Genes Co-Expressed with ESR2 Influence Clinical Outcomes in Cancer Patients: TCGA Data Analysis
Abstract
:1. Introduction
2. Results
2.1. Cancer Tissue and Corresponding Healthy Tissue Present Different ESR2 Expression Levels in Selected Cancer Types
2.2. ESR2 Expression Correlates with the Grade and Stage of Several Tumor Types
2.3. ESR2 Expression Level Affects OS and DFS in Various Cancer Types
2.4. ESR2 Affects Various Molecular Pathways in Cancer
2.5. Various Genes Present Expression Patterns Similar to That of ESR2 in Cancer
2.6. Selected Genes Present a Combined Effect with ESR2 on OS/DFS in Several Cancer Types
3. Discussion
4. Materials and Methods
4.1. Transcriptomic and Proteomic Data
4.2. Clinical Data
4.3. Databases and Bioinformatic Tools
4.3.1. cBioPortal
4.3.2. TIMER2.0
4.3.3. Human Protein Atlas
4.3.4. TISIDB
4.3.5. GSEA
4.3.6. UCSC Genome Browser
4.4. Statistical Analysis
5. Conclusions
- ESR2 mRNA expression differs between cancerous and normal tissue in various TCGA tumor types, including BRCA, COAD, KICH, CHOL, HNSC, and LUSC;
- ESR2 expression impacts patient survival in several TCGA tumor types, including BLCA, HNSC, THYM, KIRP, and THCA;
- GSEA analysis reveals ESR2 enrichment in gene sets related to epithelial–mesenchymal transition, hypoxia response, and cell cycle in cancers like PRAD and COAD;
- Twelve genes (ACIN1, CFL1, FNBP4, MDM4, NDUFB3, OCIAD2, PLIN3, POU2AF1, RAC1, SYNE2, TMEM141, TNFRSF13C) were identified as co-expressed with ESR2 and showing a combined effect with the receptor on patient survival in selected tumors, including BLCA, MESO, BRCA, COAD, and SKCM.
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
ACC | Adrenocortical carcinoma |
BLCA | Bladder urothelial carcinoma |
BRCA | Breast invasive carcinoma |
CESC | Cervical squamous cell carcinoma and endocervical adenocarcinoma |
CHOL | Cholangio carcinoma |
COAD | Colon adenocarcinoma |
DLBC | Lymphoid neoplasm diffuse large B-cell lymphoma |
ESCA | Esophageal carcinoma |
GBM | Glioblastoma multiforme |
HNSC | Head and neck squamous cell carcinoma |
KICH | Kidney chromophobe |
KIRC | Kidney renal clear cell carcinoma |
KIRP | Kidney renal papillary cell carcinoma |
LAML | Acute myeloid leukemia |
LGG | Brain lower-grade glioma |
LIHC | Liver hepatocellular carcinoma |
LUAD | Lung adenocarcinoma |
LUSC | Lung squamous cell carcinoma |
MESO | Mesothelioma |
OV | Ovarian serous cystadenocarcinoma |
PAAD | Pancreatic adenocarcinoma |
PCPG | Pheochromocytoma and paraganglioma |
PRAD | Prostate adenocarcinoma |
READ | Rectum adenocarcinoma |
SARC | Sarcoma |
SKCM | Skin cutaneous melanoma |
STAD | Stomach adenocarcinoma |
TGCT | Testicular germ cell tumor |
THCA | Thyroid carcinoma |
THYM | Thymoma |
UCEC | Uterine corpus endometrial carcinoma |
UCS | Uterine carcinosarcoma |
UVM | Uveal melanoma |
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Gene | Description | Source |
---|---|---|
ACIN1 [14q11.2] | Apoptotic chromatin condensation inducer 1 regulates chromatin condensation after activation by caspase-3 during apoptosis. Additionally, it may be involved in mRNA regulation after splicing. | [33] |
ARPC2 [2q35] | Actin-related protein 2/3 complex subunit 2 mediates actin polymerization in the nucleus and therefore regulates transcription and homolog recombination in response to DNA damage. | [34,35] |
CELF6 [15q23] | CUGBP elav-like family member 6 regulates pre-mRNA alternative splicing and may be involved in mRNA editing and translation. | [36] |
CFL1 [11q13.1] | Cofilin 1 carries out F-actin depolymerization, thus regulating cell morphology through cytoskeletal organization in epithelial cells. | [37,38] |
COL4A3 [2q36.3] | The collagen α-3(IV) chain is one of the structural components of glomerular basement membranes. Tumstatin within this domain presents anti-tumor activity. | [39,40] |
FAM30A [14q32.33] | Family with sequence similarity to 30 member A and may be a non-coding RNA. | [41] |
FCRL5 [1q23.1] | Fc receptor-like 5 is most likely involved in B-cell differentiation and may present an immunoregulatory role in marginal-zone B-cells. | [42] |
FNBP4 [11p11.2] | Formin-binding protein 4 may be involved in the regulation of cytoskeletal dynamics during cell division and migration. | [43] |
LENG8 [19q13.42] | Leukocyte receptor cluster member 8 encodes leukocyte-expressed receptors of the immunoglobulin superfamily. | [44] |
MDM4 [1q32.1] | MDM4 regulator of p53 inhibits p53- and p73-mediated cell cycle arrest and apoptosis and inhibits the degradation of MDM2. | [45,46] |
NDUFB3 [2q33.1] | NDAH–ubiquinone oxidoreductase subunit B3 is part of the electron transport chain of mitochondria on the inner membrane of the mitochondrion. | [47] |
OCIAD2 [4p11] | Ovarian carcinoma immunoreactive antigen domain containing 2 in one of the mitochondrial respiratory chain complex assembly factors. | [48] |
PLIN3 [19p13.3] | Perilipin 3 is a structural component of lipid droplets required for lipid storage in cells and is involved in mannose 6-phosphate receptor transport. | [49,50] |
POU2AF1 [11q23.1] | POU class 2 homeobox associating factor 1 is a transcriptional coactivator associated with POU2F1/OCT1 or POU2F2/OCT2 complexes; likewise, it is essential for B-cells’ ability to respond to antigens. | [51,52] |
PPP1R3E [14q11.2] | Protein phosphatase 1 regulatory subunit 3E is predicted to be involved in the positive regulation of the glycogen biosynthetic process and to be a part of the protein phosphatase type 1 complex. | [53] |
RAC1 [7p22.1] | Rac family small GTPase 1 is a plasma membrane-associated protein binding to effector proteins involved in secretion, phagocytosis, migration, and differentiation. | [54,55,56] |
RAP1GDS1 [4q23] | Rap1 GTPase-GDP dissociation stimulator 1 is a guanine nucleotide exchange factor in the GDP-GTP dissociation–binding sequence. | [57,58] |
SYNE2 [14q23.2] | Spectrin repeat containing nuclear envelope protein 2 (Nesprin-2) is a component of the LInker of Nucleoskeleton and Cytoskeleton (LINC) and regulates the spatial organization of intracellular components. | [59] |
TMEM141 [9q34.3] | Transmembrane protein 141 is predicted to be an integral component of the membrane. | [60] |
TNFRSF13C [22q13.2] | Tumor necrosis factor receptor superfamily member 13C is a B-cell-specific receptor that promotes the survival of mature B-cells and the B-cell response. | [61,62] |
TPTEP2 [22q13.1] | TPTE pseudogene 2 is a transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene. | [63] |
VAMP1 [12p13.31] | Vesicle-associated membrane protein 1 is involved in the targeting and fusion of transport vesicles to their target membrane. | [64,65] |
ZBTB25 [14q23.3] | Zinc finger- and BTB domain-containing 25 is predicted to be involved in the regulation of transcription by RNA polymerase II. | [66] |
ZFYVE26 [14q24.1] | Zinc finger FYVE-type-containing 26 encodes protein targeted to membrane lipids through interaction with phospholipids in the membrane. | [67] |
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Lipowicz, J.M.; Malińska, A.; Nowicki, M.; Rawłuszko-Wieczorek, A.A. Genes Co-Expressed with ESR2 Influence Clinical Outcomes in Cancer Patients: TCGA Data Analysis. Int. J. Mol. Sci. 2024, 25, 8707. https://doi.org/10.3390/ijms25168707
Lipowicz JM, Malińska A, Nowicki M, Rawłuszko-Wieczorek AA. Genes Co-Expressed with ESR2 Influence Clinical Outcomes in Cancer Patients: TCGA Data Analysis. International Journal of Molecular Sciences. 2024; 25(16):8707. https://doi.org/10.3390/ijms25168707
Chicago/Turabian StyleLipowicz, Julia Maria, Agnieszka Malińska, Michał Nowicki, and Agnieszka Anna Rawłuszko-Wieczorek. 2024. "Genes Co-Expressed with ESR2 Influence Clinical Outcomes in Cancer Patients: TCGA Data Analysis" International Journal of Molecular Sciences 25, no. 16: 8707. https://doi.org/10.3390/ijms25168707