Personalized oncogenomics: clinical experience with malignant peritoneal mesothelioma using whole genome sequencing

Peritoneal mesothelioma is a rare and sometimes lethal malignancy that presents a clinical challenge for both diagnosis and management. Recent studies have led to a better understanding of the molecular biology of peritoneal mesothelioma. Translation of the emerging data into better treatments and outcome is needed. From two patients with peritoneal mesothelioma, we derived whole genome sequences, RNA expression profiles, and targeted deep sequencing data. Molecular data were made available for translation into a clinical treatment plan. Treatment responses and outcomes were later examined in the context of molecular findings. Molecular studies presented here provide the first reported whole genome sequences of peritoneal mesothelioma. Mutations in known mesothelioma-related genes NF2, CDKN2A, LATS2, amongst others, were identified. Activation of MET-related signaling pathways was demonstrated in both cases. A hypermutated phenotype was observed in one case (434 vs. 18 single nucleotide variants) and was associated with a favourable outcome despite sarcomatoid histology and multifocal disease. This study represents the first report of whole genome analyses of peritoneal mesothelioma, a key step in the understanding and treatment of this disease.

Drp1 is dispensable for apoptotic cytochrome c release in primed MCF10A and fibroblast cells but affects Bcl-2 antagonist-induced respiratory changes

BACKGROUND AND PURPOSE

Dynamin-related protein 1 (Drp1) mediates mitochondrial fission and is thought to promote Bax/Bak-induced cytochrome c release during apoptosis. Conformationally active Bax, Bak and Bax/Bak-activating BH3-only proteins, such as Bim, are restrained by anti-apoptotic Bcl-2 proteins in cells that are 'primed for death'. Inhibition of Bcl-2/Bcl-xL/Bcl-w by the antagonist ABT-737 causes rapid apoptosis of primed cells. Hence, we determined whether Drp1 is required for cytochrome c release, respiratory alterations and apoptosis of cells that are already primed for death.

EXPERIMENTAL APPROACH

We tested the Drp1 inhibitor mdivi-1 for inhibition of cytochrome c release in MCF10A cells primed by Bcl-2 overexpression. We measured ATP synthesis-dependent, -independent and cytochrome c-limited maximal oxygen consumption rates (OCRs) and cell death of immortalized wild-type (WT) and Drp1 knockout (KO) mouse embryonic fibroblasts (MEFs) treated with ABT-737.

KEY RESULTS

Mdivi-1 failed to attenuate ABT-737-induced cytochrome c release. ABT-737 decreased maximal OCR measured in the presence of uncoupler in both WT and Drp1 KO MEF, consistent with respiratory impairment due to release of cytochrome c. However, Drp1 KO MEF were slightly less sensitive to this ABT-737-induced respiratory inhibition compared with WT, and were resistant to an initial ABT-737-induced increase in ATP synthesis-independent O2 consumption. Nevertheless, caspase-dependent cell death was not reduced. Pro-apoptotic Bax was unaltered, whereas Bak was up-regulated in Drp1 KO MEF.

CONCLUSIONS AND IMPLICATIONS

The findings indicate that once fibroblast cells are primed for death, Drp1 is not required for apoptosis. However, Drp1 may contribute to ABT-737-induced respiratory changes and the kinetics of cytochrome c release.

First Report of Chickpea chlorotic dwarf virus Infecting Hot Pepper in India

Hot pepper (Capsicum annuum) cultivated in India has been identified as a host of geminiviruses causing leaf curl disease such as Chilli leaf curl virus and Pepper leaf curl virus, leading to serious crop losses (3). In June 2013, hot pepper plants growing in Bangalore showed stunting and upward leaf curling. Viral DNA was extracted from a hot pepper with a Viral Gene-spin Viral DNA/RNA Extraction Kit (iNtRON Biotechnology, Seongnam, Korea) and amplified by rolling circle amplification using the illustra TempliPhi 100 Amplification Kit (GE Healthcare, Uppsala, Sweden) (2). Amplified products were digested by restriction enzyme KpnI (Takara Bio, Shiga, Japan), cloned, and sequenced (Macrogen, Seoul, Korea). Based on a BLAST search, a 2.6-kb DNA obtained from one plant sample was identified as Chickpea chlorotic dwarf virus (CpCDV), belonging to the genus Mastrevirus (family Geminiviridae) (GenBank Accession No. KF632712). The CpCDV-Bangalore isolate is 2,585 bases in length and exhibits 85.9 to 98.5% identity to previously reported CpCDV isolates. To our knowledge, this is the first report of CpCDV infecting hot pepper in India. CpCDV was recently reported from pepper plants in Oman (KF111683) (1), but it shared the lowest sequence identity (85.9%) with CpCDV-Bangalore isolate. References: (1) S. Akhtar et al. Plant Dis. 98:286, 2014. (2) E.-J. Kil et al. Arch. Virol. 159:2387. (3) D. M. J. B. Senanayake et al. Plant Pathol. 56:343, 2007.

First Report of Tomato yellow leaf curl virus Infecting Eustoma (Eustoma grandiflorum) in Korea

Eustoma (Eustoma grandiflorum), also called lisianthus, belongs to the family Gentianaceae and is cultivated for flower production globally (1), including in Korea. At least 10 viruses can infect eustoma, including Cucumber mosaic virus (genus Cucumovirus), Tobacco mosaic virus (genus Tobamovirus), Tomato spotted wilt virus (genus Tospovirus), and Tomato yellow leaf curl virus (TYLCV, genus Begomovirus) (1,2). In December 2012, disease symptoms such as leaf curling and stunting were observed on eustoma plants grown in Gumi, Korea, where TYLCV outbreak was reported on tomato farms. In a eustoma greenhouse, about 5% of eustoma plants showed the leaf curling and stunting symptoms. Total DNA was isolated from 15 symptomatic eustoma plants with a Viral Gene-spin Viral DNA/RNA Extraction Kit (iNtRON Biotechnology, Seongnam, Korea) and viral DNA was amplified by rolling circle amplification (TempliPhi Amplification Kit, GE Healthcare Life Sciences, Uppsala, Sweden) following the manufacturer's instructions. All amplicons were digested with the restriction enzyme SacI (TaKaRa Bio, Shiga, Japan) and 2.8-kb DNA fragments were verified on an agarose gel. Fifteen digested DNA fragments were purified from the gel, ligated into pGEM-T easy vector (Promega, Madison, WI), and sequenced (Macrogen, Seoul, Korea, GenBank Accession No. KF225312.1). A BLAST search exhibited a 99% identity to TYLCV previously reported in Korea (GenBank HM856911.1). This is the first report of TYLCV in eustoma plants in Korea. To identify the movement and replication of TYLCV in infected eustoma plants, PCR and Southern hybridization analysis were performed with samples from four organs (flower, leaf, stem, and root) of three individual TYLCV-infected plants. TYLCV TYL DNA from each organ sample was amplified using 2× Taq PCR MasterMix (Bioneer, Daejeon, Korea) with TYLCV-specific primers (TYLCV-F: 5'-ATATTACCGGATGGCCGCGCCT-3', CV-R: 5'-TCCACGGGGAACATCAGGGCTT-3'). Single-stranded as well as double-stranded TYLCV DNA were identified from all organs of symptomatic eustoma, indicating TYLCV can replicate and move systemically in eustoma plants. Whitefly (Bemisia tabaci)-mediated plant-to-plant viral transmission was performed with one TYLCV-infected eustoma plant and five healthy eustoma plants and revealed that 80% (4 of 5) of the eustoma plants were infected by whitefly-mediated transmission. These results indicate that TYLCV-infected eustoma plants could act as virus reservoirs to healthy eustoma plants as well as other potential TYLCV hosts, such as tomatoes. In Korea, TYLCV has been the most notorious plant virus since 2008 (3), but, until now, TYLCV infection in eustoma plants has not been reported in Korea. References: (1) C. C. Chen et al. Plant Dis. 84:506, 2000. (2) A. Kritzman et al. Plant Dis. 84:1185, 2000. (3) H. Lee et al. Mol. Cells 30:467, 2010.

Abstract P1-01-23: Increased Diagnostic Performance of Sentinel Lymph Node Biopsy Combined with Radiologic-pathologic Factors After Neoadjuvant Chemotherapy in Breast Cancer Patients with Cytologically Proven Node Metastasis at Diagnosis

Background: It is undetermined whether sentinel lymph node biopsy (SLNB) is feasible and accurate for predicting final nodal status after neoadjuvant chemotherapy (NCT) in breast cancer patients with cytologically proven node metastasis at the time of diagnosis, although currently completion node dissection is a standard surgical procedure for the management of axilla. The aim of this study was to investigate diagnostic performance of SLNB after NCT in this subgroup.

Methods: Of 374 patients with T1-T3 breast cancer who received NCT, 178 had initially biopsy proven axillary/supraclavicular metastasis and subsequently underwent SLNB using radioisotope alone followed by completion node dissection between 2008 and 2011. Detection rate, sensitivity, false negative rate (FNR), negative predictive value (NPV), and accuracy of SLNB were retrospectively analyzed and it was explored using regression analysis whether combination with clinicopathologic factors improved performance.

Results: At initial presentation, 60.7% of patients were cT2 stage and 88.2% treated with concurrent or sequential anthracycline plus taxane preoperatively. SLNB was successfully performed in 169 (94.9%) patients. The mean number of sentinel and regional nodes retrieved was 2.1 ± 1.6 and 12.8 ± 6.3, respectively. Tumoral non-responder and extensive residual nodal disease were significantly associated with detection failure of SLNB. Conversion to node-negative disease was noted in 69 (40.8%) patients. Sensitivity, FNR, NPV, and accuracy of SLNB were 78.0%, 22.0%, 75.8%, and 87.0%, respectively and diagnostic performance increased when ≥ 3 sentinel nodes were evaluated. By logistic regression model, tumoral and nodal responder, absent lymphovascular invasion (LVI), estrogen receptor (ER)-negativity, and HER2-positivity were significantly associated with node-negative disease after NCT. Area under the receiver operating characteristic curve increased from 0.890 to 0.949 when considering radiologic-pathologic factors and FNR was the lowest value of 14.3% in 46 patients with tumoral responder, absent LVI, and ER-negative tumor.

Conclusions: SLNB was technically feasible but solely showed higher FNR in this study. Improved diagnostic performance of SLNB combined with radiologic-pathologic characteristics suggests possible clinical value of SLNB after NCT in highly selected patients with node metastasis at diagnosis.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P1-01-23.

P3-14-18: Primary Tumor Response to Neoadjuvant Chemotherapy Is Significantly Associated with Nodal Pathological Complete Response in Breast Cancer Patients with Cytologically Proven Axillary Node Metastasis

Background: Axillary node status is the most significant factor for the prediction of outcome in breast cancer patients whether they received neoadjuvant chemotherapy or not. However, a reliable method to predict nodal response to neoadjuvant chemotherapy is not established yet. The aim of this study was to identify the predictive factors of axillary pathological complete response (pCR) after neoadjuvant chemotherapy in breast cancer patients with cytologically proven axillary lymph node metastases.

Patients and methods: A total of 123 patients with axillary metastases confirmed by ultrasound-guided fine-needle aspiration biopsy were subsequently treated with four cycles of anthracycline (60mg/m2) plus cyclophosphamide (600mg/m2) followed by doxetaxel (75-100mg/m2) between August 2008 and March 2011. After neoadjuvant chemotherapy, all patients underwent a definite breast surgery with complete axillary lymph node dissection. Clinicopathological parameters were evaluated using a chi-square test and logistic regression model in association with node pCR.

Results: The mean age at diagnosis was 47.9 years in all patients. Eighty-one (65.9%) patients were preoperative clinical T2 stage, 74 (60.2%) showed estrogen receptor (ER)-positivity, and 36 (29.3%) demonstrated HER2−positivity. A pCR of the axilla and breast was determined in 56 (46%) and 40 (31.7%) patients, respectively. Breast Pcr rate is significantly associated with age≤50 at diagnosis, ER(−),PR(−) and higher Ki-67 proliferation. Axillary pCR rate is significantly associated with age at diagnosis of 50 or less, smaller primary tumor size at diagnosis, tumor responsiveness to neoadjuvant chemotherapy, estrogen hormone receptors-negativity, higher Ki-67 proliferative index at diagnosis, and subtypes of HER2−enriched or triple negative breast cancer. When these factors entered logistic regression model, tumor response( SD+PD vs CR+PR: OR 8.603, P=0.007), Ki67((−) vs (+): OR 7.157, p=0.009), ER status((+) vs (−) : OR 4.943, P=0.036), pre-operation tumor size(>2cm vs ≤2cm: OR 5.116, p=0.044), HER2 status( (−) vs (+): OR 5.029,p=0.046) remained to be significant for the prediction of axillary pCR, favorable nodal response.

Conclusion: Our study suggests that primary tumor response to neoadjuvant chemotherapy is significantly associated with favorable nodal response. The factors of tumor and nodal response were similar. There are many issues remained to be determined yet.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-14-18.

P4-09-35: Co-Expression of Ki-67 Is Critical for Outcome of Cyclooxygenase-2 Positive Breast Cancer

Background

The purpose was to investigate the implications of cyclooxygenase-2 (COX-2) and Ki-67 expression on the progression and prognosis of breast cancer.

Methods: COX-2 and Ki-67 levels were immunohistochemically determined using tissue microarrays of 1,028 breast tumors treated between November 1999 and August 2005. COX-2 and Ki-67 levels were compared by tumor progression and clinicopathological parameters were investigated in association with both markers status which was divided into 3 subgroups: COX-2(+)/Ki-67(+), COX-2(+)/Ki-67(−), COX-2(−)/Ki-67(any).

Results: COX-2 expression was significantly higher in intraductal carcinoma and progressively decreased in small T1 lesions and then in T2-T4 tumors, but Ki-67 was significantly expressed at high levels in T2-T4 lesions than in intraductal or T1 carcinomas. COX-2 expression was positively associated with favorable parameters such as older age at diagnosis, smaller size, well-differentiation, hormone receptor-positivity, and was inversely associated with Ki-67 expression. Among 816 invasive tumors, COX-2 expression alone was not related to outcomes. In combination with Ki-67 expression, however, COX-2(+)/Ki-67(−) tumors were significantly associated with favorable characteristics including HER2−negativity and demonstrated favorable outcomes. COX-2(+)/Ki-67(+) tumors showed unfavorable factors and the worst outcomes. COX-2(−)/Ki-67(any) subgroup presented intermediate prognosis. Statistical significance of COX-2 combined with Ki-67 was maintained in Cox's models adjusting for clinicopathological parameters among not only whole population but also ER-positive subgroup.

Conclusions: Our study suggests that COX-2 is expressed in early phase of breast cancer development and is associated with favorable prognostic markers. But co-expression of high Ki-67 proliferative index could indicate an aggressive phenotypic change in COX-2 positive breast cancer. The mechanisms should be further investigated.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P4-09-35.

Pantothenate kinase-associated neurodegeneration in Korea: recurrent R440P mutation in PANK2 and outcome of deep brain stimulation

BACKGROUND AND PURPOSE

The purpose of this study was to evaluate the mutation status of PANK2 among Korean patients with pantothenate kinase-associated neurodegeneration (PKAN) and to document the outcome of pallidal deep brain stimulation (DBS).

METHODS

Direct sequencing and deletion/duplication analysis of PANK2 were conducted in 12 patients (11 unrelated) with PKAN, diagnosed on the basis of extrapyramidal dysfunction and the 'eye-of-the-tiger sign' on brain magnetic resonance imaging (MRI). Pallidal DBS was conducted in four patients, and the outcomes were measured using the Burke-Fahn-Marsden Dystonia Rating Scale (BFMDRS).

RESULTS

A PANK2 mutation was identified in both alleles in all patients. The most prevalent mutation was c.1319G>C (p.R440P) in 8/22 mutated alleles (36%). An intragenic deletion ranging from exons 2 to 4 was found in one allele (1/22, 4.5%) using deletion/duplication analysis. The outcome of pallidal DBS was favorable in two patients with atypical PKAN and moderate severity of dystonia. However, two patients with typical PKAN and relatively severe symptoms showed variable responses.

CONCLUSIONS

The c.1319G>C (p.R440P) mutation appears to be a founder genotype among Korean patients with PKAN. Furthermore, this study provides additional data for the recent international effort to evaluate the efficacy of pallidal DBS in the treatment of patients with PKAN.

Single nucleotide polymorphism association study for backfat and intramuscular fat content in the region between SW2098 and SW1881 on pig chromosome 6

This study was carried out to identify SNP associated with fatness traits on pig chromosome 6. In total, 11,067 putative genomic variations were detected in 125 complete bacterial artificial chromosome sequences corresponding to the region between SW2098 and SW1881, which harbors multiple QTL affecting intramuscular fat content (IMF) and backfat thickness (BFT). Among 173 putative SNP validated by MassArray, 120 SNP were used in an association study on 541 offspring produced by a cross of Korean native pig and Landrace breeds. The significance level of each SNP was determined using single marker regression analysis. Further, significant threshold values were determined using a false discovery rate. Nine out of 120 SNP showed significant effects on BFT or IMF or both. Of the 9 significant SNP, 4 were significantly associated with IMF, 7 were significantly related to BFT, and 2 SNP (Kps8172 and Kps6413) showed significant effects on both traits. Moreover, multiple regression analysis considering all significant SNP was used to correct spurious false positives due to linkage disequilibrium. Consequently, only 1 SNP (Kps6413) was significant for IMF, whereas 4 SNP including Kps6413 showed significant effects on BFT. The significant SNP had generally additive effects and on average explained 1.72% of the genetic variation for IMF and 3.92% for BFT, respectively. These markers can potentially be applied in pig breeding programs for improving IMF and BFT traits after validation in other populations.

Flexible interpretation of a decision rule by supplementary eye field neurons

Since the environment is in constant flux, decision-making capabilities of the brain must be rapid and flexible. Yet in sensory motion processing pathways of the primate brain where decision making has been extensively studied, the flexibility of neurons is limited by inherent selectivity to motion direction and speed. The supplementary eye field (SEF), an area involved in decision making on moving stimuli, is not strictly a sensory or motor structure, and hence may not suffer such limitations. Here we test whether neurons in the SEF can flexibly interpret the rule of a go/nogo task when the decision boundary in the task changes with each trial. The task rule specified that the animal pursue a moving target with its eyes if and when the target entered a visible zone. The size of the zone was changed from trial to trial in order to shift the decision boundary, and thereby assign different go/nogo significance to the same motion trajectories. Individual SEF neurons interpreted the rule appropriately, signaling go or nogo in compliance with the rule and not the direction of motion. The results provide the first evidence that individual neurons in frontal cortex can flexibly interpret a rule that governs the decision to act.

Increased abundance of the adaptor protein containing pleckstrin homology domain, phosphotyrosine binding domain and leucine zipper motif (APPL1) in patients with obesity and type 2 diabetes: evidence for altered adiponectin signalling

AIMS/HYPOTHESIS

The adiponectin signalling pathway is largely unknown, but recently the adaptor protein containing pleckstrin homology domain, phosphotyrosine binding domain and leucine zipper motif (APPL1), has been shown to interact directly with adiponectin receptor (ADIPOR)1. APPL1 is present in C2C12 myoblasts and mouse skeletal muscle, but its presence in human skeletal muscle has not been investigated.

METHODS

Samples from type 2 diabetic, and lean and non-diabetic obese participants were analysed by: immunoprecipitation and western blot; HPLC-electrospray ionisation (ESI)-mass spectrometry (MS) analysis; peak area analysis by MS; HPLC-ESI-MS/MS/MS analysis; and RT-PCR analysis of APPL1 mRNA.

RESULTS

Immunoprecipitation and western blot indicated a band specific to APPL1. Tryptic digestion and HPLC-ESI-MS analysis of whole-muscle homogenate APPL1 unambiguously identified APPL1 with 56% sequence coverage. Peak area analysis by MS validated western blot results, showing APPL1 levels to be significantly increased in type 2 diabetic and obese as compared with lean participants. Targeted phosphopeptide analysis by HPLC-ESI-MS/MS/MS showed that APPL1 was phosphorylated specifically on Ser(401). APPL1 mRNA expression was significantly increased in obese and type 2 diabetic participants as compared with lean participants. After bariatric surgery in morbidly obese participants with subsequent weight loss, skeletal muscle APPL1 abundance was significantly reduced (p < 0.05) in association with an increase in plasma adiponectin (p < 0.01), increased levels of ADIPOR1 (p < 0.05) and increased muscle AMP-activated protein kinase (AMPK) phosphorylation (p < 0.05).

CONCLUSIONS/INTERPRETATION

APPL1 abundance is significantly higher in type 2 diabetic muscle; APPL1 is phosphorylated in vivo on Ser(401). Improvements in hyperglycaemia and hypoadiponectinaemia following weight loss are associated with reduced skeletal muscle APPL1, and increased plasma adiponectin levels and muscle AMPK phosphorylation.

Characteristic Dynamic Enhancement Pattern of MR Imaging for Malignant Thyroid Tumor. Preliminary Report

The purpose of this study was to determine the characteristic dynamic enhancement pattern of MR imaging for malignant thyroid tumor. Eight patients were collected, who had pathology confirmed malignant thyroid tumor preoperatively. There were five papillary carcinomas, one medullary carcinoma, one follicular carcinoma and one FNAB proven atypical cell. All images were obtained with a 3.0-T MR imaging system with and without iv contrast administration. Pathologic report and US imaging finding were collected retrospectively. Based on preoperative MR imaging, we compared dynamic MR enhancement pattern relating to pathologic type. All biopsy proven malignant thyroid tumors show hypoechogenicity on previous US imaging, except one follicular carcinoma (isoechogenicity). On T1-weighted images, one papillary carcinoma showed high SI and one medullary carcinoma showed low SI. The other cases were not differentiated with normal parenchyma. On T2-weighted images, three papillary carcinomas and one follicular carcinoma showed high SI and one papillary carcinoma showed low SI. The other case was not differentiated with normal parenchyma. On contrast agent-enhanced dynamic T1WI, five papillary carcinomas and one medullary carcinoma showed delayed enhancement compared to normal parenchyma. One follicular carcinoma showed stronger enhancement than normal parenchyma, one papillary carcinoma showed persistently decreased enhancement than normal parenchyma. Although this study is limited by the small patient population, the data suggest that delayed enhancement on enhanced dynamic T1WI may be a characteristic MR finding of malignant thyroid tumor.

Nano-electromechanical switch-CMOS hybrid technology and its applications

Si-based CMOS technology is facing a serious challenge in terms of power consumption and variability. The increasing costs associated with physical scaling have motivated a search for alternative approaches. Hybridization of nano-electromechanical (NEM)-switch and Si-based CMOS devices has shown a theoretical feasibility for power management, but a huge technical gap must be bridged before a nanoscale NEM switch can be realized due to insufficient material development and the limited understanding of its reliability characteristics. These authors propose the use of a multilayer graphene as a nanoscale cantilever material for a nanoscale NEM switchwith dimensions comparable to those of the state-of-the-art Si-based CMOS devices. The optimal thickness for the multilayer graphene (about five layers) is suggested based on an analytical model. Multilayer graphene can provide the highest Young's modulus among the known electrode materials and a yielding strength that allows more than 15% bending. Further research on material screening and device integration is needed, however, to realize the promises of the hybridization of NEM-switch and Si-based CMOS devices.