ViroISDC: a method for calling integration sites of hepatitis B virus based on feature encoding.

BACKGROUND: Hepatitis B virus (HBV) integrates into human chromosomes and can lead to genomic instability and hepatocarcinogenesis. Current tools for HBV integration site detection lack accuracy and stability. RESULTS: This study proposes a deep learning-based method, named ViroISDC, for detecting integration sites. ViroISDC generates corresponding grammar rules and encodes the characteristics of the language data to predict integration sites accurately. Compared with Lumpy, Pindel, Seeksv, and SurVirus, ViroISDC exhibits better overall performance and is less sensitive to sequencing depth and integration sequence length, displaying good reliability, stability, and generality. Further downstream analysis of integrated sites detected by ViroISDC reveals the integration patterns and features of HBV. It is observed that HBV integration exhibits specific chromosomal preferences and tends to integrate into cancerous tissue. Moreover, HBV integration frequency was higher in males than females, and high-frequency integration sites were more likely to be present on hepatocarcinogenesis- and anti-cancer-related genes, validating the reliability of the ViroISDC. CONCLUSIONS: ViroISDC pipeline exhibits superior precision, stability, and reliability across various datasets when compared to similar software. It is invaluable in exploring HBV infection in the human body, holding significant implications for the diagnosis, treatment, and prognosis assessment of HCC.

Engineered small extracellular vesicle-mediated ferroptosis: A new frontier in cancer immunotherapy.

Ferroptosis is a novel iron-dependent form of cell death discovered in recent years, characterized by the accumulation of ferrous iron, the production of reactive oxygen species (ROS) through the Fenton reaction, and lipid peroxidation, ultimately leading to the disruption of the antioxidant system and cell membrane damage. Extensive research has found that ferroptosis plays a significant role in regulating tumor cell immune evasion, tumor development, and remodeling the tumor microenvironment. Small Extracellular vesicles (sEVs), carrying various bioactive molecules (ncRNA, DNA, proteins), are key nanoscale mediators of intercellular communication. Increasing evidence confirms that EVs can regulate the ferroptosis pathway in tumors, promoting tumor cell immune evasion and reshaping the tumor microenvironment. This article aims to comprehensively review the key mechanisms by which sEVs mediate ferroptosis in cancer and provide new insights into targeting tumor immunotherapy.

The monokaryotic filamentous fungus Ustilago sp. HFJ311 promotes plant growth and reduces Cd accumulation by enhancing Fe transportation and auxin biosynthesis.

Infection with smut fungus like Ustilago maydis decreases crop yield via inducing gall formation. However, the in vitro impact of Ustilago spp. on plant growth and stress tolerance remains elusive. This study investigated the plant growth promotion and cadmium stress mitigation mechanisms of a filamentous fungus discovered on a cultural medium containing 25 µM CdCl2. ITS sequence alignment revealed 98.7 % similarity with Ustilago bromivora, naming the strain Ustilago sp. HFJ311 (HFJ311). Co-cultivation with HFJ311 significantly enhanced the growth of various plants, including Arabidopsis, tobacco, cabbage, carrot, rice, and maize, and improved Arabidopsis tolerance to abiotic stresses like salt and metal ions. HFJ311 increased chlorophyll and Fe contents in Arabidopsis shoots and enhanced root-to-shoot Fe translocation while decreasing root Fe concentration by approximately 70 %. Concurrently, HFJ311 reduced Cd accumulation in Arabidopsis by about 60 %, indicating its potential for bioremediation in Cd-contaminated soils. Additionally, HFJ311 stimulated IAA concentration by upregulating auxin biosynthesis genes. Overexpression of the Fe transporter IRT1 negated HFJ311's growth-promotion effects under Cd stress. These results suggest that HFJ311 stimulates plant growth and inhibits Cd uptake by enhancing Fe translocation and auxin biosynthesis while disrupting Fe absorption. Our findings offer a promising bioremediation strategy for sustainable agriculture and food security.

The Effect of RhoC siRNA on the Invasiveness and Proliferation of Human Cervical Cancer Cell Line SiHa Cells / 华中科技大学学报（医学）（英德文版）

This study investigated the effect of RhoC GTPase on the proliferation and metastasis of cervical cancer cells, SiHa cells, in vitro. RhoC siRNA was introduced into SiHa cells to silence the RhoC gene. The mRNA and protein expression of RhoC, before and after RhoC siRNA transfection,was examined by RT-PCR and Western blotting, respectively. The proliferation and apoptosis of SiHa cells were examined by MTT assay and flow cytometry (FACS), respectively. Adhesive rate was evaluated by Matrigel adhesive assay, and the invasive capability and migration capability were assessed by transwell invasive assay and migration assay, respectively. The results showed that after the RhoC siRNA transfection, the mRNA and protein expression of RhoC was down-regulated in SiHa cells. The down-regulation of RhoC GTPase did not affect the cell proliferation and apoptosis (P>0.05), but it did suppress SiHa cells' adhesion to matrigel (P<0.01), the invasive capability (P<0.01) and the migration capability (P<0.01). It was concluded that RhoC obviously promotes the adhesion, invasion and migration of SiHa cells in vitro, but not proliferation and apoptosis, suggesting that RhoC plays an important rote in the progression in cervical cancer.