FOXO3a loss is a frequent early event in high-grade pelvic serous carcinogenesis.

Serous ovarian carcinoma is the most lethal gynecological malignancy in Western countries. The molecular events that underlie the development of the disease have been elusive for many years. The recent identification of the fallopian tube secretory epithelial cells (FTSECs) as the cell-of-origin for most cases of this disease has led to studies aimed at elucidating new candidate therapeutic pathways through profiling of normal FTSECs and serous carcinomas. Here we describe the results of transcriptional profiles that identify the loss of the tumor suppressive transcription factor FOXO3a in a vast majority of high-grade serous ovarian carcinomas. We show that FOXO3a loss is a hallmark of the earliest stages of serous carcinogenesis and occurs both at the DNA, RNA and protein levels. We describe several mechanisms responsible for FOXO3a inactivity, including chromosomal deletion (chromosome 6q21), upregulation of miRNA-182 and destabilization by activated PI3K and MEK. The identification of pathways involved in the pathogenesis of ovarian cancer can advance the management of this disease from being dependant on surgery and cytotoxic chemotherapy alone to the era of targeted therapy. Our data strongly suggest FOXO3a as a possible target for clinical intervention.

Improving the yield of circulating tumour cells facilitates molecular characterisation and recognition of discordant HER2 amplification in breast cancer.

BACKGROUND: Circulating tumour cells (CTCs) offer a non-invasive approach to obtain and characterise metastatic tumour cells, but their usefulness has been limited by low CTC yields from conventional isolation methods. METHODS: To improve CTC yields and facilitate their molecular characterisation we compared the Food and Drug Administration-approved CellSearch Epithelial Kit (CEK) to a simplified CTC capture method, CellSearch Profile Kit (CPK), on paired blood samples from patients with metastatic breast (n=75) and lung (n=71) cancer. Molecular markers including Human Epidermal growth factor Receptor 2 (HER2) were evaluated on CTCs by fluorescence in situ hybridisation (FISH) and compared to patients' primary and metastatic cancer. RESULTS: The median cell count from patients with breast cancer using the CPK was 117 vs 4 for CEK (P<0.0001). Lung cancer samples were similar; CPK: 145 cells vs CEK:4 cells (P<0.0001). Recovered CTCs were relatively pure (60-70%) and were evaluable by FISH and immunofluorescence. A total of 10 of 30 (33%) breast cancer patients with HER2-negative primary and metastatic tissue had HER2-amplified CTCs. CONCLUSION: The CPK method provides a high yield of relatively pure CTCs, facilitating their molecular characterisation. Circulating tumour cells obtained using CPK technology demonstrate that significant discordance exists between HER2 amplification of a patient's CTCs and that of the primary and metastatic tumour.

Molecular studies of segmental aneusomy: FISHing for the atypical cry in del(5)(p15.3).

We report a newborn male with multiple congenital anomalies including growth retardation, hypotonia, dysmorphic facies, widely-spaced nipples, micropenis, cryptorchidism, optic nerve hypoplasia, heart disease, and a striking, high-pitched cry. Chromosome analysis revealed de novo partial trisomy 11q due to a der(5)t(5;11)(p15.3;q22). Fluorescence in situ hybridization (FISH) showed loss of the 5p telomere signal on the der(5) chromosome, indicating the infant has partial monosomy 5p in addition to partial trisomy 11q. Among cases involving trisomy 11q, an unusual cry has only been documented in the presence of a der(5)t(5p;11q). This apparent dependence of the abnormal cry on monosomy 5p suggested the same genetic mechanism that occurs in Cri du chat syndrome (CDCS) may be responsible for the atypical cry in der(5)t(5p;11q) individuals. Neither a commercial CDCS probe (LSI D5S23, D5S721) nor a series of BAC clones encompassing distal regions implicated in the CDCS-associated cat-cry were deleted in our patient. These results suggest a second cry-modifying locus maps telomeric to BAC RP11-94J21 in band 5p15.33. This locus may not only cause the abnormal cry in individuals with a der(5)t(5p;11q) but could also contribute to the phenotypic variability and discordant mapping studies observed for CDCS.

[Spindle cell lipoma and 13q deletion: diagnostic utility of cytogenetic analysis]. / Lipomes à cellules fusiformes et délétion 13q: apport de la cytogénétique dans l'aide au diagnostic.

AIM: Spindle cell lipomas are rare adipose tissues tumors. Histologically, these lesions are composed of mature adipocytes and spindle cells associated with collagen bundles. Spindle cell lipomas are benign tumors that can be difficult to distinguish from malignant tumors such as spindle cell liposarcomas, myxoid liposarcomas or well-differentiated liposarcomas. RESULTS: We report herein the description of two new cases. The first case was a deeply situated and infiltrating tumor located in the retromastoidian area. The karyotype showed the presence of two chromosomal abnormalities, a partial deletion of the long arm of chromosome 13, del(13)(q12) and a balanced reciprocal translocation t(2;6)(p16~21;p21). The second case was a subcutaneous tumor of posterior cervical localization. The karyotype showed a 13q deletion associated with a complex rearrangement of chromosomes 5, 6 and 10. The presence of the 13q deletion allowed us to confirm the diagnosis of spindle cell lipoma in both cases. This deletion has been previously described in six out the eleven published karyotype reports. The 13q deletion is usually associated with partial monosomy 16. The present case confirms that it can occur independently. The 6p21 rearrangement may also play a role in the pathobiology of this tumor, as suggested by the positive HMGIY expression detected by immunohistochemistry. CONCLUSION: Our study further illustrates that spindle cell lipomas can infiltrate the surrounding muscle and emphasizes the usefulness of cytogenetic analysis in the differential diagnosis of soft tissue tumors.

Integration of cytogenetic landmarks into the draft sequence of the human genome.

We have placed 7,600 cytogenetically defined landmarks on the draft sequence of the human genome to help with the characterization of genes altered by gross chromosomal aberrations that cause human disease. The landmarks are large-insert clones mapped to chromosome bands by fluorescence in situ hybridization. Each clone contains a sequence tag that is positioned on the genomic sequence. This genome-wide set of sequence-anchored clones allows structural and functional analyses of the genome. This resource represents the first comprehensive integration of cytogenetic, radiation hybrid, linkage and sequence maps of the human genome; provides an independent validation of the sequence map and framework for contig order and orientation; surveys the genome for large-scale duplications, which are likely to require special attention during sequence assembly; and allows a stringent assessment of sequence differences between the dark and light bands of chromosomes. It also provides insight into large-scale chromatin structure and the evolution of chromosomes and gene families and will accelerate our understanding of the molecular bases of human disease and cancer.

Leiomyomata: heritability and cytogenetic studies.

Leiomyomata represent the most common gynaecological tumour in women of reproductive age, and are the primary indication for hysterectomy in the USA. Cytogenetic and genetic studies have, in recent years, advanced our understanding of the aetiology of these tumours. Cytogenetic aberrations involving chromosomes 6, 7, 12 and 14 constitute the major chromosomal abnormalities seen in leiomyomata, and suggest the possibility that disruption or dysregulation of the genes HMGIC and HMGIY may contribute to the development of these tumours. Based on the finding of a variety of chromosomal aberrations detected in fibroids, other genes with fundamental roles in the pathobiology of uterine leiomyomata await identification. Furthermore, the incidence of fibroids has been shown to be greater in African-American women than in Caucasian women. The existence of a heritability component of uterine leiomyomata has been further implicated by twin-pair studies and the existence of familial forms of leiomyomata, both of which suggest an inherited diathesis for leiomyomata formation. This paper will review the cytogenetic aberrations and gene expression, with respect to their contributions to the pathogenesis of leiomyomata, and also summarize the current understanding of heritability of these tumours.

Genetics of uterine leiomyomata.

Leiomyomata represent the most common gynecologic tumors in women of reproductive age and are the primary indication for hysterectomy in the United States. Cytogenetic and genetic studies have in recent years advanced our understanding of the etiology of these tumors. Cytogenetic aberrations involving chromosomes 6, 7, 12, and 14 constitute the major chromosomal abnormalities seen in leiomyomata and have led to the discovery that disruptions or dysregulations of HMGIC and HMGIY contribute to the development of these tumors. Based on the finding of a variety of other consistent chromosomal aberrations detected in these tumors, other genes with fundamental roles in the pathobiology of uterine leiomyomata await identification. Genes Chromosomes Cancer 28:235-245, 2000.

Identification of female carriers for Duchenne and Becker muscular dystrophies using a FISH-based approach.

Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive neuromuscular diseases caused by dystrophin gene mutations. Deletions, or more rarely duplications, of single or multiple exons within the dystrophin gene can be detected by current molecular methods in approximately 65% of DMD patients. Mothers of affected males have a two-thirds chance of carrying a dystrophin mutation, whilst approximately one-third of affected males have de novo mutations. Currently, Southern blot analysis and multiplex PCR directed against exons in deletion hot spots are used to determine female carrier status. However, both of these assays depend on dosage assessment to accurately identify carriers since, in females, the normal X chromosome is also present. To obviate quantitation of gene dosage, we have developed exon-specific probes from the dystrophin gene and applied them to a screen for potential carrier females using fluorescence in situ hybridization (FISH). Cosmid clones, representing 16 exons, were identified and used in FISH analysis of DMD/BMD families. Our preliminary work has identified multiple, informative probes for several families with dystrophin deletions and has shown that a FISH-based assay can be an effective and direct method for establishing the DMD/BMD carrier status of females.

Dysregulation of HMGIC in a uterine lipoleiomyoma with a complex rearrangement including chromosomes 7, 12, and 14.

Uterine lipoleiomyomas are extremely rare tumors consisting of a mixture of mature adipocytes and smooth muscle cells. Using G-banding and FISH, we characterized a complex rearrangement involving chromosomes 7, 8, 10, 11, 12, and 14 in one of these tumors. The region 14q23-24 was inserted into the long arm of the derivative chromosome 12, between the 3' end of HMGIC and 7q21-22, another region often rearranged in uterine leiomyomas. Other portions of chromosomes 12 and 14 were involved in derivative chromosomes 7, 11, 12, and 14. A chromosome 8 was involved in a three-way rearrangement including the derivative 7, a ring chromosome 10, and a small derivative chromosome 8 bearing segments of chromosomes 10 and 11. No abnormality of chromosome 5 was detected, in contrast to two previously reported cytogenetic analyses of uterine lipoleiomyoma. The consistent finding of chromosomes 12 and 14 on different derivatives indicates that the t(12;14) was a primary event. In addition, immunohistochemical studies showed that HMGI-C was aberrantly expressed in this tumor. These observations suggest that uterine lipoleiomyomas have a pathogenetic origin similar to that of typical leiomyomas. Genes Chromosomes Cancer 27:209-215, 2000.

[Genetics of uterine leiomyomata]. / Génétiques des léiomyomes utérines.

Uterine leiomyomata, or fibroids, represent the most common tumor in women of reproductive age. Although benign, leiomyomata constitute a major health problem, and are the most frequent indication for hysterectomy. The pathobiology of these tumors is still poorly understood. Cytogenetic and genetic studies have, in recent years, advanced our understanding of the etiology of these tumors. Specifically, cytogenetic aberrations involving chromosomes 6, 7, 12 and 14 have been shown to constitute the major chromosomal abnormalities seen in leiomyomata and have led to the discovery that HMGIC and HMGIY, two members of the non-histone high mobility group of genes, are involved in fibroid development. HMGIC and HMGIY map to 12q15 and 6p21, and their disruption or dysregulation has been shown to contribute to leiomyomata formation. Given the observation of several additional, but consistent, chromosomal aberrations, it is likely that other genes with fundamental roles in the pathobiology of uterine leiomyomata await identification. Furthermore, twin studies and the discovery of both ethnic and familial predispositions have suggested a genetic liability to develop uterine leiomyomata.

Expression of HMGIY in three uterine leiomyomata with complex rearrangements of chromosome 6.

Uterine leiomyomata (UL) are a major public health problem, yet little is known about their etiology. Genetic factors likely influence UL development and growth; for example, approximately 40% of UL have chromosomal abnormalities detectable by conventional cytogenetic analysis, including t(12;14)(q15;q23-24), rearrangements involving the short arm of chromosome 6 and interstitial deletions of the long arm of chromosome 7. Two high-mobility group (HMG) protein genes, HMGIC and HMGIY, located at 12q15 and 6p21.3, respectively, are involved in rearrangements in various mesenchymal tumors including UL. In this study, we investigated HMGIY expression in three UL with complex cytogenetic rearrangements of 6p21.3 by reverse transcriptase-polymerase chain reaction (RT-PCR) and electrophoretic shift assay (EMSA). Our findings suggest that there are multiple mechanisms for HMGIY dysregulation, which may include post-translational modification of the hmgiy protein and dysregulation due to different translocation partners. Furthermore, the mechanism dysregulating HMGIY in UL with 6p21.3 and 14q23-24 rearrangements may be similar to the mechanism dysregulating HMGIC in UL characterized as t(12;14)(q15;q23-24), because of the common involvement of an HMG gene and a gene at 14q23-24.

ORC5L, a new member of the human origin recognition complex, is deleted in uterine leiomyomas and malignant myeloid diseases.

A new member of the human origin recognition complex (ORC) was cloned and identified as ORC5L. HsORC5p is a 50-kDa protein whose sequence is 38% identical and 62% similar to ORC5p from Drosophila melanogaster. Two alleles of ORC5L were identified, one with and one without an evolutionarily conserved purine nucleotide binding motif. HsORC5p is precipitated from cell extracts with HsORC2p and HsORC4p, indicating that it is part of the putative human ORC. The bulk of HsORC5p is in an insoluble nuclear fraction, whereas the other known human ORC subunits (HsORC1p, HsORC2p, and HsORC4p) are easily extracted in the nuclear-soluble fractions and in S100 (HsORC1p). In addition, we identified an alternatively spliced mRNA from the same locus (HsORC5T). HsORC5Tp also formed a complex with HsORC4p but not with HsORC2p, suggesting it may play a regulatory role in the assembly of different ORC subcomplexes. HsORC5, HsORC5T, and HsORC4 transcripts are abundant in spleen, ovary, and prostate in addition to tissues with high levels of DNA replication like testes and colon mucosa, implicating the human ORC proteins in functions besides DNA replication. Finally, the gene for ORC5L is located at chromosome 7, band q22, in the minimal region deleted in 10% of uterine leiomyomas and in 10-20% of acute myeloid leukemias and myelodysplastic syndromes.

Differentially expressed gene products in glioblastoma cells suppressed for tumorigenicity.

The loss of large segments or an entire copy of chromosome 10 is the most common genetic alteration in human glioblastomas. To address the biological and molecular consequences of this chromosomal alteration, we transferred a human chromosome 10 into a glioma cell clone devoid of an intact copy. The hybrid cells exhibited an altered cellular morphology, a decreased saturation density, and a suppression of both anchorage-independent growth and tumor formation in nude mice. The hybrids also expressed the recently identified candidate tumor suppressor gene MMAC1/PTEN. To further identify gene products that may be involved in glioma progression, a subtractive hybridization was performed between the human glioblastoma cells and the phenotypically suppressed hybrid cells to identify differentially expressed gene products. Sixty-one clones were identified, with nine clones being preferentially expressed in the hybrid cells. Four cDNA clones represented markers of differentiation in glial cells. Two cDNA clones shared homology with platelet derived growth factor-alpha and the insulin receptor, respectively, both genes previously implicated in glioma progression. A novel gene product that was expressed predominantly in the brain, but which did not map to chromosome 10, was also identified. This clone contained an element that was also present in three additional clones, two of which also exhibited differential expression. Consequently, the presence of a functional copy of chromosome 10 in the glioma cells results in differential expression of a number of gene products, including novel genes as well as those associated with glial cell differentiation.

Suppression of transformed phenotype and tumorigenicity after transfer of chromosome 4 into U251 human glioma cells.

The development of primary human brain tumors, particularly glioblastoma multiforme (GBM), has been associated with a number of molecular and chromosomal abnormalities. In this study, a novel tumor suppressor locus was identified and localized after the transfer of a human chromosome 4 into U251 human GBM cells. Hybrid clones containing a transferred neomycin-resistance tagged chromosome 4 revealed an inability to form tumors in nude mice and a greatly decreased efficiency of soft agarose colony formation. As a control, clones containing a transferred chromosome 2 were generated, and these retained the tumorigenic phenotype of the parental U251 cells. The presence of the transferred chromosomes was demonstrated by gain of polymorphic loci and FISH analyses. Several suppressed hybrid clones were shown to contain spontaneously reduced versions of the transferred chromosome 4. A common region of the fragmented chromosome 4 was retained among these clones that included the epidermal growth factor locus at 4q24-26 and several adjacent markers. The identification of a common fragment in the suppressed clones suggests the presence of a tumor suppressor gene or genes in this region, involved in glioma oncogenesis.

Simultaneous, multilocus FISH analysis for detection of microdeletions in the diagnostic evaluation of developmental delay and mental retardation.

Many microdeletion and contiguous gene-deletion syndromes include mental retardation as a clinical feature. We have developed MultiFISH, a FISH assay using several probes to simultaneously screen for multiple microdeletion syndromes in patients who present with unexplained devleopmental delay and/or mental retardation. This screening tool can be used to determine whether a particular microdeletion syndrome is involved in the etiology of these clinical phenotypes. In this pilot study we combined probes for the commonly deleted regions of Prader-Willi, Angelman, Williams, Smith-Magenis, and DiGeorge/velocardiofacial syndromes in a single hybridization. The probes were differentially labeled, allowing multicolor detection, and 200 individual samples were screened in a blinded fashion. For all patients found by MultiFISH to have deletions, the deletions were originally identified and/or later confirmed by use of single-probe FISH analysis in our diagnostic cytogenetics laboratory. One patient, who was referred for developmental delay and was shown to have a normal G-banded karyotype, was identified by MultiFISH as having a micro-deletion at the DiGeorge/velocardiofacial commonly deleted region. Forty-six of the 200 total samples were tested for microdeletions by use of single FISH probes in the diagnostic laboratory. Ten of these cases were found to have deletions, and all deletions were subsequently detected by use of MultiFISH screen performed in a blinded fashion. Additionally, for all 200 patients tested by use of MultiFISH, no false-positive deletion results were observed. We demonstrate the ability of this technique to scan for and to identify microdeletions in a proportion of patients whose routine karyotype appears normal yet who are mentally retarded and/or developmentally delayed.

Identification of a candidate tumour suppressor gene, MMAC1, at chromosome 10q23.3 that is mutated in multiple advanced cancers.

Deletions involving regions of chromosome 10 occur in the vast majority (> 90%) of human glioblastoma multiformes. A region at chromosome 10q23-24 was implicated to contain a tumour suppressor gene and the identification of homozygous deletions in four glioma cell lines further refined the location. We have identified a gene, designated MMAC1, that spans these deletions and encodes a widely expressed 5.5-kb mRNA. The predicted MMAC1 protein contains sequence motifs with significant homology to the catalytic domain of protein phosphatases and to the cytoskeletal proteins, tensin and auxilin. MMAC1 coding-region mutations were observed in a number of glioma, prostate, kidney and breast carcinoma cell lines or tumour specimens. Our results identify a strong candidate tumour suppressor gene at chromosome 10q23.3, whose loss of function appears to be associated with the oncogenesis of multiple human cancers.

Identification of a novel gene product, RIG, that is down-regulated in human glioblastoma.

Genetic deletions to chromosome 10 have been extensively documented for human glioblastomas (GBMs). To identify gene products that may be involved in malignant progression, a subtractive hybridization was performed between GBM cells and hybrid cells suppressed for tumorigenicity following microcell transfer of chromosome 10. One novel cDNA isolated from this subtraction showed consistent upregulation (approximately 4 to 10-fold) that correlated with the nontumorigenic phenotype of the hybrid cells. Subsequent analysis resulted in the identification of a full length cDNA (2,569 bp) termed RIG (regulated in glioma). RIG expression was either not detected or detected only at low levels in cultured glioma cells and primary glioblastoma specimens compared to normal brain cells. The 2.6 kb RIG mRNA was expressed predominantly in normal brain with lower levels in heart and lung. Sequence analysis showed no significant homology to known gene products. Genomic alterations of RIG were present in approximately 25% of glioma cell lines examined. Also, RIG mapped to chromosome 11p15.1, a region that is known to be altered in malignant astrocytomas. The differential expression pattern, tissue distribution and chromosomal location of RIG suggests it serves as a molecular marker for or may play a role in the malignant progression of GBMs.

Two tumor suppressive loci on chromosome 10 involved in human glioblastomas.

A number of cytogenetic and molecular analyses have revealed very frequent and extensive losses of regions of chromosome 10 in human glioblastomas. Our recent studies have demonstrated that the transfer of a chromosome 10 into human glioblastoma cells resulted in suppression of their transformed and tumorigenic phenotype. To localize the suppressive region further, we isolated and characterized certain hybrid cells that had undergone chromosomal rearrangements to yield hybrid cells retaining only various regions of the inserted chromosome 10. One series of subclones showed the loss of the majority of the long arm of chromosome 10 (10q21-10qter) and regained the ability to grow under anchorage-independent conditions, but the cells still failed to exhibit significant tumorigenicity in nude mice. Another set of subclones exhibited major deletions of large segments of the long arm of chromosome 10 (10q21-q23; 10q26-qter), yet retained certain distal alleles associated with 10q24 to 10q26. These subclones were identical in their biological characteristics to the hybrids containing an intact chromosome 10, exhibiting no growth in soft agarose or in nude mice. These results implicate the presence of two independent phenotypically suppressive regions on chromosome 10 (10pter-q11 and 10q24-q26) that are involved in glioma progression.