Accounting for the health risk of probiotics.

Probiotics have long been associated with a myriad of health benefits, so much so that their adverse effects whether mild or severe, are often neglected or overshadowed by the enormous volume of articles describing their beneficial effects in the current literature. Recent evidence has demonstrated several health risks of probiotics that warrant serious reconsideration of their applications and further investigations. This review aims to highlight studies that report on how probiotics might cause opportunistic systemic and local infections, detrimental immunological effects, metabolic disturbance, allergic reactions, and facilitating the spread of antimicrobial resistance. To offer a recent account of the literature, articles within the last five years were prioritized. The narration of these evidence was based on the nature of the studies in the following order of preference: clinical studies or human samples, in vivo or animal models, in situ, in vitro and/or in silico. We hope that this review will inform consumers, food scientists, and medical practitioners, on the health risks, while also encouraging research that will focus on and clarify the adverse effects of probiotics.

Identification of Circular RNA Profiles in the Liver of Diet-Induced Obese Mice and Construction of the ceRNA Network.

Obesity is a major risk factor for cardiovascular, cerebrovascular, metabolic, and respiratory diseases, and it has become an important social health problem affecting the health of the population. Obesity is affected by both genetic and environmental factors. In this study, we constructed a diet-induced obese C57BL/6J mouse model and performed deep RNA sequencing (RNA-seq) on liner-depleted RNA extracted from the liver tissues of the mice to explore the underlying mechanisms of obesity. A total of 7469 circular RNAs (circRNAs) were detected, and 21 were differentially expressed (DE) in the high-fat diet (HFD) and low-fat diet (LFD) groups. We then constructed a comprehensive circRNA-associated competing endogenous RNA (ceRNA) network. Bioinformatic analysis indicated that DE circRNAs associated with lipid metabolic-related pathways may act as miRNA sponges to modulate target gene expression. CircRNA1709 and circRNA4842 may serve as new candidates to regulate the expression of PTEN. This study provides systematic circRNA-associated ceRNA profiling in HFD mouse liver, and the results can aid early diagnosis and the selection of treatment targets for obesity in the future.

EspF of Enterohemorrhagic Escherichia coli Enhances Apoptosis via Endoplasmic Reticulum Stress in Intestinal Epithelial Cells: An Isobaric Tags for Relative and Absolute Quantitation-Based Comparative Proteomic Analysis.

There have been large foodborne outbreaks related to Enterohemorrhagic Escherichia coli (EHEC) around the world. Among its virulence proteins, the EspF encoded by locus of enterocyte effacement is one of the most known functional effector proteins. In this research, we infected the HT-29 cells with the EHEC wild type strain and EspF-deficient EHEC strain. Via the emerging technique isobaric tags for relative and absolute quantitation (iTRAQ), we explored the pathogenic characteristics of EspF within host cells. Our data showed that the differences regarding cellular responses mainly contained immune regulation, protein synthesis, signal transduction, cellular assembly and organization, endoplasmic reticulum (ER) stress, and apoptosis. Notably, compared with the EspF-deficient strain, the protein processing in the ER and ribosome were upregulated during wild type (WT) infection. Our findings proved that the EspF of Enterohemorrhagic Escherichia coli induced ER stress in intestinal epithelial cells; the ER stress-dependent apoptosis pathway was also activated within the host cells. This study provides insight into the virulence mechanism of protein EspF, which will deepen our general understanding of A/E pathogens and their interaction with host proteins.

Proteomic Analysis of the Early Development of the Phalaenopsis amabilis Flower Bud under Low Temperature Induction Using the iTRAQ/MRM Approach.

Phalaenopsis amabilis, one of the most important plants in the international flower market due to its graceful shape and colorful flowers, is an orchid that undergoes vernalization and requires low-temperature treatment for flowering. There have been few reports on the proteomics of the development of flower buds. In this study, isobaric tags for relative and absolute quantification (iTRAQ) were used to identify 5064 differentially expressed proteins in P. amabilis under low-temperature treatment; of these, 42 were associated with early floral induction, and 18 were verified by mass spectrometry multi-reaction monitoring (MRM). The data are available via ProteomeXchange under identifier PXD013908. Among the proteins associated with the vernalization pathway, PEQU_11434 (glycine-rich RNA-binding protein GRP1A-like) and PEQU_19304 (FT, VRN3 homolog) were verified by MRM, and some other important proteins related to vernalization and photoperiod pathway that were detected by iTRAQ but not successfully verified by MRM, such as PEQU_11045 (UDP-N-acetylglucosamine diphosphorylase), phytochromes A (PEQU_13449, PEQU_35378), B (PEQU_09249), and C (PEQU_41401). Our data revealed a regulation network of the early development of flower buds in P. amabilis under low temperature induction.

Identification of plasma biomarkers for diffuse axonal injury in rats by iTRAQ-coupled LC-MS/MS and bioinformatics analysis.

DAI is a serious and complex brain injury associated with significant morbidity and mortality. The lack of reliable objective diagnostic modalities for DAI delays administration of therapeutic interventions. Hence, identifying reliable biomarkers is urgently needed to enable early DAI diagnosis in the clinic. Herein, we established a rat model of DAI and applied an isobaric tags for a relative and absolute quantification (iTRAQ) coupled with nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) proteomics approach to screen differentially expressed plasma proteins associated with DAI. A total of 58 proteins were found to be significantly modulated in blood plasma samples of the injury group in at least one time point compared to controls. Bioinformatics analysis of the differentially expressed proteins revealed that the pathogenesis of axonal injury underlying DAI is multi-stage biological process involved. Two significantly changed proteins, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and hemopexin (Hpx), were identified as potential diagnostic biomarkers for DAI, and were successfully confirmed by further western blot analysis. This proteomic profiling study not only identified novel plasma biomarkers that may facilitate the development of clinically diagnostic for DAI, but also provided enhanced understanding of the molecular mechanisms underlying DAI.

A proteomic adaptation of small intestinal mucosa in response to dietary protein limitation.

Dietary protein limitation (PL) is not only beneficial to human health but also applied to minimize nitrogen excretion in livestock production. However, the impact of PL on intestinal physiology is largely unknown. In this study, we identified 5275 quantitative proteins using a porcine model in which pigs suffered PL. A total of 202 proteins |log2 fold-change| > 1 were taken as differentially expressed proteins and subjected to functional and pathway enrichment analysis to reveal proteomic alterations of the jejunal mucosa. Combining with the results of western blotting analysis, we found that protein/carbohydrate digestion, intestinal mucosal tight junction and cell adhesion molecules, and the immune response to foreign antigens were increased in the jejunal mucosa of the pigs upon PL. In contrast, amino acid transport, innate and auto immunity, as well as cell proliferation and apoptosis were reduced. In addition, the expression of functional proteins that involved in DNA replication, transcription and mRNA splicing as well as translation were altered in the jejunal mucosa in response to PL. Furthermore, PL may reduce amino acid transport and cell proliferation through the depression of mTOR pathway. This study provides new insights into the molecular mechanisms underlying the small intestinal response to PL.

Maternal N-Carbamylglutamate Supplementation during Early Pregnancy Enhances Embryonic Survival and Development through Modulation of the Endometrial Proteome in Gilts.

BACKGROUND: Early pregnancy loss is a major concern in humans and animals. N-carbamylglutamate (NCG) has been found to enhance embryonic survival during early pregnancy in rats. However, little is known about the key factors in the endometrium involved in the improvement of embryonic implantation and development induced by maternal NCG supplementation. OBJECTIVES: Our objectives were to investigate whether NCG supplementation during early gestation enhanced embryonic survival and development in gilts and to uncover the related factors using the approach of endometrium proteome analysis with isobaric tags for relative and absolute quantification (iTRAQ). METHODS: Uteruses and embryos/fetuses were obtained on days 14 and 28 of gestation from gilts fed a basal diet that was or was not supplemented with 0.05% NCG. The iTRAQ-based quantitative proteomics approach was performed to explore the endometrium proteome altered by NCG supplementation. RESULTS: Maternal NCG supplementation significantly increased the number of total fetuses and live fetuses on day 28 of gestation by 1.32 and 1.29, respectively (P < 0.05), with a significant decrease in embryonic mortality (P < 0.05). iTRAQ results indicated that a total of 59 proteins showed at least 2-fold differences (P < 0.05), including 52 proteins that were present at higher abundance and 7 proteins present at lower abundance in NCG-supplemented gilts. The differentially expressed proteins primarily are involved in cell adhesion, energy metabolism, lipid metabolism, protein metabolism, antioxidative stress, and immune response. On day 14 of gestation, several proteins closely related to embryonic implantation and development, such as integrin-αv, integrin-ß3, talin, and endothelial nitric oxide synthase, were upregulated (3.7-, 4.1-, 2.4-, and 5.4-fold increases, respectively) by NCG supplementation. CONCLUSION: To our knowledge, our results provide the first evidence that altered abundance of the endometrial proteome induced by NCG supplementation is highly associated with the improvement of embryonic survival and development in gilts.

Omics evidence: single nucleotide variants transmissions on chromosome 20 in liver cancer cell lines.

Cancer genomics unveils many cancer-related mutations, including some chromosome 20 (Chr.20) genes. The mutated messages have been found in the corresponding mRNAs; however, whether they could be translated to proteins still requires more evidence. Herein, we proposed a transomics strategy to profile the expression status of human Chr.20 genes (555 in Ensembl v72). The data of transcriptome and translatome (the mRNAs bound with ribosome, translating mRNAs) revealed that ∼80% of the coding genes on Chr.20 were detected with mRNA signals in three liver cancer cell lines, whereas of the proteome identified, only ∼45% of the Chr.20 coding genes were detected. The high amount of overlapping of identified genes in mRNA and RNC-mRNA (ribosome nascent-chain complex-bound mRNAs, translating mRNAs) and the consistent distribution of the abundance averages of mRNA and RNC-mRNA along the Chr.20 subregions in three liver cancer cell lines indicate that the mRNA information is efficiently transmitted from transcriptional to translational stage, qualitatively and quantitatively. Of the 457 genes identified in mRNAs and RNC-mRNA, 136 were found to contain SNVs with 213 sites, and >40% of these SNVs existed only in metastatic cell lines, suggesting them as the metastasis-related SNVs. Proteomics analysis showed that 16 genes with 20 SNV sites were detected with reliable MS/MS signals, and some SNVs were further validated by the MRM approach. With the integration of the omics data at the three expression phases, therefore, we are able to achieve the overall view of the gene expression of Chr.20, which is constructive in understanding the potential trend of encoding genes in a cell line and exploration of a new type of markers related to cancers.

Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP.

To estimate the potential of the state-of-the-art proteomics technologies on full coverage of the encoding gene products, the Chinese Human Chromosome Proteome Consortium (CCPC) applied a multiomics strategy to systematically analyze the transciptome, translatome, and proteome of the same cultured hepatoma cells with varied metastatic potential qualitatively and quantitatively. The results provide a global view of gene expression profiles. The 9064 identified high confident proteins covered 50.2% of all gene products in the translatome. Those proteins with function of adhesion, development, reproduction, and so on are low abundant in transcriptome and translatome but absent in proteome. Taking the translatome as the background of protein expression, we found that the protein abundance plays a decisive role and hydrophobicity has a greater influence than molecular weight and isoelectric point on protein detectability. Thus, the enrichment strategy used for low-abundant transcription factors helped to identify missing proteins. In addition, those peptides with single amino acid polymorphisms played a significant role for the disease research, although they might negligibly contribute to new protein identification. The proteome raw and metadata of proteome were collected using the iProX submission system and submitted to ProteomeXchange (PXD000529, PXD000533, and PXD000535). All detailed information in this study can be accessed from the Chinese Chromosome-Centric Human Proteome Database.

Qualitative and quantitative expression status of the human chromosome 20 genes in cancer tissues and the representative cell lines.

Under the guidance of the Chromosome-centric Human Proteome Project (C-HPP), (1, 2) we conducted a systematic survey of the expression status of genes located at human chromosome 20 (Chr.20) in three cancer tissues, gastric, colon, and liver carcinoma, and their representative cell lines. We have globally profiled proteomes in these samples with combined technology of LC-MS/MS and acquired the corresponding mRNA information upon RNA-seq and RNAchip. In total, 323 unique proteins were identified, covering 60% of the coding genes (323/547) in Chr.20. With regards to qualitative information of proteomics, we overall evaluated the correlation of the identified Chr.20 proteins with target genes of transcription factors or of microRNA, conserved genes and cancer-related genes. As for quantitative information, the expression abundances of Chr.20 genes were found to be almost consistent in both tissues and cell lines of mRNA in all individual chromosome regions, whereas those of Chr.20 proteins in cells are different from tissues, especially in the region of 20q13.33. Furthermore, the abundances of Chr.20 proteins were hierarchically evaluated according to tissue- or cancer-related distribution. The analysis revealed several cancer-related proteins in Chr.20 are tissue- or cell-type dependent. With integration of all the acquired data, for the first time we established a solid database of the Chr.20 proteome.