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

Proteomics Analysis of Human Chorionic Villi Reveals Dysregulated Pathways That Contribute to Recurrent Pregnancy Loss

PURPOSE

Recurrent pregnancy loss (RPL) represents a common disorder with consequences on family and society. As more than half of the RPL cases do not have a clearly identified cause, uncovering the mechanisms behind the idiopathic RPL is urgently needed.

EXPERIMENTAL DESIGN

Using label-free data-independent LC-MS/MS acquisition coupled with ion mobility, we compared the proteome of chorionic villi from 13 RPL cases with 10 age and gestational week-matched elective pregnancies. Transcriptional levels of selected candidate biomarkers were determined in chorionic villi of 35 RPL cases and 25 controls using quantitative polymerase chain reaction (qPCR).

RESULTS

Statistically significant difference in abundance (Benjamini-Hochberg [B-H] p ≤ 0.05) and fold change ≥1.5 showed 128 proteins. Bioinformatics analysis identified complement and coagulation cascades, platelet activation, tricarboxylic acid cycle (TCA) cycle, and ferroptosis as pathways with the highest significance. Correlation with transcriptome datasets revealed a weak statistically significant positive correlation with 45% of the co-differentially expressed proteins/genes displaying the same regulation trend. The transcription levels of neurofilament light polypeptide (NEFL), dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex_mitochondrial (DLST), nitric oxide synthase 3 (NOS3), and ceruloplasmin (CP) were significantly increased in the RPL, consistent with the proteomics findings.

CONCLUSIONS AND CLINICAL RELEVANCE

Our data suggests alteration of several pathways as potential causes of idiopathic RPL from the fetal side and opens the way for investigations concerning clinical management.

Identification of protein components of the transformation system in the cell line of immortalized human keratinocytes HaCaT exposed to surfactants

Using the method of shotgun mass spectrometry, we have evaluated changes in the proteomic profile of HaCat cells in response to the treatment with sodium dodecyl sulfate (anionic surfactant) and Triton-X100 (non-ionic surfactant) in two concentrations (12.5 µg/ml and 25.0 µg/ml). The study revealed induction of orphan CYP2S1 (biotransformation phase I) in response to Triton-X100. We have identified proteins of II (glutathione-S-transferases, GSTs) and III (solute carrier proteins, SLCs) biotransformation phases, as well as antioxidant proteins (peroxiredoxins, PRDXs; catalase, CAT; thioredoxin, TXN). Thus, proteins of all three xenobiotic detoxification phases were detected. The presented results suggest a new prospect of using HaCaT keratinocytes as a model of human epidermis for studying the metabolism of drugs/toxicants in human skin in vitro.

The Application of Ejaculate-Based Shotgun Proteomics for Male Infertility Screening

Problems with the male reproductive system are of both medical and social significance. As a rule, spermatozoa and seminal plasma proteomes are investigated separately to assess sperm quality. The current study aimed to compare ejaculate proteomes with spermatozoa and seminal plasma protein profiles regarding the identification of proteins related to fertility scores. A total of 1779, 715, and 2163 proteins were identified in the ejaculate, seminal plasma, and spermatozoa, respectively. Among these datasets, 472 proteins were shared. GO enrichment analysis of the common proteins enabled us to distinguish biological processes such as single fertilization (GO:0007338), spermatid development (GO:0007286), and cell motility (GO:0048870). Among the abundant terms for GO cellular components, zona pellucida receptor complex, sperm fibrous sheath, and outer dense fiber were revealed. Overall, we identified 139 testis-specific proteins. For these proteins, PPI networks that are common in ejaculate, spermatozoa, and seminal plasma were related to the following GO biological processes: cilium movement (GO:0003341), microtubule-based movement (GO:0007018), and sperm motility (GO:0097722). For ejaculate and spermatozoa, they shared 15 common testis-specific proteins with spermatogenesis (GO:0007283) and male gamete generation (GO:0048232). Therefore, we speculated that ejaculate-based proteomics could yield new insights into the peculiar reproductive physiology and spermatozoa function of men and potentially serve as an explanation for male infertility screening.

Comparative proteoinformatics revealed the essentials of SDS impact on HaCaT keratinocytes

There is no direct evidence supporting that SDS is a carcinogen, so to investigate this fact, we used HaCaT keratinocytes as a model of human epidermal cells. To reveal the candidate proteins and/or pathways characterizing the SDS impact on HaCaT, we proposed comparative proteoinformatics pipeline. For protein extraction, the performance of two sample preparation protocols was assessed: 0.2% SDS-based solubilization combined with the 1DE-gel concentration (Protocol 1) and osmotic shock (Protocol 2). As a result, in SDS-exposed HaCaT cells, Protocol 1 revealed 54 differentially expressed proteins (DEPs) involved in the disease of cellular proliferation (DOID:14566), whereas Protocol 2 found 45 DEPs of the same disease ID. The 'skin cancer' term was a single significant COSMIC term for Protocol 1 DEPs, including those involved in double-strand break repair pathway (BIR, GO:0000727). Considerable upregulation of BIR-associated proteins MCM3, MCM6, and MCM7 was detected. The eightfold increase in MCM6 level was verified by reverse transcription qPCR. Thus, Protocol 1 demonstrated high effectiveness in terms of the total number and sensitivity of MS identifications in HaCaT cell line proteomic analysis. The utility of Protocol 1 was confirmed by the revealed upregulation of cancer-associated MCM6 in HaCaT keratinocytes induced by non-toxic concentration of SDS. Data are available via ProteomeXchange with identifier PXD035202.