Poor performance status is a risk factor for higher detection of Gram positive coccus in stone-related pyelonephritis.

INTRODUCTION: We aimed to investigate the detection rate of causative organisms in stone-related pyelonephritis and to compare their distribution according to patient backgrounds. METHODS: We retrospectively identified patients with stone-related pyelonephritis. Clinical data were collected between November 2012 and August 2020 at Wakayama Medical University Hospital, including on patient backgrounds and causative organisms. Patients were categorized by Eastern Cooperative Oncology Group performance status (PS) as the good PS group (0, 1) and the poor PS group (2-4). Bacteria were divided into Gram-positive cocci (GPC) or non-GPC groups and logistic regression analysis was used to examine factors that predict detection of GPC. RESULTS: Seventy-nine patients had stone-related pyelonephritis, 54 (68.4 %) in the good PS group and 25 (31.6 %) in the poor PS group. In the good PS group, Escherichia coli (67 %) was followed by Klebsiella species (9 %), while in the poor PS group, Escherichia coli (20 %) was followed by Enterococci and Staphylococci (12 %). GPC detection rate was significantly higher in the poor PS group than in the good PS group (40.0 % vs 14.8 %, p = 0.016), and multivariate logistic regression analysis showed that poor PS was an independent factor predicting detection of GPC (OR = 6.54, p = 0.02). CONCLUSIONS: The distribution of the causative organisms in stone pyelonephritis was similar to that in common complicated urinary tract infections. Poor PS may be an independent predictor of GPC detection in patients with stone pyelonephritis.

Alzheimer's disease brain-derived extracellular vesicles spread tau pathology in interneurons.

Extracellular vesicles are highly transmissible and play critical roles in the propagation of tau pathology, although the underlying mechanism remains elusive. Here, for the first time, we comprehensively characterized the physicochemical structure and pathogenic function of human brain-derived extracellular vesicles isolated from Alzheimer's disease, prodromal Alzheimer's disease, and non-demented control cases. Alzheimer's disease extracellular vesicles were significantly enriched in epitope-specific tau oligomers in comparison to prodromal Alzheimer's disease or control extracellular vesicles as determined by dot blot and atomic force microscopy. Alzheimer's disease extracellular vesicles were more efficiently internalized by murine cortical neurons, as well as more efficient in transferring and misfolding tau, than prodromal Alzheimer's disease and control extracellular vesicles in vitro. Strikingly, the inoculation of Alzheimer's disease or prodromal Alzheimer's disease extracellular vesicles containing only 300 pg of tau into the outer molecular layer of the dentate gyrus of 18-month-old C57BL/6 mice resulted in the accumulation of abnormally phosphorylated tau throughout the hippocampus by 4.5 months, whereas inoculation of an equal amount of tau from control extracellular vesicles, isolated tau oligomers, or fibrils from the same Alzheimer's disease donor showed little tau pathology. Furthermore, Alzheimer's disease extracellular vesicles induced misfolding of endogenous tau in both oligomeric and sarkosyl-insoluble forms in the hippocampal region. Unexpectedly, phosphorylated tau was primarily accumulated in glutamic acid decarboxylase 67 (GAD67) GABAergic interneurons and, to a lesser extent, glutamate receptor 2/3-positive excitatory mossy cells, showing preferential extracellular vesicle-mediated GABAergic interneuronal tau propagation. Whole-cell patch clamp recordings of CA1 pyramidal cells showed significant reduction in the amplitude of spontaneous inhibitory post-synaptic currents. This was accompanied by reductions in c-fos+ GAD67+ neurons and GAD67+ neuronal puncta surrounding pyramidal neurons in the CA1 region, confirming reduced GABAergic transmission in this region. Our study posits a novel mechanism for the spread of tau in hippocampal GABAergic interneurons via brain-derived extracellular vesicles and their subsequent neuronal dysfunction.

Myosteatosis as a novel predictor of urinary incontinence after robot-assisted radical prostatectomy.

OBJECTIVES: To evaluate the impact of sarcopenia and myosteatosis on urinary incontinence after prostatectomy. METHODS: We retrospectively reviewed consecutive patients who underwent robot-assisted radical prostatectomy without nerve sparing between December 2012 and March 2019. Psoas muscle index and average total psoas density, which were measured on preoperative computed tomography images at level L3, were used to evaluate sarcopenia and myosteatosis, respectively. In addition, several magnetic resonance imaging variables associated with pelvic muscles, the urethra and the prostate were measured. Urinary continence was defined as non-use or use of just one incontinence pad per day. Logistic regression analyses aimed to identify the predictors of urinary incontinence 3 and 12 months after surgery. RESULTS: Overall, 121 patients were included in the analysis. The incidence rates of urinary incontinence 3 and 12 months after surgery were 42% (51/121 cases) and 16% (19/121 cases), respectively. Logistic multivariable analysis showed that low average total psoas density was the only significant independent predictor of urinary incontinence 3 months after surgery (P < 0.01), and low obturator internus muscle thickness (P = 0.01), short membranous urethral length (P = 0.01) and low average total psoas density (P < 0.01) were significant independent predictors of urinary incontinence 12 months after surgery. By contrast, psoas muscle index was not statistically associated with urinary incontinence after surgery. CONCLUSIONS: Myosteatosis (low average total psoas density) could be a novel predictor of urinary incontinence after robot-assisted radical prostatectomy.

Enrichment of Neurodegenerative Microglia Signature in Brain-Derived Extracellular Vesicles Isolated from Alzheimer's Disease Mouse Models.

Extracellular vesicles (EVs) are secreted by any neural cells in the central nervous system for molecular clearance, cellular communications, and disease spread in multiple neurodegenerative diseases, including Alzheimer's disease (AD), although their exact molecular mechanism is poorly understood. We hypothesize that high-resolution proteomic profiling of EVs separated from animal models of AD would determine the composition of EV contents and their cellular origin. Here, we examined recently developed transgenic mice (CAST.APP/PS1), which express familial AD-linked mutations of amyloid precursor protein (APP) and presenilin-1 (PS1) in the CAST/EiJ mouse strain and develop hippocampal neurodegeneration. Quantitative proteomics analysis of EVs separated from CAST.APP/PS1 and age-matched control mice by tandem mass tag-mass spectrometry identified a total of 3444 unique proteins, which are enriched in neuron-, astrocyte-, oligodendrocyte-, and microglia-specific molecules. CAST.APP/PS1-derived EVs show significant enrichment of Psen1, APP, and Itgax and reduction of Wdr61, Pmpca, Aldh1a2, Calu, Anp32b, Actn4, and Ndufv2 compared to WT-derived EVs, suggesting the involvement of Aß-processing complex and disease-associated/neurodegenerative microglia (DAM/MGnD) in EV secretion. In addition, Itgax and Apoe, DAM/MGnD markers, in EVs show a positive correlation with Itgax and Apoe mRNA expression from brain tissue in CAST.APP/PS1 mice. These datasets indicate the significant contribution of Aß plaque and neurodegeneration-induced DAM/MGnD microglia for EV secretion in CAST.APP/PS1 mice and shed light on understanding AD pathogenesis.

Assessment of separation methods for extracellular vesicles from human and mouse brain tissues and human cerebrospinal fluids.

Extracellular vesicle (EV) is a unified terminology of membrane-enclosed vesicular species ubiquitously secreted by almost every cell type and present in all body fluids. They carry a cargo of lipids, metabolites, nucleic acids and proteins for their clearance from cells as well as for cell-to-cell communications. The exact composition of EVs and their specific functions are not well understood due to the underdevelopment of the separation protocols, especially those from the central nervous system including animal and human brain tissues as well as cerebrospinal fluids, and the low yield of proteins in the separated EVs. To understand their exact molecular composition and their functional roles, development of the reliable protocols for EV separation is necessary. Here we report the methods for EV separation from human and mouse unfixed frozen brain tissues by a sucrose step gradient ultracentrifugation method, and from human cerebrospinal fluids by an affinity capture method. The separated EVs were assessed for morphological, biophysical and proteomic properties of separated EVs by nanoparticle tracking analysis, transmission electron microscopy, and labeled and label-free mass spectrometry for protein profiling with step-by-step protocols for each assessment.

Proteomic and biological profiling of extracellular vesicles from Alzheimer's disease human brain tissues.

INTRODUCTION: Extracellular vesicles (EVs) from human Alzheimer's disease (AD) biospecimens contain amyloid beta (Aß) peptide and tau. While AD EVs are known to affect brain disease pathobiology, their biochemical and molecular characterizations remain ill defined. METHODS: EVs were isolated from the cortical gray matter of 20 AD and 18 control brains. Tau and Aß levels were measured by immunoassay. Differentially expressed EV proteins were assessed by quantitative proteomics and machine learning. RESULTS: Levels of pS396 tau and Aß1-42 were significantly elevated in AD EVs. High levels of neuron- and glia-specific factors are detected in control and AD EVs, respectively. Machine learning identified ANXA5, VGF, GPM6A, and ACTZ in AD EV compared to controls. They distinguished AD EVs from controls in the test sets with 88% accuracy. DISCUSSION: In addition to Aß and tau, ANXA5, VGF, GPM6A, and ACTZ are new signature proteins in AD EVs.

[A Case of Ureteroarterial Fistula Successfully Treated with Endovascular Stent Graft].

We report a case of right uretero-external iliac artery fistula. A 46-year-old woman diagnosed with left ovarian cancer with peritoneal dissemination underwent simple hysterectomy, bilateral adnexal removal, partial omentectomy and appendectomy. Sixteen months after the operation, a computed tomography scan showed right hydronephrosis due to the development of tumor within the pelvis. A ureteral stent was placed into the right ureter in order to preserve renal function. The ureteral stent was replaced at regular intervals. Five months after the ureteral stent placement, the patient was hospitalized urgently with gross hematuria. She was diagnosed with right uretero-external iliac artery fistula based on the angiographic examination that was conducted to detect the source of hemorrhage. She was treated successfully with endovascular stent grafting in the right external iliac artery. She has since shown no episode of hematuria.

Discovery of colorectal cancer biomarker candidates by membrane proteomic analysis and subsequent verification using selected reaction monitoring (SRM) and tissue microarray (TMA) analysis.

Recent advances in quantitative proteomic technology have enabled the large-scale validation of biomarkers. We here performed a quantitative proteomic analysis of membrane fractions from colorectal cancer tissue to discover biomarker candidates, and then extensively validated the candidate proteins identified. A total of 5566 proteins were identified in six tissue samples, each of which was obtained from polyps and cancer with and without metastasis. GO cellular component analysis predicted that 3087 of these proteins were membrane proteins, whereas TMHMM algorithm predicted that 1567 proteins had a transmembrane domain. Differences were observed in the expression of 159 membrane proteins and 55 extracellular proteins between polyps and cancer without metastasis, while the expression of 32 membrane proteins and 17 extracellular proteins differed between cancer with and without metastasis. A total of 105 of these biomarker candidates were quantitated using selected (or multiple) reaction monitoring (SRM/MRM) with stable synthetic isotope-labeled peptides as an internal control. The results obtained revealed differences in the expression of 69 of these proteins, and this was subsequently verified in an independent set of patient samples (polyps (n = 10), cancer without metastasis (n = 10), cancer with metastasis (n = 10)). Significant differences were observed in the expression of 44 of these proteins, including ITGA5, GPRC5A, PDGFRB, and TFRC, which have already been shown to be overexpressed in colorectal cancer, as well as proteins with unknown function, such as C8orf55. The expression of C8orf55 was also shown to be high not only in colorectal cancer, but also in several cancer tissues using a multicancer tissue microarray, which included 1150 cores from 14 cancer tissues. This is the largest verification study of biomarker candidate membrane proteins to date; our methods for biomarker discovery and subsequent validation using SRM/MRM will contribute to the identification of useful biomarker candidates for various cancers. Data are available via ProteomeXchange with identifier PXD000851.

Systematic Identification of Kinase-Substrate Relationship by Integrated Phosphoproteome and Interactome Analysis.

The sensitivity of phosphorylation site identification by mass spectrometry (MS)-based phosphoproteomics has improved significantly. However, the lack of kinase-substrate relationship (KSR) data has hindered improvement of the range and accuracy of kinase activity prediction using phosphoproteome data. We herein describe the application of a systematic identification of KSR by integrated phosphoproteome and interactome analysis using doxycycline (Dox)-induced target kinase-overexpressing HEK-293 cells.

hinotoriTM vs. da Vinci®: propensity score-matched analysis of surgical outcomes of robot-assisted radical prostatectomy.

hinotori™ is a recently developed surgical robot system. The present study aims to compare intraoperative and postoperative outcomes of robot-assisted radical prostatectomy (RARP) by the hinotori™ system compared with those of the longer-established da Vinci® system. This study includes 100 consecutive patients who underwent RARP by da Vinci® and 60 patients who underwent RARP by hinotori™. To minimize imbalances of patient demographics between the two groups, 1:1 propensity score-matching was performed, and 43 patients each were assigned to the da Vinci® and hinotori™ groups after matching. In the propensity score-matched cohort, we could not find significant differences in patient demographics between the two groups. Surgical outcomes, operative time, and console time in the hinotori™ group were significantly longer than those in the da Vinci® group. Meanwhile, we could not find significant differences in other outcomes between the two groups, such as estimated blood loss, intraoperative complications, major postoperative complications (Clavien-Dindo grade 3 or 4) or length of hospital stay after surgery. The rate of positive cancer margin in the hinotori™ group was higher than that in the da Vinci® group, but significant difference could not be found between the two groups. Moreover, we could not find significant differences in urinary continence rates after surgery between the da Vinci® and hinotori™ groups. Our results suggest that the hinotori™ surgical robot system could provide comparable surgical outcomes to that of the da Vinci® system for patients undergoing RARP.

Efficacy of Bisphosphonate for Urolithiasis Complicated by Osteogenesis Imperfecta.

A 44-year-old man with osteogenesis imperfecta presented with left renal colic. Non-contrast computed tomography revealed a stone (10×9 mm) in the left upper ureter. Ureteroscopic lithotripsy was performed twice and stone-free status was achieved. An analysis of the stone revealed a mixed composition including calcium oxalate and calcium phosphate. Postoperatively, we administered bisphosphonates to prevent recurrence of urolithiasis, as 24-hour urine collection revealed marked hypercalciuria. Eighteen months after surgery, the urinary calcium levels had normalized, and there was no recurrence of urolithiasis. Osteogenesis imperfecta can be complicated by urolithiasis, but bisphosphonates may be useful in preventing recurrence of this disease.

Verification of surgical factors affecting the efficiency of stone extraction with one-surgeon basketing technique using a f-URSL simulation model.

PURPOSE: Stone extraction is an important treatment option when performing flexible ureteroscopic lithotripsy (f-URSL) for upper urinary stones. We used a f-URSL simulator model to investigate surgical factors affecting the efficacy of stone extraction with the one-surgeon basketing technique. MATERIALS AND METHODS: This simulator-based study involved eight urologists and eight residents. These participants each performed two tasks, with Flexor (Cook Medical) and Navigator (Boston Scientific) ureteral access sheaths, with and without the M-arm (MC Medical) single-use basket holder, and with models representing both left and right kidneys. The two tasks were to touch each renal calix with the ureteroscope, and to extract stones. As outcomes, we recorded the number of times that the ureteroscope became stuck during insertion, the number of times a stone was dropped during removal, the number of times the basket forceps were opened and closed, and the time required to accomplish each task. RESULTS: The ureteroscope became stuck significantly more often when Navigator was used compared with Flexor overall, and for both urologists and residents (all p<0.01). Stones were dropped significantly more often on the ipsilateral side (kidney on the same side as the operator's hand) than on the contralateral side overall (p=0.01), and the basket forceps were opened and closed significantly more often on the ipsilateral side than on the contralateral side both overall and by residents (all p<0.01). CONCLUSIONS: The efficiency of stone extraction during f-URSL with the one-surgeon basketing technique was affected by differences in ureteral access sheath and the kidney side.

Impact of postoperative sexual function on health-related quality of life after robot-assisted radical prostatectomy.

Background: We investigated potential disparities in health-related quality of life, particularly concerning urinary function, between patients with preserved and those with impaired sexual function after robot-assisted radical prostatectomy (RARP). Materials and methods: Between December 2012 and April 2020, 704 men underwent RARP in our hospital. This study included 155 patients with a preoperative 5-item International Index of Erectile Function (IIEF-5) of ≥12 points and an assessable IIEF-5 at 12 months postoperatively. Health-related quality of life was assessed using the 8-item Short-Form Health Survey and Expanded Prostate Cancer Index Composite (EPIC) preoperatively and at 3, 6, and 12 months postoperatively. A logistic regression analysis and Wilcoxon rank sum tests were performed. Results: Patients were grouped according to the median IIEF-5 score 12 months after surgery: those with preserved sexual function (n = 71) and those with impaired sexual function (n = 84). The mental component summary of the 8-item Short-Form Health Survey was better in the group with preserved sexual function at 6 months postoperatively than in the group with impaired sexual function (p < 0.01). In the EPIC, the group with preserved sexual function performed better not only in the sexual domain but also in the urinary domain at all time points compared with the group with impaired sexual function (p < 0.01). In the comparison of the urinary subdomains of the EPIC, there were no significant differences in urinary function or incontinence, but there were significant differences in urinary distress and irritative/obstructive scores (p < 0.01). Conclusions: Patients with preserved postoperative sexual function after RARP showed better urinary function than those with impaired sexual function. Hence, preserved sexual function is closely associated with urinary function.

Phosphoproteomic subtyping of gastric cancer reveals dynamic transformation with chemotherapy and guides targeted cancer treatment.

There are only a few effective molecular targeted agents for advanced unresectable or recurrent advanced gastric cancer (AGC), which has a poor prognosis with a median survival time of less than 14 months. Focusing on phosphorylation signaling in cancer cells, we have been developing deep phosphoproteome analysis from minute endoscopic biopsy specimens frozen within 20 s of collection. Phosphoproteomic analysis of 127 fresh-frozen endoscopic biopsy samples from untreated patients with AGC revealed three subtypes reflecting different cellular signaling statuses. Subsequent serial biopsy analysis has revealed the dynamic mesenchymal transitions within cancer cells, along with the concomitant rewiring of the kinome network, ultimately resulting in the conversion to the epithelial-mesenchymal transition (EMT) subtype throughout treatment. We present our investigation of intracellular signaling related to the EMT in gastric cancer and propose therapeutic approaches targeting AXL. This study also provides a wealth of resources for the future development of treatments and biomarkers for AGC.

In-depth membrane proteomic study of breast cancer tissues for the generation of a chromosome-based protein list.

The Chromosome-centric Human Proteome Project (C-HPP) aims to define all proteins encoded in each chromosome and especially to identify proteins that currently lack evidence by mass spectrometry. The C-HPP also prioritizes particular protein subsets such as membrane proteins, post-translational modifications, and low-abundance proteins. In this study, we aimed to generate deep profiling of the membrane proteins of human breast cancer tissues on a chromosome-by-chromosome basis using shotgun proteomics. We identified 7092 unique proteins using membrane fractions isolated from pooled breast cancer tissues with high confidence. A total of 3282 proteins were annotated as membrane proteins by Gene Ontology analysis, which covered 45% of the membrane proteins predicted in 20,859 protein-coding genes. Furthermore, we were able to identify 851 membrane proteins that currently lack evidence by mass spectrometry in neXtProt. Our results will contribute to the accomplishment of the primary goal of the C-HPP in identifying so-called "missing proteins" and generating a whole protein catalog for each chromosome.

Identification of missing proteins in the neXtProt database and unregistered phosphopeptides in the PhosphoSitePlus database as part of the Chromosome-centric Human Proteome Project.

The Chromosome-Centric Human Proteome Project (C-HPP) is an international effort for creating an annotated proteomic catalog for each chromosome. The first step of the C-HPP project is to find evidence of expression of all proteins encoded on each chromosome. C-HPP also prioritizes particular protein subsets, such as those with post-translational modifications (PTMs) and those found in low abundance. As participants in C-HPP, we integrated proteomic and phosphoproteomic analysis results from chromosome-independent biomarker discovery research to create a chromosome-based list of proteins and phosphorylation sites. Data were integrated from five independent colorectal cancer (CRC) samples (three types of clinical tissue and two types of cell lines) and lead to the identification of 11,278 proteins, including 8,305 phosphoproteins and 28,205 phosphorylation sites; all of these were categorized on a chromosome-by-chromosome basis. In total, 3,033 "missing proteins", i.e., proteins that currently lack evidence by mass spectrometry, in the neXtProt database and 12,852 unknown phosphorylation sites not registered in the PhosphoSitePlus database were identified. Our in-depth phosphoproteomic study represents a significant contribution to C-HPP. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000089.

Integrative analysis of cancer dependency data and comprehensive phosphoproteomics data revealed the EPHA2-PARD3 axis as a cancer vulnerability in KRAS-mutant colorectal cancer.

Colorectal cancer (CRC), a common malignant tumour of the gastrointestinal tract, is a life-threatening cancer worldwide. Mutations in KRAS and BRAF, the major driver mutation subtypes in CRC, activate the RAS pathway, contribute to tumorigenesis in CRC and are being investigated as potential therapeutic targets. Despite recent advances in clinical trials targeting KRASG12C or RAS downstream signalling molecules for KRAS-mutant CRC, there is a lack of effective therapeutic interventions. Therefore, understanding the unique molecular characteristics of KRAS-mutant CRC is essential for identifying molecular targets and developing novel therapeutic interventions. We obtained in-depth proteomics and phosphoproteomics quantitative data for over 7900 proteins and 38 700 phosphorylation sites in cells from 35 CRC cell lines and performed informatic analyses, including proteomics-based coexpression analysis and correlation analysis between phosphoproteomics data and cancer dependency scores of the corresponding phosphoproteins. Our results revealed novel dysregulated protein-protein associations enriched specifically in KRAS-mutant cells. Our phosphoproteomics analysis revealed activation of EPHA2 kinase and downstream tight junction signalling in KRAS-mutant cells. Furthermore, the results implicate the phosphorylation site Y378 in the tight junction protein PARD3 as a cancer vulnerability in KRAS-mutant cells. Together, our large-scale phosphoproteomics and proteomics data across 35 steady-state CRC cell lines represent a valuable resource for understanding the molecular characteristics of oncogenic mutations. Our approach to predicting cancer dependency from phosphoproteomics data identified the EPHA2-PARD3 axis as a cancer vulnerability in KRAS-mutant CRC.

Thermography-Based Comparison of Irrigation Temperatures Between Moses Mode and Virtual Basket Mode: An In Vitro Phantom Study.

Objectives: This study aims to evaluate changes in irrigation fluid temperatures during laser activation by using thermography, with comparison between Moses mode (MM) and virtual basket mode (VBM). Materials and Methods: Experiments were performed using an unroofed pyelocaliceal model. The laser was fired for 60 seconds at 0.4 J/60 Hz. Three runs were tested per setting using short pulse mode, long pulse mode, MM contact, and VBM. The time to reach threshold of thermal injury (43°C) was evaluated using thermometer and thermography, both with and without saline irrigation (25 mL/min). These outcomes were compared between laser pulse modes. Results: In measurement of time to reach the threshold, thermography-based time was significantly shorter than thermometer-based time in all laser modes under the condition of no irrigation. Thermography measurement results indicate that the speed of temperature rise depends on laser pulse modes, and the time to reach the threshold in MM was significantly shorter than that in VBM (9.0 seconds vs 14.3 seconds, p = 0.03). When 25 mL/min saline irrigation was used, the peak temperatures by both thermometer and thermography measurements did not exceed the threshold during laser activation. Conclusions: Thermography-based evaluation suggests that irrigation temperatures near mucosa around stones can rapidly elevate during laser lithotripsy when the irrigation condition is poor. Temperature rise speed in MM may be more rapid than that in VBM. To prevent thermal injury, laser pulse modes must be used selectively according to the condition of irrigation.

Integration of pharmacoproteomic and computational approaches reveals the cellular signal transduction pathways affected by apatinib in gastric cancer cell lines.

Apatinib is known to be a highly selective vascular endothelial growth factor receptor 2 (VEGFR2) inhibitor with anti-angiogenic and anti-tumor properties. In a phase III study, the objective response rate to apatinib was low. It remains unclear why the effectivity of apatinib varies among patients and what type of patients are candidates for the treatment. In this study, we investigated the anti-tumor efficacy of apatinib against 13 gastric cancer cell lines and found that it differed depending on the cell line. Using integrated wet and dry approaches, we showed that apatinib was a multi-kinase inhibitor of c-Kit, RAF1, VEGFR1, VEGFR2, and VEGFR3, predominantly inhibiting c-Kit. Notably, KATO-III, which was the most apatinib-sensitive among the gastric cancer cell lines investigated, was the only cell line expressing c-Kit, RAF1, VEGFR1, and VEGFR3 but not VEGFR2. Furthermore, we identified SNW1 as a molecule affected by apatinib that plays an important role in cell survival. Finally, we identified the molecular network related to SNW1 that was affected by treatment with apatinib. These results suggest that the mechanism of action of apatinib in KATO-III cells is independent of VEGFR2 and that the differential efficacy of apatinib was due to differences in expression patterns of receptor tyrosine kinases. Furthermore, our results suggest that the differential efficacy of apatinib in gastric cell lines may be attributed to SNW1 phosphorylation levels at a steady state. These findings contribute to a deeper understanding of the mechanism of action of apatinib in gastric cancer cells.

Strategy for SRM-based verification of biomarker candidates discovered by iTRAQ method in limited breast cancer tissue samples.

Since LC-MS-based quantitative proteomics has become increasingly applied to a wide range of biological applications over the past decade, numerous studies have performed relative and/or absolute abundance determinations across large sets of proteins. In this study, we discovered prognostic biomarker candidates from limited breast cancer tissue samples using discovery-through-verification strategy combining iTRAQ method followed by selected reaction monitoring/multiple reaction monitoring analysis (SRM/MRM). We identified and quantified 5122 proteins with high confidence in 18 patient tissue samples (pooled high-risk (n=9) or low-risk (n=9)). A total of 2480 proteins (48.4%) of them were annotated as membrane proteins, 16.1% were plasma membrane and 6.6% were extracellular space proteins by Gene Ontology analysis. Forty-nine proteins with >2-fold differences in two groups were chosen for further analysis and verified in 16 individual tissue samples (high-risk (n=9) or low-risk (n=7)) using SRM/MRM. Twenty-three proteins were differentially expressed among two groups of which MFAP4 and GP2 were further confirmed by Western blotting in 17 tissue samples (high-risk (n=9) or low-risk (n=8)) and Immunohistochemistry (IHC) in 24 tissue samples (high-risk (n=12) or low-risk (n=12)). These results indicate that the combination of iTRAQ and SRM/MRM proteomics will be a powerful tool for identification and verification of candidate protein biomarkers.