ESTDAB: a collection of immunologically characterised melanoma cell lines and searchable databank

Cancer immunologists working in humans often require panels of tumour cell lines expressing different combinations of HLA alleles and other characteristics. Sources of cell lines are usually large cell banks carrying little immunologically relevant information on the available cells and limited numbers of different lines from the same type of tumour. Access to cells with desired combinations of characteristics is, therefore, difficult. Here, we describe an interactive database of a large collection of melanoma cell lines which have been extensively characterised for HLA genotype and surface expression, oncogene and tumour antigen expression, cytokine secretion, surface molecule expression, adhesion to extracellular matrix components, cytokine gene polymorphisms and other factors of interest to immunologists. This enables investigators to search for cells with particular constellations of HLA alleles, tumour antigens, etc., and then request these from the cell bank. This European Searchable Tumour Cell Line and Data Bank (ESTDAB) was established as a Research Infrastructure of the European Commission. For access to the databank and further details, please go to .     

Identification of cancer stem cells-associated “side population” by flow cytometry with a violet laser

The possibility of identification of a “side population” of cancer stem cells in solid tumors by a flow cytometer equipped with a 405 nm violet laser has been investigated. Ovarian cancer (Skov-3) and colorectal cancer (Colo 320) cell lines formed the “side population” after vital staining with Hoechst 33342. Analysis of cells isolated from the tumor tissue of malignant melanoma and colorectal cancer, also revealed the “side population” characterized by increased fluorescent dye exclusion. The percentage of melanoma cells included in the “side population” was the same as that of cells co-expressing the cancer stem cells markers CD34 and CD44. However, the colon cancer “side population” was significantly smaller than the minor populations of colon cancer cells identified by either CD133 expression or exclusion of Rhodamine 123 exclusion.     

Characterization of glycosylation and adherent properties of melanoma cell lines

The repertoire of oligosaccharide components of cellular glycoproteins significantly contributes to cell adhesion and communication. In tumor cells, alteration in cellular glycosylation may play a key role in giving rise to invasive and metastatic potential. Over 100 melanoma cell lines deposited in the ESTDAB Melanoma Cell Bank (Tubingen, Germany) were studied for the characteristic glycan composition related to tumor progression. Analysis of: (1) cell adhesion to extracellular matrix proteins—fibronectin, laminin, and collagen; (2) the expression of selected glycosyltransferases—α2,3(Galβ1,3)- and α2,3(Galβ1,4)-sialyltransferases, α1,2- and α1,3-fucosyltransferases, and N-acetylglucosaminyltransferase V; (3) characterization of N-glycans was carried out on uveal (4), primary cutaneous (6), and metastatic (96) melanoma cell lines. Results showed that uveal cells did not adhere to any of the substrates and, in general, possessed less glycans containing α-2,6- and α-2,3-linked sialic acid. The average number of polypeptides bearing β-1,6-branched tri- and tetra antennary glycans(characteristic of the metastatic phenotype)were similar in uveal, primary cutaneous, and metastatic melanoma cell lines. Characterization of N-glycans may open a new perspective in the search for specific glycoproteins that could become targets for the therapeutic modulation of melanoma. This article is a symposium paper from the conference “Progress in Vaccination against Cancer 2004 (PIVAC 4)”, held in Freudenstadt-Lauterbad, Black Forest, Germany, on 22–25 September 2004     

A novel cell array technique for high-throughput,cell-based analysis

Summary Microarray technology has burgeoned over the past few years from nucleic acid-based arrays to tissue microarrays (TMAs). This study aimed to develop a technique to incorporate cell lines into an array and to demonstrate the usefulness of this technique by performing immunohistochemistry for β-catenin. Cell suspensions were prepared from 23 tumor cell lines. These were fixed in formalin, suspended in agar, and embedded in paraffin to produce a cell block. A “tissue microarrayer” was used to remove triplicate, 0.6 mm-cores from each cell block and to transfer these into a recipient paraffin block at precise coordinates. Immunohistochemistry was used to identify cell lines positive for β-catenin. Cultured cells were successfully incorporated into the microarray, with preservation of cell architecture and even distribution of cells within each core. A total of 18 of 69 cores (26%) were lost in processing. A total of 16 of 23 cell lines were identified as positive for membrane and cytoplasmic β-catenin, and 6 of 23 were negative. Only one cell line was unscorable because of complete core loss. We have developed a “cell microarray” technique for analyzing antigen expression by immunohistochemistry in multiple cell lines in a single expriment. This novel application of microarrays permits high-throughput, cost-efficient analysis, with the potential to rapidly identify markers with potential diagnostic and therapeutic implications in human disease.     

Indian rice “Kasalath” contains genes that improve traits of Japanese premium rice “Koshihikari”

Rice (Oryza sativa L.) chromosome segment substitution lines (CSSLs), in which chromosomal segments of the Indian landrace “Kasalath” replace the corresponding endogenous segments in the genome of the Japanese premium rice “Koshihikari”, are available and together cover the entire genome. Chromosome regions affecting a trait (CRATs) can be identified by comparison of phenotypes with genotypes of CSSLs. We detected 99 CRATs for 15 agronomic or morphological traits. “Kasalath” had positively acting alleles in 53 CRATs. Its CRATs increased panicle number per plant by up to 23.3%, grain number per panicle by up to 30.8%, and total grain number by up to 15.1%, relative to “Koshihikari”. CRATs were identified for grain size (grain thickness and width), with positive effects of about 5.0%. A CRAT on chromosome 8 almost doubled the weight of roots in uppermost soil layers compared to “Koshihikari”. Additionally, “Kasalath” possessed CRATs for higher lodging resistance (reduction in plant height and increase in stem diameter). In some cases, multiple CRATs were detected in the same chromosome regions. Therefore, CSSLs with these chromosome segments might be useful breeding materials for the simultaneous improvement of multiple traits. Five CRATs, one for plant height on chromosome 1, one for stem diameter on chromosome 8, and three for heading date on chromosomes 6, 7, and 8 overlapped with the corresponding QTLs that already had been mapped with back-crossed inbred lines of “Nipponbare” and “Kasalath”. In both “Koshihikari” CRATs and “Nipponbare” QTLs, “Kasalath” had similar effects. Both Y. Madoka and T. Kashiwagi have contributed equally to this article.     

Characterization of HLA class I altered phenotypes in a panel of human melanoma cell lines

Background Altered HLA class I cell surface expression is one of the major mechanisms by which tumor cells escape from T lymphocytes. Immunohistochemistry-defined phenotypes of lost HLA class I expression have been described in human solid tumors, nut less information is available on melanoma cell lines. Objectives To describe the frequency and distribution of different types of HLA class I antigen alterations in 91 melanoma cell lines from the European Searchable Tumour Cell and Databank (ESTDAB). Methods The HLA class I expression was assessed by flow cytometry and HLA genotyping. Results We found various types of HLA class I cell surface alterations in about 67% of the melanoma cell lines. These alterations range from total to selective HLA class I loss due to loss of heterozygosity (LOH), haplotype loss, β2-microglobulin gene mutation, and/or total or selective down-regulation of HLA class I molecules. The most frequently observed phenotype is down-regulation of HLA-B locus that was reversible after treatment with IFN -γ. Conclusions In general, HLA class I alterations in the majority of the cells analyzed were of regulatory nature and could be restored by IFN-γ. Analysis of the frequency of distinct HLA class I altered phenotypes in these melanoma cell lines revealed specific differences compared to other types of tumors. Rosa Méndez and Teresa Rodríguez have equally contributed to this work and both should be considered as first authors.     

HLA-C “blank” alleles express class I gene products. Biochemical analysis of four different HLA-C “blank” polypeptides

Monoclonal antibodies (mAbs) W6/32, HC10, and 4E were used to precipitate class I antigens from 21 selected individuals with at least oneHLA-C “blank” allele. In 19 of these individuals, characteristicHLA-C banding patterns which could be precipitated by all three HLA class I mAbs were observed on one-dimensional isoelectric focusing gels-obviously the gene products ofHLA-C “blank”. At least four allelic HLA-C “blank” gene products with different isoelectric points could be discerned. All of them segregated withHLA-C “blank” haplotypes in informative families; two of them were associated withHLA-B51, one withHLA-B38, and one withHLA-B18. Reactivity of the HLA-C “blank” heavy chains with mAb W6/32 indicates that they are able to associated with beta-2 microglobulin, and hence are most probably expressed at the cell surface.     

Developing Microsatellite Multiplex and Megaplex PCR Systems for High-Throughput Characterization of Breeding Progenies and Linkage Maps Spanning the Apricot (<Emphasis Type="Italic">Prunus armeciaca</Emphasis> L.) Genome

One hundred and twenty apricot and peach simple sequence repeat (SSR) markers have been used in the molecular characterization of a BC1 apricot progeny of 73 seedlings derived from the cross between the F1 selection “Z506-07” (“Orange Red” × “Currot”) and the Spanish cultivar “Currot.” To reduce costs and improve the capacity of molecular characterization assays using SSR markers, a series of seven megaplex PCRs containing between six and 20 SSR markers were developed for the molecular characterization of the apricot breeding progeny studied. Amplification was successful in apricot progenitors and in the progeny with 114 of the 120 (95%) SSR markers with a suitable level of polymorphism (1.7 alleles/marker) detected in the BC1 descendants studied. In addition, the implementation of megaplex PCR increased the efficiency and reduced the cost of this type of molecular studies. The implications of these results for apricot-breeding programs and the construction of genetic linkage maps have been also discussed.     

Advanced backcross-QTL analysis in spring barley (H. vulgare ssp. spontaneum) comparing a REML versus a Bayesian model in multi-environmental field trials

A common difficulty in mapping quantitative trait loci (QTLs) is that QTL effects may show environment specificity and thus differ across environments. Furthermore, quantitative traits are likely to be influenced by multiple QTLs or genes having different effect sizes. There is currently a need for efficient mapping strategies to account for both multiple QTLs and marker-by-environment interactions. Thus, the objective of our study was to develop a Bayesian multi-locus multi-environmental method of QTL analysis. This strategy is compared to (1) Bayesian multi-locus mapping, where each environment is analysed separately, (2) Restricted Maximum Likelihood (REML) single-locus method using a mixed hierarchical model, and (3) REML forward selection applying a mixed hierarchical model. For this study, we used data on multi-environmental field trials of 301 BC₂DH lines derived from a cross between the spring barley elite cultivar Scarlett and the wild donor ISR42-8 from Israel. The lines were genotyped by 98 SSR markers and measured for the agronomic traits “ears per m2,” “days until heading,” “plant height,” “thousand grain weight,” and “grain yield”. Additionally, a simulation study was performed to verify the QTL results obtained in the spring barley population. In general, the results of Bayesian QTL mapping are in accordance with REML methods. In this study, Bayesian multi-locus multi-environmental analysis is a valuable method that is particularly suitable if lines are cultivated in multi-environmental field trials. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

New methods to approach immunotherapy of cancer – and strategies of tumours to avoid elimination

Owing to the intense effort of numerous investigators, the number of tumour antigens potentially of use for clinical immunotherapy continues to increase. At the same time, further strategies employed by tumour cells to avoid destruction by the immune system are being uncovered. A combined onslaught to target tumour cells and prevent their “escape” will be required for successful immunotherapy. Progress in this area was the subject of a meeting supported by the European Cancer Research Consortium “EUCAPS”, which was held in London in February 2000. This conference was the second of a series, the first of which was summarised previously in this journal [Pawelec G et al. (1999) Cancer Immunol Immunother 48: 214]. Received: 14 March 2000 / Accepted: 30 March 2000     

Responses to non-locomotive prey models by the praying mantis,Tenodera angustipennis Saussure

Adult females of the praying mantisTenodera angustipennis were presented with computer-generated images, and the attractiveness of “non-locomotive” prey models was examined. Mantises fixated and struck the “body and leg” model (consisting of an immobile black square on a white background with 2 black lines oscillating randomly at its sides) more frequently than the “leg” model (only oscillating lines) or the “body” model (static square only). This indicates that the model consisting of a static object and moving lines effectively elicits mantis strike behavior, although it is “non-locomotive.”     

Purification and in vitro cultivation of archaeocytes (stem cells) of the marine sponge <Emphasis Type="Italic">Hymeniacidon perleve</Emphasis> (Demospongiae)

Marine sponges (Porifera) are the best source of marine bioactive metabolites for drug discovery and development, although the sustainable production of most sponge-derived metabolites remains a difficult task. In vitro cultivation of sponge cells in bioreactors has been proposed as a promising technology. However, no continuous cell line has as yet been developed. Archaeocytes are considered to be toti/multipotent stem cells in sponges and, when purified, may allow the development of continuous sponge cell lines. As a prerequisite, we have developed a novel four-step protocol for the purification of archaeocytes from a marine sponge, Hymeniacidon perleve: (1) differential centrifugation to separate large sponge cells including archaeocytes; (2) selective agglomeration in low-Ca²⁺/Mg²⁺ artificial seawater in which living archaeocytes form small loose aggregates with some pinacocytes and collencytes; (3) differential adherence to remove anchorage-dependent pinacocytes, collencytes and other mesohyl cells; (4) Ficoll-Vrografin density gradient centrifugation to purify archaeocytes. The final purity of archaeocytes is greater than 80%. The proliferation potential of the archaeocytes has been demonstrated by high levels of BrdU incorporation, PCNA expression and telomerase activity. In 4-day primary cultures, the purified archaeocytes show a 2.5-fold increase in total cell number. This study opens an important avenue towards developing sponge cell cultures for the commercial exploitation of sponge-derived drugs. The authors are grateful for the financial support of the Chinese Academy of Sciences under the “100 Talent Project”, the “Innovation Fund” from the Dalian Institute of Chemical Physics, the “Hi-Tech Research and Development Program of China” (2001AA620404), and the European Commission (project: Silicon Biotechnology).     

Characterization of JOK-1, a human gastric epithelial cell line

Summary Human gastric epithelial cells were isolated from samples of human gastric lining and immortalized with simian virus 40 (SV40) to generate the stable human gastric epithelial cell line “JOK-1” These cells express conventional, epithelial markers (vimentin, cytokeratin-18, occludin, N-and E-cadherins, β-catenin, ZO-1, ZO-2, mucin, epithelial specific antigen) as well as SV40 large T-antigen. These cells rapidly externalized E-cadherin in response to acidic medium, and exhibited epitheliallike barrier properties that are also regulated by media pH. In contrast, the kidney epithelial cell line “MDCK” also expresses serveral epithelial markers (vimentin, cytokeratin-18, occludin, N-and E-cadherin, β-catenin, ZO-1, ZO-2, epithelial specific antigen), but does not express mucin, or large T-antigen. However, MDCK rapidly internalize their E-cadherin from the cell surface and increase the solute flux in an acidic medium. These data suggest that the JOK-1 cell line is a potentially useful cell line for developing models of gastric epithelial function, development, and disease.     

A comparative location database (CompLDB): map integration within and between species

We have adapted the Location Database (LDB) map-integration strategy of Morton et al. [Ann Hum Genet 56:223–232] (1992) as above to create an integrated map for each of several species for which fully annotated genome sequences are not yet available (sheep, cattle, pig, wallaby), using all types of partial maps for that species, including cytogenetic, linkage, somatic-cell hybrid, and radiation hybrid maps. An integrated map provides not only predictions of the kilobase location of every locus, but also predicts locations (in cM) and cytogenetic band locations for every locus. In this way a comprehensive linkage map and a comprehensive cytogenetic map are created, including all loci, irrespective of whether they have ever been linkage mapped or physically mapped, respectively. High-resolution physical maps from annotated sequenced species have also been placed alongside the integrated maps. This has created a powerful tool for comparative genomics. The LDB map-integration strategy has been extended to make use of zoo-FISH comparative information. It has also been extended to enable the creation of a “virtual” map for each species not yet sequenced by using mapping data from fully sequenced species. All of the partial maps, together with the integrated map, for each species have been placed in a database called Comparative Location Database (CompLDB), which is available for querying, browsing, or download in tabular form at . Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Single cell adhesion measuring apparatus (SCAMA): application to cancer cell lines of different metastatic potential and voltage-gated Na<Superscript>+</Superscript> channel expression

We have developed a simple yet effective apparatus, based upon negative pressure directed to the tip of a micro-pipette, to measure the adhesiveness of single cells. The “single cell adhesion measuring apparatus” (SCAMA) could differentiate between the adhesion of strongly versus weakly metastatic cancer cells as well as normal cells. Adhesion was quantified as “detachment negative pressure” (DNP) or “DNP relative to cell size” (DNPR) where a noticeable difference in cell size was apparent. Thus, for rat and human prostate and human breast cancer cell lines, adhesiveness (DNPR values) decreased in line with increased metastatic potential. Using the SCAMA, we investigated the effect of tetrodotoxin (TTX), a specific blocker of voltage-gated Na⁺ channels (VGSCs), on the adhesion of rat and human prostate cancer cell lines of markedly different metastatic potential. Following pretreatment with TTX (48 h with 1 μM), the adhesion values for the Mat-LyLu cells increased significantly 4.3-fold; there was no effect on the AT-2 cells. For the strongly metastatic PC-3M cells, TTX treatment caused a significant (∼30%) increase in adhesion. The adhesion of PNT2-C2 (“normal”) cells was not affected by the TTX pretreatment. The TTX-induced increase in the adhesiveness of the strongly metastatic cells was consistent with the functional VGSC expression in these cells and the proposed role of VGSC activity in metastatic cell behaviour. In conclusion, the SCAMA, which can be constructed easily and cheaply, offers a simple and effective method to characterise single-cell adhesion and its modulation.     

HSPVdb—the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands

T cell epitopes derived from polymorphic proteins or from proteins encoded by alternative reading frames (ARFs) play an important role in (tumor) immunology. Identification of these peptides is successfully performed with mass spectrometry. In a mass spectrometry-based approach, the recorded tandem mass spectra are matched against hypothetical spectra generated from known protein sequence databases. Commonly used protein databases contain a minimal level of redundancy, and thus, are not suitable data sources for searching polymorphic T cell epitopes, either in normal or ARFs. At the same time, however, these databases contain much non-polymorphic sequence information, thereby complicating the matching of recorded and theoretical spectra, and increasing the potential for finding false positives. Therefore, we created a database with peptides from ARFs and peptide variation arising from single nucleotide polymorphisms (SNPs). It is based on the human mRNA sequences from the well-annotated reference sequence (RefSeq) database and associated variation information derived from the Single Nucleotide Polymorphism Database (dbSNP). In this process, we removed all non-polymorphic information. Investigation of the frequency of SNPs in the dbSNP revealed that many SNPs are non-polymorphic “SNPs”. Therefore, we removed those from our dedicated database, and this resulted in a comprehensive high quality database, which we coined the Human Short Peptide Variation Database (HSPVdb). The value of our HSPVdb is shown by identification of the majority of published polymorphic SNP- and/or ARF-derived epitopes from a mass spectrometry-based proteomics workflow, and by a large variety of polymorphic peptides identified as potential T cell epitopes in the HLA-ligandome presented by the Epstein–Barr virus cells.     

DNA markers linked to eastern filbert blight resistance in ��Ratoli�� hazelnut (Corylus avellana L.)

Eastern filbert blight (EFB), caused by the pyrenomycete Anisogramma anomala (Peck) E. Müller, is a major disease problem and production constraint in orchards of European hazelnut (Corylus avellana L.) in Oregon’s Willamette Valley. Host genetic resistance is viewed as the most economical means of controlling this disease. A dominant resistance gene from “Gasaway” has been used extensively in the hazelnut breeding program at Oregon State University, but concern about the durability of a single resistance gene stimulated a search for new sources of resistance. “Ratoli,” a minor cultivar from Spain, showed no signs or symptoms of the fungus following a series of inoculations. The objective of this study was to study segregation for disease response in two progenies from crosses of Ratoli with susceptible selections and identify linked DNA markers. About half of the seedlings were resistant, suggesting control by a dominant allele at a single locus. A total of 900 random amplified polymorphic DNA (RAPD) primers and 64 amplified fragment length polymorphism (AFLP) primer combinations were screened. Four RAPD markers and two ALFP markers were identified and a linkage map constructed. On this map, disease resistance was flanked by AFLP marker C4-255 and RAPD marker G17-800 at distances of 0.4 cM and 2.8 cM, respectively. Based on co-segregation with SSR markers, Ratoli resistance was assigned to linkage group 7 while Gasaway resistance is on linkage group 6. Ratoli provides a novel source of EFB resistance, and robust RAPD marker G17-800 is useful for marker-assisted selection.