Mutation of the MXI1 gene in prostate cancer.

The Mxi1 protein negatively regulates Myc oncoprotein activity and thus potentially serves a tumour suppressor function. MXI1 maps to chromosome 10q24-q25, a region that is deleted in some cases of prostate cancer. We have detected mutations in the retained MXI1 alleles in four primary prostate tumours with 10q24-q25 deletions. Two tumours contained inactivating mutations, whereas two others contained the identical missense mutation. Fluorescence in situ hybridization also demonstrated loss of one MXI1 allele in an additional tumour lacking chromosome 10 abnormalities. MXI1 thus displays allelic loss and mutation in some cases of prostate cancer that may contribute to the pathogenesis or neoplastic evolution of this common malignancy.

Clinical laboratory implementation of cytogenomic microarrays.

Examination of the whole genome for copy number alterations by microarray is now routinely done in many laboratories. The field of cytogenetics has evolved to adapt this technology, and the current phase of transition has resulted in the need for standardization in methodologies and interpretation of data. This review will outline some of the changes addressed in the field over the last several years and briefly discuss some of the trends in data processing, analysis and interpretation.

Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH.

The discovery of complex structural variations that exist within individual genomes has prompted a need to visualize chromosomes at a higher resolution than previously possible. To address this concern, we established a robust, high-resolution fluorescence in situ hybridization (FISH) method that utilizes probes derived from high complexity libraries of long oligonucleotides (>150 mers) synthesized in massively parallel reactions. In silico selected oligonucleotides, targeted to only the most informative elements in 18 genomic regions of interest, eliminated the need for suppressive hybridization reagents. Because of the inherent flexibility in our probe design methods, we readily visualized regions as small as 6.7 kb with high specificity on human metaphase chromosomes, resulting in an overall success rate of 94%. Two-color FISH over a 479-kb duplication, initially reported as being identical in 2 individuals, revealed distinct 2-color patterns representing direct and inverted duplicons, demonstrating that visualization by high-resolution FISH provides further insight in the fine-scale complexity of genomic structures. The ability to design FISH probes for any sequenced genome along with the ease, reproducibility, and high level of accuracy of this technique suggests that it will be powerful for routine analysis of previously difficult genomic regions and structures.

Progression of metastatic human prostate cancer to androgen independence in immunodeficient SCID mice.

Prostate cancer mortality results from metastasis to bone and hormone-independent tumor growth. Models to study these progressive changes are lacking. Here we describe the propagation of advanced human prostate cancer by direct transfer of surgical samples from patients into immune-deficient male SCID mice. Explants from six of eight patients formed prostate tumors and two showed unique cytogenetic, biologic and molecular features that were retained through six or more passages. One grew in an androgen-independent fashion, whereas the second formed tumors that regressed following castration then regrew. Micrometastatic disease was detected in the hematopoietic tissues of half of the recipient mice. Thus selected specimens of advanced human prostate cancer can be propagated in SCID mice in a manner that recapitulates the clinical transition from androgen-sensitive to androgen-independent growth, accompanied by micrometastasis.

U-type exchange is the most frequent mechanism for inverted duplication with terminal deletion rearrangements.

BACKGROUND: Chromosomal rearrangements resulting in an interstitial inverted duplication with concomitant terminal deletion were first described for the short arm of chromosome 8 in 1976. Since then, this type of alteration has been identified and characterised for most chromosome arms. Three mechanisms are commonly proposed to explain the origin of this type of rearrangement. All three mechanisms involve formation of a dicentric chromosome that then breaks in a subsequent meiotic division to produce a monocentric duplicated and deleted chromosome. However, the events leading to the formation of the dicentric chromosome differ between the mechanisms. In one mechanism, either parent carries a paracentric inversion. This results in formation of a loop during meiotic pairing with a recombination event occurring in the loop. In the second mechanism, inverted low copy repeats in the same chromosome arm allow partial folding of one homologue onto itself with a recombination event between the inverted repeats. The third mechanism involves a pre-meiotic double-strand break with subsequent fusion, or U-type exchange, between the sister chromatids. The first two mechanisms require a single copy region to exist between the duplicated and deleted regions on the derivative chromosome, and therefore high resolution analysis of the rearrangement can be used to distinguish between these mechanisms. METHODS AND RESULTS: Using G-banded chromosome analysis, fluorescence in situ hybridisation (FISH) and array comparative genomic hybridisation (CGH), we describe 17 new cases of inverted duplication with terminal deletion of 2q, 4p, 5p, 6q, 8p, 9p, 10q, 13q, 15q, 18p, 18q, and 22q. CONCLUSIONS: These new cases, combined with previously described cases, demonstrate that U-type exchange is the most frequent mechanism for this rearrangement and can be observed on most, or perhaps all, chromosome arms.

Nomenclature evolution: Changes in the ISCN from the 2005 to the 2009 edition.

The Committee for the International System for Human Cytogenetic Nomenclature (ISCN) has recently met and published a revised version, ISCN 2009. Multiple changes in nomenclature guidelines are presented in that updated version. This review will highlight changes to the idiograms and specific changes in respective chapters of the 2009 version compared with the previous version of the ISCN published in 2005. These highlights are meant as a guide for the cytogeneticist to assist in the transition in the use of this updated nomenclature for describing cytogenetic and molecular cytogenetic findings in both clinical and research reports.

Expansion in size of a terminal deletion: a paradigm shift for parental follow-up studies.

BACKGROUND: Parental studies are often necessary subsequent to the identification of a chromosome abnormality. The recommended studies are based on assumptions about how chromosome rearrangements occur. One such assumption is that deletion size is stable through generations. RESULTS: We have identified a family where a small subtelomeric deletion in a phenotypically and cytogenetically normal mother expanded nearly 10-fold into a clinically consequential and cytogenetically visible deletion in her affected daughter. CONCLUSION: Traditional parental follow-up studies would have not identified this expansion, but would have rather classified the deletion in the daughter as either de novo or benign. Only by sizing the deletion by array comparative genomic hybridisation in both the mother and the daughter was the expansion recognised. Previous assumptions about chromosome behaviour suggest that this phenomenon may have been easily missed in other cases of chromosomal deletions. Therefore, this case illustrates the need for more comprehensive analyses of parental chromosome structure when characterising an abnormality in a child.

Comparison of targeted and whole genome analysis of postnatal specimens using a commercially available array based comparative genomic hybridisation (aCGH) microarray platform.

PURPOSE: The University of Utah Comparative Genomic Hybridization Microarray Laboratory was one of the first US laboratories to offer comparative genomic hybridisation (CGH) microarray testing using a commercial platform in a clinical setting. Results for 1076 patients (1598 chips) are presented. METHODS: The Spectral Genomics/PerkinElmer Constitutional Chip (targeted array), SpectralChip 2600 (whole genome array) and a "Combo" chip (both arrays run simultaneously) were the tests offered. Abnormal results were confirmed by an alternative method, most often fluorescence in situ hybridisation. RESULTS: In 669 cases with known normal cytogenetics, an abnormal detection rate of 10.8% was observed, (5.3%, 12.2% and 14.1% for the Constitutional Chip, SpectralChip 2600 and Combo assay, respectively). Known copy number variants and single clone abnormalities are not included in these rates. Single clone abnormalities are reported separately. For 1076 total cases, we report an average abnormal rate of 16.9% (8.7%, 23.7% and 18.6% for the three assays). This rate includes characterisation of some abnormalities previously identified by cytogenetics. CONCLUSIONS: CGH microarray provides a likely aetiology for the clinical phenotype in many cytogenetically normal cases, and a whole genome array generally identifies copy number changes more effectively than a targeted chip alone.

Benign copy number changes in clinical cytogenetic diagnostics by array CGH.

A database of apparently benign copy number variants (bCNVs) detected by a Spectral Genomics Inc./PerkinElmer BAC array platform has been maintained through the University of Utah Comparative Genomic Hybridization laboratory since 2005. The target population for this database represents 1,275 patients with abnormal phenotypes, primarily children referred for developmental delay and mental retardation. These bCNVs are independent of any identified copy number abnormality detected. The most common 35 bCNVs observed and their frequencies are reported here, and a subset of ten of the patients studied was evaluated on a new oligonucleotide CNV array set designed by Agilent Technologies. There was a 76% concordance of calls for these 35 bCNVs detected by both array platforms in the same patients. The higher resolution of the Agilent oligonucleotide array compared to the BAC array allowed determination of the precise breakpoints of the observed CNVs, in addition to documentation of additional CNVs of smaller sizes. As expected, observed CNVs and their frequencies were generally consistent with those of other previously published and available databases, including the Database of Genomic Variants (http://projects.tcag.ca/variation/). The availability of these data should assist other clinical laboratories in the evaluation of CNVs of unknown clinical significance.

Spontaneous immortalization rate of cultured Chinese hamster cells.

Chinese hamster cell cultures derived from either fetal cell suspensions or adult ear clippings invariably became permanent cell lines during conventional subcultivation. The immortal cell cultures arose from rare spontaneous cellular events during the in vitro cultivation of cells with limited proliferative capacity. Immortality was not related to rare, precommitted cells from the animals. The expansion of clones of cells with limited life-span to form permanent cell lines was routinely successful only when the initial, unsubdivided culture achieved a total number in excess of 10(6) cells. On the basis of this observation, a serial clonogenicity assay was developed for determining the life-span of the cells with limited proliferative capacity and for determining whether a cell population is immortal. In addition, the technique of clonal expansion was used for a fluctuation analysis to determine the rate of immortalization. This analysis yielded a rate of 1.9 X 10(6) per cell per generation.

Frequency and pattern of karyotypic abnormalities in human prostate cancer.

The cytogenetic evaluation of 30 cultured primary prostatic cancer specimens obtained during radical prostatectomies of patients with relatively early stage disease is reported. The majority of specimens examined showed a normal male karyotype, 46,XY. Nine samples contained clonally abnormal populations including five specimens which were hyperdiploid (modal range, 65-92 chromosomes), one specimen containing double minute chromosomes, and three containing structural aberrations. Loss of the Y chromosome and a partial trisomy for chromosome 4 was observed in a sample from one patient. Another sample showed a translocation between the long arms of chromosomes 5 and 7. The only tumor obtained from a previously irradiated patient contained no normal cells, a modal chromosome number of 45, loss of chromosomes 2 and Y, and multiple structural rearrangements. The appearance of any clonal cytogenetic abnormality correlated in general with a poorly differentiated state of cancer. A survey of all available previous cytogenetic data on human prostate adenocarcinoma indicated that the loss of chromosomes 1, 2, 5, and Y, the gain of chromosomes 7, 14, 20, and 22, and rearrangements involving chromosome arms 2p, 7q, and 10q are the most common changes observed. This suggests that, although the assignment of a single chromosomal aberration as a marker for early stage prostatic cancer is unlikely, several consistent "hotspots" might be of significance in the etiology of this disease.

Preneoplastic phenotype and chromosome changes of cultured human Bloom syndrome fibroblasts (strain GM 1492).

The Bloom syndrome fibroblast strain, GM 1492, was examined for phenotypic properties generally associated with neoplastic cells. A serial clonogenicity assay indicated that these cells can proliferate in culture, achieving approximately twice the number of population doublings as compared to normal human skin fibroblasts. Strain GM 1492 appeared to be partially transformed in that these cells showed a slight degree of anchorage independence when grown in methylcellulose, and also appeared to have relaxed growth requirements compared to normal fibroblasts. GM 1492 cells are heteroploid, with 20 to 80 chromosomes/cell and a modal chromosome number of 44. Cytogenetic analysis of G-banded metaphase chromosomes indicated that most cells contained at least one copy of each normal human chromosome, and many cells exhibited only aneuploidies with no detectable chromosomal rearrangements. Minute chromosomes were seen in a few of the metaphase cells examined. GM 1492 cells did not form tumors in athymic nude mice. Since many of the characteristics of GM 1492 cells are similar to those seen only in tumor cells, but the strain is nontumorigenic, we suggest that GM 1492 cells are preneoplastic and thus represent an ideal system for the in vitro study of human neoplastic progression.

Suppression of malignant phenotype in a human prostate cancer cell line by fragments of normal chromosomal region 17q.

Recent evidence obtained by in situ hybridization indicates that chromosomal region 17q is often lost in prostate tumors. To substantiate the presence of tumor suppressor genes in this chromosomal region, normal human 17q tagged with a neomycin resistance gene was transferred into a human prostate cancer cell line, PPC-1, by microcell-mediated chromosome transfer. Two hybrid clones were obtained, both of which showed decreased tumorigenicity in athymic nude mice and decreased efficiency of colony formation in soft agar with respect to PPC-1. When microcells were irradiated prior to transfer of chromosomal region 17q to determine which subchromosomal regions carry the potential tumor suppressor gene(s), 10 hybrid clones were obtained, including 6 fully malignant and 4 suppressed clones. Analysis of polymorphic loci on 17q in the series of hybrid clones suggested that a tumor suppressor gene associated with prostate cancer was located in a region no more than 28 cM long at 17q12-q22, which includes the BRCA1 gene involved in hereditary breast cancer.

Development of an antibody to actinomycin D and its application for the detection of serum levels by radioimmunoassay.

An antibody specific for actinomycin D (Act D) has been developed and used in a rapid, sensitive radioimmunoassay for detection of this anticancer drug in serum. The 2-amino group of the heterocyclic chromophore of Act D was covalently coupled to available free carboxyl groups of bovine serum albumin with carbodiimide. The resulting complex was then used for the production of a specific antibody to Act D in two male New Zealand rabbits. Antibody production was of sufficient titer in both rabbits to allow the development of a radioimmunoassay for the free drug which is rapid and sensitive enough to accurately measure 0.1 pmol of Act D. The antibody produced was characterized to be immunoglobulin G by virtue of its ability to bind to Protein A:Sepharose columns. With the use of Act-D analog, actinomine, the antibody was characterized to be specific for the pentapeptide portion of the molecule. Pharmacokinetic analysis of serial serum samples obtained from a patient who received the drug i.v. revealed a biphasic response with an alpha-serum half-life of 1.78 and a beta serum half-life of 34 min. An i.v. injection of Act D into a dog and assay of serum concentration revealed a similar biphasic response with an alpha serum half-life of 0.78 min and a beta-serum half-life of 208 min.

Suppression of the malignant phenotype of human prostate cancer cell line PPC-1 by introduction of normal fragments of human chromosome 10.

Numerous studies have detected frequent losses of heterozygosity at polymorphic loci on chromosomal arms 10p and 10q in human prostate cancers. To confirm the presence of tumor suppressor genes in these chromosomal regions, fragments of normal human chromosome 10 tagged with a neomycin resistance gene were transferred into cells from a human prostate cancer cell line. PPC-1, by microcell-mediated chromosome transfer. Two of the six hybrid clones obtained showed decreased tumorigenicity in athymic nude mice and decreased efficiency of colony formation in soft agar compared with PPC-1; the other four retained fully malignant phenotypes. Analysis of polymorphic loci on chromosome 10 in these hybrid clones suggested that a tumor suppressor gene associated with prostate cancer is located within a 17-cM region at distal 10p.

An apoptosis signaling pathway induced by the death domain of FADD selectively kills normal but not cancerous prostate epithelial cells.

The adaptor protein FADD directly, or indirectly via another adaptor called TRADD, recruits caspase 8 to death receptors of the tumor necrosis factor receptor family. Consequentially, a dominant-negative mutant (FADD-DN, which consists only of the FADD death domain) that binds to receptors but cannot recruit caspase 8 has been widely used to inhibit apoptosis by various stimuli that work via death receptors. Here, we show that FADD-DN also has another cell type- and cancer-dependent activity because it induces apoptosis of normal human prostate epithelial cells but not normal prostate stromal cells or prostate cancer cells. This activity is independent of FADD-DN's ability to bind to three known interacting proteins, Fas, TRADD or RIP suggesting that it is distinct from FADD's functions at activated death receptors. FADD-DN induces caspase activation in normal epithelial cells as demonstrated using a Fluorescence Resonance Energy Transfer assay that measures caspase activity in individual living cells. However, caspase-independent pathways are also implicated in FADD-DN-induced apoptosis because caspase inhibitors were inefficient at preventing prostate cell death. Therefore, the death domain of FADD has a previously unrecognized role in cell survival that is epithelial-specific and defective in cancer cells. This FADD-dependent signaling pathway may be important in prostate carcinogenesis.

Trisomy 17p associated with Charcot-Marie-Tooth neuropathy type 1A phenotype: evidence for gene dosage as a mechanism in CMT1A.

Charcot-Marie-Tooth neuropathy type 1A (CMT1A) is associated with a DNA duplication on chromosome 17, band p11.2, resulting in partial trisomy for this region in CMT1A patients. The 17p11.2 duplication may lead to the CMT1A phenotype either through disruption of a gene at the duplication breakpoint junction or by trisomic dosage and overexpression of a gene within the duplication. To test the latter model, we evaluated a patient with complete translocation trisomy 17p for signs of CMT1A. In addition to the dysmorphic features seen in trisomy 17p, a neurologic examination and electrophysiologic studies detected a demyelinating neuropathy, compatible with CMT1A. A karyotype on the patient's father found a balanced translocation [t(14;17)] with breakpoints on chromosome 17 in either band p11.1 or proximal p11.2. An analysis of the patient's DNA confirmed trisomy 17p and mapped the translocation breakpoint to a region in 17p11.2, proximal to the duplication breakpoint in CMT1A. Our observations in this patient with trisomy 17p are relevant to an understanding of the genetic mechanism in CMT1A and provide strong evidence that gene dosage through segmental trisomy for 17p11.2 results in the CMT1A phenotype.

Evidence by spectral karyotyping that 8q11.2 is nonrandomly involved in lipoblastoma.

We report two cases of lipoblastoma with chromosome 8-related aberrations, ie, a 92,XXYY,t(7;8Xp22;q11.2)x2 [8]/46,XY[16] in Case 1 and a 46,XY,-8,-13,add(16) (q22),+mar, +r [cp13]/46,XY[7] in Case 2. Using spectral karyotyping and fluorescence in situ hybridization techniques, the karyotype of Case 2 was redesignated as 46,XY, r(8), del(13)(q12), der(16)ins(16;8)(q22; q24q11.2)[cp13]/46,XY[7]. This report delineates a new chromosome rearrangement, ie, der(16)ins(16;8)(q22; q24q11.2) in lipoblastoma, and also confirms the t(7; 8)(p22;q11.2), reported only once previously, as a recurrent translocation involved in such a tumor. These findings provide valuable information for clinical molecular cytogenetic diagnosis of lipoblastoma. Furthermore, this report highlights the value of cytogenetic and molecular cytogenetic analysis in differential diagnosis of childhood adipose tissue tumors and adds to the number of lipoblastomas reported with chromosomal abnormalities at 8q11.2.

Natural history of Wolf-Hirschhorn syndrome: experience with 15 cases.

Wolf-Hirschhorn syndrome (WHS) is a well-known chromosomal disorder attributable to partial deletion of the short arm of chromosome 4 (4p-). Although about 120 cases have been reported so far, there is still very little data on its natural history. Information given to parents at the time of diagnosis tends to be skewed to the extreme negative. To help delineate more thoroughly the natural history of WHS, and to obtain better information to answer parents' questions in a clinical setting, we evaluated 15 patients (12 females, 3 males) in three centers with the 4p- syndrome. Four of the cases had a follow-up spanning 16 years. Thirteen cases were detected by standard cytogenetics (regular G-banding 10, high-resolution banding 3), while the remaining 2 required fluorescence in situ hybridization. A total of 5/15 (33.3%) had heart lesions; 7/15 (46. 6%) had oral facial clefts; 13/15 (86.6%) had a seizure disorder, that tended to disappear with age; and 100% had severe/profound developmental retardation. One Italian patient had sensorineural deafness and 1 Utah patient had a right split hand defect. Of note, 2 Utah patients were able to walk with support (at 4 and 12 years of age, respectively), whereas 3 Italian patients and 1 Utah patient were able to walk unassisted (at 4, 5, 5 years 9 months, and 7 years of age, respectively). Two of the 3 Italian patients also achieved sphincter control (by day). The 8 patients receiving serial electroencephalogram studies showed fairly distinctive abnormalities, usually outlasting seizures. A slow, but constant progress in development was observed in all cases, during the follow-up period. In conclusion, the combined cases of the three centers represent considerable experience, providing new information on several aspects of this important deletion syndrome.

Multiple craniofacial anomalies associated with an interstitial deletion of chromosome 1(q21->q25).

We present a patient with an interstitial deletion of the chromosome 1q21->q25 that was diagnosed by amniocentesis. Significant malformations included: microbrachycephaly, bilateral cleft lip and palate, micrognathia, short neck, and athyroidia. The autopsy results demonstrate an overlap with several other postnatally ascertained patients and document the phenotype prenatally.