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This document is a retraction note from the journal Cancer Cell International. The article titled "Circular RNA ITCH suppressed prostate cancer progression by increasing HOXB13 expression via spongy miR-17-5p" has been retracted at the request of the corresponding author. The retraction was prompted by concerns about image overlap in several figures of the article. The authors were unable to retrieve the data from a third-party biological company, leading to a loss of confidence in the presented data. The retraction was agreed upon by all authors. [Extracted from the article]

Endoplasmic reticulum (ER) stress mediates Cd-caused germ cell apoptosis in testis. The effects of 4-phenylbutyric acid (PBA), a classical chaperone, were investigated on Cd-induced apoptosis in mouse GC-1 spermatogonia cells. The cells were pretreated with PBA before Cd exposure. TUNEL and flow cytometry assays were applied to determine apoptosis. Some key biomarkers of ER stress were analyzed using RT-PCR and western blot. as expected, the apoptotic cells exposed to Cd apparently increased. The mRNA and protein expression levels of GRP78 and ATF6α, were elevated in the Cd groups. Additional experiments displayed that Cd notably increased IRE1α and JNK phosphorylation, and upregulated XBP-1 mRNA and protein expression. Moreover, p-eIF2α and CHOP expressions were clearly elevated in the Cd groups. Interestingly, PBA almost completely inhibited ER stress and protected spermatogonia against apoptosis induced by Cd. PBA alleviated Cd-induced ER stress and spermatogonia apoptosis, and may have the therapeutic role in Cd-induced male reproductive toxicity. • CdCl 2 induced spermatogonia apoptosis in vitro. • CdCl 2 triggered spermatogonia ER stress. • 4-PBA alleviated CdCl 2 -induced spermatogonia apoptosis. [ABSTRACT FROM AUTHOR]

• 1-MCP + ethylene absorbent (EA) treatment increase shelf-life of 'Fenjiao' banana. • EA does not have the negative effect on the ripening of 'Fenjiao' banana. • 1-MCP+EA repress the enzymes activity related to fruit softening. • 1-MCP +EA modulate the expression of gene related of ripening. • 1-MCP +EA treatment is easy to promote and apply in the banana industry. The 'Fenjiao' banana (Musa ABB Pisang Awak) has a high commercial and nutritional value and is harvested when it is highly plump at between 85 and 90 % commercial maturity. The fruit are less angular at this stage. However, these fruit soften rapidly after harvest. 1-Methylcyclopropene (1-MCP) significantly delays ripening, but it can cause ripening disorders when used improperly. Ethylene absorbent (EA) is also widely used to increase the postharvest life of fruit, but it has less of an effect on 'Fenjiao' banana. This study was conducted to optimize the concentrations of 1-MCP combined with EA to increase the shelf life of these bananas. The results showed that a low concentration of 1-MCP (7 g L−1) combined with EA (2 g kg−1) significantly prolonged the shelf life of the 'Fenjiao' banana and maintained its high quality. The combination of 1-MCP and EA repressed the activities of 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase, ACC synthase, pectin methylesterase, polygalacturonase and pectate lyase in the peel and pulp of 'Fenjiao' banana, as well as the corresponding levels of expression of MbACS1, MbACO1, MbPG1, MbPL1 , except for MbPME1 , which are induced by 1-MCP. This study provides a useful technique for preserving 'Fenjiao' fruit with a study on its possible physiological mechanism, which could be applied in the postharvest production of 'Fenjiao' banana. [ABSTRACT FROM AUTHOR]

Simple Summary: RNA pseudouridine modifications are present in various RNAs across different organisms and play crucial roles in regulating gene expression during biological processes. The accurate identification of pseudouridine sites within RNA sequences is essential for understanding their functional mechanisms. This study proposes a novel ensemble learning predictor named PseUpred-ELPSO, which accurately predicts RNA pseudouridine sites. The predictor demonstrates excellent performance in both cross-validation and independent testing. A user-friendly web server has been established, making it a powerful tool for pseudouridine site identification. RNA pseudouridine modification exists in different RNA types of many species, and it has a significant role in regulating the expression of biological processes. To understand the functional mechanisms for RNA pseudouridine sites, the accurate identification of pseudouridine sites in RNA sequences is essential. Although several fast and inexpensive computational methods have been proposed, the challenge of improving recognition accuracy and generalization still exists. This study proposed a novel ensemble predictor called PseUpred-ELPSO for improved RNA pseudouridine site prediction. After analyzing the nucleotide composition preferences between RNA pseudouridine site sequences, two feature representations were determined and fed into the stacking ensemble framework. Then, using five tree-based machine learning classifiers as base classifiers, 30-dimensional RNA profiles are constructed to represent RNA sequences, and using the PSO algorithm, the weights of the RNA profiles were searched to further enhance the representation. A logistic regression classifier was used as a meta-classifier to complete the final predictions. Compared to the most advanced predictors, the performance of PseUpred-ELPSO is superior in both cross-validation and the independent test. Based on the PseUpred-ELPSO predictor, a free and easy-to-operate web server has been established, which will be a powerful tool for pseudouridine site identification. [ABSTRACT FROM AUTHOR]

Background: Clear cell renal cell carcinoma (ccRCC) is associated with a high prevalence of cancer-related deaths. The survival rates of patients are significantly lower in late-stage ccRCC than in early-stage ccRCC, due to the spread and metastasis of late-stage ccRCC, surgery has not reached the goal of radical cure, and the effect of traditional radiotherapy and chemotherapy is poor. Thus, it is crucial to accurately assess the prognosis and provide personalized treatment at an early stage in ccRCC. This study aims to develop an efficient nomogram model for stratifying and predicting the survival of ccRCC patients based on tumor stage. Methods: We first analyzed the microarray expression data of ccRCC patients from the Gene Expression Omnibus (GEO) database and categorized them into two groups based on the disease stage (early and late stage). Subsequently, the GEO2R tool was applied to screen out the genes that were highly expressed in all GEO datasets. Finally, the clinicopathological data of the two patient groups were obtained from The Cancer Genome Atlas (TCGA) database, and the differences were compared between groups. Survival analysis was performed to evaluate the prognostic value of candidate genes (PSAT1, PRAME, and KDELR3) in ccRCC patients. Based on the screened gene PSAT1 and clinical parameters that were significantly associated with patient prognosis, we established a new nomogram model, which was further optimized to a single clinical variable-based model. The expression level of PSAT1 in ccRCC tissues was further verified by qRT-PCR, Western blotting, and immunohistochemical analysis. Results: The datasets GSE73731, GSE89563, and GSE150404 identified a total of 22, 89, and 120 over-expressed differentially expressed genes (DEGs), respectively. Among these profiles, there were three genes that appeared in all three datasets based on different stage groups. The overall survival (OS) of late-stage patients was significantly shorter than that of early-stage patients. Among the three candidate genes (PSAT1, PRAME, and KDELR3), PSAT1 was shown to be associated with the OS of patients with late-stage ccRCC. Multivariate Cox regression analysis showed that age, tumor grade, neoadjuvant therapy, and PSAT1 level were significantly associated with patient prognosis. The concordance indices were 0.758 and 0.725 for the 3-year and 5-year OS, respectively. The new model demonstrated superior discrimination and calibration compared with the single clinical variable model. The enhancer PSAT1 used in the new model was shown to be significantly overexpressed in tissues from patients with late-stage ccRCC, as demonstrated by the mRNA level, protein level, and pathological evaluation. Conclusion: The new prognostic prediction nomogram model of PSAT1 and clinicopathological variables combined was thus established, which may provide a new direction for individualized treatment for different-stage ccRCC patients. [ABSTRACT FROM AUTHOR]

Cadmium (Cd) is a common pollutant with reproductive toxicity. Our previous study revealed that Cd triggered spermatogonia ferroptosis. However, the underlying mechanisms remain unclear. Nuclear receptor coactivator 4 (NCOA4) mediates ferritinophagy and specific degradation of ferritin through lysosomes, resulting in the release of ferrous ions. Excessive autophagy can lead to ferroptosis. This study investigated the role of autophagy in Cd-triggered ferroptosis using GC-1 spermatogonial (spg) cells which exposed to CdCl 2 (5 μM, 10 μM, or 20 μM) for 24 without/with CQ. The cells which transfected with Ncoa4-siRNA were used to explore the role of NCOA4-mediated ferritinophagy in Cd-triggered ferroptosis. The results revealed that Cd caused mitochondrial swelling, rupture of cristae, and vacuolar-like changes. The Cd-treated cells exhibited more autophagosomes. Simultaneously, Cd increased intracellular iron, reactive oxygen species, and malondialdehyde concentrations while decreasing glutathione content and Superoxide Dismutase-2 activity. Moreover, Cd upregulated mRNA levels of ferritinophagy-associated genes (Ncoa4, Lc3b and Fth1), as well as enhanced protein expression of NCOA4, LC3B, and FTH1. While Cd decreased the mRNA and protein expression of p62/SQSTM1. These results showed that Cd caused ferritinophagy and ferroptosis. The use of chloroquine to inhibit autophagy ameliorated Cd-induced iron overload and ferroptosis. Moreover, Ncoa4 knockdown in spermatogonia significantly reduced intracellular iron concentration and alleviated Cd-triggered ferroptosis. In conclusion, our findings demonstrate that Cd activates the ferritinophagy pathway mediated by NCOA4, resulting in iron accumulation through ferritin degradation. This causes oxidative stress, ultimately initiating ferroptosis in spermatogonia. Our results may provide new perspectives and potential strategies for preventing and treating Cd-induced reproductive toxicity. [Display omitted] • Cd causes iron overload and triggers ferroptosis in spermatogonia. • Cd induces ferritinophagy in spermatogonia. • CQ antagonizes against Cd-caused iron overload in spermatogonia. • NCOA4-mediated ferritinophagy participates in Cd-triggered ferroptosis. [ABSTRACT FROM AUTHOR]

• Urinary extracellular vesicles miRNAs' expression pattern of RCC patients was examined. • uEV miR-135b-5p, miR-196b-5p, miR-200c-3p, and miR-203a-3p were upregulated in RCC patients. • A three-uEV miRNA panel could discriminate RCC patients from controls with the AUC of 0.785. • An uEV-miRNA panel could also distinguish early-stage RCC patients with the AUC of 0.786. The potential of urinary-derived extracellular vesicle (uEV) microRNAs (miRNAs) as noninvasive molecular biomarkers for identifying early-stage renal cell carcinoma (RCC) patients is rarely explored. The present study aims to explore the possibility of uEV miRNAs as novel molecular biomarkers for distinguishing early-stage RCC. uEVs were extracted by ExoQuick-TC™ kit and miRNA concentrations were measured by RT-qPCR. ROC curves and bioinformatics analysis were employed to predict the diagnostic efficacy and regulatory mechanisms of dysregulated miRNAs. Through a multiphase case-control study on uEV miRNAs screening, training, and validation in RCC cells (ACHN, Caki-1) and control cells (HK-2) and in uEVs of 125 RCC patients and 128 age- and sex-matched controls, we successfully identified four uEVs miRNAs (miR-135b-5p, miR-196b-5p, miR-200c-3p, and miR-203a-3p) were significantly and stably upregulated in RCC in vitro and in vivo. When adjusted with estimated glomerular filtration rate (eGFR), the AUC of the three-uEV miRNA panel (miR-135b-5p, miR-200c-3p, and miR-203a-3p) was 0.785 (95 % CI = 0.729–0.842, P < 0.0001) for discriminating RCC patients from controls. Notably, this panel exhibited similar performance in distinguishing early-stage (stage Ⅰ) RCC patients, with an AUC of 0.786 (95 %CI = 0.727–0.844, P < 0.0001). Bioinformatics analysis predicted that candidate miRNAs were involved in cancer progressing. Our study identified a four uEV miRNAs panel (miR-135b-5p, miR-196b-5p, miR-200c-3p, and miR-203a-3p) may serve as an auxiliary noninvasive indication of early-stage RCC. [ABSTRACT FROM AUTHOR]