Identification and characterization of differentially expressed miRNAs in HepG2 cells under normoxic and hypoxic conditions

Customized Hydrogel Films for MicroRNA Super-Resolution Imaging in Liquid Biopsies

Tissue biopsy for early diagnosis and monitoring comes with several challenges, such as its invasiveness, and issues related to tissue heterogeneity in sampling. To address these issues, researchers have proposed a noninvasive approach called liquid biopsy, which uses blood samples to detect specific noncoding RNA (microRNA, miRNA). However, the current process of isolating and amplifying miRNA can be time-consuming and yield nonspecific results. In this study, a new super-resolution imaging tool is introduced that utilizes a thin, hydrogel-based liquid view (LV) film. This film can undergo a ninefold expansion and allows the analysis of cells obtained from liquid biopsy. The potential of the LV film is validated as a tool for early diagnosis and prognosis by testing biofluids derived from a variety of diseases. This method is confirmed to accurately analyze a greater number of miRNAs with higher sensitivity in a shorter time compared to other analytical methods. These findings suggest that the LV film provides high specificity, and multiplexing in detecting small amounts of miRNAs within cells, making it suitable for 3D implementation. It is proposed that liquid biopsy with LV films can be a solution to limitations related to the invasiveness, cost, and time-consuming nature of molecular analysis.

Hypoxia-induced loss of SRSF2-dependent DNA methylation promotes CTCF-mediated alternative splicing of VEGFA in breast cancer

Alternative splicing of vascular endothelial growth factor A (VEGFA) generates numerous isoforms with unique roles in tumor angiogenesis, and investigating the underlying mechanism during hypoxia necessitates diligent pursuance. Our research systematically demonstrated that the splicing factor SRSF2 causes the inclusion of exon-8b, leading to the formation of the anti-angiogenic VEGFA-165b isoform under normoxic conditions. Additionally, SRSF2 interacts with DNMT3A and maintains methylation on exon-8a, inhibiting CCCTC-binding factor (CTCF) recruitment and RNA polymerase II (pol II) occupancy, causing exon-8a exclusion and decreased expression of pro-angiogenic VEGFA-165a. Conversely, SRSF2 is downregulated by HIF1α-induced miR-222-3p under hypoxic conditions, which prevents exon-8b inclusion and reduces VEGFA-165b expression. Furthermore, reduced SRSF2 under hypoxia promotes hydroxymethylation on exon-8a, increasing CTCF recruitment, pol II occupancy, exon-8a inclusion, and VEGFA-165a expression. Overall, our findings unveil a specialized dual mechanism of VEGFA-165 alternative splicing, instrumented by the cross-talk between SRSF2 and CTCF, which promotes angiogenesis under hypoxic conditions.

miRNA Pattern in Hypoxic Microenvironment of Kidney Cancer—Role of PTEN

MicroRNAs are post-transcriptional regulators of gene expression, and disturbances of their expression are the basis of many pathological states, including cancers. The miRNA pattern in the context of tumor microenvironment explains mechanisms related to cancer progression and provides a potential target of modern therapies. Here we show the miRNA pattern in renal cancer focusing on hypoxia as a characteristic feature of the tumor microenvironment and dysregulation of PTEN, being a major tumor suppressor. Methods comprised the CRSPR/Cas9 mediated PTEN knockout in the Renca kidney cancer cell line and global miRNA expression analysis in both in vivo and in vitro (in normoxic and hypoxic conditions). The results were validated on human cancer models with distinct PTEN status. The increase in miR-210-3p in hypoxia was universal; however, the hypoxia-induced decrease in PTEN was associated with an increase in miR-221-3p, the loss of PTEN affected the response to hypoxia differently by decreasing miR-10b-5p and increasing miR-206-3p. In turn, the complete loss of PTEN induces miR-155-5p, miR-100-5p. Upregulation of miR-342-3p in knockout PTEN occurred in the context of the whole tumor microenvironment. Thus, effective identification of miRNA patterns in cancers must consider the specificity of the tumor microenvironment together with the mutations of key suppressors.

Stronger impacts of long-term relative to short-term exposure to carbon nanomaterials on soil bacterial communities

Environmental impacts of carbon nanomaterials (CNMs) have been attracting increasing concerns in recent years. Knowledge on how short-term exposure to CNMs influences soil microbial communities is available. However, little is known about the possible difference in effects of long-term versus short-term exposure of CNMs on soil microbial communities. In this study, we systematically compared effects of fullerene (C₆₀), single-walled carbon nanotubes (SW), and graphene (GR) on soil bacterial communities over short (30 d) and long (360 d) term exposure durations. Our findings revealed that short-term exposure to all CNMs significantly increased the alpha diversity of soil bacterial communities. SW and GR exposure for 360 d relative to that for 30 d more significantly decreased their alpha diversity. Compared to short-term exposure, a long term exposure to CNMs more strongly altered the beta diversity of soil bacterial communities. LEfSe analysis showed that, GR relative to C₆₀ and SW exposure more strongly altered soil bacterial community composition especially for long-term duration at various taxonomic levels; more taxa were also identified by LEfSe analysis as biomarkers upon long-term GR exposure. More OTUs were affected by long-term GR exposure. These differences resulted from both distinct physicochemical properties of various CNMs and their exposure durations.