William G. Nash

Expression of the human c-fms proto-oncogene in hematopoietic cells and its deletion in the 5q- syndrome.

The c-fms proto-oncogene was shown to be expressed in human bone marrow and in differentiated blood mononuclear cells, suggesting that its gene product plays a role in hematopoietic maturation. The c-fms mRNA was not detected in HL-60 cells, an established promyelocytic line, whereas c-fms expression appeared 48 hr after induction when most cells had differentiated into macrophages. An acquired deletion of chromosome 5 (5q-) in bone marrow cells is associated with abnormalities in blood cell production. The normal 5 and 5q- chromosomes were segregated by construction of cell hybrids between bone marrow and rodent cells. A selective system was used that requires retention of the structural gene for dihydrofolate reductase, located on human chromosome 5. Analysis of DNA from individual hybrid clones revealed that the 5q- deletion had removed the c-fms gene. We postulate that hemizygosity at the c-fms locus leads to abnormalities in hematopoietic maturation.

ERV3, a Full-Length Human Endogenous Provirus: Chromosomal Localization and Evolutionary Relationships

A full-length human endogenous provirus termed ERV3 was isolated from a human fetal recombinant DNA library by low stringency hybridization with two probes: baboon endogenous virus LTR; and a pol-env subclone from the endogenous chimpanzee provirus, CH2. DNA sequencing within the clone and comparisons with other retroviruses revealed that ERV3 contains gag and pol gene sequences that are significantly related to those of mammalian type C retroviruses and previously described human endogenous proviruses. The ERV3 genome was determined to reside at a single locus on human chromosome 7 using a panel of rodent X human somatic cell hybrids.

Atlas of Mammalian Chromosomes

Foreword. Preface. Acknowledgments. MONOTREMATA. Order Monotremata. MARSUPIALIA. Order Didelphimorphia. Order Paucituberculata. Order Microbiotheria. Order Dasyuromorphia. Order Peramelemorphia. Order Notoryctemorphia. Order Diprotodontia. AFROTHERIA. Order Afrosoricida. Order Macroscelidea. Order Sirenia. Order Proboscidea. Order Hyracoidea. Order Tubulidentata. XENARTHRA. Order Xenarthra. EUARCHONTOGLIRES. Order Scandentia. Order Dermoptera. Order Primates. Order Rodentia. Order Lagomorpha. LAURASIATHERIA. Order Eulipotyphla. Order Chiroptera. Order Carnivora. Order Pholidota. Order Cetartiodactyla. Order Perissodactyla.

Comparative Genomics: Tracking Chromosome Evolution in the Family Ursidae Using Reciprocal Chromosome Painting

The Ursidae family includes eight species, the karyotype of which diverges somewhat, in both chromosome number and morphology, from that of other families in the order Carnivora. The combination of consensus molecular phylogeny and high-resolution trypsin G-banded karyotype analysis has suggested that ancestral chromosomal fissions and at least two fusion events are associated with the development of the different ursid species. Here, we revisit this hypothesis by hybridizing reciprocal chromosome painting probes derived from the giant panda (Ailuropoda melanoleuca), domestic cat (Felis catus), and man (Homo sapiens) to representative bear species karyotypes. Comparative analysis of the different chromosome segment homologies allowed reconstruction of the genomic composition of a putative ancestral bear karyotype based upon the recognition of 39 chromosome segments defined by painting as the smallest conserved evolutionary unit segments (pSCEUS) among these species. The different pSCEUS combinations occurring among modern bear species support and extend the postulated sequence of chromosomal rearrangements and provide a framework to propose patterns of genome reorganization among carnivores and other mammal radiations.

Chromosomal Evolution of the Canidae. I. Species with High Diploid Numbers

The Giemsa banding patterns of seven canid species, including the grey wolf (Canis lupus), the maned wolf (Chrysocyon brachyurus), the bush dog (Speothos venaticus), the crab-eating fox (Cerdocyon thous), the grey fox (Urocyon cinereoargenteus), the bat-eared fox (Otocyon megalotis), and the fennec (Fennecus zerda), are presented and compared. Relative to other members of Canidae, these species have high diploid complements (2n greater than 64) consisting of largely acrocentric chromosomes. They show a considerable degree of chromosome homoeology, but relative to the grey wolf, each species is either missing chromosomes or has unique chromosomal additions and rearrangements. Differences in chromosome morphology among the seven species were used to reconstruct their phylogenetic history. The results suggest that the South American canids are closely related to each other and are derived from a wolf-like progenitor. The fennec and the bat-eared fox seem to be recent derivatives of a lineage that branched early from the wolf-like canids and which also includes the grey fox.

The Pattern of Phylogenomic Evolution of the Canidae

Canidae species fall into two categories with respect to their chromosome composition: those with high numbered largely acrocentric karyotypes and others with a low numbered principally metacentric karyotype. Those species with low numbered metacentric karyotypes are derived from multiple independent fusions of chromosome segments found as acrocentric chromosomes in the high numbered species. Extensive chromosome homology is apparent among acrocentric chromosome arms within Canidae species; however, little chromosome arm homology exists between Canidae species and those from other Carnivore families. Here we use Zoo-FISH (fluorescent in situ hybridization, also called chromosomal painting) probes from flow-sorted chromosomes of the Japanese raccoon dog (Nyctereutes procyonoides) to examine two phylogenetically divergent canids, the arctic fox (Alopex lagopus) and the crab-eating fox (Cerdocyon thous). The results affirm intra-canid chromosome homologies, also implicated by G-banding. In addition, painting probes from domestic cat (Felis catus), representative of the ancestral carnivore karyotype (ACK), and giant panda (Ailuropoda melanoleuca) were used to define primitive homologous segments apparent between canids and other carnivore families. Canid chromosomes seem unique among carnivores in that many canid chromosome arms are mosaics of two to four homology segments of the ACK chromosome arms. The mosaic pattern apparently preceded the divergence of modern canid species since conserved homology segments among different canid species are common, even though those segments are rearranged relative to the ancestral carnivore genome arrangement. The results indicate an ancestral episode of extensive centric fission leading to an ancestral canid genome organization that was subsequently reorganized by multiple chromosome fusion events in some but not all Canidae lineages.

Cytogenetic Methodologies for Gene Mapping and Comparative Analyses in Mammalian Cell Culture Systems

Presented here are the detailed methods employed in our laboratory for gene mapping and cytogenetic analyses in human beings, in the domestic cat, and in other mammalian species. Induced in the procedures are: 1) establishment of primary fibroblast and lymphoid cell cultures; 2) heterologous cell fusion for production of rapidly proliferating cell hybrids; 3) cellular transformation of primary fibroblasts using an oncogenic retrovirus; 4) cell synchronization for high-resolution banding of promethaphase chromosomes; 5) chromosome-banding procedures, including G-banding, alkaline G-11, and Q-banding; and 6) in situ hybridization of radiolabeled molecular clones to metaphase chromosomes for regional gene localization.

Organization and chromosomal specificity of autosomal homologs of human Y chromosome repeated DNA

The human Y chromosome contains a group of repeated DNA elements, identified as 3.4-kilobase pair (kb) fragments in Hae III digests of male genomic DNA, which contain both Y-specific and non-Y-specific sequences. We have used these 3.4-kb Hae III Y fragments to explore the organizational properties and chromosomal distribution of the autosomal homologs of the non-Y-specific (NYS) 3.4-kb Hae III Y elements. Three distinct organizations, termed domains, have been identified and shown to have major concentrations on separate chromosomes. We have established that domain K is located on chromosome 15 and domain D on chromosome 16 and suggested that domain R is on chromosome 1. Our findings suggest that each domain is composed of a tandemly arrayed cluster of a regularly repeating unit containing two sets of repeated sequences: one that is homologous to the NYS 3.4-kb Hae III Y sequences and one that does not cross-react with the 3.4-kb Hae III Y repeats. Thus, these autosomal repeated DNA domains, like their Y chromosome counterparts, consist of a complex mixture of repeated DNA elements interspersed among each other in ways that lead to defined periodicities. Although each of the three identified autosomal domains cross-reacts with 3.4-kb Hae III Y fragments purified from genomic DNA, the length periodicities and sequence content of the autosomal domains are chromosome specific. The organizational properties and chromosomal distribution of these NYS 3.4-kb Hae III homologs seem inconsistent with stochastic mechanisms of sequence diffusion between chromosomes.

A comparative chromosome banding analysis of the Ursidae and their relationship to other carnivores

Trypsin G-banded karyotypes of eight species of Ursidae were prepared from retrovirus-transformed skin fibroblast cultures. The banding patterns of all bears are highly conserved, even though their diploid numbers range from 42 to 72. A comprehensive analysis of the homologous banding patterns within the Ursidae and with a hypothesized ancestral carnivore karyotype permitted the reconstruction of three significant chromosomal reorganization events that occurred during the evolution of the modern ursids. The first was a multichromosomal fissioning away from the biarmed (2n = 44) primitive carnivore karyotype, leading to six species of the Ursinae subfamily (2n = 78). The second was a comprehensive chromosome fusion in the lineage that led to the Ailuropodinae (giant panda) subfamily (2n = 44). The third event was a second, independent, but less extensive, centromeric fusion occurring in the line that led to the Tremarctinae (spectacled bear) subfamily (2n = 52). Ursidae karyotypes are not only highly conserved within the family but also exhibit extensive chromosome banding homology with other carnivore families.

Molecular cytogenetic analysis of the bladder carcinoma cell line BK-10 by spectral karyotyping.

The bladder cancer cell line BK‐10 was established from a grade III–IV transitional cell carcinoma (TCC). BK‐10 is near‐tetraploid (±4n) and consists of two subclones with 20–25 structural aberrations. Here we report the cytogenetic analysis of BK‐10 by G‐banding, spectral karyotyping (SKY), and FISH. SKY refers to the hybridization of 24 differentially labeled chromosome painting probes and the simultaneous visualization of all human chromosomes using spectral imaging. SKY enabled us to confirm 12 markers in BK‐10 previously described by G‐banding, redefine 11 aberrations, and detect 4 hidden chromosomal rearrangements, 2 of which had been identified as normal or deleted copies of chromosome 20 and 1 as a normal chromosome 3. Twenty out of 21 translocations identified were unbalanced. FISH analysis of BK‐10 using chromosome arm‐specific paints, centromere probes, and oncogene/tumor suppressor gene‐specific probes revealed a deletion of CDKN2A (p16) in all copies of chromosome 9, a low‐level amplification of MYC (five copies), and loss of one copy of TP53; detected the presence of the Y chromosome in a hidden translocation; and detected four copies of ERBB‐2. A probe set for BCR and ABL verified breakpoints for all translocations involving chromosomes 9 and 22. A new karyotype presentation, “SKY‐gram,” is introduced by combining data from G‐banding, SKY, and FISH analysis. This study demonstrates the approach of combining molecular cytogenetic techniques to characterize fully the multiple complex chromosomal rearrangements found in the bladder cancer cell line BK‐10, and to refine the chromosomal breakpoints for all translocations. Genes Chromosomes Cancer 25:53–59, 1999 Published 1999 Wiley‐Liss, Inc.