Fluorescence/electrochemical dual-mode strategy for Golgi protein 73 detection based on molybdenum disulfide/ferrocene/palladium nanoparticles and nitrogen-doped graphene quantum dots.

Golgi protein 73 (GP73) is a new serum marker associated with early diagnosis and postoperative assessment of hepatocellular carcinoma (HCC). Herein, an electrochemical/fluorescence dual-signal biosensor was designed for determination of GP73 based on molybdenum disulfide/ferrocene/palladium nanoparticles (MoS2-Fc-PdNPs) and nitrogen-doped graphene quantum dots (NGQDs). GP73 aptamer (Apt) was labeled with NGQDs to form the NGQDs-Apt fluorescence probe. MoS2-Fc-PdNPs served not only as the fluorescence quencher but also as electrochemical enhancer. The sensing platform (NGQDs-Apt/MoS2-Fc-PdNPs) was formed based on the fluorescence resonance energy transfer (FRET) mechanism. In the presence of GP73, the specific binding of NGQDs-Apt to GP73 interrupted FRET, restoring the fluorescence of NGQDs-Apt at λex/em = 348/438 nm and enhancing the oxidation current of Fc in MoS2-Fc-PdNPs at 0.04 V through differential pulse voltammetry (DPV). Under the optimal conditions, the DPV current change and fluorescence recovery have a good linear relationship with GP73 concentration from 1.00 to 10.0 ng/mL. The calibration equation for the fluorescence mode was Y1 = (0.0213 ± 0.00127)X + (0.0641 ± 0.00448) and LOD was 0.812 ng/mL (S/N = 3). The calibration equation of the electrochemical mode was Y2 = (3.41 ± 0.111)X + (1.62 ± 0.731), and LOD of 0.0425 ng/mL (S/N = 3). The RSDs of fluorescence mode and electrochemical mode after serum detection were 1.62 to 5.21% and 0.180 to 6.62%, respectively. By combining the electrochemical and fluorescence assay, more comprehensive and valuable information for GP73 was provided. Such dual-mode detection platform shows excellent reproducibility, stability, and selectivity and has great application potential.

Dimorphism of Candida tropicalis and its effect on nitrogen and phosphorus removal and sludge settleability.

Candida tropicalis PNY, a novel dimorphic strain with the capacity of simultaneous carbon, nitrogen and phosphorus removal in anaerobic and aerobic conditions, was isolated from activated sludge. Dimorphism of C. tropicalis PNY had effect on removing nitrogen and phosphorous and slightly affected COD removal under aerobic condition. Sample with high hypha formation rate (40 ± 5%) had more removal efficiencies of NH4+-N (50 mg/L) and PO43--P (10 mg/L), which could achieve 82.19% and 97.53%, respectively. High hypha cells dosage exhibited good settleability and filamentous overgrowth was not observed. According to label-free quantitative proteomics assays. Up-regulated proteins involved in the mitogen-activated protein kinase (MAPK) pathway indicated the active growth and metabolism process of sample with high hypha formation rate (40 ± 5%). And proteins concerning about glutamate synthetase and SPX domain-contain protein explain for the nutrient removal mechanism including assimilation of ammonia and polyphosphates synthesis.

A novel fluorescent strategy for Golgi protein 73 determination based on aptamer/nitrogen-doped graphene quantum dots/molybdenum disulfide @ reduced graphene oxide nanosheets.

The effective detection of biomarkers associated with hepatocellular carcinoma (HCC) is of great importance. Golgi protein 73 (GP73), a serum biomarker of HCC, has better diagnostic value than Alpha-fetoprotein (AFP) has been reported. In this paper, highly accurate fluorescence sensing platform for detecting GP73 was constructed based on fluorescence resonance energy transfer (FRET), in which nitrogen-doped graphene quantum dots (NGQDs) labelling with GP73 aptamer (GP73Apt) was used as fluorescence probe, and molybdenum disulfide @ reduced graphene oxide (MoS2@RGO) nanosheets was used as fluorescent receptors. MoS2@RGO nanosheets can quench the fluorescence of NGQDs-GP73Apt owing to FRET mechanisms. In the presence of GP73, the NGQDs-GP73Apt specifically bound with GP73 to from the deployable structures, making NGQDs-GP73Apt far away from MoS2@RGO nanosheets, blocking the FRET process, resulting in fluorescence recovery of NGQDs-GP73Apt. Under optimal conditions, the recovery intensity of fluorescence in the detection system is linearly related to the concentration of GP73 in the range of 5 ng/mL - 100 ng/mL and the limit of detection is 4.54 ng/mL (S/N = 3). Moreover, detection of GP73 was performed in human serum samples with good recovery (97.21-100.83%). This platform provides a feasible method for the early diagnosis of HCC, and can be easily extended to the detection of other biomarkers.

Integrated Analysis and Identification of mRNAs, Circular RNAs, and Long Noncoding RNAs in Immunoglobulin A Nephropathy.

Circular RNAs (circRNAs) and long noncoding RNAs (lncRNAs) have a role in monitoring the appearance and progression of a great many diseases. They are useful markers for the prognosis and diagnosis of some diseases. In previous studies, the expression patterns of mRNAs, circRNAs, and lncRNAs related to immunoglobulin A (IgA) nephropathy have not been sufficiently discussed. Active prevention methods and treatment for IgA nephropathy (IgAN) are still not used. Integrated analyses and identification of the circRNAs and lncRNAs in IgAN have not been executed. We carried out a deep RNA sequencing analysis between controls and subjects with IgAN. In total, 125 antisense lncRNAs were identified to be greatly differentially expressed between the control and experimental groups. In addition, 606 mRNAs and 1275 circRNAs with differential expression levels were found between the groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways were used as bioinformatic methods in this study. Our study showed the expression patterns of mRNAs, circRNAs, and lncRNAs in IgAN. We revealed the key roles of circRNAs and lncRNAs in the molecular mechanism of IgAN.

A label-free electrochemical aptasensor based on platinum@palladium nanoparticles decorated with hemin-reduced graphene oxide as a signal amplifier for glypican-3 determination.

Glypican-3 (GPC3) is a membrane-associated proteoglycan that is specifically upregulated in hepatocellular carcinoma (HCC) and has become one of the most promising biomarkers closely related to the occurrence and development of HCC. In this work, platinum@palladium nanoparticles decorated with hemin-reduced graphene oxide (H-rGO-Pt@Pd NPs) were used not only as a support for GPC3 aptamer (GPC3Apt) immobilization, but also as a new redox nanoprobe in electrochemical analysis for the determination of GPC3. The electrochemical aptasensor involved a reaction cell with a three-electrode system, and the differential pulse voltammetry (DPV) technique was adopted. In the presence of GPC3, the formed GPC3Apt-GPC3 complexes had stable structures and were cleaved from the electrode surface, leading to more electroactive H-rGO-Pt@Pd NPs repelling freely from the GPC3Apt/H-rGO-Pt@Pd NPs and thus to the increase of the oxidation peak current of hemin in H-rGO-Pt@Pd NPs. Under optimal conditions and a working voltage of +700 mV (vs. Ag/AgCl), the label-free electrochemical GPC3 aptasensor showed superior performance with a wider concentration linear range (0.001-10.0 µg mL-1), a lower limit of detection (LOD) (0.181 ng mL-1, S/N = 3), a higher sensitivity (0.0446 µA µM-1 cm-2) and good selectivity. Furthermore, the fabricated aptasensor was applied to GPC3 determination in human serum samples with satisfactory recoveries of 94.3%-119% and RSDs of 0.15%-5.78%. The current work provides a flexible approach for the rapid and sensitive analysis of GPC3 and has a broad application prospect in the diagnosis of HCC.

Interleukin-17A mRNA Expression is Associated with the Prognosis of Patients with Colorectal Cancer: A Pooled Meta-Analysis.

BACKGROUND: Interleukin-17A is a proinflammatory cytokine that is produced by TH17 cells, and plays a dual role in tumor progression, infectious diseases, and autoimmune disorders. Interleukin-17A is induced during colorectal tumorigenesis and angiogenesis, although some studies have reported an anti-tumor effect as well. The aim of our study was to assess the prognostic role of interleukin-17A in colorectal cancer and determine the potential mechanisms. METHODS: The GEO database was searched using the keyword "colorectal cancer", and 10 datasets were identified that included interleukin-17A mRNA expression and survival data of several colorectal cancer patient cohorts. The patients were stratified into the interleukin-17Ahigh and interleukin-17Alow groups based on the median expression level. RESULTS: Higher interleukin-17A mRNA levels were associated with better overall survival rates and the early tumor stage, indicating a protective role of interleukin-17A in colorectal cancer. Furthermore, interleukin-17A mRNA expression also correlated positively with that of TNFS11, CCR6, and CCL20, indicating that the anti-tumor effect of interleukin-17A is likely mediated by enhancing tumor antigen presentation by dendritic cells and recruiting the activated tumor-specific CD8+ cytotoxic T lymphocytes. The IL-23 and STAT3 mRNA levels were also significantly higher in the interleukin-17Ahigh group, which points to an upstream regulatory role of IL-23/STAT3 axis. Finally, the immune checkpoints PDCD1 (PD-1) and CD274 (PDL-1) were also positively correlated with interleukin-17A mRNA expression, indicating that interleukin-17A is a promising predictor of the immunotherapeutic outcome of PD-1/PDL-1 blockade in colorectal cancer. CONCLUSION: Interleukin-17A mRNA is a protective factor in colorectal cancer and a promising biomarker for assessing the prognosis and immunotherapeutic response.

Proteomics analysis of lysine crotonylation and 2-hydroxyisobutyrylation reveals significant features of systemic lupus erythematosus.

INTRODUCTION/OBJECTIVES: To seek significant features of systemic lupus erythematosus (SLE) by utilizing bioinformatics analysis. METHOD: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to quantify lysine crotonylation (Kcr) and lysine 2-hydroxyisobutyrylation (Khib) in peripheral blood mononuclear cells (PBMCs) of systemic lupus erythematosus (SLE) patients and normal controls. RESULTS: Seventy-six differentially modified proteins (DMPs) dually modified by Kcr and Khib were identified between SLE patients and healthy people. GO enrichment analysis prompted significant enrichment of seventy-six DMPs in MHC class II protein complex binding and leukocyte migration. KEGG pathways were enriched in antigen processing and presentation pathway and leukocyte transendothelial migration pathway. Six DMPs (CLTC, HSPA1B, HSPA8, HSP90AB1, HSPD1, and PDIA3) were identified in antigen processing and presentation pathway, of which HSPA8 was the core protein. Significant changes of Kcr and Khib in HSPA8 may increase ATP hydrolysis and promote antigen binding to MHC II molecule. In leukocyte transendothelial migration pathway, 7 DMPs (ACTN1, ACTN4, EZR, MSN, RAC1, RHOA, and VCL) were identified. MSN was the protein with the most modification sites in this pathway. In amino terminal ferm region of MSN, Kcr and Khib expression change may lead to the adhesion between leukocytes and endothelial cells, which was an important step of leukocyte migration. CONCLUSION: Kcr and Khib may promote the antigen presentation and jointly regulate the tissue damage mediated by leukocyte migration in SLE patients, which may play key roles in the pathogenesis of SLE probably. Key Points • Antigen processing and presentation and leukocyte transendothelial migration may play key roles in the pathogenesis of SLE.

TOX3 regulates the proliferation and apoptosis of colorectal cancer by downregulating RhoB via the activation of the MAPK pathway.

TOX high mobility group box family member 3 (TOX3) can function as tumor suppressor or oncogene in different tumors, while ras homolog family member B (RhoB) is a well-known tumor suppressor. The expression and role of TOX3 in colorectal cancer (CRC) are unknown. This study aimed to investigate the expression of TOX3 in CRC and the role of TOX3/mitogen-activated protein kinase (MAPK)/RhoB signaling in the proliferation and apoptosis of CRC cells. We showed that TOX3 messenger RNA (mRNA) and protein expression levels were significantly upregulated in CRC tissues and cell lines. High TOX3 expression was associated with high T stage, nodal invasion, and advanced tumor stage. Disease-free survival (DFS) was shortened for CRC patients with high expression of TOX3, while overall survival showed no significant difference. TOX3 promoted proliferation, inhibited apoptosis, and decreased the sensitivity to oxaliplatin of CRC cells. In addition, the inhibition of TOX3 led to the upregulation of RhoB, and RhoB overexpression suppressed the proliferation and promoted apoptosis of CRC cells. Moreover, TOX3 overexpression upregulated MAPK signaling, while MAPK signaling inhibitor U0126 induced CRC cell proliferation arrest or apoptosis, and attenuated the inhibition of RhoB in TOX3 overexpression cells. In addition, the overexpression of TOX3 increased tumor volume in nude mice. In conclusion, TOX3 may be an oncogene in CRC and can predict DFS in CRC patients. TOX3/MAPK/RhoB signaling plays an important role in the modulation of proliferation and apoptosis of CRC cells.

Compressive Strength and Chloride Resistance of Slag/Metakaolin-Based Ultra-High-Performance Geopolymer Concrete.

Ultra-high performance geopolymer concrete (UHPGC) has been favored due to its excellent sustainability and outstanding mechanical properties. This study was conducted to explore the mechanical and durability properties of slag/metakaolin-based UHPGC with steel fibers reinforcement. The uniaxial compression test and rapid chloride migration test were conducted to measure the compressive strength and chloride penetration resistance of UHPGC. A total of nine groups of mixture proportions were designed and tested to investigate the influences of steel fiber dosage and sodium hydroxide (NaOH) solution concentration. The results showed that an increased steel fiber dosage and alkali concentration can improve compressive strength, and the maximum compressive strength can reach more than 140 MPa. In addition, the rapid chloride migration test showed that the chloride penetration resistance of the slag/metakaolin-based concrete was moderate, with a non-steady chloride migration coefficient ranging from 6.5 × 10-12 m2/s to 14.1 × 10-12 m2/s. The increase in steel fiber volume content slightly enlarged chloride penetration depth, while the higher concentration of sodium hydroxide solution was beneficial as it improved chloride penetration resistance. The results suggest that although ultra-high compressive strength can be achieved, the durability issues of steel fiber reinforced slag/metakaolin-based geopolymer concrete still need considerable attention.

Transcription factor KLF2 enhances the sensitivity of breast cancer cells to cisplatin by suppressing kinase WEE1.

Cisplatin is an effective chemotherapeutic agent in facilitating the inhibition of proliferation, migration, and invasion in cancerous cells. However, the detailed mechanism of the regulation by cisplatin of human breast cancer cells is still unclear. This study aimed to investigate the mechanism of kruppel-like factor 2 (KLF2) transcription factor in cisplatin therapy for breast cancer. RT-qPCR was performed to quantify the expression of KLF2 and WEE1 in clinical tissue samples from breast cancer patients and in MDA-MB-231 cells. ChIP assay and dual-luciferase reporter assay were used to analyze the potential-binding sites of KLF2 and WEE1 promoter. Gain- or loss-of-function approaches were used to manipulate KLF2 and WEE1 in cisplatin-treated MDA-MB-231 cells, and the mechanism of KLF2 in breast cancer was evaluated both via CCK-8 assay, flow cytometry, Transwell assay, and Western blot. Further validation of the KLF2 was performed on nude mouse models. Breast cancer tissues and cells showed a relative decline of KLF2 expression and abundant WEE1 expression. Cisplatin inhibited the proliferation, migration, and invasion of MDA-MB-231 cells. Overexpression of KLF2 enhanced the inhibitory effect of cisplatin on the malignant characteristics of MDA-MB-231 cells in vitro. KLF2 targeted WEE1 and negatively regulated its expression, thus enhancing the sensitivity to cisplatin of breast cancer cells as well as tumor-bearing mice. Overall, these results suggest that KLF2 can potentially inhibit WEE1 expression and sensitize breast cancer cells to cisplatin, thus presenting a promising adjunct treatment.

Differential Expression Study of Lysine Crotonylation and Proteome for Chronic Obstructive Pulmonary Disease Combined with Type II Respiratory Failure.

Introduction: The modification of lysine crotonylation (Kcr) is another biological function of histone in addition to modification of lysine acetylation (Kac), which may play a specific regulatory role in diseases. Objectives: This study compared the expression levels of Kcr and proteome between patients with chronic obstructive pulmonary disease (COPD) combined with type II respiratory failure (RF) to study the relationship between Kcr, proteome, and COPD. Methods: We tested the Kcr and proteome of COPD combined with type II RF and normal control (NC) using croton acylation enrichment technology and liquid chromatography tandem mass spectrometry (LC-MS/MS) with high resolution. Results: We found that 32 sites of 23 proteins were upregulated and 914 sites of 295 proteins were downregulated. We performed Kyoto Encyclopedia of Genes and Genomes (KEGG), protein domain, and Gene Ontology (GO) analysis on crotonylated protein. In proteomics research, we found that 190 proteins were upregulated and 151 proteins were downregulated. Among them, 90 proteins were both modified by differentially expressed crotonylation sites and differentially expressed in COPD combined with type II RF and NC. Conclusion: Differentially expressed crotonylation sites may be involved in the development of COPD combined with type II RF. 90 proteins modified by crotonylation and differentially expressed in COPD combined with type II RF can be used as markers for the study of the molecular pathogenesis of COPD combined with type II RF.

Single-cell chromatin accessibility landscape of human umbilical cord blood in trisomy 18 syndrome.

BACKGROUND: Trisomy 18 syndrome (Edwards syndrome, ES) is a type of aneuploidy caused by the presence of an extra chromosome 18. Aneuploidy is the leading cause of early pregnancy loss, intellectual disability, and multiple congenital anomalies. The research of trisomy 18 is progressing slowly, and the molecular characteristics of the disease mechanism and phenotype are still largely unclear. RESULTS: In this study, we used the commercial Chromium platform (10× Genomics) to perform sc-ATAC-seq to measure chromatin accessibility in 11,611 single umbilical cord blood cells derived from one trisomy 18 syndrome patient and one healthy donor. We obtained 13 distinct major clusters of cells and identified them as 6 human umbilical cord blood mononuclear cell types using analysis tool. Compared with the NC group, the ES group had a lower ratio of T cells to NK cells, the ratio of monocytes/DC cell population did not change significantly, and the ratio of B cell nuclear progenitor and megakaryocyte erythroid cells was higher. The differential genes of ME-0 are enriched in Human T cell leukemia virus 1 infection pathway, and the differential peak genes of ME-1 are enriched in apopotosis pathway. We found that CCNB2 and MCM3 may be vital to the development of trisomy 18. CCNB2 and MCM3, which have been reported to be essential components of the cell cycle and chromatin. CONCLUSIONS: We have identified 6 cell populations in cord blood. Disorder in megakaryocyte erythroid cells implicates trisomy 18 in perturbing fetal hematopoiesis. We identified a pathway in which the master differential regulatory pathway in the ME-0 cell population involves human T cell leukemia virus 1 infection, a pathway that is dysregulated in patients with trisomy 18 and which may increase the risk of leukemia in patients with trisomy 18. CCNB2 and MCM3 in progenitor may be vital to the development of trisomy 18. CCNB2 and MCM3, which have been reported to be essential components of the cell cycle and chromatin, may be related to chromosomal abnormalities in trisomy 18.

Functional CYP3A variants affecting tacrolimus trough blood concentrations in Chinese renal transplant recipients.

The aim of this study was to identify novel genetic variants affecting tacrolimus trough blood concentrations. We analyzed the association between 58 single nucleotide polymorphisms (SNPs) across the CYP3A gene cluster and the log-transformed tacrolimus concentration/dose ratio (log (C0/D)) in 819 renal transplant recipients (Discovery cohort). Multivariate linear regression was used to test for associations between tacrolimus log (C0/D) and clinical factors. Luciferase reporter gene assays were used to evaluate the functions of select SNPs. Associations of putative functional SNPs with log (C0/D) were further tested in 631 renal transplant recipients (Replication cohort). Nine SNPs were significantly associated with tacrolimus log (C0/D) after adjustment for CYP3A5*3 and clinical factors. Dual luciferase reporter assays indicated that the rs4646450 G allele and rs3823812 T allele were significantly associated with increased normalized luciferase activity ratios (p < 0.01). Moreover, CYP3A7*2 was associated with higher TAC log(C0/D) in the group of CYP3A5 expressers. Age, serum creatinine and hematocrit were significantly associated with tacrolimus log (C0/D). CYP3A7*2, rs4646450, and rs3823812 are proposed as functional SNPs affecting tacrolimus trough blood concentrations in Chinese renal transplant recipients. Clinical factors also significantly affect tacrolimus metabolism.

Differential expression of transfer RNA-derived small RNAs in IgA nephropathy.

BACKGROUND: IgA nephropathy (IgAN) is one of the most common forms of primary glomerulonephritis. Recent studies have indicated that small noncoding RNAs, such as tRNA-derived small RNAs (tsRNAs), might be novel biomarkers for glomerulonephritis. We therefore investigated the potential roles and possible functions of the tsRNAs in IgAN. METHOD: Peripheral blood mononuclear cells (PBMCs) were extracted from blood samples of the patients with IgAN and healthy control groups. The expression profiles of tsRNAs were assessed by small RNA sequencing (RNA-Seq) in PBMCs of the IgAN and control groups. Dysregulated tsRNAs were selected for validation by quantitative real-time polymerase chain reaction (qRT-PCR). Target gene prediction and enrichment were performed by bioinformatics analysis. RESULTS: The results revealed that 143 significantly upregulated and 202 significantly downregulated tsRNAs were differentially altered in the IgAN group compared with the control group. Five upregulated tsRNAs (tRF-Val-AAC-007, tRF-Ala-AGC-063, tRF-Gln-CTG-010, tRF-Tyr-GTA-011 and tRF-Thr-AGT-007) and 3 downregulated tsRNAs (tiRNA-Val-TAC-004, tRF-Gly-CCC-005 and tRF-His-GTG-006) were selected for validation by qRT-PCR; the results were consistent with the sequencing data. Gene Ontology (GO) analysis revealed that the target genes predicted by upregulated tsRNAs were mostly enriched in "nucleic acid metabolic process,' "intracellular part,' and "ion binding,' whereas the target genes predicted by downregulated tsRNAs were mostly enriched in "regulation of cellular component organization,' "membrane-bound organelle,' and "ion binding.' Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the target genes predicted by upregulated tsRNAs were mostly enriched in "herpes simplex virus 1 infection,' whereas the target genes predicted by downregulated tsRNAs were mostly enriched in "circadian rhythm CONCLUSIONS:: The present study confirmed the differential expression of tsRNAs in patients with IgAN, and these dysregulated tsRNAs might be novel potential targets for the diagnosis and treatment of IgAN.

HBV integrated genomic characterization revealed hepatocyte genomic alterations in HBV-related hepatocellular carcinomas.

Hepatocellular carcinoma (HCC) is one of the most lethal malignancies that is closely associated with the Hepatitis B virus (HBV). HBV integration into host genomes can induce instability and the aberrant expression of human genomic DNA. To directly assess HBV integration breakpoints at whole genome level, four small sequencing libraries were constructed and the HBV integration profiles of four patients with HCC were characterized. In total, the current study identified 11,800,974, 11,216,998, 11,026,546 and 11,607,842 clean reads for patients 1-3 and 4, respectively, of which 92.82, 95.95, 97.21 and 97.29% were properly aligned to the hybrid reference genome. In addition, 220 HBV integration events were detected from the tumor tissues of four patients with HCC and an average of 55 breakpoints per sample was calculated. The results indicated that HBV integration events may be implicated in HCC physiologies and diseases. The results acquired may also provide insight into the pathogenesis of HCC, which may be valuable for future HCC therapy.

Proteomic analysis of differentially expressed proteins in the serum of patients with acute renal allograft rejection using iTRAQ labelling technology.

Transplantation is currently the best treatment for patients with end­stage renal disease. However, acute rejection (AR) is the major source of failure in renal transplantation. The current best practice for the diagnosis of AR involves renal biopsy, but it is invasive, time­consuming, costly and inconvenient. Sensitive and less invasive detection of AR episodes in renal transplant patients is essential to preserve allograft function. The present study applied isobaric tags for relative and absolute quantitation (iTRAQ) mass spectrometry to analyze serum protein expression in patients with AR and healthy controls. Overall, 1,399 proteins were identified. Using a cut­off of Q<0.05 and a fold change of >1.2 for the variation in expression, 109 proteins were identified to be differentially expressed between the AR and control groups, 72 of which were upregulated and 37 were downregulated. Several proteins, including properdin, keratin 1, lipoprotein(a) and vitamin D­binding protein, may have roles in the pathogenesis of AR. The present study focused on iTRAQ­based proteomic profiling of serum samples in AR. Insight from the present study may help advance the understanding of the molecular mechanisms of AR and identify potential novel biomarkers of AR for further characterization.

Correction: Characteristic analysis of TCR ß-chain CDR3 repertoire for preand post-liver transplantation.

[This corrects the article DOI: 10.18632/oncotarget.26138.].

Differential expression profile study and gene function analysis of maternal foetal-derived circRNA for screening for Down's syndrome.

Recent studies have shown that circular RNAs (circRNAs) exhibit differential expression in certain diseases. However, to the best of our knowledge, maternal fetal-derived circRNAs and mRNAs associated with Down's syndrome (DS) have not yet been investigated. A total of 12 umbilical cord blood samples were collected from pregnant women, including six women carrying fetuses with DS (diagnosed by G-banding karyotype analysis), and six women carrying fetuses without DS. In addition, 12 peripheral blood samples were obtained from children, including six children with DS and six children without DS. Gene chip technology was used to screen for differentially expressed circRNAs and mRNAs in the cord blood samples, and were subsequently verified by reverse transcription-quantitative polymerase chain reaction in peripheral blood from the children to identify potential biomarkers. Furthermore, circRNA/microRNA (miRNA) interactions were predicted using Arraystar miRNA target prediction software. There was a significant difference in the expression of hsa_circRNA_103127, hsa_circRNA_103112 and hsa_circRNA_104907 between cord blood obtained from the women carrying fetuses with and without DS, and between peripheral blood obtained from children with and without DS (P<0.01). As hsa_circRNA_103112 exhibited significant differences in expression between cord blood obtained from the women carrying fetuses with and without DS and between peripheral blood obtained from children with and without DS, its corresponding gene, ubiquitin specific peptidase 25, may be involved in the pathogenesis of the condition. These results suggested that hsa_circRNA_103112 may be upregulated in individuals with DS, resulting in an expression imbalance of diploid genes through interactions among circRNA, miRNA and mRNA. Therefore, the level of hsa_circRNA_103112 in the peripheral blood of a pregnant woman may serve as potential biomarker of fetal DS during non-invasive prenatal screening.

Quantitative analysis of protein crotonylation identifies its association with immunoglobulin A nephropathy.

Posttranslational modifications (PTMs) to histones such as lysine crotonylation are classified as epigenetic changes. Lysine crotonylation participates in various cellular processes and occurs in active promoters, directly accelerating transcription. The present study performed a proteomics analysis of crotonylation between healthy controls and patients with immunoglobulin A (IgA) nephropathy using tandem mass spectrometry and high­resolution liquid chromatography. The present results identified 353 crotonylated proteins and 770 modification sites, including 155 upregulated and 198 downregulated crotonylated proteins. In total, seven conserved motifs were identified in the present study. The present bioinformatics analysis results suggested a number of the crotonylated proteins exhibited various subcellular localization patterns, such as in the cytoplasm. Protein domains, including thioredoxin, moesin tail and myosin like IQ motif domains were markedly enriched in crotonylated proteins. Kyoto Encyclopedia of Genes and Genomes and functional enrichment analyses suggested significant enrichment of crotonylated proteins in complement and coagulation cascades, and antigen processing and presentation pathways displaying important relationships with IgA nephropathy. The present results suggested that crotonylation occurred in numerous proteins and may play key regulatory roles in IgA nephropathy.

Genotyping, generation and proteomic profiling of the first human autosomal dominant osteopetrosis type II-specific induced pluripotent stem cells.

BACKGROUND: Autosomal dominant osteopetrosis type II (ADO2) is a rare human genetic disease that has been broadly studied as an important osteopetrosis model; however, there are no disease-specific induced pluripotent stem cells (ADO2-iPSCs) that may be valuable for understanding the pathogenesis and may be a potential source of cells for autologous cell-based therapies. METHODS: To generate the first human ADO2-iPSCs from a Chinese family with ADO2 and to identify their characteristics, blood samples were collected from the proband and his parents and were used for genotyping by whole-exome sequencing (WES); the urine-derived cells of the proband were reprogrammed with episomal plasmids that contained transcription factors, such as KLF4, OCT4, c-MYC, and SOX2. The proteome-wide protein quantification and lysine 2-hydroxyisobutyrylation detection of the ADO2-iPSCs and normal control iPSCs (NC-iPSCs) were performed by high-resolution LC-MS/MS and bioinformatics analysis. RESULTS: WES with filtering strategies identified a mutation in CLCN7 (R286W) in the proband and his father, which was absent in the proband's mother and the healthy controls; this was confirmed by Sanger sequencing. The ADO2-iPSCs were successfully generated, which carried a normal male karyotype (46, XY) and the mutation of CLCN7 (R286W); the ADO2-iPSCs positively expressed alkaline phosphatase and other surface markers; and no vector and transgene were detected. The ADO2-iPSCs could differentiate into all three germ cell layers, both in vitro and in vivo. The proteomic profiling revealed similar expression of pluripotency markers in the two cell lines and identified 7405 proteins and 3664 2-hydroxyisobutyrylated peptides in 1036 proteins in the ADO2-iPSCs. CONCLUSIONS: Our data indicated that the mutation CLCN7 (R286W) may be a cause of the osteopetrosis family. The generated vector-free and transgene-free ADO2-iPSCs with known proteomic characteristics may be valuable for personalized and cell-based regenerative medicine in the future.