Identification and validation of a pyroptosis-related prognostic model for colorectal cancer based on bulk and single-cell RNA sequencing data.

BACKGROUND: Pyroptosis impacts the development of malignant tumors, yet its role in colorectal cancer (CRC) prognosis remains uncertain. AIM: To assess the prognostic significance of pyroptosis-related genes and their association with CRC immune infiltration. METHODS: Gene expression data were obtained from The Cancer Genome Atlas (TCGA) and single-cell RNA sequencing dataset GSE178341 from the Gene Expression Omnibus (GEO). Pyroptosis-related gene expression in cell clusters was analyzed, and enrichment analysis was conducted. A pyroptosis-related risk model was developed using the LASSO regression algorithm, with prediction accuracy assessed through K-M and receiver operating characteristic analyses. A nomogram predicting survival was created, and the correlation between the risk model and immune infiltration was analyzed using CIBERSORTx calculations. Finally, the differential expression of the 8 prognostic genes between CRC and normal samples was verified by analyzing TCGA-COADREAD data from the UCSC database. RESULTS: An effective pyroptosis-related risk model was constructed using 8 genes-CHMP2B, SDHB, BST2, UBE2D2, GJA1, AIM2, PDCD6IP, and SEZ6L2 (P < 0.05). Seven of these genes exhibited differential expression between CRC and normal samples based on TCGA database analysis (P < 0.05). Patients with higher risk scores demonstrated increased death risk and reduced overall survival (P < 0.05). Significant differences in immune infiltration were observed between low- and high-risk groups, correlating with pyroptosis-related gene expression. CONCLUSION: We developed a pyroptosis-related prognostic model for CRC, affirming its correlation with immune infiltration. This model may prove useful for CRC prognostic evaluation.

Copper homeostasis and cuproptosis in cancer immunity and therapy.

Copper is an essential nutrient for maintaining enzyme activity and transcription factor function. Excess copper results in the aggregation of lipoylated dihydrolipoamide S-acetyltransferase (DLAT), which correlates to the mitochondrial tricarboxylic acid (TCA) cycle, resulting in proteotoxic stress and eliciting a novel cell death modality: cuproptosis. Cuproptosis exerts an indispensable role in cancer progression, which is considered a promising strategy for cancer therapy. Cancer immunotherapy has gained extensive attention owing to breakthroughs in immune checkpoint blockade; furthermore, cuproptosis is strongly connected to the modulation of antitumor immunity. Thus, a thorough recognition concerning the mechanisms involved in the modulation of copper metabolism and cuproptosis may facilitate improvement in cancer management. This review outlines the cellular and molecular mechanisms and characteristics of cuproptosis and the links of the novel regulated cell death modality with human cancers. We also review the current knowledge on the complex effects of cuproptosis on antitumor immunity and immune response. Furthermore, potential agents that elicit cuproptosis pathways are summarized. Lastly, we discuss the influence of cuproptosis induction on the tumor microenvironment as well as the challenges of adding cuproptosis regulators to therapeutic strategies beyond traditional therapy.

Identification of driving genes of familial adenomatous polyposis by differential gene expression analysis and weighted gene co-expression network analysis.

BACKGROUND: Despite the advancement of new screening strategies and the advances in pharmacological therapies, the cancerization rates of familial adenomatous polyposis (FAP) are stable and even increased in the last years. Therefore, it necessitates additional research to characterize and understand the underlying mechanisms of FAP. OBJECTIVE: To determine the genes that drive the pathogenesis of familial adenomatous polyposis (FAP). METHODS: We performed on a cohort (GSE111156) gene profile, which consist of four group of gene expressions (the gene expressions of cancer, adenoma and normal tissue of duodenal cancer from patients with FAP were defined as Case N, Case A and Case C respectively, while that of adenoma tissue from patients with FAP who did not have duodenal cancer was Ctrl A). Tracking Tumor Immunophenotype (TIP) website was applied to reveal immune infiltration profile and signature genes of FAP. We merged the genes of key module (pink and midnight module) with signature genes to obtained the biomarkers related with FAP pathogenesis. The expression of these five biomarkers in FAP intratumoral region (IT) and tumor rim (TR) was detected with Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). RESULTS: In total, 220, 23 and 63 DEGs were determined in Cases C, A and N, in comparison to Ctrl A. In total, 196 and 10 DEGs were determined in Cases C and A, separately, as compared to Case N. A total of four biomarkers including CCL5, CD3G, CD2 and TLR3 were finally identified associated with pink module, while only one biomarker (KLF2) associated with midnight module was identified. All biomarkers were evidently raised in FAP IT tissues utilizing qRT-PCR. CONCLUSION: We identified five potential biomarkers for pathogenesis of FAP to understand the fundamental mechanisms of FAP progression and revealed some probable targets for the diagnosis or treatment of FAP.

Discovery of core gene families associated with liver metastasis in colorectal cancer and regulatory roles in tumor cell immune infiltration.

In this study, we aimed to uncover genes that drive the pathogenesis of liver metastasis in colorectal cancer (CRC), and identify effective genes that could serve as potential therapeutic targets for treating with colorectal liver metastasis patients based on two GEO datasets. Several bioinformatics approaches were implemented. First, differential expression analysis screened out key differentially expressed genes (DEGs) across the two GEO datasets. Based on gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, we identified the enrichment functions and pathways of the DEGs that were associated with liver metastasis in CRC. Second, immune infiltration analysis identified key immune signature gene sets associated with CRC liver metastasis, among which two key immune gene families (CD and CCL) identified as key DEGs were filtered by protein-protein interaction (PPI) network. Some of the members in these gene families were associated with disease free survival (DFS) or overall survival (OS) in two subtypes of CRC, namely COAD and READ. Finally, functional enrichment analysis of the two gene families and their neighboring genes revealed that they were closely associated with cytokine, leukocyte proliferation and chemotaxis. These results are valuable in comprehending the pathogenesis of liver metastasis in CRC, and are of seminal importance in understanding the role of immune tumor infiltration in CRC. Our study also identified potentially effective therapeutic targets for liver metastasis in CRC including CCL20, CCL24 and CD70.

[Current Advances in Peri-implantitis Mouse Model].

Peri-implantitis is the most common and intractable complication of dental implant-supported prothesis affecting its long-term success, and is one of the main reasons for implant failure. Due to the limitation of the research methods, the pathogenesis and pathological processes of peri-implantitis remain unclear. Animal models are indispensable tools to study the pathogenesis of diseases. With the advances of the dental implants, the peri-implantitis mouse model has been used in experimental research. This paper summarized recent studies from the following five aspects: the advantages of the mouse model, the influence of mouse strain, the design of micro-implant, the way of implant insertion, as well as the induction of peri-implantitis, aiming to provide references and help for researchers. Compared with the large animal models of peri-implantitis, the mouse model of peri-implantitis is more flexible in use. Lower costs can better control the sample number and shorter induction time can better control experimental duration. The completion of mouse genome sequencing and the progress of the genetic operating system also make the pathogenetic study possible. However, the mouse model of peri-implantitis still has some limitations. Limited by the small size of mouse oral cavity, implant insertion surgery is technically demanding, and complex surgeries are even more challenging. Moreover, due to short history of the peri-implantitis mouse model, its corresponding technical theories such as implantation methods, peri-implantitis induction methods and so on are not unified yet and still need further research and development.

High serum uric acid is associated with increased arterial stiffness in hypertension.

Serum uric acid level has been found to be associated with cerebrovascular diseases. However, whether serum uric acid level is a risk factor for arterial stiffness in the hypertension population is unclear. This study was designed to determine the relationship between serum uric acid level and arterial stiffness in the hypertension population. A total of 10450 participants were evaluated for the risk of arterial stiffness. Brachial-ankle pulse wave velocity (baPWV) was assessed, and high baPWV was determined as the highest quartile of baPWV values in a sex-specific manner. We evaluated the association between serum uric acid level and baPWV through multivariate-adjusted linear and logistic regression analyses. There was a significant difference on high baPWV between patients with quartiles of serum uric acid level in females and males (p<0.01), respectively. The odds ratios (95% CI) of the highest baPWV quartile across the sex-specific serum uric acid level were 1.0, 1.71 (1.35, 2.17), 1.75 (1.38, 2.23), and 1.95 (1.51, 2.51) in female, and 1.0, 1.33 (1.09, 1.64), 1.36 (1.11, 1.67), and 1.67 (1.36, 2.04) in male after adjusting for potential confounders. In conclusion, serum uric acid level could be considered as an important risk factor for arterial stiffness in Chinese hypertension population.

The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis.

The rubber tree, Hevea brasiliensis, produces natural rubber that serves as an essential industrial raw material. Here, we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing (SMRT) and Hi-C technologies to anchor the ∼1.47-Gb genome assembly into 18 pseudochromosomes. The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution, since the common paleopolyploid event occurred before the split of Hevea and Manihot. We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years, leading to the massive expansion by ∼65.88% (∼970 Mbp) of the whole rubber tree genome since the divergence from Manihot. We identify large-scale expansion of genes associated with whole rubber biosynthesis processes, such as basal metabolic processes, ethylene biosynthesis, and the activation of polysaccharide and glycoprotein lectin, which are important properties for latex production. A map of genomic variation between the cultivated and wild rubber trees was obtained, which contains ∼15.7 million high-quality single-nucleotide polymorphisms. We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree, some of which are involved in rubber biosynthesis. This genome assembly represents key resources for future rubber tree research and breeding, providing novel targets for improving plant biotic and abiotic tolerance and rubber production.

A comparative study of pull-out performance of bolted joints in pultruded FRP with drilled holes or punched holes.

In this study, we investigate the pull-out performance of bolted joints of pultruded fiber reinforced polymer (PFRP) profile specimens with drilled and punched holes, respectively, and investigate the effects of different resin matrices and different fiber directions on the pull-out performance of the bolted joints. The experiment results show that the pull-out performance of the bolted joints in the uni-axial polyurethane-based PFRP is better than that in the uni-axial unsaturated polyester resin-based PFRP. The pull-out capacity of bolted joints on the multi-axial PFRP specimens with drilled holes is better than that of bolted joints in the uni-axial PFRP specimens with drilled holes. The multi-axial fiber can effectively prevent longitudinal splitting of pultruded profiles and significantly improve their pull-out performance. The punching process has little impact on the pull-out performance of bolted joints in the uni-axial PFRP specimens. However, it greatly undermines the pull-out performance of the bolt hole of the multi-axial PFRP specimens. Finally, using the progressive damage analysis (PDA) model, and combined with the Hashin failure criteria, we establish a model by means of the C3D8R solid elements in ABAQUS to simulate the pull-out mechanical behavior of the bolted joints.

Synonymous mutation adenomatous polyposis coliΔ486s affects exon splicing and may predispose patients to adenomatous polyposis coli/mutY DNA glycosylase mutation­negative familial adenomatous polyposis.

Familial adenomatous polyposis (FAP) is an autosomal dominant­inherited colorectal cancer. Recent advances in genetics have indicated that the majority of patients with FAP carry germline mutations of the adenomatous polyposis coli (APC) and mutY DNA glycosylase (MUTYH) genes. However, a large subset of families with a history of FAP have undetectable pathogenic alterations, termed APC/MUTYH mutation­negative FAP. To investigate the germline mutations in the APC and MUTYH genes in Chinese patients with FAP, 13 unrelated patients were enrolled. Through genetic sequencing, four known pathogenic alterations (Lys1061LysfsTer2, Glu1309AspfsTer4, Arg283Ter and Ser1196Ter) of APC and two novel disease­associated pathogenic mutations (Tyr152Ter and Ter522Gly) in MUTYH were identified in six individuals. For samples that did not present with pathogenic alterations, the functional effects of missense, synonymous and intronic mutations were analyzed using bioinformatics tools and databases. Bioinformatics prediction suggested that the synonymous mutation Tyr486Tyr in APC (APC∆486s) was likely a disease­causing polymorphism and may have induced the exon skipping of APC. A hybrid mini­gene assay was performed, which confirmed that the synonymous single nucleotide polymorphism APC∆486s induced major splicing defects with skipping of exon 12 in APC. The data of the present study suggested that the synonymous polymorphism APC∆486s was a potential pathogenic alteration that predisposed APC/MUTYH mutation­negative patients to FAP.

Ubiquitin-specific protease USP34 controls osteogenic differentiation and bone formation by regulating BMP2 signaling.

The osteogenic differentiation of mesenchymal stem cells (MSCs) is governed by multiple mechanisms. Growing evidence indicates that ubiquitin-dependent protein degradation is critical for the differentiation of MSCs and bone formation; however, the function of ubiquitin-specific proteases, the largest subfamily of deubiquitylases, remains unclear. Here, we identify USP34 as a previously unknown regulator of osteogenesis. The expression of USP34 in human MSCs increases after osteogenic induction while depletion of USP34 inhibits osteogenic differentiation. Conditional knockout of Usp34 from MSCs or pre-osteoblasts leads to low bone mass in mice. Deletion of Usp34 also blunts BMP2-induced responses and impairs bone regeneration. Mechanically, we demonstrate that USP34 stabilizes both Smad1 and RUNX2 and that depletion of Smurf1 restores the osteogenic potential of Usp34-deficient MSCs in vitro Taken together, our data indicate that USP34 is required for osteogenic differentiation and bone formation.

A potential peptide vector that allows targeted delivery of a desired fusion protein into the human breast cancer cell line MDA-MB-231.

Effective control of breast cancer has been primarily hampered by a lack of tumor specificity in treatments. One potential way to improve targeting specificity is to develop novel vectors that specifically bind to and are internalized by tumor cells. Through a phage display library, an 11-L-amino acid peptide, PI (sequence, CASPSGALRSC), was selected. PI was labeled with fluorescein isothiocyanate (FITC) and named PI-FITC. Subsequently, the specific affinity of PI-FITC to MDA-MB-231 human breast cancer cells and other cancer cell lines was observed by confocal microscopy. Our previous study established that PI-FITC also shows affinity to Calu-1 human lung carcinoma cells and major histocompatibility complex class I antigen molecules; therefore, the cytomembrane proteins of the cell lines were analyzed to determine those that were common to the two cell lines and may be associated with transmembrane transduction. To further test the delivery ability of PI to MDA-MB-231 cells, PI-glutathione-S-transferase (GST) was constructed and the internalization of this fusion protein was visualized by immunofluorescence microscopy. The results revealed that PI exhibited specific affinity to MDA-MB-231 cells. Use of membrane transport inhibitors indicated that macropinocytosis and caveolin-mediated endocytosis may be involved in the endocytosis of PI. In addition, 11 membrane proteins common to MDA-MB-231 and Calu-1 may be associated with transmembrane transduction. In summary, PI was able to deliver PI-GST into MDA-MB-231 cells. Thus, PI could be modified to be a potential vector, and may contribute to the development of targeted therapeutic strategies for breast cancer.

Investigating polymorphisms by bioinformatics is a potential cost-effective method to screen for germline mutations in Chinese familial adenomatous polyposis patients.

The aim of this study was to investigate germline mutations of the APC, MUTYH and AXIN2 genes in Chinese patients with familial adenomatous polyposis (FAP), and further assess the value of bioinformatics in screening the pathogenic changes predisposing to FAP. APC genes from 11 unrelated FAP patients in Yunnan province in China were firstly examined by exon-specific DNA sequencing. For samples without already known pathogenic changes predisposing to FAP in the APC gene, whole-gene sequencing of MUTYH and AXIN2 was performed. Mutational analysis of each gene was performed by bioinformatics. Eleven different types of APC polymorphisms were observed in the cohort of families analyzed. Of these polymorphisms, four were missense substitutions (V1822D, V1173G, P1760H and K2057), one was a nonsense substitution (S1196X), and six were silent substitutions (Y486Y, T449T, T1493T, G1678G, S1756S and P1960P). One missense mutation (Q335H) and two intronic substitutions (c.264+11G>A and c.420+35A>G) were detected in the MUTYH gene, and four synonymous mutations (I144I, P455P, P462P and L688L) and three intonic mutations (c.1060-77G>T, c.1060-287A>G and c.1060-282 A>G) of the AXIN2 gene were observed. In addition to the already reported pathogenic mutations, by using function assessment tools and databases, the synonymous substitutions observed in the APC gene of our samples were predicted to affect splicing regulation in the translation of mRNA, while the missense mutations observed in the APC gene and MUTYH gene were predicted to be disease-related polymorphisms; however, no functional effect of the mutations was observed in the AXIN2 gene. Comprehensive screening for germline mutations in APC, MUTYH and AXIN2 genes followed by prediction of pathogenicity using bioinformatic tools contributes to a cost-effective way of screening germline mutations in Chinese familial adenomatous polyposis patients.

Pneumothorax, pneumomediastinum, pneumoperitoneum and extensive subcutaneous emphysema resulting from endoscopic mucosal resection secondary to colonoscopy: A case report.

Rectal perforation is an unusual complication of therapeutic colonoscopy. The present study reports the case of a patient with a rare manifestation of pneumothorax, pneumomediastinum, pneumoperitoneum and extensive subcutaneous emphysema that resulted from an endoscopic mucosal resection following a colonoscopy of the rectum. Only 3 cases of colonic perforation and 1 case of rectal perforation have been described previously, of which the clinical diagnoses and treatments were varied, and no results of follow-up studies were reported. In the present study, dyspnea and neck swelling were acute signs of extraluminal air that resulted from rectal perforation. Computed axial tomography was an effective diagnosis method, and is recommended for the early recognition of colorectal perforation. Appropriate management and a close follow-up are crucial for optimal results.

[Effects of antisense oligonucleotide to nuclear factor-kappaB on the development of bleomycin-induced pulmonary fibrosis and IL-4 expression therein: experiment with mice].

OBJECTIVE: To investigate the expression of nuclear factor-kappaB (NF-kappaB) in the cells in the bronchoalveolar lavage fluid (BALF) of idiopathic pulmonary fibrosis (IPF) and its effects on IL-4 expression therein, and to investigate the therapeutic role of antisense oligonucleotide (ASON) to NF-kappaB on IPF. METHODS: C57BL/6 mice were randomly divided into 4 groups: bleomycin (BLM) group (n = 35, injected with BLM through caudal vein), control group [n = 20, injected with normal saline (NS) via caudal vein], ASON group (n = 35, injected with ASON to p65, a subunit of NF-kappaB, at the dose of 900 microg), and SON group (n = 35, injected with sense oligonucleotide to p65 subunit). Six hours after intravenous injection, the BLM, ASON, and SON groups were treated with BLM-A5 (5 mg/kg dissolved in 20 microl NS) by intratracheal installation, and the control group was treated with NS (20 microl). 0.5, 1, 3, 7, 14, and 28 days following intratracheal instillation of BLM or 0.5, 1, 14 days following intratracheal instillation of NS, 5 mice of every group were sacrificed and bronchoalveolar lavage was performed. The BALF was collected and assayed with ELISA for IL-4. Immunohistochemistry (IHC) and microscope image analysis were completed to detect the expression of p65 and IL-4 in the bronchoalveolar lavage cells. Another 5 mice from each group were sacrificed 28 days after intratracheal instillation with their total right lungs taken out to undergo pathohistological examination. The content of hydroxyproline in the left lung was detected by high performance liquid chromatography and ELISA. RESULTS: (1) Twenty-eight days after intratracheal instillation, the BLM and the SON groups showed consolidation of the lung parenchyma with loss of the alveolar architecture and increased cellularity, while the ASON and control groups showed no significant pulmonary consolidation or fibrosis. (2) Twenty-eight days after intratracheal instillation, the hydroxyproline content of the BLM group was 876.8 +/- 91.1 nmol/lung, significantly higher than that of the control group (347.6 +/- 53.9 nmol/lung, t = -9.833, P < 0.001); the hydroxyproline content of the ASON group was 505.6 +/- 34.8 nmol/lung, significantly lower than that of the BLM group (t = -9.862, P < 0.001); however, the hydroxyproline content of the SON group was 775.2 +/- 68.9 nmol/lung, not significantly different from that of the BLM group (t = 2.118, P = 0.102). (3) One day after the intratracheal instillation of BLM, the value of average integral optical density of p65 in the bronchoalveolar lavage cells of the BLM, SON, and ASON groups were 275 +/- 13, 233 +/- 60, 233 +/- 60, and 126 +/- 34 respectively, all significantly higher that of the control group (38 +/- 18, t = 27.350, 8.039, and 6.107, P < 0.001, = 0.001, and = 0.004), that of the ASON group being significantly lower than those of the BLM and SON groups (t = 7.664 and -3.407, P = 0.002 and 0.027). (4) IHC showed that 1 day after the intratracheal instillation, the value of average integral optical density of IL-4 of the BLM, SON, and ASON groups were 134 +/- 16, 128 +/- 2, and 80 +/- 9 respectively, all significantly higher than that of the control group (33 +/- 12, t = 10.346, -5.927, and 5.313, P < 0.001, = 0.004, = 0.006), that of the ASON group being significantly lower than those of the BLM and SON groups (t = 6.967 and -3.591, P = 0.002 and 0.023). (5) ELISA showed that 1 day after the intratracheal instillation the IL-4 level BLM, SON, and ASON groups were (20.8 +/- 7.2) ng/L, (21.4 +/- 8.0) ng/L, and (9.7 +/- 1.4) ng/L respectively, all significantly higher than that of the control group [(1.6 +/- 3.6) ng/L, t = 6.494, 4.143, and 4.331, P = 0.003, 0.014, and 0.012], that of the ASON group being significantly lower than those of the BLM and SON groups (t = -3.553 and -3.577, P = 0.024 and 0.023) (6) Correlation analysis showed that 1 day after intratracheal instillation the expression of p65 was positively correlated with IL-4 expression in the bronchoalveolar lavage cells in the treatment group (r = 0.890, P < 0.05) and the ASON group (r = 0.909, P < 0.05). CONCLUSION: The expression of NF-kappaB is significantly increased and augments the expression of IL-4 indirectly in the BALF cells during the process of BLM-induced lung fibrosis. ASON significantly inhibits the NF-kappaB activation and the IL-4 expression, and may be useful in gene therapy for pulmonary fibrosis.