Minimally Invasive Skin Transcriptome Extraction Using a Dermal Biomarker Patch

Introduction

Advances in the scientific understanding of the skin and characteristic genomic dermal signatures continue to develop rapidly. Nonetheless, skin diagnosis remains predicated on a subjective visual examination, frequently followed by biopsy and histology. These procedures often are not sufficiently sensitive, and in the case of many inflammatory diseases, biopsies are not justified, creating a situation where high-quality samples can be difficult to obtain. The wealth of molecular information available and the pace at which new data are acquired suggest that methods for minimally invasive biomarker collection could dramatically alter our understanding of skin disease and positively impact treatment paradigms.

Methods

A chemical method was optimized to covalently modify custom dermal patches with single-stranded DNA that could bind to messenger RNA. These patches were applied to ex vivo skin samples and penetration evaluated by histological methods. Patches were then applied to both the skin of normal human subjects (lower arm) as well as lesional skin of psoriasis patients, and the transcriptome captured (N = 7; 33 unique samples). Standard RNA-Seq processing was performed to assess the gene detection rate and assessments made of the reproducibility of the extraction procedure as well as the overlap with matched punch biopsy samples from the same patient.

Results

We have developed a dermal biomarker patch (DBP) designed to be minimally invasive and extract the dermal transcriptome. Using this platform, we have demonstrated successful molecular analysis from healthy human skin and psoriatic lesions, replicating the molecular information captured with punch biopsy.

Conclusion

This DBP enables an unprecedented ability to monitor the molecular “fingerprint” of the skin over time or with various interventions, and generate previously inaccessible rich datasets. Furthermore, use of the DBP could be favored by patients relative to biopsy by limiting pain resulting from biopsy procedures. Given the large dynamic range observed in psoriatic skin, analysis of complex phenotypes is now possible, and the power of machine-learning methods can be brought to bear on dermatologic disease.

Robotic-assisted latissimus dorsi muscle flap for autologous chest reconstruction in poland syndrome

BACKGROUND

As chest reconstructions in Poland syndrome are performed for patients at young ages, patients are generally concerned about conspicuous scars. Meanwhile, a robotic-assisted latissimus dorsi (LD) muscle harvest with inconspicuous scars has been performed for autologous breast reconstruction. As our experience with robotic-assisted LD flap harvest has increased over the years, we have made improvements in surgical techniques to optimize results. The purpose of this study was to introduce and identify the role of the refined robotic-assisted LD muscle flap harvest technique in autologous chest reconstruction in patients with Poland syndrome.

METHODS

Autologous chest reconstruction using a robotic-assisted LD muscle flap harvest was performed for 21 patients with Poland syndrome. Subjective assessments were performed to evaluate improvement in chest deformity, patient satisfaction with overall outcomes, chest symmetry, and scars. Assessments by the operator and two independent evaluating investigators were carried out with patients' photographs. The complication rates and the time for robotic surgery were also evaluated.

RESULTS

At the last visit, the average patient grades for improvement in chest deformity, satisfaction with overall outcomes, chest symmetry, and scars were 4.80, 4.72, 4.18, and 4.87, respectively. Assessments by the operator and two independent evaluating investigators demonstrated that improvement in chest deformity was achieved in all patients. No serious complications such as flap loss were recorded for any patient. The time for robotic surgery markedly decreased as experience accumulated.

CONCLUSIONS

Surgical refinements for robotic-assisted LD flap harvest might be effective and reduce operative times for patients with Poland syndrome.

Epilepsy in Asia: Disease burden, management barriers, and challenges

This article reviews the burden of epilepsy in Asia, the challenges faced by people with epilepsy, and the management of epilepsy. Comparison is made with other parts of the world. For this narrative review, data were collected using specified search criteria. Articles investigating the epidemiology of epilepsy, diagnosis, comorbidities and associated mortality, stigmatization, and treatment were included. Epilepsy is a global health care issue affecting up to 70 million people worldwide. Nearly 80% of people with epilepsy live in low- and middle-income countries with limited resources. People with epilepsy are prone to physical and psychological comorbidities, including anxiety and depression, which can negatively impact their quality of life. Furthermore, people with epilepsy are at higher risk of premature death than people without epilepsy. Discrimination or stigmatization of people with epilepsy is common in Asia and can affect their education, work, and marriage opportunities. Access to epilepsy treatment varies throughout Asia. Although highly advanced treatment is available in some countries, up to 90% of people with epilepsy are not adequately treated or are not treated with conventional antiepileptic therapy in resource-limited countries. People in remote areas often do not receive any epilepsy care. First-generation antiepileptic drugs (AEDs) are available, but usually only in urban areas, and second-generation AEDs are not available in all countries. Newer AEDs tend to have more favorable safety profiles than first-generation AEDs and provide options to tailor therapy for individual patients, especially those with comorbidities. Active epilepsy surgery centers are present in some countries, although epilepsy surgery is often underutilized given the number of patients who could benefit. Further epidemiologic research is needed to provide accurate epilepsy data across the Asian region. Coordinated action is warranted to improve access to treatment and care.

Disclosure management behaviors in Korean adults with well-controlled epilepsy: Their relation to perception of stigma

PURPOSE

In spite of the fact that epilepsy is a concealable stigmatized identity, there is little evidence pertaining to disclosure management in adults living with epilepsy. We determined the factors contributing to disclosure management strategies in adults living with well-controlled epilepsy.

METHODS

This was a cross-sectional multicenter study. Korean adults whose seizures had remitted for at least one year participated in this study. Using statistical analyses, we determined whether disclosure management behaviors measured using the Disclosure Management Scale (DMS) were related to demographic, clinical, and psychosocial variables. The Stigma Scale and Hospital Anxiety Depression Scale (HADS) were used.

RESULTS

Of a total of 225 participants, 76% stated that they often or sometimes kept their epilepsy a secret, while 24% reported that they never or rarely kept their diagnosis hidden. The mean DMS score was 6.1 (SD=2.4). In univariate analyses, the DMS scores were significantly related to the HADS depression scores (r=0.187, p=0.005) and the presence of perceived stigma (p=0.001). In linear regression analyses, perceived stigma was identified only as an independent factor associated with DMS scores (p=0.031), while HADS depression lost significance (p=0.057). The presence of perceived stigma explained only 4.6% of the variance in DMS scores.

CONCLUSIONS

Our study shows that over 70% of Korean adults with well-controlled epilepsy often or sometimes keep their epilepsy a secret. Although perceived stigma is associated with concealment behaviors, it accounts for only a small proportion of the variance in disclosure management.

Abstract 1518: Lung adenocarcinoma differential expression analysis using the Maverix RNA-Seq pipeline

Background

RNA-Seq is a powerful means of identifying changes in gene expression in cancerous tissue. Widespread adoption of RNA-Seq is hampered by lack of familiarity with the appropriate analysis tools and excessive turn around time. Maverix Biomics, Inc offers a scalable, reliable, validated, and easily accessible differential expression pipeline for translational and clinical researchers to analyze and explore RNA-Seq data. Here we describe the pipeline, demonstrate the available tools and visualizations, and provide benchmarks for completion time from lung adenocarcinoma.

Results

Lung adenocarcinoma samples appear very different compared to their normal counterparts in terms of overall gene expression and exhibit many differentially expressed genes. For analysis completion time, parallelization is far superior than the theoretical curve without parallelization. It took 7.9 hours to analyze two samples, but took only 13.1 hours to analyze 25 samples. We found 2246 significant genes common to three different differential expression tools: DESeq, edgeR, and cuffdiff.

Conclusions

The Maverix RNA-Seq pipeline is demonstrated here to be highly scalable, easy to use, and includes a range of tools and visualizations for understanding differential expressions results. This pipeline is a great analytic option to accelerate translational and clinical research in the field of oncology.

Citation Format: Michael S. Fitzsimons, Mei-Chong Wendy Lee, Byung-In Lee, Lenin Subramanian. Lung adenocarcinoma differential expression analysis using the Maverix RNA-Seq pipeline. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1518.

The effect of recurrent seizures on cognitive, behavioral, and quality-of-life outcomes after 12 months of monotherapy in adults with newly diagnosed or previously untreated partial epilepsy

PURPOSE

The purpose of this study was to determine whether seizure recurrence has a negative impact on cognition, psychological function, and health-related quality of life (HRQoL) over a 12-month period of monotherapy in adults with newly diagnosed or previously untreated partial epilepsy.

METHODS

Seizure freedom (SF) was defined as no seizure recurrence during the 40-week maintenance period of medication. Neuropsychological tests, the Symptom Checklist-90 (SCL-90), and the Quality of Life in Epilepsy-31 (QOLIE-31) were administered at baseline and after 48 weeks of carbamazepine or lamotrigine monotherapy. Seventy-three patients successfully continued treatment until the 48-week follow-up time point. Fifty patients (68.5%) had SF, and the remaining 23 were not seizure-free (NSF). A seizure outcome group-by-time interaction was analyzed using a linear mixed model.

RESULTS

A group-by-time interaction was identified for the total QOLIE-31 score (p<0.05) and score on two QOLIE-31 subscales (social function: p<0.001 and seizure worry: p<0.001), with a significant improvement over time only present in the SF group (all p<0.001). There was no significant group-by-time interaction for most cognitive function tests, with the exception of the serial clustering score (p<0.01) and number of recognition hits on the California Verbal Learning Test (p<0.05). Serial clustering did not differ between the SF and NSF groups at baseline, but was significantly more used in the NSF group than in the SF group at 48 weeks (p<0.01). There was no significant group-by-time interaction for any dimension of the SCL-90.

CONCLUSION

Recurrent seizures had a significant effect on HRQoL, a subtle effect on cognitive performance, and no effect on psychological symptoms over one year in newly diagnosed or previously untreated adults with partial epilepsy.

Association of knowledge about epilepsy with mood and self-efficacy in Korean people with epilepsy

PURPOSE

We determined the level of knowledge about epilepsy in Korean people with epilepsy (PWE) and evaluated whether this is associated with self-efficacy, perceived stigma, anxiety, and depressive mood in these patients.

METHODS

This was a cross-sectional multicenter study. A total of 530 PWE participated from 31 secondary or tertiary hospitals in Korea. Knowledge about epilepsy was assessed using 34 medical items (EKP-M) of the Epilepsy Knowledge Profile-General. Additional questionnaires included the Epilepsy Self-Efficacy Scale (ESES), Stigma Scale, and Hospital Anxiety and Depression Scale (HADS). Multiple linear regression analyses were used.

RESULTS

The mean EKP-M score was 22.2 (SD: 4.1). By univariate analyses, the EKP-M was related to ESES (r=0.220, p<0.001) and HADS-D (r=-0.154, p<0.001) scores but not to the Stigma Scale or HADS-A. By linear regression analyses, after adjusting for the confounding variables, the higher EKP-M scores were independently related to both higher ESES (p<0.001) and lower HADS-D scores (p<0.05).

CONCLUSION

Korean PWE have a relatively low level of knowledge about their condition. Knowledge about epilepsy is associated with a high level of self-efficacy and less depressive symptoms in affected individuals.

Effect of Androsterone after Pilocarpine-induced Status Epilepticus in Mice

Background and Purpose:

Neurosteroids exert their antiepileptic effects via GABAA and NMDA receptors. Another cell death mechanism is excessive Ca²⁺ influx into cells. Calbindin-D28k (CB) is a protein that modulates intracellular Ca²⁺ in the nervous system. We evaluated whether androsterone up-regulates the expression of CB and has a neuroprotective effect by controlling Ca²⁺ after pilocarpine-induced status epilepticus (SE) in mice.

Methods:

SE was induced in ICR mice by injection of pilocarpine. Two hours after SE, mice were treated intraperitoneally (i.p.) with androsterone (100–200 mg/kg) or vehicle, and compared with other control groups. Two days after injection, immunohistochemical staining for CB was performed using a hippocampal slice from each mice group. We also used cresyl violet staining to compare changes in hippocampal structures.

Results:

Two days after pilocarpine-induced SE, androsterone increased the expression of CB in the hippocampus compared with control SE mice. The number of CB-positive cells was 1±0.4 cells/mm³ in pilocarpine-only group, 14±1.1 cells/mm³ in pilocarpine plus androsterone 100 mg group and 29±2.5 cells/mm³ in pilocarpine plus androsterone 200 mg group (p<0.001).

Conclusions:

These results suggest that the neuroprotective effect of androsterone after pilocarpine- induced SE may be mediated by an increased expression of CB.

ILAE official report: a practical clinical definition of epilepsy

Epilepsy was defined conceptually in 2005 as a disorder of the brain characterized by an enduring predisposition to generate epileptic seizures. This definition is usually practically applied as having two unprovoked seizures >24 h apart. The International League Against Epilepsy (ILAE) accepted recommendations of a task force altering the practical definition for special circumstances that do not meet the two unprovoked seizures criteria. The task force proposed that epilepsy be considered to be a disease of the brain defined by any of the following conditions: (1) At least two unprovoked (or reflex) seizures occurring >24 h apart; (2) one unprovoked (or reflex) seizure and a probability of further seizures similar to the general recurrence risk (at least 60%) after two unprovoked seizures, occurring over the next 10 years; (3) diagnosis of an epilepsy syndrome. Epilepsy is considered to be resolved for individuals who either had an age-dependent epilepsy syndrome but are now past the applicable age or who have remained seizure-free for the last 10 years and off antiseizure medicines for at least the last 5 years. "Resolved" is not necessarily identical to the conventional view of "remission or "cure." Different practical definitions may be formed and used for various specific purposes. This revised definition of epilepsy brings the term in concordance with common use. A PowerPoint slide summarizing this article is available for download in the Supporting Information section here.

Changing name of epilepsy in Korea; cerebroelectric disorder (noi-jeon-jeung,뇌전증,): my epilepsy story

Public misconception of epilepsy may lead to significant stigma to the disease itself, thereby causing impaired quality of life in people with epilepsy. Traditionally, epilepsy has been considered to be the consequence of evanescent spiritual forces, and even demonic possession (in many countries). The names of epilepsy in some East Asian countries originated from China, and include madness in their meaning. We recently changed the Korean name of epilepsy, gan-jil (간질, : a crazy, convulsive disease having meaning similar to ), to a neutral and scientifically explainable name: noi-jeon-jeung (뇌전증; ; cerebroelectric disorder). We expect that changing the stigmatized name of epilepsy to a neutral and scientific term with the meaning of cerebroelectric disorder will reduce the social stigma by understanding of epilepsy as one of the neurologic disorders.

NGS-based targeted RNA sequencing for expression profiling and relative quantitation of specific gene isoforms and fusions in tumor-specific panels

11108

Background: Gene expression signatures have become a useful tool for the identification of tumor subtypes and response to specific therapies. Expression of tumor, metastatic and macrophage specific transcripts utilizing alternative promoters and transcriptional start sites can further characterize these tumors . NGS is a powerful tool for gene expression analysis, however larger sample input requirements (>100ng) and excessive sequencing depth requirements (30-40M tags/sample) to detect the expression of rare isoforms or fusions in tumor samples are prohibitive for clinical assay development. We describe the development of a targeted RNA sequencing assay for the relative quantitation of specific gene expression signatures, known splice variants and gene fusions from less than 100 ng of starting material in a single tube universal amplification format. Methods: Primers for 52 genes, isoforms and gene fusion products were designed using the universal amplification strategy. 10 ng of RNA from 5 matched tumor/adjacent normal breast cancer tumor pairs were assayed. Libraries were prepared for sequencing by emPCR and sequenced on Ion Torrent PGM. Data were aligned via TMAP. Relative expression was determined vs. housekeeping genes or wild type transcripts. Results: All gene targets were detected at significant levels in at least one tumor sample. Robust expression profiling (5 log dynamic range) was obtained from FFPE macrodissected tumor and normal samples with as little as 200K reads/sample. Immune specific transcripts demonstrated differential expression (CCL3, AIF, FCGR3A and CSF1) across patients and matched pairs as well as an upregulation of CXCL12, indicative of tumor associated macrophages. Conclusions: Targeted RNAseq demonstrates detection and quantitation of relative expression levels of not only tumor subclass specific gene expression signatures, but immune cell specific transcripts from 10ng of FFPE derived total RNA derived from macrodissected tumor samples. The lower input requirements, quicker turnaround time and incredible sensitivity of targeted RNAseq make this assay a useful tool for clinical assay development.

Abstract 4143: Targeted RNA sequencing for expression analysis of breast cancer patient samples using a biomarker gene panel

Background: Gene expression profiling has been shown to be effective in the analysis of postoperative tumor samples in various cancers. However, for studies requiring the analysis of small specimens, such as core biopsies, the limited amount of available material makes multi-gene analyses exceedingly difficult. Moreover, microarray-based analyses provide somewhat limited dynamic range and multi-gene qRT-PCR analyses often require in excess of 100 ng of input RNA per sample. To this end, we describe the development of targeted RNA-sequencing methodology which combines the power of a universal RNA amplification with NGS for ultra-deep expression analysis of multiple target genes, enabling &lt;100 ng of sample input for multi-gene analysis in a single tube format. Methods: The gene expression patterns of triple-negative breast cancer FFPE samples were analyzed using a 96-gene breast cancer biomarker panel across three different platforms. Affymetrix Human Gene ST 1.0 microarrays and a pre-developed qRT-PCR panel were employed for analysis. For Targeted RNA-seq analysis, the 96-gene panel was amplified using a universal, single-tube “XP-PCR” amplification strategy followed by sequence analysis using the Ion-Torrent Personal Genome Machine. NGS-based expression analysis was performed by counting the frequency of expression tag sequences and the performance of the three expression analysis platforms were compared. Results: The performance of the three gene expression platforms was analyzed according to two different parameters. Gene pairs from four well-characterized expression modules were compared, demonstrating a positive correlation and association with expected clinical biomarker characteristics in all three platforms. Targeted RNA-seq provided the most sensitivity in terms of detection rates with &lt;100 ng FFPE RNA input and provides unlimited dynamic range with increased sequencing depth. In particular, low expressing genes, undetectable by qRT-PCR analysis from 1,000 ng input FFPE RNA, were detected and eligible for expression analysis with a significant number of sequencing reads. In addition to expression analysis, alternative transcription/splicing analysis is possible from sequence analysis of the target transcripts using targeted RNA-seq. Conclusion: By combining universally-primed pre-amplification and NGS in multi-gene expression analysis, targeted RNA-seq provides a robust, sensitive gene expression analysis methodology for a variety of clinical sample specimens. Compression issues typically associated with high pre-amplification cycles were not observed here, resulting in higher gene detection rates, at lower sample input amounts leading to high-sensitivity expression analysis.

Citation Format: Kahuku Oades, Lien Vo, Jerry Lee, Mark Landers, Yipeng Wang, Byung-In Lee, Joseph Monforte. Targeted RNA sequencing for expression analysis of breast cancer patient samples using a biomarker gene panel. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4143. doi:10.1158/1538-7445.AM2013-4143

NGS-based targeted RNA sequencing for expression analysis of patients with triple-negative breast cancer using a modulized, 96-gene biomarker panel

56

Background: Gene expression profiling has been shown to be effective in analyzing postoperative tumor samples in various cancers. However, in analyzing small specimens such as core biopsies, the limited amount of available material makes multi-gene analyses difficult or impossible. Microarray-based analyses also provide limited dynamic range. We describe the development of targeted RNA-sequencing methodology which combines the power of a universal RNA amplification with NGS for an ultra-deep expression analysis of multiple target genes, enabling <100 ng of sample input for multi-gene analysis in a single tube format. Methods: The gene expression patterns of triple-negative breast cancer FFPE samples were analyzed using a 96-gene breast cancer biomarker panel across three different platforms: Affymetrix Human Gene ST 1.0 microarrays, a pre-developed OncoScore qRT-PCR panel, and targeted RNA-seq. For targeted RNA-seq analysis, the 96-gene panel was amplified using a universal, single-tube “XP-PCR” amplification strategy followed by sequence analysis using the Ion-Torrent Personal Genome Machine. Results: Targeted RNA-seq provided the most sensitivity in terms of detection rates with <100 ng FFPE RNA input and provides unlimited dynamic range with increased sequencing depth. Expression ratio compression issues typically associated with a high number of pre-amplification cycles in standard multiplex-primed methods were not observed here. Low expressing genes, undetectable by qRT-PCR analysis from 1,000 ng input FFPE RNA, were detected and eligible for expression analysis with a significant number of sequencing reads. Alternative transcription/splicing analysis is also possible from sequence analysis of the target transcripts using targeted RNA-seq. Conclusions: By combining universally primed pre-amplification and NGS in multi-gene expression analysis, targeted RNA-seq provides the most sensitive gene expression analysis methodology.

A qPCR gene expression module test to predict resistance to cetuximab in colorectal cancers independent of KRAS mutation status

e14164

Background: While KRAS mutation predicts resistance to anti-EGFR therapy in colorectal cancer, not all KRAS wild-type patients benefit from such therapy, suggesting that complementary biomarkers capable of identifying additional non-responsive patients would have clinical utility. Methods: To search for such a biomarker, we studied the relationship of cetuximab response with twelve gene expression modules, derived from an unsupervised analysis of 20 independent microarray datasets comprising more than 2,000 colorectal cancer patients. Each module represents a set of highly co-expressed genes related to an important aspect of colorectal cancer variability. Two cetuximab-treated cohorts were studied. The first was a Phase II clinical trial (Khambata-Ford et al, J Clin Oncol, 2007) with accompanying microarray data from pre-treatment biopsies. The second was a single-institution study of cetuximab response from which formalin-fixed paraffin-embedded primary tumor specimens were available. Results: In the first study, module scores were computed by averaging co-expressed module genes in the microarray data. In the second study, module scores were generated from a qPCR gene expression module test, OncoScore Colon, which quantifies modules by averaging three representative module genes relative to housekeeping controls. Notably, in both studies, the mesenchymal module was significantly associated with cetuximab resistance, with module positive patients tending to progress on cetuximab within 10 weeks. Additionally, the status of this module was independent of KRAS mutation status—KRAS mutations occurred in both module-positive and -negative patients. Future clinical studies will continue to test the predictive capacity of the module in regards to cetuximab resistance and other mechanisms. Conclusions: In summary, this study demonstrates the value of a gene expression module-based qPCR panel for stratifying colorectal cancer patients for treatment response, and suggests that our approach may have immediate utility for cetuximab treatment response prediction.

Next-generation sequencing mutational analysis of triple-negative breast cancer patients from matched FFPE and fresh frozen samples

1058

Background: TNBC is an aggressive subtype of breast cancer accounting for 10-15% of all cases. TNBC tumors (ER-/PR-/HER-) are more common in patients with BRCA mutations. BRCA mutations leading to homologous DNA repair deficient tumors enhance the efficacy of chemotherapy and PARP inhibitors. BRCA mutations have been identified in 20% of patients without family history. Identification of germline and somatic BRCA mutations in unselected patients could increase the number of patients who benefit from these therapies. Determining BRCA mutational status from FFPE and fresh frozen specimens may enable clinical studies in these patient populations.We describe the development of an NGS BRCA mutational assay compatible with FFPE and fresh frozen samples using tumor/adjacent normal matched tissues. Methods: Matched samples were purchased from Cureline. gDNA was isolated by lysis/column purification (Qiagen) and enriched for BRCA exons/flanking regions (Halogenomics Selector). Fragment libraries were constructed (Ion Torrent frag express) and prepared for sequencing by emPCR (Ion Torrent Template Xpress). Libraries were sequenced for 65 cycles (Ion Torrent PGM) yielding 2-4M reads/sample. Variants were called from tMAP aligned reads by GATK and VarScan. Overlapped exonic variants were filtered by p-value (<0.0001) from VarScan. Results: In the first patient set normalized average depth of BRCA exon coverage was 64X and 72X per 150K reads in FFPE and fresh frozen tissues respectively covering 95-100% of target. hg19 alignment rates varied between 97-99% across all samples. Similar numbers of variants were called in both FFPE (12) vs. fresh frozen (13) with a corresponding mean duplicate removed depth of coverage of 23.3X and 42.4X at the called positions. 10/13 calls in fresh frozen overlapped with those in FFPE. A tumor specific somatic frameshift insertion in BRCA2 was detected in both FFPE and fresh frozen tissues. Conclusions: Results indicate that NGS mediated BRCA mutational analysis demonstrates equivalent utility in both FFPE and fresh frozen tumor samples although more sequencing reads are required to produce equivalent depth of coverage starting from FFPE samples.

Abstract A19: A qPCR assay, OncoScore Colon, predicts resistance to cetuximab in formalin-fixed, paraffin-embedded colorectal cancer tissue independent of KRAS status

Gene expression modules derived from an unsupervised analysis of 20 independent microarray datasets comprising more than 2,000 colorectal cancer patients were identified. Each module represents a set of highly co-expressed genes related to an important aspect of underlying cancer variability. Modules containing genes related to epithelial and mesenchymal biology associated with sensitivity and resistance to EGFR family targeted inhibitors (gefitinib and lapatinib), respectively. In retrospective analysis of clinical samples, the epithelial-mesenchymal axis associated with cetuximab response in two independent patient cohorts. The first study was a Phase II clinical trial (Khambata-Ford et al., J Clin Oncol, 2007) with accompanying microarray data from pre-treatment metastatic colorectal tumor biopsies. Expression of the modules was determined by normalizing and averaging co-expressed module genes. Patients with a more epithelial and less mesenchymal module expression profile were enriched for cetuximab response. An independent cohort of patients was analyzed using module scores that were generated from a qPCR gene expression module test, OncoScore™ Colon, which quantifies modules by averaging three representative module genes relative to housekeeping genes using formalin-fixed-paraffin-embedded primary tumor samples. In these patients, presence of the mesenchymal module was significantly associated with a decrease in progression free survival. Notably, the status of the mesenchymal module was independent of KRAS mutation status—as KRAS mutations occurred in both mesenchymal module-positive and -negative patients. Further clinical studies are ongoing to continue to support the development of the OncoScore™ Colon assay and to further test the predictive capacity of the module with regards to cetuximab resistance and other MAPK pathway inhibitors. This study demonstrates the value of a gene expression module-based qPCR panel for stratifying colorectal cancer patients for treatment response, and suggests that our approach may have immediate utility for cetuximab treatment response prediction.

Abstract 3664: Breast cancer companion diagnostic platform based on objectively defined tumor co-expression patterns stratifies multiple clinical and therapeutic endpoints comparison to existing molecular subtyping definitions

Gene expression profiles of human breast tumors have greatly expanded our understanding of the genes and pathways that underlie breast cancer. Profiling studies have also supported a molecular classification of breast cancer. The resulting molecular subtypes Luminal, Basal-like, ERBB2+, and Normal-like were shown to have different prognostic and predictive characteristics. Related studies have led to a proliferation of multigene prognostic and predictive diagnostic tests. Two independent multigene tests, OncoType Dx and MammaPrint, have been shown to be helpful in predicting the risk of recurrence of patients with early stage breast cancer. Current multigene tests consistently prioritize the proliferation, estrogen receptor (ER), and ERBB2 pathways. An alternative approach to identifying key molecular variables within breast cancer is based on a definition of objectively defined tumor co-expression patterns. To this end, we defined co-expression patterns within 56 independent breast cancer molecular profiling datasets representing &gt;5,000 unique patients. We then performed a meta-analysis across datasets to define the most robust, consistently occurring co-expression patterns. These patterns, termed modules, recapitulate the proliferation, ER, and ERBB2 pathways, but also monitor expression of other important variables including core cancer cell growth pathways, immune signaling and microenvironment, and hallmark genomic aberrations. An important feature of co-expression patterns is that a small number of genes serve as an effective surrogate for each module. Thus, we created a single multigene qPCR test that measures the expression of 18 distinct breast cancer modules and validated the test for use with formalin-fixed paraffin-embedded (FFPE) tumor samples. In retrospective microarray scoring analyses with key clinical datasets, and with analysis of FFPE specimens from breast cancer cohorts, we demonstrate that breast cancer modules can be used to recapitulate the molecular subtypes of breast cancer and to have prognostic and predictive properties similar to the current multigene tests. Because they recapitulate existing molecular tests, while also reading out many additional axes of molecular variability, breast cancer modules provide a universal assay with broad application to companion diagnostics development.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3664. doi:1538-7445.AM2012-3664

Abstract 3665: An EMT gene expression diagnostic predicts resistance to EGFR and MEK-targeted therapies in cell lines and patients

The epithelial to mesenchymal transition (EMT) in cancer cells results in the acquisition of metastatic properties and may contribute to chemoresistance. Several studies have shown that transition to a mesenchymal phenotype leads to decreased dependence on EGFR-RAS signaling and insensitivity to EGFR inhibitors. To better understand the importance of EMT as a general predictor of drug response, we defined an EMT gene signature derived from a meta-analysis of differential gene expression signatures representing genes up-regulated following transfection of breast cell lines with various EMT regulators (Taube et al., 2010 Proc Natl Acad Sci USA 107:15449-54). We then determined the expression of the EMT signature across cell line panels and determined whether it predicted sensitivity or resistance to various targeted therapies. Consistent with previous results, expression of EMT signature was significantly associated with resistance to an EGFR inhibitor, lapatinib. Similarly, the EMT signature also predicted resistance to PQIP (IGF1R), GSK1120212 (MEK), GSK690693 (AKT), and perifosine (AKT/PI3K), suggesting that EMT may be a common resistance mechanism to a number of drugs that target growth factor signaling. As more of these targeted agents are entering clinical trials, the ability to characterize the signature may have important implications for drug development. To study the relevance of the EMT signature in clinical tumors, we compared the signature to a collection of tumor co-expression patterns, known as OncoScore modules, which were defined from 40,000+ tumor microarray experiments. Notably, the EMT signature was significantly associated with a major tumor co-expression pattern representing mesenchymal and/or stromal phenotype observed in almost all major solid tumor types. In retrospective microarray scoring analyses of key clinical datasets, the mesenchymal/stromal module predicted resistance to cetuximab. This finding was validated with an independent cohort of colorectal cancer patients treated with cetuximab using the Oncoscore Colon diagnostic. Oncoscore Colon is a qPCR test optimized for formalin-fixed paraffin-embedded tissue that measures the twelve key colon cancer transcriptional modules, including the mesenchymal module. Because the mesenchymal/stromal module monitors a fundamental phenotype of cancer cells important for drug response, this validated qPCR test has broad application to companion diagnostics development and personalized medicine.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3665. doi:1538-7445.AM2012-3665

Microsatellite analysis as a tool for discriminating an interfamily hybrid between olive flounder and starry flounder

An interspecific artificial hybrid was produced between two economically important aquaculture flatfish: olive flounder (Paralichthys olivaceus) and starry flounder (P. stellatus). This hybrid displays the rapid growth characteristic of the former and tolerance to low temperatures and low salinity of the latter, but the genetics of inheritance in this hybrid have not been elucidated. Polymorphic microsatellite markers developed for P. olivaceus and P. stellatus were tested to determine if these markers can be used for analysis of parentage and genetic inheritance. Multiplex PCR using two primer sets that were specific to each species produced PCR products of different sizes; these could be used for the identification of interspecific hybrids. Among the 192 primers derived from olive flounder, 25.5% of the primer sets successfully amplified genomic DNA from starry flounder, and 23% of the 56 primer sets originating from starry flounder amplified DNA from olive flounder. Analysis of genetic inheritance in the hybrid using seven of the 62 microsatellite markers common to both species demonstrated classic Mendelian inheritance of these markers in the hybrid progeny, with the exception of one locus identified as a null allele in the hybrid. These results demonstrate that cross-specific microsatellite markers can be used tools for parentage analysis of hybrid flatfish, for mapping quantitative trait loci, for marker-assisted selective breeding, and for studies of the evolution of fish.

Cognitive and behavioral effects of lamotrigine and carbamazepine monotherapy in patients with newly diagnosed or untreated partial epilepsy

PURPOSE

In this prospective study, we compared the long-term cognitive and behavioral effects of lamotrigine (LTG) and carbamazepine (CBZ) in patients with newly diagnosed or untreated partial epilepsy.

METHODS

This was a multicenter, open-label, randomized study that compared monotherapy with LTG and CBZ in newly diagnosed or untreated patients with partial epilepsy. We employed an 8-week titration period and a 40-week maintenance period. Neuropsychological tests, Symptom Check List-90, and QOLIE-31 were assessed at baseline, 16 weeks, and 48 weeks after drug treatment. A group-by-time interaction was the primary outcome measure and was analyzed by use of the linear mixed model.

RESULTS

A total of 110 patients were eligible and 73 completed the 48-week study (LTG, n=39; CBZ, n=34). Among the cognitive tests, significant group-by-time interaction was identified only in phonemic fluency of Controlled Oral Word Association Task (p=0.0032) and Stroop Color-Word Interference (p=0.0283), with a significant better performance for LTG group. All other neuropsychological tests included did not show significant group-by-time interactions. Among the subscales of Symptom Check List-90, significant group-by-time interactions were identified in Obsessive-Compulsive (p=0.0005), Paranoid Ideation (p=0.0454), Global Severity Index (p=0.0194), and Positive Symptom Total (p=0.0197), with a significant improvement for CBZ group. QOLIE-31 did not show significant group-by-time interactions.

CONCLUSION

Our data suggest that epilepsy patients on LTG have better performance on phonemic fluency and the task of Stroop Color-Word Interference than do patients on CBZ, whereas patients on CBZ had more favorable behavioral effects on two subscales and two global scores of Symptom Check List-90 than did patients on LTG.

Inhibition of apoptosis signal-regulating kinase 1 reduces endoplasmic reticulum stress and nuclear huntingtin fragments in a mouse model of Huntington disease

Huntington's disease (HD) is characterized clinically by chorea, psychiatric disturbances, and dementia, while it is characterized pathologically by neuronal inclusions as well as striatal and cortical neurodegeneration. The neurodegeneration arises from the loss of long projection neurons in the cortex and striatum. In this study, we investigated the role of apoptosis signal-regulating kinase 1 (Ask1) in the pathogenesis of HD. We analyzed the expression of Ask1 and huntingtin (htt) within the striatum and cortex and also examined the interaction of Ask1 with htt fragments in HD (R6/2) mice. Additionally, we inhibited Ask1 and analyzed the resulting changes in brain-derived neurotrophic factor (BDNF) expression, motor function, and striatal atrophy. Ask1 activity was blocked using an Ask1 antibody raised against the C-terminus of the Ask1 protein. The anti-Ask1 antibody was infused into the striatum of the HD mice for four weeks using a micro-osmotic pump. The levels of Ask1 protein and endoplasmic reticulum (ER) stress were increased in HD mice. Binding of inactivated Ask1 to htt fragments was more prevalent in the cytosol than the nucleus of cortical neurons. Binding of inactivated Ask1 to htt fragments prevented translocation of the htt fragments into the nucleus, resulting in an improvement in motor dysfunction and atrophy. In the normal state, active Ask1 may help htt fragments enter the nucleus, while inactivated Ask1 hinders this translocation by binding to but not releasing fragmented htt into the nucleus. We propose that Ask1 may interact with htt fragments and subsequently induce ER stress. BDNF depletion may be prevented by targeting Ask1; this would decrease ER stress and possibly ameliorate behavioral or anatomical abnormalities that accompany HD. Therefore, regulating the amounts and activity of the Ask1 protein is a novel strategy for treatment of HD.

Balloon cells and dysmorphic neurons in the hippocampus associated with epileptic amnesic syndrome: a case report

Recently, we encountered a 39-year-old woman with typical epileptic amnesic syndrome. The patient underwent right anterior temporal lobectomy, which removed the right hippocampus. The patient's resected hippocampus showed typical histological features of Ammon's horn sclerosis (AHS) with dysmorphic neurons. In addition, the prominent balloon cells, admixed with dysmorphic neurons, were noted in the hippocampus. To our knowledge, this is the first reported case showing AHS with balloon cells. The presence of balloon cells reinforces the hypothesis that AHS itself might be a maldevelopment disorder.

Long-term cognitive and mood effects of zonisamide monotherapy in epilepsy patients

This study was a prospective, randomized, open-label investigation of the long-term effects of zonisamide (ZNS) monotherapy on cognition and mood of patients with epilepsy. Forty-three patients with epilepsy received ZNS, with final dose groups of 100, 200, 300, and 400mg/day. Cognitive and mood tests were done twice, at baseline and 1 year after starting medication. Nine patients were withdrawn prior to their follow-up tests. Three patients (33%) dropped out during the titration period because of cognitive and mood problems. Thirty-four patients completed follow-up neuropsychological tests. After 1 year of treatment, 16 patients (47%) complained of cognitive deficits. Only 5 patients (15%) experienced mood changes. Although ZNS decreased seizure frequency and EEG abnormalities and did not elicit significant mood changes, it had negative effects on several cognitive tests. Worse performance on delayed word recall, Trail Making Test Part B, and verbal fluency was related to dose. In conclusion, ZNS has adverse effects on cognition even after 1 year of treatment.

Lamotrigine extended-release as adjunctive therapy for partial seizures

OBJECTIVE

To evaluate the efficacy and tolerability of once-daily adjunctive lamotrigine extended-release (XR) for partial seizures in epilepsy.

METHODS

Patients more than 12 years old diagnosed with epilepsy with partial seizures and taking one to two baseline antiepileptic drugs were randomized to adjunctive once-daily lamotrigine XR or placebo in a double-blind, parallel-group trial. The study comprised a baseline phase, a 7-week double-blind escalation phase, and a 12-week double-blind maintenance phase during which doses of study medication and concomitant antiepileptic drugs were maintained.

RESULTS

Of the 243 randomized patients, 239 (118 lamotrigine XR, 121 placebo) entered the escalation phase and received study medication. Lamotrigine XR was more effective than placebo with respect to median percent reduction from baseline in weekly partial seizure frequency (primary endpoint-entire 19-week treatment phase: 46.6% vs 24.5%, p = 0.0001 [corrected] via Wilcoxon test; escalation phase: 29.8% vs 15.6%, p = 0.027; maintenance phase: 58.4% vs 26.8%, p [corrected] < 0.0001). The percentage of patients with >or=50% reduction in partial seizure frequency (44.0% vs 20.8%, p = 0.0002) [corrected] and time to >or=50% reduction in partial seizure frequency (p = 0.0001) [corrected] also favored lamotrigine XR over placebo. A similar pattern of results was observed for secondarily generalized seizures. The most common adverse events were headache (lamotrigine XR 16%, placebo 18%) [corrected] and dizziness (lamotrigine XR 19%, [corrected] placebo 5%). Differences between lamotrigine XR and placebo on health outcomes measures were not significant.

CONCLUSIONS

Once-daily adjunctive lamotrigine extended-release compared with placebo effectively reduced partial seizure frequency and was well tolerated in this double-blind study. Results support the clinical utility of this new once-daily formulation.

Diffusion PDE-based denoising technique for magnetic resonance electrical impedance tomography

Recent progress in magnetic resonance electrical impedance tomography (MREIT) research has shown that conductivity images with higher spatial resolution and accuracy are achievable. One of the most important remaining problems to be solved in MREIT before we can apply the technique to human subjects is how to reduce the amount of injection current. Since we use an MRI scanner to measure the induced magnetic flux density data subject to an injection current, the data is contaminated with random noise. In order to obtain enough signal-to-noise ratio (SNR), we need to inject a large amount of current into the subject. However, it is obvious that we must comply with the electrical safety regulations and this means that we should deal with noisy data having a low SNR due to the limited amount of injection current. Furthermore, in the developed reconstruction algorithms, the required numerical differentiations of the noisy data may result in deterioration of the reconstructed conductivity image leading to a loss of important information. We propose a PDE-based denoising technique that diminishes the degradation of reconstructed conductivity images due to the noise in measured data. The proposed PDE-based technique is advantageous in reducing the random noise while preserving useful features in MREIT.

Conductivity images of biological tissue phantoms using a 3.0 tesla MREIT system

We present cross-sectional conductivity images of a biological tissue phantom obtained by using a 3.0 Tesla magnetic resonance electrical impedance tomography (MREIT) system. Inside the cylindrical phantom with 140 mm diameter and 140 mm height, biological tissues such as bovine tongue and liver, porcine muscle, and chicken breast were placed within an agar gelatin. Injecting current of 480 mA.ms into the tissue phantom, we measured the z-component B/sub z/ of the induced magnetic flux density B=(B/sub x/, B/sub y/, B/sub z/). Using the harmonic B/sub z/ algorithm, we reconstructed cross-sectional conductivity images from the measured B/sub z/ data. Reconstructed images clearly distinguish different tissues in terms of both their shapes and conductivity values.

Reliability and Validity of the Korean Version of QOLIE-10 in Epilepsy

Background and Purpose

It is necessary in clinical practice to screen patients with epilepsy for quality-of-life factors. The purpose of this study was to develop a Korean version of the Quality of Life in Epilepsy (QOLIE)-10 survey and to determine its reliability and validity.

Methods

Data were collected from 397 adult epilepsy patients. The ten items of QOLIE-10 were derived from the Korean version of QOLIE-31. We assessed factor analysis, internal consistency, test-retest reliabilities, construct validity, and discriminant validity. Test-retest was performed in 97 patients.

Results

The ten items of QOLIE-10 were grouped into two factors: epilepsy effects/role function (driving, social, work, physical effect, mental effect, and memory) and mental health (overall quality of life, depression, and energy). The internal consistency reliability coefficient (Cronbach's α) was 0.843 for epilepsy effects/role function and 0.606 for the mental-health scale. Test - retest data revealed statistically significant correlations for individual items (range, r=0.66-0.38) and scales (range, r=0.63-0.48), except for one item, driving (r=0.21, p=0.133). QOLIE-10 was significantly correlated with the source scales in the Korean version of QOLIE-31 and with several external measures. The QOLIE-10 scores discriminated between patient groups according to their seizure severity and level of education.

Conclusions

QOLIE-10 was derived from the Korean version of QOLIE-31. The results of this study show that QOLIE-10 can be applied as a screening measure of quality of life in Korean epilepsy patients.

Association of aortic plaque with intracranial atherosclerosis in patients with stroke

OBJECTIVE

To determine whether there is a relationship between aortic plaques and intracranial (IC) atherosclerosis.

METHODS

We reviewed 922 patients with stroke who had both transesophageal echocardiography and cerebral angiography. The plaques of these patients were classified as either complex aortic plaques (CAP), which protruded > or =4 mm or were present as mobile lesions in the proximal aorta, or simple aortic plaques (SAP), which were <4 mm or present in the descending aorta. Cerebral artery atherosclerosis was classified as either an IC or extracranial (EC) atherosclerosis.

RESULTS

Among the 922 patients, we found aortic plaques in 237 patients (26%). There were 111 (47%) patients of SAP, 74 (31%) patients with CAP, and 52 (22%) patients that had both SAP and CAP. Angiography showed IC or EC atherosclerosis in 511 patients (55%). The presence of aortic plaques was significantly associated with IC or EC atherosclerosis. The significance appeared to be due to the strong association between the presence of SAP and IC atherosclerosis (51% SAP vs 35% no plaques; odds ratio = 1.94, 95% CI: 1.17 to 3.21). In the multiple logistic regression analysis, SAP were independent predictors of IC atherosclerosis

CONCLUSIONS

The presence of simple aortic plaques may be a marker of advanced vascular disease. Detection of simple aortic plaques during transesophageal echocardiography may have clinical implications because patients with these plaques frequently had concomitant intracranial atherosclerosis, a risk factor for stroke.

Physical phantom of typical Korean male for radiation protection purpose

Dose distribution within a human body can be measured using physical anthropomorphic phantoms. In an effort to establish reference Korean physical model, the first Korean physical phantom of average Korean adult male was constructed using computed tomography (CT) images of a healthy volunteer. The body dimension of the subject was close to that of average Korean male. The source images were obtained using fusion positron emission tomography machine at Radiation Health Research Institute in Korea, and ported into rapid prototyping process. The physical phantom was composed of three tissue-equivalent materials: epoxy resin, urethane foam and polyurethane representing bone, lungs and soft tissues, respectively. The densities of the tissue-equivalent materials were close to those recommended by the International Commission on Radiation Units and measurements. To facilitate dose mapping, the phantom was sliced into 2 cm sections. Hole grids for thermoluminescence (TL) dosemeter chips were drilled. To verify the appropriateness of the physical phantom, organ doses of selected organs were measured for reference photon beam, and compared with those computed by tomographic model constructed from the same CT images. Absorbed doses converted from TL relative response showed good agreement within 7% with those calculated.

Factors contributing to the stigma of epilepsy

PURPOSE

To evaluate the factors, including personality and coping styles, likely to be influential in enhancing the social stigma of epilepsy.

METHODS

Data were collected from 400 adults with epilepsy recruited from 10 epilepsy centers in Korea. Clinical information about seizures was obtained by neurologists, and other information was collected from self-completed questionnaires, including those measuring stigma scales.

RESULTS

Thirty-one percent of people with epilepsy felt stigmatized by their condition and in 9% of these the stigma was severe. Multivariate analysis identified experiences of actual discrimination from society, introverted personality, problem solving controllability, and emotional subscale of QOLIE-31 as being independently associated with the social stigma of epilepsy.

CONCLUSIONS

Episodes of discrimination, coping strategies, and personality may be important in feeling the stigma of epilepsy. These findings may provide a basis for further studies to clarify the causative factors generating the stigma of epilepsy.

Endoscopic disconnection for hypothalamic hamartoma with intractable seizure. Report of four cases

Although intractable epilepsy associated with hypothalamic hamartoma (HH) can be controlled by microsurgical resection of the lesion, excision of deep-seated lesions is often associated with morbidity and mortality. Endoscopic disconnection is less invasive and seems to be well suited for this indication. The authors discuss the role of endoscopic-assisted surgery in the management of HH-induced seizures. Four patients with HH-related intractable gelastic seizure underwent endoscopic disconnection surgery. Postoperatively, all patients exhibited improvement. Two patients became seizure free immediately after endoscopic disconnection surgery, one patient with a widespread seizure focus involving the motor strip continued to experience rare complex partial seizures but gelastic seizures ceased, and one experienced a reduced frequency of seizures but persistence of some generalized seizures. Three patients suffered postoperative disconnection-like syndrome, which continued 3 to 7 days and spontaneously disappeared. The authors advocate the endoscopic disconnection surgery as a safe and effective treatment for HH-related epilepsy by blocking the spread of epileptic discharges from the lesion.

Significance of chronic epilepsy in glial tumors and correlation with surgical strategies

PURPOSE

This study was designed to compare the frequency of postoperative epilepsy in patients with acute and chronic pre-operative epilepsy and with frontal or temporal lobe glial tumors based on the hypothesis that patients with chronic epilepsy do worse.

METHODS

We compared the clinical and diagnostic characteristics of the patients (n = 73) who had seizures preoperatively with those of the patients (n = 153) who did not. Among those who have had seizures preoperatively, we compared those (n = 32, chronic seizure group) who had seizures a year or more prior to surgery with those (n = 41, acute seizure group) who had seizures less than a year prior to surgery.

RESULTS

Among the various factors, the frequency of benign pathology and favorable neurological state were higher in the seizure group than in the non-seizure group (p < 0.05). Complex partial seizures and low-grade tumors were frequent in the chronic seizure group, whereas simple partial seizures and high-grade tumors were frequent in the acute seizure group. Seizure-free rate was significantly higher in the acute seizure group than in the chronic group (p < 0.05). Also, the difference of seizure control rate between surgical strategies was statistically significant (p < 0.05).

CONCLUSION

This study indicates that preoperative seizure duration and frequency have a close relationship with the frequency of postoperative epilepsy in patients with glial tumors. A longer duration may allow the formation of epileptogenic foci, leading to chronic epilepsy, and eventually have a negative effect on the prognosis of the patients. Factors including histopathological characteristics of the tumor, its location, seizure duration/frequency, and symptomatology should be taken into account when deciding on surgical strategies.

The surgical effect of callosotomy in the treatment of intractable seizure

We evaluated the surgical effects of the callosotomy, particularly with respect to the effect of callosotomy in some seizure types and the extent of surgery. Twenty-one patients with a minimum follow-up of two year were enrolled. The most significant effect of callosotomy was the complete suppression of the generalized seizures associated with drop attack in 12 of 21 patients and seizure reduction of more than 75% in 6 of 21 patients. The surgical effect on the partial seizures was very variable. Transient disconnection syndrome appeared in 4 patients after anterior callosotomy. Total callosotomy by staged operation significantly suppressed generalized seizures associated with drop attack without any disconnection syndrome. Our data show that callosotomy is quite a good approach to the surgical treatment of drop attacks accompanied by disabling generalized seizures.

The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biology

The TB Structural Genomics Consortium is an organization devoted to encouraging, coordinating, and facilitating the determination and analysis of structures of proteins from Mycobacterium tuberculosis. The Consortium members hope to work together with other M. tuberculosis researchers to identify M. tuberculosis proteins for which structural information could provide important biological information, to analyze and interpret structures of M. tuberculosis proteins, and to work collaboratively to test ideas about M. tuberculosis protein function that are suggested by structure or related to structural information. This review describes the TB Structural Genomics Consortium and some of the proteins for which the Consortium is in the progress of determining three-dimensional structures.

Thyrotoxic autoimmune encephalopathy: a repeat positron emission tomography study

Thyroid related autoantibodies have been related to the development of encephalopathy, known as Hashimoto's encephalopathy. However, their relation with the encephalopathy occurring in patients with Graves' disease has not been well established. The case is reported of a 51 year old woman presenting with subacute progressive dementia with evidence of hyperthyroidism. She had Graves' disease associated with high titres of thyroid related autoantibodies. Her encephalopathy was not improved by antithyroid drugs, but promptly responded to corticosteroid treatment, and stabilised with a gradual reduction of thyroid related autoantibody titres. Brain positron emission tomography initially showed a diffuse and multifocal cerebral hypometabolism with subsequent normalisation on her clinical recovery, which was consistent with the acute and reversible cerebral inflammation probably mediated by autoimmune mechanisms.

Characterization of calcium binding properties of lithostathine

The pancreas secretes primarily two types of metabolically important proteins: digestive enzymes and hormones. Lithostathine (LIT) is the only protein excreted from the pancreas that has no known digestive or hormonal activity. Human lithostathine is a 144-amino acid glycoprotein synthesized by the exocrine pancreas that has been implicated in various physiological functions, including inhibition of pancreatic stone formation. To better understand the physiological function of LIT, we expressed the recombinant LIT protein in Escherichia coli and measured its calcium binding properties by equilibrium dialysis and electron paramagnetic resonance (EPR) spectroscopy. Equilibrium dialysis with (45)Ca(2+) showed that LIT binds Ca(2+) with 1:1 stoichiometry. EPR studies using the divalent vanadyl (VO(2+)) ion as a paramagnetic substitute for Ca(2+) also showed that VO(2+) binds to LIT with a metal:protein binding stoichiometry of 1:1 and that VO(2+) competes with Ca(2+) in binding to LIT. Mutations of a cluster of acidic residues on the molecular surface (E30A, D31A, E33A, D37A, D72A, and D73A) resulted in almost complete loss (95-100%) of binding of Ca(2+) and VO(2+), showing that these residues are critical for calcium binding by LIT.

The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.

Yonsei Stroke Registry. Analysis of 1,000 patients with acute cerebral infarctions

BACKGROUND AND PURPOSE

The hospital-based stroke registry is a well-established method useful for understanding diverse clinical characteristics of stroke related to geographical, racial or environmental differences. We analyzed the data from 1,000 patients with acute cerebral infarctions registered with the Yonsei Stroke Registry (YSR) which is the first prospective hospital-based observational study in Korea.

METHODS

All patients had cerebral infarctions and presented within 7 days of onset. CT or MRI was performed in all patients and a vascular imaging study (digital subtraction or magnetic resonance angiography) was conducted in 53.9% of the patients. Subtype classification was made through a consensus approach based on the strict application of TOAST criteria.

RESULTS

The mean age of patients was 62 +/- 12 years, and 60.8% were males. Undetermined cause (UD) was the most frequent subtype (40.6%), which was followed by lacunar stroke (LS 21.5%), cardiac embolism (CE 18.3%), large-artery atherosclerosis (LAA 16.5%) and other determined causes (3.1%). Hypertension was found in 64.3%, smoking in 35.2%, diabetes mellitus in 26.9%, hypercholesterolemia in 24.1%, high hematocrit (> or = 50%) in 21.8%, clinically identified potential cardiac sources of embolism in 18.3%, a history of previous stroke in 22.0% and a history of previous transient ischemic attack in 4.7%. Recurrent stroke was associated with a higher number of risk factors (p < 0.001) and a higher incidence of LAA (p = 0.003) than the first stroke. Vertebrobasilar artery territorial infarction was found in 39.8%, which was associated with higher incidences of LAA and LS and a lower incidence of CE than carotid artery territorial lesions (p = 0.001). The 30-day mortality rate was 5.3% and cerebral herniation caused early death in 52%.

CONCLUSION

The distribution of stroke subtypes in the YSR was largely comparable with that of western registries. The highest incidence of UD might be related to the strict application of TOAST criteria.

Bcl-2 blocks cisplatin-induced apoptosis by suppression of ERK-mediated p53 accumulation in B104 cells

Bcl-2 has been reported to inhibit neurotoxicity induced by cisplatin. However, neither the mechanism of cisplatin-induced neurotoxicity nor the mechanism by which Bcl-2 confers neuroprotection is clear. In this study, the signaling pathways involved in cisplatin-induced neurotoxicity were examined using a rat neuroblastoma cell line, B104. Treatment of B104 cells with cisplatin induced apoptosis, accompanying the accumulation of p53 and Bax protein. Interestingly, extracellular signal-regulated kinase 1/2 (ERK1/2) activities of MAP kinases were markedly enhanced prior to cisplatin-induced accumulation of p53 and Bax. Inhibition of ERK1/2 activities using PD98059, a selective MEK inhibitor, blocked the apoptotic cell death preventing cisplatin-induced accumulation of p53 and Bax. These results suggest that ERK mediates cisplatin-induced p53 activation to trigger apoptosis in B104 cells. Overexpression of Bcl-2 in B104 cells resulted in the complete resistance to cisplatin-induced apoptosis blocking ERK activation and the subsequent signaling pathway of p53. Our study clearly demonstrates that the action site of Bcl-2 localizes upstream of ERK in cisplatin-induced apoptotic signaling pathway.

Crystallization and preliminary X-ray crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Saccharomyces cerevisiae

Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) from Saccharomyces cerevisiae is essential for cell viability. It has been overexpressed in Escherichia coli and has been crystallized at 296 K using polyethylene glycol (PEG) 1500 as a precipitant. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 59.48, b = 138.54, c = 157.91 A, alpha = beta = gamma = 90 degrees. Two molecules of trimeric dUTPase from S. cerevisiae are present in the asymmetric unit, giving a crystal volume per protein mass (V(M)) of 3.36 A(3) Da(-1) and a solvent content of 63%. The diffraction limit of the crystals could be significantly extended by the crystal-annealing procedure. A set of native data extending to 2.7 A resolution has been collected at 100 K using synchrotron X-rays.

Ictal automatisms with preserved responsiveness in a patient with left mesial temporal lobe epilepsy

PURPOSE

To describe the possible mechanism of ictal automatisms with preserved responsiveness (APRs) in a patient with left mesial temporal lobe epilepsy, which had not been reported previously.

METHODS

Ictal EEGs recorded from bilateral foramen ovale electrodes with scalp-sphenoidal electrodes were analyzed in respect to the ictal semiology.

RESULTS

The patient had a right hemispheric language dominance in the dextral. Electroclinical analysis revealed that the onset of oroalimentary automatisms coincided with the involvement of the left mesial and lateral temporal structures by spreading ictal discharges. The ictal discharge spreading was limited to the ipsilateral hemisphere throughout the seizure, which explained the intact consciousness and preserved responsiveness of the patient.

CONCLUSIONS

This case suggests that APRs take place in seizures originating from the nondominant temporal lobe, during which ipsilateral mesial and lateral temporal structures are diffusely involved without spreading to the contralateral side.

Crystal structure of the MJ0490 gene product of the hyperthermophilic archaebacterium Methanococcus jannaschii, a novel member of the lactate/malate family of dehydrogenases

The MJ0490 gene, one of the only two genes of Methanococcus jannaschii showing sequence similarity to the lactate/malate family of dehydrogenases, was classified initially as coding for a putative l-lactate dehydrogenase (LDH). It has been re-classified as a malate dehydrogenase (MDH) gene, because it shows significant sequence similarity to MT0188, MDH II from Methanobacterium thermoautotrophicum strain DeltaH. The three-dimensional structure of its gene product has been determined in two crystal forms: a "dimeric" structure in the orthorhombic crystal at 1.9 A resolution and a "tetrameric" structure in the tetragonal crystal at 2.8 A. These structures share a similar subunit fold with other LDHs and MDHs. The tetrameric structure resembles typical tetrameric LDHs. The dimeric structure is equivalent to the P-dimer of tetrameric LDHs, unlike dimeric MDHs, which correspond to the Q-dimer. The structure reveals that the cofactor NADP(H) is bound at the active site, despite the fact that it was not intentionally added during protein purification and crystallization. The preference of NADP(H) over NAD(H) has been supported by activity assays. The cofactor preference is explained by the presence of a glycine residue in the cofactor binding pocket (Gly33), which replaces a conserved aspartate (or glutamate) residue in other NAD-dependent LDHs or MDHs. Preference for NADP(H) is contributed by hydrogen bonds between the oxygen atoms of the monophosphate group and the ribose sugar of adenosine in NADP(H) and the side-chains of Ser9, Arg34, His36, and Ser37. The MDH activity of MJ0490 is made possible by Arg86, which is conserved in MDHs but not in LDHs. The enzymatic assay showed that the MJ0490 protein possesses the fructose-1,6-bisphosphate-activated LDH activity (reduction). Thus the MJ0490 gene product appears to be a novel member of the lactate/malate dehydrogenase family, displaying an LDH scaffold and exhibiting a relaxed substrate and cofactor specificities in NADP(H) and NAD(H)-dependent malate and lactate dehydrogenase reactions.

Enhanced detection of right-to-left shunt through patent foramen ovale by transthoracic contrast echocardiography using harmonic imaging

When the results of transesophageal echocardiography was regarded as the gold standard for detecting a patent foramen ovale (PFO) in 136 consecutive patients referred for evaluation of cardiac source of embolism, transthoracic harmonic imaging using saline contrast was superior to fundamental imaging in accuracy for detecting a PFO (sensitivity, 22.5%; specificity [p < 0.05] and sensitivity, 100%; specificity 100%, respectively.)

Diffusion-weighted image and MR spectroscopic analysis of a case of MELAS with repeated attacks

We report the clinical and MR manifestations of an 18 year-old girl with mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome. Recurrent status epilepticus caused reversible cytotoxic edema on diffusion-weighted images (DWI). Initial and one month follow-up MR spectroscopy, after seizure control, showed some discrepancies in the ratio of metabolites. N-acetylaspartate (NAA) partially recovered (NAA/creatine (Cr) ratio: 1.27-->1.84). This was because of a normalization of decreased NAA due to cellular dysfunction as a result of status epilepticus. A low ratio of NAA/Cr due to abnormal mitochondria remained in the decreased state. Reversible NAA/Cr ratios in the acute lesion suggested that NAA reflects the neuronal function as well as the level of neuronal structural damage. The altered NAA/Cr ratio better correlated with the abnormal signal intensity area of T2-weighted images (T2WI) and DWI than the lactate (Lac)/Cr ratio. With conservative treatment with anti-epileptics not accompanied by coenzyme Q or sodium dichloroacetate, lactate persistently increased (Lac/Cr ratio: 1.01-->1.21) because of the continued production of lactate in cells with respiratory deficiency, which is the main pathology of MELAS.

Radionuclide cisternography in spontaneous intracranial hypotension with simultaneous leaks at the cervicothoracic and lumbar levels

This case report clearly illustrates defined simultaneous cerebrospinal fluid leaks at the cervicothoracic and upper lumbar areas. A 53-year-old woman without a remarkable medical history was hospitalized for sudden onset of severe headache. The headache lasted more than 1 week and standing or sitting positions exaggerated the symptoms, although it was relieved when the patient was recumbent. Radionuclide cisternography was performed using 150 MBq (4 mCi) Tc-99m DTPA. It revealed two cerebrospinal fluid leaks from the cervicothoracic junction bilaterally and the left side of the upper lumbar area. Epidural blood patching was tried at the lumbar level (L1-L2) and showed only a transient effect. A second trial of this method at the level of C7-T1 performed 2 days later resulted in immediate improvement of the symptoms without recurrence. The simultaneous cerebrospinal fluid leaks were detected successfully with radionuclide cisternography using Tc-99m DTPA, which provided a useful guideline for treatment despite the limitations of delayed scanning.