P4-07-12: Identification of p53 Mutation in Whole Genome DNA from Single Circulating Tumor Cells (CTCs) and Primary Breast Cancers (BC) from Patients (pts) with Metastatic Breast Cancer (MBC)

Background: CTCs represent the source of distant metastases, and are also implied in the growth/re-growth of primary BC. Molecular/gene-level characterization of similarities and discordances between CTCs and BCs in pts with MBC may provide useful information for individualized treatment. Since somatic p53 mutations are frequently observed in primary BCs, we set out to assess the feasibility of identifying such mutations in CTCs from pts with MBCs, and compare the findings with those of the primary BCs from the same pts. Material and Method: Fiber-optic Array Scanning Technology (FAST) was used for identification and location of CTCs on large glass substrates. CTCs were identified after blood samples (10 ml) from MBC pts were stained to detect CTCs via automated digital microscopy by morphology, based on immunofuorescence staining for cytokeratin and nucleus, and the absence of CD45. Single CTCs from 10 pts with MBC were identified and removed from the glass substrates. DNA was extracted, and the whole genome of isolated CTCs was amplified by using whole genome amplification method (Sigma). P53 mutations in exon 5, exon 6, exon 7 and exon 8 were assessed. As comparison, genomic DNA from formalin-fixed and paraffin-embedded (FFPE) from primary BCs of the same pts, was amplified using the same method.

Results: p53 mutations were found in 8 out of 10 CTCs, and in 4 out of 10 in primary BC samples. Of 8 mutations detected in CTCs, one silent mutation and 7 missense mutations were seen. One particular point mutation, R181L, previously assessed as functional mutation, was observed in 4 out of 8 CTCs. None of the 4 mutations (a silent mutation, one missense mutation and two different deletions) detected in tumor samples were found in CTCs. We validated that the mutations detected in CTCs were not artifacts occurring during genome amplification, by comparing p53 mutations between unamplified tumor genomic DNA vs. amplified samples.

Conclusion: Whole genome amplification based on extracting DNA from single CTCs using FAST, and identification of mutations such as those in p53, is feasible. The quantitative and qualitative discordance in detecting p53 mutations between CTCs and primary BCs may be due to CTCs acquiring new -possibly epithelial-mesenchymal transition-like-characteristics with metastatic potential as they evolve from the primary tumors or metastatic sites, or, technical issues (analyzing FFPE-preserved vs. CTCs, tumor heterogeneity) may contribute to our findings. Further assessment of the functionality of high frequent functional mutations such as R181L is warranted.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P4-07-12.

S6-4: Protein Kinase Mutation Patterns in Human Breast Cancer

Background: We performed next generation targeted sequencing of all known human protein kinases (n=530 genes) and 56 additional cancer related genes (BRCA1,2, p53, PTEN, etc..) in 112 samples to assess the kinase mutation landscape of breast cancer. Gene expression profiling was also performed on RNA from each specimen and DNA copy number variations were assessed in a subset of 59 cases using array CGH. The three types of genomic data were mapped to canonical biological pathways to identify frequently genomically disturbed pathways in these cancers.

Methods: DNA and RNA extracted from fine needle biopsies of 92 breast cancers were analyzed, 20 samples were sequenced in duplicates or triplicates to assess technical variation of the results. Targeted sequencing was performed with Agilent SureSelect Human Kinome kit and the SOLiD sequencing platform. Gene expression profiling and array CGH were performed with Affymetrix U133A chips and Agilent 244K CGH array. Sequence data was mapped to hg19, functional impact scores were calculated with SWIFT, canonical pathways were obtained from the Broad Institute.

Results: 0.1% of the entire genome was sequenced and >80% of target base pairs had > 20-fold coverage. The mean number of single nucleic acid variants (SNV) and indels per sample were 1043 (range: 493–1583, about 60% homozygous) and 159 (range: 75–269) respectively, 97% of SNVs and 78% of indels were already represented in dbSNP or COSMIC data bases. About 20% of SNVs were predicted to alter kinase or other biological function. The mean number of functionally high impact SNVs was 28 per sample (range 11–47). In addition to known p53 and PI3K mutations we detected frequent mutations in BRCA1 (20%) and observed several predicted high impact SNVs in HER2 (20%) as well as in many MAPK family enzymes. Not all SNVs were distributed equally across disease subsets, SNVs in ULK4, BMP2K, PALB2, ALPK3 were more frequent in triple negative cancers (TNBC) whereas SNVs in EPHA2 was more common in ER+ cancers. Among TNBC, those with residual cancer after neo-adjuvant chemotherapy (n=22) had significantly higher rates of SNVs in HUNK, TRPM7, NEK1 and HER3 compared to cases with pathologic complete response (n=25). When high impact SNVs, DNA copy number alterations and gene over-expression (relative to normal breast n=45) observed in individual cases were mapped to biological pathways a complex network of anomalies emerged for each case.

Conclusion: We observed several known mutations in cancer genes and also detected many SNVs in important regulatory genes that were previously described as functional, germ-line variants with experimentally validated or suspected impact on protein function. Individual cancers have unique combinations of these events. This suggest that cancers arise in the context of complex genomic “germ line noise” which may determine which types of somatic events can or cannot “drive” individual cancers. The data also suggest therapeutic hypotheses about what biological pathways should be targeted in individuals and in subsets of cancers.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr S6-4.

Expression of ecto-ATPase NTPDase2 in human dental pulp

Dental pulpal nerve fibers express ionotropic adenosine triphosphate (ATP) receptors, suggesting that ATP signaling participates in the process of dental nociception. In this study, we investigated if the principal enzymes responsible for extracellular ATP hydrolysis, namely, nucleoside triphosphate diphosphohydrolases (NTPDases), are present in human dental pulp. Immunohistochemical and immunofluorescence experiments showed that NTPDase2 was predominantly expressed in pulpal nerve bundles, Raschkow's nerve plexus, and in the odontoblast layer. NTPDase2 was expressed in pulpal Schwann cells, with processes accompanying the nerve fibers and projecting into the odontoblast layer. Odontoblasts expressed the gap junction protein, connexin43, which can form transmembrane hemichannels for ATP release. NTPDase2 was localized close to connexin43 within the odontoblast layer. These findings provide evidence for the existence of an apparatus for ATP release and degradation in human dental pulp, consistent with the involvement of ATP signaling in the process of dentin sensitivity and dental pain.

Long-haul transmission of 35-Gb/s all-optical OFDM signal without using tunable dispersion compensation and time gating

We propose that the optical OFDM technique using all optical discrete Fourier transform (DFT) has potential as a viable alternative for upgrading long-haul optical transmission systems towards 100-Gb/s. We demonstrate transmission of 35-Gb/s (7 x 5 Gb/s NRZ-OOK) all-optical OFDM signal over ~2000-km dispersion-managed span without using tunable dispersion compensation and time gating. We achieve bit error ratio of 1.2x10(-3) (7x10(-3)) for transmission over 1980-km (2310-km) all-EDFA amplified span consisting of standard single mode fiber (SSMF) and dispersion compensating fiber (DCF). We also study the nonlinear penalty impacting the all-optical OFDM transmission and discuss potential method for its mitigation.

Analysis of altered proteins related to blast crisis in chronic myeloid leukemia by proteomic study

INTRODUCTION

Chromic myeloid leukemia (CML) blast crisis (BC) and imatinib (IM) resistance is a significant barrier to the effective treatment of the disease.

METHODS

Expression profiles of differential proteins were identified, and new biomarkers or pathways related to BC in CML were screened through proteomic analysis. Total proteins from primary bone marrow cells of CML patients in chronic phase (CP) and BC were separated via two-dimensional (2D) polyacrylamide gel electrophoresis and then analyzed by imagemaster 5.0 software to detect differential protein spots which were already identified by mass spectrometry. Based on the variation of the whole expression profile, some key proteins were picked out for Western blot to confirm the accuracy of proteomics data. Moreover, related signal pathways involving those proteins were investigated.

RESULTS

The result indicated that thirteen protein points between CML-CP and CML-BC were successfully determined. Results from Western blot of RhoA, hnRNPK, ANXA1, PSMB4, and LTA4H were similar to those from 2D polyacrylamide gel electrophoresis. Most of those proteins were involved in the proteosome pathway and the small G-protein pathway.

CONCLUSION

A group of proteins associated with BC can be obtained and the result of this study might provide clues for further research.

Suppression of local inflammation contributes to the neuroprotective effect of ginsenoside Rb1 in rats with cerebral ischemia

Local inflammation accounts for the progression of cerebral ischemic insult. Ginsenoside Rb1 (GRb1) is a natural product extracted from Panax ginseng C.A. Meyer. It has been reported to have beneficial effects in cerebral ischemia and to inhibit the inflammatory cascade in sepsis. In this study, to determine whether modulating local inflammation contributed to the neuroprotection of GRb1, male Sprague-Dawley rats were treated with GRb1 or vehicle intranasally for 1 week before being subjected to temporary occlusion of the right middle cerebral artery and reperfusion. Neuroprotection of GRb1 was evaluated with a focus on the key elements of central nervous system (CNS) inflammation, such as inflammatory cells, proinflammatory cytokines, and transcriptional factor. GRb1 reduced infarction volume by 57% (n=6, P<0.01) and significantly alleviated the neurological deficit (n=12, modified neurological severity scores [mNSS]: 6.6±1.1 vs. 8.6±1.1, P<0.05). GRb1 depressed the activation of microglia in the penumbra by 15%-27% from 24 h to 72 h after reperfusion and its further convention into phagocytic microglia/macrophages. In GRb1 group, the peak mRNA level of tumor necrosis factor α (TNF-α) mRNA was decreased by 35% 12 h after reperfusion, whereas the protein level was significantly reduced by 43%-57%. Downregulation by GRb1 of both interleukin (IL)-6 gene and protein after GRb1 administration was also observed. GRb1 partially inhibited the activation of nuclear factor-κB (NF-κB) pathway from 6 h to 72 h after ischemia and reperfusion onset, as determined by the expression of total and phosphorylated NF-κB/p65, inhibitor protein of κB (IκB)-α, and IκB-kinase complex (IKK)-α. All these results indicate that suppression of local inflammation after cerebral ischemia might be one mechanism that contributes to the neuroprotection of GRb1.

Heading date gene, dth3 controlled late flowering in O. Glaberrima Steud. by down-regulating Ehd1

Heading date in rice is an important agronomic trait controlled by several genes. In this study, flowering time of variety Dianjingyou 1 (DJY1) was earlier than a near-isogenic line (named NIL) carried chromosome segment from African rice on chromosome 3S, when grown in both long-day (LD) and short-day (SD) conditions. By analyzing a large F2 population from NIL × DJY1, the locus DTH3 (QTL for days to heading on chromosome 3) controlling early heading date in DJY1 was fine mapped to a 64-kb segment which contained only one annotated gene, a MIKC-type MADS-box protein. We detected a 6-bp deletion and a single base substitution in the C-domain by sequencing DTH3 in DJY1 compared with dth3 in NIL, and overexpression of DTH3 caused early flowering in callus. Quantitative real-time PCR revealed that the transcript level of dth3 in NIL was lower than that DTH3 in DJY1 in both LD and SD conditions. The Early heading date 1 (Ehd1) which promotes the RFT1, was up-regulated by DTH3 in both LD and SD conditions. Based on Indel and dCAPs marker analysis, the dth3 allele was only present in African rice accessions. A phylogenetic analysis based on microsatellite genotyping suggested that African rice had a close genetic relationship to O. rufipogon and O. latifolia, and was similar to japonica cultivars. DTH3 affected flowering time and had no significant effect on the main agronomic traits.

Molecular mechanics modeling of deformation and failure of super carbon nanotube networks

A generalized molecular structure mechanics (MSM) model is proposed to investigate the deformation and failure behaviors of super carbon nanotubes (SCNTs) within the quasi-static approximation. The failure mechanism of the SCNTs with Y- and X-type junctions was examined by combining a failure criterion for the breakage of the carbon-carbon bonds in the CNT networks. The carbon-carbon bonds are modeled as elastic bars with equivalent stiffness and break as their elongation ratio reaches only 19%, which means that the broken carbon-carbon bonds are ineffective in terms of the Morse potential function. It is shown that the MSM method, combined with the failure criterion of the carbon-carbon bonds, is a powerful approach to simulate the deformation and failure of both Y junctions and X junctions with different chiralities and sizes. The deformation and failure modes of these junctions which involve rotation, bending and stretching of the CNT arms are predicted using the present model and the effects of various parameters of the junctions on their mechanical behaviors are discussed.

A new approach with less damage: intranasal delivery of tetracycline-inducible replication-defective herpes simplex virus type-1 vector to brain

Gene therapy holds great potential for treating neurological disorders. However, delivering gene vectors to the brain has been either invasive or inefficacious in most studies to date. The aim of this study was to develop a safe and efficacious strategy for delivering gene vectors to the brain. A tetracycline-inducible replication-defective herpes simplex virus type-1 vector, QR9TO-LacZ, was administered to rats intranasally. QR9TO-LacZ could infect primary cortical neurons and express the reporter gene without detectable replication. QR9TO-LacZ was observed in the olfactory bulb, hippocampus, striatum, cortex, medulla, cerebellum, ventricles, and nasal septum after intranasal administration. Expression of the reporter gene could be controlled effectively by tetracycline. In vitro, introduction of QR9TO-LacZ did not change the structure of transfected neurons. In vivo, QR9TO-LacZ did not increase apoptosis in neurons and did not alter levels of interleukin 6 and tumor necrosis factor α in the brain after intranasal delivery. Our data suggest that intranasally applied QR9TO-LacZ has a wide distribution and expresses the reporter gene in the brain under the control of tetracycline with less cytotoxicity than intravenous or stereotactic delivery methods.

Gene-vitamin D interactions on food sensitization: a prospective birth cohort study

BACKGROUND

It has been hypothesized that vitamin D deficiency (VDD) contributes to the development of food sensitization (FS) and then food allergy. However, the epidemiological evidence is conflicting. We aim to examine whether cord blood VDD is associated with FS and whether such association can be modified by genetic variants in a prospective birth cohort.

METHODS

This study included 649 children who were enrolled at birth and followed from birth onward at the Boston Medical Center. We defined VDD as cord blood 25(OH)D < 11 ng/ml, and FS as specific IgE ≥ 0.35 kUA/l to any of eight common food allergens in early childhood. We genotyped potentially functional single-nucleotide polymorphisms (SNPs) in 11 genes known to be involved in regulating IgE and 25(OH)D concentrations. Logistic regressions were used to test the effects of VDD on FS individually and jointly with SNPs.

RESULTS

Among the 649 children, 44% had VDD and 37% had FS. When examined alone, VDD was not associated with FS. When examined jointly with SNPs, a significant interaction between IL4 gene polymorphism (rs2243250) and VDD (p(interaction) = 0.003, p(FDR) = 0.10) was found: VDD increased the risk of FS among children carrying CC/CT genotypes (OR = 1.79, 95%CI: 1.15-2.77). Similar but weaker interactions were observed for SNPs in MS4A2 (rs512555), FCER1G (rs2070901), and CYP24A1 (rs2762934). When all four SNPs were simultaneously considered, a strong gene-VDD interaction was evident (p(interaction) = 9 × 10(-6) ).

CONCLUSIONS

Our data demonstrate that VDD may increase the risk of FS among individuals with certain genotypes, providing evidence of gene-vitamin D interaction on FS.

Bortezomib in a phase 1 trial for patients with relapsed AL amyloidosis: cardiac responses and overall effects

BACKGROUND

Bortezomib is approved for the treatment of multiple myeloma and a role has been suggested in the treatment of systemic AL amyloidosis (AL).

METHODS

In this phase 1 dose-escalation portion of the first prospective study of single-agent bortezomib in AL, 31 patients with relapsed disease, including 14 (45%) with cardiac involvement, received bortezomib in seven dose cohorts on once-weekly (0.7, 1.0, 1.3, 1.6 mg/m(2)) and twice-weekly (0.7, 1.0, 1.3 mg/m(2)) schedules. Electrocardiographic, Holter and echocardiographic studies were evaluated in all patients to determine safety and response.

RESULTS

During therapy (median treatment period 210 days), no patient developed significant ventricular or supraventricular rhythm disturbance on 24-h Holter monitoring; however, no patient satisfied study criteria for cardiac response using echocardiographic assessment or New York Heart Association classification. Seven patients (23%) had a ≥ 10% fall in left ventricular ejection fraction, but only one met criteria for cardiac deterioration. The predominant cardiac adverse events were peripheral edema (23%), orthostatic hypotension (13%) and hypotension (10%). Two patients developed grade 3 congestive heart failure, which resolved following treatment interruption. In this Phase 1 portion, the maximum tolerated dose of bortezomib on either schedule was not reached. Hematologic responses occurred in 14 patients (45%), including seven (23%) complete responses. In non-responders mean left ventricular wall thickness increased during the course of treatment.

CONCLUSION

AL is frequently rapidly progressive; in these patients who had relapsed or progressed following previous conventional therapies, these results suggest that bortezomib may slow the progression of cardiac amyloid with limited toxicity.

Modulation of the absorption coefficient at 1.3 μm in Ge/SiGe multiple quantum well heterostructures on silicon

We report modulation of the absorption coefficient at 1.3 μm in Ge/SiGe multiple quantum well heterostructures on silicon via the quantum-confined Stark effect. Strain engineering was exploited to increase the direct optical bandgap in the Ge quantum wells. We grew 9 nm-thick Ge quantum wells on a relaxed Si0.22Ge0.78 buffer and a contrast in the absorption coefficient of a factor of greater than 3.2 was achieved in the spectral range 1290-1315 nm.

ηπ+ π- resonant structure around 1.8 GeV/c(2) and η(1405) in J/ψ → ωηπ+ π-

We present results of a study of the decay J/ψ → ωηπ+ π- using a sample of (225.2 ± 2.8) × 10(6) J/ψ events collected by the BESIII detector, and report the observation of a new process J/ψ → ωX(1870) with a statistical significance of 7.2σ, in which X(1870) decays to a(0)(±)(980)π±. Fitting to ηπ+ π- mass spectrum yields a mass M = 1877.3 ± 6.3(stat)(-7.4)(+3.4)(syst) MeV/c(2), a width Γ = 57 ± 12(stat)(-4)(+19)(syst) MeV/c(2), and a product branching fraction B(J/ψ → ωX) × B(X→a(0)(±)(980)π±) × B(a(0) (±)(980) → ηπ±) = [1.50 ± 0.26(stat)(-0.36)(+0.72) (syst)] × 10(-4). Signals for J/ψ → ωf(1)(1285) and J/ψ → ω η(1405) are also clearly observed and measured.

Colocalization of myostatin and decorin in bovine skeletal muscle

Abstract. The objectives of this study were to investigate the expression and localization of myostatin (MSTN) and decorin (DCN) in bovine skeletal muscle and to find associations with muscle fibre and adipocyte development. Samples of two muscles, known for differences in meat quality and fibre composition, namely longissimus muscle (LD) and semitendinosus muscle (ST), were obtained from 18 months old bulls of the F2 generation of a Charolais×Holstein cross. Individual muscle sections were stained for determination of size and type of muscle fibres and immunohistochemical detection of the proteins. The mRNA abundance and protein expression of MSTN and DCN were quantified by real-time PCR and Western blot, respectively. As expected, the ST had more fast fibres, less fibres of the intermediate and the slow type, and less intramuscular fat than the LD. Despite these differences, the mRNA and protein abundance of MSTN was comparable in both muscles. The protein abundance of MSTN inhibitors, namely MSTN propeptide and DCN, was greater in LD, which may have affected the biological activity of mature MSTN. Myostatin propeptide was detected in all muscle fibres; however the mature MSTN was detected to a much lower extent and mainly in slow fibres. Furthermore, MSTN was localized in close proximity to DCN in intermyocellular space, suggesting possible interactions between both proteins and effects on muscle structure and meat quality. The role of MSTN and DCN as well as their interactions in the determination of muscle composition needs to be further elucidated.

Assessment of haplotype variation in bovine &lt;i&gt;AMPD1&lt;/i&gt; gene for association with growth and carcass traits in Qinchuan beef cattle

Abstract. The AMPD1 gene plays an important role in the purine nucleotide cycle and energy metabolism in skeletal muscle. In the present study polymorphisms of the AMPD1 gene were detected by PCR-SSCP and DNA sequencing of 215 individuals of the Qinchuan beef cattle breed. DNA sequencing revealed two mutations by comparisons with the bovine genome sequence (acc. no.: NC_007301). Two single nucleotide polymorphisms (SNPs; g.19416T>C and g.19421A>G) were detected in intron 11 of the bovine AMPD1 gene. The sequencing of PCR products of animals providing different PCR-SSCP banding patterns showed that four kinds of haplotypes, named: A (T-A), B (T-G), C (C-A) and D (C-G); and the five diplotypes were segregating: AA (T-A/T-A), BC (T-G/C-A or C-G/T-A ), AC (T-A/C-A), CC (C-A/C-A) and CD (C-A/ C-G). A significant association of AMPD1 with carcass weight was shown. Animals with the new heterozygote diplotype BC (P<0.05, n=56) had greater carcass weight than those with the other diplotypes. The SNPs in AMPD1 may be used as a possible candidates for markerassisted selection in Qinchuan beef cattle breeding program.

Gene-viro-therapy targeting liver cancer by a dual-regulated oncolytic adenoviral vector harboring IL-24 and TRAIL

Cancer-targeting gene-viro-therapy is a promising cancer therapeutic strategy that strengthens the antitumor effect of oncolytic viruses by expressing an inserted foreign antitumor gene. To achieve liver cancer targeting and to improve the safety of the ZD55 vector (a widely-used E1B55KD gene-deleted oncolytic adenoviral vector (OV), we previously constructed), we designed a novel OV named Ad·AFP·D55 that selectively replicates in hepatocellular carcinoma (HCC) cells by replacing the E1A promoter with the liver-cancer specific α-Fetoprotein (AFP) promoter based on the ZD55 vector. We found that the oncolytic adenoviruses Ad·AFP·D55-IL-24 and Ad·AFP·D55-TRAIL express tumor-suppressor gene interleukin-24 (IL-24) and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), respectively, significantly suppressed the HCC cell growth in vitro by inducing apoptosis by the caspase-8 and mitochondria-dependent caspase-9 signaling pathways. Furthermore, the combined treatment of Ad·AFP·D55-IL-24 and Ad·AFP·D55-TRAIL showed strong antitumor effects in vivo by significantly inhibiting the tumor growth in HCC HuH-7 cell xenograft mice, and markedly increasing animal survival rate. Therefore, this novel HCC cell-targeting OV carrying tumor-suppressor genes may provide a promising approach for liver cancer gene therapy.

Effect of waterborne zinc exposure on metal accumulation, enzymatic activities and histology of Synechogobius hasta

The present study was conducted to determine the metal accumulation, antioxidant enzymatic response, hepatic intermediary metabolism and histological changes in Synechogobius hasta exposed to 0.35 (control), 9.7 and 19.2mg/L Zn, respectively, on the 0, 4th, 8th and 12th day. Waterborne Zn exposure significantly reduced hepatosomatic index, hepatic lipid contents and fatty liver occurrence rate, increased Zn, Fe and Mn contents and reduced the contents of Cu and Ca in liver, and increased muscle Zn content. Waterborne Zn exposure also significantly influenced enzymatic activities involved in antioxidant responses (superoxide dismutase, catalase, glutathione-S-transferase, malondialdehyde) in liver and spleen, and changed hepatic intermediary enzymatic activities (succinate dehydrogenase, malic dehydrogenase, lactate dehydrogenase, lipoprotein lipase, hepatic lipase), impaired the histological structure of the gill and spleen, and reduced vacuolated hepatocytes. Thus, our study demonstrated for the first time that waterborne Zn exposure could reduce fatty liver syndrome in S. hasta.