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Flat cultures of mammalian cells are a widely used in vitro approach for understanding cell physiology, but this system is limited in modeling solid tissues due to unnaturally rapid cell replication. This is particularly challenging when modeling mature chromatin, as fast replicating cells are frequently involved in DNA replication and have a heterogeneous polyploid population. Presented below is a workflow for modeling, treating, and analyzing quiescent chromatin modifications using a three-dimensional (3D) cell culture system. Using this protocol, hepatocellular carcinoma cell lines are grown as reproducible 3D spheroids in an incubator providing active nutrient diffusion and low shearing forces. Treatment with sodium butyrate and sodium succinate induced an increase in histone acetylation and succinylation, respectively. Increases in levels of histone acetylation and succinylation are associated with a more open chromatin state. Spheroids are then collected for isolation of cell nuclei, from which histone proteins are extracted for the analysis of their post-translational modifications. Histone analysis is performed via liquid chromatography coupled online with tandem mass spectrometry, followed by an in-house computational pipeline. Finally, examples of data representation to investigate the frequency and occurrence of combinatorial histone marks are shown.

Proteomics studies generate tables with thousands of entries. A significant component of being a proteomics scientist is the ability to process these tables to identify regulated proteins. Many bioinformatics tools are freely available for the community, some of which within reach for scientists with limited or no background in programming and statistics. However, proteomics has become popular in most other biological and biomedical disciplines, resulting in more and more studies where data processing is delegated to specialists that are not lead authors of the scientific project. This creates a risk or at least a limiting factor, as the biological interpretation of a dataset is contingent of a third-party specialist transforming data without the input of the project leader. We acknowledge in advance that dedicated scripts and software have a higher level of sophistication; but we hereby claim that the approach we describe makes proteomics data processing immediately accessible to every scientist. In this paper, we describe key steps of the typical data transformation, normalization and statistics in proteomics data analysis using a simple spreadsheet. This manuscript aims to demonstrate to those who are not familiar with the math and statistics behind these workflows that a proteomics dataset can be processed, simplified and interpreted in software like Microsoft Excel. With this, we aim to reach the community of non-specialists in proteomics to find a common language and illustrate the basic steps of -omics data processing.

The immune system has been described to play a role in the development of Alzheimer’s disease (AD), but the distribution of immunoglobulins and their subclasses in brain tissue has not been explored. In this study, examination of pathologically diagnosed frontal cortex gray matter revealed significantly higher levels of IgM and IgG in late-stage AD (Braak and Braak stages V and VI) compared to age-matched controls. While levels of IgG2 and IgG4 constant region fragments were higher in late-stage AD, concentration of native–state IgG4 with free Fc regions was increased in AD III and VI. RNA analysis did not support parenchymal B-cell production of IgG4 in AD III and V, indicating possible peripheral or meningeal B-cell involvement. Changes in the profile of IgM, IgG and IgG subclasses in AD frontal cortex may provide insight into understanding disease pathogenesis and progression.

OBJECTIVES/GOALS: Murine and clinical data suggest that antibody-dependent cellular cytotoxicity (ADCC) is associated with greater protection against disseminated neonatal HSV disease. To quantify the relative transfer of Abs with different functions and targets, we conducted a prospective study of mother-infant term and preterm dyads pre and during COVID-19 METHODS/STUDY POPULATION: Total and HSV lysate, glycoprotein D (gD) and glycoprotein B (gB)-specific IgG, IgG1 and IgG3 as well as HSV neutralizing Abs (nAbs) and ADCC were quantified in paired 3rd-trimester pregnant women and their newborns (cord) blood. Transfer ratios (TR) were defined as cord:maternal Ab levels. IgG1 and IgG3 subclass and gD or gB-specific Abs were isolated by column purification and glycan profiles were assessed by mass spectrometry. The study population included 21 term and 15 preterm dyads who were HSV-1 (+/- HSV-2) seropositive enrolled between 2018-2019 (pre-COVID) and 25 additional HSV-1 (+/- HSV-2) seropositive term dyads whose mothers were SARS-CoV-2 PCR and COVID Ab+ at delivery; 14 were asymptomatic and 11 had mild-moderate COVID disease. None of the mothers had active genital HSV lesions during delivery RESULTS/ANTICIPATED RESULTS: Anti-HSV IgG, IgG1 and IgG3 TR were higher in term vs. preterm dyads (p

DNA modifications are small covalent chemical groups that modify nucleotides to regulate DNA readout. Anomalous abundance and genome-wide localization of these modifications can negatively tune gene expression and propagate into unbalanced epigenetics regulation, which is known to be associated with multiple conditions such as cancer, diabetes and aging. We present a direct injection mass spectrometry (DI-MS) platform that offers fast, accurate and precise quantitation of global levels of DNA cytidine methylation (mC) and hydroxymethylation (hmC) in less than one minute per sample. On the contrary to most methods adopting mass spectrometry for the analysis of nucleotide modifications, in this DI-MS approach we eliminate the use of liquid chromatography, increasing throughput, eliminating issues of carryover and batch effects caused by column contamination across samples. In addition, potential biases in detection efficiency of modified nucleotides with different binding efficiency to stationary phases is eliminated, as no chromatographic separation is adopted. This method can analyze >1000 samples per day, overcoming the throughput of next-generation sequencing.•Direct injection mass spectrometry improves throughput and precision compared to liquid chromatography.•Direct injection can be used to quantify in less than one minute global levels of DNA methylation and hydroxymethylation.•The unbiased acquisition can be potentially utilized to analyze other nucleotide modifications., Graphical abstract Image, graphical abstract

The intracellular parasite Toxoplasma gondii infects a large proportion of humans worldwide and can cause adverse complications in the settings of immune-compromise and pregnancy. T. gondii thrives within many different cell types due in part to its residence within a specialized and heavily modified compartment in which the parasite divides, termed the parasitophorous vacuole. Within this vacuole, numerous proteins optimize intracellular survival following their secretion by the parasite. We investigated the contribution of one of these proteins, TgPPM3C, predicted to contain a PP2C-class serine/threonine phosphatase domain and previously shown to interact with the protein MYR1, an essential component of a putative vacuolar translocon that mediates effector export into the host cell. Parasites lacking the TgPPM3C gene exhibit a minor growth defect in vitro, are avirulent during acute infection in mice, and form fewer cysts in mouse brain during chronic infection. Phosphoproteomic assessment of TgPPM3C deleted parasite cultures demonstrated alterations in the phosphorylation status of many secreted vacuolar proteins including two exported effector proteins, GRA16 and GRA28, as well as MYR1. Parasites lacking TgPPM3C are defective in GRA16 and GRA28 export, but not in the export of other MYR1-dependant effectors. Phosphomimetic mutation of two GRA16 serine residues results in export defects, suggesting that de-phosphorylation is a critical step in the process of GRA16 export. These findings provide another example of the emerging role of phosphatases in regulating the complex environment of the T. gondii parasitophorous vacuole and influencing the export of specific effector proteins from the vacuolar lumen into the host cell., Author summary The flexible life cycle of the intracellular parasite Toxoplasma gondii allows it to infect many different types of warm-blooded hosts, as well as diverse cell types once inside the host organism. This formidable achievement is partly mediated by the establishment of a unique compartment following host cell invasion, termed the parasitophorous vacuole. While advancements have been made in cataloguing Toxoplasma secreted proteins that reside within this vacuole, the specific functions and contributions of many of these secreted parasite “tools” remain elusive. Here, we assessed the contribution of a parasite vacuolar protein called TgPPM3C, predicted to function as an enzyme that dephosphorylates other proteins. We found that deleting the TgPPM3C gene in the parasite results in a profound virulence defect during infection in mice, likely due to the dysregulated phosphorylation status of many vacuolar proteins detected by phosphoproteomic analysis of TgPPM3C-deleted parasites. We found that the phosphorylation status of one such protein, GRA16, influences its ability to cross the parasitophorous vacuole membrane and enter the host cell, where it is known to induce host transcriptional changes that benefit parasite growth. These findings illustrate the emerging role of Toxoplasma vacuolar phosphatases in regulating host-parasite interactions during infection.

Toxoplasma gondii is a highly successful parasite that infects a significant portion of the human population. As an intracellular parasite, T. gondii thrives within many different cell types due to its residence in the parasitophorous vacuole, a specialized and heavily modified compartment in which parasites divide. Within this vacuole, numerous secreted proteins facilitate functions that optimize intracellular survival. We characterized one such protein, TgPPM3C, which is predicted to contain a domain belonging to the PP2C class of serine/threonine phosphatases and is secreted by both tachyzoites and differentiating bradyzoites into the vacuolar lumen. Genetic deletion of TgPPM3C established that parasites lacking this predicted phosphatase exhibit a minor growth defect in vitro, are avirulent during acute infection in mice, and form fewer cysts in mouse brain during chronic infection. A label-free phosphoproteomic approach was utilized to identify putative TgPPM3C substrates and demonstrated several secreted proteins with altered phosphorylation status in the absence of TgPPM3C. Altered phosphorylation status was seen in MYR1, a protein essential to the process of protein effector export from the parasitophorous vacuole into the host cell, and in GRA16 and GRA28, two exported effector proteins. Defects were seen in the export of GRA16 and GRA28, but not the effector TgIST, in the TgPPM3C knockout strain. Parasites lacking TgPPM3C also exhibited defects in host c-Myc induction, a process influenced by effector export. Phosphomimetic mutations of GRA16 serine residues recapitulated export defects, implicating de-phosphorylation as an important process in facilitating the export of GRA16. These findings provide an example of the emerging critical role that phosphatases play in regulating the complex environment of the T. gondii parasitophorous vacuole.

Chromatin accessibility is a major regulator of gene expression. Histone writers/erasers have a critical role in chromatin compaction, as they “flag” chromatin regions by catalyzing/removing covalent post-translational modifications on histone proteins. Anomalous chromatin decondensation is a common phenomenon in cells experiencing aging and viral infection. Moreover, about 50% of cancers have mutations in enzymes regulating chromatin state. Numerous genomics methods have evolved to characterize chromatin state, but the analysis of (in)accessible chromatin from the protein perspective is not yet in the spotlight. We present an overview of the most used approaches to generate data on chromatin accessibility and then focus on emerging methods that utilize mass spectrometry to quantify the accessibility of histones and the rest of the chromatin bound proteome. Mass spectrometry is currently the method of choice to quantify entire proteomes in an unbiased large-scale manner; accessibility on chromatin of proteins and protein modifications adds an extra quantitative layer to proteomics dataset that assist more informed data-driven hypotheses in chromatin biology. We speculate that this emerging new set of methods will enhance predictive strength on which proteins and histone modifications are critical in gene regulation, and which proteins occupy different chromatin states in health and disease.

MGAT1 and complex N-glycans are required for spermatogenesis and fertility. Conditional deletion of Mgat1 in spermatogonia (Mgat1 cKO) causes reduced ERK1/2 signaling and the formation of multinucleated germ cells (MNC). Here we show that glycomics analysis of N-glycans released from fixed testis sections and analyzed by MALDI imaging mass spectrometry (MALDI-IMS) revealed a loss of MGAT1 activity in all germ cells based on the accumulation of the oligomannosyl substrate of MGAT1. To determine in which type of germ cell MGAT1 is essential for spermatogenesis, we generated Mgat1 cKO males that also expressed a Mgat1-HA transgene under the control of a germ cell-specific promoter – Stra8 for spermatogonia, Ldhc for spermatocytes and Prm1 for spermatids. Males expressing each Mgat1-HA transgene were fertile, and both males and females transmitted each transgene. When Stra8-Mgat1-HA was expressed in Mgat1 cKO males, spermatogenesis was rescued based on the morphology of testis sections, the complement of N-glycans on basigin, lectin histochemistry, MALDI-IMS, and fertility. By contrast, neither Ldhc-Mgat1-HA expressed in spermatocytes, nor the Prm1-Mgat1-HA transgene expressed in spermatids rescued spermatogenesis or fertility in Mgat1 cKO males. Therefore, MGAT1 must be expressed in spermatogonia for spermatogenesis to proceed normally.

We present a direct injection mass spectrometry (DI-MS) platform that accurately, precisely, and quickly quantitates global levels of DNA cytidine methylation (5mC) and hydroxymethylation (5hmC). Our platform combines an Advion TriVersa NanoMate coupled online to a Thermo Scientific Orbitrap Fusion Lumos. Following digestion to nucleosides, the DNA samples are analyzed at the rate of 0.98) and 0.13% to 1.75% (R(2) > 0.99), respectively. Accurate measurement of C, 5mC and 5hmC is achieved by optimizing in-source fragmentation to obtain a population of up to 93% of just the nucleoside base. This protocol minimizes base dimer formation and partial base-deoxyribose dissociation in gas phase and greatly improves modified base quantitation. We also demonstrate that DI-MS overcomes biases in differential chromatographic retention and issues of sample degradation in the autosampler due to its high throughput. Finally, we present an application of our workflow to quantify DNA modifications on a batch of 81 samples in about 1.5 hours.

Male germ cells are sensitive to heat stress and testes must be maintained outside the body for optimal fertility. However, no germ cell intrinsic mechanism that protects from heat has been reported. Here, we identify the germ cell specific Golgi glycoprotein MGAT4D as a protector of male germ cells from heat stress. Mgat4d is highly expressed in spermatocytes and spermatids. Unexpectedly, when the Mgat4d gene was inactivated globally or conditionally in spermatogonia, or mis-expressed in spermatogonia, spermatocytes or spermatids, neither spermatogenesis nor fertility were affected. On the other hand, when males were subjected to mild heat stress of the testis (43 °C for 25 min), germ cells with inactivated Mgat4d were markedly more sensitive to the effects of heat stress, and transgenic mice expressing Mgat4d were partially protected from heat stress. Germ cells lacking Mgat4d generally mounted a similar heat shock response to control germ cells, but could not maintain that response. Several pathways activated by heat stress in wild type were induced to a lesser extent in Mgat4d[−/−] heat-stressed germ cells (NFκB response, TNF and TGFβ signaling, Hif1α and Myc genes). Thus, the Golgi glycoprotein MGAT4D is a novel, intrinsic protector of male germ cells from heat stress.

The emergence and widespread distribution of multi-drug resistant bacteria is considered as a major public health concern. The inabilities to curb severe infections due to antibiotic resistance have increased healthcare costs as well as patient morbidity and mortality. Bacterial biofilms formed by drug-resistant bacteria add additional challenges to treatment. This study describes a sol-gel based nanoparticle system loaded with garlic extract (GE-np) that exhibits: i) slow and sustained release of garlic components; ii) stabilization of the active components; and iii) significant enhancement of antimicrobial and antibiofilm activity relative to the free garlic extract. Also, GE-np were efficient in penetrating and disrupting the well-established methicillin-resistant Staphylococcus aureus (MRSA) biofilms. Overall, the study suggests that GE-np might be a promising candidate for the treatment of chronic infections due to biofilm forming drug-resistant bacteria.

e17036 Background: ARID1A (BAF250A), a member of the SWI/SNF chromatin remodeling complex, is one of the most frequently mutated genes in human cancer. Here we report the discovery of a novel protein-protein interaction between ARID1A and the actin-binding motor protein, non-muscle myosin IIA (NM IIA) encoded by the myosin heavy chain 9 ( MYH9). Methods: The ARID1A immunoprecipitated protein complex was separated by gel electrophoresis followed by analysis of the peptide digested gel bands by C18-Reversed Phase chromatography using an Ultimate 3000 RSLCnano System (Thermo Scientific) equipped with an Acclaim PepMap C18 column (Thermo Scientific) and connected to a TriVersa NanoMate nanoelectrospray source (Advion) and a linear ion trap LTQ-XL mass spectrometer (Thermo Scientific). Protein identification was performed by Mascot search engine v. 2.5.1 (Matrix Science) against NCBI Homo sapiens database. Scaffold software v. 4.5.1 (Proteome Software Inc.) was used to validate the MS/MS peptide and protein identification based on 99% protein and 95% peptide probabilities. Immunoprecipitation and immunoblotting were done to evaluate the protein-protein interaction in ARID1A-wild type cell lines. Isogenic engineered cell lines, ES2 shRNA-control or shRNA- ARID1A stable transfection , and HCT116 control or ARID1A knockout by CRISPR-Cas9 (Horizon Discovery) were used to evaluate the effect of ARID1A loss on NM IIA expression and phosphorylation, and on cell migration by in vitro scratch assay with time lapse imaging. Results: Scaffold analysis of peptide spectra identified NM IIA with > 99% probability in the ARID1A immunopurified protein complex. In the ARID1A wildtype cell lines ES2 and KLE, endogenous NM IIA co-immunoprecipitated with ARID1A and vice versa. ES2 sh ARID1A cells had decreased total and phosphorylated NM IIA expression, and impaired cell migration compared to control cells. Similarly, HCT116 ARID1A homozygous knockout cells had impaired cell migration compared with HCT116 control cells. Conclusions: We report for the first time that ARID1A interacts with NM IIA to regulate cancer cell motility. Further investigation is ongoing to elucidate the significance of this newly identified function of ARID1A.

Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) (MALDI-IMS) provides a technical means for simultaneous analysis of precise anatomic localization and regulation of peptides. We explored the technical capability of matrix-assisted laser desorption ionization mass spectrometry for characterization of peptidomic regulation by an addictive substance along two distinct projection systems in the mouse striatum. The spatial expression patterns of substance P and proenkephalin, marker neuropeptides of two distinct striatal projection neurons, were negatively correlated at baseline. We detected 768 mass/charge (m/z) peaks whose expression levels were mostly negatively and positively correlated with expression levels of substance P and proenkephalin A (amino acids 218-228), respectively, within the dorsal striatum. After nicotine administration, there was a positive shift in correlation of mass/charge peak expression levels with substance P and proenkephalin A (218-228). Our exploratory analyses demonstrate the technical capacity of MALDI-IMS for comprehensive identification of peptidomic regulation patterns along histochemically distinguishable striatal projection pathways.

A Glycomics approach to detect disease is illustrated in the analyses of human tear fluid for rosacea. The diagnosis of ocular rosacea is particularly challenging in a subgroup of patients that do not present with typical facial skin findings but have ocular signs and symptoms. Indeed, up to 90% of patients with ocular rosacea may have neither obvious roseatic skin changes nor a previous diagnosis of rosacea. Tear fluid was collected from 37 subjects (21 controls and 16 patients with ocular rosacea) after conjunctival stimulation with filter (Schirmer) paper. O-linked oligosaccharides were released from tear fluid by beta-elimination and then purified using solid-phase extraction. Mass spectra were recorded on an external source HiResMALDI with a 7.0 T magnet. Mass spectra were obtained in both the positive and negative modes. However, signals were stronger in the negative mode. Tear fluid samples from rosacea patients yielded distinctive clusters of peaks that extend to higher masses. Patients with rosacea presented several oligomeric series that were not found in the controls. To discriminate the ocular rosacea cases from the normal controls, the sum of absolute intensities of 13 series corresponding to nearly 50 identified mass spectrum peaks was used. Thirty-six out of the 37 samples were correctly classified. This yields a sensitivity of 100% (95% CI 79.5-100) and specificity of 95.2% (95% CI 76.2-99.9). The high abundance of oligosaccharides in the tear fluid of patients with rosacea may lead to an objective diagnostic marker for the disease.

One of the principal goals of glycoprotein research is to correlate glycan structure and function. Such correlation is necessary in order for one to understand the mechanisms whereby glycoprotein structure elaborates the functions of myriad proteins. The accurate comparison of glycoforms and quantification of glycosites are essential steps in this direction. Mass spectrometry has emerged as a powerful analytical technique in the field of glycoprotein characterization. Its sensitivity, high dynamic range, and mass accuracy provide both quantitative and sequence/structural information. As part of the 2012 ABRF Glycoprotein Research Group study, we explored the use of mass spectrometry and ancillary methodologies to characterize the glycoforms of two sources of human prostate specific antigen (PSA). PSA is used as a tumor marker for prostate cancer, with increasing blood levels used to distinguish between normal and cancer states. The glycans on PSA are believed to be biantennary N-linked, and it has been observed that prostate cancer tissues and cell lines contain more antennae than their benign counterparts. Thus, the ability to quantify differences in glycosylation associated with cancer has the potential to positively impact the use of PSA as a biomarker. We studied standard peptide-based proteomics/glycomics methodologies, including LC-MS/MS for peptide/glycopeptide sequencing and label-free approaches for differential quantification. We performed an interlaboratory study to determine the ability of different laboratories to correctly characterize the differences between glycoforms from two different sources using mass spectrometry methods. We used clustering analysis and ancillary statistical data treatment on the data sets submitted by participating laboratories to obtain a consensus of the glycoforms and abundances. The results demonstrate the relative strengths and weaknesses of top-down glycoproteomics, bottom-up glycoproteomics, and glycomics methods.

Inactivating mutations of Large reduce the functional glycosylation of alpha-dystroglycan (alpha-DG) and lead to muscular dystrophy in mouse and humans. The N-terminal domain of Large is most similar to UDP-glucose glucosyltransferases (UGGT), and the C-terminal domain is related to the human i blood group transferase beta1,3GlcNAcT-1. The amino acids at conserved motifs DQD+1 and DQD+3 in the UGGT domain are necessary for mammalian UGGT activity. When the corresponding residues were mutated to Ala in mouse Large, alpha-DG was not functionally glycosylated. A similar result was obtained when a DXD motif in the beta1,3GlcNAcT-1 domain was mutated to AIA. Therefore, the first putative glycosyltransferase domain of Large has properties of a UGGT and the second of a typical glycosyltransferase. Co-transfection of Large mutants affected in the different glycosyltransferase domains did not lead to complementation. While Large mutants were more localized to the endoplasmic reticulum than wild-type Large or revertants, all mutants were in the Golgi, and only very low levels of Golgi-localized Large were necessary to generate functional alpha-DG. When Large was overexpressed in ldlD.Lec1 mutant Chinese hamster ovary (CHO) cells which synthesize few, if any, mucin O-GalNAc glycans and no complex N-glycans, functional alpha-DG was produced, presumably by modifying O-mannose glycans. To investigate mucin O-GalNAc glycans as substrates of Large, a new CHO mutant Lec15.Lec1 that lacked O-mannose and complex N-glycans was isolated and characterized. Following transfection with Large, Lec15.Lec1 cells also generated functionally glycosylated alpha-DG. Thus, Large may act on the O-mannose, complex N-glycans and mucin O-GalNAc glycans of alpha-DG.

Structural analysis of sulfated oligosaccharides from kappa-carrageenan of up to ten residues (MW2 kDa) was successfully carried out by positive mode nano-ESI-FTICR-MS together with MS/MS using sustained off-resonance irradiation-collision induced dissociation (SORI-CID). Glycosidic bond cleavage reactions via the B- and Y-types of fragmentation were observed and enabled complete sequencing of the oligosaccharide samples. The positions of the labile sulfate substituents were observable using SORI-CID, enabling the determination of the sequence of the sulfated residues.

The article by Jennifer T. Aguilan, Fabian M. Dayrit, Jinhua Zhang, Milady R. Ninonuevo and Carlito B. Lebrilla which was published in the January issue, Vol. 17, No. 1, pages 96–103, printed with an error in the title. The Greek letter “kappa” (κ) was mistakenly switched to a Greek letter “alpha” (α) in “-Carrageenan.” The actual title should have been “Structural Analysis of κ-Carrageenan Sulfated Oligosaccharides by Positive Mode Nano-ESI-FTICR-MS and MS/MS by SORI-CID” and is now published online in its corrected form on ScienceDirect. The publisher apologizes for the error.

Structural analysis of sulfated oligosaccharides from κ-carrageenan of up to ten residues (MW >2 kDa) was successfully carried out by positive mode nano-ESI-FTICR-MS together with MS/MS using sustained off-resonance irradiation-collision induced dissociation (SORI-CID). Glycosidic bond cleavage reactions via the B- and Y-types of fragmentation were observed and enabled complete sequencing of the oligosaccharide samples. The positions of the labile sulfate substituents were observable using SORI-CID, enabling the determination of the sequence of the sulfated residues.