Integrated analysis of mRNA, microRNA and protein in systemic lupus erythematosus-specific induced pluripotent stem cells from urine.

BACKGROUND: In clinical practice, it is difficult to monitor the repeating relapse in patients who have been suffering from systemic lupus erythematosus (SLE). The underlying etiology remains largely unknown. METHODS: Aiming to understand the pathogenesis of SLE, a detailed study was conducted. Renal tubular cells-derived iPSCs were successfully obtained from the urine of SLE patients and healthy controls. With the purpose to identify simultaneous expression profiling of microRNA, mRNA and protein, Illumina HiSeq™ 2000 System and iTRAQ-coupled 2D LC-MS/MS analysis were utilized in systemic lupus erythematosus-specific induced pluripotent stem cells (SLE-iPSCs) and normal control-iPSCs (NC-iPSCs). The integration of multiple profiling datasets was realized since it could facilitate the identification of non-seed miRNA targets, as well as differentially expressed mRNAs and proteins. RESULTS: For this study, profiling datasets of 1099 differentially expressed mRNAs, 223 differentially expressed microRNAs and 94 differentially expressed proteins were integrated. In order to investigate the influence of miRNA on the processes of regulating mRNAs and proteins' levels, potential targets of differentially expressed mRNAs and proteins were predicted using miRanda, TargetScan and Pictar. Multiple profiling datasets were integrated to facilitate the identification of miRNA targets, as well as differentially expressed mRNAs and proteins. Through gene ontology (GO) analysis of differentially expressed mRNAs and proteins, biological processes that drive proliferation were identified, such as mRNA processing and translation. Western blot and Q-PCR confirmed AK4 protein and mRNA up-regulation. The findings also showed that TAGLN's protein and mRNA level were down-regulated in SLE-iPSCs, both miR-371a-5p and let-7a-5p in SLE-iPSC were down-regulated and verified using Q-PCR. The up-regulation of AK4 involved in nucleotide biosynthesis suggested a general acceleration of anabolic metabolism induced by down-regulated miR-371a-5p, which might contribute to SLE. CONCLUSION: Based on high throughput analysis, integrated miRNA, mRNA, and protein expression data were generated. Differentially expressed dates were also adopted in conjunction with in-silico tools to identify potential candidates for SLE-iPSCs. Representative miRNA, mRNA and proteins were verified. It was also expected that the knowledge gained from this study can be applied to assess the usefulness of pathogenesis and novel biomarker candidates of SLE, which may develop a new way for SLE diagnosis.

Analysis of microRNAs in patients with systemic lupus erythematosus, using Solexa deep sequencing.

OBJECTIVES: Our aim in this study was to identify and examine the differential expression of microRNAs in patients with systemic lupus erythematosus (SLE). METHODS: We employed high-quality, high-throughput Solexa sequencing to clone and identify microRNAs in SLE patients and a control group. RESULTS: From the sequencing data, we identified numerous microRNAs displaying significantly different levels of expression in patients with SLE and in healthy controls. The 212 and 199 microRNAs were upregulated and downregulated, respectively. Only 61 novel microRNAs exhibited significantly different levels of expression in the two groups. The target genes of the novel microRNAs identified in the SLE group were found to have cell metabolism functions. We also analyzed the chromosomal locations of the microRNAs with high level of expression between the two groups. A profile comparison revealed that the majority of transcripts were expressed at a similar level. The functional classes of the most abundant microRNAs were equally represented on each chromosome. CONCLUSION: We identified novel and known microRNAs significantly enhancing our understanding of the microRNA expression profiles of SLE patients. These data also provide insight into the function of microRNAs in SLE and provide new strategies for future therapies.

Molecular dysfunctions in acute rejection after renal transplantation revealed by integrated analysis of transcription factor, microRNA and long noncoding RNA.

Acute rejection remains a problem in renal transplantation. To further illustrate the mechanism of rejection, we integrated protein array-based proteomics and RNA microarray-based genomics to investigate the transcription factor, microRNA and long noncoding RNA of biopsies of three patients with acute rejections and a control group. 99 transcription factors were identified in acute rejection biopsies compared to normal renal tissue. We correlated transcription factor data with microRNA and long noncoding RNA data sets and reported the expression of 5 transcription factors (AP-1, AP-4, STATx, c-Myc and p53), 12 miRNAs and 32 lncRNAs in acute rejection biopsies. Pathway analysis demonstrated that over-presentation of transcription factor pathway plays a critical role in acute rejection. This is the first study to comprehensively report the acute rejection transcription factor pathway. Integrative analysis of the transcription factor, microRNA and long noncoding RNA provided an expansive view of molecular signaling pathways in acute rejection after renal transplantation.

Association between consumption of flavonol and its subclasses and chronic kidney disease in US adults: an analysis based on National Health and Nutrition Examination Survey data from 2007-2008, 2009-2010, and 2017-2018.

Background: There is little research on the relationship between flavonol consumption and chronic kidney disease (CKD). This study aimed to examine the link between flavonol consumption and the risk of CKD among US adults, using data from the 2007-2008, 2009-2010 and 2017-2018 National Health and Nutrition Examination Survey (NHANES). Methods: A cross-sectional approach was used, drawing on data from three NHANES cycles. The flavonol consumption of the participants in this study was assessed using a 48 h dietary recall interview. CKD was diagnosed based on an estimated glomerular filtration rate below 60 mL/min/1.73 m2 or a urine albumin-to-creatinine ratio of 30 mg/g or higher. Results: Compared to the lowest quartile of flavonol intake (Q1), the odds ratios for CKD were 0.598 (95% CI: 0.349, 1.023) for the second quartile (Q2), 0.679 (95% CI: 0.404, 1.142) for the third quartile (Q3), and 0.628 (95% CI: 0.395, 0.998) for the fourth quartile (Q4), with a p value for trend significance of 0.190. In addition, there was a significant trend in CKD risk with isorhamnetin intake, with the odds ratios for CKD decreasing to 0.860 (95% CI: 0.546, 1.354) in the second quartile, 0.778 (95% CI: 0.515, 1.177) in the third quartile, and 0.637 (95% CI: 0.515, 1.177) in the fourth quartile (p for trend = 0.013). Conclusion: Our analysis of the NHANES data spanning 2007-2008, 2009-2010, and 2017-2018 suggests that high consumption of dietary flavonol, especially isorhamnetin, might be linked to a lower risk of CKD in US adults. These findings offer new avenues for exploring strategies for managing CKD.

Building an Open-Vocabulary Video CLIP Model With Better Architectures, Optimization and Data.

Despite significant results achieved by Contrastive Language-Image Pretraining (CLIP) in zero-shot image recognition, limited effort has been made exploring its potential for zero-shot video recognition. This paper presents Open-VCLIP++, a simple yet effective framework that adapts CLIP to a strong zero-shot video classifier, capable of identifying novel actions and events during testing. Open-VCLIP++ minimally modifies CLIP to capture spatial-temporal relationships in videos, thereby creating a specialized video classifier while striving for generalization. We formally demonstrate that training Open-VCLIP++ is tantamount to continual learning with zero historical data. To address this problem, we introduce Interpolated Weight Optimization, a technique that leverages the advantages of weight interpolation during both training and testing. Furthermore, we build upon large language models to produce fine-grained video descriptions. These detailed descriptions are further aligned with video features, facilitating a better transfer of CLIP to the video domain. Our approach is evaluated on three widely used action recognition datasets, following a variety of zero-shot evaluation protocols. The results demonstrate that our method surpasses existing state-of-the-art techniques by significant margins. Specifically, we achieve zero-shot accuracy scores of 88.1%, 58.7%, and 81.2% on UCF, HMDB, and Kinetics-600 datasets respectively, outpacing the best-performing alternative methods by 8.5%, 8.2%, and 12.3%. We also evaluate our approach on the MSR-VTT video-text retrieval dataset, where it delivers competitive video-to-text and text-to-video retrieval performance, while utilizing substantially less fine-tuning data compared to other methods.

Reduced circulating miR-15b is correlated with phosphate metabolism in patients with end-stage renal disease on maintenance hemodialysis.

BACKGROUND: Disorders of mineral metabolism can facilitate the progression of vascular calcification and are closely associated with adverse outcomes in end-stage renal disease (ESRD). miR-15b has been implicated in the epigenetic regulation of key metabolism, stress response, and osteoblast differentiation. METHODS AND RESULTS: In this study, we detected miR-15b in the plasma of 30 patients with ESRD and 20 healthy controls using real-time quantitative RT-PCR (RT-qPCR). Compared with healthy controls, the circulating levels of miR-15b were significantly reduced in patients with ESRD. However, there is no significant difference in circulating miR-15b levels when comparing prehemodialysis and posthemodialysis in patients with ESRD. In addition, to further estimate the potential roles of aberrantly expressed candidate miR-15b in the pathogenesis of ESRD, we utilized a bioinformatics exploratory analysis and identified gene ontology "biological process" classifications which revealed that dysregulated circulating miR-15b might be involved in phosphate metabolism. Furthermore, circulating miR-15b positively correlated with both estimated glomerular filtration rate (r = 0.502, p = 0.003) and hemoglobin levels (r = 0.432, p = 0.017) and inversely correlated with phosphate level (r = -0.516, p = 0.004). CONCLUSION: The findings indicated that the dysregulated miR-15b might contribute to the progression of ESRD by modulating genes that might be involved in the phosphate metabolism, which might have the potential of being used as a biomarker for monitoring disease.

Clinical status of patients 1 year after hospital discharge following recovery from COVID-19: a prospective cohort study.

BACKGROUND: The long-term clinical status of coronavirus disease 2019 (COVID-19) in recovered patients remains largely unknown. This prospective cohort study evaluated clinical status of COVID-19 and explored the associated risk factors. METHODS: At the outpatient visit, patients underwent routine blood tests, physical examinations, pulmonary function tests, 6-min walk test, high-resolution computed tomography (CT) of the chest, and extrapulmonary organ function tests. RESULTS: 230 patients were analyzed. Half (52.7%) reported at least one symptom, most commonly fatigue (20.3%) and sleep difficulties (15.8%). Anxiety (8.2%), depression (11.3%), post-traumatic symptoms (10.3%), and sleep disorders (26.3%) were also reported. Diffusion impairments were found in 35.4% of the patients. Abnormal chest CT scans were present in 63.5% of the patients, mainly reticulation and ground-glass opacities. Further, a persistent decline in kidney function was observed after discharge. SARS-CoV-2-specific antibodies of IgA, IgG, and IgM were positive in 56.4%, 96.3%, and 15.2% of patients, respectively. Multivariable logistic regression showed that disease severity, age, and sex were closely related to patient recovery. CONCLUSIONS: One year after hospital discharge, patients recovered from COVID-19 continued to experience both pulmonary and extrapulmonary dysfunction. While paying attention to pulmonary manifestations of COVID-19, follow-up studies on extrapulmonary manifestations should be strengthened.

Protease Inhibitor Use in COVID-19.

The outbreak of a large plaque, novel coronavirus pneumonia (NCP), which also named Coronavirus Disease 2019 (COVID-19) by the WHO, has detrimentally affected the livelihood and health of people in China. During the spread of COVID-19, colleagues who have been working at the frontline have had to face many new challenges in the treatment and prevention of NCP. Therefore, we have provided suggestions for the diagnosis, treatment, and prevention of the novel coronavirus pneumonia in the current epidemic situation based on the latest reports and the experience of doctors treating COVID-19 in our hospital. We recommend lopinavir/ritonavir as the effective drugs for antiviral treatment according to our experience in administering lopinavir/ritonavir to COVID-19 patients and the successful cases of these drugs in treating MERS and SARS, but need more clinical data to prove their efficacy in treating COVID-19.

Genome-wide analysis of histone H3 lysine 4 trimethylation in peripheral blood mononuclear cells of minimal change nephrotic syndrome patients.

BACKGROUND: Studies of the epigenome have attracted some interest in nephrology. However, to date, our knowledge about the alterations in histone modification in minimal change nephrotic syndrome (MCNS) is unknown. This study aimed to investigate the variations in histone H3 lysine 4 trimethylation (H3K4me3) in peripheral blood mononuclear cells of patients with MCNS. METHODS: H3K4me3 variations were analyzed in peripheral blood mononuclear cells, from 15 MCNS patients and 15 healthy subjects, using the ChIP-chip approach. ChIP real-time PCR is used to validate the microarray results. In addition, mRNA expression and DNA methylation status can also be further analyzed by quantitative (q) RT-PCR and methyl-DNA immunoprecipitation-q PCR, respectively. RESULTS: 848 increased and 231 decreased H3K4me3 probes displaying significant H3K4me3 differences were found in MCNS patients compared with healthy subjects. The results of ChIP real-time PCR coincided well with the microarray. Expression analysis by qRT-PCR revealed positive correlations between mRNA and H3K4me3 levels. DNA methylation alterations were found on selected positive genes (IL4R, HIVEP3, HPSE2, CDH13 and PRKD2). In addition, we also found that there is an inverse relationship between H3K4me3 and promoter DNA methylation in MCNS patients. CONCLUSION: Our studies indicate that there are significant alterations of H3K4me3 in MCNS patients. These significant H3K4me3 candidates may help to explain the immunological disturbance involved in MCNS patients.

Profiling the TRB and IGH repertoire of patients with H5N6 Avian Influenza Virus Infection by high-throughput sequencing.

Avian Influenza A (H5N6) Virus causes severe influenza disease in humans and is manifested by acute respiratory distress syndrome, multi-organ failure, and high mortality rates. T cells recognize antigens specifically through a membrane protein T cell receptor (TCR). To ward off a wide variety of pathogens, the human adaptive immune system harbors a vast array of TCRs, which are collectively referred to as the TCR repertoire. The B cell receptor (BCR) is involved in inducing the humoral immune response. The generation of a diverse T cell and B cell repertoire is essential for protection against infection. In this study, multiplex PCR based on genomic DNA amplicons and Illumina high-throughput sequencing (HTS) were applied to study the characteristics and polymorphisms of the TRB and IGH repertoire in the peripheral blood mononuclear cells (PBMCs) from two H5N6 AIV patients and six healthy donors (NC). The CDR3 average length in the AIV group was different from the NC group. The TRBV12-3, TRBV12-4, and TRBV15 gene segments and TRBV30/TRBJ1-2, TRBV12-3/TRBJ1-1 and IGHV3-11/IGHJ6 gene segment pairings also exhibited a higher usage in the PBMCs of AIV donors and may provide more information for generating more effective T/B cell targeted diagnosis/protection strategies.

Targeted next generation sequencing identified novel loss-of-function mutations in MERTK gene in Chinese patients with retinitis pigmentosa.

BACKGROUND: Retinitis pigmentosa (RP) is one of the major types of hereditary retinal dystrophies with extreme genotypic heterogeneity. To date, more than 80 genes have been identified to be associated with RP in human. METHOD: Here, we presented a clinical genetic study of three Chinese man manifested with night vision blindness and complete loss of midperipheral visual field. All of these three probands have been identified with loss of both central vision and far peripheral visual field. Gradual loss of rod cells followed by subsequent loss of cone cells have been identified in these probands. Targeted next generation sequencing and Sanger sequencing have been performed to understand the pathogenic variants underlying the disease phenotype in these three unrelated Chinese probands. RESULTS: Targeted next generation sequencing and Sanger sequencing identified three homozygous novel mutations (c.1880C>A; c.1459_1460delGA, and c.392G>A) in the MERTK gene in these three unrelated Chinese proband. In the first proband, the identified mutation (c.1880C>A) leads to the formation of a premature stop codon followed by the formation of a truncated mer-tyrosine kinase (MERTK) protein (p.Ser627*) product which predicted to be disease causing. In the second proband, the identified deletion (c.1459_1460delGA) leads to the formation of a frameshift which also finally results in the formation of a truncated MERTK protein (p.Asp487Leufs*57) product which also predicted to be disease causing. In the third proband, the identified mutation (c.392G>A) leads to the formation of a premature stop codon followed by the formation of a truncated MERTK protein (p.Trp131*) product which also predicted to be disease causing. Hence, these three mutations are loss-of-function mutations. These three mutations were absent in unaffected family members and in 100 normal healthy controls. CONCLUSION: Our present study also demonstrates the significance of targeted next generation sequencing in determining the genetic basis of RP.

Construction and identification of human tissue kallikrein gene eukaryotic expressing vector.

To clone and sequence the human tissue kallikrein gene of Chinese, and to construct eukaryotic expression recombinant of KK, total RNA was extracted from human pancreas and human tissue kallikrein gene cDNA was amplified by PCR after reverse-transcription by using Oligo(dT) primer. The original kallikrein cDNA was recovered and filled with Klenow enzyme and inserted into KS plasmid. After restriction endonuclease digestion, KK cDNA was sequenced by ABI377 analyzer. Then the KK gene was amplified from pBluescript KSKK and inserted into pcDNA3. A sequence comparison showed that the cloned kallikrein gene was only one nucleotide different from that reported in the Genbank. The coding amino acid was Asp in the Genbank gene, while the coding amino acid of Chinese kallikrein gene was Asn. The KK cDNA fragment was inserted into the eukaryotic expression vector pcDNA3. The cloned kallikrein gene and the pcDNA3KK can be used for further study in gene therapy.. .

Differential proteomics analysis of liver failure in peripheral blood mononuclear cells using isobaric tags for relative and absolute quantitation.

The aim of the present study was to examine differentially expressed proteome profiles for candidate biomarkers in peripheral blood mononuclear cells (PBMCs) of liver failure (LF) patients. Ten patients were diagnosed as LF and 10 age- and gender-matched subjects were recruited as healthy controls. Isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomic technology is efficiently applicable for identification and relative quantitation of the proteomes of PBMCs. Eight-plex iTRAQ coupled with strong cation exchange chromatography, and liquid chromatography coupled with tandem mass spectrometry were used to analyze total proteins in LF patients and healthy control subjects. Molecular variations were detected using the iTRAQ method, and western blotting was used to verify the results. LF is a complex type of medical emergency that evolves following a catastrophic insult to the liver, and its outcome remains the most ominous of all gastroenterologic diseases. Serious complications tend to occur during the course of the disease and further exacerbate the problems. Using the iTRAQ method, differentially expressed proteome profiles of LF patients were determined. In the present study, 627 proteins with different expression levels were identified in LF patients compared with the control subjects; with 409 proteins upregulated and 218 proteins downregulated. Among them, four proteins were significantly differentially expressed; acylaminoacyl-peptide hydrolase and WW domain binding protein 2 were upregulated, and resistin and tubulin ß 2A class IIa were downregulated. These proteins demonstrated differences in their expression levels compared with other proteins with normal expression levels and the significant positive correlation with LF. The western blot results were consistent with the results from iTRAQ. Thus, investigation of the molecular mechanism of the proteins involved in LF may facilitate an improved understanding of the pathogenesis of LF and elucidation of novel biomarker candidates.

[Anti-miR-145 promotes human airway smooth muscle cell proliferation and osteopontin synthesis in vitro].

OBJECTIVE: To investigate the effect of anti-miR-145 on human airway smooth muscle cell (HASMC) proliferation and osteopontin systhesis in vitro and explore the mechanisms. METHODS: HASMCs were treated with 10-100 nmol/L anti-miR-145, and the cell proliferation and apoptosis were investigated using a CCK-8 assay and flow cytometry, respectively. The changes in osteopontin synthesis after the treatment was quantified with Western blotting. RESULTS: Treatment with 10 and 50 nmol/L anti-miR-145 significantly promoted the proliferation and osteopontin synthesis in HASMCs (P<0.05 or <0.01), and 50 nmol/L anti-miR-145 obviously inhibited the cell apoptosis (P<0.01). CONCLUSION: Anti-miR-145 promotes HASMC proliferation and osteopontin synthesis and inhibits HASMC apoptosis in vitro, indicating the important role of anti-miR-145 in the pathogenesis of airway remodeling.

Integrated profiling of microRNA expression in membranous nephropathy using high-throughput sequencing technology.

The present study analyzed microRNA (miRNA) expression profiles in peripheral blood lymphocyte cells (PBLCs) from patients with membranous nephropathy (MN) and normal controls (NC), in an effort to improve the understanding of the pathogenesis of MN. High-throughput sequencing was performed on 30 MN patients and 30 healthy individuals (NC group). Known and novel miRNAs were analyzed and the results were confirmed by quantitative reverse transcription PCR (qRT-PCR). In total, 326 miRNAs showed a significant difference in expression between the MN and NC groups. This included 286 downregulated miRNAs and 40 upregulated miRNAs. In addition, there were 6 novel miRNAs that presented differential levels of expression between the MN and NC groups. The miRNAs were mapped to the genome, using a short oligonucleotide alignment program (SOAP), to analyze their expression and distribution. Twenty-five percent of the unique miRNAs in the MN group and 52.1% in the NC group were mapped to the genome. One hundred and eight mismatches were identified. Seventy-seven mismatches were detected in a higher proportion of the MN samples, compared with the NC samples. Twenty-five mismatches were detected in a higher proportion of the NC samples than the MN samples. Differential miRNA expression was also detected between 10 randomly selected pair groups, as depicted in a cluster analysis diagram. These data indicate that differential miRNA expression may be involved in the pathogenesis of MN. In addition, the discrepancies between the MN and NC groups, in the mismatched miRNAs that were mapped to the genome, strongly suggest that miRNAs play an important role in the pathogenesis of human disorders. miRNAs may provide a potential breakthrough in the research of MN and may provide a novel biomarker for the diagnosis and treatment of the disease.

Microarray analysis of long non-coding RNA expression in human acute rejection biopsy samples following renal transplantation.

Rejection is still a major obstacle in long-term allograft survival of renal transplant recipients. Long non­coding RNAs (lncRNAs) are an important class of pervasive RNAs involved in a variety of biological functions, and which are often found to be differentially expressed between healthy and pathological conditions. The aim of this study was to compare the expression profiles of lncRNAs between samples from acute rejection following kidney transplantation and control samples. Three patients were enrolled, diagnosed by renal biopsy with acute rejection upon kidney transplantation. We used lncRNA microarrays to study the lncRNA expression profiles in the kidney biopsies of these patients and in kidneys from healthy donors. Reverse transcription­quantitative polymerase chain reaction (RT-qPCR) was used to validate the microarray results. In addition, potential functions of the identified lncRNAs were further explored by searching the UCSC, RNAdb, RefSeq and NRED databases. Five candidate lncRNAs displaying differential expression in acute rejection samples were validated by RT-qPCR. The results were in agreement with the microarray data. Among the identified lncRNAs, certain have been previously identified in relevant conditions, thereby supporting previous evidence, but certain may constitute novel biomarker candidates. This is the first report to date using lncRNA microarrays to identify unique expression signatures of acute rejection in transplant biopsies. Our data indicate that lncRNAs are potentially involved in the pathogenesis of acute rejection. Our results may have important implications in the identification of diagnostic biomarkers, as well as in the understanding and treatment of acute rejection following renal transplantation.

Circulating microRNAs as candidate biomarkers in patients with systemic lupus erythematosus.

Aberrant expression of microRNAs (miRNAs) has been identified in various diseases. Recent studies demonstrated that miRNAs can be detected in the circulation and serve as potential biomarkers of various diseases. Moreover, the detection of circulating miRNAs can provide important novel information concerning diseases. In this study, a miRNA profile was used to determine the aberrantly expressed circulating miRNAs in patients with systemic lupus erythematosus (SLE) compared with patients with rheumatoid arthritis (RA) and healthy controls (HCs). To further confirm the microarray data, we identified 8 miRNAs (miR-126, miR-21, miR-451, miR-223, miR-16, miR-125a-3p, miR-155, and miR-146a) by real-time quantitative PCR (qRT-PCR) in 20 healthy controls and in 55 patients, of whom 30 patients were diagnosed with SLE and 25 were diagnosed with RA. Consistent with the microarray data, miR-126 was specifically enriched only in the blood of the SLE patients, but 4 other miRNAs (miR-21, miR-451, miR-223, and miR-16) were upregulated in the patients with SLE and were also significantly increased in the patients with RA. In contrast, miR-125a-3p, miR-155, and miR-146a showed a trend toward significantly reduced levels in the patients with SLE. In addition, to further estimate the potential roles of these differentially expressed circulating miRNAs in the pathogenesis of SLE, we used a bioinformatics exploratory analysis and identified a number of significantly enriched pathways, which implied that most dysregulated circulating miRNAs might be involved in various signal transduction pathways and cell interactions, particularly the mitogen-activated protein kinase signaling pathway. Based on these findings, we postulate that aberrantly expressed plasma miRNAs could be attractive as candidates for putative biomarkers of SLE and may help elucidate the possible pathogenesis of SLE.

Comparison of the metabolic profiling of hepatitis B virus-infected cirrhosis and alcoholic cirrhosis patients by using (1) H NMR-based metabonomics.

AIM: The aims of the present study were to depict the serum metabolic characteristics of hepatitis B virus (HBV)-infected cirrhosis and alcoholic cirrhosis patients, and to find the specific serum biomarkers associated with the diseases. METHODS: A pilot metabolic profiling study was conducted using three groups: HBV-infected cirrhosis patients (n = 21), alcoholic cirrhosis patients (n = 20) and healthy controls (n = 20). (1) H nuclear magnetic resonance (NMR)-based metabonomics was used to obtain the serum metabolic profiles of the samples. The acquired data were processed by multivariate principal component analysis (PCA) and orthogonal partial least-squares-discriminant analysis (OPLS-DA). The discriminatory metabolites between HBV-infected cirrhosis and alcoholic cirrhosis were further validated by classical biochemical assays. RESULTS: The OPLS-DA model was capable of distinguishing between HBV-infected and alcoholic cirrhosis patients. Five metabolites, creatine, acetoacetate, isobutyrate, glutamine and glutamate, were identified as the most influential factors to compare HBV-infected cirrhosis and alcoholic cirrhosis. The validation tests showed that the changes of the five metabolites were well coincident with the results of NMR. CONCLUSION: NMR spectra combined with pattern recognition analysis techniques may provide a new way to explore the pathogenesis of HBV-infected and alcoholic cirrhosis patients.

A pilot metabolic profiling study in serum of patients with chronic kidney disease based on (1) H-NMR-spectroscopy.

BACKGROUND: Chronic kidney disease (CKD) is the end point of a number of renal and systemic diseases. The metabolomics with a highly multiplexed and efficient manner is a challenging goal in nephrology. METHODS: A (1) H-NMR based metabolomics approach was applied to establish a human CKD serum metabolic profile. Serum samples were obtained from CKD patients with four stages (N= 80) and healthy controls (N= 28). The data acquired by CMPG spectrum were further processed by pattern recognition (PR) analysis. Principal components analysis (PCA) and partial least-squares-discriminant analysis (PLS-DA) was capable of clustering the disease groups and establishing disease-specific metabolites profile. RESULTS: The classification models could grade CKD patients with considerably high value of Q(2) and R(2) . The significant endogenous metabolites that contributed to distinguish CKD in different stages included the products of glycolysis (glucose, lactate), amino acids (valine, alanine, glutamate, glycine), organic osmolytes (betaine, myo-inositol, taurine, glycerophosphcholine), and so on. Based on these metabolites, the model for diagnosing patients with CKD achieved the sensitivity and specificity of 100%. CONCLUSION: The study illustrated that serum metabolic profile was altered in response to renal dysfunction and the progression of CKD. The identified metabolic biomarkers may provide useful information for the diagnosis of CKD, especially in early stages.

Circulating levels of inflammation-associated miR-155 and endothelial-enriched miR-126 in patients with end-stage renal disease.

Circulating microRNAs (miRNAs) may represent a potential noninvasive molecular biomarker for various pathological conditions. Moreover, the detection of circulating miRNAs can provide important novel disease-related information. In particular, inflammation-associated miR-155 and endothelial-enriched miR-126 are reported to be associated with vascular homeostasis. Vascular damage is a common event described in end-stage renal disease (ESRD). We hypothesized that miR-155 and miR-126 may be detectable in the circulation and serve as potential biomarkers for risk stratification. In this study, we assessed miR-155 and miR-126 in the plasma of 30 ESRD patients and 20 healthy controls using real-time quantification RT-PCR. The circulating levels of miR-155 and miR-126 were significantly reduced in patients with ESRD compared to healthy controls. However, there was no significant difference of circulating miR-155 and miR-126 levels between prehemodialysis and posthemodialysis patients. Furthermore, both circulating miR-126 and miR-155 correlated positively with estimated glomerular filtration rate (miR-126: r = 0.383, P = 0.037; miR-155: r = 0.494, P = 0.006) and hemoglobin (miR-126: r = 0.515, P = 0.004; miR-155: r = 0.598, P < 0.001) and correlated inversely with phosphate level (miR-126: r = -0.675, P < 0.001; miR-155: r = -0.399, P = 0.029). Pearson's correlation was used to compare circulating levels of miRNAs with clinical parameters. These results suggested that circulating miR-155 and miR-126 might be involved in the development of ESRD. Further studies are needed to demonstrate the role of circulating miR-155 and miR-126 as candidate biomarkers for risk estimation.