Aneuploid acute myeloid leukemia exhibits a signature of genomic alterations in the cell cycle and protein degradation machinery.

BACKGROUND: Aneuploidy occurs in more than 20% of acute myeloid leukemia (AML) cases and correlates with an adverse prognosis. METHODS: To understand the molecular bases of aneuploid acute myeloid leukemia (A-AML), this study examined the genomic profile in 42 A-AML cases and 35 euploid acute myeloid leukemia (E-AML) cases. RESULTS: A-AML was characterized by increased genomic complexity based on exonic variants (an average of 26 somatic mutations per sample vs 15 for E-AML). The integration of exome, copy number, and gene expression data revealed alterations in genes involved in DNA repair (eg, SLX4IP, RINT1, HINT1, and ATR) and the cell cycle (eg, MCM2, MCM4, MCM5, MCM7, MCM8, MCM10, UBE2C, USP37, CK2, CK3, CK4, BUB1B, NUSAP1, and E2F) in A-AML, which was associated with a 3-gene signature defined by PLK1 and CDC20 upregulation and RAD50 downregulation and with structural or functional silencing of the p53 transcriptional program. Moreover, A-AML was enriched for alterations in the protein ubiquitination and degradation pathway (eg, increased levels of UHRF1 and UBE2C and decreased UBA3 expression), response to reactive oxygen species, energy metabolism, and biosynthetic processes, which may help in facing the unbalanced protein load. E-AML was associated with BCOR/BCORL1 mutations and HOX gene overexpression. CONCLUSIONS: These findings indicate that aneuploidy-related and leukemia-specific alterations cooperate to tolerate an abnormal chromosome number in AML, and they point to the mitotic and protein degradation machineries as potential therapeutic targets.

Single nucleotide polymorphism array karyotyping: a diagnostic and prognostic tool in myelodysplastic syndromes with unsuccessful conventional cytogenetic testing.

Cytogenetic aberrations identified by metaphase cytogenetics (MC) have diagnostic, prognostic, and therapeutic implications in myelodysplastic syndromes (MDS). However, in some MDS patients MC study is unsuccesful. Single nucleotide polymorphism array (SNP-A) based karyotyping could be helpful in these cases. We performed SNP-A in 62 samples from bone marrow or peripheral blood of primary MDS with an unsuccessful MC study. SNP-A analysis enabled the detection of aberrations in 31 (50%) patients. We used the copy number alteration information to apply the International Prognostic Scoring System (IPSS) and we observed differences in survival between the low/intermediate-1 and intermediate-2/high risk patients. We also saw differences in survival between very low/low/intermediate and the high/very high patients when we applied the revised IPSS (IPSS-R). In conclusion, SNP-A can be used successfully in PB samples and the identification of CNA by SNP-A improve the diagnostic and prognostic evaluation of this group of MDS patients.

Biallelic losses of 13q do not confer a poorer outcome in chronic lymphocytic leukaemia: analysis of 627 patients with isolated 13q deletion.

Losses in 13q as a sole abnormality confer a good prognosis in chronic lymphocytic leukaemia (CLL). Nevertheless, its heterogeneity has been demonstrated and the clinical significance of biallelic 13q deletions remains controversial. We compared the clinico-biological characteristics of a series of 627 patients harbouring isolated 13q deletions by fluorescence in situ hybridization (FISH), either monoallelic (13q × 1), biallelic (13q × 2), or the coexistence of both clones (13qM). The most frequent 13q deletion was 13q × 1 (82·1%), while 13q × 2 and 13qM represented 8·6% and 9·3% of patients respectively. The median percentage of altered nuclei significantly differed across groups: 55%, 72·5% and 80% in 13q × 1, 13q × 2 and 13qM (P < 0·001). However, no significant differences in the clinical outcome among 13q groups were found. From 84 patients with sequential FISH studies, eight patients lost the remaining allele of 13q whereas none of them changed from 13q × 2 to the 13q × 1 group. The percentage of abnormal cells detected by FISH had a significant impact on the five-year cumulative incidence of treatment and the overall survival, 90% being the highest predictive power cut-off. In conclusion, loss of the remaining 13q allele is not enough to entail a worse prognosis in CLL. The presence of isolated 13q deletion can be risk-stratified according to the percentage of altered cells.

De Novo Duplication of Chromosome 9p in a Female Infant: Phenotype and Genotype Correlation.

Trisomy 9p syndrome is the fourth most frequent chromosome aberration seen in infants. Duplication of the critical region 9p22p24 leads to mental retardation, psychomotor delay, and craniofacial and digital anomalies. We report a 2-year-old Ecuadorian girl with Trisomy 9p syndrome. Although her phenotype shares characteristics of Noonan syndrome, Giemsa trypsin banding technique shows there is an extra chromosomal segment on chromosome 14, and array analysis shows that it belongs to a duplication of 38 Mb of 9p13.1p24.3. Fluorescence in situ hybridization analysis detected three signals from 9p chromosome. The duplication is de novo, being another unique case of the few reported in the literature.

A high number of losses in 13q14 chromosome band is associated with a worse outcome and biological differences in patients with B-cell chronic lymphoid leukemia.

BACKGROUND: Among patients with B-cell chronic lymphoid leukemia, those with 13q14 deletion have a favorable outcome. However, whether the percentage of cells with 13q- influences the prognosis or the biological characteristics of this disease is unknown. We analyzed the clinico-biological characteristics and outcome of patients with B-cell chronic lymphoid leukemia with loss of 13q as the sole cytogenetic aberration. DESIGN AND METHODS: Three hundred and fifty patients with B-cell chronic lymphoid leukemia were studied. Clinical data were collected and fluorescence in situ hybridization and molecular studies were carried out. In addition, a gene expression profile was obtained by microarray-based analysis. RESULTS: In 109 out of the 350 cases (31.1%) loss of 13q was the sole cytogenetic aberration at diagnosis. In the subgroup of patients with 80% or more of cells with loss of 13q (18 cases), the overall survival was 56 months compared with not reached in the 91 cases in whom less than 80% of cells had loss of 13q (p< 0.0001). The variables included in the multivariate analysis for overall survival were the percentage of losses of 13q14 (p=0.001) and B symptoms (p=0.007). The time to first therapy in the group with 80% or more vs. less than 80% of losses was 38 months vs. 87 months, respectively (p=0.05). In the multivariate analysis the variables selected were unmutated status of IgV(H) (p=0.001) and a high level of beta(2)microglobulin (p=0.003). Interestingly, these differences regarding overall survival and time to first therapy were also present when other cut-offs were considered. The gene expression profile of patients with a high number of losses in 13q14 showed a high proliferation rate, downregulation of apoptosis-related genes, and dysregulation of genes related to mitochondrial functions. CONCLUSIONS: Patients with B-cell chronic lymphoid leukemia with a high number of losses in 13q14 as the sole cytogenetic aberration at diagnosis display different clinical and biological features: short overall survival and time to first therapy as well as more proliferation and less apoptosis. A quantification of the number of cells showing a genetic abnormality should, therefore, be included in the study of the prognostic factors of B-cell chronic lymphoid leukemia.

Ring chromosome 15 - cytogenetics and mapping arrays: a case report and review of the literature.

BACKGROUND: Ring chromosome 15 has been associated in previous studies with different clinical characteristic such as cardiac problems, digit and musculoskeletal abnormalities, and mental and motor problems among others. Only 97 clinical cases of ring chromosome 15 syndrome have been reported since 1966 and a common phenotype for these patients has not been established. CASE PRESENTATION: The present case report describes a 15-month-old girl from the Amazon region of Ecuador, of Mestizo ancestry, who after cytogenetic tests showed a 46,XX,r(15) karyotype in more than 70% of metaphases observed. Her parents were healthy and non-related. The pregnancy was complicated and was positive for intrauterine growth retardation. Her birth weight was 1950 g, her length was 43.5 cm, and she had a head circumference of 29.3. In addition to postnatal growth delay, she had scant frontal hair, small eyes, hypertelorism, low-set of ears, flattened nasal bridge, anteverted nostrils, down-turned mouth, three café au lait spots, and delayed dentition. CONCLUSIONS: Despite the frequency of some phenotypes expressed in the different clinical cases reviewed and the present case, a common phenotype for patients with ring 15 could not be determined and it is restricted to the region of the chromosome lost during the ring formation.

Validation of an interphase fluorescence in situ hybridization approach for the detection of MLL gene rearrangements and of the MLL/AF9 fusion in acute myeloid leukemia.

To validate a 2-step FISH assay for the identification of the t(9;11)(p22;q23), 96 acute myeloid leukemias were studied by cytogenetic analysis, FISH and molecular biology. After a first FISH step using an MLL probe, 24/27 cases with 11q23 break showed MLL rearrangement. Southern blotting confirmed FISH data. In the second step, 24 cases with MLL rearrangement were studied using MLL and AF9 probes: 17/18 cases with t(9;11) showed MLL/AF9 fusion. In 6 patients with 11q23/MLL rearrangements other than t(9;11), FISH confirmed MLL involvement and excluded AF9 involvement. This is a reliable method for the identification of MLL/AF9 fusion in interphase cells, allowing for a reclassification of cases with suboptimal chromosome morphology. The frequency of deletion surrounding MLL and AF9 breakpoint is low.

Chromosomal imbalances identified by comparative genomic hybridization in sporadic parathyroid adenomas.

OBJECTIVE: To identify chromosomal gains and losses in sporadic parathyroid adenomas (PAs). METHODS: Fourteen sporadic PAs were studied by comparative genomic hybridization (CGH). RESULTS: The fourteen studied PAs showed chromosomal imbalances. All cases except one exhibited two or more abnormalities. Chromosomal gains were found in all cases, and three cases (21%) also presented chromosomal losses. Genomic amplification was not observed. Chromosome 9 was involved in ten cases. Recurrent genetic gain was found on 9p22-24 and on 9q34, each in 6 of 14 cases (43%). Other recurrent gains included Xq26 in 6 PAs (43%) and 4q21-28 and 8p22-23, each in 4 of 14 cases (29%). Regions of recurrent genetic loss involved whole chromosome 11 and 20q12-13, each in 2 of 14 cases (14%). CONCLUSIONS: Our findings show chromosomal imbalances in all sporadic PAs studied by CGH, partly confirming previous reports, with the exception that we observed more chromosomal gains than losses. Several regions (9p22-24, 9q34, Xq26, 4q21-28, and 8p22-23) probably deserve further investigation in order to discard the presence of genes involved in parathyroid tumorigenesis.

Impact of immunophenotype on prognosis of patients with myelodysplastic syndromes. Its value in patients without karyotypic abnormalities.

The aim of this study was simultaneously to evaluate the potential influence of cytogenetic, immunophenotypic and cell culture studies in the evolution of the myelodysplastic syndromes (MDS) with particular attention to the value of the two latter features in predicting the outcome of those patients in which karyotypic information is normal or not available. A series of 77 newly diagnosed patients with primary MDS were analyzed. Immunophenotypic studies were carried out by flow cytometry in triple color combinations: CD34/CD33/CD38, CD15/CD34/HLADR and HLADR/CD13/CD45. In all, 63% of patients showed a normal karyotype and 37% showed clonal abnormalities. In immunophenotypic analysis, overall 90% of patients displayed phenotypic aberrations and 60% showed two or more aberrations. In univariate analysis, 10 variables had a significant influence on survival: >10% bone marrow (BM) blast cells, >or=peripheral blood (PB) cytopenias, >2% of BM CD34+ cells, >85% of BM myeloid cells, >7% monocytic cells, <49% of neutrophils, a neutrophil/monocytic cell ratio <7, more than three phenotypic aberrations and >80 colony-forming units for granulocytes and macrophages (CFU-GM)/10(5) plated cells. Only the presence of >or=5% of BM blast cells (P=0.001) and cytogenetic subgroups (P=0.008) showed independent prognostic significance by multivariate analysis. In patients lacking cytogenetic information or in which the karyotype was normal additional markers had an independent prognostic value in multivariate analysis: >or=2 phenotypic aberrations (P=0.001) and >or=2 PB cytopenias (P=0.004). In summary, our results show that in patients in whom the karyotype is normal or where an insufficient amount of mitoses is obtained, immunophenotype could help to establish a prognosis.

Application of FISH 7q in MDS patients without monosomy 7 or 7q deletion by conventional G-banding cytogenetics: does -7/7q- detection by FISH have prognostic value?

Chromosomal abnormalities are detected in 40-60% of patients with de novo myelodysplastic syndromes (MDS). This study used the FISH technique in 773 patients with de novo MDS without evidence of monosomy 7 (-7) or 7q deletion (7q-) by conventional G-banding cytogenetics (CC) to analyze their prognostic impact by FISH alone. FISH detected -7/7q- in 5.2% of patients. Presence of -7/7q- was associated with shorter overall survival than absence of such aberrations. Our results suggest that FISH 7q could be beneficial in patients with intermediate WHO morphologic risk stratification and no evidence of -7/7q- by CC.

Caracterización citogenética y molecular de una paciente ecuatoriana con cromosoma 4 en anillo: análisis clínico comparativo con 37 casos internacionales / Cytogenetic and molecular characterization of a Ecuadorian patient with ring chromosome 4: comparative clinical analysis with 37 international cases

Los cromosomas en anillo son alteraciones genéticas muy inusuales, consecuencia de deleciones en las regiones terminales y de la unión de los extremos expuestos del cromosoma afectado. En un cromosoma 4 en anillo las regiones que con más frecuencia se afectan son 4p16.3 del brazo corto y 4q35.2 del brazo largo. Sujeto y métodos Se presenta el caso de una paciente con cromosoma 4 en anillo diagnosticado cuando tenía diez días de edad. Al examen clínico presentó dismorfogénesis importante: frente plana, nariz puntiforme, implantación baja de pabellones auriculares, clinodactilia del quinto dedo, microcefalia, micrognatia, un orifcio en la región lumbosacra, estatura baja y retardo mental leve. A los 10 años de edad se le realizó una evaluación citogenética con técnicas más modernas: hibridación in situ fluorescente (FISH) y mapeo genético por arrays de ADN. El fenotipo de la paciente fue comparado con 37 casos reportados en la literatura internacional. Resultados En el análisis clínico de la paciente y los 37 casos internacionales se encontró alrededor de 41 características clínicas diferentes y variables en cada sujeto. Las más frecuentes fueron retraso en el crecimiento (78%), microcefalia (67%), retardo mental (62%), bajo peso al nacer (48%), clinodactilia del quinto dedo (37%), micrognatia (29%), hipertelorismo (21%) y alguna cardiopatía (18%). El estudio citogenético de la paciente a los diez días de edad mostró un cariotipo en mosaico 46,XX/46,XX,r(4) con anillo del cromosoma 4 en el 80% de las metafases. A los diez años de edad se encontró r(4) en el 90% de las células. El análisis por FISH reveló un cariotipo 46,XX,r(4).ish r(4)(p16.3q35.2) (492870-793359-,190183811-190408149-). Los arrays evidenciaron las regiones de pérdida de los brazos cortos y largos del cromosoma 4 involucrados en la formación del anillo. Los genes que con seguridad inciden en el fenotipo de la paciente en estudio son LETM1, WHSC1, WHSC2, MIR943, TACC3, IDUA, C4orf48 para retardo mental; LETM1 y WHSC1 para microcefalia y KIAA1530 para retraso en el crecimiento.

Ring chromosomes are rare chromosomal structure abnormalities; they are formed when a chromosomal deletion leads to the fusion of both ends of the chromosome. The most frequent altered regions in ring chromosome 4 are 4p16.3 in short arm and 4q35.2 in long arm. Subject and methods Here we report a 10 days old female patient whose frst cytogenetic diagnosis showed a ring chromosome 4. Clinical examination showed congenital abnormalities including flattened forehead, prominent nose, low set ears, clinodactyly of the ffth fnger, microcephaly, micrognathia, small sacrococcygeal dimple, short stature and mild mental retardation. At the aged of ten fluorescence in situ hybridization (FISH) and DNA microarrays were performed. Finally, patient phenotype was compared with other 37 cases reported in the literature. Results The clinical analysis between the patient and the 37 cases reported showed about 41 different clinical features that vary between each individual. The most frequent features were growth retardation (78%), microcephaly (67%), mental retardation (62%), short stature at birth (48%), clinodactyly of the ffth fnger (37%), micrognathia (29%), hypertelorism (21%) and some type of cardiopathy (18%). Chromosome analysis of the patient at 10 days old appeared as a chromosomal mosaicism 46,XX/46,XX,r(4), with ring chromosome 4 in 80% of the metaphases analyzed. At 10 years old of the patient it was observed r(4) in 90% of the cells. FISH analysis showed a karyotype 46,XX,r(4).ish r(4)(p16.3q35.2) (492870-793359-,190183811-190408149-). The arrays showed deleted regions at the short and long arms of chromosome 4 involved in the formation of ring chromosome. The genes that are manifested in the patient phenotype are LETM1, WHSC1, WHSC2, MIR943, TACC3, IDUA, C4orf48 for mental retardation; LETM1 y WHSC1 for microcephaly and KIAA1530 for growth retardation.

Incidence and clinicobiologic characteristics of leukemic B-cell chronic lymphoproliferative disorders with more than one B-cell clone.

Leukemic B-chronic lymphoproliferative disorders (B-CLPDs) are generally believed to derive from a monoclonal B cell; biclonality has only occasionally been reported. In this study, we have explored the incidence of B-CLPD cases with 2 or more B-cell clones and established both the phenotypic differences between the coexisting clones and the clinicobiologic features of these patients. In total, 53 B-CLPD cases with 2 or more B-cell clones were studied. Presence of 2 or more B-cell clones was suspected by immunophenotype and confirmed by molecular/genetic techniques in leukemic samples (n = 42) and purified B-cell subpopulations (n = 10). Overall, 4.8% of 477 consecutive B-CLPDs had 2 or more B-cell clones, their incidence being especially higher among hairy cell leukemia (3 of 13), large cell lymphoma (2 of 10), and atypical chronic lymphocytic leukemia (CLL) (4 of 29). In most cases the 2 B-cell subsets displayed either different surface immunoglobulin (sIg) light chain (n = 37 of 53) or different levels of the same sIg (n = 9 of 53), usually associated with other phenotypic differences. Compared with monoclonal cases, B-CLL patients with 2 or more clones had lower white blood cell (WBC) and lymphocyte counts, more frequently displayed splenomegaly, and required early treatment. Among these, the cases in which a CLL clone coexisted with a non-CLL clone were older and more often displayed B symptoms, a monoclonal component, and diffuse infiltration of bone marrow and required early treatment more frequently than cases with monoclonal CLL or 2 CLL clones.

Leucemia linfática crónica / Chronic lymphocytic leukemia

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