Assessment of SWI/SNF chromatin remodeling complex related genes as potential biomarkers and therapeutic targets in pan-cancer.

Recent research has uncovered a surprisingly high occurrence of aberrant expression and mutations in the genes that encode subunits of the SWI/SNF chromatin-remodeling complexes (SCRC). Nevertheless, the carcinogenic effects of aberrant expression and mutations in SWI/SNF genes have only been acknowledged in recent times, resulting in a comparatively limited understanding of these modifications. In this study, we comprehensively analyzed the expression difference, somatic mutation, potential biological pathways, stromal or immune cell infiltration, and drug sensitivity of SCRC-related genes (SCRGs) in pan-cancer. Furthermore, the evolutionary trend, prognostic signature, and immunotherapy response of SCRGs in kidney renal clear cell carcinoma (KIRC) were also evaluated. The expression of SCRGs was changed in 13 out of 14 tumor types, strongly linked to prognosis, and mutated in 30.9% of tumor patients. SCRGs were also closely associated with immune-related pathways and tumor metastasis pathways. The expression of SCRGs was positively associated with the immune score or stromal score but negatively correlated with Tumor purity. Three potential drugs (FK866, Ispinesib mesylate, and WZ3105) were identified to target the SCRGs. In KIRC, scRNA-seq analysis showed that the enrichment of SCRC and the communication frequency with immune cells were significantly declined during tumor cell progression. A prognostic signature was constructed in KIRC and was effective in predicting the prognosis for KIRC. Aberrant expression of eleven prognostic genes identified from the KIRC prognostic signature and the cytotoxicity of FK866 and Ispinesib mesylate to KIRC were verified by qRT-PCR and CCK-8 assay, respectively. Our study identified SCRGs as potential biomarker and therapeutic targets, providing new insights into SCRC for tumor-targeted therapy.

Mitotically heritable epigenetic modifications of CmMYB6 control anthocyanin biosynthesis in chrysanthemum.

Flower color, which is determined by various chemical pigments, is a vital trait for ornamental plants, in which anthocyanin is a major component. However, the epigenetic regulation of anthocyanin biosynthesis remains poorly understood. During chrysanthemum cultivation, we found a heterochromatic chrysanthemum accession (YP) whose progeny generated by asexual reproduction contained both yellow-flowered (YP-Y) and pink-flowered (YP-P) plants. In this study, we aimed to elucidate the epigenetic mechanisms of different flower colors in the YP plant progeny. Metabolome and transcriptome analyses revealed that the difference in flower color between YP-Y and YP-P was caused by expression variation of the anthocyanin biosynthesis gene CmMYB6. Bisulfite sequencing revealed that methylation at the CmMYB6 promoter, especially in the CHH context, was higher in YP-Y than YP-P. After demethylation of the CmMYB6 promoter using the dCas9-TET1cd system, the flower color returned from yellow to pink. Furthermore, the methylation status of the CmMYB6 promoter was higher in YP-Y over three consecutive generations, indicating that this methylation status was heritable mitotically. Finally, investigation of other chrysanthemum cultivars showed that the methylation of CmMYB6 decreased gradually with the increase in anthocyanin content. These results lay an epigenetic foundation for the improvement of flower color in horticultural plants.

The association between changes in multifidus muscle morphology and back pain scores following discectomy surgery for lumbar disc herniation: a systematic review and meta-analysis.

PURPOSE: To evaluate the impact of discectomy on back muscles (e.g. multifidus muscle (MM)) morphology in patients with lumbar disc herniation (LDH) following discectomy surgery, address the association of back muscles morphology with pain score preoperatively and post-operatively, and investigate the relationships between the changes from pre- to post-operative back muscles measurements and pain score (primary outcome) and disability score (secondary outcome) change following discectomy if any. METHODS: We searched three online databases for randomized controlled trials (RCTs) and observational studies. In LDH patients, eligible for discectomy surgery, pre- and post-operative and the changes from pre- to post-operative of back and/or leg pain with Visual Analogue Scale (VAS) and multifidus muscle morphology, were considered as primary outcomes. Cochrane Risk-of-Bias 2 tool and Newcastle-Ottawa Scale (NOS) were used to assess the methodological quality of RCTs and observational studies, respectively. Standardize mean difference (SMD) with 95% confidence intervals (CI) was evaluated. A meta-regression analysis was conducted. GRADE approach was used to summarize the strength of evidence. RESULTS: One RCT and five observational studies were included in the analysis of 489 patients with LDH undergoing discectomy surgery. The mean overall follow-up was 64.9 weeks (6 to 148.7 weeks). There was a significant negative relationship between the change from pre- to post-operative cross-sectional area (CSA) in MM and change in VAS back pain [regression coefficient = -0.01, (95% CI = -0.02, -0.01), p = 0.044] after discectomy surgery. No significant relationship between preoperative CSA in MM and preoperative/post-operative clinical (any of the follow-up periods) scores could be established. CONCLUSION: The results of this study found very low-quality grade evidence for an association between higher reduction of CSA in MM and less reductions of back pain scores following discectomy surgery for patients with LDH. Due to the heterogeneity and methodological limitations, further studies will improve understanding and aid preoperative counselling.

Postoperative survival analysis of hepatocellular carcinoma patients with liver cirrhosis based on propensity score matching.

OBJECTIVE: Most hepatocellular carcinoma (HCC) patients in China have some degree of liver cirrhosis. The effect of cirrhosis on the long-term prognosis of HCC patients after hepatectomy is still unclear. This study aimed to investigate the effect of liver cirrhosis on the prognosis of HCC patients after hepatectomy. METHODS: Data from patients who underwent hepatectomy and had pathologically confirmed HCC were retrospectively collected. The patients' clinical pathological data were recorded. Propensity score matching (PSM) was used to eliminate the influence of potential confounding factors. The Kaplan-Meier method was used to calculate the recurrence-free survival (RFS) and overall survival (OS) rates, and Cox regression analysis was used to screen for independent risk factors affecting OS and RFS. RESULTS: A total of 1381 HCC patients who were initially treated with hepatectomy were included, including 797 patients with liver cirrhosis. The RFS and OS rates in the group with cirrhosis were significantly lower than those in the group without cirrhosis (after PSM, RFS: P < 0.001; OS: P = 0.001). Subgroup analysis showed that among patients with Barcelona Clinic Liver Cancer (BCLC) stage 0-B disease, RFS and OS were significantly lower in those with cirrhosis than in those without cirrhosis (both P < 0.05); while in patients with stage C disease, there was no significant difference between those with and without cirrhosis. In the group with cirrhosis, alpha-fetoprotein (AFP) > 400, intraoperative blood loss, tumor diameter > 5 cm, satellite lesions, and large vessel invasion were independent risk factors for RFS, while albumin-bilirubin (ALBI) grade, neutrophil-to-lymphocyte ratio (NLR), tumor diameter > 5 cm, satellite lesions, microvascular invasion, and macrovascular invasion were independent risk factors for OS. CONCLUSION: HCC with liver cirrhosis has specific characteristics. Compared with patients without cirrhosis, patients with cirrhosis have worse long-term survival after surgery. In addition, the independent risk factors for RFS and OS are different between patients with cirrhosis and without cirrhosis; liver cirrhosis is an independent risk factor for the long-term prognosis of HCC patients, especially patients with BCLC stage 0-B disease after hepatectomy.

Leaf transcriptomic response mediated by cold stress in two maize inbred lines with contrasting tolerance levels.

Maize (Zea mays L.) is a thermophilic plant and a minor drop in temperature can prolong the maturity period. Plants respond to cold stress through structural and functional modification in cell membranes as well as changes in the photosynthesis and energy metabolism. In order to understand the molecular mechanisms underlying cold tolerance and adaptation, we employed leaf transcriptome sequencing together with leaf microstructure and relative electrical conductivity measurements in two maize inbred lines, having different cold stress tolerance potentials. The leaf physiological and transcriptomic responses of maize seedlings were studied after growing both inbred lines at 5 °C for 0, 12 and 24 h. Differentially expressed genes were enriched in photosynthesis antenna proteins, MAPK signaling pathway, plant hormone signal transduction, circadian rhythm, secondary metabolites related pathways, ribosome, and proteasome. The seedlings of both genotypes employed common stress responsive pathways to respond to cold stress. However, the cold tolerant line B144 protected its photosystem II from photooxidation by upregulating D1 proteins. The sensitive line Q319 was unable to close its stomata. Collectively, B144 exhibited a cold tolerance owing to its ability to mediate changes in stomata opening as well as protecting photosystem. These results increase our understanding on the cold stress tolerance in maize seedlings and propose multiple key regulators of stress responses such as modifications in photosystem II, stomata guard cell opening and closing, changes in secondary metabolite biosynthesis, and circadian rhythm. This study also presents the signal transduction related changes in MAPK and phytohormone signaling pathways in response to cold stress during seedling stage of maize.

PMEPA1 interference activates PTEN/PI3K/AKT, thereby inhibiting the proliferation, invasion and migration of pancreatic cancer cells and enhancing the sensitivity to gemcitabine and cisplatin.

To explore the biological activity of transmembrane prostateandrogen induced RNA (PMEPA1) in human pancreatic cancer (hPAC) cells and its drug sensitivity to gemcitabine (GEM) and cisplatin (DDP). Gene Expression Profiling Interactive Analysis (GEPIA) and Cancer Cell Line Encyclopedia (CCLE) were consulted to indicate the expression of PMEPA1 in hPAC tissues and cells. Quantitative real-time PCR (RT-qPCR) and western blot were performed to verify the indication. RT-qPCR and western blot also detected the expressions of PTEN/PI3K/AKT before and after transfection of PMEPA1 siRNA plasmids. Cell counting Kit-8 (CCK-8) and EdU staining were performed to examine cell proliferation before and after transfection of phosphatase and tensin homologue delet2ed on chromosome ten (PTEN) siRNA plasmids. Transwell and wound healing detected the invasion and migration of hPAC cells. The expressions of MMP-2 and MMP-9 were detected by western blot. After GEM or DDP treatment, cell viability was observed by commercial kits and cell apoptosis by flow cytometry. GEPIA and CCLE predicted increased expression of PMEPA1 in hPAC tissues and cells, which was confirmed by quantitative reverse transcription polymerase chain reaction (RT-qPCR) and western blot. PMEPA1 was also shown to be associated with disease-free survival. Transfection of PMEPA1 siRNA plasmids affected the expressions of PTEN/PI3K/AKT. PMEPA1 interference inhibited the proliferation, invasion and migration of hPAC cells. Furthermore, PMEPA1 interference also enhanced the sensitivity of hPAC cells to GEM and DDP via PTEN interference. PMEPA1 interference inhibits the proliferation, invasion and migration of pancreatic cancer cells and enhances the sensitivity to GEM and cisplatin by activating PTEN/PI3K/AKT signaling.

Transgenerationally Transmitted DNA Demethylation of a Spontaneous Epialleles Using CRISPR/dCas9-TET1cd Targeted Epigenetic Editing in Arabidopsis.

CRISPR/dCas9 is an important DNA modification tool in which a disarmed Cas9 protein with no nuclease activity is fused with a specific DNA modifying enzyme. A previous study reported that overexpression of the TET1 catalytic domain (TET1cd) reduces genome-wide methylation in Arabidopsis. A spontaneous naturally occurring methylation region (NMR19-4) was identified in the promoter region of the PPH (Pheophytin Pheophorbide Hydrolase) gene, which encodes an enzyme that can degrade chlorophyll and accelerate leaf senescence. The methylation status of NMR19-4 is associated with PPH expression and leaf senescence in Arabidopsis natural accessions. In this study, we show that the CRISPR/dCas9-TET1cd system can be used to target the methylation of hypermethylated NMR19-4 region to reduce the level of methylation, thereby increasing the expression of PPH and accelerating leaf senescence. Furthermore, hybridization between transgenic demethylated plants and hypermethylated ecotypes showed that the demethylation status of edited NMR19-4, along with the enhanced PPH expression and accelerated leaf senescence, showed Mendelian inheritance in F1 and F2 progeny, indicating that spontaneous epialleles are stably transmitted trans-generationally after demethylation editing. Our results provide a rational approach for future editing of spontaneously mutated epialleles and provide insights into the epigenetic mechanisms that control plant leaf senescence.

Genome-wide identification and expression analysis of the AT-hook Motif Nuclear Localized gene family in soybean.

BACKGROUND: Soybean is an important legume crop and has significant agricultural and economic value. Previous research has shown that the AT-Hook Motif Nuclear Localized (AHL) gene family is highly conserved in land plants, playing crucial roles in plant growth and development. To date, however, the AHL gene family has not been studied in soybean. RESULTS: To investigate the roles played by the AHL gene family in soybean, genome-wide identification, expression patterns and gene structures were performed to analyze. We identified a total of 63 AT-hook motif genes, which were characterized by the presence of the AT-hook motif and PPC domain in soybean. The AT-hook motif genes were distributed on 18 chromosomes and formed two distinct clades (A and B), as shown by phylogenetic analysis. All the AHL proteins were further classified into three types (I, II and III) based on the AT-hook motif. Type-I was belonged to Clade-A, while Type-II and Type-III were belonged to Clade-B. Our results also showed that the main type of duplication in the soybean AHL gene family was segmented duplication event. To discern whether the AHL gene family was involved in stress response in soybean, we performed cis-acting elements analysis and found that AHL genes were associated with light responsiveness, anaerobic induction, MYB and gibberellin-responsiveness elements. This suggest that AHL genes may participate in plant development and mediate stress response. Moreover, a co-expression network analysis showed that the AHL genes were also involved in energy transduction, and the associated with the gibberellin pathway and nuclear entry signal pathways in soybean. Transcription analysis revealed that AHL genes in Jack and Williams82 have a common expression pattern and are mostly expressed in roots, showing greater sensitivity under drought and submergence stress. Hence, the AHL gene family mainly reacts on mediating stress responses in the roots and provide comprehensive information for further understanding of the AT-hook motif gene family-mediated stress response in soybean. CONCLUSION: Sixty-three AT-hook motif genes were identified in the soybean genome. These genes formed into two distinct phylogenetic clades and belonged to three different types. Cis-acting elements and co-expression network analyses suggested that AHL genes participated in significant biological processes. This work provides important theoretical basis for the understanding of AHLs biological functions in soybean.

Construction of an integrated human osteosarcoma database, HOsDb, based on literature mining, microarray analysis, and database retrieval.

BACKGROUND: Osteosarcoma (OS) is the most frequent primary malignancy of bone with a high incidence in adolescence. This study aimed to construct a publicly available, integrated database of human OS, named HOsDb. METHODS: Microarray data, current databases, and a literature search of PubMed were used to extract information relevant to human OS-related genes and their transcription factors (TFs) and single nucleotide polymorphisms (SNPs), as well as methylation sites and microRNAs (miRNAs). This information was collated for constructing the HOsDb. RESULTS: In total, we identified 7191 OS tumor-related genes, 763 OS metastasis-related genes, and 1589 OS drug-related genes, corresponding to 190,362, 21,131, and 41,135 gene-TF pairs, respectively, 3,749,490, 358,361, and 767,674 gene-miRNA pairs, respectively; and 28,386, 2532, and 3943 SNPs, respectively. Additionally, 240 OS-related miRNAs, 1695 genes with copy number variations in OS, and 18 genes with methylation sites in OS were identified. These data were collated to construct the HOsDb, which is available at www.hosdatabase.com. Users can search OS-related molecules using this database. CONCLUSION: The HOsDb provides a platform that is comprehensive, quick, and easily accessible, and it will enrich our current knowledge of OS.

miRNA-339-5p Plays an Important Role in Invasion and Migration of Pancreatic Cancer Cells.

BACKGROUND This study aimed to investigate the role of miRNA-339-5p in pancreatic cancer cell invasion and migration. MATERIAL AND METHODS The differences between exosomal miRNAs of PANC02 and PANC02-H7 were studied by microarray analysis. We measured miRNA-339-5p expression in different groups; differences in cell invasion and migration were evaluated using the Transwell and wound healing assays and expression of relative proteins (E-cadherin, vimentin and ZNF689) was measured by WB assay. The correlation between miRNA-339-5p and ZNF689 expression was evaluated by luciferase reporter gene assay. RESULTS Compared with PANC02 exosome, microarray analysis indicated that miRNA-339-5p mRNA expression was significantly suppressed (P<0.001) in the PANC02-H7 exosome. Supplementation with miR-339-5p mimics led to a significant decrease in the invasion cell number and wound healing rate (P<0.001), with significantly enhanced E-cadherin expression and suppressed vimentin expression (P<0.001). However, transfection of a miR-339-5p inhibitor led to a significant increase in the invasion cell number and wound healing rate (P<0.001), with significantly suppressed E-cadherin expression and increased vimentin expression (P<0.001). Luciferase reporter gene assay demonstrated ZNF689 gene to be the target of miR-339-5p in the PANC02-H7 cell. With miR-339-5p and ZNF689 transfection, the invasion cell number and wound healing rate were significantly increased compared with those in the miR-339-5p group (P<0.001), with significantly increased expression of ZNF689 and vimentin and suppressed E-cadherin expression (P<0.001). CONCLUSIONS miR-339-5p suppresses the invasion and migration of pancreatic cancer cells via direct regulation of ZNF689 in vitro.

Conditional survival in patients with spontaneous tumor rupture of hepatocellular carcinoma after partial hepatectomy: a propensity score matching analysis.

BACKGROUND: Spontaneous tumor rupture (STR) of hepatocellular carcinoma (HCC) is a life-threatening condition. This study investigates the influences of STR on the observed survival and conditional survival of patients received hepatectomy. METHODS: A retrospective cohort of patients who underwent hepatectomy from 2009 to 2013 was divided into tumor rupture group and non-rupture group. Propensity score matching (PSM) was used for comparison of the observed survival and conditional survival probabilities between these two groups. RESULTS: 89 pairs of patients who had comparable background and tumor characteristics were created using PSM analysis. There was significant association between STR and increased risk of OS no matter when before or after PSM (p < 0.01). STR was significantly associated with increased risks of PFS before, while not after PSM. Multivariate Cox regression analyses demonstrated that STR was an independent risk factor associated with OS. There were significant differences in two groups for conditional probabilities of OS and PFS for an additional 6 months and 1 year before PSM, while not after PSM. CONCLUSIONS: This study identified STR but not PFS as an independent risk factor influencing OS, in patients with HCC following hepatectomy. In selected patients with STRHCC, hepatectomy should be performed with acceptable outcomes.

Synergistic Effects of Transplanted Endothelial Progenitor Cells and RWJ 67657 in Diabetic Ischemic Stroke Models.

BACKGROUND AND PURPOSE: An immature vascular phenotype in diabetes mellitus may cause more severe vascular damage and poorer functional outcomes after stroke, and it would be feasible to repair damaged functional vessels using endothelial progenitor cell (EPC) transplantation. However, high glucose induces p38 mitogen-activated protein kinase activation, which can accelerate the senescence and apoptosis of EPCs. The aim of this study was to investigate the combined effects of EPC transplantation and p38 mitogen-activated protein kinase inhibitor administration on diabetic stroke outcomes. METHODS: Bone marrow-derived EPCs were injected intra-arterially into db/db mice after ischemic stroke induction. RWJ 67657 (RWJ), a p38 mitogen-activated protein kinase inhibitor, was administered orally for 7 consecutive days, with the first dose given 30 minutes before stroke induction. Functional outcome was determined at days 0, 1, 7, 14, and 21. Angiogenesis, neurogenesis, infarct volume, and Western blotting assays were performed on day 7, and white matter remodeling was determined on day 14. RESULTS: Neither EPC transplantation nor RWJ administration alone significantly improved diabetic stroke outcome although RWJ displayed a potent anti-inflammatory effect. By both improving the functioning of EPCs and reducing inflammation, EPC transplantation plus RWJ administration in vivo synergistically promoted angiogenesis and neurogenesis after diabetic stroke. In addition, the white matter remodeling, behavioral scores, and expressions of vascular endothelial growth factor and brain-derived neurotrophic factor were significantly increased in diabetic mice treated with both EPCs and RWJ. CONCLUSIONS: The combination of EPC transplantation and RWJ administration accelerated recovery from diabetic stroke, which might have been caused by increased levels of proangiogenic and neurotrophic factors.

Comprehensive analysis of genes, pathways, and TFs in nonsmoking Taiwan females with lung cancer.

PURPOSE: The aim of this study was to investigate the molecular mechanism of lung cancer among nonsmoking Taiwan females. MATERIALS AND METHODS: By using the GSE19804 microarray data accessible from Gene Expression Omnibus (GEO) database, we identified differentially expressed genes (DEGs) between nonsmoking female lung cancer patients and healthy controls (!logFC! >1.5 and p-value < 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene ontology (GO) enrichment analysis was performed using Database for Annotation, Visualization and Integrated Discovery (DAVID). The Search Tool for the Retrieval of Interacting Genes (STRING) tool was utilized to build a protein-protein interaction (PPI) network, followed by the construction of a transcriptional regulatory network based on Transcription factor (TRANSFAC) database. RESULTS: As a result, 320 DEGs were identified between nonsmoking female patients with lung cancer and healthy controls. Pathway enrichment analysis showed significantly enriched pathways such as extracellular matrix (ECM)-receptor interaction and peroxisome proliferator-activated receptor (PPAR) signaling pathway, both of which were enriched with genes COL11A1 (encoding collagen XI alpha-1 chain protein), COL1A1, cluster of differentiation 36(CD36). GO enrichment analysis found that DEGs were significantly related to chemotaxis, vasculature development and cell adhesion GO terms. IL-6 was the node of the PPI network. Critical transcription factors (TFs) including CCAAT/enhancer-binding protein delta (CEBPD) and Rel/NF-κB were also identified. CONCLUSIONS: Our study revealed that ECM-receptor interaction, PPAR signaling pathways, and important biomolecules including COL11A1, COL1A1, CD36, IL-6, CEBPD, and Rel/NF-κB might be involved in lung cancer. This study might pave the way for the development and application of targeted therapeutics of lung cancer irrelevant to smoking.

Chemotactic recruitment of adult neural progenitor cells into multifunctional hydrogels providing sustained SDF-1α release and compatible structural support.

Without chemotactic cues and structural support, cavitary brain lesions typically fail to recruit endogenous neural progenitor cells (NPCs). Toward resolving this, we engineered multifunctional biomaterials comprising injectable gelatin-hydroxyphenylpropionic acid (Gtn-HPA) hydrogels and dextran sulfate/chitosan polyelectrolyte complex nanoparticles (PCNs) that delivered stromal cell-derived factor-1α (SDF-1α). Over 7 d of interface with in vitro tissue simulant containing adult rat hippocampal NPCs (aNPCs) and their neuronal progeny, Gtn-HPA/SDF-1α-PCN hydrogels promoted chemotactic recruitment to enhance infiltration of aNPCs by 3- to 45-fold relative to hydrogels that lacked SDF-1α or vehicles to sustain SDF-1α release. When cross-linked with 0.85-0.95 mM HO, Gtn-HPA/SDF-1α-PCN hydrogels provided optimally permissive structural support for migration of aNPCs. Specific matrix metalloproteinase (MMP) inhibitors revealed that 42, 30, and 55% of cell migration into Gtn-HPA/SDF-1α-PCN hydrogels involved MMP-2, 3, and 9, respectively, demonstrating the hydrogels to be compatible toward homing endogenous NPCs, given their expression of similar MMPs. Interestingly, PCNs utilized FGF-2 found in situ to induce chemokinesis, potentiate SDF-1α chemotactic recruitment, and increase proliferation of recruited cells, which collectively orchestrated a higher number of migrated aNPCs. Overall, Gtn-HPA/SDF-1α-PCN hydrogels prove to be promising biomaterials for injection into cavitary brain lesions to recruit endogenous NPCs and enhance neural tissue repair/regeneration.

Diagnostic accuracy of low-dose dual-input computed tomography perfusion in the differential diagnosis of pulmonary benign and malignant ground-glass nodules.

This study aimed to evaluate the value of low-dose dual-input computed tomography perfusion (CTP) imaging in the differential diagnosis of benign and malignant pulmonary ground-glass opacity nodules (GGO). A retrospective study was conducted in patients with GGO who underwent CTP in our hospital from January 2021 to October 2023. All nodules were confirmed via pathological analysis or disappeared during follow-up. Postprocessing analysis was conducted using the dual-input perfusion mode (pulmonary artery and bronchial artery) of the body perfusion software to measure the perfusion parameters of the pulmonary GGOs. A total of 101 patients with pulmonary GGOs were enrolled in this study, including 43 benign and 58 malignant nodules. The dose length product of the CTP (348 mGy.cm) was < 75% of the diagnostic reference level of the unenhanced chest CT (470 mGy.cm). The effective radiation dose was 4.872 mSV. The blood flow (BF), blood volume (BV), mean transit time (MTT), and flow extraction product (FEP) of malignant nodules were higher than those of the benign nodules (p < 0.05). The FEP had the highest accuracy for the diagnosis of malignant nodules (area under the curve [AUC] = 0.821, 95% confidence interval [CI]: 0.735-0.908) followed by BV (AUV = 0.713, 95% CI 0.608-0.819), BF (AUC = 0.688, 95% CI 0.587-0.797), and MTT (AUC = 0.616, 95% CI 0.506-0.726). When the FEP was ≥ 19.12 mL/100 mL/min, the sensitivity was 91.5% and the specificity was 62.8%. To distinguish between benign nodules and malignant nodules, the AUC of the combination of BV and FEP was 0.816 (95% CI 0.728-0.903), whereas the AUC of the combination of BF, BV, MTT, and FEP was 0.814 (95% CI 0.729-0.900). Low-dose dual-input perfusion CT was extremely effective in distinguishing between benign from malignant pulmonary GGOs, with FEP exhibiting the highest diagnostic capability.

Signature of Sr isotope ratios and the contents of elements as a tool to distinguish wine regions in China.

This study investigated 120 Chinese wines from seven regions and had two objectives: to clarify the Sr isotope ratios and elemental characteristics of each region and to develop a strategy to distinguish the geographic origin of wine without authentic samples to predict its origin. The analyzed 87Sr/86Sr values ranged from 0.708256 to 0.715148, which correlated with the geological characteristics of the regions where they were grown. The Hexi Corridor exhibited the highest ratios of Sr isotopes, while Xinjiang had the lowest. The 87Sr/86Sr values were applied to establish a prediction map which was evaluated through cross-validation. The prediction error was found to be less than 0.00074. The Sr isotope ratio could remain stable for an extended period in a specific location. This map shows the feasibility of identifying wine origin and could be applied to other food products. Adding Sr isotope ratios could improve the accuracy in tracing wine origin.

Optimization of CRISPR-Cas9 system in Eustoma grandiflorum.

The optimization of the CRISPR-Cas9 system for enhancing editing efficiency holds significant value in scientific research. In this study, we optimized single guide RNA and Cas9 promoters of the CRISPR-Cas9 vector and established an efficient protoplast isolation and transient transformation system in Eustoma grandiflorum, and we successfully applied the modified CRISPR-Cas9 system to detect editing efficiency of the EgPDS gene. The activity of the EgU6-2 promoter in E. grandiflorum protoplasts was approximately three times higher than that of the GmU6 promoter. This promoter, along with the EgUBQ10 promoter, was applied in the CRISPR-Cas9 cassette, the modified CRISPR-Cas9 vectors that pEgU6-2::sgRNA-2/pEgUBQ10::Cas9-2 editing efficiency was 37.7%, which was 30.3% higher than that of the control, and the types of mutation are base substitutions, small fragment deletions and insertions. Finally we obtained an efficient gene editing vector for E. grandiflorum. This project provides an important technical platform for the study of gene function in E. grandiflorum.

Telmisartan loading thermosensitive hydrogel repairs gut epithelial barrier for alleviating inflammatory bowel disease.

Inflammatory bowel disease (IBD) remains a global health concern with a complex and incompletely understood pathogenesis. In the course of IBD development, damage to intestinal epithelial cells and a reduction in the expression of tight junction (TJ) proteins compromise the integrity of the intestinal barrier, exacerbating inflammation. Notably, the renin-angiotensin system and angiotensin II receptor type 1 (AT1R) play a crucial role in regulating the pathological progression including vascular permeability, and immune microenvironment. Thus, Telmisartan (Tel), an AT1R inhibitor, loading thermosensitive hydrogel was constructed to investigate the potential of alleviating inflammatory bowel disease through rectal administration. The constructed hydrogel exhibits an advantageous property of rapid transformation from a solution to a gel state at 37°C, facilitating prolonged drug retention within the gut while mitigating irritation associated with rectal administration. Results indicate that Tel also exhibits a beneficial effect in ameliorating colon shortening, colon wall thickening, cup cell lacking, crypt disappearance, and inflammatory cell infiltration into the mucosa in colitis mice. Moreover, it significantly upregulates the expression of TJ proteins in colonic tissues thereby repairing the intestinal barrier damage and alleviating the ulcerative colitis (UC) disease process. In conclusion, Tel-loaded hydrogel demonstrates substantial promise as a potential treatment modality for IBD.

Hypoxia Stimulates PYGB Enzymatic Activity to Promote Glycogen Metabolism and Cholangiocarcinoma Progression.

Cholangiocarcinoma (CCA) displays enhanced glycolysis, pivotal for fulfilling the heightened energy demands intrinsic to its malignant progression. Recent research has indicated that endogenous glycogen rather than exogenous glucose acts as the major carbon source for glycolysis, highlighting the need to better understand the regulation of glycogen homeostasis in CCA. Here, through comprehensive integrative analysis, we identified that glycogen phosphorylase brain form (PYGB), the main enzyme involved in glycogen homeostasis, was markedly upregulated in CCA tissues, serving as an independent prognostic indicator for human CCA patients. Moreover, elevated PYGB expression potentiated cholangiocarcinogenesis and augmented CCA cell proliferation in both organoid and xenograft models. Hypoxia stimulated PYGB activity in a phosphoglycerate kinase 1 (PGK1)-dependent manner, leading to glycogenolysis and the subsequent release of glucose-6-phosphate (G6P) and thereby facilitating aerobic glycolysis. Notably, a virtual screening pinpointed the beta-blocker carvedilol as a potent pharmacological inhibitor of PYGB that could attenuate CCA progression. Collectively, these findings position PYGB as a promising prognostic biomarker and therapeutic target for CCA.

Comparison of hepatocellular carcinoma (HCC), cholangiocarcinoma (CC), and combined HCC-CC (CHC) with each other based on microarray dataset.

Liver carcinomas have been classified into three types: hepatocellular carcinoma (HCC), cholangiocarcinoma (CC), and combined HCC-CC (CHC). We aim to find the common and different characteristic of these three types of liver cancer. The gene expression profiling of HCC, CC, and CHC were compared with each other, and enrichment pathways and processes in these three liver cancers were also identified. Using GSE15765 datasets downloaded from NCBI GEO database, the gene expression profiling of HCC, CC, and CHC were compared with each other (HCC compared with CC, HCC compared with CHC, and CC compared with HCC). Then, the differentially expressed genes (DEGs) were identified in these three groups respectively, and three PPI networks were constructed for DEGs in each group. Subsequently, the clusters in these networks were identified and further analyzed by ClusterONE and MCODE. Finally, gene set enrichment analysis enrichment analysis was performed to illustrate altered pathways and processes for each type of liver cancer. A total of 112, 530, and 64 DEGs were identified in three groups, respectively, and three PPI networks were constructed respectively for the corresponding group. Through the cluster analysis, we found some new differential marker genes for distinguishing the difference between these three types of liver cancer. We also indicated that we can distinguish HCC with CC through altered pathways and processes. Our findings develop new biomarkers for categorizing the primary liver cancer and may improve patient prognosis of these cancers. However, further validation is required since our results were based on microarray data derived from a small sample size.