Cancer-related Signaling Pathways Research Articles

Therapeutic Targeting of Hypoxia-Inducible Factors in Cancer.

In the realm of cancer therapeutics, targeting the hypoxia-inducible factor (HIF) pathway has emerged as a promising strategy. This study delves into the intricate web of HIF-associated mechanisms, exploring avenues for future anticancer therapies. Framing the investigation within the broader context of cancer progression and hypoxia response, this article aims to decipher the pivotal role played by HIF in regulating genes influencing angiogenesis, cell proliferation, and glucose metabolism. Employing diverse approaches such as HIF inhibitors, anti-angiogenic therapies, and hypoxia-activated prodrugs, the research methodologically intervenes at different nodes of the HIF pathway. Findings showcase the efficacy of agents like EZN-2968, Minnelide, and Acriflavine in modulating HIF-1α protein synthesis and destabilizing HIF-1, providing preliminary proof of HIF-1α mRNA modulation and antitumor activity. However, challenges, including toxicity, necessitate continued exploration and development, as exemplified by ongoing clinical trials. This article concludes by emphasizing the potential of targeted HIF therapies in disrupting cancer-related signaling pathways.

Exploring the mechanism of action of Sparganii Rhizoma-Curcumae Rhizoma for in treating castration-resistant prostate cancer: a network-based pharmacology and experimental validation study

Sparganii Rhizoma-Curcumae Rhizoma (SR-CR) is a classic drug pair for the treatment of castration-resistant prostate cancer (CRPC), but its mechanism has not been clarified. The study aims to elucidate the potential mechanism of SR-CR in the management of CRPC. The present study employed the TCMSP as well as the SwissTargetPrediction platform to retrieve the chemical composition and targets of SR-CR. The therapeutic targets of CRPC were identified through screening the GeneCards, Disgenet, and OMIM databases. Subsequently, the Venny online platform was utilized to identify the shared targets between the SR-CR and CRPC. The shared targets were enrichment analysis using the Bioconductor and Kyoto encyclopedia of genes and genomes (KEGG) databases. The active ingredients and core targets were verified through molecular docking and were validated using PC3 cells in the experimental validation phase. A total of 7 active ingredients and 1126 disease targets were screened from SR-CR, leading to a total of 59 shared targets. Gene Ontology (GO) analysis resulted in 1309 GO entries. KEGG pathways analysis yielded 121 pathways, primarily involving cancer-related signaling pathways. The results from molecular docking revealed stable binding interactions between the core ingredients and the core targets. In vitro cellular assays further demonstrated that SR-CR effectively suppressed the activation of the Prostate cancer signaling pathway in PC3 cells, leading to the inhibition of cell proliferation and promotion of apoptosis. The SR-CR exert therapeutic effects on CRPC by inhibiting cell proliferation and promoting apoptosis through the Prostate cancer signaling pathway.

Mechanism of Erianin anti-triple negative breast cancer based on transcriptomics methods and network pharmacology.

Triple negative breast cancer (TNBC) is a highly aggressive illness that lacks effective targeted treatments. Although Erianin has shown potential antitumor properties, its precise mechanism of action and target in TNBC remain unclear, hampering the development of drugs. The present study investigated the underlying mechanism of action of Erianin in treating TNBC by using transcriptomics and network pharmacology approaches. We evaluated Erianin's bioactivity in TNBC cell lines and xenograft tumor models. The results showed that Erianin significantly inhibited TNBC cell proliferation and impeded tumor growth. A subsequent analysis of transcriptomic and network pharmacological data identified 51 mutual targets. Analysis of protein-protein interactions identified eight hub targets. Furthermore, molecular docking indicated that the PPARA binding energy was the lowest for Erianin among the hub targets, followed by ROCK2, PDGFRB, CCND1, MUC1, and CDK1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis showed that the common targets were associated with multiple cancer-related signaling pathways, including focal adhesion, PI3K-Akt signaling pathway, Rap1 signaling pathway, microRNAs in cancer, and human papillomavirus infection. The results of the Western blot and immunohistochemistry experiment further showed that Erianin could suppress PI3K/Akt signaling pathway activation. After co-incubation with SC79, the cell inhibition rate of Erianin was decreased, which further confirmed that Erianin inhibits TNBC progression via the PI3K-AKT signaling pathway. In conclusion, our results indicated that Erianin has the potential to inhibit the proliferation of TNBC by downregulating the PI3K/AKT signaling pathway by transcriptomics and network pharmacology. Therefore, Erianin appears to be a promising compound for the effective treatment of TNBC.

Delving into the Role of Receptor-like Tyrosine Kinase (RYK) in Cancer: In Silico Insights into Its Diagnostic and Prognostic Utility

The RYK gene encodes a receptor-like tyrosine kinase crucial for several biological processes, including development, tissue homeostasis, and cancer. This study utilized data from the Cancer Genome Atlas Project (TCGA) to evaluate RYK expression at both mRNA and protein levels in various cancers, determine its prognostic significance, and explore its involvement in cancer-related signaling pathways. Elevated levels of RYK mRNA were identified in cholangiocarcinoma (CHOL), pancreatic adenocarcinoma (PAAD), glioblastoma multiforme (GBM), lung squamous cell carcinoma (LUSC), brain lower grade glioma (LGG), head and neck squamous cell carcinoma (HNSC), liver hepatocellular carcinoma (LICH), esophageal carcinoma (ESCA), and colon adenocarcinoma (COAD), while RYK protein levels were observed to be increased in colon adenocarcinoma (COAD), GBM, LICH, cervical and endocervical adenocarcinoma (CESC), and breast invasive carcinoma (BRCA). Additionally, RYK overexpression correlated with poorer prognosis in several cancers, including PAAD, LICH, BRCA, ESCA, COAD, and CESC. Furthermore, RYK showed a positive correlation with the upregulation of multiple receptors and coreceptors in the WNT signaling pathway in various types of cancer. In terms of cancer-related signaling pathways, RYK was found to potentially interact with DNA damage, TSC/mTOR, PI3K/AKT, EMT, RTK, RAS/MAPK, ER hormone, AR hormone, and the cell cycle. This study provides new and previously unreported insights into the role of RYK in cancer biology.

ICDM-GEHC: identifying cancer driver module based on graph embedding and hierarchical clustering

Due to the high heterogeneity of cancers, it is rather essential to explore driver modules with the help of gene mutation data as well as known interactions between genes/proteins. Unfortunately, latent false positive interactions are inevitable in the Protein-Protein Interaction (PPI) network. Hence in the presented method, a new weight evaluation index, based on the gene-microRNA network as well as somatic mutation profile, is introduced for weighting the PPI network first. Subsequently, the vertices in the weighted PPI network are hierarchically clustered by measuring the Mahalanobis distance of their feature vectors, extracted with the graph embedding method Node2vec. Finally, a heuristic process with dropping and extracting is conducted on the gene clusters to produce a group of gene modules. Numerous experiment results demonstrate that the proposed method exhibits superior performance to four cutting-edge identification methods in most cases regarding the capability of recognizing the acknowledged cancer-related genes, generating modules having relatively high coverage and mutual exclusivity, and are significantly enriched for specific types of cancers. The majority of the genes in the identified modules are involved in cancer-related signaling pathways, or have been reported to be carcinogenic in the literature. Furthermore, many cancer related genes detected by the proposed method are actually omitted by the four comparison methods, which has been verified in the experiments.

Exploring the mechanism of LncRNA CASC15 affecting hepatocellular carcinoma through miRNA.

This study aimed to determine the potential mechanisms through which long noncoding (Lnc) RNA cancer susceptibility candidate 15 (CASC15) affects hepatocellular carcinoma (HCC). We retrieved HCC RNA-seq and clinical information from the UCSC Xena database. The differential expression (DE) of CASC15 was detected. Overall survival was analyzed using Kaplan-Meier (K-M) curves. Molecular function and signaling pathways affected by CASC15 were determined using Gene Set Enrichment Analysis. Associations between CASC15 and the HCC microenvironment were investigated using immuno-infiltration assays. A differential CASC15-miRNA-mRNA network and HCC-specific CASC15-miRNA-mRNA ceRNA network were constructed. The overexpression of CASC15 in HCC tissues was associated with histological grade, clinical stage, pathological T stage, poor survival, more complex immune cell components, and 12 immune checkpoints. We identified 27 DE miRNAs and 270 DE mRNAs in the differential CASC15-miRNA-mRNA network, and 10 key genes that were enriched in 12 cancer-related signaling pathways. Extraction of the HCC-specific CASC15-miRNA-mRNA network revealed that IGF1R, MET, and KRAS were associated with HCC progression and occurrence. Our bioinformatic findings confirmed that CASC15 is a promising prognostic biomarker for HCC, and elevated levels in HCC are associated with the tumor microenvironment. We also constructed a disease-specific CASC15-miRNA-mRNA regulatory ceRNA network that provides a new perspective for the precise indexing of patients with elevated levels of CASC15.

Interaction of BANCR in the relationship between Hashimoto's thyroiditis and papillary thyroid carcinoma expression patterns and possible molecular mechanisms.

Previous studies have established a connection between Hashimoto's thyroiditis (HT) and an increased risk of papillary thyroid carcinoma (PTC). However, the molecular mechanisms driving this association are not well understood. The long non-coding RNA (lncRNA) BRAF-activated non-coding RNA (BANCR) has been implicated in various cancers, suggesting a potential role in the HT-PTC linkage. This study investigated the expression levels of BANCR in PTC and HT samples, compared to control tissues. We also examined the association between BANCR expression and clinicopathological features, including lymph node metastasis. Furthermore, we explored the molecular mechanisms of BANCR in PTC pathogenesis and its potential as a therapeutic target. BANCR expression was significantly lower in PTC samples than in controls, while it was moderately increased in HT samples. In PTC cases with concurrent HT, BANCR expression was markedly reduced compared to normal tissues. Our analysis revealed BANCR's role as an oncogene in PTC, influencing various cancer-related signaling pathways. Interestingly, no significant correlation was found between BANCR expression and lymph node metastasis. Our findings underscore the involvement of BANCR in the connection between HT and PTC. The distinct expression patterns of BANCR in PTC and HT, especially in PTC with concurrent HT, provide new insights into the molecular interplay between these conditions. This study opens avenues for the development of innovative diagnostic and therapeutic strategies targeting BANCR in PTC and HT.

Phytocompounds-based therapeutic approach: Investigating curcumin and green tea extracts on MCF-7 breast cancer cell line

BackgroundBreast cancer (BC) has transcended lung cancer as the most common cancer in the world. Due to the disease's aggressiveness, rapid growth, and heterogeneity, it is crucial to investigate different therapeutic approaches for treatment. According to the World Health Organization (WHO), Plant-based therapeutics continue to be utilized as safe/non-toxic complementary or alternative treatments for cancer, even in developed countries, regardless of how cutting-edge conventional therapies are. Despite their low bioavailability, curcumin (CUR) and green tea (GT) represent safer therapeutic options. Due to their potent molecular-modulating properties on various cancer-related molecules and signaling pathways, they are considered gold-standard therapeutic agents and have been incorporated into the development of one or more therapeutic strategies of BC treatment. MethodsWe investigated the modulatory role of CUR and GT extracts on significant multi molecular targets in MCF-7 BC cell line to assess their potential as BC multi-targeting agents. We analyzed the phytocompounds in GT leaves using High-performance liquid chromatography (HPLC) and Gas chromatography-mass spectrometry (GC-MS) techniques. The mRNA expression levels of Raf-1, Telomerase, Tumor necrosis factor alpha (TNF-α) and Interleukin-8 (IL-8) genes in MCF-7 cells were quantified using quantitative real-time PCR (qRT-PCR). The cytotoxicity of the extracts was assessed by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and the released Lactate dehydrogenase (LDH), a valuable marker for identifying the programmed necrosis (necroptosis). Additionally, the concentrations of the necroptosis-related proinflammatory cytokines (TNF-α and IL-8) were measured using enzyme-linked immunosorbent assay (ELISA). ResultsIn contrast to the GT, the results showed the anticancer and cytotoxic properties of CUR against MCF-7 cells, with a relatively higher level of released LDH. The CUR extract downregulated the oncogenic Raf-1, suppressed the Telomerase and upregulated the TNF-α and IL-8 genes. Results from the ELISA showed a notable increase in IL-8 and TNF-α cytokines levels after CUR treatment, which culminated after 72 h. ConclusionsAmong both extracts, only CUR effectively modulated the understudy molecular targets, achieving multi-targeting anticancer activity against MCF-7 cells. Moreover, the applied dosage significantly increased levels of the proinflammatory cytokines, which represent a component of the cytokines-targeting-based therapeutic strategy. However, further investigations are recommended to validate this therapeutic approach.

Bioinformatic Analysis and Computer-Aided Study to Investigate the Potential Application of a Bioflavonoid Compound Bilobetin in Liver Cancer Treatment.

Hepatocellular carcinoma (HCC/LIHC) is the most common type of primary liver cancer, which is a leading cause of cancer death worldwide. Patients with HCC have a short survival time after diagnosis. Unfortunately, there are no effective treatments for advanced or aggressive HCC. Thus, the rapid development of new therapeutic drugs or treatment methods for HCC is urgently needed. Bioinformatic tools and computer-aided predictions advance the processes of drug development. In this study, we incorporated bioinformatic analyses and computer-aided drug development processes to investigate the potential application of bilobetin, a bioactive compound of bioflavonoid, as a therapeutic agent for HCC treatment. Our results revealed that 4 out of 20 predicted hub target genes of bilobetin displayed functional importance in cancer-related signaling pathways in different cancers, including HCC. Importantly, the mRNA expression levels of these four key hub genes (VEGFA, SRC, MMP9, and CDK1) were significantly different between normal and HCC tumor samples. Their expression levels were significantly associated with the clinical survival outcomes of HCC patients, as well as the immune cell infiltration levels in the HCC tumor microenvironment. In addition, these four genes showed significant co-expression correlated with immune checkpoint genes, including CD274, PDCD1, CTLA4, and CD47. Furthermore, we used computer-aided approaches to investigate the binding affinity and potential binding mechanisms between bilobetin and target proteins encoded by four key hub genes. In conclusion, our study shed light on the potential application of the bioactive bioflavonoid molecule bilobetin in LIHC treatment by regulating four key hub genes.

Therapeutic and Anticancer Properties of Nerium oleander– A Poison as Medicine

Cancer is a heterogeneous disease and ranks among the most pressing health concerns faced by humans and requires a proactive treatment approach. Plants are a rich source of compounds and offer a promising avenue for cancer research. Chemotherapy has so far been effective, but it comes with some very unpleasant side effects. Nerium oleander, an evergreen plant cultivated throughout the world, has many metabolites, including cardiac glycosides, phenols, saponins and terpenoids. The plant and its derivatives have been an essential component of traditional medicine for treating several ailments from the beginning of time, notably cancer, diabetes mellitus, asthma, and cardiac disease. However, the scientific community has not gone much further into the information. This review aims to understand the therapeutic applications of N. oleander, focusing on cancer. The leaf extract, anvirzel and PBI-05204 has entered clinical trials and other derivates like oleandrin and breast in are still under in-vitro and in-vivo studies. In order to combat cancer, the plant operates on several cancer-related signaling pathways, including the Akt mTOR downstream pathway.

PP2A drives the stemness in colorectal cancer cells by decreasing the Hippo signaling pathway.

Colorectal cancer (CRC) is one of the most prevalent malignancies. Accumulating evidence suggests that Hippo signaling pathway is a crucial signaling pathway that regulates stemness in multiple cancers, including CRC. Given that, the therapeutics targeting the Hippo pathway are of great interest. At the same time, previous studies have reported that PP2A regulates the Hippo pathway in tumorigenesis. In this study, we uncover the role of PP2A in vitro and in vivo and the interaction between PP2A and Hippo signaling pathway in CRC stemness. We investigate the molecular mechanism of PP2A-mediated Hippo pathway in CRC progression from the aspect of cell stemness. Furthermore, we explore the transcription factor of PP2A in CRC. In view of circRNA's regulation of cancer-related signaling pathways in CRC, we also study the association between PP2A-mediated Hippo pathway and the CRC-related circRNA (hsa-circ-001680) confirmed in previous studies. Of note, we demonstrate how hsa-circ-001680 regulates PP2A expression. The effect of hsa-circ-001680 on PP2A stability is investigated as well. In conclusion, the study demonstrates the mechanism of PP2A-mediated pathway on CRC stemness, which may provide new sights for the treatment of CRC.

Exploring Thiazolopyridine AV25R: Unraveling of Biological Activities, Selective Anti-Cancer Properties and In Silico Target and Binding Prediction in Hematological Neoplasms.

Thiazolopyridines are a highly relevant class of small molecules, which have previously shown a wide range of biological activities. Besides their anti-tubercular, anti-microbial and anti-viral activities, they also show anti-cancerogenic properties, and play a role as inhibitors of cancer-related proteins. Herein, the biological effects of the thiazolopyridine AV25R, a novel small molecule with unknown biological effects, were characterized. Screening of a set of lymphoma (SUP-T1, SU-DHL-4) and B- acute leukemia cell lines (RS4;11, SEM) revealed highly selective effects of AV25R. The selective anti-proliferative and metabolism-modulating effects were observed in vitro for the B-ALL cell line RS4;11. Further, we were able to detect severe morphological changes and the induction of apoptosis. Gene expression analysis identified a large number of differentially expressed genes after AV25R exposure and significant differentially regulated cancer-related signaling pathways, such as VEGFA-VEGFR2 signaling and the EGF/EGFR pathway. Structure-based pharmacophore screening approaches using in silico modeling identified potential biological AV25R targets. Our results indicate that AV25R binds with several proteins known to regulate cell proliferation and tumor progression, such as FECH, MAP11, EGFR, TGFBR1 and MDM2. The molecular docking analyses indicates that AV25R has a higher binding affinity compared to many of the experimentally validated small molecule inhibitors of these targets. Thus, here we present in vitro and in silico analyses which characterize, for the first time, the molecular acting mechanism of AV25R, including cellular and molecular biologic effects. Additionally, this predicted the target binding of the molecule, revealing a high affinity to cancer-related proteins and, thus, classified AVR25 for targeted intervention approaches.

DPM2 serve as novel oncogene and prognostic marker transactivated by ESR1 in breast cancer.

Breast cancer (BRCA) is the most common malignancies worldwide with increasing rate. Dolichol phosphate mannose synthase (DPMS) is a critical mannosyltransferase involved in the posttranslational modification of proteins. At present, there is limited knowledge regarding the function of DPMS in breast cancer. In this study, silica analysis in multiple datasets found that dolichyl-phosphate mannosyltransferase subunit 2 (DPM2) is an unfavorable prognostic marker, suggesting its oncogenic role. Cell counting kit-8 and apoptosis assays show that DPM2-silenced cancer cells exhibit decreased growth potential and enhanced cell death rate. Further, transwell and wound healing assays show reduced invasion and migration capabilities in DPM2 knockdown groups, xenograft nude mice model demonstrated smaller tumor volume in DPM2 silenced BC cells. Then, the underlying downstream mechanism of DPM2 in BC was predicted and analyzed, highlighting classical tumorigenic pathways like JAK/STAT signaling pathway and oxidative phosphorylation activated in the cancer group. Finally, ChIP-seq analysis, expression correlation analysis, inhibitor treatment, and dual luciferase assays show that DPM2 is transcriptionally activated by estrogen receptor1 (ESR1). The results show that high expression of DPM2 mRNA is significantly correlated with shorter overall survival (OS) and disease-free survival (DFS) in breast cancer patients, and in vitro knockdown of DPM2 can significantly inhibit the malignant phenotypes of cells, including proliferation, invasion, migration, and apoptosis. These results suggest that DPM2 may play an important role in breast cancer. Altogether, we first uncovered the tumorigenic and prognostic role of DPM2 in breast cancer, cellular assays, and bioinformatics analysis highlighted DPM2 as oncogene via inhibited cancer-related signaling pathways in breast cancer. Besides, DPM2 is transcriptionally activated by ESR1, the signaling axis of ESR1/DPM2 provides a new strategy for BC-targeted therapy.

Targeting CD24 in Cancer Immunotherapy.

Immunotherapy is a hot area in cancer treatment, and one of the keys to this therapy is the identification of the right tumour-associated or tumour-specific antigen. Cluster of differentiation 24 (CD24) is an emerging tumour-associated antigen that is commonly and highly expressed in various tumours. In addition, CD24 is associated with several cancer-related signalling pathways and closely interacts with other molecules and immune cells to influence tumour progression. Monoclonal antibodies, antibody-drug conjugates (ADCs), chimeric antigen receptor (CAR) T-cell therapy, and CAR-NK cell therapy are currently available for the treatment of CD24. In this review, we summarise the existing therapeutic approaches and possible future directions targeting CD24.

In silico analysis of prognostic and diagnostic significance of target genes from prostate cancer cell lines derived exomicroRNAs

BackgroundCancer-secreted exovesicles are important for cell-to-cell communication by altering cancer-related signalling pathways. Exovesicles-derived miRNAs (exomiRNAs)-target genes can be useful for diagnostic and prognostic purposes.MethodsExomiRNA from prostate cancer (PCa) cells (PC-3 and LNCaP) were quantified by qRT-PCR and compared to the healthy cell line RWPE-1 by using miRNome PCR 752 miRNAs Panel. MiRNet database was used to predict exomiRNA-target genes. ExomiRNA-target genes pathway functional enrichment was performed by using Reactome database and Enrichr platform. Protein–protein interaction analysis was carried out by using the STRING database. RNA target-gene sequencing data from The Cancer Genome Atlas Prostate Adenocarcinoma (TCGA-PRAD) database was screened out in 465 PCa patients for candidate gene expression in prostate tumour (PT) tissue and non-pathologic prostate (N-PP) tissue. Signature gene candidates were statistically analysed for diagnosis and prognosis usefulness.ResultsA total of 36 exomiRNAs were found downregulated when comparing PCa cells vs a healthy cell line; and when comparing PC-3 vs LNCaP, 14 miRNAs were found downregulated and 52 upregulated. Reactome pathway database revealed altered pathways and genes related to miRNA biosynthesis, miRNA-mediated gene silencing (TNRC6B and AGO1), and cell proliferation (CDK6), among others. Results showed that TNRC6B gene expression was up-regulated in PT tissue compared to N-PP (n = 52 paired samples) and could be useful for diagnostic purposes. Likewise, gene expression levels of CDK6, TNRC6B, and AGO1 were down-regulated in high-risk PT (n = 293) compared to low-risk PCa tissue counterparts (n = 172). When gene expression levels of CDK6, TNRC6B, and AGO1 were tested as a prognostic panel, the results showed that these improve the prognostic power of classical biomarkers.ConclusionExomiRNAs-targets genes, TNRC6B, CDK6, and AGO1, showed a deregulated expression profile in PCa tissue and could be useful for PCa diagnosis and prognosis.

Inhibition of USP7 upregulates USP22 and activates its downstream cancer-related signaling pathways in human cancer cells

Deubiquitinases (DUBs) play important roles in various human cancers and targeting DUBs is considered as a novel anticancer therapeutic strategy. Overexpression of ubiquitin specific protease 7 and 22 (USP7 and USP22) are associated with malignancy, therapy resistance, and poor prognosis in many cancers. Although both DUBs are involved in the regulation of similar genes and signaling pathways, such as histone H2B monoubiquitination (H2Bub1), c-Myc, FOXP3, and p53, the interdependence of USP22 and USP7 expression has never been described. In the study, we found that targeting USP7 via either siRNA-mediated knockdown or pharmaceutical inhibitors dramatically upregulates USP22 in cancer cells. Mechanistically, the elevated USP22 occurs through a transcriptional pathway, possibly due to desuppression of the transcriptional activity of SP1 via promoting its degradation upon USP7 inhibition. Importantly, increased USP22 expression leads to significant activation of downstream signal pathways including H2Bub1 and c-Myc, which may potentially enhance cancer malignancy and counteract the anticancer efficacy of USP7 inhibition. Importantly, targeting USP7 further suppresses the in vitro proliferation of USP22-knockout (USP22-Ko) A549 and H1299 lung cancer cells and induces a stronger activation of p53 tumor suppressor signaling pathway. In addition, USP22-Ko cancer cells are more sensitive to a combination of cisplatin and USP7 inhibitor. USP7 inhibitor treatment further suppresses in vivo angiogenesis and tumor growth and induced more apoptosis in USP22-Ko cancer xenografts. Taken together, our findings demonstrate that USP7 inhibition can dramatically upregulate USP22 in cancer cells; and targeting USP7 and USP22 may represent a more effective approach for targeted cancer therapy, which warrants further study.51f9aZhqcv_kcNHk2RbtxAVideo

Circulating Extracellular Vesicle-Derived microRNAs as Novel Diagnostic and Prognostic Biomarkers for Non-Viral-Related Hepatocellular Carcinoma.

Extracellular vesicle-derived microRNAs (EV-miRNAs) are promising circulating biomarkers for chronic liver disease. In this study, we explored the potential significance of plasma EV-miRNAs in non-hepatitis B-, non-hepatitis C-related HCC (NBNC-HCC). We compared, using the NanoString method, plasma EV-miRNA profiles between NBNC-HCC and control groups including patients with non-alcoholic fatty liver disease (NAFLD) and healthy controls. The differentially expressed EV-miRNAs were validated in another set of plasma samples by qRT-PCR. A total of 66 significantly differentially expressed EV-miRNAs between the HCC and the control groups were identified in the discovery set. In the validation cohort, including plasma samples of 70 NBNC-HCC patients, 70 NAFLD patients, and 35 healthy controls, 5 plasma EV-miRNAs were significantly elevated in HCC, which included miR-19-3p, miR-16-5p, miR-223-3p, miR-30d-5p, and miR-451a. These miRNAs were found to participate in several cancer-related signaling pathways based on bioinformatic analysis. Among them, EV-miR-19-3p exhibited the best diagnostic performance and displayed a high sensitivity for detecting alpha-fetoprotein-negative HCC and early-stage HCC. In multivariate analysis, a high EV-miR-19-3p level was demonstrated as an independently unfavorable predictor of overall survival in patients with NBNC-HCC. In conclusion, our data have indicated, for the first time, that EV-miR-19-3p could serve as a novel circulating biomarker for the diagnosis and prognosis of NBNC-HCC.

Single Cell Analyses Indicate SRSF2 and TET2 Co-Mutation Results in Skewed Haematopoiesis in Myelodysplastic Syndromes

We used single-cell ATAC-seq (scATAC-seq) to study how synchronous SRSF2 and TET2 co-mutations result in skewed myelopoiesis compared with SRSF2 mutation only in subjects with myelodysplastic neoplasms (MDNs). We identified 621 differentially expressed genes in comparing of transcriptome sequencing data of bone marrow mononuclear cells ( p < 0.01; |log2FC| > 2; Figure 1 A). Up-regulated genes in the co-mutation cohort involved those expressed in pluripotent haematopoietic stem cells (HSCs), cytokine receptor interactions and cancer-related signaling pathways ( Figure 1 B). We extended our observation by interrogating data from the GSE58831 public dataset where we identified 18 similar pathways in subjects with SRSF2 and TET2 co-mutations ( Figure 1 C ). We then used scATAC-seq to verify regulatory networks with genes and transcription factors. 49,532 cells had high-quality scATAC-seq profiles and passed stringent quality filtering with a median of 12,858 fragments per cell 39% of which mapped to peaks. 16 cell types were annotated according to cell marker genes and aligned with the public single cell RNA-seq gene expression matrix of haematopoietic cell types ( Figure 1 D-E). Next, we compared transcription factor (TF) and cis-elements active during differentiation of HSC to myelopoiesis betweenthe SRSF2 and TET2 co-mutation and SRSF2 mutation-only cohorts. In the SRSF2 and TET2 co-mutation cohort we found GATA4, RUNX1, SNAI1, REL and JDP2 favour myeloid differentiation and in NF-KB related inflammatory responses. Related gene activity correlated with high activity of inflammatory cytokines such as BCL2A1, EGR1, IL-1β, and NLRP3( Figure 1 F). SRSF2 and TET2 co-mutations result in early clonal dominance at the haematopoietic stem cell stage. 19,836 peaks were accessible in SRSF2 and TET2 co-mutated samples and annotated for putative functions by GREAT ontology enrichment analysis ( Figure 1 G-H). More accessibility peaks in SRSF2 and TET2 co-mutation were restricted to cancer-related process (reactive oxygen species biosynthetic process, regulation of phagocytosis, intrinsic apoptotic signaling pathway, mRNA catabolism) and cytokine related pathways (IL-1 mediated signaling pathway) compared with SRSF2 mutation-only samples. Next, we focused on the IL-1-mediated signaling pathway, a regulator of HSC function. We isolated umbilical cord blood HSCs (CD34+) monitored their expansion in liquid culture with or without (IL-1A or IL-1B (25 ng/ml). HSCs cultured with IL-1A or IL-1B differentiated and expanded significantly faster than untreated HSCs over 7-day period ( Figure 1 I). To directly address the effects of IL-1 on HSC differentiation we used colony formation assays in methylcellulose ± IL-1. Strikingly, IL-1-treated HSCs produced almost exclusively myeloid-committed granulocyte/macrophage (GM)-type colonies containing abundant macrophages (CFU-GM), a higher proportion of immature multi-lineage granulocyte/ erythrocyte /macrophage/megakaryocyte (CFU-GEMM)-type colonies containing mostly immature myeloblasts and a lower proportion of burst-forming unit-erythroid (BFU-E). IL-1-treated HSCs also had decreased re-placing capacity ( Figure 1 J-K). Next, we constructed a SRSF2 P95H single mutation and SRSF2 P95H mutation with TET2 knockout cell lines. We found that co-mutant cells had significantly increased NLRP3 and IL-1β expression in LPS (1 ug/ml) and ATP (5 mM) treated cultures whereas no change was detected IL-1α expression ( Figure 1 L-M). In conclusion, our data preliminary indicate SRSF2 and TET2 co-mutated causes increased NLRP3-mediated IL-1β secretion resulting in skewed differentiation of HSCs in persons with MDNs.

Cancer Development in Hepatocytes by Long-Term Induction of Hypoxic Hepatocellular Carcinoma Cell (HCC)-Derived Exosomes In Vivo and In Vitro.

Hypoxic tumor cell-derived exosomes play a key role in the occurrence, development, and metastasis of tumors. However, the mechanism of hypoxia-mediated metastasis remains unclear. In this study, hypoxic hepatocellular carcinoma cell (HCC-LM3)-derived exosomes (H-LM3-exos) were used to induce hepatocytes (HL-7702) over a long term (40 passages in 120 days). A nude mouse experiment further verified the effect of H-LM3-exos on tumor growth and metastasis. The process of cancer development in hepatocytes induced by H-LM3-exos was analyzed using both biological and physical techniques, and the results showed that the proliferation and soft agar growth abilities of the transformed cells were enhanced. The concentration of tumor markers secreted by transformed cells was increased, the cytoskeleton was disordered, and the migration ability was enhanced and was accompanied by epithelial-mesenchymal transition (EMT). Transcriptome results showed that differentially expressed genes between transformed cells and hepatocytes were enriched in cancer-related signaling pathways. The degree of cancer development in transformed cells was enhanced by an increase in H-LM3-exos-induced passages. Nude mice treated with different concentrations of H-LM3-exos showed different degrees of tumor growth and liver lesions. The physical properties of the cells were characterized by atomic force microscopy. Compared with the hepatocytes, the height and roughness of the transformed cells were increased, while the adhesion and elastic modulus were decreased. The changes in physical properties of primary tumor cells and hepatocytes in nude mice were consistent with this trend. Our study linking omics with the physical properties of cells provides a new direction for studying the mechanisms of cancer development and metastasis.

Identification and validation of targets of swertiamarin on idiopathic pulmonary fibrosis through bioinformatics and molecular docking-based approach

BackgroundSwertiamarin is the main hepatoprotective component of Swertiapatens and has anti-inflammatory and antioxidation effects. Our previous study showed that it was a potent inhibitor of idiopathic pulmonary fibrosis (IPF) and can regulate the expressions of α-smooth muscle actin (α-SMA) and epithelial cadherin (E-cadherin), two markers of the TGF-β/Smad (transforming growth factor beta/suppressor of mothers against decapentaplegic family) signaling pathway. But its targets still need to be investigated. The main purpose of this study is to identify the targets of swertiamarin.MethodsGEO2R was used to analyze the differentially expressed genes (DEGs) of GSE10667, GSE110147, and GSE71351 datasets from the Gene Expression Omnibus (GEO) database. The DEGs were then enriched with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis for their biological functions and annotated terms. The protein-protein interaction (PPI) network was constructed to identify hub genes. The identified hub genes were predicted for their bindings to swertiamarin by molecular docking (MD) and validated by experiments.Results76 upregulated and 27 downregulated DEGs were screened out. The DEGs were enriched in the biological function of cellular component (CC) and 7 cancer-related signaling pathways. Three hub genes, i.e., LOX (lysyl oxidase), COL5A2 (collagen type V alpha 2 chain), and CTGF (connective tissue growth factor) were selected, virtually tested for the interactions with swertiamarin by MD, and validated by in vitro experiments.ConclusionLOX, COL5A2, and CTGF were identified as the targets of swertiamarin on IPF.