Identification of PANoptosis-related subtypes, construction of a prognosis signature, and tumor microenvironment landscape of hepatocellular carcinoma using bioinformatic analysis and experimental verification.

Background: Hepatocellular carcinoma (HCC) is one of the most lethal malignancies worldwide. PANoptosis is a recently unveiled programmed cell death pathway, Nonetheless, the precise implications of PANoptosis within the context of HCC remain incompletely elucidated. Methods: We conducted a comprehensive bioinformatics analysis to evaluate both the expression and mutation patterns of PANoptosis-related genes (PRGs). We categorized HCC into two clusters and identified differentially expressed PANoptosis-related genes (DEPRGs). Next, a PANoptosis risk model was constructed using LASSO and multivariate Cox regression analyses. The relationship between PRGs, risk genes, the risk model, and the immune microenvironment was studies. In addition, drug sensitivity between high- and low-risk groups was examined. The expression profiles of these four risk genes were elucidate by qRT-PCR or immunohistochemical (IHC). Furthermore, the effect of CTSC knock down on HCC cell behavior was verified using in vitro experiments. Results: We constructed a prognostic signature of four DEPRGs (CTSC, CDCA8, G6PD, and CXCL9). Receiver operating characteristic curve analyses underscored the superior prognostic capacity of this signature in assessing the outcomes of HCC patients. Subsequently, patients were stratified based on their risk scores, which revealed that the low-risk group had better prognosis than those in the high-risk group. High-risk group displayed a lower Stromal Score, Immune Score, ESTIMATE score, and higher cancer stem cell content, tumor mutation burden (TMB) values. Furthermore, a correlation was noted between the risk model and the sensitivity to 56 chemotherapeutic agents, as well as immunotherapy efficacy, in patient with. These findings provide valuable guidance for personalized clinical treatment strategies. The qRT-PCR analysis revealed that upregulated expression of CTSC, CDCA8, and G6PD, whereas downregulated expression of CXCL9 in HCC compared with adjacent tumor tissue and normal liver cell lines. The knockdown of CTSC significantly reduced both HCC cell proliferation and migration. Conclusion: Our study underscores the promise of PANoptosis-based molecular clustering and prognostic signatures in predicting patient survival and discerning the intricacies of the tumor microenvironment within the context of HCC. These insights hold the potential to advance our comprehension of the therapeutic contribution of PANoptosis plays in HCC and pave the way for generating more efficacious treatment strategies.

Intron-mediated regulation of ß-tubulin genes expression affects the sensitivity to carbendazim in Fusarium graminearum.

The plant pathogenic fungus, Fusarium graminearum, is known to have two ß-tubulin genes (named Fg-ß1tub and Fg-ß2tub). Mutations in Fg-ß2tub rather than in Fg-ß1tub have been shown to confer resistance to carbendazim (MBC), even though Fg-ß1tub has higher homology than Fg-ß2tub to the ß-tubulin isotypes related to benzimidazole resistance in other fungi. However, sequence alignment of ß-tubulin isotypes related to benzimidazole resistance showed that the number and position of introns in Fg-ß2tub are more consistent than Fg-ß1tub to those in other ß-tubulin genes. In detail, Fg-ß1tub lacks three introns, i.e., intron i3, i4, and i6 corresponding to positions in Fg-ß2tub of F. graminearum. To investigate the effects of the divergence introns on the function of ß-tubulins in F. graminearum, a strategy of intron deletion and insertion was used. Our results showed that deletion of the second intron from Fg-ß1tub gene increased Fg-ß1tub expression levels leading to increased sensitivity to MBC. Besides, inserting the divergence introns into Fg-ß1tub can increase Fg-ß1tub expression leading to increased sensitivity to MBC. In addition, intron-mediated Fg-ß1tub gene expression requires a splicing-competent intron within the body of the host gene. Furthermore, the insertion and deletion of introns in Fg-ß1tub gene have no significant effect on hyphal growth, conidiation and virulence in F. graminearum. Thus, we proposed that introns may be among the factors contributing to the evolution and functional divergence of two ß-tubulin genes and also significantly regulate the expression of ß-tubulin genes, which, in turn, affects sensitivity to MBC fungicides in F. graminearum.

Regulatory roles of introns in fungicide sensitivity of Fusarium graminearum.

Although the roles of introns have been much debated in eukaryotic organisms, none of them have been functionally characterized in Fusarium graminearum. In this study, we characterized the roles of introns in regulation of fungicide-sensitivity of F. graminearum. ß2 tub, cyp51A and myosin-5 are important target genes of benzimidazoles, triazoles and cyanoacrylates respectively. To explore the sensitivity regulation functions of introns in target genes, several detailed deletion studies were completed on the intronic regions of ß2 tub, cyp51A and myosin-5. Phenotypic analyses showed that deletion of the fourth intron from ß2 tub gene (designated ß2 Δi4), the sole intron from cyp51A gene (cyp51A-Δi) and the second intron from myosin-5 gene (myo5-Δi2) exhibited an increased sensitivity to corresponding fungicides. In contrast, deletion of the first or second intron from ß2 tub gene exhibited a decreased sensitivity to carbendazim. qRT-PCR showed that the mRNA transcript levels of target genes were significantly downregulated in ß2 Δi4, cyp51A-Δi and myo5-Δi2 respectively. Meanwhile, Western blot assays revealed that the protein expression levels of ß2 tub was also dramatically reduced in ß2 Δi4, but accumulated in ß2 Δi1 and ß2 Δi2. Overall, our results indicate that introns in target genes significantly regulate the fungicide-sensitivity by influencing expression of the corresponding resident genes in F. graminearum.

A meta-analysis of the efficacy of ureteroscopic lithotripsy and extracorporeal shock wave lithotripsy on ureteral calculi.

PURPOSE: To re-evaluated the clinic efficacy of ureteroscopic lithotripsy (URS) and extracorporeal shock wave lithotripsy (ESWL) on ureteral calculi with Cochrane systematic reviews in this paper. METHODS: We searched clinical randomized controlled trials and prospective controlled trials in databases such as Cochrane library, Medline, Springer, Elsevier Science Direct, PubMed. Pooled estimate of risk ratios (RRs), standard mean difference (SMD) with 95% confidence intervals (CIs) were used as measure of effect sizes. Summary effect estimates were also stratified by sample size, study design and study region. The overall effect sizes were derived using a random-effects model or fixed-effects model when appreciated, and meta-analysis were conducted with software RewMan 5.0. RESULTS: The meta-analysis suggested that there were significant differences of post-treatment stone free rate, repeat treatment rate, patients' satisfaction, incidence of postoperative complications, operation time and hospital stays between ESWL treatment cases and URS treatment cases. But in the sample sizes analysis, there were no significant differences of the post-treatment stone free rate and repeat treatment rate when the sample sizes were less than 100. CONCLUSIONS: Compared to the ureteroscopic lithotripsy treatment, extracorporeal shock wave lithotripsy treatment provided a significantly lower post-treatment stone free rate, but it also obviously brought out less postoperative complications, shorter operation time and hospital stays.

A meta-analysis of the efficacy of ureteroscopic lithotripsy and extracorporeal shock wave lithotripsy on ureteral calculi

PURPOSE: To re-evaluated the clinic efficacy of ureteroscopic lithotripsy (URS) and extracorporeal shock wave lithotripsy (ESWL) on ureteral calculi with Cochrane systematic reviews in this paper. METHODS: We searched clinical randomized controlled trials and prospective controlled trials in databases such as Cochrane library, Medline, Springer, Elsevier Science Direct, PubMed. Pooled estimate of risk ratios (RRs), standard mean difference (SMD) with 95% confidence intervals (CIs) were used as measure of effect sizes. Summary effect estimates were also stratified by sample size, study design and study region. The overall effect sizes were derived using a random-effects model or fixed-effects model when appreciated, and meta-analysis were conducted with software RewMan 5.0. RESULTS: The meta-analysis suggested that there were significant differences of post-treatment stone free rate, repeat treatment rate, patients' satisfaction, incidence of postoperative complications, operation time and hospital stays between ESWL treatment cases and URS treatment cases. But in the sample sizes analysis, there were no significant differences of the post-treatment stone free rate and repeat treatment rate when the sample sizes were less than 100. CONCLUSIONS: Compared to the ureteroscopic lithotripsy treatment, extracorporeal shock wave lithotripsy treatment provided a significantly lower post-treatment stone free rate, but it also obviously brought out less postoperative complications, shorter operation time and hospital stays. .

Gene expression profiling of human kidneys undergoing laparoscopic donor nephrectomy.

BACKGROUND AND OBJECTIVES: The objective was to compare gene expression profiles of 6 kidneys from open donor nephrectomy with 6 kidneys removed after laparoscopic donor nephrectomy and several hours of carbon dioxide pneumoperitoneum with DNA microarrays and identify small-molecule drugs. METHODS: The gene expression profile GSE3297 was downloaded from the Gene Expression Omnibus database, and the differentially expressed genes were identified by a bioinformatics approach. First, Osprey software was used to construct a differentially expressed gene associated network. Then, DAVID (Database for Annotation, Visualization, and Integrated Discovery) and FuncAssociate were used to perform functional analyses. Finally, the Connectivity Map was used to screen for small-molecule drugs. RESULTS: A total of 285 differentially expressed genes were identified, including 148 down-regulated genes and 137 up-regulated genes. In addition, the differentially expressed genes in the most significant Gene Ontology term were CASP6, KRAS, SOCS1, ESR1, TSHB, COL1A1, and MMP14. Furthermore, several differentially expressed genes, including STAT1, STAT6, SOS2, and SOCS1, participated in the most remarkable Janus kinase-signal transducer and activator of transcription signaling pathway. Finally, luteolin--with the highest score (0.887)--was identified as the small-molecule drug. CONCLUSIONS: Our data show an altered renal transcriptome induced by several hours of carbon dioxide pneumoperitoneum and laparoscopic surgery characterized by up-regulation of genes associated with acute inflammation, apoptosis, and immune injury, which could potentially result in renal injury and an enhanced immune response in the recipient after transplant.

Identifying differentially expressed genes and small molecule drugs for prostate cancer by a bioinformatics strategy.

PURPOSE: Prostate cancer caused by the abnormal disorderly growth of prostatic acinar cells is the most prevalent cancer of men in western countries. We aimed to screen out differentially expressed genes (DEGs) and explore small molecule drugs for prostate cancer. MATERIALS AND METHODS: The GSE3824 gene expression profile of prostate cancer was downloaded from Gene Expression Omnibus database which including 21 normal samples and 18 prostate cancer cells. The DEGs were identified by Limma package in R language and gene ontology and pathway enrichment analyses were performed. In addition, potential regulatory microRNAs and the target sites of the transcription factors were screened out based on the molecular signature database. In addition, the DEGs were mapped to the connectivity map database to identify potential small molecule drugs. RESULTS: A total of 6,588 genes were filtered as DEGs between normal and prostate cancer samples. Examples such as ITGB6, ITGB3, ITGAV and ITGA2 may induce prostate cancer through actions on the focal adhesion pathway. Furthermore, the transcription factor, SP1, and its target genes ARHGAP26 and USF1 were identified. The most significant microRNA, MIR-506, was screened and found to regulate genes including ITGB1 and ITGB3. Additionally, small molecules MS-275, 8-azaguanine and pyrvinium were discovered to have the potential to repair the disordered metabolic pathways, abd furthermore to remedy prostate cancer. CONCLUSIONS: The results of our analysis bear on the mechanism of prostate cancer and allow screening for small molecular drugs for this cancer. The findings have the potential for future use in the clinic for treatment of prostate cancer.

Integrated gene network analysis and text mining revealing PIK3R1 regulated by miR-127 in human bladder cancer.

BACKGROUND: Cancer is the result of a complex multistep process that involves the accumulation of sequential alterations of several genes, including those encoding microRNAs (miRNAs) that have critical roles in the regulation of gene expression.In this study, we aimed to predict potential mechanisms of bladder cancer related miRNAs and target genes by bioinformatics analyses. METHODS: Here we used the method of text mining to identify nine miRNAs in bladder cancer and adopted protein-protein interaction analysis to identify interaction sites between these miRNAs and related-target genes. RESULTS: There are two relationship types between bladder cancer and its related miRNAs: causal and unspecified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment test showed that there were three pathways related to four miRNA targeted genes. The remaining five miRNAs annotated to disease are not enriched in the KEGG pathways. Of these, PIK3R1 is the overlapping gene among 38 genes in the cancer and bladder cancer pathways. CONCLUSIONS: These findings provide new insights into the role of miRNAs in the pathway of cancer and give us a hypothesis that miR-127 might play a similar role in regulation and control of PIK3R1.

[Study on the correlation of the 5-HTTLPR polymorphism with premature ejaculation in Han Chinese population].

OBJECTIVE: To investigate the relationship between 5-HT transporter gene-linked polymorphism (5-HTTPLR) and the clinical characters of premature ejaculation in Han Chinese population. METHODS: By case-control study approach, we set primary premature ejaculation (PPE) group (119 cases), secondary premature ejaculation (SPE) group (60 cases) with IELT < 1 min in more than 90% coitus and normal control group (90 cases) with IELT ≥ 3 min. The gene polymorphism of the 5-HTT was detected by polymerase chain reaction analysis in all the cases, and the gene frequency differences among the three groups were evaluated. RESULTS: The frequency of the genotype S/S was higher in PPE group than in normal control group(51.3% vs. 37.8%,P<0.01), and the frequency of genetype L/S was lower in PPE group than in normal vontrol group(28.6% vs. 34.4%,P<0.05).The S allele was higher in PPE group than in control group (P<0.05), but there was no difference between the SPE group and the normal control group. CONCLUSION: The 5-HTTLPR polymorphism is associated with PPE, which shows that genetics may play an important role in the occurrence of PPE but not of SPE. The etiology of PPE and SPE is different.

Association between polymorphisms in the serotonin 2C receptor gene and premature ejaculation in Han Chinese subjects.

INTRODUCTION: Lifelong premature ejaculation (LPE) is characterized by persistently shorter intravaginal ejaculation latency time (IELT) than found acceptable by the patient or his partner. It has been postulated to be a neurobiological dysfunction with genetic vulnerability and is related to disturbances of central serotonin (5-hydroxytryptamine, 5-HT) neurotransmission and 5-HT receptor function. AIM: To investigate the relationship between the C-759T and G-697C polymorphisms of the 5-HT(2C) receptor and LPE. METHODS: A prospective study was conducted in 106 Han Chinese men with LPE, characterized by IELT of less than 1 min, and 84 healthy controls with IELT of more than 3 min. All subjects were genotyped for the C-759T and G-697C polymorphisms located in the promoter region of the 5-HT(2C) receptor. The frequencies of genotypes and single nucleotide mutations were compared between the two groups. RESULTS: Three genotypes were detected both in the men with LPE and in the control group: -759C/-697G, -759T/-697C, and -759C/ -697C. Genotype -759T/-697G was not detected. The frequency of genotype -759T/-697C was higher in patients with LPE than in the control group (30.2 vs. 11.9%, p < 0.05), whereas the frequency of genotype -759C/-697G was lower in patients with LPE than in the control group (66.0 vs. 83.3%, p < 0.05). No difference was found for genotype -759C/ -697C between the two groups. Mutations at -759T and -697C were more frequent in patients than in the control group (-759T: 30.2 vs. 13.3%, p < 0.05; -697C: 30.4 vs. 16.7%, p < 0.05, respectively). CONCLUSIONS: Our findings indicated that polymorphisms in the 5-HT(2C) receptor gene are associated with LPE, and men who carry the -759T or -697C genotype have increased odds of premature ejaculation. Further investigation in this field is necessary.

[Efficacy and safety of selective serotonin re-uptake inhibitors in the treatment of premature ejaculation: a systematic evaluation].

OBJECTIVE: To evaluate the efficacy and safety of selective serotonin re-uptake inhibitors (SSRIs) in the treatment of premature ejaculation (PE). METHODS: From MEDLINE (Jan, 1950-Mar, 2008), EMBASE (Jan, 1980-Mar, 2008), The Cochrane Library (Issue 1, 2008) and CNKI (Jan, 1979-Mar, 2008), we retrieved and screened the randomized controlled trials (RCT) and randomized crossover trials (RT) as well as various related data, published and unpublished, on the treatment of PE with SSRIs. The methodological quality of the included trials was evaluated by 2 reviewers. Meta-analyses were conducted with RevMan 5.0 on the homogeneous studies. RESULTS: Totally 22 studies on 4 291 patients were included. Meta-analyses showed that after treated with sertraline, fluoxetine, paroxetine, citalopram, dapoxetine and fluvoxamine, the WMD (95% CI) values of the changes in intravaginal ejaculatory latency time (IELT) were 2.63 (1.80, 3.46), 2.21 (1.50, 2.92), 4.31 (2.71, 5.91), 3.82 (3.39, 4.25), 1.57 (1.31, 1.84) and 0.01 (0.71, 0.73) respectively; the RR (95% CI) values of the sexual satisfaction rate of the patients were 1.65 (1.12, 2.43), 2.93 (0.50, 17.31), 3.08 (2.27, 4.17), 2.48 (1.99, 3.09) and 2.93 (2.36, 3.65), and those of their partners were 1.47 (0.98, 2.21), 2.88 (0.38, 21.77), 4.81 (3.15, 7.36), 5.38 (3.75, 7.72) and 2.91 (1.09, 7.78) respectively for sertraline, fluoxetine, paroxetine, citalopram and dapoxetine. CONCLUSION: All the known SSRIs but fluvoxamine could prolong IELT, and some could improve the sexual satisfaction of both the patients and their partners, but their adverse effects should be noted. The moderate possibility of selection bias and publication bias in the included studies might have a negative impact on the evidence intensity of our results. We expect more reliable evidence from more randomized controlled trials.