Hub Proteins Research Articles

Insights from 4D Label-Free Proteomic Analysis into Variation of Milk Fat Globule Membrane Proteins of Human Milk Associated with Infant's Gender.

Milk fat globule membrane (MFGM) protein profiles of breast milk collected from women in northeast China with male or female babies were investigated using a four-dimensional (4D) label-free proteomic technique. Altogether, 2538 proteins were detected and quantified and 249 were differentially expressed, with 198 decreased proteins compared to the samples of mothers with female babies. Different proteins associated with infant's gender were principally located in nuclear. The differentially expressed proteins were mainly involved in gene ontology (GO) functions of the cellular process, binding, and cell and found to be distributed in lipid-related biological processes and molecular functions to a large extent. The pathway of neurodegeneration-multiple disease ranked top for the altered proteins. The screened proteins were observed to contain some proteins related to typical functions of immunity, lipid metabolism, digestion, and growth and development. 114 proteins formed a relatively compact network (269 interactions) and dolichyl-diphospho-oligosaccharide-protein glycosyltransferase subunit 2 interacted the most with other proteins as the hub protein. MFGM proteins of breast milk were affected by the sex of offspring, and these findings may provide useful information for reasonable adjustments of infant formula powder specifically for boys or girls in the market.

Understanding the mechanism of pathogenicity through interactome studies between Arachis hypogaea L. and Aspergillus flavus

Aspergillus flavus (A. flavus) infects the peanut seeds during pre-and post-harvest stages, causing seed quality destruction for humans and livestock consumption. Even though many resistant varieties were developed, the molecular mechanism of defense interactions of peanut against A. flavus still needs further investigation. Hence, an interologous host-pathogen protein interaction (HPPI) network was constructed to understand the subcellular level interaction mechanism between peanut and A. flavus. Out of the top 10 hub proteins of both organisms, protein phosphatase 2C and cyclic nucleotide-binding/kinase domain-containing protein and different ribosomal proteins were identified as candidate proteins involved in defense. Functional annotation and subcellular localization based characterization of HPPI identified protein SGT1 homolog, calmodulin and Rac-like GTP-binding proteins to be involved in defense response against fungus. The relevance of HPPI in infectious conditions was assessed using two transcriptome data which identified the interplay of host kinase class R proteins, bHLH TFs and cell wall related proteins to impart resistance against pathogen infection. Further, the pathogenicity analysis identified glycogen phosphorylase and molecular chaperone and allergen Mod-E/Hsp90/Hsp1 as potential pathogen targets to enhance the host defense mechanism. Hence, the computationally predicted host-pathogen PPI network could provide valuable support for molecular biology experiments to understand the host-pathogen interaction. SignificanceProtein-protein interactions execute significant cellular interactions in an organism and are influenced majorly by stress conditions. Here we reported the host-pathogen protein-protein interaction between peanut and A. flavus, and a detailed network analysis based on function, subcellular localization, gene co-expression, and pathogenicity was performed. The network analysis identified key proteins such as host kinase class R proteins, calmodulin, SGT1 homolog, Rac-like GTP-binding proteins bHLH TFs and cell wall related to impart resistance against pathogen infection. We observed the interplay of defense related proteins and cell wall related proteins predominantly, which could be subjected to further studies. The network analysis described in this study could be applied to understand other host-pathogen systems generally.

Exploring molecular markers and drug candidates for colorectal cancer through comprehensive bioinformatics analysis.

Colorectal cancer (CRC) often has a poor prognosis and identifying useful and novel agents for treating CRC is urgently required. This study aimed to examine molecular markers associated with CRC prognosis and to identify potential drug candidates. The differentially expressed genes (DEGs) of CRC in TCGA were identified. The genes associated with CRC, summarized from NCBI-gene, OMIM, and the DEGs, were used to construct a co-expression network by WGCNA. Moreover, the co-expression genes from modules of interest were used to carry out functional enrichment. A total of 2742 DEGs, including 1674 upregulated and 1068 downregulated genes, were identified. Thirteen co-expression modules were constructed with WGCNA. Brown and blue co-expression modules with significant differences in disease phenotype were found. Functional enrichment analysis showed that genes in the brown module were mainly related to cell cycle, cell proliferation, DNA replication, and RNA transport. The genes in the blue module were mainly associated with fatty acid degradation, sulfur metabolism, PPAR signaling pathway and bile secretion. In addition, both the genes in brown and blue were associated with tumor staging. Some prognostic markers and candidate small molecules drugs for CRC treatment were identified. In conclusion, we revealed molecular biomarker profiles in CRC by systematic bioinformatics analysis, constructed regulatory networks of mRNA, ncRNA and transcriptional regulators (TFs), and identified potential drugs targeting hub proteins and TFs.

Comparative transcriptional analysis between virulent isolate HN1307 and avirulent isolate GD1108 of grass carp reovirus genotype II

As a widespread epidemic virus, genotype II of the grass carp reovirus poses a significant threat to the grass carp farming industry in China. Different genotype II isolates cause different degrees of virulence, although the underlying pathogenic mechanisms remain largely unknown. In this work, infections of grass carp with the virulent isolate grass carp reovirus (GCRV)-HN1307 and the avirulent isolate GCRV-GD1108 were performed to reveal a possible mutual transcriptional discrepancy. More differentially expressed genes (DEGs) were identified in the HN1307-infected group, which defined a grossly similar gene ontology (GO) pattern and different pathway landscape as the GD1108-infected group. Gene set enrichment analysis revealed that pathways related to innate immunity and metabolism were reciprocally activated and suppressed, respectively, following infection withHN1307, compared with GD1108. The trend analysis further indicated that immune-related pathways were involved in one of the four statistically significant profiles. Network analysis of transcription factor-gene interactions and protein-protein interactions on the immune-related profile suggested that among the core transcriptional factors (TFs) (UBTF, HCFC1, MAZ, MAX, and NRF1) and the hub proteins (Tlr3, Tlr7, Tlr9, Irf3, and Irf7), the latter were highly enriched in the toll-like receptor signaling pathway. Real-time quantitative PCR performed on the selected mRNAs validated the relative expression. This work will provide insights into the distinct transcriptional signatures from avirulent and virulent isolates of GCRV, which may contribute to the development of products for prevention.

Unravelling potential biomarkers for acute and chronic brucellosis through proteomic and bioinformatic approaches.

This study aimed to identify biomarkers for acute and chronic brucellosis using advanced proteomic and bioinformatic methods. Blood samples from individuals with acute brucellosis, chronic brucellosis, and healthy controls were analyzed. Proteomic techniques and differential expression analysis were used to identify differentially expressed proteins. Co-expression modules associated with brucellosis traits were identified using weighted gene co-expression network analysis (WGCNA). 763 differentially expressed proteins were identified, and two co-expression modules were found to be significantly associated with brucellosis traits. 25 proteins were differentially expressed in all three comparisons, and 20 hub proteins were identified. Nine proteins were found to be both differentially expressed and hub proteins, indicating their potential significance. A random forest model based on these nine proteins showed good classification performance. The identified proteins are involved in processes such as inflammation, coagulation, extracellular matrix regulation, and immune response. They provide insights into potential therapeutic targets and diagnostic biomarkers for brucellosis. This study improves our understanding of brucellosis at the molecular level and paves the way for further research in targeted therapies and diagnostics.

Comparative genomics and integrated system biology approach unveiled undirected phylogeny patterns, mutational hotspots, functional patterns, and molecule repurposing for monkeypox virus.

Monkeypox is a viral zoonosis with symptoms that are reminiscent of those experienced in previous smallpox cases. The GSAID database (Global Initiative on Sharing Avian Influenza Data) was used to assess 630 genomes of MPXV. The phylogenetic study revealed six primary clades, as well as a smaller percentage in radiating clades. Individual clades that make up various nationalities may have formed as a result of a particular SNP hotspot type that mutated in a specific population. The most significant mutation based on a mutational hotspot analysis was found at G3729A and G5143A. The gene ORF138, which encodes the Ankyrin repeat (ANK) protein, was found to have the most mutations. This protein mediates molecular recognition via protein-protein interactions. It was shown that 243 host proteins interacted with 10 monkeypox proteins identified as the hub proteins E3, SPI2, C5, K7, E8, G6, N2, B14, CRMB, and A41 through 262 direct connections. The interaction with chemokine system-related proteins provides further evidence that the monkeypox virus suppresses human proteins to facilitate its survival against innate immunity. Several FDA-approved molecules were evaluated as possible inhibitors of F13, a significant envelope protein on the membrane of extracellular versions of the virus. A total of 2500 putative ligands were individually docked with the F13 protein. The interaction between the F13 protein and these molecules may help prevent the monkeypox virus from spreading. After being confirmed by experiments, these putative inhibitors could have an impact on the activity of these proteins and be used in monkeypox treatments.

The Influence of Nicotine on Trophoblast-Derived Exosomes in a Mouse Model of Pathogenic Preeclampsia.

Preeclampsia (PE) is a serious complication of pregnancy with a pathogenesis that is not fully understood, though it involves the impaired invasion of extravillous trophoblasts (EVTs) into the decidual layer during implantation. Because the risk of PE is actually decreased by cigarette smoking, we considered the possibility that nicotine, a critical component of tobacco smoke, might protect against PE by modifying the content of exosomes from EVTs. We investigated the effects of nicotine on our PE model mouse and evaluated blood pressure. Next, exosomes were extracted from nicotine-treated extravillous trophoblasts (HTR-8/SVneo), and the peptide samples were evaluated by DIA (Data Independent Acquisition) proteomic analysis following nano LC-MS/MS. Hub proteins were identified using bioinformatic analysis. We found that nicotine significantly reduced blood pressure in a PE mouse model. Furthermore, we identified many proteins whose abundance in exosomes was modified by nicotine treatment of EVTs, and we used bioinformatic annotation and network analysis to select five key hub proteins with potential roles in the pathogenesis or prevention of PE. EVT-derived exosomes might influence the pathogenesis of PE because the cargo delivered by exosomes can signal to and modify the receiving cells and their environment.

Deciphering Nucleic Acid Binding Proteome of Mouse Immune Organs Reveals Hub Proteins for Aging

Profiling the nucleic acid-binding proteins (NABPs) during aging process is critical to elucidate its roles in biological systems as well as transcriptional and translational regulation. Here, we developed a comprehensive strategy to survey the NABPs of mouse immune organs by using single cell preparation and selective capture technology-based proteomics. Our approach provided a global view of tissue NABPs from different organs under normal physiological conditions with extraction specificity of 70 to 90%. Through quantitative proteomics analysis of mouse spleen and thymus at 1, 4, 12, 24, 48, and 72weeks, we investigated the molecular features of aging-related NABPs. A total of 2674 proteins were quantified in all six stages, demonstrating distinct and time-specific expression pattern of NABPs. Thymus and spleen exhibited unique aging signatures, and differential proteins and pathways were enriched across the mouse lifespan. Three core modules and 16 hub proteins associated with aging were revealed through weighted gene correlation network analysis. Significant candidates were screened for immunoassay verification, and six hub proteins were confirmed. The integrated strategy pertains the capability to decipher the dynamic functions of NABPs in aging physiology and benefit further mechanism research.

ITRAQ-based proteomic analysis provides novel insight into the postnatal testicular development of Hu sheep

Testicular development is an intricate and coordinated process in which thousands of proteins are involved in the regulation of somatic cells development and spermatogenesis. However, knowledge about the proteomic changes during postnatal testicular development in Hu sheep is still elusive. The study was conducted to characterize the protein profiles at four key stages during postnatal testicular development, including infant (0-month-old, M0), puberty (3-month-old, M3), sexual maturity (6-month-old, M6) and body maturity (12-month-old, M12), and between the large- and small-testis groups at 6 months in Hu sheep. Consequently, 5252 proteins were identified using isobaric tags for relative and absolute quantification (iTRAQ) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods, and 465, 1261, 231 and 1080 differentially abundant proteins (DAPs) were found between M0_vs_M3, M3_vs_M6L, M6L_vs_M12, and M6L_vs_M6S, respectively. GO and KEGG analysis revealed that the majority of DAPs were involved in cellular process, metabolic process and immune system-related pathways. Furthermore, a protein-protein interaction network was constructed using 86 fertility-related DAPs, and five proteins with the highest degree were represented as hub proteins, including CTNNB1, ADAM2, ACR, HSPA2 and GRB2. This study provided new insights into the regulation mechanisms of postnatal testicular development and identified several potential biomarkers for selecting the high-fertility rams. Significance of the studyTesticular development is an intricate developmental process in which thousands of proteins are involved in regulating the somatic cells development and spermatogenesis. However, knowledge about the proteome changes during postnatal testicular development in Hu sheep is still elusive. This study provides comprehensive insights into the dynamic changes in the sheep testis proteome during postnatal testicular development. Additionally, testis size is positively correlated with semen quality and ejaculation volume, also for the merits of easy measurement, high heritability and selection efficiency, is an important indicator to select candidate rams with high fertility. The functional analyses of the acquired candidate proteins may help us gain a better understanding of the molecular regulatory mechanisms of testicular development.

P-720 Biallelic variants in IQCN cause sperm flagella assembly defects and male infertility

Abstract Study question What is the effect of defects in the manchette protein IQ motif-containing N (IQCN) on sperm flagellar assembly? Summary answer Deficiency in IQCN is responsible for sperm flagella assembly defects and abnormal computer-assisted sperm analysis (CASA) parameters, which result in male infertility. What is known already Manchette is a transient structure that is involved in the shaping of the spermatid nucleus and protein transport of flagella. Most recently, our group reported that the manchette protein IQCN is essential for fertilization. Variants in IQCN led to total fertilization failure (TFF) and defective acrosome structure phenotypes. However, the related function of IQCN in sperm flagella assembly is still unknown. Study design, size, duration Fifty infertile males were recruited from the Reproductive and Genetic Hospital of China International Trust Investment Corporation (CITIC)-Xiangya from January 2014 to October 2022. Participants/materials, setting, methods Genomic DNA was extracted from the peripheral blood samples of the affected individuals for whole-exome sequencing. The ultrastructure of the flagella was detected by transmission electron microscopy (TEM). CASA was used to test the parameters of sperm motility. An Iqcn knockout (Iqcn-/-) mouse model was generated by CRISPER-Cas9 technology. Immunoprecipitation (IP) followed by liquid chromatography‒mass spectrometry was used to select the differentially expressed IQCN-binding proteins. Immunofluorescence was used to validate the localization of IQCN-binding proteins. Main results and the role of chance Biallelic variants in IQCN (c.3913A>T and c.3040A>G; c.2453_2454del) were identified in our infertile cohort. The sperm from the affected individuals showed irregular “9 + 2” structure of sperm flagella, which resulted in abnormal CASA parameters. Similar phenotypes were observed in Iqcn-/- male mice. The CASA parameters in the sperm of Iqcn-/- male mice were significantly lower than those in Iqcn+/+ male mice. The partial of peripheral doublet microtubules (DMTs) and outer dense fibers (ODFs) were absent, or the chaotic arrangement of DMTs were observed in the principal piece and end piece of sperm flagella. The hyperactivation ability of sperm from Iqcn-/- male mice was decreased than sperm from Iqcn+/+ male mice. The CDC42 and IFT protein families are hub proteins that interact with IQCN and regulate flagella assembly during spermiogenesis. Deficiency in IQCN causes the loss of binding with CDC42 and IFT74, which leads to the absence or abnormal localization of CDC42 and IFT74 in mouse and human spermatozoa. Limitations, reasons for caution More cases are needed to demonstrate the relationship between the IQCN variations and the phenotypes. Wider implications of the findings Our findings expand the genetic and phenotypic spectrum of IQCN variants in causing male infertility, thus providing a genetic marker for sperm motility deficiency and male infertility. Trial registration number N.A.

Mechanisms and Functions of Activity-Regulated Cytoskeleton-Associated Protein in Synaptic Plasticity.

Activity-regulated cytoskeleton-associated protein (Arc) is one of the most important regulators of cognitive functions in the brain regions. As a hub protein, Arc plays different roles in modulating synaptic plasticity. Arc supports the maintenance of long-term potentiation (LTP) by regulating actin cytoskeletal dynamics, while it guides the endocytosis of AMPAR in long-term depression (LTD). Moreover, Arc can self-assemble into capsids, leading to a new way of communicating among neurons. The transcription and translation of the immediate early gene Arc are rigorous procedures guided by numerous factors, and RNA polymerase II (Pol II) is considered to regulate the precise timing dynamics of gene expression. Since astrocytes can secrete brain-derived neurotrophic factor (BDNF) and L-lactate, their unique roles in Arc expression are emphasized. Here, we review the entire process of Arc expression and summarize the factors that can affect Arc expression and function, including noncoding RNAs, transcription factors, and posttranscriptional regulations. We also attempt to review the functional states and mechanisms of Arc in modulating synaptic plasticity. Furthermore, we discuss the recent progress in understanding the roles of Arc in the occurrence of major neurological disorders and provide new thoughts for future research on Arc.

How aberrant N-glycosylation can alter protein functionality and ligand binding: An atomistic view

Protein-assembly defects due to an enrichment of aberrant conformational protein variants are emerging as a new frontier in therapeutics design. Understanding the structural elements that rewire the conformational dynamics of proteins and pathologically perturb functionally oriented ensembles is important for inhibitor development. Chaperones are hub proteins for the assembly of multiprotein complexes and an enrichment of aberrant conformers can affect the cellular proteome, and in turn, phenotypes. Here, we integrate computational and experimental tools to investigte how N-glycosylation of specific residues in glucose-regulated protein 94 (GRP94) modulates internal dynamics and alters the conformational fitness of regions fundamental for the interaction with ATP and synthetic ligands and impacts substructures important for the recognition of interacting proteins. N-glycosylation plays an active role in modulating the energy landscape of GRP94, and we provide support for leveraging the knowledge on distinct glycosylation variants to design molecules targeting GRP94 disease-associated conformational states and assemblies.

Proteome changes in Neck-arm restraint and Achilles tendon suspensions during early post-mortem aging in cattle

The aging process of beef is impacted by the suspension method and aging time during the postmortem process. The neck-arm restraint (NR) suspension can accelerate the aging of beef carcasses compared with Achilles tendon (AT) suspension. However, the muscle protein changes between these two suspension methods in early postmortem aging are still unclear. This study aimed to investigate the proteomes of longissimus thoracis (LT) muscles between AT and NR suspension methods at 1 h and 72 h postmortem by the multiplexed isobaric tagging technology for relative quantitation (iTRAQ) technique and uncover the critical protein biomarkers of beef quality. A total of 59 proteins were differentially expressed between different suspension methods or postmortem aging times, which were mainly involved in actin cytoskeleton reorganization, actomyosin structure organization, response to calcium ions, and muscle contraction. Through the analysis of protein-protein interaction (PPI), we detected that ALB, APOA1, FGA, and TTN could be served as the hub proteins. Integration with the reported quantitative trait loci (QTL) of beef quality revealed that 30 differentially expressed proteins (DEPs) were involved in 46 QTL, in which, 11 proteins were differentially expressed in both the suspension method and time point comparison groups. We inferred these 11 proteins (MYL6B, MYO1A, COL3A1, AFP, CLN6, FGB, GLS2, BAG4, FGG, A2M, and WNT10A) as the most promising markers for the beef quality during the aging process.

Association analysis of hepatocellular carcinoma-related hub proteins and hub genes.

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. The occurrence and development of HCC are closely related to epigenetic modifications. Epigenetic modifications can regulate gene expression and related functions through DNA methylation. This paper presents an association analysis method of HCC-related hub proteins and hubgenes. Bioinformatics analysis of HCC-related DNA methylation data is carried out to clarify the molecular mechanism of HCC-related genes and to find hub genes (genes with more connections in the network) by constructing in the gene interaction network. This paper proposes an accurate prediction method of protein-protein interaction (PPI) based on deep learning model DeepSG2PPI. The trained DeepSG2PPI model predicts the interaction relationship between the synthetic proteins regulated by HCC-relatedgenes. This paper finds that four genes are the intersection of hub genes and hub proteins. The four genes are: FBL, CCNB2, ALDH18A1 and RPLP0. The association of RPLP0 gene with HCC is a new finding of this study. RPLP0 is expected to become a new biomarker for the treatment, diagnosis, and prognosis of HCC. The four proteins corresponding to the four genes are: ENSP00000221801, ENSP00000288207, ENSP00000360268 andENSP00000449328. The association between the hub genes with the hub proteins is analyzed. The mutual verification of the hub genes and the hub proteins can obtain more credible HCC-related genes and proteins, which is helpful for the diagnosis, treatment, and drug development ofHCC. This article is protected by copyright. All rights reserved.

An integrative network analysis to reveal network biomarkers for vulvar cancer

Vulvar cancer, accounts for 3–5% of all gynecological cancers worldwide, is a rare malignancy in women. Specific apparent symptoms are absent at the early stages of vulvar cancer, which is the crucial cause of delay in diagnosis. The study aims to identify the prospective genes for early detection of vulvar cancer through integrative bioinformatics and explainable artificial intelligence (XAI)-based methodology. Differentially expressed genes (DEGs) extracted from the RNA-Seq data of vulvar cancer were mapped to an interaction network of proteins (PPI). The PPI network was scrutinized to reveal hub proteins. A Random Forest (RF)-based machine learning (ML) classifier was constructed to select genes responsible for the disease. Shapley (SHAP) values, an explainable artificial intelligence (XAI) framework, were used to identify important genes significantly contributing to the disease. The common genes among hubs and SHAP-based importance were selected as potential biomarkers. 2760 DEGs were identified by RNA-Seq data analysis. The top 30 genes responsible for the disease were identified using SHAP-based feature importance from the RF algorithm. Five genes, namely, SNAPIN, PSMD10, CDCA8, CBX6, and UBL4A, overlap among the hubs of the PPI network and SHAP-based important genes. Exploiting these five genes may aid in the prognosis of the disease and impart essential insights into the molecular mechanisms of vulvar cancer.

Network analysis of plasma proteomes in affective disorders

The conventional differentiation of affective disorders into major depressive disorder (MDD) and bipolar disorder (BD) has insufficient biological evidence. Utilizing multiple proteins quantified in plasma may provide critical insight into these limitations. In this study, the plasma proteomes of 299 patients with MDD or BD (aged 19–65 years old) were quantified using multiple reaction monitoring. Based on 420 protein expression levels, a weighted correlation network analysis was performed. Significant clinical traits with protein modules were determined using correlation analysis. Top hub proteins were determined using intermodular connectivity, and significant functional pathways were identified. Weighted correlation network analysis revealed six protein modules. The eigenprotein of a protein module with 68 proteins, including complement components as hub proteins, was associated with the total Childhood Trauma Questionnaire score (r = −0.15, p = 0.009). Another eigenprotein of a protein module of 100 proteins, including apolipoproteins as hub proteins, was associated with the overeating item of the Symptom Checklist-90-Revised (r = 0.16, p = 0.006). Functional analysis revealed immune responses and lipid metabolism as significant pathways for each module, respectively. No significant protein module was associated with the differentiation between MDD and BD. In conclusion, childhood trauma and overeating symptoms were significantly associated with plasma protein networks and should be considered important endophenotypes in affective disorders.

Detection of Arc/Arg3.1 oligomers in rat brain: constitutive and synaptic activity-evoked dimer expression in vivo.

The immediate early gene product activity-regulated cytoskeleton-associated protein (Arc or Arg3.1) is a major regulator of long-term synaptic plasticity with critical roles in postnatal cortical development and memory formation. However, the molecular basis of Arc function is undefined. Arc is a hub protein with interaction partners in the postsynaptic neuronal compartment and nucleus. Previous in vitro biochemical and biophysical analysis of purified recombinant Arc showed formation of low-order oligomers and larger particles including retrovirus-like capsids. Here, we provide evidence for naturally occurring Arc oligomers in the mammalian brain. Using in situ protein crosslinking to trap weak Arc-Arc interactions, we identified in various preparations a prominent Arc immunoreactive band on SDS-PAGE of molecular mass corresponding to a dimer. While putative trimers, tetramers and heavier Arc species were detected, they were of lower abundance. Stimulus-evoked induction of Arc expression and dimer formation was first demonstrated in SH-SY5Y neuroblastoma cells treated with the muscarinic cholinergic agonist, carbachol, and in primary cortical neuronal cultures treated with brain-derived neurotrophic factor (BDNF). In the dentate gyrus (DG) of adult anesthetized rats, induction of long-term potentiation (LTP) by high-frequency stimulation (HFS) of medial perforant synapses or by brief intrahippocampal infusion of BDNF led to a massive increase in Arc dimer expression. Arc immunoprecipitation of crosslinked DG tissue showed enhanced dimer expression during 4 h of LTP maintenance. Mass spectrometric proteomic analysis of immunoprecipitated, gel-excised bands corroborated detection of Arc dimer. Furthermore, Arc dimer was constitutively expressed in naïve cortical, hippocampal and DG tissue, with the lowest levels in the DG. Taken together the results implicate Arc dimer as the predominant low-oligomeric form in mammalian brain, exhibiting regional differences in its constitutive expression and enhanced synaptic activity-evoked expression in LTP.

In-silico Identification and Analysis of Hub Proteins for Designing Novel First-line Anti-seizure Medications

Background: Epilepsy is a seizure-related disease with different symptoms and types, depending on the origin and propagation region of the brain. There are several marketed anti-seizure medications (ASMs) available for choice of treatment by clinicians but there is a huge paucity of ideal first-line ASMs. Objective: The present study was undertaken to identify and get an insight into the major target (hub) proteins, which can be comprehensively used as a platform for designing first-line ASMs. Method: Large-scale text mining was done to generate a data warehouse of available ASMs and their MOAs, followed by the identification of specific isoforms of target proteins for designing next-generation ASMs, using network biology and other in-silico approaches. Results: The study resulted in the identification of 3 major classes of target proteins of major ASMs and their specific isoforms, namely – GABA receptors (GABRA1, GABRB1, and GABARAP); VGSC (α- subunitSCN2A (Nav1.2)) and VGCC (α-subunitCACNA1G (Cav3.1)). The identified proteins were also observed to be concurrent with the target sites of majorly sold ASMs currently. Conclusion: The predicted hub protein families and their specific isoforms can be further validated and comprehensively used to design next-generation novel first-line ASM(s).

Splicing Modulators Are Involved in Human Polyglutamine Diversification via Protein Complexes Shuttling between Nucleus and Cytoplasm.

Length polymorphisms of polyglutamine (polyQs) in triplet-repeat-disease-causing genes have diversified during primate evolution despite them conferring a risk of human-specific diseases. To explain the evolutionary process of this diversification, there is a need to focus on mechanisms by which rapid evolutionary changes can occur, such as alternative splicing. Proteins that can bind polyQs are known to act as splicing factors and may provide clues about the rapid evolutionary process. PolyQs are also characterized by the formation of intrinsically disordered (ID) regions, so I hypothesized that polyQs are involved in the transportation of various molecules between the nucleus and cytoplasm to regulate mechanisms characteristic of humans such as neural development. To determine target molecules for empirical research to understand the evolutionary change, I explored protein-protein interactions (PPIs) involving the relevant proteins. This study identified pathways related to polyQ binding as hub proteins scattered across various regulatory systems, including regulation via PQBP1, VCP, or CREBBP. Nine ID hub proteins with both nuclear and cytoplasmic localization were found. Functional annotations suggested that ID proteins containing polyQs are involved in regulating transcription and ubiquitination by flexibly changing PPI formation. These findings explain the relationships among splicing complex, polyQ length variations, and modifications in neural development.

Dipeptidyl peptidase 4 as a potential serum biomarker for disease activity and treatment response in rheumatoid arthritis.

The treatment of rheumatoid arthritis (RA) related to the disease activity. However, the lack of highly sensitive and simplified markers limits the evaluation of disease activity. We sought to explore potential biomarkers associated with disease activity and treatment response in RA. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic analysis was performed to determine the differentially expressed proteins (DEPs) in serum collected from RA patients with moderate or high disease activity (determined by DAS28) before and after 24weeks of treatment. Bioinformatic analysis were performed for DEPs and hub proteins. In the validation cohort, 15 RA patients were enrolled. Key proteins were validated by enzyme-linked immunosorbent assay (Elisa), correlation analysis and ROC curve. We identified 77 DEPs. The DEPs enriched in humoral immune response, blood microparticle, and serine-type peptidase activity. KEGG enrichment analysis displayed that the DEPs were significantly enriched in cholesterol metabolism and complement and coagulation cascades. Activated CD4+T cell, T follicular helper cell, natural killer cell, and plasmacytoid dendritic cell significantly increased after treatment. Fifteen hub proteins were screened out. Among them, dipeptidyl peptidase 4 (DPP4) was the most significant protein associated with clinical indicators and immune cells. Serum concentration of DPP4 was testified to significantly increase after treatment and inversely correlate with disease activity indicators (ESR, CRP, DAS28-ESR, DAS28-CRP, CDAI, SDAI). Significant reduction was found in the serum CXC chemokine ligand10 (CXC10) and CXC chemokine receptor 3 (CXCR3) after treatment. Overall, our results suggest that serum DPP4 might be a potential biomarker for disease activity assessment and treatment response of RA.