Identification of WTAP-related genes by weighted gene co-expression network analysis in ovarian cancer

BACKGROUND

Wilms tumor 1 associated protein (WTAP) modulates other genes via transcriptional and post-transcriptional regulation, in particular, by acting as a N6-methyladenosine writer or binding to the 3'UTR of mRNA, and promotes a variety of tumuors. However, the roles and mechanisms of WTAP in ovarian cancer are unknown.

RESULTS

In this study, using univariate Cox analysis and online CPTA analysis, we found that WTAP was a poor prognostic factor for ovarian cancer, and its protein expression level was higher in ovarian cancer than in normal tissue. Functionally, WTAP promoted the proliferation, invasion, and migration capability of ovarian cancer, according to the results of real time cellular analysis (RTCA), EdU cell proliferation assay, transwell assay. Subsequently, we identified a module containing 133 genes that were carefully related to WTAP expression through weighted gene co-expression network analysis (WGCNA). By calculating the hazard ratios of these genes and comparing their differences in the WTAP high-expression group and the low-expression group, we observed that there was a significant positive correlation between WTAP and two poor survival-related genes, family with sequence similarity 76 member A (FAM76A) and HBS1 like translational GTPase (HBS1L), which was also verified by quantitative real-time PCR in SKOV3 and A2780 cells.

CONCLUSION

WTAP functions as an oncogenic factor that promotes the progression of ovarian cancer in which WTAP-HBS1L/FAM76A axis may be involved. Our study indicates the potential role of WTAP in prognostic biomarker and therapeutic target for ovarian cancer.

Different typical dietary lipid consumption affects the bile acid metabolism and the gut microbiota structure: an animal trial using Sprague-Dawley rats

BACKGROUND

The palm oil (PO), leaf lard oil (LO), rapeseed oil (RO), sunflower oil (SO) and linseed oil (LN) are five of the most typical dietary lipids in most Asian countries. However, their influences on gut health, and the connections between the fatty acid composition, the gut microbiota, and the bile acid metabolism are not fully understood.

RESULTS

In the present study, results showed that compared with polyunsaturated fatty acid (PUFA)-rich SO and LN, the saturated fatty acid (SFA)-rich and monounsaturated fatty acid (MUFA)-rich PO, LO and RO were more likely to decrease the re-absorption of bile acid in the colon, which was probably caused by their different role in modulating the gut microbiota structure. LO consumption significantly up-regulated the Cyp27a1, FXR and TGR5 gene expression level (P < 0.05). The correlation results suggested that the C18:0 was significantly positive correlated with these three genes, indicating that intake of SFA-rich dietary lipids, especially for the C18:0, could specifically increase the bile acid production by stimulating the bile acid alternative synthesis pathway. Although the bile acid receptor expression in the colon was increased, the re-absorption of bile acid did not show a significant increase (P > 0.05) as compared with other dietary lipids. Moreover, the C18:2-rich SO maintained the bile acid metabolic balance probably by decreasing the Romboutsia, while increasing the Bifidobacterium abundance in the colon.

CONCLUSIONS

The different dietary lipids showed different effects on the bile acid metabolism, which was probably connected with the alterations in the gut microbiota structure. The present study could provide basic understandings about the influences of the different dietary lipids consumption on gut homeostasis and bile acid metabolism. © 2021 Society of Chemical Industry.

Bendable Polycrystalline and Magnetic CoFe2O4 Membranes by Chemical Methods

The preparation and manipulation of crystalline yet bendable functional complex oxide membranes has been a long-standing issue for a myriad of applications, in particular, for flexible electronics. Here, we investigate the viability to prepare magnetic and crystalline CoFe₂O₄ (CFO) membranes by means of the Sr₃Al₂O₆ (SAO) sacrificial layer approach using chemical deposition techniques. Meticulous chemical and structural study of the SAO surface and SAO/CFO interface properties have allowed us to identify the formation of an amorphous SAO capping layer and carbonates upon air exposure, which dictate the crystalline quality of the subsequent CFO film growth. Vacuum annealing at 800 °C of SAO films promotes the elimination of the surface carbonates and the reconstruction of the SAO surface crystallinity. Ex-situ atomic layer deposition of CFO films at 250 °C on air-exposed SAO offers the opportunity to avoid high-temperature growth while achieving polycrystalline CFO films that can be successfully transferred to a polymer support preserving the magnetic properties under bending. Float on and transfer provides an alternative route to prepare freestanding and wrinkle-free CFO membrane films. The advances and challenges presented in this work are expected to help increase the capabilities to grow different oxide compositions and heterostructures of freestanding films and their range of functional properties.

Characterization of the microRNA transcriptomes and proteomics of cochlear tissue-derived small extracellular vesicles from mice of different ages after birth

The cochlea is an important sensory organ for both balance and sound perception, and the formation of the cochlea is a complex developmental process. The development of the mouse cochlea begins on embryonic day (E)9 and continues until postnatal day (P)21 when the hearing system is considered mature. Small extracellular vesicles (sEVs), with a diameter ranging from 30 to 200 nm, have been considered a significant medium for information communication in both physiological and pathological processes. However, there are no studies exploring the role of sEVs in the development of the cochlea. Here, we isolated tissue-derived sEVs from the cochleae of FVB mice at P3, P7, P14, and P21 by ultracentrifugation. These sEVs were first characterized by transmission electron microscopy, nanoparticle tracking analysis, and western blotting. Next, we used small RNA-seq and mass spectrometry to characterize the microRNA transcriptomes and proteomes of cochlear sEVs from mice at different ages. Many microRNAs and proteins were discovered to be related to inner ear development, anatomical structure development, and auditory nervous system development. These results all suggest that sEVs exist in the cochlea and are likely to be essential for the normal development of the auditory system. Our findings provide many sEV microRNA and protein targets for future studies of the roles of cochlear sEVs.

Dynamic control of circumrotation of a [2]catenane by acid-base switching

Dynamic control of the motion in a catenane remains a big challenge as it requires precise design and sophisticated well-organized structures. This paper reports the design and synthesis of a donor-acceptor [2]catenane through mechanical interlocking, employing a crown ether featuring two dibenzylammonium salts on its side arms as the host and a cyclobis(paraquat-p-phenylene) (CBPQT ⋅ 4PF6) ring as the guest molecule. By addition of external acid or base, the catenane can form self-complexed or decomplexed compounds to alter the cavity size of the crown ether ring, consequently affecting circumrotation rate of CBPQT ⋅ 4PF6 ring of the catenane. This study offers insights for the design and exploration of artificial molecular machines with intricate cascading responsive mechanisms.

Precise Error Performance of BPSK Modulated Coherent Terahertz Wireless LOS Links with Pointing Errors

One of the key advantages of terahertz (THz) communication is its potential for energy efficiency, making it an attractive option for green communication systems. Coherent THz transmission technology has recently been explored in the literature. However, there exist few error performance results for such a wireless link employing coherent THz technology. In this paper, we explore a comprehensive terrestrial channel model designed for wireless line-of-sight communication using THz frequencies. The performance of coherent THz links is analyzed, and it is found to be notably affected by two significant factors, atmospheric turbulence and pointing errors. These could occur between the terahertz transmitter and receiver in terrestrial links. The exact and asymptotic solutions are derived for bit error rate and interrupt probability for binary phase-shift keying coherent THz systems, respectively, over log-normal and Gamma-Gamma turbulent channels. The asymptotic outage probability analysis is also performed. It is shown that the presented results offer a precise estimation of coherent THz transmission performance and its link budget.

DeepPhylo: Phylogeny-Aware Microbial Embeddings Enhanced Predictive Accuracy in Human Microbiome Data Analysis

Microbial data analysis poses significant challenges due to its high dimensionality, sparsity, and compositionality. Recent advances have shown that integrating abundance and phylogenetic information is an effective strategy for uncovering robust patterns and enhancing the predictive performance in microbiome studies. However, existing methods primarily focus on the hierarchical structure of phylogenetic trees, overlooking the evolutionary distances embedded within them. This study introduces DeepPhylo, a novel method that employs phylogeny-aware amplicon embeddings to effectively integrate abundance and phylogenetic information. DeepPhylo improves both the unsupervised discriminatory power and supervised predictive accuracy of microbiome data analysis. Compared to the existing methods, DeepPhylo demonstrates superiority in informing biologically relevant insights across five real-world microbiome use cases, including clustering of skin microbiomes, prediction of host chronological age and gender, diagnosis of inflammatory bowel disease (IBD) across 15 studies, and multilabel disease classification.

Dual Targeting of Aurora-A and Bcl-xL Synergistically Reshapes the Immune Microenvironment and Induces Apoptosis in Breast Cancer

The Aurora-A kinase inhibitor MLN8237 has shown efficacy in clinical trials for advanced breast cancer; however, its use as a monotherapy is limited by significant side effects and modest efficacy. Therefore, combining MLN8237 with other agents at lower doses may provide a viable alternative. In this study, we evaluated the combination of MLN8237 with the BH3 mimetic ABT263 for the treatment of triple-negative breast cancer (TNBC). We found that this combination significantly suppressed tumor growth and metastasis in immunocompetent syngeneic mouse models, whereas its efficacy was attenuated in immunodeficient xenograft models. Mechanistic studies revealed that the combination enhanced anti-tumor immunity by increasing the presence of CD8+ T cells and NK cells, while reducing the number of immunosuppressive cells in the tumor microenvironment. This shift resulted in elevated levels of IFN-γ and granzyme B, which activated the extrinsic apoptotic pathways in cancer cells. Notably, the combination treatment did not affect tumor cell proliferation but promoted apoptosis with minimal toxicity. Furthermore, the synergistic effect of MLN8237 and ABT263 in inducing intrinsic apoptosis was primarily driven by the inhibition of the AKT-Mcl-1 and Bcl-xL survival pathways in cultured tumor cells. Together, these findings support the MLN8237-ABT263 combination as an effective treatment strategy for TNBC, promoting both immune-mediated extrinsic apoptosis and inactivation of Bcl-xL/Mcl-1-dependent intrinsic anti-apoptotic pathways.

Quantitative Detection Technology for Geometric Deformation of Pipelines Based on LiDAR

This paper introduces a novel method for enhancing underground pipeline inspection, specifically addressing limitations associated with traditional closed-circuit television (CCTV) systems. These systems, commonly used for capturing visual data of sewer system deformations, heavily rely on subjective human expertise, leading to limited accuracy in detection. Furthermore, their inability to perform quantitative analyses of deformation extent hampers overall inspection effectiveness. Our proposed method leverages laser point cloud data and employs a 3D scanner for objective detection of geometric deformations in underground pipe corridors. By utilizing this approach, we enable a quantitative assessment of blockage levels, offering a significant improvement over traditional CCTV-based methods. The key advantages of our method lie in its objectivity and quantification capabilities, ultimately enhancing detection reliability, accuracy, and overall inspection efficiency.

Aberrant LYZ expression in tumor cells serves as the potential biomarker and target for HCC and promotes tumor progression via csGRP78

Hepatocellular carcinoma (HCC) takes the predominant malignancy of hepatocytes with bleak outcomes owing to high heterogeneity among patients. Personalized treatments based on molecular profiles will better improve patients' prognosis. Lysozyme (LYZ), a secretory protein with antibacterial function generally expressed in monocytes/macrophages, has been observed for the prognostic implications in different types of tumors. However, studies about the explicit applicative scenarios and mechanisms for tumor progression are still quite limited, especially for HCC. Here, based on the proteomic molecular classification data of early-stage HCC, we revealed that the LYZ level was elevated significantly in the most malignant HCC subtype and could serve as an independent prognostic predictor for HCC patients. Molecular profiles of LYZ-high HCCs were typical of those for the most malignant HCC subtype, with impaired metabolism, along with promoted proliferation and metastasis characteristics. Further studies demonstrated that LYZ tended to be aberrantly expressed in poorly differentiated HCC cells, which was regulated by STAT3 activation. LYZ promoted HCC proliferation and migration in both autocrine and paracrine manners independent of the muramidase activity through the activation of downstream protumoral signaling pathways via cell surface GRP78. Subcutaneous and orthotopic xenograft tumor models indicated that targeting LYZ inhibited HCC growth markedly in NOD/SCID mice. These results propose LYZ as a prognostic biomarker and therapeutic target for the subclass of HCC with an aggressive phenotype.

Partial order relation-based gene ontology embedding improves protein function prediction

Protein annotation has long been a challenging task in computational biology. Gene Ontology (GO) has become one of the most popular frameworks to describe protein functions and their relationships. Prediction of a protein annotation with proper GO terms demands high-quality GO term representation learning, which aims to learn a low-dimensional dense vector representation with accompanying semantic meaning for each functional label, also known as embedding. However, existing GO term embedding methods, which mainly take into account ancestral co-occurrence information, have yet to capture the full topological information in the GO-directed acyclic graph (DAG). In this study, we propose a novel GO term representation learning method, PO2Vec, to utilize the partial order relationships to improve the GO term representations. Extensive evaluations show that PO2Vec achieves better outcomes than existing embedding methods in a variety of downstream biological tasks. Based on PO2Vec, we further developed a new protein function prediction method PO2GO, which demonstrates superior performance measured in multiple metrics and annotation specificity as well as few-shot prediction capability in the benchmarks. These results suggest that the high-quality representation of GO structure is critical for diverse biological tasks including computational protein annotation.

Creating NADP+ -Specific Formate Dehydrogenases from Komagataella phaffii by Enzymatic Engineering

Most natural formate dehydrogenases (FDHs) exhibit NAD+ specificity, making it imperative to explore the engineering of FDH cofactor specificity for NADPH regeneration systems. The endogenous FDH of Komagataella phaffii (K. phaffii), termed KphFDH, is a typical NAD+ -specific FDH. However, investigations into engineering the cofactor specificity of KphFDH have yet to be conducted. To develop an NADP+ -specific variant of KphFDH, we selected D195, Y196, and Q197 as mutation sites and generated twenty site-directed variants. Through kinetic characterization, KphFDH/V19 (D195Q/Y196R/Q197H) was identified as the variant with the highest specificity towards NADP+ , with a ratio of catalytic efficiency (kcat /KM )NADP+ /(kcat /KM )NAD+ of 129.226. Studies of enzymatic properties revealed that the optimal temperature and pH for the reduction reaction of NADP+ catalyzed by KphFDH/V19 were 45 °C and 7.5, respectively. The molecular dynamics (MD) simulation was performed to elucidate the mechanism of high catalytic activity of KphFDH/V19 towards NADP+ . Finally, KphFDH/V19 was applied to an in vitro NADPH regeneration system with Meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum (StDAPDH/H227V). This study successfully created a KphFDH variant with high NADP+ specificity and demonstrated its practical applicability in an in vitro NADPH regeneration system.