MYL6B, a myosin light chain, promotes MDM2-mediated p53 degradation and drives HCC development

IDENTIFICATION OF A NOVEL SEPSIS PROGNOSIS MODEL: BASED ON TRANSCRIPTOME AND PROTEOME ANALYSIS

ABSTRACT

Sepsis is a highly prevalent and deadly disease. Currently, there is a lack of ideal biomarker prognostis models for sepsis. We attempt to construct a model capable of predicting the prognosis of sepsis patients by integrating transcriptomic and proteomic data. Through analysis of proteomic and transcriptomic data, we identified 25 differentially expressed genes (DEGs). Single-factor Cox-Lasso regression analysis identified 16 DEGs (overall survival-DEGs) associated with patient prognosis. Through multifactor Cox-Lasso regression analysis, a prognostic model based on these 16 genes was constructed. Kaplan-Meier survival analysis and receiver operating characteristic curve analysis were used to further validate the high stability and good predictive ability of this prognostic model with internal and external data. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of overall survival-DEGs and differentially expressed genes between high and low-risk groups based on the prognostic model revealed significant enrichment in immune-related pathways, particularly those associated with viral regulation.

Seizure enhances SUMOylation and zinc-finger transcriptional repression in neuronal nuclei

A single episode of pilocarpine-induced status epilepticus can trigger the development of spontaneous recurrent seizures in a rodent model for epilepsy. The initial seizure-induced events in neuronal nuclei that lead to long-term changes in gene expression and cellular responses likely contribute toward epileptogenesis. Using a transgenic mouse model to specifically isolate excitatory neuronal nuclei, we profiled the seizure-induced nuclear proteome via tandem mass tag mass spectrometry and observed robust enrichment of nuclear proteins associated with the SUMOylation pathway. In parallel with nuclear proteome, we characterized nuclear gene expression by RNA sequencing which provided insights into seizure-driven transcriptional regulation and dynamics. Strikingly, we saw widespread downregulation of zinc-finger transcription factors, specifically proteins that harbor Krüppel-associated box (KRAB) domains. Our results provide a detailed snapshot of nuclear events induced by seizure activity and demonstrate a robust method for cell-type-specific nuclear profiling that can be applied to other cell types and models.

Dominant neoantigen verification in hepatocellular carcinoma by a single-plasmid system coexpressing patient HLA and antigen

BACKGROUND

Previous studies confirmed that most neoantigens predicted by algorithms do not work in clinical practice, and experimental validations remain indispensable for confirming immunogenic neoantigens. In this study, we identified the potential neoantigens with tetramer staining, and established the Co-HA system, a single-plasmid system coexpressing patient human leukocyte antigen (HLA) and antigen, to detect the immunogenicity of neoantigens and verify new dominant hepatocellular carcinoma (HCC) neoantigens.

METHODS

First, we enrolled 14 patients with HCC for next-generation sequencing for variation calling and predicting potential neoantigens. Then, the Co-HA system was established. To test the feasibility of the system, we constructed target cells coexpressing HLA-A*11:01 and the reported KRAS G12D neoantigen as well as specific T-cell receptor (TCR)-T cells. The specific cytotoxicity generated by this neoantigen was shown using the Co-HA system. Moreover, potential HCC-dominant neoantigens were screened out by tetramer staining and validated by the Co-HA system using methods including flow cytometry, enzyme-linked immunospot assay and ELISA. Finally, antitumor test in mouse mode and TCR sequencing were performed to further evaluate the dominant neoantigen.

RESULTS

First, 2875 somatic mutations in 14 patients with HCC were identified. The main base substitutions were C>T/G>A transitions, and the main mutational signatures were 4, 1 and 16. The high-frequency mutated genes included HMCN1, TTN and TP53. Then, 541 potential neoantigens were predicted. Importantly, 19 of the 23 potential neoantigens in tumor tissues also existed in portal vein tumor thrombi. Moreover, 37 predicted neoantigens restricted by HLA-A*11:01, HLA-A*24:02 or HLA-A*02:01 were performed by tetramer staining to screen out potential HCC-dominant neoantigens. HLA-A*24:02-restricted epitope 5'-FYAFSCYYDL-3' and HLA-A*02:01-restricted epitope 5'-WVWCMSPTI-3' demonstrated strong immunogenicity in HCC, as verified by the Co-HA system. Finally, the antitumor efficacy of 5'-FYAFSCYYDL-3'-specific T cells was verified in the B-NDG-B2m^tm1Fcrn^tm1(mB2m) mouse and their specific TCRs were successfully identified.

CONCLUSION

We found the dominant neoantigens with high immunogenicity in HCC, which were verified with the Co-HA system.

The Role of Alternative Splicing Factors hnRNP G and Fox-2 in the Progression and Prognosis of Esophageal Cancer

Aim. Alternative splicing (AS) has been widely demonstrated in the occurrence and progression of many cancers. Nevertheless, the involvement of cancer-associated splicing factors in the development of esophageal carcinoma (ESCA) remains to be explored. Method. RNA-Seq data and the corresponding clinical information of the ESCA cohort were downloaded from The Cancer Genome Atlas database. Bioinformatics methods were used to further analyzed the differently expressed AS (DEAS) events and their splicing network. Kaplan–Meier, Cox regression, and unsupervised cluster analyses were used to assess the association between AS events and clinical characteristics of ESCA patients. The splicing factors screened out were verified in vitro at the cellular level. Results. A total of 50,342 AS events were identified, of which 3,988 were DEAS events and 46 of these were associated with overall survival (OS) of ESCA patients, with a 5-year OS rate of 0.941. By constructing a network of AS events with survival-related splicing factors, the AS factors related to prognosis can be further identified. In vitro experiments and database analysis confirmed that the high expression of hnRNP G in ESCA is related to the high invasion ability of ESCA cells and the poor prognosis of ESCA patients. In contrast, the low expression of fox-2 in esophageal cancer is related to a better prognosis. Conclusion. ESCA-associated AS factors hnRNP G and Fox-2 are of great value in deciphering the underlying mechanisms of AS in ESCA and providing clues for therapeutic goals for further validation.

Arap1 loss causes retinal pigment epithelium phagocytic dysfunction and subsequent photoreceptor death

Retinitis pigmentosa (RP), a retinal degenerative disease, is the leading cause of heritable blindness. Previously, we described that Arap1^−/− mice develop a similar pattern of photoreceptor degeneration. Arap1 is an Arf-directed GTPase-activating protein shown to modulate actin cytoskeletal dynamics. Curiously, Arap1 expression was detected in Müller glia and retinal pigment epithelium (RPE), but not the photoreceptors themselves. In this study, we generated conditional knockout mice for Müller glia/RPE, Müller glia and RPE via targeting Rlbp1, Glast and Vmd2 promoters, respectively, to drive Cre recombinase expression to knock out Arap1. Vmd2-Cre Arap1^tm1c/tm1c and Rlbp1-Cre Arap1^tm1c/tm1c mice, but not Glast-Cre Arap1^tm1c/tm1c mice, recapitulated the phenotype originally observed in germline Arap1^−/− mice. Mass spectrometry analysis of human ARAP1 co-immunoprecipitation identified candidate binding partners of ARAP1, revealing potential interactants involved in phagocytosis, cytoskeletal composition, intracellular trafficking and endocytosis. Quantification of outer segment phagocytosis in vivo demonstrated a clear phagocytic defect in Arap1^−/− mice compared to Arap1^+/+ controls. We conclude that Arap1 expression in RPE is necessary for photoreceptor survival due to its indispensable function in RPE phagocytosis.

This article has an associated First Person interview with the first author of the paper.

Summary: We provide evidence that Arap1 expression in retinal pigment epithelium (RPE) is essential for maintaining photoreceptor health due to its indispensable role in RPE phagocytosis.

Lysine 2-hydroxyisobutyrylation proteomics reveals protein modification alteration in the actin cytoskeleton pathway of oral squamous cell carcinoma

As the most commonplace malignant carcinoma in the oral cavity, oral squamous cell carcinoma (OSCC) is highly invasive and prone to recurrence. The nosogenesis of OSCC are affected by epigenetics. Recently, a newly-found post-translational modification of lysine, 2-hydroxyisobutylation (Khib), has been proved to play a critical role in biological regulation. However, no research has evaluated the mechanism of Khib in oral cancer. Here, we performed liquid chromatography-mass spectrometry-based quantitative proteomics combined with bioinformatics analysis to reveal and evaluate Khib protein alterations in OSCC. Numerous proteins in OSCC undergo up-regulated modification of Khib. We quantified and identified 967 proteins with differential expression levels, and 617 2-hydroxyisobutylated proteins with 938 Khib sites. Among them, 125 proteins both differentially expressed and accompanied by obvious Khib modification were further identified and analyzed through KEGG-based and ingenuity pathway analysis (IPA). These proteins are enriched in the actin cytoskeleton regulatory pathway, and IPA predicted that they alter the state of actin aggregation and stability, hence impacting and regulating the actin cytoskeleton in OSCC. This is the first 2-hydroxyisobutylated modification proteomics performed for OSCC. Khib protein is significantly concentrated in the actin cytoskeleton regulatory pathway, indicating that this pathway may mediate the tumorigenesis or exacerbation of OSCC. SIGNIFICANCE: This is the first study that revealed the alterations of Khib protein in oral squamous cell carcinoma through LC-MS/MS-based modified proteomic. Our data showed that the protein in the actin cytoskeleton regulatory pathway was underwent significant Khib modification and abundance changes. We applied predictive function in IPA software to analyze and clarify that the aggregation of actin and the regulation of actin stability that mediated by the actin cytoskeleton regulatory pathway may be the potential mechanism of the occurrence and development of oral squamous cell carcinoma. Our research broadens the understanding of the pathogenesis of oral squamous cell carcinoma and provides new insights for future research.

Predictive Models for HCC Prognosis, Recurrence Risk, and Immune Infiltration Based on Two Exosomal Genes: MYL6B and THOC2

Introduction

Hepatocellular carcinoma (HCC) is a heterogeneous molecular disease with complex molecular pathogenesis that influences the efficacy of therapies. Exosomes play a crucial role in tumorigenesis and poor disease outcomes in HCC.

Objective

The aim of this study was to identify the optimal gene set derived from exosomes in HCC with substantial predictive value to construct models for determining prognosis, recurrence risk and diagnosis and to identify candidates suitable for immunotherapy and chemotherapy, thereby providing new ideas for the individualized treatment of patients and for improving prognosis.

Methods

Weighted correlation network analysis (WGCNA) and univariate and multivariate Cox PH regression analyses were applied to identify exosome-related signatures in the TCGA and exoRbase databases associated with clinical relevance, immunogenic features and tumor progression in HCC. Cell experiments were performed to further confirm the oncogenic effect of MYL6B and THOC2.

Results

The models for prognosis and recurrence risk prediction were built based on two exosomal genes (MYL6B and THOC2) and were confirmed to be independent predictive factors with superior predictive performance. Patients with high prognostic risk had poorer prognosis than patients with low prognostic risk in all HCC datasets, namely, the TCGA cohort (HR=2.5, P<0.001), the ICGC cohort (HR=3.15, P<0.001) and the GSE14520 cohort (HR=1.85, P=0.004). A higher recurrence probability was found in HCC patients with high recurrence risk than in HCC patients with low recurrence risk in the TCGA cohort (HR=2.44, P<0.001) and the GSE14520 cohort (HR=1.54, P=0.025). High prognostic risk patients had higher expression of immune checkpoint genes, such as PD1, B7H3, B7H5, CTLA4 and TIM3 (P<0.05). Diagnostic models based on the same two genes were able to accurately distinguish HCC patients from normal individuals and HCC from dysplastic nodules.

Conclusion

Our findings lay the foundation for identifying molecular markers to increase the early detection rate of HCC, improve disease outcomes, and determine more effective individualized treatment options for patients.

RHPN1-AS1 Drives the Progression of Hepatocellular Carcinoma via Regulating miR-596/IGF2BP2 Axis

BACKGROUND

Hepatocellular carcinoma (HCC) is one of the most deadly cancer types worldwide, and its incidence is high in China. Multiple long non-coding RNAs (lncRNAs) have been recently identified as crucial oncogenic factors or tumor suppressors. In this study, we explored the effects of LncRNA RHPN1 antisense RNA 1 (RHPN1-AS1) on the progression of HCC.

METHODS

Expression levels of RHPN1-AS1 and miR-596 in HCC samples were measured by qRT-PCR. The association between pathological indexes and the expression level of RHPN1-AS1 was also analyzed. Human HCC cell lines Huh7 and SMMC-7721 were used as cell models. CCK-8 and colony formation assays were performed to assess the effect of RHPN1-AS1 on HCC cell line proliferation. The flow cytometer instrument was used to study the effect of RHPN1-AS1 on apoptosis of HCC cells. The transwell assay was conducted to detect the effect of RHPN1-AS1 on migration and invasion. Furthermore, luciferase reporter assay was used to confirm targeting of miR-596 by RHPN1-AS1. Additionally, the regulatory function of RHPN1-AS1 on insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) was detected by western blot.

RESULTS

The expression level of RHPN1-AS1 in HCC samples was observed to significantly increase compared with normal tissues and its high expression was correlated with unfavorable pathological indexes. Highly expressed RHPN1-AS1 was associated with shorter overall survival time. RHPN1-AS1 overexpression remarkably accelerated proliferation and metastasis of HCC cells, while reduced apoptosis. Accordingly, RHPN1-AS1 knockdown suppressed the malignant phenotypes of HCC cells. RHPN1-AS1 overexpression significantly reduced miR-596 expression by sponging it, but enhanced IGF2BP2 expression.

CONCLUSION

RHPN1-AS1 acts as a sponge of tumor suppressor miR-596 in HCC that can indirectly enhance the IGF2BP2 expression and function as an oncogenic lncRNA.

Anti-tumor Drug Targets Analysis: Current Insight and Future Prospect

The incidence and mortality of malignant tumors are on the rise, which has become the second leading cause of death in the world. At present, anti-tumor drugs are one of the most common methods for treating cancer. In recent years, with the in-depth study of tumor biology and related disciplines, it has been gradually discovered that the essence of cell carcinogenesis is the infinite proliferation of cells caused by the disorder of cell signal transduction pathways, followed by a major shift in the concept of anti-tumor drugs research and development. The focus of research and development is shifting from traditional cytotoxic drugs to a new generation of anti-tumor drugs targeted at abnormal signaling system targets in tumor cells. In this review, we summarize the targets of anti-tumor drugs and analyse the molecular mechanisms of their effects, which lay a foundation for subsequent treatment, research and development.

MYL6B drives the capabilities of proliferation, invasion, and migration in rectal adenocarcinoma through the EMT process

Objective

This study was designed to explore the biological significance of myosin light chain 6B (MYL6B) in rectal adenocarcinoma.

Methods

Profiles on the Oncomine dataset, GEPIA website, and UALCAN-TCGA database were searched to assess the MYL6B expression level in rectal adenocarcinoma tissues and normal tissues. After MYL6B knockdown using siRNA strategy, cell counting kit-8 (CCK-8) and transwell assays were conducted to measure cell proliferation, migration and invasion, respectively. Flow cytometry analysis was conducted to assess cell apoptosis. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and western blot were performed to detect the expression level of mRNAs and proteins.

Results

The data showed that overexpression of MYL6B was observed in rectal adenocarcinoma tissues and correlated with a poor prognosis of patients. Functional in vitro experiments revealed that MYL6B knockdown could inhibit proliferation, migration, and invasion of rectal adenocarcinoma cells, while promote cell apoptosis. Moreover, western blot analysis suggested that increased expression of E-cadherin and decreased expression of N-cadherin and Vimentin were induced by si-MYL6B.

Conclusion

In summary, this study elaborated on the promoting effect of MYL6B in rectal adenocarcinoma progression, thus providing novel insight for strategies of clinical diagnosis and drug application in the future clinical study.

The role of MDM2-p53 axis dysfunction in the hepatocellular carcinoma transformation

Liver cancer is the second most frequent cause of cancer-related death globally. The main histological subtype is hepatocellular carcinoma (HCC), which is derived from hepatocytes. According to the epidemiologic studies, the most important risk factors of HCC are chronic viral infections (HBV, HCV, and HIV) and metabolic disease (metabolic syndrome). Interestingly, these carcinogenic factors that contributed to HCC are associated with MDM2-p53 axis dysfunction, which presented with inactivation of p53 and overactivation of MDM2 (a transcriptional target and negative regulator of p53). Mechanically, the homeostasis of MDM2-p53 feedback loop plays an important role in controlling the initiation and progression of HCC, which has been found to be dysregulated in HCC tissues. To maintain long-term survival in hepatocytes, hepatitis viruses have lots of ways to destroy the defense strategies of hepatocytes by inducing TP53 mutation and silencing, promoting MDM2 overexpression, accelerating p53 degradation, and stabilizing MDM2. As a result, genetic instability, chronic ER stress, oxidative stress, energy metabolism switch, and abnormalities in antitumor genes can be induced, all of which might promote hepatocytes' transformation into hepatoma cells. In addition, abnormal proliferative hepatocytes and precancerous cells cannot be killed, because of hepatitis viruses-mediated exhaustion of Kupffer cells and hepatic stellate cells (HSCs) and CD4+T cells by disrupting their MDM2-p53 axis. Moreover, inefficiency of hepatic immune response can be further aggravated when hepatitis viruses co-infected with HIV. Unlike with chronic viral infections, MDM2-p53 axis might play a dual role in glucolipid metabolism of hepatocytes, which presented with enhancing glucolipid catabolism, but promoting hepatocyte injury at the early and late stages of glucolipid metabolism disorder. Oxidative stress, fatty degeneration, and abnormal cell growth can be detected in hepatocytes that were suffering from glucolipid metabolism disorder, and all of which could contribute to HCC initiation. In this review, we focus on the current studies of the MDM2-p53 axis in HCC, and specifically discuss the impact of MDM2-p53 axis dysfunction by viral infection and metabolic disease in the transformation of normal hepatocytes into hepatoma cells. We also discuss the therapeutic avenues and potential targets that are being developed to normalize the MDM2-p53 axis in HCC.

Proteomic analyses reveal divergent ubiquitylation patterns in hepatocellula carcinoma cell lines with different metastasis potential

Hepatocellular carcinoma (HCC) is one of the most common malignant tumours, metastasis and recurrence remain the primary reasons for poor prognosis. Ubiquitination serves as a degradation mechanism of proteins, but it is involved in additional cellular processes including metastasis. Here, by using label-free quantification, double-glycine (di-Gly) antibody affinity purification and high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS), we investigated quantitative proteome, ubiquitylome, and the crosstalk between the two datasets in HCC cell lines with different metastasis potential to identify biomarkers associated with HCC metastasis. In total, 83 ubiquitinated proteins significantly and steadily changed their abundance according to their metastatic potential, and the participated biological processes of these ubiquitinated proteins were tightly associated with tumour metastasis. Further signaling pathway analysis revealed that the ribosome and proteasome were significantly over-activated in the highly metastatic cells. Furthermore, we analyzed the crosstalk between the whole proteome and the ubiquitylome, and further discussed the mechanism that how ubiquitination events affect HCC metastasis. Eventually, the ubiquitination of Ku80 was validated to be significantly down-regulated in the high-metastatic cells comparing with the low-metastatic cells. We believe that these findings will help us better understand the underlying molecular mechanisms of the metastasis of HCC. SIGNIFICANCE: In this manuscript, we used label free based proteomics combined with diglycine antibody (di-Gly) affinity purification approach to identify biomarkers associated with HCC recurrence/metastasis in in a serial HCC cell lines with increasing invasion and metastasis potential. And then, we analyzed the crosstalk between the whole proteome and the ubiquitylome. Eventually, the ubiquitination of Ku80 was confirm to be closely associated with invasion and migration of HCC cells. As far as we know, this is the first time to use quantitative proteomic approach to study the ubiquitylomics in HCC cell lines with increasing metastasis ability.

Design, Synthesis, and Biological Evaluation of Aromatic Amide-Substituted Benzimidazole-Derived Chalcones. The Effect of Upregulating TP53 Protein Expression

A series of benzimidazole-derived chalcones containing aromatic amide substituent were designed and synthesized. All of the chalcone compounds were tested for their in vitro antitumor activity against human cancer cell lines (HCT116, HepG2, A549, and CRL-5908). The antiproliferative activity of compounds 3, 6, 9, 14, 15, 16 against HCT116 cells was significantly better than that that of 5-Fluorouracil (IC50: 94.63 µM). The antitumor activity of these compounds showed obvious differences between the wild type HCT116 and mutant HCT116 (TP53^−/−) cells. A preliminary mechanistic study suggested that these compounds act by upregulating the expression of TP53 protein in tumor cells without inhibiting the MDM2-TP53 interaction.

A FITM1-Related Methylation Signature Predicts the Prognosis of Patients With Non-Viral Hepatocellular Carcinoma

Although great progress has been made in treatment against hepatitis virus infection, the prognosis of hepatocellular carcinoma (HCC) remains unsatisfied. Therefore, there is an unmet need to explore biomarkers or prognostic models for monitoring non-viral hepatocellular carcinoma. Accumulating evidence indicates that DNA methylation participates in carcinogenesis of malignancies. In the present study, we analyzed 101 non-viral HCC patients from TCGA database to figure out methylation-driven genes (MDGs) that might get involved in non-viral HCC pathogenesis using MethyMix algorithm. Then we picked out 8 key genes out of 137 MDGs that could affect the overall survival (OS) of both methylation and expression level. Using PCA, Uni-variate, Multi-variate, and LASSO cox regression analyses, we confirmed the potential prognostic value of these eight epigenetic genes. Ultimately, combined with immunohistochemistry (IHC), ROC, OS, and GSEA analyses, fat storage-inducing transmembrane protein1 (FITM1) was identified as a novel tumor suppressor gene in non-viral HCC and an applicable FITM1-methylation-based signature was built in a training set and validated in a testing set. Briefly, our work provides several potential biomarkers, especially FITM1, as well as a new method for disease surveillance and treatment strategy development.