NIPT-PG: empowering non-invasive prenatal testing to learn from population genomics through an incremental pan-genomic approach.

Non-invasive prenatal testing (NIPT) is a quite popular approach for detecting fetal genomic aneuploidies. However, due to the limitations on sequencing read length and coverage, NIPT suffers a bottleneck on further improving performance and conducting earlier detection. The errors mainly come from reference biases and population polymorphism. To break this bottleneck, we proposed NIPT-PG, which enables the NIPT algorithm to learn from population data. A pan-genome model is introduced to incorporate variant and polymorphic loci information from tested population. Subsequently, we proposed a sequence-to-graph alignment method, which considers the read mis-match rates during the mapping process, and an indexing method using hash indexing and adjacency lists to accelerate the read alignment process. Finally, by integrating multi-source aligned read and polymorphic sites across the pan-genome, NIPT-PG obtains a more accurate z-score, thereby improving the accuracy of chromosomal aneuploidy detection. We tested NIPT-PG on two simulated datasets and 745 real-world cell-free DNA sequencing data sets from pregnant women. Results demonstrate that NIPT-PG outperforms the standard z-score test. Furthermore, combining experimental and theoretical analyses, we demonstrate the probably approximately correct learnability of NIPT-PG. In summary, NIPT-PG provides a new perspective for fetal chromosomal aneuploidies detection. NIPT-PG may have broad applications in clinical testing, and its detection results can serve as a reference for false positive samples approaching the critical threshold.

A high-resolution haplotype-resolved Reference panel constructed from the China Kadoorie Biobank Study.

Precision medicine depends on high-accuracy individual-level genotype data. However, the whole-genome sequencing (WGS) is still not suitable for gigantic studies due to budget constraints. It is particularly important to construct highly accurate haplotype reference panel for genotype imputation. In this study, we used 10 000 samples with medium-depth WGS to construct a reference panel that we named the CKB reference panel. By imputing microarray datasets, it showed that the CKB panel outperformed compared panels in terms of both the number of well-imputed variants and imputation accuracy. In addition, we have completed the imputation of 100 706 microarrays with the CKB panel, and the after-imputed data is the hitherto largest whole genome data of the Chinese population. Furthermore, in the GWAS analysis of real phenotype height, the number of tested SNPs tripled and the number of significant SNPs doubled after imputation. Finally, we developed an online server for offering free genotype imputation service based on the CKB reference panel (https://db.cngb.org/imputation/). We believe that the CKB panel is of great value for imputing microarray or low-coverage genotype data of Chinese population, and potentially mixed populations. The imputation-completed 100 706 microarray data are enormous and precious resources of population genetic studies for complex traits and diseases.

Efficient Discrimination of Hazardous Organophosphate Flame Retardants via Cataluminescence-Based Multidimensional Ratiometric Sensing.

Emerging contaminants have recently evolved into a severe worldwide environmental issue. Organophosphate flame retardants (OPFRs) with neurotoxicity, genotoxicity, and reproductive and developmental toxicity are a class of notorious emerging contaminants that cause great concern. The development of high-efficiency and portable sensors for rapid online monitoring of OPFRs has become the primary demand for the exploration of the environmental migration and transformation of OPFRs. In this work, interestingly, the cataluminescence (CTL) phenomenon of OPFRs is first observed, and an ingenious multidimensional ratiometric CTL sensing strategy is developed for the recognition of multiple OPFRs. Three characteristic ratios are extracted from the multipeak CTL spectral curves based on energy transfer of single Tb/Eu-modified MgO sensing material, and thus a novel three-dimensional (3D) code recognition could be mapped out. This obtained 3D coordinate is found to be a unique characteristic for a given OPFR, just like an exclusive person's ID number, which can successfully discriminate and detect 10 kinds of OPFR vapors, including homologous series and isomers. More importantly, CTL mechanism investigations for OPFRs demonstrate that OPFRs undergo a series of chemical reaction processes, e.g., oxidative pyrolysis and hydroxylation, and different high-energy excited intermediates are generated, which trigger discrepant energy-transfer efficiency toward rare earth ions, leading to multipeak spectral profiles. Briefly, this proposed CTL analytical platform for OPFRs recognition initiates a new sensing principle for the efficient identification of emerging contaminants and shows significant prospects on rapid on-site detection.

Exosomal circCLIP1 regulates PM2.5-induced airway obstruction via targeting SEPT10 in vitro.

Fine particulate matter (PM2.5) exposure correlates with airway obstruction, but the mechanism remains to be fully elucidated. We aim to investigate the role of exosomal circular RNAs (circRNAs)-mediated communication between airway epithelial cells and airway smooth muscle cells in PM2.5-induced airway obstruction. RNA sequencing revealed that acute PM2.5 exposure altered the expression profiles of 2904 exosomal circRNAs. Among them, exosomal hsa_circ_0029069 (spliced from CLIP1, thus termed circCLIP1 hereafter) with a loop structure was upregulated by PM2.5 exposure and mainly encapsulated in exosomes. Then, the biological functions and the underlying mechanisms were explored by Western blot, RNA immunoprecipitation and RNA pull-down, etc. Phenotypically, exosomal circCLIP1 entered recipient cells, inducing mucus secretion in recipient HBE cells and contractility of sensitive HBSMCs. Mechanistically, circCLIP1 was upregulated by METTL3-mediated N6-methyladenine (m6A) modification in PM2.5-treated producer HBE cells and exosomes, then enhancing the expression of SEPT10 in recipient HBE cells and sensitive HBSMCs. Our study revealed that exosomal circCLIP1 played a critical role in PM2.5-induced airway obstruction and provided a new potential biomarker for the assessment of PM2.5-related adverse effects.

Candidate genes screening based on phenotypic observation and transcriptome analysis for double flower of Prunus mume.

BACKGROUND: Prunus mume is an early spring flower of Rosaceae, which owns high application value in gardens. Being an excellent ornamental trait, the double flower trait has always been one of the important breeding goals of plant breeders. However, the key regulatory genes of double flower traits of P. mume are still unclear at present. RESULTS: The floral organs' morphological differences of 20 single and 20 double flower cultivars of P. mume were compared firstly. And it was found that double flower trait of P. mume were often accompanied by petaloid stamen, multiple carpels and an increase in the total number of floral organs. Then, transcriptome sequencing of two representative cultivars P. mume 'Danban Lve' and P. mume 'Xiao Lve' were conducted at 3 Stage of flower bud development with distinct morphological differentiation. 3256 differentially expression genes (DEGs) were detected, and 20 candidate genes for double flower trait of P. mume were screened out including hub genes PmAP1-1 and PmAG-2 based on DEGs function analysis and WGCNA analysis. And it was found that epigenetic and hormone related genes may also play an important role in the process of double flower. CONCLUSIONS: This study suggested that the double flower trait of P.mume is more like accumulation origin based on morphological observation. 20 genes and co-expression network related to the formation of double flower P. mume were preliminarily screened through transcriptomics analysis. The results provided a reference for further understanding of the molecular mechanism of double flower trait in P. mume.

Efficient and effective control of confounding in eQTL mapping studies through joint differential expression and Mendelian randomization analyses.

MOTIVATION: Identifying cis-acting genetic variants associated with gene expression levels-an analysis commonly referred to as expression quantitative trait loci (eQTLs) mapping-is an important first step toward understanding the genetic determinant of gene expression variation. Successful eQTL mapping requires effective control of confounding factors. A common method for confounding effects control in eQTL mapping studies is the probabilistic estimation of expression residual (PEER) analysis. PEER analysis extracts PEER factors to serve as surrogates for confounding factors, which is further included in the subsequent eQTL mapping analysis. However, it is computationally challenging to determine the optimal number of PEER factors used for eQTL mapping. In particular, the standard approach to determine the optimal number of PEER factors examines one number at a time and chooses a number that optimizes eQTLs discovery. Unfortunately, this standard approach involves multiple repetitive eQTL mapping procedures that are computationally expensive, restricting its use in large-scale eQTL mapping studies that being collected today. RESULTS: Here, we present a simple and computationally scalable alternative, Effect size Correlation for COnfounding determination (ECCO), to determine the optimal number of PEER factors used for eQTL mapping studies. Instead of performing repetitive eQTL mapping, ECCO jointly applies differential expression analysis and Mendelian randomization analysis, leading to substantial computational savings. In simulations and real data applications, we show that ECCO identifies a similar number of PEER factors required for eQTL mapping analysis as the standard approach but is two orders of magnitude faster. The computational scalability of ECCO allows for optimized eQTL discovery across 48 GTEx tissues for the first time, yielding an overall 5.89% power gain on the number of eQTL harboring genes (eGenes) discovered as compared to the previous GTEx recommendation that does not attempt to determine tissue-specific optimal number of PEER factors. AVAILABILITYAND IMPLEMENTATION: Our method is implemented in the ECCO software, which, along with its GTEx mapping results, is freely available at www.xzlab.org/software.html. All R scripts used in this study are also available at this site. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Comprehensive copy number analysis of Y chromosome-linked loci for detection of structural variations and diagnosis of male infertility.

Infertility affects about 15% of heterosexual couples and male factors account for ~45-50% of clinical cases. Genetic factors play an important role in male infertility and thus we try to develop a cost-effective method for screening the genetic factors in male infertility. In our retrospective proof-of-concept study, we employed the high-throughput ligation-dependent probe amplification (HLPA) to examine the copy number by 115 genomic loci covering the Y chromosome, and 5 loci covering the X chromosome-specific region. We identified 8 sex chromosome aneuploid people from the low sperm concentration (LSC) group, and Y chromosome-specific microdeletion/duplications in 211 samples from the LSC group, and in 212 samples from the control group. 35 samples showed complete loss of AZFc (BPY2 to CDY1B deletion), which was not observed in controls. Nevertheless, a partial loss of AZFc (BPY2 to BPY2B deletion) was detected at comparable frequencies in both groups (68/211 vs. 108/212, respectively). And we further found structural variations in 28.6 and 26.9% samples from infertility and fertility groups. Moreover, we found that there were lower copy numbers for heterochromatic sequences in men with LSC. Especially, we reported that ultra-low relative copy number (RCN) (<0.5) type and low RCN (0.5 to <0.75) type in Yq12 were more often in the LSC group for the first time. Our results not only shed light on the potential role of low RCN in Yq12 in male infertility but also showed that HLPA can be a powerful and cost-effective tool for clinical screening in male infertility.

Chlorinated Organophosphate Flame Retardants Impair the Lung Function via the IL-6/JAK/STAT Signaling Pathway.

Toxicological studies have revealed the adverse impacts of organophosphate flame retardants (OPFRs) on the respiratory system, while there is a lack of epidemiological evidence, and information for risk assessment remains insufficient. Herein, we investigated the associations of urinary metabolites of OPFRs with the lung function in 987 adults participating in the U.S. National Health and Nutrition Examination Survey 2011-2012. The elevation of three primary metabolites of chlorinated OPFRs [bis(1,3-dichloro-2-propyl) phosphate (BDCIPP), bis(2-chloroethyl) phosphate (BCEP), and bis(1-chloro-2-propyl) phosphate (BCIPP)] was related to pulmonary dysfunction in a sample-weighted regression model. Each one-unit increase in the log-transformed levels of BDCIPP and BCEP was related to 91.52 and 79.34 mL reductions in the forced vital capacity (FVC). Each one-unit elevation in BCIPP was correlated with 130.86, 153.56, 302.26, and 148.24 mL reductions in forced expiratory volume 1st second (FEV1), FVC, peak expiratory flow rate (PEF), and forced expiratory flow at 25-75% of FVC (FEF25-75%), respectively. Then, an adverse outcome pathway (AOP) framework was constructed using the Comparative Toxicogenomics Database, the Toxicity Forecaster, and the GeneCards database. Based on the weight of the evidence, BDCIPP, BCEP, BCIPP, and their parent compounds (TDCIPP, TCEP, and TCIPP) may affect the IL-6/Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway, induce airway remodeling, and impair the lung function. Additionally, tobacco smoke exposure may modify the effects of BDCIPP on the lung function (Pint < 0.05) and affect the IL-6-mediated AOP. These results suggested that chlorinated OPFRs were associated with pulmonary dysfunction via the IL-6/JAK/STAT pathway.

Determination of organophosphate flame retardant tris(2-chloroethyl)phosphine based on the luminol-H2 O2 chemiluminescence system.

Organophosphorus flame retardants (OPFRs) are new types of environmental pollutants, therefore the rapid and sensitive detection of OPFRs is a very important objective. A new experimental phenomenon was found in which tris(2-chloroethyl)phosphine (TCEP), a type of OPFR, could effectively enhance the signal of the luminol-H2 O2 chemiluminescence (CL) system. Combined with the controllability of flow injection analysis, a rapid, stable, and sensitive CL method was established. The CL intensity responded linearly to the concentration of TCEP in the range 0.5-100 µg/L (R2 = 0.999) with a low detection limit of 33 ng/L. Relative standard deviation (RSD) was 2.2% (n = 7, c = 100 µg/L). Water samples were labelled and recycled with RSDs of 1.1-5.7% and recoveries of 88.7-116.1%. Based on these results, this study established a new CL detection method for the environmental pollutant TCEP.

Triptolide attenuates LPS-induced activation of RAW 264.7 macrophages by inducing M1-to-M2 repolarization via the mTOR/STAT3 signaling.

CONTEXT: Inflammatory bowel disease (IBD) is a chronic inflammatory disease of gastrointestinal tract, which can develop into colorectal cancer. Triptolide (TP) is a predominant bioactive ingredient of Tripterygium wilfordii Hook.F., and has been proven to have the therapeutic potential for various human diseases. OBJECTIVE: In our study, we examined the function of TP in the progression of IBD. METHODS: 3-(4,5)dimethylthiahiazo(-z-y1)-3,5-di-phenytetrazoliumromide assay was used to evaluate the viability of RAW264.7 cells. Quantitative reverse transcription polymerase chain reaction assay was performed to detect the relative gene expression. Western blot was used to detect the relative protein expression. Enzyme-linked immunosorbent assay was utilized to examine the levels of prostaglandin E2 (PGE2), tumor necrosis factor (TNF)-α, interleukin (IL)-10, and IL-6. RESULT: Our research demonstrated that TP restrained lipopolysaccharide (LPS)-caused activation of RAW264.7 cells, as evidenced by the reduction of PGE2, TNF-α, and IL-6, and increase of IL-10. TP treatment also restrained M1-type macrophage polarization and facilitated M2-type macrophage polarization of RAW 264.7 cells in the presence of LPS. Moreover, TP mitigated LPS-induced activation of the mammalian target of rapamycin (mTOR)/signal transducer and activator of transcription 3 (STAT3) signaling in RAW264.7 cells. Further, activation of the mTOR/STAT3 signaling by MHY1485 attenuated the effect of TP in regulation of macrophage polarization in RAW264.7 cells in the presence of LPS. CONCLUSION: Overall, our results indicated that TP attenuated LPS-induced activation of RAW 264.7 macrophages by inducing M1-to-M2 repolarization via repression of the mTOR/STAT3 signaling. Therefore, TP might be an effective agent for IBD treatment.

Internal heating method of loop-mediated isothermal amplification for detection of HPV-6 DNA.

Loop-mediated isothermal amplification (LAMP) is a promising diagnostic tool for genetic amplification, which is known for its rapid process, simple operation, high amplification efficiency, and excellent sensitivity. However, most of the existing heating methods are external for completion of molecular amplification with possibility of contamination of specimens. The present research provided an internal heating method for LAMP using magnetic nanoparticles (MNPs), which is called nano-LAMP. Near-infrared light with an excitation wavelength of 808 nm was employed as the heating source; hydroxy naphthol blue (HNB) was used as an indicator to conduct methodological research. We demonstrate that the best temperature was controlled at a working power of 2 W and 4.8 µg/µL concentration of nanoparticles. The lowest limit for the detection of HPV by the nano-LAMP method is 102 copies/mL, which was confirmed by a gel electrophoresis assay. In the feasibility investigation of validated clinical samples, all 10 positive HPV-6 specimens amplified by nano-LAMP were consistent with conventional LAMP methods. Therefore, the nano-LAMP detection method using internal heating of MNPs may bring a new vision to the exploration of thermostatic detection in the future.

Tanshinol alleviates ulcerative colitis by promoting the expression of VLDLR.

Tanshinol (TAN) is a widely used Chinese medicine ingredient with anti-inflammatory activity. The therapeutic effect of TAN in ulcerative colitis (UC) deserves further investigation. DSS induced UC model for mice, and TAN of different concentrations was used for in vivo therapy. Colons length was measured; expression of VLDLR in colonic mucosal tissue was evaluated by qRT-PCR, Western blot and histochemical staining. Besides, normal colorectal mucosal cell line (FHC) was treated with LPS to imitate the inflammatory process of UC in vitro. Different concentrations of TAN treated UC cell model. ELISA and qRT-PCR were applied to examine the concentrations of inflammatory cytokines (TNF-α, IL-6, IL-8, or IL-1ß). Flow cytometry and MTT was used to identify the apoptosis and viability of FHC cells, respectively. Afterwards, Western blot was performed to detect the expressions of Bax, Bcl-2, Cleaved caspase-3, and Cleaved caspase-9 in FHC cells. VLDLR was low-expressed in UC tissues as compared to the normal tissue. TAN could alleviate DSS-induced colons length shortening, colonic tissue structure destruction, inflammatory response, and VLDLR expression decrease in vivo. Further study found that TAN could alleviate LPS-induced inflammatory response, apoptosis, and viability decrease of FHC cells, and siVLDLR could partially offset the effect of TAN. TAN alleviates LPS-induced viability decrease, apoptosis, and inflammatory response in FHC cells by promoting VLDLR expression.

Headspace Volatiles and Endogenous Extracts of Prunus mume Cultivars with Different Aroma Types.

Prunus mume is a traditional ornamental plant, which owed a unique floral scent. However, the diversity of the floral scent in P. mume cultivars with different aroma types was not identified. In this study, the floral scent of eight P. mume cultivars was studied using headspace solid-phase microextraction (HS-SPME) and organic solvent extraction (OSE), combined with gas chromatography-mass spectrometry (GC-MS). In total, 66 headspace volatiles and 74 endogenous extracts were putatively identified, of which phenylpropanoids/benzenoids were the main volatile organic compounds categories. As a result of GC-MS analysis, benzyl acetate (1.55-61.26%), eugenol (0.87-6.03%), benzaldehyde (5.34-46.46%), benzyl alcohol (5.13-57.13%), chavicol (0-5.46%), and cinnamyl alcohol (0-6.49%) were considered to be the main components in most varieties. However, the volatilization rate of these main components was different. Based on the variable importance in projection (VIP) values in the orthogonal partial least-squares discriminate analysis (OPLS-DA), differential components of four aroma types were identified as biomarkers, and 10 volatile and 12 endogenous biomarkers were screened out, respectively. The odor activity value (OAV) revealed that several biomarkers, including (Z)-2-hexen-1-ol, pentyl acetate, (E)-cinnamaldehyde, methyl salicylate, cinnamyl alcohol, and benzoyl cyanide, contributed greatly to the strong-scented, fresh-scented, sweet-scented, and light-scented types of P. mume cultivars. This study provided a theoretical basis for the floral scent evaluation and breeding of P. mume cultivars.

Robust meta-analysis of biobank-based genome-wide association studies with unbalanced binary phenotypes.

With the availability of large-scale biobanks, genome-wide scale phenome-wide association studies are being instrumental in discovering novel genetic variants associated with clinical phenotypes. As increasing number of such association results from different biobanks become available, methods to meta-analyse those association results is of great interest. Because the binary phenotypes in biobank-based studies are mostly unbalanced in their case-control ratios, very few methods can provide well-calibrated tests for associations. For example, traditional Z-score-based meta-analysis often results in conservative or anticonservative Type I error rates in such unbalanced scenarios. We propose two meta-analysis strategies that can efficiently combine association results from biobank-based studies with such unbalanced phenotypes, using the saddlepoint approximation-based score test method. Our first method involves sharing the overall genotype counts from each study, and the second method involves sharing an approximation of the distribution of the score test statistic from each study using cubic Hermite splines. We compare our proposed methods with a traditional Z-score-based meta-analysis strategy using numerical simulations and real data applications, and demonstrate the superior performance of our proposed methods in terms of Type I error control.

Alternative splicing related genetic variants contribute to bladder cancer risk.

Emerging evidence has shown that aberrant alternative splicing (AS) events are involved in the carcinogenesis. The association between genetic variants in AS and bladder cancer susceptibility remains to be fully elucidated. We searched for single nucleotide polymorphisms (SNPs) which are located in splicing quantitative trait loci (sQTLs) in bladder cancer through CancerSplicingQTL database and the 1000 Genomes Project. A case-control study including 580 cases and 1,101 controls was conducted to assess the association between the functional genetic variants and bladder cancer risk. Next, we used GTEx, TCGA, and GEO databases conducting sQTL analysis and gene expression differences analysis to evaluate the potential biological function of the candidate SNPs and related genes. We found that SNP rs4383 C>G was remarkably related with the reduced risk of bladder cancer (odds ratio = 0.68, 95% confidence interval = 0.59-0.79, P = 3.91 × 10-7 ). Similar results were obtained in codominant, dominant and recessive model. Stratified analyses revealed that the effect of SNP rs4383 C>G on bladder cancer was more significant in the older subjects (age > 65), female and nonsmokers. sQTL analysis showed that SNP rs4383 was associated with the AS events of its downstream gene MAFF with a splicing event of alternative 5' splice site. The messenger RNA expression of MAFF in bladder tumor tissues was lowered compared with normal tissues. Patients with high expression of MAFF had higher survival rates. These findings indicated that SNP rs4383 related with the AS events of MAFF was associated with bladder cancer risk and could represent a possible biomarker for bladder cancer susceptibility.

MCC-SP: a powerful integration method for identification of causal pathways from genetic variants to complex disease.

BACKGROUND: Genome-wide association studies (GWAS) have successfully identified genetic susceptible variants for complex diseases. However, the underlying mechanism of such association remains largely unknown. Most disease-associated genetic variants have been shown to reside in noncoding regions, leading to the hypothesis that regulation of gene expression may be the primary biological mechanism. Current methods to characterize gene expression mediating the effect of genetic variant on diseases, often analyzed one gene at a time and ignored the network structure. The impact of genetic variant can propagate to other genes along the links in the network, then to the final disease. There could be multiple pathways from the genetic variant to the final disease, with each having the chain structure since the first node is one specific SNP (Single Nucleotide Polymorphism) variant and the end is disease outcome. One key but inadequately addressed question is how to measure the between-node connection strength and rank the effects of such chain-type pathways, which can provide statistical evidence to give the priority of some pathways for potential drug development in a cost-effective manner. RESULTS: We first introduce the maximal correlation coefficient (MCC) to represent the between-node connection, and then integrate MCC with K shortest paths algorithm to rank and identify the potential pathways from genetic variant to disease. The pathway importance score (PIS) was further provided to quantify the importance of each pathway. We termed this method as "MCC-SP". Various simulations are conducted to illustrate MCC is a better measurement of the between-node connection strength than other quantities including Pearson correlation, Spearman correlation, distance correlation, mutual information, and maximal information coefficient. Finally, we applied MCC-SP to analyze one real dataset from the Religious Orders Study and the Memory and Aging Project, and successfully detected 2 typical pathways from APOE genotype to Alzheimer's disease (AD) through gene expression enriched in Alzheimer's disease pathway. CONCLUSIONS: MCC-SP has powerful and robust performance in identifying the pathway(s) from the genetic variant to the disease. The source code of MCC-SP is freely available at GitHub ( https://github.com/zhuyuchen95/ADnet ).

Weeping candidate genes screened using comparative transcriptomic analysis of weeping and upright progeny in an F1 population of Prunus mume.

Weeping is a specific plant architecture with high ornamental value. Despite the considerable importance of the weeping habit to landscaping applications and knowledge of plant architecture biology, little is known regarding the underlying molecular mechanisms. In this study, growth and phytohormone content were analyzed among the progeny of different branch types in an F1 mapping population of Prunus mume with varying plant architecture. Bulked segregant RNA sequencing was conducted to compare differences among progeny at a transcriptional level. The weeping habit appears to be a complex process regulated by a series of metabolic pathways, with photosynthesis and flavonoid biosynthesis highly enriched in differentially expressed genes between weeping and upright progeny. Based on functional annotation and homologous analyses, we identified 30 candidate genes related to weeping that merit further analysis, including 10 genes related to IAA and GA3 biosynthesis, together with 6 genes related to secondary branch growth. The results of this study will facilitate further studies of the molecular mechanisms underlying the weeping habit in P. mume.

Value of monitoring urine ammonia at time of biopsy in patients with lupus nephritis.

OBJECTIVE: Although lupus nephritis (LN) is mostly characterized by glomerular involvement, tubular injury is indispensable in its pathogenesis and progression. The purpose of this study is to examine associations between urinary acidification function and clinical and pathological features in LN. METHODS: A total of 103 patients with renal biopsy-proven LN were included, and clinical parameters and laboratory data were obtained from the medical records. Plasma samples, 24-h urine samples and the urinary acidification function, including urine pH, titratable acid, and ammonia, were collected within 3 days before the day of renal biopsy. The correlations between defects of acid excretion and clinical and pathological features were then assessed. Logistic regression analysis was used to assess factors associated with the presence of nephrotic range proteinuria. RESULTS: The urine ammonia level was inversely correlated with SLEDAI-2 K scores, rSLEDAI scores, serum creatinine levels and proteinuria, while it was positively correlated with eGFR. And urine titratable acid was only inversely correlated with rSLEDAI scores and proteinuria. Moreover, urine ammonia had significant negative correlations with AI scores, interstitial inflammatory cell infiltration, CI scores, glomerular sclerosis, fibrous crescents, tubular atrophy and interstitial fibrosis. And urine titratable acid was mainly inversely correlated with CI scores. Furthermore, univariate logistic analyses identified that both urine titratable acid and ammonia were correlated with the presence of nephrotic range proteinuria. After the adjustment for chronicity index and eGFR in a multivariate logistic analysis, only urine titratable acid was still identified as an independent risk factor for the occurrence of nephrotic range proteinuria. CONCLUSIONS: Urine ammonia was associated with clinical and pathological features of chronicity and tubulointerstitial disease activity among patients with lupus nephritis. Furthermore, the strong association between urinary protein and titratable acid excretion at the time of kidney biopsy is significant even after adjusting for the chronicity index and eGFR at biopsy.

Mitochondrial pyruvate carrier: a potential target for diabetic nephropathy.

BACKGROUND: Mitochondrial dysfunction contributes to the pathogenesis of diabetic nephropathy (DN). Mitochondrial pyruvate carrier 1 (MPC1) and mitochondrial pyruvate carrier 2 (MPC2) play a bottleneck role in the transport of pyruvate into mitochondrial across the mitochondrial inner membrane. A previous study showed that increasing mitochondrial pyruvate carrier content might ameliorate diabetic kidney disease in db/db mice. However, the expression status of MPC1 and MPC2 in patients with DN is unclear. METHODS: Patients with primary glomerulonephropathy (PGN, n = 30), PGN with diabetes mellitus (PGN-DM, n = 30) and diabetic nephropathy (DN, n = 30) were included. MPC1 and MPC2 protein levels were examined by immunohistochemistry. The expression of MPC in different groups was evaluated by the Kruskal-Wallis test. Spearman's rank correlation was performed for correlation analysis between MPC levels and clinical factors. RESULTS: Both MPC1 and MPC2 were localized in renal tubules. Levels of MPC1 and MPC2 were lower in DN patients than in PGN patients and in PGN patients with DM, whereas there were no differences in MPC1 and MPC2 levels among DN stage II to stage IV. Moreover, both MPC1 and MPC2 levels were significantly correlated with serum creatinine, BUN and eGFR in patients with DN, whereas no analogous trend was observed in nondiabetic kidney disease. CONCLUSIONS: Our study indicated that MPC localized in renal tubules, which were significantly decreased in DN. MPC was associated with clinical features, especially those representing renal functions.

Ultraviolet-mediated peroxymonosulfate diminution of earthy and musty compound trichloroanisole in water.

Taste and odor (T&O) problem in water is one of the main obstacles to improve the quality of drinking water, and efficient water treatment processes are urgently needed to control T&O compounds. Ultraviolet-mediated peroxymonosulfate (UV/PMS) diminution of trichloroanisole (TCA) in water was investigated in this paper. The treatment of 2,3,6-trichloroanisole (2,3,6-TCA) by three advanced oxidation processes (UV, UV/H2O2 and UV/PMS) was compared, and UV/PMS stood out. SO4•- and HO• were produced in the UV/PMS, and their specific contributions to 2,3,6-TCA oxidation were investigated. The competitive kinetic model was applied to determine the second-order reaction rate between 2,3,6-TCA and SO4•- or HO•. The products of 2,3,6-TCA generated in UV/PMS were analyzed with gas chromatography/high resolution-mass spectrometry (GC/HR-MS), and the degradation mechanism was proposed. The effects of water matrices (chloride, bicarbonate and humic acid) on UV/PMS performance were studied, and the decontamination of 2,3,6-TCA in real water was carried out. The disinfection byproducts (DBPs) alteration from 2,3,6-TCA by UV/PMS - chlorination treatment was explored. Overall, UV/PMS can effectively deal with the T&O pollution of TCA in water.