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Karyotypic progression in human tumors.

Karyotypic progression may be viewed in at least two ways. One approach seeks evidence for increasing and progressive deviation from the normal chromosome pattern in tumors. The clearest examples, found in some leukemias, are those in which successive karyotypic changes are superimposed on an already aberrant cell population. Evidence of chromosomal progression within solid tumors is far less frequent, possibly because the tumors themselves are at a relatively late stage in their evolution. An alternative approach, therefore, attempts to correlate the extent of karyotypic deviation with other aspects of tumor progression. Recent data, based on classical cytogenetic analyses and flow cytometry, are presented to determine relationships between karyotype and specific origin and morphology of tumors. The predominant theme which emerges, not surprisingly, is that the more deviant chromosome patterns are associated with other measures of increased biologic malignancy. What is surprising is the degree to which these properties are expressed in primary tumors and the relative lack of evidence for further karyotypic evolution with recurrence or metastasis. Examples of genetic instability, evolution through polyploidy, gene amplification, and selection for specific chromosomal rearrangement are found in populations of premalignant and malignant human cells. There is increasing recognition of the importance of tumor-specific chromosome aberrations in the stepwise progression from the normal to the fully neoplastic cell.

Chromosome Aberrations↗

Different patterns in molecular evolution of the Triticeae.

A huge part of the genomes of most Triticeae species is formed by different families of repetitive DNA sequences. In this paper the phylogenetic distribution of two major classes of the repeats, retrotransposons and tandemly organized DNA sequences, are considered and compared with the evolution of gene-rich regions and generally accepted Triticeae phylogenetic relationships. In Hordeum, LTR-containing retrotransposons are dispersed along the chromosomes and are consistent with the existing picture of the phylogeny of Hordeum. Another retrotransposon class, LINEs, have evolved independently from LTR-retrotransposons. Different retrotransposon classes appear to have competed for genome space during the evolution of Hordeum. Another class of repeats, tandemly organized DNA sequences, tends to cluster at the functionally important regions of chromosomes, centromeres and telomeres. The distribution of a number of tandem DNA families in Triticeae is not congruent with generally accepted phylogenetic relationships. While natural selection is the dominant factor determining the structure of genic regions we suggest that the contribution of random events is important in the evolution of repetitive DNA sequences. The interplay of stochastic processes, molecular drive, and selection determines the structure of chromosomal regions, notably at centromeres and telomeres, stabilizing and differentiating species-specific karyotypes. Thus, the evolution of these regions may occur largely independently of the evolution of gene-rich regions.

Blotting, Southern↗

Genomic distribution of heterochromatic sequences in equids: implications to rapid chromosomal evolution.

We describe a molecular model for rapid chromosomal evolution that proposes tandemly repeated DNA sequences as a driving force. A prediction of this model is that when extensive rearrangements of euchromatin have been facilitated by heterochromatin, genomes will be characterized by tandemly repeated sequences that have actively changed chromosomal fields by intragenomic movement. Alternatively, it is proposed that in conservative chromosomal lineage each class of tandemly repeated sequences will be restricted to a specific chromosomal field. To provide baseline data to test this model we examined four classes of tandemly repeated elements in six species of equids (Equus). Distribution of these sequences among species, as determined from slot blot analysis, and restriction site variation, shown by Southern blot hybridization, document that these sequences are in an evolutionarily dynamic state, and in situ hybridization documents extensive intragenomic movement among nonhomologous chromosomes and chromosomal fields. These data are interpreted as being compatible with the predictions of this model. Although this is clearly not the sole molecular factor driving chromosomal evolution, the model appears to be viable as an explanation of certain patterns of chromosomal evolution such as karyotypic megaevolution and some types of karyotypic orthoselection.

Animals↗

The centromere landscapes of four karyotypically diverse Papaver species provide insights into chromosome evolution and speciation.

Understanding the roles played by centromeres in chromosome evolution and speciation is complicated by the fact that centromeres comprise large arrays of tandemly repeated satellite DNA, which hinders high-quality assembly. Here, we used long-read sequencing to generate nearly complete genome assemblies for four karyotypically diverse Papaver species, P. setigerum (2n = 44), P. somniferum (2n = 22), P. rhoeas (2n = 14), and P. bracteatum (2n = 14), collectively representing 45 gapless centromeres. We identified four centromere satellite (cenSat) families and experimentally validated two representatives. For the two allopolyploid genomes (P. somniferum and P. setigerum), we characterized the subgenomic distribution of each satellite and identified a "homogenizing" phase of centromere evolution in the aftermath of hybridization. An interspecies comparison of the peri-centromeric regions further revealed extensive centromere-mediated chromosome rearrangements. Taking these results together, we propose a model for studying cenSat competition after hybridization and shed further light on the complex role of the centromere in speciation.

Centromere↗

Evolution of the Simiiformes and the phylogeny of human chromosomes.

This paper is based on the results of Primate chromosome studies obtained using high resolution techniques in our and other laboratories. We discuss the origin and the evolution of the chromosomes in the human karyotype and the time in evolution of the Simiiformes when they acquired their present morphology. Our results indicate that the chromosomes that underwent a higher number of reorganizations during the evolution of the Simiiformes coincide with the chromosomes most often implicated in human chromosome pathology. We describe the main reorganizations that took place during Primate evolution. Centromere activation and inactivation and heterochromatin changes are discussed as mechanisms of chromosome evolution.

Animals↗

Chromosome aberrations in B-cell chronic lymphocytic leukemia. Pathogenetic and clinical implications.

Chromosome analyses were performed on leukemic cells from 102 patients with B-CLL, of whom 84 were untreated. B-cell mitogen-induced CLL cells yielded suitable metaphases in 85 patients, and 55 showed clonal chromosomal aberrations. Trisomy 12 was found in 26 patients. In nine patients the + 12 was a single aberration. A 14q + chromosome or deletions of the long arm of chromosomes 6, 11, or 13 were other recurrent aberrations. Patients with Rai stage I or more had more frequently clonal aberrations than patients with stage 0 disease (p less than .02). Patients with clonal aberrations had poorer 5-year survival than those with a normal karyotype (p less than .05). Patients with a high percentage of abnormal metaphases in the sample had poorer prognosis than patients with high admixture of normal metaphases (p less than .01). Of the specific clonal aberrations those with 14q + or trisomy 12 tended to have slightly poorer and those with 6q- or structural aberrations involving the long arm of chromosome 13 tended to have better prognosis than patients with other chromosomal aberrations. A complex karyotype tended to be an adverse prognostic sign. Clonal evolution is rare: complex karyotypes are found at diagnosis and clones with single aberrations did not acquire additional chromosome aberrations despite progressive disease and treatment. Nine hundred and seventy-nine published cases are reviewed, and pathogenetic mechanisms, such as oncogenes and gene dosage, are discussed.

Adult↗

Chromosomal banding patterns in acute nonlymphocytic leukemia.

Bone marrow chromosomes obtained from 50 of 55 consecutive adult patients with acute nonlymphocytic leukemia were analyzed with quinacrine fluorescence. Twenty-five patients showed a normal karyotype and 25 an abnormal karyotype on the initial samples available for analysis. Among the 25 patients with abnormalities, the marrow cells contained 48 chromosomes in one case, 47 in two, 46 in ten, 45 in nine, 43 in two, and 42 chromosomes in one case. Seven of the ten patients with 46 chromosomes had abnormalities, primarily balanced translocations, that were not detected with the standard Giemsa stains. The analysis of all of the data available revealed the presence of nonrandom chromosome changes such as the addition of No. 8, the loss of No. 7, and a gain or loss of one No. 21. the most frequent structural rearrangement was the translocation between the long arm of No. 8 and No. 21, which may also be associated with the loss of a sex chromosome. Chromosomal abnormalities decreased or disappeared during remission; the same abnormality recurred in relapse. Chemotherapy did not appear to produce a stable clone of aberrant cells. Evolution of the karyotype occurred in eight patients, in five of whom an additional No. 8 was observed. This pattern of chromosomal evolution in patients with acute leukemia was very similar to that observed in patients with chronic myelogenous leukemia in the blast phase.

Acute Disease↗

Karyotype in myelodysplastic syndromes: relations to morphology, clinical evolution, and survival.

One hundred eighty-eight unselected consecutive patients with "de novo" myelodysplastic syndrome (MDS) were studied cytogenetically. They were subclassified as 4 refractory anemia with ringed sideroblasts (RARS), 67 refractory anemia (RA), 58 refractory anemia with excess of blasts (RAEB), 40 RAEB in transformation (RAEB-t), and 19 chronic myelomonocytic leukemia (CMML). The overall incidence of chromosome abnormalities was 69%. The RAEB and RAEB-t patients showed karyotypic changes, more often than RA and CMML (76% and 100% vs. 56% and 42%, respectively). The most frequent single anomaly was del(5)(q13-q22q33) (22 cases), followed by monosomy 7 or del 7q (11 cases), del(11) (q14q23) (8 cases), trisomy 8 (4 cases). Complex karyotypes (defined by the presence of three or more structural or numerical abnormalities) were detected in 33 patients. With regard to the FAB classification, del (5)(q13q33) was associated with RA, and complex rearrangements with RAEB and RAEB-t. Leukemic transformation occurred in 66 patients (46%), none with a normal karyotype or del(11)(q14q23) as single abnormality. In patients carrying 5q- alone, acute evolution correlated with proximal breakpoint localization, being found in no case with del(5)(q13q33) but in three out of four cases with del(5)(q22q33). Acute leukemia (AL) progression happened in all cases with complex rearrangements and monosomy 7 or del(7q). Two of the four trisomy eight patients evolved in AL. By using the Cox proportional hazard regression analysis it was demonstrated that the karyotype abnormality was a significant predictor of leukemic transformation (P < 0.001). Patients with abnormal karyotypes without complex abnormalities had a survival (median survival 12 months) shorter than that of cases with only normal metaphases (median 83 months) (P < 0.001); patients with a mixture of normal/abnormal metaphases had a median survival of 31 months. The median survival for complex karyotypes was 7 months. Among cases with single defects, del(5)(q13q33) showed the best survival (64 months), monosomy 7 and del(7q) the worst (7 months) (P < 0.001).

Chromosome Mapping↗

The effect of imatinib mesylate on patients with Philadelphia chromosome-positive chronic myeloid leukemia with secondary chromosomal aberrations.

PURPOSE AND EXPERIMENTAL DESIGN: The acquisition of secondary chromosomal aberrations in chronic myeloid leukemia (CML) patients with Philadelphia chromosome-positive (Ph+) karyotype signifies clonal evolution associated with disease progression to accelerated/blastic phase. Therefore, these aberrations are of clinical and biological importance. We identified 58 cases with secondary abnormalities in addition to t(9;22)(q34;q11.2) or its variants in a review of 137 CML patients treated with imatinib mesylate (STI571). Clinically 13 patients were in chronic phase, 24 in accelerated phase, and 21 in blastic phase. RESULTS: More than 50% of cases showed the major routes of CML clonal evolution [+8, i(17q), +Ph, and/or +19]. The remainder exhibited minor routes of secondary abnormalities with -17/17p-, 11p-/rearr(11p), and -7/rearr(7) as the most frequent abnormalities. Of particular interest, one case developed an inv(16)(p13q22) as a secondary anomaly during blastic transformation. The bone marrow was consistent with myelomonocytic morphology with eosinophilia. Cytogenetic responses to imatinib mesylate occurred in 15 of 58 (26%) patients; 12 achieved complete cytogenetic remission, 2 had a major response, and 1 had a minor response, with most responses noted within 3-6 months. Seven patients remain in remission >17-30 months, 2 patients relapsed between 12 and 19 months on therapy, and 1 patient was treated by bone marrow transplantation. CONCLUSIONS: Although some Ph+ CML patients with clonal evolution can have a complete cytogenetic response to imatinib mesylate, responses tend to be brief, and such patients may benefit from subsequent stem cell transplantation. Therefore, CML patients with clonal evolution may require therapy additional to imatinib mesylate for maximal eradication of the Ph+ leukemic cells.

Adult↗

Comparative genomics and repetitive sequence divergence in the species of diploid Nicotiana section Alatae.

Combining phylogenetic reconstructions of species relationships with comparative genomic approaches is a powerful way to decipher evolutionary events associated with genome divergence. Here, we reconstruct the history of karyotype and tandem repeat evolution in species of diploid Nicotiana section Alatae. By analysis of plastid DNA, we resolved two clades with high bootstrap support, one containing N. alata, N. langsdorffii, N. forgetiana and N. bonariensis (called the n = 9 group) and another containing N. plumbaginifolia and N. longiflora (called the n = 10 group). Despite little plastid DNA sequence divergence, we observed, via fluorescent in situ hybridization, substantial chromosomal repatterning, including altered chromosome numbers, structure and distribution of repeats. Effort was focussed on 35S and 5S nuclear ribosomal DNA (rDNA) and the HRS60 satellite family of tandem repeats comprising the elements HRS60, NP3R and NP4R. We compared divergence of these repeats in diploids and polyploids of Nicotiana. There are dramatic shifts in the distribution of the satellite repeats and complete replacement of intergenic spacers (IGSs) of 35S rDNA associated with divergence of the species in section Alatae. We suggest that sequence homogenization has replaced HRS60 family repeats at sub-telomeric regions, but that this process may not occur, or occurs more slowly, when the repeats are found at intercalary locations. Sequence homogenization acts more rapidly (at least two orders of magnitude) on 35S rDNA than 5S rDNA and sub-telomeric satellite sequences. This rapid rate of divergence is analogous to that found in polyploid species, and is therefore, in plants, not only associated with polyploidy.

Chromosomes, Plant↗

[Heterochromatin and euchromatin regions in the chromosomes of various representatives of the subfamily Bovinae].

Heterochromatin distribution was studied in three species of subfamily Bovinae: bison (Bison bison), European bison (Bison bonasus), and gayal (Bos frontalis). In all of the studied species, C- and CMA3-banding and in situ hybridization with satellite DNAII (satDNAII) revealed the conservative distribution of heterochromatic regions in autosomes; sex chromosomes did not contain the classical constitutive heterochromatin. The Y chromosome was the most variable element of the karyotypes of both bison species and the gayal. A mechanism for formation of the acrocentric Y chromosome in B. bison was suggested. This hypothetical mechanism included breakage of the p arm at the telomeric region and subsequent translocation and inversion. The map of B. bison chromosomes (491 bands per haploid set) is presented. The data obtained are discussed in terms of speciation and the evolution of Bovinae karyotypes.

Animals↗

Cytogenetic findings in acute megakaryoblastic leukemia (ANLL-M7).

The clinical, morphologic, and cytogenetic findings in a patient with acute megakaryoblastic leukemia (ANLL-M7) are described. At the time of diagnosis, the karyotype contained three related clones: 47,XY,t(3;6)(p13;q27), +8,t(12;22)(p13;q12), +15, -21, -22, +der(22)t(21;22)(q11;p13)/47,XY, +8,del(9)(q22),t(12;22), +15, -21, -22, +der(22)/46,XY, +8, t(12;22), -21, -22, +der(22). Complete remission was achieved with intensive combination chemotherapy. At relapse 20 months later, there was clear evidence of clonal evolution, and the karyotype was now 45,XY,t(2;18)(q33;p11),del(9)(q22),t(12;22)(p13;q12), -16, +der(16)t(8;16)(q13;p13), -21, -22, +der(22)t(21;22)(q11;p13)/46,XY,t(2;18),del(9),t(12;22), -16, +der(16), -21, -22, +der(22), +mar. A comparison with the few previously cytogenetically analyzed cases of ANLL-M7 reveals that structural rearrangements of chromosomes 21 and 22 might be of primary importance in the pathogenesis of acute megakaryoblastic leukemia.

Adult↗

Multivariate analysis of chromosomal imbalances in breast cancer delineates cytogenetic pathways and reveals complex relationships among imbalances.

More than 550 breast adenocarcinomas with clonal chromosomal abnormalities have been reported. Although the aberration pattern is clearly nonrandom, no specific primary or secondary karyotypic abnormality has been identified, and furthermore the chronological order in which the aberrations appear during disease progression is not well known. The high degree of karyotypic complexity in epithelial tumors such as breast cancer is one reason why our understanding of the sequential order of cytogenetic evolution is unclear. To overcome some of these difficulties, we have used several statistical methods that allow identification and interpretation of karyotypic pathways. These methods were applied on 538 breast cancer karyotypes. The distribution of the number of imbalances/tumor showed a monomodal appearance, indicating that one single mode of karyotypic evolution is operating in this tumor type. We show that there exists a temporal order with respect to the appearance of chromosomal imbalances. The imbalances +1pq, 1q-, 3p-, and +7 appear earlier than expected from random events, and two cytogenetic pathways, one initiated by +1q and followed by 11q- and -22, the other initiated by either 3p- or 1q- and followed by 1p-, 3q-, and 6q-, can be discerned. We also show that +7 and +8q behave independently of the other imbalances and cannot, by simple means, be incorporated in the identified pathway scheme. Although the cytogenetic pathways are well separated at earlier stages, they later converge and include a common set of late imbalances.

Adenocarcinoma↗

Survival analysis and AML development in patients with de novo myelodysplastic syndromes: comparison of six different prognostic scoring systems.

A number of prognostic scoring systems for patients with myelodysplastic syndromes (MDS) have been introduced in the past. In the present study, survival and AML evolution were analyzed retrospectively in a total of 180 patients with de novo MDS (observation period: 1989-1999; median age: 71; range 27-93; f/m ratio: 1/1.2). Diagnoses were established according to FAB criteria (RARS, n=37; RA, n=53; RAEB, n=50; RAEB-t, n=19; CMML, n=21). Six different multiparameter scoring systems (the Mufti, Aul, Sanz, Morel, and Toyama scores, and the international prognostic scoring system [IPSS]) were applied. The Aul, Sanz, and Mufti scores were applied to all 180 patients, Morel and Toyama scores to 109 patients, and the IPSS to 102. As assessed by multivariate analysis, the percentage of bm-blasts, hemoglobin, platelet count, neutrophil count, LDH, and karyotype were found to be independent single variables for survival, and bm-blasts, neutrophil count, platelet count, and karyotype for AML evolution. All prognostic scoring systems applied appeared to be highly predictive for survival and AML development (P<0.001). The highest predictive values were found for the Aul, Sanz, and Toyama scores for overall survival, and the IPSS, Toyama, and Morel scores for AML-free survival. In summary, our data show that scoring systems are useful for predicting overall and AML-free survival in patients with MDS. Karyotype-based multiparameter systems appear to be particularly effective in defining MDS patients who are at high risk of transforming to leukemia.

Acute Disease↗

Unusual complex hyperdiploid karyotypes in myelodysplastic syndromes.

Over an 18-year period, 10 myelodysplastic syndrome (MDS) patients with complex hyperdiploid karyotypes were identified. According to the FAB classification, the 10 patients were subclassified as three refractory anemias (RA), three refractory anemias with excess blasts (RAEB), two RAEB in transformation (RAEB-t), and two unclassified MDS. According to the WHO classification, the diagnoses were two RA, one refractory cytopenia with multilineage dysplasia, two RAEB-1, one RAEB-2, two unclassified MDS, and two acute myeloid leukemia. Six were secondary MDS. Four patients showed marked dyserythropoiesis; three of these were secondary MDS. The chromosome number ranged from 47 to 62, and clonal evolution or composite karyotypes were noted in 7 patients. Seven patients had at least one clone with >50 chromosomes. Recurrent defects included chromosome 5, 17, and 13 abnormalities. Notably, trisomy 8 and monosomy 7 were rare in that group of patients. Three of four patients with marked dyserythropoiesis shared abnormalities of both chromosomes 13 and 17.

Aged↗

Fluorescence banding in four species of Microtidae: an analysis of the evolutive changes of the constitutive heterochromatin.

Three different fluorochrome and specific counterstain combination (DAPI/AMD, DA/DAPI and CMA/DA) treatments were applied to the chromosomes of four Microtidae (Rodentia) species. The results complete the data obtained in our previous paper (Burgos, M., Jiménez, R., & Dìaz de la Guardia, R., Genome 30:540-546, 1988) and prove that the changes in the constitutive heterochromatin in the evolution of the karyotypes of these species are not only due to gain or loss of heterochromatin, but are qualitative with respect to their nucleotide composition, repeated base pair organization or DNA-protein complex modification. These variations lead to the differential response to the fluorescence dye combinations used.

Animals↗

Multidirectional chromosome painting between the Hirola antelope (Damaliscus hunteri, Alcelaphini, Bovidae), sheep and human.

Chromosome specific painting probes of human, sheep and the Hirola antelope ( Damaliscus hunteri ) derived by flow sorting of chromosomes were used in multi directional chromosome painting experiments to better define the karyological relationship within Bovidae species (specifically, Caprini and Alcelaphini tribes) and humans. Although not all chromosomes of Damaliscus hunteri could be resolved into single peaks by flow-sorting we managed to present a complete homology map for chromosomes between the three species. When comparing the karyotype of Damaliscus hunteri with human all of the main known motives in mammalian chromosome evolution are present (i.e. associations of human homologous chromosomes 3-21, 4-8, 7-16, 14-15, 16-19 and two forms of 12-22) which were also confirmed with the sheep paint probes. Further, we observed those patterns that have been described as common derived traits for artiodactyls (i.e. associations of human homologous chromosomes 5/19 and a complex alternating pattern of hybridizations with human chromosome 14 and 15 probes). As known from classical karyotyping some of the Damaliscus chromosomes are biarmed and were supposedly involved in Robertsonian translocations frequently found in karyotype evolution of bovids. We refined these rearrangements with the molecular probes and also delineated a chromosome painting pattern that should be the result of a paracentric inversion in the Damaliscus hunteri karyotype. This study demonstrates that multidirectional chromosome painting will be a valuable tool for the investigation of the dynamics of chromosome evolution in exotic bovid species.

Animals↗

Malignant melanoma arising in a giant congenital melanocytic nevus. A case report with cytogenetic and histopathologic analyses.

A malignant melanoma developed in a 2-year-old Hispanic girl with a giant congenital melanocytic nevus (bathing-trunk type). Histopathologic evaluation showed a deep-seated tumor arising from a nonepidermal origin. Cytogenetic analysis demonstrated multiple chromosomal abnormalities in hyperdiploid cells (chromosome range, 56 to 61). No two karyotypes were identical, but many abnormalities were common to all analyzed cells, suggesting both karyotypic instability and evolution. The metaphases were monosomic for 3, 12, and 16, trisomic for 1, 2, 8, 19, 20, and 21, and included structural aberrations deletion 1 and derivatives 3 and 16. Eight markers were identified, including one ring. The extra 19 was possibly an isochromosome. No abnormalities of 6 or 10 were identified.

Chromosome Aberrations↗