Optimization of label-free nano LC-MS/MS analysis of the placental proteome

Alterations in the placental proteome in association with the presence of black carbon particles: A discovery study

BACKGROUND

Exposure to ambient air pollution is known to cause direct and indirect molecular expression changes in the placenta, on the DNA, mRNA, and protein levels. Ambient black carbon (BC) particles can be found in the human placenta already very early in gestation. However, the effect of in utero BC exposure on the entire placental proteome has never been studied to date.

OBJECTIVES

We explored whether placental proteome differs between mothers exposed to either high or low BC levels throughout the entire pregnancy.

METHODS

We used placental tissue samples from the ENVIRONAGE birth cohort, of 20 non-smoking, maternal- and neonate characteristic-matched women exposed to high (n = 10) or low (n = 10) levels of ambient BC throughout pregnancy. We modeled prenatal BC exposure levels based on the mother's home address and measured BC levels in the fetal side of the placenta. The placental proteome was analyzed by nano-liquid chromatography Q-TOF mass spectrometry. PEAKS software was used for protein identification and label-free quantification. Protein-protein interaction and functional pathway enrichment analyses were performed with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) software.

RESULTS

The accumulation of BC particles in placenta was 2.19 times higher in the high versus low exposure group (20943.4 vs 9542.7 particles/mm³; p = 0.007). Thirteen proteins showed a ≥2-fold expression difference between the two exposure groups, all overexpressed in the placentas of women prenatally exposed to high BC levels. Three protein-protein interactions were enriched within this group, namely between TIMP3 and COL4A2, SERPINE2 and COL4A2, and SERPINE2 and GP1BB. Functional pathway enrichment analysis put forward pathways involved in extracellular matrix-receptor interaction, fibrin clot formation, and sodium ion transport regulation.

DISCUSSION

Prenatal BC exposure affects the placental proteome. Future research should focus on the potential consequences of these alterations on placental functioning, and health and disease during early childhood development.

Proteomic Characterization of Human Placenta: Insights into Potential Therapeutic Applications for Osteoarthritis

Biologics have become increasingly prominent as therapeutics in recent years due to their innate immune-privileged nature, biocompatibility, and high levels of protein biofactors. The aim of the study is to characterise the biologic, lyophilized human placenta (LHP) and explore its therapeutic potential for osteoarthritis (OA). The presence of six bioactive constituents that regulate cell-extracellular matrix interaction was identified by liquid chromatography coupled to electrospray ionization and quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF/MS). Metalloproteinase inhibitor 3 (TIMP3), alpha-1 anti-trypsin (a1AT), basic fibroblast growth factor (bFGF), and transforming growth factor β1 (TGFβ1) were detected and quantified using ELISA. The total protein content present in LHP by Bradford assay was found to be 409.35 ± 0.005 μg/ml. The analytical techniques such as Attenuated Total Reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR), solid state carbon-13 Nuclear Magnetic Resonance (ssC13 NMR) spectroscopy, and Differential Scanning Calorimetry (DSC) revealed the secondary structure and conformational stability of LHP. X-Ray diffraction (XRD) studies showed its amorphous nature. Bioactivity assessment of LHP was performed in human keratinocytes (HaCaT) and human dermal fibroblasts (HDF) by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The LHP was highly proliferative against skin cells and non-toxic, based on the findings of the bioactivity assay. LHP has the potential to be used as a therapeutic agent for OA, as its characterisation unveiled its physical stability, significant concentration of bioactive components that are pertinent to cartilage repair and its conformational stability.

Discovery proteomics of human placental tissue

We describe a label-free proteomics protocol for the interrogation of the placental proteome. Step-by-step directions, including tissue cleanup and preparation, proteolytic digestion, nanoLC-MS/MS data collection and data analysis, are provided. The workflow has been applied toward exploring differential protein expression patterns in placentas from women who have been exposed to drugs during pregnancy relative to those who have not. We collected 20 tissue specimens, each representing a combination of spatially diverse sections across the placenta. These specimens were analyzed in the work described here, to survey information across the entire organ. This protocol can be scaled up or down as needed.

Protocol for Increasing the Sensitivity of MS-Based Protein Detection in Human Chorionic Villi

An important step in the proteomic analysis of missing proteins is the use of a wide range of tissues, optimal extraction, and the processing of protein material in order to ensure the highest sensitivity in downstream protein detection. This work describes a purification protocol for identifying low-abundance proteins in human chorionic villi using the proposed “1DE-gel concentration” method. This involves the removal of SDS in a short electrophoresis run in a stacking gel without protein separation. Following the in-gel digestion of the obtained holistic single protein band, we used the peptide mixture for further LC–MS/MS analysis. Statistically significant results were derived from six datasets, containing three treatments, each from two tissue sources (elective or missed abortions). The 1DE-gel concentration increased the coverage of the chorionic villus proteome. Our approach allowed the identification of 15 low-abundance proteins, of which some had not been previously detected via the mass spectrometry of trophoblasts. In the post hoc data analysis, we found a dubious or uncertain protein (PSG7) encoded on human chromosome 19 according to neXtProt. A proteomic sample preparation workflow with the 1DE-gel concentration can be used as a prospective tool for uncovering the low-abundance part of the human proteome.