Differentially Expressed Proteins
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Author(s):  
Yi-Meng Xiong ◽  
Hai-Tao Pan ◽  
Hai-Gang Ding ◽  
Yao He ◽  
Juan Zhang ◽  
...  

Abstract Recurrent pregnancy loss (RPL) is defined as the loss of two or more consecutive pregnancies before the 20 weeks of gestation. Recurrent pregnancy loss affects about 1–2% of couples trying to conceive; however, the mechanisms leading to this complication are largely unknown. Our previous studies using comparative proteomics identified 314 differentially expressed proteins (DEPs) in the placental villous. In this study, we identified 5479 proteins from a total of 34,157 peptides in decidua of patients with early recurrent pregnancy loss (Data are available via ProteomeXchange with identifier PXD023849). Further analysis identified 311 DEPs in the decidua tissue; and 159 proteins were highly expressed while 152 proteins were lowly expressed. These 311 proteins were further analyzed by using Ingenuity Pathway Analysis (IPA). The results suggested that 50 DEPs played important roles in the embryonic development. Upstream analysis of these DEPs revealed that AGT was the most important upstream regulator. Furthermore, protein - protein interaction (PPI) analysis of the embryonic development DEPs from the placental villous and decidua was performed in the STRING database. This study identified several proteins specifically associated with embryonic development in decidua of patients with early recurrent pregnancy loss. Therefore, these results provide new insights into potential biological mechanisms, that may ultimately inform recurrent pregnancy loss.


2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhudong Liu ◽  
Jie Xiao ◽  
Jianli Tang ◽  
Yang Liu ◽  
Ling Shuai ◽  
...  

Abstract Background Acetoin utilization protein (acuC) is a type I histone deacetylase which is highly conserved in bacteria. The acuC gene is related to the acetylation/deacetylation posttranslational modification (PTM) system in S. spinosa. Spinosyns, the secondary metabolites produced by Saccharopolyspora spinosa, are the active ingredients in a family of insect control agents. However, the specific functions and influences of acuC protein in S. spinosa are yet to be characterized. Results The knockout strain and overexpression strain were constructed separately with the shuttle vector pOJ260. The production of spinosyns A and D from S. spinosa-acuC were 105.02 mg/L and 20.63 mg/L, which were 1.82-fold and 1.63-fold higher than those of the wild-type strain (57.76 mg/L and 12.64 mg/L), respectively. The production of spinosyns A and D from S. spinosa-ΔacuC were 32.78 mg/L and 10.89 mg/L, respectively. The qRT-PCR results of three selected genes (bldD, ssgA and whiA) confirmed that the overexpression of acuC affected the capacities of mycelial differentiation and sporulation. Comparative proteomics analysis was performed on these strains to investigate the underlying mechanism leading to the enhancement of spinosad yield. Conclusions This study first systematically analysed the effects of overexpression acuC on the growth of S. spinosa and the production of spinosad. The results identify the differentially expressed proteins and provide evidences to understand the acetylation metabolic mechanisms which can lead to the increase of secondary metabolites.


Proteomes ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 33
Author(s):  
Eftychia Pappa ◽  
Konstantinos Vougas ◽  
Jerome Zoidakis ◽  
William Papaioannou ◽  
Christos Rahiotis ◽  
...  

Saliva, an essential oral secretion involved in protecting the oral cavity’s hard and soft tissues, is readily available and straightforward to collect. Recent studies have analyzed the salivary proteome in children and adolescents with extensive carious lesions to identify diagnostic and prognostic biomarkers. The current study aimed to investigate saliva’s diagnostic ability through proteomics to detect the potential differential expression of proteins specific for the occurrence of carious lesions. For this study, we performed bioinformatics and functional analysis of proteomic datasets, previously examined by our group, from samples of adolescents with regulated and unregulated type 1 diabetes, as they compare with healthy controls. Among the differentially expressed proteins relevant to caries pathology, alpha-amylase 2B, beta-defensin 4A, BPI fold containing family B member 2, protein S100-A7, mucin 5B, statherin, salivary proline-rich protein 2, and interleukin 36 gamma were significantly downregulated in poorly-controlled patients compared to healthy subjects. In addition, significant biological pathways (defense response to the bacterium, beta-defensin activity, proline-rich protein activity, oxygen binding, calcium binding, and glycosylation) were deregulated in this comparison, highlighting specific molecular characteristics in the cariogenic process. This analysis contributes to a better understanding of the mechanisms involved in caries vulnerability in adolescents with unregulated diabetes.


Author(s):  
Yongjie Xu ◽  
Qiu Han ◽  
Chaofeng Ma ◽  
Yaling Wang ◽  
Pengpeng Zhang ◽  
...  

Sperm cells are of unique elongated structure and function, the development of which is tightly regulated by the existing proteins and the posttranslational modifications (PTM) of these proteins. Based on the phylogenetic relationships of various swine breeds, Yorkshire boar is believed to be distinctly different from Duroc boar. The comprehensive differential proteomics and phosphoproteomics profilings were performed on spermatozoa from both Yorkshire and Duroc boars. By both peptide and PTM peptide quantification followed by statistical analyses, 167 differentially expressed proteins were identified from 1,745 proteins, and 283 differentially expressed phosphopeptides corresponding to 102 unique differentially phosphorylated proteins were measured from 1,140 identified phosphopeptides derived from 363 phosphorylated proteins. The representative results were validated by Western blots. Pathway enrichment analyses revealed that majority of differential expression proteins and differential phosphorylation proteins were primarily concerned with spermatogenesis, male gamete generation, sperm motility, energy metabolism, cilium morphogenesis, axonemal dynein complex assembly, sperm–egg recognition, and capacitation. Remarkably, axonemal dynein complex assembly related proteins, such as SMCP, SUN5, ODF1, AKAP3, and AKAP4 that play a key regulatory role in the sperm physiological functions, were significantly higher in Duroc spermatozoa than that of Yorkshire. Furthermore, phosphorylation of sperm-specific proteins, such as CABYR, ROPN1, CALM1, PRKAR2A, and PRKAR1A, participates in regulation of the boar sperm motility mainly through the cAMP/PKA signal pathway in different breeds, demonstrating that protein phosphorylation may be an important mechanism underlying the sperm diversity. Protein–protein interaction analysis revealed that the 14 overlapped proteins between differential expression proteins and differential phosphorylation proteins potentially played a key role in sperm development and motility of the flagellum, including the proteins ODF1, SMCP, AKAP4, FSIP2, and SUN5. Taken together, these physiologically and functionally differentially expressed proteins (DEPs) and differentially expressed phosphorylated proteins (DPPs) may constitute the proteomic backgrounds between the two different boar breeds. The validation will be performed to delineate the roles of these PTM proteins as modulators of Yorkshire and Duroc boar spermatozoa.


2021 ◽  
Author(s):  
Jie Li ◽  
Hamza Sohail ◽  
Muhammad Azher Nawaz ◽  
Chaowei Liu ◽  
Ping Yang

Abstract Brassinosteroids (BRs) are important in plant resistance to chilling stress. However, limited information is available regarding the specific mechanisms involved at proteomic level. We utilized iTRAQ proteomic approach, physiological assays and information obtained from cellular ultrastructure to clarify the underlying molecular mechanism of BRs to alleviate chilling stress in pepper (Capsicum annuum L.). Foliar application of 24-epibrassinolide (EBR) improved photosynthesis and improved cell structure by presenting a distinct mesophyll cell and chloroplast with well-developed thylakoid membranes in the leaves of pepper seedlings. We identified 346 differentially expressed proteins (DEPs), including 217 up-regulated proteins and 129 down-regulated proteins in plants under chilling (Chill) and Chill + EBR treated plants. Most of the DEPs were related to multiple pathways, including photosynthesis, carbohydrates metabolism, energy metabolism, protein biosynthesis, amino acids synthesis, redox and stress defence (ascorbate peroxidase, glutathione peroxidase, and superoxide dismutase). Up-regulated DEPs were associated with photosynthetic electron transfer chain, oxidative phosphorylation, GSH metabolism pathway, Calvin cycle and signaling pathway. The physiochemical analysis showed that EBR treatment improved the tolerance of pepper seedlings to chilling stress.


2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Chaonan Wang ◽  
Yuxin Wang ◽  
Hua Ru ◽  
Ting He ◽  
Nan Sun

In this study, 16S rRNA high-throughput sequencing technology was used to analyze the composition and diversity of bacterial and fungal communities in mushroom residue samples at different composting stages. During the composting process, the maximum temperature in the center of the pile can reach 52.4°C, and the temperature above 50°C has been maintained for about 8 days. The results showed that Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, and Chloroflexi were the main microorganisms in the composting process, accounting for 98.9%-99.7% of the total bacteria. Furthermore, in order to obtain the protein expressed in each stage of composting, the nonstandard quantitative method (label free) was used to analyze it quantitatively by mass spectrometry, anda total of 22815 proteins were identified. It indicated that the number of identified proteins related to cellulose decomposition and the number of differentially expressed proteins were significantly enriched, and the functional proteins related to cellulose decomposition had significant stage correspondence.


2021 ◽  
Vol 10 (14) ◽  
pp. 3060
Author(s):  
Mateusz Winiarczyk ◽  
Dagmara Winiarczyk ◽  
Katarzyna Michalak ◽  
Kai Kaarniranta ◽  
Łukasz Adaszek ◽  
...  

Macular edema and its further complications due to the leakage from the choroidal neovascularization in course of the age-related macular degeneration (AMD) is a leading cause of blindness among elderly individuals in developed countries. Changes in tear film proteomic composition have been reported to occur in various ophthalmic and systemic diseases. There is an evidence that the acute form of neovascular AMD may be reflected in the tear film composition. Tear film was collected with Schirmer strips from patients with neovascular AMD and sex- and age-matched control patients. Two-dimensional electrophoresis was performed followed by MALDI-TOF mass spectrometry for identification of differentially expressed proteins. Quantitative analysis of the differential electrophoretic spots was performed with Delta2D software. Altogether, 11 significantly differentially expressed proteins were identified; of those, 8 were downregulated, and 3 were upregulated in the tear film of neovascular AMD patients. The differentially expressed proteins identified in tear film were involved in signaling pathways associated with impaired protein clearance, persistent inflammation, and neovascularization. Tear film protein analysis is a novel way to screen AMD-related biomarkers.


2021 ◽  
Vol 15 ◽  
Author(s):  
Chunshuai Wu ◽  
Jinjuan Yu ◽  
Guanhua Xu ◽  
Hong Gao ◽  
Yue Sun ◽  
...  

Spinal cord injury (SCI) is a common but severe disease caused by traffic accidents. Coronary atherosclerotic heart disease (CHD) caused by dyslipidemia is known as the leading cause of death in patients with SCI. However, the quantitative analysis showed that the cholesterol and lipoprotein concentrations in peripheral blood (PB) did not change significantly within 48 h after SCI. Due to the presence of the Blood spinal cord barrier (BSCB), there are only few studies concerning the plasma cholesterol metabolism in the acute phase of SCI. Exosomes have a smaller particle size, which enables them relatively less limitation of BSCB. This study uses exosomes derived from the plasma of 43 patients in the acute phase of SCI and 71 patients in the control group as samples. MS proteomics and bioinformatics analysis found 590 quantifiable proteins, in which 75 proteins were upregulated and 153 proteins were downregulated, and the top 10 differentially expressed proteins are those including downregulating proteins: HIST1H4A, HIST2H3A, HIST2H2BE, HCLS1, S100A9, HIST1H2BM, S100A8, CALM3, YWHAH, and SFN, and upregulating proteins: SERPIND1, C1QB, SPTLC3, IGHV4-28, C4A, IGHV4-38-2, IGHV4-30-2, SLC15A1, C4B, and ACTG2. Enrichment analysis showed that the largest part of proteins was related to cholesterol metabolism among the downregulated proteins. The main components of cholesterol [ApoB-48 and ApoB-100 increased, ApoA-I, ApoA-II, ApoA-IV, ApoC, ApoE, and Apo(a) decreased] were changed in exosomes derived from plasma of patients. ELISA analysis showed that some components were disordered in the acute phase of SCI. These results suggested that the exosomes might be involved in cholesterol metabolism regulation in the acute phase of SCI.


Cancers ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 3432
Author(s):  
Ann-Yae Na ◽  
Soyoung Choi ◽  
Eunju Yang ◽  
Kwang-Hyeon Liu ◽  
Sunghwan Kim ◽  
...  

Identifying the biological change from hormone-naïve prostate cancer to castration-resistant prostate cancer (CRPC) is a major clinical challenge for developing therapeutic agents. Although the pathways that lead to CRPC are not fully completely understood, recent evidence demonstrates that androgen signaling is often maintained through varied mechanisms. Androgen deprivation therapy (ADT) is used as a primary treatment for preventing the progression of prostate cancer (PCa). Here we investigated PCa tissues at each stage of progression, from benign prostatic hyperplasia (BPH) to CRPC, based on quantitative proteomic technology, including tissues after ADT. In total, 4768 proteins were identified in this study, of which 4069 were quantified in the combined PCa tissues. Among the quantified proteins, 865 were differentially expressed proteins (21.2%). Based on the quantitative protein results, we performed systematic bioinformatics analysis and found that the levels of 15 proteins, including FOXA1 and HMGN1–3, increased among T3G3, T3GX, and CRPC, despite the ADT. Among all targets, we verified the increased levels of FOXA1 and HMGN1–3 in CRPC by immunoblotting and indirect enzyme-linked immunosorbent assay. In summary, we discuss the changes in intracellular factors involved in the progression of CRPC PCa despite ADT. Moreover, we suggest that FOXA1 and HMGN1–3 proteins could be used as potential CRPC-related factors in clinical therapeutic agents.


2021 ◽  
Author(s):  
Jung Hee Kim ◽  
Hyeyoon Kim ◽  
Kisoon Dan ◽  
Seong-Ik Kim ◽  
Sung-Hye Park ◽  
...  

Abstract Purpose: Craniopharyngiomas are rare epithelial tumors derived from pituitary gland embryonic tissue. This epithelial tumor can be categorized as an adamantinomatous craniopharyngioma (ACP) or papillary craniopharyngioma (PCP) subtype with histopathological and genetic differences. Genomic and transcriptomic profiles of craniopharyngiomas have been investigated; however, the proteomic profile has yet to be elucidated and added to these profiles. Recent improvements in high-throughput quantitative proteomic approaches have introduced new opportunities for a better understanding of these diseases and the efficient discovery of biomarkers. We aimed to confirm subtype-associated proteomic changes between ACP and PCP specimens.Methods: We performed a system-level proteomic study using an integrated approach that combines mass spectrometry-based quantitative proteomic, statistical, and bioinformatics analyses.Results: The bioinformatics analysis showed that differentially expressed proteins between ACP and PCP were significantly involved in mitochondrial organization, fatty acid metabolic processes, exocytosis, the inflammatory response, the cell cycle, RNA splicing, cell migration, and neuron development. Furthermore, using network analysis, we identified hub proteins that were positively correlated with ACP and PCP phenotypes.Conclusions: Our findings improve our understanding of the pathogenesis of craniopharyngiomas and provide novel insights that may ultimately translate to the development of craniopharyngioma subtype-specific therapeutics.


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