A Comprehensive Study of Gradient Conditions for Deep Proteome Discovery in a Complex Protein Matrix.

Bottom-up mass-spectrometry-based proteomics is a well-developed technology based on complex peptide mixtures from proteolytic cleavage of proteins and is widely applied in protein identification, characterization, and quantitation. A tims-ToF mass spectrometer is an excellent platform for bottom-up proteomics studies due to its rapid acquisition with high sensitivity. It remains challenging for bottom-up proteomics approaches to achieve 100% proteome coverage. Liquid chromatography (LC) is commonly used prior to mass spectrometry (MS) analysis to fractionate peptide mixtures, and the LC gradient can affect the peptide fractionation and proteome coverage. We investigated the effects of gradient type and time duration to find optimal gradient conditions. Five gradient types (linear, logarithm-like, exponent-like, stepwise, and step-linear), three different gradient lengths (22 min, 44 min, and 66 min), two sample loading amounts (100 ng and 200 ng), and two loading conditions (the use of trap column and no trap column) were studied. The effect of these chromatography variables on protein groups, peptides, and spectral counts using HeLa cell digests was explored. The results indicate that (1) a step-linear gradient performs best among the five gradient types studied; (2) the optimal gradient duration depends on protein sample loading amount; (3) the use of a trap column helps to enhance protein identification, especially low-abundance proteins; (4) MSFragger and PEAKS Studio have high similarity in protein group identification; (5) MSFragger identified more protein groups among the different gradient conditions compared to PEAKS Studio; and (6) combining results from both database search engines can expand identified protein groups by 9-11%.

Plasma pre-treatment T790M relative allelic frequency in patients with advanced EGFR-mutated non-small cell lung cancer predicts treatment response to subsequent-line osimertinib.

BACKGROUND: Approximately half of all patients with advanced EGFR-mutant NSCLC will develop acquired resistance to first or second-generation EGFR tyrosine kinase inhibitors (EGFR-TKIs) with a T790M mutation. In the AURA3 trial, patients with a T790M mutation had a response rate of 71% to osimertinib, a third-generation EGFR-TKI. The response to osimertinib may vary according to plasma T790M mutation frequency. Our aim was to determine the effect of plasma T790M mutation load on treatment response to osimertinib in an Australian multi-institutional cohort. METHODS: We performed a retrospective study on patients treated with osimertinib in the second-line setting and beyond between 2016-2018 from ten centres in Australia, who had T790M mutations detected in tumour or plasma. The primary objective was to investigate if there was a difference in disease control rate (DCR) between patients with high vs. low T790M relative allelic frequency (RAF) as detected in plasma, using a 0.3 RAF cut-off, as determined by ddPCR or BEAMing PCR. Secondary objective was to determine the survival outcomes according to high versus low plasma T790M RAF. Additional analyses were performed to investigate the survival outcome for patients with plasma versus tissue T790M positivity. RESULTS: A total of 139 patients were included in this study. Patients with higher RAF demonstrated higher DCR (74% vs. 36%, P=0.02), however there was no statistically significant difference in survival outcomes in the two groups. Exploratory analysis showed that patients with tissue T790M+ had improved DCR compared with those with plasma T790M+ (89% vs. 68%, P=0.01) and longer progression free survival (median 15.4 vs. 9.7 months; HR 0.51, 95% CI: 0.34 to 0.77, P=0.003) and overall survival (median not reached, HR 0.51, 95% CI: 0.30 to 0.86, P=0.02). Patients who were tissue T790M+ demonstrated superior survival compared to plasma T790M+ after correcting for confounding variables in a multivariate model. CONCLUSIONS: DCR was superior in patients with higher plasma T790M mutation load versus lower plasma T790M mutational load, without significant survival benefit. Plasma T790M RAF is a potential predictive biomarker which should be investigated and validated in larger prospective studies.

Severe infusion reaction due to nivolumab: A case report.

BACKGROUND: Nivolumab is an anti-PD1 immune checkpoint inhibitor commonly used for the treatment of solid organ and hematological malignancies. Severe infusion reaction due to nivolumab is quite rare. CASE: We report a case of severe infusion reaction due to nivolumab necessitating ICU admission and withdrawal of further nivolumab use in a patient with metastatic non-small cell lung cancer. CONCLUSION: Our knowledge and expertise with the use of immune checkpoint inhibitors are still evolving. This report highlights one of the rare possible side-effects that clinicians and patients may have to face with increasing indications and use of nivolumab in day to day practice.

Quantitative Proteomics Reveals Docosahexaenoic Acid-Mediated Neuroprotective Effects in Lipopolysaccharide-Stimulated Microglial Cells.

The high levels of docosahexaenoic acid (DHA) in cell membranes within the brain have led to a number of studies exploring its function. These studies have shown that DHA can reduce inflammatory responses in microglial cells. However, the method of action is poorly understood. Here, we report the effects of DHA on microglial cells stimulated with lipopolysaccharides (LPSs). Data were acquired using the parallel accumulation serial fragmentation method in a hybrid trapped ion mobility-quadrupole time-of-flight mass spectrometer. Over 2800 proteins are identified using label-free quantitative proteomics. Cells exposed to LPSs and/or DHA resulted in changes in cell morphology and expression of 49 proteins with differential abundance (greater than 1.5-fold change). The data provide details about pathways that are influenced in this system including the nuclear factor κ-light-chain-enhancer of the activated B cells (NF-κB) pathway. Western blots and enzyme-linked immunosorbent assay studies are used to help confirm the proteomic results. The MS data are available at ProteomeXchange.

Plasma next generation sequencing and droplet digital PCR-based detection of epidermal growth factor receptor (EGFR) mutations in patients with advanced lung cancer treated with subsequent-line osimertinib.

BACKGROUND: Gene mutation analysis from plasma circulating tumor DNA (ctDNA) can provide timely information regarding the mechanism of resistance that could translate to personalised treatment. We compared concordance rate of next generation sequencing (NGS) and droplet digital polymerase chain reaction (ddPCR) in the detection of the EGFR activating and T790M mutation from plasma ctDNA with diagnostic tissue biopsy-based assays. The second objective was to test whether putative osimertinib resistance associated mutations were detectable from plasma using NGS. METHODS: From January 2016 to December 2017, we prospectively collected plasma samples from patients prior to commencement of second- or third-line osimertinib therapy and upon disease progression, in a single tertiary hospital in South Western Sydney, Australia. Amplicon-based NGS and ddPCR assays were used to detect activating epidermal growth factor receptor (EGFR) and T790M mutations in 18 plasma samples from nine patients; all patients were required to have tissue biopsies with known EGFR status. RESULTS: High concordance of allelic fractions were seen in matched plasma NGS and ddPCR for activating EGFR mutations and T790M mutations (R2 = 0.92, P < 0.0001). Using tissue biopsies as reference standard, sensitivity was 100% for NGS and 94% for ddPCR. Several possible osimertinib resistance associated mutations, including PIK3CA, BRAF and TP53 mutations, were detected by NGS in samples upon progression on osimertinib therapy. CONCLUSION: ddPCR assays for EGFR mutations appear to be as sensitive and highly concordant as amplicon-based NGS. NGS has the ability to detect novel resistance mutations.

Clinical outcomes in patients with advanced epidermal growth factor receptor-mutated non-small-cell lung cancer in South Western Sydney Local Health District.

BACKGROUND: Epidermal growth factor receptor (EGFR)-mutated non-small-cell lung cancer (NSCLC) is a subgroup of oncogene addicted lung cancer that predicts response to tyrosine kinase inhibitors (TKI). However, there is variability in response and survival outcomes in patients with EGFR mutation treated with TKI. AIM: To describe clinical characteristics, treatment patterns and factors influencing outcomes in patients with EGFR-mutated NSCLC in South Western Sydney Local Health District. METHODS: Retrospective review of patients with EGFR-mutated NSCLC diagnosed between January 2010 and June 2016. RESULTS: A total of 85 EGFR-mutated NSCLC patients was identified; 80 (94%) received first-line treatment with EGFR-TKI. The median follow-up was 10.7 months with a median duration of treatment of 9 months. On disease progression (n = 44), 37% had best supportive care only, 30% received chemotherapy, 23% participated in clinical trials, 7% continued on a first generation EGFR-TKI and 3% received afatinib. Overall response rate to first-line EGFR-TKI was 66%. Median progression-free survival (PFS) was 10.7 months (range 2.7-55.9 months) and median overall survival (OS) was 23 months (range 0.4-35.8 months). Multivariate Cox regression analysis showed that patients with lower disease burden (<4 sites) had longer PFS (hazard ratio (HR) 0.36, 95% confidence interval (CI) 0.18-0.72, P = 0.004) but not OS. Good performance status predicts longer OS (HR 0.33, CI 0.14-0.77, P = 0.01). Lower (<5) pre-treatment neutrophil-to-lymphocyte ratio (NLR) was associated with better PFS (HR 0.40, 95% CI 0.18-0.87, P = 0.02) and OS (HR 0.43, 95% CI 0.19-0.94, P = 0.04). There were no survival differences when patients were stratified by age, baseline albumin level and types of EGFR mutation. CONCLUSION: Results from this community-based cohort confirm known prognostic factors in patients with EGFR-mutated NSCLC receiving TKI and suggest the negative influence of a heightened host systemic inflammatory response on patient outcomes.

CTC-mRNA (AR-V7) Analysis from Blood Samples-Impact of Blood Collection Tube and Storage Time.

Circulating tumour cells (CTCs) are an emerging resource for monitoring cancer biomarkers. New technologies for CTC isolation and biomarker detection are increasingly sensitive, however, the ideal blood storage conditions to preserve CTC-specific mRNA biomarkers remains undetermined. Here we tested the preservation of tumour cells and CTC-mRNA over time in common anticoagulant ethylene-diamine-tetra-acetic acid (EDTA) and acid citrate dextrose solution B (Citrate) blood tubes compared to preservative-containing blood tubes. Blood samples spiked with prostate cancer cells were processed after 0, 24, 30, and 48 h storage at room temperature. The tumour cell isolation efficiency and the mRNA levels of the prostate cancer biomarkers androgen receptor variant 7 (AR-V7) and total AR, as well as epithelial cell adhesion molecule (EpCAM) were measured. Spiked cells were recovered across all storage tube types and times. Surprisingly, tumour mRNA biomarkers were readily detectable after 48 h storage in EDTA and Citrate tubes, but not in preservative-containing tubes. Notably, AR-V7 expression was detected in prostate cancer patient blood samples after 48 h storage in EDTA tubes at room temperature. This important finding presents opportunities for measuring AR-V7 expression from clinical trial patient samples processed within 48 h-a much more feasible timeframe compared to previous recommendations.

Ion solvation and association in LiClO4/sulfolane solution: a vibrational spectroscopic and molecular orbital study.

Solvation interaction and ion association in solutions of lithium perchlorate/sulfolane have been studied by using infrared and Raman spectra as a function of concentration of lithium perchlorate. The band changes of antisymmetric OSO stretch, antisymmetric CSC stretch, -SO2 wag and twist suggest that there is an interaction between Li+ and sulfolane molecules, and the site of solvation is the oxygen atom of -SO2 group. The molecular orbital calculation supports this suggestion. On the other hand, the apparent solvation number was calculated, and the band fitting for the ClO4- band reveals the presence of contact ion pair, solvent separated ion pair and free ClO4- anion in the concentrated solutions.

[Surface enhanced Raman scattering of thiourea in acidic solution].

Surface enhanced Raman scattering of thiourea adsorbed on the plated silver surface in an acidic solution has been studied. The results show that the thiourea molecules are inclined to adsorbed on the silver surface via sulphur. When the concentration of HCl in the solution is increased, the plane of the thiourea molecule deviates more from the normal line of the silver surface. The experimental results also suggest that the rather strong chemical enhanced mechanism would exist in this system.

Legal and ethical issues in genetic testing and counseling for susceptibility to breast, ovarian and colon cancer.

The prediction of susceptibility to heritable breast, ovarian and colon cancer raises important legal and ethical concerns. Health care professionals have a duty to disclose sufficient information to enable patients to make informed decisions. They must also safeguard the confidentiality of patient data. These duties may come into conflict if a positive finding in one patient implies that family members are also at risk. A legal distinction is made between a breach of confidentiality and the legitimate sharing of information in a patient's interest or to prevent harm to a third party. Physicians also have a fiduciary duty to warn. Other issues concern the legal liability assumed by genetic counsellors, whose disclosures may influence decisions about childbearing, for example, and the risk of socioeconomic discrimination faced by people with a known genetic susceptibility. Traditional ethical orientations and principals may be applied to these and other questions, but feminist ethics will likely have particular importance in the development of an ethical stance toward testing and counseling for heritable breast and ovarian cancer.

[Ambulatory anesthesia in arthroscopy of the knee: proposal of an intravenous general anesthesia technique]. / L'anestesia ambulatoriale nelle artroscopie del ginocchio: proposta di una tecnica di anestesia generale e.v..

The Authors propose a technique completely i.v. for arthroscopy of the knee by means of proposal discontinuous infusion. The advantage underlined are tolerability, efficaciousness, features of awakening and a few collateral effects verified, and this leads to be conclusion that this anaesthesia system must be considered of choice in this type of surgery.