High-Throughput Fractionation Coupled to Mass Spectrometry for Improved Quantitation in Metabolomics.

Metabolomics is emerging as an important field in life sciences. However, a weakness of current mass spectrometry (MS) based metabolomics platforms is the time-consuming analysis and the occurrence of severe matrix effects in complex mixtures. To overcome this problem, we have developed an automated and fast fractionation module coupled online to MS. The fractionation is realized by the implementation of three consecutive high performance solid-phase extraction columns consisting of a reversed phase, mixed-mode anion exchange, and mixed-mode cation exchange sorbent chemistry. The different chemistries resulted in an efficient interaction with a wide range of metabolites based on polarity, charge, and allocation of important matrix interferences like salts and phospholipids. The use of short columns and direct solvent switches allowed for fast screening (3 min per polarity). In total, 50 commonly reported diagnostic or explorative biomarkers were validated with a limit of quantification that was comparable with conventional LC-MS(/MS). In comparison with a flow injection analysis without fractionation, ion suppression decreased from 89% to 25%, and the sensitivity was 21 times higher. The validated method was used to investigate the effects of circadian rhythm and food intake on several metabolite classes. The significant diurnal changes that were observed stress the importance of standardized sampling times and fasting states when metabolite biomarkers are used. Our method demonstrates a fast approach for global profiling of the metabolome. This brings metabolomics one step closer to implementation into the clinic.

Finding balance between minimally invasive surgery and laryngotracheal resection in the management of adult laryngotracheal stenosis.

Management of adult laryngotracheal stenosis is complex and several treatment options are known. The present study focuses on finding the right balance between minimally invasive surgery and laryngotracheal resection by reviewing a single institution's experiences. Retrospective analysis was performed of all adult and adolescent patients with laryngotracheal stenosis who underwent treatment in a tertiary referral center, between 1990 and 2012. Age, gender, etiology, treatment, recurrence, pre- and post-operative peak flow (PF), and pre- and post-treatment subjective complain scores (SCS) were registered. 87 patients with 267 interventions were analyzed. There were 238 dilatation tracheoscopies, 22 open surgeries and various other endoscopic procedures registered. Idiopathic stenoses required the most dilatation tracheoscopies, while post-tracheotomy stenoses required the least. Patients in the post-intubation and post-tracheotomy groups were significantly more often treated with open surgery compared to those in the granulomatosis with polyangiitis (GPA) and idiopathic groups. The gain in PF flow after dilatation tracheoscopy was significantly higher in the idiopathic group compared to the other groups. The median SCS of dyspnoea decreased in the whole population, while other SCS did not change remarkably. Repeated endoscopic procedures are recommended in patients with severe systemic disease which do not allow open surgery or when other comorbidities contraindicate open surgery. Open surgery very often offers the definitive solution in the treatment of laryngotracheal stenosis and cannot be avoided when the laryngeal or the tracheal framework is damaged. Patients' personal preferences have to be considered in the pre-operative assessment process.

Is human papillomavirus involved in laryngeal neuroendocrine carcinoma?

The purpose of this study was to detect human papillomavirus (HPV) infection in laryngeal neuroendocrine carcinoma (LNEC) and to explore the possible relationship between HPV-induced malignant transformation and prognosis in LNEC. Ten cases of LNEC from a tertiary referral hospital were retrospectively analyzed. Clinical data were subtracted from patients' files. Pretreatment biopsy material was tested for the presence of HPV6, 11, 16, and 18 using a PCR-based detection method. Immunohistochemical staining was performed for Ki-67, p16(INK4A), and p53 expression. All cases were negative for the low-risk HPV types HPV6 and HPV11 that are associated with laryngeal papillomatosis. High-risk HPV was detected in two cases; an atypical carcinoid was positive for HPV16 and a large-cell neuroendocrine carcinoma for HPV18. Both HPV-positive tumors had a high Ki-67 labeling index. Two of the four cases with a good response to therapy were hrHPV-positive (both HPV DNA positive) compared with none of the five poor responders. Our findings show that HPV may play a role in the pathogenesis of LNEC. The relationship between HPV, improved prognosis and good response to therapy for squamous cell carcinoma of the head and neck may also be true for a subset of LNEC.

The importance of multimodality therapy in the treatment of sinonasal neuroendocrine carcinoma.

Sinonasal carcinoma with neuroendocrine differentiation (SCND) is a rare group of tumors known for their aggressive behavior and poor response to treatment. The data in the literature are sparse and cover a wide range of therapeutic approaches over a protracted timeline. Therefore, it is important that institutions report on their experience with these rare neoplasms. Clinical data, such as age at diagnosis, gender, tumor subtype and stage, treatment intention and modality, recurrence, salvage treatment, and survival of patients with a SCND, diagnosed at our department between 1980 and 2010, were retrospectively analyzed. Fifteen patients were available for analysis; eight with sinonasal undifferentiated carcinoma (SNUC), five with sinonasal neuroendocrine carcinoma (SNEC), and two with small cell neuroendocrine carcinoma (SmCC). The median age at the time of diagnosis was 68 years (range 28-87). Treatment consisted of surgery (2), radiotherapy (4), a combination of these modalities (6) and palliation (3). The estimated 5-year overall survival was 60 % for SNEC, 44 % for SNUC and 0 % for SmCC. According to our institutional experience an aggressive multi-modality approach incorporating (neoadjuvant) chemoradiotherapy, radical surgery and elective treatment of the neck is the best treatment strategy for SCND. The high propensity for distant metastasis and poor prognosis of SmCC warrants consideration of the impact of treatment on the remaining quality of life in these patients.

Fractionation platform for target identification using off-line directed two-dimensional chromatography, mass spectrometry and nuclear magnetic resonance.

The unambiguous identification of unknown compounds is of utmost importance in the field of metabolomics. However, current identification workflows often suffer from error-sensitive methodologies, which may lead to incorrect structure annotations of small molecules. Therefore, we have developed a comprehensive identification workflow including two highly complementary techniques, i.e. liquid chromatography (LC) combined with mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR), and used it to identify five taste-related retention time and m/z features in soy sauce. An off-line directed two-dimensional separation was performed in order to purify the features prior to the identification. Fractions collected during the first dimension separation (reversed phase low pH) were evaluated for the presence of remaining impurities next to the features of interest. Based on the separation between the feature and impurities, the most orthogonal second dimension chromatography (hydrophilic interaction chromatography or reversed phase high pH) was selected for further purification. Unknown compounds down to tens of micromolar concentrations were tentatively annotated by MS and structurally confirmed by MS and NMR. The mass (0.4-4.2 µg) and purity of the isolated compounds were sufficient for the acquisition of one and two-dimensional NMR spectra. The use of a directed two-dimensional chromatography allowed for a fractionation that was tailored to each feature and remaining impurities. This makes the fractionation more widely applicable to different sample matrices than one-dimensional or fixed two-dimensional chromatography. Five proline-based 2,5-diketopiperazines were successfully identified in soy sauce. These cyclic dipeptides might contribute to taste by giving a bitter flavour or indirectly enhancing umami flavour.

Data-Independent Acquisition for the Quantification and Identification of Metabolites in Plasma.

A popular fragmentation technique for non-targeted analysis is called data-independent acquisition (DIA), because it provides fragmentation data for all analytes in a specific mass range. In this work, we demonstrated the strengths and weaknesses of DIA. Two types of chromatography (fractionation/3 min and hydrophilic interaction liquid chromatography (HILIC)/18 min) and three DIA protocols (variable sequential window acquisition of all theoretical mass spectra (SWATH), fixed SWATH and MSALL) were used to evaluate the performance of DIA. Our results show that fast chromatography and MSALL often results in product ion overlap and complex MS/MS spectra, which reduces the quantitative and qualitative power of these DIA protocols. The combination of SWATH and HILIC allowed for the correct identification of 20 metabolites using the NIST library. After SWATH window customization (i.e., variable SWATH), we were able to quantify ten structural isomers with a mean accuracy of 103% (91-113%). The robustness of the variable SWATH and HILIC method was demonstrated by the accurate quantification of these structural isomers in 10 highly diverse blood samples. Since the combination of variable SWATH and HILIC results in good quantitative and qualitative fragmentation data, it is promising for both targeted and untargeted platforms. This should decrease the number of platforms needed in metabolomics and increase the value of a single analysis.

Fast LC-ESI-MS/MS analysis and influence of sampling conditions for gut metabolites in plasma and serum.

In the past few years, the gut microbiome has been shown to play an important role in various disorders including in particular cardiovascular diseases. Especially the metabolite trimethylamine-N-oxide (TMAO), which is produced by gut microbial metabolism, has repeatedly been associated with an increased risk for cardiovascular events. Here we report a fast liquid chromatography tandem mass spectrometry (LC-MS/MS) method that can analyze the five most important gut metabolites with regards to TMAO in three minutes. Fast liquid chromatography is unconventionally used in this method as an on-line cleanup step to remove the most important ion suppressors leaving the gut metabolites in a cleaned flow through fraction, also known as negative chromatography. We compared different blood matrix types to recommend best sampling practices and found citrated plasma samples demonstrated lower concentrations for all analytes and choline concentrations were significantly higher in serum samples. We demonstrated the applicability of our method by investigating the effect of a standardized liquid meal (SLM) after overnight fasting of 25 healthy individuals on the gut metabolite levels. The SLM did not significantly change the levels of gut metabolites in serum.

Meta-analysis of 701 published cases of sinonasal neuroendocrine carcinoma: The importance of differentiation grade in determining treatment strategy.

The aim of this meta-analysis was to provide treatment guidelines for sinonasal neuroendocrine carcinoma (SNC) by combining all available data in the literature. A literature search for all studies concerning SNC was performed against the MEDLINE and EMBASE databases. Available clinical data was normalized, pooled, and statistically analyzed. A total of 701 cases of SNC were available for analysis, comprising 127 well or moderately differentiated sinonasal neuroendocrine carcinomas (SNEC), 459 sinonasal undifferentiated carcinoma (SNUC) and 115 sinonasal small cell carcinoma (SmCC). Tumor type was the most important predictor of survival, with a 5-year disease-specific survival (DSS) of 70.2% for SNEC, 35.9% for SNUC and 46.1% for SmCC. Tumor stage on presentation was of limited value in predicting survival or response to treatment. Overall, the application of surgery yielded significantly better results (5-year DSS 52.2% versus 30.1%, p<0.001). In SNUC, radiotherapy was a beneficial supplement to surgery (5-year DSS 54.7% versus 15.7%, p=0.027), while radiotherapy as monotherapy performed poorly (5-year DSS 17.9%). Chemotherapy did not appear to contribute to survival. Based on these findings, we can conclude that the most important predictors of survival in SNC are differentiation grade and the associated choice of treatment modality. In contrast to other head and neck cancers, tumor staging appears of limited value in predicting survival or deciding on a treatment strategy. Surgery should be the cornerstone of treatment, supplemented by radiotherapy in poorly differentiated subtypes (SNUC, SmCC). Chemotherapy does not appear to contribute to survival.

Tracking biochemical changes correlated with ultra-weak photon emission using metabolomics.

Ultra-weak photon emission (UPE) is light emitted spontaneously by biological systems without the use of specific luminescent complexes. UPE is emitted in the near-UV/UV-Vis/near-IR spectra during oxidative metabolic reactions; however, the specific pathways involved in UPE remain poorly understood. Here, we used HL-60 cells, a human promyelocytic cell line that is often used to study respiratory burst, as a model system to measure UPE kinetics together with metabolic changes. HL-60 cells were differentiated into neutrophil-like cells by culturing in all-trans-retinoic acid for 7days. We then used a targeted metabolomics approach with capillary electrophoresis-mass spectrometry to profile intracellular metabolites in HL-60 cells and to investigate the biochemical changes based on the measured UPE profile. Our analysis revealed that the levels of specific metabolites, including putrescine, creatine, ß-alanine, methionine, hydroxyproline, serine, and S-adenosylmethionine, were significantly altered in HL-60 cells after inducing respiratory burst. A comparison with recorded UPE data revealed that the changes in putrescine, glutathione, sarcosine, creatine, ß-alanine, methionine, and hydroxyproline levels were inversely correlated with the change in UPE intensity. These results suggest that these metabolic pathways, particular the methionine pathway, may play a role in the observed changes in UPE in HL-60 cells and therefore demonstrate the potential for using UPE to monitor metabolic changes.

Clinical recommendations on the treatment of neuroendocrine carcinoma of the larynx: A meta-analysis of 436 reported cases.

BACKGROUND: Current recommendations on the treatment of neuroendocrine carcinoma of the larynx (NCL) are based on anecdotal evidence. With this meta-analysis, our purpose was to provide clinicians with more substantiated guidelines in order to improve the treatment outcome of the patients affected with NCL. METHODS: A structured literature search for all research concerning NCL was performed against the MEDLINE and EMBASE databases. Available data was normalized, pooled, and statistically analyzed. RESULTS: Four hundred thirty-six cases of NCL were extracted from 182 studies, of which 23 were typical carcinoid, 163 were atypical carcinoid, 183 were small-cell neuroendocrine carcinoma, 29 were large-cell neuroendocrine carcinoma, and 38 were unspecified carcinoid tumors. The 5-year disease-specific survival (DSS) was 100% for typical carcinoid, 53% for atypical carcinoid, 19% for small-cell neuroendocrine carcinoma, and 15% for large-cell neuroendocrine carcinoma (p < .001). Patients with an atypical carcinoid treated with surgery had better DSS than those treated with radiotherapy (60% vs 54%; p = .035). Postoperative radiotherapy did not result in better DSS in atypical carcinoid. Patients with an atypical carcinoid, not undergoing surgical treatment of the neck, developed isolated regional recurrence in 30% of cases (p = .001). Radiochemotherapy yielded the best DSS for small-cell neuroendocrine carcinoma compared to other modalities (31% vs 13%; p = .001). CONCLUSION: Typical carcinoid can be treated by local excision alone. Atypical carcinoids do not seem to respond well to radiotherapy and are best managed through radical surgical excision in combination with elective neck dissection. Patients with small-cell neuroendocrine carcinoma or large-cell neuroendocrine carcinoma seem to benefit most from chemoradiotherapy.