Functional analysis of the CTNS gene exonic variants predicted to affect splicing.

Cystinosis is a severe, monogenic systemic disease caused by variants in CTNS gene. Currently, there is growing evidence that exonic variants in many diseases can affect pre-mRNA splicing. The impact of CTNS gene exonic variants on splicing regulation may be underestimated due to the lack of routine studies at the RNA level. Here, we analyzed 59 exonic variants in the CTNS gene using bioinformatics tools and identified candidate variants that may induce splicing alterations by minigene assays. We identified six exonic variants that induce splicing alterations by disrupting the ratio of exonic splicing enhancers/exonic splicing silencers (ESEs/ESSs) or by interfering with the recognition of classical splice sites, or both. Our results help in the correct molecular characterization of variants in cystinosis and inform emerging therapies. Furthermore, our work suggests that the combination of in silico and in vitro assays facilitates to assess the effects of DNA variants driving rare genetic diseases on splicing regulation and will enhance the clinical utility of variant functional annotation.

Identification of seven variants in the col4a1 gene that alter RNA splicing by minigene assay.

Type IV collagen is an integral component of basement membranes. Mutations in COL4A1, one of the key genes encoding Type IV collagen, can result in a variety of diseases. It is clear that a significant proportion of mutations that affect splicing can cause disease directly or contribute to the susceptibility or severity of disease. Here, we analyzed exonic mutations and intronic mutations described in the COL4A1 gene using bioinformatics programs and identified candidate mutations that may alter the normal splicing pattern through a minigene system. We identified seven variants that induce splicing alterations by disrupting normal splice sites, creating new ones, or altering splice regulatory elements. These mutations are predicted to impact protein function. Our results help in the correct molecular characterization of variants in COL4A1 and may help develop more personalized treatment options.

A novel heterozygous variant of the SALL1 gene with atypical Townes-Brocks syndrome phenotypes in Chinese family.

Townes-Brocks syndrome (TBS) is an autosomal dominant disorder characterised by the triad of anorectal, thumb, and ear malformations. It may also be accompanied by defects in kidney, heart, eyes, hearing, and feet. TBS has been demonstrated to result from heterozygous variants in the SALL1 gene, which encodes zinc finger protein believed to function as a transcriptional repressor. The clinical characteristics of an atypical TBS phenotype patient from a Chinese family are described, with predominant manifestations including external ear dysplasia, unilateral renal hypoplasia with mild renal dysfunction, and hearing impairment. A novel heterozygous variant c.3060T>A (p.Tyr1020*) in exon 2 of the SALL1 gene was identified in this proband. Pyrosequencing of the complementary DNA of the proband revealed that the variant transcript accounted for 48% of the total transcripts in peripheral leukocytes, indicating that this variant transcript has not undergone nonsense-mediated mRNA decay. This variant c.3060T > A is located at the terminal end of exon 2, proximal to the 3' end of the SALL1 gene, and exerts a relatively minor impact on protein function. We suggest that the atypical TBS phenotype observed in the proband may be attributed to the truncated protein retaining partial SALL1 function.

Identified eleven exon variants in PKD1 and PKD2 genes that altered RNA splicing by minigene assay.

BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is a common monogenic multisystem disease caused primarily by mutations in the PKD1 gene or PKD2 gene. There is increasing evidence that some of these variants, which are described as missense, synonymous or nonsense mutations in the literature or databases, may be deleterious by affecting the pre-mRNA splicing process. RESULTS: This study aimed to determine the effect of these PKD1 and PKD2 variants on exon splicing combined with predictive bioinformatics tools and minigene assay. As a result, among the 19 candidate single nucleotide alterations, 11 variants distributed in PKD1 (c.7866C > A, c.7960A > G, c.7979A > T, c.7987C > T, c.11248C > G, c.11251C > T, c.11257C > G, c.11257C > T, c.11346C > T, and c.11393C > G) and PKD2 (c.1480G > T) were identified to result in exon skipping. CONCLUSIONS: We confirmed that 11 variants in the gene of PKD1 and PKD2 affect normal splicing by interfering the recognition of classical splicing sites or by disrupting exon splicing enhancers and generating exon splicing silencers. This is the most comprehensive study to date on pre-mRNA splicing of exonic variants in ADPKD-associated disease-causing genes in consideration of the increasing number of identified variants in PKD1 and PKD2 gene in recent years. These results emphasize the significance of assessing the effect of exon single nucleotide variants in ADPKD at the mRNA level.

Tfcancer: a manually curated database of transcription factors associated with human cancers.

SUMMARY: Transcription factors (TFs) are critical regulation elements and its dysregulation can lead to a variety of cancers. However, currently, there are no such online resources for large-scale collection, storage and analysis of TF-cancer associations in those cancers. To fill this gap, we present a database called TFcancer (http://lcbb.swjtu.edu.cn/tfcancer/), which contains 3136 experimentally supported associations between 364 TFs and 33 TCGA cancers by manually curating more than 1800 literature. TFcancer mainly concentrates on four aspects: TF expression, molecular alteration, regulatory relationships between TFs and target genes, and biological processes and signaling pathways of TFs in cancers. TFcancer not only provides a user-friendly interface for browsing and searching but also allows flexible data downloading and user data submitting. It is believed that TFcancer is a helpful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of TFs involved in human cancers. AVAILABILITY AND IMPLEMENTATION: The TFcancer are freely available at http://lcbb.swjtu.edu.cn/tfcancer/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Supervised and Weakly Supervised Deep Learning for Segmentation and Counting of Cotton Bolls Using Proximal Imagery.

The total boll count from a plant is one of the most important phenotypic traits for cotton breeding and is also an important factor for growers to estimate the final yield. With the recent advances in deep learning, many supervised learning approaches have been implemented to perform phenotypic trait measurement from images for various crops, but few studies have been conducted to count cotton bolls from field images. Supervised learning models require a vast number of annotated images for training, which has become a bottleneck for machine learning model development. The goal of this study is to develop both fully supervised and weakly supervised deep learning models to segment and count cotton bolls from proximal imagery. A total of 290 RGB images of cotton plants from both potted (indoor and outdoor) and in-field settings were taken by consumer-grade cameras and the raw images were divided into 4350 image tiles for further model training and testing. Two supervised models (Mask R-CNN and S-Count) and two weakly supervised approaches (WS-Count and CountSeg) were compared in terms of boll count accuracy and annotation costs. The results revealed that the weakly supervised counting approaches performed well with RMSE values of 1.826 and 1.284 for WS-Count and CountSeg, respectively, whereas the fully supervised models achieve RMSE values of 1.181 and 1.175 for S-Count and Mask R-CNN, respectively, when the number of bolls in an image patch is less than 10. In terms of data annotation costs, the weakly supervised approaches were at least 10 times more cost efficient than the supervised approach for boll counting. In the future, the deep learning models developed in this study can be extended to other plant organs, such as main stalks, nodes, and primary and secondary branches. Both the supervised and weakly supervised deep learning models for boll counting with low-cost RGB images can be used by cotton breeders, physiologists, and growers alike to improve crop breeding and yield estimation.

NCR3LG1 (B7-H6) is a potential prognostic factor for bladder cancer patients.

BACKGROUND: NCR3LG1 (B7-H6) protein is selectively overexpressed on tumour and is associated with fatal disease progression of various cancer. However, its prognostic value in bladder cancer (BCa) has not been well elaborated. METHODS: We examined the expression of NCR3LG1 in human BCa and analysed its clinical significance and prognostic value. Meanwhile, the expression of NCR3LG1 was intervened in human BCa cell line 253JBV to analyse subsequent effects on tumour. RESULTS: According to TCGA data, the disease-free survival rate was statistically significant between the NCR3LG1 high expression group and the low expression group (Log Rank p = 0.006). Immunohistochemical staining showed that the expression of NCR3LG1 in BCa tissue was significantly higher than that in adjacent tissues (p < 0.0001), which was positively correlated with TNM staging (p = 0.008), histological grade (p = 0.022), and lymphoma metastasis of BCa (p = 0.032). The proliferation (p < 0.0001), invasion (p < 0.001) and migration ability (p < 0.001) of 253JBV cells are significantly inhibited by knocking down the expression of NCR3LG1, and the cell cycle arrest is induced at the G1 phase, which accelerates the apoptosis of BCa cells (p < 0.005). CONCLUSION: Our findings indicate that NCR3LG1 is involved in the progression of human BCa and may become a potential prognostic biomarker for BCa.

Silencing TTK expression inhibits the proliferation and progression of prostate cancer.

PURPOSE: The main objective of our study was to explore changes in the expression levels of differentially expressed genes associated with prostate cancer progression and to design a series of experiments to verify the function of differentially expressed genes. METHOD: The transcriptome datas of 499 cases of prostate cancer patients was downloaded from TCGA database. Differential genes associated with Gleason score were selected and filtered out by p < 0.05 and spearman coefficient >0.3. KEGG signaling pathway was enriched by differentially expressed genes, and TTK was selected as the research object. The expression of TTK was tested in prostate cancer tissues and prostate cancer cell lines. The changes of biological behavior of prostate cancer cell lines were verified after TTK was knocked out by siRNA and tumorigenic effect of TTK was verified by shRNA in vivo experiments. RESULT: The expression of TTK was positively correlated with Gleason score of prostate cancer, and the expression of protein and mRNA in metastatic prostate cancer cell lines was higher than that in non-metastatic prostate cancer cell lines. Vitro biological experiments showed that TTK gene knockout could inhibit the proliferation, invasion and migration of PC3 and DU145 cells, and promote cell apoptosis. In vivo experiments showed that TTK knockout inhibited tumorigenesis in mice. It was found that the expression of CDK2 and CCNE1 decreased after TTK was knocked out. CONCLUSION: Our results suggest that TTK is a gene associated with malignancy of PCa and could be a novel therapeutic target for clinical application.

Autonomous Navigation of a Center-Articulated and Hydrostatic Transmission Rover using a Modified Pure Pursuit Algorithm in a Cotton Field.

This study proposes an algorithm that controls an autonomous, multi-purpose, center-articulated hydrostatic transmission rover to navigate along crop rows. This multi-purpose rover (MPR) is being developed to harvest undefoliated cotton to expand the harvest window to up to 50 days. The rover would harvest cotton in teams by performing several passes as the bolls become ready to harvest. We propose that a small robot could make cotton production more profitable for farmers and more accessible to owners of smaller plots of land who cannot afford large tractors and harvesting equipment. The rover was localized with a low-cost Real-Time Kinematic Global Navigation Satellite System (RTK-GNSS), encoders, and Inertial Measurement Unit (IMU)s for heading. Robot Operating System (ROS)-based software was developed to harness the sensor information, localize the rover, and execute path following controls. To test the localization and modified pure-pursuit path-following controls, first, GNSS waypoints were obtained by manually steering the rover over the rows followed by the rover autonomously driving over the rows. The results showed that the robot achieved a mean absolute error (MAE) of 0.04 m, 0.06 m, and 0.09 m for the first, second and third passes of the experiment, respectively. The robot achieved an MAE of 0.06 m. When turning at the end of the row, the MAE from the RTK-GNSS-generated path was 0.24 m. The turning errors were acceptable for the open field at the end of the row. Errors while driving down the row did damage the plants by moving close to the plants' stems, and these errors likely would not impede operations designed for the MPR. Therefore, the designed rover and control algorithms are good and can be used for cotton harvesting operations.

LncRNA PU.1 AS regulates arsenic-induced lipid metabolism through EZH2/Sirt6/SREBP-1c pathway.

Arsenic (As) is an omnipresent metalloid toxicant, which has elicited serious environmental pollution and health risky problems. Previous studies have uncovered that the As exposure could also cause markedly reduction of serum triglycerides in mice. However, the regulation mechanisms are still largely unknown. The present study is aimed to elucidate the molecular mechanisms of lncRNAs in As-induced lipid metabolic disequilibrium. We demonstrated that lncRNA PU.1 AS was significantly induced in the liver of As-feed mice companied with lower serum triglycerides contents; further in vitro experiment confirmed that PU.1 AS regulated liver cells lipid accumulation by nile red fluorescence staining. Intensive mechanistic investigations illustrated that PU.1 AS could interact with EZH2 protein to regulate its downstream target gene expression, and As-induced PU.1 AS attenuated EZH2-supppressed Sirt6 expression, thereafter leading to a decreased SREBP-1c protein expression, as well as the diminished synthesis of triglycerides in hepatocytes. In conclusion, this study provided a new lncRNA-related regulatory signaling pathway participating in As-induced abnormal lipid metabolism.

The rice CK2 kinase regulates trafficking of phosphate transporters in response to phosphate levels.

Phosphate transporters (PTs) mediate phosphorus uptake and are regulated at the transcriptional and posttranslational levels. In one key mechanism of posttranslational regulation, phosphorylation of PTs affects their trafficking from the endoplasmic reticulum (ER) to the plasma membrane. However, the kinase(s) mediating PT phosphorylation and the mechanism leading to ER retention of phosphorylated PTs remain unclear. In this study, we identified a rice (Oryza sativa) kinase subunit, CK2ß3, which interacts with PT2 and PT8 in a yeast two-hybrid screen. Also, the CK2α3/ß3 holoenzyme phosphorylates PT8 under phosphate-sufficient conditions. This phosphorylation inhibited the interaction of PT8 with PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR1, a key cofactor regulating the exit of PTs from the ER to the plasma membrane. Additionally, phosphorus starvation promoted CK2ß3 degradation, relieving the negative regulation of PT phosphorus-insufficient conditions. In accordance, transgenic expression of a nonphosphorylatable version of OsPT8 resulted in elevated levels of that protein at the plasma membrane and enhanced phosphorus accumulation and plant growth under various phosphorus regimes. Taken together, these results indicate that CK2α3/ß3 negatively regulates PTs and phosphorus status regulates CK2α3/ß3.

Performance investigation of the polar coded FSO communication system over turbulence channel.

In this paper, for the first time, to the best of our knowledge, polar codes are introduced and experimentally implemented in a free space optical (FSO) communication system to combat atmospheric turbulence induced fading. By analyzing the characteristics of the turbulence channel, a method of evaluating the channel state information for polar decoding is proposed that can achieve good trade-off between the performance and the computational complexity of this polar coded system. To verify our scheme, an intensity modulation direct detection FSO communication experimental platform with a turbulence chamber is established. For the weak turbulence condition, comparing with the low-density parity check codes, the experimental results show that our proposed scheme has stronger error correcting capacity and lower computational complexity in combating the turbulence induced fading. Moreover, for moderate and strong turbulence conditions, the gamma-gamma turbulence model is adopted for constructing the Monte Carlo simulation. The results of the experiment and simulation both show that our proposed scheme can effectively combat atmospheric turbulence induced fading with a relatively low computational complexity in a wide range of turbulence conditions.

Data Fusion of Two Hyperspectral Imaging Systems with Complementary Spectral Sensing Ranges for Blueberry Bruising Detection.

Currently, the detection of blueberry internal bruising focuses mostly on single hyperspectral imaging (HSI) systems. Attempts to fuse different HSI systems with complementary spectral ranges are still lacking. A push broom based HSI system and a liquid crystal tunable filter (LCTF) based HSI system with different sensing ranges and detectors were investigated to jointly detect blueberry internal bruising in the lab. The mean reflectance spectrum of each berry sample was extracted from the data obtained by two HSI systems respectively. The spectral data from the two spectroscopic techniques were analyzed separately using feature selection method, partial least squares-discriminant analysis (PLS-DA), and support vector machine (SVM), and then fused with three data fusion strategies at the data level, feature level, and decision level. The three data fusion strategies achieved better classification results than using each HSI system alone. The decision level fusion integrating classification results from the two instruments with selected relevant features achieved more promising results, suggesting that the two HSI systems with complementary spectral ranges, combined with feature selection and data fusion strategies, could be used synergistically to improve blueberry internal bruising detection. This study was the first step in demonstrating the feasibility of the fusion of two HSI systems with complementary spectral ranges for detecting blueberry bruising, which could lead to a multispectral imaging system with a few selected wavelengths and an appropriate detector for bruising detection on the packing line.

The mechanism of (+) taxifolin's protective antioxidant effect for •OH-treated bone marrow-derived mesenchymal stem cells.

The natural dihydroflavonol (+) taxifolin was investigated for its protective effect on Fenton reagent-treated bone marrow-derived mesenchymal stem cells (bmMSCs). Various antioxidant assays were used to determine the possible mechanism. These included •OH-scavenging, 2-phenyl-4, 4, 5, 5-tetramethylimidazoline-1-oxyl-3-oxide radical-scavenging (PTIO•-scavenging), 1, 1-diphenyl-2-picryl-hydrazl radical-scavenging (DPPH•-scavenging), 2, 2'-azino-bis (3-ethylbenzo-thiazoline-6-sulfonic acid) radical-scavenging (ABTS+•-scavenging), Fe3+-reducing, and Cu2+-reducing assays. The Fe2+-binding reaction was also investigated using UV-Vis spectra. The results revealed that cell viability was fully restored, even increasing to 142.9 ± 9.3% after treatment with (+) taxifolin. In the antioxidant assays, (+) taxifolin was observed to efficiently scavenge •OH, DPPH• and ABTS+• radicals, and to increase the relative Cu2+- and Fe3+-reducing levels. In the PTIO•-scavenging assay, its IC50 values varied with pH. In the Fe2+-binding reaction, (+) taxifolin was found to yield a green solution with two UV-Vis absorbance peaks: λmax = 433 nm (ε =5.2 × 102 L mol-1 cm -1) and λmax = 721 nm (ε = 5.1 × 102 L mol-1 cm -1). These results indicate that (+) taxifolin can act as an effective •OH-scavenger, protecting bmMSCs from •OH-induced damage. Its •OH-scavenging action consists of direct and indirect antioxidant effects. Direct antioxidation occurs via multiple pathways, including ET, PCET or HAT. Indirect antioxidation involves binding to Fe2+.

Rice SPX1 and SPX2 inhibit phosphate starvation responses through interacting with PHR2 in a phosphate-dependent manner.

In plants, sensing the levels of external and internal nutrients is essential for reprogramming the transcriptome and adapting to the fluctuating environment. Phosphate (Pi) is a key plant nutrient, and a large proportion of Pi starvation-responsive genes are under the control of Phosphate Starvation Response Regulator 1 (PHR1) in Arabidopsis (AtPHR1) and its homologs, such as Oryza sativa (Os)PHR2 in rice. AtPHR1 and OsPHR2 expression is not very responsive to Pi starvation, raising the question as to how plants sense changes in cellular Pi levels to activate the central regulator. SPX [named after SYG1 (suppressor of yeast gpa1), Pho81 (CDK inhibitor in yeast PHO pathway), and XPR1 (xenotropic and polytropic retrovirus receptor)] proteins that harbor only the SPX domain are reported to be involved in the negative regulation of Pi starvation responses. Here, we show that the nuclear localized SPX proteins SPX1 and SPX2 are Pi-dependent inhibitors of the activity of OsPHR2 in rice. Indeed, SPX1 and SPX2 proteins interact with PHR2 through their SPX domain, inhibiting its binding to P1BS (the PHR1-binding sequence: GNATATNC). In vivo data, as well as results from in vitro experiments using purified SPX1, SPX2, and OsPHR2 proteins, showed that SPX1 and SPX2 inhibition of OsPHR2 activity is Pi-dependent. These data provide evidence to support the involvement of SPX1 and SPX2 in the Pi-sensing mechanism in plants.

A Pulsed Thermographic Imaging System for Detection and Identification of Cotton Foreign Matter.

Detection of foreign matter in cleaned cotton is instrumental to accurately grading cotton quality, which in turn impacts the marketability of the cotton. Current grading systems return estimates of the amount of foreign matter present, but provide no information about the identity of the contaminants. This paper explores the use of pulsed thermographic analysis to detect and identify cotton foreign matter. The design and implementation of a pulsed thermographic analysis system is described. A sample set of 240 foreign matter and cotton lint samples were collected. Hand-crafted waveform features and frequency-domain features were extracted and analyzed for statistical significance. Classification was performed on these features using linear discriminant analysis and support vector machines. Using waveform features and support vector machine classifiers, detection of cotton foreign matter was performed with 99.17% accuracy. Using frequency-domain features and linear discriminant analysis, identification was performed with 90.00% accuracy. These results demonstrate that pulsed thermographic imaging analysis produces data which is of significant utility for the detection and identification of cotton foreign matter.

Integrative Comparison of the Role of the PHOSPHATE RESPONSE1 Subfamily in Phosphate Signaling and Homeostasis in Rice.

Phosphorus (P), an essential macronutrient for all living cells, is indispensable for agricultural production. Although Arabidopsis (Arabidopsis thaliana) PHOSPHATE RESPONSE1 (PHR1) and its orthologs in other species have been shown to function in transcriptional regulation of phosphate (Pi) signaling and Pi homeostasis, an integrative comparison of PHR1-related proteins in rice (Oryza sativa) has not previously been reported. Here, we identified functional redundancy among three PHR1 orthologs in rice (OsPHR1, OsPHR2, and OsPHR3) using phylogenetic and mutation analysis. OsPHR3 in conjunction with OsPHR1 and OsPHR2 function in transcriptional activation of most Pi starvation-induced genes. Loss-of-function mutations in any one of these transcription factors (TFs) impaired root hair growth (primarily root hair elongation). However, these three TFs showed differences in DNA binding affinities and messenger RNA expression patterns in different tissues and growth stages, and transcriptomic analysis revealed differential effects on Pi starvation-induced gene expression of single mutants of the three TFs, indicating some degree of functional diversification. Overexpression of genes encoding any of these TFs resulted in partial constitutive activation of Pi starvation response and led to Pi accumulation in the shoot. Furthermore, unlike OsPHR2-overexpressing lines, which exhibited growth retardation under normal or Pi-deficient conditions, OsPHR3-overexpressing plants exhibited significant tolerance to low-Pi stress but normal growth rates under normal Pi conditions, suggesting that OsPHR3 would be useful for molecular breeding to improve Pi uptake/use efficiency under Pi-deficient conditions. We propose that OsPHR1, OsPHR2, and OsPHR3 form a network and play diverse roles in regulating Pi signaling and homeostasis in rice.

Genetic manipulation of a high-affinity PHR1 target cis-element to improve phosphorous uptake in Oryza sativa L.

Phosphorus (P) is an essential macronutrient for crop development and production. Phosphate starvation response 1 (PHR1) acts as the central regulator for Pi-signaling and Pi-homeostasis in plants by binding to the cis-element PHR1 binding sequence (P1BS; GNATATNC). However, how phosphate starvation-induced gene expression is regulated remains obscure. In this work, we investigated the DNA binding affinity of the PHR1 ortholog OsPHR2 to its downstream target genes in Oryza sativa (rice). We confirmed that a combination of P1BS and P1BS-like motifs are essential for stable binding by OsPHR2. Furthermore, we report that variations in P1BS motif bases affected the binding affinity of OsPHR2 and that the highest affinity motif was GaATATtC (designated the A-T-type P1BS). We also found that a combination of two A-T-type P1BS elements in tandem, namely HA-P1BS, was very efficient for binding of OsPHR2. Using the cis-regulator HA-P1BS, we modified the promoters of Transporter Traffic Facilitator 1 (PHF1), a key factor controlling endoplasmic reticulum-exit of phosphate transporters to the plasma membrane, for efficient uptake of phosphorous in an energetically neutral way. Transgenic plants with the modified promoters showed significantly enhanced tolerance to low phosphate stress in both solution and soil conditions, which provides a new strategy for crop improvement to enhance tolerance of nutrient deficiency.

ZFX is a Strong Predictor of Poor Prognosis in Renal Cell Carcinoma.

BACKGROUND: This study was designed to assay the expression of zinc finger protein X-linked (ZFX) in renal cell carcinoma (RCC) tissues and evaluate the correlation between ZFX expression and prognosis of RCC patients. MATERIAL AND METHODS: The expressions of ZFX mRNA in 53 RCC tissues and 51 normal tissues were determined by quantitative real-time polymerase chain reaction (qRT-PCR). Immunohistochemistry (IHC) technology was used to measure the expression of ZFX protein. Then chi-square test was conducted to verify the association between ZFX expression and clinical parameters. Next, we explored the overall survival rate of RCC patients with Kaplan-Meier analysis. Finally, the correlation between ZFX expression and the prognosis of RCC patients was evaluated by Cox regression analysis. RESULTS: The qRT-PCR result showed that the ZFX was significantly up-regulated in RCC tissues. As for the IHC consequence, the positive rate of ZFX expression in RCC specimens was 79.2%, while that in the normal control tissues was only 17.6%. Chi-square test showed that ZFX expression shared no close relationship with age, sex, or smoking (P>0.05), but was tightly associated with TNM stage, tumor size, and lymph node metastasis (P<0.05). Kaplan-Meier analysis showed that patients with ZFX positive expression had higher mortality than those with negative expression (P<0.05). Cox regression analysis revealed that ZFX expression had tight correlation with prognosis of RCC patients (HR=4.997, P=0.045, 95%CI=1.033-24.180). CONCLUSIONS: Our findings show that ZFX could be considered as a predictor for prognosis of RCC patients.

Dendritic cells sequester antigenic epitopes for prolonged periods in the absence of antigen-encoding genetic information.

Studies with a number of viral systems have shown, on the basis of the ability of a host to prime naïve T cells, that viral antigens persist in the infected host well beyond complete clearance of the infection and even when viral antigen is undetectable by the most sensitive methods. This has led to a reasonable assumption that the antigen persists through persistence of antigen-encoding genetic information (DNA or RNA) that resides in the host at a subdetectable level. Here, we demonstrate that epitopes, or epitope precursors, of a model antigen (ovalbumin) persist in a host for prolonged periods (weeks), well beyond the time at which the intact antigen has disappeared, and in the complete absence of genetic information encoding it. Dendritic cells are shown to be the site of this epitope sequestration in vivo, as well as in cultures in vitro. For sequestration to occur, the uptaken antigen must be significantly large, that is, the epitope and its 18-mer precursor are not sequestered. Dendritic cells are shown to create an hsp90-dependent intracellular pool of epitopes or epitope precursors that continues to release epitopes for presentation on the major histocompatibility complex I molecules for prolonged periods. Demonstration of such long-term sequestration of antigenic epitopes inside dendritic cells presents new opportunities for stimulation of immune response against cancers and viruses.