Recurrent Translocation Partner Research Articles

Chromothripsis Orchestrates Leukemic Transformation in Blast Phase MPN through Targetable Amplification of DYRK1A

Progression of myeloproliferative neoplasms to blast phase (BPMPN) is associated with lack of response to conventional therapies and dire clinical outcomes. Consequently, there is a major unmet need to develop new therapies for BPMPN. Chromothripsis, the process of catastrophic shattering and haphazard repair of chromosomes, is a key contributor to somatic variation in cancer, but this phenomenon has not yet been described in BPMPN. More broadly, whether chromothripsis might result in actionable molecular events that are amenable to targeting remains an open question. To characterise the contribution of structural variants to BPMPN, we first performed integrated copy number and mutation profiling in 64 BPMPN patients by SNP karyotyping and targeted next generation sequencing. We observed a recurrent pattern of chromothripsis that involved chromosome 21, which together with other structural variants led to amplification of a common region of chromosome 21 (‘chr21amp‘) in ~25% of patients (GISTIC q-val<0.01, Fig 1A). Chr21amp was associated with TP53 mutations and a higher number of copy number alterations. Patients with chr21amp had a particularly aggressive and treatment-resistant phenotype, with 0% surviving 12 months compared to 46% in the non-chr21amp pts ( p=0.0007), retaining significance in multivariate analysis including after correction for TP53 mutation status. Whole genome sequencing confirmed that the chromosomal rearrangements resulting in chr21amp occurred by different mechanisms, ranging from simple amplification to highly complex chromothriptic events involving multiple chromosomes. There were no recurrent translocation partners or mutations. The minimally amplified region (MAR) spanned 2.7Mb and contained 24 genes, with a median copy number of 3.5 (range 2.7-8.3) Single-cell transcriptomics combined with allelic resolution genotyping revealed that chr21amp was present in the dominant subclone and occurred subsequent to JAK2V617F and mut TP53 acquisition. Chr21amp was detectable in phenotypic HSCs and throughout early stages of hematopoiesis, but not in mature erythroid cells, consistent with a differentiation block. Of the 24 genes in the minimally amplified region, only one gene, DYRK1A, a serine threonine kinase linked to cell proliferation and survival, was both differentially expressed (single-cell and bulk RNAseq) and differentially accessible (ATACseq). To explore the functional role of DYRK1A in BPMPN we performed shRNA and CRISPR-mediated DYRK1A-knockdown and knockout (KO) in BPMPN cell lines (HEL and SET-2), which led to impaired cell proliferation. The DYRK1A inhibitors EHT1610 and GNF2133 also led to dose-dependent growth inhibition. DYRK1A-KO BPMPN HEL or SET2 cell clones showed a reduced ability to propagate leukemia in vivo with a significant survival advantage vs. wild type control mice. BPMPN chr21amp+ primary patient CD34+ cells were highly sensitive toDYRK1A inhibitors, while healthy control CD34+ cells were unaffected Prior studies have shown that DYRK1A activates the DREAM complex, a transcriptional repressor of DNA-repair pathways. In chr21amp patient cells, the DREAM DNA repair gene signature was significantly downregulated (NES -1.74, q-val <0.001), while conversely in CRISPR DYRK1A KO SET2 cells the transcriptional DNA repair signature was upregulated (NES 1.76, q-val <0.001). In functional assays, CRISPR DYRK1A KO was protective against DNA damage, with a reduction in γ-H2AX foci after etoposide treatment or irradiation ( p<0.01 for both). A second mechanism of leukemogenesis emerged from geneset enrichment analyses, which suggested enhanced JAK-STAT signaling in chr21amp BPMPN cells and downregulation in the CRISPR DYRK1A KO context. We validated this by showing that DYRK1A overexpression activates and potentiates STAT5B transcriptional activity in a luciferase reporter assay. Finally, we noted that the STAT target BCL2 was selectively upregulated in chr21amp cells. BCL2 inhibition showed strong synergy with DYRK1A inhibitors for induction of BPMPN cell apoptosis (Bliss synergy score 15). Collectively, these findings define the chr21amp event as a novel prognostic biomarker in BPMPN. We pinpoint DYRK1A amplification as a central driver of genomic instability and exacerbated JAK-STAT signalling, for the first time linking chromothripsis to a specific druggable target ( Fig 1B).

Cytogenetic analysis of 130 renal oncocytomas identify three distinct and mutually exclusive diagnostic classes of chromosome aberrations.

The cytogenetic alterations in renal oncocytoma (RO) are poorly understood. We analyzed 130 consecutive RO for karyotypic alterations. Clonal chromosome abnormalities were identified in 63 (49%) cases, which could be categorized into three classes of mutually exclusive cytogenetic categories. Class 1 (N = 20) RO had diploid karyotypes with characteristic 11q13 rearrangement in balanced translocations with 10 or more different chromosome partners in all cases. We identified recurrent translocation partners at 5q35, 6p21, 9p24, 11p13-14, and 11q23, and confirmed that CCND1 gene rearrangement at 11q13 utilizing fluorescence in situ hybridization (FISH). Class 2 RO (N = 25) exhibited hypodiploid karyotypes with loss of chromosome 1 and/or losses of Y in males and X in females in all cases. The class 3 tumors comprising of 18 cases showed diverse types of abnormalities with the involvement of two or more chromosomes exclusive of abnormalities seen in classes 1 and 2 tumors. Furthermore, karyotypically uninformative cases were subjected to FISH analysis to identify classes 1 and 2 abnormalities. In this group, we found similar frequencies of CCND1 rearrangement, loss of chromosome 1 or Y as with karyotypically abnormal cases. We validated our results against 91 tumors from the Mitelman database. Correlation of clinical data with all the three classes of ROs showed no clear evidence of overall patient survival. Our findings support the hypothesis that RO exhibit three principal cytogenetic categories, which may have different roles in initiation and/or progression. These cytogenetic markers provide a key tool in the diagnostic evaluation of RO.

Abstract 3415: Cytogenetics of renal oncocytomas identify three distinct and mutually exclusive diagnostic classes of chromosome aberrations

Abstract Christopher B. Anderson1, Michael Lipsky1, Subhadra V. Nandula2,3, Christopher E. Freeman2, Thomas Matthews2, Catlin Walsh2, Gen Li1, Matthias Szabolcs2, Mahesh M. Mansukhani 2, James M. McKiernan1, Vundavalli V. Murty 2 1Departments of Urology, 2Pathology and Cell Biology, Columbia University Medical Center, New York, New York; 3Cancer Genetics Inc, Rutherford, New Jersey The cytogenetic alterations in renal oncocytoma (RO) are poorly understood. We analyzed 130 consecutive RO for karyotypic alterations. Clonal chromosome abnormalities were identified in 63 (48.5%) cases, which could be categorized into 3 classes of mutually exclusive cytogenetic categories. Class 1 RO had diploid karyotypes with 11q13 rearrangement in balanced translocations with ten or more different chromosome partners in all 20 (31.7%) cases. We identified recurrent translocation partners at 5q35, 6p21, 9p24, 11p13-14 and 11q23, and confirmed that CCND1 gene rearrangement at 11q13 utilizing fluorescence in situ hybridization (FISH). Class 2 RO exhibited hypodiploid karyotypes with loss of chromosome 1 and concurrent losses of Y in males and X in females in 25 (39.7%) cases. The class 3 tumors comprising of 18 (30.2%) cases showed diverse types of abnormalities with the involvement of 2 or more chromosomes exclusive of abnormalities seen in Class 1 and 2 tumors. Furthermore, karyotypically uninformative cases were subjected to FISH analysis to identify class 1 and 2 abnormalities. In this group we found similar frequencies of CCND1 rearrangement, loss of 1 or Y as with karyotypically abnormal cases. We validated our results against 91 tumors from the Mittleman database. Correlation of clinical data with all the 3 classes of RO showed no clear evidence of overall patient survival. Our findings support the hypothesis that RO exhibit 3 principal cytogenetic categories, which may have different roles in initiation and/or progression. These cytogenetic markers provide a key tool in the diagnostic evaluation of RO. Citation Format: Christopher B. Anderson, Michael Lipsky, Subhadra V. Nandula, Freeman E. Christopher, Matthews Thomas, Caitlin E. Walsh, Gen Li, Matthias Szabolcs, Mahesh M. Mansukhani, James M. McKiernan, Murty V. Vundavalli. Cytogenetics of renal oncocytomas identify three distinct and mutually exclusive diagnostic classes of chromosome aberrations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3415.

Genetic basis of PD-L1 overexpression in diffuse large B-cell lymphomas

AbstractDiffuse large B-cell lymphoma (DLBCL) is one of the most common and aggressive types of B-cell lymphoma. Deregulation of proto-oncogene expression after a translocation, most notably to the immunoglobulin heavy-chain locus (IGH), is one of the hallmarks of DLBCL. Using whole-genome sequencing analysis, we have identified the PD-L1/PD-L2 locus as a recurrent translocation partner for IGH in DLBCL. PIM1 and TP63 were also identified as novel translocation partners for PD-L1/PD-L2. Fluorescence in situ hybridization was furthermore used to rapidly screen an expanded DLBCL cohort. Collectively, a subset of samples was found to be affected by gains (12%), amplifications (3%), and translocations (4%) of the PD-L1/PD-L2 locus. RNA sequencing data coupled with immunohistochemistry revealed that these cytogenetic alterations correlated with increased expression of PD-L1 but not of PD-L2. Moreover, cytogenetic alterations affecting the PD-L1/PD-L2 locus were more frequently observed in the non–germinal center B cell–like (non-GCB) subtype of DLBCL. These findings demonstrate the genetic basis of PD-L1 overexpression in DLBCL and suggest that treatments targeting the PD-1–PD-L1/PD-L2 axis might benefit DLBCL patients, especially those belonging to the more aggressive non-GCB subtype.

The DEK oncoprotein binds to highly and ubiquitously expressed genes with a dual role in their transcriptional regulation.

BackgroundThe DEK gene is highly expressed in a wide range of cancer cells, and a recurrent translocation partner in acute myeloid leukemia. While DEK has been identified as one of the most abundant proteins in human chromatin, its function and binding properties are not fully understood.MethodsWe performed ChIP-seq analysis in the myeloid cell line U937 and coupled it with epigenetic and gene expression analysis to explore the genome-wide binding pattern of DEK and its role in gene regulation.ResultsWe show that DEK preferentially binds to open chromatin, with a low degree of DNA methylation and scarce in the heterochromatin marker H3K9me3 but rich in the euchromatin marks H3K4me2/3, H3K27ac and H3K9ac. More specifically, DEK binding is predominantly located at the transcription start sites of highly transcribed genes and a comparative analysis with previously established transcription factor binding patterns shows a similarity with that of RNA polymerase II. Further bioinformatic analysis demonstrates that DEK mainly binds to genes that are ubiquitously expressed across tissues. The functional significance of DEK binding was demonstrated by knockdown of DEK by shRNA, resulting in both significant upregulation and downregulation of DEK-bound genes.ConclusionsWe find that DEK binds to transcription start sites with a dual role in activation and repression of highly and ubiquitously expressed genes.Electronic supplementary materialThe online version of this article (doi:10.1186/1476-4598-13-215) contains supplementary material, which is available to authorized users.

NPM new interacting partners and influence of NPM mutations on gene regulation

Nucleophosmin (NPM) is a multifunctional protein. NPM mutation is found in one third of all acute myeloid leukemia (AML), and in more than 60% of AML with normal karyotype. It is also a recurrent translocation partner in AML.We got interested in the NPM function as a co‐regulator of gene expression. We hypothesized that the modifications of NPM disrupt gene regulation and thereby, favour leukemia.With a combination of biochemistry and molecular biology techniques, we identified new partners of NPM involved in gene regulation. We found that NPM colocalise with different transcription regulators at specific genes. Based on our results, we propose that the effect of NPM modifications on gene regulation has a significant impact on the capacity of hematopoietic cells to receive extra‐cellular signals which favours abnormal hematopoiesis and potentially, leukemia.

Model for MLL translocations in therapy-related leukemia involving topoisomerase IIβ-mediated DNA strand breaks and gene proximity

Topoisomerase poisons such as the epipodophyllotoxin etoposide are widely used effective cytotoxic anticancer agents. However, they are associated with the development of therapy-related acute myeloid leukemias (t-AMLs), which display characteristic balanced chromosome translocations, most often involving the mixed lineage leukemia (MLL) locus at 11q23. MLL translocation breakpoints in t-AMLs cluster in a DNase I hypersensitive region, which possesses cryptic promoter activity, implicating transcription as well as topoisomerase II activity in the translocation mechanism. We find that 2-3% of MLL alleles undergoing transcription do so in close proximity to one of its recurrent translocation partner genes, AF9 or AF4, consistent with their sharing transcription factories. We show that most etoposide-induced chromosome breaks in the MLL locus and the overall genotoxicity of etoposide are dependent on topoisomerase IIβ, but that topoisomerase IIα and -β occupancy and etoposide-induced DNA cleavage data suggest factors other than local topoisomerase II concentration determine specific clustering of MLL translocation breakpoints in t-AML. We propose a model where DNA double-strand breaks (DSBs) introduced by topoisomerase IIβ into pairs of genes undergoing transcription within a common transcription factory become stabilized by antitopoisomerase II drugs such as etoposide, providing the opportunity for illegitimate end joining and translocation.

BCL2 and BCL3 are recurrent translocation partners of the IGH locus

Chromosomal translocations affecting the immunoglobulin heavy chain ( IGH) locus in chromosomal band 14q32 are the most frequent cytogenetic changes in B-cell lymphomas. We studied the presence of IGH translocations in a consecutively ascertained series of 94 classical Hodgkin lymphomas (cHL) by combined immunofluorescence for CD30 and interphase cytogenetics (FICTION technique). The Hodgkin and Reed–Sternberg cells of a total of 11 of 87 evaluable cases (13%) showed signal patterns indicative of IGH translocations. To identify the translocation partners, these cases were further studied with probes for the MYC, BCL2, BCL6, BCL3, REL/BCL11A, JAK2/PDCD1LG2 (alias PDL2) C14orf43, and C2TA loci. The IGH translocation partner could be identified in four cHL and involved BCL2 and BCL3 in two cases each. Immunohistochemistry in cases with suitable material revealed that tumor cells of the two cHL with IGH/BCL2 fusion and the cHL with IGH/BCL3 fusion expressed the BCL2 and BCL3 protein, respectively. These data indicate that BCL2 or BCL3 are recurrent translocation partners of the IGH locus in cHL; however, most of the translocation partners of IGH translocations in cHL remain to be identified.

Cytogenetic Classification of T Lineage Acute Lymphoblastic Leukaemia: Multiple Partners of BCL11B and Other Novel Rearrangements.

Increasing numbers of genetic changes are being described in T lineage acute lymphoblastic leukaemia (T ALL), which may be used to classify patients into subgroups, defining multi-step oncogenic pathways. We have integrated the significant abnormalities into a comprehensive genetic classification of T ALL, using appropriate probes for fluorescence in situ hybridization (FISH). Break-apart probes were designed, which detected rearrangements of the TCR loci. Metaphase FISH, confirmed by informative break-apart probes for the significant oncogenes, were used to identify partner genes, as shown in the table. This approach revealed new recurrent translocation partners, as well as determining the incidence and simultaneous occurrence of the different abnormalities. The series included 295 patients, children 0–14 years (n=206) and adults ≥ 15 years (n=89), with a diagnosis of T ALL, entered to one of the UK MRC/NCRI ALL treatment trials. The incidences of the common cryptic abnormalities, SIL-TAL1 fusion and TLX3 were more prevalent in children (20% and 17%, respectively) compared to adults (9% each). There was no difference in event free survival between the childhood patients with SIL-TAL1 fusion and TLX3 rearrangements. CALM-AF10 fusion and MLL rearrangements accounted for 4% each. A single patient was found with a BCR-ABL fusion, but the same probe identified nine (3%) with NUP214-ABL1 amplification. Deletions involving CDKN2A were present in 49% of patients, in association with all abnormalities. Among the patients with NUP214-ABL1 amplification, associated abnormalities were: CDKN2A deletions (n=9), TRA@-TLX1 (n=2), BCL11B-TLX3 (n=2), TRB@-TLX3 (n=1). Concurrent rearrangements were found between the TCR genes, as well as associations between MYC, IGH and the other oncogenes. For example, (1) complex abnormalities between (a) TRA@, TRG@, BCL11B (n=2) and (b) HOXA@ (n=1); (2) deletions of 3′TRB@ in association with (a) complex ring chromosomes (n=2) and (b) cytogenetically visible deletions (n=2). FISH detected several novel, recurrent rearrangements, in particular a t(6;14) involving BCL11B and the 6q26 region (n=5) and a t(9;14)(p24;q31.1) involving JAK2 (n=2), the partners of which are currently being defined. BCL11B was also involved with (a) LMO2 and (b) the 2q23 region; LMO2 was rearranged with an unidentified partner in a complex translocation with chromosomes 16 and 18; TLX1 was involved in a translocation with 3q; new partners of TRB@ were found at (a) 1q11, (b) on 12p (n=2), (c) on 21q. These findings demonstrate the valuable role of FISH analysis, with a panel of carefully selected probes, to classify T ALL patients into genetic subgroups, including rare variants, and provide information on the relationship between them. A metaphase FISH approach has facilitated the identification of potential new target genes. In particular, multiple partners of TRB@ and BCL11B, other than the known TLX3 and HOXA@ genes, have emerged, highlighting the importance of these genes in the pathogenesis of T ALL.Promotor and Oncogenes in T ALLPromotor GenesOncogenesBCL11BTRA@TRB@TRG@CDK6Novel***/UnknownTLX338*312TLX11231HOXA@151LMO11LMO2114314**LYL12TAL26NOTCH11MYC231MYB1IGH@4*includes 3 telomeric deletions, **includes 3 centromeric deletions, ***listed in text

PVRL2 Is Translocated to the TCRA Locus in t(14;19)(q11;13) Positive Peripheral T-Cell Lymphoma.

T-cell non-Hodgkin lymphomas (NHLs) are uncommon malignancies that represent approximately 15% of aggressive lymphomas in Western countries. Contrasting with B-cell lymphomas, very few recurrent chromosomal abnormalities have been identified. Nevertheless, the TCR loci and preferentially the TCRAD at chromosome band 14q11 could be involved in up to 15% of cases. We recently reported a novel and recurrent t(14;19)(q11;q13) chromosomal translocation in peripheral T-cell lymphoma (PTCL). FISH analysis performed in three cases suggested an implication of the TCRAD locus at 14q11 and of BCL3 at 19q13. We now report the molecular cloning of the genomic junctions for these three patients. Sequence analysis confirmed the involvement of the TCRAD on 14q11 and assessed the breakpoint's localisation to the TCRA variable region for all cases. In the first, the chromosomal break occurred between the J30 and the J31 segments while in the second it was in the J58 segment. Thus, both translocations probably occurred after an illegitimate V(D)J recombination. Remarkably, for the third patient, junctions with the deltaRec and psi(J)alpha elements were identified on the der(14) and der(19) respectively. Consequently this translocation probably results from an illegitimate deltarec-Psi(J)alpha rearrangement (TCRD deletion) during thymopoiesis before Valpha-Jalpha rearrangements. On chromosome 19, our results indicated a new clustering of breakpoints outside the region documented in t(14;19)(q32;q13) in chronic lymphocytic leukemia. Remarkably, all three breaks occurred ~130kb downstream from BCL3, in the PVRL2 gene. Consequently, the TCRA locus enhancer is juxtaposed to PVRL2 and BCL3 on the derivative chromosome 19. For two patients, mRNA expression levels were investigated by real time RT-PCR experiments, which confirmed a high expression of both PVRL2 and BCL3. In conclusion, we identified PVRL2 as the recurrent translocation partner of the TCRA locus in PTCL. Whether this clustering results from an important instability of the PVRL2 gene during thymopoiesis remains to be investigated. The PVRL2 overexpression itself may be an important step for T-cell lymphomagenesis.

Identification of Three Novel Chromosomal Translocation Partners Involving the Immunoglobulin Loci in Newly Diagnosed Myeloma and Human Myeloma Cell Lines.

Chromosomal translocations involving the immunoglobulin heavy-chain (IgH) locus at 14q32 are genetic hallmarks of human multiple myeloma (MM) and are likely primary oncogenic events in myeloma transformation. Common recurrent translocation partner genes of IgH account for 40–50% of cases and these rearrangements result in the transcriptional dysregulation of various proto-oncogenes such as CCND1, CCND3, FGFR3/MMSET, c-MAF, MAFB, MUM 1(IRF-4), c-MYC and it is becoming clear that these dysregulated genes play important roles in the pathogenesis and the treatment outcome of MM. Although the frequency of other partner genes of IgH translocations may be rare (<1%), it is possible that many genes not currently identified as translocation partners are functionally converged into several signal pathways and play important roles as well. Through global gene expression profiling (GEP) studies of a large population of newly diagnosed MM, we have recently reported that dysregulation of any one of the three D-type cyclins is seen in almost all newly diagnosed MM and most patients with high levels of CCND2 expression was highly correlated with expression of c-MAF, MAFB or FGFR3/MMSET. In order to identify novel translocation partner genes in MM we combined GEP and fluorescence in situ hybridization (FISH) analysis in a large population of newly diagnsoed myeloma. We investigated whether IGH-CCND2 and IGH-MAFA translocations are seen in patients exhibiting high levels of CCND2 expression but not expressing c-MAF, MAFB, or FGFR3/MMSET. We also looked for a breakpoint and targeted gene at a non-random breakpoint at the 11q23 locus in 20 MM patients with 11q23 abnormalities detected by conventional G-banding. Here we report evidence of an IGH-CCND2 fusion in a newly diagnosed case of MM and an IGH-MAFA fusion in a newly diagnosed MM and an MGUS and also mapped the 11q23 breakpoint to within 100 kb in a newly diagnosed MM and a human myeloma cell line, NCU-MM-1 and identified an IGL Pou2AF1 fusion in the NCU-MM-1 line. Importantly these translcoatios do not involve the MLL or ATM genes. These three genes were all highly expressed as detected by GEP or quantitive RT-PCR in the samples in which these genes were translocated to IG loci. Although the frequency of these 3 translocations are very rare, they further the concept of a critical role of CCND2 expression in myelomegenesis and identifed the transcriptional coactivator Pou2AF1, which specifically associates with either OCT1 or OCT2, in the B-cell response to antigens and required for the formation of germinal centers, as a potential new translocation target in myeloma. Finally, our strategy of combining GEP signatures and cytogenetic analyses appears to be a practical means of identifying new IG- mediated translocations in myeloma.

Targeting FGFR3 in t(4;14) Mutiple Myeloma: Pre-Clinical Studies of PRO-001, a Novel Anti-FGFR3 Neutralizing Antibody.

As with other B-cell malignancies, chromosomal translocations to the immunoglobulin heavy-chain (IgH) locus on chromosome 14q32 are believed to be a hallmark of multiple myeloma (MM), occurring in approximately 50% of patients. Identification of these chromosomal translocations has resulted in the discovery of powerful prognostic tools and novel molecular targets that promise to revolutionize the treatment of this malignancy. Five recurrent translocation partners have been defined, resulting in the dysregulation of the genes encoding cyclin D1 and D3, c-maf, mafB and Fibroblast Growth Factor Receptor 3 (FGFR3) together with MMSET. Genetic analysis of 14q32 translocations in MM has identified distinct groups of patients with separate clinical outcomes supporting a biological correlation of these genes in MM. In particular, the t(4;14) translocation portends a particularly bad prognosis. The association of FGFR3 expression with t(4;14) myeloma and the demonstration of the transforming potential of this receptor tyrosine kinase (RTK), make this a particularly attractive target for drug development for this poor prognosis group.We report here the development of a novel and highly specific anti-FGFR3 neutralizing antibody (PRO-001) isolated from a phage display human combinatorial antibody library. PRO-001 binds with high affinity (Kd=1.3 nM) to FGFR3 in in vitro binding assays and blocks ligand-dependent and independent FGFR3 phosphorylation and signal transduction in cell-based assays. Furthermore, PRO-001 potently inhibits FGFR3-dependent solid tumor growth in mouse xenograft models.We found that PRO-001 bound to, and competed with FGF binding to the surface of FGFR3 on human myeloma cell lines. PRO-001 inhibited FGF-induced phosphorylation of wild-type FGFR3 and downstream ERK phosphorylation in stable B9 cell transfectants (B9-WT) and FGFR3 expressing human myeloma cell lines. The antibody inhibited FGF-mediated growth of B9-WT with an IC50 of 3 μg/ml as determined by MTT proliferation assay. Growth of these cells could be rescued by IL-6 demonstrating selectivity of PRO-001 for FGFR3. PRO-001 inhibited the viability of the FGFR3 expressing, human myeloma cell line, UTMC2. Inhibition of viability was still observed when cells were co-cultured with stroma or in the presence of IL-6, a potent growth factor for MM cells. Several myeloma cell lines lacking FGFR3, showed minimal growth inhibition demonstrating selectivity and lack of non-specific toxic at effective dose concentrations. Finally, PRO-001 bound to FGFR3 on the cell surface, inhibited ERK phosphorylation, and induced cytotoxic responses in primary MM samples derived from t(4;14) positive patients. A xenograft mouse model has been established and studies assessing in vivo activity of PRO-001 are planned and will be reported. Taken together, the data demonstrate that PRO-001 is a specific and potent inhibitor of FGFR3 and that it deserves further study for targeted therapy in MM.

Molecular cytogenetic mapping of recurrent chromosomal breakpoints in tenosynovial giant cell tumors.

Tenosynovial giant cell tumor (TGCT) is the most common benign tumor of synovium and tendon sheath. Cytogenetic data indicate that 1p11-13 is the region most frequently involved in structural rearrangements. With the aim of eventually identifying the genes associated with TGCT development, we have investigated 1p11-13 breakpoints using fluorescence in situ hybridization (FISH) analysis, with a panel of yeast artificial chromosome (YAC) probes covering 1p11-21. Twenty-six tumors were analyzed by G-banding, and 24 of these showed a breakpoint in 1p11-13. The cytogenetic findings add to previous observations that, among a variety of translocations involving 1p11-13, chromosome 2 is the most common translocation partner, with a breakpoint in 2q35-37. This aberration was found in eight cases. Other recurrent translocation partners, found in two or three cases, were 5q22-31, 11q11-12, and 8q21-22. Material from 21 tumors was available for FISH analysis, which revealed that the breakpoints clustered to one region spanned by two YAC probes, 914F6 and 885F12 located in 1p13.2, in 18 cases. Bacterial artificial chromosome probes were used to map the recurrent breakpoint on chromosome 2. In four of seven cases there was a breakpoint within the sequence covered by probe 260J21, where the RDC1 gene is located, a gene reported to fuse with HMGIC in lipomas with a 2;12 translocation.

Identification of NFIB as recurrent translocation partner gene of HMGIC in pleomorphic adenomas.

Approximately 12% of all pleomorphic adenomas of the salivary glands are characterized by chromosome aberrations involving the chromosome segment 12q13-15. Several chromosomes have been found as translocation partners of chromosome 12, and some of these recurrently. Recently, the HMGIC gene was identified as the target gene affected by the 12q13-15 aberrations. Here, we report the identification and characterization of a new translocation partner gene of HMGIC in pleomorphic adenomas. 3'-RACE analysis of a primary adenoma with an apparently normal karyotype revealed an HMGIC fusion transcript containing ectopic sequences derived from the human NFIB gene, previously mapped to chromosome band 9p24.1. The HMGIC NFIB fusion transcript was also confirmed by RT-PCR. Since the chromosome segment 9p12-24 is repeatedly involved as translocation partner of chromosome 12q13-15 in pleomorphic adenomas, we tested whether NFIB might be a recurrent partner of HMGIC. RT-PCR analysis of a second adenoma with an ins(9;12)(p23;q12q15) as the sole anomaly, revealed that also in this tumor an HMGIC/NFIB hybrid transcript was present. The reciprocal NFIB/HMGIC fusion transcript, however, could not be detected in any of these tumors. Nucleotide sequence analysis of the fusion transcripts indicated that the genetic aberration in both tumors resulted in the replacement of a carboxy-terminal segment of HMGIC by the last five amino acids of NFIB. In conclusion, our results reveal the recurrent involvement of the NFIB gene as translocation partner gene of HMGIC in pleomorphic adenomas.