A novel family of plant nuclear envelope-associated proteins

This paper describes the characterisation of a new family of higher plant nuclear envelope-associated proteins (NEAPs) that interact with other proteins of the nuclear envelope. In the model plant Arabidopsis thaliana, the family consists of three genes expressed ubiquitously (AtNEAP1-3) and a pseudogene (AtNEAP4). NEAPs consist of extensive coiled-coil domains, followed by a nuclear localisation signal and a C-terminal predicted transmembrane domain. Domain deletion mutants confirm the presence of a functional nuclear localisation signal and transmembrane domain. AtNEAP proteins localise to the nuclear periphery as part of stable protein complexes, are able to form homo- and heteromers, and interact with the SUN domain proteins AtSUN1 and AtSUN2, involved in the linker of nucleoskeleton and cytoskeleton (LINC) complex. An A. thaliana cDNA library screen identified a putative transcription factor called AtbZIP18 as a novel interactor of AtNEAP1, which suggest a connection between NEAP and chromatin. An Atneap1 Atneap3 double-knockout mutant showed reduced root growth, and altered nuclear morphology and chromatin structure. Thus AtNEAPs are suggested as inner nuclear membrane-anchored coiled-coil proteins with roles in maintaining nuclear morphology and chromatin structure.

Murine solid tumours as a novel model to study bacterial biofilm formation in vivo

Bacteria of many species are able to invade and colonize solid tumours in mice. We have focused on Salmonella enterica serovar Typhimurium. Detailed analysis revealed that such tumour-invading Salmonella form biofilms, thus providing a versatile in vivo test system for studying bacterial phenotypes and host-pathogen interactions. It appears that biofilm formation by S. typhimurium is induced as a defence against the immune system of the host, and in particular against neutrophils. Further, we extended our work to the clinically more relevant biofilm infection by Pseudomonas aeruginosa. The induction of P. aeruginosa biofilms in neoplastic tissue appears to be elicited as a reaction against the immune system. Reconstitution experiments reveal that T cells are responsible for biofilm induction. Isogenic mutants that are no longer able to form biofilms can be used for comparison studies to determine antimicrobial resistance, especially therapeutic efficacy against P. aeruginosa located in biofilms.

Protein interactions at the higher plant nuclear envelope: evidence for a linker of nucleoskeleton and cytoskeleton complex

Following the description of SAD1/UNC84 (SUN) domain proteins in higher plants, evidence has rapidly increased that plants contain a functional linker of nucleoskeleton and cytoskeleton (LINC) complex bridging the nuclear envelope (NE). While the SUN domain proteins appear to be highly conserved across kingdoms, other elements of the complex are not and some key components and interactions remain to be identified. This mini review examines components of the LINC complex, including proteins of the SUN domain family and recently identified plant Klarsicht/Anc/Syne-1 homology (KASH) domain proteins. First of these to be described were WIPs (WPP domain interacting proteins), which act as protein anchors in the outer NE. The plant KASH homologs are C-terminally anchored membrane proteins with the extreme C-terminus located in the nuclear periplasm; AtWIPs contain a highly conserved X-VPT motif at the C-terminus in contrast to PPPX in opisthokonts. The role of the LINC complex in organisms with a cell wall, and description of further LINC complex components will be considered, together with other potential plant-specific functions.

Genomic and mutational profiling of ductal carcinomas in situ and matched adjacent invasive breast cancers reveals intra-tumour genetic heterogeneity and clonal selection

The mechanisms underlying the progression from ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) of the breast are yet to be fully elucidated. Several hypotheses have been put forward to explain the progression from DCIS to IDC, including the selection of a subpopulation of cancer cells with specific genetic aberrations, and the acquisition of new genetic aberrations or non-genetic mechanisms mediated by the tumour microenvironment. To determine whether synchronously diagnosed ipsilateral DCI and IDCs have modal populations with distinct repertoires of gene copy number aberrations and mutations in common oncogenes, matched frozen samples of DCIS and IDC were retrieved from 13 patients and subjected to microarray-based comparative genomic hybridization (aCGH) and Sequenom MassARRAY (Oncocarta v 1.0 panel). Fluorescence in situ hybridization and Sanger sequencing were employed to validate the aCGH and Sequenom findings, respectively. Although the genomic profiles of matched DCI and IDCs were similar, in three of 13 matched pairs amplification of distinct loci (ie 1q41, 2q24.2, 6q22.31, 7q11.21, 8q21.2 and 9p13.3) was either restricted to, or more prevalent in, the modal population of cancer cells of one of the components. Sequenom MassARRAY identified PIK3CA mutations restricted to the DCIS component in two cases, and in a third case the frequency of the PIK3CA mutant allele reduced from 49% in the DCIS to 25% in the IDC component. Despite the genomic similarities between synchronous DCIS and IDC, our data provide strong circumstantial evidence to suggest that in some cases the progression from DCIS to IDC is driven by the selection of non-modal clones that harbour a specific repertoire of genetic aberrations.

A whole-genome massively parallel sequencing analysis of BRCA1 mutant oestrogen receptor-negative and -positive breast cancers

BRCA1 encodes a tumour suppressor protein that plays pivotal roles in homologous recombination (HR) DNA repair, cell-cycle checkpoints, and transcriptional regulation. BRCA1 germline mutations confer a high risk of early-onset breast and ovarian cancer. In more than 80% of cases, tumours arising in BRCA1 germline mutation carriers are oestrogen receptor (ER)-negative; however, up to 15% are ER-positive. It has been suggested that BRCA1 ER-positive breast cancers constitute sporadic cancers arising in the context of a BRCA1 germline mutation rather than being causally related to BRCA1 loss-of-function. Whole-genome massively parallel sequencing of ER-positive and ER-negative BRCA1 breast cancers, and their respective germline DNAs, was used to characterize the genetic landscape of BRCA1 cancers at base-pair resolution. Only BRCA1 germline mutations, somatic loss of the wild-type allele, and TP53 somatic mutations were recurrently found in the index cases. BRCA1 breast cancers displayed a mutational signature consistent with that caused by lack of HR DNA repair in both ER-positive and ER-negative cases. Sequencing analysis of independent cohorts of hereditary BRCA1 and sporadic non-BRCA1 breast cancers for the presence of recurrent pathogenic mutations and/or homozygous deletions found in the index cases revealed that DAPK3, TMEM135, KIAA1797, PDE4D, and GATA4 are potential additional drivers of breast cancers. This study demonstrates that BRCA1 pathogenic germline mutations coupled with somatic loss of the wild-type allele are not sufficient for hereditary breast cancers to display an ER-negative phenotype, and has led to the identification of three potential novel breast cancer genes (ie DAPK3, TMEM135, and GATA4).

Abstract 5076: Integrative genomic and transcriptomic analysis of metaplastic carcinomas of the breast

Background Metaplastic breast carcinomas (MBCs) are characterised by neoplastic cells that display differentiation towards squamous epithelium or mesenchymal elements. These tumours are of triple-negative phenotype and have an aggressive clinical behaviour. The aims of this study were to characterise a series of MBCs at the genomic and transcriptomic level to identify potential drivers of this breast cancer special type. Design Twenty-five frozen MBCs and two MBC cell lines (HCC1569 and Hs578T) were subjected to genotyping (Affymetrix SNP6), 32K BAC microarray comparative genomic hybridisation (aCGH), microarray gene expression profiling (Illumina HT12) and massively parallel mRNA-sequencing (RNA-seq, Illumina GAII). Novel chimaeric transcripts were identified using Chimerascan v0.4.3. 10 cases with available germline DNA were subjected to targeted exomic sequencing (Illumina HiSeq). Somatic variants were called using the Genome Analysis Toolkit (GATK) using best practice guidelines. Fusion genes and mutations were validated using (RT)-PCR and Sanger sequencing, respectively. Results MBCs displayed a complex pattern of gene copy number aberrations, with multiple copy number gains and losses throughout the genome. Recurrent amplifications/ high-level gains at 3q25.2-q27.1, 8p11.21-q24.3 and 12p13.33 and recurrent homozygous deletions on 9p21.3 (CDKN2A/2B) and 10q23.31 (PTEN) were found. Unsupervised clustering of gene expression showed that MBCs associated with chondroid differentiation separated into a distinct cluster, whereas MBC's with spindle and epithelial morphology did not cluster apart. Integration of SNP6 copy number and gene expression data identified 198 genes overexpressed when amplified. RNA-seq revealed 1025 unique nominated fusion gene events (43-119 per tumour), including 254 fusions predicted to be in-frame. These included a promoter swap involving TBXLR1 fused to PIK3CA and a recurrent promoter swap involving NF1 that was also seen in the MBC cell line Hs578T. Targeted exome sequencing identified 402 somatic coding variants (12-96 per tumour), including recurrent mutations in TP53 (5/10) and genes involved in PI3K signaling. Conclusion Our results demonstrate that MBCs have complex genomes and are heterogeneous at both the genomic and transcriptomic levels. TP53, CDKN2A/2B and PTEN mutations and/ or homozygous deletions, and activation of the PI3K pathway are recurrent events in these tumours.

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 5076. doi:1538-7445.AM2012-5076

Immunophenotypic and genomic characterization of papillary carcinomas of the breast

Papillary carcinomas are a special histological type of breast cancer and have a relatively good outcome. We characterized the genomic and phenotypic characteristics of papillary carcinomas to determine whether they would constitute an entity distinct from grade- and oestrogen receptor (ER)-matched invasive ductal carcinomas of no special type (IDC-NSTs). The phenotype of 63 papillary carcinomas of the breast and grade- and ER-matched IDC-NSTs was determined by immunohistochemistry. DNA of sufficient quality was extracted from 49 microdissected papillary carcinomas and 49 microdissected grade- and ER-matched IDC-NSTs. These samples were subjected to high-resolution microarray-based comparative genomic hybridization (aCGH) and Sequenom MassARRAY sequencing analysis of 19 known oncogenes. Papillary carcinomas were predominantly of low histological grade, expressed immunohistochemical markers consistent with a luminal phenotype, and a lower rate of lymph node metastasis and p53 expression than grade- and ER-matched IDC-NSTs. Papillary carcinomas displayed less genomic aberrations than grade- and ER-matched IDC-NSTs; however, the patterns of gene copy number aberrations found in papillary carcinomas were similar to those of ER- and grade-matched IDC-NSTs, including 16q losses. Furthermore, PIK3CA mutations were found in 43% and 29% of papillary carcinomas and grade- and ER-matched IDC-NSTs, respectively. The genomic profiles of encapsulated, solid and invasive papillary carcinomas, the three morphological subtypes, were remarkably similar. Our results demonstrate that papillary carcinomas are a homogeneous special histological type of breast cancer. The similarities in the genomic profiles of papillary carcinomas and grade- and ER-matched IDC-NSTs suggest that papillary carcinomas may be best positioned as part of the spectrum of ER-positive breast cancers, rather than as a distinct entity. Furthermore, the good prognosis of papillary carcinomas may stem from the low rates of lymph node metastasis and p53 expression, low number of gene copy number aberrations and high prevalence of PIK3CA mutations.

High-throughput detection of fusion genes in cancer using the Sequenom MassARRAY platform

Fusion genes have pivotal roles in the development and progression of human cancer and offer potential for rational drug design. Massively parallel sequencing has identified a panoply of in-frame expressed fusion genes, but early reports suggest that the majority of these are present at very low prevalence or are private events. Conventional methods for the identification of recurrent expressed fusion genes in large cohorts of cancers (eg fluorescence in situ hybridization (FISH) and reverse transcriptase PCR (RT-PCR)) are time consuming and prone to artifacts. Here, we describe a novel high-throughput strategy for the detection of recurrent fusion genes in cancer based on the Sequenom MassARRAY platform. Fusion genes were initially identified by massively parallel sequencing of breast cancer cell lines. For each fusion gene, two Sequenom probes were designed. Primary human breast cancers and cancer cell lines were interrogated for 10 fusion genes. Sensitivity, specificity, and predictive values of the MassARRAY method were then determined using FISH and qRT-PCR as the 'gold standard.' By combining two probes per fusion gene, the negative and positive predictive values were 100 and 71.4%, respectively. All fusion genes identified by massively parallel sequencing were accurately detected. No recurrent fusion genes were found. The MassARRAY-based approach described here may, therefore, be employed as a high-throughput screening tool for known fusion genes in human cancer. In keeping with other highly sensitive assays, further refinement of this technique is necessary to reduce the number of false-positive results.

Eeyarestatin 1 interferes with both retrograde and anterograde intracellular trafficking pathways

BACKGROUND

The small molecule Eeyarestatin I (ESI) inhibits the endoplasmic reticulum (ER)-cytosol dislocation and subsequent degradation of ERAD (ER associated protein degradation) substrates. Toxins such as ricin and Shiga/Shiga-like toxins (SLTx) are endocytosed and trafficked to the ER. Their catalytic subunits are thought to utilise ERAD-like mechanisms to dislocate from the ER into the cytosol, where a proportion uncouples from the ERAD process, recovers a catalytic conformation and destroys their cellular targets. We therefore investigated ESI as a potential inhibitor of toxin dislocation.

METHODOLOGY AND PRINCIPAL FINDINGS

Using cytotoxicity measurements, we found no role for ES(I) as an inhibitor of toxin dislocation from the ER, but instead found that for SLTx, ESI treatment of cells was protective by reducing the rate of toxin delivery to the ER. Microscopy of the trafficking of labelled SLTx and its B chain (lacking the toxic A chain) showed a delay in its accumulation at a peri-nuclear location, confirmed to be the Golgi by examination of SLTx B chain metabolically labelled in the trans-Golgi cisternae. The drug also reduced the rate of endosomal trafficking of diphtheria toxin, which enters the cytosol from acidified endosomes, and delayed the Golgi-specific glycan modifications and eventual plasma membrane appearance of tsO45 VSV-G protein, a classical marker for anterograde trafficking.

CONCLUSIONS AND SIGNIFICANCE

ESI acts on one or more components that function during vesicular transport, whilst at least one retrograde trafficking pathway, that of ricin, remains unperturbed.

Development of a RP-HPLC Method for Analysis of Triphala Curna and its Applicability to Test Variations in Triphala Curna Preparations

A sensitive, rapid, reverse phase HPLC method is reported for analysis of Triphala Curna using gallic acid, chebulagic acid and chebulinic acid as markers. Validation data for the method has been provided. Unlike methods of recovery testing adopted for synthetic chemicals, a modified approach has been presented here for a formulation like Triphala Curna having three myrobalans in its composition. Data has been provided to demonstrate applicability of the method developed to assess the variation in the Triphala Curna preparations.

Abstract 4829: Massively parallel RNA sequencing analysis of micropapillary carcinomas of the breast

Micropapillary carcinomas of the breast are a special type of breast cancer that account for up to 3% of breast cancers and which have an aggressive clinical behaviour. They are preferentially of intermediate to high histological grade and consistently express oestrogen receptor (ER). Previous genomic studies have demonstrated that micropapillary carcinomas are characterized by a constellation of genetic aberrations that is distinct from that of grade and ER-matched ductal carcinomas of the breast. Akin to sarcomas and leukaemias, it has recently been demonstrated that some special types of breast cancer (e.g. secretory and adenoid cystic carcinomas) are characterised by recurrent specific chromosomal translocations leading to the formation of oncogenic fusion genes. The aim of this study was to investigate whether micropapillary carcinomas of the breast harbour novel recurrent fusion genes. A series of six pure micropapillary carcinomas and two secretory carcinomas (positive controls harbouring the ETV6-NTRK3 translocation) were subjected to paired-end massively parallel RNA sequencing (RNA-seq). cDNA libraries were prepared according to standard mRNA prep Illumina protocols and run on the GAII sequencers (read length of each mate pair = 54bp; 2 lanes per sample). Data were aligned to the genome and transcriptome using Eland and mate-pairs supporting novel chimeras identified using previously validated pipelines. Fusion genes identified were validated using reverse transcription PCR (RT-PCR), Sanger sequencing and investigated in separate cohorts of micropapillary carcinomas (n=25) and other types of breast cancer (n=163) using fluorescence in situ hybridisation and RT-PCR. The sensitivity of the approach was validated by the analysis of the two secretory carcinomas, as the ETV6-NTRK3 reciprocal fusion gene was identified using our pipeline. Analysis of micropapillary carcinomas identified four novel intra-chromosomal fusion genes. Three of the fusions; SLC2A1-FAF1, ELMO2-RAE1, BCAS4-AURKA were present in a single tumour and spanned breakpoints of amplification. A fourth, TSPAN14-DYDC2, was a copy neutral event in a separate tumour sample. We also observed that the three fusions from a single patient were also present in the lymph node metastasis. All fusions were validated with RT-PCR, Sanger sequencing and/or FISH. One of the fusion genes was shown to be recurrent (index case and a mixed micropapillary carcinoma). Our results demonstrate that a proportion of micropapillary carcinomas of the breast harbour fusion transcripts. Further investigations are being undertaken to determine the functionality of these fusion genes.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4829. doi:10.1158/1538-7445.AM2011-4829

CyberKnife for prostate cancer: Is it cost-effective?

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Background: The study assessed the cost-effectiveness of CyberKnife (CK) compared to surgery and radiation therapy for the treatment of prostate cancer (PC) from a third-party and societal perspective.

Methods: For patients > 65 yrs with localized PC, a Markov model compared treatment with CK, intensity modulated radiation therapy (IMRT), surgery or proton therapy (PT). Following treatment, patients were at risk of long-term toxicity: genitourinary (GU); gastrointestinal (GI); and sexual dysfunction (SD). Long-term toxicity was defined as adverse events >grade 2 on Radiation Therapy Oncology Group scale occurring at least 12 months following treatment. Markov states included all possible combinations of GI, GU, and SD long-term toxicities, no toxicity, and death. During each year patients remained in the same Markov state or died. Costs and utilities were assigned using published sources. Toxicity probabilities were derived using meta-analytical techniques to pool results from multiple studies. It was assumed that long-term disease control would not differ across treatments. The model projected expected lifetime costs and quality adjusted life years (QALYs) for each treatment and incremental cost-effectiveness of CK vs comparators as cost per QALY gained. Costs from societal perspective included lost productivity. Extensive sensitivity analyses were conducted.

Results: Surgery was the least expensive treatment option followed by CK. CK patients had higher expected QALYs (8.11) than other treatment options (7.72- 8.06). From a payer perspective, total lifetime costs were $25,904, $22,295, $38,915, and $58,100 for CK, surgery, IMRT and PT, respectively. Incremental cost per QALY gained for CK versus Surgery was $9,200/QALY. Compared to IMRT and PT, CK was less costly and resulted in higher QALYs (dominance). At a threshold of $50,000/QALY, CK was cost effective in 86%, 79%, and 91% of simulations compared to surgery, IMRT, and PT, respectively. From a societal perspective, CK costs $4,200/QALY compared to surgery and remained dominant vs IMRT and PT. Results were most sensitive to costs of surgery and CK.

Conclusions: Initial CK costs are higher than surgery, but CK patients have better quality of life. CK patients have lower lifetime costs and higher QALYs than IMRT and PT patients.

[Table: see text]

RNAi screening of Drosophila (Sophophora) melanogaster S2 cells for ricin sensitivity and resistance

The ribosome-inhibiting toxin ricin binds exposed β1→4 linked galactosyls on multiple glycolipids and glycoproteins on the cell surface of most eukaryotic cells. After endocytosis, internal cell trafficking is promiscuous, with only a small proportion of ricin proceeding down a productive (cytotoxic) trafficking route to the endoplasmic reticulum (ER). Here, the catalytic ricin A chain traverses the membrane to inactivate the cytosolic ribosomes, which can be monitored by measuring reduction in protein biosynthetic capacity or cell viability. Although some markers have been discovered for the productive pathway, many molecular details are lacking. To identify a more comprehensive set of requirements for ricin intoxication, the authors have developed an RNAi screen in Drosophila S2 cells, screening in parallel the effects of individual RNAi treatments alone and when combined with a ricin challenge. Initial screening of 806 gene knockdowns has revealed a number of candidates for both productive and nonproductive ricin trafficking, including proteins required for transport to the Golgi, plus potential toxin interactors within the ER and cytosol.

Use of Hydrogenophaga pseudoflava penetration to quantitatively assess the impact of filtration parameters for 0.2-micrometer-pore-size filters

Filters rated as having a 0.2-microm pore size (0.2-microm-rated filters) are used in laboratory and manufacturing settings for diverse applications of bacterial and particle removal from process fluids, analytical test articles, and gasses. Using Hydrogenophaga pseudoflava, a diminutive bacterium with an unusual geometry (i.e., it is very thin), we evaluated passage through 0.2-microm-rated filters and the impact of filtration process parameters and bacterial challenge density. We show that consistent H. pseudoflava passage occurs through 0.2-microm-rated filters. This is in contrast to an absence of significant passage of nutritionally challenged bacteria that are of similar size (i.e., hydrodynamic diameter) but dissimilar geometry.

Unilateral thoracic canal stenosis

Two unusual cases of thoracic spinal canal stenosis are reported. The cord compression was a result of unilateral hypertrophy of the lamina and facet joint. Bony decompression resulted in rapid neurological recovery.