Partially tryptic peptides are often identified in shotgun proteomics using trypsin as the proteolytic enzyme; however, their sources have been controversial. Herein we investigate the impact of in-source fragmentation on shotgun proteomics profiling of three biological samples: a standard protein mixture, a mouse brain tissue homogenate, and mouse plasma. Since the in-source fragments of peptide ions have the same LC elution time as its parental peptide, partially tryptic peptide ions from in-source fragmentation can be distinguished from the other partially tryptic peptides based on their elution time differences from those computationally predicted data. The percentage of partially tryptic peptide identifications resulting from in-source fragmentation in a standard protein digest was observed to be ~60 %. In more complex mouse brain or plasma samples, in-source fragmentation contributed to a less degree of 1–3 % of all identified peptides due to the limit dynamic range of LC-MS/MS measurements. The other major source of partially tryptic peptides in complex biological samples is presumably proteolytic cleavage by endogenous proteases in the samples. Our work also provides a method to identify such proteolytic-derived partially tryptic peptides due to endogenous proteases in the samples by removing in-source fragmentation artifacts from the identified peptides.
in-source fragmentation; partially tryptic; trypsin specificity; predicted elution time
Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used to identify and quantify peptides in complex biological samples. In particular, label-free shotgun proteomics is highly effective for the identification of peptides and subsequently obtaining a global protein profile of a sample. As a result, this approach is widely used for discovery studies. Typically, the objective of these discovery studies is to identify proteins that are affected by some condition of interest (e.g., disease, exposure). However, for complex biological samples, label-free LC-MS proteomics experiments measure peptides and do not directly yield protein quantities. Thus, protein quantification must be inferred from one or more measured peptides. In recent years many computational approaches to compute relative protein quantification of label-free LC-MS data have been published. In this review, we examine the most commonly employed quantification approaches to compute relative protein abundance from peak intensity values, evaluate their individual merits, and discuss challenges in the use of the various computational approaches.
label-free; peak intensity; protein quantification; relative
Antibiotic resistance among highly pathogenic strains of bacteria and fungi is a growing concern in the face of the ability to sustain life during critical illness with advancing medical interventions. The longer patients remain critically ill, the more likely they are to become colonized by multidrug-resistant (MDR) pathogens. The human gastrointestinal tract is the primary site of colonization of many MDR pathogens and is a major source of life-threatening infections due to these microorganisms. Eradication measures to sterilize the gut are difficult if not impossible and carry the risk of further antibiotic resistance. Here, we present a strategy to contain rather than eliminate MDR pathogens by using an agent that interferes with the ability of colonizing pathogens to express virulence in response to host-derived and local environmental factors. The antivirulence agent is a phosphorylated triblock high-molecular-weight polymer (here termed Pi-PEG 15–20) that exploits the known properties of phosphate (Pi) and polyethylene glycol 15-20 (PEG 15-20) to suppress microbial virulence and protect the integrity of the intestinal epithelium. The compound is nonmicrobiocidal and appears to be highly effective when tested both in vitro and in vivo. Structure functional analyses suggest that the hydrophobic bis-aromatic moiety at the polymer center is of particular importance to the biological function of Pi-PEG 15-20, beyond its phosphate content. Animal studies demonstrate that Pi-PEG prevents mortality in mice inoculated with multiple highly virulent pathogenic organisms from hospitalized patients in association with preservation of the core microbiome.
The underlying mechanisms that lead to dramatic differences between closely related pathogens are not always readily apparent. For example, the genomes of Yersinia pestis (YP) the causative agent of plague with a high mortality rate and Yersinia pseudotuberculosis (YPT) an enteric pathogen with a modest mortality rate are highly similar with some species specific differences; however the molecular causes of their distinct clinical outcomes remain poorly understood. In this study, a temporal multi-omic analysis of YP and YPT at physiologically relevant temperatures was performed to gain insights into how an acute and highly lethal bacterial pathogen, YP, differs from its less virulent progenitor, YPT. This analysis revealed higher gene and protein expression levels of conserved major virulence factors in YP relative to YPT, including the Yop virulon and the pH6 antigen. This suggests that adaptation in the regulatory architecture, in addition to the presence of unique genetic material, may contribute to the increased pathogenenicity of YP relative to YPT. Additionally, global transcriptome and proteome responses of YP and YPT revealed conserved post-transcriptional control of metabolism and the translational machinery including the modulation of glutamate levels in Yersiniae. Finally, the omics data was coupled with a computational network analysis, allowing an efficient prediction of novel Yersinia virulence factors based on gene and protein expression patterns.
Computational prediction of protein function is frequently error-prone and incomplete. In Mycobacterium tuberculosis (Mtb), ~25% of all genes have no predicted function and are annotated as hypothetical proteins, severely limiting our understanding of Mtb pathogenicity. Here, we utilize a high throughput, quantitative, activity-based protein profiling (ABPP) platform to probe, annotate, and validate ATP-binding proteins in Mtb. We experimentally validate prior in silico predictions of >250 proteins and identify 72 hypothetical proteins as novel ATP binders. ATP interacts with proteins with diverse and unrelated sequences, providing a new and expanded view of adenosine nucleotide binding in Mtb. Several hypothetical ATP binders are essential or taxonomically limited, suggesting specialized functions in mycobacterial physiology and pathogenicity.
Non-syndromic hearing loss (NSHL) is the most common sensory
impairment in humans. Until recently its extreme genetic heterogeneity
precluded comprehensive genetic testing. Using a platform that couples
targeted genomic enrichment (TGE) and massively parallel sequencing (MPS) to
sequence all exons of all genes implicated in NSHL, we test 100 persons with
presumed genetic NSHL and in so doing establish sequencing requirements for
maximum sensitivity and define MPS quality score metrics that obviate Sanger
validation of variants.
We examined DNA from 100 sequentially collected probands with
presumed genetic NSHL without exclusions due to inheritance, previous
genetic testing, or type of hearing loss. We performed TGE using
post-capture multiplexing in variable pool sizes followed by Illumina
sequencing. We developed a local Galaxy installation on a high
performance-computing cluster for bioinformatics analysis.
To obtain maximum variant sensitivity with this platform
3.2–6.3 million total mapped sequencing reads per sample are
required. Quality score analysis showed that Sanger validation is not
required for 95% of variants. Our overall diagnostic rate was
42% but varied by clinical features from 0% for persons with
asymmetric hearing loss to 56% for persons with bilateral autosomal
These findings will direct the use of TGE and MPS strategies for
genetic diagnosis for NSHL. Our diagnostic rate highlights the need for
further research on genetic deafness focused on novel gene identification
and an improved understanding of the role of non-exonic mutations. The
unsolved families we have identified provide a valuable resource to address
Deafness; hearing loss; targeted genomic enrichment; sequence capture; massively parallel sequencing
Use of elevated electric fields and helium-rich gases has recently enabled differential IMS with resolving power up to R ~ 300. Here we applied that technique to a protein (namely, ubiquitin), achieving R up to ~80 and separating many previously unresolved conformers. While still limited by conformational multiplicity, this resolution is some four times greater than that previously reported using either conventional (drift-tube or traveling-wave) or differential IMS. The capability for fine resolution of protein conformers may open new avenues for proteoform separations in top-down and intact-protein proteomics.
Microbial glycoside hydrolases play a dominant role in the biochemical conversion of cellulosic biomass to high-value biofuels. Anaerobic cellulolytic bacteria are capable of producing multicomplex catalytic subunits containing cell-adherent cellulases, hemicellulases, xylanases, and other glycoside hydrolases to facilitate the degradation of highly recalcitrant cellulose and other related plant cell wall polysaccharides. Clostridium thermocellum is a cellulosome producing bacterium that couples rapid reproduction rates to highly efficient degradation of crystalline cellulose. Herein, we have developed and applied a suite of difluoromethylphenyl aglycone, N-halogenated glycosylamine, and 2-deoxy-2-fluoroglycoside activity-based protein profiling (ABPP) probes to the direct labeling of the C. thermocellum cellulosomal secretome. These activity-based probes (ABPs) were synthesized with alkynes to harness the utility and multimodal possibilities of click chemistry, and to increase enzyme active site inclusion for LC-MS analysis. We directly analyzed ABP-labeled and unlabeled global MS data, revealing ABP selectivity for glycoside hydrolase (GH) enzymes, in addition to a large collection of integral cellulosome-containing proteins. By identifying reactivity and selectivity profiles for each ABP, we demonstrate our ability to widely profile the functional cellulose degrading machinery of the bacterium. Derivatization of the ABPs, including reactive groups, acetylation of the glycoside binding groups, and mono- and disaccharide binding groups, resulted in considerable variability in protein labeling. Our probe suite is applicable to aerobic and anaerobic microbial cellulose degrading systems, and facilitates a greater understanding of the organismal role associated with biofuel development.
The Risk Model is a validated outcome predictor for patients with head and neck squamous cell carcinoma (Brandwein-Gensler et al. in Am J Surg Pathol 20:167–178, 2005; Am J Surg Pathol 34:676–688, 2010). This model may potentially shift treatment paradigms for patients with low-stage cancers, as current protocols dictate that they might receive only primary surgery. Here we test the hypothesis that the Risk Model has added prognostic value for low-stage oral cavity squamous cell carcinoma (OCSCC) patients. 299 patients with Stage I/II OCSCC were characterized according to the Risk Model (Brandwein-Gensler et al. in Am J Surg Pathol 20:167–178, 2005; Am J Surg Pathol 34:676–688, 2010). Cumulative incidence and competing risk analysis were performed for locoregional recurrence (LRR) and disease-specific survival (DSS). Receiver operating characteristic analyses were performed for worst pattern of invasion (WPOI) and the risk categories. 292 patients were analyzed; 30 T1N0 patients (17 %) and 26 T2N0 patients (23 %) developed LRR. Disease-specific mortality occurred in 9 T1N0 patients (6 %) and 9 T2N0 patients (10 %). On multivariable analysis, the Risk Model was significantly predictive of LRR (p = 0.0012, HR 2.41, 95 % CI 1.42, 4.11) and DSS (p = 0.0005, HR 9.16, 95 % CI 2.65, 31.66) adjusted for potential confounders. WPOI alone was also significantly predictive for LRR adjusted for potential confounders with a cut-point of either WPOI-4 (p = 0.0029, HR 3.63, 95 % CI 1.56, 8.47) or WPOI-5 (p = 0.0008, HR 2.55, 95 % CI 1.48, 4.41) and for DSS (cut point WPOI-5, p = 0.0001, HR 6.34, 95 % CI 2.50, 16.09). Given a WPOI-5, the probability of developing locoregional recurrence is 42 %. Given a high-risk classification for a combination of features other than WPOI-5, the probability of developing locoregional recurrence is 32 %. The Risk Model is the first validated model that is significantly predictive for the important niche group of low-stage OCSCC patients.
Risk Model; Low-stage; Oral cavity; Pattern of invasion; Squamous cell carcinoma
Recruitment and retention of health workers is a major concern. Policy initiatives emphasize financial incentives, despite mixed evidence of their effectiveness. Qualitative studies suggest that nurses especially may be more driven by altruistic motivations, but quantitative research has overlooked such values. This paper adds to the literature through characterizing the nature and determinants of nurses’ altruism, based on a cross-country quantitative study.
An experimental ‘dictator game’ was undertaken with 1064 final year nursing students in Kenya, South Africa and Thailand between April 2007 and July 2008. This presents participants with a real financial endowment to split between themselves and another student, a patient or a poor person. Giving a greater share of this financial endowment to the other person is interpreted as reflecting greater altruism.
Nursing students gave over 30% of their initial endowment to others (compared with 10% in similar experiments undertaken in other samples). Respondents in all three countries showed greater generosity to patients and the poor than to fellow students.
Consideration needs to be given to how to appeal to altruistic values as an alternative strategy to encourage nurses to enter the profession and remain, such as designing recruitment strategies to increase recruitment of altruistic individuals who are more likely to remain in the profession.
economics; health services
Patients with advanced squamous cell carcinoma of the head and neck (SCCHN) have limited treatment options. Inhibition of histone deacetylases (HDACs) represents a novel therapeutic approach warranting additional investigation in solid tumors.
A phase II trial of single agent romidepsin, an HDAC inhibitor, was performed in 14 patients with SCCHN who provided consent for pre- and post-therapy samples of accessible tumor, blood and uninvolved oral mucosa. Romidepsin was administered at 13 mg/m2 as a 4-hour intravenous infusion on days 1, 8 and 15 of 28 day cycles, with response assessment by RECIST every 8 weeks.
Objective responses were not observed, although 2 heavily pretreated patients had brief clinical disease stabilization. Observed toxicities were expected, including frequent severe fatigue. Immunohistochemical analysis of 7 pre- and post-treatment tumor pairs demonstrated induction of p21Waf1/Cip1 characteristic of HDAC inhibition, as well as decreased Ki67 staining. Exploratory microarray analyses of mucosal and tumor samples detected changes in gene expression following romidepsin treatment that were most commonly associated with regulation of transcription, cell cycle control, signal transduction, and electron transport. Treatment with romidepsin did not alter the extent of DNA methylation of candidate gene loci (including CDH1 and hMLH1) in SCCHN tumors.
Single agent romidepsin has limited activity for the treatment of SCCHN but can effectively achieve tumor-associated HDAC inhibition. Although tolerability of romidepsin in this setting may be limiting, further evaluation of other HDAC inhibitors in combination with active therapies may be justified.
romidepsin; head and neck cancer; squamous cell carcinoma; histone deacetylase (HDAC) inhibitors; phase II trial
blaSHV genes from Escherichia coli and Salmonella enterica isolates from chicken (n = 19) and pork (n = 1) were identified as blaSHV-2 (n = 5) or blaSHV-2a (n = 15). Eighteen were on plasmids of the incI1 (n = 15), incP (n = 2), and incFIB (n = 1) incompatibility groups. These plasmids were all transferable by conjugation between E. coli and S. enterica.
This study identified and characterized enteropathogenic Escherichia coli (EPEC) in the Canadian food supply. Eighteen of 450 E. coli isolates from food animal sources were identified as atypical EPEC (aEPEC). Several of the aEPEC isolates identified in this study possessed multiple virulence genes, exhibited adherence and attaching and effacing (A/E) lesion formation, disrupted tight junctions, and were coclassified with the extraintestinal pathogenic E. coli (ExPEC) and enterotoxigenic E. coli (ETEC) pathotypes.
Plants represent a large reservoir of organic carbon comprised primarily of recalcitrant polymers that most metazoans are unable to deconstruct. Many herbivores gain access to nutrients in this material indirectly by associating with microbial symbionts, and leaf-cutter ants are a paradigmatic example. These ants use fresh foliar biomass as manure to cultivate gardens composed primarily of Leucoagaricus gongylophorus, a basidiomycetous fungus that produces specialized hyphal swellings that serve as a food source for the host ant colony. Although leaf-cutter ants are conspicuous herbivores that contribute substantially to carbon turnover in Neotropical ecosystems, the process through which plant biomass is degraded in their fungus gardens is not well understood. Here we present the first draft genome of L. gongylophorus, and, using genomic and metaproteomic tools, we investigate its role in lignocellulose degradation in the gardens of both Atta cephalotes and Acromyrmex echinatior leaf-cutter ants. We show that L. gongylophorus produces a diversity of lignocellulases in ant gardens and is likely the primary driver of plant biomass degradation in these ecosystems. We also show that this fungus produces distinct sets of lignocellulases throughout the different stages of biomass degradation, including numerous cellulases and laccases that likely play an important role in lignocellulose degradation. Our study provides a detailed analysis of plant biomass degradation in leaf-cutter ant fungus gardens and insight into the enzymes underlying the symbiosis between these dominant herbivores and their obligate fungal cultivar.
Nitrogen is one of the major nutrients limiting microbial productivity in the ocean, and as a result, most marine microorganisms have evolved systems for responding to nitrogen stress. The highly abundant alphaproteobacterium “Candidatus Pelagibacter ubique,” a cultured member of the order Pelagibacterales (SAR11), lacks the canonical GlnB, GlnD, GlnK, and NtrB/NtrC genes for regulating nitrogen assimilation, raising questions about how these organisms respond to nitrogen limitation. A survey of 266 Alphaproteobacteria genomes found these five regulatory genes nearly universally conserved, absent only in intracellular parasites and members of the order Pelagibacterales, including “Ca. Pelagibacter ubique.” Global differences in mRNA and protein expression between nitrogen-limited and nitrogen-replete cultures were measured to identify nitrogen stress responses in “Ca. Pelagibacter ubique” strain HTCC1062. Transporters for ammonium (AmtB), taurine (TauA), amino acids (YhdW), and opines (OccT) were all elevated in nitrogen-limited cells, indicating that they devote increased resources to the assimilation of nitrogenous organic compounds. Enzymes for assimilating amine into glutamine (GlnA), glutamate (GltBD), and glycine (AspC) were similarly upregulated. Differential regulation of the transcriptional regulator NtrX in the two-component signaling system NtrY/NtrX was also observed, implicating it in control of the nitrogen starvation response. Comparisons of the transcriptome and proteome supported previous observations of uncoupling between transcription and translation in nutrient-deprived “Ca. Pelagibacter ubique” cells. Overall, these data reveal a streamlined, PII-independent response to nitrogen stress in “Ca. Pelagibacter ubique,” and likely other Pelagibacterales, and show that they respond to nitrogen stress by allocating more resources to the assimilation of nitrogen-rich organic compounds.
Pelagibacterales are extraordinarily abundant and play a pivotal role in marine geochemical cycles, as one of the major recyclers of labile dissolved organic matter. They are also models for understanding how streamlining selection can reshape chemoheterotroph metabolism. Streamlining and its broad importance to environmental microbiology are emerging slowly from studies that reveal the complete genomes of uncultured organisms. Here, we report another remarkable example of streamlined metabolism in Pelagibacterales, this time in systems that control nitrogen assimilation. Pelagibacterales are major contributors to metatranscriptomes and metaproteomes from ocean systems, where patterns of gene expression are used to gain insight into ocean conditions and geochemical cycles. The data presented here supply background that is essential to interpreting data from field studies.
Quantitative proteomics analysis of cortical samples of ten Alzheimer’s disease (AD) brains versus ten normally aged brains was performed by following the accurate mass and time tag (AMT) approach with the high resolution LTQ Orbitrap mass spectrometer. More than 1400 proteins were identified and quantitated. A conservative approach of selecting only the consensus results of four normalization methods was suggested and used. A total of 197 proteins were shown to be significantly differentially abundant (p-values<0.05, corrected for multiplicity of testing) in AD versus control brain samples. Thirty seven of these proteins were reported as differentially abundant or modified in AD in the previous proteomics and transcriptomics publications. The rest to the best of our knowledge are new. Mapping of the discovered proteins with bioinformatic tools revealed significant enrichment with differentially abundant proteins of pathways and processes known to be important in AD, including signal transduction, regulation of protein phosphorylation, immune response, cytoskeleton organization, lipid metabolism, energy production, and cell death.
Alzheimer’s disease; brain; cortical samples; proteomics; bioinformatics; normalization
Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.
Human serum glycan profiling with mass spectrometry (MS) has been employed to study several disease conditions and is demonstrating promise for e.g. clinical biomarker discovery. However, the low glycan ionization efficiency and the large dynamic range of glycan concentrations in human sera hinder comprehensive profiling. In particular, large glycans are problematic because they are present at low concentrations and prone to fragmentation. Here we show that, following liquid chromatographic separation on graphite columns, the sub-ambient pressure ionization with nanoelectrospray (SPIN)-MS can expand the serum glycome profile when compared with the conventional atmospheric pressure electrospray ionization (ESI)-MS with a heated capillary inlet. Notably, the ions generated by the SPIN interface were observed at higher charge states for 50% of the annotated glycans. Out of a total of 130 detected glycans, 34 were only detected with the SPIN-MS, resulting in improved coverage of glycan families as well as of glycans with larger numbers of labile monosaccharides.
Salmonella virulence is largely mediated by two type III secretion systems (T3SS) that deliver effector proteins from the bacterium to a host cell; however, the secretion signal is poorly defined. Effector N termini are thought to contain the signal, but they lack homology, possess no identifiable motif, and adopt intrinsically disordered structures. Alternative studies suggest that RNA-encoded signals may also be recognized and that they can be located in the 5′ untranslated leader sequence. We began our study by establishing the minimum sequence required for reporter translocation. Untranslated leader sequences predicted from 42 different Salmonella effector proteins were fused to the adenylate cyclase reporter (CyaA′), and each of them was tested for protein injection into J774 macrophages. RNA sequences derived from five effectors, gtgA, cigR, gogB, sseL, and steD, were sufficient for CyaA′ translocation into host cells. To determine the mechanism of signal recognition, we identified proteins that bound specifically to the gtgA RNA. One of the unique proteins identified was Hfq. Hfq had no effect upon the translocation of full-length CigR and SteD, but injection of intact GtgA, GogB, and SseL was abolished in an hfq mutant, confirming the importance of Hfq. Our results demonstrated that the Salmonella pathogenicity island 2 (SPI-2) T3SS assembled into a functional apparatus independently of Hfq. Since particular effectors required Hfq for translocation, Hfq-RNA complexes may participate in signal recognition.
Liquid chromatography coupled with mass spectrometry is the predominant platform used to analyze proteomics samples consisting of large numbers of proteins and their proteolytic products (e.g., truncated polypeptides) and spanning a wide range of relative concentrations. This review provides an overview of advanced capillary liquid chromatography techniques and methodologies that greatly improve separation resolving power and proteomics analysis coverage, sensitivity, and throughput.
Liquid chromatography; Proteomics; Peptides; Proteins; Column technologies
‘Medical Tourism’ – the phenomenon of people travelling abroad to access medical treatment - has received increasing attention in academic and popular media. This paper reports findings from a study examining effect of inbound and outbound medical tourism on the UK NHS, by estimating volume of medical tourism and associated costs and benefits. A mixed methods study it includes analysis of the UK International Passenger Survey (IPS); interviews with 77 returning UK medical tourists, 63 policymakers, NHS managers and medical tourism industry actors policymakers, and a review of published literature. These informed costing of three types of treatments for which patients commonly travel abroad: fertility treatment, cosmetic and bariatric surgery. Costing of inbound tourism relied on data obtained through 28 Freedom-of-Information requests to NHS Foundation Trusts. Findings demonstrate that contrary to some popular media reports, far from being a net importer of patients, the UK is now a clear net exporter of medical travellers. In 2010, an estimated 63,000 UK residents travelled for treatment, while around 52,000 patients sought treatment in the UK. Inbound medical tourists treated as private patients within NHS facilities may be especially profitable when compared to UK private patients, yielding close to a quarter of revenue from only 7% of volume in the data examined. Costs arise where patients travel abroad and return with complications. Analysis also indicates possible savings especially in future health care and social costs averted. These are likely to be specific to procedures and conditions treated. UK medical tourism is a growing phenomenon that presents risks and opportunities to the NHS. To fully understand its implications and guide policy on issues such as NHS global activities and patient safety will require investment in further research and monitoring. Results point to likely impact of medical tourism in other universal public health systems.
Mucoepidermoid carcinoma (MEC) is a relatively common salivary tumor with varying potential for aggressive behavior. Mucoepidermoid carcinoma grading has evolved from descriptive two-tiered schemata to more objective three-tiered systems. In 2001, we published a grading system Brandwein et al. in Am J Surg Pathol 25:835–845, (2001) which modified the prevailing criteria of Auclair et al. in Cancer 69:2021–2030 (1992), and included additional features of aggressive MEC. Here we seek to validate our modified grading system in a new multicenter cohort. The retrospective cohort consisted of 76 patients with confirmed MEC and known outcome data. The resection specimens were reviewed and uniformly graded according to our modified criteria Brandwein et al. in Am J Surg Pathol 25:835–845 (2001), and the Auclair criteria Auclair et al. in Cancer 69:2021–2030, (1992), Goode et al. in Cancer 82:1217–1224, (1998). Case distribution was as follows: Montefiore Medical Center: 41 (1977–2009), University of Alabama at Birmingham: 21 (1999–2010), and Rhode Island Hospital: 14, (1995–2011). Patient age ranged from 7 to 81 years (mean 51 years). The female to male ratio was 3:1. The most commonly involved sites were: parotid: n = 39 (51 %), palate: n = 10 (13 %), retromolar trigone: n = 6 (8 %), buccal: n = 5 (7 %), and submandibular gland: n = 5 (7 %). The modified criteria upgraded 41 % MEC; 20/25 MEC from AFIP Grade 1 to Grade 2 and 5/25 from AFIP Grade 1 to Grade 3. Eleven patients had positive lymph nodes; the AFIP MEC grade for cases were: Grade 1–3/11, Grade 2–1/11, and Grade 3–7/11; the modified grading criteria distribution for these cases were Grade 1: 0/11, Grade 2: 1/11, and Grade 3: 10/11. Nine patients developed disease progression after definitive treatment. High-stage and positive lymph node status were significantly associated with disease progression (p = 0.0003 and p < 0.0001, respectively). For the nine patients with disease progression, the modified grading schema classified eight MEC as Grade 3 and one as Grade 2. By comparison, the AFIP grading schema classified three of these MEC as Grade 1, and the remaining six as Grade 3. Despite the fact that this multicenter retrospective study accrued 76 patients with outcome, the predictive performance of the two grading schema could not be compared due to the few patients who experienced disease progression and were also reclassified with respect to grade (n = 3).
Mucoepidermoid carcinoma; Grading; Pattern of invasion; AFIP; Modified criteria
During acute Lyme disease, bacteria can disseminate to the central nervous system (CNS) leading to the development of meningitis and other neurologic symptoms. Here we have analyzed pooled cerebrospinal fluid (CSF) allowing a deep view into the proteome for patients diagnosed with early-disseminated Lyme disease and CSF inflammation. Additionally, we analyzed individual patient samples and quantified differences in protein abundance employing label-free quantitative mass spectrometry based methods. We identified 108 proteins that differ significantly in abundance in patients with acute Lyme disease from controls. Comparison between infected patients and control subjects revealed differences in proteins in the CSF associated with cell death localized to brain synapses and others that likely originate from brain parenchyma.
Proteomics; mass spectrometry; Lyme disease; cerebrospinal fluid; Lyme neuroborreliosis