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Sporadic clear cell renal cell carcinoma (cRCC) is genetically characterized by the recurrent loss of the short arm of chromosome 3, with a hotspot for copy number loss in the 3p21 region. We applied a method called “gene identification by nonsense-mediated mRNA decay inhibition” to a panel of 10 cRCC cell lines with 3p21 copy number loss to identify biallelic inactivated genes located at 3p21. This revealed inactivation of the histone methyltransferase gene SETD2, located on 3p21.31, as a common event in cRCC cells. SETD2 is nonredundantly responsible for trimethylation of the histone mark H3K36. Consistent with this function, we observed loss or a decrease of H3K36me3 in 7 out of the 10 cRCC cell lines. Identification of missense mutations in 2 out of 10 primary cRCC tumor samples added support to the involvement of loss of SETD2 function in the development of cRCC tumors. Cancer Res; 70(11); 4287–91. ©2010 AACR.

Supplementary Figure 1 from Histone Methyltransferase Gene SETD2 Is a Novel Tumor Suppressor Gene in Clear Cell Renal Cell Carcinoma

Supplementary Figure 3 from Histone Methyltransferase Gene SETD2 Is a Novel Tumor Suppressor Gene in Clear Cell Renal Cell Carcinoma

Supplementary Table 3 from Histone Methyltransferase Gene SETD2 Is a Novel Tumor Suppressor Gene in Clear Cell Renal Cell Carcinoma

Supplementary Table 4 from Histone Methyltransferase Gene SETD2 Is a Novel Tumor Suppressor Gene in Clear Cell Renal Cell Carcinoma

Supplementary Figure 2G from Histone Methyltransferase Gene SETD2 Is a Novel Tumor Suppressor Gene in Clear Cell Renal Cell Carcinoma

Supplementary Table 2 from Histone Methyltransferase Gene SETD2 Is a Novel Tumor Suppressor Gene in Clear Cell Renal Cell Carcinoma

Supplementary Table 1 from Histone Methyltransferase Gene SETD2 Is a Novel Tumor Suppressor Gene in Clear Cell Renal Cell Carcinoma

Population-based studies that contain detailed clinical data on patients with myelodysplastic syndrome (MDS) are scarce. This study focused on the real-world overall survival (OS) of MDS patients in association with comorbidities, specifically malignancies. An observational population-based study using the HemoBase registry was performed, including all patients with MDS diagnosed between 2005 and 2017 in Friesland, a Dutch province. Detailed information about diagnosis, patient characteristics, previous treatment of malignancies, and comorbidities according to the Charlson Comorbidity Index (CCI) was collected from electronic health records. Patients were followed up until June 2019. Kaplan-Meier plots and Cox regression analyses were used to study survival differences. In the 291 patients diagnosed with MDS, the median OS was 25.3 months (95% confidence interval [CI], 20.3-30.2). OS was significantly better for patients with CCI score

Background Patients with hematological malignancies (HMs) carry a wide range of chromosomal and molecular abnormalities that impact their prognosis and treatment. Since no current technique can detect all relevant abnormalities, technique(s) are chosen depending on the reason for referral, and abnormalities can be missed. We tested targeted transcriptome sequencing as a single platform to detect all relevant abnormalities and compared it to current techniques. Material and Methods We performed RNA-sequencing of 1385 genes (TruSight RNA Pan-Cancer, Illumina) in bone marrow from 136 patients with a primary diagnosis of HM. We then applied machine learning to expression profile data to perform leukemia classification, a method we named RANKING. Gene fusions for all the genes in the panel were detected, and overexpression of the genes EVI1, CCND1, and BCL2 was quantified. Single nucleotide variants/indels were analyzed in acute myeloid leukemia (AML), myelodysplastic syndrome and patients with acute lymphoblastic leukemia (ALL) using a virtual myeloid (54 genes) or lymphoid panel (72 genes). Results RANKING correctly predicted the leukemia classification of all AML and ALL samples and improved classification in 3 patients. Compared to current methods, only one variant was missed, c.2447A>T in KIT (RT-PCR at 10−4), and BCL2 overexpression was not seen due to a t(14; 18)(q32; q21) in 2% of the cells. Our RNA-sequencing method also identified 6 additional fusion genes and overexpression of CCND1 due to a t(11; 14)(q13; q32) in 2 samples. Conclusions Our combination of targeted RNA-sequencing and data analysis workflow can improve the detection of relevant variants, and expression patterns can assist in establishing HM classification.

Therapeutic decision making is often challenging in older AML patients. We collected retrospective data of 355 consecutive AML patients (>= 60 years) who were treated with intensive chemotherapy (IC) (n=155), hypomethylating agents (HMA) (n=83), or best supportive care (BSC) (n=117) between 2002 and 2017. Overall survival (OS) and response rates after therapy were analyzed. Multivariate Cox regression was performed to analyze the impact of different treatment strategies on survival. The median OS was not significantly different between patients treated with IC or HMA (14.9 vs 10.9 months; HR=1.32, p=0.076)), despite a difference in complete remission rate (59% after IC vs 35% after HMA). Patients who received a allogeneic hematopoietic cell transplantation (allo HCT) after treatment with IC or HMA had a significant survival benefit compared to patient who didn't proceed to allo HCT (median OS 65 vs 8 months, respectively, p

Chromosomal breakpoints involving the MYC gene locus, frequently referred to as MYC rearrangements (MYC - R+), are a diagnostic hallmark of Burkitt lymphoma and recurrent in many other subtypes of B-cell lymphomas including follicular lymphoma, diffuse large B-cell lymphoma and other high-grade B-cell lymphomas and are associated with an aggressive clinical course. In remarkable contrast, in MCL, only few MYC - R+ cases have yet been described. In the current study, we have retrospectively analysed 16 samples (MYC - R+, n = 15, MYC - R-, n = 1) from 13 patients and describe their morphological, immunophenotypic and (molecular) genetic features and clonal evolution patterns. Thirteen out of fifteen MYC - R+ samples showed a non-classical cytology including pleomorphic (centroblastic, immunoblastic), anaplastic or blastoid. MYC translocation partners were IG-loci in 4/11 and non-IG loci in 7/11 analysed cases. The involved IG-loci included IGH in 3 cases and IGL in one case. PAX5 was the non-IG partner in 2/7 patients. The MYC - R+ MCL reported herein frequently displayed characteristics associated with an aggressive clinical course including high genomic-complexity (6/7 samples), frequent deletions involving the CDKN2A locus (7/10 samples), high Ki-67 proliferation index (12/13 samples) and frequent P53 expression (13/13 samples). Of note, in 4/14 samples, SOX11 was not or only focally expressed and 3/13 samples showed focal or diffuse TdT-positivity presenting a diagnostic challenge as these features could point to a differential diagnosis of diffuse large B-cell lymphoma and/or lymphoblastic lymphoma/leukaemia.

BACKGROUND Over 500 translocations have been identified in acute leukemia. To detect them, most diagnostic laboratories use karyotyping, fluorescent in situ hybridization, and reverse transcription PCR. Targeted locus amplification (TLA), a technique using next-generation sequencing, now allows detection of the translocation partner of a specific gene, regardless of its chromosomal origin. We present a TLA multiplex assay as a potential first-tier screening test for detecting translocations in leukemia diagnostics. METHODS The panel includes 17 genes involved in many translocations present in acute leukemias. Procedures were optimized by using a training set of cell line dilutions and 17 leukemia patient bone marrow samples and validated by using a test set of cell line dilutions and a further 19 patient bone marrow samples. Per gene, we determined if its region was involved in a translocation and, if so, the translocation partner. To balance sensitivity and specificity, we introduced a gray zone showing indeterminate translocation calls needing confirmation. We benchmarked our method against results from the 3 standard diagnostic tests. RESULTS In patient samples passing QC, we achieved a concordance with benchmarking tests of 81% in the training set and 100% in the test set, after confirmation of 4 and nullification of 3 gray zone calls (in total). In cell line dilutions, we detected translocations in 10% aberrant cells at several genetic loci. CONCLUSIONS Multiplex TLA shows promising results as an acute leukemia screening test. It can detect cryptic and other translocations in selected genes. Further optimization may make this assay suitable for diagnostic use.

AimsLow-grade follicular lymphoma (FL) (grade 1/2, FL1/2) has an annual risk of transformation of approximate to 3%, which is associated with aberrations in CDKN2A/B, TP53, and MYC. As in diffuse large B-cell lymphoma, high MYC expression in transformed FL (tFL) might predict a MYC breakpoint.Methods and resultsWe quantified MYC expression by immunohistochemistry and digital analysis in 41 paired biopsies from 20 patients with FL1/2 with subsequent transformation and in four isolated biopsies of tFL. As controls, 28 biopsies of FL1/2 without transformation (median follow-up of 105 months) and nine biopsies of FL3A/B were analysed. In the 20 FL1/2-tFL pairs, MYC expression was significantly higher in tFL than in the initial FL1/2 biopsies (median 54% versus 6%; 7% in FL3A, and 35% in FL3B). MYC breaks (MYC-R) were detected in eight of 21 (38%) tFLs analysed by fluorescence in-situ hybridization (FISH), with a median MYC score of 86%. In two of the analysed tFL cases, the translocation was already detected in antecedent FL1/2. MYC partners were immunoglobulin (IG) loci in three of eight cases (one IGL, one IGH, and one IGK) and non-IG in five of eight cases (two PAX5, one BCL6, and two unknown). Of the eight MYC-R+ cases, six were BCL2+/MYC+ double-hit, one was BCL2+/BCL6+/MYC+ triple-hit, and one was MYC+ single-hit. All three IG-MYC+ cases showed a MYC expression level of >85%, whereas the five cases with a non-IG MYC partner had a wider range of expression (median 68%, range 13-86%). Among the 13 MYC-R- tFLs, two groups with almost dichotomous MYC expression could be observed (three cases showed 90% MYC expression), suggesting alternative mechanisms of MYC activation.Conclusionswe show an increase in MYC expression from FL1/2 to tFL. MYC breakpoints were present in approximate to 40% of the cases, which is markedly higher than in de novo DLBCL. MYC expression was uniformly high in cases with an IG-MYC translocation but much more heterogeneous and in part independent of the presence of a MYC break in non-IG-MYC and MYC-negative cases.

Complex karyotype (CK) identified by chromosome-banding analysis (CBA) has shown prognostic value in chronic lymphocytic leukemia (CLL). Genomic arrays offer high-resolution genome-wide detection of copy-number alterations (CNAs) and could therefore be well equipped to detect the presence of a CK. Current knowledge on genomic arrays in CLL is based on outcomes of single center studies, in which different cutoffs for CNA calling were used. To further determine the clinical utility of genomic arrays for CNA assessment in CLL diagnostics, we retrospectively analyzed 2293 arrays from 13 diagnostic laboratories according to established standards. CNAs were found outside regions captured by CLL FISH probes in 34% of patients, and several of them including gains of 8q, deletions of 9p and 18p (p, This study was partly funded by an unrestricted contribution from Janssen Pharmaceuticals and from GILEAD Sciences SA. A.C.L. is supported by the Peters van der Laan foundation. J.C.S. was funded by Bloodwise (11052, 12036), the Kay Kendall Leukaemia Fund (873), Cancer Research UK (C34999/A18087, ECMC C24563/A15581), Wessex Medical Research and the Bournemouth Leukaemia Fund. K.P., M.J., and S.P. are supported by the project MHCR DRO no. 65269705, the research infrastructures NCMG LM2015091, and EATRIS-CZ LM2015064, and the project CEITEC2020 LQ1601, funded by MEYS CR. R.R. is supported by Swedish Cancer Society, the Swedish Research Council, the Knut and Alice Wallenberg Foundation, Karolinska Institutet, Karolinska University Hospital, and Radiumhemmets Forskningsfonder, Stockholm.

Ring sideroblasts (RS) emerge as result of aberrant erythroid differentiation leading to excessive mitochondrial iron accumulation, a characteristic feature for myelodysplastic syndromes (MDS) with mutations in the spliceosome gene SF3B1. However, RS can also be observed in patients diagnosed with acute myeloid leukemia (AML). The objective of this study was to characterize RS in patients with AML. Clinically, RS-AML is enriched for ELN adverse risk (55%). In line with this finding, 35% of all cases had complex cytogenetic aberrancies, and TP53 was most recurrently mutated in this cohort (37%), followed by DNMT3A (26%), RUNX1 (25%), TET2 (20%), and ASXL1 (19%). In contrast to RS-MDS, the incidence of SF3B1 mutations was low (8%). Whole-exome sequencing and SNP array analysis on a subset of patients did not uncover a single genetic defect underlying the RS phenotype. Shared genetic defects between erythroblasts and total mononuclear cell fraction indicate common ancestry for the erythroid lineage and the myeloid blast cells in patients with RS-AML. RNA sequencing analysis on CD34+ AML cells revealed differential gene expression between RS-AML and non RS-AML cases, including genes involved in megakaryocyte and erythroid differentiation. Furthermore, several heme metabolism-related genes were found to be upregulated in RS- CD34+ AML cells, as was observed in SF3B1mut MDS. These results demonstrate that although the genetic background of RS-AML differs from that of RS-MDS, they have certain downstream effector pathways in common.

Genetic profiling is important for disease evaluation and prediction of prognosis or responsiveness to therapy in neoplasia. Microarray technologies, including array comparative genomic hybridization and single-nucleotide polymorphism-detecting arrays, have in recent years been introduced into the diagnostic setting for specific types of haematological malignancies and solid tumours. It can be used as a complementary test or depending on the neoplasia investigated, also as a standalone test. However, comprehensive and readable presentation of frequently identified complex genomic profiles remains challenging. To assist diagnostic laboratories, standardization and minimum criteria for clinical interpretation and reporting of acquired genomic abnormalities detected through arrays in neoplastic disorders are presented.

Background: We studied two cases of rare fibrous bone tumors, namely desmoplastic fibroma (DF) and low-grade central osteosarcoma (LGCOS) resembling desmoplastic fibroma (DF-like LGCOS). As the clinical presentation, imaging features and histopathology of DF and DF-like LGOS show much overlap, the objective of this study was to investigate the value of cytogenetic analysis, molecular pathology and immunohistochemistry in discrimination of these two mimickers.Case presentation: A mutation in CTNNB (S45F) and nuclear beta-catenin immunostaining were observed in DF. DF-LGCOS had amplification of CDK4 and showed strong nuclear expression of CDK4 by IHC. Moreover, the karyotype of DF-LGCOS showed an interstitial heterozygous deletion of the long arm of chromosome 13 (q12q32), associated with loss of the RB1 tumor suppressor gene.Conclusions: Karyotyping and molecular genetic analysis may contribute to a conclusive diagnosis.

Cytogenetic and molecular genetic data are of paramount importance in the diagnosis, prognosis, and risk stratification of patients with malignant diseases. Sometimes they even directly guide the choice of therapy.1 Disease-specific abnormalities, particularly translocations, can provide essential information to assist the Pathologist and/or Oncologist in assigning a diagnosis. In several diseases, tumour genetics correlate strongly with clinical risk; thus, cytogenetic information may help the Oncologist counsel the patient, choose a specific treatment, and/or modulate treatment intensity. Clinical trials may involve cytogenetic classification of patients to the appropriate treatment regimens. Currently, the provision of specific assays for acquired neoplasiaspecific genomic changes varies among and within countries as a range of laboratories offer diagnostic solid tumour genetics; these may include Cytogenetic, Pathology, Haematology, and Molecular Genetics laboratories. Technical standards and general guidelines for the analysis and the report of results on most solid tumours are lacking. To address these deficits, a tumour best practice meeting with invited tumour experts without conflict of interest was held on 23rd April 2013 in Oxford, United Kingdom. The aim was to produce professional guidelines for tumour genetic laboratories and to incorporate the standards imposed by generic European guidelines,2 regulatory bodies (ISO15189, 2012 Medical laboratories – requirements for quality and competence),3 reporting guidelines,4 ISCN,5 and acquired best practice guidelines, while taking into account the current practice in Europe. The guidelines are aimed principally at giving guidance on the minimum, standard cytogenetic analyses, which are applicable to different types of laboratories operating under different regulatory arrangements and are relevant if more specific recommendations are not available. It was universally acknowledged that information on ancillary techniques in use in most cytogenetic laboratories (eg, RTPCR) or advanced techniques not always extensively performed in all laboratories (eg, next-generation sequencing (NGS)) were considered. The process for developing these evidence-based consensus guidelines included agreement on the need of general uniform rules on solid tumour analysis and reporting, discussion on the architecture of the guidelines, working group formation with different tasks (collection, analysis and comparison of any existing guidelines on this subject, type of tumours to be included according to published data and database consultation, method of analysis to be included, report formulation), circulation of the working group activities, formulation and circulation of the initial recommendations, draft and discussion, final consensus, and approval. It is noted that some elements of the tumour diagnostic service not subject to statute may be varied according to local constraints and agreements. Therefore, these guidelines are minimum requirements and additional professional judgment may be of paramount importance under many circumstances. In addition, as new techniques, particularly NGS, as well as clinical evidence, are becoming available all the time, these should be kept under constant review. Notes: The use of ‘must’ in this document indicates a requirement and the use of ‘should’ indicates a recommendation. Where there appears to be contradiction between available guidelines, the most recently published ones should be taken to apply to all. All diagnostic laboratories should be accredited to national or internationally accepted standards (ISO15189).3,6 Laboratories should participate in an External Quality Assessment Scheme7 in all aspects of their service for which a scheme is available.

Malignant peripheral nerve sheath tumor is a rare and aggressive disease with poor treatment response, mainly affecting adolescents and young adults. Few molecular biomarkers are used in the management of this cancer type, and although TP53 is one of few recurrently mutated genes in malignant peripheral nerve sheath tumor, the mutation prevalence and the corresponding clinical value of the TP53 network remains unsettled. We present a multi-level molecular study focused on aberrations in the TP53 network in relation to patient outcome in a series of malignant peripheral nerve sheath tumors from 100 patients and 38 neurofibromas, including TP53 sequencing, high-resolution copy number analyses of TP53 and MDM2, and gene expression profiling. Point mutations in TP53 were accompanied by loss of heterozygosity, resulting in complete loss of protein function in 8.2% of the malignant peripheral nerve sheath tumors. Another 5.5% had MDM2 amplification. TP53 mutation and MDM2 amplification were mutually exclusive and patients with either type of aberration in their tumor had a worse prognosis, compared to those without (hazard ratio for 5-year disease-specific survival 3.5, 95% confidence interval 1.78-6.98). Both aberrations had similar consequences on the gene expression level, as analyzed by a TP53-associated gene signature, a property also shared with the copy number aberrations and/or loss of heterozygosity at the TP53 locus, suggestin g a common "P53-mutated phenotype" in as many as 60% of the tumors. This was a poor prognostic phenotype (hazard ratio = 4.1, confidence interval: 1.7-9.8), thus revealing a TP53-non-aberrant patient subgroup with a favorable outcome. The frequency of the " TP53-mutated phenotype" warrants explorative studies of stratified treatment strategies in malignant peripheral nerve sheath tumor.

Therapy-related myeloid neoplasms (tMNs) are severe adverse events that can occur after treatment with autologous hematopoietic stem cell transplantation (ASCT). This study aimed to investigate the development of tMNs following ASCT at the molecular level by whole-exome sequencing (WES) and targeted deep sequencing (TDS) in sequential (pre-) tMN samples. WES identified a significantly higher number of mutations in tMNs as compared with de novo myelodysplastic syndrome (MDS) (median 27 vs 12 mutations; P = .001). The mutations found in tMNs did not carry a clear aging-signature, unlike the mutations found in de novo MDS, indicating a different mutational mechanism. In some patients, tMN mutations were identified in both myeloid and T cells, suggesting that tMNs may originate from early hematopoietic stem cells (HSCs). However, the mutational spectra of tMNs and the preceding malignancies did not overlap, excluding common ancestry for these malignancies. By use of TDS, tMN mutations were identified at low variant allele frequencies (VAFs) in transplant material in 70% of the patients with tMNs. Reconstruction of clonal patterns based on VAFs revealed that premalignant clones can be present more than 7 years preceding a tMN diagnosis, a finding that was confirmed by immunohistochemistry on bone marrow biopsies. Our results indicate that tMN development after ASCT originates in HSCs bearing (pre-) tMN mutations that are present years before disease onset and that post-ASCT treatment can influence the selection of these clones. Early detection of premalignant clones and monitoring of their evolutionary trajectory may help to predict the development of tMNs and guide early intervention in the future.

Background. Malignant peripheral nerve sheath tumor (MPNST) is a rare and highly aggressive disease with no evidence of effect from adjuvant therapy. It is further associated with the hereditary syndrome neurofibromatosis type 1 (NF1). Silencing of the tumor suppressor gene RASSF1A through DNA promoter hypermethylation is known to be involved in cancer development, but its impact in MPNSTs remains unsettled.Methods. The RASSF1A promoter was analyzed by methylation-specific PCR in 113 specimens, including 44 NF1-associated MPNSTs, 47 sporadic MPNSTs, 21 benign neurofibromas, and 1 nonneoplastic nerve sheath control.Results. RASSF1A methylation was found only in the malignant samples (60%) and identified a subgroup among patients with NF1-associated MPNST with a poor prognosis. These patients had a mean 5-year disease-specific survival of 27.3 months (95% CI: 17.2-37.4) versus 47.4 months (95% CI: 37.5-57.2) for NF1 patients with unmethylated promoters, P = 0.014. In multivariate Cox regression analysis, methylated RASSF1A remained an adverse prognostic factor independent of clinical risk factors, P = .013 (hazard ratio: 5.2; 95% CI: 1.4-19.4).Conclusion. A considerable number of MPNST samples display hypermethylation of the RASSF1A gene promoter, and for these tumors, this is the first molecular marker that if validated can characterize a subgroup of patients with inferior prognosis, restricted to individuals with NF1.

Despite numerous studies reporting deregulated microRNA (miRNA) and gene expression patterns in clear cell renal cell carcinoma (ccRCC), no direct comparisons have been made to its presumed normal counterpart: the renal proximal tubular epithelial cells (PTECs). The aim of this study was to determine the miRNA expression profiles of 10 ccRCC-derived cell lines and short-term cultures of PTEC and to correlate these with their gene expression and copy-number profiles. Using microarray-based methods, a significantly altered expression level in ccRCC cell lines was observed for 23 miRNAs and 1630 genes. The set of miRNAs with significantly decreased expression levels include all members of the miR-200 family known to be involved in the epithelial to mesenchymal transition process. Expression levels of 13 of the 47 validated target genes for the downregulated miRNAs were increased more than twofold. Our data reinforce the importance of the epithelial to mesenchymal transition process in the development of ccRCC.

Clear cell renal cell carcinomas are characterized by 3p loss, and by inactivation of Von Hippel Lindau (VHL), a tumorsuppressor gene located at 3p25. Recently, SETD2, located at 3p21, was identified as a new candidate ccRCC tumor-suppressor gene. The combined mutational frequency in ccRCC tumors of VHL and SETD2 suggests that there are still undiscovered tumor-suppressor genes on 3p. We screened all genes on 3p for mutations in 10 primary ccRCC tumors using exome-sequencing. We identified inactivating mutations in VHL, PBRM1, and BAP1. Sequencing of PBRM1 in ccRCC-derived cell lines confirmed its frequent inactivation in ccRCC. PBRM1 encodes for BAF180, the chromatin targeting subunit of the SWI/SNF complex. BAP1 encodes for BRCA1 associated protein-1, involved in histone deubiquitination. Taken together, the accumulating data suggest an important role for aberrant chromatin regulation in ccRCC development. Hum Mutat 33:10591062, 2012. (c) 2012 Wiley Periodicals, Inc.

The isocitrate dehydrogenase 1 gene (IDH1) was in 2008 identified as a new glioblastoma pathogenesis candidate gene by Parsons et al.1 Following this discovery, IDH1/2 mutated tumors have been studied more carefully, and in 2010 the IDH1 mutation was found to be associated with a glioma cytosine–phosphate–guanine island methylator phenotype (G-CIMP).2 Today, it is clear that the common mutations in the IDH genes result in an IDH enzyme with de novo activity producing 2-hydroxyglutarate.3 This metabolite is an inhibitor of α-ketoglutarate–dependent dioxygenases, leading to genome-wide methylation alterations subsequently changing gene expression.4,5 Although large series of different tumor types have been analyzed, IDH1/2 mutations have been reported at significant frequencies in only a few other neoplastic diseases, such as central and periosteal cartilaginous tumors, intrahepatic cholangiocarcinoma, acute myeloid leukemia, blast-phase myeloproliferative neoplasms, and angioimmunoblastic T-cell lymphoma.6–15 The IDH mutation frequency is relatively high in oligodendrogliomas. Hence, we hypothesized that IDH mutations could also be frequent in malignant peripheral nerve sheath tumors (MPNSTs), tumors composed of Schwann cells, which are the peripheral nervous system's functional equivalent to oligodendrocytes. Previously, no IDH1 R132 mutations were detected in a small series of 17 schwannomas7 or in a series of 24 MPNSTs.16 We sequenced the glioma mutation hotspots R132 and R172 in IDH1 and IDH2, respectively, in gliomas and one of the world's largest series of MPNSTs. Tumor samples (n = 161) from 157 glioma patients who underwent surgery at Oslo University Hospital–Rikshospitalet, Oslo, Norway from 2005 to 2010 were included in this study. High-grade gliomas from patients with known prior low-grade glioma were regarded as secondary, while other high-grade gliomas were regarded as primary. Histological diagnoses were reviewed by a neuropathologist (D.S.). MPNST tissue samples (n = 93, from 91 patients) diagnosed in the period 1973–2008 were collected from Oslo University Hospital; Skane University Hospital, Lund, Sweden; University Medical Center Groningen, Groningen, Netherlands; and Istituto Ortopedico Rizzoli, Bologna, Italy. Histological diagnoses were determined by sarcoma reference pathologists. The biobanks and projects were approved according to national legislations. DNA was extracted from fresh frozen tissue. From gliomas where fresh frozen tissue was not available we used tissue stored in RNAlater. Regions of IDH1 and IDH2 including the mutation hotspots were amplified with primers in separate PCR reactions. Primer sequences for the IDH1 reaction were 5′-GCA-CGG-TCT-TCA-GAG-AAG-CCA-3′ (forward, our design) and 5′-AGG-GGA-TCC-TAT-TGT-GCA-GCC-AG-3′ (reverse, our design), and for the IDH2 reaction 5′-AGC-CCA-TCA-TCT-GCA-AAA-AC-3′ (forward17) and 5′-CTA-GGC-GAG-GAG-CTC-CAG-T-3′ (reverse17). Results were reviewed independently by 2 of the authors (A.B.H., H.H.). All mutations were technically validated in a separate run. The detected IDH1 mutation frequencies in the 161 gliomas (Table 1) are in line with earlier reports18 and confirm that IDH1 mutations are frequent in World Health Organization (WHO) grades II and III astrocytomas, oligoastrocytomas, oligodendrogliomas, and secondary glioblastomas. From 4 glioma patients included in the study, 2 samples of different grades were examined. The same mutation status was found in both samples. No mutation was detected in the IDH2 hotspot R172, which, based on earlier reported IDH2 mutation frequencies and our number of examined gliomas, is not surprising. This is particularly so because we found a relatively high frequency of IDH1 mutations, and IDH1 and IDH2 mutations do not appear to occur together.17 Table 1. Frequency of IDH1 mutations in codon R132 The WHO grade III gliomas were divided into primary and secondary tumors depending on absence or presence of preexisting lower-grade lesions. All anaplastic oligodendrogliomas (n = 8) were IDH1 mutated, regardless of primary/secondary status. In the subgroups anaplastic oligoastrocytoma and anaplastic astrocytoma, all primary tumors but one were IDH1 nonmutated, whereas all secondary tumors were mutated. Interestingly, the only primary anaplastic astrocytoma with IDH1 mutation had areas with low-grade histology, suggesting that this may in fact have been a secondary tumor. We found that 2 primary glioblastomas harbored the IDH1 mutation. Both patients had a short clinical history and therefore no evidence of a preexisting low-grade glioma. Our neuropathologist found one of these primary glioblastomas to be diagnostically intermediate between an anaplastic oligoastrocytoma and a glioblastoma with a large oligodendroglial component. Nonetheless, the patient received standard glioblastoma treatment and was therefore included as a primary glioblastoma patient in our analyses. No mutations were detected in the samples from the 91 MPNST patients, either in the hereditary cases (n = 44) or in the sporadic cases (n = 47). Our results suggest that although principally composed of functionally equivalent cells, gliomas and MPNSTs pursue different pathogenetic pathways. We cannot rule out the possibility of mutations occurring in other IDH1/2 codons. However, few other IDH1/2 mutations have so far been reported, and only a few of these have resulted in the same de novo activity as the glioma hotspot mutations.19 In conclusion, when analyzing 161 glioma samples, we detected the expected mutations in the analyzed IDH1/2 glioma mutation hotspots at frequencies on a par with previous studies.18 Furthermore, it would be interesting to analyze a larger series of WHO grade III gliomas to confirm our observations indicating that IDH1 mutations are more frequent in secondary than primary anaplastic oligoastrocytomas and anaplastic astrocytomas. No IDH1/2 glioma hotspot mutations were detected in MPNSTs, indicating that these pathologically similar but peripherally occurring tumors are pathogenetically different from CNS gliomas.

Purpose Karyotype is an independent indicator of prognosis in acute myeloid leukemia (AML) that is widely applied to risk-adapted therapy. Because AML is rare in children, the true prognostic significance of individual chromosomal abnormalities in this age group remains unclear. Patients and Methods This cytogenetic study of 729 childhood patients classified them into 22 subgroups and evaluated their incidence and risk. Results Rearrangements of 11q23 were the most frequent abnormality found in approximately 16% of patients, with 50% of these in infants. The outcome for all patients with 11q23 abnormalities was intermediate; no difference was observed for those with t(9;11)(p21-22;q23). The core binding factor leukemias with the translocations t(8;21)(q22;q22) and inv(16)(p13q22) occurred at incidences of 14% and 7%, respectively, predominantly in older children, and their prognosis was favorable. An adverse outcome was observed in patients with monosomy 7, abnormalities of 5q, and t(6;9)(p23;q34). Abnormalities of 3q and complex karyotypes, in the absence of favorable-risk features, have been associated with an adverse outcome in adults, but the results were not significant in this childhood series. However, the presence of 12p abnormalities predicted a poor outcome. Conclusion Because the spectrum of chromosomal changes and their risk association seem to differ between children and adults with AML, biologic differences are emerging, which will contribute to the redefinition of risk stratification for different age groups in the future.

Insects are highly valued as food in many cultures but have only recently gained interest in the West as a sustainable alternative to reduce the environmental impact of meat production. Despite the growing consumer interest in insect consumption, there is still a great disparity between curious trying and actual acceptance. The aim of this study was to examine how the product preparation, familiarity and individual traits (e.g. food neophobia) influence the consumer acceptance of insects as food. Dutch consumers (n = 976) evaluated 8 mealworm product images on 4 acceptability measures (product appropriateness, expected sensory-liking, willingness to buy, willingness to try). Product images varied according to mealworm visibility (visible/invisible), carrier flavour (savoury/sweet) and carrier origin (Western/Asian). High product acceptability was not simply achieved by adding mealworms to familiar foods. Acceptability depended very much on the perceived appropriateness of mealworms as food and the perceived appropriateness of the product combination. However, mealworm products were always expected to be inferior to the carrier products, even when visually identical. Familiarity with mealworms and individual traits played a relatively minor role, and influenced the willingness to try more than the other acceptability measures. We conclude that appropriate product design is important but insufficient to achieve consumer acceptance of insects as food in the West. Additional incentives are required to encourage acceptance beyond the mere willingness to try. We discuss the complexities underlying the consumer acceptance of insects as food and reflect on how acceptance might be increased in the future.

Genetic profiling is important for disease evaluation and prediction of prognosis or responsiveness to therapy in neoplasia. Microarray technologies, including array comparative genomic hybridization and single-nucleotide polymorphism-detecting arrays, have in recent years been introduced into the diagnostic setting for specific types of haematological malignancies and solid tumours. It can be used as a complementary test or depending on the neoplasia investigated, also as a standalone test. However, comprehensive and readable presentation of frequently identified complex genomic profiles remains challenging. To assist diagnostic laboratories, standardization and minimum criteria for clinical interpretation and reporting of acquired genomic abnormalities detected through arrays in neoplastic disorders are presented.

Diagnostic cytogenetic abnormalities are considered important prognostic factors in patients with acute myeloid leukaemia (AML). However, the prognostic assessments have mainly been derived from patients with AML aged

Despite the fact that numerous studies have been performed on diffuse large B-cell lymphoma (DLBCL), only few have concerned extranodal lymphomas occurring in the testis. We performed a cytogenetic and molecular study of 17 testicular non-Hodgkin lymphomas, of which 14 were proven primary DLBCL of the testis. Cytogenetic analysis revealed in 8 out of 11 evaluable cases a structural abnormality of the long arm of chromosome 6, with deletion or addition of material of unknown origin, and with breakpoints spanning the region 6q12-6q23. The cytogenetic findings were confirmed by fluorescent in situ hybridization (FISH) with a chromosome 6 painting probe. Using array based-comparative genomic hybridization on 16 evaluable cases, including 5 cases not tested by cytogenetics or FISH, 14 (88%) showed chromosome 6q deletions. We identified two regions of minimal deletion (RMD), at 104-113 Mb (6q16.3-q21) and 137.5-138.8 Mb (6q23.3), respectively. In one case, we observed a 2.7 Mb homozygous deletion ranging from 135.3 to 138.0 Mb that partly overlapped with the RMD at 6q23.3. Our study indicates that 6q deletions play a major pathogenetic role in DLBCL of the testis and that many of these deletions are part of unbalanced translocations. (c) 2006 Wiley-Liss, Inc.

DEV is the only cell line derived from nodular lymphocyte predominance type of Hodgkin's lymphoma (NLPHL); however, a comprehensive report about the genetic and immunophenotypic profile of this unique cell line is lacking. We analyzed DEV with respect to immunophenotype and genetic aberrations. The immunostaining revealed positivity for CD45, CD20, CD22, CD79a, IgA2, CD80, CD86, CD74, and BCL6. Cytogenetically, DEV has complex chromosome 3 translocations involving chromosomes 7, 14, and 22. A detailed analysis of the 3q27 breakpoint of the der(3)t(3;14)(p14;q32)t(3;22)(q27;q11.2) revealed a break in the BCL6 alternative breakpoint region. Using array comparative genomic hybridization, a 3-megabase homozygous deletion at 17q24.1-24.2 was identified. Fluorescence in situ hybridization indicated the presence of 2 chromosome 17 homologues, each of which carried a small interstitial deletion. Eight microsatellite markers flanking the homozygously deleted region all showed a homozygous pattern suggesting loss of one of the parental alleles. D17S1809 and D17S1816 could not be amplified using DEV DNA, in keeping with a location within the homozygously deleted segment. In conclusion, DEV has an immunophenotype that is consistent with the neoplastic cells of NLPHL cases, the lymphocytic and histiocytic cells. We demonstrated involvement of the BCL6 gene based on the presence of a breakpoint in the alternative breakpoint region and nuclear staining for BCL6 protein and identified a homozygously deleted region at 17q24. (c) 2006 Elsevier Inc. All rights reserved.

The molecular biology underlying the development of highly malignant peripheral nerve sheath tumors (MPNSTs) remains mostly unknown. In the present study, the expression pattern of 10 selected cell cycle components is investigated in a series of 15 MPNSTs from patients with (n = 9) or without (n = 5) neurofibromatosis type 1 (NF1). Thirteen tumors did not express the cyclin-dependent kinase inhibitor, p16(INK4A), an observation that was related to homozygote gene deletions in three tumors, heterozygote deletions in five, and gross gene rearrangements in five. The absence of protein expression in the tumors with one seemingly intact allele was not caused by promoter hypermethylation of p16(INK4A) or p14(ARF). All tumor samples expressed normal sized RB1, cyclin D3, CDK2, CDK4, p21(CIP1), and p27(KlP1) proteins, and only a single tumor showed an aberrant protein band for one of these proteins, p21(CIP1). Cyclin D1 was absent in four tumors; all except one tumor showed expression of TP53 protein, and three of nine MPNSTs had expression of normal-sized MDM2. In conclusion, this study shows that the vast majority of MPNSTs had gross rearrangements of the p16(INK4A) gene, explaining the absence of the encoded protein in the same tumors. The level of expression was equally distributed between the familial (NF1) and sporadic cases, although it should be noted that the 2 cases with p16(INK4A) expression were sporadic. The data imply that the complete absence of p16(INK4A) is sufficient for activation of the cell cycle in most MPNSTs; thus, it is not necessary for tumor proliferation to further stimulate the cycle through alteration of other central components.

Translocations involving band 3q27, affecting the major breakpoint region (MBR) of BCL6, are common in diffuse large B-cell lymphomas (DLBCLs). Recent data suggest an alternative breakpoint cluster region (ABR) located between 245 and 285 kb 5' of BCL6, which might be associated with Follicular Lymphoma (FL). Ten DLBCLs and 9 FLs grade 3B with cytogenetic rearrangements at 3q27 were studied by fluorescence in situ hybridization (FISH) to discriminate between breakpoints at the ABR and MBR. Eight DLBCLs contained a breakpoint in the MBR, and 6 FL grade 3B (FL3B) cases contained a breakpoint in the ABR. No specific chromosomal partners could be identified in both groups. Previously published data have suggested that FL3B cases with 3q27 aberrations are closely related to the majority of DLBCLs of germinal center cell origin. However, our findings suggest that the mechanism of 3q27 rearrangement in FL3B cases is similar to the mechanism in follicular lymphomas grade 1,2, and 3A cases. (c) 2005 Wiley-Liss, Inc.

Cyclosporin A (CsA) inhibits the P-gp pump that can be responsible for failure of cytostatic treatment in acute myeloid leukaemia (AML). Eighty patients with relapsing/refractory AML were randomly assigned to mitoxantrone (M) and etoposide (VP) (MVP) in unmitigated antileukaemic doses with or without CsA, to investigate if toxicity was manageable and if antileukaemic therapy could be improved. CsA did not delay haematological recovery, but fewer CsA patients received post-induction therapy because of haematological and non-haematological toxicity. CR rate was 43% for MVP and 53% for CsA; DFS was 9 and 8 months, and OS 8 and 9 months, respectively. Seventeen of 38 CR patients proceeded to stem cell transplantation (SCT). After a median follow-up of 66 months, six patients were still alive. Addition of CsA did not improve treatment outcome, possibly due to inadequate post-induction therapy as a result of increased toxicity.

The histological transformation from a follicular lymphoma (FL) to a diffuse large B-cell lymphoma (DLBL) occurs in 22% to 30% of all cases of FL. The aim of this study was to identify specific chromosomal gains/losses associated with transformation of FL to DLBL, in addition to the well-known mechanisms like p53 mutation and protein expression and c-myc translocation and up-regulation. This is the first study to meet 2 important conditions for such a comparison. First, we demonstrate that the FL and the DLBL were clonally related, based on identical immunoglobulin gene rearrangements in 5 of the 6 cases. Second, we used laser microdissection microscopy to isolate only the neoplastic cells from the initial FL samples. The results indicate that no single chromosomal abnormality seems to be responsible for the transformation of FL to DLBL. P53 protein overexpression was found in 4 and c-myc translocation in 3 of the 6 transformed DLBLs, but not in the initial FL samples. Additional chromosomal abnormalities were detected by comparative genomic hybridization in all 6 cases when the DLBL was compared with the FL. In the 5 cases with transformation of grade 1 or 2 FL to DLBL, gains at chromosomes 7 (5 of 5 cases), 10p1 (3 of 5 cases), 12 (3 of 5 cases), and 20p13 (2 of 5 cases) and loss at 9q (4 of 5 cases) were the most frequently found abnormalities. A gain on chromosome 7p, in combination with a loss on 9q, was found in 4 of the 5 DLBL that transformed from FL grade 1 or 2.

Splenic marginal zone lymphoma (SMZL) is a rare non-Hodgkin's lymphoma that recently has been recognized as an entity. The first goal of this study was to identify potential chromosomal aberrations in this entity by cytogenetic analysis and comparative genomic hybridization (CGH). The second goal was to assess the frequency of 7q31-32 allelic imbalances in SMZL with primary involvement of the spleen and the typical immunophenotype (IgM+; IgD(dim); and CD5-, CD10-, and CD23-). We applied CGH and cytogenetics to 13 cases of SMZL with primary splenic involvement. By CGH, we found DNA copy number changes in 11 of 13 cases. Overall chromosomal gains were more frequent than chromosomal losses. Gains were most frequently detected for chromosome X, chromosome 3, and chromosome 18. Losses commonly involved chromosome 7 and chromosome 6.CGH and cytogenetic analysis showed a deletion in chromosome 7q31 in 4 cases. Loss of heterozygosity (LOH) analysis using three microsatellite markers located at 7q31 revealed LOH in 9 cases. Remarkably, 2 of the 4 cases that lacked a 7q31 deletion had an atypical immunophenotype because they were partially CD23 positive. The other 2 cases were not informative. The findings indicate that SMZL with primary splenic presentation and the typical IgM+, IgDdim, CD5-, CD10-, CD23- immunophenotype is characterized by the presence of deletions in chromosome 7q31-32.

We describe several relatives within one renal cell cancer (RCC) family sharing a constitutional t(2;3) (q35;q21). Based on molecular studies on several independent primary tumors in this family, a causative role for this translocation in tumor development was suggested. Subsequent positional cloning of the 3q21 chromosomal breakpoint revealed that this breakpoint disrupts a novel gene, DIRC2 (disrupted in renal cancer 2). This gene encodes an evolutionary conserved transmembrane protein and represents a novel member of the MFS superfamily of transporters. To evaluate whether DIRC2 is also targeted in sporadic RCC cases with cytogenetically defined 3q21 breakpoints, fluorescence in situ hybridization analysis was performed on metaphase spreads and/or interphase nuclei of 12 primary sporadic RCC using genomic clones from a 3q21 breakpoint-spanning contig as probes. Three breakpoints were mapped proximal to the familial breakpoint and nine breakpoints were mapped distal to this breakpoint. Two of the latter breakpoints were mapped in the contig within 1 Mb distance from the familial breakpoint. Because these clustered 3q21 breakpoints do not coincide with the familial 3q21 breakpoint, they most likely affect genes distinct from DIRC2.

Soft tissue sarcomas (STSs) are rare tumors, notorious for early hematogenous metastasizing. Metastatic disease is seldom amenable to curative treatment; therefore new treatment modalities are required. Treatment-related and tumor-related prognostic factors can be assessed to estimate the risk for subsequent metastases, as will be discussed. By this means, high-risk patients can be defined; they are the candidates for clinical trials mandatory for treatment development. The metastatic process as well as the reaction to chemotherapy depends on the biological make-up of the tumor. Current chemotherapy regimens do not improve the survival rates of patients with metastatic disease, due to resistance mechanisms of tumor cells. New drugs with direct access to the cell death machinery in tumor cells might contribute to more effective treatment of STS patients.

Purpose: Leiomyosarcomas (LMS) of deep and superficial tissues were examined to identify prognostic markers explaining their different biological behaviour and to define differences between cutaneous and subcutaneous LMS. LMS and leiomyomas (LM) of the skin were compared to and consistent differences that could aid in the (sometimes difficult) diagnosis.Patients: Material was obtained from 27 patients with a deep LMS, 14 with a superficial LMS, and 21 with a LM.Methods: Proliferation markers (mitotic and Ki-67 indices), DNA ploidy, size, grade, and the amount of apoptosis were studied. Statistical analysis was performed and survival curves were constructed by the Kaplan-Meier method and compared by the log-rank test.Results: Superficial LMS were smaller than deep LMS (p < 0.05), and the overall survival of patients with a superficial LMS was better than with a deep LMS (p < 0.05).Within the group of superficial LMS only entirely subcutaneous, and not cutaneous tumors metastasized.No differences were found in the other examined parameters. Proliferation and apoptotic indices were significantly higher in superficial LMS compared to superficial LM.Discussion: The difference in clinical outcome between patients with a superficial and deep LMS, seems to be related to site and size.The metastatic potential of subcutaneous LMS, however, seems to be related to location alone and not to size.The amount of apoptosis and proliferation can be used as additional criteria in the differentiation between superficial LMS and LM.

Cardiac myxomas are significant causes of cardiovascular morbidity and mortality. Their genetic background is presently unknown. Recently, linkage analysis in cardiac myxomas of Carney complex patients has indicated that 2p16 and 17q2 might carry genes responsible for the development of hereditary cardiac myxomas. Less is known about sporadic cardiac myxomas. To date, cytogenetic analysis has been performed on 13 sporadic cases, and no specific rearrangement has been deduced. We studied 15 sporadic cardiac myxomas and reviewed the literature. Ten of the present cases revealed abnormal karyotypes with clonal and nonclonal rearrangements including dicentric chromosomes and telomeric associations. No cytogenetic evidence was found for a role of 2p16 in the development of sporadic cases. Region 17q2 was involved in structural rearrangements, but to a lesser extent than other regions. Structural rearrangements involving regions 12p1 and 17p1 are more frequently present and might therefore harbor genes important for the development of sporadic cardiac myxomas.

BACKGROUND. Multidrug resistance (MDR) is associated with expression of P-glycoprotein (P-gp), multidrug resistance-associated protein 1 (MRP1), and lung resistance-related protein (LRP). Tumor necrosis factor (TNF-alpha) is able to modify the expression of these three proteins in different cell types. The effect of TNF-alpha in the clinical situation on patients with soft tissue sarcomas (STS) is indeterminate. METHODS, Thirty-seven patients with a locally advanced extremity STS underwent hyperthermic isolated limb perfusion (HILP) with TNF-alpha and melphalan; 15 patients received additional interferon gamma, Clinical and histologic responses were documented and used to define the overall response. Samples before and after HILP were analyzed immunohistochemically for P-gp! MRP1, and LRP, Samples were scored as negative or positive (less than or equal to 5% or > 5% positive tumor cells). RESULTS, Six patients had an overall complete response, 25 patients had a partial response, and 4 patients with STS revealed no change; in 2 patients, the response remained unclear. The percentage STS samples that were positive for all three proteins dropped from 92% before HILP to 85% after HILP. P-gp positive samples were encountered more often than MRP1 positive samples (P