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

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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The Role of PAX2 in Breast Cancer: A Study Based on Bioinformatics Analysis and in Vitro Validation

10.21203/rs.3.rs-738037/v1 ◽

2021 ◽

Author(s):

Shan Yang ◽

Wei Gao ◽

Haoqi Wang ◽

Xi Zhang ◽

Yunzhe Mi ◽

...

Keyword(s):

Breast Cancer ◽

Cell Growth ◽

Expression Profiles ◽

Enrichment Analysis ◽

Mapk Signaling ◽

Gene Set Enrichment Analysis ◽

Functional Enrichment ◽

Migration And Invasion ◽

Clinical Samples

Abstract Background: Breast cancer (BC) is the most frequently diagnosed cancer in women and is the second most common cancer among newly diagnosed cancers worldwide. Studies have shown that paired box 2 (PAX2) participates in the tumorigenesis of some cancer cells. However, the functions of PAX2 in the BC context are still unclear.Methods: Transcriptome expression proﬁles and clinicopathological information of BC were download from the TCGA database. Then the expression level and prognostic value in TCGA database were explored. Gene Set Enrichment Analysis (GSEA) and functional enrichment analysis were performed to investigate the functions and pathways of PAX2. Moreover, RT-qPCR was used to determine the expression of PAX2 in BC tissues, and the predictive value of PAX2 in clinical samples was assessed. CCK-8 assay was used to evaluate cell growth. The migration and invasion capacities of cells were assessed by wound healing assay and Transwell assay.Results: PAX2 was up-regulated in the TCGA-BC datasets. GSEA analysis suggested that PAX2 might be involved in the regulation of MAPK signaling pathways and so on. Moreover, PAX2 was overexpressed in BC tissues, and PAX2 expression was associated with menopause. PAX2 deficiency could inhibit the growth, migration, and invasion of BC cells.Conclusion: This study suggested that PAX2 was up-regulated in BC, which inhibited BC cell growth, migration, and invasion. Thus, PAX2 could be a potential therapeutic target for BC.

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Connecting gene expression subtypes of colorectal cancer (CRC) with cell lines and drug resistance.

Journal of Clinical Oncology ◽

10.1200/jco.2013.31.15_suppl.e14544 ◽

2013 ◽

Vol 31 (15_suppl) ◽

pp. e14544-e14544

Author(s):

Eva Budinska ◽

Jenny Wilding ◽

Vlad Calin Popovici ◽

Edoardo Missiaglia ◽

Arnaud Roth ◽

...

Keyword(s):

Gene Expression ◽

Cell Line ◽

Clinical Significance ◽

Cell Lines ◽

Drug Response ◽

Drug Sensitivity ◽

Expression Profiles ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis

e14544 Background: We identified CRC gene expression subtypes (ASCO 2012, #3511), which associate with established parameters of outcome as well as relevant biological motifs. We now substantiate their biological and potentially clinical significance by linking them with cell line data and drug sensitivity, primarily attempting to identify models for the poor prognosis subtypes Mesenchymal and CIMP-H like (characterized by EMT/stroma and immune-associated gene modules, respectively). Methods: We analyzed gene expression profiles of 35 publicly available cell lines with sensitivity data for 82 drug compounds, and our 94 cell lines with data on sensitivity for 7 compounds and colony morphology. As in vitro, stromal and immune-associated genes loose their relevance, we trained a new classifier based on genes expressed in both systems, which identifies the subtypes in both tissue and cell cultures. Cell line subtypes were validated by comparing their enrichment for molecular markers with that of our CRC subtypes. Drug sensitivity was assessed by linking original subtypes with 92 drug response signatures (MsigDB) via gene set enrichment analysis, and by screening drug sensitivity of cell line panels against our subtypes (Kruskal-Wallis test). Results: Of the cell lines 70% could be assigned to a subtype with a probability as high as 0.95. The cell line subtypes were significantly associated with their KRAS, BRAF and MSI status and corresponded to our CRC subtypes. Interestingly, the cell lines which in matrigel created a network of undifferentiated cells were assigned to the Mesenchymal subtype. Drug response studies revealed potential sensitivity of subtypes to multiple compounds, in addition to what could be predicted based on their mutational profile (e.g. sensitivity of the CIMP-H subtype to Dasatinib, p<0.01). Conclusions: Our data support the biological and potentially clinical significance of the CRC subtypes in their association with cell line models, including results of drug sensitivity analysis. Our subtypes might not only have prognostic value but might also be predictive for response to drugs. Subtyping cell lines further substantiates their significance as relevant model for functional studies.

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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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Distinctive Cellular and Metabolic Reprogramming in Porcine Lung Mononuclear Phagocytes Infected With Type 1 PRRSV Strains

Frontiers in Immunology ◽

10.3389/fimmu.2020.588411 ◽

2020 ◽

Vol 11 ◽

Author(s):

Elisa Crisci ◽

Marco Moroldo ◽

Thien-Phong Vu Manh ◽

Ammara Mohammad ◽

Laurent Jourdren ◽

...

Keyword(s):

Expression Profiles ◽

Enrichment Analysis ◽

Cellular Reprogramming ◽

Mononuclear Phagocytes ◽

Gene Set Enrichment Analysis ◽

Metabolic Reprogramming ◽

Specific Expression ◽

Data Set

Porcine reproductive and respiratory syndrome (PRRS) has an extensive impact on pig production. The causative virus (PRRSV) is divided into two species, PRRSV-1 (European origin) and PRRSV-2 (North American origin). Within PRRSV-1, PRRSV-1.3 strains, such as Lena, are more pathogenic than PRRSV-1.1 strains, such as Flanders 13 (FL13). To date, the molecular interactions of PRRSV with primary lung mononuclear phagocyte (MNP) subtypes, including conventional dendritic cells types 1 (cDC1) and 2 (cDC2), monocyte-derived DCs (moDC), and pulmonary intravascular macrophages (PIM), have not been thoroughly investigated. Here, we analyze the transcriptome profiles of in vivo FL13-infected parenchymal MNP subpopulations and of in vitro FL13- and Lena-infected parenchymal MNP. The cell-specific expression profiles of in vivo sorted cells correlated with their murine counterparts (AM, cDC1, cDC2, moDC) with the exception of PIM. Both in vivo and in vitro, FL13 infection altered the expression of a low number of host genes, and in vitro infection with Lena confirmed the higher ability of this strain to modulate host response. Machine learning (ML) and gene set enrichment analysis (GSEA) unraveled additional relevant genes and pathways modulated by FL13 infection that were not identified by conventional analyses. GSEA increased the cellular pathways enriched in the FL13 data set, but ML allowed a more complete comprehension of functional profiles during FL13 in vitro infection. Data indicates that cellular reprogramming differs upon Lena and FL13 infection and that the latter might keep antiviral and inflammatory macrophage/DC functions silent. Although the slow replication kinetics of FL13 likely contribute to differences in cellular gene expression, the data suggest distinct mechanisms of interaction of the two viruses with the innate immune system during early infection.

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TNF-α Triggers RIP1/FADD/Caspase-8-Mediated Apoptosis of Astrocytes and RIP3/MLKL-Mediated Necroptosis of Neurons Induced by Angiostrongylus cantonensis Infection

Cellular and Molecular Neurobiology ◽

10.1007/s10571-021-01063-w ◽

2021 ◽

Author(s):

Hongli Zhou ◽

Minyu Zhou ◽

Yue Hu ◽

Yanin Limpanon ◽

Yubin Ma ◽

...

Keyword(s):

Cell Death ◽

Enrichment Analysis ◽

Angiostrongylus Cantonensis ◽

Gene Set Enrichment Analysis ◽

Caspase 8 ◽

Cns Injury ◽

Vitro Assay ◽

Tnf Α

AbstractAngiostrongylus cantonensis (AC) can cause severe eosinophilic meningitis or encephalitis in non-permissive hosts accompanied by apoptosis and necroptosis of brain cells. However, the explicit underlying molecular basis of apoptosis and necroptosis upon AC infection has not yet been elucidated. To determine the specific pathways of apoptosis and necroptosis upon AC infection, gene set enrichment analysis (GSEA) and protein–protein interaction (PPI) analysis for gene expression microarray (accession number: GSE159486) of mouse brain infected by AC revealed that TNF-α likely played a central role in the apoptosis and necroptosis in the context of AC infection, which was further confirmed via an in vivo rescue assay after treating with TNF-α inhibitor. The signalling axes involved in apoptosis and necroptosis were investigated via immunoprecipitation and immunoblotting. Immunofluorescence was used to identify the specific cells that underwent apoptosis or necroptosis. The results showed that TNF-α induced apoptosis of astrocytes through the RIP1/FADD/Caspase-8 axis and induced necroptosis of neurons by the RIP3/MLKL signalling pathway. In addition, in vitro assay revealed that TNF-α secretion by microglia increased upon LSA stimulation and caused necroptosis of neurons. The present study provided the first evidence that TNF-α was secreted by microglia stimulated by AC infection, which caused cell death via parallel pathways of astrocyte apoptosis (mediated by the RIP1/FADD/caspase-8 axis) and neuron necroptosis (driven by the RIP3/MLKL complex). Our research comprehensively elucidated the mechanism of cell death after AC infection and provided new insight into targeting TNF-α signalling as a therapeutic strategy for CNS injury.

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Connectivity Map Analysis Indicates PI3K/Akt/mTOR Inhibitors as Potential Anti-Hypoxia Drugs in Neuroblastoma

Cancers ◽

10.3390/cancers13112809 ◽

2021 ◽

Vol 13 (11) ◽

pp. 2809

Author(s):

Paolo Uva ◽

Maria Carla Bosco ◽

Alessandra Eva ◽

Massimo Conte ◽

Alberto Garaventa ◽

...

Keyword(s):

Expression Profiles ◽

Gene Expression Profiles ◽

Drug Repurposing ◽

Enrichment Analysis ◽

Mtor Inhibitors ◽

Gene Set Enrichment Analysis ◽

Low Oxygen ◽

Connectivity Map ◽

Hypoxic Conditions ◽

Connectivity Score

Neuroblastoma (NB) is one of the deadliest pediatric cancers, accounting for 15% of deaths in childhood. Hypoxia is a condition of low oxygen tension occurring in solid tumors and has an unfavorable prognostic factor for NB. In the present study, we aimed to identify novel promising drugs for NB treatment. Connectivity Map (CMap), an online resource for drug repurposing, was used to identify connections between hypoxia-modulated genes in NB tumors and compounds. Two sets of 34 and 21 genes up- and down-regulated between hypoxic and normoxic primary NB tumors, respectively, were analyzed with CMap. The analysis reported a significant negative connectivity score across nine cell lines for 19 compounds mainly belonging to the class of PI3K/Akt/mTOR inhibitors. The gene expression profiles of NB cells cultured under hypoxic conditions and treated with the mTORC complex inhibitor PP242, referred to as the Mohlin dataset, was used to validate the CMap findings. A heat map representation of hypoxia-modulated genes in the Mohlin dataset and the gene set enrichment analysis (GSEA) showed an opposite regulation of these genes in the set of NB cells treated with the mTORC inhibitor PP242. In conclusion, our analysis identified inhibitors of the PI3K/Akt/mTOR signaling pathway as novel candidate compounds to treat NB patients with hypoxic tumors and a poor prognosis.

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A broadly neutralizing monoclonal antibody induces broad protection against heterogeneous PRRSV strains in piglets

Veterinary Research ◽

10.1186/s13567-021-00914-0 ◽

2021 ◽

Vol 52 (1) ◽

Author(s):

Zhigang Zhang ◽

Tianshu Zhai ◽

Mingshuo Li ◽

Kun Zhang ◽

Jingrui Li ◽

...

Keyword(s):

Monoclonal Antibody ◽

Neutralizing Antibodies ◽

Antigenic Variation ◽

Profile Analysis ◽

Expression Profiles ◽

Enrichment Analysis ◽

Antibody Isotype ◽

Hilar Lymph Node

AbstractNeutralizing antibodies (NAbs) have attracted attention as tools for achieving PRRSV control and prevention, but viral antigenic variation undermines the abilities of NAbs elicited by attenuated PRRSV vaccines to confer full protection against heterogeneous PRRSV field isolates. As demonstrated in this study, the monoclonal antibody (mAb) mAb-PN9cx3 exhibited broad-spectrum recognition and neutralizing activities against PRRSV-1 and PRRSV-2 strains in vitro. Furthermore, in vivo experiments revealed that the administration of two 10-mg doses of mAb-PN9cx3 before and after the inoculation of piglets with heterologous PRRSV isolates (HP-PRRSV-JXA1 or PRRSV NADC30-like strain HNhx) resulted in significant reduction of the PRRSV-induced pulmonary pathological changes and virus loads in porcine alveolar macrophages (PAMs) compared with the results obtained with mAb-treated isotype controls. Moreover, minimal hilar lymph node PRRSV antigen levels were observed in mAb-PN9cx3-treated piglets. A transcriptome profile analysis of PAMs extracted from lung tissues of piglets belonging to different groups (except for antibody-isotype controls) indicated that mAb-PN9cx3 treatment reversed the PRRSV infection-induced alterations in expression profiles. A gene ontology (GO) enrichment analysis of these genes traced their functions to pathways that included the immune response, inflammatory response, and response to steroid hormone, and their functions in oogenesis and positive regulation of angiogenesis have been implicated in PRRSV pathogenesis. Overall, NADC30-like HNhx infection affected more gene pathways than HP-PRRSV infection. In conclusion, our research describes a novel immunologic approach involving the use of mAbs that confer cross-protection against serious illness resulting from infection with heterogeneous PRRSV-2 isolates, which is a feat that has not yet been achieved through vaccination. Ultimately, mAb-PN9cx3 will be a powerful addition to our current arsenal for achieving PRRSV prevention and eradication.

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Robust Metabolic Transcriptional Components in 34,494 Patient-Derived Samples and Cell Lines

10.21203/rs.3.rs-659596/v1 ◽

2021 ◽

Author(s):

Vincent Christiaan Leeuwenburgh ◽

Carlos G. Urzúa-Traslaviña ◽

Arkajyoti Bhattacharya ◽

Marthe T.C. Walvoort ◽

Mathilde Jalving ◽

...

Keyword(s):

Cell Lines ◽

Expression Profiles ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Metabolic Processes ◽

Gene Sets ◽

Transcriptional Changes ◽

Cancer Tissues ◽

Tumor Biopsies ◽

Transcriptional Landscape

Abstract Background: Patient-derived bulk expression profiles of cancers can provide insight into transcriptional changes that underlie reprogrammed metabolism in cancer. These profiles represent the average expression pattern of all heterogeneous tumor and non-tumor cells present in biopsies of tumor lesions. Hence, subtle transcriptional footprints of metabolic processes can be concealed by other biological processes and experimental artifacts. However, consensus Independent Component Analyses (c-ICA) can capture statistically independent transcriptional footprints, of both subtle and more pronounced metabolic processes. Methods: We performed c-ICA with 34,494 bulk expression profiles of patient-derived tumor biopsies, non-cancer tissues, and cell lines. Gene set enrichment analysis with 608 gene sets that describe metabolic processes was performed to identify transcriptional components enriched for metabolic processes (mTCs). The activity of these mTCs were determined in all samples to create a metabolic transcriptional landscape. Results: A set of 555 mTCs were identified of which many were robust across different datasets, platforms, and patient-derived tissues and cell lines. We demonstrate how the metabolic transcriptional landscape defined by the activity of these mTCs in samples can be used to explore associations between the metabolic transcriptome and drug sensitivities, patient outcomes, and the composition of the immune tumor microenvironment. Conclusions: To facilitate the use of our transcriptional metabolic landscape, we have provided access to all data via a web portal ( www.themetaboliclandscapeofcancer.com ). We believe this resource will contribute to the formulation of new hypotheses on how to metabolically engage the tumor or its (immune) microenvironment.

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Abstract 392: The Plasma Proteome of Tangier Disease Patients Reveals Perturbations of Diabetic and Inflammatory Pathways

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvb.36.suppl_1.392 ◽

2016 ◽

Vol 36 (suppl_1) ◽

Author(s):

James T McParland ◽

Evanthia Pashos ◽

Daniel J Rader ◽

Marina Cuchel

Keyword(s):

Inflammatory Response ◽

Type Ii Diabetes ◽

Enrichment Analysis ◽

Nonparametric Test ◽

Type Ii Diabetes Mellitus ◽

Gene Set Enrichment Analysis ◽

P Value ◽

Type Ii ◽

Tangier Disease ◽

Inflammatory Pathways

Aim: The ATP-binding cassette transporter 1 (ABCA1) is a membrane protein well known for its role in cholesterol efflux and HDL formation. Recently, ABCA1 has been implicated as playing a key role in other processes, such as insulin secretion and inflammatory response. We sought to further investigate these potential roles through a quantitative proteomics approach. Specifically, we hypothesized that we could detect differential protein signatures in the plasma of Tangier patients that correspond to pathways involved in diabetes and inflammation. Methods: We used SOMAscan® technology (SomaLogic, Boulder, CO, USA) to analyze plasma collected from 5 Tangier disease patients (homozygotes or compound heterozygotes for functional ABCA1 mutations) and 7 normolipidemic controls. We tested for differences in the levels of approximately 1,000 plasma proteins using a nonparametric test (KS). We then performed Ingenuity Canonical Pathway analysis to examine if proteins linked to diabetes and inflammation pathways were significantly more likely to be differentially abundant in the plasma. We corroborated the results using Gene Set Enrichment Analysis (GSEA). Results: We found an enrichment in differentially abundant proteins involved in type II diabetes mellitus signaling (p-value=0.0002) and inflammatory pathways, such as granulocyte adhesion and diapedesis (p-value=2.2*10 -12 ). These results were also corroborated by GSEA, where gene sets corresponding to GO biological processes such as immune response (p-value=0.008) and inflammatory response (p-value=0.032) ranked at the top of the enrichment results. Conclusions: The results from this pilot study support the concept that ABCA1 is implicated in pathways affecting immune and inflammatory response and type II diabetes.

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Transmembrane p24 Trafficking Protein 2 Regulates Inflammation Through the TLR4/NF-κB Signaling Pathway in Lung Adenocarcinoma

10.21203/rs.3.rs-794174/v1 ◽

2021 ◽

Author(s):

Longhua Feng ◽

Pengjiang Cheng ◽

Zhengyun Feng ◽

Xiaoyu Zhang

Keyword(s):

Lung Adenocarcinoma ◽

Signaling Pathway ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Inflammatory Factors ◽

Normal Tissues ◽

Kaplan Meier ◽

New Strategy

Abstract Background: To investigate the role of transmembrane p24 trafficking protein 2 (TMED2) in lung adenocarcinoma (LUAD) and determine whether TMED2 knockdown could inhibit LUAD in vitro and in vivo.Methods: TIMER2.0, Kaplan-Meier plotter, gene set enrichment analysis (GSEA), Target Gene, and pan-cancer systems were used to predict the potential function of TMED2. Western blotting and immunohistochemistry were performed to analyze TMED2 expression in different tissues or cell lines. The proliferation, development, and apoptosis of LUAD were observed using a lentivirus-mediated TMED2 knockdown. Bioinformatics and western blot analysis of TMED2 against inflammation via the TLR4/NF-κB signaling pathway were conducted. Results: TMED2 expression in LUAD tumor tissues was higher than that in normal tissues and positively correlated with poor survival in lung cancer and negatively correlated with apoptosis in LUAD. The expression of TMED2 was higher in tumors or HCC827 cells. TMED2 knockdown inhibited LUAD development in vitro and in vivo and increased the levels of inflammatory factors via the TLR4/NF-κB signaling pathway. TMED2 was correlated with TME, immune score, TME-associated immune cells, their target markers, and some mechanisms and pathways, as determined using the TIMER2.0, GO, and KEGG assays.Conclusions: TMED2 may regulate inflammation in LUAD through the TLR4/NF-κB signaling pathway, and enhance the proliferation, development, and prognosis of LUAD by regulating inflammation, which provide a new strategy for treating LUAD by regulating inflammation.

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