Consistent DNA losses on the short arm of chromosome 1 in a series of malignant gastrointestinal stromal tumors

Fourteen malignant gastrointestinal stromal tumors (GISTs), characterized by immunohistochemistry, were analyzed by comparative genomic hybridization (CGH). The most striking feature was the detection of consistent DNA losses on the short arm of chromosome 1 in these 14 malignant tumors. Additional recurrent imbalances were also found: significant gains, which could be indicative of tumor progression, were frequent on the long arm of chromosome 1, as were losses of DNA copy number detected in chromosomes 13, 14, 15 and 22.

Leiomyosarcomas and most malignant fibrous histiocytomas share very similar comparative genomic hybridization imbalances: an analysis of a series of 27 leiomyosarcomas

Twenty-seven tumor samples with a diagnosis of leiomyosarcomas (LMS) were characterized by comparative genomic hybridization. The results were compared with immunohistochemical analysis of the smooth muscle profile of the tumors and expression of the RB1 gene protein. The comparative genomic hybridization profiles suggested that 7 of the 27 tumors might have been misclassified. High levels of DNA amplification were detected in 20 different small regions and recurrently involved bands 1p34, q21, 12q13-15, 17p, and 22q. Most recurrent simple gains were noted at sites such as 1p3, 1q21, 15q12-15, 16p, 17p and 17q, 19, 20q, 22q, and Xp. Significant losses of chromosome 13 were detected in 19 of the 27 tumors with a putative common region of loss in bands 13q14-21. Losses of chromosomes 1q, 2p and 2q, 4q, 9p, 10p and 10q, 11p and 11q23, and 16q were also highly recurrent. A comparative analysis between the most frequent genomic imbalances observed in this study of LMS and the genomic imbalances observed in a large proportion of malignant fibrous histiocytomas (MFH) from a previous study demonstrated that both types of tumors had similar recurrent imbalances. Although MFH were once thought to be a separate member of the soft tissue sarcoma family, our observations support the hypothesis that MFH are a morphologic modulation in the tumoral progression of other sarcomas, particularly LMS.

Molecular analysis of chromosome arm 17q gain in neuroblastoma

Complete or partial gain of the long arm of chromosome 17 (17q) has been shown recently by molecular cytogenetic techniques to be the most frequent chromosomal change in neuroblastoma and to be associated with adverse prognosis. Few reports, however, have focused on the precise mapping of the commonly overrepresented region. We have investigated 17q gain by the analysis of allelic imbalances at microsatellite loci dispersed along chromosome 17 in a series of 69 neuroblastomas. Allelic imbalances for at least two consecutive loci were observed in 39/59 informative cases, that is in agreement with previously reported frequencies of 17q gain. In a subset of the cases, comparative genomic hybridization analysis established the relationship between these allelic imbalances and the gain of 17q material. A partial 17q gain was observed in 9 cases, delineating a common region of 17q gain between the marker D17S787 (75 cM, 360 cR) and the telomere. In most cases, molecular results were suggestive of partial tri- or tetrasomy, whereas in 4 cases a higher copy number was documented. Our results also confirm that the presence of additional 17q material is closely associated with 1p36 deletion, MYCN amplification, and diploid or tetraploid chromosomal content. Genes Chromosomes Cancer 28:276-284, 2000.

FISH analysis of translocations involving the short arm of chromosome 9 in lymphoid malignancies

Deletion of the short arm of chromosome 9 (9p), resulting in the loss of the p16INK4a/MTS1 gene, now called CDKN2, has been found to occur frequently in acute lymphoblastic leukemia, even in the absence of a microscopically visible deletion. In this study, we have used YAC probes encompassing the CDKN2 locus to analyze by fluorescence in situ hybridization patients with leukemia and lymphoma and translocations involving 9p in order to establish the CDKN2 status in relation to the karyotype. We found that, in leukemic cells exhibiting loss of heterozygosity at the CDKN2 locus, the deleted allele was from the cytogenetically normal chromosome 9, whereas the other allele was located on a rearranged chromosome. This finding suggests that CDKN2 gene loss is nonrandomly associated with 9p translocation in lymphoid proliferations. Genes Chromosom.

Faconi anemia and bone marrow clonal chromosome abnormalities

Clonal chromosome abnormalities were detected in bone marrow cells of 20 patients with Fanconi anemia investigated at various stages of the disease. Two presented with acute leukemia, six with myelodysplastic syndrome, and 12 had minor or no morphological abnormalities of hematopoietic cells. Abnormalities of chromosome 7 were detected in nine patients (monosomy, isochromosome, or other structural rearrangement), and chromosome 1 was rearranged in four. The types and the significance of clonal chromosome abnormalities which may be present without apparent evolution toward acute leukemia or myelodysplastic syndrome in Fanconi anemia patients are discussed.

Translocation (2;3)(p22;q28) is associated with myeloid disorders

Chromosome studies carried out in two children with acute myeloblastic leukemia (AML, M2) showed a t(2;3)(p22;q28). This abnormality was associated with monosomy 7 and del(12)(p12) in the first patient and was found only in relapse in the second patient. Comparison with the other previously published t(2;3) suggests that this translocation is a nonrandom abnormality involving a pluripotent stem cell and occurring as a secondary chromosome abnormality in AML.

Inversion-associated translocations in acute myelomonocytic leukemia with eosinophilia

Cytogenetic studies of three acute myelomonocytic leukemias with bone marrow eosinophilia (M4EO) revealed chromosome 16 inversion associated with additional abnormalities. The inverted chromosome 16 was involved in two patients. Fluorescence in situ hybridization (FISH) experiments with a YAC probe detecting inv(16) showed that the translocation breakpoints involving chromosome 16 did not implicate the inversion breakpoints. FISH can thus distinguish between true variant translocations and translocations with other breakpoints on chromosome 16 in M4EO.

Distinct MLL gene rearrangements associated with successive acute monocytic and lymphoblastic leukemias in the same patient

A patient with acute monocytic leukemia (AMoL) and t(6;11)(q27;q23) developed acute lymphoblastic leukemia (ALL) and t(4;11)(q21;23), 10 months after complete remission of the AMoL. The MLL gene, normally located at band 11q23, appeared differently rearranged in the cells of these two leukemias, showing a different origin for the two malignant clones. The responsibility of etoposide, used in treatment of the AML, in the occurrence of the ALL is probable in this patient.

Translocation t(11;11)(q13;q23) and HRX gene rearrangement associated with therapy-related leukemia in a child previously treated with VP16

A child with acute myelomonocytic leukemia, bone marrow eosinophilia and inv(16) received first-line therapy including etoposide (VP-16). Cytopenia and monocytosis appeared 7 months after complete remission while the child was treated with maintenance chemotherapy. Blood abnormalities persisted after discontinuation of treatment. Nine months after complete remission, t(11;11)(q13;q23) and HRX rearrangement were detected. Five months later, overt leukemia of monocytic type occurred. The responsibility of VP-16 therapy in this treatment-related acute myelocytic leukemia is discussed.

Whole arm translocation t(17;18): a non-random abnormality of myeloid cell proliferation

Whole arm translocation t(17;18) was detected in two patients, one with acute monocytic leukemia and the other with acute transformation of chronic myelocytic leukemia. Dual-color fluorescence in situ hybridization (FISH) to interphase nuclei with alphoid probes specific to chromosomes 17 and 18 showed the presence of two very close spots. This feature was interpreted as the conservation of the pericentromeric region of the two chromosomes involved in the translocation. The present cases add to eight previously reported other patients with whole arm translocation t(17;18) (one with FISH studies). Since these patients had either myeloid leukemia or myelodysplastic syndrome, it is suggested that the t(17;18)(p10;q10) translocation is a new non-random abnormality associated with myeloid cell proliferations.

In situ hybridization to interphase nuclei in acute leukemia

Numerical chromosome abnormalities were studied in 17 acute lymphoblastic leukemias and one hyperdiploid acute myeloblastic leukemia by fluorescence in situ hybridization (FISH) using YAC clones specific to chromosomes 21 and 6. The results agreed well with cytogenetic findings. Hyperdiploid leukemias with more than 50 chromosomes usually had 4 copies of chromosome 21 and three of chromosome 6, while diploid and pseudodiploid cases were confirmed to have two copies of the two chromosomes. Interesting discrepancies were also observed. In one patient, trisomy 6 was detected by FISH but not by cytogenetics because of the probable inclusion of a chromosome 6 segment within a marker chromosome. The percentages of nuclei with 3 or 4 spots (chromosome 21) and three spots (chromosome 6) in hyperdiploid cells were significantly different in some patients, whereas they might be identical from cytogenetic data.

Rearrangements of the retinoic acid receptor alpha and promyelocytic leukemia zinc finger genes resulting from t(11;17)(q23;q21) in a patient with acute promyelocytic leukemia

Cytogenetic study of a patient with acute promyelocytic leukemia (APL) showed an unusual karyotype 46,xy,t(11;17) (q23;21) without apparent rearrangement of chromosome 15. Molecular studies showed rearrangements of the retinoic acid receptor alpha (RAR alpha) gene but no rearrangement of the promyelocytic leukemia gene consistent with the cytogenetic data. Similar to t(15;17) APL, all-trans retinoic acid treatment in this patient produced an early leukocytosis which was followed by a myeloid maturation, but the patient died too early to achieve remission. Further molecular analysis of this patient showed a rearrangement between the RAR alpha gene and a newly discovered zinc finger gene named PLZF (promyelocytic leukemia zinc finger). The fusion PLZF-RAR alpha gene found in this case, was not found in DNA obtained from the bone marrow of normals, APL with t(15;17) and in one patient with AML-M2 with a t(11;17). Fluorescence in situ hybridization using a PLZF specific probe localized the PLZF gene to chromosomal band 11q23.1. Partial exon/intron structure of the PLZF gene flanking the break point on chromosome 11 was also established and the breakpoint within the RAR alpha gene was mapped approximately 2 kb downstream of the exon encoding the 5' untranslated region and the unique A2 domain of the RAR alpha 2 isoform.

Abnormalities of chromosome 18 in myelodysplastic syndromes and secondary leukemia

Monosomy 18 and partial deletion of 18q are nonrandom events in myelodysplastic syndromes (MDS) and secondary acute myeloblastic leukemia (sAML). They are part of complex chromosome abnormalities, as shown in the present study of six patients with MDS and sAML. We compared occurrence of chromosome 18 abnormalities in these syndromes with that in de novo AML.

The genes for MHC class II regulatory factors RFX1 and RFX2 are located on the short arm of chromosome 19

RFX1 is a transacting DNA-binding regulatory factor involved in the control of MHC class II gene expression. RFX2 is a structurally very similar protein with identical DNA binding features. A member of the family of RFX factors is affected in an autosomal recessive disease, MHC class II deficient combined immunodeficiency (CID), caused by a defect in a trans-acting regulatory factor controlling MHC class II gene expression. In situ hybridization with 3H-labeled RFX1 cDNA has allowed us to identify two distinct targets on the short arm of chromosome 19 (19p13.1 and 19p13.2-p13.3). With the use of biotinylated genomic cosmid clones specific for RFX1 and RFX2, respectively, it was then possible to localize RFX1 at 19p13.1 and RFX2 at 19p13.2-p13.3. These two regulatory genes are thus assigned to a region of high gene density and RFX1 is close to another DNA-binding factor, LYL1.

5q- anomaly in acute lymphoblastic leukemia

We report two new cases of common acute lymphoblastic leukemia (ALL) with 5q-. This abnormality, which is uncommon in ALL, was previously reported in 14 cases of ALL of various subtypes and appears to occur less frequently in common ALL than in other types of ALL.

Loss of chromosome 22 in patients with refractory anemia with excess of blasts (RAEB) in transformation and acute leukemia after RAEB

We report studies of 12 patients with refractory anemia and excess of blasts in transformation (RAEB-t) and 17 with acute myeloblastic leukemia (AML) after RAEB. Besides chromosome 5 and 7 abnormalities, five patients with complex karyotypic changes had monosomy 22. This association is discussed in relation to the hypothesis of a suppressor gene located on chromosome 22.

The 11q23 breakpoint in acute leukemia with t(11;19)(q23;p13) is distal to those of t(4;11), t(6;11) and t(9;11)

Thirteen cosmid probes were mapped on the long arm of chromosome 11 between 11q22 and 11q24 by nonradioactive in situ hybridization. Starting with these localizations and those of other probes mapped to 11q23, four acute leukemias with translocations involving 11q23 were studied with the same method. The translocation breakpoints of the t(4;11)(q21;q23), t(6;11)(q27;q23), t(9;11)(p21-p22;q23), and t(11;19)(q23;p13) were confirmed to be distal to CD3D. The probe cC111-304 was proximal to the t(11;19) breakpoint while distal to the breakpoints of the other rearrangements. In view of the diversity of chromosomal abnormalities involving band 11q23, our finding extends the molecular heterogeneity of the breakpoint localization in leukemias with rearrangements involving 11q23.

The gene for the type II (p75) tumor necrosis factor receptor (TNF-RII) is localized on band 1p36.2-p36.3

The gene encoding the type II (p75) tumor necrosis factor receptor (TNF-RII) has been localized on human chromosome 1, band 1p36.2 by nonradioactive in situ hybridization. The gene encoding the type I (p55) TNF-R, which is structurally homologous to the type II (p75) TNF-R, has been previously localized on chromosome 12 band 12p13. Thus, despite their probable common ancestry, the genes for the two TNF-Rs are localized on different chromosomes.

Cytogenetic studies in acute promyelocytic leukemia: a survey of secondary chromosomal abnormalities

A series of 105 patients with acute promyelocytic leukemia (APL) has been cytogenetically investigated at the Department of Hematology of the Saint-Louis Hospital (Paris) between 1977 and 1990. Sixty-two patients were examined at diagnosis, 32 in relapse, and 11 both at diagnosis and in relapse. The typical t(15;17)(q22;q12) or variants of this translocation were observed in all but four patients. The t(15;17) was the only change in 47 cases at diagnosis and in 21 examined in relapse. The most frequent secondary change was trisomy 8 (17% at diagnosis). More or less complex chromosomal abnormalities in addition to t(15;17) were present in six patients at diagnosis, and in 17 patients in relapse. Rearrangements of 2q35-q37 and del(11p) were observed only in relapse and may thus be nonrandom secondary changes. Cytogenetic studies performed on 19 patients treated with all-trans retinoic acid did not indicate that this treatment induces chromosomal abnormalities.

Partial deletion of chromosome 2 in non-Hodgkin lymphoma

Six patients with non-Hodgkin malignant lymphoma (NHL) in a series of 151 cases showed partial deletion of chromosome 2 when studied cytogenetically. Three had deletions of bands 2p14-p22 and three others had a deletion of bands 2q22-q24 in common. The deletions were associated with other abnormalities in each case and were not associated with a particular subtype of NHL. These deletions are secondary, apparently nonrandom, new abnormalities associated with NHL.

Deletion of (7p13p14) in non-Hodgkin's lymphoma

Deletion of the short arm of chromosome 7 at 7(p13p14) has been occasionally reported in non-Hodgkin's malignant lymphoma (NHL). The inclusion of this abnormality within the list of nonrandom changes awaited further data. We report three partial deletions of 7p with breakpoint at 7p13, found in various subtypes of NHL, and one deletion covering these bands (7p11 to 7p15). The association of 7p- with other chromosomal changes in the same NHL suggests that partial 7p deletion is a nonrandom secondary abnormality.

In situ hybridization ascertains the presence of a translocation t(6;11) in an acute monocytic leukemia

In situ hybridization was performed in a case of acute monoblastic leukemia (FAB type M5b) with a rearrangement of the long arm of chromosome 11. Cytogenetic analysis after R- and G-banding showed an apparent deletion of 11q with a breakpoint at 11q23, and a translocation t(6;11) was suspected in certain metaphases. In situ hybridization with a biotinylated cosmid probe hybridizing at 11q25 confirmed the translocation t(6;11)(q27;q23). Use of nonradioactive in situ hybridization techniques for more precise characterization of chromosomal rearrangements in malignant cells is emphasized.

Cytogenetic studies of 44 T-cell acute lymphoblastic leukemias

Cytogenetic studies on 44 patients with T-cell acute lymphoblastic leukemia (ALL) were reported. The incidence of leukemia without detectable chromosomal changes was 25%. Hyperdiploidy with more than 50 chromosomes was found in only one patient. Previously described nonrandom abnormalities like 6q-, 9p-, and 12p- were observed, and it was confirmed that they are not specific for a particular type of ALL. The incidence of chromosomal rearrangements on chromosomes 7 and 14 where the T-cell receptor gene loci are located was 36% of those with abnormal karyotypes and 27% of the total. This was clearly different from the frequency of rearrangements of these bands found in T-cell lymphoma. Finally, a rearrangement on bands 11q14-q21 was detected in five cases.

Secondary nonrandom chromosomal abnormalities of band 13q34 in Burkitt lymphoma-leukemia

Clonal abnormalities of the long arm of chromosome 13 were detected in 9 of 54 patients with Burkitt lymphoma-leukemia. All abnormalities involved band 13q34, in three patients as t(1;13). The 13q34 abnormalities are thus the second most frequent secondary chromosomal abnormalities, after those of chromosome I, in these lymphoid proliferations.

Chromosomal rearrangement on chromosome 11q14-q21 in T cell acute lymphoblastic leukemia

Deletion and translocation involving the bands 11q14 and 11q21 have been detected in five patients with T cell acute lymphoblastic leukemia (ALL). The breakpoint on chromosome 11 was on the same band as that previously described in some acute nonlymphocytic leukemias: monocytic or myelomocytic. The existence of a new nonrandom rearrangement involving bands 11q14-q21 is postulated in ALL. An unusual rearrangement on 11q13 in a patient with T cell ALL is also reported.

Cytogenetic studies on acute nonlymphocytic leukemia in relapse

Karyotypic abnormalities were compared in 42 acute nonlymphocytic leukemia patients at diagnosis and in relapse. Clonal changes were observed in 21 cases. The types of changes were the appearance of clonal abnormalities in relapse in four patients without clonal changes at diagnosis, the detection of new abnormalities superimposed on preexisting ones in 11 cases, and the selection of an abnormal clone in six others. Nonclonal structural abnormalities, mainly involving chromosomes 17 and 12p, were detected in relapse in 17 patients, compared to seven at diagnosis. The appearance of totally new clonal changes at relapse and the role of individual sensitivity to chemotherapy are discussed.

Cytogenetic studies on 519 consecutive de novo acute nonlymphocytic leukemias

Cytogenetic studies were performed in the same laboratory on 519 untreated cases of de novo acute nonlymphocytic leukemia (ANLL) between 1977 and 1985. The overall incidence of clonal chromosome abnormalities was 54.3%; higher in children (67.5%) than in adults (50.4%). The distribution of chromosome abnormalities was uneven, according to the categories of the FAB nomenclature. The highest frequency of chromosome changes was observed in ANLL-M3 and the lowest in M1 and M6. The frequency of specific chromosome abnormalities and of their associated changes were also estimated. Monosomy 7 was detected in three patients with acute megakaryocytic leukemia (M7). Six cases with two abnormal chromosomally unrelated clones were observed and six constitutional chromosome abnormalities were detected. A clearer knowledge of the incidence of various chromosomal changes in ANLL seems necessary for better differentiation between the so-called primary and secondary chromosome abnormalities and for prognostic evaluation.