Project description:Recurrent miscarriage (RM) is the occurrence of repeated pregnancies that end in miscarriage of the fetus before 20 weeks of gestation. Recurrent miscarriages affect about 1-2% of couples trying to conceive; however, mechanisms leading to this complication are largely unknown. Our previous studies using comparative proteomics identified 314 differentially expressed proteins (DEPs) in placental villous. In this study, we identified 5479 proteins from a total of 34157 peptides in decidua of patients with early recurrent miscarriage. Further analysis identified 311 DEPs in the decidua tissue; 159 proteins showed the increased expression while 152 proteins showed decreased expression. These 311 proteins were further analyzed using Ingenuity Pathway Analysis (IPA). The results suggested that 50 DEPs could play important roles in the embryonic development. Furthermore, network analysis of the placental villous and decidua embryonic development DEPs was performed in STRING database to find the core gene. This study identifies several proteins that are specifically associated with embryonic development in decidua of patients with early recurrent miscarriage, these results provide new insights into potential biological mechanisms and may ultimately inform recurrent miscarriage.
Project description:The objective of this project was to characterize the salivary proteome of patients with recurrent aphthous stomatitis using mass spectrometry-based proteomics(nLC-MS/MS) and assess its clinical usefulness in identifying the most representative biological and molecular processes during the course of lesions. To do this, we conducted a case-control study, analyzing the saliva of healthy controls and patients with recurrent aphthous stomatitis during a complete ulcerative cycle (active ulcers and absence of lesions).
Project description:In this experiment we generated Affymetrix gene expression data for T Follicular Helper (TFH) cells from tonsils of healthy volunteers (4 biological replicates) and naive CD4-positive helper T cells (2 biological replicates). TFH cells provide a model relevant to SLE as TFH operate upstream of the activation of pathogenic autoantibody-producing B cells during the disease. This experiment accompanies promoter capture-C and ATAC-seq experiments on the same cell types.
Project description:Cigarette smoking is the major cause of cancers of the respiratory tract, including non-small cell lung cancer (NSCLC) and head and neck cancer (HNC). In order to better understand carcinogenesis of the lung and upper airways, we have compared the gene expression profiles of tumour-distant, histologically normal bronchial biopsy specimens obtained from current smokers with NSCLC or HNC (SC, considered as a single group), as well as non-smokers (NS) and smokers without cancer (SNC). RNA from a total of 97 biopsies was used for gene expression profiling (Affymetrix HG-U133 Plus 2.0 array). Differentially expressed genes were used to compare NS, SNC, and SC, and functional analysis was carried out using Ingenuity Pathway Analysis (IPA). Smoking-related cancer of the respiratory tract was found to affect the expression of genes encoding xenobiotic biotransformation proteins, as well as proteins associated with crucial inflammation/immunity pathways and other processes that protect the airway from the chemicals in cigarette smoke or contribute to carcinogenesis. Finally, we used the prediction analysis for microarray (PAM) method to identify gene signatures of cigarette smoking and cancer, and uncovered a 15-gene signature that distinguished between SNC and SC with an accuracy of 83%. Thus, gene profiling of histologically normal bronchial biopsy specimens provided insight into cigarette-induced carcinogenesis of the respiratory tract and gene-signatures of cancer in smokers.
Project description:High uterine artery Doppler (UtAD) resistance indices (RI), indicative of poor uterine blood flow, have been shown to be predictive of placental complications of pregnancy such as pre-eclampsia (PE), fetal growth restriction (FGR) and stillbirth. A comparative analysis of gene expression in High vs normal risk pregnancies in placental tissue from first trimester was undertaken. Patients were stratified by their risk of developing placental complications as determined by Doppler resistance indices. High-resistance cases were defined as those with bilateral uterine diastolic notches and a mean RI >95th percentile whilst Normal-resistance cases had a mean RI of <95th percentile. A direct comparison of gene expression in Placental villous tissue obtained folowing terminations at of 9 to 14 weeks gestation.
Project description:Acute myeloid leukemia with complex karyotype (CK-AML) is characterized by three or more chromosomal aberrations, and comprises 10–12% of AML patients. It is associated with complex chromosomal rearrangements, intra-tumor heterogeneity, therapy resistance and poor overall survival. We aimed to transcriptionally characterize CK-AML by performing RNA sequencing on blasts from 4 CK-AML patient samples.
Project description:There are histological and functional differences between human deciduous and permanent pediodontal ligament (PDL) tissues. The purpose of this study was to determine the differences between these two types of tissue at the molecular level by comparative gene expression analysis. PDL samples were obtained from permanent premolars (n=38) and anterior deciduous teeth (n=31) extracted from 40 healthy persons. Comparative cDNA microarrary analysis revealed several differences in gene expression between the deciduous and permanent PDL tissues.
Project description:It is of paramount importance to unravel the molecular mechanisms underlying PCa progression to develop novel diagnostic and therapeutic approaches. MicroRNA (miRNA) profiling through microarrays is an invaluable tool to identify a miRNA signature, which is required to determine the general and specific expression alterations between distinct types of tissues. In this study, it is aimed to compare the miRNA profile of recurrent and non-recurrent prostate tumor tissues to explore a possible involvement of miRNAs in PCa progression.
Project description:Expression of proteins regulating apoptosis (BCL-2, MCL-1, BCL-X and BAX) in acute myeloid leukemia (AML) blasts at diagnosis have been shown to be associated with disease-free survival. We previously found that the initially high apoptosis-resistance of AML cells decreased after therapy, while regaining high levels at relapse. This suggested a dynamic regulation of apoptosis. This data is from the lysate fraction of the secretomes described in PXD001476.
Project description:Expression of proteins regulating apoptosis (BCL-2, MCL-1, BCL-X and BAX) in acute myeloid leukemia (AML) blasts at diagnosis have been shown to be associated with disease-free survival. We previously found that the initially high apoptosis-resistance of AML cells decreased after therapy, while regaining high levels at relapse. This suggested a dynamic regulation of apoptosis. Herein, we further explored this aspect of apoptosis in AML. Firstly, the intra-individual ex vivo apoptosis-related profiles of normal lymphocytes and AML blasts showed a strong correlation, with expression values far beyond control lymphocytes. Secondly, we demonstrated that apoptosis-resistant primary AML blasts, as opposed to apoptosis-sensitive cells, were able to up-regulate BCL-2 expression in sensitive AML blasts in contact cultures (p=0.0067 and p=1.0 respectively). Using proteomics we further set out to identify novel proteins possibly engaged in apoptosis regulation. Proteomics analysis revealed that major functional protein clusters upregulated in secretomes of apoptosis-resistant AML, were presumably engaged in global gene regulation including mRNA splicing, protein translation and chromatin remodeling.