Improvement of trypsin method for banding chromosomes

Karyotypic analysis and isolation of four DNA markers of the scleractinian coral Favitespentagona (Esper, 1795) (Scleractinia, Anthozoa, Cnidaria)

We performed conventional and molecular cytogenetic studies on the Favitespentagona Esper, 1795, a scleractinian coral mostly found along the west coast of Japan. Karyotype analysis of F.pentagona by G-banding revealed a karyogram containing a homogenously staining region (HSR) on chromosome 10 in more than 50% of the examined metaphase spreads. This HSR consisted of sequences from 18S ribosomal RNA (rRNA) genes, as demonstrated by fluorescence in situ hybridization (FISH) and DNA sequencing. We highlighted the development of four chromosomal FISH markers from repetitive genes such as U2 small nuclear RNA linked to 5S rRNA sequence (U2 snRNA-5S), 18S rRNA, histone H3, and uncharacterized gene FP-9X. The chromosomal locations of the U2 snRNA-5S and 18S RNA were on the terminal end of long arm of chromosomes 2 and 10, respectively, while the histone H3 and the uncharacterized gene were located near the centromeres of chromosomes 1 and 9, respectively. These FISH markers will improve the karyotyping of F.pentagona from mitotic preparations which helps in widening our understanding of coral genetic structure and chromosome organization. In addition, these improvements in karyotyping will provide the basis in constructing of chromosome-level genome assembly for F.pentagona.

Identification of homogeneously staining regions by G-banding and chromosome microdissection, and FISH marker selection using human Alu sequence primers in a scleractinian coral Coelastrea aspera Verrill, 1866 (Cnidaria)

Karyotype analysis was performed on the scleractinian coral Coelastrea aspera Verrill, 1866, commonly found along temperate coasts in Japan (30-35°N) and in coastal waters in the Indian and Pacific oceans. G-banding of Coelastrea aspera was successfully performed, although the banding pattern was not as clear as that in mammals. The karyogram clearly revealed that this coral had a homogeneously staining region (hsr) in chromosome 11. This hsr consisted of ribosomal RNA (rRNA) related genes, which was demonstrated by fluorescence in situ hybridization (FISH) with probes generated using 28S ribosomal DNA (rDNA) primers and those generated through chromosome microdissection. In addition, we conducted silver-stained nucleolus organizer region (Ag-NOR) analysis and found Ag depositions in the interphase nuclei but not on rRNA gene loci and hsr(s) in the mitotic stage. The hsr of this coral was observed in approximately 50% of the metaphase spreads analyzed. This may explain the diversity of coral rDNA based on the molecular study of sequence analysis. Furthermore, it was discovered that human telomere and Alu repeated sequences were present in this Coelastrea aspera. Probes derived from human Alu sequences are expected to play an important role in the classification of corals. Overall, our data can be of great value in discriminating among scleractinian coral species and understanding their genetics, including chromosomal evolution.

The genome landscape of the african green monkey kidney-derived vero cell line

Continuous cell lines that originate from mammalian tissues serve as not only invaluable tools for life sciences, but also important animal cell substrates for the production of various types of biological pharmaceuticals. Vero cells are susceptible to various types of microbes and toxins and have widely contributed to not only microbiology, but also the production of vaccines for human use. We here showed the genome landscape of a Vero cell line, in which 25,877 putative protein-coding genes were identified in the 2.97-Gb genome sequence. A homozygous ∼9-Mb deletion on chromosome 12 caused the loss of the type I interferon gene cluster and cyclin-dependent kinase inhibitor genes in Vero cells. In addition, an ∼59-Mb loss of heterozygosity around this deleted region suggested that the homozygosity of the deletion was established by a large-scale conversion. Moreover, a genomic analysis of Vero cells revealed a female Chlorocebus sabaeus origin and proviral variations of the endogenous simian type D retrovirus. These results revealed the genomic basis for the non-tumourigenic permanent Vero cell lineage susceptible to various pathogens and will be useful for generating new sub-lines and developing new tools in the quality control of Vero cells.

Classical and molecular cytogenetic analysis

Cytogenetic analysis is performed on cell cultures for several reasons, notably, to perform identity checks by verifying species of origin or the retention of key chromosome rearrangements in cell lines described previously. De novo chromosome analysis is usually performed when characterizing cancer cell lines for the presence of neoplastic rearrangements associated with specific tumors. This usually involves fluorescence in situ hybridization (FISH) using clones covering gene loci near recurrent chromosome breakpoints. Chromosome breakage is an important endpoint in radiation biology and mutagenesis, enabling cell lines to be used for measuring genotoxic dosage and repair. Finally, cytogenetic analysis may be performed to monitor stability in culture. Unlike most preparative techniques, chromosome preparation resists standardization. Hence, procedures must be optimized for each cell line. Thus, evidence-based protocols are described for hypotonic harvesting, rapid G-banding, FISH, and Spectral Karyotyping (SKY) analysis of cell cultures to allow troubleshooting and fine-tuning to suit the requirements of individual cell lines.

Cytogenetic analysis of cancer cell lines

Cancer genes are often deregulated by genomic rearrangements. Accordingly, analysis of the participant chromosomes responsible now occupies a key role in characterizing and identifying cancer cell lines. Cytogenetics may also be used to study the nature and extent of chromosome breakage induced by radiation or chemicals ("clastogenesis"), to distinguish individual cells or clones within a tumor cell population and to monitor the stability of chromosome rearrangements. This chapter describes cytogenetic procedures for characterizing cancer cells in culture. Cell lines allow the use of a wider range of harvesting and hypotonic treatments to optimize metaphase chromosome preparations than that possible with primary cultures. This assists improved banding, fluorescence in situ hybridization (FISH), and Spectral Karyotyping (SKY) analysis for research, rendering cell lines ideal tools for oncogenomics, ideally in parallel with transcriptomic analysis of the same cells. The experience of the writers with more than 800 cell lines has shown that no single hypotonic harvesting protocol is adequate consistently to deliver satisfactory chromosome preparations. Thus, evidence-based protocols are described for hypotonic harvesting, rapid G-banding, and FISH and SKY analysis of cell cultures to allow troubleshooting and fine-tuning to suit the requirements of individual cell lines.

Cytogenetic harvesting of commonly used tumor cell lines

Tumor cell lines are widely used both as disease models and, increasingly, as genomic resources for the ascertainment of new cancer genes. Cytogenetic analysis remains a major route to uncovering the cancer genome. However, cancer cell lines vary inexplicably in their harvesting preferences, which must, therefore, be determined by trial and error. This article describes harvesting protocols optimized empirically for 550 commonly used, mainly human, cancer cell lines together with evidence-based procedures to assist in determining conditions for unlisted cell lines and subsidiary protocols for cytogenetic analysis using G-banding and fluorescence in situ hybridization.

Cryptic and complex chromosomal rearrangements and the deletion of TP53 gene in a patient with leukemic mantle cell lymphoma

We present a case of leukemic mantle cell lymphoma with cryptic and complex chromosomal rearrangements, including multiple-way translocations involving chromosomes 8q24, 14q11/q32, 17p13.3, 17p13.1, 21q22, and 21q22; a deletion of the long arm of chromosome 10 [del(10)(q24)]; and a deletion of the TP53 gene in addition to t(11;14). We speculate that this series of chromosomal changes may disrupt the IgH gene, activate the c-MYC oncogene, inactivate the p53 tumor suppressor gene, and disrupt other cancer-related genes either within or flanking the chromosomal breakpoints. This combinational effect causes the progression of mantle cell lymphoma.

Periodontal Status in Two Siblings With Severe Congenital Neutropenia: Diagnosis and Mutational Analysis of the Cases

BACKGROUND

Severe congenital neutropenia (SCN), also known as Kostmann syndrome, was originally reported as an autosomal recessive disease of neutrophil production. The disease is characterized by a maturation arrest of neutrophil precursors at the promyelocytic stage of differentiation and by extremely low levels of mature neutrophils in peripheral blood.

METHODS

A 6-year-old male presented with a complaint of gingival swelling and bleeding, and swelling at the left side of his face. Upon clinical examination, severe inflammation of all gingival tissues was apparent, and a periapical abscess with mobility was noted on the left mandibular second molar. Medical and dental histories revealed numerous recurrent bacterial infections associated with oral and non-oral tissues. His medical history with recurrent infections led us to evaluate his 3-year-old sister to determine the status of her oral health. Inflammation of her oral tissues and recurrent bacterial infections were apparent. Their consanguineous parents were in good health. To assist in identifying possible systemic diseases underlying the inflammatory situation in the siblings, consultations were requested from the Pediatric Hematology Department at Selcuk University and Pediatric Oncology Department at Gulhane Military Medical Academy.

RESULTS

Based on absolute neutrophil count (< or =200/mm(3)) and bone marrow aspiration findings consistent with early maturation arrest in myelopoiesis, the cases were diagnosed as SCN. No chromosomal abnormality was detected upon cytogenetic examination. Sequencing analysis also revealed no mutation in the neutrophil elastase or growth factor independent-1 (GFI-1) genes in these patients. Severe periodontal disease, attachment loss, and mobility for over 50% of the deciduous teeth were noted. Within 6 months, the male sibling lost all of his deciduous teeth due to periapical and periodontal infections. His sister presented with tooth mobility for all mandibular incisors. Monthly visits, including scaling, polishing, and 0.2% chlorhexidine digluconate irrigation were performed to support their oral hygiene and to avoid recurrent oral infections. We have been able to stabilize these patients' periodontal conditions during a 2-year follow-up period.

CONCLUSION

This case report emphasizes the role of periodontists and pediatric dentists in the diagnosis of diseases linked with neutrophil and other systemic disorders and highlights the need to optimize the health of oral tissues with regular appointments.

A variant t(8;10;21) in a patient with pathological features mimicking atypical chronic myeloid leukemia

We report the case of an 11-year-old girl who was initially diagnosed with a chronic myeloproliferative disorder, possibly chronic myelogenous leukemia (CML), based on laboratory and blood and marrow morphological findings. The patient's high leukocyte count did not respond to hydroxyurea, a standard initial therapy for CML. Chromosomal analysis revealed that the patient did not have t(9;22), but a complex t(8;10;21)(q22;q24;q22), a variant of t(8;21). The treatment regime was switched to an acute myeloid leukemia (AML) protocol; the patient responded well and is now in remission. This case demonstrates again that routine clinical cytogenetic analysis plays an important role in the clinical diagnosis, guidance of treatment, and prognostication in hematological disorders.

Down syndrome with pure partial trisomy 21q22 due to a paternal insertion (4;21) uncovered by uncultured amniotic fluid interphase FISH

OBJECTIVE

To emphasize the usefulness and reliability of fluorescence in situ hybridization (FISH) on uncultured amniotic fluid cells in the prenatal diagnosis of common chromosomal aneuploidies.

METHODS

FISH analyses utilizing centromeric, locus-specific or whole chromosome paint DNA probes specific for chromosomes X, Y, 13, 18, 21, and 4 were performed on uncultured amniotic fluid cells or the peripheral blood specimen from the father. Routine chromosome analysis was carried out as well.

RESULTS

A prenatal case with partial trisomy 21 due to a paternal cryptic insertion (4;21) was ascertained by a rapid overnight FISH on uncultured amniotic fluid cells. The fetus was delivered at term and had classical features of Down syndrome.

CONCLUSION

Our results stress the importance of FISH on uncultured amniotic fluid cells to supplement routine cytogenetics, especially in cases with abnormal ultrasound findings.

Duplication 15q in a patient with t(8;21) acute myeloblastic leukemia (M2)

We present unique chromosomal abnormalities found in a patient with acute myeloblastic leukemia (AML) of French-American-British subtype M2. The patient was referred for an evaluation of chromosomal anomaly associated with AML. She was found to have an abnormal karyotype 46,XX,t(8;21)(q22;q22), and a questionable dup(15)(q15q22) in the majority of cells analyzed. Two cells had the same chromosomal anomalies plus a duplicated derivative chromosome 21 [der(21)t(8;21)(q22;q22)]. These cytogenetic findings were confirmed by fluorescence in situ hybridization utilizing the appropriate DNA probes. To our knowledge, this is the first case report of a combination of the translocation between chromosomes 8 and 21, a duplication of chromosome 15 [dup(15)(q15q22), and a duplicated derivative chromosome 21 [der(21)t(8;21)(q22;q22)].

Cytogenetic studies on a patient with prepubertal breast cancer: a case report

Cytogenetic studies were carried in a 10 year old girl with prepubertal breast cancer for assessing inherited genetic susceptibility to chromosome breakage. The girl presented with a tumour in the left breast. Histologically it was diagnosed as secretory carcinoma (SC). Chromosome anomalies observed in phytohemagglutinin (PHA-P) stimulated lymphocytes were del(2)(q33), del(3)(p24), del(7)(q22) and dup(12)(p11p12). The regions involved have been reported in breast tumors. These loci, detected in peripheral blood lymphocytes (PBL), could be the sites susceptible to breakage, its subsequent effect being manifested in the target (breast) tissue.

Chromosomal localisation of a pseudoautosomal growth gene(s)

Although recent molecular studies in patients with sex chromosome aberrations are consistent with a growth gene(s) being present in the pseudoautosomal region (PAR), the precise location has not been determined. In this report, we describe a Japanese boy and his mother with an interstitial deletion in Xp22.3 and review the correlation between genotype and stature in six cases of partial monosomy of the PAR. The results indicate that the region from DXYS20 to DXYS15 is the critical region for the putative growth gene(s).

Sex reversal in a child with a 46,X,Yp+ karyotype: support for the existence of a gene(s), located in distal Xp, involved in testis formation

We report on a sex reversed Japanese child with a 46,X,Yp+ karyotype, minor dysmorphic features, and no testicular development. The Yp+ chromosome was derived by translocation of an Xp fragment (Xp21-Xp22.3) to Yp11.3. This has resulted in deletion of distal part of the Y chromosome pseudoautosomal region (DXYS15-telomere) and duplication of the X specific region (DXS84-PABX) and proximal part of the pseudoautosomal region (MIC2-DXYS17). No deletion of the Y specific region was detected nor was any mutation found in SRY. Cytogenetic analysis suggests that the proximal part of the Xp fragment is the most distal part of the short arm of the Yp+ chromosome (Xp21----Xp 22.3::Yp11.3----Yqter). No chromosomal mosaicism was detected. These results are similar to previous reports of sex reversal in four subjects with a 46,Y,Xp+ karyotype. We conclude that the sex reversal is a direct, or indirect, consequence of having two active copies of the distal part of Xp and may indicate the presence of a gene(s) which acts in the testis determination or differentiation pathway.

The uptake of iron and transferrin by the human malignant melanoma cell

The role of the transferrin homologue, melanotransferrin (p97), in iron metabolism has been studied using the human melanoma cell line, SK-MEL-28, which expresses this antigen in high concentrations. The mechanisms of iron and transferrin uptake were investigated using human transferrin labelled with iodine-125 and iron-59. Internalised and membrane-bound iron and transferrin were separated using the proteinase, pronase. The uptake of iron from transferrin occurred by at least two processes. The first process was saturable and consistent with receptor-mediated endocytosis, involving internalisation of transferrin bound to specific binding sites. Uptake of iron also occurred by a second process which was non-saturable up to 0.06 mg/ml (0.75 microM) and was of higher efficiency than the saturable process. This process of iron uptake may be the dominant one at physiological serum transferrin concentrations. A membrane-bound, pronase-sensitive, temperature-dependent, iron-binding component was also identified. The number of binding sites was estimated to be approx. 340,000 per cell (assuming 2 atoms of iron per site) and it is suggested that this binding component may be melanotransferrin.

Goat-mouse hybridomas secreting goat immunoglobulins

Monoclonal antibodies specific for an allotypic marker of goat IgG2 were used to select goat-mouse hybrid cells secreting goat IgG2. Four of these hybrid cell clones continued to synthesize goat IgG2 (5-15 micrograms/ml) for over eight months. They will be used to study goat IgG gene regulation.

A ring X chromosome, 46,Y,r(X)(p22.33q28), as a cause of extreme short stature in a male

We describe a 15 10/12-year-old boy (Tanner stage 4, peak growth velocity 7 cm/year) with a ring X chromosome who presented with extreme short stature (mean -5.3 SD) as the sole recognizable abnormality. His chromosome constitution was determined to be 46,Y,r(X)(p22.33q28) in 174 of 182 peripheral blood cells and in 35 skin fibroblasts. Of the remaining eight peripheral blood cells, five had a dicentric double-size ring and three had a smaller ring. Other laboratory studies for short stature were noncontributory. We suspect that the ring's specific behavior in mitosis or its effect on expression of the statural determinant on the X chromosome short arm may be responsible for short stature in this patient.

Chromosomal analysis in Ewing sarcoma

Two cases of Ewing sarcoma were karyotyped by using a fluorodeoxyuridine synchronisation procedure on short term cultures of fresh tumour material. This procedure enables rapid cytogenetic analysis of such material. Both showed relatively simple karyotypes, 48,XX, +2, +7,t(11;22)(q24;q12), ?dup(12)(q21----q24) and 47,XX,i(1q),t(11;22)(q24;q12). These results further support this translocation between chromosomes 11 and 22 as a specific marker for Ewing sarcoma. Cytogenetic studies in such cases are an important adjunct to histological studies and in some cases may contribute to the resolution of the diagnosis.

PER-117: a new human ALL cell line with an immature thymic phenotype

A new cell line, PER-117, was established from bone marrow cells of an eighteen months old boy with an acute lymphoblastic leukaemia (ALL). The leukaemic origin of cell line PER-117 is indicated by its cytochemical, immunological and cytogenetic similarity to the patient's fresh leukaemic cells. PER-117 carries a marker chromosome which was identified as a translocation between chromosomes 1 and 11. The surface marker analysis revealed that the phenotype of PER-117 is RFB-1+, RFT-1+ (CD5), 3A1+ (CD7), OKT 9+, OKT 10+ and HLA-DR-. Thus, this cell line appears to represent a prothymocyte or stage I thymocyte and preliminary data suggest that it can be induced in vitro to further differentiate.

Rearrangement and possible amplification of the ribosomal RNA gene sites in the human chronic myelogenous leukemia cell line K562

We have studied the location of the nucleolar organizer regions (NORs) in the human chronic myeloid leukemia cell line K562. In man, the NORs are normally found on the short arms of the acrocentric chromosomes. We show that in the K562 line, the NORs are substantially rearranged with both insertional and terminal NORs. In addition, the putative t(15;17) marker chromosome had three insertional NORs that may have arisen through gene amplification.

Acoustic microscopy of human metaphase chromosomes

Acoustic micrographs of human metaphase chromosomes have been recorded with wavelengths as short as 470 nm using liquid argon near 85 K as the acoustic wave coupling medium. Chromosomes prepared by trypsin-Giemsa staining exhibit acoustic banding patterns similar to the G-bands seen in optical images. Unstained chromosomes exhibit acoustic markings that do not correspond to traditional banding patterns. The observed acoustic contrast may arise from spatial variations in chromosomal mechanical properties, or from thickness variations in the fixed chromosomes.