A Transcriptomic Approach Reveals Selective Ribosomal Remodelling in the Tumour Versus the Stromal Compartment of Metastatic Colorectal Cancer

Because of its high incidence and poor prognosis, colorectal cancer (CRC) represents an important health issue in several countries. As with other carcinomas, the so-called tumour microenvironment (TME) has been shown to play key roles in CRC progression and related therapeutical outcomes, even though a deeper understanding of the underlying molecular mechanisms is needed to devise new treatment strategies. For some years now, omics technologies and consolidated bioinformatics pipelines have allowed scientists to access large amounts of biologically relevant information, even when starting from small tissue samples; thus, in order to shed new light upon the role of the TME in CRC, we compared the gene expression profiles of 6 independent tumour tissues (all progressed towards metastatic disease) to the expression profile of the surrounding stromata. To do this, paraffin-embedded whole tissues were first microdissected to obtain samples enriched with tumour and stromal cells, respectively. Afterwards, RNA was extracted and analysed using a microarray-based approach. A thorough bioinformatics analysis was then carried out to identify transcripts differentially expressed between the two groups and possibly enriched functional terms. Overall, 193 genes were found to be significantly downregulated in tumours compared to the paired stromata. The functional analysis of the downregulated gene list revealed three principal macro areas of interest: the extracellular matrix, cell migration, and angiogenesis. Conversely, among the upregulated genes, the main alterations detected by the functional annotation were related to the ribosomal proteins (rProteins) of both the large (60S) and small (40S) subunits of the cytosolic ribosomes. Subsequent gene set enrichment analysis (GSEA) confirmed the massive overexpression of most cytosolic—but not mitochondrial—ribosome rProteins.

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LMNB2 promotes the progression of colorectal cancer by silencing p21 expression

Cell Death and Disease ◽

10.1038/s41419-021-03602-1 ◽

2021 ◽

Vol 12 (4) ◽

Author(s):

Chen-Hua Dong ◽

Tao Jiang ◽

Hang Yin ◽

Hu Song ◽

Yi Zhang ◽

...

Keyword(s):

Colorectal Cancer ◽

Cell Cycle ◽

Cell Proliferation ◽

Cell Cycle Progression ◽

Molecular Mechanisms ◽

Gene Set Enrichment Analysis ◽

Molecular Therapy ◽

Cycle Progression ◽

Cancer Tissues

AbstractColorectal cancer is the second common cause of death worldwide. Lamin B2 (LMNB2) is involved in chromatin remodeling and the rupture and reorganization of nuclear membrane during mitosis, which is necessary for eukaryotic cell proliferation. However, the role of LMNB2 in colorectal cancer (CRC) is poorly understood. This study explored the biological functions of LMNB2 in the progression of colorectal cancer and explored the possible molecular mechanisms. We found that LMNB2 was significantly upregulated in primary colorectal cancer tissues and cell lines, compared with paired non-cancerous tissues and normal colorectal epithelium. The high expression of LMNB2 in colorectal cancer tissues is significantly related to the clinicopathological characteristics of the patients and the shorter overall and disease-free cumulative survival. Functional analysis, including CCK8 cell proliferation test, EdU proliferation test, colony formation analysis, nude mouse xenograft, cell cycle, and apoptosis analysis showed that LMNB2 significantly promotes cell proliferation by promoting cell cycle progression in vivo and in vitro. In addition, gene set enrichment analysis, luciferase report analysis, and CHIP analysis showed that LMNB2 promotes cell proliferation by regulating the p21 promoter, whereas LMNB2 has no effect on cell apoptosis. In summary, these findings not only indicate that LMNB2 promotes the proliferation of colorectal cancer by regulating p21-mediated cell cycle progression, but also suggest the potential value of LMNB2 as a clinical prognostic marker and molecular therapy target.

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Colorectal Cancer Growth Retardation through Induction of Apoptosis, Using an Optimized Synergistic Cocktail of Axitinib, Erlotinib, and Dasatinib

Cancers ◽

10.3390/cancers11121878 ◽

2019 ◽

Vol 11 (12) ◽

pp. 1878 ◽

Cited By ~ 6

Author(s):

Robert H. Berndsen ◽

Nathalie Swier ◽

Judy R. van Beijnum ◽

Patrycja Nowak-Sliwinska

Keyword(s):

Colorectal Cancer ◽

Cell Lines ◽

Kinase Inhibitors ◽

Expression Profiles ◽

Chorioallantoic Membrane ◽

Treatment Strategies ◽

Tumor Growth Inhibition ◽

Clinical Implementation

Patients with advanced colorectal cancer (CRC) still depend on chemotherapy regimens that are associated with significant limitations, including resistance and toxicity. The contribution of tyrosine kinase inhibitors (TKIs) to the prolongation of survival in these patients is limited, hampering clinical implementation. It is suggested that an optimal combination of appropriate TKIs can outperform treatment strategies that contain chemotherapy. We have previously identified a strongly synergistic drug combination (SDC), consisting of axitinib, erlotinib, and dasatinib that is active in renal cell carcinoma cells. In this study, we investigated the activity of this SDC in different CRC cell lines (SW620, HT29, and DLD-1) in more detail. SDC treatment significantly and synergistically decreased cell metabolic activity and induced apoptosis. The translation of the in-vitro-based results to in vivo conditions revealed significant CRC tumor growth inhibition, as evaluated in the chicken chorioallantoic membrane (CAM) model. Phosphoproteomics analysis of the tested cell lines revealed expression profiles that explained the observed activity. In conclusion, we demonstrate promising activity of an optimized mixture of axitinib, erlotinib, and dasatinib in CRC cells, and suggest further translational development of this drug mixture.

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Association between cetuximab response and differential immunologic gene expression signatures in colorectal cancer metastases.

Journal of Clinical Oncology ◽

10.1200/jco.2016.34.4_suppl.558 ◽

2016 ◽

Vol 34 (4_suppl) ◽

pp. 558-558 ◽

Cited By ~ 1

Author(s):

Michael Sangmin Lee ◽

Benjamin Garrett Vincent ◽

Autumn Jackson McRee ◽

Hanna Kelly Sanoff

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

T Cells ◽

T Cell ◽

Immune Cell ◽

Expression Profiles ◽

Gene Set Enrichment Analysis ◽

Activated T Cells ◽

Gene Sets

558 Background: Different immune cell infiltrates into colorectal cancer (CRC) tumors are associated with different prognoses. Tumor-associated macrophages contribute to immune evasion and accelerated tumor progression. Conversely, tumor infiltrating lymphocytes at the invasive margin of CRC liver metastases are associated with improved outcomes with chemotherapy. Cetuximab is an IgG1 monoclonal antibody against epidermal growth factor receptor (EGFR) and stimulates antibody-dependent cellular cytotoxicity (ADCC) in vitro. However, it is unclear in humans if response to cetuximab is modulated by the immune response. We hypothesized that different immune patterns detected in gene expression profiles of CRC metastases are associated with different responses to cetuximab. Methods: We retrieved gene expression data from biopsies of metastases from 80 refractory CRC patients treated with cetuximab monotherapy (GEO GSE5851). Samples were dichotomized by cetuximab response as having either disease control (DC) or progressive disease (PD). We performed gene set enrichment analysis (GSEA) with GenePattern 3.9.4 using gene sets of immunologic signatures obtained from the Molecular Signatures Database v5.0. Results: Among the 68 patients with response annotated, 25 had DC and 43 had PD. In the PD cohort, 59/1910 immunologic gene sets had false discovery rate (FDR) < 0.1. Notably, multiple gene sets upregulated in monocyte signatures were associated with PD. Also, gene sets consistent with PD1-ligated T cells compared to control activated T cells (FDR = 0.052) or IL4-treated CD4 T cells compared to controls (FDR = 0.087) were associated with PD. Conclusions: Cetuximab-resistant patients tended to have baseline increased expression of gene signatures reflective of monocytic infiltrates, consistent with also having increased expression of the IL4-treated T-cell signature. Cetuximab resistance was also associated with increased expression of the PD1-ligated T cell signature. These preliminary findings support further evaluation of the effect of differential immune infiltrates in prognosis of metastatic CRC treated with cetuximab.

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Stromal genes discriminate preinvasive from invasive disease, predict outcome, and highlight inflammatory pathways in digestive cancers

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0909797107 ◽

2010 ◽

Vol 107 (5) ◽

pp. 2177-2182 ◽

Cited By ~ 102

Author(s):

Amel Saadi ◽

Nicholas B. Shannon ◽

Pierre Lao-Sirieix ◽

Maria O’Donovan ◽

Elaine Walker ◽

...

Keyword(s):

Expression Profiles ◽

Enrichment Analysis ◽

Invasive Disease ◽

Gene Set Enrichment Analysis ◽

In Vitro Assays ◽

Stromal Compartment ◽

Inflammatory Pathways ◽

Digestive Cancers ◽

Stromal Signature

The stromal compartment is increasingly recognized to play a role in cancer. However, its role in the transition from preinvasive to invasive disease is unknown. Most gastrointestinal tumors have clearly defined premalignant stages, and Barrett’s esophagus (BE) is an ideal research model. Supervised clustering of gene expression profiles from microdissected stroma identified a gene signature that could distinguish between BE metaplasia, dysplasia, and esophageal adenocarcinoma (EAC). EAC patients overexpressing any of the five genes (TMEPAI, JMY, TSP1, FAPα, and BCL6) identified from this stromal signature had a significantly poorer outcome. Gene ontology analysis identified a strong inflammatory component in BE disease progression, and key pathways included cytokine–cytokine receptor interactions and TGF-β. Increased protein levels of inflammatory-related genes significantly up-regulated in EAC compared with preinvasive stages were confirmed in the stroma of independent samples, and in vitro assays confirmed functional relevance of these genes. Gene set enrichment analysis of external datasets demonstrated that the stromal signature was also relevant in the preinvasive to invasive transition of the stomach, colon, and pancreas. These data implicate inflammatory pathways in the genesis of gastrointestinal tract cancers, which can affect prognosis.

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Identification of IL10RA by Weighted Correlation Network Analysis and in vitro Validation of Its Association With Prognosis of Metastatic Melanoma

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2020.630790 ◽

2021 ◽

Vol 8 ◽

Author(s):

Si Cheng ◽

Zhe Li ◽

Wenhao Zhang ◽

Zhiqiang Sun ◽

Zhigang Fan ◽

...

Keyword(s):

Network Analysis ◽

Metastatic Melanoma ◽

Large Scale ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Migration And Invasion

Skin cutaneous melanoma (SKCM) is the major cause of death for skin cancer patients, its high metastasis often leads to poor prognosis of patients with malignant melanoma. However, the molecular mechanisms underlying metastatic melanoma remain to be elucidated. In this study we aim to identify and validate prognostic biomarkers associated with metastatic melanoma. We first construct a co-expression network using large-scale public gene expression profiles from GEO, from which candidate genes are screened out using weighted gene co-expression network analysis (WGCNA). A total of eight modules are established via the average linkage hierarchical clustering, and 111 hub genes are identified from the clinically significant modules. Next, two other datasets from GEO and TCGA are used for further screening of biomarker genes related to prognosis of metastatic melanoma, and identified 11 key genes via survival analysis. We find that IL10RA has the highest correlation with clinically important modules among all identified biomarker genes. Further in vitro biochemical experiments, including CCK8 assays, wound-healing assays and transwell assays, have verified that IL10RA can significantly inhibit the proliferation, migration and invasion of melanoma cells. Furthermore, gene set enrichment analysis shows that PI3K-AKT signaling pathway is significantly enriched in metastatic melanoma with highly expressed IL10RA, indicating that IL10RA mediates in metastatic melanoma via PI3K-AKT pathway.

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DDX10 Promotes the Proliferation and Metastasis of Colorectal Cancer Cells via Splicing RPL35

10.21203/rs.3.rs-907936/v1 ◽

2021 ◽

Author(s):

Xin Zhou ◽

Zhihong Liu ◽

Cuifeng Zhang ◽

Manman Jiang ◽

Yuxiao Jin ◽

...

Keyword(s):

Colorectal Cancer ◽

Molecular Mechanisms ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Migration And Invasion ◽

Ppi Network ◽

Interacting Protein ◽

Network Analyses ◽

Potential Biomarker

Abstract Background: Colorectal cancer (CRC) has become the second deadliest cancer in the world and severely threatens human health. An increasing number of studies have focused on the role of the RNA helicase DEAD-box (DDX) family in CRC. However, the mechanism of DDX10 in CRC has not been elucidated.Methods: In our study, we analysed the expression data of CRC samples from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Subsequently, we performed cytological experiments and animal experiments to explore the role of DDX10 in CRC cells. Furthermore, we performed Gene Ontology (GO)/ Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and protein-protein interaction (PPI) network analyses. Finally, we predicted the interacting protein of DDX10 by LC-MS/MS and verified it by coimmunoprecipitation (Co-IP) and qPCR.Results: In the present study, we identified that DDX10 mRNA was extremely highly expressed in CRC tissues compared with normal colon tissues in the TCGA and GEO databases. The protein expression of DDX10 was measured by immunochemistry (IHC) in 17 CRC patients. The biological roles of DDX10 were explored via cell and molecular biology experiments in vitro and in vivo and cell cycle assays. We found that DDX10 knockdown markedly reduced CRC cell proliferation, migration and invasion. Then, we constructed a PPI network with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). GO and KEGG enrichment analysis and gene set enrichment analysis (GSEA) showed that DDX10 was closely related to RNA splicing and E2F targets. Using LC-MS/MS and Co-IP assays, we discovered that RPL35 is the interacting protein of DDX10. In addition, we hypothesize that RPL35 is related to the E2F pathway and the immune response in CRC.Conclusions: In conclusion, provides a better understanding of the molecular mechanisms of DDX10 in CRC and provides a potential biomarker for the diagnosis and treatment of CRC.

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Immune cell infiltration characteristics and related core genes in lupus nephritis: results from bioinformatic analysis

10.21203/rs.2.12276/v1 ◽

2019 ◽

Author(s):

Yiling Cao ◽

Weihao Tang ◽

Wanxin Tang

Keyword(s):

Gene Expression ◽

Lupus Nephritis ◽

Molecular Mechanisms ◽

Immune Cell ◽

Expression Profiles ◽

Gene Set Enrichment Analysis ◽

Cell Infiltration ◽

Immune Cell Infiltration ◽

Spearman Correlation ◽

Core Genes

Abstract Objects Lupus nephritis (LN) is a common complication of systemic lupus erythematosus that presents a high risk of end-stage renal disease. In the present study, we used CIBERSORT and gene set enrichment analysis (GSEA) of gene expression profiles to identify immune cell infiltration characteristics and related core genes in LN. Methods Datasets from the Gene Expression Omnibus, GSE32591 and GSE113342, were downloaded for further analysis. The GSE32591 dataset, which included 32 LN glomerular biopsy tissues and 14 glomerular tissues of living donors, was analyzed by CIBERSORT. Different immune cell types in LN were analyzed by the Limma software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis based on GSEA were performed by clusterProfiler software. Lists of core genes were derived from Spearman correlation between the most significant GO term and differentially expressed immune cell gene from CIBERSORT. GSE113342 was employed to validate the association between selected core genes and clinical manifestation. Result Five types of immune cells revealed important associations with LN, and monocytes emerged to be the prominent differences. GO and KEGG analyses indicated that immune response pathways are significantly enriched in LN. The Spearman correlation indicated that 15 genes, including FCER1G, CLEC7A, MARCO, CLEC7A, PSMB9, and PSMB8, were closely related to clinical features. Conclusion This study is the first to identify immune cell infiltration with microarray data of glomeruli in LN by using CIBERSORT analysis and provides novel evidence and clues for further research of the molecular mechanisms of LN.

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OTEH-7. Molecular characterization of tumor stiffness in glioblastoma

Neuro-Oncology Advances ◽

10.1093/noajnl/vdab070.046 ◽

2021 ◽

Vol 3 (Supplement_2) ◽

pp. ii11-ii12

Author(s):

Skarphedinn Halldorsson ◽

Siri Fløgstad Svensson ◽

Henriette Engen Berg ◽

Denise Wolrab ◽

Frode Rise ◽

...

Keyword(s):

Molecular Mechanisms ◽

Immune Cell ◽

Treatment Strategies ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Tissue Stiffness ◽

Cancer Proliferation ◽

Polar Metabolites ◽

Novel Treatment Strategies ◽

Tumor Stiffness

Abstract Tumor heterogeneity is one of the hallmarks of glioblastoma multiforme (GBM). Morphology within a given GBM tumor can be extremely variable where some regions of the tumor have a soft, gel-like structure while other areas are dense and fibrous. Abnormal mechanical stress and tissue stiffening caused by cancer proliferation are believed to affect vascularity by compressing structurally weak blood vessels and restricting the supply of nutrients and oxygen to the tissue. These effects contribute to a hypoxic microenvironment that promotes disease progression and chemoresistance. The genetic and molecular mechanisms that govern tissue stiffness within GBM tumors, however, are largely unknown. Magnetic Resonance Elastography (MRE) is an emerging technique for quantifying tissue stiffness non-invasively. We have evaluated 10 GBM patients by MRE imaging obtained prior to surgical resection. During surgery, 2–7 stereotactically navigated biopsies were collected from locations within the tumor with varying degrees of measured stiffness. Biopsies were processed to extract RNA, proteins, polar metabolites and lipids. Biomolecules were analyzed on relevant -omics platforms (RNA sequencing, MS-proteomics and lipidomics, NMR of polar metabolites). Differential expression and gene set enrichment analysis of patient paired biopsies indicate an overall increase in macrophage infiltration and extracellular matrix re-organization associated with increased tumor stiffness. Among the most highly upregulated genes in stiff tumor tissue were lymphatic endothelial hyaluronic acid receptor 1 (LYVE-1) and macrophage receptor with collagenous structure (MARCO), both of which have been associated with immune cell infiltration and tissue stiffness. Our preliminary findings offer novel insights into tumor morphology in GBM that can be inferred from imaging prior to surgery. This can be used to identify tumor regions with high risk of progression and infiltration, thereby informing and guiding surgical strategy and may ultimately lead to novel treatment strategies.

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An autophagy-related long non-coding RNA signature for patients with colorectal cancer

Physiology International ◽

10.1556/2060.2021.00125 ◽

2021 ◽

Author(s):

Dongyan Zhao ◽

Xizhen Sun ◽

Sidan Long ◽

Shukun Yao

Keyword(s):

Colorectal Cancer ◽

Overall Survival ◽

High Risk ◽

Cox Regression ◽

Risk Group ◽

Expression Profiles ◽

High Risk Group ◽

Low Risk ◽

Gene Set Enrichment Analysis ◽

Cox Regression Analysis

AbstractAimLong non-coding RNAs (lncRNAs) have been identified to regulate cancers by controlling the process of autophagy and by mediating the post-transcriptional and transcriptional regulation of autophagy-related genes. This study aimed to investigate the potential prognostic role of autophagy-associated lncRNAs in colorectal cancer (CRC) patients.MethodsLncRNA expression profiles and the corresponding clinical information of CRC patients were collected from The Cancer Genome Atlas (TCGA) database. Based on the TCGA dataset, autophagy-related lncRNAs were identified by Pearson correlation test. Univariate Cox regression analysis and the least absolute shrinkage and selection operator analysis (LASSO) Cox regression model were performed to construct the prognostic gene signature. Gene set enrichment analysis (GSEA) was used to further clarify the underlying molecular mechanisms.ResultsWe obtained 210 autophagy-related genes from the whole dataset and found 1187 lncRNAs that were correlated with the autophagy-related genes. Using Univariate and LASSO Cox regression analyses, eight lncRNAs were screened to establish an eight-lncRNA signature, based on which patients were divided into the low-risk and high-risk group. Patients’ overall survival was found to be significantly worse in the high-risk group compared to that in the low-risk group (log-rank p = 2.731E-06). ROC analysis showed that this signature had better prognostic accuracy than TNM stage, as indicated by the area under the curve. Furthermore, GSEA demonstrated that this signature was involved in many cancer-related pathways, including TGF-β, p53, mTOR and WNT signaling pathway.ConclusionsOur study constructed a novel signature from eight autophagy-related lncRNAs to predict the overall survival of CRC, which could assistant clinicians in making individualized treatment.

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Bioinformatic Analysis of Gene Expression Profile in Plasma of Hypertensive Patients

American Journal of Hypertension ◽

10.1093/ajh/hpaa040 ◽

2020 ◽

Vol 33 (6) ◽

pp. 581-581

Author(s):

Yan-zhen Li ◽

Hao-jie Xu ◽

Jia-min Hu ◽

Shi-zhu Lin ◽

Na Zhang ◽

...

Keyword(s):

Messenger Rna ◽

Noncoding Rna ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Therapeutic Interventions ◽

Total Rna ◽

Hormone Synthesis ◽

Public Data

Abstract Background To analyze expression profiles of long noncoding RNA (lncRNA) and messenger RNA (mRNA) in patients with essential hypertension (EH) and normotensive adults. Methods The gene chip dataset GSE76845, which was generated from 5 plasma samples from patients with EH and 5 normotensives, was downloaded from the National Biotechnology Information Center Public Data Platform. Each sample (total RNA) was pooled from the total RNA of 3 age- and gender-matched subjects (EH patients or healthy controls). A ClusterProfiler package including gene set enrichment analysis (GSEA) was used to identify differentially expressed genes. The target microRNA and mRNA were predicted by microcode, microDB, microTarBase, and TargetScan databases. Finally, a competing endogenous RNAs (ceRNA) regulatory network was constructed. Results Compared with the healthy control adults, 191 differential lncRNAs (90 upregulated and 101 downregulated) and 1,187 differential mRNAs (533 upregulated and 654 downregulated) were identified in EH patients. GSEA analysis showed that 17 pathways, including ubiquinone and terpenoid-quinone biosynthesis, parathyroid hormone synthesis secretion and action, fatty acid metabolism, and steroid hormone biosynthesis are involved in hypertension. A ceRNA network consisting of 150 nodes and 488 interactive pairs was constructed. Conclusions lncRNA and mRNA profile analysis provides new insight into molecular mechanisms of EH pathogenesis and potential targets for therapeutic interventions.

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