Interplay between orphan nuclear receptors and androgen receptor-dependent or-independent growth signalings in prostate cancer

GraphPath: a graph attention model for molecular stratification with interpretability based on the pathway-pathway interaction network

MOTIVATION

Studying the molecular heterogeneity of cancer is essential for achieving personalized therapy. At the same time, understanding the biological processes that drive cancer development can lead to the identification of valuable therapeutic targets. Therefore, achieving accurate and interpretable clinical predictions requires paramount attention to thoroughly characterizing patients at both the molecular and biological pathway levels.

RESULTS

Here, we present GraphPath, a biological knowledge-driven graph neural network with multi-head self-attention mechanism that implements the pathway-pathway interaction network. We train GraphPath to classify the cancer status of patients with prostate cancer based on their multi-omics profiling. Experiment results show that our method outperforms P-NET and other baseline methods. Besides, two external cohorts are used to validate that the model can be generalized to unseen samples with adequate predictive performance. We reduce the dimensionality of latent pathway embeddings and visualize corresponding classes to further demonstrate the optimal performance of the model. Additionally, since GraphPath's predictions are interpretable, we identify target cancer-associated pathways that significantly contribute to the model's predictions. Such a robust and interpretable model has the potential to greatly enhance our understanding of cancer's biological mechanisms and accelerate the development of targeted therapies.

AVAILABILITY AND IMPLEMENTATION

https://github.com/amazingma/GraphPath.

MALAT1 promotes FOXA1 degradation by competitively binding to miR-216a-5p and enhancing neuroendocrine differentiation in prostate cancer

OBJECTIVES

Prostate cancer (PC) is a leading cause of cancer-related death in males worldwide. Neuroendocrine differentiation (NED) is a feature of PC that often goes undetected and is associated with poor patient outcomes. Long non-coding RNAs (lncRNAs), microRNAs (miRNAs/miRs), and messenger RNAs (mRNAs) play important roles in the development and progression of PC.

METHODS

In this study, we used transcriptome sequencing and bioinformatics analysis to identify key regulators of NED in PC. Specifically, we examined the expression of PC-related lncRNAs, miRNAs, and mRNAs in PC cells and correlated these findings with NED phenotypes.

RESULTS

Our data revealed that metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and zinc finger protein 91 (ZFP91) were upregulated in PC, while miR-216a-5p was down-regulated. Ectopic expression of MALAT1 induced NED and promoted malignant phenotypes of PC cells. Furthermore, we found that MALAT1 competitively bound to miR-216a-5p, upregulated ZFP91, and promoted the degradation of forkhead box A1 (FOXA1), a key gene involved in NED of PC.

CONCLUSION

Taken together, these results suggest that MALAT1 plays an oncogenic role in NED and metastasis of PC via the miR-216a-5p/ZFP91/FOXA1 pathway. Our study highlights the potential of targeting this pathway as a novel therapeutic strategy for PC.

EWS/FLI1 Characterization, Activation, Repression, Target Genes and Therapeutic Opportunities in Ewing Sarcoma

Despite their clonal origins, tumors eventually develop into complex communities made up of phenotypically different cell subpopulations, according to mounting evidence. Tumor cell-intrinsic programming and signals from geographically and temporally changing microenvironments both contribute to this variability. Furthermore, the mutational load is typically lacking in childhood malignancies of adult cancers, and they still exhibit high cellular heterogeneity levels largely mediated by epigenetic mechanisms. Ewing sarcomas represent highly aggressive malignancies affecting both bone and soft tissue, primarily afflicting adolescents. Unfortunately, the outlook for patients facing relapsed or metastatic disease is grim. These tumors are primarily fueled by a distinctive fusion event involving an FET protein and an ETS family transcription factor, with the most prevalent fusion being EWS/FLI1. Despite originating from a common driver mutation, Ewing sarcoma cells display significant variations in transcriptional activity, both within and among tumors. Recent research has pinpointed distinct fusion protein activities as a principal source of this heterogeneity, resulting in markedly diverse cellular phenotypes. In this review, we aim to characterize the role of the EWS/FLI fusion protein in Ewing sarcoma by exploring its general mechanism of activation and elucidating its implications for tumor heterogeneity. Additionally, we delve into potential therapeutic opportunities to target this aberrant fusion protein in the context of Ewing sarcoma treatment.

Screening of Endocrine Disrupting Potential of Surface Waters via an Affinity-Based Biosensor in a Rural Community in the Yellow River Basin, China

Overcoming the limitations of traditional analytical methods and developing technologies to continuously monitor environments and produce a comprehensive picture of potential endocrine-disrupting chemicals (EDCs) has been an ongoing challenge. Herein, we developed a portable nuclear receptor (NR)-based biosensor within 90 min to perform highly sensitive analyses of a broad range of EDCs in environmental water samples. Based on the specific binding of the fluorescence-labeled NRs with their ligands, the receptors were attached to the EDC-functionalized fiber surface by competing with EDCs in the samples. The biosensor emitted fluorescence due to the evanescent wave excitation, thereby resulting in a turn-off sensing mode. The biosensor showed a detection limit of 5 ng/L E₂-binding activity equivalent (E₂-BAE) and 93 ng/L T₃-BAE. As a case study, the biosensor was used to map the estrogenic binding activities of surface waters obtained from a rural community in the Yellow River basin in China. When the results obtained were compared with those from the traditional yeast two-hybrid bioassay, a high correlation was observed. It is anticipated that the good universality and versatility exhibited by this biosensor for various EDCs, which is achieved by using different NRs, will significantly promote the continuous assessment of global EDCs.

N-glycosylation of GDF15 abolishes its inhibitory effect on EGFR in AR inhibitor-resistant prostate cancer cells

Castration-resistance of prostate cancer is one of the most challenging clinical problems. In the present study, we have performed proteomics and glycomics using LNCaP model. Growth differentiation factor-15 (GDF15) level is increased in androgen receptor (AR) inhibitor-resistant cells and the inhibitory effect of GDF15 on epithelial growth factor receptor (EGFR) pathway is relieved by GDF15 N70 glycosylation. Interference of GDF15 (siRNA or N70Q dominant negative) or EGFR pathway (inhibitor or siRNA for EGFR, SRC or ERK) decreases the resistant-cell survival in culture and tumor growth in mice. Our study reveals a novel regulatory mechanism of prostate cancer AR inhibitor resistance, raises the possibility of AR/SRC dual-targeting of castration-resistance of prostate cancer, and lays foundation for the future development of selective inhibitors of GDF15 glycosylation.

5-Hydroxymethylfurfural Exerts Negative Effects on Gastric Mucosal Epithelial Cells by Inducing Oxidative Stress, Apoptosis, and Tight Junction Disruption

5-Hydroxymethylfurfural (5-HMF) is a processing byproduct present in foods that are consumed daily by humans, and the diet is the principal route for human exposure to it. However, its adverse effects on gastric epithelial cells are not fully understood. Based on the half inhibitory concentration value, concentrations of HMF of 2, 4, 8, and 16 mM were selected for this study. After 5-HMF treatment for 24 h, the number of living cells decreased to 89.61 ± 0.48, 77.30 ± 0.57, 58.75 ± 0.36, and 19.61 ± 0.40% of the control, respectively. Apoptosis activated through both the death receptor and mitochondrial pathways was confirmed to be the primary mode of HMF-induced cell death. Further analysis revealed that the reactive oxygen species (ROS) levels in GES-1 cells increased 1.7-6.5 fold after exposure to 5-HMF. Moreover, the inhibition of ROS by N-acetylcysteine blocked HMF-induced apoptosis and cell proliferation suppression, indicating that oxidative stress was important in HMF-induced apoptosis. Besides, after 5-HMF treatment, the gene expressions of occludin and ZO-1 were reduced by 1.1-3.4 fold and 2.0-9.4 fold, respectively. The cell surface morphology and tight junction-related protein expression analysis also revealed the destructive effect of 5-HMF on tight junction integrity. Our research highlights a potential mechanism of HMF-induced toxicity in GES-1 cells and provides additional information on the health risks of 5-HMF exposure to the human gastric epithelium.

Mesenchymal stem cells: ideal seeds for treating diseases

Mesenchymal stem cells (MSCs), a kind of multipotent stem cells with self-renewal ability and multi-differentiation ability, have become the “practical stem cells” for the treatment of diseases. MSCs have immunomodulatory properties and can be used to treat autoimmune diseases, such as systemic lupus erythematosus (SLE) and Crohn’s disease. MSCs also can be used in cancer and aging. At present, many clinical experiments are using MSCs. MSCs can reduce the occurrence of inflammation and apoptosis of tissue cells, and promote the proliferation of endogenous tissue and organ cells, so as to achieve the effect of repairing tissue and organs. MSCs presumably also play an important role in Corona Virus Disease 2019 (COVID-19) infection.

Role of Microgliosis and NLRP3 Inflammasome in Parkinson's Disease Pathogenesis and Therapy

Parkinson's disease (PD) is a neurodegenerative disorder marked primarily by motor symptoms such as rigidity, bradykinesia, postural instability and resting tremor associated with dopaminergic neuronal loss in the Substantia Nigra pars compacta (SNpc) and deficit of dopamine in the basal ganglia. These motor symptoms can be preceded by pre-motor symptoms whose recognition can be useful to apply different strategies to evaluate risk, early diagnosis and prevention of PD progression. Although clinical characteristics of PD are well defined, its pathogenesis is still not completely known, what makes discoveries of therapies capable of curing patients difficult to be reached. Several theories about the cause of idiopathic PD have been investigated and among them, the key role of inflammation, microglia and the inflammasome in the pathogenesis of PD has been considered. In this review, we describe the role and relation of both the inflammasome and microglial activation with the pathogenesis, symptoms, progression and the possibilities for new therapeutic strategies in PD.