Rescue in vitro maturation (IVM) of immature oocytes in stimulated cycles in women with low functional ovarian reserve (LFOR)

Rescue in vitro maturation (IVM) is currently not a routine procedure in association with in vitro fertilization (IVF). We compared in a prospectively cohort study of 10 patients with normal functional ovarian reserve (NFOR) and of 25 with low functional ovarian reserve (LFOR), defined by abnormally high FSH and/or abnormally low AMH levels), IVM dynamics of immature oocytes. Following controlled ovarian hyperstimulation in IVF cycles, only immature oocytes underwent rescue IVM (for up to 48 h). Oocyte maturation dynamics, fertilization rates, embryo development, and pregnancy rates were then compared between NFOR and LFOR patients. Though proportion of MI and GV oocytes reaching MII stages within 48 h and rate of maturation of MI oocytes did not differ, in women with LFOR significantly more GV oocytes reached MII stage within 24 h (30.4 vs. 66.9 %; P = 0.013), while fertilization rates and embryo generation numbers were similar between both groups. Rescue IVM, thus, produced 1.5 additional embryos for transfer in women with LFOR and 1.6 in patients with NFOR, a highly significant difference in relative improvement in available embryo numbers for LFOR (+60.0 %) and NFOR women (+16.5 %). Rescue IVM, thus, not only demonstrates different time dynamics between women with LFOR and NFOR but also disproportionate efficacy in improving available embryo numbers for transfer in favor of LFOR patients. 1/7 patients, who reached embryo transfer with only embryos produced via rescue IVF conceived and delivered, proving that rescue IVF in women with LFOR also improves pregnancy and delivery chances. Because of the small number of embryos LFOR patients produce, every additional embryo is of considerable potential clinical significance for them, suggesting that rescue IVM in women with LFOR should become routine practice.

Glycerol-3-phosphate acyltransferase-1 upregulation by O-GlcNAcylation of Sp1 protects against hypoxia-induced mouse embryonic stem cell apoptosis via mTOR activation

Oxygen signaling is critical for stem cell regulation, and oxidative stress-induced stem cell apoptosis decreases the efficiency of stem cell therapy. Hypoxia activates O-linked β-N-acetyl glucosaminylation (O-GlcNAcylation) of stem cells, which contributes to regulation of cellular metabolism, as well as cell fate. Our study investigated the role of O-GlcNAcylation via glucosamine in the protection of hypoxia-induced apoptosis of mouse embryonic stem cells (mESCs). Hypoxia increased mESCs apoptosis in a time-dependent manner. Moreover, hypoxia also slightly increased the O-GlcNAc level. Glucosamine treatment further enhanced the O-GlcNAc level and prevented hypoxia-induced mESC apoptosis, which was suppressed by O-GlcNAc transferase inhibitors. In addition, hypoxia regulated several lipid metabolic enzymes, whereas glucosamine increased expression of glycerol-3-phosphate acyltransferase-1 (GPAT1), a lipid metabolic enzyme producing lysophosphatidic acid (LPA). In addition, glucosamine-increased O-GlcNAcylation of Sp1, which subsequently leads to Sp1 nuclear translocation and GPAT1 expression. Silencing of GPAT1 by gpat1 siRNA transfection reduced glucosamine-mediated anti-apoptosis in mESCs and reduced mammalian target of rapamycin (mTOR) phosphorylation. Indeed, LPA prevented mESCs from undergoing hypoxia-induced apoptosis and increased phosphorylation of mTOR and its substrates (S6K1 and 4EBP1). Moreover, mTOR inactivation by rapamycin (mTOR inhibitor) increased pro-apoptotic proteins expressions and mESC apoptosis. Furthermore, transplantation of non-targeting siRNA and glucosamine-treated mESCs increased cell survival and inhibited flap necrosis in mouse skin flap model. Conversely, silencing of GPAT1 expression reversed those glucosamine effects. In conclusion, enhancing O-GlcNAcylation of Sp1 by glucosamine stimulates GPAT1 expression, which leads to inhibition of hypoxia-induced mESC apoptosis via mTOR activation.

Metal allergy in eyelid dermatitis and the evaluation of metal contents in eye shadows

BACKGROUND

Allergic contact dermatitis is a common diagnosis in eyelid dermatitis. Sensitization to metals is prevalent in eyelid dermatitis and colour cosmetic products are frequently suspected as the source of metal exposure.

OBJECTIVE

To investigate the contact allergens for eyelid dermatitis and to assess metal contents in eye shadow products.

METHODS

Data were collected in the department of dermatology of Ewha Womans University hospital from December 1998 to February 2014. A total of 983 patients were patch tested during the period and 67 patients had eyelid dermatitis among them. To examine metal elements in colour cosmetic products for eyes, randomly selected 10 eye shadows were analysed.

RESULTS

Frequent allergens were metals, thiomersal and phenylenediamine in patients with eyelid dermatitis. The sensitization rates of individual allergens were not significantly different between patients with eyelid dermatitis and without eyelid dermatitis. All 10 eye shadow products contained more than 5 ppm of at least one element, nickel, cobalt or chromium.

CONCLUSION

Metals were top-rank allergens in patients with eyelid dermatitis as in the remaining patients patch tested. The eye shadow products contained significant amount of nickel, cobalt or chromium to elicit allergic reactions.

Mesenchymal stem cell-based gene therapy for erectile dysfunction

Despite the overwhelming success of PDE5 inhibitor (PDE5I), the demand for novel pharmacotherapeutic and surgical options for ED continues to rise owing to the increased proportion of elderly individuals in the population, in addition to the growing percentage of ED patients who do not respond to PDE5I. Surgical treatment of ED is associated with many complications, thus warranting the need for nonsurgical therapies. Moreover, none of the above-mentioned treatments essentially corrects, cures or prevents ED. Although gene therapy is a promising option, many challenges and obstacles such as local inflammatory response and random transgene expression, in addition to other safety issues, limit its use at the clinical level. The use of stem cell therapy alone also has many shortcomings. To overcome these inadequacies, many scientists and clinicians are investigating new gene and stem cell therapies.

Abstract P3-07-56: Predictive value of tertiary lymphoid structure assessed by high endothelial venule count in neoadjuvant setting of triple-negative breast cancer

Background

Tertiary lymphoid structure (TLS) is an ectopic lymph node-like structure characterized by lymphoid aggregation with high endothelial venules (HEVs), and is an important source of tumor-infiltrating lymphocytes (TILs). TILs have a strong prognostic and predictive significance, particularly in triple-negative breast cancer (TNBC). We previously analyzed expression of immune-related genes in pre-neoadjuvant chemotherapy (NAC) biopsy samples using NanoString assay and showed that gene expression of follicular helper T cell marker CXCL13, which is closely associated with TLSs, was an independent predictive factor for pathologic complete remission (pCR) in TNBC. However, measuring gene expression of biopsy sample is not easy to perform in daily pathology practice. Therefore, we evaluated TLSs by assessing hematoxylin and eosin (H&E) stained slides and immunohistochemistry, and investigated their clinical importance.

Methods

A total of 108 patients diagnosed with primary TNBC and treated with NAC (anthracycline, cyclophosphamide, and taxane) were included. The amounts of TILs and TLSs were histopathologically measured in H&E slides. Immunohistochemical studies were done in 55 cases with available tissue samples. The numbers of CD3-, CD8-, and CD20- immunopositive cells in tumor areas were counted by the image analyzer. MECA79- immunopositive HEV densities were calculated. Their relationship to CXCL13 gene expression by NanoString assay was also analyzed.

Results

The overall rate of pCR was 30.6% (33 of 108 tumors). Lower pre-NAC clinical T stage and higher level of TIL and TLS assessed by H&E slides were predictors of pCR in all cases. The mean number of MECA 79-immunopositive HEV in pre-NAC biopsy samples was 12 (range, 0-72). The amounts of TILs and TLSs, numbers of CD3-, CD8-, and CD20- positive cells, HEV density, and expression of CXCL13 showed good correlation with one another. Higher HEV density, CD20- positive cell number, and CXCL13 expression were predictors of pCR. Higher CD8- positive cell numbers and CXCL13 expression were associated with better disease-free survival rate.

Conclusion

The amount of TLSs assessed by H&E slides and MECA 79-immunopositive HEV densities was well correlated with level of TILs, numbers of CD3-, CD8-, and CD20-positive cells, and gene expression of CXCL13, and was significantly associated with pCR in TNBCs. Therefore, assessing HEV density by MECA 79 immunohistochemistry in pre-NAC biopsy samples might be an objective and valuable tool for predicting pCR of TNBC in routine pathology practice. Further investigation of mechanism of TLS development might help to improve immunotherapeutic strategy.

Citation Format: Song IH, Lee HJ, Park IA, Yu JH, Ahn J-H, Gong G. Predictive value of tertiary lymphoid structure assessed by high endothelial venule count in neoadjuvant setting of triple-negative breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-56.

Abstract P3-07-34: Predictive role of stromal tumor infiltrating lymphocytes (TILs) in patients with metastatic HER2-positive breast cancer (BC) treated with trastuzumab

Background:Prognostic significance of stromal TILs in metastatic BC has been suggested in various BC subtypes. However, predictive role of stromal TILs for the efficacy of trastuzumab has not been established in patients with HER2-positive BC. This study was performed to evaluate whether the stromal TILs are associated with the efficacy of trastuzumab in patients with metastatic HER2-positve BC.

Method:Between June 2006 and March 2013, a total of 60 women with recurrent or metastatic HER2-positive BC treated with trastuzumab were included in this retrospective analysis. In these patients, trastuzumab was administered either as single agent or combination with taxanes. Stromal TILs were assessed using immunohistochemistry in surgical specimen (n=39, 65%) and biopsy specimen of metastatic lesion (n=21, 35%) by the academic pathologist (HJL). Primary endpoint of this study was progression-free survival (PFS), and secondary endpoints were response rate and overall survival (OS).

Result:Median age was 54 year old (range, 36-76), and all patients had invasive ductal carcinoma. Hormone receptor was positive in 34 patients (57%) and 18 patients (30%) initially presented with metastatic disease. Nine patients (15%) received cytotoxic chemotherapy without trastuzumab before the administration of trastuzumab. Patients were grouped according to the TILs (< 10% [n=50] and >10% [n=10]), and there was no significant difference in age (p=0.68), histologic grade (p=1.00), metastatic sites (p>0.05), and number of lines of chemotherapy before the administration of trastuzumab(p=0.33) among patients with low and high stromal TILs. High TILs were more common in hormone receptor (HR)-negative tumor compared with HR–positive tumor (31% vs 6%; p=0.02). In overall, median PFS and OS were 15.0 months (95% CI, 9.7-20.2) and 35.0 months (95% CI, 29.8-40.2), respectively. Median PFS in patients with high stromal TILs were numerically longer than that in those with low TILs (22.0 months [95% CI, 9.6-34.4] vs 14.0 months [95% CI, 9.6-18.4]; p=0.057). There was no difference in response rates (p=0.43) and OS (p=0.94) according to the stromal TILs. FcR genotype was not significantly correlated with objective response rate, PFS and OS.

Conclusion:This study suggests that the stromal TILs might be associated with the clinical outcomes of HER2-targeted therapy in patients with metastatic HER2-positive BC. Our finding should be validated in future studies based on a large sample size.

Keywords: Breast cancer, tumor infiltrating lymphocyte. Trastzumab, HER2.

Citation Format: Yoon JA, Yoo C, Lee HJ, Kim K-P, Kim J, Ahn J-H, Jung KH, Gong G, Kim S-B. Predictive role of stromal tumor infiltrating lymphocytes (TILs) in patients with metastatic HER2-positive breast cancer (BC) treated with trastuzumab. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-34.

Abstract P1-14-15: A randomized phase lll trial of neoadjuvant sequential chemotherapy with 4 cycles of adriamycin plus cyclophosphamide followed by 4 cycles of docetaxel (AC4-D4) versus shorter 3 cycles of FEC followed by 3 cycles of docetaxel (FEC3-D3) in node-positive breast cancer (Neo-Shorter): First report of efficacy & toxicity profile

Background: The addition of a taxane to anthracycline-based chemotherapy provided an improved outcome in neoadjuant setting. Two neoadjuvant chemotherapy with 4 cycles of AC followed by 4 cycles of docetaxel (AC4-D4) and 3 cycles of FEC followed by 3 cycles of docetaxel (FEC3-D3) are widely used. Short duration of chemotherapy, 6 cycles rather than 8 cycles might be an attractive approach.

Methods: This is a randomized, single-center, prospective, parallel group, comparative phase III trial (NCT02001506). Patients (pts) with breast cancer of clinically stage II or III, or sized  1.5 cm with histologically proven lymph-node involvement were included. Pts were stratified according to hormone receptor and HER2 expression status and randomized to AC4-D4 and 3 cycles of FEC3-D3 treatment. The primary endpoint was pathological complete response, defined as the absence of invasive disease in the breast and axillary lymph nodes, analyzed by intention to treat.

Results: At the time of submission, a total of 207 pts were enrolled; 1 pt failed screening; 25 pts dropped out (5 pts in AC4-D4 arm and 2 pts in FEC3-D3 arm discontinue treatment due to progressive disease); 39 pts are still receiving neoadjuvant chemotherapy; 142 pts, who received surgery, were included for this analysis. In AC4-D4 arm, among 64 pts, 57 pts achieved clinical response (6 complete response [CR] and 51 partial response [PR]) and among them 9 pts achieved pathologic complete response [pCR]. In FEC3-D3 arm, among 78 pts, 66 pts achieved clinical response (7 CR and 59 PR) and among them 11 pts achieved pCR. Addition of docetaxel increased clinical response in both arms. The most common adverse event was febrile neutropenia. Without prophylactic G-CSF, grade ≥3 febrile neutropenia (FN) occurred 23/661 cycles (3.5%) in AC4-D4 arm and 23/552 cycles (4.2%) in FEC3-D3 arm, respectively. Grade 3 and 4 toxicities other than FN were reported at expected levels in both groups. Sixty-one severe adverse events were reported; 33 (including 23 FN) in AC4-D4 arm and 28 (including 23 FN) in FEC3-D3 arm.

Conclusion: Compared to AC4-D4, shorter duration of FEC3-D3 neoadjuvant chemotherapy showed similar efficacy of pCR rate of 14.0% (versus 14.1% in AC4-D4 arm). The most common and important adverse event was febrile neutropenia in both arms. Updated study findings will be provided.

Citation Format: Kim JE, Ahn J-H, Jung KH, Lee HJ, Gong G-Y, Lee E-M, Ha EJ, Son B-H, Ahn S-H, Ahn SD, Kim H-H, Shin HJ, Kim S-B. A randomized phase lll trial of neoadjuvant sequential chemotherapy with 4 cycles of adriamycin plus cyclophosphamide followed by 4 cycles of docetaxel (AC4-D4) versus shorter 3 cycles of FEC followed by 3 cycles of docetaxel (FEC3-D3) in node-positive breast cancer (Neo-Shorter): First report of efficacy & toxicity profile. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-14-15.

Abstract P5-04-20: TLE1 protein expression in HER2-positive and triple-negative breast cancer

Purpose

Transducin-like enhancer protein 1 (TLE1) is a member of the Groucho (Gro)/TLE family of transcriptional co-repressors that regulate the transcriptional activity of a wide range of genes. TLE1 has been shown to be a specific and diagnostically useful immunohistochemical marker for synovial sarcoma. However, there have been few reports of the status of TLE1 in breast cancers. The purpose of this study was to clarify the nuclear expression of TLE1 in 511 Korean breast cancers by immunohistochemistry (IHC) and to correlate the findings to clinicopathologic variables including prognostic significance.

Methods

IHC was performed on tissue microarrays (TMAs) in 511 cases of breast cancer. Associations between the TLE1 expression and the clinicopathologic characteristics were retrospectively analyzed. Progression-free survival and disease-specific survival was assessed by the Kaplan–Meier method and Cox regression model.

Results

Of 511 cases of breast cancer, high expression of the TLE1 was detected in 63 (12.3%) cases. TLE1-high expression was strongly associated with HER2-positive breast cancer phenotype (p < 0.001) and triple-negative breast cancer phenotype (p < 0.001). Furthermore, high TLE1was significantly associated with high histologic grade (p < 0.001), node-negative (p =0.011), estrogen receptor negativity (p < 0.001), progesterone receptor negativity (p < 0.001), CK5/6 positivity (p < 0.001), epidermal growth factor receptor positivity (p < 0.001), high ki-67 proliferative index (p < 0.001) and high p53 expression (p < 0.001). Survival analysis demonstrated no significant association between TLE1 expression and disease progression and cancer-related death (p =0.112 and p =0.068, respectively).

Conclusion

Our results show that high TLE1expression is significantly associated with HER2-positive and triple-negative breast cancer. TLE1 may represent a potential therapeutic target for this aggressive disease, which warrants further investigation.

Citation Format: Lee HJ, Oh M-H, Lee J-H, Cho HD, Jang S-H, Jung HY, Kim K-J. TLE1 protein expression in HER2-positive and triple-negative breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-04-20.

Development of a highly immunogenic Newcastle disease virus chicken vaccine strain of duck origin

Newcastle disease virus (NDV) strain NDRL0901 was developed as a live vaccine candidate for control of Newcastle disease. NDV isolate KR/duck/13/07 (DK1307) of duck origin was used as the selected vaccine strain. DK1307 was passaged 6 times in chickens. Then a single clone from the chicken-adapted virus (DK1307C) was finally selected, and the vaccine strain was named NDRL0901. DK1307C and the clone NDRL0901 viruses showed enhanced immunogenicity compared to the DK1307 virus. Principal component analysis based on fusion and hemagglutinin-neuraminidase genes revealed the codon usage pattern in the dataset is distinct separating duck viral sequences and avian sequences, and passage of the duck origin virus into the chicken host causes deviation in the codon usage pattern. The NDRL0901 virus was avirulent and did not acquire viral virulence even after 7 back passages in chickens. When day-old chicks were vaccinated with the NDRL0901 virus via spray, eye drops, and drinking water, the vaccinated birds showed no clinical signs and had significant protection efficacy (>80%) against very virulent NDV (Kr005 strain) infection regardless of the administration route employed. The results indicate that the NDRL0901 strain is safe in chickens and can offer protective immunity.

Measurement of body joint angles for physical therapy based on mean shift tracking using two low cost Kinect images

Range of motion (ROM) is commonly used to assess a patient's joint function in physical therapy. Because motion capture systems are generally very expensive, physical therapists mostly use simple rulers to measure patients' joint angles in clinical diagnosis, which will suffer from low accuracy, low reliability, and subjective. In this study we used color and depth image feature from two sets of low-cost Microsoft Kinect to reconstruct 3D joint positions, and then calculate moveable joint angles to assess the ROM. A Gaussian background model is first used to segment the human body from the depth images. The 3D coordinates of the joints are reconstructed from both color and depth images. To track the location of joints throughout the sequence more precisely, we adopt the mean shift algorithm to find out the center of voxels upon the joints. The two sets of Kinect are placed three meters away from each other and facing to the subject. The joint moveable angles and the motion data are calculated from the position of joints frame by frame. To verify the results of our system, we take the results from a motion capture system called VICON as golden standard. Our 150 test results showed that the deviation of joint moveable angles between those obtained by VICON and our system is about 4 to 8 degree in six different upper limb exercises, which are acceptable in clinical environment.

Body Temperature Monitoring Using Subcutaneously Implanted Thermo-loggers from Holstein Steers

Body temperature (BT) monitoring in cattle could be used to early detect fever from infectious disease or physiological events. Various ways to measure BT have been applied at different locations on cattle including rectum, reticulum, milk, subcutis and ear canal. In other to evaluate the temperature stability and reliability of subcutaneous temperature (ST) in highly fluctuating field conditions for continuous BT monitoring, long term ST profiles were collected and analyzed from cattle in autumn/winter and summer season by surgically implanted thermo-logger devices. Purposes of this study were to assess ST in the field condition as a reference BT and to determine any location effect of implantation on ST profile. In results, ST profile in cattle showed a clear circadian rhythm with daily lowest at 05:00 to 07:00 AM and highest around midnight and rather stable temperature readings (mean±standard deviation [SD], 37.1°C to 37.36°C±0.91°C to 1.02°C). STs are 1.39°C to 1.65°C lower than the rectal temperature and sometimes showed an irregular temperature drop below the normal physiologic one: 19.4% or 36.4% of 54,192 readings were below 36.5°C or 37°C, respectively. Thus, for BT monitoring purposes in a fever-alarming-system, a correction algorithm is necessary to remove the influences of ambient temperature and animal resting behavior especially in winter time. One way to do this is simply discard outlier readings below 36.5°C or 37°C resulting in a much improved mean±SD of 37.6°C±0.64°C or 37.8°C±0.55°C, respectively. For location the upper scapula region seems the most reliable and convenient site for implantation of a thermo-sensor tag in terms of relatively low influence by ambient temperature and easy insertion compared to lower scapula or lateral neck.

Rapid enlargement of endometrial stromal sarcoma after uterine fibroid embolization for presumed adenomyosis: a case report and literature review

Uterine sarcomas have rarely been diagnosed after uterine artery embolization. It remains unclear whether the diagnostic work-up is required prior to such embolization to prevent a missed diagnosis of sarcomas and a delay in providing definitive treatment. Because of the rarity and heterogeneity of endometrial stromal neoplasms, little is known about their epidemiology, pathogenesis, and molecular pathology. The authors report a case of low-grade endometrial stromal sarcoma (ESS) diagnosed after uterine fibroid embolization. Although they performed laparoscopic biopsy of the rapidly growing uterine mass, they could not detect the ESS. Although rare, ESS should be considered in the differential diagnosis of uterine fibroid enlargement. It is essential to assess the risk of malignancy by taking into account the patient's clinical symptoms, results of the physical exam, and imaging findings prior to uterine artery embolization. Pathologic diagnosis should include an adequate biopsy sample and the use of molecular genetic testing.

Abstract A1-41: Automated pipeline for high confidence variant calling and functional annotation, for matched tumor/normal samples sequenced by next-generation sequencing (NGS)

As the time required to sequence a genome using NGS sequencers is decreasing rapidly, the use of genomic data in the clinic to inform patient care, is becoming feasible. One area that needs to be addressed is the computational time required to align reads to a reference genome and call variants, which is now a larger proportion of the overall process. Standardization and repeatability of processing is critical in a clinical setting. To satisfy these criteria, we have developed a bioinformatics pipeline which starts with deep targeted resequencing from gene sets and related loci, and then automates the alignment, variant calling and functional annotation using an open source workflow tool.

Given that tumor samples are often heterogenous mixtures - indicating either subclonal populations or fractions of normal tissue, deep sequencing is crucial in accurate detection of less prevalent minor allele somatic mutations. We used Oligonucleotide-Selective Sequencing (OS-Seq) as a targeted resequencing approach to provide deep coverage over the target region, with high specificity. With OS-Seq, the inner surface of an Illumina flow cell is modified with primer probe oligos, turning it into an enrichment platform for DNA sequencing libraries. The required steps from modification to a ready to sequence flow cell are fully automated and integrated into the standard Illumina sequencing preparation using cBot.

The computational workflow for this project was developed using the open source tool bpipe. Once a library of bioinformatics steps has been defined in bpipe, these steps can be used as building blocks and put together in various ways to develop different pipelines. Bpipe also provides comprehensive audit trails and logs so that results are traceable and repeatable. For this particular workflow, steps for alignment to the genome using Burrows-Wheeler Aligner (BWA), steps for differentiation and filtering for each OS-Seq primer probe; variant calling using muTect; and variant filtering and annotation using custom scripts which access resources such as Single Nucleotide Polymorphisms Database (dbSNP), Combined Annotation Dependent Depletion (CADD), Catalogue of Somatic Mutations in Cancer (COSMIC), The Cancer Genome Atlas (TCGA), Drug Gene Interaction Database (DGIdb), are included.

As a pilot for a larger study on the underlying genetics of Gastric cancer (GC [MIM 137215]) we analyzed matched tumor/normal samples from ten GC patients (6 intestinal, 4 diffuse) using this automated pipeline. We targeted the exons of 74 driver genes involved in several pathways commonly implicated in gastrointestinal cancers, such as RTK-RAS signaling. A median sequencing depth of 1300-2700 was achieved over these 20 samples, resulting in an average of four high-confidence somatic mutations in the target genes per patient, predicted to be deleterious by CADD. All variants were fully annotated with amino acid change, CADD score, and any match to mutations curated in COSMIC or reported in TCGA, plus possible drug targets as reported in DGIdb.

By reducing the data processing turnaround time required to provide clinically actionable mutations, this study has significant implications in the development of precision cancer medicine. Our open source bioinformatics analysis approach provides mutations in a format readily accessible to the physician, and which can inform patient care.

Citation Format: Susan M. Grimes, HoJoon Lee, Stephanie Greer, Jae-Ho Cheong, Hanlee P. Ji. Automated pipeline for high confidence variant calling and functional annotation, for matched tumor/normal samples sequenced by next-generation sequencing (NGS). [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-41.

Abstract A1-32: The Stanford-TCGA portal: An interactive web/mobile interface for exploring the clinical phenotypic relevance of specific cancer drivers

The Stanford-TCGA Portal (http://genomeportal.stanford.edu/pan-tcga) enables users to easily navigate cancer genomic/proteomic data of cancer patients with their clinical information from the Cancer Genome Atlas (TCGA) project. As of 2014 January, the TCGA processed thousands of samples from over 20 cancer types and the data is publically available. This huge data set can offer many valuable insights about cancer research. However, exploring data from TCGA remains a challenge, particularly for researchers and others who lack formal bioinformatics training. With the Stanford-TCGA Portal, anyone can use a personal device such as laptops or smart phones to explore the TCGA data in regards to clinically relevant questions. For example, “What genes are associated with advanced breast cancer?”, “What is the difference in the frequency of TP53 mutations between diffuse and intestinal gastric cancers?”, or “What is the frequency of copy number deletion of APC for samples with/without PIK3CA mutations?”.

While several websites such as cBio portal or UCSC cancer genomics browser was developed in order to make TCGA data more accessible to a community, there are few interactive features that enable querying of clinically-relevant phenotypic associations with drivers and modifier genes. The Stanford-TCGA portal allows users to navigate TCGA data in three different ways; i) search for clinically relevant genes/micro RNAs (miRs)/proteins by names, cancer types or clinical parameters, ii) profile genomic/proteomic changes by clinical parameters in a cancer type, or iii) test two-hit hypothesis. Thus, one can address specific questions regarding the association of cancers drivers with clinical parameters and outcome.

We identify clinically relevant genes/miRs/proteins by our rigorous statistical analysis, which has been previously published, from 17 cancer types with 19 clinical parameters such as clinical stage or smoking history. Basically, elastic-net method estimates an optimal multiple linear regularized regression of the clinical parameters on the space of genomic/proteomic features. This analysis identified the set of top gene predictors of each clinical parameter in each cancer type respectively. Users can easily access the lists of these identified genes through the Stanford-TCGA Portal.

In summary, the Stanford-TCGA Portal enables the cancer research community and others to fully utilize TCGA data. It provides simple yet clinically relevant information for web and mobile interface, thus one can examine queries and test hypothesis regarding genomic/proteomic alterations in cancers from any time and place. This will be an important step towards translation of genomic/proteomic data into clinics.

Citation Format: HoJoon Lee, Jennifer Palm, Hanlee Ji. The Stanford-TCGA portal: An interactive web/mobile interface for exploring the clinical phenotypic relevance of specific cancer drivers. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-32.

Left ventricular end diastolic pressure for detection of intracoronary ergonovine-induced myocardial ischemia

BACKGROUND

Recent consensus on variant angina defines significant spasm as total or subtotal occlusion of a coronary artery. However, the clinical significance of "less-than-subtotal" spasm needs to be reappraised, especially if the coronary spasm is combined with chest pain. Therefore, we evaluated the feasibility of left ventricular end diastolic pressure (LVEDP) as a tool to detect myocardial ischemia during ergonovine provocation testing.

METHODS

After achieving two access sites, 29 patients underwent successful LVEDP monitoring using 5-Fr pigtail catheters during ergonovine provocation tests. Patients were divided into two groups based on the occurrence of anginal symptoms.

RESULTS

Of the 29 patients, 16 (55 %) patients had anginal symptoms. LVEDP was significantly increased in the symptomatic group compared with the nonsymptomatic group (∆LVEDP 5.6 ± 4.2 vs. 1.2 ± 2.0 mmHg, p = 0.002). However, of the 16 patients with anginal symptoms, positive provocation test results were confirmed in only six patients (38 %) as per the traditional standard (> 90 % inducible spasm of the epicardial coronary artery).

CONCLUSION

Compared with the traditional standard, LVEDP may have advantages in terms of elucidating anginal symptoms in patients suspected of having coronary vasospasm when performing ergonovine provocation tests.

The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinical-genomic driver associations

Background

The Cancer Genome Atlas (TCGA) project has generated genomic data sets covering over 20 malignancies. These data provide valuable insights into the underlying genetic and genomic basis of cancer. However, exploring the relationship among TCGA genomic results and clinical phenotype remains a challenge, particularly for individuals lacking formal bioinformatics training. Overcoming this hurdle is an important step toward the wider clinical translation of cancer genomic/proteomic data and implementation of precision cancer medicine. Several websites such as the cBio portal or University of California Santa Cruz genome browser make TCGA data accessible but lack interactive features for querying clinically relevant phenotypic associations with cancer drivers. To enable exploration of the clinical–genomic driver associations from TCGA data, we developed the Cancer Genome Atlas Clinical Explorer.

Description

The Cancer Genome Atlas Clinical Explorer interface provides a straightforward platform to query TCGA data using one of the following methods: (1) searching for clinically relevant genes, micro RNAs, and proteins by name, cancer types, or clinical parameters; (2) searching for genomic/proteomic profile changes by clinical parameters in a cancer type; or (3) testing two-hit hypotheses. SQL queries run in the background and results are displayed on our portal in an easy-to-navigate interface according to user’s input. To derive these associations, we relied on elastic-net estimates of optimal multiple linear regularized regression and clinical parameters in the space of multiple genomic/proteomic features provided by TCGA data. Moreover, we identified and ranked gene/micro RNA/protein predictors of each clinical parameter for each cancer. The robustness of the results was estimated by bootstrapping. Overall, we identify associations of potential clinical relevance among genes/micro RNAs/proteins using our statistical analysis from 25 cancer types and 18 clinical parameters that include clinical stage or smoking history.

Conclusion

The Cancer Genome Atlas Clinical Explorer enables the cancer research community and others to explore clinically relevant associations inferred from TCGA data. With its accessible web and mobile interface, users can examine queries and test hypothesis regarding genomic/proteomic alterations across a broad spectrum of malignancies.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-015-0226-3) contains supplementary material, which is available to authorized users.

Free-electron X-ray laser measurements of collisional-damped plasmons in isochorically heated warm dense matter

We present the first highly resolved measurements of the plasmon spectrum in an ultrafast heated solid. Multi-keV x-ray photons from the Linac Coherent Light Source have been focused to one micrometer diameter focal spots producing solid density aluminum plasmas with a known electron density of n_{e}=1.8×10^{23}  cm^{-3}. Detailed balance is observed through the intensity ratio of up- and down-shifted plasmons in x-ray forward scattering spectra measuring the electron temperature. The plasmon damping is treated by electron-ion collision models beyond the Born approximation to determine the electrical conductivity of warm dense aluminum.

Direct Observation of Melting in Shock-Compressed Bismuth With Femtosecond X-ray Diffraction

The melting of bismuth in response to shock compression has been studied using in situ femtosecond x-ray diffraction at an x-ray free electron laser. Both solid-solid and solid-liquid phase transitions are documented using changes in discrete diffraction peaks and the emergence of broad, liquid scattering upon release from shock pressures up to 14 GPa. The transformation from the solid state to the liquid is found to occur in less than 3 ns, very much faster than previously believed. These results are the first quantitative measurements of a liquid material obtained on shock release using x-ray diffraction, and provide an upper limit for the time scale of melting of bismuth under shock loading.

Cell-Mediated Dexamethasone Release from Semi-IPNs Stimulates Osteogenic Differentiation of Encapsulated Mesenchymal Stem Cells

Scaffold-based delivery of bioactive molecules capable of directing stem cell differentiation is critical to the development of point-of-care cell therapy for orthopedic repair. Dexamethasone-conjugated hyaluronic acid (HA-DXM) was synthesized and combined with hydrolytically degradable, photo-cross-linkable PEG-bis(2-acryloyloxy propanoate) (PEG-bis-AP) to form semi-IPNs. Dexamethasone (DX) release was limited in physiological buffer and substantially increased in the presence of encapsulated human mesenchymal stem cells (hMSCs) or exogenous hyaluronidase, confirming that release occurred primarily by a cell-mediated enzymatic mechanism. hMSCs encapsulated in PEG-bis-AP/HA-DXM semi-IPNs increased osteoblast-specific gene expression, alkaline phosphatase activity, and matrix mineralization, attaining levels that were not significantly different from positive controls consisting of hMSCs in PEG-bis-AP/native HA cultured with DX supplementation in the culture medium. These studies demonstrate that PEG-bis-AP/HA-DXM semi-IPNs can provide cell-mediated release of bioactive free DX that induces hMSC osteogenic differentiation. This approach offers an efficient system for local delivery of osteogenic molecules empowering point of care applications.

Association between information provision and decisional conflict in cancer patients

BACKGROUND

In this study, we aimed to identify demographic and clinical variables that correlate with perceived information provision among cancer patients and determine the association of information provision with decisional conflict (DC).

PATIENTS AND METHODS

We enrolled a total of 625 patients with cancer from two Korean hospitals in 2012. We used the European Organization for Research and Treatment of Cancer (EORTC) quality-of-life questionnaire (QLQ-INFO26) to assess patients' perception of the information received from their doctors and the Decisional Conflict Scale (DCS) to assess DC. To identify predictive sociodemographic and clinical variables for adequate information provision, backward selective logistic regression analyses were conducted. In addition, adjusted multivariate logistic regression analyses were carried out to identify clinically meaningful differences of perceived level of information subscales associated with high DC.

RESULTS

More than half of patients with cancer showed insufficient satisfaction with medical information about disease (56%), treatment (73%), other services (83%), and global score (80%). In multiple logistic regression analyses, lower income and education, female, unmarried status, type of cancer with good prognosis, and early stage of treatment process were associated with patients' perception of inadequate information provision. In addition, Information about the medical tests with high DCS values clarity [adjusted odds ratio (aOR), 0.54; 95% confidence interval (CI) 0.30-0.97] and support (aOR, 0.53; 95% CI 0.33-0.85) showed negative significance. For inadequate information perception about treatments and other services, all 5 DCS scales (uncertainty, informed, values clarity, support, and effective decision) were negatively related. Global score of inadequate information provision also showed negative association with high DCS effective decision (aOR, 0.43; 95% CI 0.26-0.71) and DCS uncertainty (aOR, 0.46; 95% CI 0.27-0.77).

CONCLUSION

This study found that inadequate levels of perceived information correlated with several demographic and clinical characteristics. In addition, sufficient perceived information levels may be related to low levels of DC.

Long-term efficacy of biofeedback therapy in patients with dyssynergic defecation: results of a median 44 months follow-up

BACKGROUND

The beneficial effect of biofeedback therapy (BFT) over a period of more than 2 years has not been studied in a large group of patients. The aim of this study was to evaluate the long-term efficacy of BFT for dyssynergic defecation (DD).

METHODS

We evaluated the results for 347 consecutive constipated patients with DD who underwent BFT for a median of five sessions between 2004 and 2009. Initial responses were assessed immediately after the completion of BFT. A responder was defined as a subject with at least a three-point improvement from before to after BFT on an 11-point global bowel satisfaction (GBS) scale, or a two-point improvement if the baseline GBS was more than six points. The probability of remaining a responder was estimated by non-parametric maximum likelihood estimation.

KEY RESULTS

The initial response rate to BFT was 72.3% (n = 251), Parkinson's disease and higher baseline GBS scores were associated with initial non-response. The long-term efficacy of BFT was analyzed in 103 patients who were followed up for more than 6 months; the initial effects of BFT were maintained in 85 of the patients (82.5%) during a median of 44 months of follow-up (IQR = 12-68). The probability of remaining a responder was 60% at 2 years, and 58% at 5 years.

CONCLUSIONS & INFERENCES

The efficacy of BFT is maintained for more than 2 years after BFT in a considerable proportion of constipated patients with DD. BFT is effective and durable treatment for managing DD.

Further morphological observations on hearts with twisted atrioventricular connections (criss-cross hearts)

A superior and anterior location of the tricuspid valve in the setting of malalignment between the atrial and ventricular septal structures was the characteristic unifying morphologic feature of seven autopsied hearts with twisted atrioventricular connections. The peculiar angiocardiographic appearances of this lesion could be readily explained by the findings of unusual recesses in the right atrium, in the right ventricle, and in the left ventricle. The recess in the morphologically left ventricle was seen in each case at the right posterior part (or, in the hearts with left-handed ventricles, at the left part) of the chamber. Displacement of the right-sided atrioventricular valve far from the inferior caval vein (vena cava) had produced the recess in the morphologically right atrium; this feature was most prominent in the heart in which the atrioventricular connections were discordant. The recess within the right ventricular outflow tract was seen in four hearts, in all of which the inlet and apical trabecular components of the right ventricle were hypoplastic.

Shot-to-shot intensity and wavefront stability of high-harmonic generation

We report on the shot-to-shot stability of intensity and spatial phase of high-harmonic generation (HHG). The intensity stability is measured for each high-harmonic (HH) order with a spectrometer. Additionally, the spatial phase is measured with an XUV wavefront sensor for a single HH order measured in a single shot, which according to our knowledge was not reported before with a Hartmann wavefront sensor. Furthermore, we compare the single-shot measurement of the spatial phase with time-integrated measurements and we show that the XUV wavefront sensor is a useful tool to simultaneously optimize the spatial phase and intensity of HHG within the available HHG parameter range used in this study.

The ossification pattern in paediatric occipito-cervical spine: is it possible to estimate real age?

AIM

To retrospectively analyse the synchondrosis from the occipital bone to the whole cervical spine and determine the feasibility and validity of age estimation using computed tomography (CT) images.

MATERIAL AND METHODS

A total of 231 cervical spine or neck CT images of young children (<7 years of age) were examined. Twelve ossification centres were assessed (occiput: n = 2; atlas: n = 2; axis, n = 6; whole sub-axial vertebra: n = 2), and the ossification process was graded as open (O, fully lucent), osseous bridging (B, partially ossified), and fusion (F, totally ossified). After the first analysis was completed, the resulting chronological chart was used to estimate the age of 10 new cases in order to confirm the usefulness of the chart.

RESULTS

Infancy was easily estimated using the sub-axial or C2 posterior ossification centres, while the posterior occipital regions provided good estimation of age between 1-2 years. The most difficult period for accurate age estimation was between 2-4 years. However, the C2 anterior (neurocentral ossification) and C1 posterior regions did yield information to help determine the age around 3 years. The anterior occipital region was useful for age estimation between 4-5 years, and the C1-anterior region was potentially useful to help decide among the other parameters. The test for age estimation (TAE) had a very high ICC score (0.973) among the three observers.

CONCLUSION

Segmentalised analysis can enhance the ability to estimate real age, at least by the year. The analysis of the occipital bone made a strong contribution to the usefulness of the chorological chart. An organised chronological chart can provide readily available information for age estimation, and the primary application of the above data (TAE) demonstrated the validity of this approach.

Arachidonic acid promotes skin wound healing through induction of human MSC migration by MT3-MMP-mediated fibronectin degradation

Arachidonic acid (AA) is largely released during injury, but it has not been fully studied yet how AA modulates wound repair with stem cells. Therefore, we investigated skin wound-healing effect of AA-stimulated human umbilical cord blood-derived mesenchymal stem cells (hUCB-MSCs) in vivo and its molecular mechanism in vitro. We found that transplantation of hUCB-MSCs pre-treated with AA enhanced wound filling, re-epithelization, and angiogenesis in a mouse skin excisional wound model. AA significantly promoted hUCB-MSCs migration after a 24 h incubation, which was inhibited by the knockdown of G-protein-coupled receptor 40 (GPR40). AA activated mammalian target of rapamycin complex 2 (mTORC2) and Akt^ser473 through the GPR40/phosphoinositide 3-kinase (PI3K) signaling, which was responsible for the stimulation of an atypical protein kinase C (PKC) isoform, PKCζ. Subsequently, AA stimulated phosphorylation of p38 MAPK and transcription factor Sp1, and induced membrane type 3-matrix metalloproteinase (MT3-MMP)-dependent fibronectin degradation in promoting hUCB-MSCs motility. Finally, the silencing of MT3-MMP in AA-stimulated hUCB-MSCs failed to promote the repair of skin wounds owing to impaired cell motility. In conclusion, AA enhances skin wound healing through induction of hUCB-MSCs motility by MT3-MMP-mediated fibronectin degradation, which relies on GPR40-dependent mTORC2 signaling pathways.

Comparison of computed tomographic findings in pulmonary mucormycosis and invasive pulmonary aspergillosis

Because there are no available molecular markers for pulmonary mucormycosis (PM), which has low culture sensitivity, early diagnosis and treatment rely heavily on imaging modes such as computed tomography (CT). However, there are limited data comparing CT findings for PM with those for invasive pulmonary aspergillosis (IPA). Adult patients who met the modified criteria for proven and probable PM (over an 11-year period) and IPA (over a 6-year period, owing to the availability of the galactomannan assay) according to the modified European Organization for Research and Treatment of Cancer/Mycosis Study Group definitions were retrospectively enrolled. IPA cases were selected at a 1 : 4 (PM/IPA) ratio. Thoracic CT scans were reviewed by two experienced radiologists blinded to the patients' demographics and clinical outcomes. A total of 24 patients with PM, including 20 (83%) with proven PM and four (17%) with probable PM, and 96 patients with IPA, including 12 (13%) with proven IPA and 84 (87%) with probable IPA, were eventually analysed. The reverse halo sign was more common in patients with PM (54%) than in those with IPA (6%, p < 0.001), whereas some airway-invasive features, such as clusters of centrilobular nodules, peribronchial consolidations, and bronchial wall thickening, were more common in patients with IPA (IPA 52% vs. PM 29%, p 0.04; IPA 49% vs. PM 21%, p 0.01; IPA 34% vs. PM 4%, p 0.003, respectively). The reverse halo sign was more common, and airway-invasive features were less common, in patients with PM than in those with IPA. These findings may help physicians to initiate Zygomycetes-active antifungal treatment earlier.

Investigation of femtosecond collisional ionization rates in a solid-density aluminium plasma

The rate at which atoms and ions within a plasma are further ionized by collisions with the free electrons is a fundamental parameter that dictates the dynamics of plasma systems at intermediate and high densities. While collision rates are well known experimentally in a few dilute systems, similar measurements for nonideal plasmas at densities approaching or exceeding those of solids remain elusive. Here we describe a spectroscopic method to study collision rates in solid-density aluminium plasmas created and diagnosed using the Linac Coherent light Source free-electron X-ray laser, tuned to specific interaction pathways around the absorption edges of ionic charge states. We estimate the rate of collisional ionization in solid-density aluminium plasmas at temperatures ~30 eV to be several times higher than that predicted by standard semiempirical models.

Blockade of CD40-CD154 costimulatory pathway promotes long-term survival of full-thickness porcine corneal grafts in nonhuman primates: clinically applicable xenocorneal transplantation

The porcine cornea may be a good solution for the shortage of human donor corneas because its size and refractive properties are comparable to those of the human cornea. However, antigenic differences need to be overcome to apply xenocorneal transplantation in actual clinical practice. We aimed to investigate the feasibility of full-thickness porcine corneas as human corneal substitutes using a CD40-CD154 costimulatory pathway blocking strategy in a clinically applicable pig-to-nonhuman primate corneal transplantation model. As a result, the mean survival time of the xenocorneal grafts in recipients who received anti-CD154 antibody-based immunosuppressants (POD318 (n = 4); >933, >243, 318 and >192) was significantly longer than that in controls (POD28 (n = 3); 21, 28 and 29; p = 0.010, log-rank test). Administration of anti-CD154 antibodies markedly reduced inflammatory cellular infiltrations (predominantly CD8 T cells and macrophages) into the xenocorneal grafts and almost completely blocked xenoantigen-triggered increases in Th1-associated cytokines, chemokines and C3a in the aqueous humor. Moreover, systemic expansion of memory T cells was effectively controlled and responses of anti-Gal/donor pig-specific antibodies were considerably diminished by programmed injection of anti-CD154 antibodies. Consequently, porcine corneas might be promising human corneal substitutes when the transplantation is accompanied by potent immunosuppression such as a CD40-CD154 costimulatory pathway blockade.

Spontaneous Zone III rupture of the flexor tendons of the ulnar three digits in elderly Korean farmers

Spontaneous flexor tendon rupture is a rare condition and the aetiology is not clear. We report 12 elderly Korean farmers with spontaneous flexor tendon ruptures. We found the rupture in the dominant hand in ten patients. A rupture in the little finger was found in all 12 patients (seven with both flexor tendons ruptured and five with only the profundus ruptured), in the ring finger in four patients (the profundus ruptured in all and both flexor tendons in two patients), and in the middle finger a partial rupture of the profundus in one patient. The tendons were ruptured close to the hook of the hamate. Repetitive friction between the flexor tendons and the hamate hook may cause the ruptures. The hamate hook was excised and the ruptured profundus tendons were reconstructed with tendon transfers with quite favourable functional recovery at follow-up of 1 to 2 years. The ruptured superficialis tendons were not reconstructed. Level of Evidence IV.

Poly(ethylene glycol) diacrylate/hyaluronic acid semi-interpenetrating network compositions for 3-D cell spreading and migration

To serve as artificial matrices for therapeutic cell transplantation, synthetic hydrogels must incorporate mechanisms enabling localized, cell-mediated degradation that allows cell spreading and migration. Previously, we have shown that hybrid semi-interpenetrating polymer networks (semi-IPNs) composed of hydrolytically degradable poly(ethylene glycol) diacrylates (PEGdA), acrylate-PEG-GRGDS and native hyaluronic acid (HA) support increased cell spreading relative to fully synthetic networks that is dependent on cellular hyaluronidase activity. This study systematically investigated the effects of PEGdA/HA semi-IPN network composition on 3-D spreading of encapsulated fibroblasts, the underlying changes in gel structure responsible for this activity, and the ability of optimized gel formulations to support long-term cell survival and migration. Fibroblast spreading exhibited a biphasic response to HA concentration, required a minimum HA molecular weight, decreased with increasing PEGdA concentration and was independent of hydrolytic degradation at early time points. Increased gel turbidity was observed in semi-IPNs, but not in copolymerized hydrogels containing methacrylated HA, which did not support cell spreading. This suggests that there is an underlying mechanism of polymerization-induced phase separation that results in HA-enriched defects within the network structure. PEGdA/HA semi-IPNs were also able to support cell spreading at relatively high levels of mechanical properties (∼10kPa elastic modulus) compared to alternative hybrid hydrogels. In order to support long-term cellular remodeling, the degradation rate of the PEGdA component was optimized by preparing blends of three different PEGdA macromers with varying susceptibility to hydrolytic degradation. Optimized semi-IPN formulations supported long-term survival of encapsulated fibroblasts and sustained migration in a gel-within-gel encapsulation model. These results demonstrate that PEGdA/HA semi-IPNs provide dynamic microenvironments that can support 3-D cell survival, spreading and migration for a variety of cell therapy applications.

Telbivudine protects renal function in patients with chronic hepatitis B infection in conjunction with adefovir-based combination therapy

Previous studies have demonstrated that the treatment of chronic hepatitis B (CHB) infection with adefovir (ADV) can impair renal function. In contrast, treatment with telbivudine (LdT) improves renal function in CHB patients. The aim of this study was to evaluate the renoprotective effect of LdT in CHB patients receiving ADV-based combination therapy. The effects of treatment with ADV + LdT on renal function were compared to those resulting from treatment with ADV + entecavir (ETV), ADV + lamivudine (LAM), ADV alone and ETV alone. The consecutive cohort analysis included 831 CHB patients who received ADV + LdT, ADV + LAM, ADV + ETV, ADV alone or ETV alone for 96 weeks. Alterations in estimated glomerular filtration rate (eGFR) were compared between the five groups using a linear mixed-effects model. HBV DNA levels were also compared between the five groups during the 96-week period. Among the five treatment groups, significant improvements in eGFR were observed in the ADV + LdT and ADV + LAM groups over time (P < 0.001 for each group compared with baseline eGFR). In patients with a baseline eGFR between 50 and 90 mL/min, the change in eGFR was the most significant in the ADV + LdT group (+0.641 mL/min; P < 0.001). Age, gender, baseline eGFR and treatment option were significant predictive factors for eGFR changes. In conclusion, our results suggest that the combination therapy of LdT and ADV is significantly associated with renoprotective effects in CHB patients when compared with other ADV-based combination or single therapies.

Role of resistin in the inflammatory response induced by nicotine plus lipopolysaccharide in human periodontal ligament cells in vitro

BACKGROUND AND OBJECTIVE

Resistin was recently reported to play a role in inflammation-related diseases such as arthritis. However, the precise role of resistin in chronic inflammatory diseases, such as periodontal disease, remains unclear. The aim of this study was to investigate the combined effects of nicotine and lipopolysaccharide (LPS) on the expression of resistin and to assess whether resistin expression influences the levels of inflammatory cytokines, extracellular matrix (ECM) molecules and MMPs in human periodontal ligament cells (PDLCs) stimulated with both nicotine and LPS.

MATERIAL AND METHODS

PDLCs were pretreated with isoproterenol or resistin-specific small interfering RNA (siRNA), stimulated with LPS plus nicotine for 24 h, and then monitored for the production of inflammatory mediators. The concentrations of prostaglandin E2 (PGE2) and nitric oxide (NO) were measured by radioimmunoassay and the Griess method, respectively. RT-PCR and western blot analysis were used to measure the levels of mRNA and protein, respectively. Western blot analysis was also used to assess the activation of various signal-transduction pathways.

RESULTS

Treatment with nicotine plus LPS up-regulated the expression of resistin mRNA and the production of resistin protein in PDLCs in a time- and concentration-dependent manner. Isoproterenol-mediated interference with the function of resistin, or siRNA-mediated knockdown of resistin expression, markedly attenuated the LPS plus nicotine-mediated stimulation of PGE2 and NO production, the production of cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase proteins and the expression of proinflammatory cytokines [tumor necrosis factor-α, interleukin (IL)-1β, IL-6 and IL-12] and MMPs (MMP-1, MMP-2 and MMP-9); however, these treatments restored the expression of ECM molecules. Furthermore, pretreatment with isoproterenol or resistin-specific siRNA blocked nicotine plus LPS-induced activation of phosphoinositide-3-kinase, glycogen synthase kinase-3 beta, β-catenin, p38, ERK, JNK and nuclear factor-κB.

CONCLUSION

This is the first study to show that the inhibition of resistin, by either a pharmacological or a genetic silencing approach, has anti-inflammatory effects. These effects include decreased levels of inflammatory cytokines and the prevention of ECM breakdown in a nicotine plus LPS-stimulated PDLC model.

New experimental platform to study high density laser-compressed matter

We have developed a new experimental platform at the Linac Coherent Light Source (LCLS) which combines simultaneous angularly and spectrally resolved x-ray scattering measurements. This technique offers a new insights on the structural and thermodynamic properties of warm dense matter. The < 50 fs temporal duration of the x-ray pulse provides near instantaneous snapshots of the dynamics of the compression. We present a proof of principle experiment for this platform to characterize a shock-compressed plastic foil. We observe the disappearance of the plastic semi-crystal structure and the formation of a compressed liquid ion-ion correlation peak. The plasma parameters of shock-compressed plastic can be measured as well, but requires an averaging over a few tens of shots.

Exploring Mbar shock conditions and isochorically heated aluminum at the Matter in Extreme Conditions end station of the Linac Coherent Light Source (invited)

Recent experiments performed at the Matter in Extreme Conditions end station of the Linac Coherent Light Source (LCLS) have demonstrated the first spectrally resolved measurements of plasmons from isochorically heated aluminum. The experiments have been performed using a seeded 8-keV x-ray laser beam as a pump and probe to both volumetrically heat and scatter x-rays from aluminum. Collective x-ray Thomson scattering spectra show a well-resolved plasmon feature that is down-shifted in energy by 19 eV. In addition, Mbar shock pressures from laser-compressed aluminum foils using velocity interferometer system for any reflector have been measured. The combination of experiments fully demonstrates the possibility to perform warm dense matter studies at the LCLS with unprecedented accuracy and precision.

Prognostic and predictive values of EGFR overexpression and EGFR copy number alteration in HER2-positive breast cancer

Background:

Epidermal growth factor receptor (EGFR) is overexpressed in a subset of human epidermal growth factor receptor 2 (HER2)-positive breast cancers, and coexpression of HER2 and EGFR has been reported to be associated with poor clinical outcome. Moreover, interaction between HER2 and EGFR has been suggested to be a possible basis for trastuzumab resistance.

Methods:

We analysed the clinical significance of EGFR overexpression and EGFR gene copy number alterations in 242 HER2-positive primary breast cancers. In addition, we examined the correlations between EGFR overexpression, trastuzumab response and clinical outcome in 447 primary, and 112 metastatic HER2-positive breast cancer patients treated by trastuzumab.

Results:

Of the 242 primary cases, the level of EGFR overexpression was 2+ in 12.7% and 3+ in 11.8%. High EGFR gene copy number was detected in 10.3%. Epidermal growth factor receptor overexpression was associated with hormone receptor negativity and high Ki-67 proliferation index. In survival analyses, EGFR overexpression, but not high EGFR copy number, was associated with poor disease-free survival in all patients, and in the subgroup not receiving adjuvant trastuzumab. In 447 HER2-positive primary breast cancer patients treated with adjuvant trastuzumab, EGFR overexpression was also an independent poor prognostic factor. However, EGFR overexpression was not associated with trastuzumab response, progression-free survival or overall survival in the metastatic setting.

Conclusions:

Epidermal growth factor receptor overexpression, but not high EGFR copy number, is a poor prognostic factor in HER2-positive primary breast cancer. Epidermal growth factor receptor overexpression is a predictive factor for trastuzumab response in HER2-positive primary breast cancer, but not in metastatic breast cancer.

Smoking cession decreases mean platelet volume in healthy Korean populations

BACKGROUND

Smoking is considered as a major modifiable risk factor for cardiovascular diseases. It has been shown that smoking cessation drops the risk of cardiovascular diseases such as myocardial infarction and also improves platelet function. Because mean platelet volume (MPV) is a simple and convenient indicator for platelet activation, we planned to investigate the effect of smoking status on MPV in healthy populations.

METHODS

This study was conducted on 398 individuals who visited our hospital for regular medical check-ups and were confirmed not to have diabetes or hypertension. MPV was measured using EDTA blood on an Advia 2120 (Siemens Healthcare Diagnostics Inc., Tarrytown, NY, USA) within 2 hours.

RESULTS

Present smokers showed higher MPV levels than present non-smokers. When MPV was compared by taking previous smoking history and present smoking status into account, the smoking cessation group showed significantly lower MPV levels than other groups.

CONCLUSIONS

Because this finding was significant only in the female group, the change in MPV according to smoking status was found to be different by gender. We carefully suggest that smoking cessation can lower the risk of cardiovascular diseases through the change in MPV, which can be more effective for women than men.

Abstract 4174: An integrative genomic analysis for clinically relevant cancer genetic aberration and targeted therapeutic prediction

While the genomic and genetic basis of many cancers has been partly elucidated, less is known about the identity of specific cancer genes that are associated with clinical parameters such as clinical stage, metastasis, and survival. To address this question, we compiled multiple genomic data types (mutations, copy number alterations, gene expression and methylation status) as well as clinical meta-data for twelve different cancers in the Cancer Genome Atlas Project. We used an elastic-net regularized regression method on the combined genomic data to identify genetic aberrations and their associated cancer genes that are indicators of clinical parameters in each cancer type. To facilitate the identification of clinically actionable genetic aberrations from this cancer genomic data, we utilized genomic and drug response data from the Cancer Cell Line Encyclopedia (CCLE). These expansive data sets of hundreds of cancer cell lines include three genomic data types (mutations, copy number alterations, gene expression) and drug response data. To demonstrate the performance and validity of this approach, we demonstrated that our bioinformatics pipeline successfully identified i) synthetic genes that have their CNVs perfectly associated with stages from a simulated data ii) mutations of TGFBR2, methylation of MLH1 and other driver genes that have genetic changes associated with colorectal cancer (CRC) that demonstrate microsatellite instability CRC from TCGA data, and iii) IDH1 that obtained mutations associated with survival according to glioblastoma (GBM) data. We identify the top ranked genes that delineate key clinical features such as survival analysis or clinical stages for 13 cancers. A fit of the elastic-net regularized regression to more than 200 samples/cancer type and integrative analysis of integrative genomic platforms identified the set of top gene predictors of clinical parameters (TCGA data) and drug response (CCLE data). There are several genes ranked top in multiple cancer types while most of them are unique to a cancer type. These results provide us with new insights into the underlying genetic similarities and differences among 13 cancers; namely, common genetic characteristics that have implications for clinical phenotype. Finally, we are identifying the core set of gene aberrations that are both clinically relevant and drug responsible.

Citation Format: HoJoon Lee, Hanlee P. Ji. An integrative genomic analysis for clinically relevant cancer genetic aberration and targeted therapeutic prediction. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4174. doi:10.1158/1538-7445.AM2014-4174

Absolute pulse energy measurements of soft x-rays at the Linac Coherent Light Source

This paper reports novel measurements of x-ray optical radiation on an absolute scale from the intense and ultra-short radiation generated in the soft x-ray regime of a free electron laser. We give a brief description of the detection principle for radiation measurements which was specifically adapted for this photon energy range. We present data characterizing the soft x-ray instrument at the Linac Coherent Light Source (LCLS) with respect to the radiant power output and transmission by using an absolute detector temporarily placed at the downstream end of the instrument. This provides an estimation of the reflectivity of all x-ray optical elements in the beamline and provides the absolute photon number per bandwidth per pulse. This parameter is important for many experiments that need to understand the trade-offs between high energy resolution and high flux, such as experiments focused on studying materials via resonant processes. Furthermore, the results are compared with the LCLS diagnostic gas detectors to test the limits of linearity, and observations are reported on radiation contamination from spontaneous undulator radiation and higher harmonic content.

Genotoxic stress/p53-induced DNAJB9 inhibits the pro-apoptotic function of p53

DNAJB9 is a recently isolated member of the molecular chaperone gene family, whose precise function is largely unknown. In the present study, we have identified DNAJB9 as an inducible gene of the tumor suppressor p53. DNAJB9 expression was induced by p53 or genotoxic stress in a p53-dependent manner, which was mediated by the Ras/Raf/ERK pathway. In addition, depletion of DNAJB9 by using siRNAs greatly increased genotoxic stress/p53-induced apoptosis, suggesting that DNAJB9 inhibits the pro-apoptotic function of p53. We also found that DNAJB9 physically interacts with p53 through its J domain, through which it inhibits the pro-apoptotic function of p53. Moreover, DNAJB9 colocalized with p53 in both cytoplasm and nucleus under genotoxic conditions. Together, these results demonstrate that DNAJB9 is a downstream target of p53 that belongs to the group of negative feedback regulators of p53.

Effects of microbial additives on chemical composition and fermentation characteristics of barley silage

This study examined the effects of bacterial inoculants on chemical composition and fermentation indices of barley silage. Barley forage (Youngyang) was harvested at 24% dry matter (DM) and wilted to 47.9% DM. The wilted barley forage was chopped to 3–5 cm length and applied with no inoculant (CON), L. plantarum (1×10¹⁰ cfu/g, LP) or Effective Microorganisms (0.5×10⁹ cfu/g, EM). Then the forages were ensiled in four replications for each treatment in 20 L mini silos and stored for 100 days. The contents of crude protein and ether extract were higher in CON silage ensiled for 100-d, while the contents of DM and crude ash were higher in EM silage (p<0.05). The contents of ADF, NDF and hemicellulose as well as the in vitro DM digestibility were not affected by microbial inoculation (p>0.05). The pH, ammonia-N concentration and lactate to acetate ratio were higher (p<0.05) in CON silage, while lactate concentrations were higher (p<0.05) in CON and LP silage. Acetate concentration and lactic acid bacteria was increased (p<0.05) by both inoculants (LP and EM), but propionate concentration and yeast was increased (p<0.05) by EM and LP, respectively. These results indicated that the fermentation quality of barley silage was improved by the application of bacterial inoculants.

Detection of quantitative trait Loci affecting fat deposition traits in pigs

Quantitative trait loci (QTL) associated with fat deposition traits in pigs are important gene positions in a chromosome that influence meat quality of pork. For QTL study, a three generation resource population was constructed from a cross between Korean native boars and Landrace sows. A total of 240 F2 animals from intercross of F1 were produced. 80 microsatellite markers covering chromosomes 1 to 10 were selected to genotype the resource population. Intervals between adjacent markers were approximately 19 cM. Linkage analysis was performed using CRIMAP software version 2.4 with a FIXED option to obtain the map distances. For QTL analysis, the public web-based software, QTL express (http://www.qtl.cap.ed.ac.uk) was used. Two significant and two suggestive QTL were identified on SSC 6, 7, and 8 as affecting body fat and IMF traits. For QTL affecting IMF, the most significant association was detected between marker sw71 and sw1881 on SSC 6, and a suggestive QTL was identified between sw268 and sw205 on SSC8. These QTL accounted for 26.58% and 12.31% of the phenotypic variance, respectively. A significant QTL affecting IMF was detected at position 105 cM between markers sw71 and sw1881 on SSC 6.

Effect of inter-cycle interval on oocyte production in humans in the presence of the weak androgen DHEA and follicle stimulating hormone: a case-control study

BACKGROUND

In various animal models androgens have been demonstrated to enhance follicle stimulating hormone (FSH) activity on granulosa cells during small growing follicle stages. To assess whether similar synergism may also exist in humans we investigated women on androgen (dehydroepiandrosterone, DHEA) supplementation with varying concomitant FSH exposure.

METHODS

In a case controlled cohort study we determine if time interval between IVF cycles of IVF treatment with FSH had an effect on ovarian response to ovulation induction in women supplemented with DHEA. Among 85 women with known low functional ovarian reserve (LFOR), supplemented with DHEA, and undergoing at least 3 consecutive IVF cycles, 68 demonstrated short (<120 days) intervals between repeated cycles (Group 1) and were, therefore, considered to have consistent FSH exposure. In contrast 17 women (Group 2) demonstrated long (>=120 days) intervals between repeated cycles and, therefore, were considered to demonstrate inconsistent FSH exposure. Trends in oocyte yields were compared between these groups, utilizing mixed model repeated measures ANOVA, adjusted for initial age and FSH dose.

RESULTS

Only women in Group I demonstrated a linear increase in oocyte yields across their three cycles of treatments (F=7.92; df 1, 68.6; p=0.017). Moreover, the analysis revealed a significant interaction between the two patient groups and cycle number for retrieved oocytes (F=6.32, df=2, 85.9, p=0.003).

CONCLUSIONS

This study offers preliminary confirmatory evidence that repeated short interval exposure to androgens in combination with FSH improves human FOR. A higher level of evidence will require prospectively randomized studies.

Absence of BRCA/FMR1 correlations in women with ovarian cancers

Previously reported findings in Austrian BRCA1/2 mutation carriers suggested a possible dependency of embryos with BRCA1/2 mutations on so-called low alleles of the fragile X mental retardation 1 (FMR1) gene, characterized by less than 26 CGG repeats (CGG(n<26)). The hypothesis arose from a study reporting highly statistically significant enrichment of low FMR1 alleles, significantly exceeding low allele prevalence in a general population, suggesting embryo lethality of BRCA1/2 mutations, "rescued" by presence of low FMR1 alleles. Such a dependency would also offer an explanation for the so-called "BRCA-paradox," characterized by BRCA1/2 deficient embryonic tissues being anti-proliferative (thereby potentially causing embryo-lethality) but proliferative in malignant tumors, including breast and ovarian cancers. Follow up investigations by other investigators, however, at most demonstrated trends towards enrichment but, mostly, no enrichment at all, raising questions about the original observation and hypothesis. We in this study, therefore, investigated CGGn of the FMR1 gene of 86 anonymized DNA samples from women with various forms of ovarian cancer, and were unable to demonstrate differences in prevalence of low FMR1 alleles either between positive and negative ovarian cancer patients for BRCA1/2 or between ovarian cancer patients and reported rates in non-cancer populations. This raises further questions about a suggested dependency between BRCA1/2 and FMR1, but also raises the possibility that investigated Austrian BRCA1/2 carrier populations differ from those in other countries. Either only selected BRCA1/2 mutations, therefore, interact with low FMR1 alleles or the Austrian data reflect only coincidental observations.

Utilizing FMR1 gene mutations as predictors of treatment success in human in vitro fertilization

CONTEXT

Mutations of the fragile X mental retardation 1 (FMR1) gene are associated with distinct ovarian aging patterns.

OBJECTIVE

To confirm in human in vitro fertilization (IVF) that FMR1 affects outcomes, and to determine whether this reflects differences in ovarian aging between FMR1 mutations, egg/embryo quality or an effect on implantation.

DESIGN, SETTING, PATIENTS

IVF outcomes were investigated in a private infertility center in reference to patients' FMR1 mutations based on a normal range of CGG(n = 26-34) and sub-genotypes high (CGG(n>34)) and low (CGG(<26)). The study included 3 distinct sections and study populations: (i) A generalized mixed-effects model of morphology (777 embryos, 168 IVF cycles, 125 infertile women at all ages) investigated whether embryo quality is associated with FMR1; (ii) 1041 embryos in 149 IVF cycles in presumed fertile women assessed whether the FMR1 gene is associated with aneuploidy; (iii) 352 infertile patients (< age 38; in 1st IVF cycles) and 179 donor-recipient cycles, assessed whether the FMR1 gene affects IVF pregnancy chances via oocyte/embryo quality or non-oocyte maternal factors.

INTERVENTIONS

Standardized IVF protocols.

MAIN OUTCOME MEASURES

Morphologic embryo quality, ploidy and pregnancy rates.

RESULTS

(i) Embryo morphology was reduced in presence of a low FMR1 allele (P = 0.032). In absence of a low allele, the odds ratio (OR) of chance of good (vs. fair/poor) embryos was 1.637. (ii) FMR1 was not associated with aneuploidy, though aneuploidy increased with female age. (iii) Recipient pregnancy rates were neither associated with donor age or donor FMR1. In absence of a low FMR1 allele, OR of clinical pregnancy (vs. chemical or no pregnancy) was 2.244 in middle-aged infertility patients.

CONCLUSIONS

A low FMR1 allele (CGG(<26)) is associated with significantly poorer morphologic embryo quality and pregnancy chance. As women age, low FMR1 alleles affect IVF pregnancy chances by reducing egg/embryo quality by mechanisms other than embryo aneuploidy.

Equilibration dynamics and conductivity of warm dense hydrogen

We investigate subpicosecond dynamics of warm dense hydrogen at the XUV free-electron laser facility (FLASH) at DESY (Hamburg). Ultrafast impulsive electron heating is initiated by a ≤ 300-fs short x-ray burst of 92-eV photon energy. A second pulse probes the sample via x-ray scattering at jitter-free variable time delay. We show that the initial molecular structure dissociates within (0.9 ± 0.2) ps, allowing us to infer the energy transfer rate between electrons and ions. We evaluate Saha and Thomas-Fermi ionization models in radiation hydrodynamics simulations, predicting plasma parameters that are subsequently used to calculate the static structure factor. A conductivity model for partially ionized plasma is validated by two-temperature density-functional theory coupled to molecular dynamic simulations and agrees with the experimental data. Our results provide important insights and the needed experimental data on transport properties of dense plasmas.

Esophageal mucosal mast cell infiltration and changes in segmental smooth muscle contraction in noncardiac chest pain

Mast cells release potent mediators that alter enteric nerve and smooth muscle functions and may contribute to the pathogenesis of functional gastrointestinal disorders. The goal of this study was to determine if mucosal mast cell infiltration was associated with smooth muscle segmental changes in esophageal contraction. All patients with noncardiac chest pain (NCCP) were divided into two groups consisting of patients with non-erosive reflux disease or functional chest pain (FCP) according to the results of ambulatory 24 hours esophageal pH monitoring and high-resolution manometry. Pressure-volume (PV) was calculated by multiplying the length of the esophageal segment, duration of the contraction, and mean pressure over the entire space-time box (P mean). Quantification of mast cells was performed in five consecutive nonoverlapping immunostained sections. Spearman correlation analysis showed that the distal segment PV correlated with the mast cell count in all of the patients combined and in patients with FCP with correlation coefficients of 0.509 and 0.436, respectively (P = 0.004 and P = 0.042). Similar findings were observed for the segmental ratio of distal to proximal smooth muscle PV in all patients and in patients with FCP (correlation coefficients 0.566; P = 0.001 and correlation coefficients 0.525; P = 0.012, respectively). Mucosal mast cell infiltration was associated with distal esophageal contraction as a key pathophysiologic factor of NCCP.