Association Signals Unveiled by a Comprehensive Gene Set Enrichment Analysis of Dental Caries Genome-Wide Association Studies

Gene set-based analysis of genome-wide association study (GWAS) data has recently emerged as a useful approach to examine the joint effects of multiple risk loci in complex human diseases or phenotypes. Dental caries is a common, chronic, and complex disease leading to a decrease in quality of life worldwide. In this study, we applied the approaches of gene set enrichment analysis to a major dental caries GWAS dataset, which consists of 537 cases and 605 controls. Using four complementary gene set analysis methods, we analyzed 1331 Gene Ontology (GO) terms collected from the Molecular Signatures Database (MSigDB). Setting false discovery rate (FDR) threshold as 0.05, we identified 13 significantly associated GO terms. Additionally, 17 terms were further included as marginally associated because they were top ranked by each method, although their FDR is higher than 0.05. In total, we identified 30 promising GO terms, including 'Sphingoid metabolic process,' 'Ubiquitin protein ligase activity,' 'Regulation of cytokine secretion,' and 'Ceramide metabolic process.' These GO terms encompass broad functions that potentially interact and contribute to the oral immune response related to caries development, which have not been reported in the standard single marker based analysis. Collectively, our gene set enrichment analysis provided complementary insights into the molecular mechanisms and polygenic interactions in dental caries, revealing promising association signals that could not be detected through single marker analysis of GWAS data. © 2013 Wang et al

Mechanism of herpesvirus UL24 protein regulating viral immune escape and virulence

Herpesviruses have evolved a series of abilities involved in the process of host infection that are conducive to virus survival and adaptation to the host, such as immune escape, latent infection, and induction of programmed cell death for sustainable infection. The herpesvirus gene UL24 encodes a highly conserved core protein that plays an important role in effective viral infection. The UL24 protein can inhibit the innate immune response of the host by acting on multiple immune signaling pathways during virus infection, and it also plays a key role in the proliferation and pathogenicity of the virus in the later stage of infection. This article reviews the mechanism by which the UL24 protein mediates herpesvirus immune escape and its effects on viral proliferation and virulence by influencing syncytial formation, DNA damage and the cell cycle. Reviewing these studies will enhance our understanding of the pathogenesis of herpesvirus infection and provide evidence for new strategies to combat against viral infection

High Expression of VSTM2L Induced Resistance to Chemoradiotherapy in Rectal Cancer through Downstream IL-4 Signaling

Background. Preoperative chemoradiotherapy (pCRT) is a common and essential therapeutic strategy for patients with locally advanced rectal cancer (LARC), but poor tumor response and therapeutic resistance to chemoradiotherapy have appeared usually among persons and affected those patients’ survival prognosis. The resistance to chemoradiotherapy in rectal cancer is difficult to predict. This study was aimed at evaluating the role of V-set and transmembrane domain containing 2 like protein (VSTM2L) in resistance to chemoradiotherapy in rectal cancer. Methods. Analysis of the GEO profiling datasets of rectal cancer patients receiving pCRT disclosed that VSTM2L as a candidate gene was significantly upregulated in nonresponders of rectal cancer with pCRT. The mRNA and protein expression of VSTM2L was detected by quantitate real-time PCR, western blotting, and immunohistochemistry in six rectal cancer biopsy tissues before pCRT. Furthermore, the rectal cancer patient-derived organoids were cultured to evaluate the association of VSTM2L expression and tumor response to CRT. Overexpression of VSTM2L in cancer cells treated with CRT was analyzed for the function of cell proliferation and viability, clone formation, DNA damage repair, and apoptosis ability. The GSEA and RNA-sequence analysis were used to find the downstream mechanism of VSTM2L overexpression in cells treated with CRT. Results. The mRNA levels of VSTM2L were significantly downregulated in normal rectal tissues compared to tumor tissues and were upregulated in nonresponders of rectal cancer patients receiving pCRT and positively correlated with poor survival prognosis from GEO datasets. High expression of VSTM2L was significantly associated with tumor regression after pCRT (P=0.030). Moreover, high expression of VSTM2L reduced γ-H2AX expression in rectal cancer patient-derived organoids treated with CRT. The overexpression of VSTM2L in colorectal cancer cells induced resistance to CRT via promoting cell proliferation and inhibiting apoptosis. The molecular mechanism revealed that the overexpression of VSTM2L induced resistance to CRT through downstream IL-4 signaling affecting the progress of cell proliferation and apoptosis. Conclusion. The high expression of VSTM2L induced resistance to CRT, and adverse survival outcomes served as a prognostic factor in patients with rectal cancer receiving pCRT, suggesting that VSTM2L high expression may be a potential resistant predictable biomarker for LARC patients receiving pCRT

Empirical Method for Evaluating Resilient Modulus of Saturated Silty Clay under Cyclic Loading

Resilient modulus of soil is crucial for the design of a structure on a foundation subjected to a cyclic loading (e.g., traffic load or machine vibration load). This paper conducted a series of dynamic triaxial tests of saturated silty clay, considering the influence of the factors of cyclic stress ratio (CSR), static deviatoric stress ratio (SDR), and overconsolidation ratio (OCR) on the resilient modulus and dynamic damping ratio of the soil. A cyclic loading with a form of half sine wave was used to model the traffic loading. The results showed that the soil was prone to failure under a higher SDR, even though the applied CSR was less than the critical CSR. The saturated silty clay performed a strain softening behavior and its dynamic properties deteriorated significantly when higher CSR and SDR and lower OCR were involved. Based on the test results, an empirical method with a form of exponential function was proposed to evaluate the resilient modulus of the soil, considering the combined effects of CSR and SDR and OCR. The proposed method was verified through a comparison with the test results in this study and from literatures, and some recommendations for its application were offered

PSSM-Distil: Protein Secondary Structure Prediction (PSSP) on Low-Quality PSSM by Knowledge Distillation with Contrastive Learning

Protein secondary structure prediction (PSSP) is an essential task in computational biology. To achieve the accurate PSSP, the general and vital feature engineering is to use multiple sequence alignment (MSA) for Position-Specific Scoring Matrix (PSSM) extraction. However, when only low-quality PSSM can be obtained due to poor sequence homology, previous PSSP accuracy (merely around 65%) is far from practical usage for subsequent tasks. In this paper, we propose a novel PSSM-Distil framework for PSSP on low-quality PSSM, which not only enhances the PSSM feature at a lower level but also aligns the feature distribution at a higher level. In practice, the PSSM-Distil first exploits the proteins with high-quality PSSM to achieve a teacher network for PSSP in a full-supervised way. Under the guidance of the teacher network, the low-quality PSSM and corresponding student network with low discriminating capacity are effectively resolved by feature enhancement through EnhanceNet and distribution alignment through knowledge distillation with contrastive learning. Further, our PSSM-Distil supports the input from a pre-trained protein sequence language BERT model to provide auxiliary information, which is designed to address the extremely low-quality PSSM cases, i.e., no homologous sequence. Extensive experiments demonstrate the proposed PSSM-Distil outperforms state-of-the-art models on PSSP by 6% on average and nearly 8% in extremely low-quality cases on public benchmarks, BC40 and CB513

Construction of a Protein Crystalline Inclusion-Based Enzyme Immobilization System for Biosynthesis of PAPS from ATP and Sulfate

3′-Phosphoadenosine-5′-phosphosulfate (PAPS) is the bioactive form of sulfate and is involved in all biological sulfation reactions. The enzymatic transformation method for PAPS is promising, but the low efficiency and high cost of enzyme purification and storage restrict its practical applications. Here, we reported PAPS biosynthesis with a protein crystalline inclusion (PCI)-based enzyme immobilization system. First, the in vivo crystalline inclusion protein CipA was identified as an efficient auto-assembly tag for immobilizing the bifunctional PAPS synthase (ASAK). After characterizing the pyrophosphokinase activity of a polyphosphate exonuclease PaPPX from Pseudomonas aeruginosa, and optimizing the linker fragment, auto-assembled enzymes ASAK-PT-CipA and PaPPX-PT-CipA were constructed. Then, the auto-assembled enzymes ASAK-PT-CipA and PaPPX-PT-CipA with high stability were co-expressed and immobilized for constructing a transformation system. The highest transformation rate of PAPS from ATP and sulfate reached 90%, and the immobilized enzyme can be reused 10 times. The present work provided a convenient, efficient, and easy to be enlarged auto-immobilization system for PAPS biosynthesis from ATP and sulfate. The immobilization system also represented a new approach to reduce the production cost of PAPS by facilitating the purification, storage, and reuse of related enzymes, and it would boost the studies on biotechnological production of glycosaminoglycans and sulfur-containing natural compounds