Genetic events during the transformation of a tamoxifen-sensitive human breast cancer cell line into a drug-resistant clone.

Tamoxifen resistance is a serious clinical problem commonly encountered in the management of patients with breast cancer. The mechanisms leading to its development are unclear. Tamoxifen acts via multiple pathways and has diverse effects. Hence transformation from a tamoxifen-sensitive to a resistant phenotype could involve multiple genetic events. Knowledge of the genetic pathways leading to resistance may facilitate the development of novel therapeutic strategies. In this study, a variation of conventional comparative genomic hybridization (CGH) has been employed to detect genetic alterations associated with tamoxifen resistance. MCF-7, a tamoxifen-sensitive human breast cancer cells line, and its tamoxifen-resistant clone, CL-9 were used. Both cell lines showed extensive areas of concordance but consistent differences were seen with the acquisition of tamoxifen resistance. These differences included the amplification of 2p16.3 approximately p23.2, 2q21 approximately q34, 3p12.3 approximately p14.1, 3p22 approximately p26, 3q, 12q13.2 approximately q22, 13q12 approximately q14, 17q21.3 approximately q23, 20q11.2 approximately q13.1 and 21q11.2 approximately q21 as well as the deletion of 6p21.1, 6p23 approximately p25, 7q11.1 approximately q31, 7q35 approximately q36, 11p15, 11q24, 13q33, 17p, 18q12 approximately q21.1, 19p, 19q13.3, 22q13.1 approximately q13.2. These findings were supported by conventional cytogenetics and chromosome painting. The regions identified by CGH potentially harbor genes that could be important in the development of tamoxifen resistance.

Yeast artificial chromosome cloning and chromosomal localization of the abundant odontogenic keratocyst protein elafin.

An imbalance in human leucocyte elastase (HLE) activity is widely recognized to play an important pathological role in a number of human diseases. An earlier report has described greater transcription of elafin, an endogenous inhibitor of HLE, in epithelia of odontogenic keratocysts of the jaw than in normal oral mucosa. The elafin gene was now localized to chromosome 20q11.2-13.1 using a combination of somatic cell-hybrid panel screening and fluorescence in situ hybridization using a biotinylated DNA probe prepared from isolated yeast artificial chromosomes. No other positive fluorescent signals were observed. This eliminates the elafin gene as a candidate gene for naevoid basal-cell carcinoma syndrome, as the gene for this syndrome localizes to chromosome 9q23.1-31. The elafin yeast artificial chromosome DNA is to be subcloned to identify polymorphic microsatellite markers that will establish whether this gene is frequently amplified in oral neoplastic tissue.

Haematopoietic repopulating activity in human cord blood CD133+ quiescent cells.

We have demonstrated previously that cord blood CD133(+) cells isolated in the G(0) phase of the cell cycle are highly enriched for haematopoietic stem cell (HSC) activity, in contrast to CD133(+)G(1) cells. Here, we have analysed the phenotype and functional properties of this population in more detail. Our data demonstrate that a large proportion of the CD133(+)G(0) cells are CD38 negative (60.4%) and have high aldehyde dehydrogenase activity (75.1%) when compared with their CD133(+)G(1) counterparts (13.5 and 4.1%, respectively). This suggests that stem cell activity resides in the CD133(+)G(0) population. In long-term BM cultures, the CD133(+)G(0) cells generate significantly more progenitors than the CD34(+)G(0) population (P<0.001) throughout the culture period. Furthermore, a comparison of CD133(+)G(0) versus CD133(+)G(1) cells revealed that multilineage reconstitution was obtained only in non-obese diabetic/SCID animals receiving G(0) cells. We conclude that CD133(+) cells in the quiescent phase of the cell cycle have a phenotype consistent with HSCs and are highly enriched for repopulating activity when compared with their G(1) counterparts. This cell population should prove useful for selection and manipulation in ex vivo expansion protocols.

Marker gene transfer into human haemopoietic cells using a herpesvirus saimiri-based vector.

Herpesvirus-based gene therapy vectors offer an attractive alternative to retroviral vectors because of their episomal nature and ability to accommodate large transgenes. Saimiriine herpesvirus 2 (HVS) is a prototypical gamma-2 herpesvirus that can latently infect numerous different cell types. A cosmid-generated HVS vector in which transforming genes have been deleted and the marker gene encoding enhanced green fluorescent protein (HVS-GFP) has been incorporated was evaluated for its potential to transduce CD34+ haemopoietic progenitors selected from cord blood. Expression of GFP could subsequently be readily detected in cells of the erythroid lineage in both CFU-GEMM assays and liquid differentiation cultures. These results confirm the potential of HVS as a candidate vector for gene therapy applications using primitive haemopoietic cells and suggest that it may be applicable to disorders affecting cells of the erythroid lineage.

Human glucokinase regulatory protein (GCKR): cDNA and genomic cloning, complete primary structure, and chromosomal localization.

Null mutations in the glucokinase (GCK) gene can cause autosomal dominant type 2 diabetes (maturity onset diabetes of the young, MODY); however, MODY is genetically heterogeneous. In both liver and pancreatic islet, glucokinase is subject to inhibition by a regulatory protein (GCKR). Given the role of GCK in MODY, GCKR is itself a candidate type 2 diabetes susceptibility gene. Here we describe the structure of full-length (2.2 kb) cDNA for human GCKR, from the hepatoblastoma cell line HepG2. The human GCKR translation product has 625 amino acids and a predicted molecular weight of 68,700. It has 88% amino acid identity to rat GCKR. Yeast artificial chromosomes (YAC clones) containing human GCKR were isolated, and the gene was mapped to Chromosome (Chr) 2p23 by fluorescent in situ hybridization and somatic cell hybrid analysis.

Identification of a novel microsatellite marker tightly linked to the KAI-1 gene for predicting prostate cancer progression.

BACKGROUND: We have mapped the human prostate-specific membrane antigen (PSM) gene to the chromosome 11p11.2 region at 62.5 cM, a region which also contains the prostatic cancer metastasis suppressor gene KAI-1. The genetic marker D11S1344 has been utilised for loss of heterozygosity (LOH) studies on the KAI-1 gene in a large series of prostate cancer specimens. The results were negative and it was concluded that deletions of the KAI-1 gene were not involved in the development of the metastatic phenotype in these tumours. One possible explanation for this result could be that D11S1344 is not sufficiently tightly linked to the KAI-1 gene to detect small deletions. OBJECTIVE: To attempt to identify a genetic marker more tightly linked to the KAI-1 gene than D11S1344. METHODS: Yeast artificial chromosome (YAC) clones containing the KAI-1 gene and the neighbouring marker D11S1344 were analysed by the fluorescent in situ hybridisation technique. The human genomic inserts in these novel clones were sized by pulsed field gel electrophoresis. For more accurate mapping of the KAI-1 gene, YACs containing it were screened for polymorphic markers (including D11S1344) from the 11p11.2 region. RESULTS: The novel YAC clones localised exclusively to the 11p11.2 region, with single hybridisation signals compared to the dual signals consistently obtained with nearby PSM-containing YACs. All the KAI-1 clones found had small inserts (<300 kb). The only known microsatellite which gave amplification products with these YACs was D11S986 which has been mapped at 61.3 cM on human chromosome 11. CONCLUSIONS: We have precisely localised KAI-1 at 61.3 cM on human chromosome 11. This is some 1.2 cM away from the previously utilised LOH microsatellite marker, D11S1344. We suggest that the very tightly linked microsatellite D11S986 may be a more accurate marker to assess LOH of the KAI-1 gene and thus predict progression of prostate cancer. The region of genetic duplication around the PSM gene does not extend as far distally on 11p as KAI-1.

Clinical value of serum immunoreactive trypsin concentration.

The clinical value of estimation of serum concentrations of immunoreactive trypsin was evaluated by studying 46 healthy controls, 23 controls in hospital, 44 patients with chronic pancreatic disease, and 184 patients with non-pancreatic conditions in which pancreatic disease commonly enters into the differential diagnosis. Serum trypsin concentration had a log normal distribution in the controls, and the calculated normal range was considerably wider than that previously reported. The concentration was abnormal in only 13 out of 27 patients with chronic pancreatitis and was extremely variable in patients with pancreatic cancer. Abnormal results occurred in 11% of the patients with non-pancreatic disease. Eighteen patients had a subnormal trypsin concentration, of whom six did not have pancreatic disease and 12 had either chronic pancreatitis or pancreatic cancer. There was no correlation between serum trypsin concentration and mean tryptic activity as measured by the Lundh test. Of 11 patients with pancreatic steatorrhoea, only seven had subnormal trypsin concentrations. There results suggest that the serum concentrations of immunoreactive trypsin has a low specificity and sensitivity for pancreatic disease and does no reflect the degree exocrine insufficiency in patients with proved chronic pancreatitis.

Genomic organization of the human ubiquitin-conjugating enzyme gene, UBE2L6 on chromosome 11q12.

The human UBE2L6 gene encodes UbcH8(Kumar), a ubiquitin-conjugating enzyme (E2) highly simliar in primary structure to UbcH7 which is encoded by UBE2L3. Like UBC4 and UBC5 in yeast, these proteins demonstrate functional redundancy. Herein we report the intron/exon structure of UBE2L6. Comparison of the genomic organization of UBE2L6 with UBE2L3 demonstrates that these genes remain highly conserved at the genomic as well as at the protein level. We also describe the chromosomal localization of UBE2L6, which maps to chromosome 11q12.

Characterisation of the human and mouse orthologues of the Drosophila ariadne gene.

The specificity of the ubiquitin degradation system is regulated through interaction between individual ubiquitin-conjugating enzymes (E2s) and multiple ubiquitin-protein ligases (E3s). Here we describe the characterisation of a novel gene (ARIH1) that encodes the human homologue of Drosophila ariadne which interacts with the E2s, UbcH7 and UbcH8 and represents a component of an E3 complex. Three PACs (189N19, 142P17 and 179H7) were isolated that contain this gene. Using these PACs as probes, we mapped ARIH1 to human chromosome 15q24 by fluorescence in situ hybridisation (FISH). Sequencing of the ARIH1 PACs showed that the gene has 13 introns. In addition, we isolated two PACs (345D8 and 571P19) containing the mouse orthologue (Arih1) of ARIH1. The intron-exon structure of Arih1 was identical to ARIH1 and the proteins demonstrated a 98% identity at the amino acid level. Furthermore, comparison of Drosophila ariadne with ARIH1 indicates an identity at the amino acid level of 70% and introns at 3/7 identical sites. The high degree of homology demonstrated by the mouse and human orthologues of Drosophila ariadne indicates an important, conserved biological function, consistent with a putative role in ubiquitylation.

Characterization of human SHC p66 cDNA and its processed pseudogene mapping to Xq12-q13.1.

SHC is an adapter protein in the Ras-MAPkinase pathway that is involved in the regulation of cell growth and differentiation. The p46 and p52 isoforms are thought to be produced by the use of two alternative translation initiation sites in a 3.4-kb transcript from the SHCA gene, which maps to chromosome 1q21. The p66 isoform could be encoded by a different 3.8- or 2.8-kb transcript of the same gene or alternatively by a SHC-related gene. To characterize other putative genes coding for SHC-like proteins, primers from the 3' UTR of the SHCA gene were used to screen a yeast artificial chromosome (YAC) library by polymerase chain reaction (PCR). Two YAC clones, 20D11B and 36D1D, were isolated and used as probes for fluorescence in situ hybridization analysis. Both these probes hybridized to chromosome Xq12-q13.1. This novel SHC-related sequence was characterized by direct sequencing of vectorette library PCR products produced from clone 20D11B. A transcript of 3.2 kb that was 85% identical to the mouse Shc cDNA encoding the p66 isoform was identified. Sequence analysis demonstrated the presence of multiple stop codons identifying this isoform of SHC as a processed pseudogene. Using primers designed on the basis of the nucleotide sequence of the pseudogene, we have now amplified and sequenced a human cDNA that encodes the SHC p66 protein. Thus, we have characterized the human SHC p66 isoform cDNA and identified a processed SHC pseudogene that maps to chromosome Xq12-q13.1.

Human sequences homologous to the gene for the cochlear protein Ocp-II do not map to currently known non-syndromic hearing loss loci.

The abundant and almost exclusive expression of OCP-II protein in the mammalian cochlea has fuelled speculation that mutations in the OCP2 gene may result in inherited forms of hearing impairment. We have identified several human sequences related to OCP2 and sublocalised three of these OCP2 related loci to 4q12-p14 or 4p16.2-pter, 5q15-q21.3 and 7p22-q22 by PCR. 2 YACs with sequence consistent with the chromosome 7 locus were also used for FISH analysis and hybridised to chromosome 7q11. Our data suggest that the cytogenetic localisations of these OCP2 related sequences do not correlate with the precise chromosomal positions of deafness loci so far identified.

Detailed genetic mapping around a putative prostate-specific membrane antigen locus on human chromosome 11p11.2.

Physical mapping of the human prostate-specific membrane antigen gene (FOLH) has not been straightforward. Previously, localisations of this gene to either 11p11.2 or 11q14 have been described. This raised the possibility of the presence of more than one related FOLH gene in man. We now present detailed characterisation of the region around a FOLH gene in a 500-kb non-chimaeric YAC clone, putatively assigned to 11p11.2. This clone contains two known microsatellites, D11S1326 and D11S1357 which have been previously mapped unequivocally to the 11p11.2 region at 62.5 cM. This data strongly supports the original 11p11.2 localisation of FOLH. The YAC clone also has a putative EST at each of its ends and these have thus been physically positioned on this chromosome. However, the two regions previously highlighted at 11p11.2 and 11q14 are apparently extensively duplicated, as evidenced by the appearance of dual FISH signals with a number of different genomic probes selected across this 500-kb 11p11.2 region.

Rapid isolation of genomic clones for individual members of human multigene families: identification and localisation of UBE2L4, a novel member of a ubiquitin conjugating enzyme dispersed gene family.

We describe a rapid, PCR-based, screening procedure for the isolation of human genomic clones in lambda bacteriophage, containing sequences coding for individual homologous members of a multigene family. The approach is based upon the identification, by dilution, of sub-pools of the genomic library that contain members of the gene family, prior to phage isolation. The presence of specific genes is established by PCR of aliquots of individually amplified library pools, using consensus primers and subsequent sequencing. We have used the approach to isolate a fourth member of the UBE2L gene family, UBE2L4, and located it on chromosome 19q13.1-->q13.2. This PCR-based approach to library screening has wider applicability in that it could be used to isolate alternate-spliced products from cDNA libraries.

Novel translocation of the BCL10 gene in a case of mucosa associated lymphoid tissue lymphoma.

Interest has focused on a recently identified gene, BCL10, thought to play an important role in the genesis of extranodal, marginal zone (MALT) lymphomas. This gene belongs to a family containing caspase recruitment domains (CARD), that are involved in the apoptotic pathway. Translocations of the BCL10 gene to the immunoglobulin heavy chain locus at 14q32 have been described. We report herein a case of MALT lymphoma showing t(1; 2)(p22; p12). The translocation was shown to involve the BCL10 gene and the immunoglobulin kappa light chain locus by fluorescence in situ hybridization.

Characterization of a human ubiquitin-conjugating enzyme gene UBE2L3.

Ubiquitin-conjugating enzymes (E2s) are essential components of the post-translational protein ubiquitination pathway, mediating the transfer of activated ubiquitin to substrate proteins. We have identified a human gene, UBE2L3, localized on Chromosome (Chr) 22q11. 2-13.1, encoding an E2 almost identical to that encoded by the recently described human L-UBC (UBE2L1) gene present on Chr 14q24.3. Using chromosome-specific vectorette PCR, we have determined the intron/exon structure of UBE2L3. In contrast to the intronless UBE2L1 gene, the coding sequence of UBE2L3 is interrupted by three large introns. UBE2L3-derived mRNA appears to be the predominant species in most tissues rather than the transcript from UBE2L1 or another homologous gene UBE2L2, which maps to Chr 12q12. We also present additional evidence that these genes are members of a larger multigene family. The primary sequence of the protein encoded by UBE2L3 is identical to partial peptide sequence derived from the rabbit E2 'E2-F1,' suggesting that we have identified the human homolog of this protein. This latter E2 has been demonstrated to participate in transcription factor NF-kappaB maturation, c-fos degradation, and human papilloma virus-mediated p53 degradation in vitro.

A human ubiquitin conjugating enzyme, L-UBC, maps in the Alzheimer's disease locus on chromosome 14q24.3.

We have identified a novel ubiquitin conjugating enzyme gene, L-UBC, which maps to human Chromosome (Chr) 14q24.3. This is also the location of the major early onset familial Alzheimer's disease gene (FAD3). L-UBC encodes a protein that demonstrates homology to the yeast ubiquitin conjugating enzyme, UBC-4, and human UbcH5. Their functions are to ubiquitinate specific proteins targeted for degradation. The protein also exhibits very strong homology to a rabbit protein, E2-F1, which mediates p53 degradation driven by papilloma virus E6 protein in vitro. The accumulation of specific proteins that have undergone aberrant processing in neurofibrillary tangles and amyloid plaques is the classic pathological feature in brains of Alzheimer's disease patients. Abnormal ubiquitination has previously been suggested to play a role in the etiology of Alzheimer's disease. This gene therefore represents a plausible candidate gene for FAD3.

A locus for isolated cleft palate, located on human chromosome 2q32.

We present evidence for the existence of a novel chromosome 2q32 locus involved in the pathogenesis of isolated cleft palate. We have studied two unrelated patients with strikingly similar clinical features, in whom there are apparently balanced, de novo cytogenetic rearrangements involving the same region of chromosome 2q. Both children have cleft palate, facial dysmorphism, and mild learning disability. Their karyotypes were originally reported as 46, XX, t(2;7)(q33;p21) and 46, XX, t(2;11)(q33;p14). However, our molecular cytogenetic analyses localize both translocation breakpoints to a small region between markers D2S311 and D2S116. This suggests that the true location of these breakpoints is 2q32 rather than 2q33. To obtain independent support for the existence of a cleft-palate locus in 2q32, we performed a detailed statistical analysis for all cases in the human cytogenetics database of nonmosaic, single, contiguous autosomal deletions associated with orofacial clefting. This revealed 2q32 to be one of only three chromosomal regions in which haploinsufficiency is significantly associated with isolated cleft palate. In combination, our data provide strong evidence for the location at 2q32 of a gene that is critical to the development of the secondary palate. The close proximity of these two translocation breakpoints should also allow rapid progress toward the positional cloning of this cleft-palate gene.