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1.
Medicine (Baltimore) ; 102(50): e36476, 2023 Dec 15.
Article in English | MEDLINE | ID: mdl-38115247

ABSTRACT

Idiopathic membranous nephropathy (IMN) is a common type of primary glomerulonephritis, which pathogenesis are highly involved protein and immune regulation. Therefore, we investigated protein expression in different microregions of the IMN kidney tissue. We used laser capture microdissection and mass spectrometry to identify the proteins in the kidney tissue. Using MSstats software to identify the differently expressed protein (DEP). Gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were used to predict and enrich the potential functions of the DEPs, and DEPs were compared to the Public data in the gene expression omnibus (GEO) database for screening biomarkers of IMN. Immune infiltration analysis was used to analyze the immune proportion in IMN. Three significantly up-regulated proteins were identified in the glomeruli of patients with IMN; 9 significantly up-regulated and 6 significantly down-regulated proteins were identified in the interstitium of patients with IMN. Gene ontology analysis showed that the DEPs in the glomerulus and interstitium were mostly enriched in "biological regulation, the immune system, and metabolic processes." Kyoto Encyclopedia of Genes and Genomes analysis showed that the DEPs in the glomerulus and interstitium were mostly enriched in the "immune system" and the "complement and coagulation cascades. " According to the public information of the GEO database, DEPs in our study, Coatomer subunit delta Archain 1, Laminin subunit alpha-5, and Galectin-1 were highly expressed in the IMN samples from the GEO database; in the immune infiltration analysis, the proportion of resting memory CD4 T cells and activated NK cells in IMN were significantly higher than in the normal group. This study confirmed that there were significant differences in protein expression in different micro-regions of patients with IMN, The protein Coatomer subunit delta Archain 1, Laminin subunit alpha 5, Galectin-1 are potential biomarkers of IMN, the memory T cells CD4 and NK cells, maybe involved in the immunologic mechanism in the development of IMN.


Subject(s)
Glomerulonephritis, Membranous , Humans , Glomerulonephritis, Membranous/genetics , Glomerulonephritis, Membranous/diagnosis , Galectin 1 , Coatomer Protein , Proteomics , Kidney/pathology , Biomarkers , Laminin
2.
Transpl Immunol ; 81: 101929, 2023 12.
Article in English | MEDLINE | ID: mdl-37683736

ABSTRACT

OBJECTIVE: At present, little is known about the immune mechanism of liver transplantation caused by decompensated cirrhosis. Lymphocytes play an essential important role in the immune rejection of liver transplantation. In this study, we aimed to comprehensively analyze changes in complementary determinant 3 (CDR3) repertoire of T cell receptor ß chain (TRß) and immunoglobulin heavy chain (IGH) in liver transplantation patients and healthy controls (HC). METHODS: High-throughput sequencing technology was used to study the characteristics of TRß/IGH CDR3 repertoire, and identify the amino acid sequences of TRß and IGH associated with liver transplantation patients and HC. RESULTS: We found that some TRß and IGH CDR3 repertoire characteristics differed between liver transplant patients and HC. The diversity of TRß CDR3 increased in the liver transplantation group. First and seven days after live transplantation patients showed a lower degree of T cell clone amplification compared to the HC group. The CDR3 repertoire of the TRß/IGH chain was certainly biased in the use of some V, D, and J gene segments, TRß/IGH V-J combined frequency was also skewed and TRß CDR3 clonotypes were shared at a higher degree in the liver transplantation patients. Importantly, one amino acid sequence in the decompensated cirrhosis group was significantly higher than that in the healthy group. It should be noted that the frequency of some CDR3 sequences is closely correlated with the different stages of liver transplantation, and these sequences may play a key role in liver transplantation. CONCLUSION: Based on the above results, we can better understand the dynamic changes of TCß/IGH CDR3 repertoire in patients during liver transplantation.


Subject(s)
Complementarity Determining Regions , Liver Transplantation , Humans , Complementarity Determining Regions/genetics , Immunoglobulin Heavy Chains , T-Lymphocytes , Receptors, Antigen, T-Cell, alpha-beta/genetics , Receptors, Antigen, T-Cell, alpha-beta/metabolism , Liver Cirrhosis/metabolism
3.
Nat Metab ; 5(1): 29-40, 2023 01.
Article in English | MEDLINE | ID: mdl-36624157

ABSTRACT

Human pluripotent stem cell-derived islets (hPSC islets) are a promising alternative to primary human islets for the treatment of insulin-deficient diabetes. We previously demonstrated the feasibility of this approach in nonhuman primates; however, the therapeutic effects of hPSC islets can be limited by the maladaptive processes at the transplantation site. Here, we demonstrate successful implantation of hPSC-derived islets in a new transplantation site in the abdomen, the subanterior rectus sheath, in eight nonhuman primates (five male and three female). In this proof-of-principle study, we find that hPSC islets survive and gradually mature after transplantation, leading to improved glycemic control in diabetic primates. Notably, C-peptide secretion responds to meal challenge from 6 weeks post-transplantation (wpt), with stimulation indices comparable to those of native islets. The average post-prandial C-peptide level reaches approximately 2.0 ng ml-1 from 8 wpt, which is five times higher than the peak value we previously obtained after portal vein infusion of hPSC islets and was associated with a decrease of glycated hemoglobin levels by 44% at 12 wpt. Although additional studies in larger cohorts involving long-term follow-up of transplants are needed, our results indicate that the subanterior rectus sheath supports functional maturation and maintenance of hPSC islets, suggesting that it warrants further exploration as a transplantation target site in the context of for hPSC-based cell-replacement therapies.


Subject(s)
Islets of Langerhans Transplantation , Islets of Langerhans , Animals , Male , Humans , Female , Islets of Langerhans Transplantation/methods , C-Peptide , Primates , Abdomen
4.
Clin Immunol ; 245: 109162, 2022 12.
Article in English | MEDLINE | ID: mdl-36243349

ABSTRACT

PURPOSE: The dynamic immunity of kidney transplant patients has not been fully elucidated. In this study, we explored the repertoire features of B/T cell receptor (BCR/TCR) of kidney transplant patients. METHODS: Using combined multiplex PCR amplification and high-throughput sequencing technique, we analyzed the uremic patients' BCR H chain and TCR beta chain repertoire which obtained 1 day before kidney transplantation (PRE-1), 1 day and 7 day after kidney transplantation (POST-1 and POST-7). RESULTS: Our analysis results showed the diversity of TCRß CDR3 in POST-7 group was highest. In addition, there were specific skewed usage of TRBV gene subfamilies, and V-J combinations in different time points during kidney transplantation. Moreover, the overlap degrees of BCR-H (TCR-ß) CDR3 repertoire among each group were identified. Notably, the abundance of some TCR-ß CDR3 sequences changed regularly in the time point of kidney transplantation. CONCLUSIONS: The BCR-H (TCR-ß) CDR3 repertoire of kidney transplant patients changed dynamically.


Subject(s)
Complementarity Determining Regions , Kidney Transplantation , Receptors, Antigen, B-Cell , Receptors, Antigen, T-Cell , Humans , Complementarity Determining Regions/genetics , High-Throughput Nucleotide Sequencing/methods , Receptors, Antigen, B-Cell/genetics , Receptors, Antigen, T-Cell/genetics
5.
Proteomics Clin Appl ; 16(1): e2000069, 2022 01.
Article in English | MEDLINE | ID: mdl-34543527

ABSTRACT

PURPOSE: Membranous nephropathy (MN) is a common cause of nephrotic syndrome in adults. However, the underlying mechanisms of its occurrence and development are not completely clear. Thus, it is essential to explore the mechanisms. EXPERIMENTAL DESIGN: Here, we employed label-free quantification and liquid chromatography-tandem mass spectrometry analysis techniques to investigate the proteomic and phosphoproteomic alterations in renal biopsy tissues of MN patients. Samples were collected from 16 MN patients and 10 controls. Immunohistochemistry (IHC) was performed to validate the hub phosphoprotein. RESULTS: We focused on the changes in the phosphoproteome in MN group versus control group (CG). Totally, 1704 phosphoproteins containing 3241 phosphosites were identified and quantified. The phosphorylation levels of 216 phosphoproteins containing 297 phosphosites were differentially regulated in stage II MN group versus CG, and 333 phosphoproteins containing 461 phosphosites were differentially phosphorylated in stage III MN group versus CG. In each comparison, several differential phosphoproteins were factors, kinases and receptors involved in cellular processes, biological regulation and other biological processes. The subcellular location of most of the differential phosphoproteins was the nucleus. Protein-protein interaction analysis showed that the connections among the differential phosphoproteins were extremely complex, and several signalling pathways probably associated with MN were identified. The hub phosphoprotein was validated by IHC. CONCLUSIONS AND CLINICAL RELEVANCE: This investigation can provide direct insight into the global phosphorylation events in MN group versus CG and may help to shed light on the potential pathogenic mechanisms of MN.


Subject(s)
Glomerulonephritis, Membranous/diagnosis , Kidney/pathology , Phosphopeptides/analysis , Proteome/analysis , Proteomics/methods , Case-Control Studies , Chromatography, High Pressure Liquid , Glomerulonephritis, Membranous/metabolism , Glomerulonephritis, Membranous/pathology , Humans , Kidney/metabolism , Phosphorylation , Protein Interaction Maps/genetics , Severity of Illness Index , Signal Transduction/genetics , Tandem Mass Spectrometry
6.
Pharmacogenomics J ; 21(3): 376-389, 2021 06.
Article in English | MEDLINE | ID: mdl-33649515

ABSTRACT

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.


Subject(s)
Cytochrome P-450 CYP3A/genetics , Immunosuppressive Agents/pharmacokinetics , Kidney Transplantation , Tacrolimus/pharmacokinetics , Adult , Aging/metabolism , Asian People , Cohort Studies , Creatinine/blood , Female , Genetic Variation , Hematocrit , Humans , Male , Middle Aged , Polymorphism, Single Nucleotide , Transplant Recipients
7.
Ren Fail ; 43(1): 520-529, 2021 Dec.
Article in English | MEDLINE | ID: mdl-33719820

ABSTRACT

BACKGROUND: Kidneys obtained from deceased donors increase the incidence of delayed graft function (DGF) after renal transplantation. Here we investigated the influence of the risk factors of donors with DGF, and developed a donor risk scoring system for DGF prediction. METHODS: This retrospective study was conducted in 1807 deceased kidney donors and 3599 recipients who received donor kidneys via transplants in 29 centers in China. We quantified DGF associations with donor clinical characteristics. A donor risk scoring system was developed and validated using an independent sample set. RESULTS: The incidence of DGF from donors was 19.0%. Six of the donor characteristics analyzed, i.e., age, cause of death, history of hypertension, terminal serum creatinine, persistence of hypotension, and cardiopulmonary resuscitation (CPR) time were risk factors for DGF. A 49-point scoring system of donor risk was established for DGF prediction and exhibited a superior degree of discrimination. External validation of DGF prediction revealed area under the receiver-operating characteristic (AUC) curves of 0.7552. CONCLUSIONS: Our study determined the deceased donor risk factors related to DGF after renal transplantation pertinent to the Chinese cohort. The scoring system developed here had superior diagnostic significance and consistency and can be used by clinicians to make evidence-based decisions on the quality of kidneys from deceased donors and guide renal transplantation therapy.


Subject(s)
Delayed Graft Function/etiology , Kidney Transplantation/adverse effects , Tissue Donors/statistics & numerical data , Adult , Brain Death , China , Cold Ischemia/adverse effects , Creatinine/analysis , Delayed Graft Function/therapy , Female , Graft Survival , Humans , Incidence , Kidney/physiopathology , Male , Middle Aged , ROC Curve , Renal Dialysis/statistics & numerical data , Retrospective Studies , Risk Factors , Transplantation, Homologous , Transplants/physiopathology
8.
Biol Open ; 10(2)2021 02 15.
Article in English | MEDLINE | ID: mdl-33589441

ABSTRACT

Human induced pluripotent stem cells (iPSCs) are important source for regenerative medicine. However, the links between pluripotency and oncogenic transformation raise safety issues. To understand the characteristics of iPSC-derived cells at single-cell resolution, we directly reprogrammed two human iPSC lines into cardiomyocytes and collected cells from four time points during cardiac differentiation for single-cell sequencing. We captured 32,365 cells and identified five molecularly distinct clusters that aligned well with our reconstructed differentiation trajectory. We discovered a set of dynamic expression events related to the upregulation of oncogenes and the decreasing expression of tumor suppressor genes during cardiac differentiation, which were similar to the gain-of-function and loss-of-function patterns during oncogenesis. In practice, we characterized the dynamic expression of the TP53 and Yamanaka factor genes (OCT4, SOX2, KLF4 and MYC), which were widely used for human iPSCs lines generation; and revealed the co-occurrence of MYC overexpression and TP53 silencing in some of human iPSC-derived TNNT2+ cardiomyocytes. In summary, our oncogenic expression atlas is valuable for human iPSCs application and the single-cell resolution highlights the clues potentially associated with the carcinogenic risk of human iPSC-derived cells.


Subject(s)
Cell Differentiation/genetics , Gene Expression Profiling , Gene Expression Regulation , Induced Pluripotent Stem Cells/cytology , Myocytes, Cardiac/metabolism , Oncogenes , Single-Cell Analysis , Cell Line , Computational Biology/methods , Humans , Karyotype , Myocytes, Cardiac/cytology , Single-Cell Analysis/methods
9.
Nephrol Dial Transplant ; 36(4): 599-608, 2021 03 29.
Article in English | MEDLINE | ID: mdl-31883338

ABSTRACT

BACKGROUND: Immune aberrations in end-stage renal disease (ESRD) are characterized by systemic inflammation and immune deficiency. The mechanistic understanding of this phenomenon remains limited. METHODS: We generated 12 981 and 9578 single-cell transcriptomes of peripheral blood mononuclear cells (PBMCs) that were pooled from 10 healthy volunteers and 10 patients with ESRD by single-cell RNA sequencing. Unsupervised clustering and annotation analyses were performed to cluster and identify cell types. The analysis of hallmark pathway and regulon activity was performed in the main cell types. RESULTS: We identified 14 leukocytic clusters that corresponded to six known PBMC types. The comparison of cells from ESRD patients and healthy individuals revealed multiple changes in biological processes. We noticed an ESRD-related increase in inflammation response, complement cascade and cellular metabolism, as well as a strong decrease in activity related to cell cycle progression in relevant cell types in ESRD. Furthermore, a list of cell type-specific candidate transcription factors (TFs) driving the ESRD-associated transcriptome changes was identified. CONCLUSIONS: We generated a distinctive, high-resolution map of ESRD-derived PBMCs. These results revealed cell type-specific ESRD-associated pathways and TFs. Notably, the pooled sample analysis limits the generalization of our results. The generation of larger single-cell datasets will complement the current map and drive advances in therapies that manipulate immune cell function in ESRD.


Subject(s)
Gene Expression Regulation , Kidney Failure, Chronic/genetics , Leukocytes, Mononuclear/metabolism , Single-Cell Analysis/methods , Transcriptome , Case-Control Studies , Female , Humans , Kidney Failure, Chronic/pathology , Male , Middle Aged
10.
Medicine (Baltimore) ; 99(48): e23437, 2020 Nov 25.
Article in English | MEDLINE | ID: mdl-33235128

ABSTRACT

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.


Subject(s)
Glomerulonephritis, IGA/genetics , RNA, Small Untranslated/metabolism , RNA, Transfer/metabolism , Adult , Case-Control Studies , Down-Regulation , Female , High-Throughput Nucleotide Sequencing , Humans , Leukocytes, Mononuclear/metabolism , Male , Real-Time Polymerase Chain Reaction , Sequence Analysis, RNA , Up-Regulation
11.
Mol Clin Oncol ; 13(6): 79, 2020 Dec.
Article in English | MEDLINE | ID: mdl-33062269

ABSTRACT

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.

12.
Mol Med Rep ; 22(3): 2329-2341, 2020 09.
Article in English | MEDLINE | ID: mdl-32705285

ABSTRACT

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.


Subject(s)
Graft Rejection/diagnosis , Kidney Failure, Chronic/therapy , Kidney Transplantation/adverse effects , Proteomics/methods , Adult , Case-Control Studies , Chromatography, Liquid , Female , Gene Expression Profiling , Gene Expression Regulation , Graft Rejection/blood , Humans , Keratin-1/blood , Lipoprotein(a)/blood , Male , Middle Aged , Properdin/metabolism , Tandem Mass Spectrometry , Transplantation, Homologous , Vitamin D-Binding Protein/blood
13.
Ann Transplant ; 25: e921844, 2020 Jun 23.
Article in English | MEDLINE | ID: mdl-32572018

ABSTRACT

BACKGROUND There are many situations of abnormal metabolism influencing liver graft function. This study aims to provide data for the development of liver function recovery after liver transplantation by dynamically analyzing metabolites of bile acids pathway in serum. MATERIAL AND METHODS A comprehensive metabolomics profiling of serum of 9 liver transplantation patients before transplantation, on the 1st, 3rd, and 7th days after liver transplantation, and healthy individuals were performed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). Multivariate data and dynamic analysis were used to search for biomarkers between the metabolomics profiles present in perioperative liver transplantation and normal controls. RESULTS Thirty-three differential endogenous metabolites were screened by the threshold of variable importance in the projection (VIP) from an orthogonal partial least square discriminant analysis (OPLS-DA) greater than 1.0, q-value <0.05, and fold change (FC) ≤0.8 or ≥1.2 between the preoperative group and the normal controls in negative mode. The metabolite intensities of taurocholic acid, taurochenodeoxycholic acid, chenodeoxycholic acid glycine conjugate, and glycocholic acid pre-transplantation were significantly higher than those of normal controls. The average metabolite intensities of taurocholic acid and taurochenodesoxycholic acid on the first day after liver transplantation were lower than those observed pre-transplantation. The average metabolite intensities on day 3 after liver transplantation showed a sudden increase and then decreased after 7 postoperative days. The average metabolite intensities of glycocholic acid and chenodeoxycholic acid glycine conjugate showed an increasing trend on the 1st, 3rd, and 7th days after liver transplantation. CONCLUSIONS Use of taurocholic acid and taurochenodeoxycholic acid-related bile secretion, liver regeneration, and de novo bile acid synthesis may help clinical evaluation and provide data for the development of liver function recovery after liver transplantation.


Subject(s)
Bile Acids and Salts/blood , Carcinoma, Hepatocellular/metabolism , Graft Survival/physiology , Liver Neoplasms/metabolism , Liver Transplantation , Liver/metabolism , Adult , Biomarkers/blood , Carcinoma, Hepatocellular/blood , Carcinoma, Hepatocellular/pathology , Carcinoma, Hepatocellular/surgery , Chenodeoxycholic Acid/blood , Chromatography, Liquid , Female , Glycocholic Acid/blood , Humans , Liver/pathology , Liver Neoplasms/blood , Liver Neoplasms/pathology , Liver Neoplasms/surgery , Male , Metabolomics , Middle Aged , Tandem Mass Spectrometry , Taurochenodeoxycholic Acid/blood , Taurocholic Acid/blood , Treatment Outcome
14.
Oncotarget ; 11(18): 1679, 2020 May 05.
Article in English | MEDLINE | ID: mdl-32405342

ABSTRACT

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

15.
Mol Med Rep ; 21(3): 1242-1250, 2020 03.
Article in English | MEDLINE | ID: mdl-32016442

ABSTRACT

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.


Subject(s)
Gene Expression Regulation , Glomerulonephritis, IGA/metabolism , Histones/analysis , Protein Processing, Post-Translational , Proteomics , Adult , Amino Acid Motifs , Antigen Presentation , Chromatography, Liquid , Computational Biology , Down-Regulation , Female , Glomerulonephritis, IGA/immunology , Histones/metabolism , Humans , Lysine/metabolism , Male , Middle Aged , Promoter Regions, Genetic/genetics , Tandem Mass Spectrometry , Up-Regulation
16.
Exp Ther Med ; 19(2): 1006-1016, 2020 Feb.
Article in English | MEDLINE | ID: mdl-32010263

ABSTRACT

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.

17.
Ren Fail ; 41(1): 1-13, 2019 Nov.
Article in English | MEDLINE | ID: mdl-31880216

ABSTRACT

Background/Aims: End-stage renal disease (ESRD), characterized by progressive loss of rental function during the disease course, has been reported to be correlated with immune dysregulation. To date, a majority of previous studies on immune response to ESRD have been focused on the T-cell response. This prospective study was to assess the B-cell receptor (BCR) heavy chain repertoire in ESRD patients.Materials and methods: A total of 10 ESRD patients and six healthy controls were prospectively enrolled in this study. BCR immunoglobulin heavy chain (IGH) repertoire in the peripheral blood from ESRD patients and healthy individuals were analyzed by means of next generation sequencing (NGS) in combination with multiplex PCR, Illumina sequencing, and the international ImMunoGeneTics database (IMGT).Results: Abnormal BCR complementary-determining region 3 (CDR3) sequences were identified in relation to ESRD. We also found that the degree of the B-cell clonal expansion in the ESRD group was significantly greater than that in the control group (p < .05), whereas the distributions of BCR CDR3, V, D, J, and V-J gene segments were comparable between the ESRD and control groups. T-test for analysis of the distribution ratio of the V, D, J, and V-J genes revealed five up-regulated genes and nine down-regulated genes associated with ESRD, and there were significant differences between the ESRD and control groups (p < .05).Conclusions: We have provided a successful approach to analyzing peripheral B-cell repertoire in ESRD patients, and the results suggest a direct correlation between the BCR repertoire and ESRD. The ESRD-specific BCR CDR3 sequences may hold promise for potentially therapeutic benefit.


Subject(s)
Antigens, Differentiation, B-Lymphocyte/genetics , B-Lymphocytes/metabolism , Kidney Failure, Chronic/immunology , Adult , Case-Control Studies , High-Throughput Nucleotide Sequencing , Humans , Middle Aged , Prospective Studies , Young Adult
18.
Genes Genomics ; 41(12): 1493-1503, 2019 12.
Article in English | MEDLINE | ID: mdl-31576517

ABSTRACT

BACKGROUND: Bladder cancer (BCa) is a tumor associated with high morbidity and mortality and its incidence is increasing worldwide. However, the pathogenesis of bladder cancer is not well understood. OBJECTIVE: To further illustrate the molecular mechanisms involved in the pathogenesis of BCa and identify potential therapeutic targets, we combined the transcriptomic analysis with RNA sequencing and tandem mass tags (TMT)-based proteomic methods to quantitatively screen the differentially expressed genes and proteins between bladder cancer tissues (BC) and adjacent normal tissues (AN). RESULTS: Transcriptome and proteome studies indicated 7094 differentially expressed genes (DEGs) and 596 differentially expressed proteins (DEPs) between BC and AN, respectively. GO enrichment analyses revealed that cell adhesion, calcium ion transport, and regulation of ATPase activity were highly enriched in BCa. Moreover, several key signaling pathway were identified as of relevance to BCa, in particular the ECM-receptor interaction, cell adhesion molecules (CAMs), and PPAR signaling pathway. Interestingly, 367 genes were shared by DEGs and DEPs, and a significant positive correlation between mRNA and translation profiles was found. CONCLUSION: In summary, this joint analysis of transcript and protein profiles provides a comprehensive reference map of gene activity regarding the disease status of BCa.


Subject(s)
Urinary Bladder Neoplasms/genetics , Urinary Bladder Neoplasms/metabolism , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Gene Ontology , Humans , Protein Interaction Mapping , Proteome , Proteomics , Real-Time Polymerase Chain Reaction , Signal Transduction
19.
Stem Cell Res Ther ; 10(1): 251, 2019 08 14.
Article in English | MEDLINE | ID: mdl-31412925

ABSTRACT

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.


Subject(s)
Biomarkers/analysis , Chloride Channels/genetics , Induced Pluripotent Stem Cells/pathology , Mutation , Neoplasms/pathology , Osteopetrosis/pathology , Proteome/analysis , Adult , Animals , Apoptosis , Cell Proliferation , Female , Gene Expression Profiling , Gene Expression Regulation , Genotype , Humans , Induced Pluripotent Stem Cells/metabolism , Kruppel-Like Factor 4 , Male , Mice , Mice, Inbred NOD , Mice, SCID , Neoplasms/genetics , Neoplasms/metabolism , Osteopetrosis/genetics , Osteopetrosis/metabolism , Tumor Cells, Cultured , Xenograft Model Antitumor Assays
20.
Oncotarget ; 10(26): 2508-2514, 2019 Apr 02.
Article in English | MEDLINE | ID: mdl-31069013

ABSTRACT

Liver cancer is the second leading cause of cancer mortality worldwide. Safer and more effective diagnostic methods for liver cancer are desirable, and biomarkers represent a potentially alternative method for diagnosis. The present study was designed to identify liver cancer biomarkers. We quantified the changes in serum protein levels between liver transplantation and healthy (control) females using isobaric tags for relative and absolute quantitation (iTRAQ) as well as proteomic analysis. A total of 1399 proteins were identified; of these, three proteins showed significantly different concentrations between the before transplantation group and the control group. These proteins may thus be relevant to liver cancer and constitute potential liver cancer biomarkers.

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