Two-dimensional Liquid Chromatography-tandem Mass Spectrometry Research Articles

Genetic regulation of human brain proteome reveals proteins implicated in psychiatric disorders.

Psychiatric disorders are highly heritable yet polygenic, potentially involving hundreds of risk genes. Genome-wide association studies have identified hundreds of genomic susceptibility loci with susceptibility to psychiatric disorders; however, the contribution of these loci to the underlying psychopathology and etiology remains elusive. Here we generated deep human brain proteomics data by quantifying 11,608 proteins across 268 subjects using 11-plex tandem mass tag coupled with two-dimensional liquid chromatography-tandem mass spectrometry. Our analysis revealed 788 cis-acting protein quantitative trait loci associated with the expression of 883 proteins at a genome-wide false discovery rate <5%. In contrast to expression at the transcript level and complex diseases that are found to be mainly influenced by noncoding variants, we found protein expression level tends to be regulated by non-synonymous variants. We also provided evidence of 76 shared regulatory signals between gene expression and protein abundance. Mediation analysis revealed that for most (88%) of the colocalized genes, the expression levels of their corresponding proteins are regulated by cis-pQTLs via gene transcription. Using summary data-based Mendelian randomization analysis, we identified 4 proteins and 19 genes that are causally associated with schizophrenia. We further integrated multiple omics data with network analysis to prioritize candidate genes for schizophrenia risk loci. Collectively, our findings underscore the potential of proteome-wide linkage analysis in gaining mechanistic insights into the pathogenesis of psychiatric disorders.

Development and validation of a multi-class analysis of pesticides in corn products by comprehensive two-dimensional liquid chromatography-tandem mass spectrometry

Due to the growing trend of organic food, there is still concern over the use of chemicals and pesticides in agriculture. In recent years, several procedures have been validated for the control of pesticides in food. In the present research, a comprehensive two-dimensional liquid chromatography coupled with tandem mass spectrometry is proposed for the first time for a multi-class analysis of 112 pesticides in corn-based products. Notably, a “reduced” QuEChERS-based method as extraction and clean-up procedure prior to the analysis, was successfully employed. Limits of quantification values were lower than the ones fixed by the European legislation; intra-day and inter-day precision were lower than 12.9% and 15.1%, respectively (at the 500 μg/kg concentration levels). Over 70% of the analytes provided recoveries between 70% and 120% range (at 50, 500 and 1000 µg/kg concentration levels) with standard deviation values below 20%. In addition, matrix effect values were in the range between 13% to 161%. The method was applied to the analysis of real samples, and three pesticides were detected at trace levels in both samples. The findings of this work pave the way for the treatment of complex matrices such as corn products.

Proteomics Profiling Reveals Regulation of Immune Response to Salmonella enterica Serovar Typhimurium Infection in Mice.

Regulation of the immune response to Salmonella enterica serovar Typhimurium (S. Typhimurium) infection is a complex process, influenced by the interaction between genetic and environmental factors. Different inbred strains of mice exhibit distinct levels of resistance to S. Typhimurium infection, ranging from susceptible (e.g., C57BL/6J) to resistant (e.g., DBA/2J) strains. However, the underlying molecular mechanisms contributing to the host response remain elusive. In this study, we present a comprehensive proteomics profiling of spleen tissue from C57BL/6J and DBA/2J strains with different doses of S. Typhimurium infection by tandem mass tag labeling coupled with two-dimensional liquid chromatography-tandem mass spectrometry (TMT-LC/LC-MS/MS). We identified and quantified 3,986 proteins, resulting in 475 differentially expressed proteins (DEPs) between C57BL/6J and DBA/2J strains. Functional enrichment analysis unveiled that the mechanisms of innate immune responses to S. Typhimurium infection could be associated with several signaling pathways, including the interferon (IFN) signaling pathway. We experimentally validated the roles of the IFN signaling pathway in the innate immune response to S. Typhimurium infection using an IFN-γ neutralization assay. We further illustrated the importance of macrophage and proinflammatory cytokines in the mechanisms underlying the resistance to S. Typhimurium using quantitative reverse transcription-PCR (qRT-PCR). Taken together, our results provided new insights into the genetic regulation of the immune response to S. Typhimurium infection in mice and might lead to the discovery of potential protein targets for controlling salmonellosis.

A sensitive, heart-cutting, two-dimensional liquid chromatography–tandem mass spectrometry method for the determination of mometasone furoate in human plasma: Application for a bioequivalence study in nasal spray formulations

AbstractWe developed and validated a sensitive, heart-cutting, two-dimensional liquid chromatography–tandem mass spectrometry (2D-LC‒MS/MS) method to determine the concentration of mometasone furoate in human plasma after nasal spray administration. Isotopically labeled mometasone furoate-13C,d6 was used as an internal standard (IS). Plasma samples were prepared using a solid-phase extraction (SPE) method. With this 2D-LC strategy, the analytes were trapped in the first dimension (1D) column, and only judiciously selected portions of the 1D effluent were transferred to the second dimension (2D) column for further separation to obtain high-resolution information. MS/MS quantification was performed in positive ionization mode via multiple-reaction monitoring (MRM). This analytical method was fully validated according to related regulatory guidance, and the results showed that the method is robust and sensitive enough for pharmacokinetic investigation of mometasone furoate with satisfactory linearity from 0.25 to 30 pg mL−1. This method was successfully applied to a bioequivalence (BE) study of mometasone furoate aqueous nasal sprays in healthy volunteers.

Evaluation of indirect-ELISA using eluted antigens from Trichinella spiralis muscle larvae for diagnosis of swine trichinellosis

Trichinellosis is caused by Trichinella spiralis muscle larvae (TsML), which is transmitted to human when they eat infected raw or undercooked meat. T. spiralis infection is detected by an enzyme-linked immunosorbent assay (ELISA) using excretory–secretory antigens (ESAg); however, the preparation of ESAg is challenging, and yields are low, which hampers screening efforts. In this study, crude somatic antigens (CSAg) of TsML with molecular weights (MWs) of 43, 79 and 101 kDa have been identified in swine trichinellosis sera with less cross-reaction with uninfected sera and other parasitic infected sera. After that, the CSAg at MWs of 43, 79 and 101 kDa (TsCSAg-43, TsCSAg-79, and TsCSAg-101, respectively) were isolated from sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The eluted antigens were analyzed by IgG-ELISA for sensitivity and specificity, and specific antigens from the three regions were identified by two-dimensional polyacrylamide gel electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS-MS). The sensitivity of IgG-ELISA using the three eluted antigens was 100% with specificities of 97.77%, 95.54%, 90.63% and for TsCSAg-43, TsCSAg-79, and TsCSAg-101, respectively. The LC-MS-MS results of immunomics showed that 18/20 spots of the antigens with MWs of 43, 79, and 101 kDa represent 11 different proteins identified. TsCSAg-43 showed the highest specificity, indicating that the specific proteins identified, including 45 kDa antigen–trichina [fragment], DNA topoisomerase 2-alpha antigen targeted by protective antibodies, and a conserved hypothetical protein (gi339234223), should be developed and produced in large volumes for further immunodiagnostic studies.

Nanocomposite packaging regulates energy metabolism of mushrooms (Flammulina filiformis) during cold storage: A study on mitochondrial proteomics

Energy deficit leads to quality deterioration of fresh mushrooms. To investigate the metabolic energy differences between Flammulina filiformis packaged with nanocomposite (NP) and conventional polyethylene (CP) bags, tandem mass tags (TMT) labeling combined with two-dimensional liquid chromatography-tandem mass spectrometry technique and biochemical analysis were applied. Results showed that the ATP and energy charge level in NP group were higher with a delayed decrease compared to those in CP. The enzyme activities in EMP and TCA processes were inhibited by NP, while Mn-SOD activity and gene expression of electron transport chain complexes were enhanced. TMT-based proteomic analysis revealed that the most differentially expressed proteins were mitochondria proteins and NP could inhibit the carbohydrate and energy metabolism bioprocesses. In summary, the mitochondrial integrity and function of NP packed F. filiformis were protected and the balance of energy supplement was maintained, resulting in better postharvest quality during cold storage.

Downregulation of Calreticulin and Annexin A2 Expression in Acquired Middle Ear Cholesteatoma by 2-DE Analysis.

Many factors are thought to be associated with the development of cholesteatoma, while the mechanisms of its formation remain unclear. This study aimed to identify the potential mechanisms of the proliferation and growth of cholesteatoma by analysis of the differential expressions of proteins in cholesteatoma and retroauricular skin tissue collected from the same patients. The present study is a retrospective study performed in an academic medical center. Comparative proteomics analyses using two-dimensional gel electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), in addition to immunohistochemical analysis, were conducted to identify differentially-expressed proteins in cholesteatoma tissue as compared with retroauricular skin tissue. Western blotting was also employed to verify the expression patterns of the specific proteins identified by 2-DE and to measure the changes in potential modulators related to cholesteatoma proliferation and growth. Calreticulin (CRT) and annexin A2 (AnxA2) were identified as being differentially-expressed in cholesteatoma by 2-DE and LC-MS/MS, the results of which were in agreement with the results of immunohistochemical analysis and western blotting. Downregulation of CRT and AnxA2 were observed in cholesteatoma. Our data suggests that CRT and AnxA2 downregulation are seen in cholesteatoma compared to retroauricular skin. We speculate that the reduced expression of CRT and the persistent inflammatory response play important roles in the epithelial proliferation of cholesteatoma.

Diverse Aquatic Animal Matrices Play a Key Role in Survival and Potential Virulence of Non-O1/O139 Vibrio cholerae Isolates.

Vibrio cholerae can cause pandemic cholera in humans. The waterborne bacterium is frequently isolated from aquatic products worldwide. However, current literature on the impact of aquatic product matrices on the survival and pathogenicity of cholerae is rare. In this study, the growth of eleven non-O1/0O139 V. cholerae isolates recovered from eight species of commonly consumed fish and shellfish was for the first time determined in the eight aquatic animal matrices, most of which highly increased the bacterial biomass when compared with routine trypsin soybean broth (TSB) medium. Secretomes of the V. cholerae isolates (draft genome size: 3,852,021–4,144,013 bp) were determined using two-dimensional gel electrophoresis (2DE-GE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques. Comparative secretomic analyses revealed 74 differential extracellular proteins, including several virulence- and resistance-associated proteins secreted by the V. cholerae isolates when grown in the eight matrices. Meanwhile, a total of 8,119 intracellular proteins were identified, including 83 virulence- and 8 resistance-associated proteins, of which 61 virulence-associated proteins were absent from proteomes of these isolates when grown in the TSB medium. Additionally, comparative genomic and proteomic analyses also revealed several strain-specific proteins with unknown functions in the V. cholerae isolates. Taken, the results in this study demonstrate that distinct secretomes and proteomes induced by the aquatic animal matrices facilitate V. cholerae resistance in the edible aquatic animals and enhance the pathogenicity of the leading waterborne pathogen worldwide.

ITRAQ-Based Proteomic Analysis Reveals Potential Serum Biomarkers for Pediatric Non-Hodgkin's Lymphoma.

Non-Hodgkin’s lymphoma (NHL) is the third most common malignant tumor among children. However, at initial NHL diagnosis, most cases are at an advanced stage because of nonspecific clinical manifestations and currently limited diagnostic methods. This study aimed to screen and verify potential serum biomarkers of pediatric NHL using isobaric tags for relative and absolute quantification (iTRAQ)-based proteomic analysis. Serum protein expression profiles from children with B-NHL (n=20) and T-NHL (n=20) and healthy controls (n=20) were detected by utilizing iTRAQ in combination with two-dimensional liquid chromatography-tandem mass spectrometry (2D LC–MS/MS) and analyzed by applying Ingenuity Pathway Analysis (IPA). The candidate biomarkers S100A8 and LRG1 were further validated by using enzyme-linked immunosorbent assays (ELISAs). Receiver operating characteristic (ROC) analysis based on ELISA data was used to evaluate diagnostic efficacy. In total, 534 proteins were identified twice using iTRAQ combined with 2D LC–MS/MS. Further analysis identified 79 and 73 differentially expressed proteins in B-NHL and T-NHL serum, respectively, compared with control serum according to our defined criteria; 34 proteins were overexpressed and 45 proteins underexpressed in B-NHL, whereas 45 proteins were overexpressed and 28 proteins underexpressed in T-NHL (p < 0.05). IPA demonstrated a variety of signaling pathways, including acute phase response signaling and liver X receptor/retinoid X receptor (LXR/RXR) activation, to be strongly associated with pediatric NHL. S100A8 and LRG1 were elevated in NHL patients compared to normal controls according to ELISA (p < 0.05), which was consistent with iTRAQ results. The areas under the ROC curves of S100A8, LRG1, and the combination of S100A8 and LRG1 were 0.873, 0.898 and 0.970, respectively. Our findings indicate that analysis of the serum proteome using iTRAQ combined with 2D LC–MS/MS is a feasible approach for biomarker discovery. Serum S100A8 and LRG1 are promising candidate biomarkers for pediatric NHL, and these differential proteins illustrate a novel pathogenesis and may be clinically helpful for NHL diagnosis in the future.

DIA Comparative Proteomic Analysis of Retro-oil Fluid and Vitreous Fluid From Retinal Detachment Patients.

Objectives: There have been reports of unexplained visual loss following intra-ocular silicone oil (SiO) tamponade in retinal detachment patients, yet the underlying mechanism is unknown. The aim of this study was to investigate the mechanisms behind retinal toxicity following intra-ocular SiO tamponade in retinal detachment patients. Methods and Results: Vitreous fluid samples were acquired from 27 patients (27 eyes). Twelve eyes for data-independent acquisition (DIA) were divided into four groups: pars plana vitrectomy (PPV) for rhegmatogenous retinal detachment (RD group), SiO removal after successful retinal reattachment (SO group), cataract surgery after successful retinal reattachment with sterilized air tamponade (FA group), and PPV for epiretinal membrane (ERM group). The remaining 15 eyes were used for enzyme-linked immunosorbent assay analysis. DIA was combined with two-dimensional liquid chromatography–tandem mass spectrometry to find expression changes in the proteome of vitreous. Mean number mass spectra, statistically differentially expressed proteins, gene ontology (GO), pathway representations, and protein interactions were analyzed. GO analysis showed that the protein categories of synapse organization, cell adhesion, and regulation of cell migration in the SO group were differentially expressed compared to the control or FA groups (p < 0.05). Through Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, lysosome and cell adhesion were found to be significantly enriched in the SO group compared to the FA and control groups (p < 0.05). Cadherin 2, transferrin, and lysosome function may partially contribute to silicone oil-related vision loss. Conclusion: Vision loss-inducing novel molecular signatures and pathways that may be associated with SiO toxicity were identified. Transferrin may be a potential visual outcome biomarker for SiO tamponade.

Comparative proteomics and secretomics revealed virulence, and coresistance-related factors in non O1/O139 Vibrio cholerae recovered from 16 species of consumable aquatic animals

Vibrio cholerae can cause pandemic cholera in humans. The bacterium resides in aquatic environments worldwide. Identification of risk factors of V. cholerae in aquatic products is imperative for assuming food safety. In this study, we determined virulence-associated genes, cross-resistance between antibiotics and heavy metals, and genome fingerprinting profiles of non O1/O139 V. cholerae isolates (n = 20) recovered from 16 species of consumable aquatic animals. Secretomes and proteomes of V. cholerae with distinct genotypes and phenotypes were obtained by using two-dimensional gel electrophoresis (2D-GE) and/or liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques. Comparative secretomic analysis revealed 4 common and 45 differential extracellular proteins among 20 V. cholerae strains, including 13 virulence- and 8 resistance-associated proteins. A total of 21,972 intracellular proteins were identified, and comparative proteomic analysis revealed 215 common and 913 differential intracellular proteins, including 22 virulence- and 8 resistance-associated proteins. Additionally, different secretomes and proteomes were observed between V. cholerae isolates of fish and shellfish origins. A number of novel proteins with unknown function and strain-specific proteins were also discovered in the V. cholerae isolates. SignificanceV. cholerae can cause pandemic cholera in humans. The bacterium is distributed in aquatic environments worldwide. Identification of risk factors of V. cholerae in aquatic products is imperative for assuming food safety. Non-O1/O139 V. cholerae has been reported to cause sporadic cholera-like diarrhea and bacteremia diseases, which indicates virulence factors rather than the major cholera toxin (CT) exist. This study for the first time investigated proteomes and secretomes of non-O1/O139 V. cholerae originating from aquatic animals. This resulted in the identification of a number of virulence and coresistance-related factors, as well as novel proteins and strain-specific proteins in V. cholerae isolates recovered from 16 species of consumable aquatic animals. These results fill gaps for better understanding of pathogenesis and resistance of V. cholerae, and also support the increasing need for novel diagnosis and vaccine targets against the leading waterborne pathogen worldwide.

Screening Serum Differential Proteins in Children with Acute Promyelocytic Leukemia Based on iTRAQ Technique

To screen the serum differentially expressed proteins of APL in children. Serum protein expression profiles from 20 cases of normal healthy controls, and 20 cases of APL patients were detected by iTRAQ (isobaric tag for relative and absolute quantification)labeling coupled with two-dimensional liquid chromatography-tandem mass spectrometry(2DLC-MS/MS), and analyzed by bioinformatics software. S100A8, LRG1 and SPARC were validated by ELISA. ROC was built by SPSS 20.0 software. Analysis identified 83 differentially expressed proteins in APL serum compared with control according to our defined criteria, of which 33 proteins were up-regulated and 50 proteins were down-regulated (P<0.05)．IPA analysis revealed that these differentially expressed proteins were related to the function of Cellular Movement, Immune Cell Trafficking, Hematological System Development and Function, Cell-To-Cell Signaling and Interaction, Tissue Development, and involved in a variety of signalling Pathways, the most representative pathways including LXR/RXR Activation and Acute Phase Response Signaling. S100A8 and LRG1 were found to be elevated and SPARC was markedly down-regulated in serum of childhood APL when compared to the normal controls as examined by ELISA (P<0.05), which was consistent with the iTRAQ result. The overall predictive accuracy of each protein was reflected by the area under the ROC curve(AUC), S100A8,LRG1 and SPARC with ROC areas of 0.841,1.000 and 0.944 respectively. S100A8,LRG1 and SPARC may be serve as serum candidate biomarkers for pediatric APL.

Strategy for high-throughput identification of protein complexes by array-based multi-dimensional liquid chromatography-mass spectrometry

Comprehensive elucidation of the composition of multiprotein complexes in model organisms is essential to understand conserved biological systems, but large-scale mapping physical association networks is still challenging due to limited throughput of present methods. In this work, a strategy coupling array-based online two-dimensional liquid chromatography (array-based 2D-LC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was demonstrated for high throughput and in-depth identification of protein complexes from cultured human HeLa cell extracts. Mixed-bed ion-exchange column was employed as the first dimensional (1stD) separating mode and an array consisting of eight reversed phase columns was developed as the second dimensional (2ndD) mode. Taking advantage of array parallel strategy, this online system showed an 8-fold increase in throughput. After array-based online 2D-LC separation, altogether 256 × 2ndD fractions were collected for further LC-MS/MS analysis. Public databases of protein-protein interaction (PPI) and co-elution curves identified by LC-MS were applied to reconstruct the protein complexes. A rigorous inspection was operated by cataloging the protein complexes into chromatographic fractions to minimize the number of false positives. As result, a total number of 4,436 proteins were identified and 26,092 elution curves were graphed. A network consisting of 47,745 PPIs was established among 2,201 proteins and presented 1,530 putative protein complexes with high confidence. Most of the identified PPIs were linked to diverse biological processes and may reveal further disease mechanism and therapeutic strategy.

Acupuncture Regulates Serum Differentially Expressed Proteins in Patients with Chronic Atrophic Gastritis: A Quantitative iTRAQ Proteomics Study.

Objective To identify differentially expressed proteins (DEPs) in sera of patients with chronic atrophic gastritis (CAG) using isobaric tags for relative and absolute quantitation (iTRAQ) and to explore acupuncture's mechanism in CAG. Methods Peripheral sera from 8 healthy volunteers (HC), 8 chronic nonatrophic gastritis (NAG) patients, 8 CAG patients, and 8 CAG patients who underwent acupuncture treatment (CAG + ACU) were collected followed by labeling with iTRAQ reagent for protein identification and quantification using two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS). Representative DEPs were selected through bioinformatics, and proteins were verified by enzyme-linked immunosorbent assay (ELISA). Results A total of 4,448 unique peptides were identified, corresponding to 816 nonredundant proteins. A 1.4-fold difference was used as the threshold. Compared with the HC group, 75 and 106 DEPs were identified from CAG and NAG groups, respectively. Compared with the CAG group, 110 and 66 DEPs were identified from the NAG and CAG + ACU groups, respectively. The DEPs were mainly involved in protein binding and the Notch signaling pathway-related proteins, and the upregulated proteins included actin-binding proteins (thymosin beta-4, tropomyosin-4, profilin-1, transgelin-2), while the downregulated proteins included Notch2 and Notch3. After acupuncture, the expression of these proteins in CAG patients was less differentiated from that in healthy people. The level of the above 6 proteins were verified by ELISA, and the results were similar to the results of iTRAQ analysis. Conclusions Actin-binding proteins and Notch signaling pathway-related proteins were correlated with the development and progression of CAG and thus are potential diagnostic markers for CAG. Acupuncture may play a role in regulating actin-binding proteins and Notch signaling pathway-related proteins to play a therapeutic role in CAG.

Proteomic analysis of human frontal and temporal cortex using iTRAQ-based 2D LC-MS/MS

BackgroundThe human brain is the most complex organ in the body, and it is important to have a better understanding of how the protein composition in the brain regions contributes to the pathogenesis of associated neurological disorders.MethodsIn this study, a comparative analysis of the frontal and temporal cortex proteomes was conducted by isobaric tags of relative and absolute quantification (iTRAQ) labeling and two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS). Brain protein was taken from relatively normal tissue that could not be avoided of damage during emergent surgery of the TBI (traumatic brain injury) patients admitted in Beijing Tiantan Hospital from 2014 to 2017. Eight cases were included. Four frontal lobes and 4 temporal lobes proteome were analyzed and the proteins were quantitated. Gene Ontology (GO), Ingenuity Pathway Analysis (IPA), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used to analyze the biological function of identified proteins, unchanged proteins, and differentially expressed proteins (DEPs).ResultsA total number of 2127 protein groups were identified in the frontal and temporal lobe proteomes. A total of 1709 proteins could be quantitated in both the frontal and temporal cortex. Among 90 DEPs, 14 proteins were screened highly expressed in the temporal cortex, including MAPT, SNCG, ATP5IF1, GAP43, HSPE1, STMN1, NDUFS6, LDHB, SNCB, NDUFA7, MRPS36, EPDR1, CISD1, and RALA. In addition, compared to proteins expressed in the frontal cortex, 14 proteins including EDC4, NIT2, VWF, ASTN1, TGM2, SSB, CLU, HBA1, STOM, CRP, LRG1, SAA2, S100A4, and VTN were a low expression in the temporal cortex. The biological process enrichment showed that unchanged proteins between the frontal and temporal cortex mainly take part in regulated exocytosis, axon guidance, and vesicle-mediated transport. The KEGG pathway analysis showed that unchanged proteins between the frontal and temporal cortex mainly take part in oxidative phosphorylation, carbon metabolism, Huntington’s disease, and Parkinson’s disease.ConclusionsThe majority of proteins are unchanged between the frontal and temporal cortex, and unchanged proteins are closely related to its function. Among DEPs, MATP (tau) is upregulated in the temporal cortex, closely related to Alzheimer’s disease (AD), and is one of the targets for the treatment of AD. CLU is downregulated in the temporal cortex which functions as an extracellular chaperone that prevents aggregation of non-native proteins. It was suggested that the temporal lobe may not be the “functional dumb area” of the traditional view, but could be involved in important neural metabolic circuits.

Vitamin D status at birth and acute respiratory infection hospitalisation during infancy

Hospital admission for acute respiratory infections (ARIs) during early childhood is a global public health concern. Vitamin D deficiency is prevalent during pregnancy and infancy. Evidence indicates that vitamin D supplementation prevents ARIs. To determine whether vitamin D deficiency at birth is associated with ARI hospitalisations during infancy. We performed a nested case-control study in children aged 0-12months. Cases had ≥1 ARI hospitalisation and 4 controls were individually matched to each case. Newborn 25(OH)D concentration was measured on dried blood spots using two-dimensional liquid chromatography-tandem mass spectrometry. Hospital admissions were measured using health care records. Median serum 25(OH)D concentration in cases and controls was compared, and covariates of ARI hospitalisation during infancy were assessed using conditional logistic regression analysis. Six per cent of the cohort (n=384) had an ARI hospitalisation during infancy, and 1536 controls were matched to cases. Median DBS [25(OH)D] was lower among ARI cases than controls (46nmol/l vs. 61nmol/L). Median 25(OH)D levels were lower for those hospitalised ≥2 times (47, IQR 36, 58) vs. those hospitalised once (52, IQR 42, 62) vs. the controls and also lower for those who stayed in the hospital for ≥3days (45, IQR 36, 54) vs 1-2days (48, IQR 38, 59) compared to the controls. After adjustment for season of birth and covariates describing demographic, antenatal, perinatal, and infant characteristics, DBS 25(OH)D concentration (<50nmol/L) at birth was associated with increased odds of ARI hospitalisation during infancy (odds ratio 2.20, 95% confidence interval 1.48, 2.91). Vitamin D deficiency at birth is associated with increased odds of ARI hospitalisations in infants. The findings have implications for a developed country like New Zealand where vitamin D supplementation is not routinely recommended and the burden of ARI hospitalisation in young children is high.

Combined signatures of serum proteome and transcriptome in patients with recurrent aphthous ulcer.

Recurrent aphthous ulcer (RAU) is a common oral disease with unclear mechanism. This study aimed to explore the serum signatures of RAU patients via proteomic and transcriptomic analysis. This study was based on clinical observation. Part of serum was used for clinical tests, while the rest was processed for isobaric tags for relative and absolute quantitation (ITRAQ) labeling coupled with two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS) combined with microRNA (miRNA) microarrays. Bioinformatic analysis was then used to obtain significant signatures, which was verified by ELISA, qRT-PCR, and dual-luciferase reporter gene assays. Clinical data showed that triglyceride level, white blood cell count, and neutrophils percentage were increased in RAU group, while lymphocytes percentage was decreased. ITRAQ-2D LC-MS/MS identified 22 upregulated and 33 downregulated proteins in RAU group. Simultaneously, miRNA microarrays identified 64 upregulated and 31 downregulated miRNAs. After integrative bioinformatic analysis and verification, three miRNA-protein pairs, mainly involved in oxidative stress and inflammation responses, were obtained. Additionally, the interaction network indicated the crucial role of complement and coagulation cascade pathway in RAU. Our study revealed that complement and coagulation cascade pathway, oxidative stress, and inflammation responses may act as vital factors in pathogenesis of RAU.

Abstract PS18-38: Comparative analysis of differentially abundant proteins quantified by LC-MS/MS between flash frozen and laser microdissected OCT-embedded breast tumor samples

Abstract Background: Proteomic studies are typically conducted using flash-frozen (FF) samples utilizing tandem mass spectrometry. However, FF samples are comprised of multiple cell types, making it difficult to ascertain the proteomic profiles of specific cells. Conversely, OCT-embedded (Optimal Cutting Temperature compound) specimens can undergo laser microdissection (LMD) to capture and study specific cell types separately from the cell mixture. In the current study, we compared proteomic data obtained from FF and OCT samples to determine if samples that are stored and processed differently produce comparable results. Methods: Proteins were extracted from FF and OCT-embedded invasive breast tumors from 5 female patients. FF samples were lysed via homogenization (FF/HOM) while OCT-embedded specimens underwent LMD to collect only tumor cells (OCT/LMD-T) or both tumor and stromal cells (OCT/LMD-TS) followed by incubation at 37°C. Proteins were extracted using the illustra triplePrep kit and then trypsin-digested, TMT-labeled, and processed by two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS). Proteins were identified and quantified with Proteome Discoverer v1.4 and comparative analyses performed to identify proteins that were significantly differentially expressed amongst the different processing methods. Results: Among 4,950 proteins consistently quantified across all samples, 216 and 171 proteins were significantly differentially expressed (adjusted p-value &amp;lt; 0.05; |log2 FC| &amp;gt; 1) between FF/HOM vs. OCT/LMD-T and FF/HOM vs. OCT/LMD-TS, respectively, with most proteins being more highly abundant in the FF/HOM samples. PCA and unsupervised hierarchical clustering analysis with these 216 and 171 proteins were able to distinguish FF/HOM from OCT/LMD-T and OCT/LMD-TS samples, respectively. Likewise, PCA analysis and unsupervised clustering analysis using the 402 and 60 significantly differentially enriched GO terms (adjusted p-value (BH) &amp;lt; 0.2) in the FF/HOM vs. OCT/LMD-T and FF/HOM vs OCT/LMD-TS comparisons, respectively, not only distinguished OCT/LMD from FF/HOM samples but also separated LA and LB1 breast cancer subtypes within each storage/preparation method from one another. Although FF/HOM appears to be more similar to OCT/LMD-TS than OCT/LMD-T based on the number of differentially enriched proteins (216 vs. 171; p=0.022) and GO terms (402 vs. 60; p &amp;lt; 2.2 x 10-16), FF/HOM shows no greater similarity to OCT/LMD-TS than OCT/LMD-T based on PCA analysis with either proteins or GO terms ( based on weighted distance for pairwise samples, p = 0.97 from paired t-test). No significantly differentially enriched proteins or GO terms were detected between the OCT/LMD-T and OCT/LMD-TS samples but trended differences were detected. Conclusions: The proteomic profiles of the OCT/LMD-TS samples were more similar to those from OCT/LMD-T samples than FF/HOM samples, suggesting a strong influence from the sample processing methods. These results indicate that in LC-MS/MS proteomic studies, FF/HOM samples exhibit different protein profiles from OCT/LMD samples and thus, results from these two different methods cannot be directly compared. Our study also provides preliminary data for designing new studies to explore why OCT/LMD-TS samples are more similar to OCT/LMD-T than to FF/HOM samples, and to separate LA from LB1 samples. Disclaimer: The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views, opinions or policies of USUHS, HJF, the DOD or the Departments of the Army, Navy or Air Force. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government. Citation Format: Lori A. Sturtz, Guisong Wang, Punit Shah, Richard Searfoss, Praveen-Kumar Raj-Kumar, Jeffrey A. Hooke, J. Leigh Fantacone-Campbell, Brenda Deyarmin, Mary Lou Cutler, Rangaprasad Sarangarajan, Niven R. Narain, Hai Hu, Michael A. Kiebish, Albert J. Kovatich, Craig D. Shriver. Comparative analysis of differentially abundant proteins quantified by LC-MS/MS between flash frozen and laser microdissected OCT-embedded breast tumor samples [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS18-38.

Quantitative proteomic profiling of Cervicovaginal fluid from pregnant women with term and preterm birth

BackgroundPreterm birth (PTB) is one of major causes of perinatal mortality and neonatal morbidity, but knowledge of its complex etiology is still limited. Here we present cervicovaginal fluid (CVF) protein profiles of pregnant women who subsequently delivered at spontaneous preterm or term, aiming to identify differentially expressed CVF proteins in PTB and term birth.MethodsThe CVF proteome of women who sequentially delivered at preterm and term was analyzed using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with two-dimensional nanoflow liquid chromatography-tandem mass spectrometry (2D-nLC-MS/MS). We compared the CVF proteome of PTB (n = 5) and control subjects (term birth, n = 7) using pooled control CVF (term birth, n = 20) as spike-in standard.ResultsWe identified 1294 CVF proteins, of which 605 were newly identified proteins. Of 990 proteins quantified in both PTB and term birth, 52 proteins were significantly up/down-regulated in PTB compared to term birth. The differentially expressed proteins were functionally associated to immune response, endopeptidase inhibitors and structural constituent of cytoskeleton. Finally, we confirm the down-regulation of SERPINB7 (a serine-type protease inhibitor) in PTB compared to control by Western blot.ConclusionsTaken together, our study provide quantitative CVF proteome profiles of pregnant women who ultimately delivered at preterm and term. These promising results could help to improve the understanding of PTB etiology and to discover biomarkers for asymptomatic PTB.

Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells.

T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) to histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis by MS can detect species missed by bottom-up approaches. We used a novel approach of online two-dimensional liquid chromatography-tandem MS with high-resolution reversed-phase liquid chromatography (RPLC), alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. The first online RPLC separation sorted histone families, then RPLC or weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative identifications were assigned by matching proteoform masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for histone-intact protein PTM mapping (HiPTMap) to identify and quantify proteoforms purified from CD8 T cells after in vivo influenza infection. Activation significantly altered PTMs following influenza infection, histone maps changed as T cells migrated to the site of infection, and T cells responding to secondary infections had significantly more transcription enhancing modifications. Thus, HiPTMap identified and quantified proteoforms and determined changes in CD8 T cell histone PTMs over the course of infection.