Isolation and genetic characterization of human KB cell lines resistant to multiple drugs

Human KB cell lines resistant to high levels of colchicine were isolated by several successive single-step selections. Most of these selection steps resulted in cross-resistance to vincristine, vinblastine, adriamycin, actinomycin D, and puromycin; however, at the highest levels of colchicine resistance, increased cross-resistance to other drugs was not observed. There was no major change in protein synthesis or alteration in protein phosphorylation or [^14C]glucosamine labeling patterns accompanying the development of multiple drug resistance as measured by analysis of metabolically labeled proteins on SDS gels. Cell-cell hybridization experiments showed that the colchicine-resistant and multiple drug-resistant phenotypes were incompletely dominant. In addition, colchicine resistance was found to segregate independently from resistance to other drugs in one somatic cell hybrid, suggesting that complex genetic loci are involved in the development of the multiple drug-resistant phenotype. These mutants should be useful for the study of the clinically important problem of multiple drug resistance in human cancer.     

Molecular cytogenetic characterization of rhabdomyosarcoma cell lines

Alveolar rhabdomyosarcomas (ARMS) are soft-tissue tumors that are genetically characterized by the presence of reciprocal translocations that generate the fusion gene PAX3-FOXO1A or PAX7-FOXO1A. For the study of the biologic consequences of such rearrangements, several cell lines have been generated. However, established cell lines accumulate chromosome and genetic aberrations that make it difficult to draw significant conclusions. We have applied a set of techniques that includes spectral karyotyping, fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), and microarray CGH, to the most commonly used cell lines carrying the two fusion genes that are present in ARMS. We have identified the bacterial artificial chromosomes that cover the breakpoints at genes PAX3, PAX7, and FOXO1A, which can be used as FISH probes for the translocations. The RH30 cell line, positive for the PAX3-FOXO1A fusion gene, was found to be highly complex: wide range of chromosome number, more than 50 chromosome rearrangements, amplification of the hybrid gene, 24 DNA changes detected by conventional CGH, and 21 gene copy changes detected by microarray CGH (including several high-level amplifications). RMZ-RC2 cell line, positive for the PAX7-FOXO1A, was in the near-tetraploid range with only nonclonal structural rearrangements, amplification of the hybrid gene, 24 DNA changes by CGH, and 8 gene copy changes, confirming the previously reported high-level amplification of MYCN.     

Molecular cytogenetic characterization of non-Hodgkin lymphoma cell lines.

Spectral karyotyping (SKY) and comparative genomic hybridization (CGH) have greatly enhanced the resolution of cytogenetic analysis, enabling the identification of novel regions of rearrangement and amplification in tumor cells. Here we report the analysis of 10 malignant non-Hodgkin lymphoma (NHL) cell lines derived at the Ontario Cancer Institute (OCI), Toronto, designated as OCI-Ly1, OCI-Ly2, OCI-Ly3, OCI-LY4, OCI-Ly7, OCI-Ly8, OCI-Ly12, OCI-Ly13.2, OCI-Ly17, and OCI-Ly18, by G-banding, SKY, and CGH, and we present their comprehensive cytogenetic profiles. In contrast to the 52 breakpoints identified by G-banding, SKY identified 87 breakpoints, which clustered at 1q21, 7p15, 8p11, 13q21, 13q32, 14q32, 17q11, and 18q21. G-banding identified 10 translocations, including the previously described recurring translocations, t(8;14)(q24;q32) and t(14;18)(q32;q21). In contrast, SKY identified 60 translocations, including five that were recurring, t(8;14)(q24;q32), t(14;18)(q32;q21), t(4;7)(p12;q22), t(11;18)(q22;q21), and t(3;18)(q21;p11). SKY also identified the source of all the marker chromosomes. In addition, 10 chromosomes that were classified as normal by G-banding were found by SKY to be rearranged. CGH identified seven sites of high-level DNA amplification, 1q31-32, 2p12-16, 8q24, 11q23-25, 13q21-22, 13q32-34, and 18q21-23; of these, 1q31-32, 11q23-25, 13q21-22, and 13q32-34 have previously not been described as amplified in NHL. This comprehensive cytogenetic characterization of 10 NHL cell lines identified novel sites of rearrangement and amplification; it also enhances their value in experimental studies aimed at gene discovery and gene function.     

Chromosome 8 genetic analysis and phenotypic characterization of 21 ovarian cancer cell lines

The short arm of chromosome 8 undergoes frequent loss of heterozygosity (LOH) in ovarian adenocarcinomas. Fine mapping has identified several distinct critical regions within 8p which undergo rates of LOH of 50% or greater, suggesting that there may be more than one tumor suppressor gene located on this chromosome arm. In an effort to refine the location of these putative tumor suppressor genes by homozygosity-mapping-of-deletion analysis, we have analyzed 21 ovarian cancer cell lines with 19 polymorphic microsatellite markers from 8p. Eleven of the cell lines (55%) were homozygous at every marker, indicating loss of an entire 8p arm. No smaller extended regions of hemizygosity were identified. Refinement of these 8p target regions was therefore not possible, but this analysis did identify the ovarian cancer cell lines that would be most appropriate for microcell-mediated chromosome transfer to complement the hypothesized mutation in the target tumor suppressor gene(s) on 8p. The 11 cell lines that had undergone 8p LOH were therefore characterized for colony formation in soft agar and tumor formation in nude mice. We identified four cell lines (JAM, OVCA4, OVCA5, and OVCA8) that were hemizygous for 8p and that formed colonies in soft agar and tumors in nude mice, making them ideal cell lines for chromosome 8 or candidate gene transfer.     

Cytogenetic and biological characterization of two new human plasma cell lines

Two new human plasma cell lines designated as ACB-885 and ACB-1085 have been established from a 39-year-old patient with multiple myeloma. These cell lines have definitive plasma cell features by morphologic examination, and essentially all of the cells are positive for cytoplasmic IgG kappa immunoglobulin. These cells are negative for standard T-cell surface markers and mature B-cell markers, such as B1, B2, and HLA-DR, but are strongly positive for the antigen defined by OKT-10. The cells are negative for Epstein-Barr virus. The cell lines have a doubling time of 30-35 hours and a growth fraction approaching 100%. Cytogenetic analysis showed a 2n chromosome number of 45-46 with very similar karyotypic abnormalities in both the plasma cell lines and the original tumor material. One of the chromosomes in each of the pairs of chromosomes number #1, #2, #6, #7, #8, #10, #12, #13, and #22 were consistently missing. These were replaced by eight marker chromosomes that resulted from chromosomal rearrangements involving mainly these missing chromosomes. Almost all of the breakpoints occurring in the marker chromosomes were identified, and eight of these breakpoints have been reported in other studies of myeloma plasma cells. Homogeneously staining regions were observed in two marker chromosomes suggesting gene amplification in these chromosomal regions.     

Comparison of diphtheria intoxication in human and nonhuman cell lines and their resistant variants.

Differences in sensitivity to diphtheria toxin of several toxin-sensitive and toxin-resistant human and non-human cell lines were compared. A method is described whereby it is possible to compare the sensitivity of one cell line with another and obtain meaningful quantitative results. Based on the concentration of toxin required to produce 50% inhibition of protein synthesis after 24 h of exposure the ID50 (24) value toxin-resistant cells were found to be 105 to 106 times more resistant to toxin than toxin-sensitive cells. There was little variation in the ID50 (24) values for cells in each of the two groups. The toxin-resistant cells used in this study, naturally resistant as well as selected variants, possess elongation factor 2 which is susceptible to inactivation by toxin. It is suggested that they are capable of activation of toxin but either cannot bind toxin or are unable to transport toxin across the plasma membrane. Protein synthesis is inhibited when these resistant cells are exposed to high concentrations of toxin. Under these conditions it is likely that enough toxin is able to bypass the block in toxin-specific entry and reach the cytosol by a second, less efficient, nonspecific mechanism to catalyze the inactivation of elongation factor 2 and inhibit protein synthesis.     

Selection and characterization of canine, swine and rabbit cell lines resistant to bovine viral diarrhea virus

Contamination of cell cultures with adventitious viruses may pose serious risks for virology diagnosis, research and vaccine production. This article reports the selection and characterization of three cell lines resistant to bovine viral diarrhea virus (BVDV), a major contaminant of cell cultures. The resistant cells were obtained from canine (MDCK), swine (PK-15) and rabbit (RK-13) parental cell lines by expanding and cloning cells that survived lytic infection with BVDV. All three selected cell lines were resistant to three standard BVDV strains and to 10 field isolates as demonstrated by immunofluorescence for viral antigens and by co-cultivation with susceptible cells. Inoculation of selected cells with BVDV (10 TCID50/cell) resulted in frequencies of infection of <10(-5) (MDCK-R, PK-15R) and 3.3 x 10(-4) (RK-13R). Comparing to the parental cell lines, these cells were >10,000-, >20,000- and 600-fold less susceptible to BVDV, respectively. Inoculation of resistant cells with BVDV in the presence of polyethylene-glycol increased the frequency of infection in the order of >437-, >346- and 87-fold, respectively, indicating that resistance is probably due to a block in viral entry. Nevertheless, each resistant cell line retained the susceptibility to three other viruses that replicate in the parental cells. Thus, these cells may be useful for many virology purposes, with a very low risk of BVDV contamination.     

Molecular characterization of human multiple myeloma cell lines by integrative genomics: insights into the biology of the disease

To investigate the patterns of genetic lesions in a panel of 23 human multiple myeloma cell lines (HMCLs), we made a genomic integrative analysis involving FISH, and both gene expression and genome-wide profiling approaches. The expression profiles of the genes targeted by the main IGH translocations showed that the WHSC1/MMSET gene involved in t(4;14)(p16;q32) was expressed at different levels in all of the HMCLs, and that the expression of the MAF gene was not restricted to the HMCLs carrying t(14;16)(q32;q23). Supervised analyses identified a limited number of genes specifically associated with t(4;14) and involved in different biological processes. The signature related to MAF/MAFB expression included the known MAF target genes CCND2 and ITGB7, as well as genes controlling cell shape and cell adhesion. Genome-wide DNA profiling allowed the identification of a gain on chromosome arm 1q in 88% of the analyzed cell lines, together with recurrent gains on 8q, 18q, 7q, and 20q; the most frequent deletions affected 1p, 13q, 17p, and 14q; and almost all of the cell lines presented LOH on chromosome 13. Two hundred and twenty-two genes were found to be simultaneously overexpressed and amplified in our panel, including the BCL2 locus at 18q21.33. Our data further support the evidence of the genomic complexity of multiple myeloma and reinforce the role of an integrated genomic approach in improving our understanding of the molecular pathogenesis of the disease. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.     

Establishing standards for the characterization of human embryonic stem cell lines

As of August 2005, 22 human embryonic stem cell (hESC) lines listed on the National Institutes of Health (NIH) hESC Registry were being distributed to investigators. At a June 2005 meeting of NIH-supported hESC researchers, we proposed that a set of shared standards should be available in order to characterize the cells unambiguously in multiple laboratories. Here, we elaborate such a plan to identify a set of standard methods and to initiate collaborative efforts to validate the standards. The standard assays we propose should be comprehensive enough to ensure that hESC banks can provide a consistent and reliable product for NIH researchers, and inexpensive enough that individual laboratories can afford to use at least some of the methods routinely in their laboratories. We expect that as data accumulate and standards evolve, a core set of tests will become the norm for routine assessment of hESC cultures and that these tests will lay the groundwork for clinical applications of these cells.     

Molecular genetic analysis of chromosome 9 candidate tumor-suppressor loci in bladder cancer cell lines

Underrepresentation of chromosome 9 is a common finding in bladder cancer. Frequent loss of the whole chromosome suggests the presence of at least one relevant tumor suppressor gene on each arm. Candidate regions identified by loss of heterozygosity (LOH) analysis include a region at 9p21 containing CDKN2A, which encodes p16 and p14(ARF), a large region at 9q12-31 including PTCH and many other genes, a small region at 9q32-33, which includes the DBCCR1 gene, and a region at 9q34 including the TSC1 gene. Experimental replacement of genes or chromosomes into tumor cells with appropriate deletions or mutations represents an important approach to test the functional significance of candidate tumor suppressor genes. Loss of an entire copy of chromosome 9 in many bladder tumor cell lines provides no indication of which gene or genes are affected, and selection of appropriate recipient cells for gene replacement is difficult. We have investigated three candidate tumor suppressor genes on chromosome 9 (CDKN2A, DBCCR1, and TSC1), at the DNA level and by expression analysis in a panel of bladder tumor cell lines, many of which have probable LOH along the length of the chromosome, as indicated by homozygosity for multiple polymorphic markers. Cytogenetically, we found no reduction in the numbers of chromosomes 9 relative to total chromosome count. Homozygous deletion of the CDKN2A locus was frequent but homozygous deletion of TSC1 was not found. A new cell line, DSH1, derived from a pT1G2 transitional cell carcinoma with known homozygous deletion of DBCCR1, is described. This study identifies suitable cell lines for future functional analysis of both CDKN2A and DBCCR1.     

Karyotypic characterization of established cell lines and short-term cultures of human lung cancers

Karyotypic patterns were analyzed from the four major histopathologic groups of human lung cancer: small cell (SCC), squamous cell (SQC), large cell (LCC), and adenocarcinoma (ADC). The studies were performed on banded chromosomes from direct preparations of pleural fluids (one case of SQC and LCC, respectively) and on cell lines. All metaphases were aneuploid and showed highly rearranged chromosomes, with the exception of the direct preparation of the SQC, which was pseudodiploid. The number of marker chromosomes varied-from tumor to tumor. No consistent aberrations could be detected. Special attention was paid to chromosomes 3p-, which was earlier reported to be a characteristic marker chromosome for SCC. We could confirm the presence of that abnormality in two of our six SCC lines. However, we also found a 3p- in a primary SQC culture, in one LCC cell line, and in one ADC cell line. The breakpoint on 3p was not consistent. In some lines, numerical and structural changes of chromosomes #1, #12, #14, and #22 were also noteworthy, although none of these chromosome abnormalities seemed to be correlated to a certain histopathologic group.     

Cytogenetic characterization of three human and three rat medullary thyroid carcinoma cell lines

Medullary thyroid carcinoma (MTC) is a neuroendocrine tumor of the thyroid C-cells. MTC may arise as a sporadic tumor or as a component of one of three autosomal dominant familial cancer syndromes, MEN 2A, MEN 2B, or familial MTC. Recent studies have identified mutations of the RET protooncogene in the proximal long arm of chromosome 10, which are thought to be causative for these syndromes. To facilitate the search for other genes involved in the development of MTC, we characterized cytogenetically three human MTC cell lines and three rat MTC cell lines. The human cell lines studied were TT and RO-H85-1, previously reported, and an uncharacterized cell line, MZ-CRC-1, derived from a malignant pleural effusion from a patient with metastatic MTC. The rat MTC cell lines characterized were CA-77, 6–23C₆, and 44-2. Cytogenetic abnormalities present in the human and rat cell lines were compared with 13 reported cytogenetic studies of human MTC tumors and three other cytogenetically analyzed MTC cell lines. The human 9q/rat 3 and human 3p/rat 15 chromosomes were affected in six of the comparable cell lines and tumors. These findings suggest human chromosome regions 9q and 3p may contain genes involved in the pathogenesis of MTC.     

Production and characterization of human 293 cell lines expressing the site-specific recombinase Cre

We have constructed 293 cell lines expressing the site-specific Cre recombinase from bacteriophage P1, that acts on a 34 bp target sequence calledloxP. Stably transformed cells were obtained by transfection with a plasmid containing Cre and a selectable marker under the control of viral promoters. The resulting 293 Cre cell lines could be used to induce expression from adenovirus vectors containing reporter genes under the control of a Cre responsive “molecular switch” High efficiency recombination was observed for Ad viral DNA containingloxP sites. The Cre expressing cell lines described here are likely to be useful for several purposes: For expression of toxic gene products from Cre inducible viral vectors, to induce recombination betweenloxP sites in transfected plasmids, and to induce deletions or rearrangements of genes defined byloxP sites in viral genomes.