Differential Protein Expression Research Articles

Proteomic study of the inhibitory effects of tannic acid on MRSA biofilm

IntroductionThe mechanism of tannic acid (TA) intervention on methicillin-resistant Staphylococcus aureus (MRSA, USA 300) biofilm formation was explored using proteomics.MethodsThe minimum inhibitory concentration (MIC) of TA against the MRSA standard strain USA 300 was determined by two-fold serial dilution of the microbroth. The effects of TA were studied using crystal violet staining. The morphology of TA-treated USA 300 cells was observed by scanning electron microscopy and confocal laser scanning microscopy. Differentially expressed proteins (DEPs) were screened using proteomic and biological information analyses, and their transcriptional levels were verified using real-time quantitative polymerase chain reaction.ResultsThe MIC of TA was 0.625 mg/mL, whereas 1/2 MIC (0.3125 mg/mL) of TA significantly inhibited biofilm formation without affecting the bacterial growth (p < 0.01) and prevented the formation of a complete three-dimensional biofilm structure. Using 1/2 MIC of TA, 208 DEPs were identified, of which 127 were upregulated and 81 were downregulated. The transcriptional levels of the genes corresponding to five randomly selected DEPs (glnA, ribD, clpB, gap, and lukE) were consistent with the proteomics data (p < 0.05). Bioinformatic analysis showed that the changes in the MRSA strains after TA intervention primarily involved pyrimidine and purine metabolisms, arginine biosynthesis, and the citric acid cycle.ConclusionTA exerts an antibacterial effect on MRSA and can be used as a potential candidate for the development of anti-biofilm drugs, thereby laying a foundation for the treatment of MRSA biofilm-induced infections.

Effect of Seminal Plasma on the Freezability of Boar Sperm

Background: Seminal plasma is an important component of semen and has a significant effect on sperm function. However, the relationship between seminal plasma and sperm freezing capacity has not been fully studied. Purpose: Exploring metabolites and proteins related to the boar sperm freezing capacity in seminal plasma, by metabolomic and proteomic approaches, and directly verifying the protective effect of seminal plasma on the cryopreservation of boar sperm using high and low freezability seminal plasma as base freezing extender. Methods: Semen samples were collected from 30 different boars, 11 high and 11 low freezing-resistant boars were selected after freezing 2~4 times, and seminal plasma was selected at the same time. Sperm motility and movement parameters were analyzed using a CASA system. Reproductive hormones (Testosterone, progesterone, estradiol, prolactin, prostaglandin F2α, luteinoid hormone) in seminal plasma were detected by ELISA. Analysis of proteins and metabolites in high and low freezing-resistant seminal plasma by proteomics and metabolomics techniques. Results: The six reproductive hormones tested were not significantly associated with sperm freezing resistance. A total of 13 differentially expressed metabolites (DEMs) and 38 differentially expressed proteins (DEPs) were identified, while a total of 348 metabolites and 1000 proteins were identified. These DEMs were related to energy metabolism, drugs, or environmental pollutants, while the DEPs were mainly involved in the cytoskeletal dynamics and cell adhesion processes. There were 33 metabolites and 70 proteins significantly associated with mean progress motility (PM) at 10 min and 2 h after thawing. The 70 related proteins were associated with cell division and cycle regulation in gene ontology (GO) terms, as well as KEGG pathways, thermogeneration, and pyruvate metabolism. Using highly freezable boar SP as a base freezing extender made no difference from using lowly freezable boar SP, and both were not as good as the commercial control. Conclusion: There were significant differences in seminal plasma with different freezability, but the similarity was much greater than the difference. The protection effect of seminal plasma is not remarkable, and it does not exhibit superior cryoprotective properties compared to commercial semen cryoelongators. Significance: This study provides a deeper understanding of how seminal plasma composition affects sperm freezabilty. It provides potential biomarkers and targets for improving sperm cryopreservation techniques.

Proteomic profiling of neonatal herpes simplex virus infection on dried blood spots

Background:Neonatal herpes simplex virus (HSV) infection is life-threatening, with a mortality of up to 70–80% when disseminated, often due to vague symptoms and delayed treatment. Neonatal screening using dried blood spot (DBS) samples is among the most impactful preventative health measures ever implemented, but screening for HSV has not been investigated.Methods:We investigated high throughput multiplexed proteomics on DBS samples collected on days 2–3 of life from a nationwide cohort of neonates with HSV infection (n = 53) and matched controls. We measured 2941 proteins using the Olink Explore 3072 panels and proximity extension assays, followed by differential protein expression by Analysis of Variance with post-hoc correction and functional annotation.Results:Here, we show distinct protein profiles in neonates with disseminated HSV disease, with differences in 20 proteins compared to controls. These proteins are associated with innate and adaptive immune responses and cytokine activation.Conclusions:Our findings indicate the potential of neonatal screening for disseminated HSV disease to ensure early treatment and reduce the high mortality.

Myeloid-specific deletion of autotaxin inhibits rheumatoid arthritis and osteoclastogenesis

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by joint swelling, pain, and bone remodeling. We previously reported that autotaxin (ATX) deficiency disrupts lipid rafts in macrophages. Lipid raft disruption results in the dysregulation of RANK signaling, which is crucial for osteoclastogenesis and the pathogenesis of RA. Therefore, we evaluated the effect of ATX deficiency on joint inflammation and osteoclast differentiation. A collagen-induced arthritis mouse model was used with myeloid lineage-restricted Atx-knockout (AtxΔME/ΔME) mice and DBA/1 mice treated with the ATX inhibitor PF-8380. Joint inflammation and bone erosion were visualized using hematoxylin and eosin staining and micro-computed tomography. Osteoclast differentiation was assessed by tartrate-resistant acid phosphatase staining. ATX deficiency suppressed joint inflammation, bone resorption, osteoclast differentiation, and pro-inflammatory protein expression in both AtxΔME/ΔME mice and PF-8380-treated mice compared to controls. Mean disease score of Atx+/+ mice at the end of experiment was 3.813, but that of AtxΔME/ΔME was 0.185 (p < 0.05). The differentiation of bone marrow-derived macrophages into osteoclasts was reduced in AtxΔME/ΔME cells compared to Atx+/+ cells. ATX deficiency suppressed RANKL-induced phosphorylation of ERK and Akt and the interaction between RANK and TRAF6. ATX deficiency disrupted lipid rafts and dysregulated RANK distribution in RAW264.7 cells. Actin ring formation was also inhibited in AtxΔME/ΔME osteoclasts. ATX deficiency suppressed RA and osteoclast differentiation by disrupting lipid rafts and altering the RANK signaling pathway. This suggests that ATX inhibition may be an effective strategy for developing new disease-modifying antirheumatic drugs.

Integrated analysis of proteome and transcriptome revealed changes in multiple signaling pathways involved in immunity in the northern snakehead (Channa argus) during Nocardia seriolae infection

The northern snakehead (Channa argus) is a valuable aquaculture species across certain Asian countries, contributing significantly to economic prosperity and dietary needs. However, its productivity faces significant challenges, particularly from diseases such as nocardiosis, caused by Nocardia seriolae. To date, the majority of research efforts have focused on describing the observed phenomena related to N. seriolae infection. However, there remains a notable gap in knowledge concerning the infectivity of N. seriolae and the immune response it elicits. To better understand the modulation of the immune responses to N. seriolae infection in snakeheads, we investigated the splenic proteome profiles. Specifically, we compared the profiles between uninfected northern snakehead specimens and those infected with N. seriolae at 96 h using the label-free data-independent acquisition methodology. A total of 700 differentially expressed proteins (DEPs) were obtained. Of these, 353 proteins exhibited upregulation, whereas 347 proteins displayed downregulation after the infection. The DEPs were mapped to the reference canonical pathways in Kyoto Encyclopedia of Genes and Genomes database, revealing several crucial pathways that were activated following N. seriolae infection. Noteworthy, among these were pathways such as ferroptosis, complement and coagulation cascades, chemokine signaling, tuberculosis, natural killer cell-mediated cytotoxicity, and Th17 cell differentiation. Furthermore, protein–protein interaction networks were constructed to elucidate the interplay between immune-related DEPs. These results revealed expression changes in multiple signaling pathways during the initial colonization phase of N. seriolae. This discovery offers novel insights into the infection mechanisms and host interaction dynamics associated with N. seriolae.

Growth and physiological response of Yulu Hippophae rhamnoides to drought stress and its omics analysis

ABSTRACT Hippophae rhamnoides (H. rhamnoides) is the primary tree species known for its ecological and economic benefits in arid and semi-arid regions. Understanding the response of H. rhamnoides roots to drought stress is essential for promoting the development of varieties. One-year-old Yulu H. rhamnoides was utilized as the experimental material, and three water gradients were established: control (CK), moderate (T1) and severe (T2), over a period of 120 days. The phenotypic traits and physiological indies were assessed and analyzed, while the roots were subjected by RNA-Seq transcriptome and Tandem Mass Tags (TMT) proteome analysis. Drought stress significantly reduced the plant height, ground diameter, root biomass and superoxide dismutase activity; however, the main root length increased. In comparison with CK, a total of 5789 and 5594 differential genes, as well as 63 and 1012 differential proteins, were identified in T1 and T2, respectively. The combined analysis of transcriptome and proteome showed that the number of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) associated with T1, T2 and CK was 28 and 126, respectively, with 7 and 36 genes achieving effective KEGG annotation. In T1 and T2, the differential genes were significantly enriched in the plant hormone signal transduction pathway, but there was no significant enrichment in the protein expression profile. In T2, 38 plant hormone signal transduction function genes and 10 peroxisome related genes were identified. With the increase of drought stress, the combined expression of DEGs and DEPs increased. Yulu H. rhamnoides may allocate more resources toward CAT while simultaneously decreasing SOD and POD to mitigate the oxidative stress induced by drought. Furthermore, the molecular mechanisms underlying plant hormone signal transduction and peroxisome-related genes in the roots of H. rhamnoides were discussed in greater detail.

Differential proteomic profiles between cognitive frail and robust older adults from the MELoR cohort.

The present study explored for the first time the blood-based proteomic signature that could potentially distinguish older adults with and without cognitive frailty (CF). The participants were recruited under the Malaysian Elders Longitudinal Research (MELoR) study. Cognition and physical frailty were determined using the Montreal Cognitive Assessment (MoCA) and Fried's criteria, respectively. The differential protein expression in the blood samples (38 CF vs 40 robust) were then determined using the Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH) analysis. A total of 294 proteins were found to be differentially expressed in the CF group as opposed to the robust group. Considering proteins with fold change (FC) ≥ ± 2 and p-values < 0.05, 13 proteins were significantly upregulated and nine proteins significantly downregulated in the CF group when compared to the robust group. Subsequent correlation analysis identified nine dysregulated proteins, namely APOA1, APOA2, APOA4, APOC1, APOE, GPX3, RBP4, SERPINC1 and TTR, to exhibit significantly and moderately strong correlations with parameters of cognitive and/or frailty assessments. These proteins could potentially serve as useful proteomic signature of CF given their sensitivity > 78%, specificity > 75%, accuracy > 80% and area under the curve (AUC) > 0.8. The major biological pathways that could be potentially dysregulated by the nine proteins were associated with lipid metabolism and the retinoid system. The present findings warrant further validation in future studies that involve a larger cohort.

Cell-Specific Control of Mammalian Gene Expression Using DNA Repair Inducible Ribozyme Switches.

The ability to control gene expression is vital for elucidating gene functions and developing next-generation therapeutics. Current techniques are challenged by the lack of cell-specific control designs or immunogenicity risk from foreign proteins. We develop a DNA repair inducible ribozyme switch that enables cell-specific control of gene expression in cells and in vivo. This strategy designs plasmids with a DNA lesion (8-oxoG and O6-MeG) site-specifically installed within the ribozyme encoding region, generating active hammerhead ribozyme for mRNA degradation due to transcriptional mutagenesis, whereas DNA repair yields a single-base mismatch in the ribozyme to abrogate its activity. This strategy is demonstrated to allow specific control of gene expression in cancer cells with overexpressed DNA repair enzymes such as MutY DNA glycosylase and O6-methylguanine-DNA-methyltransferases. It also shows the capability of conditionally regulating the expression of different proteins for signal reporting and gene editing, enabling DNA repair monitoring and targeted gene therapy in cancer cells. This strategy is demonstrated using the inducible CRISPR/Cas9 system for in vivo editing of oncogenic Polo-like kinase 1 in a mouse model, resulting in significant tumor growth suppression. The DNA repair inducible ribozyme switch may provide a compact system for cell-specific gene expression control toward precise gene therapy.

Cell‐Specific Control of Mammalian Gene Expression Using DNA Repair Inducible Ribozyme Switches

The ability to control gene expression is vital for elucidating gene functions and developing next‐generation therapeutics. Current techniques are challenged by the lack of cell‐specific control designs or immunogenicity risk from foreign proteins. We develop a DNA repair inducible ribozyme switch that enables cell‐specific control of gene expression in cells and in vivo. This strategy designs plasmids with a DNA lesion (8‐oxoG and O6‐MeG) site‐specifically installed within the ribozyme encoding region, generating active hammerhead ribozyme for mRNA degradation due to transcriptional mutagenesis, whereas DNA repair yields a single‐base mismatch in the ribozyme to abrogate its activity. This strategy is demonstrated to allow specific control of gene expression in cancer cells with overexpressed DNA repair enzymes such as MutY DNA glycosylase and O6‐methylguanine‐DNA‐methyltransferases. It also shows the capability of conditionally regulating the expression of different proteins for signal reporting and gene editing, enabling DNA repair monitoring and targeted gene therapy in cancer cells. This strategy is demonstrated using the inducible CRISPR/Cas9 system for in vivo editing of oncogenic Polo‐like kinase 1 in a mouse model, resulting in significant tumor growth suppression. The DNA repair inducible ribozyme switch may provide a compact system for cell‐specific gene expression control toward precise gene therapy.

Proteomic Analysis Reveals Differentially Expressed Proteins in Cordyceps militaris Cultured with Different Media.

Cordyceps militaris is rich in high quality protein, which is an excellent protein supplement. In this study, proteins were extracted from C. militaris cultured with tussah pupa and C. militaris cultured with wheat and analyzed by liquid chromatography coupled with mass spectrometer. Results showed that a total of 83 differentially expressed proteins (DEPs) were identified. KEGG analysis showed that the number of DEPs involved in amino sugar and nucleotide sugar metabolism and metabolic pathways was the largest. The expression levels of chitinase, tubulin alpha chain and heat shock 70 kDa protein were upregulated in C. militaris cultured with tussah pupa, and these key DEPs were mainly related to immune modulation and disease resistance. The results revealed the nutritional and functional differences in the fruiting bodies of C. militaris cultured with tussah pupa and wheat, respectively. The findings provide a theoretical basis for further studies on the biological function of proteins in C. militaris.

Novel plasma cytokines identified and validated in children during lead exposure according to the new updated BLRV

Lead is a pervasive environmental contaminant with significant health risks, particularly to children. It is known for its neurotoxic and immunotoxic effects, causing developmental, cognitive, and behavioral impairments. Despite extensive research, the mechanisms of lead toxicity remain unclear. Cytokines, which are critical in immune response and inflammation, have emerged as potential biomarkers for lead toxicity. The recent Centers for Disease Control and Prevention (CDC) update to the blood lead reference value (BLRV) to 3.5 µg/dL emphasizes the need to explore novel biomarkers and mechanisms. The study involved 100 healthy children aged 1 to 5 years, divided into two groups based on BLRV: elevated (≥ 3.5 µg/dL) and low (< 3.5 µg/dL). The research consisted of two phases: discovery and validation. Plasma samples were analyzed using RayBio® Human Cytokine Antibody Arrays and Enzyme-linked immunosorbent assay (ELISA) for cytokine levels. Ethical approval was obtained, and statistical analyses included t-tests, chi-squared tests, pearson correlations, and multivariate logistic regression. Protein-protein interaction (PPI), Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted to explore the roles of significant differentially expressed proteins (DEPs). No significant differences in age, gender, or BMI between the two groups, but BLRV levels were significantly higher in the elevated BLRV group compared to the low BLRV group. In the discovery phase, significant changes in cytokine expression were identified, including increased levels of IL-6, IL-8, and IL-17, and decreased levels of BDNF, BMP-4, IGF-1, IL-7, IL-10, and Leptin. These findings were validated in the second phase using ELISA. Significant positive correlations were found between BLRV and IL-6, IL-8, and IL-17. Negative correlations were observed with BDNF, BMP-4, IGF-1, IL-7, IL-10, and Leptin. Multivariate regression confirmed that BLRV significantly affects these cytokine levels. PPI networks revealed that DEPs had strong interactions with multiple proteins, indicating their central role in lead toxicity. GO and KEGG analyses highlighted pathways related to neurotoxicity and inflammatory responses, including “negative regulation of myotube differentiation,” “neurotrophin signaling pathway,” and “alcoholism.” This study provides insights into the role of cytokines as biomarkers for lead toxicity and offers a comprehensive analysis of the mechanisms involved. The findings underscore the importance of early detection and intervention based on updated BLRV thresholds.

A multi-omics approach identifies the key role of disorders of sphingolipid metabolism in Ang II-induced hypertensive cardiomyopathy myocardial remodeling

Hypertension-induced myocardial remodelling encompasses both structural and functional changes in cardiac muscle tissue, such as myocardial hypertrophy, fibrosis, and inflammation. These alterations not only impair the systolic and diastolic functions of the heart but also elevate the risk of cardiovascular events and heart failure. One of the primary contributors to hypertensive cardiomyopathy (HTN-CM) is the over-activation of the renin-angiotensin-aldosterone system (RAAS), which subsequently induces myocardial remodeling. Although conventional therapeutic strategies aim to suppress RAAS and slow the progression of heart failure, the primary challenge in treating HTN-CM remains the lack of sensitive and specific biomarkers for early detection of myocardial remodelling. Combined multi-omics analyses, complemented by experimental validation, offer a systematic understanding of the landscape of gene/protein/metabolite expression in HTN-CM, revealing the underlying mechanisms of angiotensin II (Ang II)-induced myocardial remodeling in HTN-CM. Transcriptomic analysis revealed that differentially expressed genes (DEGs) are implicated in sphingolipid metabolic processes and are associated with collagen synthesis and inflammatory responses, collectively contributing to myocardial remodeling in HTN-CM. Proteomic analysis demonstrated that differentially expressed proteins (DEPs) are also involved in inflammatory and fibrotic processes, with associations to sphingolipid signaling pathways, particularly manifested through elevated expression of IL6, COL4A1, FGG, FGB, CREBBP and SPHK2 proteins. Metabolomic profiling further elucidated the increased expression of bioactive sphingolipid metabolites S1P and Sa1P in the myocardium of HTN-CM. Integrative multi-omics analysis revealed that HTN-CM is primarily influenced by the sphingolipid signaling pathway, with additional associations to the HIF-1α and FoxO signaling pathways. Correlation analysis has highlighted strong associations between sphingolipids and genes/proteins related to fibrosis and inflammation, as well as their connection to the HIF-1α and FoxO signalling pathways. Furthermore, certain key indicators were validated through ELISA and Western blot analyses in both plasma and myocardial tissue. In conclusion, the findings of this study suggest that excessive Ang II may induce abnormalities in sphingolipid metabolism, resulting in increased levels of S1P in both circulating and myocardial tissues. This elevation in S1P is implicated in myocardial inflammatory and fibrotic alterations, highlighting its pivotal role in myocardial remodeling. The specific mechanism underlying the sphingolipid signaling pathway in myocardial remodeling may involve downstream biological processes, including oxidative stress and excessive mitochondrial autophagy, mediated by HIF-1α and FoxO.

A Comparative Transcriptomic and Proteomic Analysis of the Pileus of Agaricus bisporus During Its Different Developmental Phases

The analysis of the developmental stages of Agaricus bisporus, a major edible and medicinal mushroom, has always been an important focus in this research area. The process of the growth and development of edible mushrooms is complex and involves the regulation of multiple genes and metabolic pathways. Less data exist on the mechanism of their growth and development at the overall level. In this study, RNA sequencing analyses (RNA-Seq) and data-independent acquisition (DIA) proteomic analyses were carried out at the button phase (BP), harvesting phase (HP), and opening phase (OP) stages of Agaricus bisporus ‘Shuangbao 106’ to reveal the changes in gene expression during the different growth periods of its substrates. The authors screened and explored 3351 differentially expressed genes (DEGs) with a difference factor of ≥2.0, including 2080 up-regulated and 1271 down-regulated genes. After proteome sequencing, 1156 differentially expressed proteins (DEPs) were screened, including 524 up-regulated and 632 down-regulated genes. The expression in TPM of glycoside hydrolase, catalytic core, and chitinase II decreased during both the HP and OP compared with the BP. This may be because mushrooms require higher levels of glycoside hydrolase, catalytic core, and chitinase II activity during the BP to cope with external threats and the need for cell wall remodeling. Conversely, the growth of mushrooms slowed down and the need for cell wall remodeling decreased during the HP and OP, leading to a decrease in the expression of glycoside hydrolase, catalytic core, and chitinase II. This change is related to the need for environmental adaptation, immune defense, and cell wall remodeling, and may regulate the post-growth process of A. bisporus via the hydrolysis of cell wall chitin and glycoside hydrolase. It may also inhibit the growth of mushroom pilei.

Proteomic profiling identifies classic Hodgkin lymphoma patients at risk of bleomycin pulmonary toxicity

Advances in treating classic Hodgkin lymphoma (cHL) have improved cure rates, with overall survival exceeding 80%, resulting in a growing population of survivors at risk of long-term complications, particularly cardiac and pulmonary toxicity. Bleomycin, a key component of combination chemotherapy, is associated with bleomycin-induced pulmonary toxicity (BPT). Using label-free quantification nano liquid chromatography-tandem mass spectrometry, protein expression in diagnostic lymphoma samples from patients with and without BPT was compared. Results showed differential protein expression and disrupted cellular pathways, suggesting biological differences in BPT risk. Immunohistochemical analysis revealed higher expression of JAK3, BID, and MMP9, and lower expression of CD20, TPD52, and PIK3R4 in patients with BPT. High BID and low CD20 expression were associated with inferior overall survival, while high BID and low JAK3 and CD20 expression were linked to poorer progression-free survival. These findings highlight altered protein profiles in pretreatment cHL biopsies associated with BPT development.

Daidzein Inhibits Non-small Cell Lung Cancer Growth by Pyroptosis.

Non-Small-Cell Lung Cancer (NSCLC) represents the leading cause of cancer deaths in the world. We previously found that daidzein, one of the key bioactivators in soy isoflavone, can inhibit NSCLC cell proliferation and migration, while the molecular mechanisms of daidzein in NSCLC remain unclear. We developed an NSCLC nude mouse model using H1299 cells and treated the mice with daidzein (30 mg/kg/day). Mass spectrometry analysis of tumor tissues from daidzein-treated mice identified 601 differentially expressed proteins (DEPs) compared to the vehicle-treated group. Gene enrichment analysis revealed that these DEPs were primarily associated with immune regulatory functions, including B cell receptor and chemokine pathways, as well as natural killer cell-mediated cytotoxicity. Notably, the NOD-like receptor signaling pathway, which is closely linked to pyroptosis, was significantly enriched. Further analysis of key pyroptosis-related molecules, such as ASC, CASP1, GSDMD, and IL-1β, revealed differential expression in NSCLC versus normal tissues. High levels of ASC and CASP1 were associated with a favorable prognosis in NSCLC, suggesting that they may be critical effectors of daidzein's action. In NSCLC-bearing mice treated with daidzein, RT-qPCR and Western blot analyses showed elevated mRNA and protein levels of ASC, CASP1, and IL-1β but not GSDMD, which was consistent with the proteomic data. In summary, this study demonstrated that daidzein inhibits NSCLC growth by inducing pyroptosis. Key pathway modulators ASC, CASP1, and IL-1β were identified as primary targets of daidzein. These findings offer insights into the molecular mechanisms underlying the anti-NSCLC effects of daidzein and could offer dietary recommendations for managing NSCLC.

Proteomic analysis of plasma and duodenal tissue in celiac disease patients reveals potential noninvasive diagnostic biomarkers

The pathogenesis of celiac disease (CeD) remains incompletely understood. Traditional diagnostic techniques for CeD include serological testing and endoscopic examination; however, they have limitations. Therefore, there is a need to identify novel noninvasive biomarkers for CeD diagnosis. We analyzed duodenal and plasma samples from CeD patients by four-dimensional data-dependent acquisition (4D-DIA) proteomics. Differentially expressed proteins (DEPs) were identified for functional analysis and to propose blood biomarkers associated with CeD diagnosis. In duodenal and plasma samples, respectively, 897 and 140 DEPs were identified. Combining weighted gene co-expression network analysis(WGCNA) with the DEPs, five key proteins were identified across three machine learning methods. FGL2 and TXNDC5 were significantly elevated in the CeD group, while CHGA expression showed an increasing trend, but without statistical significance. The receiver operating characteristic curve results indicated an area under the curve (AUC) of 0.7711 for FGL2 and 0.6978 for TXNDC5, with a combined AUC of 0.8944. Exploratory analysis using Mfuzz and three machine learning methods identified four plasma proteins potentially associated with CeD pathological grading (Marsh classification): FABP, CPOX, BHMT, and PPP2CB. We conclude that FGL2 and TXNDC5 deserve exploration as potential sensitive, noninvasive diagnostic biomarkers for CeD.

Multi-omics joint screening of biomarkers related to M2 macrophages in gastric cancer

BackgroundDue to high mortality rate and limited treatments in gastric cancer (GC), call for deeper exploration of M2 macrophages as biomarkers is needed.MethodsThe data for this study were obtained from the Gene Expression Omnibus (GEO) and Genomic Data Commons (GDC). The Seurat package was utilized for single-cell RNA sequencing (scRNA-seq) analysis. FindAllMarkers was used to identify genes highly expressed among different cell subsets. DESeq2 package was leveraged to screen differentially expressed genes (DEGs), while limma package was utilized for identifying differentially expressed proteins (DEPs). Enrichment analyses of the genes were conducted using KOBAS-i database. MultipleROC was applied to evaluate the diagnostic potential of biomarkers, and rms package was utilized to construct diagnostic models. hTFtarget database was utilized to predict potential transcription factors (TFs). Finally, cell-based assays were performed to validate the expression and potential biological functions of the screened key markers.ResultsThis study found that M2 macrophages were enriched in protein, endoplasmic reticulum, and virus-related pathways. A total of 4146 DEGs and 1946 DEPs were obtained through screening, with 254 common DEGs/DEPs. The results of gene function enrichment analysis suggested that it may affect the occurrence and development of GC through DNA replication and cell cycle. This study identified three biomarkers, HSPH1, HSPD1, and IFI30, and constructed a diagnostic model based on these three genes. The AUC value greater than 0.8 proved the reliability of the model. Through screening TFs, SPI1 and KLF5 were found to be the common TFs for the three biomarkers. The expression of the three genes IFI30, HSPD1 and HSPH1 was up-regulated in GC cells, and IFI30 may play a facilitating role in the migration and invasion of GC cells.ConclusionThis study identified three biomarkers and constructed a diagnostic model, providing a new perspective for the research and treatment of GC.

Differential tumor protein expression at follicular lymphoma diagnosis reveals dysregulation of key molecular pathways associated with histological transformation

Follicular lymphoma (FL) is the most common low-grade lymphoma. Despite its indolent nature, FL carries an inherent risk of histological transformation (HT) to a more aggressive lymphoma. Existing biomarkers are insufficient to predict HT, indicating the need for more robust biological predictors. Previously, we used mass spectrometry-based proteomics to identify differentially expressed proteins in diagnostic FLs with and without subsequent HT. This study sought to further investigate identified proteins in transformation of FL, generally acting in important cellular pathways such as (i) apoptosis (BID), (ii) cell cycle (CDC26, CDK6, SRSF1, SRSF2), (iii) GTPase signaling (IQGAP2, MEK1), (iv) cytoskeletal rearrangement and cellular migration (ACTB, CD11a, MMP9, SEPT6), and (v) immune processes (CD81, IgG, MPO, PIK3AP1). We analyzed pre-therapeutic samples from 48 FL patients, either non-transforming FL (nt-FL, n = 30) or subsequently-transforming FL (st-FL, n = 18), the latter with histologically-confirmed transformation after their initial FL diagnosis. Paired high-grade lymphomas (tFL, n = 18) from the time of transformation were also analyzed. We used immunohistochemistry and digital image analysis to quantify protein levels. In all five pathway classes, several proteins were differentially expressed between either the diagnostic nt-FL and st-FL samples, or between the paired st-FL and tFL samples (p < 0.05). Interestingly, we found correlation between expression levels of several proteins, indicating a complex involvement between several pathways. Differential expression of most proteins was also associated with shorter transformation-free survival (p < 0.05). These findings emphasize underlying differences in FL biology predictive of subsequent transformation, highlighting deregulation of important interconnected cellular pathways.

Mechanistic insights into retinoic-acid treatment for autism in the improvement of social behavior: evidence from a multi omics study in rats

BackgroundAutism spectrum disorder (ASD) is a lifelong condition. It is characterized by complex etiologies, including disruptions in exogenous retinoic acid (RA) signaling, which may serve as an environmental risk factor. Targeting the RA pathway presents a promising therapeutic avenue, though the precise mechanisms remain to be elucidated. MethodsFemale Sprague–Dawley rats were treated with valproic acid (VPA) during pregnancy to induce an ASD model in their offspring. Some offspring received RA treatment postnatally. Social behavior and brain-functional connectivity were assessed using behavioral tests and functional magnetic resonance imaging (fMRI), respectively. Transcriptomics analysis and proteomics analysis of the hypothalamus identified differentially expressed genes (DEGs) and differentially expressed proteins (DEPs). These were intersected with ASD pathogenic genes (APGs) and ASD pathogenic proteins (APPs) to identify differentially expressed APGs (DE-APGs) and differentially expressed APPs (DE-APPs), which were validated by real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blotting. Analyses of enrichment of signaling pathways were done using the Kyoto Encyclopedia of Genes and Genomes database. ResultsRA treatment significantly improved social behaviors and revealed distinct patterns of hypo- and hyper-connectivity across various brain regions, with notable changes involving the hypothalamus and facial nerve. Differential analysis revealed 4165 DEGs (DEG 1) and 329 DEPs (DEP 1) between control and VPA groups, and 1610 DEGs (DEG 2) and 197 DEPs (DEP 2) between VPA and RA supplementation (RAS) groups. Twenty-two DE-APGs and five DE-APPs were identified, with key associations found between proteins such as Tbl1xr1 and Myo5a and >13 genes including Nrxn1, Cacna1e, and Gabrb2. Significant alterations in DE-APGs, including Grin2b, Nrxn1, Cacna1e, and Gabrb2, were confirmed via real-time RT-PCR and western blotting. In addition, 22 key signaling pathways were enriched in DEPs and DEGs. ConclusionRA supplementation in ASD rats induced by VPA may ameliorate social deficits and modulated functional connectivity, especially in the hypothalamus and facial nerve regions. This suggests potential therapeutic benefits for neural circuitry dysregulation in ASD. Additionally, RA altered critical gene and protein expressions in hypothalamus, implicating its role in modulating key signaling pathways to mitigate social deficits in ASD. This study provides new insights into the molecular mechanisms of ASD and supports the development of novel therapeutic strategies.

Alterations in the nutrient composition, muscle quality, and proteomics of two Sepiidae species (Sepiella maindroni and Sepia esculenta) during storage

The present study compared muscle protein characteristics between Sepiella maindroni (S. maindroni) and Sepia esculenta (S. esculenta). We analyzed the nutrient composition, myofibrillar protein properties, and proteomic changes in muscle tissue under freezing conditions. Amino acid analysis revealed 17 hydrolyzed amino acids in both species’ muscle tissues, with tryptophan identified as the first limiting amino acid. Essential amino acids (EAAs) constituted more than 31% of total amino acids (TAAs), aligning closely with the FAO/WHO recommended ideal protein pattern. The Essential Amino Acid Index (EAAI) for S. maindroni was high at 82.99. Twenty fatty acids were identified in both species, with total contents of C20:5n-3 (EPA) and C22:6n-3 (DHA) exceeding 40%. S. maindroni had significantly more such fatty acids than S. esculenta. During the freezing process, the total sulfhydryl content and Ca2+-ATPase activity of both species showed a decreasing trend, while carbonyl content exhibited an overall increase. After 60 days of freezing, the total sulfhydryl content and Ca2+-ATPase activity in the muscles of both species decreased to minimum levels. Compared to fresh samples, both species’ muscle tissues exhibited varying degrees of deterioration in microscopic structure after 60 days of freezing. A total of 350 differentially expressed proteins (DEPs) comprising 208 upregulated and 142 downregulated proteins were identified in S. maindroni and S. esculenta. After 60 days of freezing, 322 DEPs, including 181 upregulated and 141 downregulated proteins, were detected in both species. COG functional classification indicated that low-temperature storage affected DEPs in the muscle tissue, influencing the flavor, texture, and protein functionality of the species.