The p-MYH9/USP22/HIF-1α axis promotes lenvatinib resistance and cancer stemness in hepatocellular carcinoma.

Lenvatinib is a targeted drug used for first-line treatment of hepatocellular carcinoma (HCC). A deeper insight into the resistance mechanism of HCC against lenvatinib is urgently needed. In this study, we aimed to dissect the underlying mechanism of lenvatinib resistance (LR) and provide effective treatment strategies. We established an HCC model of acquired LR. Cell counting, migration, self-renewal ability, chemoresistance and expression of stemness genes were used to detect the stemness of HCC cells. Molecular and biochemical strategies such as RNA-sequencing, immunoprecipitation, mass spectrometry and ubiquitination assays were used to explore the underlying mechanisms. Patient-derived HCC models and HCC samples from patients were used to demonstrate clinical significance. We identified that increased cancer stemness driven by the hypoxia-inducible factor-1α (HIF-1α) pathway activation is responsible for acquired LR in HCC. Phosphorylated non-muscle myosin heavy chain 9 (MYH9) at Ser1943, p-MYH9 (Ser1943), could recruit ubiquitin-specific protease 22 (USP22) to deubiquitinate and stabilize HIF-1α in lenvatinib-resistant HCC. Clinically, p-MYH9 (Ser1943) expression was upregulated in HCC samples, which predicted poor prognosis and LR. A casein kinase-2 (CK2) inhibitor and a USP22 inhibitor effectively reversed LR in vivo and in vitro. Therefore, the p-MYH9 (Ser1943)/USP22/HIF-1α axis is critical for LR and cancer stemness. For the diagnosis and treatment of LR in HCC, p-MYH9 (Ser1943), USP22, and HIF-1α might be valuable as novel biomarkers and targets.

RNA sequencing identifies lung cancer lineage and facilitates drug repositioning.

Recent breakthrough therapies have improved survival rates in non-small cell lung cancer (NSCLC), but a paradigm for prospective confirmation is still lacking. Patientdatasets were mainly downloaded from TCGA, CPTAC and GEO. We conducted downstream analysis by collecting metagenes and generated 42-gene subtype classifiers to elucidate biological pathways. Subsequently, scRNA, eRNA, methylation, mutation, and copy number variation were depicted from a phenotype perspective. Enhancing the clinical translatability of molecular subtypes, preclinical models including CMAP, CCLE, and GDSC were utilized for drug repositioning. Importantly, we verified the presence of previously described three phenotypes including bronchioid, neuroendocrine, and squamoid. Poor prognosis was seen in squamoid and neuroendocrine clusters for treatment-naive and immunotherapy populations. The neuroendocrine cluster was dominated by STK11 mutations and 14q13.3 amplifications, whose related methylated loci are predictive of immunotherapy. And the greatest therapeutic potential lies in the bronchioid cluster. We further estimated the relative cell abundance of the tumor microenvironment (TME), specific cell types could be reflected among three clusters. Meanwhile, the higher portion of immune cell infiltration belonged to bronchioid and squamoid, not the neuroendocrine cluster. In drug repositioning, MEK inhibitors resisted bronchioid but were squamoid-sensitive. To conceptually validate compounds/targets, we employed RNA-seq and CCK-8/western blot assays. Our results indicated that dinaciclib and alvocidib exhibited similar activity and sensitivity in the neuroendocrine cluster. Also, a lineage factor named KLF5 recognized by inferred transcriptional factors activity could be suppressed by verteporfin.

Characterization of Key Aroma Compounds of Soy Sauce-like Aroma Produced in Ferment of Soybeans by Bacillus subtilis BJ3-2.

Fermented soybeans are popular among many for their rich soy sauce-like aroma. However, the precise composition of this aroma remains elusive, with key aroma compounds unidentified. In this study, we screened the candidate genes ilvA and serA in BJ3-2 based on previous multi-omics data, and we constructed three mutant strains, BJ3-2-ΔserA, BJ3-2-ΔilvA, and BJ3-2-ΔserAΔilvA, using homologous recombination to fermented soybeans with varying intensities of soy sauce-like aroma. Our objective was to analyze samples that exhibited different aroma intensities resulting from the fermented soybeans of BJ3-2 and its mutant strains, thereby exploring the key flavor compounds influencing soy sauce-like aroma as well analyzing the effects of ilvA and serA on soy sauce-like aroma. We employed quantitative descriptive sensory analysis (QDA), gas chromatography-olfactometry-mass spectrometry (GC-O-MS), relative odor activity value analysis (rOAV), principal component analysis (PCA), orthogonal partial least squares-discriminant analysis (OPLS-DA), and partial least squares regression analysis (PLSR). QDA revealed the predominant soy sauce-like aroma profile of roasted and smoky aromas. GC-MS detected 99 volatile components, predominantly pyrazines and ketones, across the four samples, each showing varying concentrations. Based on rOAV (>1) and GC-O, 12 compounds emerged as primary contributors to soy sauce-like aroma. PCA and OPLS-DA were instrumental in discerning aroma differences among the samples, identifying five compounds with VIP > 1 as key marker compounds influencing soy sauce-like aroma intensity levels. Differential analyses of key aroma compounds indicated that the mutant strains of ilvA and serA affected soy sauce-like aroma mainly by affecting pyrazines. PLSR analysis indicated that roasted and smoky aromas were the two most important sensory attributes of soy sauce-like aroma, with pyrazines associated with roasted aroma and guaiacol associated with smoky aroma. In addition, substances positively correlated with the intensity of soy sauce-like aroma were verified by additional experiments. This study enhances our understanding of the characteristic flavor compounds in soy sauce-like aroma ferments, provides new perspectives for analyzing the molecular mechanisms of soy sauce-like aroma formation, and provides a theoretical framework for the targeted enhancement of soy sauce-like aroma in various foods.

Characterization of key aroma compounds of fried pepper sauce under different pretreatment processes.

Fried pepper sauce (FPS) is renowned among consumers for its distinct aroma profile and rich nutritional composition. However, the primary aroma components of FPSs, crucial for quality assurance, remain unclear. Therefore, this study aimed to delve deeper into the unique aroma profile of FPSs by analyzing samples subjected to various pretreatment methods (including three heat-moisture treatment processes: soaking at 60 °C, soaking at 100 °C, and steaming, and three crushing processes: mashing, mincing, and horizontal knife cutting). FPS samples were analyzed by quantitative descriptive sensory analysis (QDA), gas chromatography-olfactometry-mass spectrometry (GC-O-MS), relative odor activity value analysis (rOAV), principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA) and partial least squares regression analysis (PLSR). The QDA results revealed that the overall aroma profile of FPS products was characterized by chili-like, fatty, and herbal notes. GC-MS identified 115 volatile components in FPSs, primarily alkenes, ketones, and acids, with varying concentrations across samples. According to the rOAV (>1) and GC-O, 11 compounds were identified as key aroma contributors to FPS aroma, including 2-methylpropanal, acetic acid, 3-methylbutanal, methional, eucalyptol, benzeneacetaldehyde, linalool, (E)-2-nonenal, (2E)-2-decenal, (2E,4E)-deca-2,4-dienal, and (E,Z)-2,4-decadienal. PCA and PLS-DA were employed to assess aroma differences among nine FPS samples. Screening for VIP > 1 and p < 0.05 identified 8 and 12 key marker compounds influenced by different crushing methods or heat-moisture treatments, respectively. PLSR indicated that the sensory attributes were greatly related to most aroma-active compounds. These findings provide novel insights into FPS aroma attributes, facilitating precise processing and quality control of fried pepper sauce products.

Improvement in Noodle Quality and Changes in Microstructure and Disulfide Bond Content through the Addition of Pepper Straw Ash Leachate.

Every year, a significant amount of pepper stalks are wasted due to low utilization. The ash produced from pepper stalks contains a significant amount of alkaline salts, which are food additives that can enhance the quality of noodles. Therefore, utilizing natural pepper straw ash to improve the quality of noodles shows promising development prospects. In this study, pepper straw ash leachate (PSAL) was extracted and added to noodles. The quality of the noodles gradually improved with the addition of PSAL, with the best effect observed at a concentration of 18% (PSAL mass/flour mass). This addition resulted in a 57.8% increase in noodle hardness, a 55.43% increase in chewiness, a 19.41% rise in water absorption rate, and a 13.28% increase in disulfide bond content. These alterations rendered the noodles more resilient during cooking, reducing their tendency to soften and thus enhancing chewiness and palatability. Incorporating PSAL also reduced cooking loss by 57.79%. Free sulfhydryl groups decreased by 5.1%, and scanning electron microscopy revealed a denser gluten network structure in the noodles, with more complete starch wrapping. This study significantly enhanced noodle quality and provided a new pathway for the application of pepper straw resources in the food industry.

Genome-wide characterization and expression analysis of the HD-Zip II gene family in response to drought and GA3 stresses in Nicotiana tabacum.

BACKGROUND: Homeodomain-leucine ZIPper (HD-ZIP) transcription factors play crucial roles in plant growth, development, and stress responses. The HD-ZIP family is categorised into four groups (HD-ZIP I-IV). While extensive genome-wide studies have been conducted on the HD-ZIP I, III, and IV subfamily in Nicotiana tabacum (tobacco), comprehensive reports on the HD-ZIP II subfamily genes are limited. METHODS: Bioinformatics resources and tools were utilised to analyse molecular characteristics, phylogenetic homology, and protein interactions. Expression pattern analyses in various tissues and the relative expression of NtHD-ZIP II genes under drought and GA3 treatment were assessed by qRT-PCR. RESULTS: In this study, 24 HD-ZIP II members were systematically identified and categorised into seven independent clades through phylogenetic analysis involving tobacco and other plant species. We found that 19 NtHD-ZIP II genes exhibited tissue-specific expression. The transcripts of NtHD-ZIPII3, 4, 14, 23, 24 were notably induced under the drought treatments, while those of NtHD-ZIPII7, 11, 12, 20 were suppressed. Furthermore, NtHD-ZIPII15 transcripts decreased following GA3 treatment, whereas the transcripts of NtHD-ZIPII7, 8, 11, 12 were induced after GA3 treatment. Notably, an increase in trichomes was observed in tobacco leaves treated with GA3 and subjected to drought. CONCLUSIONS: The expression levels of some HD-ZIP II genes were altered, and an increase in glandular trichomes was induced under GA3 and drought treatments in tobacco. Overall, our findings provide insights into the expression patterns of NtHD-ZIP II genes and will facilitate their functional characterisation in future studies.

mTOR inhibitor reduces nontumour-related death in liver transplantation for hepatocellular carcinoma.

Sirolimus is a regularly applied immunosuppressant for patients undergoing liver transplantation (LT) for hepatocellular carcinoma (HCC). Sirolimus not only significantly inhibits HCC recurrence but also protects renal function. However, the improvement effect of sirolimus on nontumour-related death in patients is still unknown. The aim of our study was to investigate the therapeutic effect of sirolimus on nontumour-related deaths. In this study, we retrospectively enrolled 403 LT patients with HCC from January 1, 2015, to December 31, 2018. The median follow-up time was 47.1 months. The patients were divided into the sirolimus group (N = 184) and the sirolimus-free group (N = 219). There were no significant differences between the sirolimus group and the sirolimus-free group in survival (P = 0.054). In transplant patients who exceeded the Milan or Hangzhou criteria, the sirolimus group achieved higher survival than the sirolimus-free group (P = 0.005; P = 0.02). Moreover, multivariate analysis showed that sirolimus strongly reduced the hazard ratio (HR) for nontumour-related death in LT patients who exceeded the Milan (HR: 0.42; 95% CI: 0.18-1; P = 0.05) or Hangzhou criteria (HR: 0.26; 95% CI: 0.08-0.89; P = 0.032). HCC recurrence increased the risk of nontumour-related death. In conclusion, sirolimus-based immunosuppression can significantly reduce nontumour-related death in LT patients who exceed the criteria for transplantation. In addition, this finding will further promote the application of sirolimus after liver transplantation for hepatocellular carcinoma.

Role of tumor cell pyroptosis in anti-tumor immunotherapy.

Peripheral tumor-specific CD8+ T cells often fail to infiltrate into tumor parenchyma due to the immunosuppression of tumor microenvironment (TME). Meanwhile, a significant portion of tumor-specific CD8+ T cells infiltrated into TME are functionally exhausted. Despite the enormous success of anti-PD-1/PD-L1 immune-checkpoint blockade (ICB) treatment in a wide variety of cancer types, the majority of patients do not respond to this treatment largely due to the failure to efficiently drive tumor-specific CD8+ T cell infiltration and reverse their exhaustion states. Nowadays, tumor cell pyroptosis, a unique cell death executed by pore-forming gasdermin (GSDM) family proteins dependent or independent on inflammatory caspase activation, has been shown to robustly promote immune-killing of tumor cells by enhancing tumor immunogenicity and altering the inflammatory state in the TME, which would be beneficial in overcoming the shortages of anti-PD-1/PD-L1 ICB therapy. Therefore, in this review we summarize the current progresses of tumor cell pyroptosis in enhancing immune function and modulating TME, which synergizes anti-PD-1/PD-L1 ICB treatment to achieve better anti-tumor effect. We also enumerate several strategies to better amply the efficiency of anti-PD-1/PD-L1 ICB therapy by inducing tumor cell pyroptosis.

Key candidate genes for male sterility in peppers unveiled via transcriptomic and proteomic analyses.

This study aimed to enhance the use of male sterility in pepper to select superior hybrid generations. Transcriptomic and proteomic analyses of fertile line 1933A and nucleic male sterility line 1933B of Capsicum annuum L. were performed to identify male sterility-related proteins and genes. The phylogenetic tree, physical and chemical characteristics, gene structure characteristics, collinearity and expression characteristics of candidate genes were analyzed. The study identified 2,357 differentially expressed genes, of which 1,145 and 229 were enriched in the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, respectively. A total of 7,628 quantifiable proteins were identified and 29 important proteins and genes were identified. It is worth noting that the existence of CaPRX genes has been found in both proteomics and transcriptomics, and 3 CaPRX genes have been identified through association analysis. A total of 66 CaPRX genes have been identified at the genome level, which are divided into 13 subfamilies, all containing typical CaPRX gene conformal domains. It is unevenly distributed across 12 chromosomes (including the virtual chromosome Chr00). Salt stress and co-expression analysis show that male sterility genes are expressed to varying degrees, and multiple transcription factors are co-expressed with CaPRXs, suggesting that they are involved in the induction of pepper salt stress. The study findings provide a theoretical foundation for genetic breeding by identifying genes, metabolic pathways, and molecular mechanisms involved in male sterility in pepper.

Population-based high-dimensional analyses identify multiple intrinsic characters for cancer vaccines against lung squamous cell carcinoma.

In lung squamous cell carcinoma (LUSC), current cancer vaccines show promising effects, despite a lack of benefit for a large number of patients. We first identified the tumor antigens into shared and private antigens, and determined the population by clustering analysis in public datasets. For vaccine development, The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) were collected. WGCNA method was furthermore applied to construct a consensus gene co-expression network based on TCGA and CPTAC datasets. The main analyses in bulk sequencing included survival, clinical features, tumor microenvironment (TME), and pathways enrichment. In addition, single-cell RNA (scRNA) analysis of cancer epithelium dissected consensus subtype. We identified the ideal population for cancer vaccines, and candidate neoantigens including AOC1, COL5A2, LGI2, and POSTN. According to subtype analysis, Lung squamous 1 (LSQ1) type exhibited a higher tumor mutational load (TMB) and copy number but no immune infiltration, whereas lung squamous 2 (LSQ2) tumors had a higher global methylation level and more fibroblasts but had less stemness. Meanwhile, trajectory analysis further revealed that the evolution of TME influenced prognosis. We emphasized specific pathways or targets with the potential for combination immunotherapy by consensus network and single-cell RNA analyses. Anti-androgen therapy has been validated in vitro experiments of LUSC as proof of concept. In conclusion, LSQ1 was linked to immune exclusion and might be utilized for vaccination, while LSQ2 was linked to immune dysfunction and could be used for programmed cell death protein 1 (PD1) blocking therapy.

Ubiquitin-specific protease 22 promotes tumorigenesis and progression by an FKBP12/mTORC1/autophagy positive feedback loop in hepatocellular carcinoma.

Ubiquitin-specific protease 22 (USP22) has been identified as a potential marker for cancer stem cells in hepatocellular carcinoma (HCC). It can promote HCC stemness, which is considered a driver of tumorigenesis. Here, we sought to determine the role of USP22 in tumorigenesis, elucidate its underlying mechanism, and explore its therapeutic significance in HCC. As a result, we found that tissue-specific Usp22 overexpression accelerated tumorigenesis, whereas Usp22 ablation decelerated it in a c-Myc/NRasGV12-induced HCC mouse model and that the mammalian target of rapamycin complex 1 (mTORC1) pathway was activated downstream. USP22 overexpression resulted in increased tumorigenic properties that were reversed by rapamycin in vitro and in vivo. In addition, USP22 activated mTORC1 by deubiquitinating FK506-binding protein 12 (FKBP12) and activated mTORC1, in turn, further stabilizing USP22 by inhibiting autophagic degradation. Clinically, HCC patients with high USP22 expression tend to benefit from mTOR inhibitors after liver transplantation (LT). Our results revealed that USP22 promoted tumorigenesis and progression via an FKBP12/mTORC1/autophagy positive feedback loop in HCC. Clinically, USP22 may be an effective biomarker for selecting eligible recipients with HCC for anti-mTOR-based therapy after LT.

TP53/mTORC1-mediated bidirectional regulation of PD-L1 modulates immune evasion in hepatocellular carcinoma.

BACKGROUND: Immunotherapy has facilitated great breakthroughs in the treatment of hepatocellular carcinoma (HCC). However, the efficacy and response rate of immunotherapy are limited and vary among different patients with HCC. TP53 mutation substantially affects the expression of immune checkpoint molecules in multiple cancers. However, the regulatory relationship between programmed death ligand 1 (PD-L1) and TP53 is poorly studied in HCC. We aimed to elucidate the regulatory mechanism of PD-L1 in HCC with different TP53 statuses and to assess its role in modulating immune evasion in HCC. METHODS: HCC mouse models and cell lines with different TP53 statuses were constructed. PD-L1 levels were detected by PCR, western blotting and flow cytometry. RNA-seqencing, immunoprecipitation, chromatin immunoprecipitation and transmission electron microscopy were used to elucidate the regulatory mechanism in HCC with different TP53 status. HCC mouse models and patient with HCC samples were analyzed to demonstrate the preclinical and clinical significance of the findings. RESULTS: We report that loss of p53 promoted PD-L1 expression and reduced CD8+ T-cell infiltration in patient with HCC samples and mouse models. Mammalian target of rapamycin (mTOR) pathway was activated in p53-loss-of-function HCC or after knocking down TP53. The transcription factor E2F1 was found to bind to the p53 protein in TP53 wild-type HCC cells, and inhibiting mammalian target of rapamycin complex 1 (mTORC1) disrupted this binding and enhanced E2F1 translocation to the nucleus, where it bound to the PD-L1 promoter and transcriptionally upregulated PD-L1. In p53-loss-of-function HCC cells, autophagosomes were activated after mTORC1 suppression, promoting the degradation of PD-L1 protein. The combination of mTOR inhibitor and anti-PD-L1 antibody enhanced CD8+ T-cell infiltration and tumor suppression in TP53 wild-type HCC mouse models, but no benefit was observed in p53-loss-of-function HCC mouse models. In patients with TP53 wild-type HCC, PD-L1 levels were significantly higher in the high E2F1 group than in the low E2F1 group, and the low E2F1 level group had significantly superior survival. CONCLUSION: We revealed the bidirectional regulatory mechanism of PD-L1 mediated by TP53/mTORC1 in HCC. The combination of mTOR inhibitor and anti-PD-L1 antibody could be a novel precise immunotherapy scheme for TP53 wild-type HCC.

A nomogram model for predicting the risk of checkpoint inhibitor-related pneumonitis for patients with advanced non-small-cell lung cancer.

OBJECTIVE: Immunotherapy extensively treats advanced non-small-cell lung cancer (NSCLC). Although immunotherapy is generally better tolerated than chemotherapy, it can cause multiple immune-related adverse events (irAEs) involving multiple organs. Checkpoint inhibitor-related pneumonitis (CIP) is a relatively uncommon irAE that, in severe cases, can be fatal. Potential risk factors for the occurrence of CIP are currently poorly understood. This study sought to develop a novel scoring system for predicting the risk of CIP based on a nomogram model. METHODS: We retrospectively collected advanced NSCLC patients who received immunotherapy at our institution between January 1, 2018, and December 30, 2021. All patients who met the criteria were randomly divided into the training set and testing set (in a ratio of 7:3), and cases fulfilling the CIP diagnostic criteria were screened. The patients' baseline clinical characteristics, laboratory tests, imaging, and treatment information were extracted from the electronic medical records. The risk factors associated with the occurrence of CIP were identified based on the results of logistic regression analysis on the training set, and a nomogram prediction model was developed. The discrimination and prediction accuracy of the model was evaluated using the receiver operating characteristic (ROC) curve, the concordance index (C-index), and the calibration curve. Decision curve analysis (DCA) was used to evaluate the clinical applicability of the model. RESULTS: The training set comprised 526 (CIP: 42 cases), and the testing set comprised 226 (CIP: 18 cases) patients, respectively. In the training set, the final multivariate regression analysis revealed that age (p = 0.014; odds ratio [OR] = 1.056; 95% Confidence Interval [CI] =1.011-1.102), Eastern Cooperative Oncology Group performance status (p = 0.002; OR = 6.170; 95% CI = 1.943-19.590), history of prior radiotherapy (p < 0.001; OR = 4.005; 95% CI = 1.920-8.355), baseline white blood cell count (WBC) (p < 0.001; OR = 1.604; 95% CI = 1.250-2.059), and baseline absolute lymphocyte count (ALC) (p = 0.034; OR = 0.288; 95% CI = 0.091-0.909) were identified as independent risk factors for the occurrence of CIP. A prediction nomogram model was developed based on these five parameters. The area under the ROC curve and C-index of the prediction model in the training set and testing set were 0.787 (95% CI: 0.716-0.857) and 0.874 (95% CI: 0.792-0.957), respectively. The calibration curves are in good agreement. The DCA curves indicate that the model has good clinical utility. CONCLUSION: We developed a nomogram model that proved to be a good assistant tool for predicting the risk of CIP in advanced NSCLC. This model has the potential power to help clinicians in making treatment decisions.

Biocontrol Capabilities of Bacillus subtilis E11 against Aspergillus flavus In Vitro and for Dried Red Chili (Capsicum annuum L.).

As a condiment with extensive nutritional value, chili is easy to be contaminated by Aspergillus flavus (A. flavus) during field, transportation, and storage. This study aimed to solve the contamination of dried red chili caused by A. flavus by inhibiting the growth of A. flavus and detoxifying aflatoxin B1 (AFB1). In this study, Bacillus subtilis E11 (B. subtilis) screened from 63 candidate antagonistic bacteria exhibited the strongest antifungal ability, which could not only inhibit 64.27% of A. flavus but could also remove 81.34% of AFB1 at 24 h. Notably, scanning electron microscopy (SEM) showed that B. subtilis E11 cells could resist a higher concentration of AFB1, and the fermentation supernatant of B. subtilis E11 could deform the mycelia of A. flavus. After 10 days of coculture with B. subtilis E11 on dried red chili inoculated with A. flavus, the mycelia of A. flavus were almost completely inhibited, and the yield of AFB1 was significantly reduced. Our study first concentrated on the use of B. subtilis as a biocontrol agent for dried red chili, which could not only enrich the resources of microbial strains for controlling A. flavus but also could provide theoretical guidance to prolong the shelf life of dried red chili.

The predictive value of the modified AFP model for liver transplantation outcomes in multinodular hepatocellular carcinoma patients.

BACKGROUND: There is a lack of studies focusing on the benefit of liver transplantation (LT) in hepatocellular carcinoma (HCC) patients with > 3 tumors. This study aims to establish a model to effectively predict overall survival in Chinese HCC patients with multiple tumors (> 3 tumors) who undergo LT. METHODS: This retrospective study included 434 HCC liver transplant recipients from the China Liver Transplant Registry. All HCC patients had more than 3 tumor nodules. Three selection criteria systems (i.e., AFP, Metroticket 2.0, and Up-to-7) were compared regarding the prediction of HCC recurrence. The modified AFP model was established by univariate and multivariate competing risk analyses. RESULTS: The AFP score 2 and the AFP score ≥ 3 groups had 5-year recurrence rates of 19.6% and 40.5% in our cohort. The prediction of HCC recurrence based on the AFP model was associated with a c-statistic of 0.606, which was superior to the Up-to-7 and Metroticket 2.0 models. AFP level > 1000 ng/mL, largest tumor size ≥ 8 cm, vascular invasion, and MELD score ≥ 15 were associated with overall survival. The 5-year survival rate in the modified AFP score 0 group was 71.7%. CONCLUSIONS: The AFP model is superior in predicting tumor recurrence in HCC patients with > 3 tumors prior to LT. With the modified AFP model, patients likely to derive sufficient benefit from LT can be identified.

The predictive value of plasma exosomal lncRNAs/mRNAs in NSCLC patients receiving immunotherapy.

PURPOSE: There is an urgent need to explore the use of plasma-derived exosomal long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) as potential biomarkers to select the most suitable patient population to receive immunotherapy for advanced NSCLC with no actionable molecular markers. PATIENTS AND METHODS: In the present study, 7 patients with advanced NSCLC who received nivolumab were enrolled for molecular studies. Plasma-derived exosomal lncRNAs/mRNAs expression profiles differed between patients exhibiting differential immunotherapy efficacy. RESULTS: In the non-responders, 299 differentially expressed exosomal mRNAs and 154 lncRNAs were significantly upregulated. In GEPIA2, 10 mRNAs were upregulated in the NSCLC patients compared to that of the normal population. The up-regulation of CCNB1 related to the cis-regulation of lnc-CENPH-1 and lnc-CENPH-2. KPNA2, MRPL3, NET1 and CCNB1 were trans-regulated by lnc-ZFP3-3. In addition, IL6R exhibited a trend of increased expression in the non-responders at baseline, and this expression was further downregulated after treatment in responders. The association between CCNB1 with lnc-CENPH-1 and lnc-CENPH-2, as well as the lnc-ZFP3-3-TAF1 pair, may represent potential biomarkers of poor immunotherapy efficacy. Patients may obtain increased effector T cell function when IL6R is suppressed by immunotherapy. CONCLUSIONS: Our study suggests that plasma-derived exosomal lncRNA and mRNA expression profiles differ between responders and non-responders to nivolumab immunotherapy. Lnc-ZFP3-3-TAF1-CCNB1 pair and IL6R might be key factors predicting efficiency of immunotherapy. Large scale clinical studies seem warranted to further validate the potential of plasma-derived exosomal lncRNAs and mRNAs as a biomarker to aid the selection of NSCLC patients for nivolumab immunotherapy.

Systemic analysis identifying PVT1/DUSP13 axis for microvascular invasion in hepatocellular carcinoma.

BACKGROUND: Microvascular invasion (MVI) is an independent detrimental risk factor for tumor recurrence and poor survival in hepatocellular carcinoma (HCC). Competitive endogenous RNA (ceRNA) networks play a pivotal role in the modulation of carcinogenesis and progression among diverse tumor types. However, whether the ceRNA mechanisms are engaged in promoting the MVI process in patients with HCC remains unknown. METHODS: A ceRNA regulatory network was constructed based on RNA-seq data of patients with HCC from The Cancer Genome Atlas (TCGA) database. In total, 10 hub genes of the ceRNA network were identified using four algorithms: "MCC," "Degree," "Betweenness," and "Stress." Transcriptional expressions were verified by in situ hybridization using clinical samples. Interactions between ceRNA modules were validated by luciferase reporting assay. Logistic regression analysis, correlation analysis, enrichment analysis, promoter region analysis, methylation analysis, and immune infiltration analysis were performed to further investigate the molecular mechanisms and clinical transformation value. RESULTS: The ceRNA regulatory network featuring a tumor invasion phenotype consisting of 3 long noncoding RNAs, 3 microRNAs, and 93 mRNAs was constructed using transcriptional data from the TCGA database. Systemic analysis and experimentally validation identified a ceRNA network (PVT1/miR-1258/DUSP13 axis) characterized by lipid regulatory potential, immune properties, and abnormal methylation states in patients with HCC and MVI. Meanwhile, 28 transcriptional factors were identified as potential promotors of PVT1 with 3 transcriptional factors MXD3, ZNF580, and KDM1A promising as therapeutic targets in patients with HCC and MVI. Furthermore, miR-1258 was an independent predictor for MVI in patients with HCC. CONCLUSION: The PVT1/DUSP13 axis is significantly associated with MVI progression in HCC patients. This study provides new insight into mechanisms related to lipids, immune phenotypes, and abnormal epigenetics in oncology research.

A Novel Therapeutic Target for Small-Cell Lung Cancer: Tumor-Associated Repair-like Schwann Cells.

Small-cell lung cancer (SCLC), representing 15-20% of all lung cancers, is an aggressive malignancy with a distinct natural history, poor prognosis, and limited treatment options. We have previously identified Schwann cells (SCs), the main glial cells of the peripheral nervous system, in tumor tissues and demonstrated that they may support tumor spreading and metastasis formation in the in vitro and in vivo models. However, the role of SCs in the progression of SCLC has not been investigated. To clarify this issue, the cell proliferation assay, the annexin V apoptosis assay, and the transwell migration and invasion assay were conducted to elucidate the roles in SCLC of tumor-associated SCs (TA-SCs) in the proliferation, apoptosis, migration, and invasion of SCLC cells in vitro, compared to control group. In addition, the animal models to assess SC action's effects on SCLC in vivo were also developed. The result confirmed that TA-SCs have a well-established and significant role in facilitating SCLC cell cancer migration and invasion of SCLC in vitro, and we also observed that SC promotes tumor growth of SCLC in vivo and that TA-SCs exhibited an advantage and show a repair-like phenotype, which allowed defining them as tumor-associated repair SCs (TAR-SCs). Potential molecular mechanisms of pro-tumorigenic activity of TAR-SCs were investigated by the screening of differentially expressed genes and constructing networks of messenger-, micro-, and long- non-coding RNA (mRNA-miRNA-lncRNA) using DMS114 cells, a human SCLC, stimulated with media from DMS114-activated SCs, non-stimulated SCs, and appropriate controls. This study improves our understanding of how SCs, especially tumor-activated SCs, may promote SCLC progression. Our results highlight a new functional phenotype of SCs in cancer and bring new insights into the characterization of the nervous system-tumor crosstalk.

Integration of metabolome and transcriptome analyses reveals the mechanism of anthocyanin accumulation in purple radish leaves.

Anthocyanins are natural pigments and play significant roles in multiple growth, development, and stress response processes in plants. The vegetables with high anthocyanin content have better colours, higher antioxidant activity than green vegetables and are potent antioxidants with health benefits. However, the mechanism of anthocyanin accumulation in purple and green leaves of Raphanus sativus (radish) is poorly understood and needs further investigation. In the present study, the pigment content in a green leaf cultivar "RA9" and a purple-leaf cultivar "MU17" was characterized and revealed that the MU17 had significantly increased accumulation of anthocyanins and reduced content of chlorophyll and carotenoid compared with that in RA9. Meanwhile, these two cultivars were subjected to a combination of metabolomic and transcriptome studies. A total of 52 massively content-changed metabolites and 3463 differentially expressed genes were discovered in MU17 compared with RA9. In addition, the content of significantly increased flavonoids (such as pelargonidin and cyanidin) was identified in MU17 compared to RA9 using an integrated analysis of metabolic and transcriptome data. Moreover, the quantitative real-time polymerase chain reaction results also confirmed the differences in the expression of genes related to pathways of flavonoids and anthocyanin metabolism in MU17 leaves. The present findings provide valuable information for anthocyanin metabolism and further genetic manipulation of anthocyanin biosynthesis in radish leaves. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01245-w.