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Objective To explore the effect of copy number variation on the occurrence and development of hepatocellular carcinoma by using copy number variation and transcriptome experiment of hepatocellular carcinoma combined with public clinical data. Methods The copy number variation found in hepatoma cell lines HepG2 and Huh7 was identified by optical genome mapping. The function of the copy number variant genes in the two cell lines was analyzed, and the protein interaction network was mapped according to the enrichment pathway. Key genes in the core network of two cell lines were selected to analyze the relationship between copy number variation and gene expression in hepatocellular carcinoma. The relationship between gene expression and clinical survival was analyzed by GEPIA database. RNA-seq assay and public data were used to verify gene expression levels. Results HepG2 cells mainly showed increased copy number, and related genes were enriched in estrogen signaling pathway and Staphylococcus aureus infection pathway. Huh7 cells showed both increased and decreased copy number, and related genes mainly concentrated in olfactory conduction and cytokine-cytokine receptor interaction pathways. The copy number of key genes SRC, MAPK3 and MAP3K7 was proportional to gene expression, and survival was significantly reduced in patients with high expression of these genes (P＜0.05). Compared with HEK293T cell line, the expression of SRC and MAP3K7 genes in the two hepatocellular carcinoma lines was significantly increased(P＜0.001), suggesting the specific variation of hepatocellular carcinoma. MAPK3 had no difference. Conclusions The expression of copy number variant genes SRC and MAP3K7 in hepatocellular carcinoma is significantly correlated with the prognosis of patients, and may significantly affect the development and heterogeneity of hepatocellular carcinoma.

To systematically assess the effect of negative pressure wound therapy (NPWT) on postoperative surgical wound infection, length of hospital stay and postoperative complications after spinal surgery. Relevant studies on the application of NPWT in spinal surgery were conducted via a computerised database search, including PubMed, EMBASE, Web of Science, MEDLINE, Cochrane Library, China National Knowledge Infrastructure (CNKI) and Wanfang, from inception to June 2023. The identified literature was rigorously screened and data extraction was performed by two investigators independently. The quality of the relevant studies was evaluated using the Newcastle–Ottawa scale (NOS). The effect size for count data was determined by the odds ratio (OR), while the impact size for measurement data was expressed as the standardised mean difference (SMD). The 95% confidence interval (CI) was calculated for each effect magnitude. Stata 17.0 software was used for the meta‐analysis. Ten papers, totalling 1448 patients, were finally included. This study demonstrated that NPWT led to a statistically significant reduction in the occurrence of postoperative surgical wound infections (OR: 0.377, 95% CI: 0.238–0.598, p < 0.001), fewer postoperative complications (OR: 0.526, 95% CI: 0.360–0.770, p = 0.001) and a shortened hospital stay (SMD: −0.678, 95%CI: −1.324 to −0.031, p = 0.040) after spinal surgery compared with the control group. When compared with other treatment approaches, NPWT also demonstrated a substantial reduction in surgical wound infections and postoperative complications, as well as a shorter duration of hospitalisation after spinal surgery. [ABSTRACT FROM AUTHOR]

Emerging evidence reveals that the three-dimensional (3D) chromatin architecture plays a key regulatory role in various biological processes of plants. However, information on the 3D chromatin architecture of the legume model plant Medicago truncatula and its potential roles in the regulation of response to mineral nutrient deficiency are very limited. Using high-resolution chromosome conformation capture sequencing, we identified the 3D genome structure of M. truncatula in terms of A/B compartments, topologically associated domains (TADs) and chromatin loops. The gene density, expressional level, and active histone modification were higher in A compartments than in B compartments. Moreover, we analysed the 3D chromatin architecture reorganization in response to phosphorus (P) deficiency. The intra-chromosomal cis -interaction proportion was increased by P deficiency, and a total of 748 A/B compartment switch regions were detected. In these regions, density changes in H3K4me3 and H3K27ac modifications were associated with expression of P deficiency-responsive genes involved in root system architecture and hormonal responses. Furthermore, these genes enhanced P uptake and mobilization by increasing root surface area and strengthening signal transduction under P deficiency. These findings advance our understanding of the potential roles of 3D chromatin architecture in responses of plants in general, and in particular in M. truncatula , to P deficiency. [ABSTRACT FROM AUTHOR]

Higher-order chromatin structures play important roles in regulating multiple biological processes such as growth and development as well as biotic and abiotic stress response. However, little is known about three-dimensional chromatin structures in Paulownia or about whole-genome chromatin conformational changes that occur in response to Paulownia witches' broom (PaWB) disease. We used high-throughput chromosome conformation capture (Hi-C) to obtain genome-wide profiles of chromatin conformation in both healthy and phytoplasma-infected Paulownia fortunei genome. The heat map results indicated that the strongest interactions between chromosomes were in the telomeres. We confirmed that the main structural characteristics of A/B compartments, topologically associated domains, and chromatin loops were prominent in the Paulownia genome and were clearly altered in phytoplasma-infected plants. By combining chromatin immunoprecipitation sequencing, Hi-C signals, and RNA sequencing data, we inferred that the chromatin structure changed and the modification levels of three histones (H3K4me3/K9ac/K36me3) increased in phytoplasma-infected P . fortunei , which was associated with changes of transcriptional activity. We concluded that for epigenetic modifications, transcriptional activity might function in combination to shape chromatin packing in healthy and phytoplasm-infected Paulownia. Finally, 11 genes (e.g., RPN6 , Sec61 subunit- α) that were commonly located at specific topologically associated domain boundaries, A/B compartment switching and specific loops, and had been associated with histone marks were identified and considered as closely related to PaWB stress. Our results provide new insights into the nexus between gene regulation and chromatin conformational alterations in nonmodel plants upon phytopathogen infection and plant disease resistance.