Loss of PMFBP1 Disturbs Mouse Spermatogenesis by Downregulating HDAC3 Expression

PURPOSE

Polyamine modulating factor 1 binding protein (PMFBP1) acts as a scaffold protein for the maintenance of sperm structure. The aim of this study was further to identify the new role and molecular mechanism of PMFBP1 during mouse spermatogenesis.

METHODS AND RESULTS

We identified a profile of proteins interacting with PMFBP1 by immunoprecipitation combined with mass spectrometry and demonstrated that class I histone deacetylases, particularly HDAC3 and chaperonin-containing TCP1 subunit 3 (CCT3), were potential interaction partners of PMFBP1 based on network analysis of protein-protein interactions and co-immunoprecipitation. Immunoblotting and immunochemistry assays showed that loss of Pmfbp1 would result in a decline in HDACs and change the proteomic profile of mouse testis, in which differently expressed proteins are associated with spermatogenesis and assembly of flagella, which was proved by proteomic analysis of testis tissue obtained from Pmfbp1^-/- mice. After integrating with transcriptome data for Hdac3^-/- and Sox30^-/- round sperm obtained from a public database, RT-qPCR confirmed ring finger protein 151 (Rnf151) and ring finger protein 133 (Rnf133) were key downstream response factors of the Pmfbp1-Hdac axis affecting mouse spermatogenesis.

CONCLUSION

Taken together, this study indicates a previously unidentified molecular mechanism of PMFBP1 in spermatogenesis whereby PMFBP1 interacts with CCT3, affecting the expression of HDAC3, followed by the downregulation of RNF151 and RNF133, resulting in an abnormal phenotype of sperm beyond the headless sperm tails. These findings not only advance our understanding of the function of Pmfbp1 in mouse spermatogenesis but also provide a typical case for multi-omics analysis used in the functional annotation of specific genes.

Modulation of cellular transcriptome and proteome composition by azidohomoalanine-implications on click chemistry-based secretome analysis

The analysis of the secretome provides important information on proteins defining intercellular communication and the recruitment and behavior of cells in specific tissues. Especially in the context of tumors, secretome data can support decisions for diagnosis and therapy. The mass spectrometry-based analysis of cell-conditioned media is widely used for the unbiased characterization of cancer secretomes in vitro. Metabolic labeling using azide-containing amino acid analogs in combination with click chemistry facilitates this type of analysis in the presence of serum, preventing serum starvation-induced effects. The modified amino acid analogs, however, are less efficiently incorporated into newly synthesized proteins and may perturb protein folding. Combining transcriptome and proteome analysis, we elucidate in detail the effects of metabolic labeling with the methionine analog azidohomoalanine (AHA) on gene and protein expression. Our data reveal that 15-39% of the proteins detected in the secretome displayed changes in transcript and protein expression induced by AHA labeling. Gene Ontology (GO) analyses indicate that metabolic labeling using AHA leads to induction of cellular stress and apoptosis-related pathways and provide first insights on how this affects the composition of the secretome on a global scale. KEY MESSAGES: Azide-containing amino acid analogs affect gene expression profiles. Azide-containing amino acid analogs influence cellular proteome. Azidohomoalanine labeling induces cellular stress and apoptotic pathways. Secretome consists of proteins with dysregulated expression profiles.

Anterior blepharitis is associated with elevated plectin levels consistent with a pronounced intracellular response

PURPOSE

Anterior blepharitis is a frequent ocular condition which may result in severe ocular surface disease. In this study, advanced proteome analysis was performed to elucidate biological mechanisms underlying anterior blepharitis.

METHODS

All patients underwent full ophthalmological examination including Ocular Surface Disease Index score (OSDI). Measurement of non-invasive break-up time (NBUT), Oxford score, and meibography were performed. Tear film samples from treatment naïve patients with anterior blepharitis (n = 15) and age-matched controls (n = 11) were collected with Schirmer filtration paper. The samples were analyzed with label-free quantification nano liquid chromatography - tandem mass spectrometry (LFQ nLC-MS/MS). Significantly regulated proteins were identified with a permutation-based calculation with a false discovery rate at 0.05.

RESULTS

Among the 927 proteins detected, a total of 162 proteins were significantly changed. Regulated proteins were involved in cytoplasmic translation, positive regulation of B cell activation, complement activation and phagocytosis. High levels of plakin proteins, a group of proteins involved in cytoskeleton organization, were observed in anterior blepharitis, including plectin, desmoplakin, envoplakin, epiplakin, periplakin, and vimentin. The upregulation of plectin was confirmed with single reaction monitoring. Patients with anterior blepharitis had lower levels of immunoglobulin chains, VEGF coregulated chemokine 1 (CXCL17), and platelet-derived growth factor C.

CONCLUSIONS

Anterior blepharitis was associated with a high level of plectin indicating a pronounced intracellular response with cytoskeletal reorganization. Our data suggest a lack of immunoglobulin chains and CXCL17 in anterior blepharitis with potential alterations in the ocular surface immune response.

Proteomics reveals defective peroxisomal fatty acid oxidation during the progression of acute kidney injury and repair

Acute kidney injury (AKI) is characterized by a rapid decrease in renal function with high mortality and risk of progression to chronic kidney disease (CKD). Ischemia and reperfusion injury (IRI) is one of the major causes of AKI. However, the cellular and molecular responses of the kidney to IRI are complex and not fully understood. Herein, we conducted unbiased proteomics and bioinformatics analyses in an IRI mouse model on days 3, 7, and 21, and validated the results using IRI, unilateral ureteral obstruction (UUO), and biopsies from patients with AKI or CKD. The results indicated an obvious temporal expression profile of differentially expressed proteins and highlighted impaired lipid metabolism during the progression of AKI to CKD. Acyl-coenzyme A oxidase 1 (Acox1), the first rate-limiting enzyme of peroxisomal fatty acid beta-oxidation, was then selected, and its disturbed expression in the two murine models validated the proteomic findings. Accordingly, Acox1 expression was significantly downregulated in renal biopsies from patients with AKI or CKD, and its expression was negatively correlated with kidney injury score. Furthermore, in contrast to the decreased Acox1 expression, lipid droplet accumulation was remarkably increased in these renal tissues, suggesting dysregulation of fatty acid oxidation. In conclusion, our results suggest that defective peroxisomal fatty acid oxidation might be a common pathological feature in the transition from AKI to CKD, and that Acox1 is a promising intervention target for kidney injury and repair.

High-throughput proteomics of breast cancer subtypes: Biological characterization and multiple candidate biomarker panels to patients' stratification

BACKGROUND AND AIMS

The actual classification of breast tumors in subtypes represents an attempt to stratify patients into clinically cohesive groups, nevertheless, clinicians still lack reproducible and reliable protein biomarkers for breast cancer subtype discrimination. In this study, we aimed to access the differentially expressed proteins between these tumors and its biological implications, contributing to the subtype's biological and clinical characterization, and with protein panels for subtype discrimination.

METHODS

In our study, we applied high-throughput mass spectrometry, bioinformatic, and machine learning approaches to investigate the proteome of different breast cancer subtypes.

RESULTS

We identified that each subtype depends on different protein expression patterns to sustain its malignancy, and also alterations in pathways and processes that can be associated with each subtype and its biological and clinical behaviors. Regarding subtype biomarkers, our panels achieved performances with at least 75% of sensibility and 92% of specificity. In the validation cohort, the panels obtained acceptable to outstanding performances (AUC = 0.740 to 1.00).

CONCLUSIONS

In general, our results expand the accuracy of breast cancer subtypes' proteomic landscape and improve the understanding of its biological heterogeneity. In addition, we identified potential protein biomarkers for the stratification of breast cancer patients, improving the repertoire of reliable protein biomarkers.

SIGNIFICANCE

Breast cancer is the most diagnosed cancer type worldwide and the most lethal cancer in women. As a heterogeneous disease, breast cancer tumors can be classified into four major subtypes, each presenting particular molecular alterations, clinical behaviors, and treatment responses. Thus, a pivotal step in patient management and clinical decisions is accurately classifying breast tumor subtypes. Currently, this classification is made by the immunohistochemical detection of four classical markers (estrogen receptor, progesterone receptor, HER2 receptor, and the Ki-67 index); however, it is known that these markers alone do not fully discriminate the breast tumor subtypes. Also, the poor understanding of the molecular alterations of each subtype leads to a challenging decision-making process regarding treatment choice and prognostic determination. This study, through high-throughput label-free mass-spectrometry data acquisition and downstream bioinformatic analysis, advances in the proteomic discrimination of breast tumors and achieves an in-depth characterization of the subtype's proteomes. Here, we indicate how the variations in the subtype's proteome can influence the tumor's biological and clinical differences, highlighting the variation in the expression pattern of oncoproteins and tumor suppressor proteins between subtypes. Also, through our machine-learning approach, we propose multi-protein panels with the potential to discriminate the breast cancer subtypes. Our panels achieved high classification performance in our cohort and in the independent validation cohort, demonstrating their potential to improve the current tumor discrimination system as complements to the classical immunohistochemical classification.

Venom phenotype conservation suggests integrated specialization in a lizard-eating snake

Biological specialization reduces the size of niche space while increasing efficiency in the use of available resources. Specialization often leads to phenotypic changes via natural selection aligning with niche space constraints. Commonly observed changes are in size, shape, behavior, and traits associated with feeding. One often selected trait for dietary specialization is venom, which, in snakes, often shows variation dependent on diet across and within species. The Neotropical Blunt-headed Treesnake (Imantodes cenchoa) is a highly specialized, rear-fanged, arboreal, lizard hunter that displays a long thin body, enlarged eyes, and a large Duvernoy's gland. However, toxin characterization of I. cenchoa has never been completed. Here, we use RNA-seq and mass spectrometry to assemble, annotate, and analyze the venom gland transcriptomes of four I. cenchoa from across their range. We find a lack of significant venom variation at the sequence and expression levels, suggesting venom conservation across the species. We propose this conservation provides evidence of a specialized venom repertoire, adapted to maximize efficiency of capturing and processing lizards. Importantly, this study provides the most complete venom gland transcriptomes of I. cenchoa and evidence of venom specialization in a rear-fanged snake, giving insight into selective pressures of venom across all snake species.

Proteome reveals the mechanism of selenium-sulfur interaction in regulating isothiocyanate biosynthesis and the physiological metabolism of broccoli sprouts

Broccoli sprouts have a strong ability to accumulate isothiocyanate and selenium. In this study, the isothiocyanate content increased significantly as a result of ZnSO₄ stress. Particularly, based on the isothiocyanate content is not affected, the combined ZnSO₄ and Na₂SeO₃ treatment alleviated the inhibition of ZnSO₄ and induced selenium content. Gene transcription and protein expression analyses revealed the changes in isothiocyanate and selenium metabolite levels in broccoli sprouts. ZnSO₄ combined with Na₂SeO₃ was proven to activate a series of isothiocyanate metabolite genes (UGT74B1, OX1, and ST5b) and selenium metabolite genes (BoSultr1;1, BoCOQ5-2, and BoHMT1). The relative abundance of the total 317 and 203 proteins, respectively, in 4-day-old broccoli sprouts varied, and the metabolic and biosynthetic pathways for secondary metabolites were significantly enriched in ZnSO₄/control and ZnSO₄ combined Na₂SeO₃/ZnSO₄ comparisons. The findings demonstrated how ZnSO₄ combined with Na₂SeO₃ treatment reduced stress inhibition and the accumulation of encouraged selenium and isothiocyanates during the growth of broccoli sprouts.

Comparative transcriptome and proteome analysis explores the antitumor key regulators of ergosterone in H22 tumor-bearing mice

Ergosterone has been proved to have potential antitumor effect on H22 tumor-bearing mice, but the antitumor mechanism and key regulators are still unclear. The current study was aimed to explore the key regulators responsible for antitumor of ergosterone using whole transcriptome and proteome analysis in H22 tumor-bearing mice model. The model of H22 tumor-bearing mice was constructed according to the histopathological data and biochemical parameters. The isolated tumor tissues of different treatment groups were subjected to transcriptomic and proteomic analysis. Our findings demonstrated that 472 differentially expressed genes and 658 proteins were identified in the tumor tissue of different treatment groups through RNA-Seq and liquid chromatography with tandem mass spectrometry-based proteomic analysis, respectively. The combined omics analysis revealed three critical genes/proteins, including Lars2, Sirpα and Hcls1 that could play a role in antitumor pathways. Furthermore, Lars2, Sirpα and Hcls1 genes/proteins, as key regulators of the antitumor effect of ergosterone, were verified by qRT-PCR and western blotting methods, respectively. In summary, our study provides new insights into analysing the antitumor mechanism of ergosterone from the point of view of gene and protein expression and will encourage further development of the antitumor pharmaceutical industry.

Physiological and proteomic analyses reveal the important role of arbuscular mycorrhizal fungi on enhancing photosynthesis in wheat under cadmium stress

Arbuscular mycorrhizal fungi (AMF) are important in the phytoremediation of cadmium (Cd). Improving photosynthesis under Cd stress helps to increase crop yields. However, the molecular regulatory mechanisms of AMF on photosynthetic processes in wheat (Triticum aestivum) under Cd stress remain unclear. This study utilized physiological and proteomic analyses to reveal the key processes and related genes of AMF that regulate photosynthesis under Cd stress. The results showed that AMF promoted the accumulation of Cd in the roots of wheat but significantly reduced the content of Cd in the shoots and grains. The photosynthetic rates, stomatal conductance, transpiration rates, chlorophyll content, and accumulation of carbohydrates under Cd stress were increased by AMF symbiosis. Proteomic analysis showed that AMF significantly induced the expression of two enzymes involved in the chlorophyll biosynthetic pathway (coproporphyrinogen oxidase and Mg-protoporphyrin IX chelatase), improved the expression of two proteins related to CO₂ assimilation (ribulose-1,5-bisphosphate carboxylase and malic enzyme), and increased the expression of S-adenosylmethionine synthase, which positively regulates abiotic stress. Therefore, AMF may regulate photosynthesis under Cd stress by promoting chlorophyll biosynthesis, carbon assimilation, and S-adenosylmethionine metabolism.

Physiological and molecular response and tolerance of Macleaya cordata to lead toxicity

BACKGROUND

Macleaya cordata is a traditional medicinal herb, and it has high tolerance and accumulation ability to heavy metals, which make it a good candidate species for studying phytoremediation. The objectives of this study were to investigate response and tolerance of M. cordata to lead (Pb) toxicity based on comparative analysis of transcriptome and proteome.

RESULTS

In this study, the seedlings of M. cordata cultured in Hoagland solution were treated with 100 µmol·L^- 1 Pb for 1 day (Pb 1d) or 7 days (Pb 7d), subsequently leaves of M. cordata were taken for the determination of Pb accumulation and hydrogen peroxide production (H₂O₂), meanwhile a total number of 223 significantly differentially expressed genes (DEGs) and 296 differentially expressed proteins (DEPs) were screened between control and Pb treatments. The results showed leaves of M. cordata had a special mechanism to maintain Pb at an appropriate level. Firstly, some DEGs were iron (Fe) deficiency-induced transporters, for example, genes of vacuolar iron transporter and three ABC transporter I family numbers were upregulated by Pb, which can maintain Fe homeostasis in cytoplasm or chloroplast. In addition, five genes of calcium (Ca²⁺) binding proteins were downregulated in Pb 1d, which may regulate cytoplasmic Ca²⁺ concentration and H₂O₂ signaling pathway. On the other hand, the cysteine synthase upregulated, glutathione S-transferase downregulated and glutathione reductase downregulated in Pb 7d can cause reduced glutathione accumulation and decrease Pb detoxification in leaves. Furthermore, DEPs of eight chlorophyll a/b binding proteins, five ATPases and eight ribosomal proteins can play a pivotal role on chloroplast turnover and ATP metabolism.

CONCLUSIONS

Our results suggest that the proteins involved in Fe homeostasis and chloroplast turnover in mesophyll cells may play key roles in tolerance of M. cordata to Pb. This study offers some novel insights into Pb tolerance mechanism of plants, and the potential valuable for environmental remediation of this important medicinal plant.

Ecological threat caused by malathion and its chiral metabolite in a honey bee-rape system: Stereoselective exposure risk and the mechanism revealed by proteome

Honey bees play an important role in the ecological environment. Regrettably, a decline in honey bee colonies caused by chemical insecticides has occurred throughout the world. Potential stereoselective toxicity of chiral insecticides may be a hidden source of danger to bee colonies. In this study, the stereoselective exposure risk and mechanism of malathion and its chiral metabolite malaoxon were investigated. The absolute configurations were identified using an electron circular dichroism (ECD) model. Ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used for chiral separation. In pollen, the initial residues of malathion and malaoxon enantiomers were 3571-3619 and 397-402 μg/kg, respectively, and R-malathion degraded relatively slowly. The oral LD₅₀ values of R-malathion and S-malathion were 0.187 and 0.912 μg/bee with 5 times difference, respectively, and the malaoxon values were 0.633 and 0.766 μg/bee. The Pollen Hazard Quotient (PHQ) was used to evaluate exposure risk. R-malathion showed a higher risk. An analysis of the proteome, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and subcellular localization, indicated that energy metabolism and neurotransmitter transport were the main affected pathways. Our results provide a new scheme for the evaluation of the stereoselective exposure risk of chiral pesticides to honey bees.

Maternal pre-conceptional glyphosate exposure impacts the offspring hepatic and ovarian proteome

Glyphosate (GLY) is an herbicide used for rural and urban weed control. Urinary GLY in women is associated with shortened gestational length yet effects of GLY on offspring due to maternal exposure are unclear. This study tested the hypothesis that maternal chronic pre-conceptional GLY exposure would cause phenotypic and molecular changes in F1 offspring. Female C57BL/6 mice (7 wk old; n = 40) received saline vehicle control (CT; n = 20) or GLY (2 mg/Kg; n = 20) daily per os for ten weeks. At dosing completion, females were housed with unexposed males and divided into Cohort 1 who were euthanized at gestation day (GD) 14 (n = 10 per treatment), and Cohort 2 who completed gestation (n = 10 per treatment). F1 female ovarian and liver samples underwent LC-MS/MS and bioinformatic analysis. Maternal exposure did not affect litter (P > 0.05) sex ratio, or embryonic or neonatal gross phenotypes. In Cohort 2 offspring, no treatment effect on (P > 0.05) offspring anogenital distance, puberty onset or ovarian follicular composition was noted. Body weight was increased (P < 0.05) in male GLY-exposed compared to CT dam offspring. F1 females from GLY-exposed dams, had altered (P < 0.05) abundance of 54 ovarian and 110 hepatic proteins. Pathways altered in the ovary (FDR ≤ 0.07) included thermogenesis and PI3K-AKT signaling and in liver (FDR ≤ 0.08) included metabolic, glutathione metabolism, oxidative phosphorylation, non-alcoholic fatty liver disease, and thermogenesis. Thus, pre-conceptional GLY exposure affected offspring phenotypic and molecular profiles potentially impacting reproductive health.

Functional proteomics based on protein microarray technology for biomedical research

This chapter traces a route through Proteomics from its origins to the present day. The different proteomics applications are discussed with a focus on microarray technology. Analytical microarrays, functional microarrays and reverse phase microarrays and their different applications are discussed. Several studies are mentioned where the great versatility of this approach is shown. Finally, the advantages and future challenges of microarray technology are outlined.

Cooperation is the key: the CCN biological system as a gate to high complex protein superfamilies' signaling

Cellular signaling is generally understood as the support of communication between contiguous cells belonging to the same tissue or cells being far apart of each other, at a molecular scale, when the message emitted by the transmitters is traveling in liquid or solid matter to reach recipient targets. Subcellular signaling is also important to ensure the proper cell constitution and functioning. However cell signaling is mostly used in the first understanding, to describe how the message sent from one point to another one, will reach a target where it will be interpreted. The Cellular Communication Network (CCN) factors (Perbal et al. 2018) constitute a family of biological regulators thought to be responsible for signaling pathways coordination (Perbal 2018). Indeed, these proteins interact with a diverse group of cell receptors, such as integrins, low density lipoprotein receptors, heparan sulfate proteoglycan receptors (HSPG), and the immunoglobulin superfamily expressed exclusively in the nervous system, or with soluble factors such as bone morphogenetic proteins (BMPS) and other growth factors such as vascular endothelial growth factor, fibroblastic growth factor, and transforming growth factor (TGFbeta). Starting from the recapitulation of basic concepts in enzymology and protein-ligands interactions, we consider, in this manuscript, interpretations of the mechanistic interactions that have been put forward to explain the diversity of CCN proteins biological activities. We suggest that the cross-talks between superfamilies of proteins under the control of CCNs might play a central role in the coordination of developmental signaling pathways.

Adaptive mechanisms of Bacillus to near space extreme environments

Earth's near space is an extreme atmosphere environment with high levels of radiation, low atmospheric pressure and dramatic temperature fluctuations. The region is above the flight altitude of aircraft but below the orbit of satellites, which has special and Mars-like conditions for investigating the survival and evolution of life. Technical limitations including flight devices, payloads and technologies/methodologies hinder microbiological research in near space. In this study, we investigated microbial survival and adaptive strategies in near space using a scientific balloon fight mission and multi-omics analyses. Methods for sample preparation, storage, protector and vessel were optimized to prepare the exposed microbial samples. After 3 h 17 min of exposure at a float altitude of ~32 km, only Bacillus strains were alive with survival efficiencies of 0-10^-6. Diverse mutants with significantly altered metabolites were generated, firstly proving that Earth's near space could be used as a new powerful microbial breeding platform. Multi-omics analyses of mutants revealed cascade changes at the genome, transcriptome and proteome levels. In response to environmental stresses, two mutants had similar proteome changes caused by different genomic mutations and mRNA expression levels. Metabolic network analysis combined with proteins' expression levels revealed that metabolic fluxes of EMP, PPP and purine synthesis-related pathways were significantly altered to increase/decrease inosine production. Further analysis showed that proteins related to translation, molecular chaperones, cell wall/membrane, sporulation, DNA replication/repair and anti-oxidation were significantly upregulated, enabling cells to efficiently repair DNA/protein damages and improve viability against environmental stress. Overall, these results revealed genetic and metabolic responses of Bacillus to the harsh conditions in near space, providing a research basis for bacterial adaptive mechanisms in extreme environments.

Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes

BACKGROUND

Diplonemid flagellates are among the most abundant and species-rich of known marine microeukaryotes, colonizing all habitats, depths, and geographic regions of the world ocean. However, little is known about their genomes, biology, and ecological role.

RESULTS

We present the first nuclear genome sequence from a diplonemid, the type species Diplonema papillatum. The ~ 280-Mb genome assembly contains about 32,000 protein-coding genes, likely co-transcribed in groups of up to 100. Gene clusters are separated by long repetitive regions that include numerous transposable elements, which also reside within introns. Analysis of gene-family evolution reveals that the last common diplonemid ancestor underwent considerable metabolic expansion. D. papillatum-specific gains of carbohydrate-degradation capability were apparently acquired via horizontal gene transfer. The predicted breakdown of polysaccharides including pectin and xylan is at odds with reports of peptides being the predominant carbon source of this organism. Secretome analysis together with feeding experiments suggest that D. papillatum is predatory, able to degrade cell walls of live microeukaryotes, macroalgae, and water plants, not only for protoplast feeding but also for metabolizing cell-wall carbohydrates as an energy source. The analysis of environmental barcode samples shows that D. papillatum is confined to temperate coastal waters, presumably acting in bioremediation of eutrophication.

CONCLUSIONS

Nuclear genome information will allow systematic functional and cell-biology studies in D. papillatum. It will also serve as a reference for the highly diverse diplonemids and provide a point of comparison for studying gene complement evolution in the sister group of Kinetoplastida, including human-pathogenic taxa.

Post-mortem muscle proteome of crossbred bulls and steers: Relationships with carcass and meat quality

This study investigated the skeletal muscle proteome of crossbred bulls and steers with the aim of explaining the differences in carcass and meat quality traits. Therefore, 640 post-weaning Angus-Nellore calves were fed a high-energy diet for a period of 180 days. In the feedlot trial, comparisons of steers (n = 320) and bulls (n = 320) showed lower (P < 0.01) average daily gain (1.38 vs. 1.60 ± 0.05 kg/d), final body weight (547.4 vs. 585.1 ± 9.3 kg), which resulted in lower hot carcass weight (298.4 vs. 333.7 ± 7.7 kg) and ribeye area (68.6 vs. 81.0 ± 2.56 cm²). Steers had higher (P < 0.01) carcass fatness, meat color parameters (L*, a*, b*, chroma (C*), hue (h°)) and lower ultimate pH. Moreover, lower (P < 0.01) Warner-Bratzler shear force (WBSF) were observed in steers compared to bulls (WBSF = 3.68 vs. 4.97 ± 0.08 kg; and 3.19 vs. 4.08 ± 0.08 kg). The proteomic approach using two-dimensional electrophoresis, mass spectrometry and bioinformatics procedures revealed several differentially expressed proteins between steers and bulls (P < 0.05). Interconnected pathways and substantial changes were revealed in biological processes, molecular functions, and cellular components between the post-mortem muscle proteomes of the compared animals. Steers had increased (P < 0.05) abundance of proteins related to energy metabolism (CKM, ALDOA, and GAPDH), and bulls had greater abundance of proteins associated with catabolic (glycolysis) processes (PGM1); oxidative stress (HSP60, HSPA8 and GSTP1); and muscle structure and contraction (TNNI2 and TNNT3). The better carcass (fatness and marbling degree) and meat quality traits (tenderness and color parameters) of steers were associated with higher abundance of key proteins of energy metabolism and lower abundance of enzymes related to catabolic processes, oxidative stress, and proteins of muscle contraction SIGNIFICANCE: Sexual condition of cattle is known to be an important factor affecting animal performances and growth as well as the carcass and meat quality traits. The investigation of skeletal muscle proteome help a better understanding of the origin of the differences in quality traits between bulls and steers. The inferior meat quality of bulls was found to be due to the greater expression of proteins associated with primary and catabolic processes, oxidative stress, and muscle contraction. Steers had greater expression of proteins, from which several are known biomarkers of beef quality (mainly tenderness).

Identification of novel prognostic indicators for oral squamous cell carcinoma based on proteomics and metabolomics

BACKGROUND

The low 5-year survival rate of oral squamous cell carcinoma (OSCC) suggests that new prognostic indicators need to be identified to aid the clinical management of patients.

METHODS

Saliva samples from OSCC patients and healthy controls were collected for proteomic and metabolomic sequencing. Gene expressed profiling was downloaded from TCGA and GEO databases. After the differential analysis, proteins with a significant impact on the prognosis of OSCC patients were screened. Correlation analysis was performed with metabolites and core proteins were identified. Cox regression analysis was utilized to stratify OSCC samples based on core proteins. The prognostic predictive ability of the core protein was then evaluated. Differences in infiltration of immune cells between the different strata were identified.

RESULTS

There were 678 differentially expressed proteins (DEPs), 94 intersected DEPs among them by intersecting with differentially expressed genes in TCGA and GSE30784 dataset. Seven core proteins were identified that significantly affected OSCC patient survival and strongly correlated with differential metabolites (R² > 0.8). The samples were divided into high- and low-risk groups according to median risk score. The risk score and core proteins were well prognostic factor in OSCC patients. Genes in high-risk group were enriched in Notch signaling pathway, epithelial mesenchymal transition (EMT), and angiogenesis. Core proteins were strongly associated with the immune status of OSCC patients.

CONCLUSIONS

The results established a 7-protein signatures with the hope of early detection and the capacity for risk assessment of OSCC patient prognosis. Further providing more potential targets for the treatment of OSCC.

Proteomic analysis reveals differential responsive mechanisms in Solanum nigrum exposed to low and high dose of cadmium

Cadmium (Cd) contamination is becoming a widespread environmental problem. However, the differential responsive mechanisms of Cd hyperaccumulator Solanum nigrum to low or high dose of Cd are not well documented. In this study, phenotypic and physiological analysis firstly suggested that the seedlings of S. nigrum showed slight leaf chlorosis symptoms under 25 μM Cd and severe inhibition on growth and photosynthesis under 100 μM Cd. Further proteomic analysis identified 105 differentially expressed proteins (DEPs) in the Cd-treated leaves. Under low dose of Cd stress, 47 DEPs are mainly involved in primary metabolic processes, while under high dose of Cd stress, 92 DEPs are mainly involved in photosynthesis, energy metabolism, production of phytochelatin and reactive oxygen species (ROS). Protein-protein interaction (PPI) network analysis of DEPs support above differential responses in the leaves of S. nigrum to low and high dose of Cd treatments. This work provides the differential responsive mechanisms in S. nigrum to low and high dose of Cd, and the theoretical foundation for the application of hyperaccumulating plants in the phytoremediation of Cd-contaminated soils.

Saliva proteome of partially- and fully-engorged adult female Haemaphysalis flava ticks

Tick saliva is a reservoir of bioactive proteins. Saliva protein compositions change dynamically during blood-feeding. Decipherment of protein profiles in different blood-feeding stages may bring deeper insight into tick feeding physiology and provide targets for immunologic control alternatives. However, having the infancy of tick genome sequencing, assembly, annotation, and limited knowledge of tick salivary proteins restrain the data interpretation. Here, we aimed to depict the saliva protein profile in partially- (PE) and fully-engorged (FE) Haemaphysalis flava ticks, with a special focus on the analysis of those uncharacterized proteins. Saliva was collected from PE and FE adult female H. flava ticks. Saliva proteins were analyzed by high-performance liquid chromatography-tandem mass spectrometry (HPLC/MS-MS). MS data were searched against an in-house salivary gland transcriptome library for identification of tick-derived proteins. Abundances of proteins were compared between PE and FE ticks. The uncharacterized proteins detected in saliva were further bioinformatically analyzed. In total, 614 proteins were identified including 94 host proteins and 520 tick-derived proteins. The 226 tick-derived high-confidence proteins were classified into 10 categories: transporters, enzymes, protease inhibitors, immunity-related proteins, lipocalins, glycine-rich proteins, muscle proteins, secreted proteins, uncharacterized proteins and others. A total of 98 proteins were shared in both PE and FE with 74 only in PE and 54 only in FE. Abundances of 24 shared proteins were significantly higher in PE. The profile of top 15 most abundant proteins was also different between PE and FE ticks. The 65 uncharacterized proteins detected in tick saliva were branched into subclusters 1 A, 1B, 2, 3 A, 3B and 3 C based on particular motifs like RGD, LRR, indicating their diverse predicted functions like anti-coagulation, regulation of innate immune, or other functions. This study provides and compares saliva proteomes of H. flava ticks in two feeding stages with special cluster analysis on the uncharacterized proteins. Further investigations are needed to confirm the roles of these uncharacterized proteins in ticks.

Analysis of differentially expressed proteins after EHP-infection and characterization of caspase 3 protein in the whiteleg shrimp (Litopenaeus vannamei)

Whiteleg shrimp (Litopenaeus vannamei) is the most important species of shrimp farmed worldwide in terms of its economic value. Enterocytozoon hepatopenaei (EHP) infects the hepatopancreas, resulting in the hepatopancreatic microsporidiosis (HPM) of the host, which causes slow growth of the shrimp and poses a threat to the farming industry. In this study, differentially expressed proteins (DEPs) between EHP-infected and uninfected shrimp were investigated through proteomics sequencing. A total of 9908 peptides and 2092 proteins were identified. A total of 69 DEPs were identified in the hepatopancreas (HP), of which, 28 were upregulated and 41 were downregulated. Our results showed that the differences among the level of multiple proteins involved in the apoptosis were significant after the EHP infection, which indicated that the apoptosis pathway was activated in whiteleg shrimp. In addition, expression leve of caspase 3 gene were identified related to the EHP infection. Furthermore, predictions of spatial structure, analysis of phylogeny and chromosome-level linearity of the caspase 3 protein were performed as well. In conclusion, a relatively complete proteomic data set of hepatopancreas tissues in whiteleg shrimp were established in this study. Findings about genes involved in the apoptosis here will provide a further understanding of the molecular mechanism of EHP infection in the internal immunity of whiteleg shrimp.

Multi-omics analysis revealed the brain dysfunction induced by energy metabolism in Pelteobagrus vachelli under hypoxia stress

Hypoxia in water environment has become increasingly frequent and serious due to global warming and environmental pollution. Revealing the molecular mechanism of fish hypoxia adaptation will help to develop markers of environmental pollution caused by hypoxia. Here, we used a multi-omics method to identify the hypoxia-associated mRNA, miRNA, protein, and metabolite involved in various biological processes in Pelteobagrus vachelli brain. The results showed that hypoxia stress caused brain dysfunction by inhibiting energy metabolism. Specifically, the biological processes involved in energy synthesis and energy consumption are inhibited in P. vachelli brain under hypoxia, such as oxidative phosphorylation, carbohydrate metabolism and protein metabolism. Brain dysfunction is mainly manifested as blood-brain barrier injury accompanied by neurodegenerative diseases and autoimmune diseases. In addition, compared with previous studies, we found that P. vachelli has tissue specificity in response to hypoxia stress and the muscle suffers more damage than the brain. This is the first report to the integrated analysis of the transcriptome, miRNAome, proteome, and metabolome in fish brain. Our findings could provide insights into the molecular mechanisms of hypoxia, and the approach could also be applied to other fish species. DATA AVAILABILITY: The raw data of transcriptome has been uploaded to NCBI database (ID: SUB7714154 and SUB7765255). The raw data of proteome has been uploaded to ProteomeXchange database (PXD020425). The raw data of metabolome has been uploaded to Metabolight (ID: MTBLS1888).

Alterations in the root phenylpropanoid pathway and root-shoot vessel system as main determinants of the drought tolerance of a soybean genotype

Climate change increases precipitation variability, particularly in savanna environments. We have used integrative strategies to understand the molecular mechanisms of drought tolerance, which will be crucial for developing improved genotypes. The current study compares the molecular and physiological parameters between the drought-tolerant Embrapa 48 and the sensitive BR16 genotypes. We integrated the root-shoot system's transcriptome, proteome, and metabolome to understand drought tolerance. The results indicated that Embrapa 48 had a greater capacity for water absorption due to alterations in length and volume. Drought tolerance appears to be ABA-independent, and IAA levels in the leaves partially explain the higher root growth. Proteomic profiles revealed up-regulated proteins involved in glutamine biosynthesis and proteolysis, suggesting osmoprotection and explaining the larger root volume. Dysregulated proteins in the roots belong to the phenylpropanoid pathways. Additionally, PR-like proteins involved in the biosynthesis of phenolics may act to prevent oxidative stress and as a substrate for modifying cell walls. Thus, we concluded that alterations in the root-shoot conductive vessel system are critical in promoting drought tolerance. Moreover, photosynthetic parameters from reciprocal grafting experiments indicated that the root system is more essential than the shoots in the drought tolerance mechanism. Finally, we provided a comprehensive overview of the genetic, molecular, and physiological traits involved in drought tolerance mechanisms.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01307-7.

Mechanisms for the increase in lipid production in cyanobacteria during the degradation of antibiotics

This study evaluated the responses of cell density, photosynthesis activity, dry cell weight, lipid productivity, proteome and metabolome in two non-toxic cyanobacterial species (Synechococcus sp. and Chroococcus sp.) exposed to two frequently detected antibiotics (sulfamethoxazole and ofloxacin) at test concentrations of 0.2-20.0 μg L^-1 in a 4-day culture period. Upregulated antioxidant enzymes and oxidoreductases contributed to antibiotic biodegradation in Synechococcus sp.; whereas, upregulated carotenoid protein contributed to antibiotic biodegradation in Chroococcus sp. The 4-day removal efficiencies of sulfamethoxazole and ofloxacin by cyanobacteria were 35.98-66.23% and 33.01-61.92%, respectively. In cyanobacteria, each antibiotic induced hormetic responses, such as increase in cell density, dry cell weight, and photosynthetic activity; upregulation of photosynthesis-related proteins; and elevation of lipid expression by up to 2.05-fold. Under antibiotic stress, the two cyanobacterial species preferred to store energy in the form of lipids rather than ATP, with fructose-bisphosphate aldolase playing an essential role in lipid synthesis. The downregulation of lipid transporters also facilitated lipid accumulation in Synechococcus sp. In general, the two non-toxic cyanobacterial species achieved a good combination of lipid deposition and antibiotic treatment performance, especially in Chroococcus sp. exposed to sulfamethoxazole.

Experimental design considerations for studies of human tear proteins

PURPOSE

Human tears contain abundant, diverse sets of proteins that may serve as biomarkers of ocular surface health. There is a need for reproducible methods that consider multiple factors influencing the tear proteome, in addition to the variable of interest. Here we examined a workflow for proteomic analysis of tear proteins without the need to pool tear samples from multiple individuals, thus allowing for analyses based on individual factors, and increasing opportunities for protein biomarker discovery.

METHODS

Tears were collected by Schirmer strip following topical ocular anesthetic application then individually stored at -80 °C prior to processing for proteomics. Tear proteins were extracted from Schirmer strips, digested using suspension trapping spin columns (S-Trap), and labeled with high multiplicity tandem mass tags (TMT). Peptide digests were then extensively fractionated by two-dimensional chromatography and analyzed by mass spectrometry to identify and measure changes in protein abundance in each sample. Analysis of select samples was performed to test protocols and to compare the impact of clinically relevant parameters. To facilitate comparison of separate TMT experiments, common pool samples were included in each TMT instrument run and internal reference scaling (IRS) was performed.

RESULTS

Differences in subsets of tear proteins were noted for: geographic site of tear collection, contact lens use, and differences in tear fluid volume among individuals.

CONCLUSION

These findings demonstrate that proteomic analysis of human tear proteins can be performed without the need to pool samples, and that development of analytic workflows must consider factors that may affect outcomes in studies focused on diverse clinical samples.

Chronic stress targets mitochondrial respiratory efficiency in the skeletal muscle of C57BL/6 mice

Episodes of chronic stress can result in psychic disorders like post-traumatic stress disorder, but also promote the development of metabolic syndrome and type 2 diabetes. We hypothesize that muscle, as main regulator of whole-body energy expenditure, is a central target of acute and adaptive molecular effects of stress in this context. Here, we investigate the immediate effect of a stress period on energy metabolism in Musculus gastrocnemius in our established C57BL/6 chronic variable stress (Cvs) mouse model. Cvs decreased lean body mass despite increased energy intake, reduced circadian energy expenditure (EE), and substrate utilization. Cvs altered the proteome of metabolic components but not of the oxidative phosphorylation system (OXPHOS), or other mitochondrial structural components. Functionally, Cvs impaired the electron transport chain (ETC) capacity of complex I and complex II, and reduces respiratory capacity of the ETC from complex I to ATP synthase. Complex I-OXPHOS correlated to diurnal EE and complex II-maximal uncoupled respiration correlated to diurnal and reduced nocturnal EE. Bioenergetics assessment revealed higher optimal thermodynamic efficiencies (ƞ-opt) of mitochondria via complex II after Cvs. Interestingly, transcriptome and methylome were unaffected by Cvs, thus excluding major contributions to supposed metabolic adaptation processes. In summary, the preclinical Cvs model shows that metabolic pressure by Cvs is initially compensated by adaptation of mitochondria function associated with high thermodynamic efficiency and decreased EE to manage the energy balance. This counter-regulation of mitochondrial complex II may be the driving force to longitudinal metabolic changes of muscle physiological adaptation as the basis of stress memory.

A serum protein signature at the time of Uveal Melanoma diagnosis predicts long-term patient survival

PURPOSE

To develop a prognostic test based on a single blood sample obtained at the time of uveal melanoma diagnosis.

METHODS

83 patients diagnosed with posterior uveal melanoma between 1996 and 2000 were included. Peripheral serum samples were obtained at diagnosis and kept at -80 °C until this analysis. Protein profiling of 84 cancer-related proteins was used to screen for potential biomarkers and a prognostic test that stratifies patients into metastatic risk categories was developed (serUM-Px) in a training cohort and then tested in a validation cohort.

RESULTS

Low serum leptin levels and high osteopontin levels were found to identify patients with poor prognosis and were therefore selected for inclusion in the final test. In the validation cohort, patient sex and American Joint Committee on Cancer stages were similarly distributed between the low, intermediate, and high metastatic risk categories. With increasing metastatic risk category, patients had shorter metastasis-free- and overall survival, as well as greater cumulative incidence of uveal melanoma-related mortality in competing risk analysis (P = 0.007, 0.018 and 0.029, respectively). In multivariate Cox regression, serUM-Px was an independent predictor of metastasis with tumor size and patient sex as covariates (hazard ratio 3.2, 95% CI 1.5-6.9).

CONCLUSIONS

A prognostic test based on a single peripheral venous blood sample at the time of uveal melanoma diagnosis stratifies patients into low, intermediate, and high metastatic risk categories. Prospective validation will facilitate its clinical utility.

Morphological alterations in corneal nerves of patients with dry eye and associated biomarkers

The purposes of the present study were to (1) identify the relationship between dry eye symptoms and morphological changes in corneal subbasal nerves/ocular surfaces, and (2) discover tear film biomarkers indicating morphological changes in the subbasal nerves. This was a prospective cross-sectional study conducted between October and November 2017. Adults with dry eye disease (DED, n = 43) and healthy eyes (n = 16) were evaluated based on their subjective symptoms and ophthalmological findings. Corneal subbasal nerves were observed using confocal laser scanning microscopy. Nerve lengths, densities, branch numbers, and nerve fiber tortuosity were analyzed using ACCMetrics and CCMetrics image analysis systems; tear proteins were quantified by mass spectroscopy. Compared with the control group, the DED group had significantly lower tear breakup times (TBUT) and pain tolerance capacity, and significantly higher corneal nerve branch density (CNBD) and corneal nerve total branch density (CTBD). CNBD and CTBD showed significant negative correlations with TBUT. Six biomarkers (cystatin-S, immunoglobulin kappa constant, neutrophil gelatinase-associated lipocalin, profilin-1, protein S100-A8, and protein S100-A9) showed significant positive correlations with CNBD and CTBD. The significantly higher CNBD and CTBD in the DED group suggests that DED is associated with morphological alterations in corneal nerves. The correlation of TBUT with CNBD and CTBD further supports this inference. Six candidate biomarkers that correlate with morphological changes were identified. Thus, morphological changes in corneal nerves are a hallmark of DED, and confocal microscopy may help in the diagnosis and treatment of dry eyes.

Proteomic analysis reveals the non-coding small RNA Qrr5 influences autoaggregation and growth competition in Vibrio parahaemolyticus

Vibrio parahaemolyticus, a sea-born bacterial pathogen, is a primary inducement of food-borne gastroenteritis. Previous studies have shown that non-coding small RNA plays a vital role in the regulation of multiple biological processes in pathogenic bacteria, especially autoaggregation and growth competition. However, the inherent mechanisms have not yet to be fully understood. As important regulators in Vibrios, the involvement of Qrr sRNAs in V. parahaemolyticus is largely unknown. Here, we carried out the Qrr5 deletion mutant and utilized a proteomic method to describe global proteomic alterations in response to Qrr5 deletion. A total of 297 significantly expressed proteins were determined between the Qrr5 deletion mutant and wild-type strain, among which 137 proteins were upregulated and 160 proteins were downregulated. The upregulated proteins principally participated in membrane transporters and signal transcription, while the downregulated proteins participated in the two-component system and transcription factor binding. Notably, transcriptional regulator LysR, outer membrane protein OmpA, and conjugal transfer protein TraA-related proteins were upregulated, causing the promotion of autoaggregation ability and growth competition ability against E. coli. This study provides insights into the regulatory network of sRNA in this bacterium, which will facilitate further explorations of important biological processes in pathogenic bacteria. SIGNIFICANCE: sRNA Qrr5 is an important regulator involved in bacterial multiple physiological processes, including auto-aggregation and growth competition among food-borne pathogens Vibrio parahaemolyticus. Here, utilizing a TMT-labeling proteomic approach, we identified 137 proteins were upregulated and 160 proteins were downregulated between the Qrr5 deletion mutant and wild-type strain. The upregulated proteins were involved in membrane transporters and signal transcription, while downregulated proteins were involved in the two-component system and transcription factor binding. Moreover, the LysR, OmpA, and TraA proteins were significantly upregulated, causing the promotion of autoaggregation and commensal growth competition ability. The mechanism of how Qrr5 regulates the targeted genes remains unclarified and need great efforts to explore.

Comparative Analyses of Human Exosome Proteomes

Exosomes are responsible for cell-to-cell communication and serves as a valuable drug delivery vehicle. However, exosome heterogeneity, non-standardized isolation methods and proteomics/bioinformatics approaches limit its clinical applications. To better understand exosome heterogeneity, biological function and molecular mechanism of its biogenesis, secretion and uptake, techniques in proteomics or bioinformatics were applied to investigate human embryonic kidney cell (293T cell line)-derived exosome proteome and enable an integrative comparison of exosomal proteins and protein-protein interaction (PPI) networks of eleven exosome proteomes extracted from diverse human samples, including 293T (two datasets), dermal fibroblast, mesenchymal stem cell, thymic epithelial primary cell, breast cancer cell line (MDA-MB-231), patient neuroblastoma cell, plasma, saliva, serum and urine. Mapping of exosome biogenesis/secretion/uptake-related proteins onto exosome proteomes highlights exosomal origin-specific routes of exosome biogenesis/secretion/uptake and exosome-dependent intercellular communication. The finding provides insight into comparative exosome proteomes and its biogenesis, secretion and uptake, and potentially contributes to clinical applications.

Venom comparisons of endemic and micro-endemic speckled rattlesnakes Crotalus mitchellii, C. polisi and C. thalassoporus from Baja California Peninsula

A high diversity of rattlesnake species can be found in the Baja California peninsula and the island of the Gulf of California, nevertheless, their venom has been poorly evaluated. The aim of this work was to present the first characterization of endemic Crotalus mitchellii, micro endemic C. polisi and C. thalassoporus venoms. All samples provoke human plasma coagulation showing doses in the rank of 2.3-41.0 μg and also produce rapid hydrolysis of the alpha chain of bovine fibrinogen while the beta chain is attacked at larger incubation periods by C. polisi and especially by C. thalassoporus. Phospholipase activity ranging from 23.2 to 173.8 U/mg. The venoms of C. thalassoporus and C. polisi show very high hemorrhagic activity (from 0.03 to 0.31 μg). A total of 130 toxin-related proteins were identified and classified into ten families. Crotalus mitchellii venom was characterized by high abundance of crotoxin-like and other phospholipase proteins (34.5%) and serine proteinases (29.8%). Crotalus polisi showed a similar proportion of metalloproteinases (34%) and serine proteinases (22.8%) components with important contribution of C-type lectins (14.3%) and CRiSP (14.0%) proteins. Venom of C. thalassoporus is dominated by metalloproteases that amount to more than 66% of total toxin proteins. These results provide a foundation for comprehending the biological, ecological and evolutionary significance of venom composition of speckled rattlesnake from the Baja California peninsula.

Proteome derangement in malignant epithelial cells and its stroma following exposure to 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone

Discovering novel changes in the proteome of malignant lung epithelial cells and/or the tumor-microenvironment is paramount for diagnostic, prognostic, and/or therapy development. A time-dependent 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK)-induced mouse lung tumor model was used to screen the proteome of lung tumors. NNK-transformed human lung epithelial BEAS-2B cells were then established to evaluate the epithelial cell-specific protein changes. A duration-dependent increase of tumor burden was observed in NNK-treated mice, 2/12 (17%), 8/12 (67%), 9/12 (75%), and 10/10 (100%) at weeks 8, 12, 16, and 20 after the NNK exposure, respectively. A total of 25 differentially expressed proteins (≥ twofold change), predominantly structural, signaling, and metabolic proteins, were detected by two-dimensional difference gel electrophoresis and identified by mass spectrometry. Calregulin, ezrin, histamine releasing factor (HRF), and inorganic pyrophosphatase 1 (PPA1) exhibited changes and were further confirmed via immunoblotting. In addition, immunohistochemistry (IHC) analysis indicated upregulated E-cadherin and decreased vimentin expression in epithelial cells of tumor tissues. Acquisition of a neoplastic phenotype in NNK-transformed BEAS-2B cells was demonstrated by enhanced wound closure and increased anchorage independent colony formation. In transformed BEAS-2B cells, protein expression of E-cadherin, ezrin, and PPA1 (but not calregulin and HRF) was upregulated, as was observed in tumor tissues IHC staining using mouse lung tumor tissues further revealed that HRF upregulation was not lung epithelial cell specific. Altogether, tumorigenesis after NNK exposure may be initiated by protein dysregulation in lung epithelial cells together with proteome derangement derived from other cell types existing in the tumor-microenvironment.

Proteome-Wide Discovery of Cortical Proteins That May Provide Motor Resilience to Offset the Negative Effects of Pathologies in Older Adults

BACKGROUND

Motor resilience proteins have not been identified. This proteome-wide discovery study sought to identify proteins that may provide motor resilience.

METHODS

We studied the brains of older decedents with annual motor testing, postmortem brain pathologies, and proteome-wide data. Parkinsonism was assessed using 26 items of a modified United Parkinson Disease Rating Scale. We used linear mixed-effect models to isolate motor resilience, defined as the person-specific estimate of progressive parkinsonism after controlling for age, sex, and 10 brain pathologies. A total of 8 356 high-abundance proteins were quantified from dorsal lateral prefrontal cortex using tandem mass tag and liquid chromatography-mass spectrometry.

RESULTS

There were 391 older adults (70% female), mean age 80 years at baseline and 89 years at death. Five proteins were associated with motor resilience: A higher level of AP1B1 (Estimate -0.504, SE 0.121, p = 3.12 × 10-5) and GNG3 (Estimate -0.276, SE 0.068, p = 4.82 × 10-5) was associated with slower progressive parkinsonism. By contrast, a higher level of TTC38 (Estimate 0.140, SE 0.029, p = 1.87 × 10-6), CARKD (Estimate 0.413, SE 0.100, p = 3.50 × 10-5), and ABHD14B (Estimate 0.175, SE 0.044, p = 6.48 × 10-5) was associated with faster progressive parkinsonism. Together, these 5 proteins accounted for almost 25% of the variance of progressive parkinsonism above the 17% accounted for by 10 indices of brain pathologies.

DISCUSSION

Cortical proteins may provide more or less motor resilience in older adults. These proteins are high-value therapeutic targets for drug discovery that may lead to interventions that maintain motor function despite the accumulation of as yet untreatable brain pathologies.

Adiponectin can be a good predictor of urodynamic detrusor underactivity: a prospective study in men with lower urinary tract symptoms

PURPOSE

To investigate whether circulating adiponectin, which is considered a possible marker of anti-atherogenic effects, is a useful predictor of bladder function, especially detrusor underactivity (DU), in men with lower urinary tract symptoms (LUTS).

METHODS

A total of 130 treatment-naïve men with non-neurogenic LUTS were prospectively stratified into two groups (the DU and non-DU groups) based on the presence or absence of DU, where DU is defined as a bladder contractility index < 100 and bladder outlet obstruction index (BOOI) < 40. The impact of serum adiponectin levels on urodynamic function, including DU, was assessed using univariate, binomial logistic regression, and receiver operating characteristic (ROC) curve analyses.

RESULTS

In total, data from 118 men were analyzed; 39 (33.0%) had DU (DU group) and 79 (67.0%) did not have DU (non-DU group). The median serum adiponectin in the DU group was significantly lower than in the non-DU group (6.2 vs 12.6 µg/mL, p < 0.001). In the binomial logistic regression analysis, lower adiponectin, smaller intravesical prostatic protrusion, and lower bladder voiding efficiency were significant factors related to DU. In the ROC analyses, serum adiponectin had the highest area under the curve value for DU diagnosis (0.849). Additionally, a cutoff value of 7.9 µg/mL for serum adiponectin level was identified for DU, which yielded a sensitivity and specificity of 79% and 90%, respectively.

CONCLUSIONS

The serum adiponectin level was significantly associated with bladder function and may be a useful marker for predicting DU in men with LUTS.

Changes on proteomic and metabolomic profiling of cryopreserved sperm effected by melatonin

Cryopreservation may reduce sperm fertility due to cryodamage including physical-chemical and oxidative stress damages. As a powerful antioxidant, melatonin has been reported to improve cryoprotective effect of sperm. However, the molecular mechanism of melatonin on cryopreserved ram sperm hasn't been fully understand. Give this, this study aimed to investigate the postthaw motility parameters, antioxidative enzyme activities and lipid peroxidation, as well as proteomic, metabolomic changes of Huang-huai ram spermatozoa with freezing medium supplemented with melatonin. Melatonin was firstly replenished to the medium to yield five different final concentrations: 0.1, 0.5, 1.0, 1.5, and 2.0 mM. A control (NC) group without melatonin replenishment was included. Protective effects of melatonin as evidenced by postthaw motility, activities of T-AOC, T-SOD, GSH-Px, CAT, contents of MDA, 4-HNE, as well as acrosome integrity, plasma membrane integrity, with 0.5 mM being the most effective concentration (MC group). Furthermore, 29 differentially abundant proteins involving in sperm functions were screened among Fresh, NC and MC groups of samples (n = 5) based on the 4D-LFQ, with 7 of them upregulated in Fresh and MC groups. 26 differentially abundant metabolites were obtained involving in sperm metabolism among the three groups of samples (n = 8) based on the UHPLC-QE-MS, with 18 of them upregulated in Fresh and MC groups. According to the bioinformatic analysis, melatonin may have positive effects on frozen ram spermatozoa by regulating the abundance changes of vital proteins and metabolites related to sperm function. Particularly, several proteins such as PRCP, NDUFB8, NDUFB9, SDHC, DCTN1, TUBB6, TUBA3E, SSNA1, as well as metabolites like L-histidine, L-targinine, ursolic acid, xanthine may be potential novel biomarkers for evaluating the postthaw quality of ram spermatozoa. In conclusion, a dose-dependent replenishment of melatonin to freezing medium protected ram spermatozoa during cryopreservation, which can improve motility, antioxidant enzyme activities, reduce levels of lipid peroxidation products, modify the proteomic and metabolomic profiling of cryopreserved ram spermatozoa through reduction of oxidative stress, maintenance of OXPHOS and microtubule structure. SIGNIFICANCE: Melatonin, a powerful antioxidant protects ram spermatozoa from cryopreservation injuries in a dose-dependent manner, with 0.5 mM being the most effective concentration. Furthermore, sequencing results based on the 4D-LFQ combined with the UHPLC-QE-MS indicated that melatonin modifies proteomic and metabolomic profiling of ram sperm during cryopreservation. According to the bioinformatic analysis, melatonin may have positive effects on frozen ram spermatozoa by regulating the expression changes of vital proteins and metabolites related to sperm metabolism and function. Particularly, several potential novel biomarkers for evaluating the postthaw quality of ram spermatozoa were acquired, proteins such as PRCP, NDUFB8, NDUFB9, SDHC, DCTN1, TUBB6, TUBA3E, SSNA1, as well as metabolites like L-histidine, L-targinine, ursolic acid, xanthine.

TMT-based comparative proteomic analysis of Dezhou donkey spermatozoa related to freezability

The freezability difference between donkey ejaculates is a limiting factor of sperm cryopreservation. Our recent study shows that the freezability of donkey semen is related to the seminal plasma proteome. In this study, we aimed to identify the different abundance sperm proteins in good freezability ejaculates (GFEs) and poor freezability ejaculates (PFEs) using a Tandem Mass Tag (TMT) peptide labeling coupled with LC-MS/MS approach. A total of 2682 proteins were identified, among which 58 were significantly up-regulated in GFEs and 16 were down-regulated compared with PFEs. Bioinformatic analysis results revealed that the majority of different abundance proteins (DAPs) participated in copper and calcium binding, regulation of RNA biosynthetic process, positive regulation of innate immune response, and negative regulation of programmed cell death. KEGG pathway enrichment analysis showed the up-regulated proteins in GF group were mainly involved in N-Glycan biosynthesis and protein processing in endoplasmic reticulum. Our study was the first to analyze the proteome of sperm from donkey ejaculates with different freezabilities. The identified candidate proteins might be used to explore the molecular mechanism related to donkey sperm cryotolerance and might improve the screening of jacks with good sperm freezability. SIGNIFICANCE: Cryopreserved semen has been widely used in assisted reproductive technology. However, semen cryopreservation is a damaging process, which can cause oxidative stress, reduce sperm motility and motility. There are differences in sperm freezability reported to exist between or within breeds, and even between fractions coming from the same ejaculate. The freezability difference between donkey ejaculates is a limiting factor of sperm cryopreservation. The mechanisms that affect the freezing difference in sperm quality remain to be investigated, and freezability differences was found to be related to protein composition of spermatozoa. Some protein markers that can indicate good freezability or poor freezability semen have been identified in mammals. Until now, there is no information about the relationship between donkey spermatozoa proteome and freezability. Additional novel biomarkers of semen freezability in donkey spermatozoa are also needed. The identified candidate proteins might be used to explore the molecular mechanism related to donkey sperm cryotolerance and might improve the screening of jacks with good sperm freezability.

OSppc: A web server for online survival analysis using proteome of pan-cancers

Prognostic biomarker, as a feasible and objective indicator, is valuable in the assessment of cancer risk. With the development of high-throughput sequencing technology, the screening of prognostic biomarkers has become easy, but it is difficult to screen prognostic markers based on proteomic data. In this study we developed a tool named Online consensus Survival analysis web server based on Proteome of Pan-cancers, abbreviated as OSppc, to evaluate the prognostic values of protein biomarkers. >8000 cancer cases with proteomic data, transcriptomic data and clinical follow-up information were collected from TCGA and CPTAC. 14,038 proteins (including proteins and their phosphorylated forms) analyzed by reverse-phase protein arrays and mass spectrometry in 33 types of cancers were collected. In OSppc, three analysis modules are provided, including Survival Analysis, Differential Analysis and Correlation Analysis. Survival analysis module exhibits HR with 95% CI and KM curves with log-rank p value of protein and mRNA levels of input genes. Differential analysis module shows the box plots of protein expression levels in different tissues. Correlation analysis module provides scatter plot with pearson's and spearman's correlation coefficient of the protein and its corresponding mRNA. OSppc can be accessed at http://bioinfo.henu.edu.cn/Protein/OSppc.html. SIGNIFICANCE: OSppc can analyze the association between protein, mRNA and prognosis, the correlation between proteome data and gene expression profiles, the differential expression of proteome data between subgroups such as normal and cancer as well. OSppc is registration-free and very valuable to evaluate the prognostic potency of protein of interests. OSppc is very valuable for researchers and clinicians to screen, develop and validate potential protein prognostic biomarkers in pan-cancers, and offers the opportunities to investigate the clinical important functional genes and therapeutic targets of cancers.

Systemic proinflammatory-profibrotic response in aortic stenosis patients with diabetes and its relationship with myocardial remodeling and clinical outcome

BACKGROUND

Previous studies have mainly focused more on how diabetes affects the valve than the myocardium in aortic stenosis (AS). In the pressure-overloaded heart, myocardial fibrosis is an important driver of the progression from compensated hypertrophy to heart failure. Using comprehensive noninvasive imaging and plasma proteomics, we investigated whether and how diabetes aggravates the remodeling of the myocardium and its relation with prognosis in AS patients.

METHODS

Severe AS patients were enrolled in two prospective cohorts for imaging and biomarker analysis. The imaging cohort (n = 253) underwent echocardiography and cardiac magnetic resonance, and the biomarker cohort (n = 100) blood sampling with multiplex proximity extension assay for 92 proteomic biomarkers. The composite outcome of hospitalization for heart failure admissions and death was assessed in the imaging cohort.

RESULTS

Diabetic patients were older (70.4 ± 6.8 versus 66.7 ± 10.1 years) with more advanced ventricular diastolic dysfunction and increased replacement and diffuse interstitial fibrosis (late gadolinium enhancement % 0.3 [0.0-1.6] versus 0.0 [0.0-0.5], p = 0.009; extracellular volume fraction % 27.9 [25.7-30.1] versus 26.7 [24.9-28.5], p = 0.025) in the imaging cohort. Plasma proteomics analysis of the biomarker cohort revealed that 9 proteins (E-selectin, interleukin-1 receptor type 1, interleukin-1 receptor type 2, galectin-4, intercellular adhesion molecule 2, integrin beta-2, galectin-3, growth differentiation factor 15, and cathepsin D) were significantly elevated and that pathways related to inflammatory response and extracellular matrix components were enriched in diabetic AS patients. During follow-up (median 6.3 years), there were 53 unexpected heart failure admissions or death in the imaging cohort. Diabetes was a significant predictor of heart failure and death, independent of clinical covariates and aortic valve replacement (HR 1.88, 95% CI 1.06-3.31, p = 0.030).

CONCLUSIONS

Plasma proteomic analyses indicate that diabetes potentiates the systemic proinflammatory-profibrotic milieu in AS patients. These systemic biological changes underlie the increase of myocardial fibrosis, diastolic dysfunction, and worse clinical outcomes in severe AS patients with concomitant diabetes.

Improving the genome and proteome annotations of the marine model diatom Thalassiosira pseudonana using a proteogenomics strategy

Diatoms are unicellular eukaryotic phytoplankton that account for approximately 20% of global carbon fixation and 40% of marine primary productivity; thus, they are essential for global carbon biogeochemical cycling and climate. The availability of ten diatom genome sequences has facilitated evolutionary, biological and ecological research over the past decade; however, a complimentary map of the diatom proteome with direct measurements of proteins and peptides is still lacking. Here, we present a proteome map of the model marine diatom Thalassiosira pseudonana using high-resolution mass spectrometry combined with a proteogenomic strategy. In-depth proteomic profiling of three different growth phases and three nutrient-deficient samples identified 9526 proteins, accounting for ~ 81% of the predicted protein-coding genes. Proteogenomic analysis identified 1235 novel genes, 975 revised genes, 104 splice variants and 234 single amino acid variants. Furthermore, our quantitative proteomic analysis experimentally demonstrated that a considerable number of novel genes were differentially translated under different nutrient conditions. These findings substantially improve the genome annotation of T. pseudonana and provide insights into new biological functions of diatoms. This relatively comprehensive diatom proteome catalog will complement available diatom genome and transcriptome data to advance biological and ecological research of marine diatoms.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00161-y.

Proteome-Wide Mendelian Randomization Identifies Causal Links Between Blood Proteins and Acute Pancreatitis

BACKGROUND & AIMS

Acute pancreatitis (AP) is a complex disease and the leading cause of gastrointestinal disease-related hospital admissions. Few therapeutic options exist for AP prevention. Blood proteins with causal evidence may represent promising drug targets, but few have been causally linked with AP. Our objective was to identify blood proteins linked with AP by combining genome-wide association meta-analysis and proteome-wide Mendelian randomization (MR) studies.

METHODS

We performed a genome-wide association meta-analysis totalling 10,630 patients with AP and 844,679 controls and a series of inverse-variance weighted MR analyses using cis-acting variants on 4719 blood proteins from the deCODE study (n = 35,559) and 4979 blood proteins from the Fenland study (n = 10,708).

RESULTS

The meta-analysis identified genome-wide significant variants (P <5 × 10^-8) at 5 loci (ABCG5/8, TWIST2, SPINK1, PRSS2 and MORC4). The proteome-wide MR analyses identified 68 unique blood proteins that may causally be associated with AP, including 29 proteins validated in both data sets. Functional annotation of these proteins confirmed expression of many proteins in metabolic tissues responsible for digestion and energy metabolism, such as the esophagus, adipose tissue, and liver as well as acinar cells of the pancreas. Genetic colocalization and investigations into the druggable genome also identified potential drug targets for AP.

CONCLUSIONS

This large genome-wide association study meta-analysis for AP identified new variants linked with AP as well as several blood proteins that may be causally associated with AP. This study provides new information on the genetic architecture of this disease and identified pathways related to AP, which may be further explored as possible therapeutic targets for AP.

Linalool controls the viability of Escherichia coli by regulating the synthesis and modification of lipopolysaccharide, the assembly of ribosome, and the expression of substrate transporting proteins

Escherichia coli (E. coli) is a Gram-negative bacterium and some pathogenic types may cause serious diseases, foods or food environments were the primary routes for its infection. Citrus aurantium L. var. amara Engl., a variety of sour orange, were used as a kind of non-conventional edible plant in China, but its antimicrobial activity and mechanisms were not well studied. Thus, in this study, EO from the flower of Citrus aurantium L. var. amara Engl. (CAEO) were studied as a kind of natural antimicrobial agent to control E. coli, our results showed that both of CAEO and its main component (linalool) exhibited strong antibacterial efficacy. Further, transcriptomic and proteomic analysis were carried out to explore cell response under linalool treatment and the main results included: (1) The synthesis and modification of lipopolysaccharide (LPS) was significantly influenced. (2) Ribosomal assembly and protein synthesis were significantly inhibited. (3) The expression of proteins related to the uptake of several essential substances was significantly changed. In all, our results would supply a theoretical basis for the proper use of CAEO and linalool as a promising antimicrobial agent to prevent and control E. coli infection in the future.

Functional pleiotropy of calcium binding protein Regucalcin in signaling and diseases

Regucalcin (Mr ∼ 33.38 kDa) is a calcium binding protein, discovered in rat liver. In humans, gene for regucalcin is located on chromosome-11 (p11.3-q11.2) consisting of seven exons and six introns. The protein differs from other calcium binding protein in the way that it lacks EF-hand motif of calcium binding domain. It is also called as Senescence Marker Protein-30 (SMP-30) as previously its weight assumes to be 30 kDa and expression of this protein decreases with aging in androgen independent manner. Among vertebrates, it is a highly conserved protein showing gene homology in Drosophila, Xenopus, fireflies and others too. It is primarily expressed in liver and kidney in addition to brain, lungs, and skeletal muscles. Regucalcin acts as a Ca²⁺ regulatory protein and controls various cellular functions in liver and other organs. It suppresses protein phosphatase, protein kinase, DNA and RNA synthesis. Published evidences suggest regucalcin to be a reliable biomarker in various disorders of liver, kidney, brain and ocular. In over expressed state, it subdues apoptosis in cloned rat hepatoma cells and also induces hyperlipidemia and osteoblastogenesis by regulating various factors. Owing to the multi-functionality of regucalcin this review is presented to elaborate its importance in order to understand its involvement in cellular signaling during various pathologies.

Influence of sex, age and diabetes on brain transcriptome and proteome modifications following cerebral ischemia

Ischemic stroke is a major cause of death and disability worldwide. Translation into the clinical setting of neuroprotective agents showing promising results in pre-clinical studies has systematically failed. One possible explanation is that the animal models used to test neuroprotectants do not properly represent the population affected by stroke, as most of the pre-clinical studies are performed in healthy young male mice. Therefore, we aimed to determine if the response to cerebral ischemia differed depending on age, sex and the presence of comorbidities. Thus, we explored proteomic and transcriptomic changes triggered during the hyperacute phase of cerebral ischemia (by transient intraluminal middle cerebral artery occlusion) in the brain of: (1) young male mice, (2) young female mice, (3) aged male mice and (4) diabetic young male mice. Moreover, we compared each group's proteomic and transcriptomic changes using an integrative enrichment pathways analysis to disclose key common and exclusive altered proteins, genes and pathways in the first stages of the disease. We found 61 differentially expressed genes (DEG) in male mice, 77 in females, 699 in diabetics and 24 in aged mice. Of these, only 14 were commonly dysregulated in all groups. The enrichment pathways analysis revealed that the inflammatory response was the biological process with more DEG in all groups, followed by hemopoiesis. Our findings indicate that the response to cerebral ischemia regarding proteomic and transcriptomic changes differs depending on sex, age and comorbidities, highlighting the importance of incorporating animals with different phenotypes in future stroke research studies.

Comparison of urine proteomes from tumor-bearing mice with those from tumor-resected mice

Objective

This study aimed to address on the most important concern of surgeons-whether to completely resect tumor. Urine can indicate early changes associated with physiological or pathophysiological processes. Based on these ideas, we conducted experiments to explore changes in the urine proteome between tumor-bearing mice and tumor-resected mice.

Method

The tumor-bearing mouse model was established with MC38 mouse colon cancer cells, and the mice were divided into the control group, tumor-resected group, and tumor-bearing group. Urine was collected 7 and 30 days after tumor resection. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used to identify the urine proteome, which was analyzed for differentially expressed proteins and functional annotation.

Results

(1) Seven days after tumor resection, 20 differentially expressed proteins distinguished the tumor-resected group and the tumor-bearing group. The identified biological processes included circadian rhythm, Notch signaling pathway, leukocyte cell-cell adhesion, and heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules. (2) Thirty days after tumor resection, 33 differentially expressed proteins distinguished the tumor-resected group and the tumor-bearing group. The identified biological processes included cell adhesion; complement activation, the alternative pathway; the immune system process; and angiogenesis. (3) The difference in the urine proteome between the tumor-resected group and the healthy control group was smaller 30 days after tumor resection.

Conclusion

Changes in the urinary proteome can reflect the complete resection of MC38 tumors.

Proteomic analysis of postprandial high-density lipoproteins in healthy subjects

The relationship between the functionality and composition of high-density lipoproteins (HDL) is yet not fully studied, and little is known about the influence of the diet in HDL proteome. Therefore, the aim of this research was to elucidate the HDL proteome associated to postprandial hyperlipidemia. Male volunteers were recruited for an interventional study with high fatty acid-based meals. Blood samples were collected before the intake (baseline), and 2-3 (postprandial peak) and 5-6 (postprandial post peak) hours later. HDL were purified and the protein composition was quantified by LC-MS/MS. Statistical analysis was performed by lineal models (amica) and by ANOVA and multi-t-test of the different conditions (MetaboAnalyst). Additionally, a clustering of the expression profiles of each protein was done with coseq R package (RStudio). Initially, 320 proteins were identified but only 119 remained after the filtering. APOM, APOE, APOB, and APOA2, proteins previously identified in the HDL proteome, were the only proteins with a statistically significant altered expression in postprandial hyperlipidemia when compared to baseline (p values <0.05 and logFC >1). In conclusion, we have been able to describe several behaviors of the whole HDL proteome during the postprandial hyperlipidemic metabolism.

Proteomics dataset on detached and purified Arabidopsis thaliana rosette leaf trichomes

Trichomes are highly specialized uni- or multicellular outgrowths of epidermal cells of plant organs that, in the case of leaves, contribute to plant resistance against abiotic and biotic stress. The model plant Arabidopsis thaliana features single-celled non-glandular rosette leaf trichomes that are dispensable under laboratory conditions. Trichomes have therefore become a successful model to identify plant genes involved in cellular differentiation and cell wall development. We have recently devised an improved method for the enrichment of plant leaf trichomes that relies on the biochemical weakening of the trichome-leaf junctions and a magnetic stirrer-based mechanical stimulus for trichome release followed by density gradient purification of trichomes. Here we provide detailed information on a label-free quantitative (LFQ) shotgun proteomics dataset collected at four stages while applying this protocol to isolate trichomes from rosette leaves of A. thaliana, from (i) whole seedlings before enrichment, from (ii) trichome-depleted material after separation, from (iii) detached trichomes, and from (iv) enriched trichomes after sucrose density gradient centrifugation. Proteins were extracted, digested with trypsin and the resulting peptides identified by nanoflow-chromatography coupled to tandem mass spectrometry. This dataset informs on proteins and biochemical processes present and/or enriched in A. thaliana rosette leaf trichomes, complementing recent large-scale proteome maps. The data further enables comparative analysis with trichome proteomic data from other plant species, may be reanalyzed using different software packages or search settings, and may serve as a reference benchmark for future method refinement.

Proteome profiling of ductal carcinoma in situ

BACKGROUND AND AIM

DCIS is the most common type of non-invasive breast cancer, accounting for about 15 to 30%. Proteome profile is used to detect biomarkers in the tissues of breast cancer patients by mass spectrometry. This study aimed to obtain the expression profile of DCIS proteome, and the expression profile of invasive biomarkers, and finally to introduce a dedicated biomarker panel to facilitate the prognosis and early detection for in situ breast cancer patients.

METHODS AND MATERIALS

In this study, 10 patients with breast cancer (DCIS) were studied. Benign (marginal) and cancerous tissue samples were obtained from patients for proteomics experiments. Initially, all tissue proteins were extracted using standard methods, and the proteins were separated using two-dimensional electrophoresis. Then, the expression amount of the extracted proteins was determined by ITRAQ. The data were analysed by R software, and gene ontology was utilised for describing the protein in detail.

RESULTS

30 spots on gel electrophoresis were found in the tumor tissue group (sample), and 15 spots in the margin group (control) with P < 0.05. Healthy and cancerous tissue gels showed that 5 spots had different expression. VWF, MMP9, ITGAM, MPO and PLG protein spots were identified using the site www.ebi.ac.uk/IPI. Finally, protein biomarkers for breast tumor tissue with margin were introduced with the names of P04406, P49915, P05323, P06733, and P02768.

DISCUSSION

There are 5 critical proteins in inducing cancer pathways especially complement and coagulation cascades. The hall markers of a healthy cell to be cancerous are proliferation, invasion, angiogenesis, and changes in the immune system. Hence, regulation of protein plays a key role in developing recurrence to breast cancer in margins.

Comparative proteomic analysis of seminal plasma exosomes in buffalo with high and low sperm motility

BACKGROUND

Exosomes are nanosized membranous vesicles secreted by various types of cells, which facilitate intercellular communication by transporting bioactive compounds. Exosomes are abundant in biological fluids including semen, and their protein composition and the potential of seminal plasma exosomes (SPEs) as fertility biomarkers were elucidated in humans, however, little information is available regarding buffalo (Bubalus bubalis). Here, we examined protein correlation between spermatozoa, seminal plasma (SP), and SPEs, and we compared and analyzed protein differences between high-motility (H-motility) and low-motility (L-motility) SPEs in buffalo.

RESULTS

SPEs were concentrated and purified by ultracentrifugation combined with sucrose density gradient centrifugation, followed by verification using western blotting, nanoparticle tracking analysis, and transmission electron microscopy. Protein composition in spermatozoa, SP and SPEs, and protein difference in H- and L-motility SPEs were identified by LC-MS/MS proteomic analysis and were functionally analyzed through comprehensive bioinformatics. Many SPEs proteins originated from spermatozoa and SP, and nearly one third were also present in spermatozoa and SP. A series of proteins associated with reproductive processes including sperm capacitation, spermatid differentiation, fertilization, sperm-egg recognition, membrane fusion, and acrosome reaction were integrated in a functional network. Comparative proteomic analyses showed 119 down-regulated and 41 up-regulated proteins in L-motility SPEs, compared with H-motility SPEs. Gene Ontology (GO) enrichment of differentially expressed proteins (DEPs) showed that most differential proteins were located in sperm and vesicles, with activities of hydrolase and metalloproteinase, and were involved in sperm-egg recognition, fertilization, single fertilization, and sperm-zona pellucida binding processes, etc. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that differential proteins were mainly involved in the PPRP signaling pathway, calcium signaling pathway, and cAMP signaling pathway, among others. Furthermore, 6 proteins associated with reproduction were validated by parallel reaction monitoring analysis.

CONCLUSION

This study provides a comprehensive description of the seminal plasma exosome proteome and may be of use for further screening of biomarkers associated with male infertility.

Comparative transcriptome, digital gene expression and proteome profiling analyses provide insights into the brachyurization from the megalopa to the first juvenile in Eriocheir sinensis

Eriocheir sinensis larva normally experiences 11 stages. The reduced abdomen folded beneath the thorax is the most prominent characteristic of morphological alteration from megalopa to juvenile crab. Up to date, the molecular mechanisms of brachyurization remain a mystery. Here, transcriptome library, digital gene expression (DGE) libraries and proteome libraries at two developmental stages [the megalopa stage of E. sinensis (stage M) and the first stage of juvenile crab (stage J1)] of the Chinese mitten crab larva were constructed for RNA sequencing and iTRAQ approaches followed by bioinformatics analysis, respectively. In total, 1106 genes and 871 proteins were differentially expressed between the stage M and stage J1. Moreover, several important pathways were identified, including biosynthesis of secondary metabolites, metabolic pathways, focal adhesion, and some disease pathways. Besides, muscle contraction, oxidative phosphorylation, calcium signaling, PI3K-Akt, DNA replication pathway, and integrin signaling pathway also had important functions in brachyurization process. Furthermore, the components, actin, actin-related protein, collagens, filamin-A/B, laminin, integrins, paxillin, and fibronectin had up-regulated expression levels in M stage compared to J1 stage.

The feasibility of skin mucus replacing exosome as a pool for bacteria-infected markers development via comparative proteomic screening in teleost

In fish, skin mucus forms a protective barrier between the body surface and the external water environment, thus providing the most direct and intuitive clues to monitor the subject's health condition. To explore the impact of the Vibrio harveyi pathogen on teleost, the proteome of epidermal mucus from control and sick Cynoglossus semilaevis were screened through iTRAQ followed with LC-MS/MS. 1531 credible proteins were obtained relating to structural, metabolic and immunological functions. 335 different expressed proteins (DEPs) were identified, with 166 up-regulated and 169 down-regulated in MS. 62 proteins were characterized, including 22 up-regulated proteins and 40 down-regulated proteins. Integrated analysis of DE-miRNAs and DEPs from miRomics and proteomics were conducted to show the indirect regulatory relationship. Comparative analysis of DEPs between mucus and exosomes demonstrated that exosomes contributed the most DEPs of all mucus DEPs. 125 proteins are DEPs only in exosomes, which presented minor difference in total mucus. Expression of Aminopeptidase (anpep), Calcium-transporting ATPase, Histone H2B and H2A confirmed implied fine discriminative power with infected C. semilaevis, among which Calcium-transporting ATPase and H2B also appeared in list of exosomal markers. This study might shed the light on effective biomarker digging at other extended screening scenarios.