Exploring the role of ubiquitin regulatory X domain family proteins in cancers: bioinformatics insights, mechanisms, and implications for therapy.

UBXD family (UBXDF), a group of proteins containing ubiquitin regulatory X (UBX) domains, play a crucial role in the imbalance of proliferation and apoptotic in cancer. In this study, we summarised bioinformatics proof on multi-omics databases and literature on UBXDF's effects on cancer. Bioinformatics analysis revealed that Fas-associated factor 1 (FAF1) has the largest number of gene alterations in the UBXD family and has been linked to survival and cancer progression in many cancers. UBXDF may affect tumour microenvironment (TME) and drugtherapy and should be investigated in the future. We also summarised the experimental evidence of the mechanism of UBXDF in cancer, both in vitro and in vivo, as well as its application in clinical and targeted drugs. We compared bioinformatics and literature to provide a multi-omics insight into UBXDF in cancers, review proof and mechanism of UBXDF effects on cancers, and prospect future research directions in-depth. We hope that this paper will be helpful for direct cancer-related UBXDF studies.

Space-time mapping on the sagittal axis in congenital blindness.

Previous evolutionary perspectives proposed that the space-time mapping on the sagittal axis originates from visuo-locomotion coupling when walking/running forward. Accordingly, the congenitally blind could not have developed a sagittal mental timeline if the latter depends on such a visuo-locomotion coupling. However, this conclusion was reached in only a single empirical study (Rinaldi et al. in J Exp Psychol General 147:444-450, 2018), and its theoretical underpinnings are not entirely convincing as locally static and continuous auditory input undergoes a relatively similar change as function of self-locomotion, but this type of sensory-locomotion coupling is spared even in congenital blindness. Therefore, the present study systematically explored whether the congenitally blind show space-time mappings on the sagittal axis using different paradigms in three experiments. In Experiment 1, using a typical implicit RT task, the congenitally blind showed the same preferred space-time mapping in the sagittal dimension as normally sighted participants did. In Experiment 2, this space-time mapping occurred even automatically when temporal relations were task-irrelevant in a naming task. In Experiment 3, in an explicit space-time mapping task, the congenitally blind were more likely to locate the past behind and the future in front of their bodies. Moreover, most blind participants used spatial metaphors for their space-time mapping on the sagittal axis. These results supported the conclusion that the congenitally blind have a sagittal mental timeline, and that their sensory-locomotion coupling experience was either more similar to that of sighted participants or not critical for the space-time mapping. The present study, thus, also helps to clarify the origin of the sagittal mental timeline.

Neural correlates of bribe-taking decision dilemma: An fNIRS study.

Bribe-taking decision is a social dilemma for individuals: the pursuit of economic self-interest vs. compliance with social norms. Despite the well-known existence of the conflict in deciding whether to accept bribes, little is known about its neural responses. Using functional near-infrared imaging (fNIRS) technology and the bribe-taking decision game (economic gambling game as a control condition), the current study dissociated the neural correlates of the different motivations in the bribery dilemma, as well as the inhibitory effect of social norms on bribery and its underlying brain mechanisms in supra-cortical regions. Findings revealed that if individuals are more motivated by economic interest, rejecting money (vs. accepting money) accompanies higher activity in the dorsolateral prefrontal cortex (DLPFC) and frontopolar cortex (FPC), which reflects impulse inhibition and decision evaluation; whereas, if individuals are more consider social norms, their DLPFC is more active when they accept bribes (vs. reject bribes), which reflects their fear of punishment. Additionally, the key brain region where social norms inhibit bribery involves the left DLPFC. The current findings contribute to the literature on the neural manifestations of corrupt decisions and provide some insights into the anti-corruption movement.

Does walking/running experience shape the sagittal mental time line?

A growing body of evidence suggested that time could be separately represented either on the lateral or sagittal axis. And the lateral mental time line has an origin associated with sensorimotor experience, e.g., reading/writing. However, it is still not clear whether the sagittal mental time line also originates from sensorimotor experience, e.g., walking/running. To address this question, we examined how the movement experience affected the space-time mapping on the lateral and sagittal axes using the virtual reality technique in two experiments. The results showed that the virtual movement experience had significant effects on the space-time mapping on the lateral axis (Experiment 1), but not on the sagittal axis (Experiment 2). This finding supported that the space-time mapping on the lateral axis does originate from sensorimotor experience, while the space-time mapping on the sagittal axis more likely originates from spatial metaphors in languages or other cultural experiences.

Role of Guanxi (interpersonal relationship) in bribe-taking behaviors: evidence from China.

Bribery, an illegal conspiracy between two transactional parties, has a wide range of destructive effects on society. From an interpersonal interaction perspective, we explored how Guanxi (interpersonal relationships, including direct and indirect ones) influences individuals, especially government officials' bribe-taking probability, using behavioral experiments and questionnaires. The findings suggested that direct Guanxi promoted individuals' acceptance of bribes (Study 1a), and indirect Guanxi had the same role and effect sizes (Study 1b). However, the mechanisms were slightly different. Government officials were more likely to accept bribes from family members and friends (direct Guanxi) (than strangers) because they had more trust and felt more responsible and obligated to help them (Study 2). However, accepting bribes from those who contacted them through their family or friends (indirect Guanxi) (vs. strangers) was only driven by trust (Study 3). The present study explores the lubricant role of Guanxi in corruption, extends the literature on why bribery occurs from a new perspective, and provides suggestions for fighting corruption.

Small numerosity advantage for sequential enumeration on RSVP stimuli: an object individuation-based account.

Although there is a large literature demonstrating rapid and accurate enumeration of small sets of simultaneously presented items (i.e., subitizing), it is unclear whether this small numerosity advantage (SNA) can also manifest in sequential enumeration. The present study thus has two aims: to establish a robust processing advantage for small numerosities during sequential enumeration using a rapid serial visual presentation (RSVP) paradigm, and to examine the underlying mechanism for a SNA in sequential enumeration. The results indicate that a small set of items presented in fast sequences can be enumerated accurately with a high precision and a SOA (stimulus onset asynchrony)-sensitive capacity limit, essentially generalizing the large literature on small numerosity advantage from spatial domain to temporal domain. A resource competition hypothesis was proposed and confirmed in further experiments. Specifically, sequential enumeration and other cognitive process, such as visual working memory (VWM), compete for a shared resource of object individuation by which items are segregated as individual entities. These results implied that the limited resource of object individuation can be allocated within time windows of flexible temporal scales during simultaneous and sequential enumerations. Taken together, the present study calls for attention to the dynamic aspect of the enumeration process and highlights the pivotal role of object individuation in underlying a wide range of mental operations, such as enumeration and VWM.

Bromo- and extraterminal domain protein inhibition improves immunotherapy efficacy in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) represents the majority of liver cancer and is the fourth most common cause of cancer-related death. Although advances in molecular targeted therapy have shown promise, none of these agents has yet demonstrated significant clinical benefit. Bromo- and extraterminal domain (BET) protein inhibitors have been considered potential therapeutic drugs for HCC but the biological activity remains unclear. This study found that BET protein inhibition did not effectively suppress the progression of HCC, using a transgenic HCC mouse model. Mechanistically, the BET protein inhibitor JQ1 upregulated the expression of programmed cell death-ligand 1 (PD-L1) on the plasma membrane in vivo and in vitro. Moreover, JQ1 enhanced the expression of Rab8A, which upregulated the expression of PD-L1 on the plasma membrane. This study also showed that JQ1 combined with anti-PD-L1 Ab effectively suppressed HCC progression, and this benefit was obtained by enhancing the activation and cytotoxic capabilities of CD8 T cells. These results revealed the crucial role and regulation of BET protein inhibition on the expression of PD-L1 in HCC. Thus, combining BET protein inhibition with immune checkpoint blockade offers an efficient therapeutic approach for HCC.

Analysis of LncRNA expression in cell differentiation.

Lineage-specific cell differentiation is a precise and coordinated biological process. To explore the roles of long noncoding RNA (lncRNA) in this process, the expression of polyA-minus RNAs was comparatively studied during the course of myocyte and adipocyte differentiation. In addition to identifying thousands of novel lncRNAs, distinct lncRNA profiles were revealed during lineage-specific differentiation, showing their active involvement in this process. This study further found that lncRNAs were organized in clusters and are co-regulated, constituting transcription open domains (TODs). In myocyte differentiation of C2C12 cells, loss-of-function screening identified three myogenic lncRNAs. Knockdown of their expression compromised not only the differentiation process, but also the essential signaling pathway. In addition to showing that lncRNAs are actively involved in cell differentiation, our results start to reveal a comprehensive signaling pathway, involving both protein and lncRNA factors.

Linc-RoR promotes c-Myc expression through hnRNP I and AUF1.

Linc-RoR was originally identified to be a regulator for induced pluripotent stem cells in humans and it has also been implicated in tumorigenesis. However, the underlying mechanism of Linc-RoR-mediated gene expression in cancer is poorly understood. The present study demonstrates that Linc-RoR plays an oncogenic role in part through regulation of c-Myc expression. Linc-RoR knockout (KO) suppresses cell proliferation and tumor growth. In particular, Linc-RoR KO causes a significant decrease in c-Myc whereas re-expression of Linc-RoR in the KO cells restores the level of c-Myc. Mechanistically, Linc-RoR interacts with heterogeneous nuclear ribonucleoprotein (hnRNP) I and AU-rich element RNA-binding protein 1 (AUF1), respectively, with an opposite consequence to their interaction with c-Myc mRNA. While Linc-RoR is required for hnRNP I to bind to c-Myc mRNA, interaction of Linc-RoR with AUF1 inhibits AUF1 to bind to c-Myc mRNA. As a result, Linc-RoR may contribute to the increased stability of c-Myc mRNA. Although hnRNP I and AUF1 can interact with many RNA species and regulate their functions, with involvement of Linc-RoR they would be able to selectively regulate mRNA stability of specific genes such as c-Myc. Together, these results support a role for Linc-RoR in c-Myc expression in part by specifically enhancing its mRNA stability, leading to cell proliferation and tumorigenesis.

Drug response to HER2 gatekeeper T798M mutation in HER2-positive breast cancer.

The gatekeeper T798M mutation in HER2 kinase domain has been observed to considerably shift drug sensitivity to HER2 in breast cancer therapy. Here, drug response of clinical tyrosine kinase inhibitors (TKIs) to the mutation was profiled using a synthetic biology protocol. It was found that TKIs can be grouped into three classes in terms of their response behavior to T798M mutation: class I inhibitors exhibit drug resistance upon the mutation, such as lapatinib, TAK-285 and AEE788; class II inhibitors are insensitive to the mutation, such as erlotinib and gefitinib; and class III inhibitors can be sensitized by the mutation, such as staurosporine. However, kinetic study indicated that the mutation has only a modest effect on the binding of substrate ATP to HER2. Binding free energy analysis revealed that the drug response is primarily determined by direct interaction between the kinase and inhibitors, but not by indirect kinase interaction with competitive ATP. This is different to the molecular mechanism of "generic" drug resistance conferring from EGFR gatekeeper T790M mutation, which is caused by increased ATP affinity upon the mutation. Structural analysis of kinase-inhibitor complexes unraveled that HER2 T798M mutation induces significant steric hindrance to class I inhibitors, but can establish additional nonbonded interactions for class III inhibitors.

MicroRNA-155 targets cyb561d2 in zebrafish in response to fipronil exposure.

MicroRNAs (miRNAs), which are a class of small noncoding RNAs, can modulate the expression of many protein-coding genes when an organism is exposed to an environmental chemical. We previously demonstrated that miR-155 was significantly downregulated in adult zebrafish (Danio rerio) in response to fipronil (5-amino-1-[2,6-dichloro-4-(trifluoromethyl) phenyl]-4-[(trifluoromethyl) sulphinyl]-1H-pyrazole-3-carbonitrile) exposure. However, the regulation of this miRNA's predicted target gene cyb561d2, which is a member of the cytochrome b561 (cyt b561) family involved in electron transfer, cell defence, and chemical stress, has not been experimentally validated to date. In this study, we evaluated the effects of fipronil on miR-155 and cyb561d2 in zebrafish. The expression of miR-155 was downregulated, whereas cyb561d2 was upregulated in both mRNA and protein level in a dose-dependent manner upon stimulation of fipronil. The dual luciferase report assay demonstrated that miR-155 interacted with cyb561d2 3'-untranslated regions (3'-UTR). The expression of cyb561d2 was reduced in both mRNA and protein levels when ZF4 cells were transfected with an miR-155 mimic, whereas its expression levels of both mRNA and protein were increased when endogenous miR-155 was inhibited by transfection with an miR-155 inhibitor. The results improved our understanding of molecular mechanism of toxicity upon fipronil exposure, and presents miR-155 as a potential novel toxicological biomarker for chemical exposure. © 2014 Wiley Periodicals, Inc. Environ Toxicol 31: 877-886, 2016.

Overexpression of ILK1 in breast cancer associates with poor prognosis.

Integrin-linked kinase 1 (ILK1), a member of the serine/threonine kinases, has been demonstrated to be associated with numerous biological and pathological processes. However, the role of ILK1 in breast cancer has not been thoroughly elucidated. The purpose of this study was to assess ILK1 expression and to explore its contribution to breast cancer. The ILK1 mRNA expression was measured by real-time quantitative reverse transcriptase-polymerase chain reaction. In addition, ILK1 expression was analyzed by immunohistochemistry in 163 clinicopathologically characterized breast cancer cases. The relationship between ILK1 expression and clinicopathological features was analyzed by appropriate statistics. Kaplan-Meier analysis and Cox proportional hazard regression models were used to investigate the correlation between ILK1 expression and prognosis of breast cancer patients. The relative mRNA expression of ILK1 was significantly higher in breast cancer tissues than in adjacent noncancerous tissues (P < 0.001). In addition, ILK1 expression was significantly correlated with tumor size (P = 0.016), grade (P = 0.024), stage (P = 0.029), lymph node metastases (P = 0.007), and estrogen receptor status (P = 0.002). Kaplan-Meier analysis indicated that patients with high ILK1 expression had poor overall survival (P < 0.001). Multivariate analysis showed that high ILK1 expression was an independent predictor of overall survival. In conclusion, our data suggest for the first time that the increased expression of ILK1 in breast cancer is associated significantly with aggressive progression and poor prognosis. ILK1 may be an important molecular marker for predicting the carcinogenesis, progression, and prognosis of breast cancer.

Development of a single-tube multiplex real-time PCR for detection and identification of five pathogenic targets by using melting-curve analysis with EvaGreen.

SYBR Green I (SG) is widely used in real-time PCR applications as an intercalating dye. Preferential binding of SG during PCR and inhibition of PCR often result in failure to detect multiple amplicons in multiplex reactions. In the present study, a novel single-tube, multiplex real-time PCR with EvaGreen dye (EG) was developed and evaluated for simultaneous detection of pathogenic targets by using five potato viruses as models. The PCR products obtained using five sets of specific primers were analyzed by melting curve analysis. The assay could specifically detect and differentiate the five potato viruses by producing a distinct peak for each amplification product and exhibited a high reproducibility with coefficients of variation from 0.01 to 0.25 %. Detection sensitivity of the assay ranged from 100 to 500 copies/µL for each virus. The results of this study demonstrate that multiplex real-time PCR and melting-curve analysis with EG is a sensitive, specific and inexpensive method for simultaneous detection of multiple pathogens.

RNA-seq identified a super-long intergenic transcript functioning in adipogenesis.

RNA transcripts are generally classified into polyA-plus and polyA-minus subgroups due to the presence or absence of a polyA tail at the 3' end. Even though a number of physiologically and pathologically important polyA-minus RNAs have been recently identified, a systematic analysis of the expression and function of these transcripts in adipogenesis is still elusive. To study the potential function of the polyA-minus RNAs in adipogenesis, a dynamic expressional profiling was performed in the induced differentiation of 3T3-L1 cells. In addition to identifying thousands of novel intergenic transcripts, differentiation-synchronized expression was characterized for many of them. Among these, several large intergenic transcripts were found to be upregulated by more than 19-fold during differentiation. Further study demonstrated a fat tissue-specific expression pattern for these regions and identified an adipogenesis-associated long non-coding RNA. Collectively, these lines of evidence contribute to the characterization of a super-long intergenic transcript functioning in adipogenesis.

The Emerging Roles of circRNAs in Papillary Thyroid Carcinoma: Molecular Mechanisms and Biomarker Potential.

Papillary thyroid carcinoma (PTC) is a common endocrine malignant tumor. The incidence of PTC has increased in the past decades and presents a younger trend. Accumulating evidence indicates that circular RNAs (circRNAs), featured with non-linear, closed-loop structures, play pivotal roles in tumorigenesis and regulate cell biological processes, such as proliferation, migration, and invasion, by acting as microRNA (miRNA) sponges. Additionally, due to their unique stability, circRNAs hold promising potential as diagnostic biomarkers and effective therapeutic targets for PTC treatment. In this review, we systematically arrange the expression level of circRNAs, related clinical characteristics, circRNA-miRNA-mRNA regulatory network, and molecular mechanisms. Furthermore, related signaling pathways and their potential ability of diagnostic biomarkers and therapeutic targets are discussed, which might provide a new strategy for PTC diagnosis, monitoring, and prognosis.

Regulation of LncRNAs and microRNAs in neuronal development and disease.

Non-coding RNAs (ncRNAs) are RNAs that do not encode proteins but play important roles in regulating cellular processes. Multiple studies over the past decade have demonstrated the role of microRNAs (miRNAs) in cancer, in which some miRNAs can act as biomarkers or provide therapy target. Accumulating evidence also points to the importance of long non-coding RNAs (lncRNAs) in regulating miRNA-mRNA networks. An increasing number of ncRNAs have been shown to be involved in the regulation of cellular processes, and dysregulation of ncRNAs often heralds disease. As the population ages, the incidence of neurodegenerative diseases is increasing, placing enormous pressure on global health systems. Given the excellent performance of ncRNAs in early cancer screening and treatment, here we attempted to aggregate and analyze the regulatory functions of ncRNAs in neuronal development and disease. In this review, we summarize current knowledge on ncRNA taxonomy, biogenesis, and function, and discuss current research progress on ncRNAs in relation to neuronal development, differentiation, and neurodegenerative diseases.

Diagnostic implications of lncRNA NORAD in breast cancer.

This study aimed to assess the expression levels of non-coding RNA activated by DNA damage (NORAD) in the cells, tissues, and serum of breast cancer (BRCA) patients and benign breast nodules and investigate its association with clinicopathological characteristics and prognosis in BRCA. NORAD was analyzed using TCGA-BRCA, GSE77308, Cellminer, and Sangerbox databases, revealing its significance in BRCA prognosis, immune microenvironment, and cell function. Serum samples from 38 BRCA patients, 80 patients with benign breast nodules (50 fibroadenoma and 30 breast adenosis cases), and 42 healthy individuals were collected from Zhejiang Xiaoshan Hospital. NORAD expression was quantified using quantitative reverse transcription PCR (RT-qPCR). Differential NORAD expression between benign and malignant breast nodules and its relationship to clinicopathological characteristics were assessed. NORAD demonstrated elevated expression in BRCA patient serum compared to healthy individuals and those with benign breast nodules (P < 0.05). Moreover, its expression correlated with TNM-stage, lymph node metastasis, and luminal classification. These findings highlight the elevated NORAD expression in BRCA patient serum and its correlation with clinicopathological characteristics, providing insights into its potential as a diagnostic biomarker or therapeutic target.

Machine learning modeling and prognostic value analysis of invasion-related genes in cutaneous melanoma.

In this study, we aimed to develop an invasion-related risk signature and prognostic model for personalized treatment and prognosis prediction in skin cutaneous melanoma (SKCM), as invasion plays a crucial role in this disease. We identified 124 differentially expressed invasion-associated genes (DE-IAGs) and selected 20 prognostic genes (TTYH3, NME1, ORC1, PLK1, MYO10, SPINT1, NUPR1, SERPINE2, HLA-DQB2, METTL7B, TIMP1, NOX4, DBI, ARL15, APOBEC3G, ARRB2, DRAM1, RNF213, C14orf28, and CPEB3) using Cox and LASSO regression to establish a risk score. Gene expression was validated through single-cell sequencing, protein expression, and transcriptome analysis. Negative correlations were discovered between risk score, immune score, and stromal score using ESTIMATE and CIBERSORT algorithms. High- and low-risk groups exhibited significant differences in immune cell infiltration and checkpoint molecule expression. The 20 prognostic genes effectively differentiated between SKCM and normal samples (AUCs >0.7). We identified 234 drugs targeting 6 genes from the DGIdb database. Our study provides potential biomarkers and a risk signature for personalized treatment and prognosis prediction in SKCM patients. We developed a nomogram and machine-learning prognostic model to predict 1-, 3-, and 5-year overall survival (OS) using risk signature and clinical factors. The best model, Extra Trees Classifier (AUC = 0.88), was derived from pycaret's comparison of 15 classifiers. The pipeline and app are accessible at https://github.com/EnyuY/IAGs-in-SKCM.

Biomarker of Pulmonary Inflammatory Response in LUAD: miR-584-5p Targets RAB23 to Suppress Inflammation Induced by LPS in A549 Cells.

BACKGROUND: Pulmonary inflammatory response (PIR) is one of the prognostic risk factors of lung adenocarcinoma (LUAD), with a high mortality rate. OBJECTIVES: This study aims to investigate prognostic microRNA (miRNA) to improve clinical prognosis prediction and postoperative inflammation treatment in LUAD patients. METHODS: About 201 differentially expressed microRNAs (DE-miRNAs) in LUAD were mined by differential analysis. Univariate/multivariate Cox analyses established and validated prognostic risk miRNAs in TCGA-LUAD. KEGG and GO were used to link risk signatures and biological functions. After 48 hours of exposure to 50 ng/mL LPS, the miR-584-5p/RAB23 regulatory network was verified in qRT-PCR, Western Blotting, and the Luciferase Reporter Assay in A549 cells. RESULTS: MiR-584-5p and miR-101-3p were validated as riskscore correlated with LUAD patients' 1-year survival (p < 0.001) and participate in multiple inflammation-related pathways. RAB23, a RAS oncogene, is involved in inflammatory MAPK signaling. Evidence suggests that miR-584-5p regulates inflammation in LUAD by targeting RAB23. A549 cells were transfected with the mimic and inhibitor of miR-584-5p, confirming the negative regulatory relationship between miR-584-5p and RAB23. In the A549 induced by LPS, either over-expression of miR-584-5p or knock-down of RAB23 expression decreased the expression of inflammatory factors and increased cell viability. CONCLUSION: Prognostic-related risk miR-584-5p can regulate the expression of RAB23 at both the mRNA and protein levels, thereby influencing the development of a PIR in LUAD. This will have significant implications for the clinical prognosis prediction and therapy decision-making of LUAD patients with PIR.

Characterization of a carcinogenesis-associated long non-coding RNA.

A negative selection strategy was used in the present study to isolate long polyA-minus RNAs from the total transcriptome and a long non-coding RNA named Yiya was identified. Yiya is a 1.9 kb long intergenic ncRNA gene mapped to chromosome 1q41, a well-established cancer susceptibility locus. Expression profiling revealed a general and regulated expression pattern of Yiya in major tissues, and more interestingly, identified elevated mRNA levels in different cancers. Quantitative analysis further demonstrated a dynamic regulation of Yiya expression in cell cycle progression, suggesting that it was involved in cell cycle regulation. Supporting this, overexpression of Yiya promotes cell cycle progression at the G1/S transition, therefore identifying Yiya as a cell-cycle-associated long non-coding RNA.