Differential profiling of breast cancer plasma proteome by isotope-coded affinity tagging method reveals biotinidase as a breast cancer biomarker

<p>Abstract</p> <p>Background</p> <p>Breast cancer is one of the leading causes of women's death worldwide. It is important to discover a reliable biomarker for the detection of breast cancer. Plasma is the most ideal source for cancer biomarker discovery since many cells cross-communicate through the secretion of soluble proteins into blood.</p> <p>Methods</p> <p>Plasma proteomes obtained from 6 breast cancer patients and 6 normal healthy women were analyzed by using the isotope-coded affinity tag (ICAT) labeling approach and tandem mass spectrometry. All the plasma samples used were depleted of highly abundant 6 plasma proteins by immune-affinity column chromatography before ICAT labeling. Several proteins showing differential abundance level were selected based on literature searches and their specificity to the commercially available antibodies, and then verified by immunoblot assays.</p> <p>Results</p> <p>A total of 155 proteins were identified and quantified by ICAT method. Among them, 33 proteins showed abundance changes by more than 1.5-fold between the plasmas of breast cancer patients and healthy women. We chose 5 proteins for the follow-up confirmation in the individual plasma samples using immunoblot assay. Four proteins, α1-acid glycoprotein 2, monocyte differentiation antigen CD14, biotinidase (BTD), and glutathione peroxidase 3, showed similar abundance ratio to ICAT result. Using a blind set of plasmas obtained from 21 breast cancer patients and 21 normal healthy controls, we confirmed that BTD was significantly down-regulated in breast cancer plasma (Wilcoxon rank-sum test, <it>p </it>= 0.002). BTD levels were lowered in all cancer grades (I-IV) except cancer grade zero. The area under the receiver operating characteristic curve of BTD was 0.78. Estrogen receptor status (<it>p </it>= 0.940) and progesterone receptor status (<it>p </it>= 0.440) were not associated with the plasma BTD levels.</p> <p>Conclusions</p> <p>Our study suggests that BTD is a potential serological biomarker for the detection of breast cancer.</p

Effect of the Presence of Brain-Derived Neurotrophic Factor Val66Met Polymorphism on the Recovery in Patients With Acute Subcortical Stroke

Objective : To investigate the effect of brain-derived neurotrophic factor (BDNF) Valmet polymorphism on the recovery after subcortical stroke, using the modified Rankin Scale (mRS). Methods : Subcortical stroke patients with copies of BDNF Valmet polymorphism (n=7) were compared to their controls (n=7) without a copy of BDNF Valmet polymorphism after matching for initial severity, location and type of stroke. The mRS scores at 1 and 3 months after discharge from the neurorehabilitation unit were compared between the groups. Results : A repeated measures ANOVA for mRS revealed significant interaction between time and group (F(2, 24) =37.2, p<0.001) and a significant effect of time (F(2, 24)=10.8, p<0.001), thereby reflecting significant differences between the Met allele (+) group and the Met allele (-) group. There was a significant difference in mRS scores at 3 months post-discharge between the two groups (p=0.01) although no difference was evident in mRS scores at 1 month post-discharge between the two groups. There were significant improvements between mRS scores on admission and mRS scores at 1 month post-discharge (p=0.02), and between mRS scores at 1 month post-discharge and mRS scores at 3 months post-discharge (p=0.004) in the Met allele (-) group. Conclusion : BDNF Valmet polymorphism may be associated with worse functional outcome in Korean patients with subcortical stroke. Therefore, BDNF Valmet polymorphism should be considered as an important prognostic factor for recovery and responses to rehabilitation therapies after stroke in Korean patients. There is a need for developing different rehabilitation strategies for the population with BDNF Valmet polymorphism. Further studies assessing different outcomes for various functional domains of stroke recovery are needed to clarify the role of BDNF Valmet polymorphism.This research was supported by SK Chemicals Co. through Seoul National University R&DB Foundation (Grant No. 800-2010095).OAIID:oai:osos.snu.ac.kr:snu2013-01/102/0000005165/4SEQ:4PERF_CD:SNU2013-01EVAL_ITEM_CD:102USER_ID:0000005165ADJUST_YN:YEMP_ID:A075663DEPT_CD:801CITE_RATE:0FILENAME:첨부된 내역이 없습니다.DEPT_NM:의학과EMAIL:[email protected]:

Genomic profile of metastatic breast cancer patient-derived xenografts established using percutaneous biopsy.

BACKGROUND: Metastatic breast cancer (mBC) is a complex and life-threatening disease and although it is difficult to cure, patients can benefit from sequential anticancer treatment, including endocrine therapy, targeted therapy and cytotoxic chemotherapy. The patient-derived xenograft (PDX) model is suggested as a practical tool to predict the clinical outcome of this disease as well as to screen novel drugs. This study aimed to establish PDX models in Korean patients and analyze their genomic profiles and utility for translational research. METHODS: Percutaneous core needle biopsy or punch biopsy samples were used for xenotransplantation. Whole exome sequencing and transcriptome analysis were performed to assess the genomic and RNA expression profiles, respectively. Copy number variation and mutational burden were analyzed and compared with other metastatic breast cancer genomic results. Mutational signatures were also analyzed. The antitumor effect of an ATR inhibitor was tested in the relevant PDX model. RESULTS: Of the 151 cases studied, 40 (26%) PDX models were established. Notably, the take rate of all subtypes, including the hormone receptor-positive (HR +) subtype, exceeded 20%. The PDX model had genomic fidelity and copy number variation that represented the pattern of its donor sample. TP53, PIK3CA, ESR1, and GATA3 mutations were frequently found in our samples, with TP53 being the most frequently mutated, and the somatic mutations in these genes strengthened their frequency in the PDX model. The ESR1 mutation, CCND1 amplification, and the APOBEC signature were significant features in our HR + HER2- PDX model. Fulvestrant in combination with palbociclib showed a partial response to the relevant patient\u27s tumor harboring the ESR1 mutation, and CCND1 amplification was found in the PDX model. AZD6738, an ATR inhibitor, delayed tumor growth in a relevant PDX model. CONCLUSIONS: Our PDX model was established using core needle biopsy samples from primary and metastatic tissues. Genomic profiles of the samples reflected their original tissue characteristics and could be used for the interpretation of clinical outcomes

Genetic and Epigenetic Alterations of the NF2 Gene in Sporadic Vestibular Schwannomas

BACKGROUND: Mutations in the neurofibromatosis type 2 (NF2) tumor-suppressor gene have been identified in not only NF2-related tumors but also sporadic vestibular schwannomas (VS). This study investigated the genetic and epigenetic alterations in tumors and blood from 30 Korean patients with sporadic VS and correlated these alterations with tumor behavior. METHODOLOGY/PRINCIPAL FINDINGS: NF2 gene mutations were detected using PCR and direct DNA sequencing and three highly polymorphic microsatellite DNA markers were used to assess the loss of heterozygosity (LOH) from chromosome 22. Aberrant hypermethylation of the CpG island of the NF2 gene was also analyzed. The tumor size, the clinical growth index, and the proliferative activity assessed using the Ki-67 labeling index were evaluated. We found 18 mutations in 16 cases of 30 schwannomas (53%). The mutations included eight frameshift mutations, seven nonsense mutations, one in-frame deletion, one splicing donor site, and one missense mutation. Nine patients (30%) showed allelic loss. No patient had aberrant hypermethylation of the NF2 gene and correlation between NF2 genetic alterations and tumor behavior was not observed in this study. CONCLUSIONS/SIGNIFICANCE: The molecular genetic changes in sporadic VS identified here included mutations and allelic loss, but no aberrant hypermethylation of the NF2 gene was detected. In addition, no clear genotype/phenotype correlation was identified. Therefore, it is likely that other factors contribute to tumor formation and growth

Can a routine follow-up blood culture be justified in Klebsiella pneumoniae bacteremia? a retrospective case–control study

Background : The need for mandatory confirmation of negative conversion in Klebsiella pneumoniae bacteremia (KpB) has not been adequately addressed. We conducted a retrospective case–control study of adult patients with KpB over a 5-year period in two tertiary-care hospitals to determine the risk factors for persistent bacteremia and to reevaluate the necessity of follow-up blood culture in KpB. Methods : Persistent KpB is defined as the finding of K. pneumoniae in more than two separate blood-culture samples for longer than a two-day period in a single episode. The case- and control-groups were patients with persistent and non-persistent KpB, respectively, and they were matched 1-to-3 according to age and gender. Results : Among 1068 KpB episodes analyzed after excluding polymicrobial infection and repeated KpB, follow-up blood cultures were performed in 862 cases (80.7%), 62 of which (7.2%) were persistent. Independent risk factors for persistence were intra-abdominal infection, higher Charlsons comorbidity weighted index score, prior solid organ transplantation, and unfavorable treatment response, which was defined as positivity for at least two parameters among fever, leukocytosis, and no decrease of C-reactive protein on the second day after initial culture. A proposed scoring system using four variables, namely, intra-abdominal infection, nosocomial KpB, fever and lack of C-reactive protein decrease, the last two being assessed on the second day after the initial blood culture, showed that only 4.9% of the patients with no risk factors or with only intra-abdominal infection had persistent KpB. Conclusions : Though persistent KpB is uncommon, follow-up blood culture was performed in as many as 80% of the cases in this study. A more careful clinical assessment is warranted to reduce the cost and patient inconvenience involved in follow-up blood culture.Peer Reviewe

The heme oxygenase-1 genotype is a risk factor to renal impairment of IgA nephropathy at diagnosis, which is a strong predictor of mortality

The induction of heme oxygenase-1 (HO-1) ameliorates oxidative stress and inflammatory process, which play important roles in IgA nephropathy. We hypothesized length polymorphism in the promoter region of the HO-1 gene, which is related to the level of gene transcription, is associated with disease severity of IgA nephropathy. The subjects comprised 916 patients with IgA nephropathy and gene data. Renal impairment was defined as an estimated glomerular filtration rate less than 60 mL/min/1.73 m(2) at diagnosis. The short (S: 28) (GT) repeats in the HO-1 gene was determined. The frequencies of S/S, S/M, M/M, S/L, L/M, and L/L genotypes were 7.2%, 6.9%, 3.1%, 30.8%, 22.7%, and 29.4%, respectively. The baseline characteristics were not different. In the S/S genotypic group, the renal impairment rate was 18.2%, which was lower than 32.2% in the group with M/M, L/M, or L/L genotype. The odds ratio of renal impairment in S/S genotype, compared to that in M/M, L/M, or L/L genotype, was 0.216 (95% confidence interval, 0.060-0.774, p=0.019). The HO-1 gene promoter length polymorphism was related to the renal impairment of IgA nephropathy at diagnosis, which is an important risk factor for mortality in IgA nephropathy patients

Multi-Range Conditional Random Field for Classifying Railway Electrification System Objects Using Mobile Laser Scanning Data

Railways have been used as one of the most crucial means of transportation in public mobility and economic development. For safe railway operation, the electrification system in the railway infrastructure, which supplies electric power to trains, is an essential facility for stable train operation. Due to its important role, the electrification system needs to be rigorously and regularly inspected and managed. This paper presents a supervised learning method to classify Mobile Laser Scanning (MLS) data into ten target classes representing overhead wires, movable brackets and poles, which are key objects in the electrification system. In general, the layout of the railway electrification system shows strong spatial regularity relations among object classes. The proposed classifier is developed based on Conditional Random Field (CRF), which characterizes not only labeling homogeneity at short range, but also the layout compatibility between different object classes at long range in the probabilistic graphical model. This multi-range CRF model consists of a unary term and three pairwise contextual terms. In order to gain computational efficiency, MLS point clouds are converted into a set of line segments to which the labeling process is applied. Support Vector Machine (SVM) is used as a local classifier considering only node features for producing the unary potentials of the CRF model. As the short-range pairwise contextual term, the Potts model is applied to enforce a local smoothness in the short-range graph; while long-range pairwise potentials are designed to enhance the spatial regularities of both horizontal and vertical layouts among railway objects. We formulate two long-range pairwise potentials as the log posterior probability obtained by the naive Bayes classifier. The directional layout compatibilities are characterized in probability look-up tables, which represent the co-occurrence rate of spatial relations in the horizontal and vertical directions. The likelihood function is formulated by multivariate Gaussian distributions. In the proposed multi-range CRF model, the weight parameters to balance four sub-terms are estimated by applying the Stochastic Gradient Descent (SGD). The results show that the proposed multi-range CRF can effectively classify individual railway elements, representing an average recall of 97.66% and an average precision of 97.07% for all classes