Split-signal FISH for detection of chromosome aberrations in acute lymphoblastic leukemia.

Chromosome aberrations are frequently observed in precursor-B-acute lymphoblastic leukemias (ALL) and T-cell acute lymphoblastic leukemias (T-ALL). These translocations can form leukemia-specific chimeric fusion proteins or they can deregulate expression of an (onco)gene, resulting in aberrant expression or overexpression. Detection of chromosome aberrations is an important tool for risk classification. We developed rapid and sensitive split-signal fluorescent in situ hybridization (FISH) assays for six of the most frequent chromosome aberrations in precursor-B-ALL and T-ALL. The split-signal FISH approach uses two differentially labeled probes, located in one gene at opposite sites of the breakpoint region. Probe sets were developed for the genes TCF3 (E2A) at 19p13, MLL at 11q23, ETV6 at 12p13, BCR at 22q11, SIL-TAL1 at 1q32 and TLX3 (HOX11L2) at 5q35. In normal karyotypes, two colocalized green/red signals are visible, but a translocation results in a split of one of the colocalized signals. Split-signal FISH has three main advantages over the classical fusion-signal FISH approach, which uses two labeled probes located in two genes. First, the detection of a chromosome aberration is independent of the involved partner gene. Second, split-signal FISH allows the identification of the partner gene or chromosome region if metaphase spreads are present, and finally it reduces false-positivity.     

Rapid and sensitive detection of all types of MLL gene translocations with a single FISH probe set.

The MLL gene on chromosome 11 band q23 is frequently involved in chromosome translocations in acute lymphoblastic leukemia and acute myeloid leukemia. The translocation results in the formation of a fusion gene on the derivative 11 chromosome consisting of the 5' part of the MLL gene and the 3' part of another gene; already more than 30 different partner chromosome regions have been described. MLL gene rearrangements are generally correlated with a poor prognosis. Therefore the presence of an 11q23 aberration has direct implications for treatment stratification, making early and rapid detection of utmost importance. In this study, we developed a FISH probe set for detection of MLL gene rearrangements according to strict design criteria. The cosmid probes are derived from the flanking regions of the MLL breakpoint region on chromosome 11 and when used in dual colored FISH experiments give rise to a split of the normally colocalizing (fused) signals in case of a translocation. This split signal was observed in seven out of 10 cases with an 11q23 translocation with various partner chromosomes. In the three other cases, a deletion of the 3' part of the MLL gene, downstream of the breakpoint region was also found. A low false positive value of only 1.7% was obtained for interphase cells in contrast to conventional dual colored FISH where the creation of a fusion signal has cut off values of at least 5-10%. A major advantage of our type of probe set is the application of a single FISH experiment to detect all types of MLL translocations. Moreover, since this cosmid probe set can be used for either interphase or metaphase studies, metaphases are no longer a prerequisite for detecting the presence of an 11q23 translocation. Nevertheless, metaphase FISH with the new probe set is helpful in determining the partner chromosome and therefore may lead to the identification of new partner genes.     

Identification of novel cryptic translocations involving IGH in B-cell non-Hodgkin's lymphomas

Chromosomal rearrangements involving the immunoglobulin heavy chain gene (IGH) at 14q32 are observed in approximately 50% of patients with B-cell non-Hodgkin's lymphoma (NHL). The 5' end of the IGH gene is located within 8 kb of the telomeric repeats of 14q. Translocations involving the IGH locus and the telomeric band of a partner chromosome are difficult to identify, because most terminal bands of human chromosomes appear pale by conventional G-banding techniques. To determine whether there are cryptic translocations involving the IGH locus, we used dual-color fluorescence in situ hybridization (FISH) of 5' and 3' IGH genomic clones containing the variable sequences, or the J(H) and the 5' constant regions, respectively. We examined cells from 51 patients with B-cell NHL who had a normal karyotype (3 patients), clonal abnormalities not involving 14q32 (35 patients), or alterations of 14q32 other than recurring translocations, i.e., add(14)(q32) (13 patients). FISH detected 17 IGH translocations in 16 of 51 (31%) cases. Of the 13 cases with add(14)(q32), FISH identified the partner chromosome in 9 cases (69%; 3q27, 6 cases; 2p13, 19p13.3, and 18q21.3, 1 case each). Six of thirty-eight (16%) patients without visible alterations of 14q32 and 2 of 13 (15%) patients with an abnormality of one chromosome 14 had masked (5 patients) or cryptic IGH translocations (3 patients), involving 3q27 (3 patients), 5p15.3 (2 patients), 19p13.3 (3 patients), or 14q32 (1 patient; 1 patient had two rearrangements). We identified two novel, recurring, cryptic translocations: t(5;14)(p15.3;q32) (2 patients) and t(14;19)(q32;p13.3) (3 patients). In summary, FISH permitted the detection of cryptic or masked IGH rearrangements in approximately 20% of lymphoma cases without visible rearrangements of 14q32 analyzed retrospectively.     

Evolutionary sequence of cytogenetic aberrations during the oncogenesis of plasma cell disorders. Direct evidence at single cell level

Bone marrow specimens from 185 patients with plasma cell disorders (PCD) were investigated by fluorescence in situ hybridization (FISH) in order to determine the temporal sequence of cytogenetic aberrations. In 25 cases combined FISH analysis has also been performed at single cell level. Clonal evolution was observed in 16% of cases. The Δ13 was preceded by t(4;14)(p16;q32) and t(14;16)(q32;q23) translocations. Deletion of p53 gene was a secondary aberration compared to Δ13 and t(11;14)(q13;q32) translocation. In 22% of all cases with recurrent IGH translocation, this aberration was presented only in a subset of purified plasma cells questioning its initiating role.     

The t(8;9)(p22;p24) translocation in atypical chronic myeloid leukaemia yields a new PCM1-JAK2 fusion gene

Several tyrosine kinase genes are involved in chromosomal translocations in chronic myeloproliferative disorders, but there are still uncharacterized translocations in some cases. We report two such cases corresponding to atypical chronic myeloid leukaemia with a t(8;9)(p22;p24) translocation. By fluorescence in situ hybridisation (FISH) on the corresponding metaphases with a bacterial artificial chromosome probe encompassing the janus kinase 2 (JAK2) gene at 9p24, we observed a split for both patients, suggesting that this gene was rearranged. The locus at 8p22 contains different candidate genes including the pericentriolar material 1 gene (PCM1), already implicated in reciprocal translocations. The rearrangement of the PCM1 gene was demonstrated by FISH, for both patients. By RT-PCR, we confirmed the fusion of 3' part of JAK2 with the 5' part of PCM1. Sequence analysis of the chimeric PCM1-JAK2 mRNA suggests that the putative protein displays the coiled-coil domains of PCM1 and the tyrosine kinase domain of JAK2. This new translocation identifies JAK2 as a possible therapeutic target for compounds with anti-tyrosine kinase activity.     

Identification of MLL partner genes in 27 patients with acute leukemia from a single cytogenetic laboratory

Chromosomal rearrangements involving the MLL gene have been associated with many different types of hematological malignancies. Fluorescent in situ hybridization with a panel of probes coupled with long distance inverse-PCR was used to identify chromosomal rearrangements involving the MLL gene. Between 1995 and 2010, 27 patients with an acute leukemia were found to have a fusion gene involving MLL. All seven ALL patients with B cell acute lymphoblastic leukemia were characterized by the MLL/AFF1 fusion gene resulting from a translocation (5 patients) or an insertion (2 patients). In the 19 AML patients with acute myeloblastic leukemia, 31.6% of all characterized MLL fusion genes were MLL/MLLT3, 21.1% MLL/ELL, 10.5% MLL/MLLT6 and 10.5% MLL/EPS15. Two patients had rare or undescribed fusion genes, MLL/KIAA0284 and MLL/FLNA. Seven patients (26%) had a complex chromosomal rearrangement (three-way translocations, insertions, deletions) involving the MLL gene. Splicing fusion genes were found in three patients, leading to a MLL/EPS15 fusion in two and a MLL/ELL fusion in a third patient. This study showed that fusion involving the MLL gene can be generated through various chromosomal rearrangements such as translocations, insertions and deletions, some being complex or cryptic. A systematic approach should be used in all cases of acute leukemia starting with FISH analyses using a commercially available MLL split signal probe. Then, the analysis has to be completed, if necessary, by further molecular cytogenetic and genomic PCR methods.     

急性淋巴细胞白血病常见融合基因检测的研究

 【摘要】　目的　探讨联合应用多重巢式反转录聚合酶链反应（RT-PCR）技术和染色体核型分析对急性淋巴细胞白血病（ALL）常见融合基因的表达和克隆性染色体异常的检出情况。方法　采用多重巢式RT-PCR技术对189例ALL患者进行检测,同时进行染色体R或G显带。结果　189例ALL患者中69例（36.5 %）检出10种融合基因（E2A-PBX1、TEL-AML1、bcr-abl、MLL-AF4、MLL-AF6、MLL-AF9、MLL-AF10、MLL-ELL、SIL-TAL1、TLS-ERG）,染色体R或G显带可供分析的152例中,86例（56.6 %）检出染色体结构和数目异常;二者联合可使ALL克隆性染色体异常检出率增至69.3%（131例）。90例成年ALL患者中33例（36.7 %）检测阳性,其中bcr-abl 22例,未见TEL-AML1,99例儿童ALL患者中阳性36例（36.4 %）,其中TEL-AML1 24例,bcr-abl 2例。成年人组与儿童组bcr-abl 、TEL-AML1的表达率差异有统计学意义（均P＜0.01）。MLL相关融合基因、E2A-PBX1、SIL-TAL1、TLS-ERG等表达率差异无统计学意义（均P＞0.05）。66例正常核型的ALL患者检测出有bcr-abl 、TEL-AML1融合基因的存在。结论 成年人和儿童ALL融合基因表达各有侧重,多重巢式RT-PCR可用于初诊时染色体畸变的筛选,可在核型正常的ALL患者中检出隐匿的染色体易位,提供与预后相关的重要信息。     

Chromosome Imbalances and Alterations in the p53 Gene inUterine Myomas from the Same Family Members: FamilialLeiomyomatosis in Turkey

Uterine leiomyomas (UL) are extremely common neoplasms in women of reproductive age, and are associatedwith a variety of characteristic choromosomal aberrations (CAs). The p53 gene has been reported to play acrucial role in suppressing the growth of a variety of cancer cells. Therefore, the present study investigated theeffects of CAs and the p53 gene on ULs. We performed cytogenetic analysis by G-banding in 10 cases undergoingmyomectomy or hysterectomy. Fluorescence in situ hybridization (FISH) with a p53 gene probe was alsoused on interphase nuclei to screen for deletions. In patients, CAs were found in 23.4% of 500 cells analysed,significantly more frequent than in the control group (p<0.001). In the patients, 76% of the abnormalities werestructural aberrations (deletions, translocations and breaks), and only 24% were numerical. Deletions were themost common structural aberration observed in CAs. Among these CAs, specific changes in five loci 1q11, 1q42,2p23, 5q31 and Xp22 have been found in our patients and these changes were not reported previously in UL.The chromosome breaks were more frequent in cases, from high to low, 1, 2, 6, 9, 3, 5, 10 and 12. Chromosome22, X, 3, 17 and 18 aneuploidy was observed to be the most frequent among all numerical aberrations. Weobserved a low frequency of p53 losses (2-11%) in our cases. The increased incidence of autosomal deletions,translocations, chromatid breaks and aneuploidy, could contribute to the progression of the disease along withother chromosomal alterations.     

Five Most Common Prognostically Important FusionOncogenes are Detected in the Majority of Pakistani Pediatric Acute Lymphoblastic Leukemia Patients and are Strongly Associated with Disease Biology and Treatment Outcome

Background and Objectives: Acute lymphoblastic leukemia (ALL) is a complex genetic disease involvingmany fusion oncogenes (FO) having prognostic significance. The frequency of various FO can vary in differentethnic groups, with important implications for prognosis, drug selection and treatment outcome. Method: Westudied fusion oncogenes in 101 pediatric ALL patients using interphase FISH and RT-PCR, and their associationswith clinical features and treatment outcome. Results: Five most common fusion genes i.e. BCR-ABL t (22;9), TCF3-PBX1 (t 1; 19), ETV6-RUNX1 (t 12; 21), MLL-AF4 (t 4; 11) and SIL-TAL1 (del 1p32) were foundin 89/101 (88.1%) patients. Frequency of BCR-ABL was 44.5% (45/101). BCR-ABL positive patients had asignificantly lower survival (43.7±4.24 weeks) and higher white cell count as compared to others, except patientswith MLL-AF4. The highest relapse-free survival was documented with ETV6-RUNX1 (14.2 months) followedclosely by those cases in which no gene was detected (13.100). RFS with BCR-ABL, MLL-AF4, TCF3-PBX1and SIL-TAL1 was less than 10 months (8.0, 3.6, 5.5 and 8.1 months, respectively). Conclusions: This is the firststudy from Pakistan correlating molecular markers with disease biology and treatment outcome in pediatricALL. It revealed the highest reported frequency of BCR-ABL FO in pediatric ALL, associated with poor overallsurvival. Our data indicate an immediate need for incorporation of tyrosine kinase inhibitors in the treatmentof BCR-ABL+ pediatric ALL in this population and the development of facilities for stem cell transplantation.     

Prognostically Significant Fusion Oncogenes in Pakistani Patients with Adult Acute Lymphoblastic Leukemia and their Association with Disease Biology and Outcome

Background and objectives: Chromosomal abnormalities play an important role in genesis of acute lymphoblastic leukemia (ALL) and have prognostic implications. Five major risk stratifying fusion genes in ALL are BCR-ABL, MLL-AF4, ETV6-RUNX11, E2A-PBX1 and SIL-TAL1. This work aimed to detect common chromosomal translocations and associated fusion oncogenes in adult ALL patients and study their relationship with clinical features and treatment outcome. Methods: We studied fusion oncogenes in 104 adult ALL patients using RT-PCR and interphase-FISH at diagnosis and their association with clinical characteristics and treatment outcome. Results: Five most common fusion genes i.e. BCR-ABL (t 9; 22), TCF3-PBX1 (t 1; 19), ETV6-RUNX1 (t 12; 21), MLL-AF4 (t 4; 11) and SIL-TAL1 (Del 1p32) were found in 82/104 (79%) patients. TCF3-PBX1 fusion gene was associated with lymphadenopathy, SIL-TAL positive patients had frequent organomegaly and usually presented with a platelets count of less than 50 x109/l. Survival of patients with fusion gene ETV6-RUNX1 was better when compared to patients harboring other genes. MLL-AF4 and BCR-ABL positivity characterized a subset of adult ALL patients with aggressive clinical behaviour and a poor outcome. Conclusions: This is the first study from Pakistan which investigated the frequency of 5 fusion oncogenes in adult ALL patients, and their association with clinical features, treatment response and outcome. Frequencies of some of the oncogenes weredifferent from those reported elsewhere and they appear to be associated with distinct clinical characteristics and treatment outcome. This information will help in the prognostic stratification and risk adapted management of adult ALL patients.     

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.     

儿童急性淋巴细胞白血病TEL-AML1融合基因检测

 目的　检测儿童急性淋巴细胞白血病（ALL）中TEL-AML1融合基因的阳性率,探讨TEL-AML1融合基因的检测方法及其临床应用价值。方法　在形态学、免疫分型、细胞遗传学基础上,采用巢式反转录-聚合酶链反应（RT-PCR）和荧光原位杂交技术（FISH）检测31例ALL患儿骨髓单核细胞中TEL-AML1融合基因。结果　巢式RT-PCR技术和FISH技术均可以显著提高TEL-AML1融合基因的检出率,应用上述两种方法,31例患儿中检测出7例TEL-AML1阳性,占儿童初发ALL的22.6 %（7／31）,在B系ALL中的阳性率为25.9 %（7／27）。结论　t(12;21)形成TEL-AML1融合基因是儿童ALL最常见的染色体易位,常规染色体核型分析极难发现,需用巢式RT-PCR或FISH等分子检测方法加以证实。     

Derivative chromosome 9 deletions are a significant feature of childhood Philadelphia chromosome positive acute lymphoblastic leukaemia.

Deletions from the derivative chromosome 9, der(9), of the translocation, t(9;22)(q34;q11), at the site of the ABL/BCR fusion gene, have been demonstrated by fluorescence in situ hybridisation (FISH), in both Philadelphia chromosome (Ph)-positive chronic myeloid leukaemia (CML) and acute lymphoblastic leukaemia (ALL). In CML they occur in 10-15% of cases and appear to indicate a worse prognosis, whereas in ALL, the situation is unclear. This study presents the findings of dual fusion FISH used to detect such deletions in a series of 27 BCR/ ABL-positive childhood ALL patients. Metaphase FISH was essential for the accurate interpretation of interphase FISH signal patterns. Three cases (11%) had a single fusion signal, resulting from deletions of the der(9). Three other patients with variant translocations and one with an insertion, also had a single fusion, but with no evidence of deletions. Gain of a fusion in approximately one-third of patients indicated a second Ph, which appears to be a diagnostic marker of Ph-positive ALL. This study shows that the incidence of deletions from the der(9) in childhood ALL is at least as high as that reported for CML.