Evaluation of the selenotranscriptome expression in two hepatocellular carcinoma cell lines

Selenoprotein K at the intersection of cellular pathways

Selenoprotein K (selenok) is linked to the integrated stress response, which helps cells combat stressors and regain normal function. The selenoprotein contains numerous protein interaction hubs and post-translational modification sites and is involved in protein palmitoylation, vesicle trafficking, and the resolution of ER stress. Anchored to the endoplasmic reticulum (ER) membrane, selenok interacts with protein partners to influence their stability, localization, and trafficking, impacting various cellular functions such as calcium homeostasis, cellular migration, phagocytosis, gene expression, and immune response. Consequently, selenok expression level is linked to cancer and neurodegenerative diseases. Because it contains the reactive amino acid selenocysteine, selenok is likely to function as an enzyme. However, highly unusual for enzymes, the protein segment containing the selenocysteine lacks a stable secondary or tertiary structure, yet it includes multiple interaction sites for protein partners and post-translational modifications. Currently, the reason(s) for the presence of the rare selenocysteine in selenok is not known. Furthermore, of selenok's numerous interaction sites, only some have been sufficiently characterized, leaving many of selenok's potential protein partners to be discovered. In this review, we explore selenok's role in various cellular pathways and its impact on human health, thereby highlighting the links between its diverse cellular functions.

Dysregulation of Transcription Profile of Selenoprotein in Patients with Kashin-Beck Disease and Its Effect on Se Deficiency-Induced Chondrocyte Apoptosis

Kashin-Beck disease (KBD) is a chronic, degenerative osteoarthropathy related to selenium (Se) deficiency. Se participates in the synthesis of selenoprotein in the form of selenocysteine. In total, 25 selenoproteins, encoded by 25 genes, are currently found in humans; however, the effects of selenoprotein genes on chondrocyte apoptosis, particularly in apoptosis-related genes, remain poorly elucidated. Therefore, in the current study, the expression of selenoprotein genes and apoptosis-related genes were determined by RT-qPCR in patients and chondrocytes and the correlations between them were analyzed using Pearson and Spearman's rank correlation, and the chondrocyte apoptosis rate was detected by Annexin V-FITC/PI. The results showed that the mRNA levels of 17 selenoprotein genes were downregulated, whereas two genes were upregulated in patients with KBD. The BAX/BCL2 ratio and the mRNA levels of BAX and P53 were increased, but the mRNA levels of BCL2 and NF-κB p65 were decreased in patients with KBD. The mRNA levels of GPX2, GPX3, DIO1, TXNRD1, TXNRD3, and SPS2 were most closely associated with apoptosis-related genes in patients with KBD. Moreover, in the Se deficiency group, the mRNA levels of GPX3, DIO1, and TXNRD1 were downregulated and GPX activity was decreased, but the late apoptosis rate, the mRNA levels of BAX and P53, and the BAX/BCL2 ratio were increased; the opposite trend was observed in the Se supplement group. Collectively, these results indicate that selenoprotein transcription profile is dysregulated in patients with KBD. Furthermore, the expression of GPX3, DIO1, and TXNRD1 genes might be involved in the development of chondrocyte apoptosis by affecting antioxidant capacity.

Gene expression evaluation of antioxidant enzymes in patients with hepatocellular carcinoma: RT-qPCR and bioinformatic analyses

Any condition leading to chronic liver disease is a potential oncogenic agent for hepatocellular carcinoma (HCC). Alterations in the expression of antioxidant enzymes could alter the redox balance. Our aim was to evaluate the expression of the genes GPX1, GPX4, SEP15, SELENOP, SOD1, SOD2, GSR, CAT, and NFE2L2 in patients with HCC. Differential gene expression analysis was performed using RNA-Seq data from the TCGA and GTEx databases, and RT-qPCR data from HCC patient samples. Bioinformatic analysis revealed significant differential expression in most genes. GPX4 expression was significantly increased (p=0.02), while SOD2 expression was significantly decreased (p=0.04) in experimental data. In TCGA samples, alpha-fetoprotein levels (mg/dL) were negatively correlated with the expression of SEP15 (p<0.001), SELENOP (p<0.001), SOD1 (p<0.001), SOD2 (p<0.001), CAT (p<0.001), and NFE2L2 (p=0.004). Alpha-fetoprotein levels were positively correlated with the expression of GPX4 (p=0.02) and SELENOP (p=0.01) in the experimental data. Low expression of GPX1 (p=0.006), GPX4 (p=0.01), SELENOP (p=0.006), SOD1 (p=0.007), CAT (p<0.001), and NFE2L2 (p<0.001), and higher levels of GSR, were associated with low overall survival at 12 months. These results suggest a significant role for these antioxidant enzymes in HCC pathogenesis and severity.

System-Wide Pollution of Biomedical Data: Consequence of the Search for Hub Genes of Hepatocellular Carcinoma Without Spatiotemporal Consideration

Biomedical institutions rely on data evaluation and are turning into data factories. Big-data storage centers, supercomputing systems, and increased algorithmic efficiency allow us to analyze the ever-increasing amount of data generated every day in biomedical research centers. In network science, the principal intrinsic problem is how to integrate the data and information from different experiments on genes or proteins. Data curation is an essential process in annotating new functional data to known genes or proteins, undertaken by a biobank curator, which is then reflected in the calculated networks. We provide an example of how protein-protein networks today have space-time limits. The next step is the integration of data and information from different biobanks. Omics data and networks are essential parts of this step but also have flawed protocols and errors. Consider data from patients with cancer: from biopsy procedures to experimental tests, to archiving methods and computational algorithms, these are continuously handled so require critical and continuous "updates" to obtain reproducible, reliable, and correct results. We show, as a second example, how all this distorts studies in cellular hepatocellular carcinoma. It is not unlikely that these flawed data have been polluting biobanks for some time before stringent conditions for the veracity of data were implemented in Big data. Therefore, all this could contribute to errors in future medical decisions.

Selenoprotein V protects against endoplasmic reticulum stress and oxidative injury induced by pro-oxidants

Selenoprotein V (SELENOV) contains a thioredoxin-like fold and a conserved CxxU motif with a potential redox function. This study was to assess its in vivo and in vitro roles and mechanisms in coping with different oxidant insults. In Experiment (Expt.)1, SELENOV knockout (KO) and wild type (WT) mice (male, 8-wk old) were given an ip injection of saline, diquat (DQ, 12.5 mg/kg), or N-acetyl-para-aminophenol (APAP, 300 mg/kg) (n = 10), and killed 5 h after the injection. In Expt. 2, primary hepatocytes of WT and KO were treated with DQ (0-0.75 mM) or APAP (0-6 mM) for 12 h. In Expt. 3, 293 T cells overexpressing Selenov gene (OE) were treated with APAP (0-4 mM) for 24 h or H₂O₂ (0-0.4 mM) for 12 h. Compared with the WT, the DQ- and APAP-injected KO mice had higher (P < 0.05) serum alanine aminotransferase activities and hepatic malondialdehyde (MDA), protein carbonyl, endoplasmic reticulum (ER) stress-related proteins (BIP and CHOP), apoptosis-related proteins (FAK and caspase-9), and 3-nitrotyrosine, along with lower total anti-oxidizing-capability (T-AOC) and severer hepatic necrosis. Likewise, the DQ and APAP-treated KO hepatocytes had elevated (P < 0.05) cell death (10-40%), decreased (P < 0.05) T-AOC (63-83%), glutathione (26-87%), superoxide dismutase (SOD) activity (28-36%), mRNA levels of redox enzymes (Cat, Gcs, Gpx3, and Sod) and (or) sharper declines (P < 0.05) in cellular respiration and ATP production than that of the WT cells. In contrast, the OE cells had greater viability and T-AOC and lower MDA, and carbonyl contents after the APAP and H₂O₂ exposures (all at P < 0.05) than the controls. Moreover, the OE cells had greater (P < 0.05) redox enzyme activities (GPX, TrxR, and SOD), and lower (P < 0.05) expressions of ER stress-related genes (Atf4, Atf6, Bip, Xbp1t, Xbp1s, and Chop) and proteins (BIP, CHOP, FAK, and caspase-9) than the control cells after the treatment of H₂O₂ (0.4 mM). In conclusion, SELENOV conferred protections in vivo and in vitro against the reactive oxygen and nitrogen species-mediated ER stress-related signaling and oxidative injuries.

Emerging roles for non-selenium containing ER-resident glutathione peroxidases in cell signaling and disease

Maintenance of cellular redox control is pivotal for normal cellular functions and cell fate decisions including cell death. Among the key cellular redox systems in mammals, the glutathione peroxidase (GPX) family of proteins is the largest conferring multifaceted functions and affecting virtually all cellular processes. The endoplasmic reticulum (ER)-resident GPXs, designated as GPX7 and GPX8, are the most recently added members of this family of enzymes. Recent studies have provided exciting insights how both enzymes support critical processes of the ER including oxidative protein folding, maintenance of ER redox control by eliminating H₂O₂, and preventing palmitic acid-induced lipotoxicity. Consequently, numerous pathological conditions, such as neurodegeneration, cancer and metabolic diseases have been linked with altered GPX7 and GPX8 expression. Studies in mice have demonstrated that loss of GPX7 leads to increased differentiation of preadipocytes, increased tumorigenesis and shortened lifespan. By contrast, GPX8 deficiency in mice results in enhanced caspase-4/11 activation and increased endotoxic shock in colitis model. With the increasing recognition that both types of enzymes are dysregulated in various tumor entities in man, we deem a review of the emerging roles played by GPX7 and GPX8 in health and disease development timely and appropriate.

Integrated Analysis to Study the Relationship between Tumor-Associated Selenoproteins: Focus on Prostate Cancer

Selenoproteins are proteins that contain selenium within selenocysteine residues. To date, twenty-five mammalian selenoproteins have been identified; however, the functions of nearly half of these selenoproteins are unknown. Although alterations in selenoprotein expression and function have been suggested to play a role in cancer development and progression, few detailed studies have been carried out in this field. Network analyses and data mining of publicly available datasets on gene expression levels in different cancers, and the correlations with patient outcome, represent important tools to study the correlation between selenoproteins and other proteins present in the human interactome, and to determine whether altered selenoprotein expression is cancer type-specific, and/or correlated with cancer patient prognosis. Therefore, in the present study, we used bioinformatics approaches to (i) build up the network of interactions between twenty-five selenoproteins and identify the most inter-correlated proteins/genes, which are named HUB nodes; and (ii) analyze the correlation between selenoprotein gene expression and patient outcome in ten solid tumors. Then, considering the need to confirm by experimental approaches the correlations suggested by the bioinformatics analyses, we decided to evaluate the gene expression levels of the twenty-five selenoproteins and six HUB nodes in androgen receptor-positive (22RV1 and LNCaP) and androgen receptor-negative (DU145 and PC3) cell lines, compared to human nontransformed, and differentiated, prostate epithelial cells (EPN) by RT-qPCR analysis. This analysis confirmed that the combined evaluation of some selenoproteins and HUB nodes could have prognostic value and may improve patient outcome predictions.

Dysregulation of Redox Status in Urinary Bladder Cancer Patients

The alteration of redox homeostasis constitutes an important etiological feature of common human malignancies. We investigated DNA damage, selenium (Se) levels and the expression of cytoprotective genes involved in (1) the KEAP1/NRF2/ARE pathway, (2) selenoprotein synthesis, and (3) DNA methylation and histone deacetylation as putative key players in redox status dysregulation in the blood of urinary bladder cancer (UBC) patients. The study involved 122 patients and 115 control individuals. The majority of patients presented Ta and T1 stages. UBC recurrence occurred within 0.13 to 29.02 months. DNA damage and oxidative DNA damage were significantly higher in the patients compared to the controls, while plasma Se levels were significantly reduced in the cases compared to the controls. Of the 25 investigated genes, elevated expression in the peripheral blood leukocytes in patients was observed for NRF2, GCLC, MMP9 and SEP15, while down-regulation was found for KEAP1, GSR, HMOX1, NQO1, OGG1, SEPW1, DNMT1, DNMT3A and SIRT1. After Bonferroni correction, an association was found with KEAP1, OGG1, SEPW1 and DNMT1. Early recurrence was associated with the down-regulation of PRDX1 and SRXN1 at the time of diagnosis. Peripheral redox status is significantly dysregulated in the blood of UBC patients. DNA strand breaks and PRDX1 and SRXN1 expression may provide significant predictors of UBC recurrence.

Combination Suicide Gene Delivery with an Adeno-Associated Virus Vector Encoding Inducible Caspase-9 and a Chemical Inducer of Dimerization Is Effective in a Xenotransplantation Model of Hepatocellular Carcinoma

Current treatment approaches for hepatocellular carcinoma (HCC) have a narrow therapeutic index and alternate modes of treatment are thus required. We have utilized a gene delivery vector containing inducible caspase 9 (iCasp9) gene, which is a synthetic analogue based on the mammalian caspase 9 and fused to a human FK506 binding protein that allows its conditional dimerization to a synthetic, small molecule [chemical inducer of dimerization, AP20187] and results in target cell apoptosis. In our studies, we have tested these synthetic vectors based on an adeno-associated virus platform for their potential anti-tumorigenic effect in human HCC cells in vitro and in a HCC tumor model developed in nude mice. Our data demonstrates that the iCasp9-AP20187 bioconjugate is able to trigger terminal effectors of cellular apoptosis and presents a viable approach for the potential treatment of HCC.

HMGB1 and SEPP1 as predictors of hepatocellular carcinoma in patients with viral C hepatitis: Effect of DAAs

BACKGROUND

Hepatitis C viral infection (HCV) and hepatocellular carcinoma (HCC) are potential health problems. New directly acting antivirals (DAAs) changed HCV treatment strategies. Selenoprotein P1 (SEPP1) is a hepatokine implicated in HCC pathogenesis. High mobility group box1 (HMGB1), a nuclear DNA-binding protein, involved in immune and inflammatory responses in HCV and HCC. Therefore, the aim of current study was to investigate HMGB1 and SEPP1 levels in HCV and HCV + HCC patients and exploring DAAs effect on them.

METHODS

15 healthy volunteers, 25 HCV and 25 HCV + HCC patients were included. Liver function tests, alpha fetoprotein (AFP), SEPP1 and HMGB1 serum levels were evaluated. For HCV group blood samples before and after treatment with sofosbuvir/daclatasvir combination were collected.

RESULTS

HMGB1 was significantly higher in HCV + HCC group than in control and HCV groups (p < .05). SEPP1 decreased significantly in HCV and HCV + HCC groups compared to control group (p < .001). SEPP1 significantly elevated after treatment with DAAs (p = .001). HMGB1 and SEPP1 were negatively correlated with each other in HCV group (p = .047). Logistic regression analysis showed that HMGB1 and SEPP1 could be used as predictors for HCC in HCV infected patients (p = .02,p = .002) respectively. Receiver operating characteristic curve (ROC) revealed HMGB1 had 32% sensitivity and 100% specificity in differentiating HCV from HCV + HCC patients, both SEPP1 and HMGB1 had high sensitivity (92%,60%) and 93% specificity in differentiating healthy from HCV + HCC group.

CONCLUSION

HMGB1 and SEPP1 are involved in pathogenesis of HCV and HCV induced HCC. Both of them could serve as predictive biomarkers for HCC in HCV patients.

Transcriptional Regulation of Selenoprotein F by Heat Shock Factor 1 during Selenium Supplementation and Stress Response

Changes of Selenoprotein F (SELENOF) protein levels have been reported during selenium supplementation, stressful, and pathological conditions. However, the mechanisms of how these external factors regulate SELENOF gene expression are largely unknown. In this study, HEK293T cells were chosen as an in vitro model. The 5′-flanking regions of SELENOF were analyzed for promoter features. Dual-Glo Luciferase assays were used to detect promoter activities. Putative binding sites of Heat Shock Factor 1 (HSF1) were predicted in silico and the associations were further proved by chromatin immunoprecipitation (ChIP) assay. Selenate and tunicamycin (Tm) treatment were used to induce SELENOF up-regulation. The fold changes in SELENOF expression and other relative proteins were analyzed by Q-PCR and western blot. Our results showed that selenate and Tm treatment up-regulated SELENOF at mRNA and protein levels. SELENOF 5′-flanking regions from −818 to −248 were identified as core positive regulatory element regions. Four putative HSF1 binding sites were predicted in regions from −1430 to −248, and six out of seven primers detected positive results in ChIP assay. HSF1 over-expression and heat shock activation increased the promoter activities, and mRNA and protein levels of SELENOF. Over-expression and knockdown of HSF1 showed transcriptional regulation effects on SELENOF during selenate and Tm treatment. In conclusion, HSF1 was discovered as one of the transcription factors that were associated with SELENOF 5′-flanking regions and mediated the up-regulation of SELENOF during selenate and Tm treatment. Our work has provided experimental data for the molecular mechanism of SELENOF gene regulation, as well as uncovered the involvement of HSF1 in selenotranscriptomic for the first time.

PIWI-interacting RNA-36712 restrains breast cancer progression and chemoresistance by interaction with SEPW1 pseudogene SEPW1P RNA

Background

Breast cancer is one of the most common malignancies and the major cause of cancer-related death in women. Although the importance of PIWI-interacting RNAs (piRNAs) in cancer has been increasingly recognized, few studies have been explored the functional mechanism of piRNAs in breast cancer development and progression.

Methods

We examined the top 20 highly expressed piRNAs based on the analysis of TCGA breast cancer data in two patient cohorts to test the roles of piRNAs in breast cancer. The effects of piRNA-36,712 on the malignant phenotypes and chemosensitivity of breast cancer cells were detected in vitro and in vivo. MS2-RIP and reporter gene assays were conducted to identify the interaction and regulation among piRNA-36,712, miRNAs and SEPW1P. Kaplan-Meier estimate with log-rank test was used to compare patient survival by different piRNA-36,712 expression levels.

Results

We found piRNA-36,712 level was significantly lower in breast cancer than in normal breast tissues and low level was correlated with poor clinical outcome in patients. Functional studies demonstrated that piRNA-36,712 interacts with RNAs produced by SEPW1P, a retroprocessed pseudogene of SEPW1, and subsequently inhibits SEPW1 expression through competition of SEPW1 mRNA with SEPW1P RNA for microRNA-7 and microRNA-324. We also found that higher SEPW1 expression due to downregulation of piRNA-36,712 in breast cancer may suppress P53, leading to the upregulated Slug but decreased P21 and E-cadherin levels, thus promoting cancer cell proliferation, invasion and migration. Furthermore, we found that piRNA-36,712 had synergistic anticancer effects with the paclitaxel and doxorubicin, two chemotherapeutic agents for breast cancer.

Conclusions

These findings suggest that piRNA-36,712 is a novel tumor suppressor and may serve as a potential predictor for the prognosis of breast cancer patients.

Electronic supplementary material

The online version of this article (10.1186/s12943-019-0940-3) contains supplementary material, which is available to authorized users.

Role of Selenoprotein F in Protein Folding and Secretion: Potential Involvement in Human Disease

Selenoproteins form a group of proteins of which its members contain at least one selenocysteine, and most of them serve oxidoreductase functions. Selenoprotein F (SELENOF), one of the 25 currently identified selenoproteins, is located in the endoplasmic reticulum (ER) organelle and is abundantly expressed in many tissues. It is regulated according to its selenium status, as well as by cell stress conditions. SELENOF may be functionally linked to protein folding and the secretion process in the ER. Several studies have reported positive associations between SELENOF genetic variations and several types of cancer. Also, altered expression levels of SELENOF have been found in cancer cases and neurodegenerative diseases. In this review, we summarize the current understanding of the structure, expression, and potential function of SELENOF and discuss its possible relation with various pathological processes.

Participation of selenoproteins localized in the ER in the processes occurring in this organelle and in the regulation of carcinogenesis-associated processes

The functions performed by the ER are diverse: synthesis of steroid hormones, synthesis of proteins for the plasma membrane, lysosomes, as well as proteins meant for exocytosis, protein folding, formation of disulfide bonds, N-linked glycosylation, etc. Selenoproteins localized in this organelle are definitely involved in the processes occurring in it, and the most common of them include participation in protein degradation, regulation of ER stress and redox metabolism. ER stress has been registered in many types of cancer cells. The ability to persist under prolonged ER stress increases their survival, resistance to drugs and immunity. Disturbances in the redox regulation of the cell cycle, which result in the accumulation of misfolded proteins in the ER, viral infection, disruption of Ca²⁺ regulation, are known to cause an evolutionarily conserved reaction - unfolded protein response (UPR) and, ultimately, lead to ER stress. Since selenoproteins, as oxidoreductases, possess antioxidant properties, and their role in the regulation of important processes, such as carcinogenesis and ER stress, has been actively studied in the recent decades, the subject of this review is highly relevant.

Selenoprotein K Mediates the Proliferation, Migration, and Invasion of Human Choriocarcinoma Cells by Negatively Regulating Human Chorionic Gonadotropin Expression via ERK, p38 MAPK, and Akt Signaling Pathway

Selenoprotein K (SelK), a member of selenoprotein family, is identified as a single endoplasmic reticulum (ER) transmembrane protein. Although over-expression of SelK inhibits adherence and migration of human gastric cancer BGC-823 cells, the effects of SelK in human choriocarcinoma (CCA) are not well understood. In this study, the expression levels of SelK in three CCA cell lines, BeWo, JEG-3, and JAR, were examined. The effects of silencing or over-expressing SelK on expression of human chorionic gonadotropin beta subunit (β-hCG) were detected by western blotting. The results show that the protein level of β-hCG was reciprocally regulated by down- or up-regulation of SelK (*P < 0.05; #P < 0.05). The proliferative, migratory, and invasive capabilities of JEG-3 cells with reduced or over-expressed SelK were then tested using the cell counting kit-8 (CCK-8), wound healing, and transwell chamber assays. We found that these cellular activities were markedly increased by the loss of SelK in JEG-3 cells. Conversely, over-expressing SelK in JEG-3 cells suppressed these phenotypes. In addition, SelK expression after down- or up-regulation of β-hCG was also measured. Surprisingly, we found that level of SelK was affected by β-hCG (*P < 0.05; #P < 0.05). The proliferation, migration, and invasion were determined in JEG-3 cells after each over-expression and reduction of β-hCG. The results confirmed that β-hCG functions as a promoter of human choriocarcinoma. Furthermore, ERK/p38 MAPK and Akt signaling pathways were found to involve in these cellular functions. This work suggests that SelK may act as a tumor suppressor in human choriocarcinoma cells by negatively regulating β-hCG expression via ERK, p38 MAPK, and Akt signaling pathways. These findings revealed that selenoprotein K may serve as a novel target for human choriocarcinoma therapy in vitro.

Endoplasmic reticulum-resident selenoproteins as regulators of calcium signaling and homeostasis

The human selenoprotein family contains 25 members that share the common feature of containing the amino acid, selenocysteine (Sec). Seven selenoproteins are localized to the endoplasmic reticulum (ER) and exhibit different structural features contributing to a range of cellular functions. Some of these functions are either directly or indirectly related to calcium (Ca²⁺) flux or homeostasis. The presence of the unique Sec residue within these proteins allows some to exert oxidoreductase activity, while the function of the Sec in other ER selenoproteins remains unclear. Some functional insight has been achieved by identifying domains within the ER selenoproteins or through the identification of binding partners. For example, selenoproteins K and N (SELENOK AND SELENON) have been characterized through interactions detected with the inositol 1,4,5-triphosphate receptors (IP3Rs) and the SERCA2b pump, respectively. Others have been linked to chaperone functions related to ER stress or Ca²⁺ homeostasis. This review summarizes the details gathered to date regarding the ER-resident selenoproteins and their effect on Ca²⁺ regulated pathways and outcomes in cells.

Comparison of the seleno-transcriptome expression between human non-cancerous mammary epithelial cells and two human breast cancer cell lines

Breast cancer is the second most common cause of mortality in women; therefore, the identification of novel putative markers is required to improve its diagnosis and prognosis. Selenium is known to protect mammary epithelial cells from oxidative DNA damage, and to inhibit the initiation phase of carcinogenesis by stimulating DNA repair and apoptosis regulation. Consequently, the present study has focused attention on the selenoprotein family and their involvement in breast cancer. The present study performed a global analysis of the seleno-transcriptome expression in human breast cancer MCF-7 and MDA-MB231 cell lines compared with healthy breast MCF-10A cells using reverse transcription-quantitative polymerase chain reaction. The present data revealed the presence of differently expressed genes in MCF-7 and MDA-MB231 cells compared with MCF-10A cells: Four downregulated [glutathione peroxidase (GPX)1, GPX4, GPX5 and GPX7] and three upregulated (deiodinase iodothyronine, type II, GPX2 and GPX3) genes. Additionally, interactomic investigation were performed by the present study to evaluate the association between the downregulated and upregulated genes, and to identify putative HUB nodes, which represent the centers of association between the genes that are capable of direct control over the gene networks. Network analysis revealed that all differentially regulated genes, with the exception of selenoprotein T, are implicated in the same network that presents three HUB nodes interconnected to the selenoprotein mRNAs, including TP53, estrogen receptor 1 and catenin-β1 (CTNNB1). Overall, these data demonstrated for the first time, a profile of seleno-mRNAs specific for human breast cells, indicating that these genes alter their expression on the basis of the ER-positivity or negativity of breast cancer cells.

Contribution of mammalian selenocysteine-containing proteins to carcinogenesis

Oxidative stress caused by a sharp growth of free radicals in the organism is a major cause underlying the occurrence of all kinds of malignant formations. Selenium is an important essential trace element found in selenoproteins in the form of selenocysteine, an amino acid differing from cysteine for the presence of selenium instead of sulfur and making such proteins highly active. To date the role of selenium has been extensively investigated through studying the functions of selenoproteins in carcinogenesis. Analysis of the obtained results clearly demonstrates that selenoproteins can act as oncosuppressors, but can also, on the contrary, favor the formation of malignant tumors.

A study on the structural features of SELK, an over-expressed protein in hepatocellular carcinoma, by molecular dynamics simulations in a lipid-water system

Human SELK is a small trans-membrane selenoprotein characterized by a single trans-membrane helix, while the N-terminal region protrudes into the lumen and the long C-terminal domain into the cytoplasm. SELK is over-expressed in some cancers, like hepatocellular carcinoma; however its precise role in cancer development is presently unknown. SELK is involved in promoting the calcium flux, catalyzing palmitoylation reactions and protein degradation in the endoplasmic reticulum (ER). Therefore, this protein should bind many different proteins like p97/VCP in the supramolecular complex involved in the ER degradation pathway. To study the structural features of SELK in the membrane, we have modeled the protein and then subjected it to molecular dynamics simulations in a lipid-water system. The model shows a N-terminal domain with three β-strands and a short helix, a well-defined trans-membrane helix and a C-terminal domain that lacks a persistent secondary structure and contains long disordered regions. The trajectory analysis during the simulation evidences that: (i) the N-terminal region explores a limited conformational space and is stabilized by intra-peptide H-bonds as well with membrane lipids and water, (ii) the trans-membrane helix was found to be quite stable and (iii) the disordered C-terminal region is stabilized by H-bonds with clustered water molecules as well as by rapidly interchanging intra-peptidic H-bonds, with a structural tendency to compact around the four HUB residues found for this domain. Moreover, N-terminal and C-terminal clusters are distributed differently in the conformational space suggesting that their dynamics are coupled complicatedly through the membrane. Further analyses have shown that the N-terminal has a tendency to pivot around the insertion with the TM-helix through the fluctuations of the three β-strands, which, in turn, show features similar to WW-domains. These results will be useful to study the SELK, SELS and VCP complex representing an interesting druggable target for cancer.

Human MiR-544a Modulates SELK Expression in Hepatocarcinoma Cell Lines

Hepatocellular carcinoma (HCC) is a multi-factorial cancer with a very poor prognosis; therefore, there are several investigations aimed at the comprehension of the molecular mechanisms leading to development and progression of HCC and at the definition of new therapeutic strategies. We have recently evaluated the expression of selenoproteins in HCC cell lines in comparison with normal hepatocytes. Recent results have shown that some of them are down- and others up-regulated, including the selenoprotein K (SELK), whose expression was also induced by sodium selenite treatment on cells. However, so far very few studies have been dedicated to a possible effect of microRNAs on the expression of selenoproteins and their implication in HCC. In this study, the analysis of SELK 3'UTR by bioinformatics tools led to the identification of eight sites potentially targeted by human microRNAs. They were then subjected to a validation test based on luciferase reporter constructs transfected in HCC cell lines. In this functional screening, miR-544a was able to interact with SELK 3'UTR suppressing the reporter activity. Transfection of a miR-544a mimic or inhibitor was then shown to decrease or increase, respectively, the translation of the endogenous SELK mRNA. Intriguingly, miR-544a expression was found to be modulated by selenium treatment, suggesting a possible role in SELK induction by selenium.

Deducing the functional characteristics of the human selenoprotein SELK from the structural properties of its intrinsically disordered C-terminal domain

The intrinsically disordered proteins (IDPs) cannot be described by a single structural representation but, due to their high structural fluctuation, through conformational ensembles. Certainly, molecular dynamics (MD) simulations represent a useful tool to study their different conformations capturing the conformational distribution. Our group is focusing on the structural characterization of proteins belonging to the seleno-proteome due to their involvement in cancer. They present disordered domains central for their biological function, and, in particular, SELK is a single-pass transmembrane protein that resides in the endoplasmic reticulum membrane (ER) with a C-terminal domain exposed to the cytoplasm that is known to interact with different components of the endoplasmic reticulum associated to the protein degradation (ERAD) pathway. This protein is found to be up-expressed in hepatocellular carcinoma and in other cancers. In this work we performed a detailed analysis of the C-terminal domain sequence of SELK and discovered that it is characterized by many prolines, and four negatively and eleven positively charged residues, which are crucial for its biological activity. This region can be considered as a weak polyelectrolyte and, specifically, a polycation, with high disordered propensity and different phosphorylation sites dislocated along the sequence. Then, we modeled its three-dimensional structure by performing MD simulations in water at neutral pH to analyze the structural stability as well as to identify the presence of HUB residues that play a key structural role as evidenced by the residue-residue interaction network analysis. Through this approach, we demonstrate that the C-terminal domain of SELK (i) presents a poor content of regular secondary structure elements, (ii) is dynamically stabilized by a network of intra-molecular H-bonds and H-bonds with water molecules, (iii) is highly fluctuating and, therefore, can be described only through a conformational ensemble, where we evidenced a distribution of equilibrium conformers which continuously inter-change their conformations. Finally to verify the specific role played by the negative charges, we also performed MD simulations at acidic pH. Overall, all the obtained results evidenced that SELK has the dynamic structural features to be defined as a HUB protein able to interact with multiple members. Therefore, considering the possible role that this protein can have in cancer development and progression, it can represent a target for drug design studies.

GPX4 and GPX7 over-expression in human hepatocellular carcinoma tissues

Hepatocellular carcinoma (HCC) is the most common type of liver cancer and is still one of the most fatal cancers. Hence, it needs to identify always new putative markers to improve its diagnosis and prognosis. The selenium is an essential trace mineral implicated as a key factor in the early stage of cancer and exerts its biological function through the selenoproteins. In the last years our group has been studying the involvement of some selenoproteins in HCC. However, no many data are reported in literature about the correlation between HCC and the glutathione peroxidases (GPXs), both selenium and non selenium-containing GPXs.

In this paper we have evaluated the GPX4 and GPX7 expression in some paraffin-embedded tissues from liver biopsy of patients with hepatitis C virus (HCV)-related cirrhosis and HCC by immunohistochemistry and RT-qPCR analysis. Our results evidenced that i) GPX4 and GPX7 had a statistically significant over-expression in HCC tissues compared to cirrhotic counterparts used as non tumor tissues, and ii) their expression was higher in grade III HCC tissues with respect to grade I-II samples. Therefore, we propose to use GPX4 and GPX7 as possible markers for improving HCC diagnosis/prognosis.