Extracellular vesicles for precision medicine in prostate cancer - Is it ready for clinical translation?

Biofluid-based biomarker tests hold great promise for precision medicine in prostate cancer (PCa) clinical practice. Extracellular vesicles (EV) are established as intercellular messengers in cancer development with EV cargos, including protein and nucleic acids, having the potential to serve as biofluid-based biomarkers. Recent clinical studies have begun to evaluate EV-based biomarkers for PCa diagnosis, prognosis, and disease/therapy resistance monitoring. Promising results have led to PCa EV biomarker validation studies which are currently underway with the next challenge being translation to robust clinical assays. However, EV research studies generally use low throughput EV isolation methods and costly molecular profiling technologies that are not suitable for clinical assays. Here, we consider the technical hurdles in translating EV biomarker research findings into precise and cost-effective clinical biomarker assays. Novel microfluidic devices coupling EV extraction with sensitive antibody-based biomarker detection are already being explored for point-of-care applications for rapid provision in personalised medicine approaches.

Defining the relationship between cellular and extracellular vesicle (EV) content in breast cancer via an integrative multi-omic analysis.

Much recent research has been dedicated to exploring the utility of extracellular vesicles (EVs) as circulating disease biomarkers. Underpinning this work is the assumption that the molecular cargo of EVs directly reflects the originating cell. Few attempts have been made, however, to empirically validate this on the -omic level. To this end, we have performed an integrative multi-omic analysis of a panel of breast cancer cell lines and corresponding EVs. Whole transcriptome analysis validated that the cellular transcriptome remained stable when cultured cells are transitioned to low serum or serum-free medium for EV collection. Transcriptomic profiling of the isolated EVs indicated a positive correlation between transcript levels in cells and EVs, including disease-associated transcripts. Analysis of the EV proteome verified that HER2 protein is present in EVs, however neither the estrogen (ER) nor progesterone (PR) receptor proteins are detected regardless of cellular expression. Using multivariate analysis, we derived an EV protein signature to infer cellular patterns of ER and HER2 expression, though the ER protein could not be directly detected. Integrative analyses affirmed that the EV proteome and transcriptome captured key phenotypic hallmarks of the originating cells, supporting the potential of EVs for non-invasive monitoring of breast cancers.

Factors associated with cardiac implantable electronic device-related infections, New South Wales, 2016-21: a retrospective cohort study.

OBJECTIVES: To quantify the rate of cardiac implantable electronic device (CIED)-related infections and to identify risk factors for such infections. DESIGN: Retrospective cohort study; analysis of linked hospital admissions and mortality data. SETTING, PARTICIPANTS: All adults who underwent CIED procedures in New South Wales between 1 January 2016 and 30 June 2021 (public hospitals) or 30 June 2020 (private hospitals). MAIN OUTCOME MEASURES: Proportions of patients hospitalised with CIED-related infections (identified by hospital record diagnosis codes); risk of CIED-related infection by patient, device, and procedural factors. RESULTS: Of 37 675 CIED procedures (23 194 men, 63.5%), 500 were followed by CIED-related infections (median follow-up, 24.9 months; interquartile range, 11.2-40.8 months), including 397 people (1.1%) within twelve months of their procedures, and 186 of 10 540 people (2.5%) at high risk of such infections (replacement or upgrade procedures; new cardiac resynchronisation therapy with defibrillator, CRT-D). The overall infection rate was 0.50 (95% confidence interval [CI], 0.45-0.54) per 1000 person-months; it was highest during the first month after the procedure (5.60 [95% CI, 4.89-6.42] per 1000 person-months). The risk of CIED-related infection was greater for people under 65 years of age than for those aged 65-74 years (adjusted hazard ratio [aHR], 1.71; 95% CI, 1.32-2.23), for people with CRT-D devices than for those with permanent pacemakers (aHR, 1.46; 95% CI, 1.02-2.08), for people who had previously undergone CIED procedures (two or more v none: aHR, 1.51; 95% CI, 1.02-2.25) or had CIED-related infections (aHR, 11.4; 95% CI, 8.34-15.7), or had undergone concomitant cardiac surgery (aHR, 1.62; 95% CI, 1.10-2.39), and for people with atrial fibrillation (aHR, 1.33; 95% CI, 1.11-1.60), chronic kidney disease (aHR, 1.54; 95% CI, 1.27-1.87), chronic obstructive pulmonary disease (aHR, 1.37; 95% CI, 1.10-1.69), or cardiomyopathy (aHR 1.60; 95% CI, 1.25-2.05). CONCLUSIONS: Knowledge of risk factors for CIED-related infections can help clinicians discuss them with their patients, identify people at particular risk, and inform decisions about device type, upgrades and replacements, and prophylactic interventions.

Real-world evidence on the association between cardiac implantable electronic device infection and all-cause mortality.

AIMS: An infection following cardiac implantable electronic device (CIED) procedure is a serious complication, but its association with all-cause mortality is inconsistent across observational studies. To quantify the association between CIED infection and all-cause mortality in a large, contemporary cohort from New South Wales, Australia. METHODS AND RESULTS: This retrospective cohort study used linked hospital and mortality data and included all patients aged >18 years who underwent a CIED procedure between July 2017 and September 2022. Cardiac implantable electronic device infection was defined by the presence of relevant diagnosis codes. Cox regression to estimate adjusted hazard ratios (aHRs) with 95% confidence intervals (CIs) for the association of CIED infection with mortality, at 1-year, and at the end of follow-up, with CIED infection included as a time-dependent variable, and other potential risk factors for mortality included as fixed covariates. We followed 37,750 patients with CIED procedures {36% female, mean age [standard deviation (SD)] 75.8 [12.7] years}, and 487 (1.3%) CIED infections were identified. We observed 5771 (15.3%) deaths during an average follow-up of 25.2 (SD 16.8) months. Compared with no infection group, patients with CIED infection had a higher Kaplan-Meier mortality rate (19.4 vs. 6.8%) and adjusted hazard of mortality (aHR 2.73, 95% CI 2.10-3.54) at 12 months post-procedure. These differences were attenuated but still remained significant at the end of follow-up (aHR 1.83, 95% CI 1.52-2.19). CONCLUSION: In a complete, state-wide cohort of CIED patients, infection was associated with higher risks of both short-term and long-term mortality.

LipidSuite: interactive web server for lipidomics differential and enrichment analysis.

Advances in mass spectrometry enabled high throughput profiling of lipids but differential analysis and biological interpretation of lipidomics datasets remains challenging. To overcome this barrier, we present LipidSuite, an end-to-end differential lipidomics data analysis server. LipidSuite offers a step-by-step workflow for preprocessing, exploration, differential analysis and enrichment analysis of untargeted and targeted lipidomics. Three lipidomics data formats are accepted for upload: mwTab file from Metabolomics Workbench, Skyline CSV Export, and a numerical matrix. Experimental variables to be used in analysis are uploaded in a separate file. Conventional lipid names are automatically parsed to enable lipid class and chain length analyses. Users can interactively explore data, choose subsets based on sample types or lipid classes or characteristics, and conduct univariate, multivariate and unsupervised analyses. For complex experimental designs and clinical cohorts, LipidSuite offers confounding variables adjustment. Finally, data tables and plots can be both interactively viewed or downloaded for publication or reports. Overall, we anticipate this free, user-friendly webserver to facilitate differential lipidomics data analysis and re-analysis, and fully harness biological interpretation from lipidomics datasets. LipidSuite is freely available at http://suite.lipidr.org.

Structure of human endo-α-1,2-mannosidase (MANEA), an antiviral host-glycosylation target.

Mammalian protein N-linked glycosylation is critical for glycoprotein folding, quality control, trafficking, recognition, and function. N-linked glycans are synthesized from Glc3Man9GlcNAc2 precursors that are trimmed and modified in the endoplasmic reticulum (ER) and Golgi apparatus by glycoside hydrolases and glycosyltransferases. Endo-α-1,2-mannosidase (MANEA) is the sole endo-acting glycoside hydrolase involved in N-glycan trimming and is located within the Golgi, where it allows ER-escaped glycoproteins to bypass the classical N-glycosylation trimming pathway involving ER glucosidases I and II. There is considerable interest in the use of small molecules that disrupt N-linked glycosylation as therapeutic agents for diseases such as cancer and viral infection. Here we report the structure of the catalytic domain of human MANEA and complexes with substrate-derived inhibitors, which provide insight into dynamic loop movements that occur on substrate binding. We reveal structural features of the human enzyme that explain its substrate preference and the mechanistic basis for catalysis. These structures have inspired the development of new inhibitors that disrupt host protein N-glycan processing of viral glycans and reduce the infectivity of bovine viral diarrhea and dengue viruses in cellular models. These results may contribute to efforts aimed at developing broad-spectrum antiviral agents and help provide a more in-depth understanding of the biology of mammalian glycosylation.

An Update on SARS-CoV-2 Clinical Trial Results-What We Can Learn for the Next Pandemic.

The coronavirus disease 2019 (COVID-19) pandemic has claimed over 7 million lives worldwide, providing a stark reminder of the importance of pandemic preparedness. Due to the lack of approved antiviral drugs effective against coronaviruses at the start of the pandemic, the world largely relied on repurposed efforts. Here, we summarise results from randomised controlled trials to date, as well as selected in vitro data of directly acting antivirals, host-targeting antivirals, and immunomodulatory drugs. Overall, repurposing efforts evaluating directly acting antivirals targeting other viral families were largely unsuccessful, whereas several immunomodulatory drugs led to clinical improvement in hospitalised patients with severe disease. In addition, accelerated drug discovery efforts during the pandemic progressed to multiple novel directly acting antivirals with clinical efficacy, including small molecule inhibitors and monoclonal antibodies. We argue that large-scale investment is required to prepare for future pandemics; both to develop an arsenal of broad-spectrum antivirals beyond coronaviruses and build worldwide clinical trial networks that can be rapidly utilised.

Nursing Care of the Acute Ischemic Stroke Endovascular Thrombectomy Patient.

Nurses are an integral part of the multidisciplinary team caring for a patient eligible for endovascular thrombectomy. Their care includes obtaining health history, performing clinical assessments, using critical thinking to anticipate the care path, and communicating findings to other team members. The prehospital and emergency department nurses utilize stroke severity scales to identify a possible thrombectomy candidate and help expedite intervention. In the interventional laboratory, nursing collaborates with radiology technologists and interventionalists to ensure patient safety and monitor for intraprocedural complications. Post-procedure, the intensive care nurse delivers complex care to ensure optimal neurological outcome and assess for postprocedural complications. Nursing is essential in every phase of care along with collaboration with other disciplines.

Increased lipid metabolism impairs NK cell function and mediates adaptation to the lymphoma environment.

Natural killer (NK) cells play critical roles in protection against hematological malignancies but can acquire a dysfunctional state, which limits antitumor immunity. However, the underlying reasons for this impaired NK cell function remain to be uncovered. We found that NK cells in aggressive B-cell lymphoma underwent substantial transcriptional reprogramming associated with increased lipid metabolism, including elevated expression of the transcriptional regulator peroxisome activator receptor-γ (PPAR-γ). Exposure to fatty acids in the lymphoma environment potently suppressed NK cell effector response and cellular metabolism. NK cells from both diffuse large B-cell lymphoma patients and Eµ-myc B-cell lymphoma-bearing mice displayed reduced interferon-γ (IFN-γ) production. Activation of PPAR-γ partially restored mitochondrial membrane potential and IFN-γ production. Overall, our data indicate that increased lipid metabolism, while impairing their function, is a functional adaptation of NK cells to the fatty-acid rich lymphoma environment.

Comparison of care accessibility, costs, and quality with face-to-face and telehealth epilepsy clinic visits.

During the COVID-19 pandemic, restrictions on reimbursement for telehealth visits were lifted and this visit type was suddenly available to patients around the United States of America. Telehealth visits offer potential cost savings for patients and families, which may vary by region of the world studied. Also, aggressiveness of the care patients receive may differ, and patients or families may be more likely to choose one visit type over another based on seizure control. This is a prospective face-to-face clinic versus telehealth clinic visit comparison study involving patients with seizures, their legal guardians, and caretakers who attend clinic. We compared travel distance, work-related factors, childcare, satisfaction of care, changes in seizure medication or diagnostics tests ordered, and willingness to cancel appointments to better understand the behavioral patterns of patients, caretakers, and providers. Our results indicate that many patients and families still prefer in-person interactions with their medical providers. Patient and family satisfaction levels were equal with both visit types. No significant difference was seen in medical management between face-to-face and telehealth visits. Also, prior seizure control did not dictate the type of visit chosen. Telehealth participants were significantly more willing to cancel appointments if asked to switch to face-to-face then face-to-face participants asked to complete telehealth visits. Surprisingly, we found that patients and families choosing telehealth were not statistically more likely to be employed or take less time off work. Also, distance from home to office was not significantly shorter for participants choosing face-to-face visits. Offering a combination of telehealth and face-to-face visits appears to be the optimal strategy in caring for patients with controlled and uncontrolled seizure disorders to ensure adherence with clinic visits and satisfaction with care. Our study suggests that providers are equally willing to adjust medications or order additional diagnostic testing regardless of visit type. Patients and families may be less likely to cancel telehealth visits than face-to-face visits; this finding may translate to improved seizure control and long-term decreased cost of care.

Pathogen-induced inflammation is attenuated by the iminosugar MON-DNJ via modulation of the unfolded protein response.

Sepsis is a life-threatening condition involving a dysregulated immune response to infectious agents that cause injury to host tissues and organs. Current treatments are limited to early administration of antibiotics and supportive care. While appealing, the strategy of targeted inhibition of individual molecules in the inflammatory cascade has not proved beneficial. Non-targeted, systemic immunosuppression with steroids has shown limited efficacy and raises concern for secondary infection. Iminosugars are a class of small molecule glycomimetics with distinct inhibition profiles for glycan processing enzymes based on stereochemistry. Inhibition of host endoplasmic reticulum resident glycoprotein processing enzymes has demonstrated efficacy as a broad-spectrum antiviral strategy, but limited consideration has been given to the effects on host glycoprotein production and consequent disruption of signalling cascades. This work demonstrates that iminosugars inhibit dengue virus, bacterial lipopolysaccharide and fungal antigen-stimulated cytokine responses in human macrophages. In spite of decreased inflammatory mediator production, viral replication is suppressed in the presence of iminosugar. Transcriptome analysis reveals the key interaction of pathogen-induced endoplasmic reticulum stress, the resulting unfolded protein response and inflammation. Our work shows that iminosugars modulate these interactions. Based on these findings, we propose a new therapeutic role for iminosugars as treatment for sepsis-related inflammatory disorders associated with excess cytokine secretion.

Addressing Delicate and Variable Cancer Morphology in Spectral Histopathology Using Canine Visceral Hemangiosarcoma.

Spectral histopathology has shown promise for the classification and diagnosis of tumors with defined morphology, but application in tumors with variable or diffuse morphologies is yet to be investigated. To address this gap, we evaluated the application of Fourier transform infrared (FTIR) imaging as an accessory diagnostic tool for canine hemangiosarcoma (HSA), a vascular endothelial cell cancer that is difficult to diagnose. To preserve the delicate vascular tumor tissue structure, and potential classification of single endothelial cells, paraffin removal was not performed, and a partial least square discrimination analysis (PLSDA) and Random Forest (RF) models to classify different tissue types at individual pixel level were established using a calibration set (24 FTIR images from 13 spleen specimens). Next, the prediction capability of the PLSDA model was tested with an independent test set (n = 11), resulting in 74% correct classification of different tissue types at an individual pixel level. Finally, the performance of the FTIR spectropathology and chemometric algorithm for diagnosis of HSA was established in a blinded set of tissue samples (n = 24), with sensitivity and specificity of 80 and 81%, respectively. Taken together, these results show that FTIR imaging without paraffin removal can be applied to tumors with diffuse morphology, and this technique is a promising tool to assist in canine splenic HSA differential diagnosis.

Rapid Classification of COVID-19 Severity by ATR-FTIR Spectroscopy of Plasma Samples.

The coronavirus disease 2019 (COVID-19) pandemic continues to ravage the world, with many hospitals overwhelmed by the large number of patients presenting during major outbreaks. A rapid triage for COVID-19 patient requiring hospitalization and intensive care is urgently needed. Age and comorbidities have been associated with a higher risk of severe COVID-19 but are not sufficient to triage patients. Here, we investigated the potential of attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy as a rapid blood test for classification of COVID-19 disease severity using a cohort of 160 COVID-19 patients. A simple plasma processing and ATR-FTIR data acquisition procedure was established using 75% ethanol for viral inactivation. Next, partial least-squares-discriminant analysis (PLS-DA) models were developed and tested using data from 130 and 30 patients, respectively. Addition of the ATR-FTIR spectra to the clinical parameters (age, sex, diabetes mellitus, and hypertension) increased the area under the ROC curve (C-statistics) for both the training and test data sets, from 69.3% (95% CI 59.8-78.9%) to 85.7% (78.6-92.8%) and 77.8% (61.3-94.4%) to 85.1% (71.3-98.8%), respectively. The independent test set achieved 69.2% specificity (42.4-87.3%) and 94.1% sensitivity (73.0-99.0%). Diabetes mellitus was the strongest predictor in the model, followed by FTIR regions 1020-1090 and 1588-1592 cm-1. In summary, this study demonstrates the potential of ATR-FTIR spectroscopy as a rapid, low-cost COVID-19 severity triage tool to facilitate COVID-19 patient management during an outbreak.

Correction: Detecting antimicrobial resistance in Escherichia coli using benchtop attenuated total reflectance-Fourier transform infrared spectroscopy and machine learning.

Correction for 'Detecting antimicrobial resistance in Escherichia coli using benchtop attenuated total reflectance-Fourier transform infrared spectroscopy and machine learning' by Hewa G. S. Wijesinghe et al., Analyst, 2021, DOI: 10.1039/d1an00546d.

Detecting antimicrobial resistance in Escherichia coli using benchtop attenuated total reflectance-Fourier transform infrared spectroscopy and machine learning.

The widespread dissemination of resistance to third-generation cephalosporins in the Enterobacterales through the production of extended-spectrum ß-lactamase (ESBL) is considered a critical global crisis requiring urgent attention of clinicians and scientists alike. Rapid diagnostic methods that can identify microbial resistance profiles closer to the point of care are crucial to minimize the overuse of antimicrobial agents and improve patient outcomes. Although Fourier transform infrared (FTIR) microscopy has shown promise in distinguishing between bacterial species, the high cost and technical requirements of the IR microscope may limit broad clinical use. To address the practical needs of a clinical microbiology laboratory, here, we examine the ability of a lower cost portable benchtop attenuated total reflectance (ATR)-FTIR spectrometer to achieve antimicrobial resistance detection, using a simple, clinically aligned sampling protocol. The technical reproducibility was confirmed through multi-day analysis of an Escherichia coli type strain, which serves as quality control. We generated a dataset of 100 E. coli clinical bloodstream isolates with 63 ceftriaxone resistant blaCTX-M ESBL gene variant strains and developed a classifier for blaCTX-M genotype detection. After assessing 35 machine learning methods using the training set (n = 71), four methods were further optimised, and the best performing method was evaluated using the held-out testing set (n = 29). A tuned support vector machine model with a polynomial kernel, using the 700-1500 cm-1 range achieved a sensitivity of 89.2%, and specificity of 66.7% for detecting blaCTX-M in independent testing, approaching the reported performance of FTIR microscopy. With further algorithm improvement, these data suggest the potential deployment of a portable FTIR spectrometer as a rapid antimicrobial susceptibility prediction platform to enable the efficient use of antimicrobials.

Systematic Review of Evidence-Based Guidelines for Prehospital Care.

Introduction: Multiple national organizations have identified a need to incorporate more evidence-based medicine in emergency medical services (EMS) through the creation of evidence-based guidelines (EBGs). Tools like the Appraisal of Guidelines for Research and Evaluation (AGREE) II and criteria outlined by the National Academy of Medicine (NAM) have established concrete recommendations for the development of high-quality guidelines. While many guidelines have been created that address topics within EMS medicine, neither the quantity nor quality of prehospital EBGs have been previously reported. Objectives: To perform a systematic review to identify existing EBGs related to prehospital care and evaluate the quality of these guidelines using the AGREE II tool and criteria for clinical guidelines described by the NAM. Methods: We performed a systematic search of the literature in MEDLINE, EMBASE, PubMED, Trip, and guidelines.gov, through September 2018. Guideline topics were categorized based on the 2019 Core Content of EMS Medicine. Two independent reviewers screened titles for relevance and then abstracts for essential guideline features. Included guidelines were appraised with the AGREE II tool across 6 domains by 3 independent reviewers and scores averaged. Two additional reviewers determined if each guideline reported the key elements of clinical practice guidelines recommended by the NAM via consensus. Results: We identified 71 guidelines, of which 89% addressed clinical aspects of EMS medicine. Only 9 guidelines scored >75% across AGREE II domains and most (63%) scored between 50 and 75%. Domain 4 (Clarity of Presentation) had the highest (79.7%) and domain 5 (Applicability) had the lowest average score across EMS guidelines. Only 38% of EMS guidelines included a reporting of all criteria identified by the NAM for clinical practice guidelines, with elements of a systematic review of the literature most commonly missing. Conclusions: EBGs exist addressing a variety of topics in EMS medicine. This systematic review and appraisal of EMS guidelines identified a wide range in the quality of these guidelines and variable reporting of key elements of clinical guidelines. Future guideline developers should consider established methodological and reporting recommendations to improve the quality of EMS guidelines.

RaftProt V2: understanding membrane microdomain function through lipid raft proteomes.

Cellular membranes feature dynamic submicrometer-scale lateral domains termed lipid rafts, membrane rafts or glycosphingolipid-enriched microdomains (GEM). Numerous proteomics studies have been conducted on the lipid raft proteome, however, interpretation of individual studies is limited by potential undefined contaminant proteins. To enable integrated analyses, we previously developed RaftProt (http://lipid-raft-database.di.uq.edu.au/), a searchable database of mammalian lipid raft-associated proteins. Despite being a highly used resource, further developments in annotation and utilities were required. Here, we present RaftProt V2 (http://raftprot.org), an improved update of RaftProt. Besides the addition of new datasets and re-mapping of all entries to both UniProt and UniRef IDs, we have implemented a stringent annotation based on experimental evidence level to assist in identification of possible contaminant proteins. RaftProt V2 allows for simultaneous search of multiple proteins/experiments at the cell/tissue type and UniRef/Gene level, where correlations, interactions or overlaps can be investigated. The web-interface has been completely re-designed to enable interactive data and subset selection, correlation analysis and network visualization. Overall, RaftProt aims to advance our understanding of lipid raft function through integrative analysis of datasets collected from diverse tissue and conditions. Database URL: http://raftprot.org.

lipidr: A Software Tool for Data Mining and Analysis of Lipidomics Datasets.

The rapid evolution of mass spectrometry (MS)-based lipidomics has enabled the simultaneous measurement of numerous lipid classes. With lipidomics datasets becoming increasingly available, lipidomic-focused software tools are required to facilitate data analysis as well as mining of public datasets, integrating lipidomics-unique molecular information such as lipid class, chain length, and unsaturation. To address this need, we developed lipidr, an open-source R/Bioconductor package for data mining and analysis of lipidomics datasets. lipidr implements a comprehensive lipidomic-focused analysis workflow for targeted and untargeted lipidomics. lipidr imports numerical matrices, Skyline exports, and Metabolomics Workbench files directly into R, automatically inferring lipid class and chain information from lipid names. Through integration with the Metabolomics Workbench API, users can search, download, and reanalyze public lipidomics datasets seamlessly. lipidr allows thorough data inspection, normalization, and uni- and multivariate analyses, displaying results as interactive visualizations. To enable interpretation of lipid class, chain length, and total unsaturation data, we also developed and implemented a novel lipid set enrichment analysis. A companion online guide with two live example datasets is presented at https://www.lipidr.org/. We expect that the ease of use and innovative features of lipidr will allow the lipidomics research community to gain novel detailed insights from lipidomics data.

Antibody-Free Targeted Proteomics Assay for Absolute Measurement of α-Tubulin Acetylation.

Acetylation of α-tubulin at conserved lysine 40 (K40) amino acid residue regulates microtubule dynamics and controls a wide range of cellular activities. Dysregulated microtubule dynamics characterized by differential α-tubulin acetylation is a hallmark of cancer, neurodegeneration, and other complex disorders. Hence, accurate quantitation of α-tubulin acetylation is required in human disease and animal model studies. We developed a novel antibody-free proteomics assay to measure α-tubulin acetylation targeting protease AspN-generated peptides harboring K40 site. Using the synthetic unmodified and acetylated stable isotope labeled peptides DKTIGGG and DKTIGGGD, we demonstrate assay linearity across 4 log magnitude and reproducibility of <10% coefficient of variation. The assay accuracy was validated by titration of 10-80% mixture of acetylated/nonacetylated α-tubulin peptides in the background of human olfactory neurosphere-derived stem (ONS) cell matrix. Furthermore, in agreement with antibody-based high content microscopy analysis, the targeted proteomics assay reported an induction of α-tubulin K40 acetylation upon Trichostatin A stimulation of ONS cells. Independently, we found 35.99% and 16.11% α-tubulin acetylation for mouse spinal cord and brain homogenate tissue, respectively, as measured by our assay. In conclusion, this simple, antibody-free proteomics assay enables quantitation of α-tubulin acetylation, and is applicable across various fields of biology and medicine.

Antibody-Free Multiplex Measurement of 23 Human Cytokines in Primary Cell Culture Secretome Using Targeted Mass Spectrometry.

Cytokines are commonly measured by immunoassays; however, these have limited multiplexing capacity, are costly, and can exhibit cross-reactivity. Multiple reaction monitoring (MRM) mass spectrometry is a robust method to quantify analytes with high specificity and multiplexing ability, hence we aimed to investigate its suitability as an alternative cost-effective method for cytokine measurement. Human keratinocyte conditioned media spiked with recombinant cytokines was used as an experimental system to evaluate sensitivity, linearity, and reproducibility of an MRM assay targeting 79 peptides representing 23 human cytokines. Our MRM method was able to identify 21 cytokines by two or more unique peptides and two cytokines by a single unique peptide. In a serum-free matrix, the median LOD and LOQ for cytokine peptides was 130 and 433 pg/mL, respectively. The presence of serum increased median LOD and LOQ by about 2.3-fold. The assay shows excellent replicate consistency with 8% intra- and 12% interday coefficient of variations. We found high pH reversed-phase fractionation a useful tool to increase assay sensitivity with the drawback of increasing its variability by approximately 10%. Overall, our results suggest utility of a multiplex cytokine MRM for routine measurement of secreted cytokines in cellular experiments under low serum conditions. Additional enrichment steps will be required in high complexity matrices such as serum.