Maria Soller

Confirmation of the high frequency of the TMPRSS2/ERG fusion gene in prostate cancer.

In a recent study by Tomlins et al., (2005), it was shown that a large subset of prostate cancer harbors the fusion genes TMPRSS2/ERG and TMPRSS2/ ETV1, generated through cryptic interand intrachromosomal rearrangements. A gene fusion of the 50 untranslated region of TMPRSS2 to ERG or ETV1 was identified in 23 (79%) of 29 prostate cancer samples. As yet, however, there have not been any confirmatory reports. In the present study, total RNA was extracted from 18 prostate adenocarcinoma biopsies using the Trizol reagent (Invitrogen, Carlsbad, CA) and cDNA synthesis was conducted in a 20 ll reaction mixture which contained 2.5 lg of total RNA, 13 first strand buffer, 10 mM DTT, 1 mM of each dNTP, 20 U RNase inhibitor (RNA guard, Amersham, Biosciences, Piscataway, NJ), 500 pmol random hexamers, and 200 U M-MLV reverse transcriptase (Invitrogen). The reaction was carried out at 378C for 60 min, heated for 10 min at 658C, and then kept at 48C. PCR amplifications were performed using 1 ll cDNA as template in a final volume of 50 ll containing 13 PCR buffer, 0.2 mM of each dNTP, 1.25 mM MgCl2, 0.5 lM of each of the TMPRSS2-1F and ERG-541R primers (Table 1) for the amplification of the TMPRSS2/ERG transcript or TMPRSS2-1F and ETV1-580R for the TMPRSS2/ETV1 transcript, and 1U Platinum Taq DNA polymerase (Invitrogen). One microliter of the first PCR product was then used as template in a second PCR with primers TMPRSS2-20F and ERG-450R (for TMPRSS2/ERG) or TMPRSS220F and ETV1-502R (TMPRSS2/ETV1). The PCR was run on a PCT-200 DNA Engine (MJ Research, Waltham, MA), and both amplifications had an identical cycling profile: an initial denaturation at 948C for 5 min, followed by 30 cycles of 1 min at 948C, 1 min at 608C, and 1 min at 728C, and a final extension for 10 min at 728C. Amplified fragments were run on a 1.5% agarose gel, stained with ethidium bromide, purified using the QIAquick gel extraction kit (Qiagen, Hilden, Germany), and directly sequenced using the dideoxy procedure with an ABI Prism BigDye terminator v1.1 cycle sequencing ready reaction kit (Applied Biosystems, Foster City, CA) on the Applied Biosystems

Midline carcinoma with t(15;19) and BRD4-NUT fusion oncogene in a 30-year-old female with response to docetaxel and radiotherapy

BackgroundPoorly differentiated midline carcinoma with a translocation between chromosomes 15 and 19, i.e. t(15;19), has been recognized as a distinct clinical entity for over a decade. This tumor affects young individuals, shows a rapidly fatal clinical course despite intensive therapy. The t(15;19) results in the fusion oncogene BRD4-NUT. Information concerning treatment of this rare disorder is scarce.Case presentationA 30-year-old woman was admitted with a rapidly progressing tumor in the mediastinum, cervical lymph nodes, vertebral column and the epidural space. Pathological, cytogenetic, FISH and PCR analysis revealed a glycogenated carcinoma rarely expressing cytokeratins and showing t(15;19) and BRD4-NUT gene rearrangement. The patient was initially treated with a Ewing sarcoma chemotherapy regimen, but had rapid progression after two cycles. She then received docetaxel and radiotherapy, which resulted in almost complete disappearance of the tumor.ConclusionDocetaxel may be considered for initial chemotherapy in young patients presenting with a midline carcinoma with bone marrow involvement and cytogenetic and molecular genetic finding of a t(15;19)/BRD4-NUT-rearrangement. We herein describe, in detail, the laboratory methods by which the BRD4-NUT -rearrangement can be detected.

Molecular Analysis Expands the Spectrum of Phenotypes Associated with GLI3 Mutations

A range of phenotypes including Greig cephalopolysyndactyly and Pallister‐Hall syndromes (GCPS, PHS) are caused by pathogenic mutation of the GLI3 gene. To characterize the clinical variability of GLI3 mutations, we present a subset of a cohort of 174 probands referred for GLI3 analysis. Eighty‐one probands with typical GCPS or PHS were previously reported, and we report the remaining 93 probands here. This includes 19 probands (12 mutations) who fulfilled clinical criteria for GCPS or PHS, 48 probands (16 mutations) with features of GCPS or PHS but who did not meet the clinical criteria (sub‐GCPS and sub‐PHS), 21 probands (6 mutations) with features of PHS or GCPS and oral‐facial‐digital syndrome, and 5 probands (1 mutation) with nonsyndromic polydactyly. These data support previously identified genotype–phenotype correlations and demonstrate a more variable degree of severity than previously recognized. The finding of GLI3 mutations in patients with features of oral–facial–digital syndrome supports the observation that GLI3 interacts with cilia. We conclude that the phenotypic spectrum of GLI3 mutations is broader than that encompassed by the clinical diagnostic criteria, but the genotype–phenotype correlation persists. Individuals with features of either GCPS or PHS should be screened for mutations in GLI3 even if they do not fulfill clinical criteria. Hum Mutat 31:1142–1154, 2010.

CHD7 mutation spectrum in 28 Swedish patients diagnosed with CHARGE syndrome

CHARGE syndrome is a disorder characterized by Coloboma, Heart defect, Atresia choanae, Retarded growth and/or development, Genital hypoplasia and Ear anomalies. Heterozygous mutations in the chromodomain helicase DNA‐binding protein 7 (CHD7) gene have been identified in about 60% of individuals diagnosed with CHARGE syndrome. We performed a CHD7 mutation screening by direct exon sequencing in 28 index patients (26 sporadic cases, 1 familial case consisting of a brother and sister and 1 case consisting of monozygotic twins) diagnosed with CHARGE syndrome in order to determine the mutations in a cohort of Swedish CHARGE syndrome patients. The patients without a detectable CHD7 mutation, or with a missense mutation, were further investigated by multiplex ligation‐dependent probe amplification (MLPA) in order to search for intragenic deletions or duplications. Thirteen novel mutations and five previously reported mutations were detected. The mutations were scattered throughout the gene and included nonsense, frameshift and missense mutations as well as intragenic deletions. In conclusion, CHD7 mutations were detected in a large proportion (64%) of cases diagnosed with CHARGE syndrome. Screening for intragenic deletions with MLPA is recommended in cases where mutations are not found by sequencing. In addition, a CDH7 mutation was found in an individual without temporal bone malformation.

Mutation update for the PORCN gene.

Mutations in the PORCN gene were first identified in Goltz‐Gorlin syndrome patients in 2007. Since then, several reports have been published describing a large variety of genetic defects resulting in the Goltz‐Gorlin syndrome, and mutations or deletions were also reported in angioma serpiginosum, the pentalogy of Cantrell and Limb‐Body Wall Complex. Here we present a review of the published mutations in the PORCN gene to date and report on seven new mutations together with the corresponding clinical data. Based on the review we have created a Web‐based locus‐specific database that lists all identified variants and allows the inclusion of future reports. The database is based on the Leiden Open (source) Variation Database (LOVD) software, and is accessible online at http://www.lovd.nl/porcn. At present, the database contains 106 variants, representing 68 different mutations, scattered along the whole coding sequence of the PORCN gene, and 12 large gene rearrangements, which brings up to 80 the number of unique mutations identified in Goltz‐Gorlin syndrome patients. Hum Mutat 32:1–6, 2011.

Array based characterization of a terminal deletion involving chromosome subband 15q26.2: an emerging syndrome associated with growth retardation, cardiac defects and developmental delay

BackgroundSubtelomeric regions are gene rich and deletions in these chromosomal segments have been demonstrated to account for approximately 2.5% of patients displaying mental retardation with or without association of dysmorphic features. However, cases that report de novo terminal deletions on chromosome arm 15q are rare.MethodsIn this study we present the first example of a detailed molecular genetic mapping of a de novo deletion in involving 15q26.2-qter, caused by the formation of a dicentric chromosome 15, using metaphase FISH and tiling resolution (32 k) genome-wide array-based comparative genomic hybridization (CGH).ResultsAfter an initial characterization of the dicentric chromosome by metaphase FISH, array CGH analysis mapped the terminal deletion to encompass a 6.48 megabase (Mb) region, ranging from 93.86–100.34 Mb on chromosome 15.ConclusionIn conclusion, we present an additional case to the growing family of reported cases with 15q26-deletion, thoroughly characterized at the molecular cytogenetic level. In the deleted regions, four candidate genes responsible for the phenotype of the patient could be delineated: IGFR1, MEF2A, CHSY1, and TM2D3. Further characterization of additional patients harboring similar 15q-aberrations might hopefully in the future lead to the description of a clear cut clinically recognizable syndrome.

Deletion of the SCN gene cluster on 2q24.4 is associated with severe epilepsy: An array-based genotype-phenotype correlation and a comprehensive review of previously published cases.

PURPOSE To characterize a deletion of chromosome 2q at the molecular level in a patient suffering from severe epilepsy resembling severe myoclonic epilepsy of infancy/Dravets syndrome (SMEI/DS) and to correlate other cases harboring deletions in the same region to morphological and clinical data. METHODS Array-based comparative genomic hybridization (array CGH) was performed on DNA from the patient. Forty-three previously published cases reporting deletions within region 2q21-q31 were collected and analyzed regarding their cytogenetic and clinical data. RESULTS A del(2)(q24.3q31.1) was detected in the patient, spanning a 10.4-megabase (Mb) region between 165.18 and 175.58Mb, harboring 47 genes. FISH analysis was performed, confirming this deletion. Twenty-two of the 43 previously published cases were seizure-positive. The most common dysmorphic features were ear abnormalities, microcephaly, micrognathia and brachysyndactyly for all patients as well as for solely the seizure-positive and -negative ones. For the 22 seizure-positive cases chromosome subband 2q24.3 constituted the smallest commonly deleted region among the majority of the cases, where subbands 2q22.1 and 2q33.3 represented the most proximal and distal breakpoint, respectively. CONCLUSIONS Based on the early age of presentation and the severity of the epilepsy reported for the majority of the seizure-positive cases it was concluded that SMEI/DS could be the epileptic encephalopathy associated with deletions within the 2q22.1-q33.3 region, due to haploinsuffiency of SCN1A and/or complete or partial deletion of other voltage-gated sodium channel genes caused by the aberration. Furthermore, our study supports that array CGH is a competent technique for screening SCN1A mutation-negative patients diagnosed with SMEI/DS-like epilepsies and dysmorphic features, generating rapid and high-resolution data of genomic imbalances present in the patients.

Cytogenetic findings and clinical course in a consecutive series of Wilms tumors

Wilms tumor (WT) is characterized by a nonrandom pattern of chromosome aberrations, but the clinical significance of different cytogenetic patterns is unknown. The present study describes the cytogenetic findings and the clinical course in a cohort of 39 children with WT. Samples for short-term culturing and cytogenetic analysis were obtained during a 15-year period. Clonal chromosome aberrations were detected in 23 samples from 19 patients. Tumors that relapsed more often showed clonal aberrations than did tumors that did not. However, this association my have been due to sampling bias. Among the cases with karyotypically abnormal samples, the modal chromosome number was in the near-diploid range in 10, hyperdiploid/hypotriploid in 8, and hypodiploid in 1. The most common changes were trisomy 12 and gain of 1q material (8 cases each), trisomy/tetrasomy 8 (7 cases), and trisomy 13 (5 cases). None of these frequently occurring abnormalities, or the ploidy level, showed any association with clinical outcome, using tumor relapse as an end-point. Nor could any relationship between cytogenetic features and histopathologic subtype be discerned. Although the number of informative cases was too small for proper evaluation, the present study did not contradict the previous notion that loss of material from the long arm of chromosome 16 is associated with poor clinical outcome. All three patients with deletion of 16q developed metastases.

Relation between smoking history and gene expression profiles in lung adenocarcinomas

BackgroundLung cancer is the worldwide leading cause of death from cancer. Tobacco usage is the major pathogenic factor, but all lung cancers are not attributable to smoking. Specifically, lung cancer in never-smokers has been suggested to represent a distinct disease entity compared to lung cancer arising in smokers due to differences in etiology, natural history and response to specific treatment regimes. However, the genetic aberrations that differ between smokers and never-smokers’ lung carcinomas remain to a large extent unclear.MethodsUnsupervised gene expression analysis of 39 primary lung adenocarcinomas was performed using Illumina HT-12 microarrays. Results from unsupervised analysis were validated in six external adenocarcinoma data sets (n=687), and six data sets comprising normal airway epithelial or normal lung tissue specimens (n=467). Supervised gene expression analysis between smokers and never-smokers were performed in seven adenocarcinoma data sets, and results validated in the six normal data sets.ResultsInitial unsupervised analysis of 39 adenocarcinomas identified two subgroups of which one harbored all never-smokers. A generated gene expression signature could subsequently identify never-smokers with 79-100% sensitivity in external adenocarcinoma data sets and with 76-88% sensitivity in the normal materials. A notable fraction of current/former smokers were grouped with never-smokers. Intriguingly, supervised analysis of never-smokers versus smokers in seven adenocarcinoma data sets generated similar results. Overlap in classification between the two approaches was high, indicating that both approaches identify a common set of samples from current/former smokers as potential never-smokers. The gene signature from unsupervised analysis included several genes implicated in lung tumorigenesis, immune-response associated pathways, genes previously associated with smoking, as well as marker genes for alveolar type II pneumocytes, while the best classifier from supervised analysis comprised genes strongly associated with proliferation, but also genes previously associated with smoking.ConclusionsBased on gene expression profiling, we demonstrate that never-smokers can be identified with high sensitivity in both tumor material and normal airway epithelial specimens. Our results indicate that tumors arising in never-smokers, together with a subset of tumors from smokers, represent a distinct entity of lung adenocarcinomas. Taken together, these analyses provide further insight into the transcriptional patterns occurring in lung adenocarcinoma stratified by smoking history.

The Expression of Pluripotency Marker Oct 3/4 in Prostate Cancer and Benign Prostate Hyperplasia

Oct 3/4 (Octamer 3/4), a member of POU family has been considered as an important stem cell marker and essential transcription factor during human embryogenesis. In recent years, there have also been reports on presence of Oct 3/4 in differentiated benign and malignant human cells. The objective of this study was to investigate the transcription and the protein expression of Oct 3/4 isoforms in prostate cancer and benign prostate tissue.