Proteomic analysis of amniotic fluids from healthy mid-gestation pregnancy
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
SUBMITTER: 
Michele Costanzo
LAB HEAD: Michele Costanzo
PROVIDER: PXD077489 | Pride | 2026-05-06
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DIANN_IDs_AF_CTRLs.xlsx | Xlsx | |||
| Experimental_Design.txt | Txt | |||
| TOTALRAW_AF_CTRLs.zip | Other | |||
| checksum.txt | Txt |
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Project description:Amniotic fluid (AF) is a complex biological material that provides a unique window into the developing human. Residual AF supernatant contains cell-free fetal RNA. The objective of this study was to develop an understanding of the AF core transcriptome by identifying the transcripts ubiquitously present in the AF supernatant of euploid midtrimester fetuses. We detected 476 well-annotated genes present in all twelve AF samples. Functional analysis identified 6 physiological systems represented in the AF core transcriptome, including musculoskeletal and nervous system development and function and embryonic/ organismal development. mTOR signaling was identified as a key canonical pathway. Twenty-three highly organ-specific transcripts were identified; six of these are known to be highly expressed by fetal brain. This study demonstrates that AF cell-free fetal RNA can provide biological information about multiple fetal organ systems. This was an in silico investigation of gene expression in 12 euploid midtrimester AF samples acquired primarily for advanced maternal age. We focused on the transcripts called M-bM-^@M-^\presentM-bM-^@M-^] in all of the samples. Functional analyses were performed using Ingenuity software. Fetal-organ specificity was examined for each transcript using the GNF Gene Expression Atlas. For fetal organs not represented in the atlas, manual literature searching and Ingenuity analysis were used.
2012-01-11 | E-GEOD-33168 | biostudies-arrayexpress
Project description:Preterm neonates are susceptible to gastrointestinal (GI) disorders such as necrotizing enterocolitis (NEC). Maternal milk, and especially colostrum, protects against NEC via growth promoting, immunomodulatory and antimicrobial factors. The fetal enteral diet, amniotic fluid (AF), contains similar bioactive components and we hypothesized that postnatal AF administration would reduce inflammatory responses and NEC in preterm neonates. Thirty preterm pigs (92% gestation) were delivered by caesarean section and fed total parental nutrition (TPN) for 48 h followed by enteral porcine colostrum (COLOS, n=7), infant formula (FORM, n=13) or formula + porcine AF (AF, n=10). Using a previously validated model of NEC in preterm pigs, we determined the structural, functional, microbiological and immunological responses to AF when administered prior to and after introduction of a suboptimal enteral formula diet. Keywords: Healthy versus inflammed tissues in relation to necrotizing enterocolitis Pigs from each treatment group (COLOS, n=4; FORM, n=6; and AF, n=7) were randomly selected for microarray analysis of frozen distal small intestine samples. The FORM group was further divided into formula-fed healthy pigs (F-HEA, n=3) and formula-fed NEC pigs (F-NEC, n=3) in order to compare sick versus healthy formula fed pigs. Equal amounts of total distal small intestinal RNA from all pigs were pooled to make the reference sample. Samples and reference pool were labelled with Oyster 550 and 650, respectively. The in-house spotted porcine oligonucleotide microarray version 4 (POM4) is a low density microarray consisting of 384 different oligonucleotide probes representing more than 200 different immune related genes.
2010-05-06 | E-GEOD-13515 | biostudies-arrayexpress
Project description:Cannabis use during pregnancy is associated with adverse neurodevelopmental outcomes. However, the underlying mechanisms and effects of cannabis on fetal development are relatively unknown. We determined the impact of chronic delta-9-tetrahydrocannabinol (THC, cannabis’s main psychoactive component) exposure on fetal development in a rhesus macaque model using advanced imaging combined with molecular and tissue studies. Animals were divided into control (n=5) or THC-exposed (n=5) groups, which received a daily THC edible pre-conception and throughout pregnancy. Animals underwent fetal brain T2-weighted MRI at gestational days 85 (G85), G110, G135 and G155 (term is ~G168) to assess brain development. All animals underwent cesarean delivery with fetal cerebral spinal fluid (CSF) and brain collection at G155 for microRNA (miRNA) and histologic analysis. THC exposure did not demonstrate any fetal brain volumetric changes. However, histological findings in THC-exposed brains suggested brain dysregulation that may have long-term developmental implications. We identified two extracellular-vesicle-associated miRNAs (mir-448 and mir-199a-3p) with>2-fold change in CSF with maternal THC use. Amniotic fluid (AF) was collected at the 4 gestational ages (GA) and relative protein abundance changes measured with isobaric labeling quantitative proteomics. Changes in AF were observed across the GAs and in response to THC-treatment.
2025-07-18 | PXD042447 | Pride
Project description:Despite numerous studies on fetal therapy for myelomeningoceles (MMC), the pathophysiology of this malformation remains poorly understood. This study aimed to analyze the biochemical profile and proteome of amniotic fluid (AF) supernatants from MMC fetuses to explore the prenatal pathophysiology. Proteome analysis was conducted in 18 MMC and 18 healthy singleton fetuses, as well as in 5 dichorionic pregnancies with MMC fetuses and their healthy co-twins. ELISA tests were used to validate proteome results. Biochemical analysis revealed anal incontinence in 37% of MMC cases (p<0.0001), while controls had a normal profile. Proteomics identified 2453 quantified proteins, with 39 significantly up-regulated and 10 down-regulated in MMC. Up-regulated proteins included ectodomains of CHL1, APLP1, SEZ6, SEZ6L, which are generated by the Alzheimer’s disease-linked protease BACE1. Some proteins varied with disease and gestational age, e.g., CNTN1, NEO1, and DRAXIN. COL11A2 and EFNB1 decreased in MMC, rising in controls. Contrary to the in-utero inflammation or meconium neurotoxicity hypothesis, our results suggest a CSF leak in AF. Abundance of brain and spinal cord proteins may aid diagnosis, characterizing cases and informing prognosis for couples.
2025-03-13 | PXD048510 | Pride
Project description:Background – Although many studies have been conducted to develop fetal therapy for myelomeningoceles (MMC), pathophysiology of this malformation remains poorly understood. The purpose of our study was to compare amniotic fluid (AF) of fetuses with MMC and healthy fetuses using biochemical and proteomic analysis to explore the prenatal pathophysiology of MMC. Methods – The biochemical analysis of 61 AF samples from MMC singletons fetuses was compared to those of 45 AF samples from healthy singletons fetuses. This analysis included the dosage of urea, uric acid, creatinine, amylase, total proteins, and the assay of the following enzyme activities: gamma-glutamyl transpeptidase, aminopeptidase M, alkaline phosphatase isoenzymes. A cohort of 36 AF samples from singletons fetuses was analysed using data independent analysis MS. The strongest candidates were validates by western blot. AF samples from five MMC fetuses from dichorionic twin pregnancies and those of their healthy co-twins were also analysed using using high-resolution mass spectrometry. Results – Biochemical analysis showed an increase in enzymes activities of aminopeptidase M (AMP), alkaline phosphatase isoenzymes (tALP) and intestinal alkaline phosphatase isoenzyme (iALP) in the MMC group, compared to the control group. The biochemical profile comparison of the two groups revealed an anal incontinence profile in 37% of the MMC cases and a normal profile in all the controls (p<0.0001). No significant differences were found in creatinine, uric acid, urea, and amylase levels between both groups. AF proteome comparison of the singleton cohort of showed an increase in 37 proteins and a decrease in 8 proteins in MMC AF samples compared to control AF samples. It also highlighted an evolution in some proteins abundance according the gestation week. We therefore analyzed AF samples for twin pregnancy, which largely confirmed and refined the candidates previously found. Among the increased proteins, eleven (CHL1, ALPLP1, SEZ6, SEZ6L, APP…..) correspond to substrates for the BACE1 secretase, and three were validated by western blot. APOB was also found elevated in all MMC AF and was validated by ELISA. The elevated proteins found in the AF strongly correlated with the neonatal CSF previously reported, rendering the AF analysis a preview if the neonatal CSF in the second trimester of gestation. Conclusion – Our study is the first to suggest an association between MMC and secretase BACE1 with an overexpression or a functional dysregulation of BACE1 in fetuses with MMC. The study also suggests that amniotic fluid (AF) analysis is a preview of the cerebrospinal fluid (CSF) from the newborn, and that it could be used to help predict the prognosis of the fetus.
2026-01-21 | PXD047861 | Pride
Project description:Amniotic fluid volume (AFV) is determined primarily by the rate of intramembranous (IM) transport of AF cross the amnion. Intramembranous transport is characterized as vesicular endocytotic and transcytotic processes regulated by fetal urine-derived stimulators and AF inhibitors. Our objectives were to utilize a large-scale multiomics approach to decipher the vesicular transport pathways in the amnion and to identify potential transport regulators in AF and fetal urine. We utilized fetal sheep to experimentally induce alterations in IM transport rate and analyze the expression profiles of transcripts and proteins in amnion, AF and fetal urine. Four experimental groups were studied: control (C), urine drainage with reduced IM transport rate and AFV (UD), urine drainage and fluid replacement with decreased IM transport rate but increased AFV (UDR), and intra-amniotic fluid infusion with increased IM transport rate and AFV (IA). Amnion and fluid samples were subjected to transcriptomics (RNA-Seq) and isobaric labeling proteomics studies followed by bioinformatics analyses using Ingenuity Pathway Analysis software. The analyses revealed 9 functional transport pathways and a panel of differentially expressed transcripts and proteins that are known mediators of vesicular transport and cellular trafficking. During UD, expression of transport and trafficking mediators were reduced as compared to controls. With UDR, expression of energy metabolism activators increased while trafficking mediators decreased. During IA, expression of vesicular uptake molecules increased while trafficking mediators decreased. Co-expression of the motor protein, cytoplasmic dynein light chain-1, in both AF and fetal urine suggest that this molecule may function as a urine-derived stimulator of IM transport.
2021-07-21 | PXD013135 | Pride
Project description:Atrial fibrillation (AF) is the most common persistent arrhythmia that affect 1–2% of the general population. People with AF display an array of complications cardiogenic stroke and systemic embolism caused by hemodynamic instability and blood hypercoagulability in clinical practice. However, it’s still unclear whether and how ubiquitylated proteins react to AF in the left atrial appendage of patients with AF and valvular heart disease. This theory focuses on the changes of ubiquitylated proteins in atrial fibrillation associated with heart valve disease. We firstly widely analysis the proteins ubiquitination in patients with atrial fibrillation.
2021-12-24 | PXD030397 | Pride
Project description:Background: Horses and humans are among the few mammals prone to developing spontaneous atrial fibrillation (AF), both suffering from high recurrence rates after treatment. Treatment resistance is often attributed to functional, structural, and metabolic remodeling of the atria. The aim of this explorative study was to evaluate the molecular pathways associated with early stages of AF in horses and to compare the AF proteomes between horses and humans. Methods: We performed data-independent acquisition mass spectrometry on myocardial biopsies collected from the right atrium (RA), left atrium (LA), and left ventricular chamber (LV) in horses with early stages of naturally occurring persistent AF and controls (n=8 in each group). Results: We identified a total of 3400 quantifiable proteins, several of which were differentially regulated between AF horses and controls (268 in RA, 324 in LA, and 284 in LV, p<0.05). Pathway enrichment analyses identified changes in metabolic, contractile, and extracellular matrix (ECM) proteins. Atrial hypocontractility and ECM remodeling were confirmed by echocardiography and histology, respectively. Key proteomic changes in horses with AF overlapped with human AF public datasets, underscoring the translational relevance of the equine AF model. Particularly, contractile proteins, such as cardiac troponins (TNNT2), myosin (MYH6) and tropomyosin (TPM2), along with metabolic regulators as heat shock protein family A (HSPA4) and Proteasome 26S Subunit, Non-ATPase 13 (PSMD13) were shared between horses and humans with AF. Moreover, a significant increase in several ECM glycoproteins was detected in both species, highlighting the importance of early ECM remodeling that extends beyond the fibrotic changes often associated with AF. Conclusion: The horse and human cardiac proteome share similar AF-related changes. Metabolic, functional, and structural protein changes identified in early-stage AF may provide clues to pharmacological targets for preventing AF-associated atrial remodeling and improving treatment success across species.
2025-05-28 | PXD052818 | Pride
Project description:ABSTRACT Primary human distal lung/parenchymal fibroblasts (DLF) exhibit a different phenotype from airway fibroblasts (AF), including the expression of high levels of a-smooth muscle actin (a-SMA). The scope of the differences and the mechanisms driving them are unknown. To determine whether distinct fibroblast characteristics and function based on lung region are predicted by a broad range of genomic differences in AF vs DLF. Matched human fibroblast pairs isolated from proximal and distal lung in 18 asthmatic and 4 normal subjects were studied. Microarray analysis was performed on 12 matched fibroblast pairs (8 asthmatic and 4 normal subjects) and validated by quantitative real-time PCR (qRT-PCR). The functional impact of these molecular differences on AF and DLF was then revealed using computational approaches. Microarray data demonstrated 474 transcripts upregulated in AF, and 611 transcripts upregulated in DLF, when the asthmatic and normal fibroblasts were combined for all the analysis. Further gene ontology (GO) and network analysis identified distinct pathway activation patterns between AF and DLF, including identification of the SMAD3 and MAPK8 signaling pathways. These results demonstrated that marked molecular and functional differences exist between these two lung regional fibroblast populations. These striking differences identify multiple potential mechanisms by which AF and DLF differ in their responses to injury, regeneration and remodeling in the lungs. In order to better identify the underlying molecular differences between AF and DLF, microarray analysis was performed on 12 different matched pairs of fibroblasts (4 pairs from normal subjects and 8 pairs from asthmatics).
2011-07-21 | E-GEOD-27335 | biostudies-arrayexpress
Project description:Transcriptional profiling of human amniotic fluid-derived mesenchymal stem cells (AF-MSCs) comparing normal condition-cultured AF-MSCs with hypoxia condition-culture AF-MSCs ES cells. The latter improves the proliferation and survival of AF-MSCs, and makes AF-MSCs secret more growth factors. Goal was to determine the effects of hypoxia condition on global AF-MSCs gene expression. Two-condition experiment, Nor AF-MSCs vs. Hypo AF-MSCs. Experimantal replicates: 2 (1-1 vs. 1-2; 2-1 vs. 2-2). Biological replicates: 2 normal replicates, 2 treated replicates.
2013-12-18 | E-GEOD-53402 | biostudies-arrayexpress