Nuclear gene OPA1, encoding a mitochondrial dynamin-related protein, is mutated in dominant optic atrophy.

Optic atrophy type 1 (OPA1, MIM 165500) is a dominantly inherited optic neuropathy occurring in 1 in 50,000 individuals that features progressive loss in visual acuity leading, in many cases, to legal blindness. Phenotypic variations and loss of retinal ganglion cells, as found in Leber hereditary optic neuropathy (LHON), have suggested possible mitochondrial impairment. The OPA1 gene has been localized to 3q28-q29 (refs 13-19). We describe here a nuclear gene, OPA1, that maps within the candidate region and encodes a dynamin-related protein localized to mitochondria. We found four different OPA1 mutations, including frameshift and missense mutations, to segregate with the disease, demonstrating a role for mitochondria in retinal ganglion cell pathophysiology.

Deregulation of the platelet-derived growth factor B-chain gene via fusion with collagen gene COL1A1 in dermatofibrosarcoma protuberans and giant-cell fibroblastoma.

Dermatofibrosarcoma protuberans (DP), an infiltrative skin tumour of intermediate malignancy, presents specific features such as reciprocal translocations t(17;22)(q22;q13) and supernumerary ring chromosomes derived from the t(17;22). In this report, the breakpoints from translocations and rings in DP and its juvenile form, giant cell fibroblastoma (GCF), were characterised on the genomic and RNA level. These rearrangements fuse the platelet-derived growth factor B-chain (PDGFB, c-sis proto-oncogene) and the collagen type I alpha 1 (COL1A1) genes. PDGFB has transforming activity and is a potent mitogen for a number of cell types, but its role in oncogenic processes is not fully understood. COL1A1 is a major constituent of the connective tissue matrix. Neither PDGFB nor COL1A1 have so far been implicated in any tumour translocations. These gene fusions delete exon 1 of PDGFB, and release this growth factor from its normal regulation.

Translocation of oncogene c-sis from chromosome 22 to chromosome 11 in a Ewing sarcoma-derived cell line.

Somatic cell hybrids, obtained after fusion of translocation (11;22)-positive Ewing sarcoma cells and Chinese hamster fibroblasts, were assayed for the presence of immunoglobulin C lambda, Philadelphia chromosome breakpoint cluster region, and c-sis oncogene sequences. It was found that c-sis was translocated from chromosome 22 to chromosome 11 in the Ewing sarcoma cells used, indicating that the breakpoint must be proximal to this locus. Moreover, we found that the chromosome 22-linked C lambda and breakpoint cluster region sequences are not translocated. This result confirms an earlier cytogenetic observation that the Ewing sarcoma-associated breakpoint in chromosome 22 is distal to those observed in translocation (8;22)-positive Burkitt lymphoma and in Philadelphia chromosome-positive chronic myeloid leukemia.

Chimeric EWS-FLI1 transcript in a Ewing cell line with a complex t(11;22;14) translocation.

Peripheral neuroectodermal tumors include the differentiated neuroepithelioma and the undifferentiated Ewing's tumor. Despite clinical and pathological differences, both malignancies are characterized by a t(11;22)(q24;q12) translocation which is observed in > 90% of the cases. Molecularly, the translocation is underlaid by a rearrangement between the EWS and Fli-1 genes on chromosomes 22 and 11, respectively. Because of the difficulties in the differential diagnosis between various small round cell tumors of childhood, including Ewing's tumor, a molecular diagnostic assay would be desirable. A prerequisite for predicting the reliability of such a test resides in the molecular elucidation of the peripheral neuroectodermal tumor cases which do not exhibit the prototypical translocation. We have analyzed one such case of Ewing's tumor-derived cell line with a t(11;22;14)(q24;q12;q11) translocation. An EWS-Fli-1 fusion transcript was evidenced by polymerase chain reaction amplification of a reverse transcription product obtained from total RNA. Direct sequencing was performed to demonstrate that the molecular rearrangement in this particular Ewing sample resulted in a fusion transcript similar to those observed in tumors with the prototypical translocation.

Ring 22 chromosomes in dermatofibrosarcoma protuberans are low-level amplifiers of chromosome 17 and 22 sequences.

Ring chromosomes have been found with some regularity as solid tumors have come increasingly under cytogenetic study. The full genetic content and significance of these rings remain unclear. Dermatofibrosarcoma protuberans, a tumor of the deep dermis, consistently has supernumerary ring chromosomes, sometimes as the sole detectable cytogenetic change. Using a modified method for comparative genomic hybridization and fluorescent in situ hybridization with a panel of various probes, we found that these ring chromosomes consistently contain the chromosome 22 centromere along with interstitial sequences from chromosomes 17 and 22, specifically from regions 17q23-24 and 22q11-12. The ring chromosomes in dermatofibrosarcoma protuberans are vehicles for a particular pattern of relatively low-level genomic amplification of selected sequences.

Myxoid liposarcoma with t(12;16) (q13;p11) contains site-specific differences in methylation patterns surrounding a zinc-finger gene mapped to the breakpoint region on chromosome 12.

The q13 to q15 region of human chromosome 12 is frequently and consistently rearranged in malignant and benign adipose tissue tumors as well as benign tumors of smooth muscle and salivary glands. A reciprocal translocation, (12;16) (q13;p11), is characteristic of the myxoid subtype of liposarcoma, whereas translocations within 12q13-14 are frequently observed in benign lipomas. We are using pulsed-field gel electrophoresis to study the 12q13-q14 region in order to detect and clone the respective translocation breakpoints in these tumors. The locus GLI, which encodes a zinc-finger protein, has been mapped to the same region as the myxoid liposarcoma breakpoint. Pulsed-field analysis of myxoid liposarcoma and lipoma DNA has allowed us to construct a 600-kilobase physical map surrounding the GLI locus, which shows that breakpoints in both types of tumor are outside this region. However, myxoid liposarcoma DNA samples contained altered restriction fragments detectable with GLI probes that were highly specific and reproducible from case to case. These altered fragments are due to highly specific and reproducible methylation differences that are unique to myxoid liposarcoma DNA. These methylation changes may prove to be useful clinically as a diagnostic tool to differentiate subtypes of liposarcoma.

In vitro karyotypic and immunophenotypic characterisation of primitive neuroectodermal tumours: similarities to malignant gliomas.

Monoclonal antibody (Mab) mediated immunotherapy of brain tumours requires the identification of tumour-restricted cell surface antigens. We have characterised four primitive neuroectodermal tumours, which included pineoblastoma, medulloblastoma and ependymoblastoma cultures, that demonstrated in vitro evidence of malignant behaviour (anchorage-independent growth and nu/nu xenograft tumour formation). The cytogenetic findings ranged from normal G-banded and Q-banded karyotypes through mixed near-diploid/hyperdiploid. These cultures resembled the cell surface immunophenotypic spectrum of malignant gliomas. They were distinguished from normal glia in vitro by the expression of restricted fetal mesenchymal, neuronal, myoblastic, melanocytic, epidermal, chondrocytic, lymphoid and epithelial antigens. Certain antigens appeared sufficiently represented among central nervous system (CNS) neoplasms to afford potential targets for Mab-mediated immunotherapy.

Chromosomal changes in soft-tissue sarcomas. A new diagnostic parameter.

A cytogenetic study was performed on short-term cultures from fresh surgical specimens obtained from 41 patients with soft-tissue sarcomas of various histologic origins. The results demonstrated that myxoid liposarcomas (five tumors) were associated with a specific translocation between chromosomes 12 and 16 and that synovial sarcomas (six tumors) were associated with a specific translocation between the X chromosome and chromosome 18. These chromosomal data have been used to differentiate myxoid liposarcoma from other myxoid tumors exhibiting a non-characteristic histologic picture, as well as to ascertain the diagnosis of synovial sarcoma in undifferentiated soft-tissue sarcomas. The results to date indicate that identification of specific chromosomal changes in sarcomas may provide a new diagnostic criterion for these tumors and possibly improve prognostication with regard to survival and response to treatment.

Normal blood lymphocytes from patients with adipose tissue tumors with rearrangements at 12q13-q14 do not express the fragile site fra(12)(q13.1).

An association between chromosomal fragile sites and cancer-specific breakpoints has been found to be statistically significant. Cancer patients have been shown to be carriers of fragile sites in chromosome regions involved in rearrangements in malignant cells. Based on these observations it has been hypothesized that fragile sites may be involved in the pathogenesis of human tumors. We have recently described a new recurrent cancer breakpoint at chromosomal region 12q13-q14 in adipose tissue tumors. The possible involvement in these tumors of the rare folate-sensitive fragile site 12q13.1 has been investigated in PHA-stimulated peripheral blood cells from three patients carrying the t(12;16)(q13;p11) in their liposarcoma cells and one patient with the t(3;12)(q28;q14) in his lipoma cells. No expression of the fragile site 12q13.1 could be detected in the blood lymphocytes of any of the patients. The involvement of the fragile site 12q13.1 in the pathogenesis of adipose tissue tumors with a 12q13-q14 breakpoint remains to be established.

Chromosomes in Ewing's sarcoma. II. Nonrandom additional changes, trisomy 8 and der(16)t(1;16).

Chromosomal data from 82 informative, unrelated Ewing's sarcoma (ES) specimens (including 20 personal specimens) were reviewed for secondary changes additional to the t(11;22)(q24;q12). Additional numerical and/or structural changes were found in 75 specimens. Trisomy 8 was observed consistently in half of the 43 cases selected for analysis of numerical changes. A nonrandom der(16) was observed as a result of an unbalanced t(1;16) in 18% of the 82 analyzed for structural changes. Consistent involvement of chromosome #16 in rearrangements with chromosome #1 may be an additional chromosome change specifically associated with ES.

Consistent involvement of band 12q14 in two different translocations in three lipomas from the same patient.

We studied cytogenetically three distinct lipomas from a patient with multiple subcutaneous lipomas in the left shoulder area. A breakpoint at 12q14 was involved in structural rearrangements in the three lipomas resulting in two different reciprocal translocations, i.e., t(3;12)(q28;q14) in two and a t(1;12)(q34.2;q14) in the third. These results confirm the consistency of involvement of the breakpoint at 12q14 in lipomas and give support to the hypothesis that multiple lipomas evolve from different stem cells.

Translocation (7;21) in a lipoma.

Cytogenetic analysis was performed on a solitary lipoma from the flank of a 38-year-old male. A translocation t(7;21)(p22;q11.2) was found as the sole clonal chromosomal abnormality. The results are discussed in relation to other cytogenetic abnormalities found in benign adipose tumors.

Cytogenetic studies of adipose tissue tumors. I. A benign lipoma with reciprocal translocation t(3;12)(q28;q14).

Detailed clinical histories and cytogenetic investigations using short-term cultures are reported in three typical benign lipomas. Although a diploid (normal) karyotype was observed in two cases, a reciprocal chromosome translocation t(3;12)(q28;q14) was found in the third case, which was briefly reported previously. These data are discussed in light of a lipoma with similar karyotypic changes reported by Heim et al. and a similar translocation observed by us in malignant myxoid liposarcomas. The nonrandom involvement of segment 12q13-q14 in benign and malignant lipomatous tumors suggest a common basis for at least one of the possible multiple steps in the genesis of neoplastic processes.

Cytogenetic studies of adipose tissue tumors. II. Recurrent reciprocal translocation t(12;16)(q13;p11) in myxoid liposarcomas.

Detailed chromosome studies, briefly reported previously, from short-term cultures of tumor cells from myxoid liposarcomas are reported. A common reciprocal translocation, t(12;16)(q13;p11), was found in three cases and a complex t(1;12;16)(p11;q13;p11) in the fourth one. This nonrandom primary change, not described before in solid tumors, could characterize the myxoid form of liposarcoma. The involvement of a closely located breakpoint on chromosome #12 in a reciprocal t(3;12)(q28;q14) described in a lipoma in the previous article of this series, suggests a common basis in the biological process of proliferation of tumors sharing a common histogenesis.

Association of breakpoint 14q23 with uterine leiomyoma.

A chromosomal study of short-term cultured tumor cells from a benign uterine leiomyoma showed a clonal insertion, dir ins(14;6)(q23;p23p25) as a unique change. This finding supports the hypothesis of a specific association of the breakpoint 14q23 with uterine leiomyoma.

Breakpoints in benign lipoma may be at 12q13 or 12q14.

Chromosomal investigations in two unrelated lipoma samples are reported. The breakpoint involving 12q in chromosomal rearrangements could be assigned to band 12q13 in one case and 12q14 in the other case. Evidence is provided that cytogenetically distinct breakpoints on 12q may be found in lipoma cells, resolving previous disagreements based on interpretational difficulties.

Multiple chromosomal mechanisms generate an EWS/FLI1 or an EWS/ERG fusion gene in Ewing tumors.

The t(11;22)(q24;q12) translocation is found in about 85% of Ewing tumors and leads in all cases to an EWS/FLI1 fusion gene. In a few instances, complex translocations, involving chromosomes 11, 22 and a third chromosome or other variant translocations not involving chromosome 11 also have been reported. These rearrangements generate an active fusion gene between the EWS gene and either the human FLI1 gene or other members of the ETS gene family: the ERG gene localized in band 21q22.2, the ETV1 gene localized in band 7p22, or the E1AF gene localized in band 17q12. Using fluorescence in situ hybridization (FISH) on interphase nuclei or metaphases, we report here the characterization of particular karyotypes in Ewing tumors, namely a complex t(2;11;22) translocation, a variant t(12;22) translocation, and one Ewing tumor without specific rearrangements but with an EWS/ERG fusion gene demonstrated by molecular analysis. These molecular cytogenetic methods allowed us (1) to precisely localize the genomic breakpoints within-EWSR1 and EWSR2 and to identify the chromosome carrying the fusion gene; (2) to determine the nature of events generating the fusion genes; (3) to demonstrate that some variant translocations represent masked complex translocations; and (4) to show that the generation of an EWS/ERG fusion gene cannot be obtained through a simple balanced translocation.

Comparative genomic hybridization reveals novel chromosome deletions in 90 primary soft tissue tumors.

Comparative genomic hybridization (CGH) was used to detect chromosomal gains and losses in a series of 90 frozen soft tissue primary tumors (STTs), all untreated. The material consisted of 69 malignant sarcomas, including 20 malignant fibrous histiocytomas (MFH), 23 liposarcomas (LPS), 6 leiomyosarcomas (LMS), 4 synovial sarcomas, 4 primitive neuroectodermal tumors (PNETs), and various others subtypes, in addition to 21 benign tumors. Within the benign tumors, only 2 of the 3 schwannomas showed genetic changes. In malignant sarcomas, genetic changes were detected in 64 of the 69 samples analyzed (92%), with a mean of 4.5 per sample (range 0-10). Gains and losses on chromosome 13 were observed in 32% of the sarcomas with genomic imbalance. Recurring low-level copy number increases were found at new sites on chromosomes 7 (6 MFH samples, 30%) and 8 (10 LPS samples, 43%), the minimal common regions being 7p15-pter and 8q24. No new recurring high-level amplifications were found. Surprisingly, losses of DNA sequences were more frequent than gains; particularly, losses were the main feature in LMS, with highly recurrent common minimal losses at 11q14-qter and 13q21-q22 (4 samples, 66%, and 5 samples, 83%, respectively). Losses of chromosome 2 sequences (minimal common regions at 2p24-pter and 2q32-qter) were observed in 50% of the MFH analyzed. New recurrent losses of whole or part of chromosome 14 were found in 57% of the pleomorphic LPS (PLPS) analyzed. This study uncovers new clues for the diagnosis of malignant STTs and shows the importance of deletions as events in the early steps involved in the tumorigenesis of STTs.

Consistent breakpoints in region 14q22-q24 in uterine leiomyoma.

The chromosomes of nine consecutive human benign leiomyomas of the uterus were studied with banding methods following short-term culture. All of the tumors had a typical benign histology. Five exhibited clonal chromosome changes including three with consistent involvement of chromosomes 12 and 14 in a translocation, t(12;14)(q14-15;q23-q24), a direct insertion, dir ins(12;14)(p11.2;q22q24.1), and a direct insertion, dir ins(14;12)(q22-q23;q14-q15q23-q24.1). Thus, this study demonstrated the presence of consistent chromosome changes in another benign proliferation. Strikingly, the breakpoint observed at 12q14-q15 in two specimens is also involved nonrandomly in other benign proliferations such as mixed salivary gland tumors and lipomas. However, region 14q22-q24, which was involved in three specimens, may contain a DNA sequence critical for the genesis of uterine leiomyoma.

Recurrent breakpoints at 9q31 and 22q12.2 in extraskeletal myxoid chondrosarcoma.

A cytogenetic study of extraskeletal myxoid chondrosarcoma cells revealed a complex t(9;22;15)(q31;q12.2;q25) as a primary chromosome change. A reciprocal translocation involving identical breakpoints on chromosomes #9 and #22 in this tumor has been reported in the literature. We suggest that the breakpoints 9q31 and 22.q12.2 are associated with extraskeletal myxoid chondrosarcoma, a comparatively rare tumor of adulthood.