rationally, and to avoid the adverse effects associated with the combination of Chinese herbal medicines and warfarin. Methods: A computerized literature search of electronic databases, including PubMed, MEDLINE, Cochrane Library, Web of Science (WOS), China National Knowledge Infrastructure (CNKI) and WANFANG Data was performed. Key words used in the literature search were "warfarin", "Chinese medicine", "traditional Chinese medicine", "Chinese patent medicine" etc. and their combinations in a time limit from January 1, 1990 to May 1, 2021. A total of 64 articles were obtained following the selection process, including clinical reports, pharmacological experiments and in vitro experiments which were reviewed to determine the mechanism of the anticoagulant effect of herbal medicine on warfarin. Results: The mechanisms affecting the anticoagulant effect of warfarin are complex, and herbal medicines may enhance and diminish the anticoagulant effect of warfarin through a variety of mechanisms; thus, clinical use needs to be cautious. Some herbal medicines have shown inconsistent results in both in vivo and ex vivo experiments, pharmacology and clinical studies, and should be the focus of future research. Conclusion: With the widespread use of TCM, the combination of warfarin and TCM is more common. This article will promote clinicians' knowledge and understanding of the TCMs which interact with warfarin, in order to avoid the occurrence of adverse clinical treatment processes, and improve the efficacy and safety.

Small cell lung cancer (SCLC) is the most devastating subtype of lung cancer with no clinically available prognostic biomarkers. N6 -methyladenosine (m6 A) and noncoding RNAs play critical roles in cancer development and treatment response. However, little is known about m6 A-related long noncoding RNAs (lncRNAs) in SCLC. We used 206 limited-stage SCLC (LS-SCLC) samples from two cohorts to undertake the first and most comprehensive exploration of the m6 A-related lncRNA profile in SCLC and constructed a relevant prognostic signature. In total, 289 m6 A-related lncRNAs were screened out. We then built a seven-lncRNA-based signature in the training cohort with 48 RNA sequencing data using univariate and multivariate Cox regression models. The signature was well validated in an independent cohort containing 158 cases with quantitative PCR data. In both cohorts, the signature divided patients into high- and low-risk groups with significantly different survival rates (both p < 0.001). Our signature predicted chemotherapy survival benefit in patients with LS-SCLC. Receiver operating characteristic and C-index analyses indicated that the signature was better at predicting prognosis and chemotherapy benefit than other clinicopathologic features. Moreover, the signature was identified as an independent predictor of prognosis and chemotherapy response in different cohorts. Furthermore, functional analysis showed that multiple activated immune-related pathways were enriched in the low-risk group. Additionally, the signature was also closely related to various immune checkpoints and inflammatory responses. We generated the first clinically available m6 A-related lncRNA signature to predict prognosis and chemotherapy benefit in patients with LS-SCLC. Our findings could help optimize the clinical management of patients with LS-SCLC and inform future therapeutic targets for SCLC.

ATP-binding cassette transporters (ABC transporters) play crucial physiological roles in plants, such as being involved in the growth and development of organs, nutrient acquisition, response to biotic and abiotic stress, disease resistance, and the interaction of the plant with its environment. The ABCG subfamily of proteins are involved in the process of plant vegetative organ development. In contrast, the functions of the ABCG36 and ABCG40 transporters have received considerably less attention. Here, we investigated changes in the transcriptomic data of the stem tissue of transgenic tobacco (Nicotiana tabacum) with LkABCG36 and LkABCG40 (Larix kaempferi) overexpression, and compared them with those of the wild type (WT). Compared with the WT, we identified 1120 and 318 differentially expressed genes (DEGs) in the LkABCG36 and LkABCG40 groups, respectively. We then annotated the function of the DEGs against the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The results showed enrichment in cell wall biogenesis and hormone signal transduction functional classes in transgenic LkABCG36 tobacco. In transgenic LkABCG40 tobacco, the enrichment was involved in metabolic and biosynthetic processes, mainly those related to environmental adaptation. In addition, among these DEGs, many auxin-related genes were significantly upregulated in the LkABCG36 group, and we found key genes involved in environmental adaptation in the LkABCG40 group, including an encoding resistance protein and a WRKY transcription factor. These results suggest that LkABCG36 and LkABCG40 play important roles in plant development and environmental adaptation. LkABCG36 may promote plant organ growth and development by increasing auxin transport, whereas LkABCG40 may inhibit the expression of WRKY to improve the resistance of transgenic tobacco. Our results are beneficial to researchers pursuing further study of the functions of ABCG36 and ABCG40.

Cytokines have been reported to alter the response to immune checkpoint inhibitors (ICIs) in patients with the tumor in accordance with their plasma concentrations. Here, we aimed to identify the key cytokines which influenced the responses and stimulated resistance to ICIs and tried to improve immunological response and develop novel clinical treatments in non-small cell lung cancer (NSCLC).

Renal fibrosis is the ultimate presentation of chronic kidney disease, which progresses to end-stage renal disease. Hydroxychloroquine (HCQ) has been adapted for the treatment of autoimmune diseases; however, the potential mechanism underlying the role of HCQ in renal fibrosis remains unclear. C57BL/6 J mice were randomly divided into three groups (sham group, UUO group, and UUO + HCQ group (20 mg/kg)). HE and Masson staining were performed to assess kidney tissue damage and fibrosis, and western blotting was performed to assess the expression of epithelial-mesenchymal transition (EMT), extracellular matrix (ECM), PI3K/AKT, and NF-κB-related proteins. PCR and TUNEL were adopted to detect inflammatory factors and cell apoptosis. HK-2 cells treated with TGF-β1 were used for the in vitro experiments. HCQ may potentially have therapeutic effects on renal fibrosis mediated through 122 target genes, and the Kyoto Encyclopedia of Genes and Genomes pathways of these genes were enriched for PI3K/AKT signaling based on network pharmacology. UUO mice that received HCQ demonstrated significantly less tubular damage than the UUO mice. HCQ treatment additionally blunted EMT in UUO kidneys and TGF-β1-treated renal tubular epithelial cells, and alleviated ECM deposition in kidney tissue. Furthermore, HCQ treatment reduced UUO-induced inflammation and apoptosis. Mechanistically, HCQ treatment suppressed the activation of the PI3K/Akt and NF-kB pathways. This study demonstrated that HCQ ameliorated renal fibrosis by inhibiting the PI3K/AKT and NF-κB signaling pathways to attenuate inflammatory factors and the apoptotic function of renal tubular epithelial cells, thus providing renewed theoretical evidence for HCQ treatment of renal fibrosis.