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Proteins are the main functional executor of cellular function. Due to the fact that proteins could not be amplified in vitro, the development of single-cell proteomics technology lags behind single-cell genomics and transcriptomics technologies. The traditional proteomics technology detects the average protein expression levels from large amounts of cells; nevertheless, it is unable to address the cell subtypes and heterogeneity among individual cells. Analysis of proteins at the single-cell level can help characterize the molecular basis of cell phenotypes and heterogeneity. With the rapid development of mass spectrometers, mass spectrometry-based methods have pushed single-cell proteomics to a new level. In this review, we summarized the recent research progress of single-cell proteomics methods based on LC-MS/MS, including single cell selection, sample preparation, isotope labelling technology, peptide separation, mass spectrometry analysis and data analysis, and its applications in biomedical research. The challenges and prospects of single-cell proteomics in the future are also prospected. Advances in single cell proteomics will provide new ideas and methods for biomedical research and deepen our understanding of human health and disease.

Bacterial Mn(II) oxidation is believed to play a dominant role in accelerating the rate of Mn biomineralization in nature. Commonly, bacteria employ two ways involving Mn(II) oxidases and reactive oxygen species to oxidize Mn(II). In this study, a new strategy for bacterial Mn(II) oxidation involving the pyocyanin, a greenish blue phenazine pigment from Pseudomonas aeruginosa, was discovered. To begin with, a bacterial strain L3 was isolated from soils and identified as Pseudomonas aeruginosa, which exhibited the ability of Mn(II) oxidation. Next, the pyocyanin was purified from strain L3 cultures and proven to be involved in Mn(II) oxidation. Particularly, the oxidation of Mn(II) by pyocyanin was dependent on its ambient pH. In comparison with pH of 5 and 7, pyocyanin (the initial value of OD387 was 0.56 at pH of 2) showed a stronger capability of oxidizing Mn(II) at pH of 9, reaching 144.03 μg L−1 of Mn oxides after 108 h of Mn(II) oxidation, while pyocyanin ultimately produced 43.81 μg L−1 at pH of 7 and 3.32 μg L−1 at pH of 5, respectively. Further, strain L3 cultures were fractionated into three parts, i.e., the cell culture solution, fermentation supernatant, and cell suspension, and the Mn(II)-oxidizing activity was found to be distributed in the cell culture solution and fermentation supernatant, as evidenced by the formation of blackish glossy Mn oxides. Specifically, in the first half, the rate of Mn(II) oxidation by the fermentation supernatant was higher than that by the cell culture solution, whereas in the second half, the cell culture solution showed the much higher Mn(II)-oxidizing activity compared to the fermentation supernatant. Last but not least, the collective results from mineral characterization demonstrated that, the Mn oxides produced by P. aeruginosa strain L3, either by the cell culture solution or by the fermentation supernatant, were bixbyite-type Mn2O3 with poor crystallinity. [ABSTRACT FROM AUTHOR]

Multiplexed single-cell proteomes (SCPs) quantification by mass spectrometry greatly improves the SCP coverage. However, it still suffers from a low number of protein identifications and there is much room to boost proteins identification by computational methods. In this study, we present a novel framework DeepSCP, utilizing deep learning to boost SCP coverage. DeepSCP constructs a series of features of peptide-spectrum matches (PSMs) by predicting the retention time based on the multiple SCP sample sets and fragment ion intensities based on deep learning, and predicts PSM labels with an optimized-ensemble learning model. Evaluation of DeepSCP on public and in-house SCP datasets showed superior performances compared with other state-of-the-art methods. DeepSCP identified more confident peptides and proteins by controlling q-value at 0.01 using target–decoy competition method. As a convenient and low-cost computing framework, DeepSCP will help boost single-cell proteome identification and facilitate the future development and application of single-cell proteomics. [ABSTRACT FROM AUTHOR]

Objectives: Accumulating evidences show that the regulatory network of m6A modification is essential for mammalian spermatogenesis. However, as an m6A reader, the roles of YTHDF2 remain enigmatic due to the lack of a proper model. Here, we employed the germ cell conditional knockout mouse model and explored the function of YTHDF2 in spermatogenesis. Materials and methods: Ythdf2 germ cell conditional knockout mice were obtained by crossing Ythdf2‐floxed mice with Vasa‐Cre and Stra8‐Cre mice. Haematoxylin and eosin (HE) staining, immunofluorescent staining and Western blotting were used for phenotyping. CASA, IVF and ICSI were applied for sperm function analysis. RNA‐seq, YTHDF2‐RIP‐seq and quantitative real‐time PCR were used to explore transcriptome changes and molecular mechanism analysis. Results: Our results showed that YTHDF2 was highly expressed in spermatogenic cells. The germ cell conditional knockout males were sterile, and their sperm displayed malformation, impaired motility, and lost fertilization ability. During differentiated spermatogonia transiting to pachytene spermatocyte, most m6A‐modified YTHDF2 targets that were degraded in control germ cells persisted in pachytene spermatocytes of Ythdf2‐vKO mice. These delayed mRNAs were mainly enriched in pathways related to the regulation of transcription, and disturbed the transcriptome of round spermatid and elongated spermatid subsequently. Conclusion: Our data demonstrate that YTHDF2 facilitates the timely turnover of phase‐specific transcripts to ensure the proper progression of spermatogenesis, which highlights a critical role of YTHDF2 in spermatogenesis. [ABSTRACT FROM AUTHOR]

Aging has many effects on the female reproductive system, among which decreased oocyte quality and impaired embryo developmental potential are the most important factors affecting female fertility. However, the mechanisms underlying oocyte aging are not yet fully understood. Here, we selected normal reproductively aging female mice and constructed a protein expression profile of metaphase II (MII) oocytes from three age groups. A total of 187 differentially expressed (DE) proteins were identified, and bioinformatics analyses showed that these DE proteins were highly enriched in RNA splicing. Next, RNA‐seq was performed on 2‐cell embryos from these three age groups, and splicing analysis showed that a large number of splicing events and genes were discovered at this stage. Differentially spliced genes (DSGs) in the two reproductively aging groups versus the younger group were enriched in biological processes related to DNA damage repair/response. Binding motif analysis suggested that PUF60 might be one of the core splicing factors causing a decline in DNA repair capacity in the subsequent development of oocytes from reproductively aging mice, and changing the splicing pattern of its potential downstream DSG Cdk9 could partially mimic phenotypes in the reproductively aging groups. Taken together, our study suggested that the abnormal expression of splicing regulation proteins in aged MII oocytes would affect the splicing of nascent RNA after zygotic genome activation in 2‐cell embryos, leading to the production of abnormally spliced transcripts of some key genes associated with DNA damage repair/response, thus affecting the developmental potential of aged oocytes. [ABSTRACT FROM AUTHOR]

(E) Two spEV protein biomarker for noninvasive differential diagnosis of azoospermia (NOA vs. However, the choices for high sensitivity and specificity in the noninvasive differential diagnosis of azoospermia are limited.3 Extracellular vesicles (EVs) are increasingly being considered as a promising source of novel diagnostic biomarkers due to their noninvasive nature and high reproducibility.4 In this study, we revealed that two proteins SLC5A12 and HIST1H2BA from human seminal plasma extracellular vesicle (spEV) could differentially diagnose azoospermia with high sensitivity and specificity. Dear Editor, Azoospermia, which accounts for about 10%-15% of infertile men, is generally classified as obstructive azoospermia (OA) due to male reproductive tract obstruction and nonobstructive azoospermia (NOA) due to testicular failure.1 NOA has three major forms: hypospermatogenesis (HS), germ cell arrest (MA), and Sertoli cell-only (SCO) based on the histopathological examination of testicular tissue.2 An accurate diagnosis of the subtype of azoospermia is crucial and mandatory, as the treatment approach differs between NOA and OA. Thus, significant decrease of spEV SLC5A12 is expected in OA patients, but not NOA patients. [Extracted from the article]

Myotubularin related protein 7 (MTMR7), a key member of the MTMR family, depicts phosphatase activity and is involved in myogenesis and tumor growth. We have previously identified MTMR7 in the proteomic profile of mouse spermatogonial stem cell (SSC) maturation and differentiation, implying that MTMR7 is associated with neonatal testicular development. In this study, to further explore the distribution and function of MTMR7 in mouse testis, we studied the effect of Mtmr7 knockdown on neonatal testicular development by testicular and SSC culture methods. Our results revealed that MTMR7 is exclusively located in early germ cells. Deficiency of MTMR7 by morpholino in neonatal testis caused excessive SSC proliferation, which was attributable to the aberrant PI3K/AKT signaling activation. Altogether, our study demonstrates that MTMR7 maintains SSC homeostasis by inhibiting PI3K/AKT signaling activation. [ABSTRACT FROM AUTHOR]

Oligoasthenozoospermia is a major cause of male infertility; however, its etiology and pathogenesis are unclear and may be associated with specific gene abnormalities. This study focused on Tppp2 (tubulin polymerization promoting protein family member 2), whose encoded protein localizes in elongating spermatids at stages IV‐VIII of the seminiferous epithelial cycle in testis and in mature sperm in the epididymis. In human and mouse sperm, in vitro inhibition of TPPP2 caused significantly decreased motility and ATP content. Studies on Tppp2 knockout (KO) mice demonstrated that deletion of TPPP2 resulted in male subfertility with a significantly decreased sperm count and motility. In Tppp2−/− mice, increased irregular mitochondria lacking lamellar cristae, abnormal expression of electron transfer chain molecules, lower ATP levels, decreased mitochondrial membrane potential and increased apoptotic index were observed in sperm, which could be the potential causes for its oligoasthenozoospermia phenotype. Moreover, we identified a potential TPPP2‐interactive protein, eEf1b (eukaryotic translation elongation factor 1 beta), which plays an important role in protein translation extension. Thus, TPPP2 is probably a potential pathogenic factor in oligoasthenozoospermia. Deficiency of TPPP2 might affect the translation of specific proteins, altering the structure and function of sperm mitochondria, and resulting in decreased sperm count, motility and fertility. [ABSTRACT FROM AUTHOR]

Acidithiobacillus ferrooxidans showed the compensate growth and oxidation after re-feeding with sufficient ferrous materials after starvation. Compensatory phenomena were first detected in chemoautotrophic organisms. Starvation stress of Acidithiobacillus ferrooxidans was achieved via culturing in low concentrations of iron. During compensation, growth and ferrous oxidation took place faster than in controls. In addition, some genes related to ferrous oxidation (such as rus) and carbon assimilation ( cbbR, csoS3) were expressed in different patterns in the low energy environments. Their expression patterns can account for this increased growth and oxidation. Other groups of genes ( cspAB, feoAB, fur) were suppressed in response to starvation stress. The presence of pyrite and joint cold stress can render compensation nearly undetectable. This may be why the compensation phenomena observed under these conditions was not the same as that observed under single starvation stress conditions. Gene expression reflected a possible mechanism of tolerance to starvation in Acidithiobacillus ferrooxidans, which would allow the organism to adapt and survive in ferrous-limited environments. [ABSTRACT FROM AUTHOR]

Introduction: Intrahepatic cholestasis of pregnancy (ICP) usually occurs in the third trimester and associated with increased risks in fetal complications. Currently, the exact cause of this disease is unknown. In this study we aim to investigate the potential proteins in placenta, which may participate in the molecular mechanisms of ICP-related fetal complications using iTRAQ-based proteomics approach. Methods: The iTRAQ analysis combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to separate differentially expressed placental proteins from 4 pregnant women with ICP and 4 healthy pregnant women. Bioinformatics analysis was used to find the relative processes that these differentially expressed proteins were involved in. Three apoptosis related proteins ERp29, PRDX6 and MPO that resulted from iTRAQ-based proteomics were further verified in placenta by Western blotting and immunohistochemistry. Placental apoptosis was also detected by TUNEL assay. Results: Proteomics results showed there were 38 differentially expressed proteins from pregnant women with ICP and healthy pregnant women, 29 were upregulated and 9 were downregulated in placenta from pregnant women with ICP. Bioinformatics analysis showed most of the identified proteins was functionally related to specific cell processes, including apoptosis, oxidative stress, lipid metabolism. The expression levels of ERp29, PRDX6 and MPO were consistent with the proteomics data. The apoptosis index in placenta from ICP patients was significantly increased. Conclusion: This preliminary work provides a better understanding of the proteomic alterations of placenta from pregnant women with ICP and may provide us some new insights into the pathophysiology and potential novel treatment targets for ICP. [ABSTRACT FROM AUTHOR]

A number of genes involved in zygotic genome activation (ZGA) have been identified, but the RNA‐binding maternal factors that are directly related to ZGA in mice remain unclear. The present study shows that maternal deletion of Igf  2bp2 (also commonly known as Imp2) in mouse embryos causes early embryonic developmental arrest in vitro at the 2‐cell‐stage. Transcriptomics and proteomics analyses of 2‐cell‐stage embryos in mice reveal that deletion of IMP2 downregulates the expression of Ccar1 and Rps14, both of which are required for early embryonic developmental competence. IGF2, a target of IMP2, when added in culture media, increases the proportion of wild‐type embryos that develop successfully to the blastocyst stage: from 29% in untreated controls to 65% (50 × 10−9m IGF2). Furthermore, in an experiment related to embryo transfer, foster mothers receiving IGF2‐treated embryos deliver more pups per female than females who receive untreated control embryos. In clinically derived human oocytes, the addition of IGF2 to the culture media significantly enhances the proportion of embryos that develop successfully. Collectively, the findings demonstrate that IMP2 is essential for the regulation and activation of genes known to be involved in ZGA and reveal the potential embryonic development‐related utility of IGF2 for animal biotechnology and for assisted reproduction in humans. [ABSTRACT FROM AUTHOR]

Objective To assess the long-term effects of repeated controlled ovarian hyperstimulation (COH) on ovarian structure and function. Design Experimental study. Setting Laboratory. Animal(s) Adult female rhesus macaques. Intervention(s) A repeated COH rhesus macaque model (superovulation group) with spontaneously ovulating macaques used as controls (normal group) and samples of serum and ovarian tissue collected over a 5-year period. Main Outcome Measure(s) Steroid hormone levels, and structural, functional, and protein changes in ovaries. Result(s) The follicular histology, proportion of follicles at each developmental stage, and expression levels of oocyte-specific genes showed no statistically significant differences between the two groups. However, the superovulation group exhibited mitochondrial abnormalities in the granulosa cells and a low expression of genes involved in steroid hormone synthesis compared with the normal group. A comparison of protein expression in the ovaries of both groups using tandem mass tag labeling with mass spectrometry revealed that most of the differentially-expressed proteins were down-regulated in the superovulation group. These proteins were mainly localized in the mitochondria and cytosol, and changes in protein levels in the superovulation group mainly inhibited cell proliferation and differentiation but promoted apoptosis. Conclusion(s) Our study indicates that repeated COH could change the expression of many proteins in the ovaries even after several years, potentially affecting the development and function of ovarian cells. [ABSTRACT FROM AUTHOR]