Sulfoproteomics Workflow with Precursor Ion Accurate Mass Shift Analysis Reveals Novel Tyrosine Sulfoproteins in the Golgi

Tyrosine sulfation in the Golgi of secreted and membrane proteins is an important post-translational modification (PTM). However, its labile nature has limited analysis by mass spectrometry (MS), a major reason why no sulfoproteome studies have been previously reported. Here, we show that a phosphoproteomics experimental workflow, which includes serial enrichment followed by high resolution, high mass accuracy MS, and tandem MS (MS/MS) analysis, enables sulfopeptide coenrichment and identification via accurate precursor ion mass shift open MSFragger database search. This approach, supported by manual validation, allows the confident identification of sulfotyrosine-containing peptides in the presence of high levels of phosphorylated peptides, thus enabling these two sterically and ionically similar isobaric PTMs to be distinguished and annotated in a single proteomic analysis. We applied this approach to isolated interphase and mitotic rat liver Golgi membranes and identified 67 tyrosine sulfopeptides, corresponding to 26 different proteins. This work discovered 23 new sulfoproteins with functions related to, for example, Ca2+-binding, glycan biosynthesis, and exocytosis. In addition, we report the first preliminary evidence for crosstalk between sulfation and phosphorylation in the Golgi, with implications for functional control.

Quantitative Imaging Assessment for Clinical Trials in Oncology

BACKGROUND

Objective radiographic assessment is crucial for accurately evaluating therapeutic efficacy and patient outcomes in oncology clinical trials. Imaging assessment workflow can be complex; can vary with institution; may burden medical oncologists, who are often inadequately trained in radiology and response criteria; and can lead to high interobserver variability and investigator bias. This article reviews the development of a tumor response assessment core (TRAC) at a comprehensive cancer center with the goal of providing standardized, objective, unbiased tumor imaging assessments, and highlights the web-based platform and overall workflow. In addition, quantitative response assessments by the medical oncologists, radiologist, and TRAC are compared in a retrospective cohort of patients to determine concordance.

PATIENTS AND METHODS

The TRAC workflow includes an image analyst who pre-reviews scans before review with a board-certified radiologist and then manually uploads annotated data on the proprietary TRAC web portal. Patients previously enrolled in 10 lung cancer clinical trials between January 2005 and December 2015 were identified, and the prospectively collected quantitative response assessments by the medical oncologists were compared with retrospective analysis of the same dataset by a radiologist and TRAC.

RESULTS

This study enlisted 49 consecutive patients (53% female) with a median age of 60 years (range, 29-78 years); 2 patients did not meet study criteria and were excluded. A linearly weighted kappa test for concordance for TRAC versus radiologist was substantial at 0.65 (95% CI, 0.46-0.85; standard error [SE], 0.10). The kappa value was moderate at 0.42 (95% CI, 0.20-0.64; SE, 0.11) for TRAC versus oncologists and only fair at 0.34 (95% CI, 0.12-0.55; SE, 0.11) for oncologists versus radiologist.

CONCLUSIONS

Medical oncologists burdened with the task of tumor measurements in patients on clinical trials may introduce significant variability and investigator bias, with the potential to affect therapeutic response and clinical trial outcomes. Institutional imaging cores may help bridge the gap by providing unbiased and reproducible measurements and enable a leaner workflow.

Integrative whole exome, transcriptome, and clinical profiling of biliary tract cancers (BTCs)

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Background: BTC is clinically and genomically heterogeneous and next generation sequencing may identify disease subsets with distinct prognostic and therapeutic implications. Methods: Patients (pts) with BTC underwent whole exome and transcriptome sequencing via the Michigan Oncology Sequencing (MI-ONCOSEQ) platform between 09/2011 and 07/2017. Results: 53 pts (47.2% female) with median age 60 (range 17-72) years had 38 intrahepatic, 6 perihilar, and 4 extrahepatic distal cholangiocarcinoma (CCA) while 3 had gallbladder and 2 mixed CCA/hepatocellular carcinoma. Forty-one pts (77.3%) had advanced BTC at diagnosis and 40 (75.5%) received platinum doublet as first line therapy. The most frequent somatic mutations were TP53 (35.8%), BAP1 (18.9%), KRAS (17.0%), IDH1 (15.1%), PBRM1 (13.2%), ARID1A (11.3%), and SMAD4 (11.3%). Median overall survival (OS) in 8 pts with IDH1 mutation was 16.8 months (none received IDH1 inhibitor). Putative pathogenic germline variants were noted in 6 (11.3%) pts of which 4 were biallelic (MSH2, BRCA1, BRCA2 and MUTYH) and 2 monoallelic (ATM and FH). Germline mutation in FH has not been reported in BTC. Biallelic DNA damage repair pathway mutations were noted in 14 (26.4%; 11 somatic, 3 germline) pts and their median OS was 16.8 months. Of these 9 pts with advanced BTC received 1st line platinum therapy and had a median PFS of 9.3 months (4 PR, 3 SD). Nine (17%) pts had FGFR2 fusion (6 partners); median OS not yet reached (6 alive; 5 received FGFR inhibitor). Potentially targetable molecular alterations (IDH1, MSH2, BRCA1/2, PALB2, ATM, FGFR2, ERBB2) were identified in 27 (50.9%) pts. Copy number profile shows frequent loss of chr1p, chr3p, chr4, chr6q, chr8p, chr9, and gain of chr1q, chr7, and chr8q. Immune profiling & pathway analysis of BTCs with clinical correlation is ongoing. Conclusions: Integrative sequencing of BTCs with clinical profiling will lead to more precise treatment of pts with BTCs.

Characterization of O-sulfopeptides by negative ion mode tandem mass spectrometry: superior performance of negative ion electron capture dissociation

Positive ion mode collision-activated dissociation tandem mass spectrometry (CAD MS/MS) of O-sulfopeptides precludes determination of sulfonated sites due to facile proton-driven loss of the highly labile sulfonate groups. A previously proposed method for localizing peptide and protein O-sulfonation involves derivatization of nonsulfonated tyrosines followed by positive ion CAD MS/MS of the corresponding modified sulfopeptides for diagnostic sulfonate loss. This indirect method relies upon specific and complete derivatization of nonsulfonated tyrosines. Alternative MS/MS activation methods, including positive ion metastable atom-activated dissociation (MAD) and metal-assisted electron transfer dissociation (ETD) or electron capture dissociation (ECD) provide varying degrees of sulfonate retention. Sulfonate retention has also been reported following negative ion MAD and electron detachment dissociation (EDD), which also operates in negative ion mode in which sulfonate groups are less labile than in positive ion mode. However, an MS/MS activation technique that can effectively preserve sulfonate groups while providing extensive backbone fragmentation (translating to sequence information, including sulfonated sites) with little to no noninformative small molecule neutral loss has not previously been realized. Here, we report that negative ion CAD, EDD, and negative ETD (NETD) result in sulfonate retention mainly at higher charge states with varying degrees of fragmentation efficiency and sequence coverage. Similar to previous observations from CAD of sulfonated glycosaminoglycan anions, higher charge states translate to a higher probability of deprotonation at the sulfonate groups thus yielding charge-localized fragmentation without loss of the sulfonate groups. However, consequently, higher sulfonate retention comes at the price of lower sequence coverage in negative ion CAD. Fragmentation efficiency/sequence coverage averaged 19/6% and 33/20% in EDD and NETD, respectively, both of which are only applicable to multiply-charged anions. In contrast, the recently introduced negative ion ECD showed an average fragmentation efficiency of 69% and an average sequence coverage of 82% with complete sulfonate retention from singly- and doubly-deprotonated sulfopeptide anions.

Examining the Proteome of Drosophila Across Organism Lifespan

A survey of the proteome of Drosophila melanogaster at nine time points across the adult lifespan based on several mass-spectrometry-based techniques is presented. In total, there is evidence for 5902 unique peptides corresponding to 1699 different proteins. Of hundreds of relatively abundant components, many appear to be highly dynamic as the adult fly ages. Of those proteins that we observe changing with age, a majority, associated with metabolism, reproduction, and development, are down-regulated. Other biological pathways such as defense response also show variable changes, where some proteins are down-regulated and others are up-regulated. The observed variations are compared with a report of genome-wide changes at the transcriptome level at different ages and the similarities and differences are presented.

Management of drug-interaction alerts in community pharmacies

BACKGROUND AND OBJECTIVE

Drug-interaction alert systems are commonly used in community pharmacies to identify potential drug-drug interactions. However, depending on the software default setting, pharmacists may override alerts because they are too numerous. We explored the handling of drug-interaction alerts by community pharmacies in Switzerland.

METHODS

Data were collected by 15 trained pharmacy students in 15 Swiss community pharmacies. The medication history and the drug-interaction alerts of 600 patients who had >or=2 drugs on prescription were assessed, and the pharmacists in charge were interviewed about their management of drug-interaction alerts.

RESULTS

In the 15 pharmacies studied, the computer systems were programmed to flag only 'severe' drug interactions in four, 'severe or moderate' in six or 'severe, moderate or minor' in five pharmacies. The median frequency of drug-interaction alerts increased with decreasing default severity level from 0.5 to 40, respectively, to 76 per 40 patient visits and pharmacy. Because of these default settings, 277 (35 x 2%) of 787 potential drug-interaction alerts on new or repeated prescriptions were overridden by the computer systems. Only 256 (32 x 5%) of 787 potential drug interactions emerged from new prescriptions. The alert systems produced 656 alerts of which 146 were irrelevant because of multiple alerting of the same interaction or of drug combinations currently no longer taken. Of the 510 remaining relevant drug-interaction alerts, 289 (56 x 7%) were overridden by community pharmacists without any action taken. If the pharmacist took care of a patient's prescription him- or herself (as opposed to just controlling a prescription after a technician took care of the patient), fewer drug-interaction alerts were overridden by the pharmacist [Odds ratio (OR) 0 x 6, 95% confidence interval (CI) 0 x 42-0 x 98; P=0 x 042). Technical overrides (by default settings) and pharmacists' overrides together accounted for 71 x 9% (566 of 787 potential drug interactions). Of the remaining 211 interactions alerts, 87 (41 x 2%) were checked more closely by consulting the literature, contacting the prescribing physician or discussion with the patient. This led to 55 (63 x 2%) interventions (close monitoring, adjustment of dose or ingestion time, therapy stop or switching to alternative therapy). Determinants associated with action taken after an interaction alert were potential high severity (severe or moderate) (OR 3 x 34, 95% CI 1 x 77-6 x 31; P<0 x 001) and alert flagged for the first time (OR 3 x 76, 95% CI 1 x 98-7 x 14; P<0 x 001). All severe potential drug interactions (n=10) generated an alert and all caused an intervention.

CONCLUSIONS

Pharmacists override a substantial proportion of drug-interaction alerts of minor or moderate potential severity by ignoring them or by programming the system to only flag drug interactions of potentially high severity. More sophisticated systems with improved sensitivity and specificity are required. Until these become available, it is important to ensure that at least potentially severe drug interactions are not missed; a goal that seems to be largely achieved.

Prevalence and patient awareness of selected potential drug interactions with self-medication

BACKGROUND AND OBJECTIVE

In community pharmacies potential drug interactions between prescription only medicines (POM) and over-the-counter (OTC) drugs purchased for self-medication arise mainly in two situations: (i) if an OTC drug is purchased by a passer-by customer whose prescribed drug therapy is not known; or (ii) if a POM or an OTC drug is requested by a regular customer whose prescribed drug therapy is usually recorded. With this study we aimed to assess the prevalence of potential drug interactions with selected POM and OTC drugs in passer-by and regular customers as well as their awareness of these potential drug interactions.

METHODS

Data were collected in 14 community pharmacies in the region of Basel, Switzerland by observation of customer contacts and interviews with passer-by customers purchasing selected OTC drugs, and telephone-interviews with regular customers treated with selected POMs identified in community pharmacies' databases. The selected POMs and OTC drugs are drugs which could lead to clinically relevant drug interactions of varying severity but manageable through different interventions such as adjustment of dose and its timing and/or monitoring of the therapy, and avoidance of the combination by choosing an alternative treatment.

RESULTS

Of 1183 passer-by customers observed, 164 (14 x 4%) purchased at least one of the selected OTC drugs. One hundred and two (62 x 2%) of those subjects were interviewed. Forty-three (42 x 2%) mentioned taking prescribed drugs, and three of them were exposed to potential drug interactions of moderate severity. Out of 592 regular customers selected from the community pharmacy database, 434 (73 x 3%) could be interviewed. Sixty-nine (15 x 9%) of them were exposed to a potential drug interaction between purchased OTC drug for self-medication and their POM. Furthermore, 116 (26 x 7%) regular customers were exposed to potential drug interactions within their prescribed drugs and in 28 (6 x 5%) multiple (>or=2) potential drug interactions were found. Two hundred and three (46 x 8%) regular customers were aware of potential drug interactions between their POM and OTC drugs. Ninety-six (47 x 3%) of them were informed by their prescribing physician and 52 (25 x 6%) by their community pharmacist. Awareness of potential drug interaction was higher in younger customers [odds ratio (OR) 0 x 95; 95% confidence intervals (CI) 0 x 93, 0 x 97, P<0 x 0001] and higher for drug interactions classified as 'severe' [OR 1 x 79; 95% CI 1 x 16, 2 x 77, P=0 x 009].

CONCLUSION

Efforts to increase awareness of potential drug interactions is needed. Although community pharmacies are adequately equipped with computerized drug interaction surveillance systems this is often not applied to self-medication. Vigilance for potential interactions of all drugs, including those sold over the counter, should be increased.

[Application aids in pharmacotherapy]

The actual administration of pharmacotherapy is in most cases entirely up to the patient. Correct application can often be only achieved with application aids. They are already part of many preparations: printed blister packages, measures for dosing liquids, applicators for topical use, dosage sprays, and supports for eye drop containers. Special needs can be covered by additional application aids like dosage syringes for child medication, spacers for asthma sprays, devices for splitting or crunching tablets. Filling the medicines in containers better manageable by the patient, in week dispensers or week blisters, may also be crucial to guarantee correct dosing and regimen. Application aids often play a significant part in the success of a therapy. Needed are evidence based criteria for the selection of devices and instructions. Such criteria need to be developed because they are still largely lacking.

Screening for sleep disorders in community pharmacies - evaluation of a campaign in Switzerland

BACKGROUND

In 2003 the Swiss federation of pharmacists organized a campaign "sleep disturbances--daytime sleepiness". The goal was to assist pharmacy clients in detecting likely causes of any sleep disturbance or daytime sleepiness through a free of charge screening, and to deliver targeted counselling. For pharmacy practice there are no screening or triage guidelines to assess the severity of sleep and wakefulness disturbances and potential causes for those disturbances. In this paper the outcome of the campaign in terms of feasibility, participation, observed response patterns, sale of over-the-counter (OTC) sleeping pills, and counselling activities is evaluated.

METHODS

The Stanford sleep disorders questionnaire and the Epworth sleepiness scale served to identify patterns of symptoms suggestive of four major categories of sleep disorders. The questionnaires were posted on a web-site and the clients' data were entered online in the pharmacies. A report was automatically generated and immediately available online to the pharmacists. The pharmacists documented separately their counselling activities in a pharmacist's activity report.

RESULTS

Six hundred and twenty-two (23%) of 2743 pharmacy clients had response patterns suggestive of obstructive sleep apnoea, 418 (15%) of restless-legs-syndrome, 39 (1%) of a sleep disorder potentially associated with a psychiatric condition and 79 (3%) of narcolepsy. An Epworth sleepiness score >10 points was found in 567 (21%). After screening, 2345 (86%) pharmacy clients received targeted counselling. Only 216 (8%) purchased an OTC sleeping pill and 704 (26%) were recommended to consult a physician, but of these, 446 (63%) were already under medical supervision.

CONCLUSIONS

The online screening tool for sleep disorders and daytime sleepiness was successfully introduced in Swiss pharmacies. Pharmacies were able to assess the pattern of individual sleep disorders and to identify a possible cause in nearly one-third of the cases.

[Return of unused drugs to pharmacies]

For the first time unused drugs have been analyzed in Switzerland. The two non profit organizations MEDI HELP DIRECT in Zurich and Pharmaciens sans Frontières in Neuchâtel collected the unused drugs with the aim to examine the quality and the quantity of the medication returned to the pharmacies. In both cantons about 5000 units have been registered and examined with the respect to shelf-life, contents, requirement of prescription and reimbursement by health companies. Two thirds of the drugs have 50-100% contents left over. Prescribed medicines returned faster to the pharmacies and are less often expired.