Long-distance Inverse Research Articles

Targeted Next Generation Sequencing Reveals a Third Breakpoint Cluster Region and New Partner Genes in the KMT2A Recombinome

Chromosomal rearrangements of the KMT2A gene are associated with acute leukemias and myelodysplastic syndromes. The large number of known KMT2A fusions (>100) renders a precise diagnosis a demanding task. More than 50% of all KMT2A partner genes have been analyzed at the DCAL, including the novel partner genes BCAS4, FAM13A, RANBP3, and STK4. Even though all KMT2A rearrangements are associated with high-risk acute leukemia, the outcome (poor or very poor) is influenced by the partner gene. So far, we have analyzed more than 3,200 patients positive for a KMT2A rearrangement. The breakpoints of these cases are located mainly in the major breakpoint cluster region (bcr1) and to a small extent in the recently described minor bcr (bcr2). A small number of breakpoints were also found outside of these two bcrs.Most of these patients were analyzed by long distance inverse (LDI)- or multiplex-PCR which only cover bcr1. More recently, we used targeted KMT2A-NGS with whole gene coverage in over 450 patients, which was initially applied selectively in patients negative by LDI- and multiplex-PCR and then used more widely.Within the KMT2A-NGS group, 410 patients had bcr1 breakpoints mainly between the KMT2A exons 7 and 13, while 46 patients bcr2 breakpoints mainly between exons 20 and 24. Of note, five patients had their breakpoint outside of these two bcrs: three of them within intron 2 and no functional KMT2A rearrangement; the other two within intron 35 and intron 36, fusing almost the whole KMT2A gene in frame to the respective partner genes ARHGEF12 and MLLT4. These two breakpoints may define a third and rare bcr (bcr3), although further cases are needed to support this hypothesis. Interestingly, 70 patients displayed a 3‘-KMT2A deletion, indicating that the number of terminal deletions is higher than described previously. Two patients had a 5‘-KMT2A deletion. All deletions started or ended in bcr1 and bcr2.We also observed a striking difference in the distribution of partner genes between bcr1 and bcr2. The most frequent translocation partners fused to bcr1 sites are transcription factors, while the partner genes linked to bcr2 sites generally code for cytosolic proteins. In bcr1, the 4 most frequent partner genes AFF1, MLLT3, MLLT1, and MLLT10, found in 80% of cases, all code for transcription factors that are part of the super elongation complex (SEC). These fusions therefore all lead to disruption of the hematopoietic lineage commitment.In contrast in bcr2, 3 partner genes USP2, MLLT4, and USP8 account for 85% of the cases. USP2 and USP8 are ubiquitin specific peptidases involved in cell signaling and exclusively fused to bcr2 in KMT2A. While MLLT4 is found as a partner in bcr1, bcr2 and bcr3 fusions; unlike other recurrent KMT2A partners linked to bcr1, it is not a transcription factor and it exerts oncogenic potential via dimerization like other cytosolic partners. We hypothesize that the oncogenic properties of USP2 and USP8 are dependent on dimerization like MLLT4 and that the most frequent fusions involving at different bcrs favor different oncogenic mechanisms: bcr1 transactivation and bcr2 dimerization. Further studies are needed to explain why USP2 and USP8 are exclusively associated with bcr2, and why the most frequent partner genes AFF1 and MLLT3 of the bcr1 are less frequent in bcr2.In conclusion, targeted NGS combined with bioinformatic analysis has expanded our knowledge of the KMT2A recombinome to include more fusion partners and has generated new hypotheses for future research on oncogenic mechanisms. DisclosuresNo relevant conflicts of interest to declare.

Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR.

Long interspersed nuclear elements 1 (LINE-1s) are the only family of mobile genetic elements in the human genome that can move autonomously. They do so by a process called retrotransposition wherein they transcribe to form an mRNA intermediate which is then consequently inserted into the genome by reverse transcription. Despite being silent in normal cells, LINE-1s are highly active in different epithelial tumors. De novo LINE-1 insertions can potentially drive tumorigenesis, and hence it is important to systematically study LINE-1 retrotransposition in cancer. Out of ~150 retrotransposition-competent LINE-1s present in the human genome, only a handful of LINE-1 loci, also referred to as "hot" LINE-1s, account for the majority of de novo LINE-1 insertion in different cancer types. We have developed a simple polymerase chain reaction (PCR)-based method to monitor retrotransposition activity of these hot LINE-1s. This method, based on long-distance inverse (LDI)-PCR, takes advantage of 3´ transduction, a mechanism by which a LINE-1 mobilizes its flanking non-repetitive region, which can subsequently be used to identify de novo LINE-1 3´ transduction events stemming from a particular hot LINE-1.

Inverse synthetic aperture LADAR demonstration: system structure, imaging processing, and experiment result.

A long-distance inverse synthetic aperture LADAR (ISAL) imaging experiment outdoors over 1km for cooperative targets is demonstrated, which gets a two-dimensional high-resolution image with resolution exceeding 2.5cm. The system utilizes an electro-optic in-phase and quadrature modulator to output a linear frequency-modulated continuous waveform (LFMCW) with a bandwidth of 6GHz and pulse repetition frequency (PRF) of 16.7KHz. For the problem of the coherence of the laser, the effects of the coherent processing interval (CPI) and time delay of the local oscillator (LO) on the coherence are discussed. The fiber delay line is set and the CPI is reduced to lower the requirement of the frequency stability of the laser source. The images are formed by two-dimensional Fourier transform and joint time-frequency transform methods, respectively. In this paper, we present the system structure, imaging processing, and the experiment result in detail. The experiment result validates the performance of our system for ISAL imaging.

The novel double-hit, t(8;22)(q24;q11)/MYC-IGL and t(14;15)(q32;q24)/IGH-BCL2A1, in diffuse large B-cell lymphoma

An 82-year-old woman presented with generalized lymphadenopathy and skin involvement. Lymph node biopsy revealed diffuse large B-cell lymphoma with a high proliferation index. G-banding and fluorescence in situ hybridization showed a hypertetraploid karyotype with two copies of t(8;22)(q24;q11), generating the fusion of MYC and the immunoglobulin λ chain gene (IGL), and two copies of the novel immunoglobulin heavy chain gene (IGH) translocation, t(14;15)(q32;q24). A long-distance inverse polymerase chain reaction (PCR) using nested primer combinations designed for each constant gene of IGH showed that Cγ4 was juxtaposed to the downstream sequence of the BCL2A1 (BCL2-related protein A1) gene through the Sγ4 switch region. As a result of t(14;15)(q32;q24), BCL2A1 and IGH Sγ4-Cγ4 were aligned in the same transcriptional orientation at a distance of 64 kb. Reverse transcriptase-mediated PCR showed high BCL2A1 mRNA levels in a lymphoma specimen. Since BCL2A1, mapped at 15q24.3 or 15q25.1, encodes a protein that is an anti-apoptotic member of the BCL2 protein family, we herein described the novel double-hit, t(8;22)(q24;q11)/MYC-IGL and t(14;15)(q32;q24)/IGH-BCL2A1, in which BCL2A1 is considered to play a role equivalent to that of BCL2 in the most frequent double-hit, MYC/BCL2.

Detection and screening of chromosomal rearrangements in uterine leiomyomas by long-distance inverse PCR.

Genome instability is a hallmark of many tumors and recently, next-generation sequencing methods have enabled analyses of tumor genomes at an unprecedented level. Studying rearrangement-prone chromosomal regions (putative "breakpoint hotspots") in detail, however, necessitates molecular assays that can detect de novo DNA fusions arising from these hotspots. Here we demonstrate the utility of a long-distance inverse PCR-based method for the detection and screening of de novo DNA rearrangements in uterine leiomyomas, one of the most common types of human neoplasm. This assay allows in principle any genomic region suspected of instability to be queried for DNA rearrangements originating there. No prior knowledge of the identity of the fusion partner chromosome is needed. We used this method to screen uterine leiomyomas for rearrangements at genomic locations known to be rearrangement-prone in this tumor type: upstream HMGA2 and within RAD51B. We identified a novel DNA rearrangement upstream of HMGA2 that had gone undetected in an earlier whole-genome sequencing study. In more than 30 additional uterine leiomyoma samples, not analyzed by whole-genome sequencing previously, no rearrangements were observed within the 1,107 bp and 1,996 bp assayed in the RAD51B and HMGA2 rearrangement hotspots. Our findings show that long-distance inverse PCR is a robust, sensitive, and cost-effective method for the detection and screening of DNA rearrangements from solid tumors that should be useful for many diagnostic applications.

Complex MLLrearrangement in non-infiltrated bone marrow in an infant with stage II precursor B-lymphoblastic lymphoma

Precursor B-lymphoblastic lymphoma cells are indistinguishable by morphology, and immune phenotype from lymphoblasts in acute leukemia which in infancy is associated with MLL rearrangements and a poor prognosis. The role of MLL gene deregulation in rare cases of isolated lymphoblastic lymphoma in infants is obscure. We report the case of a 10-month-old child who presented with a cutaneous nodule on the left foot. Histological diagnosis was precursor B-lymphoblastic lymphoma. The young age of the patient motivated us to investigate the presence of an MLL rearrangement. Cytogenetic analysis was performed by fluorescence in situ hybridization (FISH), and the genomic fusion partner of MLL was identified by long-distance inverse (LDI-)PCR and confirmed by direct PCR. Fluorescence in situ hybridization screening of paraffin-embedded formalin-fixed tissue indeed revealed the presence of an MLL rearrangement. The genomic fusion partner was identified as AF10 by DNA sequencing of the MLL breakpoint region. The MLL-AF10 fusion gene was further detected in cytologically normal pretreated bone marrow. Treatment was started with standard four-drug induction chemotherapy. Because of the unfavorable outcome associated with MLL rearrangements in infant leukemia, we intensified postremission treatment according to the Interfant-06 study protocol. The child is in continuous first remission 36 months after diagnosis. This is the first report of submicroscopic bone marrow involvement in MLL-rearranged isolated cutaneous B-cell precursor lymphoma in an infant. To prospectively address the role of MLL rearrangements in extramedullary B-lymphoblastic malignancies in infants, we suggest to assess both tumors and non-infiltrated bone marrow for the presence of this genetic abnormality.

Molecular methods for genomic analyses of variantPML-RARAor otherRARA-related chromosomal translocations in acute promyelocytic leukemia

TO THE EDITOR: We read an interesting paper by Palta et al. in a recent issue of the Korean Journal of Hematology titled, variant of acute promyelocytic leukemia with tuberculosis: a case report and review of literature [1]. We would like to add some comments to their article and suggest additional molecular methods to confirm variant translocations in acute promyelocytic leukemia (APL). Apart from its characteristic morphology, APL is strongly correlated with presence of the PML-RARA fusion gene due to a t(15;17) translocation. Patients displaying cryptic PML-RARA gene rearrangements or other translocations involving RARA are very rare. Since RARA generates chimeric fusion genes with various partners such as ZBTB16 at 11q23, NUMA1 at 11q13, NPM1 at 5q35, FIP1L1 at 4q12, and STAT5b at 17q11.2 (Fig. 1), confirmatory molecular methods to detect gene rearrangements are necessary when unique or unusual chromosomal translocations are found in APL cases. Palta et al. reported a case of APL accompanied by tuberculosis where cytogenetic study showed a variant chromosomal translocation, t(11;17)(q23;q21). First, although they describe this case as APL with t(11;17)(q23;q21) through bone marrow (BM), immunophenotyping, and cytogenetic studies, we noted an absence of results based on molecular methods. To demonstrate the existence of the ZBTB16-RARA fusion gene, a single specific reverse transcriptase-polymerase chain reaction (RT-PCR) with a specific primer to detect the gene rearrangement or multiplex RT-PCR (e.g. HemaVision) to detect ZBTB16-RARA could have provided an accurate molecular diagnostic result. Second, the authors' reference to a paper by Kang et al. was puzzling despite the fact that it was cited as a similar case with chromosomal translocations at a similar location, in cases of AML with chromosomal translocation t(11;17) [2]. In the first case, cytogenetic analysis from BM aspirate showed t(11;17)(q23;q21) in 18 out of 20 cells while the MLL probe in fluorescence in situ hybridization (FISH) showed split-out signals in 98.5% of interphase cells. The second case also showed t(11;17)(q23;q25) in the chromosome study while the FISH assay showed split-out signals in 79% of interphase cells. However, normal fluorescence patterns were found in 200 cells in additional FISH assays when a dual-color single-fusion PML-RARA probe was used for both cases, which led to the conclusion that the MLL gene was involved in the 11q23 breakpoint and RARA was not involved in the 17q breakpoint. Hence, the authors' citation of this study to explain the ZBTB16-RARA fusion gene appears inadequate, and a molecular study could unambiguously identify the involvement of ZBTB16 at 11q23 in their case. Fig. 1 Various RARA partner genes in acute promyelocytic leukemias. We suggest the authors conduct RT-PCR analysis of the ZBTB16-RARA fusion gene if any remnant RNA or cDNA samples from their APL patient are available. However, if only genomic DNA is available, analyzing the genomic breakpoints by multiplex long distance-polymerase chain reaction (LD-PCR) would be helpful. LD-PCR or long distance inverse (LDI)-PCR can identify known or unknown partner genes, monitor minimal residual disease (MRD), and identify multi-way chromosomal translocations such as three-way or four-way translocations [3]. We have recently used LD-PCR to confirm APL cases showing unusual karyotypes or discrepant results between conventional cytogenetics and molecular studies. More precisely, we identified a novel PML-ADAMTS17-RARA rearrangement and confirmed the genomic fusion breakpoints of cryptic PML-RARA rearrangement in 2 APL patients [3-5]. In conclusion, detection of leukemia-associated fusion genes is important due to their direct relevance to diagnosis, MRD assessment, and treatment response. Since APL patients with ZBTB16-RARA are resistant to all-trans-retinoic acid (ATRA), molecular methods with higher resolution than chromosome studies must be conducted to detect fusion genes and facilitate selection of the most appropriate treatment. We believe that molecular techniques such as FISH, RT-PCR, and LD-PCR should be used in addition to morphology and cytogenetic studies in APL diagnosis and evaluation so that atypical PML-RARA or RARA variant gene rearrangements are not missed.

Molecular analysis of the t(2;8)/MYC–IGK translocation in high‐grade lymphoma/leukemia by long‐distance inverse PCR

Burkitt lymphoma and a subset of diffuse large B-cell lymphomas are characterized by chromosomal alterations affecting the MYC oncogene on 8q24. In most cases MYC is found juxtaposed to the immunoglobulin heavy chain (IGH) gene locus. Translocations to the immunoglobulin kappa (IGK) gene locus on 2p11 are observed in around 5-10% of cases. Little data exist on the molecular mechanisms leading to this aberration. The chromosomal breakpoints on chromosome 8 have been found dispersed over a large area 3' of MYC. In order to obtain a better understanding of this chromosomal translocation we developed a long-distance inverse (LDI) PCR method for the identification of chromosomal translocations affecting the IGK locus. We investigated a number of cytogenetically mostly uncharacterized high-grade lymphoma samples and identified a MYC-IGK juxtaposition in seven patients and three t(2;8)-positive cell lines. The chromosomal breakpoints were molecularly characterized and analyzed. The linear distance of the breakpoints on chromosome 8 to MYC ranged from some 100 bp to more than 0.5 MB. The reciprocal translocated allele could be characterized in the majority of cases. This study represents the largest series of t(2;8)-positive cases analyzed so far. The LDI PCR method developed here should also be useful for the analysis of chromosomal translocations affecting the IGK locus in general.

Molecular Analysis of the t(2;8)/MYC-IGK Translocation in High-Grade Lymphoma/Leukemia by Long-Distance Inverse PCR

Abstract 4407 Background:Burkitt lymphoma and a subset of diffuse large B-cell lymphomas are characterized by chromosomal alterations affecting the MYC oncogene on 8q24. In most cases MYC is found juxtaposed to the immunoglobulin heavy chain (IGH) gene locus. Translocations to the immunoglobulin kappa (IGK) gene locus on 2p11 are observed in around 10% of cases. Little data exist on the molecular mechanisms leading to this aberration. The chromosomal breakpoints on chromosome 8 have been found dispersed over a large area 3' of MYC. Currently, molecular cytogenetics (FISH) and cytogenetics are the methods of choice to detect the t(2;8) translocation and until now there exists no PCR method to reliably detect it. Objectives:In order to obtain a better understanding of this chromosomal translocation we developed a long-distance inverse (LDI) PCR method for the identification of chromosomal translocations affecting the IGK locus. The LDI PCR method takes advantage of the fact that the chromosomal breaks occur on chromosome 2 in the vicinity of the IGK joining segments. Using this method we investigated a number of cytogenetically mostly uncharacterized high-grade lymphoma samples. Results:A MYC-IGK juxtaposition was identified in 7 patients and three t(2;8)-positive cell lines. The chromosomal breakpoints were molecularly characterized and analyzed. The linear distance of the breakpoints on chromosome 8 to MYC ranged from some 100 bp to more than 0.5 MB. The breakpoints appeared to be clustered in distinctive regions, however, the number is still to small to draw definitive conclusions. The reciprocal translocated allele could be characterized in the majority of cases and putative break mechanisms are proposed. No larger sequence homologies were detected at the break sites. A minority of breaks were located near putative recombination signal sequences (RSS). Conclusions:This study represents the largest series of t(2;8)-positive cases analyzed so far and the LDI PCR developed therein is the first universally applicable PCR-based method to detect this aberration. This LDI PCR should furthermore in general be useful for the molecular analysis of chromosomal translocations affecting the IGK locus. These aberrations have been detected in various lymphoma entities but are currently largely unexplored. Disclosures:No relevant conflicts of interest to declare.

Abstract 4699: Oncogenic fusion genes resulting from 7q34 deletions constitute a novel mechanism of MAPK pathway activation in pilocytic astrocytoma

Abstract Pilocytic astrocytoma (PA) is the most common brain tumor in children. Underlying genetic driver aberrations can currently be determined for 75-80% of cases. In particular, we and others have recently shown that tandem duplication at 7q34, resulting in BRAF fusion genes and constitutive activation of the MAPK signaling pathway, is a hallmark genetic lesion in PA development. Alternative mechanisms of MAPK activation include BRAF and KRAS point mutations, RAF1 fusions, and Neurofibromatosis-associated NF1 mutations. In order to examine more precisely the spectrum of alterations in PA, we screened 79 tumor samples for RAF fusion genes and mutations in KRAS, NRAS, PTPN11, BRAF and RAF1. We used multiplex and long-distance inverse (LDI) PCR to identify BRAF and RAF1 fusion genes and direct sequencing for detailed breakpoint mapping. Strikingly, LDI-PCR revealed a novel BRAF fusion gene with an uncharacterized gene, FAM131B, as a partner. Array-based comparative genomic hybridization (aCGH), revealed an interstitial deletion of ∼2.5 Mb as a novel mechanism forming the FAM131B-BRAF fusion. As with the more common duplication, this deletion removes the N-terminal auto-inhibitory domain of BRAF kinase, resulting in constitutive kinase activity. Functional characterization of the novel fusion gene demonstrated constitutive MEK phosphorylation potential and transforming activity in NIH 3T3 cells. The same fusion gene was also identified in one PA in an additional series from Cambridge, UK (n=7, with no previously identified alteration). Furthermore, we have detected a larger deletion at 7q in one additional case from our series, in which the alternative fusion partner is currently being identified. Overall, gene fusions targeting RAF kinases were identified in 68% (54/79) of PA. Detailed analysis of genomic DNA mapped 96% (52/54) of the breakpoints to the same breakpoint cluster region in intron 8 of the BRAF gene. Moreover, we identified the first non-intronic breakpoint in exon 8 of BRAF and two novel SRGAP3-RAF1 fusion variants. BRAF, KRAS or NF1 mutations were observed as alternative mechanisms of MAPK activation in 9 tumors in which no RAF duplication was detected, as well as in two cases in our series which concomitantly harbored two or even three hits in the MAPK pathway. In summary, we have identified a novel, recurrent BRAF fusion gene resulting in MAPK pathway activation in PA caused by a genomic deletion rather than amplification at 7q34, suggesting the possibility of further undiscovered fusion variants targeting RAF genes in this and other tumor types. Being a hallmark of PA tumorigenesis, these RAF fusion genes are expected to have clinical utility as both a specific marker for PA and a tumor-specific therapeutic target, which offers promise for applying novel treatment strategies in the near future. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4699. doi:10.1158/1538-7445.AM2011-4699

Therapy-related acute myeloid leukemia with t(2;11)(q37;q23) after treatment for osteosarcoma

The survival rate for children with osteosarcoma (OS) has improved dramatically with the introduction of multiagent chemotherapy. As the number of pediatric cancer survivors increases, there is a concern about the development of secondary malignant neoplasms. Secondary acute myeloid leukemia (AML) has been rarely reported after treatment for OS. We describe a 14-year-old boy with OS of the left ileum who developed secondary AML 15 months after completion of treatment. Cytogenetic analysis of the leukemic cells demonstrated deletion 11q23, whereas fluorescence in situ hybridization revealed rearrangement of the MLL gene. Only the addition of the long-distance inverse polymerase chain reaction technique identified the SEPT2 as the MLL fusion partner resulting in t(2;11)(q37;q23) that was reported in a very few secondary AML cases. Because of the cryptic nature of MLL translocations that cannot be detected by conventional cytogenetics or may misinterpreted as deletion, additional molecular techniques are required to identify the precise translocation partner. Because long-distance inverse polymerase chain reaction is not available in most molecular laboratories, the true incidence of t(2;11)(q37;q23) and the involvement of SEPT2 as the MLL translocation partner could be more prevalent in secondary AML.

Abstract 1178: Identification of a novel BRAF fusion partner in pilocytic astrocytoma

Abstract Pilocytic astrocytoma (PA) constitutes the most common brain tumor in children. Recently, we and others have demonstrated that tandem duplications at chromosome 7q34 targeting the BRAF locus define a hallmark genetic lesion in PA development, resulting in BRAF fusion genes and constitutive activation of the MAPK signaling pathway. NF1, KRAS and activating BRAF mutations as well as RAF1 tandem duplications were identified as alternative mechanisms mostly in tumors without BRAF duplication. To identify BRAF and RAF1 fusion genes and to discover novel fusion partners, we screened a total of 62 PA by using multiplex and long-distance inverse (LDI) PCR. Direct genomic sequencing was performed for detailed breakpoint mapping and to detect activating mutations. All translocations identified by PCR-based methods were validated by fluorescence in situ hybridization. Overall, gene fusions targeting RAF kinases occurred in 71% (44/62) of PA. Sequencing of cDNA of the retrieved fusion transcripts confirmed all previously reported variants of the KIAA1549-BRAF fusion gene. Further detailed analysis of genomic DNA mapped 95% (42/44) of the breakpoints to the same breakpoint cluster region in intron 8 of the BRAF gene. Moreover, we identified the first non-intronic breakpoint in exon 8 of BRAF and detected one fusion gene product which additionally displayed an internal rearrangement of the remaining BRAF fragment. Fusion of SRGAP3 to RAF1 in two cases and activating mutations of BRAF, KRAS or NF1 in eleven cases were observed as alternative mechanisms of MAPK activation in tumors in which no BRAF or RAF1 duplication was detected. Interestingly, LDI-PCR analysis revealed fusion of BRAF to the first intron of the yet uncharacterized gene, FAM131B. Notably, all fusion events replaced the N-terminal auto-inhibitory domain of the respective RAF kinase with segments of the complementary fusion partner and retained the complete, in-frame coding sequence for the kinase domain enabling constitutive activation of the RAF kinase protein. In summary, we identified fusion events targeting RAF kinase genes to be the predominant cause for aberrant MAPK activation in PA, accompanied by activating mutations as a complementary mechanism. This study significantly extends our knowledge of the high frequency and striking similarity of rearrangements resulting in KIAA1549-BRAF or SRGAP3-RAF1 fusion genes by discovering hitherto unreported fusion variants. Most importantly, we identified a novel fusion oncogene between BRAF and the so far uncharacterized gene FAM131B, representing the first report of a BRAF fusion partner in PA other than KIAA1549. Taken together, our results strengthen the role of BRAF fusion genes as a hallmark of PA tumorigenesis and highlight the potential of RAF kinase fusion products as a specific marker for PA and a promising tumor-specific therapeutic target which may open the avenue for developing novel treatment strategies in the future. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1178.

NRIP3: a novel translocation partner of MLL detected in a pediatric acute myeloid leukemia with complex chromosome 11 rearrangements

NRIP3: a novel translocation partner of MLL detected in a pediatric acute myeloid leukemia with complex chromosome 11 rearrangements

Micro-RNA Gene Deregulation by Chromosome Translocations with Fragile Genomic Regions in B-Cell Lymphoma Cells

Micro-RNA (miR) genes posttranscriptionally modulate target gene expression via imperfect 3′-UTR matching sequences and play key roles in development, homeostasis and cancer. Little is known how miR genes are themselves regulated, or deregulated in cancer. Chief paradigm for neoplastic miR deregulation concerns miR-17/92 cluster members subject to genomic amplification in B-cell lymphoma. While the repeated occurrence of oncogenic miR genes at or near chromosomal breakpoints in cancer links chromosome fragility to oncogenic miR deregulation, direct evidence of a causal connection remains tenuous. We found that t(3;7)(q27;q32) in a B-cell lymphoma cell line joins 5′-BCL6 to a noncoding region of chromosome 7 inside a common chromosomal fragile site (FRA7H). In these cells hybrid mRNA was absent, unlike canonical BCL6 translocations which involve promoter exchange yielding hybrid mRNA. Affected cells instead showed downregulation of miR-29b-1, the only gene located within FRA7H - a recurrent transcriptional feature of B-cell lymphoma subsets. In another BCL6 translocation, t(3;13)(q27;q31)t(13;12)(q31;p11), which 5′-RACE also showed to be non-fusogenic, long distance inverse (LDI)-PCR revealed junction of 5′-BCL6 to chromosome 13 sequences inside the miR-17/92 host gene MIRH1 (alias c13orf25). FISH using a sensitive tyramide amplification protocol with c13orf25 clones confirmed the presence of a cryptic BCL6-MIRH1 rearrangement. Surprisingly, reverse transcriptase quantitative (q) PCR assay revealed weak MIRH1 expression using 3′-primers. In contrast, repeating the assay using more central primers covering the miR-17/92 coding region showed massive upregulation. 3′-RACE confirmed a novel high level MIRH1 transcript truncated by 3.1 kbp. Quantitative genomic PCR and FISH excluded miR-17/92 genomic copy number alteration, while LDI-PCR analysis showed that formation of truncated MIRH1 involved multiple DNA cuts at 3q27 (x1), 12p11 (x1), and 13q31 (x5) – the last including a complex excision/inversion/insertion rearrangement. Stress induced DNA duplex destabilization (SIDD) analysis revealed that 6 of 7 breaks precisely coincided with fragility peaks. Taken together, these data suggest a novel role for BCL6 translocations in the deregulation of miR genes near sites of chromosome or DNA instability. BCL6 has been shown to suppress p53 in germinal center B-cells thus protecting B-cells from apoptosis induced by DNA damage, offering a possible explanation for chromosome rearrangements associated with genomic fragility therein. Chromosomal MIRH1 dysregulation is not limited to BCL6 expressing lymphomas, however: cytogenetic investigations performed on diverse leukemia-lymphoma cell lines, including those derived from multiple myeloma and plasma cell leukemia, showed 11/50 with cytogenetic rearrangements at or near MIRH1. In sister cell lines sequentially established at diagnosis and relapse of multiple myeloma, only the latter showed miR-17/92 chromosomal rearrangement and upregulation. Interestingly miR overexpression was limited to miR-92, while miR-17/18 were barely expressed. FISH analysis and qPCR showed that discrepant expression was associated with rearrangement upstream of MIRH1. In brief, our data show that like other cancer genes, oncogenic miRs are subject to dysregulation mediated by structural chromosome rearrangements.

Usefulness of long‐distance inverse polymerase chain reaction for molecular detection of 14q32 translocation in a clinical setting

All mature B‐cell leukaemias and lymphomas have a clonal Ig gene recombination, and half of them have a reciprocal chromosomal translocation involving the 14q32 locus. The 14q32 translocation partners are variable, such as BCL‐2, BCL‐1 and BCL‐6, thus accounting for the difficulty in molecular detection by the current genomic polymerase chain reaction (PCR) method. To identify B‐cell clones efficiently with an Ig gene rearrangement and reciprocal inter‐chromosomal translocation, we verified the usefulness, in a practical laboratory setting, of our modified long‐distance inverse (LDI) PCR method for detecting IgH gene rearrangements involving inter‐ and intra‐chromosomal segments. The total run time of this LDI PCR method was 5.5 h. Using 24 samples of mature B‐cell leukaemias and lymphomas, the modified LDI PCR gave clonally rearranged amplicons in 83 % (20/24) of cases. Direct sequencing results of the amplicons revealed inter‐chromosomal translocations in 5 cases (25 %) and intra‐chromosomal rearrangements in the remaining 15 cases (75 %). The partners of the inter‐chromosomal translocation consisted of the 11q13.3 segment containing a partial BCL1 sequence in 3 cases; 18q21.3 segment containing a partial BCL2 sequence in one case; and a segment of 7q11.2 in one case. We present an LDI PCR‐based methodology for the efficient identification of 14q32 translocations, with modifications to reduce the total run time to within one day.

Five members of the CEBP transcription factor family are targeted by recurrent IGH translocations in B-cell precursor acute lymphoblastic leukemia (BCP-ALL)

AbstractCCAAT enhancer-binding protein (CEBP) transcription factors play pivotal roles in proliferation and differentiation, including suppression of myeloid leukemogenesis. Mutations of CEBPA are found in a subset of acute myeloid leukemia (AML) and in some cases of familial AML. Here, using cytogenetics, fluorescence in situ hybridization (FISH), and molecular cloning, we show that 5 CEBP gene family members are targeted by recurrent IGH chromosomal translocations in BCP-ALL. Ten patients with t(8;14)(q11;q32) involved CEBPD on chromosome 8, and 9 patients with t(14;19)(q32;q13) involved CEBPA, while a further patient involved CEBPG, located 71 kb telomeric of CEBPA in chromosome band 19q13; 4 patients with inv(14)(q11q32)/t(14;14)(q11;q32) involved CEBPE and 3 patients with t(14;20)(q32;q13) involved CEBPB. In 16 patients the translocation breakpoints were cloned using long-distance inverse–polymerase chain reaction (LDI-PCR). With the exception of CEBPD breakpoints, which were scattered within a 43-kb region centromeric of CEBPD, translocation breakpoints were clustered immediately 5′ or 3′ of the involved CEBP gene. Except in 1 patient with t(14;14)(q11;q32), the involved CEBP genes retained germ-line sequences. Quantitative reverse transcription (RT)–PCR showed overexpression of the translocated CEBP gene. Our findings implicate the CEBP gene family as novel oncogenes in BCP-ALL, and suggest opposing functions of CEBP dysregulation in myeloid and lymphoid leukemogenesis.

A case of acute myelogenous leukemia with MLL–AF10 fusion caused by insertion of 5′ MLL into 10p12, with concurrent 3′ MLL deletion

Structural abnormalities involving the mixed-lineage leukemia ( MLL) gene on 11q23 have been associated with hematological malignancies. The rearrangement of MLL occurs during translocations and insertions involving a variety of genes on the partner chromosome. We report a rare case of acute myelogenous leukemia (AML-M2) with 11q23 abnormalities. Fluorescence in situ hybridization (FISH) using a commercial dual-color MLL probe detected an atypical signal pattern: one fusion signal, two green signals smaller than those usually detected, and no orange signals. Spectral karyotyping (SKY) analysis indicated that one green signal was detected on the short arm of derivative chromosome 10, and the other green signal on the long arm of a derivative chromosome 11, on which no orange signal was detected. A long-distance inverse polymerase chain reaction (LDI-PCR) identified the fusion partner gene, in which intron 6 of MLL was fused with intron 8 of AF10 on 10p12 in the 5′ to 3′ direction. Our observations indicated that the MLL– AF10 fusion gene resulted from the insertion of part of the region that included the 5′ MLL insertion into 10p12; this was concurrent with the deletion of 3′ MLL.