po 450 interplay between coding and non coding genome in human parathyroid tumours

Introduction Parathyroid tumours are the second most common endocrine neoplasia in women, after thyroid cancer. Mutations in the oncosuppressor CDC73 are the key event in most carcinomas whereas alterations in the tumour suppressor MEN1 (located at 11q13.1) occur in up to a third of sporadic adenomas. Although lncRNAs play a regulatory role in endocrine cancer pathogenesis, a lncRNAs profiling in human parathyroid tumours is still missing. Here, we identified a 'molecular signature' able to distinguish among parathyroid histotypes and a new potential epigenetic role of MEN1 in lncRNAs regulation. Material and methods Ninety lncRNAs were investigated in 4 parathyroid carcinomas (PCas), 12 adenomas (PAds) and 2 normal glands (PaNs). Hierarchical clustering (HCL) and Significance Analysis of Microarray (SAM) were performed to identify differences in lncRNAs expression. Significant lncRNAs were validated in additional 7 PCas, 26 PAds, 6 atypical PAds (aPAds) and 4 PaNs. CDC73 and MEN1 genes mutations were detected by Sanger sequencing. PAds genomic characterisation was obtained by array Comparative Genomic Hybridization (aCGH). HEK293 cells were transiently silenced for MEN1 expression to analyse MEN1-lncRNAs correlation. Results and discussions Nine lncRNAs were identified as differentially expressed in parathyroid tissues. Specifically, KCNQ1OT1 and SNHG6 were enriched in PaNs, reduced HAR1B, MEG3, HOXA3as and NEAT1 expression characterised PAds, whereas BC200, HOXA6as and WT1-AS were upregulated in PCas. HCL identified 3 clusters in which PaNs and PCas were distinctly separated, while aPAds were closer to PCas. Moreover, PAds clustered in a highly heterogeneous way. Notably, PCas and aPAds harbouring CDC73-mutations overexpressed the majority of the lncRNAs, compared to CDC73 wild-type samples. Interestingly, BACE1-AS, KCNQ1OT1, NEAT1 and SNHG6 levels in PAds were positively correlated with MEN1 levels. aCGH analysis revealed that Chr11 loss of heterozygosity (LOH) was the main chromosomal aberration in PAds. Of note, Chr11 LOH was associated with significant HAR1B upregulation and these data were confirmed in HEK293 cells knocked-down for MEN1. Conclusion Parathyroid histotypes are characterised by different lncRNAs signatures, suggesting a correlation with tumour aggressiveness and pathogenetic mechanisms. Further, our data highlight that lncRNAs profiles are related to CDC73 gene mutation status, chromosome 11 derangements and MEN1 inactivation

MGMT-Methylated Alleles Are Distributed Heterogeneously Within Glioma Samples Irrespective of IDH Status and Chromosome 10q Deletion

Several molecular markers drive diagnostic classification, prognostic stratification, and/or prediction of response to therapy in patients with gliomas. Among them, IDH gene mutations are valuable markers for defining subtypes and are strongly associated with epigenetic silencing of the methylguanine DNA methyltransferase (MGMT) gene. However, little is known about the percentage of MGMT-methylated alleles in IDH-mutated cells or the potential association between MGMT methylation and deletion of chromosome 10q, which encompasses the MGMT locus. Here, we quantitatively assessed MGMT methylation and IDH1 mutation in 208 primary glioma samples to explore possible differences associated with the IDH genotype. We also explored a potential association between MGMT methylation and loss of chromosome 10q. We observed that MGMT methylation was heterogeneously distributed within glioma samples irrespective of IDH status suggesting an incomplete overlap between IDH1-mutated and MGMT-methylated alleles and indicating a partial association between these two events. Moreover, loss of one MGMT allele did not affect the methylation level of the remaining allele. MGMT was methylated in about half of gliomas harboring a 10q deletion; in those cases, loss of heterozygosity might be considered a second hit leading to complete inactivation of MGMT and further contributing to tumor progression

Evidence of Distinct Tumour-Propagating Cell Populations with Different Properties in Primary Human Hepatocellular Carcinoma

Increasing evidence that a number of malignancies are characterised by tumour cell heterogeneity has recently been published, but there is still a lack of data concerning liver cancers. The aim of this study was to investigate and characterise tumour-propagating cell (TPC) compartments within human hepatocellular carcinoma (HCC).After long-term culture, we identified three morphologically different tumour cell populations in a single HCC specimen, and extensively characterised them by means of flow cytometry, fluorescence microscopy, karyotyping and microarray analyses, single cell cloning, and xenotransplantation in NOD/SCID/IL2Rγ/⁻ mice.The primary cell populations (hcc-1, -2 and -3) and two clones generated by means of limiting dilutions from hcc-1 (clone-1/7 and -1/8) differently expressed a number of tumour-associated stem cell markers, including EpCAM, CD49f, CD44, CD133, CD56, Thy-1, ALDH and CK19, and also showed different doubling times, drug resistance and tumorigenic potential. Moreover, we found that ALDH expression, in combination with CD44 or Thy-1 negativity or CD56 positivity identified subpopulations with a higher clonogenic potential within hcc-1, hcc-2 and hcc-3 primary cell populations, respectively. Karyotyping revealed the clonal evolution of the cell populations and clones within the primary tumour. Importantly, the primary tumour cell population with the greatest tumorigenic potential and drug resistance showed more chromosomal alterations than the others and contained clones with epithelial and mesenchymal features.Individual HCCs can harbor different self-renewing tumorigenic cell types expressing a variety of morphological and phenotypical markers, karyotypic evolution and different gene expression profiles. This suggests that the models of hepatic carcinogenesis should take into account TPC heterogeneity due to intratumour clonal evolution

Cytogenetic mapping of a novel locus for type II Waardenburg syndrome

An Italian family in which Waardenburg syndrome type II (WS2) segregates together with a der(8) chromosome from a (4p;8p) balanced translocation was studied. Cytogenetic analysis by painting and subtelomeric probe hybridization positioned the chromosome 8 breakpoint at p22-pter. Fluorescence in situ hybridization analysis with yeast artificial chromosomes from a contig spanning the 8p21-pter region refined the breakpoint in an interval of less than 170 kb between markers WI-3823 and D8S1819. The only cloned gene for WS2 is that for microphtalmia (MITF) on chromosome 3p. In this family, MITF mutations were excluded by sequencing the whole coding region. The 8p23 region may represent a third locus for WS2 (WS2C)

Insights into 6q21-q22 : Refinement of the critical region for acro-cardio-facial syndrome

Deletions on chromosome 6q are rarely reported in the literature, and genotype-phenotype correlations are poorly understood. We report a child with a deletion of the 6q21-q22 chromosomal region, providing some intriguing results about the correlation between this region and acro-cardio-facial syndrome, congenital heart disease, split hand and foot malformation, and epilepsy

Complex genomic alterations and intellectual disability: an interpretative challenge

Background: Complex chromosomal rearrangements (CCRs) are structural rearrangements involving more than three chromosomes or having more than two breaks; approximately 70% are not associated with any clinical phenotype. Here, we describe a CCR segregating in a two-generation family. Method: A 4-year-old male was evaluated for developmental delay, mild intellectual disability and epicanthus. Karyotype, fluorescence in situ hybridisation (FISH) analysis and array comparative genomic hybridisation (aCGH) analysis were performed on the patient and of all family members. Result: Array CGH analysis of the proband detected two non-contiguous genomic gains of chromosome 2 at bands q32.3q33.2 and bands q36.1q36.3. Both karyotype and FISH analysis revealed a recombinant chromosome 2 with a direct insertion of regions q32.3q33.2 and q36.1q36.3 into region q12. Both of these regions were also present in their original location. Karyotype and FISH analysis of the father revealed a de novo direct insertion of regions q32.3q33.2 and q36.1q36.3 into region q12. Moreover, a de novo balanced translocation involving the q arm of the same chromosome 2 and the p arm of chromosome 10 was observed in the father of the proband. The single nucleotide polymorphism (SNP) array analysis and haplotype reconstruction confirmed the paternal origin of the duplications. Karyotype, FISH analysis and array CGH analysis of other family members were all normal. Conclusion: This report underlines the importance of using different methods to correctly evaluate the origin and the structure of CCRs in order to provide an appropriate management of the patients and a good estimation of the reproductive risk of the family

Otorhinolaringologic manifestation of Smith-Magenis syndrome

Smith-Magenis syndrome (SMS) is a multiple congenital anomaly/mental retardation (MCA/MR) syndrome link to a contiguous-gene deletion syndrome, involving chromosome 1 7p 11.2,whose incidence is estimated to be 1:25 000 livebirth. SMS is characterised by a specific physical, behavioural and developmental pattern. The main clinical features consist of a broad flat midface with brachycefaly, broad nasal bridge, brachydactily, speech delay, hoarse deep voice and peripheral neuropathy. Behavioural abnormalities include hypermotility, self-mutilation and sleep disturbance. This report defines the otorhinolaryngological aspects of a new case of SMS, confirmed by cytogenetic-molecular analysis, in a 9 year old girl affected by chronic otitis media, deafness and sinusitis, who presented with typical clinical signs and symptoms. (C) 2001 Elsevier Science Ireland Ltd. All rights reserved

Trisomic zygote rescue revealed by DNA polymorphism analysis in confined placental mosaicism

Uniparental disomy can be caused by different genetic mechanisms such as gamete complementation, chromosome duplication in monosomic zygote, or post-zygotic aneuploidy correction. This last mechanism is well documented in human reproduction and is related to placental mosaicism. In the case of a trisomic zygote which has originated by paternal or maternal non-disjunction at the first or second meiotic cell division, mosaicism will result from chromosome loss and restoration of a 'normalized' diploid fetal karyotype. In order to enrich the literature with new observations on this subject, we studied by DNA polymorphism analysis ten cases of confined placental mosaicism (CPM). The finding in placental DNA of three different alleles at polymorphic loci of chromosomes 13, 16, and 20 demonstrated the trisomic status of the zygote in three cases. On the basis of these results, we believe that systematic DNA polymorphism analysis could give useful additional information to improve knowledge on aneuploidy correction in human reproduction

Molecular cytogenetic characterization of a 2q35-q37 duplication and a 4q35.1-q35.2 deletion in two cousins : a genotype-phenotype analysis

The 2q3 duplication and 4q3 deletion are two distinct conditions with variable phenotypes including developmental delay, intellectual disability, Pierre Robin sequence (PRS), and cardiovascular, craniofacial, digital and skeletal anomalies. We describe two cousins, a 37-year-old man (Patient 1) and a 17-year-old girl (Patient 2), with a derivative chromosome leading to a 4q35 deletion-2q35q37 duplication. Conventional karyotype showed in both patients the same rearrangement derived from unbalanced segregation of a parental reciprocal translocation involving the long arms of chromosome 2 and 4. Patient 1's father and Patient 2's mother were identified as the carriers of a balanced translocation t(2;4)(q35;q35). Array-CGH analysis, performed to characterize the rearrangement, documented in both patients the presence of a 26Mb duplication of the 2q35-q37.3 region of chromosome 2 and a 6.3Mb deletion of the 4q35.1-q35.2 region of chromosome 4. Both patients showed intellectual disability, minor facial, and digital anomalies, hearing, ocular, and genitourinary abnormalities. The comparison of their features with those of published cases of 2q3 duplication and 4q3 deletion allowed us to further delineate the genotype-phenotype correlation as well as the combined effect of partial 2q duplication and 4q deletion syndromes in adulthood