Localization of the human interferon-induced, ds-RNA activated p68 kinase gene (PRKR) to chromosome 2p21-p22

The interferon-induced dsRNA-activated protein kinase (PRKR) belongs to a subclass of serine/threonine kinases, involved in the regulation of protein synthesis by phosphorylation of the alpha subunit of initiation factor eIF2. Somatic cell hybrids segregating human chromosomes were used to assign this kinase to human chromosome 2. Fluorescence in situ hybridization confirmed this assignment and further localized the gene (PRKR) to the boundary region of bands p21 and 22.

Astroblastoma: report of a case with ultrastructural, cell kinetic, and cytogenetic analysis

Astroblastomas are rare tumors of cerebral hemispheres of young adults. We report an astroblastoma in a 15-year-old girl and present the first descriptions of cytogenetic abnormalities in this tumor. The tumor was relatively well demarcated from the brain and revealed prominent perivascular rosettes as well as intervascular clear cells that contained abundant glycogen. Cytogenetic analysis revealed an abnormal hypodiploid karyotype with 45 chromosomes and monosomies of chromosomes 10, 21, and 22 and two marker chromosomes in all cells examined. The tumor had a Ki-67 labelling index of 4.7% and assessment of ploidy by flow cytometry revealed 96% of cells in the G0G1 phase and 4% of cells in the G2M phase. Assessment of proliferation and ploidy indices in further cases may provide important prognostic data for this poorly understood entity. Further cytogenetic studies will also help to identify if there are consistent karyotypic abnormalities in these enigmatic tumors.

Characterization of abnormal one pronuclear human oocytes by morphology, cytogenetics and in-situ hybridization

The morphology, chromosomal constitution and developmental capability of abnormal human oocytes (94/3500 oocytes; 2.7%) which after insemination exhibited only one pronucleus were examined. The majority of one pronuclear oocytes exhibited two or more distinct polar bodies. Dividing oocytes showed irregular chromosome distribution from haploid to diploid. Embryos resulting from abnormal oocytes displayed limited developmental potential. Many of them underwent fragmentation or were arrested at the 2- or 8-cell stage of development, and only some reached the morula or blastocyst state (11/35 oocytes). In approximately 45% (15/33) of examined oocytes, decondensed sperm heads or tiny nucleus-like structures were found in addition to a single nucleus. Chromosome Y was also detected in chromosomal preparations in approximately 10% of the oocytes by in-situ hybridization utilizing the human Y chromosome-specific DNA probe (DYZ3). These observations provided strong evidence that many of these oocytes originated from fertilized oocytes. The origin of the other one pronuclear oocytes could not be determined. Parthenogenetic activation of some oocytes cannot be excluded and other explanations concerning the origin of abnormal oocytes are discussed.

Time-resolved studies of crossbridge movement: why use X-rays? Why use fish muscle?

The advantages of using time-resolved X-ray diffraction as a means of probing myosin cross-bridge behaviour in active muscle are outlined, together with the reasons that bony fish muscle has advantages in such studies. We show that the observed X-ray diffraction patterns from fish muscle can be analysed in a way that is rigorous enough to allow reliable information about crossbridge activity to be defined. Among the advantages of this muscle are that diffraction patterns from resting, active and rigor muscles are all well-sampled at least out to the 30 row-line, that the resting myosin layer-line pattern can be 'solved' crystallographically to define the starting position of the crossbridges in resting muscle, and that the equatorial intensity distribution, which in all patterns from vertebrate skeletal muscles comprises overlapping peaks from the A-band and the Z-band, can be analysed sufficiently rigorously to allow separation of the two patterns, both of which change when the muscle is active. Finally, we present results both on a new set of myosin-based layer-lines in patterns from active muscle (consistent with the presence of low-force bridges as also indicated by the time-courses of the intensity changes on the equator and the changing mass distribution in the A-band unit cell) and also on changes of the actin-based layer-lines (consistent with stereospecific labelling of the actin filaments by force-producing crossbridges). Our results to date, which demonstrate the enormous power of time-resolved X-ray diffraction studies, strongly support the swinging of myosin heads on actin as part of the contractile cycle.

Molecular genetic, cytogenetic, and immunohistochemical characterization of alveolar soft-part sarcoma. Implications for cell of origin

BACKGROUND

Alveolar soft-part sarcoma is a rare tumor of uncertain histogenesis.

METHODS

The authors report a patient who was studied using immunohistochemistry, cytogenetic analysis, and molecular probes for MyoD1 and MYCN (N-myc proto-oncogene).

RESULTS

By immunoperoxidase, the tumor was focally positive for vimentin, neuron-specific enolase, and S-100 protein but negative for muscle-specific actin, desmin, and low-molecular-weight keratin. Direct chromosome analysis of primary tumor cells using G-banded preparations yielded two clonally abnormal lines: one demonstrated trisomy 47,XX+5; the other demonstrated 46,XX,1p-,17q+. Expression of the MYCN RNA was detectable at a low level, and MYCN was single copy at the DNA level. Expression of the myogenic molecular marker MyoD1 was not detected by Northern blotting analysis.

CONCLUSIONS

This is the first detailed study to address the molecular biology and tumor cytogenetics of alveolar soft-part sarcoma. The results of this study indicate a neurogenic origin for this unusual tumor and fail to provide support for the notion of a myogenic origin.

High-resolution mapping of mammalian genes by in situ hybridization to free chromatin

Fluorescence in situ hybridization to metaphase chromosomes or chromatin fibers in interphase nuclei is a powerful technique in mapping genes and DNA segments to specific chromosome region. We have been able to release the chromatin fibers from cells arrested at G1 and G2 phases using different drugs and a simple alkaline lysis procedure. We have also demonstrated specific hybridization of fluorescence-labeled probes to single-copy genomic DNA sequences on the free chromatins. Fluorescence in situ hybridization signals have been detected for sequences separated as close as 21 kilobase pairs and as far as 350 kilobase pairs, with excellent correspondence between the observed and expected distances. The resolution of this technique should approach 10 kilobase pairs and its coverage should span millions of base pairs. Therefore, free chromatin mapping can be generally used to study the structure and organization of mammalian genomes.

Infrequent genomic rearrangement and normal expression of the putative RB1 gene in retinoblastoma tumors

Retinoblastoma (RB) tumors develop when both alleles of a gene (RB1) are mutated and unable to function normally. Recently, Friend et al. [S. H. Friend, R. Bernards, S. Rogelj, R. A. Weinberg, J. M. Rapaport, D. M. Albert, and T. P. Dryja, Nature (London) 32:643-646, 1986] reported the cloning of a gene, 4.7R, with some properties expected for the RB1 gene, namely, a high frequency (30%) of genomic rearrangements in tumors and absence of message in all RB tumors examined. To extend the characterization of this gene, we used 4.7R probes to search for genomic rearrangements of DNA and to study the expression of the 4.7R gene in RB tumors, osteosarcoma (OS) tumors arising in RB patients, and other normal and malignant tissues. In 34 previously unreported RB and OS tumors arising in RB patients, we observed only four (12%) with genomic abnormalities. Transcripts of 4.7R were present in 12 of 17 RB tumors, 2 of 2 OS tumors, and all non-RB tumors and normal tissues tested. We were unable to confirm the high frequency of truncated messages of 4.7R in RB tumors reported by Lee et al. (W. H. Lee, R. Bookstein, F. Hong, L. J. Young, J. Y. Shaw, and E. Y. Lee, Science 235:1394-1399, 1987) and Fung et al. (Y. K. Fung, A. L. Murphree, A. Tang, J. Qian, S. H. Hinrichs, and W. F. Benedict, Science 236:1657-1661, 1987) but did confirm the presence of a truncated transcript in the RB cell line Y79. Of the RB and RB-related OS tumors which appeared normal on Southern blots, 2 of 26 or 12% had abnormal transcripts, giving a combined frequency of 22% abnormalities in the 4.7R gene detectable by Southern and Northern (RNA) blot analyses.

Re-evaluation of the sublocalization of esterase D and its relation to the retinoblastoma locus by in situ hybridization

In situ hybridization of a cDNA probe for the esterase D gene (ESD) was carried out on human chromosomes. The probe hybridized most strongly to 13q14.2 and 13q14.3. This observation raises doubts concerning the most recently published assignment of ESD to 13q14.1. A deletion in an individual with retinoblastoma was reported to separate the closely linked ESD and retinoblastoma (RB1) loci, placing ESD proximal to RB1. Quantitative in situ hybridization studies of this deletion do not confirm this interpretation. Rather, they suggest that ESD is missing from the deleted chromosome 13 and duplicated on the normal homolog. From these findings, we conclude that the deletion in this individual cannot be used to determine the orientation nor the sublocalization of ESD and RB1 within the 13q14 region.

Cloning of the esterase D gene: a polymorphic gene probe closely linked to the retinoblastoma locus on chromosome 13

The study of recessive oncogenes such as those responsible for retinoblastoma and Wilms tumor is difficult because the gene products involved are unknown and because the diseases are not associated with unique cellular or molecular phenotypes suitable for genetic manipulation. Since the gene for esterase D (ESD) is known to be tightly linked to the retinoblastoma locus (RB1) in the q14.1 band of chromosome 13, we have cloned the ESD gene from a human cDNA library by using oligonucleotides specific for a partial amino acid sequence of the purified enzyme to provide a genetic marker for further studies on retinoblastoma. The putative ESD gene codes for a message of 1.2 kilobases, which is present in all cell types examined, and maps to 13q14.1, thus confirming that it is the ESD gene. Restriction enzyme analysis reveals a restriction fragment length polymorphism with Apa I; this polymorphism results from the heterozygosity of 32% of the individuals tested and is shown to be useful in identifying carriers of the mutation responsible for retinoblastoma. A preliminary screen of 24 retinoblastoma tumors by Southern blot did not reveal any homologous deletions or rearrangements of the ESD locus.

Tumour induction by the retinoblastoma mutation is independent of N-myc expression

Retinoblastoma (RB) tumours form in the eyes of young children when homozygosity for a mutation at the Rb-1 locus develops in a somatic retinal cell. A similar shift to homozygosity for the RB mutation has been observed in osteogenic sarcoma (OS) tumours that commonly arise as second tumours in children who survive RB. This observation suggests that the Rb-1 locus controls the expression of genes with oncogenic potential; a possible target is the oncogene N-myc, which is sometimes amplified and over-expressed in the neuroectodermal tumours neuroblastoma and RB. However, N-myc is developmentally regulated in normal murine embryogenesis, and an alternative possibility is that the expression of the gene in tumour cells reflects their embryonic origin and is unrelated to the RB mutation. We have therefore examined N-myc expression in various fetal, adult and tumour tissues, and report here that the gene is expressed in fetal but not in adult brain and retina and in near-diploid RB tumour samples at levels similar to those observed in normal fetal retina. Only RB tumours with genomic amplification of the N-myc gene exhibited increased levels of expression; and no N-myc transcripts were detected in osteogenic sarcomas initiated by mutations at the Rb-1 locus. We therefore conclude that the expression of N-myc in RB tumours probably reflects the origin of the tumour from an embryonic tissue normally expressing the gene and is not directly associated with the mutation at the RB locus.

"Crystalline" myosin cross-bridge array in relaxed bony fish muscle. Low-angle x-ray diffraction from plaice fin muscle and its interpretation

Detailed structural analysis of muscles normally used to study myosin cross-bridge behavior (e.g., frog sartorius muscle, insect flight muscle) is extremely difficult due to the statistical disorder inherent in their myosin filament arrays. Bony fish muscle is different from all other muscle types in having a myosin filament (A-Band) array with good three-dimensional (crystalline) regularity that is coherent right across each myofibril. Rigorous structure analysis is feasible with fish muscle. We show that low-angle x-ray diffraction patterns from plaice fin muscle contain characteristic vertebrate layer lines at orders of 429 (+/- 0.2) A, that these layer lines are well sampled by row-lines from a simple hexagonal lattice of a-spacing 470 (+/- 2.0) A at rest length and that there are meridional reflections, due to axial perturbations of the basic helix of myosin heads, similar in position to those from frog muscle but differing in relative intensities. Clear trends based on modeling to a resolution of 130 A of the observed intensities in the low angle x-ray diffraction pattern from relaxed plaice fin muscle suggest that: (a) the pattern out to 130 A is more sensitive to the distribution of the two heads than it is to details of the head shape, (b) both heads in one myosin molecule probably tilt axially in the same direction by approximately 20-40 degrees relative to a normal to the thick filament backbone, (c) the center of mass of the heads is at 145 to 160 A radius, and (d) the two heads form a compact structure by lying closely adjacent to each other and almost parallel. Little rotational disorder of the heads can occur. Because of its crystallinity, bony fish muscle provides a uniquely useful structural probe of myosin cross-bridge behavior in other muscle states such as rigor and active contraction.

Resting myosin cross-bridge configuration in frog muscle thick filaments

Clear images of myosin filaments have been seen in shadowed freeze-fracture replicas of single fibers of relaxed frog semitendinosus muscles rapidly frozen using a dual propane jet freezing device. These images have been analyzed by optical diffraction and computer averaging and have been modelled to reveal details of the myosin head configuration on the right-handed, three-stranded helix of cross-bridges. Both the characteristic 430-A and 140-150-A repeats of the myosin cross-bridge array could be seen. The measured filament backbone diameter was 140-160 A, and the outer diameter of the cross-bridge array was 300 A. Evidence is presented that suggests that the observed images are consistent with a model in which both of the heads of one myosin molecule tilt in the same direction at an angle of approximately 50-70 degrees to the normal to the filament long axis and are slewed so that they lie alongside each other and their radially projected density lies along the three right-handed helical tracks. Any perturbation of the myosin heads away from their ideal lattice sites needed to account for x-ray reflections not predicted for a perfect helix must be essentially along the three helical tracks of cross-bridges. Little trace of the presence of non-myosin proteins could be seen.

A detailed analysis of chromosomal changes in heritable and non-heritable retinoblastoma

Full cytogenetic analysis of 27 different retinoblastoma tumors is presented. Gross aneuploidy of chromosome arms 6p and 1q were very common, being observed in 15/27 and 21/27 tumors, respectively. However, we found that chromosome 13 was rarely missing: only 3/27 had a detectable monosomy affecting 13q14. Monosomy of chromosome 13 by small deletion or rearrangement was also not observed in any of 12 retinoblastoma tumor lines analyzed detail at the 300-400 chromosome band level. A novel observation in retinoblastoma was the discovery of non-random translocations at three specific breakpoints, 14q32 (4/12), 17p12 (5/12), and 10q25 (3/12). Genomic rearrangements similar to those described involving C-myc in Burkitt lymphoma 14q+ cells could not be demonstrated in the four 14q+ retinoblastoma lines using molecular techniques, and a probe mapping to the site implicated to have an activating role in lymphoma. These data suggest that there is a target for rearrangement at 14q32 but it is not the same sequence used in some Burkitt lymphomas. Two other breakpoints (2p24 and 8q24) coincided with the mapped position of cellular oncogenes, but also failed to show a molecular rearrangement with the oncogene probes. The breakpoints, 10q25 and 17p12, are constitutional fragile sites which may predispose these regions to act as acceptors of translocations in malignant cells. One line had double minute chromosomes, and was the only one of 16 (6%) tested with the N-myc probe which had an amplification. Different tumors from single patients with multifocal heritable retinoblastoma showed independent karyotype evolution. Unilateral non-heritable tumors exhibited a high level of karyotype stability throughout both in vivo and in vitro growth. The various common patterns of aneuploidy and translocations probably confer an early selective advantage to malignant cells, rather than induce malignant transformation.

Isochromosome 6p, a unique chromosomal abnormality in retinoblastoma: verification by standard staining techniques, new densitometric methods, and somatic cell hybridization

Study of chromosome rearrangements in retinoblastoma tumors revealed that all tumors contained either an unusual isochromosome and/or extra copies of chromosome 1q. Extra copies of chromosome 1q occur in many malignancies. The pattern of G-bands suggested that the isochromosome was derived from either the short arm of chromosome 6, i(6p), or the long arm of chromosome 17, i(17q). Standard staining techniques using G-, C-, Q-, and R-banding; high resolution G-banding; and density profile analysis were consistent with the characteristic isochromosome of retinoblastoma being i(6p), rather than i(17q). This conclusion was substantiated by the analysis of segregants derived from retinoblastoma X mouse hybrid cells which had been grown in bromodeoxyuridine to select for loss of chromosome 17. The unique isochromosome was not lost under these conditions confirming that it is an i(6p) rather than an i(17q). The i(6p) abnormality has not been observed frequently in other tumors, but occurs in 60% of retinoblastoma tumors. Thus, although the mutation predisposing to retinoblastoma is known to map at 13q14, somatic amplification of genes on 1q and 6p may play a role in the pathogenesis of this tumor.

Muscle crossbridge positions from equatorial diffraction data: an approach towards solving the phase problem

Following a discussion of the problems involved in the analysis of X-ray diffraction data from muscle, a description is given of a possible procedure for solving the phase problem in the case of equatorial diffraction data. The approach involves the use of the Patterson Function which can be determined unambiguously from the observed diffracted intensities. The method is tested using five different muscle-like model density distributions for which the correct phases can be calculated directly. It is then applied to the equatorial X-ray diffraction data from relaxed frog sartorius muscle where it selects a phase set which is also the most likely to be correct on the basis of other available data on frog muscle. This phase set gives rise to a Fourier synthesis map in which the crossbridges form a uniform shelf of density around the myosin filament backbones. Possible lateral movements of the crossbridges from this relaxed configuration in active and rigor muscle are discussed. The approach to solving the phase problem is now being applied to data from fish muscle, insect flight muscle and crab muscle. It should also have its application to other fibrous materials apart from muscle.

Somatic inactivation of genes on chromosome 13 is a common event in retinoblastoma

Through family studies and analysis of patients with congenital chromosome abnormalities, the germ-line mutation responsible for the hereditary form of the eye tumour, retinoblastoma, has been assigned to the q14 region on chromosome 13 and closely linked to an enzyme called esterase D (ESD). Knudson has proposed that as few as one somatic event in addition to the germ-line mutation is required to induce tumours in patients with the hereditary form of retinoblastoma; the non-hereditary form requires two somatic events to occur in the same cell. The somatic event(s) may involve either mutation of the remaining normal gene at 13q14 or mutation of a gene at another site in the genome. Here we have examined six retinoblastoma patients who are heterozygous for electrophoretic variants of ESD. Although the normal cells of all six patients expressed both variants, the tumour cells of four patients expressed enzyme from only one of the two ESD alleles. We tentatively conclude that induction of a retinoblastoma tumour requires the somatic inactivation of genes near the ESD locus including the remaining normal gene at the retinoblastoma (RB) locus.

Muscle structure, cryo-methods and image analysis

Negatively stained cryo-sections from glutaraldehyde fixed, anti-freeze treated muscle, quench-frozen in Freon cooled by liquid nitrogen, show improved preservation of axial structure of the myofibrils compared with conventional plastic sections. Such sections are being used both to characterize the structural differences inthe M-bands of different vertebrate muscles and fibre types and also to define the axial distribution of myosin crossbridges and non-myosin proteins in the crossbridge region of the A-band. Combined with analysis of the transverse A-band structure from plastic sections, the cryo-sections are helping to reconstruct a three-dimensional picture of the molecular architecture of the A-band. This, in turn, is providing the necessary structural background with which to interpret the wealth of published X-ray diffraction data on muscle. Such data should reveal the nature of the contractile event itself. Since good X-ray diffraction patterns can be obtained from living muscles, these can be compared with optical diffraction patterns from muscle cryo-sections as a means of testing the degree of preservation in the sections. Muscle is therefore an excellent tissue with which to evaluate new cryo-techniques.