Setting out the frame conditions for feasible use of FFPE derived RNA

Introduction

The usage of formalin-fixed paraffin embedded (FFPE) tissue is characterized by its long shelf-life and simple handling. Therefore it is the most commonly available tissue specimen in routine diagnostics and histological studies. Formaldehyde fixation may result in RNA degradation and cross linking with proteins, while storage conditions also affect RNA integrity. The present study was designed to investigate the influence of these factors on RNA analysis.

Prenatal diagnosis and characterization of an unbalanced whole arm translocation resulting in monosomy for 18p

Monosomy for the short arm of chromosome 18 is one of the most frequent autosomal deletions observed. While most cases result from terminal deletion of 18p, 16% of cases reported were as a result of an unbalanced whole arm translocation resulting in monosomy 18p. The origin and structure of these derivative chromosomes were reported in only a few cases. We report the prenatal diagnosis and characterization of a new case of monosomy 18p as a result of an unbalanced whole arm translocation. Amniocentesis was performed at 15 weeks of gestation on a 34-year-old woman initially referred for advanced maternal age. Holoprosencephaly was identified by ultrasound at the time of amniocentesis. Karyotype analysis showed an unbalanced whole arm translocation between the long arm of one chromosome 18 and the long arm of one chromosome 22, 45,XX,der(18;22)(q10;q10), in all metaphases. In effect, the fetus had monosomy for 18p. Parental karyotypes were normal, suggesting a de novo origin for the der(18;22). Fluorescence in situ hybridization (FISH) analysis was performed with alpha-satellite probes D18Z1 and D14Z1/D22Z1 to identify the origin of the centromere on the der(18;22). Signal was observed with both probes, indicating that the centromere was composed of alpha-satellite DNA from both constituent chromosomes. Genotyping of the fetus and her parents with chromosome 18p STS marker D18S391 showed only the paternal 187 bp allele was present in the fetus, indicating that it was the maternal chromosome 18 involved in the der(18;22). This case and previous reports show that de novo unbalanced whole arm translocations are more likely to retain alpha-satellite sequences from the two chromosomes involved.     

Regional differences in the compaction of chromatin in human G0/G1 interphase nuclei

The large-scale structure of chromatin corresponding to G- and R-bands in human G₀/G₁ interphase nuclei was compared. Fluorescence in situ hybridization (FISH) was used to measure the interphase distance between 42 pairs of probes separated by 0.1–1.5Mbp. The probe pairs were derived from 21q22.2 and Xp21.3, G-band positive regions, and from 4p16.3, 6p21.3, and Xq28, R-band positive regions. Distributions of measured interphase distances in all regions approximated a Rayleigh distribution, suggesting that the chromatin follows a random-walk path over this range. A linear correlation of mean-square interphase distance and genomic separation, also indicative of random-walk folding, was observed in all regions. The slope of the correlation observed using probes from G-band regions was systematically lower than that from R-band regions. The difference in the slope between Xp21.3 and Xq28 was particularly striking and was observed in normal fibroblast cells, fixed alternatively with methanol and acetic acid or paraformaldehyde, and HeLa cells. These results demonstrate regional differences in large-scale chromosome structure during interphase, with the more openly configured chromatin corresponding to R-bands.This revised version was published online in November 2005 with corrections to the Cover Date.     

Antibody penetration of viable human cells. I. Increased penetration of human lymphocytes by anti-RNP IgG.

Antibody penetration of viable cells and interaction with intracellular antigens may have major consequences for immunopathological processes in connective tissue diseases. We have reported previously that antibody can penetrate viable human lymphocytes. To assess further the role of antinuclear antibodies in this process, peripheral blood lymphocytes (PBMC) were incubated with FITC-conjugated IgG fractions from sera containing anti-RNP (anti-RNP IgG), Ro(SS-A), La(SS-B) and dsDNA antibodies and control sera for 24 h. Using crystal violet to quench cell surface staining, intracellular fluorescence of viable lymphocytes was quantified on the flow cytometer. It was noted that anti-RNP IgG entered 46.4 +/- 7.2% of lymphocytes which was significantly higher than anti-Ro(SS-A) (29.9 +/- 4.1%, P less than 0.05), La(SS-B) (22.0 +/- 7.5%, P less than 0.01) IgG and control IgG (28.8 +/- 2.1%, P less than 0.05) and not statistically different from anti-dsDNA IgG (32.6 +/- 14.3%). Inhibition experiments showed that the increased number of cells penetrated by anti-RNP IgG was a specific process. Time-course studies showed that anti-RNP IgG entry into cells was different from pooled control IgG. With anti-RNP IgG, positive-staining lymphocytes gradually increased in number from 12 to 24 h incubation, whilst with pooled control IgG, the peak was reached within 5 min. Dual staining experiments suggested that whereas both anti-RNP IgG and pooled control IgG entered B and NK cells, anti-RNP IgG also entered T cells. Using IgG F(ab')2 and Fc fragments from either anti-RNP IgG or pooled control IgG to compete with their FITC-conjugated counterparts indicated that the entry of anti-RNP IgG into-viable cells appeared to involve both F(ab')2 and Fc fragments, and pooled control IgG depended exclusively on the Fc portion of IgG. Further investigation by incubating anti-RNP IgG with 35S-methionine-labelled monocyte-depleted PBMC (MD-PBMC) suggested that anti-RNP IgG might react with the corresponding antigens either on the cell surface or within the cytoplasm.     

A molecular and FISH analysis of structurally abnormal Y chromosomes in patients with Turner syndrome

Fourteen patients with Turner syndrome and a structurally abnormal Y chromosome were analysed by PCR amplification and fluorescence in situ hybridisation for the presence of sequences specific to defined regions of the Y chromosome. Thirteen patients had a mosaic karyotype including a 45,X cell line and one case was non-mosaic in cultured lymphocytes. Ten patients had a pseudodicentric Yp chromosome, two an isodicentric Yq, one a pseudodicentric Yq, and one a derived Y chromosome. Two of the patients with a psu dic(Yp) chromosome had complex karyotypes with more than two cell lines, one of which exhibited five morphologically distinct mar(Y) chromosomes, presumably derived from a progenitor psu dic(Yp). Nine of the ten psu dic(Yp) chromosomes were positive for all Yp and Yq probes used except DYZ1 which maps to Yq12, suggesting a common breakpoint near the Yq euchromatin/heterochromatin boundary. In the three patients with a dicentric Yq chromosome two different breakpoints were observed; in two it was between PABY and the subtelomeric repeat sequence and in one it was between DYZ5 and AMGY in proximal Yp. Our results suggest that the great majority of structurally abnormal Y chromosomes found in Turner syndrome mosaics contain two copies of virtually all of the functional Y chromosome euchromatin.     

肝癌细胞微细胞介导染色体转移方法学的建立与探讨

目的建立肝癌细胞微细胞介导染色体转移方法，为肝癌转移抑制基因的染色体功能定位建立技术平台。方法人单染色体供体细胞通过微核化、出核、融合步骤将随机标记有耐药neo基因的正常人8号染色体导入到大鼠肝癌高转移细胞系C5F中，对微细胞杂交克隆进行药物筛选和单细胞克隆，并填序列标签位点-PCR和全染色体涂染荧光原位杂交方法验证人染色体转移的结果。结果获得具有G418和HAT双重抗性的微细胞杂交细胞，通过单细胞分离克隆方法获得15个具有双重抗性的微细胞杂交克隆，序列标签位点-PCR结果发现导入染色体的随机片段丢失，全染色体涂染荧光原位杂交结果发现导入的人8号染色体与大鼠染色体发生了稳定的重组。结论成功建立微细胞介导的染色体转移技术，为肝癌转移抑制基因的染色体功能定位奠定了技术基础。     

伴有22三体的t(5;17)变异易位急性早幼粒细胞白血病

目的 探讨一例核型为47,XY,t(5;17),+22的少见急性早幼粒细胞白血病(acute promyelo-cytic leukemia,APL)的临床和实验特征.方法 在常规核型分析的基础上,应用荧光原位杂交(fluorescencein situ hybridization,FISH)和多重荧光原位杂交(multiplex fluorescence in situ hybridization,M-FISH)技术进一步检测该病例的细胞遗传学异常,并结合文献分析此类少见变异易位的临床特点.结果 FISH检测PML-RARa阴性,但77%的细胞显示存在17号RARa基因的重排或复制;BCR-ABL阴性,但74%的细胞显示有22号染色体的复制或重排.M-FISH明确RARa基因重排系5号与17号染色体易位所致,并证实了22号三体的存在.结论 变异型t(5;17)易位,形成NPM-RARa融合基因的急性早幼粒细胞白血病是APL中少见的类型.骨髓形态表现为奥氏小体缺如,核型中常伴有其它附加染色体异常,全反式维甲酸(all-trans retinoicacid,ATRA)联合化疗有效,但易复发,合并弥漫性血管内凝血及高白细胞者预后凶险.     

Chromosomal integrity maintained in five human embryonic stem cell lines after prolonged in vitro culture

There have been recent reports of human embryonic stem cell (hESC) lines developing chromosomal aberrations after long-term culture, indicating an unstable genomic status due to the in vitro milieu. This raises concern, since it would limit their use in therapeutics. In this study the chromosomal status of five well-characterized hESC lines, SA002, SA002.5, AS034.1.1, SA121 and SA461, was monitored during long-term in vitro culture. The criteria of defined hESCs were met by all of the five hESC lines (four diploid and one trisomic for chromosome 13). The genomes were screened for chromosomal aberrations and rearrangements using comparative genomic hybridization (CGH), interphase fluorescence in situ hybridization (FISH) and traditional karyotyping on several occasions while in culture. The genomic integrity was shown to be maintained after repeated freeze-thaw procedures and continuous culture in vitro for up to 22 months (148 passages). We discuss the most common de novo chromosomal aberrations reported in hESCs, as well as their possible origin.     

Comparative chromosome mapping of sex-linked genes and identification of sex chromosomal rearrangements in the Japanese wrinkled frog (Rana rugosa, Ranidae) with ZW and XY sex chromosome systems

There are regional variations of sex chromosome morphologies in the Japanese wrinkled frog, Rana rugosa (2n = 26): heterogametic ZZ/ZW-type and XX/XY-type sex chromosomes, and two different types of homomorphic sex chromosomes. To search for homology between the ZW and XY sex chromosomes and the chromosome rearrangements that have occurred during sex chromosomal differentiation in R. rugosa, we performed chromosome mapping of sexual differentiation genes for R. rugosa by FISH. Three genes, AR, SF-1/Ad4BP and Sox3, were localized to both the ZW and XY chromosomes, and their locations were all different between the Z and W and between the X and Y. AR and SF-1/Ad4BP were located on the short arms of the W and X and the long arms of Z and Y, and Sox3 was mapped to the different locations on the long arms between the Z and W and between the X and Y, probably as a result of multiple rearrangements that occurred during the process of sex chromosome differentiation. However, the chromosomal locations of three genes were almost consistent between the Z and Y and between the W and X, indicating that the Z and Y chromosomes and the W and X chromosomes were respectively derived from the same origins. Dmrt1, which is located on avian sex chromosomes, was localized to autosomes in R. rugosa with both the ZW and XY sex chromosomes, suggesting that Dmrt1 might not be related to sex determination in this species.     

Intratumorous distribution of catecholaminergic clone cells of human neuroblastoma

Summary The intratumorous distribution of catecholaminergic clone cells in 23 human neuroblastomas was studied using Falck-Hillarp's method, and the findings compared with the catecholamine (CA) content within the tumour. All the specimens contained elements with CA fluorescence, and the pattern of fluorescence was classified from the distribution of CA-positive cells and neurofibrils, as diffuse cellular (DC); diffuse fibrillary (DF), sporadic (S), clustered (C), island-shaped (I), and bundled (B). The strength of CA fluorescence of both cellular and fibrillary elements correlated well with the CA content within the tumour. In addition, all tumours of urinary VMA-negative cases also contained significantly larger amounts of CA than other, non-functioning, tumours in the paediatric age group. The results of this study suggest that firstly, the ratio of CA-positive cells to CA-positive neuronal processes is proportionately higher in the poorly-differentiated neuroblastomas and that secondly, even tumours negative for urinary VMA or HVA might be polyclonal and contain catecholaminergic elements.This study was supported in part by a Research Grant from the Ministry of Education, Japan (No. 59570549)