Incisional hernia following colorectal cancer surgery according to suture technique: Hughes Abdominal Repair Randomized Trial (HART)

BACKGROUND

Incisional hernias cause morbidity and may require further surgery. HART (Hughes Abdominal Repair Trial) assessed the effect of an alternative suture method on the incidence of incisional hernia following colorectal cancer surgery.

METHODS

A pragmatic multicentre single-blind RCT allocated patients undergoing midline incision for colorectal cancer to either Hughes closure (double far-near-near-far sutures of 1 nylon suture at 2-cm intervals along the fascia combined with conventional mass closure) or the surgeon's standard closure. The primary outcome was the incidence of incisional hernia at 1 year assessed by clinical examination. An intention-to-treat analysis was performed.

RESULTS

Between August 2014 and February 2018, 802 patients were randomized to either Hughes closure (401) or the standard mass closure group (401). At 1 year after surgery, 672 patients (83.7 per cent) were included in the primary outcome analysis; 50 of 339 patients (14.8 per cent) in the Hughes group and 57 of 333 (17.1 per cent) in the standard closure group had incisional hernia (OR 0.84, 95 per cent c.i. 0.55 to 1.27; P = 0.402). At 2 years, 78 patients (28.7 per cent) in the Hughes repair group and 84 (31.8 per cent) in the standard closure group had incisional hernia (OR 0.86, 0.59 to 1.25; P = 0.429). Adverse events were similar in the two groups, apart from the rate of surgical-site infection, which was higher in the Hughes group (13.2 versus 7.7 per cent; OR 1.82, 1.14 to 2.91; P = 0.011).

CONCLUSION

The incidence of incisional hernia after colorectal cancer surgery is high. There was no statistical difference in incidence between Hughes closure and mass closure at 1 or 2 years.

REGISTRATION NUMBER

ISRCTN25616490 (http://www.controlled-trials.com).

Optimization of Microflow LC Coupled with Scanning SWATH and Its Application in Hepatocellular Carcinoma Tissues

Scanning SWATH coupled with normal-flow LC has been recently introduced for high-content, high-throughput proteomics analysis, which requires a relatively large amount of sample injection. Here we established the microflow LC coupled with Scanning SWATH for samples with relatively small quantities. First, we optimized several key parameters of the LC and MS settings, including C18 particle size for the analytical column, LC gradient and flow rate, as well as effective ion accumulation time and isolation window width for MS acquisition. We then compared the optimized Scanning SWATH method with the conventional variable window SWATH (referred to as SWATH) method. Results showed that the total ion chromatogram signals in Scanning SWATH were 10 times higher than that of SWATH, and Scanning SWATH identified 12.2-22.2% more peptides than SWATH. Finally, we employed 120 min Scanning SWATH to acquire the proteomes of 62 formalin-fixed, paraffin-embedded (FFPE) tissue samples from 31 patients with hepatocellular carcinoma (HCC). Altogether, 92 334 peptides and 8516 proteins were quantified. Besides the reported biomarkers, including ANXA2, MCM7, SUOX, and AKR1B10, we identified new potential HCC biomarkers such as CST5, TP53, CEBPB, and E2F4. Taken together, we present an optimal workflow integrating microflow LC and Scanning SWATH that effectively improves the protein identification and quantitation.

High-throughput proteomics of nanogram-scale samples with Zeno SWATH MS

The possibility to record proteomes in high throughput and at high quality has opened new avenues for biomedical research, drug discovery, systems biology, and clinical translation. However, high-throughput proteomic experiments often require high sample amounts and can be less sensitive compared to conventional proteomic experiments. Here, we introduce and benchmark Zeno SWATH MS, a data-independent acquisition technique that employs a linear ion trap pulsing (Zeno trap pulsing) to increase the sensitivity in high-throughput proteomic experiments. We demonstrate that when combined with fast micro- or analytical flow-rate chromatography, Zeno SWATH MS increases protein identification with low sample amounts. For instance, using 20 min micro-flow-rate chromatography, Zeno SWATH MS identified more than 5000 proteins consistently, and with a coefficient of variation of 6%, from a 62.5 ng load of human cell line tryptic digest. Using 5 min analytical flow-rate chromatography (800 µl/min), Zeno SWATH MS identified 4907 proteins from a triplicate injection of 2 µg of a human cell lysate, or more than 3000 proteins from a 250 ng tryptic digest. Zeno SWATH MS hence facilitates sensitive high-throughput proteomic experiments with low sample amounts, mitigating the current bottlenecks of high-throughput proteomics.

MetaboKit: a comprehensive data extraction tool for untargeted metabolomics

We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identities from reference spectral libraries, adducts, dimers, in-source fragments (ISF), MS/MS fragmentation spectra, and more importantly the retention time information unique to the chromatography system used in the experiment. Using the customized library, the software performs targeted peak integration for precursor ions in DDA analysis and for precursor and product ions in data independent acquisition (DIA) analysis. With its stringent identification algorithm requiring matches by both MS and MS/MS data, MetaboKit provides identification results with significantly greater specificity than the competing software packages without loss in sensitivity. The proposed MS/MS-based screening of ISFs also reduces the chance of unverifiable identification of ISFs considerably. MetaboKit's quantification module produced peak area values highly correlated with known concentrations in a DIA analysis of the metabolite standards at both MS1 and MS2 levels. Moreover, the analysis of Cdk1Liv-/- mouse livers showed that MetaboKit can identify a wide range of lipid species and their ISFs, and quantitatively reconstitute the well-characterized fatty liver phenotype in these mice. In DIA data, the MS1-level and MS2-level peak area data produced similar fold change estimates in the differential abundance analysis, and the MS2-level peak area data allowed for quantitative comparisons in compounds whose precursor ion chromatogram was too noisy for peak integration.

Ultra-fast proteomics with Scanning SWATH

Accurate quantification of the proteome remains challenging for large sample series and longitudinal experiments. We report a data-independent acquisition method, Scanning SWATH, that accelerates mass spectrometric (MS) duty cycles, yielding quantitative proteomes in combination with short gradients and high-flow (800 µl min-1) chromatography. Exploiting a continuous movement of the precursor isolation window to assign precursor masses to tandem mass spectrometry (MS/MS) fragment traces, Scanning SWATH increases precursor identifications by ~70% compared to conventional data-independent acquisition (DIA) methods on 0.5-5-min chromatographic gradients. We demonstrate the application of ultra-fast proteomics in drug mode-of-action screening and plasma proteomics. Scanning SWATH proteomes capture the mode of action of fungistatic azoles and statins. Moreover, we confirm 43 and identify 11 new plasma proteome biomarkers of COVID-19 severity, advancing patient classification and biomarker discovery. Thus, our results demonstrate a substantial acceleration and increased depth in fast proteomic experiments that facilitate proteomic drug screens and clinical studies.

A comprehensive CHO SWATH-MS spectral library for robust quantitative profiling of 10,000 proteins

Sequential window acquisition of all theoretical fragment-ion spectra (SWATH) is a data-independent acquisition (DIA) strategy that requires a specific spectral library to generate unbiased and consistent quantitative data matrices of all peptides. SWATH-MS is a promising approach for in-depth proteomic profiling of Chinese hamster Ovary (CHO) cell lines, improving mechanistic understanding of process optimization, and real-time monitoring of process parameters in biologics R&D and manufacturing. However, no spectral library for CHO cells is publicly available. Here we present a comprehensive CHO global spectral library to measure the abundance of more than 10,000 proteins consisting of 199,102 identified peptides from a CHO-K1 cell proteome. The robustness, accuracy and consistency of the spectral library were validated for high confidence in protein identification and reproducible quantification in different CHO-derived cell lines, instrumental setups and downstream processing samples. The availability of a comprehensive SWATH CHO global spectral library will facilitate detailed characterization of upstream and downstream processes, as well as quality by design (QbD) in biomanufacturing. The data have been deposited to ProteomeXchange (PXD016047).

Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study

BACKGROUND

This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery.

METHODS

This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery.

RESULTS

A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498).

CONCLUSION

There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.

Expanding the Use of Spectral Libraries in Proteomics

The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

Liquid chromatography coupled to tandem mass spectrometry is the main method for high-throughput identification and quantification of peptides and inferred proteins. Within this field, data-independent acquisition (DIA) combined with peptide-centric scoring, exemplified by SWATH-MS, emerged as a scalable method to achieve deep and consistent proteome coverage across large-scale datasets. Here we discuss the adaptation of statistical concepts developed for discovery proteomics based on spectrum-centric scoring to large-scale DIA experiments analyzed with peptide-centric scoring strategies and provide guidance on their application. We show that optimal tradeoffs between sensitivity and specificity require careful considerations of the relationship between proteins in the samples and proteins represented in the spectral library. We propose the application of a global analyte constraint to prevent accumulation of false positives across large-scale datasets. Furthermore, to increase the quality and reproducibility of published proteomic results, well-established confidence criteria should be reported for detected peptide queries, peptides and inferred proteins.

SWATH-ID: An instrument method which combines identification and quantification in a single analysis

Data-independent acquisition (DIA) approaches, such as SWATH^® -MS, are showing great potential to reliably quantify significant numbers of peptides and proteins in an unbiased manner. These developments have enhanced interest in developing a single DIA method that integrates qualitative and quantitative analysis, eliminating the need of a prebuilt library of peptide spectra, which are created through data-dependent acquisition methods or from public repositories. Here, we introduce a new DIA approach, referred to as "SWATH-ID," which was developed to allow peptide identification as well as quantitation. The SWATH-ID method is composed of small Q1 windows, achieving better selectivity and thus significantly improving high-confidence peptide extractions from data files. Furthermore, the SWATH-ID approach transmits precursor ions without fragmentation as well as their fragments within the same SWATH acquisition period. This provides a single scan that includes all precursor ions within the isolation window as well as a record of all of their fragment ions, substantially negating the need for a survey scan. In this way all precursors present in a small Q1 window are associated with their fragment ions, improving the identification specificity and providing a more comprehensive and in-depth view of protein and peptide species in complex samples.

Abstract P6-01-14: Dissection of the Abl interactor 1 signaling in metastatic breast cancer cells

Abl interactor 1 (Abi1) is a key component of WAVE regulatory complex (WRC) that regulates actin cytoskeleton reorganization, membrane receptor signaling, and intracellular trafficking. Recent in vitro and in vivo studies as well as the studies of human patient samples suggest that Abi1 may play an important role in breast cancer (BC) metastasis. To determine if Abi1 is deregulated in metastatic breast cancer cells, we compared the expression of Abi1 in a panel of human breast cancer cell lines exhibiting distinct metastatic properties. In comparison with low-metastatic ER+/PR+ BC lines MCF-7 and T47D and a non-transforming mammary epithelial cell line MCF-10A, two ER-BC lines CN34 and MDA 231 and their sublines selected by high metastatic potential to bone (231Bo), brain (231Br and CN34Br), and lung (231LM2) show significantly reduced Abi1 protein levels, with greater reduction found in highly metastatic sublines. It is unlikely that the down-regulation of Abi1 expression in these metastatic BC cells occurs at mRNA level, because RT-PCR analysis shows no significant difference in Abi1 mRNA levels among the cells analyzed. Interestingly, despite a reduction in protein level, the tyrosine phosphorylation of Abi1 was increased in CN34, MDA231, and their metastatic sublines compared to low-metastatic BC cells. The tyrosine phosphorylation of Abi1 is stimulated by epidermal growth factor (EGF) in these cells and Abi1 is recruited to EGF receptor (EGFR) upon EGF stimulation. The deregulation of Abi1 in metastatic BC cells is mediated by Abl tyrosine kinases, as the inhibition of Abl family kinases by imatinib not only attenuates EGF-stimulated Abi1 tyrosine phosphorylation but also rescue the down-regulation of Abi1 protein in metastatic BC cells.

These findings are consistent with a role of the EGFR-Abl-Abi1 signaling in BC metastasis. The studies suggest that this pathway may serve as a biomarker for diagnosis and/or prognosis of metastatic breast cancer. We have identified the tyrosine 213 in Abi1 as a major phosphorylation site stimulated by Abl kinases and have generated a unique conditional Abi1 depletion/re-expression system to dissect how the deregulation of the Abi1 signaling contributes to BC metastasis.

Citation Format: Jiang P, Tang H, Hogan H, Tate S, Ryan W, Paul L, Liu X, Zonghan D. Dissection of the Abl interactor 1 signaling in metastatic breast cancer cells [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-01-14.

Population-based cohort study of variation in the use of emergency cholecystectomy for benign gallbladder diseases

Background

The aims of this prospective population-based cohort study were to identify the patient and hospital characteristics associated with emergency cholecystectomy, and the influences of these in determining variations between hospitals.

Methods

Data were collected for consecutive patients undergoing cholecystectomy in acute UK and Irish hospitals between 1 March and 1 May 2014. Potential explanatory variables influencing the performance of emergency cholecystectomy were analysed by means of multilevel, multivariable logistic regression modelling using a two-level hierarchical structure with patients (level 1) nested within hospitals (level 2).

Results

Data were collected on 4744 cholecystectomies from 165 hospitals. Increasing age, lower ASA fitness grade, biliary colic, the need for further imaging (magnetic retrograde cholangiopancreatography), endoscopic interventions (endoscopic retrograde cholangiopancreatography) and admission to a non-biliary centre significantly reduced the likelihood of an emergency cholecystectomy being performed. The multilevel model was used to calculate the probability of receiving an emergency cholecystectomy for a woman aged 40 years or over with an ASA grade of I or II and a BMI of at least 25·0 kg/m2, who presented with acute cholecystitis with an ultrasound scan showing a thick-walled gallbladder and a normal common bile duct. The mean predicted probability of receiving an emergency cholecystectomy was 0·52 (95 per cent c.i. 0·45 to 0·57). The predicted probabilities ranged from 0·02 to 0·95 across the 165 hospitals, demonstrating significant variation between hospitals.

Conclusion

Patients with similar characteristics presenting to different hospitals with acute gallbladder pathology do not receive comparable care.

Modular emergency general surgery training: A pilot study of a novel programme

Introduction Pan-speciality consensus guidance advocates mandatory emergency general surgery (EGS) training modules for specialist registrars (StRs). This pilot study evaluated the impact of EGS modules aimed at StRs over 1 year. Methods Eleven StRs were allocated a focused 4-week EGS module, in addition to the standard 1:12 on-call duty rota, in a tertiary surgical centre. Primary outcome measures included the number of indicative emergency operations and validated Procedure Based Assessments (PBAs) performed, both during the EGS module and over the training year. Results StRs performed a median of 11 (range 5-15) laparotomies during the EGS module versus 31 (range 9-49) over the whole training year. StRs attended 43.7% of available laparotomies during the module (range 24.1-63.7%). EGS modules provided more than one-third of the total emergency laparotomy experience, and a quarter of the emergency colectomy, appendicectomy and Hartmann's procedure experience. There were no differences in EGS module-related outcomes between junior and senior StRs. Significantly more PBAs related to laparotomy and segmental colectomy were completed during EGS modules than the on-call duty rota, at 32% versus 14% (p<0.001) and 48% versus 22% (p=0.019), respectively. Performance levels were maintained following module completion. Conclusions These findings provide an important baseline when considering future modular EGS training.

Abstract IA19: Regulation of signaling interactomes in cancer

With the advent of next generation DNA sequencing technologies, the pace of discovery of cancer-associated sequence variants has greatly accelerated, leading to the realization that tumors (and especially solid tumors) harbor hundreds of mutations. Ongoing statistical analysis across multiple laboratories worldwide is progressing rapidly, helping to identify which of these mutations are likely drivers of the cancer phenotype. However, in spite of rapid progress in mapping of cancer related signaling and interaction networks, there has been an increasing disconnect between the identification of a cancer variant, and the mechanistic understanding of transformation induced by the mutation. Such molecular understanding is crucial for developing therapeutic interventions. In particular, frequent consequences of cancer-related mutations are specific alterations of protein-protein interactions affecting downstream signaling networks: an analysis of these altered interactions offers novel therapeutic avenues. At the same time, we still need to gain more knowledge regarding the protein-protein interactions targeted by anticancer drugs, in order to validate on-target effects and identify potential off-target modulation. For both of these objectives, we require the development of approaches that can quantify both gain and loss of interactions, in a sensitive manner, and as much as possible, under conditions that recapitulate the cellular context.

Our research team has coupled affinity purification of a protein to quantitative mass spectrometry approaches. Key to our success has been the expression at near endogenous levels of a recombinant bait protein (as wild type or sequence variants) in human cells, followed by affinity purification using an antibody directed against the epitope tag and simultaneous identification and quantification by mass spectrometry.

In particular, we are reporting here on our efforts to apply the novel data-independent mass spectrometric acquisition (DIA) method known as SWATH to these questions (see Lambert et al., Nature Methods, 2013; Tsou et al., Nature Methods, 2015). We are demonstrating how the approach can be used to profile the differential interactomes of cancer-associated mutants of kinase and phosphatase proteins (CDK4, PPP2R1A, PPP6C), and identify potentially actionable interactions. We are further demonstrating, using JQ1, an inhibitor of the interaction between acetyl-lysine modified histones and the bromodomain and extra-terminal (BET) protein family, (BRD2, BRD3, BRD4 and BRDT) that our approach permits to globally study the modulation of interactions following exposure to an anticancer agent. We reveal that JQ1 induces a rapid rewiring of the interactome of each BET protein, both decreasing interactions with acetylated histones as expected, but also modulating BET association with numerous interaction partners. Furthermore, multiple new interactions were induced upon JQ1 treatment that may alter the compound's potency. Taken together, our results demonstrate that the AP-SWATH-MS allows for the characterization of dynamically modulated interactomes for a wide array of cancer-associated proteins.

Citation Format: Jean-Philippe Lambert, Yiwang Zhou, Amber Couzens, Chih-Chiang Tsou, Sarah Picaud, Gordana Ivosev, Stephen Tate, Alexey Nesvizhskii, Panagis Filippakopoulos, Anne-Claude Gingras. Regulation of signaling interactomes in cancer. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr IA19.

A randomised clinical trial of the effectiveness of home-based health care with telemonitoring in patients with COPD

We studied the effect of telemonitoring in addition to usual care compared to usual care alone in patients with chronic obstructive pulmonary disease (COPD). A total of 110 patients with moderate to severe COPD were recruited from a specialist respiratory service in Northern Ireland. Patients had at least two of: emergency department admissions, hospital admissions or emergency general practitioner (GP) contacts in the 12 months before the study. Exclusion criteria were patients who had any respiratory disorder other than COPD, or were cognitively unable to learn the process of monitoring. Patients were randomised to receive six months of home telemonitoring with usual care, or six months of usual care. The primary outcome measure was disease-specific quality of life, as measured by the St George’s Respiratory Questionnaire for COPD patients (SGRQ-C). Of 100 patients completing the study, 48 patients were randomised to telemonitoring and 52 patients were randomised to the control group. The SGRQ-C scores improved significantly in the intervention group compared to usual care ( P = 0.001). The HADS anxiety score was significantly higher in the telehealth group compared to the usual care group ( P = 0.01). There were significantly more contacts with the Community Respiratory Team in the telemonitoring group compared to the control group ( P = 0.029). There were no significant between group differences in EQ-5D scores, HADS depression scores, GP activity, emergency department visits, hospital admissions or exacerbations. The total cost to the health service of the intervention over the 6-month study period was £2039, giving an estimated ICER of £203,900. In selected patients with COPD, telemonitoring was effective in improving health-related quality of life and anxiety, but was not a cost-effective intervention.

A repository of assays to quantify 10,000 human proteins by SWATH-MS

Mass spectrometry is the method of choice for deep and reliable exploration of the (human) proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets of proteins in a complex biological matrix and is used in studies that rely on the quantitatively accurate and reproducible measurement of proteins across multiple samples. It requires the one-time, a priori generation of a specific measurement assay for each targeted protein. SWATH-MS is a mass spectrometric method that combines data-independent acquisition (DIA) and targeted data analysis and vastly extends the throughput of proteins that can be targeted in a sample compared to selected reaction monitoring (SRM). Here we present a compendium of highly specific assays covering more than 10,000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research. Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35).

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

Characterizing changes in protein-protein interactions associated with sequence variants (e.g. disease-associated mutations or splice forms) or following exposure to drugs, growth factors or hormones is critical to understanding how protein complexes are built, localized and regulated. Affinity purification (AP) coupled with mass spectrometry permits the analysis of protein interactions under near-physiological conditions, yet monitoring interaction changes requires the development of a robust and sensitive quantitative approach, especially for large-scale studies where cost and time are major considerations. To this end, we have coupled AP to data-independent mass spectrometric acquisition (SWATH), and implemented an automated data extraction and statistical analysis pipeline to score modulated interactions. Here, we use AP-SWATH to characterize changes in protein-protein interactions imparted by the HSP90 inhibitor NVP-AUY922 or melanoma-associated mutations in the human kinase CDK4. We show that AP-SWATH is a robust label-free approach to characterize such changes, and propose a scalable pipeline for systems biology studies.

Pyruvate kinase is a dosage-dependent regulator of cellular amino acid homeostasis

The glycolytic enzyme pyruvate kinase (PK) is required for cancer development, and has been implicated in the metabolic transition from oxidative to fermentative metabolism, the Warburg effect. However, the global metabolic response that follows changes in PK activity is not yet fully understood. Using shotgun proteomics, we identified 31 yeast proteins that were regulated in a PK-dependent manner. Selective reaction monitoring confirmed that their expression was dependent on PK isoform, level and activity. Most of the PK targets were amino acid metabolizing enzymes or factors of protein translation, indicating that PK plays a global regulatory role in biosynthethic amino acid metabolism. Indeed, we found strongly altered amino acid profiles when PK levels were changed. Low PK levels increased the cellular glutamine and glutamate concentrations, but decreased the levels of seven amino acids including serine and histidine. To test for evolutionary conservation of this PK function, we quantified orthologues of the identified PK targets in thyroid follicular adenoma, a tumor characterized by high PK levels and low respiratory activity. Aminopeptidase AAP-1 and serine hydroxymethyltransferase SHMT1 both showed PKM2- concentration dependence, and were upregulated in the tumor. Thus, PK expression levels and activity were important for maintaining cellular amino acid homeostasis. Mediating between energy production, ROS clearance and amino acid biosynthesis, PK thus plays a central regulatory role in the metabolism of proliferating cells.

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis

Most proteomic studies use liquid chromatography coupled to tandem mass spectrometry to identify and quantify the peptides generated by the proteolysis of a biological sample. However, with the current methods it remains challenging to rapidly, consistently, reproducibly, accurately, and sensitively detect and quantify large fractions of proteomes across multiple samples. Here we present a new strategy that systematically queries sample sets for the presence and quantity of essentially any protein of interest. It consists of using the information available in fragment ion spectral libraries to mine the complete fragment ion maps generated using a data-independent acquisition method. For this study, the data were acquired on a fast, high resolution quadrupole-quadrupole time-of-flight (TOF) instrument by repeatedly cycling through 32 consecutive 25-Da precursor isolation windows (swaths). This SWATH MS acquisition setup generates, in a single sample injection, time-resolved fragment ion spectra for all the analytes detectable within the 400-1200 m/z precursor range and the user-defined retention time window. We show that suitable combinations of fragment ions extracted from these data sets are sufficiently specific to confidently identify query peptides over a dynamic range of 4 orders of magnitude, even if the precursors of the queried peptides are not detectable in the survey scans. We also show that queried peptides are quantified with a consistency and accuracy comparable with that of selected reaction monitoring, the gold standard proteomic quantification method. Moreover, targeted data extraction enables ad libitum quantification refinement and dynamic extension of protein probing by iterative re-mining of the once-and-forever acquired data sets. This combination of unbiased, broad range precursor ion fragmentation and targeted data extraction alleviates most constraints of present proteomic methods and should be equally applicable to the comprehensive analysis of other classes of analytes, beyond proteomics.

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis

Most proteomic studies use liquid chromatography coupled to tandem mass spectrometry to identify and quantify the peptides generated by the proteolysis of a biological sample. However, with the current methods it remains challenging to rapidly, consistently, reproducibly, accurately, and sensitively detect and quantify large fractions of proteomes across multiple samples. Here we present a new strategy that systematically queries sample sets for the presence and quantity of essentially any protein of interest. It consists of using the information available in fragment ion spectral libraries to mine the complete fragment ion maps generated using a data-independent acquisition method. For this study, the data were acquired on a fast, high resolution quadrupole-quadrupole time-of-flight (TOF) instrument by repeatedly cycling through 32 consecutive 25-Da precursor isolation windows (swaths). This SWATH MS acquisition setup generates, in a single sample injection, time-resolved fragment ion spectra for all the analytes detectable within the 400-1200 m/z precursor range and the user-defined retention time window. We show that suitable combinations of fragment ions extracted from these data sets are sufficiently specific to confidently identify query peptides over a dynamic range of 4 orders of magnitude, even if the precursors of the queried peptides are not detectable in the survey scans. We also show that queried peptides are quantified with a consistency and accuracy comparable with that of selected reaction monitoring, the gold standard proteomic quantification method. Moreover, targeted data extraction enables ad libitum quantification refinement and dynamic extension of protein probing by iterative re-mining of the once-and-forever acquired data sets. This combination of unbiased, broad range precursor ion fragmentation and targeted data extraction alleviates most constraints of present proteomic methods and should be equally applicable to the comprehensive analysis of other classes of analytes, beyond proteomics.

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis

Most proteomic studies use liquid chromatography coupled to tandem mass spectrometry to identify and quantify the peptides generated by the proteolysis of a biological sample. However, with the current methods it remains challenging to rapidly, consistently, reproducibly, accurately, and sensitively detect and quantify large fractions of proteomes across multiple samples. Here we present a new strategy that systematically queries sample sets for the presence and quantity of essentially any protein of interest. It consists of using the information available in fragment ion spectral libraries to mine the complete fragment ion maps generated using a data-independent acquisition method. For this study, the data were acquired on a fast, high resolution quadrupole-quadrupole time-of-flight (TOF) instrument by repeatedly cycling through 32 consecutive 25-Da precursor isolation windows (swaths). This SWATH MS acquisition setup generates, in a single sample injection, time-resolved fragment ion spectra for all the analytes detectable within the 400-1200 m/z precursor range and the user-defined retention time window. We show that suitable combinations of fragment ions extracted from these data sets are sufficiently specific to confidently identify query peptides over a dynamic range of 4 orders of magnitude, even if the precursors of the queried peptides are not detectable in the survey scans. We also show that queried peptides are quantified with a consistency and accuracy comparable with that of selected reaction monitoring, the gold standard proteomic quantification method. Moreover, targeted data extraction enables ad libitum quantification refinement and dynamic extension of protein probing by iterative re-mining of the once-and-forever acquired data sets. This combination of unbiased, broad range precursor ion fragmentation and targeted data extraction alleviates most constraints of present proteomic methods and should be equally applicable to the comprehensive analysis of other classes of analytes, beyond proteomics.

A cost-benefit analysis of multidimensional fractionation of affinity purification-mass spectrometry samples

Affinity purification coupled to mass spectrometry (AP-MS) is gaining widespread use for the identification of protein-protein interactions. It is unclear, however, whether typical AP sample complexity is limiting for the identification of all protein components using standard one-dimensional LC-MS/MS. Multidimensional sample separation is useful for reducing sample complexity prior to MS analysis and increases peptide and protein coverage of complex samples. Here, we monitored the effects of upstream protein or peptide separation techniques on typical mammalian AP-MS samples, generated by FLAG affinity purification of four baits with different biological functions and/or subcellular distribution. As a first separation step, we employed SDS-PAGE, strong cation exchange LC, or reversed-phase LC at basic pH. We also analyzed the benefits of using an instrument with a faster scan rate, the new TripleTOF 5600 mass spectrometer. While all multidimensional approaches yielded a clear increase in spectral counts, the increase in unique peptides and additional protein identification was modest and came at the cost of increased instrument and handling time. The use of a high duty-cycle instrument achieved similar benefits without these drawbacks. An increase in spectral counts is beneficial when data analysis methods relying on spectral counts, including Significance Analysis of INTeractome (SAINT), are used.

Structure-function analysis of core STRIPAK Proteins: a signaling complex implicated in Golgi polarization

Cerebral cavernous malformations (CCMs) are alterations in brain capillary architecture that can result in neurological deficits, seizures, or stroke. We recently demonstrated that CCM3, a protein mutated in familial CCMs, resides predominantly within the STRIPAK complex (striatin interacting phosphatase and kinase). Along with CCM3, STRIPAK contains the Ser/Thr phosphatase PP2A. The PP2A holoenzyme consists of a core catalytic subunit along with variable scaffolding and regulatory subunits. Within STRIPAK, striatin family members act as PP2A regulatory subunits. STRIPAK also contains all three members of a subfamily of Sterile 20 kinases called the GCKIII proteins (MST4, STK24, and STK25). Here, we report that striatins and CCM3 bridge the phosphatase and kinase components of STRIPAK and map the interacting regions on each protein. We show that striatins and CCM3 regulate the Golgi localization of MST4 in an opposite manner. Consistent with a previously described function for MST4 and CCM3 in Golgi positioning, depletion of CCM3 or striatins affects Golgi polarization, also in an opposite manner. We propose that STRIPAK regulates the balance between MST4 localization at the Golgi and in the cytosol to control Golgi positioning.

The application of a newly developed linear stapler preloaded with tissue reinforcement for distal pancreatectomy in the management of ovarian cancer

Advanced ovarian cancer may extend into the spleen, and even the pancreatic tail, in which a splenectomy associated with distal pancreatectomy is crucial for optimal cytoreduction. A new linear stapler preloaded with tissue reinforcement is currently introduced. We herein report the first three cases of successful application of this device for distal pancreatectomy performed during cytoreductive surgery for ovarian cancer.

Does endocarditis require routine coagulation screening?

We report a case of probable iatrogenic vitamin K deficiency in the context of antibiotic treatment for endocarditis. The patient was initially admitted with breathlessness and treated for an exacerbation of chronic obstructive pulmonary disease. However, during this period the patient was further diagnosed with endocarditis following repeated temperature spikes. Following initiation of antibiotic treatment for endocarditis the patient was noted to become increasingly anaemic. The patient was noted to have prolonged prothrombin time despite no anticoagulants. Antibiotics have been reported to alter the gut flora causing vitamin K deficiency; thereby, resulting in coagulopathy. We give a brief overview and literature review regarding potential vitamin K deficiency in this clinical context.

The risk of post-molar gestational trophoblastic neoplasia is higher in heterozygous than in homozygous complete hydatidiform moles

BACKGROUND

Complete hydatidiform mole (CHM) is a high-risk pregnancy for gestational trophoblastic neoplasia (GTN). Patients with CHM have a 10-30% chance of trophoblastic sequelae. CHM includes androgenic homozygous (monospermic) and androgenic heterozygous (dispermic) moles. It is controversial whether the risk of GTN is higher with heterozygous than with homozygous CHM. A prospective cohort study was conducted to assess risk of GTN in homozygous and heterozygous CHM using short tandem repeat (STR) polymorphisms, and a meta-analysis of previous reports.

METHODS

Twenty-eight consecutive molar pregnancies were evacuated and followed by regular hCG measurements to detect GTN. Persistent GTN was diagnosed according to the International Federation of Gynecology and Obstetrics 2000 system. Cytogenesis of the mole was determined by STR polymorphisms of molar tissue and parental blood. A meta-analysis of the GTN rate from previous reports was conducted using Mantel-Haenszel methods.

RESULTS

Of 28 molar pregnancies, 24 were homozygous and three were heterozygous CHM. The remaining mole was diandric triploidy (a partial hydatidiform mole). Of the 24 homozygous CHMs, six (25%) cases developed GTN and received chemotherapy. Meanwhile, all three cases (100%) of heterozygous mole developed GTN and needed chemotherapy. The GTN risk was higher in heterozygous (P = 0.029, Fisher's exact test) than homozygous moles. A systematic review revealed only five previous reports (with more than 15 cytogenetically diagnosed cases), and the pooled relative risk of persistent GTN for heterozygous mole was not significant (odds ratio, 2.0; 95% confidence interval, 0.98-4.07).

CONCLUSIONS

Heterozygous CHM had a higher risk for GTN than homozygous CHM.

Serum YKL-40 as a marker for cervical adenocarcinoma

BACKGROUND

The current study examined the clinical usefulness of YKL-40 in detection and prognosis of uterine cervical cancer.

PATIENTS AND METHODS

Serum levels of YKL-40, cancer antigen 125 (CA 125), carbohydrate antigen 19-9 (CA19-9), and squamous cell carcinoma (SCC) antigen were determined by enzyme-linked immunosorbent assay in women with benign gynecologic disease (n=24), cervical malignancy (SCC, n=104; adenocarcinoma, n=37), and age-matched healthy controls (n=45). Immunohistochemical analysis for local YKL-40 expression was carried out on 28 adenocarcinomas.

RESULTS

Receiver operating characteristic curve analysis showed that YKL-40 [area under the curve (AUC)=0.882] was significantly better at discriminating adenocarcinoma from healthy control than SCC antigen, CA 125, and CA19-9. For SCC, YKL-40 (AUC=0.898) carried out similarly to SCC antigen and was better than CA 125 and CA19-9. Using a cut-off YKL-40 value of 92.2 ng/ml, sensitivity of YKL-40 in stage I adenocarcinoma (68%) was higher than that of the other three markers (11%-21%). Tumor-associated macrophages showed immunoreactivity for YKL-40 in 2 of 28 adenocarcinoma tissue samples, but adenocarcinoma cells themselves were nonimmunoreactive in all samples. Multivariate Cox regression analysis revealed that elevated pretreatment YKL-40 levels predicted unfavorable prognosis, independent of International Federation of Gynecology and Obstetrics stage and age at diagnosis.

CONCLUSIONS

Pretreatment serum YKL-40 level is a possible prognosticator of cervical adenocarcinoma.

Instrumental and experimental effects in LC-MS-based metabolomics

The experimental complexity of a metabolomics study can cause uncontrolled variance that is not related to the biological effect being studied and may distort or obscure the data analysis. While some sources can be controlled with good experimental techniques and careful sample handling, others are inherent in the analytical technique used and cannot easily be avoided. We discuss the sources and appearance of some of these artifacts and show ways in which they can be detected using visualization and statistical tools, allowing appropriate treatment prior to multivariate analysis (MVA).

Instrumental and experimental effects in LC-MS-based metabolomics

The experimental complexity of a metabolomics study can cause uncontrolled variance that is not related to the biological effect being studied and may distort or obscure the data analysis. While some sources can be controlled with good experimental techniques and careful sample handling, others are inherent in the analytical technique used and cannot easily be avoided. We discuss the sources and appearance of some of these artifacts and show ways in which they can be detected using visualization and statistical tools, allowing appropriate treatment prior to multivariate analysis (MVA).

Concurrent daily cisplatin and extended-field radiation therapy for carcinoma of the cervix

The aim of this study was to assess acute toxicities of concurrent low-dose daily cisplatin and extended-field radiation therapy (EFRT) for carcinoma of the uterine cervix. Fifteen women with cervical cancer who were treated with concurrent daily low-dose cisplatin and EFRT were analyzed. Daily cisplatin dose was fixed to 8 mg/m(2), which was determined in the preceding phase I study using pelvic radiotherapy. Twelve patients underwent either combined external beam radiation therapy and intracavitary brachytherapy or external beam radiation therapy alone. Three other patients were treated with adjuvant chemoradiotherapy after surgery. A total dose of EFRT ranged from 40 to 45 Gy, with an additional boost to the gross tumor volume up to 50.4-55 Gy. A median total dose of cisplatin during entire radiation therapy course was 224 mg/m(2) (range, 200-240 mg/m(2)). In 14 of 15 patients (93%), daily cisplatin could be delivered continuously as planned without any modification. Administration of cisplatin had to be interrupted in only one patient for only 3 days. Fourteen patients developed grade 2 or worse leukopenia including five after treatment, grade 2 in four, grade 3 in eight, and grade 4 in two. Grade 3 thrombocytopenia was observed in three patients. Grade 2 or worse anemia was observed in 12. Three patients had grade 3 nonhematologic toxicities, diarrhea in two, and nausea/vomiting in one. Although moderate to severe hematologic toxicities are common, this study suggests that concurrent low-dose daily cisplatin and EFRT are feasible. A cumulative cisplatin dose of greater than 200 mg/m(2) during radiation therapy could be achieved by using daily cisplatin dose of 8 mg/m(2).

Serum YKL-40 levels are usuful diagnostic tumor markers for adenocarcinoma of the uterine cervix

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Background: YKL-40 is secreted by cancer cells, macrophages, and neutrophils. It may be a growth factor, play a role in angiogenesis, or prevent apoptosis. The current study examined serum YKL-40 levels in patients with adenocarcinoma of the cervix to determine if it is a serum marker. Methods: The serum YKL-40 level was assayed by enzyme-linked immunosorbent assay in 24 patients with benign gynecologic disease, in 104 patients with squamous cell carcinonma , in 37 patietns with adenocarcinoma, and in 45 healthy controls, Serum squamous cell carcinoma antigen (SCC) and CA125 and CA19–9 values were obtained. Results: The serum YKL-40 level was higher in patients with cervical carcinoma than in the healthy controls (p<0.0001). YKL-40 concentrations increased significantly in patients with squamous cell carcinoma and in those with adenocarcinoma (vs. normal control: p<0.0001 and p<0.0001, respectively). Judging from the receiver operating curves (ROC), the serum YKL-40 was more sensitive than other serum markers at identifying adenocarcinoma. In squamous cell carcinoma, this ability of serum YKL-40 was equal to that of SCC. YKL-40 was elevated in 68.4% of patients with stage I adenocarcinoma. The pretherapeutic serum level of YKL-40 correlated significantly with the International Federation of Gynecology and Obstetrics advanced stage in patients with adenocarcinoma of the cervix. Furthermore, the pretherapeutic serum level of YKL-40 correlated with disease persistence or recurrence. Conclusions: The serum YKL-40 level has potential usefulness as a diagnostic marker of adenocarcinoma of the cervix.

[Table: see text]

No significant financial relationships to disclose.

Sodium channel Nav1.8 immunoreactivity in painful human dental pulp

BACKGROUND

The tetrodotoxin-resistant voltage-gated sodium channel Nav1.8 (SNS1/PN3) is expressed by nociceptors and may play a role in pain states.

METHODS

Using specific antibodies for immunohistochemistry, we studied Nav1.8 immunoreactivity in human dental pulp in relation to the neuronal marker neurofilament. Human tooth pulp was extracted from teeth harvested from a total of twenty-two patients (fourteen without dental pain, eight patients with dental pain).

RESULTS

Fibres immunoreactive for Nav1.8, were significantly increased on image analysis in the painful group: median (range) Nav1.8 to Neurofilament % area ratio, non-painful 0.059 (0.006-0.24), painful 0.265 (0.13-0.5), P = 0.0019.

CONCLUSION

Nav1.8 sodium channels may thus represent a therapeutic target in trigeminal nerve pain states.

Progress towards gene therapy for cystic fibrosis

A decade ago it was widely anticipated that cystic fibrosis would be one of the first diseases to be treated by gene therapy. The difficult hurdle of cloning the responsible gene had been accomplished, its function was established and the lung appeared readily accessible for gene replacement. Since the first clinical trials for cystic fibrosis lung disease in the early 1990s it has become increasingly apparent that successful lung-directed gene therapy is significantly more complex than was first envisioned. Numerous obstacles including vector toxicity, inefficient transgene expression and limited vector production have delayed progress. An increased understanding of vector biology and host interaction has led to the development of novel strategies to enhance the efficiency and selectivity of gene delivery to the lung. Although significant challenges remain, there is now a realistic prospect of a clinically effective treatment in the next 10 years.

Effects of breathing pattern and inspired air conditions on breath condensate volume, pH, nitrite, and protein concentrations

BACKGROUND

The effects of breathing pattern and inspired air conditions on the volume and content of exhaled breath condensate (EBC) were investigated.

METHODS

Total exhaled water (TEW), EBC volume, pH, nitrite and protein concentrations were measured in three groups of 10 healthy subjects breathing into a condenser at different target minute ventilations (Vm), tidal volumes (Vt), and inspired air conditions.

RESULTS

The volumes of both TEW and EBC increased significantly with Vm. For Vm 7.5, 15 and 22.5 l/min, mean (SD) EBC was 627 (258) microl, 1019 (313) microl, and 1358 (364) microl, respectively (p<0.001) and TEW was 1879 (378) microl, 2986 (496) microl, and 4679 (700) microl, respectively (p<0.001). TEW was significantly higher than EBC, reflecting a condenser efficiency of 40% at a target Vm of 7.5 l/min which reduced to 29% at Vm 22.5 l/min. Lower Vt gave less TEW than higher Vt (26.6 v 30.7 microl/l, mean difference 4.1 (95% CI 2.6 to 5.6), p<0.001) and a smaller EBC volume (4.3 v 7.6 microl/l, mean difference 3.4 (95% CI 2.3 to 4.5), p<0.001). Cooler and drier inspired air yielded less water vapour and less breath condensate than standard conditions (p<0.05). Changes in the breathing pattern had no effect on EBC protein and nitrite concentrations and pH.

CONCLUSION

These results show that condensate volume can be increased by using high Vt and increased Vm without compromising the dilution of the sample.

Proteomics Analysis of Rat Brain Postsynaptic Density

The postsynaptic density contains multiple protein complexes that together relay the presynaptic neurotransmitter input to the activation of the postsynaptic neuron. In the present study we took two independent proteome approaches for the characterization of the protein complement of the postsynaptic density, namely 1) two-dimensional gel electrophoresis separation of proteins in conjunction with mass spectrometry to identify the tryptic peptides of the protein spots and 2) isolation of the trypsin-digested sample that was labeled with isotope-coded affinity tag, followed by liquid chromatography-tandem mass spectrometry for the partial separation and identification of the peptides, respectively. Functional grouping of the identified proteins indicates that the postsynaptic density is a structurally and functionally complex organelle that may be involved in a broad range of synaptic activities. These proteins include the receptors and ion channels for glutamate neurotransmission, proteins for maintenance and modulation of synaptic architecture, sorting and trafficking of membrane proteins, generation of anaerobic energy, scaffolding and signaling, local protein synthesis, and correct protein folding and breakdown of synaptic proteins. Together, these results imply that the postsynaptic density may have the ability to function (semi-) autonomously and may direct various cellular functions in order to integrate synaptic physiology.

Transfection efficiency and toxicity following delivery of naked plasmid DNA and cationic lipid–DNA complexes to ovine lung segments

We defined, using a novel large animal model system, the acute pathologic response to localized pulmonary administration of either naked plasmid DNA (pDNA) or cationic lipid-pDNA complexes (pDNA:GL67) and related such responses to concomitant indicators of transfection efficiency, namely levels of chloramphenicol acetyl transferase (CAT) protein and mRNA in specific lung tissue compartments. We instilled doses of 0.2, 1, and 5 mg pDNA to spatially distinct lung segments in six anesthetized sheep and doses of 0.2, 1, and 5 mg pDNA:GL67 to a further six sheep. Twenty-four hours after gene delivery the sheep were euthanized and necropsy examination with sampling of relevant tissues was carried out. Levels of plasmid-derived CAT-specific mRNA and CAT protein in samples derived from segments treated with either pDNA or pDNA:GL67 increased in relation to the administered dose. Levels of mRNA and protein expression were greater for pDNA:GL67 than for pDNA alone. A significant correlation was observed between mRNA and protein expression in samples derived from airways treated with pDNA:GL67. Histopathological changes following administration of both pDNA and pDNA:GL67 were characterized by a neutrophilic inflammation predominantly oriented on airways. The severity of the inflammatory response appeared to correlate with the administered dose of DNA and was generally more severe for pDNA:GL67.

Structural comparison between wild-type and P25S human cystatin A by NMR spectroscopy. Does this mutation affect the alpha-helix conformation?

The effect of substituting Pro25, located in the alpha-helical region of the cystatin A structure, with Ser has been studied. The structures of wild type and P25S cystatin A were determined by multidimensional NMR spectroscopy under comparable conditions. These two structures were virtually identical, and the alpha-helix between Glu15-Lys30 exists with uninterrupted continuity, with a slight bend at residue 25. In order to characterize the possible substitution effects of Pro25 with Ser on the alpha-helix, the chemical shifts of the amide nitrogens and protons, the generalized order parameters obtained by the analyses of the 15N-1H relaxation data, the amide proton exchange rates, and the NOE networks among the alpha-helical and surrounding residues were carefully compared. None of these parameters indicated any significant static or dynamic structural differences between the alpha-helical regions of the wild-type and P25S cystatin A proteins. We therefore conclude that our previous structure of the wild-type cystatin A, in which the alpha-helix exhibited a sharp kink at Pro25, must be revised. The asymmetric distribution of hydrophobic interactions between the side-chain residues of the alpha-helix and the rolled beta-sheet surface, as revealed by NOEs, may be responsible for the slight bend of the alpha-helix in both variants and for the destabilized hydrogen bonding of the alpha-helical residues that follow Pro25/Ser25, as evidenced by increased amide exchange rates.

Airways in cystic fibrosis are acidified: detection by exhaled breath condensate

BACKGROUND

The loss of cystic fibrosis transmembrane conductance regulator (CFTR) mediated chloride conductance does not fully explain the diverse pathologies evident in patients with cystic fibrosis (CF). Bicarbonate (HCO(3)(-)) secretion is also impaired in CFTR expressing tissues and CFTR is thought to regulate HCO(3)(-) secretion at the apical membrane of epithelial cells. We hypothesised that the epithelial lining fluid (ELF) of patients with CF would be acidified and that this may be worsened during an infective exacerbation due to the increased inflammatory burden.

METHODS

pH and nitrite levels in exhaled breath condensate (EBC) from 12 healthy non-smoking controls and 30 patients with CF (11 of whom were in an infective exacerbation) were measured. A further nine patients were studied before and after intravenous antibiotic treatment for an exacerbation of CF.

RESULTS

The pH of EBC was significantly lower in patients with stable CF than in controls (5.88 (0.32) v 6.15 (0.16), p=0.017), and was further reduced in CF patients with an exacerbation (5.32 (0.38), p=0.001) compared with stable CF patients. EBC pH increased significantly following antibiotic treatment from 5.27 (0.42) to 5.71 (0.42), p=0.049). Nitrite levels in EBC were increased in CF patients with an exacerbation compared with control subjects (4.4 (4.0) micro m v 1.6 (1.6) micro m p=0.047). No correlation was found between EBC pH and nitrite levels.

CONCLUSIONS

These findings support the hypothesis that airway acidification occurs in CF. This acidity is in part a function of inflammation as the pH of the EBC of patients increased significantly with treatment of an exacerbation, although not to control levels. Acidic pH of the ELF may play a role in the pathophysiology of CF lung disease and requires further investigation.

A novel15N-labeling method to selectively observe15NH2resonances of proteins in1H-detected heteronuclear correlation spectroscopy

An experimental method to selectively label side-chain NH2 groups of glutamine and asparagine in proteins with 15N is proposed. This selective labeling method enables to observe only 15NH2 resonances and thus, to discriminate between 15NH and 15NH2 resonances in a 1H-detected heteronuclear correlation spectrum. This method gives results with approximately two times higher sensitivity than those obtained by elaborate pulse sequences such as DEPT-HSQC and will be useful for studying the molecular interaction involving the side chains of Asn and Gln residues.

Increased sodium channel SNS/PN3 immunoreactivity in a causalgic finger

The sodium channels SNS/PN3 and NaN/SNS2 are regulated by the neurotrophic factors-nerve growth factor (NGF) and glial-derived neurotrophic factor (GDNF), and may play an important role in the development of pain after nerve injury or inflammation. These key molecules have been studied in an amputated causalgic finger and control tissues by immunohistochemistry. There was a marked increase in the number and intensity of SNS/PN3-immunoreactive nerve terminals in the affected finger, while GDNF-immunoreactivity was not observed, in contrast to controls. No differences were observed for NGF, trk A, NT-3 or NaN/SNS2-immunoreactivity. While further studies are required, these findings suggest that accumulation of SNS/PN3 and/or loss of GDNF may contribute to pain in causalgia, and that selective blockers of SNS/PN3 and/or rhGDNF may provide effective novel treatments.