Pathogenic microorganism DNA high-throughput genetic sequencing to diagnose peritoneal dialysis-associated peritonitis due to Mycobacterium tuberculosis infection.

Peritoneal dialysis-associated peritonitis is a serious complication of peritoneal dialysis, and the prevention and treatment of this condition are important for improving the long-term survival and quality of life of patients. However, peritoneal dialysis-associated peritonitis due to Mycobacterium tuberculosis infection is relatively rare and not easily diagnosed. Here, we present a case of peritoneal dialysis-associated peritonitis caused by Mycobacterium tuberculosis identified by pathogenic microbial DNA high-throughput genetic sequencing. This case demonstrates that pathogenic microbial DNA high-throughput genetic sequencing could be used to improve the detection rate of pathogenic microorganisms in patients with complex conditions, thereby allowing for earlier initiation of treatment.

Research progress on measurement methods and evaluation of the hemodialysis adequacy index Kt/V.

The most common form of replacement therapy for end-stage renal disease (ESRD) is hemodialysis, and the adequacy of hemodialysis is strongly associated with the quality of life and long-term survival of patients. Kt/V is currently one of the most important indicators for evaluating the adequacy of hemodialysis. There are many methods for measuring Kt/V, such as blood collection and measurement, dialysate measurement, bioresistive resistance, WinNonlin software analysis, and artificial intelligence. There are different views on the importance of Kt/V as an indicator of the adequacy of hemodialysis. This article provides a literature review of the various methods of measuring Kt/V and on different perspectives on Kt/V as an evaluation of hemodialysis adequacy.

ERBB2 is a potential diagnostic and prognostic biomarker in renal clear cell carcinoma.

Renal clear cell carcinoma (ccRCC) is a common parenchymal tumor of the kidney, and the discovery of biomarkers for early and effective diagnosis of ccRCC can improve the early diagnosis of patients and thus improve long-term survival. Erb-b2 receptor tyrosine kinase 2 (ERBB2) mediates the processes of cell proliferation, differentiation, and apoptosis inhibition. The purpose of this study was to investigate the diagnostic and prognostic role of ERBB2 in ccRCC. We analyzed the expression levels of ERBB2 in various cancers from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. RNA-seq data were analyzed using R packages to identify differentially expressed genes between the high and low ERBB2 expression groups in the TCGA-KIRC dataset. Spearman correlation analysis was performed to determine the correlation between ERBB2 expression and immune cell infiltration, immune checkpoint expression, and PTEN expression. DNA methylation changes and genetic alterations in ERBB2 were assessed using the MethSurv and cBioPortal databases. Logistic regression analysis was performed to determine the correlation between ERBB2 expression and the clinicopathological characteristics of ccRCC patients. The diagnostic and prognostic value of ERBB2 was assessed using Kaplan‒Meier (K‒M) survival curves, diagnostic ROC curves, time-dependent ROC curves, nomogram models, and Cox regression models. The expression level of ERBB2 is lower in tumor tissues of ccRCC patients than in the corresponding control tissues. Differentially expressed genes associated with ERBB2 were significantly enriched in the pathways "BMP2WNT4FOXO1 pathway in primary endometrial stromal cell differentiation" and "AMAN pathway". In ccRCC tissues, ERBB2 expression levels were associated with immune cell infiltration, immune checkpoints, and PTEN. The DNA methylation status of 10 CpG islands in the ERBB2 gene was associated with the prognosis of ccRCC. ERBB2 expression levels in ccRCC tissues were associated with race, sex, T stage, M stage, histological grade, and pathological stage. Cox regression analysis showed that ERBB2 was a potential independent predictor of overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) in ccRCC patients. ROC curve analysis showed that the expression level of ERBB2 could accurately distinguish between ccRCC tissue and adjacent normal renal tissue. Our study showed that ERBB2 expression in ccRCC tissues can be of clinical importance as a potential diagnostic and prognostic biomarker.

Risk Factors for Cerebrospinal Fluid Leakage After Extradural Spine Surgery: A Meta-Analysis and Systematic Review.

BACKGROUND: Cerebrospinal fluid (CSF) leakage is 1 of the common complications of spine surgery and is largely caused by intraoperative or postoperative dural tears. Associations of different factors with postoperative CSF leakage have not been consistent. In this study we aimed to identify demographic, disease-related, and surgical risk factors for CSF leakage after extradural spine surgery in a systematic review and meta-anlysis. METHODS: The PubMed, EMBASE, Web of Science, Cochrane Library, Chinese National Knowledge Infrastructure, Chinese Wanfang data, Chinese Weipu Database, and SinoMed databases were searched from inception until October 24, 2022. Fixed-effects or random-effects models were used to calculate odds ratios and 95% confidence intervals. The quality of observational studies was evaluated using the Newcastle-Ottawa scale instrument. RESULTS: A total of 15 observational studies with 1,719,923 participants were included in this systematic review. All studies had a Newcastle-Ottawa scale score greater than or equal to 6. Age older than 70 years, smoking, ossification of the posterior longitudinal ligament, adhesion of spinal dura, spinal canal stenosis, cervical fracture, spondylolisthesis, revision surgery, and multiple surgical segments were all related to CSF leakage in the pooled analysis. Obesity and disease duration>1 year were not associated with the leakage of CSF. CONCLUSIONS: This study will provide a reference for the identification of patients at high risk of developing CSF leakage, which suggests clinicians to strengthen the observation of drainage fluid in high-risk groups.

Biomechanical and histomorphological analysis of the mandible in rats with chronic kidney disease.

The present study aimed to investigate the biomechanical and histomorphological features of mandibles in an adenine-induced chronic kidney disease-mineral and bone disorder (CKD-MBD) rat model of CKD. A total of 14 Sprague-Dawley rats were randomized into the following two groups: control group and CKD group. At the end of the sixth week, all rats were euthanized, and serum was collected for biochemical marker tests. Macroscopic bone growth and biomechanical parameters were measured in the right hemimandible, while the left hemimandible was used for bone histomorphometric analysis. Compared to the control group, the CKD group showed a significant increase in serum creatinine, blood urea nitrogen, and serum parathyroid hormone at the end of the sixth week. The biomechanical structural properties significantly decreased in the CKD group compared to the control group. Bone histomorphometric analysis indicated that the trabecular bone volume of rats in the CKD group was significantly lower than that of the control group. In the CKD groups, the bone formation parameters of the trabecular bone were significantly increased, while the bone mineralization apposition rates of both the trabecular bone and periosteal cortical bone were significantly increased. The rat CKD model showed deteriorated structural mechanics, low trabecular bone volume, high trabecular bone formation, increased trabecular bone mineralization apposition rate, and increased cortical bone mineralization apposition rate, which met the characteristics of osteitis fibrosa, indicating that this model is a useful tool for the study of mandible diseases in CKD patients.

EGFR Inhibition Overcomes Resistance to FGFR4 Inhibition and Potentiates FGFR4 Inhibitor Therapy in Hepatocellular Carcinoma.

Aberrant activation of the FGF19-FGFR4 signaling pathway plays an essential role in the tumorigenesis of hepatocellular carcinoma (HCC). As such, FGFR4 inhibition has emerged as a novel therapeutic option for the treatment of HCC and has shown preliminary efficacy in recent clinical trials for patients exhibiting aberrant FGF19 expression. Resistance to kinase inhibitors is common in oncology, presenting a major challenge in the clinical treatment process. Hence, we investigated the potential mechanisms mediating and causing resistance to FGFR4 inhibition in HCC. Upon the successful establishment of a battery of cellular models developing resistance to FGFR4 inhibitors, we have identified the activation of EGFR, MAPK, and AKT signaling as the primary mechanisms mediating the acquired resistance. Combination of inhibitors against EGFR or its downstream components restored sensitivity to FGFR4 inhibitors. In parental HCC cell lines, EGF treatment also resulted in resistance to FGFR4 inhibitors. This resistance was effectively reverted by inhibitors of the EGFR signaling pathway, suggesting that EGFR activation is a potential cause of intrinsic resistance. We further confirmed the above findings in vivo in mouse xenograft tumor models. Genomic analysis of patient samples from The Cancer Genome Atlas confirmed that a segment of patients with HCC harboring FGF19 overexpression indeed exhibited increased activation of EGFR signaling. These findings conclusively indicate that both induced and innate activation of EGFR could mediate resistance to FGFR4 inhibition, suggesting that dual blockade of EGFR and FGFR4 may be a promising future therapeutic strategy for the treatment of FGF19-FGFR4 altered HCC.

Genome-wide pathogenesis interpretation using a heat diffusion-based systems genetics method and implications for gene function annotation.

BACKGROUND: Genetics is best dedicated to interpreting pathogenesis and revealing gene functions. The past decade has witnessed unprecedented progress in genetics, particularly in genome-wide identification of disorder variants through Genome-Wide Association Studies (GWAS) and Phenome-Wide Association Studies (PheWAS). However, it is still a great challenge to use GWAS/PheWAS-derived data to elucidate pathogenesis. METHODS: In this study, we used HotNet2, a heat diffusion-based systems genetics algorithm, to calculate the networks for disease genes obtained from GWAS and PheWAS, with an attempt to get deeper insights into disease pathogenesis at a molecular level. RESULTS: Through HotNet2 calculation, significant networks for 202 (for GWAS) and 167 (for PheWAS) types of diseases were identified and evaluated, respectively. The GWAS-derived disease networks exhibit a stronger biomedical relevance than PheWAS counterparts. Therefore, the GWAS-derived networks were used for pathogenesis interpretation by integrating the accumulated biomedical information. As a result, the pathogenesis for 64 diseases was elucidated in terms of mutation-caused abnormal transcriptional regulation, and 47 diseases were preliminarily interpreted in terms of mutation-caused varied protein-protein interactions. In addition, 3,802 genes (including 46 function-unknown genes) were assigned with new functions by disease network information, some of which were validated through mice gene knockout experiments. CONCLUSIONS: Systems genetics algorithm HotNet2 can efficiently establish genotype-phenotype links at the level of biological networks. Compared with original GWAS/PheWAS results, HotNet2-calculated disease-gene associations have stronger biomedical significance, hence provide better interpretations for the pathogenesis of genome-wide variants, and offer new insights into gene functions as well. These results are also helpful in drug development.

Heat Diffusion Kernel Algorithm-Based Interpretation of the Disease Intervention Mechanism for DHA.

Docosahexaenoic acid (DHA) is effective in the prevention and treatment of cancer, congenital disorders, and various chronic diseases. According to the omnigenic hypothesis, these complex diseases are caused by disordered gene regulatory networks comprising dozens to hundreds of core genes and a mass of peripheral genes. However, conventional research on the disease intervention mechanism of DHA only focused on specific types of genes or pathways instead of examining genes at the network level, resulting in conflicting conclusions. In this study, we used HotNet2, a heat diffusion kernel algorithm, to calculate the gene regulatory networks of connectivity map (cMap)-derived agents (including DHA) based on gene expression profiles, aiming to interpret the disease intervention mechanism of DHA at the network level. As a result, significant gene regulatory networks for DHA and 676 cMap-derived agents were identified respectively. The biological functions of the DHA-regulated gene network provide preliminary insights into the mechanism by which DHA intervenes in disease. In addition, we compared the gene regulatory networks of DHA with those of cMap-derived agents, which allowed us to predict the pharmacological effects and disease intervention mechanism of DHA by analogy with similar agents with clear indications and mechanisms. Some of our analysis results were supported by experimental observations. Therefore, this study makes a significant contribution to research on the disease intervention mechanism of DHA at the regulatory network level, demonstrating the potential application value of this methodology in clarifying the mechanisms about nutrients influencing health.

[Effects of Fuzheng Yiliu Granule-medicated serum on apoptosis of liver cancer cells from mice and its mechanism].

OBJECTIVE: To study the effects of Fuzheng Yiliu Granule (FZYLG)-medicated serum on apoptosis of liver cancer cells H22 from mice and its mechanism. METHODS: Liver cancer cells H22 from mice were incubated in culture media containing sera from rabbits medicated with different doses of FZYLG. Flow cytometry was used to examine the cell cycle and analyze the apoptotic rate of the H22 cells. The morphological changes of the H22 cells were observed by transmission electron microscope and the apoptosis related proteins Bcl-2 and Bax were examined by streptavidin-biotin peroxidase complex (SABC) method. RESULTS: FZYLG-medicated serum could influence the cell cycle and stop the proliferation of H22 cells at the G(1)/G(0) phase with apoptotic peak being detected. In culture media with FZYLG-medicated sera, the expression of Bcl-2 decreased while that of Bax increased as compared with that in culture medium with non-medicated serum (P<0.05). CONCLUSION: FZYLG-medicated serum can induce apoptosis of the liver cancer cells H22 by influencing the cell cycle, down-regulating the expression of Bcl-2 and up-regulating the expression of Bax.

Studies on structures and activities of initial Maillard reaction products by electrospray ionisation mass spectrometry combined with liquid chromatography in processing of red ginseng.

Electrospray ionisation-mass spectrometry (ESI-MS) was applied to analyse the water-soluble extract of red ginseng (RG). Several new compounds were produced from the Maillard reaction during the steaming and drying process for preparing RG. Both the tandem electrospray ionisation (ESI-MS(n)) and Fourier transform ion cyclotron resonant mass spectrometric (FT-ICR-MS) data of these products proved that they were the initial Maillard reaction products (MRPs) of maltose with glutamic acid/aspartic acid, which were specific components in RG. In addition, their anti-diabetic and antioxidant activities were examined in vitro. The anti-diabetic activities were evaluated by studying the α-glucosidase inhibition using ultrafiltration LC-MS/MS techniques, while the antioxidant activities were investigated by UPLC-ESI-MS method. The results demonstrated that four initial MRPs in RG were identified as α-glucosidase inhibitors, and showed marked scavenging effect on the hydroxyl radical ((·)OH). Based on these studies, the processing method of RG was improved to generate more active compounds.

KRAS and PIK3CA but not BRAF genes are frequently mutated in Chinese cholangiocarcinoma patients.

Cholangiocarcinoma (CCA) is a rare but lethal malignancy arising from the biliary tract epithelium. It has a poor prognosis largely due to the difficulties of early diagnosis and the lack of effective therapies. It is thus imperative to develop new and effective treatments for CCA, which depends heavily on the mechanistic understanding of the disease. Previous studies have suggested that somatic mutations in KRAS, BRAF, and PIK3CA genes are frequently found in several types of human cancers including colon, breast, and lung carcinomas as well as CCA. Yet, the frequency and the involvement of these oncogenic mutations in CCA in Chinese population have not been investigated. In this study, we evaluated the hotspot mutations of KRAS, BRAF, and PIK3CA genes in 34 Chinese CCA patients. Sequencing analysis revealed 13 (38.2%) and 11 (32.4%) patients bearing KRAS and PIK3CA mutations, in which two (5.9%) of them harbored both KRAS and PIK3CA mutations. Surprisingly, no BRAF mutation was detected in all 34 CCA samples. Our findings indicate that somatic mutations in KRAS and PIK3CA but not BRAF oncogenes are closely associated with the development of CCA in Chinese population and provide new potential targets for future therapeutic treatments of the disease.

[Ultrasound-mediated microbubble destruction enhances LMP-1 gene transfection into dendritic cells in vivo].

OBJECTIVE: To investigate the transfection efficiency and the optimal conditions of delivering latent membrane protein-1 (LMP-1) gene to dendritic cells (DCs) by ultrasound exposure combined with contrast agent. METHODS: Human DCs were cultured in vivo and transfected with the recombinant plasmid pEGFP-C3-LMP1 under varying conditions including ultrasound intensities, exposure time and microbubble contrast agent concentration. The transfection efficiency was assessed by fluorescent microscopy and flow cytometry, and the cell viability by trypan blue exclusion test. RESULTS: An exposure time of 60 s at MI 1.0 with a microbubble contrast agent concentration of 20% resulted in the optimal effect of delivering the recombinant plasmid pEGFP-C3-LMP1 into the DCs, with a transfection efficiency of (14.37∓2.12)%. Over 90% of the transfected cells were viable after the transfection. CONCLUSION: Microbubble contrast agent combined with ultrasound exposure can enhance the delivery of recombinant plasmid pEGFP-C3-LMP1 into the DCs.