RESUMEN
Osteosarcoma is the primary malignant cancer of bone and particularly affects adolescents and young adults, causing debilitation and sometimes death. As a model for human osteosarcoma, we have been studying p53(+/-) mice, which develop osteosarcoma at high frequency. To discover genes that cooperate with p53 deficiency in osteosarcoma formation, we have integrated array comparative genomic hybridization, microarray expression analyses in mouse and human osteosarcomas, and functional assays. In this study, we found seven frequent regions of copy number gain and loss in the mouse p53(+/-) osteosarcomas but have focused on a recurrent amplification event on mouse chromosome 9A1. This amplicon is syntenic with a similar chromosome 11q22 amplicon identified in several human tumor types. Three genes on this amplicon, the matrix metalloproteinase gene MMP13 and the antiapoptotic genes Birc2 (cIAP1) and Birc3 (cIAP2), show elevated expression in mouse and human osteosarcomas. We developed a functional assay using clonal osteosarcoma cell lines transduced with lentiviral short hairpin RNA vectors to show that down-regulation of MMP13, Birc2, or Birc3 resulted in reduced tumor growth when transplanted into immunodeficient recipient mice. These experiments revealed that high MMP13 expression enhances osteosarcoma cell survival and that Birc2 and Birc3 also enhance cell survival but only in osteosarcoma cells with the chromosome 9A1 amplicon. We conclude that the antiapoptotic genes Birc2 and Birc3 are potential oncogenic drivers in the chromosome 9A1 amplicon.
Asunto(s)
Neoplasias Óseas/genética , Proteínas Inhibidoras de la Apoptosis/genética , Metaloproteinasa 13 de la Matriz/genética , Osteosarcoma/genética , Proteína p53 Supresora de Tumor/deficiencia , Proteínas Adaptadoras Transductoras de Señales/biosíntesis , Proteínas Adaptadoras Transductoras de Señales/deficiencia , Proteínas Adaptadoras Transductoras de Señales/genética , Animales , Proteína 3 que Contiene Repeticiones IAP de Baculovirus , Neoplasias Óseas/enzimología , Proteínas de Ciclo Celular , Transformación Celular Neoplásica/genética , Hibridación Genómica Comparativa , Amplificación de Genes , Inestabilidad Genómica , Humanos , Proteínas Inhibidoras de la Apoptosis/deficiencia , Metaloproteinasa 13 de la Matriz/biosíntesis , Ratones , Ratones Endogámicos C57BL , Osteosarcoma/enzimología , Fosfoproteínas/biosíntesis , Fosfoproteínas/deficiencia , Fosfoproteínas/genética , ARN Neoplásico/biosíntesis , ARN Neoplásico/genética , Células Tumorales Cultivadas , Proteína p53 Supresora de Tumor/genética , Ubiquitina-Proteína Ligasas , Proteínas Señalizadoras YAPRESUMEN
BACKGROUND: Most machine-learning classifiers output label predictions for new instances without indicating how reliable the predictions are. The applicability of these classifiers is limited in critical domains where incorrect predictions have serious consequences, like medical diagnosis. Further, the default assumption of equal misclassification costs is most likely violated in medical diagnosis. RESULTS: In this paper, we present a modified random forest classifier which is incorporated into the conformal predictor scheme. A conformal predictor is a transductive learning scheme, using Kolmogorov complexity to test the randomness of a particular sample with respect to the training sets. Our method show well-calibrated property that the performance can be set prior to classification and the accurate rate is exactly equal to the predefined confidence level. Further, to address the cost sensitive problem, we extend our method to a label-conditional predictor which takes into account different costs for misclassifications in different class and allows different confidence level to be specified for each class. Intensive experiments on benchmark datasets and real world applications show the resultant classifier is well-calibrated and able to control the specific risk of different class. CONCLUSION: The method of using RF outlier measure to design a nonconformity measure benefits the resultant predictor. Further, a label-conditional classifier is developed and turn to be an alternative approach to the cost sensitive learning problem that relies on label-wise predefined confidence level. The target of minimizing the risk of misclassification is achieved by specifying the different confidence level for different class.
Asunto(s)
Inteligencia Artificial , Biología Computacional/economía , Biología Computacional/métodos , Técnicas y Procedimientos Diagnósticos , Técnicas y Procedimientos Diagnósticos/economía , Almacenamiento y Recuperación de la Información , Modelos Estadísticos , Reconocimiento de Normas Patrones Automatizadas/métodosRESUMEN
Separase is an endopeptidase that separates sister chromatids by cleaving cohesin Rad21 during the metaphase-to-anaphase transition. Conditional expression of Separase in tetracycline-inducible diploid FSK3 mouse mammary epithelial cells with both p53 WT and mutant (Ser-233-234) alleles of unknown physiological significance develops aneuploidy within 5 days of Separase induction in vitro. Overexpression of Separase induces premature separation of chromatids, lagging chromosomes, and anaphase bridges. In an in vivo mouse mammary transplant model, induction of Separase expression in the transplanted FSK3 cells for 3-4 weeks results in the formation of aneuploid tumors in the mammary gland. Xenograft studies combined with histological and cytogenetic analysis reveal that Separase-induced tumors are clonal in their genomic complements and have a mesenchymal phenotype suggestive of an epithelial-mesenchymal transition. Induction of Separase resulted in trisomies for chromosomes 8, 15, and 17; monosomy for chromosome 10; and amplification of the distal region of chromosomes 8 and 11. Separase protein is found to be significantly overexpressed in human breast tumors compared with matched normal tissue. These results collectively suggest that Separase is an oncogene, whose overexpression alone in mammary epithelial cells is sufficient to induce aneuploidy and tumorigenesis in a p53 mutant background.
Asunto(s)
Aneuploidia , Neoplasias de la Mama/enzimología , Proteínas de Ciclo Celular/metabolismo , Endopeptidasas/metabolismo , Neoplasias Mamarias Experimentales/enzimología , Anafase , Animales , Western Blotting , Línea Celular Tumoral , Cromátides/enzimología , Inestabilidad Cromosómica , Células Epiteliales/enzimología , Células Epiteliales/patología , Femenino , Humanos , Metafase , Ratones , Hibridación de Ácido Nucleico , Separasa , TetraciclinaRESUMEN
Osteosarcoma is a primary malignant tumor of bone arising from primitive bone-forming mesenchymal cells and accounts for approximately 60% of malignant bone tumors. Our comparative genomic hybridization (CGH) studies have identified frequent amplification at 6p12-p21, 12q13-q15, and 17p11.2 in osteosarcoma. Of these amplified regions, 6p12-p21 is particularly interesting because of its association with progression and poor prognosis in patients with osteosarcoma. In an attempt to identify aberrantly expressed gene(s) mapping to the 6p12-p21 amplicon, a region-specific array was generated using 108 overlapping BAC and P1 clones covering a 28.8-Mb region at 0.26-Mb intervals. Based on array CGH analysis, the 6p amplicon was refined to 7.9 Mb between the clones RP11-91E11 and RP1-244F2 and 10 amplified clones, with possible target genes, were identified. To study the expression pattern of the target genes from the hotspot amplicon and known candidate genes from 6p12-21, we did quantitative reverse transcription-PCR analysis of MAPK14, MAPK13, CDKN1A, PIM1, MDGA1, BTB9, DNAH8, CCND3, PTK7, CDC5L, and RUNX2 on osteosarcoma patient samples and seven cell lines. The combined array CGH and quantitative reverse transcription-PCR analysis identified amplification and overexpression of CDC5L, CCND3, and RUNX2. We screened these three genes for protein expression by Western blotting and immunohistochemistry and detected overexpression of CDC5L. Furthermore, we used an in vivo assay to show that CDC5L possesses potential oncogenic activity. These results indicate that CDC5L, a cell cycle regulator important for the G2-M transition, is the most likely candidate oncogene for the 6p12-p21 amplicon found in osteosarcoma.
Asunto(s)
Neoplasias Óseas/genética , Proteínas de Ciclo Celular/genética , Cromosomas Humanos Par 6 , Amplificación de Genes , Osteosarcoma/genética , Proteínas de Unión al ARN/genética , Animales , Neoplasias Óseas/metabolismo , Línea Celular Tumoral , Mapeo Cromosómico , Femenino , Genes cdc , Humanos , Masculino , Ratones , Células 3T3 NIH , Oncogenes , Osteosarcoma/metabolismo , ARN Mensajero/metabolismoRESUMEN
Fluorescence in situ hybridization (FISH) banding approaches are standard for the exact characterization of simple, complex, and even cryptic chromosomal aberrations within the human genome. The most frequently applied FISH banding technique is the multicolor banding approach, also abbreviated as m-band, MCB, or in its whole genomic variant multitude MCB (mMCB). MCB allows the differentiation of chromosome region-specific areas at the GTG band and sub-band level and is based on region-specific microdissection libraries, producing changing fluorescence intensity ratios along the chromosomes. The latter are used to assign different pseudocolors to specific chromosomal regions. Here we present the first bacterial artificial chromosome (BAC) array comparative genomic hybridization (aCGH) mapped, comprehensive, genome-wide human MCB probe set. All 169 region-specific microdissection libraries were characterized in detail for their size and the regions of overlap. In summary, the unique possibilities of the MCB technique to characterize chromosomal breakpoints in one FISH experiment are now complemented by the feature of being anchored within the human DNA sequence at the BAC level.
Asunto(s)
Bandeo Cromosómico/métodos , ADN/genética , Colorantes Fluorescentes , Hibridación Fluorescente in Situ/métodos , Cromosomas Artificiales Bacterianos/genética , Color , Genoma Humano/genética , Humanos , Hibridación de Ácido Nucleico , Análisis de Secuencia por Matrices de OligonucleótidosRESUMEN
Phosphatase and tensin homologue deleted from chromosome 10 (Pten) is expressed aberrantly in non-small cell lung cancer cells, but the role of Pten in lung neoplasia has not been fully elucidated. In this study, we used a genetic approach to inactivate Pten in the bronchial epithelium of mice. Although, by itself, Pten inactivation had no discernible effect on bronchial epithelial histology, it accelerated lung tumorigenesis initiated by oncogenic K-ras, causing more rapid lethality than that induced by oncogenic K-ras alone (8 weeks versus 24 weeks of median duration of survival, respectively). Lung tumors arose in K-ras mutant, Pten-deficient mice that rapidly obstructed bronchial lumina and replaced alveolar spaces. Relative to K-ras mutant tumors, the K-ras mutant, Pten-deficient tumors exhibited more advanced histologic severity and more prominent inflammation and vascularity. Thus, Pten inactivation cooperated with oncogenic K-ras in promoting lung tumorigenesis.
Asunto(s)
Transformación Celular Neoplásica/genética , Genes ras , Neoplasias Pulmonares/genética , Fosfohidrolasa PTEN/genética , Adenocarcinoma Bronquioloalveolar/irrigación sanguínea , Adenocarcinoma Bronquioloalveolar/genética , Adenocarcinoma Bronquioloalveolar/metabolismo , Adenocarcinoma Bronquioloalveolar/patología , Alelos , Animales , Transformación Celular Neoplásica/metabolismo , Quimiocinas/biosíntesis , Quimiocinas/genética , Modelos Animales de Enfermedad , Regulación Neoplásica de la Expresión Génica , Silenciador del Gen , Inmunohistoquímica , Péptidos y Proteínas de Señalización Intercelular/biosíntesis , Péptidos y Proteínas de Señalización Intercelular/genética , Neoplasias Pulmonares/irrigación sanguínea , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/patología , Ratones , Ratones Endogámicos C57BL , Fosfohidrolasa PTEN/biosíntesis , Fosfohidrolasa PTEN/deficiencia , Fosfatidilinositol 3-Quinasas/metabolismo , Transducción de SeñalRESUMEN
Glioma pathogenesis-related protein 1 (GLIPR1), a novel p53 target gene, is down-regulated by methylation in prostate cancer and has p53-dependent and -independent proapoptotic activities in tumor cells. These properties suggest an important tumor suppressor role for GLIPR1, yet direct genetic evidence of a tumor suppressor function for GLIPR1 is lacking and the molecular mechanism(s), through which GLIPR1 exerts its tumor suppressor functions, has not been shown. Here, we report that the expression of GLIPR1 is significantly reduced in human prostate tumor tissues compared with adjacent normal prostate tissues and in multiple human cancer cell lines. Overexpression of GLIPR1 in cancer cells leads to suppression of colony growth and induction of apoptosis. Mice with an inactivated Glipr1 gene had significantly shorter tumor-free survival times than either Glipr1(+/+) or Glipr1(+/-) mice in both p53(+/+) and p53(+/-) genetic backgrounds, owing to their development of a unique array of malignant tumors. Mechanistic analysis indicated that GLIPR1 up-regulation increases the production of reactive oxygen species (ROS) leading to apoptosis through activation of the c-Jun-NH(2) kinase (JNK) signaling cascade. Thus, our results identify GLIPR1 as a proapoptotic tumor suppressor acting through the ROS-JNK pathway and support the therapeutic potential for this protein.
Asunto(s)
Apoptosis , Proteínas Quinasas JNK Activadas por Mitógenos/metabolismo , Proteínas de Neoplasias/fisiología , Proteínas del Tejido Nervioso/fisiología , Especies Reactivas de Oxígeno/metabolismo , Animales , Apoptosis/genética , Apoptosis/fisiología , Proteínas Reguladoras de la Apoptosis/genética , Proteínas Reguladoras de la Apoptosis/fisiología , Transformación Celular Neoplásica/genética , Femenino , Regulación Neoplásica de la Expresión Génica , Genes Supresores de Tumor/fisiología , Predisposición Genética a la Enfermedad , Células HCT116 , Humanos , Masculino , Proteínas de la Membrana , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Proteínas de Neoplasias/genética , Neoplasias/genética , Proteínas del Tejido Nervioso/genética , Transducción de Señal/fisiologíaRESUMEN
Despite the widespread application of microarray imaging for biomedical imaging research, barriers still exist regarding its reliability for clinical use. A critical major problem lies in accurate spot segmentation and the quantification of gene expression level (mRNA) from the microarray images. A variety of commercial and research freeware packages are available, but most cannot handle array spots with complex shapes such as donuts and scratches. Clustering approaches such as k-means and mixture models were introduced to overcome this difficulty, which use the hard labeling of each pixel. In this paper, we apply fuzzy clustering approaches for spot segmentation, which provides soft labeling of the pixel. We compare several fuzzy clustering approaches for microarray analysis and provide a comprehensive study of these approaches for spot segmentation. We show that possiblistic c-means clustering (PCM) provides the best performance in terms of stability criterion when testing on both a variety of simulated and real microarray images. In addition, we compared three statistical criteria in measuring gene expression levels and show that a new asymptotically unbiased statistic is able to quantify the gene expression level more accurately.
RESUMEN
Array-based comparative genomic hybridization (array CGH) is becoming a prominent genomic technology with many important applications in biomedical research. Although several platforms of this technology have been published, successful implementation of this technology still demands technical expertise. Here, we describe the technology that has been developed and improved in the past few years are described. Our array CGH technology is primarily based on robust and readily implemented array production method. We also developed related protocols for using our bacterial artifical chromosomes CGH microarrays. This technology was successfully used to detect DNA copy-number alterations in various mouse and human samples.
Asunto(s)
ADN/análisis , Dosificación de Gen , Genoma , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Animales , Reactivos de Enlaces Cruzados/farmacología , Fluorescencia , Humanos , Ratones , Silanos/químicaRESUMEN
Mutations in ras and p53 are the most prevalent mutations found in human nonmelanoma skin cancers. Although some p53 mutations cause a loss of function, most result in expression of altered forms of p53, which may exhibit gain-of-function properties. Therefore, understanding the consequences of acquiring p53 gain-of-function versus loss-of-function mutations is critical for the generation of effective therapies for tumors harboring p53 mutations. Here we describe an inducible mouse model in which skin tumor formation is initiated by activation of an endogenous K-ras(G12D) allele. Using this model we compared the consequences of activating the p53 gain-of-function mutation p53(R172H) and of deleting the p53 gene. Activation of the p53(R172H) allele resulted in increased skin tumor formation, accelerated tumor progression, and induction of metastasis compared with deletion of p53. Consistent with these observations, the p53(R172H) tumors exhibited aneuploidy associated with centrosome amplification, which may underlie the mechanism by which p53(R172H) exerts its oncogenic properties. These results clearly demonstrate that p53 gain-of-function mutations confer poorer prognosis than loss of p53 during skin carcinogenesis and have important implications for the future design of therapies for tumors that exhibit p53 gain-of-function mutations.
Asunto(s)
Neoplasias Cutáneas/metabolismo , Neoplasias Cutáneas/patología , Proteína p53 Supresora de Tumor/metabolismo , Alelos , Aneuploidia , Animales , Arginina/genética , Arginina/metabolismo , Transformación Celular Neoplásica/genética , Transformación Celular Neoplásica/metabolismo , Transformación Celular Neoplásica/patología , Centrosoma , Modelos Animales de Enfermedad , Activación Enzimática , Regulación Neoplásica de la Expresión Génica , Glicina/genética , Glicina/metabolismo , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/patología , Neoplasias Pulmonares/secundario , Metástasis Linfática/patología , Ratones , Ratones Endogámicos C57BL , Mutación/genética , Neoplasias Cutáneas/genética , Proteína p53 Supresora de Tumor/genética , Proteínas ras/genética , Proteínas ras/metabolismoRESUMEN
The underlying genetic cause of mental retardation (MR) remains unknown in about half of the cases. Recently, using whole genome array comparative genomic hybridization (array-CGH), submicroscopic genetic imbalances have been detected in up to 20% of patients with an unexplained MR, dysmorphic features, and apparently normal karyotype. Here, we present a 12-year-old girl with features of basal cell nevus syndrome (BCNS), pulmonary valve stenosis, and MR, in whom array-CGH identified a 7.7 Mb deletion on 9q22.1-q22.32. The deleted region includes, among others, the ROR2 and PTCH genes. Haploinsufficiency of PTCH causes the BCNS syndrome and mutations in ROR2 have been found in an autosomal recessive Robinow syndrome and a dominantly inherited brachydactyly type 1B. We speculate that haploinsufficiency of ROR2 may contribute to pulmonary valve stenosis. Because of an age-dependent penetrance, BCNS may be challenging for diagnosis particularly when the features are not part of a typical clinical spectrum of BCNS. Early diagnosis of BCNS is important for preventing the development of associated tumors and better care of the patient. Our data confirm the previous observations that application of the whole genome array-CGH should be considered in selected patients with undiagnosed MR and dysmorphic features.
Asunto(s)
Síndrome del Nevo Basocelular/genética , Deleción Cromosómica , Cromosomas Humanos Par 9 , Discapacidad Intelectual/genética , Receptores de Superficie Celular/genética , Anomalías Múltiples/diagnóstico , Anomalías Múltiples/genética , Síndrome del Nevo Basocelular/diagnóstico , Síndrome del Nevo Basocelular/patología , Niño , Cromosomas Artificiales Bacterianos , Facies , Femenino , Genoma Humano , Humanos , Hibridación Fluorescente in Situ , Discapacidad Intelectual/diagnóstico , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Receptores Patched , Receptor Patched-1 , Receptores Huérfanos Similares al Receptor Tirosina Quinasa , Receptores de Superficie Celular/metabolismoRESUMEN
Serial analysis of gene expression from aggressive mammary tumors derived from transplantable p53 null mouse mammary outgrowth lines revealed significant up-regulation of Tfdp1 (transcription factor Dp1), Lamp1 (lysosomal membrane glycoprotein 1) and Gas6 (growth arrest specific 6) transcripts. All of these genes belong to the same linkage cluster, mapping to mouse chromosome band 8A1. BAC-array comparative genomic hybridization and fluorescence in situ hybridization analyses revealed genomic amplification at mouse region ch8A1.1. The minimal region of amplification contained genes Cul4a, Lamp1, Tfdp1, and Gas6, highly overexpressed in the p53 null mammary outgrowth lines at preneoplastic stages, and in all its derived tumors. The same amplification was also observed in spontaneous p53 null mammary tumors. Interestingly, this region is homologous to human chromosome 13q34, and some of the same genes were previously observed amplified in human carcinomas. Thus, we further investigated the occurrence and frequency of gene amplification affecting genes mapping to ch13q34 in human breast cancer. TFDP1 showed the highest frequency of amplification affecting 31% of 74 breast carcinomas analyzed. Statistically significant positive correlation was observed for the amplification of CUL4A, LAMP1, TFDP1, and GAS6 genes (P < 0.001). Meta-analysis of publicly available gene expression data sets showed a strong association between the high expression of TFDP1 and decreased overall survival (P = 0.00004), relapse-free survival (P = 0.0119), and metastasis-free interval (P = 0.0064). In conclusion, our findings suggest that CUL4A, LAMP1, TFDP1, and GAS6 are targets for overexpression and amplification in breast cancers. Therefore, overexpression of these genes and, in particular, TFDP1 might be of relevance in the development and/or progression in a significant subset of human breast carcinomas.
Asunto(s)
Neoplasias de la Mama/genética , Cromosomas Humanos Par 13/genética , Amplificación de Genes , Neoplasias Mamarias Experimentales/genética , Animales , Northern Blotting , Mapeo Cromosómico , ADN de Neoplasias/genética , Expresión Génica , Perfilación de la Expresión Génica , Humanos , Hibridación Fluorescente in Situ , Ratones , Familia de Multigenes , Hibridación de Ácido Nucleico , Reacción en Cadena de la Polimerasa de Transcriptasa InversaRESUMEN
Small supernumerary marker chromosomes (sSMCs) are a morphologically heterogeneous group of additional structurally abnormal chromosomes that cannot be identified unambiguously by conventional banding techniques alone. Molecular cytogenetic methods enable detailed characterization of sSMCs; however, in many cases interpretation of their clinical significance is problematic. The aim of our study was to characterize precisely sSMCs identified in three patients with dysmorphic features, psychomotor retardation and multiple congenital anomalies. We also attempted to correlate the patients' genotypes with phenotypes by inclusion of data from the literature. The sSMCs were initially detected by G-banding analysis in peripheral blood lymphocytes in these patients and were subsequently characterized using multicolor fluorescence in situ hybridization (M-FISH), (sub)centromere-specific multicolor FISH (cenM-FISH, subcenM-FISH), and multicolor banding (MCB) techniques. Additionally, the sSMCs in two patients were also studied by hybridization to whole-genome bacterial artificial chromosome (BAC) arrays (array-CGH) to map the breakpoints on a single BAC clone level. In all three patients, the chromosome origin, structure, and euchromatin content of the sSMCs were determined. In patient RS, only a neocentric r(2)(q35q36) was identified. It is a second neocentric sSMC(2) in the literature and the first marker chromosome derived from the terminal part of 2q. In the other two patients, two sSMCs were found, as M-FISH detected additional sSMCs that could not be characterized in G-banding analysis. In patient MK, each of four cell lines contained der(4)(:p11.1-->q12:) accompanied by a sSMC(18): r(18)(:p11.2-->q11.1::p11.2-->q11.1:), inv dup(18)(:p11.1-->q11.1::q11.1-->p11.1:), or der(18) (:p11.2-->q11.1::q11.1-->p11.1:). In patient NP, with clinical features of trisomy 8p, three sSMCs were characterized: r(8)(:p12-->q11.1::q11.1-->p21:) der(8) (:p11.22-->q11.1::q11.1-->p21::p21-->p11.22:) and der(21)(:p11.1-->q21.3:). The BAC array results confirmed the molecular cytogenetic results and refined the breakpoints to the single BAC clone resolution. However, the complex mosaic structure of the marker chromosomes derived from chromosomes 8 and 18 could only be identified by molecular cytogenetic methods. This study confirms the usefulness of multicolor FISH combined with whole-genome arrays for comprehensive analyses of marker chromosomes.
Asunto(s)
Aneuploidia , Cromosomas Humanos/genética , Preescolar , Pintura Cromosómica , Cromosomas Artificiales Bacterianos/genética , Femenino , Marcadores Genéticos , Humanos , Hibridación Fluorescente in Situ , Masculino , Repeticiones de Microsatélite , Mosaicismo , FenotipoRESUMEN
We describe our findings in a 46,XY female with a clinical features of Genitopatellar syndrome (GPS) and confirmed hermaphroditism with ovotestes, and five additional patients with GPS. GPS is a genetic disorder characterized by renal and genital anomalies, joint dislocation, aplastic or hypoplastic and often displaced patellae, minor facial anomalies, and mental retardation. The genital anomalies clearly distinguish GPS from nail-patella syndrome (NPS) that has similar features, but additionally shows hypoplastic finger- and toenails as found in the 46,XY female. In our patients no mutation was found in the coding regions of WNT4, WNT7A, TBX4, and LMX1B. Fluorescent in situ hybridization (FISH) and array-based comparative genome hybridization (aCGH) analysis showed a 3 Mb deletion of LMX1B, NR6A1, and NR5A1 (SF1) in the 46,XY female. This is the first report of a microdeletion causing haploinsuffiency of LMX1B and NR5A1. The deletion of LMX1B is responsible for the knee anomalies and the deletion of NR5A1 likely causes the sex reversal. Cytogenetic analysis of the five additional patients with diagnosed GPS failed to identify a similar microdeletion, or inversion of a potentially regulatory element between the two genes. This suggests that the locus 9q33-9q34 can be excluded for GPS and that the presented case is unique in its combination of GPS and NPS features caused by a microdeletion associated with loss of function of LMX1B and NR5A1.
Asunto(s)
Anomalías Múltiples/genética , Deleción Cromosómica , Cromosomas Humanos Par 9 , Trastornos del Desarrollo Sexual , Gónadas/anomalías , Proteínas de Homeodominio/genética , Rótula/anomalías , Receptores Citoplasmáticos y Nucleares/genética , Factores de Transcripción/genética , Niño , Preescolar , Bandeo Cromosómico , Análisis Mutacional de ADN , Femenino , Humanos , Lactante , Proteínas con Homeodominio LIM , Masculino , Factor Esteroidogénico 1 , SíndromeRESUMEN
The Aurora-A kinase gene is amplified in a subset of human tumors and in radiation-induced lymphomas from p53 heterozygous mice. Normal tissues from p53-/- mice have increased Aurora-A protein levels, but lymphomas from these mice exhibit heterozygous deletions of Aurora-A and/or reduced protein expression. A similar correlation between low p53 levels and Aurora-A gene deletions and expression is found in human breast cancer cell lines. In vitro studies using mouse embryo fibroblasts demonstrate that inhibition of Aurora-A can have either positive or negative effects on cell growth as a function of p53 status. These data have implications for the design of approaches to targeted cancer therapy involving the crosstalk between Aurora-A kinase and p53 pathways.
Asunto(s)
Neoplasias de la Mama/metabolismo , Linfoma/metabolismo , Neoplasias Inducidas por Radiación/metabolismo , Proteínas Serina-Treonina Quinasas/genética , Neoplasias del Timo/metabolismo , Proteína p53 Supresora de Tumor/fisiología , Animales , Apoptosis , Aurora Quinasa A , Aurora Quinasas , Neoplasias de la Mama/patología , Células Cultivadas , Regulación hacia Abajo , Embrión de Mamíferos/citología , Embrión de Mamíferos/metabolismo , Femenino , Fibroblastos/citología , Fibroblastos/metabolismo , Eliminación de Gen , Dosificación de Gen , Perfilación de la Expresión Génica , Inestabilidad Genómica , Heterocigoto , Linfoma/genética , Linfoma/patología , Masculino , Ratones , Ratones Noqueados , Análisis por Micromatrices , Neoplasias Inducidas por Radiación/genética , Neoplasias Inducidas por Radiación/patología , Proteínas Serina-Treonina Quinasas/metabolismo , Tasa de Supervivencia , Neoplasias del Timo/genética , Neoplasias del Timo/patología , Proteína p53 Supresora de Tumor/genética , Irradiación Corporal TotalRESUMEN
Tumours develop from clonally expanded population of cells harbouring aberrations of oncogenes and tumour suppressor genes. In this study, metaphase and array comparative genomic hybridization showed good correlation of aberration profiles in lung adenocarcinoma cell lines from patients with different tobacco exposure. Recurrent DNA gains were found at chromosomes 1, 7, 8, 17, 20, and deletions at 1, 3, 8, 9, 10, 12, 17, 18, 19. Candidate tumour loci and encompassed genes at 7p21 (AGR2), 8q21(TPD52), 20q13 (ZNF217, WFDC2, EEF1A2) and 10p15 (KLF6) were analyzed by dual colour FISH for genomic changes and quantitative PCR for expression changes. Results indicated that EEF1A2 and KLF6 were strong candidates of oncogene and tumour suppressor genes, respectively. This study illustrates, a practical strategy for identifying candidate cancer genes from microarray data.
Asunto(s)
Adenocarcinoma/genética , Aberraciones Cromosómicas , Predisposición Genética a la Enfermedad/genética , Neoplasias Pulmonares/genética , Hibridación de Ácido Nucleico/métodos , Adenocarcinoma/patología , Anciano , Femenino , Dosificación de Gen , Regulación Neoplásica de la Expresión Génica , Genoma Humano , Humanos , Hibridación Fluorescente in Situ , Neoplasias Pulmonares/patología , Masculino , Metafase/genética , Análisis por Micromatrices/métodos , Persona de Mediana Edad , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Células Tumorales CultivadasRESUMEN
In this report we present a spontaneous mouse mutant, named Polypodia (Ppd), that primarily exhibits ectopic, ventral/caudal limbs and associated pelvic girdle malformation or duplication. Less penetrant features include diphallia, microphthalmia, small kidney, curled or kinked tail, forelimb anomaly, and skin papillae. Ppd mice have a normal karyotype and no large-scale genomic deletions or insertions by BAC-based array comparative genomic hybridization (CGH). Ppd is X-linked dominant with approximately 20% penetrance on the C3H background and maps to X:61.6 Mb-X:71.24 Mb. The limb and a subset of the nonlimb anomalies are similar to those in offspring from retinoic acid-treated dams at E4.5-5.5 and feature overlap with the Disorganization mouse mutant and human patients with ectopic legs. We hypothesize that Ppd affects very early steps in the formation of caudal structures including limb and appendage number. The existence of noncaudal anomalies implies the involvement of Ppd in a broad array of cell fate decisions.
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Genes Dominantes , Genes Ligados a X , Deformidades Congénitas de las Extremidades Inferiores/genética , Anomalías Múltiples/genética , Animales , Mapeo Cromosómico , Extremidades/anatomía & histología , Regulación del Desarrollo de la Expresión Génica , Deformidades Congénitas de las Extremidades Inferiores/embriología , Ratones , Ratones Mutantes , Linaje , FenotipoRESUMEN
This article summarizes the proceedings of a symposium presented at the 2005 annual meeting of the Research Society on Alcoholism in Santa Barbara, California. The organizer was James M. Sikela, and he and Michael F. Miles were chairs. The presentations were (1) Genomewide Surveys of Gene Copy Number Variation in Human and Mouse: Implications for the Genetics of Alcohol Action, by James M. Sikela; (2) Regional Differences in the Regulation of Brain Gene Expression: Relevance to the Detection of Genes Associated with Alcohol-Related Traits, by Robert Hitzemann; (3) Identification of Ethanol Quantitative Trait Loci Candidate Genes by Expression Profiling in Inbred Long Sleep/Inbred Short Sleep Congenic Mice, by Robnet T. Kerns; and (4) Quantitative Proteomic Analysis of AC7-Modified Mice, by Kathleen J. Grant.
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Etanol/farmacología , Análisis de Secuencia por Matrices de Oligonucleótidos , Proteómica , Alcoholismo/genética , Animales , Ambiente , Femenino , Perfilación de la Expresión Génica , Humanos , Masculino , Ratones , Sitios de Carácter Cuantitativo , Sueño/genética , Especificidad de la EspecieRESUMEN
Although radiation can directly induce DNA damage and is a known human and animal carcinogen, the number of genetic changes in radiation-induced tumors, and the pathways responsible for generating them, are unknown. We have used high-density BAC arrays covering >95% of the mouse genome for analysis of genomic patterns of aberrations in spontaneous and radiation-induced mouse lymphomas. The majority of radiation-induced tumors exhibit one of three 'signatures' based on gene copy number changes. Some exhibit extensive scrambling of the genome, with very high numbers of recurrent gains and losses. Two other signatures are characterized by excess gains but relatively few losses, or vice versa. Changes in spontaneous tumors often involve whole chromosomes, whereas radiation-induced tumors exhibit a high frequency of localized deletion/amplification events. The number of copy number abnormalities does not correlate with the latency or pathology of the tumors. We propose that specific early events following radiation exposure induce changes in 'caretaker' genes that control specific downstream pathways involved in DNA damage repair. The nature of these early events may determine the overall genomic signature observed in the resulting tumor.
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Daño del ADN/efectos de la radiación , Genes p53 , Inestabilidad Genómica/efectos de la radiación , Linfoma/etiología , Linfoma/genética , Neoplasias Inducidas por Radiación/genética , Neoplasias del Timo/genética , Animales , Reparación del ADN , Femenino , Amplificación de Genes , Eliminación de Gen , Perfilación de la Expresión Génica , Masculino , Ratones , Ratones Endogámicos C57BL , Neoplasias del Timo/etiologíaRESUMEN
Molecular cytogenetics allows the identification of cryptic chromosome rearrangements, which is clinically useful in mentally retarded and/or dysmorphic individuals with normal results from conventional cytogenetics analysis. We report on a 3-year-old girl with mental retardation, growth deficiency, speech delay, and dysmorphic features including hypertelorism, upslanting palpebral fissures, midfacial hypoplasia, and posteriorly rotated ears. The G-banding analysis showed a 46,XX,t(3;8)(q26.2;p21.1)mat karyotype. However, her clinical features were suggestive of the 18q syndrome. Subtelomeric FISH analysis revealed a der(18) translocated material from chromosome 17. Array-based comparative genomic hybridization (array-CGH) with subtelomeric BAC and PAC clones confirmed the abnormality and refined the breakpoints to 18q22.3-qter and 17p13.2-pter (deletion of 8.5 Mb and duplication of 3.9 Mb, respectively). This case demonstrates the diagnostic utility of combining conventional cytogenetics with molecular chromosome analyses for the identification of subtle chromosome abnormalities.