EMTome: a resource for pan-cancer analysis of epithelial-mesenchymal transition genes and signatures

Abstract Background The epithelial-mesenchymal transition (EMT) enables dissociation of tumour cells from the primary tumour mass, invasion through the extracellular matrix, intravasation into blood vessels and colonisation of distant organs. Cells that revert to the epithelial state via the mesenchymal-epithelial transition cause metastases, the primary cause of death in cancer patients. EMT also empowers cancer cells with stem-cell properties and induces resistance to chemotherapeutic drugs. Understanding the driving factors of EMT is critical for the development of effective therapeutic interventions. Methods This manuscript describes the generation of a database containing EMT gene signatures derived from cell lines, patient-derived xenografts and patient studies across cancer types and multiomics data and the creation of a web-based portal to provide a comprehensive analysis resource. Results EMTome incorporates (i) EMT gene signatures; (ii) EMT-related genes with multiomics features across different cancer types; (iii) interactomes of EMT-related genes (miRNAs, transcription factors, and proteins); (iv) immune profiles identified from The Cancer Genome Atlas (TCGA) cohorts by exploring transcriptomics, epigenomics, and proteomics, and drug sensitivity and (iv) clinical outcomes of cancer cohorts linked to EMT gene signatures. Conclusion The web-based EMTome portal is a resource for primary and metastatic tumour research publicly available at www.emtome.org.

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Pan-Cancer Analysis Shows Enrichment of Macrophages, Overexpression of Checkpoint Molecules, Inhibitory Cytokines, and Immune Exhaustion Signatures in EMT-High Tumors

Frontiers in Oncology ◽

10.3389/fonc.2021.793881 ◽

2022 ◽

Vol 11 ◽

Author(s):

Jayesh Kumar Tiwari ◽

Shloka Negi ◽

Manju Kashyap ◽

Sheikh Nizamuddin ◽

Amar Singh ◽

...

Keyword(s):

Cancer Progression ◽

Immune Escape ◽

The Cancer Genome Atlas ◽

Mesenchymal Transition ◽

Gene Signatures ◽

Immune Exhaustion ◽

Cancer Types ◽

Tcga Dataset ◽

Pan Cancer

Epithelial–mesenchymal transition (EMT) is a highly dynamic process that occurs under normal circumstances; however, EMT is also known to play a central role in tumor progression and metastasis. Furthermore, role of tumor immune microenvironment (TIME) in shaping anticancer immunity and inducing the EMT is also well recognized. Understanding the key features of EMT is critical for the development of effective therapeutic interventions. Given the central role of EMT in immune escape and cancer progression and treatment, we have carried out a pan-cancer TIME analysis of The Cancer Genome Atlas (TCGA) dataset in context to EMT. We have analyzed infiltration of various immune cells, expression of multiple checkpoint molecules and cytokines, and inflammatory and immune exhaustion gene signatures in 22 cancer types from TCGA dataset. A total of 16 cancer types showed a significantly increased (p < 0.001) infiltration of macrophages in EMT-high tumors (mesenchymal samples). Furthermore, out of the 17 checkpoint molecules we analyzed, 11 showed a significant overexpression (p < 0.001) in EMT-high samples of at least 10 cancer types. Analysis of cytokines showed significant enrichment of immunosuppressive cytokines—TGFB1 and IL10—in the EMT-high group of almost all cancer types. Analysis of various gene signatures showed enrichment of inflammation, exhausted CD8+ T cells, and activated stroma signatures in EMT-high tumors. In summary, our pan-cancer EMT analysis of TCGA dataset shows that the TIME of EMT-high tumors is highly immunosuppressive compared to the EMT-low (epithelial) tumors. The distinctive features of EMT-high tumors are as follows: (i) the enrichment of tumor-associated macrophages, (ii) overexpression of immune checkpoint molecules, (iii) upregulation of immune inhibitory cytokines TGFB1 and IL10, and (iv) enrichment of inflammatory and exhausted CD8+ T-cell signatures. Our study shows that TIMEs of different EMT groups differ significantly, and this would pave the way for future studies analyzing and targeting the TIME regulators for anticancer immunotherapy.

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Integrated Genomic Analysis of Hypoxia Genes across Cancer Types Identifies Significant Associations with Cancer Hallmarks

10.1101/403717 ◽

2018 ◽

Author(s):

Lingjian Yang ◽

Laura Forker ◽

Christina S. Fjeldbo ◽

Robert G. Bristow ◽

Heidi Lyng ◽

...

Keyword(s):

Environmental Factor ◽

Epithelial Mesenchymal Transition ◽

Tumour Progression ◽

The Cancer Genome Atlas ◽

Silent Mutation ◽

Multiple Cancer ◽

Mesenchymal Transition ◽

Cancer Types ◽

Pan Cancer

ABSTRACTHypoxia is a generic micro-environmental factor in most solid tumours. While most published literature focused on in vitro or single tumour type investigations, we carried out the first multi-omics pan cancer analysis of hypoxia with the aim of gaining a comprehensive understanding of its implication in tumour biology. A core set of 52 mRNAs were curated based on experimentally validated hypoxia gene sets from multiple cancer types. The 52 mRNAs collectively stratified high- and low-hypoxia tumours from The Cancer Genome Atlas (TCGA) database (9698 primary tumours) in each of the 32 cancer types available. High- hypoxia tumours had high expression of not only mRNA but also protein and microRNA markers of hypoxia. In a pan cancer transcriptomic analysis, ≥70% of the known cancer hallmark pathways were enriched in high-hypoxia tumours, most notably epithelial mesenchymal transition potential, proliferation (G2M checkpoint, E2F targets, MYC targets) and immunology response. In a multi-omics analysis, gene expression-determined high- hypoxia tumours had a higher non-silent mutation rate, DNA damage repair deficiency and leukocyte infiltration. The associations largely remained significant after correcting for confounding factors, showing a profound impact of hypoxia in tumour evolution across cancer types. High-hypoxia tumours determined using the core gene set had a poor prognosis in 16/32 cancer types, with statistical significances remaining in five after adjusting for tumour stage and omics biomarkers. In summary, this first comprehensive in vivo map of hypoxia in cancers highlights the importance of this micro-environmental factor in driving tumour progression.

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Pan-Cancer Analysis Reveals Distinct Metabolic Reprogramming in Different Epithelial–Mesenchymal Transition Activity States

Cancers ◽

10.3390/cancers13081778 ◽

2021 ◽

Vol 13 (8) ◽

pp. 1778

Author(s):

Ji-Yong Sung ◽

Jae-Ho Cheong

Keyword(s):

Energy Metabolism ◽

Epithelial Mesenchymal Transition ◽

Metabolic Reprogramming ◽

The Cancer Genome Atlas ◽

Cancer Type ◽

Mesenchymal Transition ◽

Significant Difference ◽

Cancer Types ◽

Using Data ◽

Patient Prognosis

Epithelial–mesenchymal transition (EMT) is critical for cancer development, invasion, and metastasis. Its activity influences metabolic reprogramming, tumor aggressiveness, and patient survival. Abnormal tumor metabolism has been identified as a cancer hallmark and is considered a potential therapeutic target. We profiled distinct metabolic signatures by EMT activity using data from 9452 transcriptomes across 31 different cancer types from The Cancer Genome Atlas. Our results demonstrated that ~80 to 90% of cancer types had high carbohydrate and energy metabolism, which were associated with the high EMT group. Notably, among the distinct EMT activities, metabolic reprogramming in different immune microenvironments was correlated with patient prognosis. Nine cancer types showed a significant difference in survival with the presence of high EMT activity. Stomach cancer showed elevated energy metabolism and was associated with an unfavorable prognosis (p < 0.0068) coupled with high expression of CHST14, indicating that it may serve as a potential drug target. Our analyses highlight the prevalence of cancer type-dependent EMT and metabolic reprogramming activities and identified metabolism-associated genes that may serve as potential therapeutic targets.

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Pan-Cancer Analysis of VIM Expression in Human Cancer Tissues

10.21203/rs.3.rs-646169/v1 ◽

2021 ◽

Author(s):

Małgorzata Blatkiewicz ◽

Piotr Białas ◽

Olga Taryma-Leśniak ◽

Beata Hukowska-Szematowicz

Keyword(s):

Protein Interactions ◽

Promoter Methylation ◽

Epithelial Mesenchymal Transition ◽

Human Cancer ◽

Gene Promoter ◽

The Cancer Genome Atlas ◽

Intermediate Filament Protein ◽

Biological Regulation ◽

Mesenchymal Transition ◽

Cancer Types

Abstract In 2020, more than 19 million cancer cases were diagnosed. One of the best paths to more effective treatment with a chance of being cured for patients is early detection. Vimentin (VIM), as an intermediate filament protein, is broadly expressed in mesenchymal cells. VIM is responsible for several biological processes such as cellular component organization and biogenesis, metabolic processes, and biological regulation. A growing body of literature indicates that expression of the VIM gene (VIM) is disrupted in carcinomas during epithelial–mesenchymal transition. Herein, we broadly analyzed the gene expression and promoter methylation profile of VIM in 19 cancer types across The Cancer Genome Atlas (TCGA). Furthermore, the protein–protein interactions (GeneMANIA and Search Tool for the Retrieval of Interacting Genes (STRING) database) and the alteration frequency of mutations (cBioPortal database) in VIM were analyzed. We proved that VIM is overexpressed in seven of the 19 studied cancer types. For two of them, we observed an association of VIM expression with gene promoter methylation. It must be emphasized that VIM overexpression can be a potential diagnostic biomarker in selected types of cancers.

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A novel prognostic model based on epithelial-mesenchymal transition-related genes predicts patient survival in gastric cancer

World Journal of Surgical Oncology ◽

10.1186/s12957-021-02329-9 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Wanting Song ◽

Yi Bai ◽

Jialin Zhu ◽

Fanxin Zeng ◽

Chunmeng Yang ◽

...

Keyword(s):

Gene Expression ◽

Gastric Cancer ◽

Risk Model ◽

Cox Regression ◽

Epithelial Mesenchymal Transition ◽

Risk Groups ◽

The Cancer Genome Atlas ◽

Critical Function ◽

Mesenchymal Transition ◽

Patient Prognosis

Abstract Background Gastric cancer (GC) represents a major malignancy and is the third deathliest cancer globally. Several lines of evidence indicate that the epithelial-mesenchymal transition (EMT) has a critical function in the development of gastric cancer. Although plentiful molecular biomarkers have been identified, a precise risk model is still necessary to help doctors determine patient prognosis in GC. Methods Gene expression data and clinical information for GC were acquired from The Cancer Genome Atlas (TCGA) database and 200 EMT-related genes (ERGs) from the Molecular Signatures Database (MSigDB). Then, ERGs correlated with patient prognosis in GC were assessed by univariable and multivariable Cox regression analyses. Next, a risk score formula was established for evaluating patient outcome in GC and validated by survival and ROC curves. In addition, Kaplan-Meier curves were generated to assess the associations of the clinicopathological data with prognosis. And a cohort from the Gene Expression Omnibus (GEO) database was used for validation. Results Six EMT-related genes, including CDH6, COL5A2, ITGAV, MATN3, PLOD2, and POSTN, were identified. Based on the risk model, GC patients were assigned to the high- and low-risk groups. The results revealed that the model had good performance in predicting patient prognosis in GC. Conclusions We constructed a prognosis risk model for GC. Then, we verified the performance of the model, which may help doctors predict patient prognosis.

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Phospholipase C Delta 3 inhibits apoptosis and promotes proliferation, migration, and invasion of thyroid cancer cells via Hippo pathway

Acta Biochimica et Biophysica Sinica ◽

10.1093/abbs/gmab016 ◽

2021 ◽

Vol 53 (4) ◽

pp. 481-491

Author(s):

Lizhi Lin ◽

Jialiang Wen ◽

Bangyi Lin ◽

Hao Chen ◽

Adheesh Bhandari ◽

...

Keyword(s):

Thyroid Cancer ◽

Phospholipase C ◽

Cell Lines ◽

Epithelial Mesenchymal Transition ◽

Hippo Pathway ◽

Suppressive Effect ◽

The Cancer Genome Atlas ◽

Disease Stage ◽

Migration And Invasion ◽

Mesenchymal Transition

Abstract In recent decades, the incidence of thyroid cancer (TC) has rapidly increased, leading us to explore the complex underlying mechanisms. We identified the gene Phospholipase C Delta 3 (PLCD3) as a potential oncogene in TC by conducting the whole transcriptome sequencing. Our study is to understand the oncogenic role of PLCD3 in TC. We verified the overexpression of PLCD3 in TC from The Cancer Genome Atlas, Gene Expression Omnibus databases, and a locally validated cohort. Clinical correlation analysis showed that PLCD3 expression was related to histological type, T stage, lymph node metastasis (LNM), and disease stage. The high expression of PLCD3 could be a distinguishing factor for TC and its LNM. The biological function was examined using small interfering RNA-transfected TC cell lines. Silenced PLCD3 could inhibit colony formation, migration, and invasion ability and promote apoptosis of TC cell lines. PLCD3 silencing reversed the epithelial-mesenchymal transition but induced the apoptotic progress. Further exploration revealed that PLCD3 might be associated with critical genes of the Hippo pathway. The expressions of RHOA, YAP1/TAZ, and their downstream targets were decreased significantly when PLCD3 was down-regulated. YAP1 overexpression rescued the tumor-suppressive effect caused by PLCD3 silencing. This study demonstrates that PLCD3 is an oncogene that supports tumorigenesis and progression in TC, and PLCD3 may be a potential target gene for TC treatment.

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Carboxypeptidase E-ΔN promotes migration, invasiveness, and epithelial–mesenchymal transition of human osteosarcoma cells via the Wnt–β-catenin pathway

Biochemistry and Cell Biology ◽

10.1139/bcb-2018-0236 ◽

2019 ◽

Vol 97 (4) ◽

pp. 446-453 ◽

Cited By ~ 9

Author(s):

Shuli Fan ◽

Xiang Gao ◽

Peng Chen ◽

Xu Li

Keyword(s):

Cell Migration ◽

Tumor Metastasis ◽

Molecular Mechanisms ◽

Epithelial Mesenchymal Transition ◽

Mesenchymal Transition ◽

Human Osteosarcoma ◽

Carboxypeptidase E ◽

Human Osteosarcoma Cells ◽

Cancer Types ◽

Interfering Rna

Osteosarcoma (OS) is the most common malignant bone tumor in children and adolescents, and metastatic OS is the major cause of OS-related death. Carboxypeptidase E (CPE) is known to be highly expressed in some cancer types, and its N-terminal truncated form, CPE-ΔN, is implicated in tumor metastasis and poor prognosis. In this study, we investigated the effect of CPE-ΔN on cell migration, invasiveness, and the epithelial–mesenchymal transition (EMT) of OS cells, and illustrated the molecular mechanisms. We first constructed CPE-ΔN overexpressing human OS cell lines (143B and U2OS cells), and found that ectopic CPE-ΔN expression in OS cells enhanced cell migration and invasiveness, and promoted the EMT process. Further, overexpression of CPE-ΔN increased the levels of c-myc and nuclear β-catenin in OS cells, which suggested the CPE-ΔN promotes activation of the Wnt–β-catenin pathway in OS cells. Treatment with β-catenin small interfering RNA (siRNA) inhibited the migration and invasiveness of CPE-ΔN-overexpressing cells, and reduced the expression of E-cadherin. Together, these results suggest that CPE-ΔN promotes migration, invasiveness, and the EMT of OS cells via the Wnt–β-catenin signaling pathway.

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Characterizing Intercellular Communication of Pan-Cancer Reveals SPP1+ Tumor-Associated Macrophage Expanded in Hypoxia and Promoting Cancer Malignancy Through Single-Cell RNA-Seq Data

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.749210 ◽

2021 ◽

Vol 9 ◽

Author(s):

Jinfen Wei ◽

Zixi Chen ◽

Meiling Hu ◽

Ziqing He ◽

Dawei Jiang ◽

...

Keyword(s):

Single Cell ◽

Cancer Cells ◽

Cancer Progression ◽

Epithelial Mesenchymal Transition ◽

Single Cells ◽

Matrix Remodeling ◽

Rna Seq ◽

Mesenchymal Transition ◽

Tumor Associated Macrophage ◽

Cancer Types

Hypoxia is a characteristic of tumor microenvironment (TME) and is a major contributor to tumor progression. Yet, subtype identification of tumor-associated non-malignant cells at single-cell resolution and how they influence cancer progression under hypoxia TME remain largely unexplored. Here, we used RNA-seq data of 424,194 single cells from 108 patients to identify the subtypes of cancer cells, stromal cells, and immune cells; to evaluate their hypoxia score; and also to uncover potential interaction signals between these cells in vivo across six cancer types. We identified SPP1+ tumor-associated macrophage (TAM) subpopulation potentially enhanced epithelial–mesenchymal transition (EMT) by interaction with cancer cells through paracrine pattern. We prioritized SPP1 as a TAM-secreted factor to act on cancer cells and found a significant enhanced migration phenotype and invasion ability in A549 lung cancer cells induced by recombinant protein SPP1. Besides, prognostic analysis indicated that a higher expression of SPP1 was found to be related to worse clinical outcome in six cancer types. SPP1 expression was higher in hypoxia-high macrophages based on single-cell data, which was further validated by an in vitro experiment that SPP1 was upregulated in macrophages under hypoxia-cultured compared with normoxic conditions. Additionally, a differential analysis demonstrated that hypoxia potentially influences extracellular matrix remodeling, glycolysis, and interleukin-10 signal activation in various cancer types. Our work illuminates the clearer underlying mechanism in the intricate interaction between different cell subtypes within hypoxia TME and proposes the guidelines for the development of therapeutic targets specifically for patients with high proportion of SPP1+ TAMs in hypoxic lesions.

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Comprehensive Analysis of The Significance of Hypoxia-Related Genes in Ovarian Cancer

10.21203/rs.3.rs-457769/v1 ◽

2021 ◽

Author(s):

Wancheng Zhao ◽

Lili Yin

Keyword(s):

Ovarian Cancer ◽

Epithelial Mesenchymal Transition ◽

Principal Component ◽

Vital Role ◽

The Cancer Genome Atlas ◽

Consensus Clustering ◽

Mesenchymal Transition ◽

Cancer Genome Atlas ◽

Pca Algorithm

Abstract Background: Hypoxia-related genes have been reported to play important roles in a variety of cancers. However, their roles in ovarian cancer (OC) have remained unknown. The aim of our research was to explore the significance of hypoxia-related genes in OC patients.Methods: In this study, 15 hypoxia-related genes were screened from The Cancer Genome Atlas (TCGA) database to group the ovarian cancer patients using the consensus clustering method. Principal component analysis (PCA) was performed to calculate the hypoxia score for each patient to quantify the hypoxic status. Results: The OC patients from TCGA-OV dataset were divided into two distinct hypoxia statuses (cluster.A and cluster.B) based on the expression level of the 15 hypoxia-related genes. Most hypoxia-related genes were expressed more highly in the cluster.A group than in the cluster.B group. We also found that patients in the cluster.A group exhibited higher expression of immune checkpoint-related genes, epithelial-mesenchymal transition-related genes, and immune activation-related genes, as well as elevated immune infiltrates. PCA algorithm indicated that patients in the cluster.A group had higher hypoxia scores than that in in the cluster.B group.Conclusions: In summary, our research elucidated the vital role of hypoxia-related genes in immune infiltrates of OC. Our investigation of hypoxic status may be able to improve the efficacy of immunotherapy for OC.

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Identification of a Novel Epithelial-Mesenchymal Transition Gene Signature Regulated by KEAP1-NRF2 Pathway in Esophageal Carcinoma

10.21203/rs.3.rs-77379/v1 ◽

2020 ◽

Author(s):

Mohamed Elshaer ◽

Ahmed Hammad ◽

Xiu Jun Wang ◽

Xiuwen Tang

Keyword(s):

Cell Lines ◽

Epithelial Mesenchymal Transition ◽

Cancer Cell Line ◽

Enrichment Analysis ◽

Gene Signature ◽

Gene Set Enrichment Analysis ◽

The Cancer Genome Atlas ◽

Mesenchymal Transition ◽

Gene Set ◽

Over Expression

Abstract BackgroundKEAP1-NRF2 pathway alterations were identified in many cancers including, esophageal cancer (ESCA). Identifying biomarkers that are associated with mutations in this pathway will aid in defining this cancer subset; and hence in supporting precision and personalized medicine. MethodsIn this study, 182 tumor samples from the Cancer Genome Atlas (TCGA)-ESCA RNA-Seq V2 level 3 data were segregated into two groups KEAP1-NRF2-mutated (22) and wild-type (160).The two groups were subjected to differential gene expression analysis, and we performed Gene Set Enrichment Analysis (GSEA) to determine all significantly affected biological pathways. Then, the enriched gene set was integrated with the differentially expressed genes (DEGs) to identify a gene signature regulated by the KEAP1-NRF2 pathway in ESCA. Furthermore, we validated the gene signature using mRNA expression data of ESCA cell lines provided by the Cancer Cell Line Encyclopedia (CCLE). The identified signature was tested in 3 independent ESCA datasets to assess its prognostic value.ResultsWe identified 11 epithelial-mesenchymal transition (EMT) genes regulated by the KEAP1-NRF2 pathway in ESCA patients. Five of the 11 genes showed significant over-expression in KEAP1-NRF2-mutated ESCA cell lines. In addition, the over-expression of these five genes was significantly associated with poor survival in 3 independent ESCA datasets, including the TCGA-ESCA dataset.ConclusionAltogether, we identified a novel EMT 5-gene signature regulated by the KEAP1-NRF2 axis and this signature is strongly associated with metastasis and drug resistance in ESCA. These 5-genes are potential biomarkers and therapeutic targets for ESCA patients in whom the KEAP1-NRF2 pathway is altered.

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