Kirsi Autio

DNA Copy Number Losses in Human Neoplasms

This review summarizes reports of recurrent DNA sequence copy number losses in human neoplasms detected by comparative genomic hybridization. Recurrent losses that affect each of the chromosome arms in 73 tumor types are tabulated from 169 reports. The tables are available online at http://www.amjpathol.org and http://www. helsinki.fi/ approximately lglvwww/CMG.html. The genes relevant to the lost regions are discussed for each of the chromosomes. The review is supplemented also by a list of known and putative tumor suppressor genes and DNA repair genes (see Table 1, online). Losses are found in all chromosome arms, but they seem to be relatively rare at 1q, 2p, 3q, 5p, 6p, 7p, 7q, 8q, 12p, and 20q. Losses and their minimal common overlapping areas that were present in a great proportion of the 73 tumor entities reported in Table 2 (see online) are (in descending order of frequency): 9p23-p24 (48%), 13q21 (47%), 6q16 (44%), 6q26-q27 (44%), 8p23 (37%), 18q22-q23 (37%), 17p12-p13 (34%), 1p36.1 (34%), 11q23 (33%), 1p22 (32%), 4q32-qter (31%), 14q22-q23 (25%), 10q23 (25%), 10q25-qter (25%),15q21 (23%), 16q22 (23%), 5q21 (23%), 3p12-p14 (22%), 22q12 (22%), Xp21 (21%), Xq21 (21%), and 10p12 (20%). The frequency of losses at chromosomes 7 and 20 was less than 10% in all tumors. The chromosomal regions in which the most frequent losses are found implicate locations of essential tumor suppressor genes and DNA repair genes that may be involved in the pathogenesis of several tumor types.

Online Access to CGH Data of DNA Sequence Copy Number Changes

Listing of thechromosomal locations of recurrent DNA copy numberchanges in 73 tumor types from 283 reports available atthe end of last year can be accessed online at http://www.helsinki.fi/;lgl_www/CMG.html.When reviewing the CGH literature, we encounteredseveral problems, mainly the following:1. Different CGH systems (software applications) hadbeen used.2. There were no consensus criteria for thresholds oflosses, gains, and amplifications. In our compilation, wechose to apply an intensity ratio of 1.5 or higher as thethreshold value for amplifications.3. The results, with some exceptions, had not beenconfirmed using other techniques.Thus, one should be careful in comparing the originalpaper and our data file.The online files include a figure constructed from thecomposite profiles of the listed recurrent DNA copy num-ber sequence changes (Figure 1). Major data updates ofthe files are scheduled for July and December 2000. Inthe meantime, occasional reports will be added to thecompilation.Sakari KnuutilaKirsi AutioYan Aalto

Human chronic lymphocytic leukemia: Karyotypes in different lymphocyte populations

Abstract Karyotypes of different lymphocyte populations from 10 patients with chronic lymphocytic leukemia (CLL) showed two types of chromosome abnormalities. In cultures containing mitogens for T cells (leukoagglutinin (LA)) as well as T and B cells (pokeweed mitogen (PWM); protein A (PA)) random structural aberrations or trisomies were seen. However, one patient had a clone with trisomy 12 in LA- as well as PA-cultured cells. This clone represented about 10–20% of all mitoses, and was observed over a time period of 4 years. Nonrandom rearrangements were found in lipopolysaccharide B (LPS)-stimulated B lymphocytes from one individual in 11 cells analyzed. All these cells had multiple chromosome rearrangements. The cells probably represented a clone, since the karyotype was almost identical in all 11 cells, and the following reciprocal translocations could be identified: t(6;7), t(7;13), and t(11;14).

Outcome of ETV6/RUNX1-positive childhood acute lymphoblastic leukaemia in the NOPHO-ALL-1992 protocol: frequent late relapses but good overall survival

The prognostic impact of t(12;21)(p13;q22) [ETV6/RUNX1 fusion] in paediatric acute lymphoblastic leukaemia (ALL) has been extensively debated, particularly with regard to the frequency of late relapses and appropriate treatment regimens. We have retrospectively collected 679 ALLs with known ETV6/RUNX1 status, as ascertained by fluorescence in situ hybridization or reverse‐transcription polymerase chain reaction, treated according to the Nordic Society of Paediatric Haematology and Oncology ‐ALL‐1992 protocol. The assigned risk groups/treatment modalities for the 171 (25%) patients with t(12;21)‐positive ALLs were 74 (43%) standard risk, 71 (42%) intermediate risk and 26 (15%) high risk. The 5‐ and 10‐year event‐free survival (EFS) of the 171 patients was 80% and 75% respectively, with no significant differences among the three risk groups. Most of the relapses occurred in boys and were late, with almost 50% of all relapses occurring ≥5 years after diagnosis. Of all relapses after 6 years, 80% occurred in the t(12;21)‐positive group. The overall survival was 94% at 5 years and 88% at 10 years; thus, the treatment of patients in second or later remission is usually successful. As yet, there is no reliable plateau in the EFS curve, a fact that raises the question as to when the prognostic ramifications of ALLs harbouring ETV6/RUNX1 should be evaluated.

Cytogenetic and immunologic characterization of mitotic cells in chronic lymphocytic leukaemia.

Lymphocytes from 14 patients with chronic B‐cell leukaemia (B‐CLL) and one with chronic T‐cell leukaemia (T‐CLL) were studied by the MAC (Morphology, Antibodies, Chromosomes) method, which allows simultaneous analysis of the morphology, immunologic phenotype and karyotype of the same mitotic cell. Use of the MAC‐method in present studies has yielded new information about the cytogenetics of CLL. Although most of the interphase cells from patients with B‐CLL were positive for B‐cell markers, many of the mitotic cells turned out to be T cells, supporting the notion that the cells studied by conventional chromosome analysis are often non‐neoplastic T cells. In some B‐CLL cases with normal karyotype in the conventional chromosome study, however, most of the mitotic cells were B cells, indicating that neoplastic B cells may also have a normal karyotype. The patient with T‐CLL had normal karyotype even though most of the mitoses were T cells. The chromosome abnormalities found were restricted to cells with light chain clonality. Our results show that clonal chromosome abnormalities do occur in neoplastic B cells of patients with B‐CLL.

Chromosome changes in human chronic lymphocytic leukemia.

Karyotypes were studied in B- and T-lymphocyte cultures from 66 patients with B-cell CLL and two patients wtih T-cell CLL. Thirty-one of the B-cell cases had not been treated for their disease; 35 had received radiotherapy, corticosteroids, or cytostatic drugs. Only one of the untreated patients had a clone with an abnormal karyotype. This was present in all her mitotic cells found in cultures containing lipopolysaccharide B (LPS, a B-cell mitogen) and 10% of those in cultures with pokeweed mitogen (PWM, a T- and B-cell mitogen). The karyotype of this clone was 46,XX,t(6;7),t(7;13),t(11;14). Four of the treated patients had clones with specific chromosome changes. These were 47,XY,+12 in 10% of leukoagglutinin (LA, T-cell mitogen) and protein A (PA, T- and B-cell mitogen) cultures in one case; 47,XX,+12,del(14) in 80% of LPS cultures and in all spontaneously dividing cells in another case; 46,XY,t(6;20) in all LPS cultures in another; and 46,XX,t(1;8) in all PA cultures in another. Both structural and numerical nonclonal chromosome aberrations (9%) were found in 24% of the different cultures of cells from untreated patients, and in 15% of the cells in 20% of the different cultures in the patient who had received treatment. Both patients with T-cell CLL had receive) in all PA cultures in another. Both structural and numerical nonclonal chromosome aberrations (9%) were found in 24% of the different cultures of cells from untreated patients, and in 15% of the cells in 20% of the different cultures in the patient who had received treatment. Both patients with T-cell CLL had receive) in all PA cultures in another. Both structural and numerical nonclonal chromosome aberrations (9%) were found in 24% of the different cultures of cells from untreated patients, and in 15% of the cells in 20% of the different cultures in the patient who had received treatment. Both patients with T-cell CLL had received treatment for their disease, and had a normal karyotype in all cultures.

Cytogenetic patterns in ETV6/RUNX1-positive pediatric B-cell precursor acute lymphoblastic leukemia: A Nordic series of 245 cases and review of the literature

Between 1992 and 2004, 1,140 children (1 to <15 years) were diagnosed with B‐cell precursor acute lymphoblastic leukemia (ALL) in the Nordic countries. Of these, 288 (25%) were positive for t(12;21)(p13;q22) [ETV6/RUNX1]. G‐banding analyses were successful in 245 (85%); 43 (15%) were karyotypic failures. The modal chromosome numbers, incidence, types, and numbers of additional abnormalities, genomic imbalances, and chromosomal breakpoints in the 245 karyotypically informative cases, as well as in 152 previously reported cytogenetically characterized t(12;21)‐positive ALLs in the same age group, were ascertained. The most common modal numbers among the 397 cases were 46 (67%), 47 (16%), 48 (6%), and 45 (5%). High‐hyperdiploidy, triploidy, and tetraploidy were each found in ∼1%; none had less than 40 chromosomes. Secondary chromosomal abnormalities were identified by chromosome banding in 248 (62%) of the 397 ALLs. Of these, 172 (69%) displayed only unbalanced changes, 14 (6%) only balanced aberrations, and 26 (10%) harbored both unbalanced and balanced abnormalities; 36 (15%) were uninformative because of incomplete karyotypes. The numbers of secondary changes varied between 1 and 19, with a median of 2 additional aberrations per cytogenetically abnormal case. The most frequent genomic imbalances were deletions of 6q21‐27 (18%), 8p11‐23 (6%), 9p13‐24 (7%), 11q23‐25 (6%), 12p11‐13 (27%), 13q14‐34 (7%), loss of the X chromosome (8%), and gains of 10 (9%), 16 (6%), and 21 (29%); no frequent partial gains were noted. The chromosome bands most often involved in structural rearrangements were 3p21 (2%), 5q13 (2%), 6q12 (2%), 6q14 (2%), 6q16 (2%), 6q21 (10%), 6q23 (6%), 6q25 (3%), 9p13 (2%), 11q13 (2%), 11q23 (2%), 12p11 (6%), 12p12 (7%), 12p13 (25%), 21q10 (6%), and 21q22 (6%). Considering that the t(12;21) is known to arise in utero and that the postnatal latency period is protracted, additional mutations are most likely necessary for overt ALL. The frequently rearranged chromosome regions may harbor genes of importance for the transformation and/or progression of an initial preleukemic t(12;21)‐positive clone.

High modal number and triple trisomies are highly correlated favorable factors in childhood B-cell precursor high hyperdiploid acute lymphoblastic leukemia treated according to the NOPHO ALL 1992/2000 protocols

Between 1992 and 2008, 713 high hyperdiploid acute lymphoblastic leukemias in children aged 1–15 years were diagnosed and treated according to the Nordic Society for Pediatric Hematology and Oncology acute lymphoblastic leukemia 1992/2000 protocols. Twenty (2.8%) harbored t(1;19), t(9;22), der(11q23), or t(12;21). The median age of patients with “classic” high hyperdiploidy was lower than that of patients with translocation-positive high hyperdiploidy (P<0.001). Cases with triple trisomies (+4, +10, +17), comprising 50%, had higher modal numbers than the triple trisomy-negative cases (P<0.0001). The probabilities of event-free survival and overall survival were lower for those with white blood cell counts ≥50×109/L (P=0.017/P=0.009), ≥5% bone marrow blasts at day 29 (P=0.001/0.002), and for high-risk patients (P<0.001/P=0.003), whereas event-free, but not overall, survival, was higher for cases with gains of chromosomes 4 (P<0.0001), 6 (P<0.003), 17 (P=0.010), 18 (P=0.049), and 22 (P=0.040), triple trisomies (P=0.002), and modal numbers >53/55 (P=0.020/0.024). In multivariate analyses, modal number and triple trisomies were significantly associated with superior event-free survival in separate analyses with age and white blood cell counts. When including both modal numbers and triple trisomies, only low white blood cell counts were significantly associated with superior event-free survival (P=0.009). We conclude that high modal chromosome numbers and triple trisomies are highly correlated prognostic factors and that these two parameters identify the same subgroup of patients characterized by a particularly favorable outcome.

Clinical and cytogenetic features of a population-based consecutive series of 285 pediatric T-cell acute lymphoblastic leukemias: Rare T-cell receptor gene rearrangements are associated with poor outcome.

Clinical characteristics and cytogenetic aberrations were ascertained and reviewed in a population‐based consecutive series of 285 pediatric T‐cell acute lymphoblastic leukemias (T‐ALLs) diagnosed between 1992 and 2006 in the Nordic countries. Informative karyotypic results were obtained in 249 (87%) cases, of which 119 (48%) were cytogenetically abnormal. Most (62%) of the aberrant T‐ALLs were pseudodiploid. Structural changes were more common than numerical ones; 86% displayed at least one structural abnormality and 41% at least one numerical anomaly. The most frequent abnormalities were T‐cell receptor (TCR) gene rearrangements (20%) [TCR;11p13 (10%), TCR;10q24 (3%), TCR;other (8%)], del(9p) (17%), +8 (14%), del(6q) (12%), and 11q23 rearrangements (6%). The TCR;other group comprised the rare rearrangements t(X;14)(p11;q11), t(X;7)(q22;q34), t(1;14)(p32;q11), ins(14;5)(q11;q?q?), inv(7)(p15q34), t(8;14)(q24;q11), t(7;11)(q34;p15), and t(12;14)(p13;q11). The clinical characteristics of this Nordic patient cohort agreed well with previous larger series, with a median age of 9.0 years, male predominance (male/female ratio 3.1), median white blood cell (WBC) count of 66.5 × 109/l, and a high incidence of mediastinal mass and central nervous system involvement (59% and 9.5%, respectively). These features did not differ significantly among the various genetic subgroups. 5‐year event‐free survival (EFS) and overall survival for all patients were 0.61 (±0.03) and 0.67 (±0.03), respectively. In a multivariate analysis, two factors affected negatively the EFS, namely a WBC count of ≥200 × 109/l (P < 0.001) and the presence of rare TCR rearrangements (P = 0.001). In conclusion, in this large series of childhood T‐ALLs from the Nordic countries, the cytogenetic findings were not associated with risk of therapy failure with the exception of the TCR;other group. However, further prospective and collaborative investigations of this genetically heterogeneous entity are needed to confirm these results.

Clinical and cytogenetic features of pediatric dic(9;20)(p13.2;q11.2)-positive B-Cell precursor acute lymphoblastic leukemias: A nordic series of 24 cases and review of the literature

Although dic(9;20)(p13.2;q11.2) is a characteristic abnormality in childhood B‐cell precursor acute lymphoblastic leukemias (BCP ALL), little is known about its clinical impact or the type and frequency of additional aberrations it may occur together with. We here review the clinical and cytogenetic features of a Nordic pediatric series of 24 patients with dic(9;20)‐positive BCP ALL diagnosed 1996–2006, constituting 1.3% of the BCP ALL, as well as 47 childhood cases from the literature. Consistent immunophenotypic features of the Nordic cases included positivity for HLA‐DR, CD10, CD19, CD20, and CD22 and negativity for T‐cell and myeloid markers; no detailed immunophenotypes were reported for the previously published cases. In the entire cohort of 71 cases, the modal chromosome distribution was 45 (62%), 46 (21%), 47 (7%), 48 (4%), 49 (3%), 44 (1%), and 50 (1%). Additional changes were present in 63%, the most frequent of which were homozygous loss of CDKN2A (33%) and gains of chromosomes 21 (28%) and X (10%). The median patient age was 3 years, the female/male ratio was 2.0, the median white blood cell count was 24 × 109/l, 11% had central nervous system involvement, and 5% had a mediastinal mass at diagnosis. Risk group stratification was nonstandard risk in 79%. The event‐free survival and overall survival at 5 years for the 24 Nordic cases was 0.62 and 0.82, respectively. Thus, although relapses are quite common, postrelapse treatment of many patients is successful. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045‐2257/suppmat.