
RPS27 selectively regulates the expression and alternative splicing of inflammatory and immune response genes in thyroid cancer cells.
Advances in clinical and experimental medicine : official organ Wroclaw Medical University
BACKGROUND:The expression of ribosomal protein S27 (RPS27) is upregulated in multiple human malignancies. In thyroid cancer, the expression of RPS27 is associated with patient outcomes. However, the carcinogenic mechanisms of RPS27 and functions of RPS27 in the initiation and progression of thyroid cancer are still not clear. OBJECTIVES:To investigate the carcinogenic mechanisms of RPS27 and functions of RPS27 in the initiation and progression of thyroid cancer. MATERIAL AND METHODS:The RPS27 gene was overexpressed in BTH101 cells and the influence on the level of gene expression and alternative splicing (AS) was then analyzed by comparing the transcriptomes of the overexpressing cells with the controls. The procedures included cloning and plasmid construction of RPS27, cell culture and transfection, evaluation of RPS27 overexpression, library preparation and sequencing, RNA-Seq raw data clean and alignment, differentially expressed genes (DEGs) analysis, AS analysis, quantitative real-time polymerase chain reaction (qRT-PCR) validation of DEGs and AS events (ASEs), and functional enrichment analysis. RESULTS:The results demonstrated that RPS27 could selectively regulate the expression of genes associated with autoimmune thyroid disease, inflammatory/immune response and AS of genes associated with TRIF-dependent toll-like receptor signaling pathway and apoptotic process. The genes in question are BMP6, SERPINA3, IL17B, IL1RN, HLA-B, PF4, HLA-DOB, MADCAM1, HLA-DQA1, TPO, HLA-B, HLA-DQA1, HLA-DOB, HLA-C, KRT8, CFLAR, HMGA1, CASP8, CCNH, UBE2D3, and MAPK9, among others. CONCLUSIONS:The RPS27 selectively regulated the expression and alternative splicing of genes involved in inflammatory/immune response and TRIF-dependent toll-like receptor signaling pathway, which were tightly associated with the initiation and progression of thyroid cancer. These results extend our knowledge on the molecular functions of RPS27 in thyroid cancer cells and have a potential value in thyroid cancer treatment.
10.17219/acem/147271
A metabolic phenotype based on mitochondrial ribosomal protein expression as a predictor of lymph node metastasis in papillary thyroid carcinoma.
Lee Jandee,Seol Mi-Youn,Jeong Seonhyang,Lee Cho Rok,Ku Cheol Ryong,Kang Sang-Wook,Jeong Jong Ju,Shin Dong Yeob,Nam Kee-Hyun,Lee Eun Jig,Chung Woong Youn,Jo Young Suk
Medicine
Metabolic reprogramming has been regarded as an essential component of malignant transformation. However, the clinical significance of metabolic heterogeneity remains poorly characterized. The aim of this study was to characterize metabolic heterogeneity in thyroid cancers via the analysis of the expression of mitochondrial ribosomal proteins (MRPs) and genes involved in oxidative phosphorylation (OxPhos), and investigate potential prognostic correlations. Gene set enrichment analysis (GSEA) verified by reverse transcription polymerase chain reaction and gene network analysis was performed using public repository data. Cross-sectional observational study was conducted to classify papillary thyroid cancer (PTC) by the expression of MRP L44 (MRPL44) messenger RNA (mRNA), and to investigate the clinicopathological features. GSEA clearly showed that the expression of OxPhos and MRP gene sets was significantly lower in primary thyroid cancer than in matched normal thyroid tissue. However, 8 of 49 primary thyroid tumors (16.3%) in the public repository did not show a reduction in OxPhos mRNA expression. Remarkably, strong positive correlations between MRPL44 expression and those of OxPhos and MRPs such as reduced nicotinamide adenine dinucleotide dehydrogenase (ubiquinone) 1 α subcomplex, 5; succinate dehydrogenase complex, subunit D; cytochrome c, somatic; adenosine triphosphate synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9); and MRP S5 (MRPS5) (P < 0.0001) were clearly denoted, suggesting that MRPL44 is a representative marker of OxPhos and MRP expressions. In laboratory experiments, metabolic heterogeneity in oxygen consumption, extracellular acidification rates (ECARs), and amounts of OxPhos complexes were consistently observed in BCPAP, TPC1, HTH-7, and XTC.UC1 cell lines. In PTCs, metabolic phenotype according to OxPhos amount defined by expression of MRPL44 mRNA was significantly related to lymph node metastasis (LNM) (P < 0.001). Furthermore, multivariate analysis clearly indicated that expression of MRPL44 is associated with an increased risk of lateral neck LNM (odds ratio 9.267, 95% confidence interval 1.852-46.371, P = 0.007). MRPL44 expression may be a representative marker of metabolic phenotype according to OxPhos amount and a useful predictor of LNM.
10.1097/MD.0000000000000380
Ribosomal protein S3 mediates drug resistance of proteasome inhibitor: potential therapeutic application in multiple myeloma.
Haematologica
Multiple myeloma (MM) remains incurable due to drug resistance. Ribosomal protein S3 (RPS3) has been identified as a non-Rel subunit of NF-κB. However, the detailed biological roles of RPS3 remain unclear. Here, we report for the first time that RPS3 is necessary for MM survival and drug resistance. RPS3 was highly expressed in MM, and knockout of RPS3 in MM inhibited cell growth and induced cell apoptosis both in vitro and in vivo. Overexpression of RPS3 mediated the proteasome inhibitor resistance of MM and shortened the survival of MM tumor-bearing animals. Moreover, our present study found an interaction between RPS3 and the thyroid hormone receptor interactor 13 (TRIP13), an oncogene related to MM tumorigenesis and drug resistance. We demonstrated that the phosphorylation of RPS3 was mediated by TRIP13 via PKCδ, which played an important role in activating the canonical NF-κB signaling and inducing cell survival and drug resistance in MM. Notably, the inhibition of NF-κB signaling by the small-molecule inhibitor targeting TRIP13, DCZ0415, was capable of triggering synergistic cytotoxicity when combined with bortezomib in drug-resistant MM. This study identifies RPS3 as a novel biomarker and therapeutic target in MM.
10.3324/haematol.2023.282789
The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity.
Cell
During eukaryotic evolution, ribosomes have considerably increased in size, forming a surface-exposed ribosomal RNA (rRNA) shell of unknown function, which may create an interface for yet uncharacterized interacting proteins. To investigate such protein interactions, we establish a ribosome affinity purification method that unexpectedly identifies hundreds of ribosome-associated proteins (RAPs) from categories including metabolism and cell cycle, as well as RNA- and protein-modifying enzymes that functionally diversify mammalian ribosomes. By further characterizing RAPs, we discover the presence of ufmylation, a metazoan-specific post-translational modification (PTM), on ribosomes and define its direct substrates. Moreover, we show that the metabolic enzyme, pyruvate kinase muscle (PKM), interacts with sub-pools of endoplasmic reticulum (ER)-associated ribosomes, exerting a non-canonical function as an RNA-binding protein in the translation of ER-destined mRNAs. Therefore, RAPs interconnect one of life's most ancient molecular machines with diverse cellular processes, providing an additional layer of regulatory potential to protein expression.
10.1016/j.cell.2017.05.022
TERT accelerates BRAF mutant-induced thyroid cancer dedifferentiation and progression by regulating ribosome biogenesis.
Science advances
TERT reactivation occurs frequently in human malignancies, especially advanced cancers. However, in vivo functions of TERT reactivation in cancer progression and the underlying mechanism are not fully understood. In this study, we expressed TERT and/or active BRAF ( V600E) specifically in mouse thyroid epithelium. While V600E alone induced papillary thyroid cancer (PTC), coexpression of V600E and TERT resulted in poorly differentiated thyroid carcinoma (PDTC). Spatial transcriptome analysis revealed that tumors from mice coexpressing V600E and TERT were highly heterogeneous, and cell dedifferentiation was positively correlated with ribosomal biogenesis. Mechanistically, TERT boosted ribosomal RNA (rRNA) expression and protein synthesis by interacting with multiple proteins involved in ribosomal biogenesis. Furthermore, we found that CX-5461, an rRNA transcription inhibitor, effectively blocked proliferation and induced redifferentiation of thyroid cancer. Thus, TERT promotes thyroid cancer progression by inducing cancer cell dedifferentiation, and ribosome inhibition represents a potential strategy to treat TERT-reactivated cancers.
10.1126/sciadv.adg7125
Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data.
Tonner Peter,Srinivasasainagendra Vinodh,Zhang Shaojie,Zhi Degui
BMC genomics
BACKGROUND:Ribosomal proteins (RPs) have about 2000 pseudogenes in the human genome. While anecdotal reports for RP pseudogene transcription exists, it is unclear to what extent these pseudogenes are transcribed. The RP pseudogene transcription is difficult to identify in microarrays due to potential cross-hybridization between transcripts from the parent genes and pseudogenes. Recently, transcriptome sequencing (RNA-seq) provides an opportunity to ascertain the transcription of pseudogenes. A challenge for pseudogene expression discovery in RNA-seq data lies in the difficulty to uniquely identify reads mapped to pseudogene regions, which are typically also similar to the parent genes. RESULTS:Here we developed a specialized pipeline for pseudogene transcription discovery. We first construct a "composite genome" that includes the entire human genome sequence as well as mRNA sequences of real ribosomal protein genes. We then map all sequence reads to the composite genome, and only exact matches were retained. Moreover, we restrict our analysis to strictly defined mappable regions and calculate the RPKM values as measurement of pseudogene transcription levels. We report evidences for the transcription of RP pseudogenes in 16 human tissues. By analyzing the Human Body Map 2.0 study RNA-sequencing data using our pipeline, we identified that one ribosomal protein (RP) pseudogene (PGOHUM-249508) is transcribed with RPKM 170 in thyroid. Moreover, three other RP pseudogenes are transcribed with RPKM > 10, a level similar to that of the normal RP genes, in white blood cell, kidney, and testes, respectively. Furthermore, an additional thirteen RP pseudogenes are of RPKM > 5, corresponding to the 20-30 percentile among all genes. Unlike ribosomal protein genes that are constitutively expressed in almost all tissues, RP pseudogenes are differentially expressed, suggesting that they may contribute to tissue-specific biological processes. CONCLUSIONS:Using a specialized bioinformatics method, we identified the transcription of ribosomal protein pseudogenes in human tissues using RNA-seq data.
10.1186/1471-2164-13-412
Effects of thyroid-stimulating hormone on adhesion molecules and pro-inflammatory cytokines secretion in human umbilical vein endothelial cells.
Research in pharmaceutical sciences
Atherosclerosis is a multifactorial disorder, which affects the arterial wall. It has been reported that, hypothyroidism and thyroid hormone deficiency are related to cardiovascular disorders. Also, endothelial dysfunction plays an essential role in the development of atherosclerosis. We aimed to evaluate the effects of thyroid-stimulating hormone (TSH) on pro-inflammatory tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), angiogenic vascular endothelial growth factor (VEGF) and leukocyte adhesion, intercellular adhesion molecule 1 (ICAM-1) and E-selectin in human umbilical vein endothelial cells (HUVECs). In this study, HUVEC cells were treated with 1 and 2 μM of TSH in different treatment times. The gene and protein expression of ICAM-1, VEGF, and E-selectin were performed by real-time polymerase chain reaction and western blotting, respectively. Likewise, TNF-α and IL-6 protein levels were determined by the ELISA method. VEGF, ICAM-1, and E-selectin as endothelial dysfunction markers and also, TNF-α and IL-6 as pro-inflammatory cytokines were detectable in HUVEC. Besides, the results of this study revealed that TSH treatment down-regulates TNF-α and IL-6. Evaluating the gene and protein expression data revealed the upregulation of ICAM-1, E-selectin, and VEGF in TSH treated cases in different periods of exposure. Considering the multiple actions of TSH, it could be concluded that TSH plays a controversial role in atherogenesis by anti-inflammatory effects and on the other side, angiogenesis and leukocyte adhesion induction which is related to vascular cell proliferation.
10.4103/1735-5362.245966
Effect of metformin alone and in combination with etoposide and epirubicin on proliferation, apoptosis, necrosis, and migration of B-CPAP and SW cells as thyroid cancer cell lines.
Research in pharmaceutical sciences
Background and purpose:There has not been a comprehensive study on the simultaneous effects of metformin, etoposide, and epirubicin on thyroid cancer cells. Hence, the current research proposed the study on the effect of metformin alone and in combination with etoposide and epirubicin on the rate of proliferation, apoptosis, necrosis, and migration against B-CPAP and SW-1736 cells as thyroid cancer cell lines. Experimental approach:MTT-based proliferation assay, combination index method, flow cytometry, and scratch wound healing assays were used to evaluate the simultaneous effects of the three approved drugs against thyroid cancer cells. Findings/Results:This study showed that the toxic concentration of metformin on normal Hu02 cells was more than 10 folds higher than B-CPAP and SW cancerous cells. Metformin in combination with epirubicin and etoposide could increase percentages of B-CPAP and SW cells in early and late apoptosis and necrosis phases in comparison with their single concentrations, significantly. Metformin in combination with epirubicin and etoposide could arrest the S phase in B-CPAP and SW cells, significantly. Metformin in combination with epirubicin and etoposide could reduce ~100% migration rate, whereas single concentrations of epirubicin and etoposide could reduce ~50% migration rate. Conclusion and implication:Combined treatment of metformin with anticancer drugs epirubicin and etoposide can increase the mortality in thyroid cancer cell lines and reduce the toxicity of these drugs on the normal cell line, which could be the starting point for proposing a new combination strategy in the therapy of thyroid cancer to induce more potency and reduce acute toxicity.
10.4103/1735-5362.367797
Pan-cancer analysis of the prognostic and immunological role of RPL4.
Heliyon
Ribosomal proteins (RPs) play an important role in the overall stability, function, and integrity of ribosomes. Ribosomal protein L4 (RPL4), which is encoded by , is assumed to play different roles in different cancers due to the strong correlation between them. However, research based on the underlying mechanisms of this correlations is limited. Therefore, this study investigated the biological role of RPL4 in various cancers. The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases were used to compare the differential expression of RPL4 in tumor and normal tissues. The Sangerbox database and Kaplan-Meier method were employed to assess RPL4's impact on the prognosis of pan-cancer. Analyses using the cBioPortal tool, Shiny Methylation Analysis Resource Tool (SMART), and MethSurv provided insights into the methylation and epigenetic alterations of . Gene enrichment analysis revealed that is involved in ribosome biogenesis through multiple pathways, and its enrichment in signaling pathways directly or indirectly influence tumor development. Tumor Immune Single-cell Hub (TISCH) was used to analyze expression levels and cellular functions in the tumor microenvironment. Tumor Immune Estimation Resource Database 2.0 (TIMER2.0) and Tumor-Immune System Interactions Database (TISIDB) tools revealed that RPL4 affected the immune infiltration potential of tumors. Furthermore, the application of the ROC mapper and CellMiner databases indicated an association between RPL4 and sensitivity to multiple antitumor drugs. Additionally, RPL4 was found to remodel the tumor immune microenvironment, leading to the development of chemoresistance. In conclusion, the findings suggest that RPL4 can be used as a potential tumor biomarker and may serve as a target for immunotherapy in various cancers. Genetic testing of RPL4 provides a foundation for the diagnosis, prognosis, and treatment of clinical tumors.
10.1016/j.heliyon.2024.e34461
uS5/Rps2 residues at the 40S ribosome entry channel enhance initiation at suboptimal start codons in vivo.
Genetics
The eukaryotic 43S pre-initiation complex (PIC) containing Met-tRNAiMet in a ternary complex (TC) with eIF2-GTP scans the mRNA leader for an AUG codon in favorable "Kozak" context. AUG recognition triggers rearrangement of the PIC from an open conformation to a closed state with more tightly bound Met-tRNAiMet. Yeast ribosomal protein uS5/Rps2 is located at the mRNA entry channel of the 40S subunit in the vicinity of mRNA nucleotides downstream from the AUG codon or rRNA residues that communicate with the decoding center, but its participation in start codon recognition was unknown. We found that nonlethal substitutions of conserved Rps2 residues in the entry channel reduce bulk translation initiation and increase discrimination against poor initiation codons. A subset of these substitutions suppress initiation at near-cognate UUG start codons in a yeast mutant with elevated UUG initiation, and also increase discrimination against AUG codons in suboptimal Kozak context, thus resembling previously described substitutions in uS3/Rps3 at the 40S entry channel or initiation factors eIF1 and eIF1A. In contrast, other Rps2 substitutions selectively discriminate against either near-cognate UUG codons, or poor Kozak context of an AUG or UUG start codon. These findings suggest that different Rps2 residues are involved in distinct mechanisms involved in discriminating against different features of poor initiation sites in vivo.
10.1093/genetics/iyab176