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S W Scherer

Publications and source records attributed to S W Scherer.

At least 73 records · Page 4Linked to original sources
PubMed1999

cDNA cloning, characterization and chromosome mapping of the gene encoding human cartilage associated protein (CRTAP).

We have recently isolated and characterized cDNA clones coding for a novel developmentally regulated avian and mouse embryo protein, CASP for Cartilage Associated Protein. Here we describe the isolation and characterization of the gene coding for the human CASP. The comparison of the putative human and mouse protein sequences with the chick sequence revealed an overall high identity (89% and 51%, respectively). Homology search with known DNA and protein sequences showed that CASPs are related to two mammalian nuclear proteins. Here we demonstrate definitively that CASPs are distinct from these nuclear proteins. However, sequence comparison analyses suggest that all of these proteins belong to a new family. In all human tissues examined two CASP mRNA species were detected, whereas a single mRNA and three mRNAs were found in chick and mouse, respectively. The human CASP gene (CRTAP) was assigned to chromosome 3p22 by fluorescence in situ hybridization.

Amino Acid Sequence↗
PubMed1999

Characterization of the human myeloid leukemia-derived cell line GF-D8 by multiplex fluorescence in situ hybridization, subtelomeric probes, and comparative genomic hybridization.

The human myeloid leukemia cell line GF-D8 was established from the peripheral blood blasts of a patient with acute myeloid leukemia FAB subtype MI (AML-MI). The karyotype, which has not changed significantly over several years of culture, was described initially as 44,XY,-5,del(7q),inv(7q),add(8q),add(11q),del(12p),-15,-17,+mar. With the advent of multicolor fluorescence in situ hybridization (FISH) techniques, the prospect of accurately characterizing this complex karyotype became feasible. In the present study, we applied 24-color whole-chromosome painting and analyzed the results using a filter-based detection system and proprietary software for multiplex FISH (M-FISH). This resulted in the refinement of the karyotype and the identification of hitherto unsuspected chromosome rearrangements. M-FISH identified the origin of the add(8q) and add(11q) as well as the small marker chromosome. Both the del(7q) and del(12p) were redefined as unbalanced translocations and an apparently normal chromosome 11 was shown to be t(11;17). Importantly, the del(12p) was shown to be a der(12)t(7;12). Single-color whole-chromosome painting studies confirmed these findings, but also identified a cryptic t(Y;12) not seen in the original M-FISH analysis. We then carried out a FISH screening assay using a complete set of chromosome-specific subtelomeric probes. This allowed the identification of p and q subtelomeric regions involved in the translocations and indicated amplification of the 8q subtelomeric region. Comparative genomic hybridization (CGH) revealed a highly unbalanced karyotype, as deletions accompanied the majority of translocations, and identified the regions of amplification as 8q22.3-qter and 11q21-qter. Finally, conventional FISH with centromeric and unique sequence probes was necessary to elucidate all of the rearrangements.

Aged↗
PubMed1998

The BCL7 gene family: deletion of BCL7B in Williams syndrome.

The BCL7A gene, which maps to human chromosome 12q24.13, was cloned through its direct involvement with MYC and IGH in a three-way translocation in a Burkitt lymphoma cell line. Here, we describe the identification of two related human genes, BCL7B and BCL7C, which share 90% identity to the amino-terminal 51 amino acids of human BCL7A, as well as 41% identity in the same region to Drosophila melanogaster, Caenorhabditis elegans, and Brugia malayi EST sequences. This degree of relatedness in the amino-terminal domain suggests we have defined a new gene family of unknown function. There was little sequence conservation between the family members outside this conserved domain and no identified protein motifs could be deduced. Human BCL7B and BCL7C mapped to chromosome 7q11.23, and 16p11, respectively. No chromosomal rearrangements affecting BCL7B or BCL7C were detected in lymphoid malignancies. BCL7B did, however, map within the region of 7q11.23 which is commonly deleted in the congenital disorder, Williams syndrome.

Amino Acid Sequence↗
PubMed1998

Human GBF1 is a ubiquitously expressed gene of the sec7 domain family mapping to 10q24.

We present the cDNA sequence of human GBF1 along with data on expression pattern and genomic attributes. The deduced polypeptide encodes a putative guanine nucleotide exchange factor of 206.5 kDa, containing a centrally positioned Sec7 domain and a proline-rich region at the extreme C terminus. Its mRNA transcripts are found in 17 tissues and cell lines, likely suggesting a housekeeping role for GBF1p. The gene maps to 10q24, 2.33 cR from D10S540. It is fully contained within YAC 822C1 and covers at most 450 kb. Its Sec7 domain-encoding region harbors four introns.

Amino Acid Sequence↗
PubMed1998

Molecular cytogenetic characterization of a critical region in bands 7q35-q36 commonly deleted in malignant myeloid disorders.

Loss of chromosome 7 (-7) or deletion of the long arm (7q-) are recurring chromosome abnormalities in myeloid leukemias. The association of -7/7q- with myeloid leukemia suggests that these regions contain novel tumor suppressor gene(s), whose loss of function contribute to leukemic transformation or tumor progression. Based on chromosome banding analysis, two critical regions have been identified, one in band q22 and another in bands q32-q35. Presently there are no data available on the molecular delineation of the distal critical region. In this study we analyzed bone marrow and blood samples from 13 patients with myeloid leukemia (de novo myelodysplastic syndrome [MDS], n = 3; de novo acute myeloid leukemia [AML], n = 9; therapy-related (t-) AML, n = 1) which, on chromosome banding analysis, exhibited deletions (n = 12) or in one case a balanced translocation involving bands 7q31-qter using fluorescence in situ hybridization (FISH). As probes we used representative clones from a contig map of yeast artificial chromosome (YAC) clones that spans chromosome bands 7q31.1-qter. In the 12 cases with loss of 7q material, we identified a commonly deleted region of approximately 4 to 5 megabasepairs in size encompassing the distal part of 7q35 and the proximal part of 7q36. Furthermore, the breakpoint of the reciprocal translocation from the patient with t-AML was localized to a 1,300-kb sized YAC clone that maps to the proximal boundary of the commonly deleted region. Interestingly, in this case both homologs of chromosome 7 were affected: one was lost (-7) and the second exhibited the t(7q35). The identification and delineation of translocation and deletion breakpoints provides the first step toward the identification of the gene(s) involved in the pathogenesis of 7q35-q36 aberrations in myeloid disorders.

Chromosome Mapping↗
PubMed1998

Clustering of human chromosome fragments on the mouse genome by chromosome-mediated gene transfer.

Pieces of metaphase chromosomes prepared from mouse cells containing neo-tagged human chromosome 7 were transferred to mouse cells with calcium phosphate to isolate G418-resistant clones. FISH analysis revealed that the majority of them contained human DNA at a single site on their genome. These transformants contained STS markers mapped to various regions of chromosome 7. It is thus suggested that pieces of human chromosomes tend to assemble and integrate on the mouse genome.

Animals↗
PubMed1998

Molecular characterization of a common fragile site (FRA7H) on human chromosome 7 by the cloning of a simian virus 40 integration site.

Common fragile sites are chromosomal loci prone to breakage and rearrangement, hypothesized to provide targets for foreign DNA integration. We cloned a simian virus 40 integration site and showed by fluorescent in situ hybridization analysis that the integration event had occurred within a common aphidicolin-induced fragile site on human chromosome 7, FRA7H. A region of 161 kb spanning FRA7H was defined and sequenced. Several regions with a potential unusual DNA structure, including high-flexibility, low-stability, and non-B-DNA-forming sequences were identified in this region. We performed a similar analysis on the published FRA3B sequence and the putative partial FRA7G, which also revealed an impressive cluster of regions with high flexibility and low stability. Thus, these unusual DNA characteristics are possibly intrinsic properties of common fragile sites that may affect their replication and condensation as well as organization, and may lead to fragility.

Base Sequence↗
PubMed1998

Genomic structure of the human congenital chloride diarrhea (CLD) gene.

Congenital chloride diarrhea (CLD) is caused by mutations in a gene which encodes an intestinal anion transporter. We report here the complete genomic organization of the human CLD gene which spans approximately 39kb, and comprises 21 exons. All exon/intron boundaries conform to the GT/AG rule. An analysis of the putative promoter region sequence shows a putative TATA box and predicts multiple transcription factor binding sites. The genomic structure was determined using DNA from several sources including multiple large-insert libaries and genomic DNA from Finnish CLD patients and controls. Exon-specific primers developed in this study will facilitate mutation screening studies of patients with the disease. Genomic sequencing of a BAC clone H_RG364P16 revealed the presence of another, highly homologous gene 3' of the CLD gene, with a similar genomic structure, recently identified as the Pendred syndrome gene (PDS).

Base Sequence↗
PubMed1998

Structural characterization and mapping of the normal epithelial cell-specific 1 gene.

The normal epithelial cell-specific 1 (NES1) gene is a recently identified novel serine protease-like gene which is down-regulated during breast cancer progression. The gene product has 34-42% identity with the members of three distinct serine protease families: the trypsin-like family, activators of kringle domain-containing growth factors, and the kallikrein family (X. L. Liu et al., (1996) Cancer Res 56, 3371-3379). Although the cDNA of this gene has been cloned, its genomic structure and chromosomal position are not as yet known. Here, we report the genomic characterization and mapping of the NES1 gene. By subcloning and sequencing a PAC clone containing the complete NES1 gene, we were able to characterize the structure of this gene. The NES1 gene spans 5.5 kb and is composed of five coding exons and one untranslated exon. The positions of the introns were similar to trypsinogen, prostate specific antigen (PSA), and tissue plasminogen activator (TPA). NES1 gene was also localized with somatic cell mapping, radiation hybrid mapping, and fluorescence in situ hybridization techniques to chromosome 19q13.3-q13.4, the same region where the human kallikrein gene family resides. Taken together, our results suggest that the NES1 gene originates from the same ancestor as trypsinogen, PSA, and TPA, but remains in close proximity to PSA.

Amino Acid Sequence↗
PubMed1998

Human PON2 gene at 7q21.3: cloning, multiple mRNA forms, and missense polymorphisms in the coding sequence.

We report the cloning and characterization of human PON2, a paraoxonase-related gene-2 that is physically linked with PON1 and PON3 on 7q2l.3. PON2 is ubiquitously expressed and we identified several mRNA forms produced by alternative splicing, or by the use of a second transcription start site. We also describe two polymorphisms in the coding sequences that, in the protein deduced from the longest open reading frame, predict an alanine-to-glycine substitution at residue 147 and a serine-to-cysteine substitution at residue 310.

Amino Acid Sequence↗
PubMed1998

Localization of 67 exons on a YAC contig spanning 1.5 Mb around the multidrug resistance gene region of human chromosome 7q21.1.

A contig of 21 nonchimeric yeast artificial chromosomes (YACs) was previously assembled across 1.5 Mb of the multidrug resistance (MDR) gene (PGY1 and PGY3) region of human chromosome 7q21.1. This region of the human genome has now been subjected to exon amplification to detect the presence of additional genes. Exon trapping was performed directly on the YACs. Sixty-seven gene fragments were isolated and characterized by sequence analysis and comparison with public databases. The localization of these exons in the 1.5-Mb region was determined by hybridization to YAC clones, and they were localized in 11 subregions of YAC contigs. The exon collection includes 21 exons that were identical to known cDNA sequences of PGY1, PGY3, sorcin (SRI), the cDNA similar to the delta subunit of the human amiloride-sensitive Na- channel (SCNED), and 4 cDNAs with unknown function; 43 exons that showed homology/similarity to known cDNA sequences of mouse DMP1, rat COT, mouse and human NADHD, human MDC, 3 cDNAs encoding possible membrane proteins, and 21 other cDNAs; and 3 exons that shared no homology/similarity with any sequence in public databases. The nucleotide sequences of all the PGY1 and PGY3 exons were identical to the corresponding cDNA sequences previously determined, and these exons were localized to the expected positions on the appropriate YAC clones. No other member of the MDR gene family thus appeared to be present in the 1.5-Mb region. The integrated physical and exon maps should prove valuable for both fine mapping and determination of a complete gene map of this segment of the genome.

ATP Binding Cassette Transporter, Subfamily B↗
PubMed1998

Cloning and mapping of a cDNA for methionine synthase reductase, a flavoprotein defective in patients with homocystinuria.

Methionine synthase catalyzes the remethylation of homocysteine to methionine via a reaction in which methylcobalamin serves as an intermediate methyl carrier. Over time, the cob(I)alamin cofactor of methionine synthase becomes oxidized to cob(II)alamin rendering the enzyme inactive. Regeneration of functional enzyme requires reductive methylation via a reaction in which S-adenosylmethionine is utilized as a methyl donor. Patients of the cblE complementation group of disorders of folate/cobalamin metabolism who are defective in reductive activation of methionine synthase exhibit megaloblastic anemia, developmental delay, hyperhomocysteinemia, and hypomethioninemia. Using consensus sequences to predicted binding sites for FMN, FAD, and NADPH, we have cloned a cDNA corresponding to the "methionine synthase reductase" reducing system required for maintenance of the methionine synthase in a functional state. The gene MTRR has been localized to chromosome 5p15.2-15.3. A predominant mRNA of 3.6 kb is detected by Northern blot analysis. The deduced protein is a novel member of the FNR family of electron transferases, containing 698 amino acids with a predicted molecular mass of 77,700. It shares 38% identity with human cytochrome P450 reductase and 43% with the C. elegans putative methionine synthase reductase. The authenticity of the cDNA sequence was confirmed by identification of mutations in cblE patients, including a 4-bp frameshift in two affected siblings and a 3-bp deletion in a third patient. The cloning of the cDNA will permit the diagnostic characterization of cblE patients and investigation of the potential role of polymorphisms of this enzyme as a risk factor in hyperhomocysteinemia-linked vascular disease.

5-Methyltetrahydrofolate-Homocysteine S-Methyltran↗
PubMed1998

The hyaluronidase gene HYAL1 maps to chromosome 3p21.2-p21.3 in human and 9F1-F2 in mouse, a conserved candidate tumor suppressor locus.

We recently cloned and expressed the major hyaluronidase activity from human plasma, HYAL1, and found that the protein is 40% identical to the testicular hyaluronidase, PH-20. The HYAL1 mRNA sequence was used in a homology search of the mouse database of expressed sequence tags (dbEST). Two ESTs were obtained and, in combination with 5'RACE-PCR, were used to clone the mouse HYAL1 ortholog (Hyal1). Hyal1 codes for a protein of 462 amino acids that is 73% identical to the human sequence. Hyal1 stably expressed in human embryonic kidney cells resulted in a 20,000-fold increase of hyaluronidase activity. Sequence-tagged sites derived from the HYAL1 gene from both species were used to isolate P1 genomic clones that were used as probes for fluorescence in situ hybridization. The human gene was localized to chromosome 3p21 and the mouse gene to a syntenic region on chromosome 9F1-F2. In mouse, serum hyaluronidase polymorphism has previously been mapped by an interspecific backcross to 60 cM from the centromere of chromosome 9, which corresponds to a cytogenetic location of 9F1-F2. The mouse Hyal1 gene is therefore very likely to be responsible for the hyaluronidase polymorphism linked to this locus. We also present evidence that human HYAL1 is identical to an uncharacterized gene positionally cloned by others from chromosome 3p21.3 that is homozygously deleted in several small-cell lung carcinoma cell lines.

Amino Acid Sequence↗
PubMed1998

Analysis of the human Sonic Hedgehog coding and promoter regions in sacral agenesis, triphalangeal thumb, and mirror polydactyly.

The human Sonic Hedgehog gene (SHH) is one of the vertebrate homologs related to the Drosophila segment polarity gene hedgehog. The entire coding and promoter region of the SHH gene, including 2 kb 5' of the transcriptional start site has been screened for mutations in families with autosomal dominant sacral agenesis and autosomal dominant triphalangeal thumb, two conditions previously known to be linked to 7q36. We have also studied the SHH gene in five families with mirror polydactyly associated with tibial hemimelia and in 51 unrelated patients with neural tube defects. Except for two sequence variants in exon 3, no mutations were found in these disease categories. OFF

Abnormalities, Multiple↗