A new complex variant Philadelphia chromosome, t(1;9;22)ins(17;22), characterized by fluorescence in situ hybridization in an adult ALL

A new complex variant Philadelphia chromosome was detected in a 65-year-old man with acute, pre-B, lymphoblastic leukemia (ALL). The classic cytogenetic analysis identified an apparently balanced three-way translocation t(1;9;22)(q25;q34;q11.2). Fluorescence in situ hybridization (FISH) studies confirmed the translocation and showed bcr/abl fusion on the der(22). However, these studies revealed that the distal part of the bcr gene was not translocated onto chromosome 1 at 1q25, but inserted into chromosome 17 at 17p12-13. This complex variant translocation was described as a t(1;9;22)(q25;q34;q11.2)ins(17;22)(p12-13;q11.2q11.2). Secondary changes including +8, an inversion of the derivative chromosome 9, a translocation t(14;20)(q11;q13), and an additional derivative 22 were also identified in most of the abnormal cells. The patient died from systemic fungemia and multiorgan failure 9 months after the diagnosis of ALL. The clinical significance of complex variant Philadelphia chromosomes in ALL is reviewed and discussed.     

Multicolor spectral karyotyping identifies novel translocations in childhood acute lymphoblastic leukemia.

We used a recently described molecular cytogenetic method, spectral karyotyping (SKY), to analyze metaphase chromosomes from 30 pediatric patients with acute lymphoblastic leukemia (ALL). This group included 20 patients whose leukemic blast cells lacked chromosomal abnormalities detected by conventional cytogenetics and 10 patients whose blast cells had multiple chromosomal abnormalities that could not be completely identified by G-banding analysis. In two of the 20 patients (10%) with apparently normal karyotypes, SKY identified three cryptic translocations: a t(7;8)(q34-35;q24.1) in one patient and a t(13;17)(q22;q21) and a der(19)t(17;19)(q22;p13) in another. Fluorescence in situ hybridization using subtelomeric probes proved the latter translocation to be a t(17;19). SKY analysis was also successful in defining the nature of the chromosomal abnormalities in four of the 10 patients with marker and derivative chromosomes. The identified abnormalities in the latter group included three novel translocations: a der(X)t(X;5)(p11.4;q31), a der(21)t(X;21)(p11.4;p11.2) and a t(X;9)(p11.4;p13). The presence of the t(X;9) was suggested by conventional cytogenetics. The application of fluorescence in situ hybridization using chromosome-specific painting probes and locus-specific probes complemented the SKY analysis by confirming the nature of the chromosome rearrangements defined by SKY and by identifying the amplification of the AML1/CBFA2 gene in one patient with a duplicated 21q. Our study demonstrates the utility of SKY in identifying novel translocations and in refining the identity of chromosomal abnormalities in leukemias.     

t(1;7) in acute myeloblastic leukemia following myelodysplastic syndrome (RAEB-T)

A case is described of myelodysplastic syndrome (MDS) refractory anemia type with an excess of blasts in transformation with early leukemic evolution (AML-M1). All bone marrow cells examined showed an unbalanced translocation t(1;7). The karyotype was 45, xy, -21, -7, + der dic t(1;7) (q12;q21). There are reports in the literature of the translocation t(1;7) (p11;p11), which leads to trisomy of the long arms of chromosome #1 and monosomy of the long arms of chromosome #7. In the case here described the breakpoints of the chromosomes involved in the translocation differ from the classic ones: in this case there is trisomy of the region 1q12----1qter and monosomy of the region 7q21----7qter. Some clinical and cytogenetic considerations are suggested.     

T(1;21;8)(p34;q22;q22): a novel variant of t(8;21) in acute myeloblastic leukemia with maturation

The complex variants of t(8;21) involving chromosomes 8 and 21 as well as another chromosome account for approximately 3% of acute myeloid leukemia patients. We report here a 30-year-old male patient with AML-M2. Fluorescence in situ hybridization analysis using dual-color fluorescence ETO and AML1 probes located at 8q22 and 21q22 respectively showed an AML1/ETO fusion signal on the derivative chromosome 8. Whole chromosome painting probes were used for chromosome 1, 8 and 21 and revealed a three-way translocation (1;21;8)(p34 ~ p35;q22;q22). Involvement of chromosome region 1p34 has never been reported earlier, although region 1p35 as a variant in AML with t(8;21) has been reported with an AML1/ETO fusion signal on the 1p35 rather than der(8). In conclusion, combining conventional karyotype, FISH or RT-PCR analyses are a rational strategy for the identification of the complex variants of t(8;21) translocation which could be critical events responsible for leukemogenesis.     

Complexity of an apparently simple variant Ph translocation in chronic myeloid leukemia

A patient with chronic myeloid leukemia (CML) presented with an apparently simple Ph translocation t(19;22)(q13;q11). In-situ hybridization revealed movement of the c-abl oncogene from a cytogenetically normal chromosome 9 to the Ph. Bcr-3' and c-sis probes hybridized to distal 1p and not to the 19q+ chromosome as expected from the cytogenetic findings. We concluded that this patient had a complex translocation involving four chromosomes: t(1;9;19;22)(p36;q34;q13;q11).     

Abnormalities of chromosome bands 15q13-15 in childhood acute lymphoblastic leukemia

BACKGROUND: Recurring breakpoints in chromosome bands 15q13-15 occur infrequently in leukemia. To the authors' knowledge, the clinical significance of these breakpoints in childhood acute lymphoblastic leukemia (ALL) has not been previously investigated. METHODS: Centrally reviewed karyotypes of children with newly diagnosed ALL enrolled on Children's Cancer Group protocols from 1988 to 1995 formed the basis of the current report. Statistical analyses used chi-square tests for homogeneity of proportions, and outcome was analyzed using life table methods and associated statistics. RESULTS: Of 1946 cases with centrally reviewed and accepted cytogenetic analyses, 23 cases (1%) had breakpoints in chromosome bands 15q13-15. Most patients with 15q13-15 breakpoints had standard risk ALL, although breakpoints in 15q13-15 occurred more frequently in infants than in older children. The majority of these patients (16 patients; 70%) had balanced 15q13-15 rearrangements. Additional chromosomal abnormalities not involving 15q included abnormal 12p, abnormal 9p, Philadelphia chromosome, deletion 6q, and an 11q23 breakpoint. Thirteen (57%) 15q13-15 breakpoints occurred in pseudodiploid karyotypes; five (22%) were in hyperdiploid karyotypes with 47-50 chromosomes; two (9%) were in hyperdiploid karyotypes with > 50 chromosomes; and three (13%) were in hypodiploid karyotypes. Of the 23 patients with 15q13-15 breakpoints, 21 were survivors, 18 survived event-free for 2.2-9.3 years, and 3 were alive 1 to 3 years after a relapse at time of writing. CONCLUSIONS: The current study suggests that genes at 15q13-15 may be involved in the leukemogenesis of some cases of childhood ALL, but that with current intensive therapy such aberrations do not confer increased risk of treatment failure.     

A complex translocation t(5;9;22) in Philadelphia cells involving the short arm of chromosome 5 in a case of chronic myelogenous leukemia

Chronic myelogenous leukemia (CML) is genetically characterized by the reciprocal translocation of chromosome 9 and 22, t(9;22)(q34;q11) which results in the fusion of BCR/ABL gene observed on the derivative chromosome 22 called Philadelphia (Ph') chromosome. About 5-8% of Philadelphia positive patients with CML show various complex translocations involving one or more other chromosomes, in addition to chromosome 9 and 22. In our report we discuss one case with CML, his cytogenetic study revealed a complex translocation t(5;9;22)(p15.1; q34; q11.2), del 5p15.1-->pter, translocation BCR(22q11.2-->qter) to der(5), positive Ph-chromosome and positive t(BCR\ABL). Further confirmation of complex translocation was done by FISH study using the LSI BCR/ABL dual color dual fusion (DF) translocation probe, chromosome 5 and 22 whole paint probes.     

Prognostic significance of the balanced t(1;19) and unbalanced der(19)t(1;19) translocations in acute lymphoblastic leukemia.

The recurring chromosomal 1;19 translocation in acute lymphoblastic leukemia (ALL) occurs in balanced t(1;19) (q23;p13) and unbalanced, -19, +der(19)t(1;19)(q23;p13) forms. The clinical features and outcome were compared for 30 patients with the t(1;19) and 36 patients with the der(19) forms. These were 45 children (less than 1-14 years) and 21 adults (15-54 years) (median age 9.0 years), 41 females, 25 males, with median white blood count (WBC) 20.9 x 10(9)/1. Patients were classified by karyotype thus: t(1;19) 11 cases; t(1;19) with additional change (+A) 19 cases; der(19) 17 cases; and der(19) +A, 19 cases. Non-random additional structural abnormalities included involvement of 1q, 6q, i(7q), i(9q), 9p, and 13q. The only significant difference in clinical or blast cell features between patients with the t(1;19) and the der(19) was the greater age of adults with t(1;19) (p less than 0.05). Projected median event-free survival and survival of all cases together was 22 months and greater than 112 months respectively. Neither age nor WBC contributed significantly to prognosis. For patients at all ages, prognosis of der(19) was better than t(1;19). This was statistically significant for event-free and overall survival in childhood (p = 0.02 and p = 0.01 respectively) and was independent of age (p = 0.04 and p = 0.008 respectively) and WBC (p = 0.03 and p = 0.04 respectively). Future studies should examine separately the outcome for patients with the balanced and unbalanced forms of the t(1;19).     

Seven novel and stable translocations associated with oncogenic gene expression in malignant melanoma

Cytogenetics has not only precipitated the discovery of several oncogenes, but has also led to the molecular classification of numerous malignancies. The correct identification of aberrations in many tumors has, however, been hindered by extensive tumor complexity and the limitations of molecular cytogenetic techniques. In this study, we have investigated five malignant melanoma (MM) cell lines from at least three different passages using high-resolution R-banding and the recently developed methods of comparative genomic hybridization and multicolor or multiplex fluorescence in situ hybridization. We subsequently detected nine consistent translocations, seven of which were novel: dic(1;11)(p10;q14), der(9)t(3;9)(p12;p11), der(4)t(9;4;7)(q33:p15-q23:q21), der(14)t(5;14)(q12;q32), der(9)t(9;22)(p21;q11), der(19)t(19;20)(p13.3;p11), der(10)t(2;12;7;10)(q31:p12-->pter:q11.2-->q31:q21), der(19)t(10;19)(q23;q13), and der(20)t(Y;20)(q11.23;q13.3). Furthermore, using the human HG-U133A GeneChip, positive expression levels of oncogenes or tumor-related genes located at the regions of chromosomal breakpoints were identified, including AKT1, BMI1, CDK6, CTNNB1, E2F1, GPNMB, GPRK7, KBRAS2, LDB2, LIMK1, MAPK1, MEL, MP1, MUC18, NRCAM, PBX3, RAB22A, RAB38, SNK, and STK4, indicating an association between chromosomal breakpoints and altered gene expression. Moreover, we also show that growth of all five cell lines can be significantly reduced by downregulating CDK6 gene expression with small interfering RNA (siRNA). Because the majority of these breakpoints have been reported previously in MM, our results support the idea of common mechanisms in this disease.     

Cytogenetic findings in 14 benign cartilaginous neoplasms

Benign cartilaginous tumors represent a spectrum of neoplastic processes with variable clinical and pathologic presentations. These tumors are histologically characterized by the presence of chondrocytes surrounded by a cartilaginous matrix. Few studies describe karyotypic abnormalities in these benign lesions. We report a series of 14 chondromas from a single institution. Conventional cytogenetics was performed on short term cultures from all cases. Clonal chromosome aberrations were found in nine tumors. One soft tissue chondroma contained three clones with t(6;12)(q12;p11.2), t(3;7)(q13;p12), and der(2)t(2;18)(p11.2;q11.2). Three periosteal chondromas displayed random structural aberrations of chromosomes 2, 3, 6, 7, and 11 and loss of chromosome 13. Among the enchondromas, three tumors displayed chromosome losses, one contained a complex translocation involving chromosomes 12, 15, and 21 as well as an inv(2)(p21q31),t(12;15;21)(q13;q14;q22) and a separate enchondroma showed a translocation involving chromosomes 12 and 22. Our data suggest that considerable cytogenetic heterogeneity exists among benign chondromatous tumors.     

The utility of spectral karyotyping in the cytogenetic analysis of newly diagnosed pediatric acute lymphoblastic leukemia.

We applied multicolor spectral karyotyping (SKY) to a panel of 29 newly diagnosed pediatric pre B-cell ALLs with normal and abnormal G-banded karyotypes to identify cryptic translocations and define complex chromosomal rearrangements. By this method, it was possible to define all add chromosomes in six cases, a cryptic t(12;21)(p13;q11) translocation in six cases, marker chromosomes in two cases and refine the misidentified aberrations by G-banding in two cases. In addition, we identified five novel non-recurrent translocations - t(2;9)(p11.2;p13), t(2;22) (p11.2;q11.2), t(6;8)(p12;p11), t(12;14)(p13;q32) and t(X;8)(p22.3;q?). Of these translocations, t(2;9), t(2;22) and t(12;14) were identified by G-banding analysis and confirmed by SKY. We characterized a t(12;14)( p13;q32) translocation by FISH, and identified a fusion of TEL with IGH for the first time in ALL. We identified a rearrangement of PAX5 locus in a case with t(2;9)(p11.2;p13) by FISH and defined the breakpoint telomeric to PAX5 in der(9)t(3;9)(?;p13). These studies demonstrate the utility of using SKY in combination with G-banding and FISH to augment the precision with which chromosomal aberrations may be identified in tumor cells.     

M-FISH cytogenetic analysis of non-Hodgkin lymphomas with t(14;18)(q32;q21) and add(1)(p36) as a secondary abnormality shows that the extra material often comes from chromosome arm 17q

The most common translocation in non-Hodgkin lymphomas (NHL) is a t(14;18)(q32;q21) recombining the immunoglobulin heavy-chain gene (IGH) on chromosome 14 with the B cell leukemia/lymphoma 2 (BCL2) gene on chromosome 18. Although NHLs carrying a t(14;18) typically begin as low-grade, follicular lymphomas, they have a tendency towards transformation to more aggressive disease, something that is accompanied, presumably caused, by the acquisition of secondary chromosomal changes. One such common change is add(1)(p36), in which material of unknown origin is added to the tip of the short arm of chromosome 1. We used multicolor fluorescence in situ hybridization (M-FISH), a new FISH-based screening technique, to better characterize the rearrangement. Whenever doubt persisted after M-FISH, hybridization with chromosome-specific probes was also performed. In 5 out of 14 informative cases, the extra material on 1p36 could be shown to have come from 17q, more specifically 17q11-21 --> qter, whereas it came from 6p and 11q in two cases each and from 3p, 8p, 8q, 9q, and 12p in one case each. It appears, therefore, that der(1)t(1;17)(p36;q11-21) is a common secondary aberration in NHLs with t(14;18) as the primary abnormality, accounting for about one-third of all add(1)(p36) chromosomes seen in this cytogenetic subset.     

Cyclin D1 amplification in chromosomal band 11q13 is associated with overrepresentation of 3q21-q29 in head and neck carcinomas

Eight cytogenetically characterized head and neck squamous cell carcinomas (HNSCCs) with CCND1 amplification in the form of a homogeneously staining region (hsr) in 11q13 were studied by COBRA FISH and FISH with specific probes to identify and characterize chromosomal segments added to the derivative chromosomes 11. In 4 of the tumors, it could be recognized that the material added was derived from the long arm of chromosome 3. The rearrangements were interpreted as der(11)hsr(11)(q13)t(3;11)(q21;q13) in 3 cases and as der(11)hsr(11)(q13)t(3;11)(q14;q13) in 1 case. In the other 4 cases, material from chromosomes 1, 16, or 19 was added to the derivative chromosomes 11. By further FISH analysis with 14 YAC clones spanning 3q13-q21 in the 4 tumors with der(11)hsr(11)t(3;11), it could be shown that they had different breakpoints at the molecular level, excluding the possibility that a particular gene was rearranged by the translocations. More surprisingly, gain of the 3q21-q29 segment was found in all 8 tumors with hsr in 11q13 and loss of 3p was seen in 7 of the tumors. These findings strongly indicate a synergistic effect of CCND1 amplification, loss of distal 11q, 3q gain and 3p deletion in HNSCC development and also suggests a mechanistic link between intrachromosomal amplification at 11q13 and recombination with distal 3q.     

Characterization of the translocation breakpoint in a patient with Philadelphia positive, bcr negative acute lymphoblastic leukaemia

Approximately 5% of children and 10-20% of adults with acute lymphoblastic leukaemia (ALL) have a chromosome translocation t(9;22) which at the cytogenetic level appears identical to that in chronic myeloid leukaemia (CML). The t(9;22) translocation was first recognised in CML patients by its 22q- or Philadelphia (Ph) chromosome. While all Ph positive CML patients so far described have a chromosome 22 breakpoint within the breakpoint cluster region (bcr) located in the 3' part of the phl gene, only some Ph positive ALL patients have breakpoints in bcr. We have cloned the breakpoint of the 9q+ chromosome from the DNA of a Ph positive ALL patient in whom there is no breakpoint in the bcr. The non-chromosome 9 sequences of the breakpoint region are shown to be derived from chromosome 22. The breakpoint in chromosome 22 is shown to be the first intron of the phl gene about 66kb upstream of the bcr. Using probes from this intron, rearrangements were detected in the DNA of two out of twelve additional Ph positive, bcr negative ALL patients.     

Possible evidence for acquired genetic activity at both chromosomal breakpoints of the Philadelphia translocation in chronic myeloid leukemia

The Philadelphia (Ph1) chromosome (22q-), found in more than 90% of patients with chronic myeloid leukemia (CML), is one part of a reciprocal translocation, t(9;22) (q34;q11), in which the oncogene c-abl moves from 9q34 to 22q11. The translocation results in the translation of an aberrant abl-related protein with tyrosine kinase activity. Genetically active genes are known to have chromatin which is hypersensitive to deoxyribonuclease I (DNase I) and to be hypomethylated. Using an in situ nick translation technique on metaphase chromosomes, we have examined DNase I sensitivity and methylation status at the breakpoints 9q34 and 22q11 in bone marrow cells from controls (two cases) and CML patients (three cases). In CML cells DNase I sensitivity was significantly increased, at both breakpoints, in the translocated chromosomes compared with their normal homologues in CML cells and with both homologues in control marrows. A hypermethylated site, seen at 22q11 in normal 22s was hypomethylated on 22q-. The 9q34 region was hypomethylated in normal and translocated chromosomes. DNase I sensitivity, seen at 22q13 in CML cells, was lost following translocation in one of three cases. This technique demonstrates alterations in chromatin conformation and methylation status at translocation breakpoints which may be related to acquired genetic activity at one or both of these sites.     

A complex karyotype involving chromosomes 3, 6, 11, 12, and 22 in adult acute lymphoblastic leukemia

Complex chromosomal abnormalities are rare in adult patients with acute lymphoblastic leukemia (ALL). Using molecular methods, we characterized a complex karyotype involving chromosomes 3, 6, 11, 12, and 22 in a 38-year-old man with ALL. Cytogenetic analysis revealed the following karyotype: 46,XY,der(3)t(3;?6)(q22;?p21), - 6,add(11)(q23),add(12)(p13), + mar[10]/46,XY[19]. Because patients with 11q23 abnormalities have a poor prognosis and require aggressive treatment, we used fluorescence in situ hybridization (FISH) to fully characterize the abnormalities. FISH analysis showed no rearrangement of the MLL or ETV6-CBFA2 (TEL-AML1) genes; the wild-type ETV6 allele was deleted in most cells. The revised karyotype after the FISH analysis was as follows: 46,XY,der(3)t(3;12)(p13;p?13)del(3)(q21),der(6)inv(6)(p21q21)ins(6;3)(q21;q21q25),der(11)t (3; 11)(q25;q23),der(12)t(11; 12)(q23;p?12),t(12;22)(p13;q13). Although structural abnormalities involving 11q23 and 12p13 bands were identified by conventional cytogenetics, this report clearly demonstrates that molecular assays are needed to fully characterize gene rearrangements, complex translocations as well as to assign patients to the appropriate treatment group.     

Pathogenesis of jumping translocations: a molecular cytogenetics study

BACKGROUND/AIMS: Jumping translocations are rare cytogenetic aberrations in haematological malignancies, the pathogenesis of which remains to be fully characterised. We investigated the mechanism of formation of jumping translocations in a case of adult common acute lymphoblastic leukaemia (ALL) positive for the Ph translocation. METHODS: Interphase and metaphase fluorescence in situ hybridisation (FISH) was performed using several probe systems. Results were correlated with findings on conventional cytogenetics. Granulocytes, T-cells and leukaemic B-cells in peripheral blood were sorted by immunomagnetic method and the terminal restriction fragment (TRF) length of these cellular populations was determined by Southern blot analysis. RESULTS: Duplicated BCR-ABL fusion signals were found on a dic(14;22)der(22)t(9;22) chromosome. Clonal jumping translocations, existing as evolutionary changes, involved the donor chromosomal segment distal to 1q12 jumping onto the telomere ends of 11q, 15p, 19p and 20p. Telomere length was decreased in the neoplastic B-cell population and contributed to the formation of the dicentric chromosome that showed absence of telomere repeats at fusion ends. Subsequent pericentromeric heterochromatin decondensation of chromosome 1q occurred, and this donor segment was randomly fused to the shortened telomere ends of non-homologous chromosomes. CONCLUSIONS: Both telomere shortening and pericentromeric heterochromatin decondensation contribute to the formation of jumping translocations, which is most probably a multi-stage process.