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Cancer cells exhibit nonrandom and complex chromosome abnormalities. The role of genomic changes in cancer is well established. However, the identification of complex and cryptic chromosomal changes is beyond the resolution of conventional banding methods. The fluorescence microscopy afforded by imaging technologies, developed recently, facilitates a precise identification of these chromosome alterations in cancer. The three most commonly utilized molecular cytogenetics methods comparative genomic hybridization, spectral karyotype, and fluorescence in situ hybridization, that have already become benchmark tools in cancer cytogenetics, are described in this chapter. Comparative genomic hybridization is a powerful tool for screening copy-number changes in tumor genomes without the need for preparation of metaphases from tumor cells. Multicolor spectral karyotype permits visualization of all chromosomes in one experiment permitting identification of precise chromosomal changes on metaphases derived from tumor cells. The uses of fluorescence in situ hybridization are diverse, including mapping of alteration in single copy genes, chromosomal regions, or entire chromosomes. The opportunities to detect genetic alterations in cancer cells continue to evolve with the use of these methodologies both in diagnosis and research.

An increased incidence of acute myeloid leukemia (AML) has recently been documented in patients post-solid organ transplantation but the incidence and types of myelodysplastic syndromes (MDS) occurring in this patient population are not known. We identified 5 patients (3M, 2F, age 48-64 years) who developed MDS ranging from 1.8 to 25 years (median 4.2 years) post-solid organ transplantation, only 2 patients had received azathioprine. The cumulative incidence of MDS in heart and lung transplant recipients at 15 years was 0.5% and 1.8%, respectively, which is markedly higher compared to the general population. Low-risk types of MDS predominated, 3 of 5 patients are alive (median 3.9 years) since diagnosis. Deletions of chromosome 20q, which have not been previously reported in post-transplant MDS/AML, were identified in 3 cases. Our findings expand the morphologic and cytogenetic spectrum of MDS occurring post-solid organ transplantation and suggest that mechanisms beside azathioprine toxicity might be important in disease pathogenesis.

Background Post-transplant lymphoproliferative disorders (PTLDs) encompass heterogeneous entities with different histomorphology and behavior. T/NK-cell PTLDs (T/NK-PTLDs) are rare, accounting for 2-15% of all PTLD, which are often EBV-negative and associated with a poor prognosis. The pathogenesis of T/NK-PTLDs and the underlying molecular alterations are presently unknown. In order to better understand their pathogenesis, we performed high resolution DNA profiling for copy number alterations and targeted mutational analyses of 18T/NK-PTLDs. Methods Cases of T/NK-PTLD were selected from the archives of two institutions. Morphological features were assessed and immunohistochemistry (IHC) was performed to classify lymphomas according to the WHO 2008 criteria. DNA was extracted from formalin-fixed paraffin-embedded tissue. Copy number analysis (n=16; Affymetrix Oncoscan FFPE Assay) and targeted next-generation sequencing for 467 cancer-associated genes, after capture of all exons or select whole genes (n=17; Illumina HiSeq 2500), were performed. Variants with allele frequency 1% in 1000 genomes project, read depth Results The T/NK-PTLDs represented virtually the entire spectrum of currently recognized T- and NK-cell lymphomas. Peripheral T-cell lymphoma (PTCL), NOS were the most frequent (n=6), extranodal location was common (n=14, 78%) and only a minority were EBV+ (n=2, 11%). Copy number alterations were observed in 13 cases (81%; complex =11, simple=2). In contrast to B-cell PTLDs, EBV+ T/NK-PTLDs showed more complex copy number changes than EBV- cases. Somatic mutations were detected in 17/18 cases (94%). Overall, 343 variants were identified: 277 missense (80%), 40 indels (12%) and 14 nonsense (4%). An average of 20.1 variants/case was observed with an average 594.8-fold coverage. Mutations of epigenetic mediators and chromatin remodeling complex genes, including TET2 (n=5), MLL2 (n=4), MLL3 (n=4), DNMT3a (n=3), ARID1B (n=3) and ARID2 (n=2), were the most frequent alterations, seen in 11/17 (65%) cases. Disruption of TP53 was identified in 6/18 (33%) cases; biallelic inactivation in 3 cases with co-occurrence of missense (n=2) or nonsense (n=1) mutation and 17p LOH, monoallelic missense mutations in two cases, and loss of 17p encompassing the p53 locus in one case. Mutually exclusive activating STAT3 and STAT5B mutations were identified in 5/17 (29%) cases. Mutations targeting the STAT3 SH2 domain were seen in one EBV- cutaneous anaplastic large cell lymphoma and two EBV+ PTLDs (PTCL, NOS and extranodal NK/T cell lymphoma (ENKTCL)). Both EBV+ cases also showed LOH of the STAT3 locus on 17q and 6q loss encompassing PTPRK, the phosphorylase responsible for downregulation of STAT3 signaling. A JAK3 variant (S568P) adjacent a known hotspot was also identified in the ENKTCL. Missense mutations in RHOA and FYN were detected in one angioimmunoblastic T-cell lymphoma (AITL). Mutations were also observed in genes not previously implicated in T/NK-cell lymphomas, including potentially damaging missense variants in MED12 (n=3) and TBX3 (n=3), and a novel missense MTOR mutation (W1456L) involving the FAT domain. Recurrent copy number alterations comprised gains of 7q (n=4, including 2 hepatosplenic T-cell lymphomas [HSTCL]), 8q (n=3; MYC) and 9q (n=2; ABL1, SYK), and losses of 7p (n=4) and 6q (n=3; FOXO3, PRDM1). Contrary to prior reports, MSI was uncommon in our series despite use of azathioprine therapy (n=9), with only 1 of 3 cases harboring mutations in mismatch repair genes was confirmed to be MSI-H. Conclusion Our analysis of a large series of T/NK-PTLDs represents the first survey of genomic and genetic changes in these lymphomas, and adds to the growing list of genes and pathways altered in T/NK-cell neoplasms. Our findings suggest shared genomic and molecular aberrations with T-cell lymphomas occurring in "immunocompetent" individuals. Functional studies are needed to assess if some of the observed genetic alterations could serve as therapeutic targets for these aggressive neoplasms. Figure 1. Figure 1. Disclosures No relevant conflicts of interest to declare.

We describe the clinical course of a recurrent case of congenital fibrosarcoma diagnosed in a 9-mo-old boy with a history of hemimelia. Following complete surgical resection of the primary tumor, the patient subsequently presented with bulky bilateral pulmonary metastases 6 mo following surgery. Molecular characterization of the tumor revealed the absence of the prototypical ETV6-NTRK3 translocation. However, tumor characterization incorporating cytogenetic, array comparative genomic hybridization, and RNA sequencing analyses, revealed a somatic t(2;15)(2p21;15q25) translocation resulting in the novel fusion of EML4 with NTRK3. Cloning and expression of EML4-NTRK3 in murine fibroblast NIH 3T3 cells revealed a potent tumorigenic phenotype as assessed in vitro and in vivo. These results demonstrate that multiple fusion partners targeting NTRK3 can contribute to the development of congenital fibrosarcoma.

The transit of T cell-activated B cells through the germinal center (GC) is controlled by sequential activation and repression of key transcription factors, executing the pre- and post-GC B cell program. B cell lymphoma (BCL) 6 and IFN regulatory factor (IRF) 8 are necessary for GC formation and for its molecular activity in Pax5+PU.1+ B cells. IRF4, which is highly expressed in BCL6− GC B cells, is necessary for class switch recombination and the plasma cell differentiation at exit from the GC. In this study, we show at the single-cell level broad coexpression of IRF4 with BCL6, Pax5, IRF8, and PU.1 in pre- and post-GC B cells in human and mouse. IRF4 is down-regulated in BCL6+ human GC founder cells (IgD+CD38+), is absent in GC centroblasts, and is re-expressed in positive regulatory domain 1-positive centrocytes, which are negative for all the B cell transcription factors. Activated (CD30+) and activation-induced cytidine deaminase-positive extrafollicular blasts coexpress Pax5 and IRF4. PU.1-negative plasma cells and CD30+ blasts uniquely display the conformational epitope of IRF4 recognized by the MUM1 Ab, an epitope that is absent from any other IRF4+PU.1+ lymphoid and hemopoietic subsets. Low grade B cell lymphomas, representing the malignant counterpart of pre- and post-GC B cells, accordingly express IRF4. However, a fraction of BCL6+ diffuse large B cell lymphomas express IRF4 bearing the MUM1 epitope, indicative of a posttranscriptional modification of IRF4 not seen in the normal counterpart.

In early and polymorphic post-transplant lymphoproliferative disorders (PTLD) Epstein-Barr virus (EBV), through its latency proteins, drives the proliferation of B lymphocytes, a process which in immunocompetent individuals leads to the establishment of latently infected memory B cells.We analyzed 11 cases, which included early and polymorphic PTLD, and 12 controls for latency of EBV infection and their antigenic profile.We identified a minority of terminally differentiated EBER+ IRTA1+ memory B cells and EBER+ CD138+ PRDM1+ plasma cells in these samples. These elements were identified both in PTLD and in tumor-free tonsils from post-transplant patients but not in EBV- control tonsils. The expression of EBV latency proteins is heterogeneous, and is associated with activation of the NF-kB pathway. EBV signaling (through EBNA2, LMP1 and LMP2A) and NF-kB activation correlated with upregulation of target proteins: cMYC, JunB, CCL22, TRAF1 and IRF4. EBV-infected lymphocytes in early and polymorphic PTLDs represent a mixture of latencies II, III and, in at least 1/3 of infected cells, of latency 0.EBV infection correlates with NF-kB activation, with EBV-dependent cell signaling, and lastly, with the presence of EBV-infected plasma cells and memory cells.

Activating mutations in NOTCH1 are present in over 50% of human T-cell lymphoblastic leukemia (T-ALL) samples and inhibition of NOTCH1 signaling with gamma-secretase inhibitors (GSI) has emerged as a potential therapeutic strategy for the treatment of this disease. Here, we report a new human T-cell lymphoma line CUTLL1, which expresses high levels of activated NOTCH1 and is extremely sensitive to gamma-secretase inhibitors treatment. CUTLL1 cells harbor a t(7;9)(q34;q34) translocation which induces the expression of a TCRB-NOTCH1 fusion transcript encoding a membrane-bound truncated form of the NOTCH1 receptor. GSI treatment of CUTLL1 cells blocked NOTCH1 processing and caused rapid clearance of activated intracellular NOTCH1. Loss of NOTCH1 activity induced a gene expression signature characterized by the downregulation of NOTCH1 target genes such as HES1 and NOTCH3. In contrast with most human T-ALL cell lines with activating mutations in NOTCH1, CUTLL1 cells showed a robust cellular phenotype upon GSI treatment characterized by G1 cell cycle arrest and increased apoptosis. These results show that the CUTLL1 cell line has a strong dependence on NOTCH1 signaling for proliferation and survival and supports that T-ALL patients whose tumors harbor t(7;9) should be included in clinical trials testing the therapeutic efficacy NOTCH1 inhibition with GSIs.

Background Cervical Cancer (CC) exhibits highly complex genomic alterations. These include hemizygous deletions at 4p15.3, 10q24, 5q35, 3p12.3, and 11q24, the chromosomal sites of Slit-Robo pathway genes. However, no candidate tumor suppressor genes at these regions have been identified so far. Slit family of secreted proteins modulates chemokine-induced cell migration of distinct somatic cell types. Slit genes mediate their effect by binding to its receptor Roundabout (Robo). These genes have shown to be inactivated by promoter hypermethylation in a number of human cancers. Results To test whether Slit-Robo pathway genes are targets of inactivation at these sites of deletion, we examined promoter hypermethylation of SLIT1, SLIT2, SLIT3, ROBO1, and ROBO3 genes in invasive CC and its precursor lesions. We identified a high frequency of promoter hypermethylation in all the Slit-Robo genes resulting in down regulated gene expression in invasive CC, but the inhibitors of DNA methylation and histone deacetylases (HDACs) in CC cell lines failed to effectively reactivate the down-regulated expression. These results suggest a complex mechanism of inactivation in the Slit-Robo pathway in CC. By analysis of cervical precancerous lesions, we further show that promoter hypermethylation of Slit-Robo pathway occurs early in tumor progression. Conclusion Taken together, these findings suggest that epigenetic alterations of Slit-Robo pathway genes (i) play a role in CC development, (ii) further delineation of molecular basis of promoter methylation-mediated gene regulation provides a potential basis for epigenetic-based therapy in advanced stage CC, and (iii) form epigenetic signatures to identify precancerous lesions at risk to progression.

Acute promyelocytic leukemia (APL) is characterized by the translocation t(15;17)(q22;q21), resulting in the promyelocytic leukemia (PML)-retinoic acid receptor alpha (RARA) fusion protein in 95% cases whereas variant translocations involving PLZF (11q23), NPM (5q35), NUMA (11q13) and STAT5b (17q23) account for the rest. Leukemias with PML-RARA translocations respond well to all-trans retinoic acid (ATRA) or arsenic trioxide (ATO) therapy whereas those with PLZF-RARA fusions respond poorly. Although primary resistance to ATRA is rare, secondary or acquired resistance is frequently observed in patients treated with ATRA alone or in combination with other chemotherapy regimens. However, molecular abnormalities mediating resistance to ATRA therapy are underexplored. Here, we report two cases of APL with RARA-PML deletions on der(17) or der(15), which displayed clinical evidence of primary and secondary resistance to therapy, respectively.

Gain-of-function mutations in exon 3 of beta-catenin (CTNNB1) are specific for Wilms' tumors that have lost WT1, but 50% of WT1-mutant cases lack such "hot spot" mutations. To ask whether stabilization of beta-catenin might be essential after WT1 loss, and to identify downstream target genes, we compared expression profiles in WT1-mutant versus WT1 wild-type Wilms' tumors. Supervised and nonsupervised hierarchical clustering of the expression data separated these two classes of Wilms' tumor. The WT1-mutant tumors overexpressed genes encoding myogenic and other transcription factors (MOX2, LBX1, SIM2), signaling molecules (TGFB2, FST, BMP2A), extracellular Wnt inhibitors (WIF1, SFRP4), and known beta-catenin/TCF targets (FST, CSPG2, CMYC). Beta-Catenin/TCF target genes were overexpressed in the WT1-mutant tumors even in the absence of CTNNB1 exon 3 mutations, and complete sequencing revealed gain-of-function mutations elsewhere in the CTNNB1 gene in some of these tumors, increasing the overall mutation frequency to 75%. Lastly, we identified and validated a novel direct beta-catenin target gene, GAD1, among the WT1-mutant signature genes. These data highlight two molecular classes of Wilms' tumor, and indicate strong selection for stabilization of beta-catenin in the WT1-mutant class. Beta-Catenin stabilization can initiate tumorigenesis in other systems, and this mechanism is likely critical in tumor formation after loss of WT1.

SummaryPten−/− cells display a partially defective checkpoint in response to ionizing radiation (IR). The checkpoint defect was traced to the ability of AKT to phosphorylate CHK1 at serine 280, since a nonphosphorylated mutant of CHK1 (S280A) complemented the checkpoint defect and restored CDC25A degradation. CHK1 phosphorylation at serine 280 led to covalent binding of 1 to 2 molecules of ubiquitin and cytoplasmic CHK1 localization. Primary breast carcinomas lacking PTEN expression and having elevated AKT phosphorylation had increased cytoplasmic CHK1 and displayed aneuploidy (p < 0.005). We conclude that loss of PTEN and subsequent activation of AKT impair CHK1 through phosphorylation, ubiquitination, and reduced nuclear localization to promote genomic instability in tumor cells.

MAD2 inhibits the anaphase-promoting complex when chromosomes are unattached to the mitotic spindle. It acts as a tumor suppressor gene because MAD2+/–cells enter anaphase early and display chromosome instability, leading to the formation of lung tumors in mice. Complete MAD2 inactivation has not been identified in human tumors, although partial defects are prevalent. By employing RNA interference in human somatic cells, we found that severe reduction of MAD2 protein levels results in mitotic failure and extensive cell death arising from defective spindle formation, incomplete chromosome condensation, and premature mitotic exit leading to multinucleation. Cyclin B is degraded prematurely in the MAD2 short interfering RNA-treated cells but not in MAD2+/– cells, suggesting an explanation for the spindle failure and mitotic catastrophe in the MAD2 knockdown cells. Thus, anaphase-promoting complex substrates exhibit distinct sensitivities in the presence of different MAD2 doses, which in turn determine MAD2's role as either a tumor suppressor or an essential gene.

Background Carcinoma of uterine cervix is the second most common cancers among women worldwide. Combined radiation and chemotherapy is the choice of treatment for advanced stages of the disease. The prognosis is poor, with a five-year survival rate ranging from about 20–65%, depending on stage of the disease. Therefore, genetic characterization is essential for understanding the biology and clinical heterogeneity in cervical cancer (CC). Methods We used a genome-wide screening method – comparative genomic hybridization (CGH) to identify DNA copy number changes in 77 patients with cervical cancer. We applied categorical and survival analyses to analyze whether chromosomal changes were related to clinico-pathologic characteristics and patients survival. Results The CGH analysis revealed a loss of 2q33-q37 (57.1%), gain of 3q (54.5%) and chromosomal amplifications (20.77%) as frequent genetic changes. A total of 15 amplified chromosomal sites were detected in 16 cases that include 1p31, 2q32, 7q22, 8q21.2-q24, 9p22, 10q21, 10q24, 11q13, 11q21, 12q15, 14q12, 17p11.2, 17q22, 18p11.2, and 19q13.1. Recurrent amplified sites were noted at 11q13, 11q21, and 19q13.1. The genomic alterations were further evaluated for prognostic significance in CC patients, and we did not find any correlation with a number of clinical or histological parameters. The tumors harboring HPV18 exhibited higher genomic instability compared to tumors with HPV 16. Conclusions This study demonstrated that 2q33-q37 deletions, 3q gains and chromosomal amplifications as characteristic changes in invasive CC. These genetic alterations will aid in the identification of novel tumor suppressor gene(s) at 2q33-q37 and oncogenes at amplified chromosomal sites. Molecular characterization of these chromosomal changes utilizing the current genomic technologies will provide new insights into the biology and clinical behavior of CC.

The human fibroblast activation protein {alpha} (FAP{alpha}) is an inducible cell surface glycoprotein of M{sub r} 95,000 recognized by a number of monoclonal antibodies (mAbs), including the prototype mAb F19. Immunohistochemical studies have shown that FAP{alpha} expression in vivo is tightly regulated, with transient expression in some fetal mesenchymal tissues but absence of expression in most normal adult tissues. Reexpression of FAP{alpha} is observed in the reactive stromal fibroblasts of several common types of epithelial cancers, including >90% of breast, colorectal, and lung carcinomas and healing wounds. Cloning and sequence analysis of an FAP{alpha}-specific cDNA has revealed that the molecule is encoded by a novel gene, FAP, which shows sequence similarity to members of the serine protease family of integral membrane proteins, namely dipeptidyl peptidase IV (DPPIV, also known as lymphocyte activation antigen, CD26, or adenosine dearoinase binding protein) and DPPX, a DPPIV-related molecule of unknown function. 15 refs., 1 fig.

We performed comparative genomic hybridization (CGH) and high-resolution deletion mapping of the long arm of chromosome 2 (2q) in invasive cervical carcinoma (CC). The CGH analyses on 52 CCs identified genetic losses at 2q33–q36, gain of 3q26–q29, and frequent chromosomal amplifications. Characterization of 2q deletions by loss of heterozygosity (LOH) in 60 primary tumors identified two sites of minimal deleted regions at 2q35–q36.1 and 2q36.3–q37.1. To delineate the stage at which these genetic alterations occur in CC progression, we analysed 33 cervical intraepithelial neoplasia (CIN) for LOH. We found that 89% of high-grade (CINII and CINIII) and 40% of low-grade (CINI) CINs exhibited LOH at 2q. To identify the target tumor suppressor gene (TSG), we performed an extensive genetic and epigenetic analyses of a number of candidate genes mapped to the deleted regions. We did not find inactivating mutations in CASP10, BARD1, XRCC5, or PPP1R7 genes mapped to the deleted regions. However, we did find evidence of downregulated gene expression in CFLAR, CASP10 and PPP1R7 in CC cell lines. We also found reactivated gene expression in CC cell lines in vitro after exposure to demethylating and histone deacetylase (HDAC) inhibiting agents. Thus, these data identify frequent chromosomal amplifications in CC, and sites of TSGs at 2q35–q36.1 and 2q36.3–q37.1 that are critical in CC development.

Two groups of renal oncocytomas have been cytogenetically defined by the loss of one or both of chromosomes Y and 1 or by structural rearrangement involving 11q12~q13. We report five renal oncocytomas with structural chromosomal rearrangements involving 11q13 with previously unreported partner chromosomes (namely, 1, 6, and 7). For two of the five cases, a t(6;11)(p21;q13) translocation was revealed; the others had t(1;11)(p13;q13), t(7;11)(q11.2;q13), and t(5;11)(q35; q13). Fluorescence in situ hybridization confirmed translocation of CCND1 at 11q13 to partner chromosomes 5, 6, and 7. Overexpression of cyclin D1, the protein product of CCND1, was detected in three of the five cases (60%) by means of immunohistochemical staining of formalin-fixed, paraffin-embedded tumor sections. In three cases for which fresh tissue was available, Southern blot analysis using the MDL-5 probe for the BCL1 breakpoint did not reveal rearrangement of BCL1. In addition, six consecutive renal oncocytomas diagnosed at our institution between 1999 and 2002 whose karyotypes did not show 11q13 translocations were all negative for cyclin D1 overexpression under immunohistochemical analysis. The findings of CCND1 rearrangement with FISH and correlation with cyclin D1 overexpression under immunohistochemical analysis suggest that cyclin D1 alterations play a role in the subset of renal oncocytomas with 11q translocations, although other genes may also be involved.

We applied a combination of molecular cytogenetic methods, including comparative genomic hybridization (CGH), spectral karyotyping (SKY), and fluorescence in situ hybridization (FISH), to characterize the genetic aberrations in eight widely used cervical cancer (CC) cell lines. CGH identified the most frequent chromosomal losses including 2q, 3p, 4q, 6q, 8p, 9p, 10p, 13q, and 18q; gains including 3q, 5p, 5q, 8q, 9q, 11q, 14q, 16q, 17q, and 20q; and high-level chromosomal amplification at 3q21, 7p11, 8q23–q24, 10q21, 11q13, 16q23–q24, 20q11.2, and 20q13. Several recurrent structural chromosomal rearrangements, including der(5)t(5;8)(p13;q23) and i(5)(p10); deletions affecting chromosome bands 5p11, 5q11, and 11q23; and breakpoint clusters at 2q31, 3p10, 3q25, 5p13, 5q11, 7q11.2, 7q22, 8p11.2, 8q11.2, 10p11.2, 11p11.2, 14q10, 15q10, 18q21, and 22q11.2 were identified by SKY. We detected integration of HPV16 sequences by FISH on the derivative chromosomes involving bands 18p10 and 18p11 in cell line C-4I, 2p16, 5q21, 5q23, 6q, 8q24, 10, 11p11, 15q, and 18p11 in Ca Ski, and normal chromosome 17 at 17p13 in ME-180. FISH analysis was also used further to determine the copy number changes of PIKA3CA and MYC. This comprehensive cytogenetic characterization of eight CC cell lines enhances their utility in experimental studies aimed at gene discovery and functional analysis. © 2003 Wiley-Liss, Inc.

BCL8 is a novel human gene family initially identified through cloning of BCL8A, located at the t(14;15)(q32;q11-q13) translocation breakpoint, in a case of diffuse large B-cell lymphoma. Multiple copies of BCL8A map to the 1-Mb proximal duplicated region at 15q. We identified additional copies on human chromosomes 13 (BCL8B), 22 (BCL8C), 2 (BCL8D), and 10 (BCL8E) by cDNA cloning and sequence analysis. BCL8A, BCL8C, BCL8D, and BCL8E are truncated at the genomic level and are presumably pseudogenes or sterile transcripts. BCL8B is expressed predominantly in human brain and encodes a 327-kDa protein with extensive homology to the Drosophila melanogaster protein kinase A anchoring protein RG. LRBA, a human gene with a ubiquitous expression pattern mapping to 4q32, encodes a protein closely related to BCL8. The phylogenetically conserved BCL8 gene family evolved by transchromosomal and intrachromosomal duplications within the human genome.

At least eight genes clustered in 1 Mb of DNA on human chromosome (Chr) 11p15.5 are subject to parental imprinting, with monoallelic expression in one or more tissues. Orthologues of these genes show conserved linkage and imprinting on distal Chr 7 of mice. The ex- tended imprinted region has a bipartite structure, with at least two differentially methylated DNA elements (DMRs) controlling the imprinting of two sub-domains. We pre- viously described three biallelically expressed genes (MRPL23, 2G7 and TNNT3) in 100 kb of DNA immedi- ately downstream of the imprinted H19 gene, suggesting that H19 marks one border of the imprinted region. Here we extend this analysis to two additional downstream genes, HRAS and MUCDHL (mu-protocadherin). We find that these genes are biallelically expressed in multiple fe- tal and adult tissues, both in humans and in mice. The mouse orthologue of a third gene, DUSP8, located be- tween H19 and MUCDHL, is also expressed biallelically. The DMR immediately upstream of H19 frequently shows a net gain of methylation in Wilms tumors, either via Chr 11p15.5 loss of heterozygosity (LOH) or loss of imprinting (LOI), but changes in methylation in CpG-rich sequences upstream and within the MUCDHL gene are rare in these tumors and do not correlate with LOH or LOI. These findings are further evidence for a border of the imprinted region immediately downstream of H19, and the data allow the construction of an imprinting map that includes more than 20 genes, distributed over 3 Mb of DNA on Chr 11p15.5.

Therapy-related myelodysplastic syndrome and acute myelogenous leukemia (t-MDS/AML) are serious complications of chemotherapy and radiotherapy for cancer. High-dose chemotherapy followed by autologous stem cell transplantation (ASCT) may be associated with an increased incidence of these complications. The frequency of t-MDS/AML after ASCT for breast cancer is uncertain. We reviewed our database of 379 consecutive breast cancer ASCT patients treated with alkylator-based chemotherapy, followed for a median of 1.52 years (range 0-8.97), with a median survival of 6.16 years. Three patients have developed tMDS/AML. The probability of developing this complication at 5 years is 0.032 in our series. We have used pathologic, cytogenetic and molecular methods to evaluate which portions of therapy may have predisposed to the development of this complication. Cytogenetic abnormalities were not found in the stem cell harvests of these patients by metaphase analysis or by fluorescence in situ hybridization (FISH). One patient demonstrated a clonal X chromosome inactivation pattern in her stem cell harvest, indicating pre-transplant chemotherapy may have been responsible for the development of her leukemia. As two of our patients developed this complication at greater than 4 years post-transplant, the number of cases may increase with longer follow-up. While the incidence appears to be low, further prospective and retrospective analysis will be necessary to determine which portions of therapy predispose to the development of t-MDS/AML in patients undergoing ASCT for treatment of breast cancer.

The mitotic checkpoint protein hsMad2 is required to arrest cells in mitosis when chromosomes are unattached to the mitotic spindle. The presence of a single, lagging chromosome is sufficient to activate the checkpoint, producing a delay at the metaphase-anaphase transition until the last spindle attachment is made. Complete loss of the mitotic checkpoint results in embryonic lethality owing to chromosome mis-segregation in various organisms. Whether partial loss of checkpoint control leads to more subtle rates of chromosome instability compatible with cell viability remains unknown. Here we report that deletion of one MAD2 allele results in a defective mitotic checkpoint in both human cancer cells and murine primary embryonic fibroblasts. Checkpoint-defective cells show premature sister-chromatid separation in the presence of spindle inhibitors and an elevated rate of chromosome mis-segregation events in the absence of these agents. Furthermore, Mad2+/- mice develop lung tumours at high rates after long latencies, implicating defects in the mitotic checkpoint in tumorigenesis.

Cre-mediated deletion of exons 3 and 4 of the mouse Brca2 gene occurring specifically in mammary epithelial cells of conditional female mutants carrying a combination of loxP-modified and null Brca2 alleles resulted in a high incidence (77%) of breast tumors that were often palpable and developed in one or more glands after long latency (time for median tumor-free survival of approximately 1.4 years; total of 40 tumors in 20 animals). These invasive adenocarcinomas were histologically quite uniform, exhibiting predominantly a solid, nodular tumor pattern with very few variants, in striking contrast to the morphological heterogeneity of analogous Brca1-associated tumors. The karyotypes of tumor cells lacking Brca2 had various chromosomal aberrations and ranged from diploid to hypertetraploid, but this wide variability was incongruous with the histological appearance of carcinomas that was comparable between specimens. The implications of these observations in the context of models positing that Brca2 is involved in the maintenance of genomic stability are discussed.

The beclin 1 (BECN1) gene encodes a 60-kDa coiled-coil protein that interacts with the prototypic apoptosis inhibitor Bcl-2. Previous studies indicate that beclin 1 maps to a region approximately 150 kb centromeric to BRCA1 on chromosome 17q21 that is commonly deleted in breast, ovarian, and prostate cancer. The complete cDNA sequence of beclin 1 encodes a 2098-bp transcript, with a 120-bp 5' UTR, 1353-bp coding region, and 625-bp 3' UTR. Hybridization screening of a human genomic PAC library identified PAC 452O8, which contains the complete beclin 1 gene. Determination of the exon-intron structure of beclin 1 reveals 12 exons, ranging from 61 to 794 bp, which extend over 12 kb of the human genome. FISH analysis of human breast carcinoma cell lines using PAC 452O8 as probe identified allelic beclin 1 deletions in 9 of 22 cell lines. Sequencing of genomic DNA from 10 of these cell lines revealed no mutations in coding regions or splice junctions. Additionally, Northern blot analysis of 11 cell lines did not identify any abnormalities in beclin 1 transcripts. These results indicate that human breast carcinoma cell lines frequently contain allelic deletions of beclin 1, but not beclin 1 coding mutations.

Cytogenetic and molecular genetic analyses have shown that the 12q22 region is recurrently deleted in male germ cell tumors (GCTs), suggesting that this site may harbor a tumor suppressor gene (TSG). Previous loss of heterozygosity (LOH) analyses identified a consensus minimal deleted region between the markers D12S377 andD12S296, and a YAC clone contig covering the region was generated. Here, we describe a high-resolution sequence-ready physical map of this contig covering a 3-Mb region. The map comprised of 52 cosmids, 49 PACs, and 168 BACs that were anchored to the previous YAC contig; 99 polymorphic, nonpolymorphic, EST, and gene-based markers are now placed on this map in a unique order. Of these, 61 markers were isolated in the present study, including one that was polymorphic. In addition, we have narrowed the minimal deletion to ∼830 kb betweenD12S1716 (proximal) and P382A8-AG (distal) by LOH analysis of 108 normal-tumor DNAs from GCT patients using 21 polymorphic STSs. These physical and deletion maps should prove useful for identification of the candidate TSG in GCTs, provide framework to generate complete DNA sequence, and ultimately generate a gene map of this segment of the chromosome 12.[The sequence data described in this paper have been submitted to the Genome Survey Sequence under accession nos. AQ254896–AQ254955 andAQ269251–AQ269266. Online supplementary material is available athttp://www.genome.org]

Background: Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis and increased risk of progression to acute myeloid leukemia (AML). A hallmark of MDS is increased apoptosis, while AML undergoes decreased apoptosis and increased proliferation. BCL2, an anti-apoptotic protein, is overexpressed in high grade MDS and AML and may confer poor prognosis and increased chemotherapy resistance. In this study we examined the DNA methylation status of BCL2 in MDS and AML. Methods: We conducted DNA methylation profiling on genomic DNA extracted from bone marrows of 22 refractory anemia with ringed sideroblasts (RARS), 8 refractory anemia with excess blasts (RAEB), 21 de novo AML, 21 therapy related AML, and 7 normal volunteers. We used both Illumina 27K BeadChip and 450K BeadChip methylation arrays to assess CpG methylation. Standard student T-test was used to screen differentially methylated MDS and AML CpG sites compared to normal samples. We validated the microarray data by combined bisulfite restriction analysis (COBRA) and bisulfite sequencing. Results: We identified a region in the BCL2 gene body that was among the most differentially methylated in MDS and AML versus normal bone marrow. Within that amplicon, BCL2 in both RARS, a low grade MDS, and RAEB, a high grade MDS, were hypermethylated compared to normal bone marrow (43% vs 18%, 48% vs 18%, respectively, p Conclusions: Our study identifies a region of BCL2 that is hypermethylated in both low and high risk MDS while hypomethylated in AML compared to normal bone marrows. We hypothesize aberrant epigenetic modification of BCL2 plays a key role in apoptosis and transformation from MDS to AML, and our data support the idea of combining demethylating drugs with BCL2 antagonists. We are currently investigating whether BCL2 protein expression correlates with methylation, and plan to map the histone marks with CHIP-seq to correlate chromatin accessibility and DNA methylation in BCL2. Citation Format: Sangmin Lee, Naomi Galili, Stephen Nimer, Mark D. Minden, Vundavalli V. Murty, Suresh Jhanwar, Azra Raza, Benjamin Tycko. Loss of methylation in a regulatory region of BCL2 in MDS/AML. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2989. doi:10.1158/1538-7445.AM2013-2989

Deletion of 9p21–22 is a common genetic alteration in dysplastic, in situ, and invasive head and neck squamous cell carcinoma (HNSCC). However, a candidate tumor suppressor gene (TSG) at this site has thus far not been identified in HNSCC. We report homozygous deletion of the recently identified multiple tumor suppressor I (MTSI)/cyclin-dependent kinase-4-inhibitor (CDKN2) gene mapped to 9p21, which encodes the p16 protein, a regulator of cyclin-dependent kinase 4, in six of 16 HNSCC cell lines. We also show absence of the CDKN2 mRNA in all cell lines with CDKN2 deletion as well as in an additional two cell lines without deletion. Overall, we have identified 9p abnormalities in 12 of 16 (75%) cell lines, at least nine of which involved CDKN2. We further demonstrate that the CDKN2 deletion in HNSCC is located within a previously described region of allelic loss between D9S171 and IFNW, which spans a 4 cM region of 9p. However, examination of 36 primary tumors revealed genetic alterations in only seven of 36 (19%) tumors. These results suggest that genetic alterations at CDKN2 are frequent in HNSCC cell lines, but the role of this gene in primary tumors is less compelling. CDKN2 does not appear to be the only TSG on 9p21 in HNSCC, and our results suggest that another region of deletion exists proximal to the IFNW locus. © 1995 Wiley-Liss, Inc.

Background : Development of uterine cervical cancer is preceded by preneoplastic proliferative changes in the cervical epithelium called intra-epithelial neoplasia or dysplasia. The genetic basis of the origin and progression of such preneoplastic lesions is not known. By analysis of carcinomas for loss of constitutional heterozygosity (LOH), we have previously shown a high frequency of allelic loss in the short arm of chromosome 5 (5p), suggesting loss of a candidate tumor suppressor gene located in 5p and associated with the development of this tumor. Purpose : To further understand the role of genetic alterations that affect 5p in cervical carcinogenesis, we evaluated the status of microsatellite polymorphisms at five loci mapped to 5p14-ter in precancerous and cancerous lesions. Methods : Biopsy specimens from two groups of patients were analyzed for genetic alterations affecting 5p. One group comprised 14 cases of precancerous lesions (i.e., dysplasias) and five cases of carcinoma in situ (CIS) ; the second group comprised 46 previously untreated patients with invasive carcinoma. Tumor and normal DNAs were analyzed by polymerase chain reaction for genetic losses and instability at five polymorphic microsatellite loci (D5S392, D5S406, D5S208, D5S117, and D5S432) mapped to 5p. Results : LOH was observed in 25 (55.6%) of 45 informative invasive carcinomas, one (20%) of five cases of CIS, and three (21%) of 14 precancerous lesions. Among the loci tested, D5S406 (5p15.1-15.2) exhibited LOH in 12 (48%) of 25 invasive carcinomas, one (33%) of three cases of CIS, and three (60%) of five precancerous lesions, suggesting this to be the site in 5p of the novel candidate tumor suppressor gene. In addition, replication error-type alterations were noted in the 5p14-ter region in six (13%) of 46 invasive carcinomas, two (40%) of five cases of CIS, and three (21%) of 14 precancerous lesions. Instability affected D5S406 in eight (66.7%) of 12 instances that showed microsatellite instability. Conclusion : These observations suggest that allelic loss and microsatellite instability in the region of D5S406 may play a role early in the development of cervical carcinoma and identify the site of a candidate tumor suppressor gene. These genetic markers (allelic loss and microsatellite instability) may also define CIS and precancerous lesions at high risk for progression to invasive cancer. Implications : The future molecular cloning of the candidate tumor suppressor gene at 5p15.1-15.2 may provide new insights into the genetic mechanisms of cervical carcinogenesis. Analysis and clinical follow-up of a large cohort of prospectively ascertained cases of precancerous lesions would help to validate the usefulness of these markers. [J Natl Cancer Inst 87 :742-745, 1995]

Publisher Summary This chapter discusses molecular genetics in germ cell tumors (GCT). GCTs in the male arise in spermatogonial cells; they are heterogeneous, and some subsets exhibit embryonal-like differentiation. Therefore, they provide unusual opportunities for the analysis of the genetic basis of malignant transformation and differentiation in a stem cell system of unique destiny. GCTs are present in gonadal or extragonadal sites and histologically comprise seminomas and nonseminomas. The genetic basis of transformation in germ cells and regulation of in vivo differentiation in this complex tumor system remain largely unknown. This chapter presents a summary of current results of the cytogenetic and molecular analyses of male GCTs. These studies have led to a new model of transformation of a germ cell in differentiation. The model, unlike the currently well-established models of tumorigenic transformation calls for rescue, by amplification and over expression of a key gene or genes, of a cell otherwise destined to die because of inability to complete the developmental program. The chapter also discusses the studies initiated to identify specific genetic alterations that may release constraints on embryonal-like differentiation of a germ cell independently of fertilization.

Abstract 2635 BACKGROUND: Hairy cell leukemia (HCL) is a rare type of B-cell non Hodgkin lymphoma (B-NHL), which is characterized by neoplastic cells exhibiting slender cytoplasmic projections and an activated phenotype. Unlike other B-NHL, HCL lacks characteristic recurrent chromosome abnormalities and its etiology remains elusive. Recently, the BRAF V600E mutation was described to occur at a high frequency in HCL in contrast to other B-NHL, suggesting that the BRAF V600E mutation could represent a disease defining lesion and a possible therapeutic target. In this study, we determined the prevalence of the BRAF V600E mutation in a large series of low and intermediate grade B-NHL and assessed the relationship of this mutation, if any, with microsatellite instability (MSI). METHODS: DNA was extracted from various low and intermediate grade B-NHL (n=100), as defined by the 2008 World Health Organization Classification, which comprised HCL (n=10 from 6 patients), chronic lymphocytic leukemia/small lymphocytic lymphoma (n=22), mantle cell lymphoma (n=19), marginal zone lymphoma (n=22), follicular lymphoma (n=20) and lymphoplasmacytic lymphoma (n=7). Percentage of neoplastic cells was assessed by flow cytometry (n=99) or immunohistochemistry (n=1). Presence of BRAF V600E mutation was determined using a real time PCR assay using allele-specific hydrolysis (“Taqman”) probes. The detection limit of the assay was determined by diluting DNA extracted from a fresh HCL sample with normal high molecular weight DNA extracted by the same method. MSI analysis was performed using a multiplex reaction for 5 quasi monomorphic mononucleotide repeat markers (BAT-25, BAT-26, MONO-27, NR-21 and NR-24) and two highly polymorphic penta nucleotide markers (Penta C and Penta D) as sample identifiers. In the absence of normal DNA for comparison, a sample was considered MSI-H if greater than two markers showed an altered pattern, indeterminate if only two showed an alteration and MSS if no marker showed an altered allele. RESULTS: The ubiquitous occurrence and high specificity of the BRAF V600E mutation for HCL was confirmed in our series of B-NHL. The HCL samples consisted of 10 specimens from 6 patients and were the initial diagnostic specimen in 2 patients. The percentage of neoplastic cells in these samples ranged from 1% to 78.4% (median 18.2%). The BRAF V600E mutation was detected in 7 of 10 (70%) samples of HCL from 5 of 6 (83%) patients. The proportion of hairy cells was ≤5% in samples where the mutation was not detected. All 90 of the other low and intermediate grade B-NHL (>50% tumor burden) were negative for the V600E mutation. Compared to the reported sensitivity of approximately 30% tumor cells for detecting the BRAF V600E mutation by Sanger sequencing, our real time PCR assay allowed detection of the mutation in samples containing ≥9.8% tumor cells. Analysis of the HCL cases for MSI revealed that all cases had a microsatellite stable (MSS) phenotype. CONCLUSIONS: The BRAF V600E mutation appears specific for HCL among low and intermediate grade B-NHL and is not associated with microsatellite instability. These characteristics thus warrant inclusion in disease definition. Further refinements of a realtime PCR based approach for detecting the BRAF V600E mutation might be of utility in diagnosis and disease monitoring, as the neoplastic cellular yield is often limited in HCL due to underlying myelofibrosis. Disclosures: No relevant conflicts of interest to declare.

We have used an in situ hybridization method for analysis of expression of BCL2 and MYC on cytospun preparations of normal and malignant lymphoid cell lines and tissue sections of normal and malignant lymph nodes. The probes comprised 50-mer antisense oligonucleotides starting at the ATG codons of exon 3 of BCL2 and exon 2 of MYC. We studied the expression of these two genes in frozen tissue sections of biopsy specimens derived from normal and hyperplastic lymph nodes, B-cell lymphomas carrying the t(14;18)(q32;q21) and t(8;14)(q24;q32) translocations, and T-cell lymphomas with clonal chromosome abnormalities. While all proliferating cells expressed both genes, BCL2 expression was increased two- to threefold in follicular lymphomas with t(14;18) and MYC expression was increased two- to four-fold in high-grade lymphomas with t(8;14). These results are consistent with previous data on deregulated expression of these genes obtained from study of lymphoma cell lines carrying the relevant translocations.

Human male germ cell tumors (GCTs) result from malignant transformation of premeiotic or early meiotic germ cells and exhibit embryonal-like differentiation of the three germinal layers. The genetic basis of origin and expression of differentiated phenotypes by GCTs are poorly understood. Our recent cytogenetic analysis of a large series of GCTs has shown that two chromosome 12 abnormalities, an isochromosome for the short arm [i(12p)] and deletions in the long arm [del(12q)], characterize these tumors, which led us to suggest that the deletions represent loss of one or more candidate tumor suppressor genes whose products regulate the normal proliferation of the spermatogonial stem cells. We undertook a molecular mapping of the deletions by comparing germ-line and tumor genotypes of eight polymorphic loci in paired normal/tumor DNA samples from 45 GCT patients. Analysis of loss of constitutional heterozygosity at these loci revealed two regions of frequent loss (> 40%), one at 12q13 and the other at 12q22, identifying the sites of the postulated tumor suppressor genes. One tumor (no. 143A) exhibited a homozygous deletion of a region of 12q22, which included the MGF gene. The KIT and MGF genes have been shown to play key roles in embryonal and postnatal development of germ cells; therefore, we evaluated their expression by Northern blot analysis in a panel of three GCT cell lines and 24 fresh GCT biopsies. Deregulated expression of MGF and KIT, which was discordant between seminomatous and nonseminomatous lesions, was observed.

Distinct cell-cycle-dependent changes in the conformation of centromeric chromatin in a specific human chromosome containing α-satellite DNA have been demonstrated by fluorescence in situ hybridization (FISH). This method, based upon specific FISH signal morphology, allows simultaneous analysis of chromosomal aneuploidy and detection of specific cell-cycle stage(s) of human tumor and/or normal cell populations in a single preparation of interphase cells. This interphase cytogenetic procedure might prove useful for both basic and clinical research involving human cells.

The BCL10 gene has recently been cloned from the chromosomal translocation t(1;14)(p22;q32) in a low-grade mucosa-associated lymphoid tissue (MALT) lymphoma, and was implicated in the pathogenesis of this and several other tumor types (Willis et al. 1999xWillis, T.G., Jadayel, D.M., Du, M.-Q., Peng, H., Perry, A.R., Abdul-Rauf, M., Price, H., Karran, L., Majekodunmi, O., Wlodarska, I., Pan, L., Crook, T., Hamoudi, R., Isaacson, P.G., and Dyer, M.J.S. Cell. 1999; 96: 35–45Abstract | Full Text | Full Text PDF | PubMed | Scopus (470)See all ReferencesWillis et al. 1999). BCL10 is a cellular homolog of the equine herpesvirus-2 E10 gene, which contains an amino-terminal caspase recruitment domain (CARD) and plays a role in apoptosis. Willis et al. 1999xWillis, T.G., Jadayel, D.M., Du, M.-Q., Peng, H., Perry, A.R., Abdul-Rauf, M., Price, H., Karran, L., Majekodunmi, O., Wlodarska, I., Pan, L., Crook, T., Hamoudi, R., Isaacson, P.G., and Dyer, M.J.S. Cell. 1999; 96: 35–45Abstract | Full Text | Full Text PDF | PubMed | Scopus (470)See all ReferencesWillis et al. 1999 also showed that BCL10 exhibits hypermutations in MALT lymphomas with t(1;14) as well as frequent mutations in 45% of B and T cell lineage lymphomas without the 1p22 chromosomal rearrangements. In addition, they reported BCL10 mutations in cell lines derived from several solid tumor types including three each of male germ cell tumors (GCTs) and mesotheliomas, suggesting that it may be commonly involved in the pathogenesis of many human malignancies. The 1p22 region is affected by frequent deletions in male GCTs (Mathew et al. 1994xMathew, S., Murty, V.V.S., Bosl, G.J., and Chaganti, R.S.K. Cancer Res. 1994; 54: 6265–6299PubMedSee all ReferencesMathew et al. 1994) and mesotheliomas (Lee et al. 1996xLee, W.C., Balsara, B., Liu, Z., Jhanwar, S.C., and Testa, J.R. Cancer Res. 1996; 56: 4297–4301PubMedSee all ReferencesLee et al. 1996), suggesting that inactivation of a critical gene in this region may play a role in the genesis of these tumors.In order to validate a possible role for BCL10 in male GCT and lymphoma pathogenesis, we performed mutation analysis of its coding region in a panel of 59 GCTs (41 primary tumors and 18 cell lines) (Murty et al. 1994xMurty, V.V.V.S., Bosl, G.J., Houldsworth, J., Meyers, M., Mukherjee, A.B., Reuter, V., and Chaganti, R.S.K. Oncogene. 1994; 9: 2245–2251PubMedSee all ReferencesMurty et al. 1994), 15 MALT lymphomas, and 15 follicular lymphomas (Offit et al. 1993xOffit, K., Parsa, N.Z., Gaidano, G., Filippa, D.A., Louie, D., Pan, D., Jhanwar, S.C., Dalla-Favera, R., and Chaganti, R.S.K. Blood. 1993; 82: 2157–2162PubMedSee all ReferencesOffit et al. 1993). The coding region of BCL10 was amplified as described (Willis et al. 1999xWillis, T.G., Jadayel, D.M., Du, M.-Q., Peng, H., Perry, A.R., Abdul-Rauf, M., Price, H., Karran, L., Majekodunmi, O., Wlodarska, I., Pan, L., Crook, T., Hamoudi, R., Isaacson, P.G., and Dyer, M.J.S. Cell. 1999; 96: 35–45Abstract | Full Text | Full Text PDF | PubMed | Scopus (470)See all ReferencesWillis et al. 1999) and SSCP analysis was performed by standard methods (Orita et al. 1989xOrita, M., Suzuki, Y., Sekiya, T., and Hayashi, K. Genomics. 1989; 5: 874–879Crossref | PubMed | Scopus (2705)See all ReferencesOrita et al. 1989). We reasoned that if BCL10 is the target gene deleted, it should exhibit mutations in cases with loss of heterozygosity (LOH), and we included 11 such tumors in the panel of 41 primary GCTs (Mathew et al. 1994xMathew, S., Murty, V.V.S., Bosl, G.J., and Chaganti, R.S.K. Cancer Res. 1994; 54: 6265–6299PubMedSee all ReferencesMathew et al. 1994). Among the cell lines studied, we also included the Tera-1, Tera-2, and GCT-44 cell lines studied by Willis et al. 1999xWillis, T.G., Jadayel, D.M., Du, M.-Q., Peng, H., Perry, A.R., Abdul-Rauf, M., Price, H., Karran, L., Majekodunmi, O., Wlodarska, I., Pan, L., Crook, T., Hamoudi, R., Isaacson, P.G., and Dyer, M.J.S. Cell. 1999; 96: 35–45Abstract | Full Text | Full Text PDF | PubMed | Scopus (470)See all ReferencesWillis et al. 1999. Conformational changes were noted with high frequency in both GCTs and lymphomas in exon 1 and in 11 cases in exon 3 (5 GCTs and 6 lymphomas) (Table 1Table 1). No variants were found in either tumor in exon 2. All SSCP variants in exon 3 in both tumors were identical while exon 1 variants exhibited a complex pattern (Figure 1AFigure 1A). In order to determine if the SSCP variants represent somatic mutations or genetic polymorphisms, we analyzed paired normal-tumor DNAs by SSCP in 14 of 15 exon 1 variants and all 5 exon 3 variants in GCTs. We found identical SSCP variants in all cases, suggesting that these represent genetic polymorphisms.Figure 1Genetic Analysis of BCL10 in Germ Cell Tumors (GCTs) and B Cell Lymphomas(A) PCR-SSCP analysis. (a) and (c), GCT; (b) and (d), lymphoma. (a) and (b), exon 1; (c) and (d), exon 3.2. Arrows indicate conformational changes. N, normal; T, tumor; CL, cell line; tumor numbers are indicated on top.(B) PCR sequence analysis. (a) and (b), Tera-1; (c), GCT-44; (d) and (e), Tera-2; (f), T-243A; (g)–(i), 240A. Panels (a)–(e) show absence of mutations in GCT cell lines in relation to Willis et al. 1999xWillis, T.G., Jadayel, D.M., Du, M.-Q., Peng, H., Perry, A.R., Abdul-Rauf, M., Price, H., Karran, L., Majekodunmi, O., Wlodarska, I., Pan, L., Crook, T., Hamoudi, R., Isaacson, P.G., and Dyer, M.J.S. Cell. 1999; 96: 35–45Abstract | Full Text | Full Text PDF | PubMed | Scopus (470)See all ReferencesWillis et al. 1999 report, where boxes indicate base change and upward arrow indicates insertion positions. Positions in coding region of cDNA are: (a), 172 bp; (b), 653 bp; (c), 172 bp; (d), 58 bp; (e), insertion at 499 bp. Panel (f), A/G heterozygosity at position 2 of codon 213. Panels (g)–(i) indicate loss of heterozygosity at codon 5 (underlined) in tumor and cell line 240A. Panel (g), normal DNA; panel (h), tumor DNA; panel (i) cell line DNA. The residual peak of G in panel (h) indicates the presence of contaminating normal cells.(C) Multiplex RT-PCR analysis of BCL10 expression in GCT. Primer from the 5′ coding region (5′-GGACCCGGAAGAAGCGCCATCTCC-3′ and 5′-AAGTAGTCTAACAATTTTCCAGCCC-3′) spanning two different exons were used to amplify a 249 bp PCR product. PCR was performed utilizing AmpliTaq DNA polymerase (PE Applied Biosystems, Foster City, CA). The 450 bp PCR product represents β-actin as control. Marker, PhiX HaeIII; tumor and cell line numbers are shown on top.View Large Image | View Hi-Res Image | Download PowerPoint SlideTable 1Analysis of BCL10 Sequence Alterations in GCT and NHLTumor TypeNo. StudiedSSCP VariantsPosition of Sequence Variation in cDNA (amino acid)Germ cell tumor59Exon 1–Intron 115 (25.5%)703 G/T (Ala/Ser) 714 G/C (Leu/Leu) Intron 1, 58 G/CExon 35 (8.5%)1328 G/A (Gly/Glu)Non-Hodgkin's Lymphoma30Exon 1–Intron 110 (33.3%)703 G/T (Ala/Ser) 714 G/C (Leu/Leu) Intron 1, 58 G/CExon 36 (20.0%)1328 G/A (Gly/Glu)To identify the nature of alterations associated with conformation variations, we determined the sequences of 9 exon 3 (paired normal-tumor DNAs in 5 GCTs and 4 lymphomas) variants and 12 exon 1 variants (paired normal-tumor DNAs in 7 GCTs and 4 lymphomas) (Table 1Table 1). We found identical sequences in both normal and tumor DNAs in each case. Although we did not find SCCP variants in the 3 GCT cell lines (Tera-1, Tera-2, and GCT-44), we sequenced the exons and found no sequence alterations (Figure 1BFigure 1B). This analysis also identified the sequence variation reflected in SSCP variants. The region amplified for exon 1 exhibited 3 different polymorphisms, 2 in the coding region and one in 5′ intron 1. These included G/T in the first base of codon 5, G/C at the third base of codon 8, and a C/G polymorphism in intron 1. The polymorphism in exon 3 was G/A at second base of codon 213. Consistent with the reported high frequency of LOH at the 1p22 region in GCT, the tumor and the cell line from GCT-240A were reduced to homozygosity at all polymorphic loci in exon 1–intron 1 compared to germline heterozygosity (Figure 1BFigure 1B). Thus, these data are at variance with the results reported by Willis et al. 1999xWillis, T.G., Jadayel, D.M., Du, M.-Q., Peng, H., Perry, A.R., Abdul-Rauf, M., Price, H., Karran, L., Majekodunmi, O., Wlodarska, I., Pan, L., Crook, T., Hamoudi, R., Isaacson, P.G., and Dyer, M.J.S. Cell. 1999; 96: 35–45Abstract | Full Text | Full Text PDF | PubMed | Scopus (470)See all ReferencesWillis et al. 1999. The changes noted by them, mostly truncations or missense mutations supported a tumor suppressor gene (TSG) role for BCL10. Our data contradict this presumption in GCTs and B cell lymphomas, and provide evidence for polymorphisms in BCL10 coding region.Lack of mutation in the BCL10 coding region may not exclude it as a deleted TSG. Other genetic or epigenetic mechanisms such as alterations in promoter or methylation patterns can silence gene expression (1xBaylin, S.B., Herman, J.G., Graff, J.R., Vertino, P.M., and Issa, J.P. Adv. Cancer Res. 1998; 72: 141–196Crossref | PubMedSee all References, 2xForget, B.G. Ann. N.Y. Acad. Sci. 1998; 30;850: 38–44Crossref | Scopus (91)See all References). In order to examine this possibility, we employed a multiplex RT-PCR strategy to analyze BCL10 expression. This analysis revealed detectable levels of expression in 14 of 16 GCTs (10 cell lines and 6 primary tumors) examined. BCL10 message could not be detected in the remaining 2 cells lines, 577M-F and 2102E-R, after 45 cycles of PCR amplification (Figure 1CFigure 1C). Thus, the present analysis rules out a role for BCL10 as a TSG in the majority of GCTs. On the basis of the data presented, we conclude that BCL10 is not a target TSG at 1p22 in male GCTs or B cell lymphomas.‡To whom correspondence should be addressed (e-mail: vvm2@columbia.edu).

Marginal zone lymphoma (MZL) is a B-cell non-Hodgkin lymphoma (B-NHL) derived from marginal-zone B-cells. The current WHO classification recognizes three types of MZLs, which comprise extranodal MZL (EMZL), nodal MZL (NMZL), and splenic MZL (SMZL). Four recurrent and mutually exclusive chromosomal translocations: t(11;18)(q21;q21), t(1;14)(p22;q32), t(14;18)(q32;q21), and t(3;14)(p14.1;q32) have been described in EMZLs, but not in NMZLs or SMZLs, with frequencies ranging from 0–40% depending on differing anatomic sites and geographic regions. At least three of these translocations, t(11;18) API2/MALT1, t(1;14) IgH/BCL10, and t(14;18) IgH/MALT, result in constitutive activation of nuclear factor-kB (NF-kB), a transcription factor complex regulating multiple cellular processes including cell growth and survival. Approximately 25% of MZL however, lack any recognizable recurrent genetic alteration. Recently, biallelic deletions of the chromosomal region 6q23.3-q24.1 containing the tumor necrosis factor alpha-induced protein 3 (TNFAIP3, A20), which is a negative regulator of NF-kB, were detected in ocular adnexal MZLs, suggesting a role for A20 as a tumor suppressor in this disease entity. Here, we investigated a panel of 32 cases representing all three types of MZLs by PCR amplification and sequencing of the A20 coding exons. FISH was also performed using locus specific probes for A20 and Blimp1. Five 1–2 bp deletions and a single bp insertion, all leading to premature stop codons, were identified in 5/20 (25%) non-splenic MZLs and 1/12 (8.3%) SMZLs. The somatic nature of the mutations was confirmed by analyzing matched normal DNA in 4 cases. All A20 mutations were predictive of severely truncated polypeptides lacking functionally relevant domains. Genetic loss of A20 was detected by FISH in 4/20 (20%) non-splenic MZLs, including 1 with biallelic loss, but not in SMZLs. Two of the four A20 deletions seen by FISH were also observed by array-CGH. Deletions encompassing Blimp1 were not detected in cases with A20 deletions. No evidence for epigenetic silencing of A20 via promoter methylation of CpG islands was found in 10 MZLs analyzed. Thus, biallelic inactivation of A20, either via deletion of both alleles or frameshift mutations of one allele and loss of the second allele was identified in 3/20 (15%) non-splenic MZLs, while an additional 4/20 (20%) non-splenic MZLs displayed monoallelic A20 inactivation by mutations (N=3) or deletion (N=1). When we determined the relationship between A20 inactivation and trisomy 18 or the translocations associated with constitutive activation of NF-kB, A20 inactivation appeared mutually exclusive with these cytogenetic aberrations, with the exception of one case that had trisomy 18. In summary, our results indicate that A20 is mono- or biallelically inactivated in approximately one third of MZLs, arising in both nodal (3/9, 33.3%) and extranodal sites (4/11, 36.4%), and in a minority of SMZLs (1/12, 8.3%). Evidence of a classic two-hit mechanism was observed in 3/20 (15%) non-splenic MZL. In addition, detection of MZLs with monoallelic inactivation suggests a haploinsufficient role of A20 as a tumor suppressor. Thus, A20 inactivation may represent a common mechanism for constitutive activation of the NF-kB pathway, which, in turn, may contribute to lymphomagenesis by stimulating cell proliferation and survival. The identification of genetic lesions in MZLs that deregulate NF-kB activity offers the possibility of targeted therapeutic intervention.

We report the karyotypic analysis of seven testicular and one ovarian germ cell tumor (GCT) cell lines, a number of which have previously been partially investigated. An i(12p) was found in each of the testicular GCT cell lines, while it was absent in the ovarian GCT cell line. Thus, our study extends to cell lines the observation from fresh tumor tissues that i(12p) is a highly nonrandom chromosomal abnormality of testicular GCT. Additional consistent nonrandom abnormalities in the testicular GCT cell lines included the following: del(1)(p22), del(1)(q21), i(1q), del(7)(q11.2), and del(12)(q14). The del(12)(q14) abnormality was identified in five of the cell lines investigated. This observation, together with previous detection of this marker chromosome in fresh tumor specimens by us and others, suggests that loss of genetic material on 12q may represent a primary change associated with malignant transformation of testicular germ cells. As reported in a previous study, a t(15;20)(p11;q11) translocation was identified in the ovarian GCT cell line. Interestingly, it also was seen in one testicular GCT cell line. In addition, a der(15)t(15;20)(p11;q11) marker chromosome was identified in two other testicular GCT cell lines. Thus, this reinvestigation of GCT cell lines has resolved the discrepancy regarding the occurrence of i(12p) in fresh tumors versus established cell lines and identified additional nonrandom abnormalities of potential importance to the development of GCTs.

ContextTGFBR1*6A is a common polymorphism of the type I transforming growth factor β receptor (TGFBR1). Epidemiological studies suggest that TGFBR1*6A may act as a tumor susceptibility allele. How TGFBR1*6A contributes to cancer development is largely unknown.ObjectivesTo determine whether TGFBR1*6A is somatically acquired by primary tumors and metastases during cancer development and whether the 3–amino acid deletion that differentiates TGFBR1*6A from TGFBR1 is part of the mature receptor or part of the signal sequence and to investigate TGFBR1*6A signaling in cancer cells.Design, Setting, and PatientsTumor and germline tissues from 531 patients with a diagnosis of head and neck, colorectal, or breast cancer recruited from 3 centers in the United States and from 1 center in Spain from June 1, 1994, through June 30, 2004. In vitro translation assays, MCF-7 breast cancer cells stably transfected with TGFBR1*6A, TGFBR1, or the vector alone, DLD-1 colorectal cancer cells that endogenously carry TGFBR1*6A, and SW48 colorectal cancer cells that do not carry TGFBR1*6A.Main Outcome MeasuresTGFBR1*6A somatic acquisition in cancer. Determination of the amino terminus of the mature TGFBR1*6A and TGFBR1 receptors. Determination of TGF-β–dependent cell proliferation.ResultsTGFBR1*6A was somatically acquired in 13 of 44 (29.5%) colorectal cancer metastases, in 4 of 157 (2.5%) of colorectal tumors, in 4 of 226 (1.8%) head and neck primary tumors, and in none of the 104 patients with breast cancer. TGFBR1*6A somatic acquisition is not associated with loss of heterozygosity, microsatellite instability, or a mutator phenotype. The signal sequences of TGFBR1 and TGFBR1*6A are cleaved at the same site resulting in identical mature receptors. TGFBR1*6A may switch TGF-β growth inhibitory signals into growth stimulatory signals in MCF-7 breast cancer cells and in DLD-1 colorectal cancer cells.ConclusionsTGFBR1*6A is somatically acquired in 29.5% of liver metastases from colorectal cancer and may bestow cancer cells with a growth advantage in the presence of TGF-β. The functional consequences of this conversion appear to be mediated by the TGFBR1*6A signal sequence rather than by the mature receptor. The results highlight a new facet of TGF-β signaling in cancer and suggest that TGFBR1*6A may represent a potential therapeutic target in cancer.

Background Male germ cell tumor (GCT) is a highly curable malignancy, which exhibits exquisite sensitivity to cisplatin treatment. The genetic pathway(s) that determine the chemotherapy sensitivity in GCT remain largely unknown.

Cervical cancer (CC), a leading cause of cancer-related deaths in women worldwide, has been causally linked to genital human papillomavirus (HPV) infection. Although a host of genetic alterations have been identified, molecular basis of CC development is still poorly understood. We examined the role of promoter hypermethylation, an epigenetic alteration that is associated with the silencing tumor suppressor genes in human cancer, by studying 16 gene promoters in 90 CC cases. We found a high frequency of promoter methylation in CDH1, DAPK, RARB, and HIC1 genes. Correlation of promoter methylation with clinical characteristics and other genetic changes revealed the following: a) overall promoter methylation was higher in more advanced stage of the disease, b) promoter methylation of RARB and BRCA1 predicted worse prognosis, and c) the HIC1 promoter methylation was frequently seen in association with microsatellite instability. Promoter methylation was associated with gene silencing in CC cell lines. Treatment with methylation or histone deacetylation-inhibiting agents resulted in profound reactivation of gene expression. These results may have implications in understanding the underlying epigenetic mechanisms in CC development, provide prognostic indicators, and identify important gene targets for treatment.

Background Previous studies have shown that the short arm of chromosome 5 (5p) exhibit frequent genetic changes in invasive cervical carcinoma (CC), and that these changes arise early during the carcinogenesis, in precancerous lesions. These data therefore suggest that loss of candidate tumor suppressor genes located on 5p is associated with the development of CC. However, the precise location of 5p deletions is not known.

Human male germ cell tumors (GCTs) arise from undifferentiated primordial germ cells (PGCs), a stage in which extensive methylation reprogramming occurs. GCTs exhibit pluripotentality and are highly sensitive to cisplatin therapy. The molecular basis of germ cell (GC) transformation, differentiation, and exquisite treatment response is poorly understood. To assess the role and mechanism of promoter hypermethylation, we analyzed CpG islands of 21 gene promoters by methylation-specific PCR in seminomatous (SGCT) and nonseminomatous (NSGCT) GCTs. We found 60% of the NSGCTs demonstrating methylation in one or more gene promoters whereas SGCTs showed a near-absence of methylation, therefore identifying distinct methylation patterns in the two major histologies of GCT. DNA repair genes MGMT, RASSF1A, and BRCA1, and a transcriptional repressor gene HIC1, were frequently methylated in the NSGCTs. The promoter hypermethylation was associated with gene silencing in most methylated genes, and reactivation of gene expression occured upon treatment with 5-Aza-2' deoxycytidine in GCT cell lines. Our results, therefore, suggest a potential role for epigenetic modification of critical tumor suppressor genes in pathways relevant to GC transformation, differentiation, and treatment response.

The FES oncogene was previously localized to human chromosome 15 by analysis of mouse × human somatic cell hybrids and to 15q26 by in situ hybridization of a radioacively labeled probe. In the present study, using fluorescence in situ hybridization, we have determined the precise map position of FES at 15q26.1.

Genomic DNA segments for the coagulation factor VIIIc gene (F8C), which exhibits only limited restriction length polymorphism, map to the proximal region of band Xq28 by somatic cell hybridization analysis and in situ hybridization. Using somatic cell hybrids, we have obtained data which place probes DX13 (used to detect locus DXS15) and Stl4 (used to detect DXS52) distal to F8C, within band Xq28. Previous studies have mapped the factor IX gene (F9) and probe 52A (used to detect DXS51) proximal to F8C, in Xq26→q27 and Xq27, respectively (Camerino et al., 1984; Drayna et al, 1984; Mattei et al., 1985). Thus, the relative order of genetic marker loci in the Xq27→qter region is most likely cen-F9-DXS51-F8C-(DXS15, DXS52)-Xqter* The collection of these molecular probes is thus potentially useful in three-factor crosses of factor VIII gene segregation.

We have used serologic, biochemical, and genetic methods to characterize two stage-specific human differentiation antigens of neural and melanocytic cells: A42 (57,000 Mr glycoprotein) and J143 (140,000/30,000 Mr glycoprotein). The genes determining A42 and J143 cell surface expression in rodent-human hybrids were chromosomally mapped, and the respective human chromosomes were introduced into rodent cells derived from distinct differentiation lineages. Serologic analysis of the resulting hybrid clones has permitted the identification of two types of regulatory signals determining A42 and J143 expression. First, both antigens are expressed in hybrids constructed with antigen-positive human cells and also in certain hybrids constructed with antigen-negative human cells, indicating that intrinsic signals provided by the differentiation program of the rodent fusion partner induce antigen expression. Second, a series of human-mouse neuroblastoma hybrids, which are A42- or J143- when cultured on plastic surfaces, can be induced to express the antigens when cultured on substrates coated with extracellular matrix (ECM) produced by bovine corneal endothelial cells or fibronectin. This induction of antigen expression by extrinsic, ECM-derived signals is accompanied in the neuroblastoma hybrids by increased substrate adhesiveness and cell spreading and by characteristic changes in cell morphology. A similar program of phenotypic changes is also seen in spontaneous variants of human neuroblastoma and Ewing's sarcoma cells and in ECM-induced Ewing's sarcoma cells. These findings suggest that ECM-derived signals have a role analogous to mitogens and soluble differentiation factors in modulating differentiation phenotypes and tissue-specific patterns of cell surface antigen expression.