The Glomerulus Multiomics Analysis Provides Deeper Insights into Diabetic Nephropathy.

Although diabetic nephropathy (DN) is the leading cause of the end-stage renal disease, the exact regulation mechanisms remain unknown. In this study, we integrated the transcriptomics and proteomics profiles of glomeruli isolated from 50 biopsy-proven DN patients and 25 controls to investigate the latest findings about DN pathogenesis. First, 1152 genes exhibited differential expression at the mRNA or protein level, and 364 showed significant association. These strong correlated genes were divided into four different functional modules. Moreover, a regulatory network of the transcription factors (TFs)-target genes (TGs) was constructed, with 30 TFs upregulated at the protein levels and 265 downstream TGs differentially expressed at the mRNA levels. These TFs are the integration centers of several signal transduction pathways and have tremendous therapeutic potential for regulating the aberrant production of TGs and the pathological process of DN. Furthermore, 29 new DN-specific splice-junction peptides were discovered with high confidence; these peptides may play novel functions in the pathological course of DN. So, our in-depth integrative transcriptomics-proteomics analysis provided deeper insights into the pathogenesis of DN and opened the potential avenue for finding new therapeutic interventions. MS raw files were deposited into the proteomeXchange with the dataset identifier PXD040617.

A time-resolved multi-omic atlas of the developing mouse liver.

Liver organogenesis and development are composed of a series of complex, well-orchestrated events. Identifying key factors and pathways governing liver development will help elucidate the physiological and pathological processes including those of cancer. We conducted multidimensional omics measurements including protein, mRNA, and transcription factor (TF) DNA-binding activity for mouse liver tissues collected from embryonic day 12.5 (E12.5) to postnatal week 8 (W8), encompassing major developmental stages. These data sets reveal dynamic changes of core liver functions and canonical signaling pathways governing development at both mRNA and protein levels. The TF DNA-binding activity data set highlights the importance of TF activity in early embryonic development. A comparison between mouse liver development and human hepatocellular carcinoma (HCC) proteomic profiles reveal that more aggressive tumors are characterized with the activation of early embryonic development pathways, whereas less aggressive ones maintain liver function-related pathways that are elevated in the mature liver. This work offers a panoramic view of mouse liver development and provides a rich resource to explore in-depth functional characterization.

A Systematic Review and Meta-Analysis: Hyponatremia Predicted All-Cause and Cardiovascular Mortality in Dialysis Population.

BACKGROUND: Hyponatremia is one of the most common disorders of electrolytes. Some research studies reported that hyponatremia was closely associated with mortality in patients with dialysis. However, this viewpoint remains controversial. OBJECTIVE: We aimed to do a systematic review and meta-analysis to assess the influence of hyponatremia on mortality in patients with dialysis. METHODS: We identified the eligible studies that investigated the association between hyponatremia and mortality risk in patients under dialysis by searching systematically a series of databases including PubMed, Embase, Cochrane, Web of science, and Ovid from January 2011 to June 2020. Adjusted hazard ratios (HRs) with 95% confidence intervals (95% CIs) were pooled. RESULTS: From 1,116 records identified, 12 studies including prospective and retrospective cohort studies met our inclusion criteria. We found hyponatremia both at baseline (HR: 1.50 and 95% CI: 1.41-1.59) and in time-varying (HR: 1.63 and 95% CI: 1.44-1.84) were significantly correlated to all-cause mortality after multivariable adjusted. By the subgroup analysis, the same results were presented in hemodialysis (HR: 1.48 and 95% CI: 1.38-1.59) or peritoneal dialysis patients (HR: 1.52 and 95% CI: 1.37-1.70). We also observed that lower serum sodium was independently associated with cardiovascular death. CONCLUSIONS: Hyponatremia was independently associated with all-cause and cardiovascular mortality, and it might predict adverse outcomes of patients under dialysis.

Functional dissection of regulatory models using gene expression data of deletion mutants.

Genome-wide gene expression profiles accumulate at an alarming rate, how to integrate these expression profiles generated by different laboratories to reverse engineer the cellular regulatory network has been a major challenge. To automatically infer gene regulatory pathways from genome-wide mRNA expression profiles before and after genetic perturbations, we introduced a new Bayesian network algorithm: Deletion Mutant Bayesian Network (DM_BN). We applied DM_BN to the expression profiles of 544 yeast single or double deletion mutants of transcription factors, chromatin remodeling machinery components, protein kinases and phosphatases in S. cerevisiae. The network inferred by this method identified causal regulatory and non-causal concurrent interactions among these regulators (genetically perturbed genes) that are strongly supported by the experimental evidence, and generated many new testable hypotheses. Compared to networks reconstructed by routine similarity measures or by alternative Bayesian network algorithms, the network inferred by DM_BN excels in both precision and recall. To facilitate its application in other systems, we packaged the algorithm into a user-friendly analysis tool that can be downloaded at http://www.picb.ac.cn/hanlab/DM_BN.html.

[Engineering and heterologous expression of a nikkomycin biosynthetic gene cluster].

OBJECTIVE: We expressed a nikkomycin biosynthetic gene cluster in the well-characterized surrogate Streptomyces coelicolor M1146. METHODS: By using PCR-targeting method, we replaced the promoters of sanG and sanF in pNIK, which contains nikkomycin biosynthetic gene cluster, with the hrdB promoter to generate pNIKm. We transferred pNIK and pNIKm into S. coelicolor M1146 by intergeneric conjugation and obtained M1146-NIK and M1146-NIKm, respectively. We then evaluated expression of the gene cluster in the heterologous host by RT-PCR. Furthermore, we also compared the antifugal activity and nikkomycin production of M1146-NIK and M1146-NIKm by bioassay against Alternaria longipes and HPLC analysis. RESULTS: M1146-NIK and M1146-NIKm exhibited antifungal activity, and they can produce a trace amount of nikkomycin X, nikkomycin Z and pseudo-Z. There was a substantial accumulation of uridine in M1146-NIK, whereas substantial accumulations of uridine, ribofuranosyl-4-formyl-4-imidazolone and pyridylhomothreonine were observed in M1146-NIKm. CONCLUSION: We successfully expressed the nikkomycin biosynthetic gene cluster in the heterologous host and identified nikkomycins and some of its key biosynthetic intermediates. This study will provide the basis for enzymatic reaction of the condensation between the two nikkomycin moieties and for the generation of hybrid antibiotics by combinatorial biosynthesis.

Effects of myo-inositol on regulating glucose and lipid metabolism and alternative splicing events coexpressed with lncRNAs in the liver tissues of diabetic mice.

Objective: Recent studies have shown that gene alternative splicing (AS) and long noncoding RNAs (lncRNAs) are involved in diabetes mellitus (DM) and its complications. Currently, myo-inositol (MI) is considered as effective for the treatment of insulin resistance and lipid metabolism disorders in diabetes patients. We hope to better explore the potential roles of gene AS and lncRNAs in liver glucose and lipid metabolism in diabetes, as well as the effects of myo-inositol treatment, through transcriptome analysis. Methods: This study analysed glucose and lipid metabolism-related biochemical indicators and liver HE staining in four groups of mice: the control group (Ctrl group), the diabetes group (DM group), the myo-inositol treatment group (MI group), and the metformin treatment group (Met group). The changes in relevant gene-regulated alternative splicing events (RASEs) and lncRNAs were analysed by RNA sequencing of liver tissue, and coexpression analysis and functional enrichment analysis were used to predict the possible lncRNAs and RASEs involved in liver glucose and lipid metabolism. Result: Metformin and myo-inositol alleviated insulin resistance, lipid metabolism disorders, and hepatic steatosis in diabetic mice. Transcriptome sequencing analysis revealed differential splicing events of genes related to lipid metabolism and differentially expressed lncRNAs (DElncRNAs). Six different lncRNAs and their potentially interacting splicing events were predicted. Conclusion: The present study revealed novel changes in RASEs and lncRNAs in the livers of diabetic mice following treatment with myo-inositol, which may shed light on the potential mechanisms by which myo-inositol delays and treats the progression of hepatic glucose and lipid metabolism in diabetes.

A review of research progress on mechanisms of peritoneal fibrosis related to peritoneal dialysis.

Peritoneal dialysis (PD) is an effective alternative treatment for patients with end-stage renal disease (ESRD) and is increasingly being adopted and promoted worldwide. However, as the duration of peritoneal dialysis extends, it can expose problems with dialysis inadequacy and ultrafiltration failure. The exact mechanism and aetiology of ultrafiltration failure have been of great concern, with triggers such as biological incompatibility of peritoneal dialysis solutions, uraemia toxins, and recurrent intraperitoneal inflammation initiating multiple pathways that regulate the release of various cytokines, promote the transcription of fibrosis-related genes, and deposit extracellular matrix. As a result, peritoneal fibrosis occurs. Exploring the pathogenic factors and molecular mechanisms can help us prevent peritoneal fibrosis and prolong the duration of Peritoneal dialysis.

Polyploid Induction and Identification of Rosa roxburghii f. eseiosa.

Rosa roxburghii f. eseiosa Ku is a variety of Rosa roxburghii, with two known genotypes: Wuci 1 and Wuci 2. The lack of prickle on the peel of R. roxburghii f. eseiosa makes it easy to pick and process, but its fruit size is small. Therefore, we aim to induce polyploidy in order to obtain a larger fruit variety of R. roxburghii f. eseiosa. In this study, current-year stems of Wuci 1 and Wuci 2 were used as materials for polyploid induction, which was carried out through colchicine treatment coupled with tissue culture and rapid propagation technology. Impregnation and smearing methods were effectively used to produce polyploids. Using flow cytometry and a chromosome counting method, it was found that one autotetraploid of Wuci 1 (2n = 4x = 28) was obtained by the impregnation method before primary culture, with a variation rate of 1.11%. Meanwhile, seven Wuci 2 bud mutation tetraploids (2n = 4x = 28) were produced by smearing methods during the training seedling stage. When tissue-culture seedlings were treated with 20 mg/L colchicine for 15 days, the highest polyploidy rate was up to 60%. Morphological differences between different ploidys were observed. The side leaflet shape index, guard cell length, and stomatal length of the Wuci 1 tetraploid were significantly different from those of the Wuci 1 diploid. The terminal leaflet width, terminal leaflet shape index, side leaflet length, side leaflet width, guard cell length, guard cell width, stomatal length, and stomatal width of the Wuci 2 tetraploid were significantly different from those of the Wuci 2 diploid. Additionally, the leaf color of the Wuci 1 and Wuci 2 tetraploids changed from light to dark, with an initial decrease in chlorophyll content followed by an increase. In summary, this study established an effective method for inducing polyploids in R. roxburghii f. eseiosa, which could provide a foundation for the breeding and development of new genetic resources for R. roxburghii f. eseiosa and other R. roxburghii varieties in the future.

F-box protein 43 promoter methylation as a novel biomarker for hepatitis B virus-associated hepatocellular carcinoma.

Background: Hepatocellular carcinoma (HCC) has a high prevalence and poor prognosis worldwide. Therefore, it is urgent to find effective and timely diagnostic markers. The objective of this study was to evaluate the diagnostic value of F-box protein 43 promoter methylation in peripheral blood mononuclear cells (PBMCs) for HCC. Method: A total of 247 participants were included in this study, comprising individuals with 123 hepatitis B virus-associated HCC, 79 chronic hepatitis B, and 45 healthy controls. F-box protein 43 methylation and mRNA levels in PBMCs were detected by MethyLight and quantitative real-time PCR. Result: F-box protein 43 promoter methylation levels were significantly lower in HCC PBMCs than the chronic hepatitis B (P < 0.001) and healthy control PBMCs (P < 0.001). Relative mRNA expression levels of F-box protein 43 in HCC PBMCs were significantly higher than those in chronic hepatitis B (P < 0.001) and healthy control PBMCs (P < 0.001). Receiver operating characteristic analysis of F-box protein 43 promoter methylation levels yielded an area under curve (AUC) of 0.793 with 76.42% sensitivity and 68.35% specificity when differentiating HCC from chronic hepatitis. These values for the F-box protein 43 promoter methylation level were superior to those of the alpha-fetoprotein serum (AFP) level (AUC: 0.780, sensitivity: 47.97%, and specificity: 96.20%), with increments in values for the combination of F-box protein 43 promoter methylation AFP levels (AUC: 0.888, sensitivity: 76.42%, and specificity: 86.08%). Conclusion: Hypomethylation of the F-box protein 43 promoter in PBMCs is a promising biochemical marker for HBV-associated HCC.

Effect of intradermal needle therapy at combined acupoints on patients' gastrointestinal function following surgery for gastrointestinal tumors.

BACKGROUND: Postoperative gastrointestinal function recovery is critical for rapid rehabilitation of patients with gastrointestinal tumors. Traditional Chinese medicine offers considerable advantages for gastrointestinal disease treatment. However, no study has reported the clinical efficacy of intradermal needle therapy (INT) at the Yuan-source, Luo-connecting, and He-sea points of the corresponding meridian for gastrointestinal function in patients following surgery for gastrointestinal tumors. AIM: To investigate the effect of INT at combined acupoints on patients' gastrointestinal function following surgery for gastrointestinal tumors. METHODS: This randomized controlled trial was conducted at the Second Affiliated Hospital of Xi'an Jiaotong University on patients with diagnosed gastrointestinal cancer, no distant metastases or organ failure, and hospitalized for elective radical tumor resection, who did not receive preoperative radiotherapy or chemotherapy. Participants were randomly allocated to either the intervention (n = 32) or the control (n = 32) group. Participants in the control group received enhanced recovery care, while those in the intervention group received enhanced recovery care combined with INT at the Yuan-source, Luo-connecting, and He-sea points. After surgery, INT was performed immediately upon the patient's return to the ward, and continued for seven consecutive days. The independent samples t-test, chi-square test, and generalized estimating equations were used for data analysis. RESULTS: The participants' ages ranged from 40 to 80 years (average 63 ± 10.1 years). Most participants underwent surgery for either gastric (43.8%) or colon cancer (39.1%) and had adenocarcinoma (87.5%). Significant differences were noted in time to first postoperative flatus passage (66 ± 27 h vs 103 ± 41 h, P < 0.001), time to first defecation (106 ± 44 h vs 153 ± 50 h, P < 0.001), and time to first oral feeding (73 ± 30 h vs 115 ± 38 h, P < 0.001) between the intervention and control groups. Gastrointestinal symptoms, including abdominal distension, nausea, and fatigue 48 h and 72 h after surgery, were significantly alleviated in the intervention group compared with that observed in the control group (P < 0.05). CONCLUSION: INT at the Yuan-source, Luo-connecting, and He-sea points can promote recovery of gastrointestinal function and ease gastrointestinal symptoms in patients following surgical resection of gastrointestinal tumors.

MTA2 sensitizes gastric cancer cells to PARP inhibition by induction of DNA replication stress.

Poly (ADP-ribose) polymerase (PARP) inhibitor olaparib selectively kills cancer cells with BRCA-deficiency and is approved for BRCA-mutated breast, ovarian and pancreatic cancers by FDA. However, phase III study of olaparib failed to show a significant improvement in overall survival in patients with gastric cancer (GC). To discover an effective biomarker for GC patient-selection in olaparib treatment, we analyzed proteomic profiling of 12 GC cell lines. MTA2 was identified to confer sensitivity to olaparib by aggravating olaparib-induced replication stress in cancer cells. Mechanistically, we applied Cleavage Under Targets and Tagmentation assay to find that MTA2 proteins preferentially bind regions of replication origin-associated DNA sequences, which could be enhanced by olaparib treatment. Furthermore, MTA2 was validated here to render cancer cells susceptible to combination of olaparib with ATR inhibitor AZD6738. In general, our study identified MTA2 as a potential biomarker for olaparib sensitivity by aggravating olaparib-induced replication stress.

sanN encoding a dehydrogenase is essential for Nikkomycin biosynthesis in Streptomyces ansochromogenes.

Nikkomycins are a group of peptidyl nucleoside antibiotics with potent fungicidal, insecticidal, and acaricidal activities. sanN was cloned from the partial genomic library of Streptomyces ansochromogenes 7100. Gene disruption and complementation analysis demonstrated that sanN is essential for nikkomycin biosynthesis in S. ansochromogenes. Primer extension assay indicated that sanN is transcribed from two promoters (sanN-P1 and sanN-P2), and sanN-P2 plays a more important role in nikkomycin biosynthesis. Purified recombinant SanN acts as a dehydrogenase to convert benzoate-CoA to benzaldehyde in a random-order mechanism in vitro, with respective Kcat/Km values of 3.8 mM-1s-1 and 12.0 mM-1s-1 toward benzoate-CoA and NADH, suggesting that SanN catalyzes the formation of picolinaldehyde during biosynthesis of nikkomycin X and Z components in the wild-type stain. These data would facilitate us to understand the biosynthetic pathway of nikkomycins and to consider the combinatorial synthesis of novel antibiotic derivatives.

A time-resolved multi-omic atlas of the developing mouse stomach.

The mammalian stomach is structurally highly diverse and its organ functionality critically depends on a normal embryonic development. Although there have been several studies on the morphological changes during stomach development, a system-wide analysis of the underlying molecular changes is lacking. Here, we present a comprehensive, temporal proteome and transcriptome atlas of the mouse stomach at multiple developmental stages. Quantitative analysis of 12,108 gene products allows identifying three distinct phases based on changes in proteins and RNAs and the gain of stomach functions on a longitudinal time scale. The transcriptome indicates functionally important isoforms relevant to development and identifies several functionally unannotated novel splicing junction transcripts that we validate at the peptide level. Importantly, many proteins differentially expressed in stomach development are also significantly overexpressed in diffuse-type gastric cancer. Overall, our study provides a resource to understand stomach development and its connection to gastric cancer tumorigenesis.

Study on Post-Treatment Relapse in HBeAg Positive CHB Patients.

BACKGROUND: Many factors are associated with post-treatment relapse in CHB patients, and there are no effective factors to predict relapse. In this study, we investigate the influence factors associated with post-treatment relapse and their predictive value in HBeAg positive CHB (eP-CHB). METHODS: The factors associated with post-treatment relapse were analyzed firstly by a retrospective study in eP-CHB. Variables included age, sex, regimen, baseline HBeAg and HBV DNA level, total course of treatment as well as duration of consolidation therapy after HBeAg seroconversion. The predictive effects of the influence factors were evaluated in an eP-CHB prospective cohort. RESULTS: 89 patients were enrolled in the retrospective study, 42(47.2%) relapsed after discontinuation of treatment. Factors related to post-treatment relapse were total course of treatment, duration of consolidation therapy and baseline HBV DNA level. Relapse rates in patients with total course >36 months, consolidation duration >12 months and baseline HBV DNA level < 1.0E+5IU/ml were lower than those of total course <24 months (P = 0.002), consolidation duration≤12 months (P = 0.011) and baseline HBV DNA level > 1.0E+7IU/ml (P = 0.01) respectively. Patients with HBV DNA≥1.0E+7IU/ml plus HBeAg<200COI at baseline had the highest relapse rate and cumulative relapse rate than the other three arms (P = 0.048 and 0.008 respectively). Logistic regression analysis demonstrated that baseline HBV DNA level, duration of consolidation therapy and combination of baseline HBV DNA and HBeAg (IgDNA/IgHBeAg) were independent factors to predict post-treatment relapse. The model based on baseline IgDNA/IgHBeAg and consolidation duration worked well in predicting post-treatment relapse in the prospective study and the accuracy, specificity, sensitivity, PPV and NPV for prediction were 80.3%, 81.1%, 79.2%, 73.1% and 85.7% respectively. CONCLUSIONS: Virological factors including baseline HBV DNA, HBeAg and treatment course were major influence factors associated with post-treatment relapse in eP-CHB. Patients with higher HBV DNA and lower HBeAg levels at baseline, shorter total course as well as consolidation therapy were more likely to develop relapse after discontinuation of therapy. The antiviral therapy in eP-CHB patients should be individually managed at different levels. It is better to treat those with higher viral load and lower HBeAg levels at baseline for a longer course, especially longer consolidation duration so as to decrease the relapse rate.

[Changes in diversity of culturable microorganisms on leaf surface of transgenic Bt cotton].

In a field study, the quantitative changes of bacterial, actinomycetic and fungal populations on the leaf surface of transgenic Bt cotton (GK-12) and non-transgenic Bt cotton (Simian No. 3) were monitored at seedling, squaring, flowering and boll-opening stages, respectively, and the diversity of bacterial physiological groups was analyzed at flowering and boll-opening stages. The results showed that there was a positive correlation between the quantity of culturable microorganisms and the development of cotton. The total number of bacteria, fungi and actinomyces began to rise at seedling stage, reached its peak at flowering stage, and decreased markedly at boll-opening stage. The Simpson index, Shannon-Wiener index, and evenness index of bacterial physiological groups were higher at flowering stage, but lower at boll-opening stage on GK-12 than on Simian No. 3.