Exosomal miR-4488 and miR-1273g-5p inhibit the epithelial-mesenchymal transition of transforming growth factor β2-mediated retinal pigment epithelial cells by targeting ATP-binding cassette A4

A deep learning method to integrate extracelluar miRNA with mRNA for cancer studies

MOTIVATION

Extracellular miRNAs (exmiRs) and intracellular mRNAs both can serve as promising biomarkers and therapeutic targets for various diseases. However, exmiR expression data is often noisy, and obtaining intracellular mRNA expression data usually involves intrusive procedures. To gain valuable insights into disease mechanisms, it is thus essential to improve the quality of exmiR expression data and develop noninvasive methods for assessing intracellular mRNA expression.

RESULTS

We developed CrossPred, a deep-learning multi-encoder model for the cross-prediction of exmiRs and mRNAs. Utilizing contrastive learning, we created a shared embedding space to integrate exmiRs and mRNAs. This shared embedding was then used to predict intracellular mRNA expression from noisy exmiR data and to predict exmiR expression from intracellular mRNA data. We evaluated CrossPred on three types of cancers and assessed its effectiveness in predicting the expression levels of exmiRs and mRNAs. CrossPred outperformed the baseline encoder-decoder model, exmiR or mRNA-based models, and variational autoencoder models. Moreover, the integration of exmiR and mRNA data uncovered important exmiRs and mRNAs associated with cancer. Our study offers new insights into the bidirectional relationship between mRNAs and exmiRs.

AVAILABILITY AND IMPLEMENTATION

The datasets and tool are available at https://doi.org/10.5281/zenodo.13891508.

Linking ABC transporters to the hallmarks of cancer

Human ATP-binding cassette (ABC) transporters are ubiquitously expressed and transport a broad range of endogenous and xenobiotic substrates across extra- and intracellular membranes. Mutations in ABC genes cause 21 monogenic diseases, and polymorphisms in these genes are associated with susceptibility to complex diseases. ABC transporters also play a major role in drug bioavailability, and they mediate multidrug resistance in cancer. At least 13 ABC transporters were shown to be involved in drug resistance in vitro. In the past decade, efforts have been made to elucidate their roles in tumor biology. Herein, we explore their involvement in tumorigenesis, focusing on the hallmarks of cells as they make their way from normalcy to neoplastic growth states.

The role and application of vesicles in triple-negative breast cancer: Opportunities and challenges

Extracellular vesicles (EVs) carry DNA, RNA, protein, and other substances involved in intercellular crosstalk and can be used for the targeted delivery of drugs. Triple-negative breast cancer (TNBC) is rich in recurrent and metastatic disease and lacks therapeutic targets. Studies have proved the role of EVs in the different stages of the genesis and development of TNBC. Cancer cells actively secrete various biomolecules, which play a significant part establishing the tumor microenvironment via EVs. In this article, we describe the roles of EVs in the tumor immune microenvironment, metabolic microenvironment, and vascular remodeling, and summarize the application of EVs for objective delivery of chemotherapeutic drugs, immune antigens, and cancer vaccine adjuvants. EVs-based therapy may represent the next-generation tool for targeted drug delivery for the cure of a variety of diseases lacking effective drug treatment.

DCLRE1A Contributes to DNA Damage Repair and Apoptosis in Age-Related Cataracts by Regulating the lncRNA/miRNA/mRNA Axis

PURPOSE

Age-related cataract (ARC) is associated with the deregulation of transcription and defects in DNA repair in lens epithelial cells (LECs). DCLRE1A acted in DNA interstrand cross-links pathway to improve DNA replication and transcription. The aim of this study was to examined the further regulatory effect on DCLRE1A in the lncRNA-miRNA-mRNA network using a cell model of DCLRE1A overexpression (OE-DCLRE1A) in LECs.

METHODS

The expression level of DCLRE1A in ARC tissues and SRA01/04 cells after H2O2 treatment was measured as protein and mRNA by qRT-PCR and Western Blot(WB). CCK8, and TUNEL assays detected the change in cell viability and apoptosis, respectively. Furthermore, Immunofluorescence assays detect the expression of DNA damaged and repair marker proteins after OE-DCLRE1A. The global expression profiles of lncRNAs, miRNAs, and mRNAs were determined using high-throughput sequencing. KEGG and GO enrichment analysis disclose the possible function of differentially expressed (DE) lncRNA, miRNA, and mRNA.

RESULTS

The protein and mRNA of DCLRE1A were decreased in the anterior capsule of ARC and SRA01/04 cells treated by H2O2. OE-DCLRE1A improved damaged-DNA repair and enhanced cell viability against apoptosis after H2O2 treatment. Furthermore, we demonstrated the DE-molecules between the OE-DCLRE1A and control groups including 595 DE-lncRNAs, 221 DE-miRNAs, and 4718 DE-mRNAs. Next, bioinformatics analysis not only found that the DE-mRNAs are mainly involved in DNA repair-related signaling pathways after OE-DCLRE1A, but also screened two lncRNA-miRNA-mRNA networks focusing on DNA damage activated by OE-DCLRE1A, which involved 2 lncRNAs, 2 miRNAs, and 53 mRNAs.

CONCLUSION

We revealed that DCLRE1A activated the lncRNA/miRNA/DNA-repair network to take part in DNA repair processes, which not only represents a new regulatory mechanism employed by DCLRE1A but also uncovers the screening lncRNA may hold potential therapeutic values in ARC formation. However, these conclusions will need to be confirmed by future studies in vitro and in vivo models.

Salivary Exosomes in Health and Disease: Future Prospects in the Eye

Exosomes are a group of vesicles that package and transport DNA, RNA, proteins, and lipids to recipient cells. They can be derived from blood, saliva, urine, and/or other biological tissues. Their impact on several diseases, such as neurodegenerative, autoimmune, and ocular diseases, have been reported, but not fully unraveled. The exosomes that are derived from saliva are less studied, but offer significant advantages over exosomes from other sources, due to their accessibility and ease of collection. Thus, their role in the pathophysiology of diseases is largely unknown. In the context of ocular diseases, salivary exosomes have been under-utilized, thus creating an enormous gap in the literature. The current review discusses the state of exosomes research on systemic and ocular diseases and highlights the role and potential of salivary exosomes as future ocular therapeutic vehicles.

ABC transporters affects tumor immune microenvironment to regulate cancer immunotherapy and multidrug resistance

Multidrug resistance (MDR) is the phenomenon in which cancer cells simultaneously develop resistance to a broad spectrum of structurally and mechanistically unrelated drugs. MDR severely hinders the effective treatment of cancer and is the major cause of chemotherapy failure. ATP-binding cassette (ABC) transporters are extensively expressed in various body tissues, and actively transport endogenous and exogenous substrates through biological membranes. Overexpression of ABC transporters is frequently observed in MDR cancer cells, which promotes efflux of chemotherapeutic drugs and reduces their intracellular accumulation. Increasing evidence suggests that ABC transporters regulate tumor immune microenvironment (TIME) by transporting various cytokines, thus controlling anti-tumor immunity and sensitivity to anticancer drugs. On the other hand, the expression of various ABC transporters is regulated by cytokines and other immune signaling molecules. Targeted inhibition of ABC transporter expression or function can enhance the efficacy of immune checkpoint inhibitors by promoting anticancer immune microenvironment. This review provides an update on the recent research progress in this field.

Puerarin suppresses hypoxia-induced vascular endothelial growth factor upregulation in human retinal pigmented epithelial cells by blocking JAK2/STAT3 pathway

The purpose of this study was to explore the mechanism by which puerarin regulated the expression of hypoxia-inducible factor 1α (HIF-1α) and vascular endothelial growth factor (VEGF) in humans' retinal pigment epithelial (RPE) cells under hypoxia. RPE cells (ARPE-19 and D407 cells) and a rat model of oxygen-induced retinopathy were used in the current study. Western blotting and ELISA were performed to detect the level of JAK2, phosphorylated JAK2, STAT3, phosphorylated STAT3, HIF-1α, and VEGF in cells. In addition, the interaction between JAK2 and STAT3 was determined using with a co-immunoprecipitation assay. We found puerarin inhibited hypoxia-induced upregulation of VEGF at both the mRNA and protein level via decreasing HIF-1α expression in RPE cells. Moreover, puerarin attenuated the interaction between JAK2 and STAT3, and subsequently blocking p-STAT3 nucleus translocation in vitro and in vivo. In conclusion, puerarin could effectively inhibit hypoxia-induced VEGF upregulation in RPE cells via mediated JAK2/STAT3 pathway.

A Microfluidic Platform to Monitor Real-Time Effects of Extracellular Vesicle Exchange between Co-Cultured Cells across Selectively Permeable Barriers

Exosomes and other extracellular vesicles (EVs) play a significant yet poorly understood role in cell-cell communication during homeostasis and various pathological conditions. Conventional in vitro and in vivo approaches for studying exosome/EV function depend on time-consuming and expensive vesicle purification methods to obtain sufficient vesicle populations. Moreover, the existence of various EV subtypes with distinct functional characteristics and submicron size makes their analysis challenging. To help address these challenges, we present here a unique chip-based approach for real-time monitoring of cellular EV exchange between physically separated cell populations. The extracellular matrix (ECM)-mimicking Matrigel is used to physically separate cell populations confined within microchannels, and mimics tissue environments to enable direct study of exosome/EV function. The submicron effective pore size of the Matrigel allows for the selective diffusion of only exosomes and other smaller EVs, in addition to soluble factors, between co-cultured cell populations. Furthermore, the use of PEGDA hydrogel with a very small pore size of 1.2 nm in lieu of Matrigel allows us to block EV migration and, therefore, differentiate EV effects from effects that may be mediated by soluble factors. This versatile platform bridges purely in vitro and in vivo assays by enabling studies of EV-mediated cellular crosstalk under physiologically relevant conditions, enabling future exosome/EV investigations across multiple disciplines through real-time monitoring of vesicle exchange.

Methyltransferase-like (METTL)14-mediated N6-methyladenosine modification modulates retinal pigment epithelial (RPE) activity by regulating the methylation of microtubule-associated protein (MAP)2

The expression of METTL14 is significantly reduced in patients with retinitis pigmentosa (RP). To clarify the significance of the N6-methyladenosine (m⁶A) RNA modification in RP, we examined phagocytosis, apoptosis, and cell cycle distribution in a human RPE cell line, ARPE-19, following lentivirus-mediated knockdown of METTL14. Differentially expressed genes and changes in m⁶A level were evaluated by RNA sequencing (RNA-seq) and methylated RNA immunoprecipitation sequencing (MeRIP-seq), respectively. The results showed that phagocytosis and proliferation were decreased whereas apoptosis was increased in RPE cells by METTL14 silencing. We found that METTL14 directly regulated m⁶A level and the expression of MAP2, as determined by RNA-seq, MeRIP-seq, MeRIP quantitative PCR, and the RNA pull-down assay. Additionally, MAP2 could bind to neuronal differentiation (NEUROD)1, a pathogenic gene in RPE-associated diseases. A family member of the YTH domain, (YTHDF)2 was recognized as an m⁶A reader of MAP2 mRNA. MAP2 overexpression had the same effects as METTL14 knockdown in RPE cells. Thus, METTL14 regulates the expression of MAP2 via the modification of m⁶A, resulting in the dysregulation of NEUROD1 and pathologic changes in RPE cells. These findings suggest that therapeutic strategies targeting the m⁶A modification of MAP2 or the METTL14/YTHDF2/MAP2/NEUROD1 signaling axis may be effective in the treatment of RPE-associated ocular diseases.