Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 22
Filtrar
Mais filtros










Base de dados
Intervalo de ano de publicação
1.
EClinicalMedicine ; 40: 101099, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34490415

RESUMO

Background: Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there has been increasing urgency to identify pathophysiological characteristics leading to severe clinical course in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Human leukocyte antigen alleles (HLA) have been suggested as potential genetic host factors that affect individual immune response to SARS-CoV-2. We sought to evaluate this hypothesis by conducting a multicenter study using HLA sequencing. Methods: We analyzed the association between COVID-19 severity and HLAs in 435 individuals from Germany (n = 135), Spain (n = 133), Switzerland (n = 20) and the United States (n = 147), who had been enrolled from March 2020 to August 2020. This study included patients older than 18 years, diagnosed with COVID-19 and representing the full spectrum of the disease. Finally, we tested our results by meta-analysing data from prior genome-wide association studies (GWAS). Findings: We describe a potential association of HLA-C*04:01 with severe clinical course of COVID-19. Carriers of HLA-C*04:01 had twice the risk of intubation when infected with SARS-CoV-2 (risk ratio 1.5 [95% CI 1.1-2.1], odds ratio 3.5 [95% CI 1.9-6.6], adjusted p-value = 0.0074). These findings are based on data from four countries and corroborated by independent results from GWAS. Our findings are biologically plausible, as HLA-C*04:01 has fewer predicted bindings sites for relevant SARS-CoV-2 peptides compared to other HLA alleles. Interpretation: HLA-C*04:01 carrier state is associated with severe clinical course in SARS-CoV-2. Our findings suggest that HLA class I alleles have a relevant role in immune defense against SARS-CoV-2. Funding: Funded by Roche Sequencing Solutions, Inc.

2.
J Mol Diagn ; 23(4): 399-406, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33497835

RESUMO

Formalin-fixed, paraffin-embedded (FFPE) tissue is the most commonly used material for tumor molecular profiling, therapy selection, and prognostication. Tumor tissue enrichment by tissue dissection is highly recommended to generate quality data reproducibly for use in downstream assays, such as real-time PCR and next-generation sequencing. The aim of this study was to evaluate the performance of the automated tissue dissection tool AVENIO Millisect System compared with a manual dissection method using 18 FFPE tissue specimens. The study assessed performance of these two methods with paraffinized and deparaffinized sections at 5- and 10-µm thickness as well as at low (5% to 10%) and high (>50%) tumor content. In addition, compatibility with various nucleic acid and protein extraction methods was assessed. Overall, dissection by Millisect resulted in statistically significantly higher yields of nucleic acids and protein compared with manual dissection (P = 0.00524). In downstream analysis on a statistically nonpowered sample set, EGFR mutation testing by PCR led to highly concordant results, and next-generation sequencing testing yielded significantly higher allelic frequencies when tissue was dissected by Millisect compared with manual scraping, demonstrating noninferiority of the automated method. In summary, the AVENIO Millisect System may replace manual labor and support automation of FFPE tumor tissue workflows in clinical molecular laboratories with high testing volumes with adequate validation.

3.
J Mol Med (Berl) ; 87(6): 633-44, 2009 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-19399471

RESUMO

Wiskott-Aldrich syndrome (WAS) predisposes patients to leukemia and lymphoma. WAS is caused by mutations in the protein WASP which impair its interaction with the WIPF1 protein. Here, we aim to identify a module of WIPF1-coexpressed genes and to assess its use as a prognostic signature for colorectal cancer, glioma, and breast cancer patients. Two public colorectal cancer microarray data sets were used for discovery and validation of the WIPF1 co-expression module. Based on expression of the WIPF1 signature, we classified more than 400 additional tumors with microarray data from our own experiments or from publicly available data sets according to their WIPF1 signature expression. This allowed us to separate patient populations for colorectal cancers, breast cancers, and gliomas for which clinical characteristics like survival times and times to relapse were analyzed. Groups of colorectal cancer, breast cancer, and glioma patients with low expression of the WIPF1 co-expression module generally had a favorable prognosis. In addition, the majority of WIPF1 signature genes are individually correlated with disease outcome in different studies. Literature gene network analysis revealed that among WIPF1 co-expressed genes known direct transcriptional targets of c-myc, ESR1 and p53 are enriched. The mean expression profile of WIPF1 signature genes is correlated with the profile of a proliferation signature. The WIPF1 signature is the first microarray-based prognostic expression signature primarily developed for colorectal cancer that is instrumental in other tumor types: low expression of the WIPF1 module is associated with better prognosis.


Assuntos
Proteínas do Citoesqueleto/genética , Perfilação da Expressão Gênica , Peptídeos e Proteínas de Sinalização Intracelular/genética , Neoplasias/diagnóstico , Apoptose , Neoplasias Encefálicas/diagnóstico , Neoplasias Encefálicas/genética , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/genética , Linhagem Celular Tumoral , Proliferação de Células , Neoplasias Colorretais/diagnóstico , Neoplasias Colorretais/genética , Feminino , Redes Reguladoras de Genes , Humanos , Neoplasias/genética , Prognóstico , Proteínas Proto-Oncogênicas c-myc/genética , Proteína Supressora de Tumor p53/genética , Proteína Neuronal da Síndrome de Wiskott-Aldrich/genética , Proteína Neuronal da Síndrome de Wiskott-Aldrich/metabolismo
4.
Mol Cancer ; 6: 79, 2007 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-18081933

RESUMO

Colorectal tumors have characteristic genome-wide expression patterns that allow their distinction from normal colon epithelia and facilitate clinical prognosis. The expression heterogeneity within a primary colorectal tumor has not been studied on a genome scale yet. Here we investigated three compartments of colorectal tumors, the invasion front, the inner tumor mass, and surrounding normal epithelial tissue by microdissection and microarray-based expression profiling. In both tumor compartments many genes were differentially expressed when compared to normal epithelium. The sets of significantly deregulated genes in both compartments overlapped to a large extent and revealed various interesting known and novel pathways that could have contributed to tumorigenesis. Cells from the invasion front and inner tumor mass, however, did not show significant differences in their expression profile, neither on the single gene level nor on the pathway level. Instead, gene expression differences between individuals are more pronounced as all patient-matched tumor samples clustered in close proximity to each other. With respect to invasion front and inner tumor mass we conclude that the specific tumor cell micro-environment does not have a strong influence on expression patterns: largely similar genome-wide expression programs operate in the invasion front and interior compartment of a colorectal tumor.


Assuntos
Neoplasias Colorretais/genética , Regulação Neoplásica da Expressão Gênica , Invasividade Neoplásica/genética , Neoplasias Colorretais/patologia , Humanos , Hibridização de Ácido Nucleico , Análise de Sequência com Séries de Oligonucleotídeos
5.
Mol Cancer ; 5: 37, 2006 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-16982006

RESUMO

BACKGROUND: Cancer development is accompanied by genetic phenomena like deletion and amplification of chromosome parts or alterations of chromatin structure. It is expected that these mechanisms have a strong effect on regional gene expression. RESULTS: We investigated genome-wide gene expression in colorectal carcinoma (CRC) and normal epithelial tissues from 25 patients using oligonucleotide arrays. This allowed us to identify 81 distinct chromosomal islands with aberrant gene expression. Of these, 38 islands show a gain in expression and 43 a loss of expression. In total, 7.892 genes (25.3% of all human genes) are located in aberrantly expressed islands. Many chromosomal regions that are linked to hereditary colorectal cancer show deregulated expression. Also, many known tumor genes localize to chromosomal islands of misregulated expression in CRC. CONCLUSION: An extensive comparison with published CGH data suggests that chromosomal regions known for frequent deletions in colon cancer tend to show reduced expression. In contrast, regions that are often amplified in colorectal tumors exhibit heterogeneous expression patterns: even show a decrease of mRNA expression. Because for several islands of deregulated expression chromosomal aberrations have never been observed, we speculate that additional mechanisms (like abnormal states of regional chromatin) also have a substantial impact on the formation of co-expression islands in colorectal carcinoma.


Assuntos
Aberrações Cromossômicas , Neoplasias Colorretais/genética , Regulação Neoplásica da Expressão Gênica , Mapeamento Cromossômico , Perfilação da Expressão Gênica , Genes Neoplásicos , Genoma Humano , Humanos , Análise de Sequência com Séries de Oligonucleotídeos , RNA Mensageiro/metabolismo
6.
Clin Cancer Res ; 12(13): 3950-60, 2006 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-16818692

RESUMO

PURPOSE: The aim of the present study was to identify human genes that might prove useful in the diagnosis and therapy of primary breast cancer. EXPERIMENTAL DESIGN: Twenty-four matched pairs of invasive ductal breast cancer and corresponding benign breast tissue were investigated by a combination of laser microdissection and gene expression profiling. Differential expression of candidate genes was validated by dot blot analysis of cDNA in 50 pairs of matching benign and malignant breast tissue. Cellular expression of candidate genes was further validated by RNA in situ hybridization, quantitative reverse transcription-PCR, and immunohistochemistry using tissue microarray analysis of 272 nonselected breast cancers. Multivariate analysis of factors on overall survival and recurrence-free survival was done. RESULTS: Fifty-four genes were found to be up-regulated and 78 genes were found to be down-regulated. Dot blot analysis reduced the number of up-regulated genes to 15 candidate genes that showed at least a 2-fold overexpression in >15 of 50 (30%) tumor/normal pairs. We selected phosphatidic acid phosphatase type 2 domain containing 1A (PPAPDC1A) and karyopherin alpha2 (KPNA2) for further validation. PPAPDC1A and KPNA2 RNA was up-regulated (fold change >2) in 84% and 32% of analyzed tumor/normal pairs, respectively. Nuclear protein expression of KPNA2 was significantly associated with shorter overall survival and recurrence-free survival. Testing various multivariate Cox regression models, KPNA2 expression remained a highly significant, independent and adverse risk factor for overall survival. CONCLUSIONS: Gene expression profiling of laser-microdissected breast cancer tissue revealed novel genes that may represent potential molecular targets for breast cancer therapy and prediction of outcome.


Assuntos
Biomarcadores Tumorais/genética , Neoplasias da Mama , Carcinoma Ductal de Mama , Perfilação da Expressão Gênica , Lasers , Microdissecção/métodos , alfa Carioferinas/genética , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/enzimologia , Neoplasias da Mama/genética , Carcinoma Ductal de Mama/diagnóstico , Carcinoma Ductal de Mama/enzimologia , Carcinoma Ductal de Mama/genética , Intervalo Livre de Doença , Feminino , Seguimentos , Humanos , Imuno-Histoquímica , Pessoa de Meia-Idade , Análise Multivariada , Estadiamento de Neoplasias , Fosfatidato Fosfatase/genética , Prognóstico , RNA/genética , Análise de Regressão , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Sulfotransferases/genética , Taxa de Sobrevida , Análise Serial de Tecidos/métodos , Regulação para Cima/genética
7.
J Pathol ; 205(1): 21-8, 2005 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-15586368

RESUMO

The identification of novel disease-associated genes in gynaecological tumours has important implications for understanding the process of tumourigenesis and the development of novel treatment regimens. cDNA libraries from disease tissues may represent a valuable source to identify such genes. Recently, a bio-informatic procedure based on an 'electronic Northern' approach was established to screen expressed sequence tag (EST) libraries for genes differentially expressed in tumour and normal tissues, and identified 450 candidate genes differentially expressed in breast and ovarian cancer. In this report, the validation of an initial set of 40 candidate genes, which were selected due to their localization in chromosomal regions frequently altered in gynaecological tumours, is described. Differential expression of 29 of these genes, including three uncharacterized novel genes, was confirmed by applying cancer profiling arrays with 106 matched pairs of tumour/normal cDNAs and quantitative reverse transcription-polymerase chain reaction (RT-PCR) on 60 clinical specimens. The majority of these differentially expressed genes have not been described previously in the context of breast and ovarian cancer, and may constitute novel diagnostic markers for these tumour entities.


Assuntos
Neoplasias da Mama/genética , Regulação Neoplásica da Expressão Gênica , Neoplasias Ovarianas/genética , Carcinoma Ductal de Mama/genética , DNA Complementar/genética , DNA de Neoplasias/genética , Etiquetas de Sequências Expressas , Feminino , Perfilação da Expressão Gênica , Marcadores Genéticos , Humanos , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Neoplasias Ovarianas/metabolismo , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos
8.
J Pathol ; 205(3): 359-76, 2005 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-15532095

RESUMO

In order to screen for differentially expressed genes that might be useful in diagnosis or therapy of prostate cancer we have used a custom made Affymetrix GeneChip containing 3950 cDNA fragments. Expression profiles were obtained from 42 matched pairs of mRNAs isolated from microdissected malignant and benign prostate tissues. Applying three different bioinformatic approaches to define differential gene expression, we found 277 differentially expressed genes, of which 98 were identified by all three methods. Fourteen per cent of these genes were not found in other expression studies, which were based on bulk tissue. Resultant candidate genes were further validated by quantitative RT-PCR, mRNA in situ hybridization and immunohistochemistry. AGR2 was over-expressed in 89% of prostate carcinomas, but did not have prognostic significance. Immunohistologically detected over-expression of MEMD and CD24 was identified in 86% and 38.5% of prostate carcinomas respectively, and both were predictive of PSA relapse. Combined marker analysis using MEMD and CD24 expression proved to be an independent prognostic factor (RR = 4.7, p = 0.006) in a Cox regression model, and was also superior to conventional markers. This combination of molecular markers thus appears to allow improved prediction of patient prognosis, but should be validated in larger studies.


Assuntos
Molécula de Adesão de Leucócito Ativado/metabolismo , Antígenos CD/metabolismo , Biomarcadores Tumorais/metabolismo , Perfilação da Expressão Gênica , Glicoproteínas de Membrana/metabolismo , Neoplasias da Próstata/metabolismo , Molécula de Adesão de Leucócito Ativado/genética , Antígenos CD/genética , Biomarcadores Tumorais/genética , Antígeno CD24 , Análise por Conglomerados , Expressão Gênica , Humanos , Masculino , Glicoproteínas de Membrana/genética , Microdissecção , Pessoa de Meia-Idade , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Prognóstico , Antígeno Prostático Específico/sangue , Neoplasias da Próstata/genética , Neoplasias da Próstata/patologia , RNA Mensageiro/genética , RNA Neoplásico/genética , Análise de Sobrevida
9.
Oncogene ; 23(57): 9295-302, 2004 Dec 09.
Artigo em Inglês | MEDLINE | ID: mdl-15489893

RESUMO

We have identified a gene, ST18 (suppression of tumorigenicity 18, breast carcinoma, zinc-finger protein), within a frequent imbalanced region of chromosome 8q11 as a breast cancer tumor suppressor gene. The ST18 gene encodes a zinc-finger DNA-binding protein with six fingers of the C2HC type (configuration Cys-X5-Cys-X12-His-X4-Cys) and an SMC domain. ST18 has the potential to act as transcriptional regulator. ST18 is expressed in a number of normal tissues including mammary epithelial cells although the level of expression is quite low. In breast cancer cell lines and the majority of primary breast tumors, ST18 mRNA is significantly downregulated. A 160 bp region within the promoter of the ST18 gene is hypermethylated in about 80% of the breast cancer samples and in the majority of breast cancer cell lines. The strong correlation between ST18 promoter hypermethylation and loss of ST18 expression in tumor cells suggests that this epigenetic mechanism is responsible for tumor-specific downregulation. We further show that ectopic ST18 expression in MCF-7 breast cancer cells strongly inhibits colony formation in soft agar and the formation of tumors in a xenograft mouse model.


Assuntos
Neoplasias da Mama/genética , Cromossomos Humanos Par 8 , Proteínas de Ligação a DNA/genética , Genes Supressores de Tumor , Animais , Sequência de Bases , Neoplasias da Mama/patologia , Linhagem Celular Tumoral , Metilação de DNA , Primers do DNA , Humanos , Hibridização in Situ Fluorescente , Perda de Heterozigosidade , Camundongos , Regiões Promotoras Genéticas , RNA Mensageiro/genética , Proteínas Repressoras , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Frações Subcelulares/metabolismo
10.
Genomics ; 84(1): 69-81, 2004 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-15203205

RESUMO

Fragile sites appear visually as nonstaining gaps on chromosomes that are inducible by specific cell culture conditions. Expansion of CGG/CCG repeats has been shown to be the molecular basis of all five folate-sensitive fragile sites characterized molecularly so far, i.e., FRAXA, FRAXE, FRAXF, FRA11B, and FRA16A. In the present study we have refined the localization of the FRA10A folate-sensitive fragile site by fluorescence in situ hybridization. Sequence analysis of a BAC clone spanning FRA10A identified a single, imperfect, but polymorphic CGG repeat that is part of a CpG island in the 5'UTR of a novel gene named FRA10AC1. The number of CGG repeats varied in the population from 8 to 13. Expansions exceeding 200 repeat units were methylated in all FRA10A fragile site carriers tested. The FRA10AC1 gene consists of 19 exons and is transcribed in the centromeric direction from the FRA10A repeat. The major transcript of approximately 1450 nt is ubiquitously expressed and codes for a highly conserved protein, FRA10AC1, of unknown function. Several splice variants leading to alternative 3' ends were identified (particularly in testis). These give rise to FRA10AC1 proteins with altered COOH-termini. Immunofluorescence analysis of full-length, recombinant EGFP-tagged FRA10AC1 protein showed that it was present exclusively in the nucleoplasm. We show that the expression of FRA10A, in parallel to the other cloned folate-sensitive fragile sites, is caused by an expansion and subsequent methylation of an unstable CGG trinucleotide repeat. Taking advantage of three cSNPs within the FRA10AC1 gene we demonstrate that one allele of the gene is not transcribed in a FRA10A carrier. Our data also suggest that in the heterozygous state FRA10A is likely a benign folate-sensitive fragile site.


Assuntos
Sítios Frágeis do Cromossomo/genética , Fragilidade Cromossômica/genética , Metilação de DNA , Proteínas Nucleares/genética , Expansão das Repetições de Trinucleotídeos/genética , Repetições de Trinucleotídeos/genética , Alelos , Processamento Alternativo/genética , Sequência de Aminoácidos , Humanos , Espaço Intranuclear/metabolismo , Dados de Sequência Molecular , Proteínas Nucleares/metabolismo , Especificidade de Órgãos/genética , Alinhamento de Sequência , Transcrição Genética/genética
11.
Oncogene ; 23(26): 4536-55, 2004 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-15064704

RESUMO

To understand the relationship between oncogenic signaling and the reprogramming of gene expression, we performed transcriptional profiling in rat ovarian surface epithelial cells (ROSE), in which neoplastic transformation is driven by a mutated KRAS oncogene. We identified >200 genes whose expression was elevated or reduced following permanent KRAS expression. Deregulated KRAS-responsive genes encode transcriptional regulators, signaling effectors, proteases, extracellular matrix and adhesion proteins, transformation-suppressing proteins and negative growth regulators. Many of them have not been previously identified in cells expressing oncogenic RAS genes or in other well-studied models of oncogenic signaling. The number of critical genes related to the execution of anchorage-independent proliferation and epithelial-mesenchymal transition was narrowed down to 79 by selectively inhibiting the mitogen-activated protein kinase (MAPK/ERK) and phosphatidylinositol 3-kinase (PI3K) pathways. Blocking MAPK/ERK-signaling caused reversion to the normal epithelial phenotype in conjunction with the reversal of deregulated target transcription to pretransformation levels. In addition, silencing of the overexpressed transcriptional regulator Fra-1 by RNA interference resulted in growth reduction, suggesting that this factor partially contributes to, but is not sufficient for the proliferative capacity of KRAS-transformed epithelial cells.


Assuntos
Transformação Celular Neoplásica/genética , Genes ras , Ovário/patologia , Transcrição Genética , Animais , Cromonas/farmacologia , Inibidores Enzimáticos/farmacologia , Células Epiteliais/efeitos dos fármacos , Células Epiteliais/metabolismo , Células Epiteliais/patologia , Feminino , Flavonoides/farmacologia , Regulação Neoplásica da Expressão Gênica , Proteínas Quinases Ativadas por Mitógeno , Morfolinas/farmacologia , Ovário/efeitos dos fármacos , Ovário/fisiologia , Fosfatidilinositol 3-Quinases/metabolismo , Inibidores de Fosfoinositídeo-3 Quinase , Proteínas Proto-Oncogênicas c-fos/efeitos dos fármacos , Proteínas Proto-Oncogênicas c-fos/genética , Proteínas Proto-Oncogênicas c-raf/efeitos dos fármacos , Proteínas Proto-Oncogênicas c-raf/metabolismo , Ratos , Transdução de Sinais
12.
Bioessays ; 26(5): 567-81, 2004 May.
Artigo em Inglês | MEDLINE | ID: mdl-15112237

RESUMO

Recently, the first investigation of nucleoli using mass spectrometry led to the identification of 271 proteins. This represents a rich resource for a comprehensive investigation of nucleolus evolution. We applied a protocol for the identification of known and novel conserved protein domains of the nucleolus, resulting in the identification of 115 known and 91 novel domain profiles. The phyletic distribution of nucleolar protein domains in a collection of complete proteomes of selected organisms from all domains of life confirms the archaebacterial origin of the core machinery for ribosome maturation and assembly, but also reveals substantial eubacterial and eukaryotic contributions to nucleolus evolution. We predict that, in different phases of nucleolus evolution, protein domains with different biochemical functions were recruited to the nucleolus. We suggest a model for the late and continuous evolution of the nucleolus in early eukaryotes and argue against an endosymbiotic origin of the nucleolus and the nucleus. Supplementary material for this article can be found on the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html.


Assuntos
Evolução Biológica , Nucléolo Celular , Proteínas Nucleares/química , Proteínas Nucleares/classificação , Proteínas Arqueais/metabolismo , Proteínas de Bactérias/metabolismo , Nucléolo Celular/química , Nucléolo Celular/metabolismo , Bases de Dados Factuais , Modelos Biológicos , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Filogenia , Estrutura Terciária de Proteína , Proteoma/análise , Proteínas Ribossômicas , Ribossomos/metabolismo
13.
Cancer Lett ; 204(1): 69-77, 2004 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-14744536

RESUMO

The inter-alpha-trypsin inhibitor (ITI) family constitutes a group of proteins built up from one light chain and a variable set of heavy chains. Originally identified as plasma protease inhibitors, recent data indicate that ITI plays a role in extracellular matrix (ECM) stabilization and in prevention of tumor metastasis. Here we describe cloning as well as phylogenetic and expression analysis of a novel member of the heavy chain gene family, ITIH5. ITIH5 contains the two domains conserved in all known ITIHs, the vault protein inter-alpha-trypsin (VIT) domain and a von Willebrand type A (vWA) domain. However, ITIH5 diverged early from a common ancestor of the other subfamilies. We found strong downregulation of ITIH5 expression in breast tumors by real-time PCR and RNA in situ hybridization. While normal breast epithelial cells clearly express ITIH5, expression is consistantly lost or strongly downregulated in invasive ductal carcinoma. ITIH5 mRNA was neither detectable in cancerous nor benign breast cell lines. We propose that loss of ITIH5 expression may be involved in breast cancer development.


Assuntos
Neoplasias da Mama/genética , Proteínas de Transporte/genética , Sequência de Aminoácidos , Northern Blotting , Neoplasias da Mama/metabolismo , Neoplasias da Mama/patologia , Carcinoma Ductal/genética , Carcinoma Ductal/metabolismo , Carcinoma Ductal/patologia , Proteínas de Transporte/metabolismo , Clonagem Molecular , DNA Antissenso/farmacologia , Progressão da Doença , Regulação para Baixo , Regulação Neoplásica da Expressão Gênica , Humanos , Hibridização In Situ , Dados de Sequência Molecular , Neoplasias/genética , Neoplasias/metabolismo , Neoplasias/patologia , Filogenia , Proteínas Secretadas Inibidoras de Proteinases , RNA Mensageiro/metabolismo , Homologia de Sequência de Aminoácidos
14.
Cell Signal ; 16(4): 435-56, 2004 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-14709333

RESUMO

Immunoreceptor tyrosine-based inhibitory motifs (ITIMs) are short sequences of the consensus (ILV)-x-x-Y-x-(LV) in the cytoplasmic tail of immune receptors. The phosphorylation of tyrosines in ITIMs is known to be an important signalling mechanism regulating the activation of immune cells. The shortness of the motif makes it difficult to predict ITIMs in large protein databases. Simple pattern searches find ITIMs in approximately 30% of the protein sequences in the RefSeq database. The majority are false positive predictions. We propose a new database search strategy for ITIM-bearing transmembrane receptors based on the use of sequence context, i.e. the predictions of signal peptides, transmembrane helices (TMs) and protein domains. Our new protocol allowed us to narrow down the number of potential human ITIM receptors to 109 proteins (0.7% of RefPep). Of these, 36 have been described as ITIM receptors in the literature before. Many ITIMs are conserved between orthologous human and mouse proteins which represent novel ITIM receptor candidates. Publicly available DNA array expression data revealed that ITIM receptors are not exclusively expressed in blood cells. We hypothesise that ITIM signalling is not restricted to immune cells, but also functions in diverse solid organs of mouse and man.


Assuntos
Biologia Computacional , Proteoma , Receptores Imunológicos/química , Tirosina/metabolismo , Humanos , Fosforilação , Relação Estrutura-Atividade
15.
Genes Chromosomes Cancer ; 37(4): 421-6, 2003 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-12800155

RESUMO

Deletions in the long arm of chromosome 6 (6q) are among the most frequent chromosome aberrations in lymphoid neoplasms. Recently, the region of minimal deletion (RMD1) in 6q27 was narrowed down to 5-9 Mb. In the present study, we aimed to define the distal border of the commonly lost region in 6q27 more precisely and to identify and investigate tumor-suppressor genes (TSGs) from this region. Twenty-nine cases, in which our previous fluorescence in situ hybridization (FISH) screening that used a set of 36 YAC probes revealed loss in 6q25-27, were further investigated by means of FISH. In all cases, deletions of 6q27 extended from yeast artificial chromosome (YAC) 977e10 spanning the proximal border of RMD1 to the most telomeric YAC 933f7 within the recently established YAC-contig of this region. An interstitial homozygous deletion, flanked by the telomeric probe TelVysion6q and YAC 971g12, was detected, which substantially narrows down the RMD1. To identify candidate TSGs down-regulated in malignant lymphomas from this region of homozygous loss, we performed electronic profiling of expressed sequences mapped to this region. This analysis suggested the gene PDCD2 originally thought to be involved in programmed cell death to be probably down-regulated in malignant B-cell lymphomas compared to normal B lymphocytes. Nevertheless, mutation analyses failed to identify mutations in the coding region of PDCD2 in nine lymphomas with FISH-proved 6q27 deletions. Furthermore, epigenetic studies in these nine and an additional 48 lymphomas did not show altered methylation of the PDCD2 locus in these tumors. Possibly haploinsufficiency is effectual in accelerating tumor progression.


Assuntos
Mapeamento Cromossômico/métodos , Cromossomos Humanos Par 6/genética , Deleção de Genes , Perfilação da Expressão Gênica/métodos , Genes Supressores de Tumor , Linfoma de Células B/genética , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Linhagem Celular Transformada , Regulação Neoplásica da Expressão Gênica/genética , Humanos , Células Tumorais Cultivadas
16.
Oncogene ; 22(19): 2972-83, 2003 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-12771949

RESUMO

Loss of heterozygosity (LOH) and in silico expression analysis were applied to identify genes significantly downregulated in breast cancer within the genomic interval 6q23-25. Systematic comparison of candidate EST sequences with genomic sequences from this interval revealed the genomic structure of a potential target gene on 6q24.3, which we called SAM and SH3 domain containing 1 (SASH1). Loss of the gene-internal marker D6S311, found in 30% of primary breast cancer, was significantly correlated with poor survival and increase in tumor size. Two SASH1 transcripts of approximately 4.4 and 7.5 kb exist and are predominantly transcribed in the human breast, lung, thyroid, spleen, placenta and thymus. In breast cancer cell lines, SASH1 is only expressed at low levels. SASH1 is downregulated in the majority (74%) of breast tumors in comparison with corresponding normal breast epithelial tissues. In addition, SASH1 is also downregulated in tumors of the lung and thyroid. Analysis of the protein domain structure revealed that SASH1 is a member of a recently described family of SH3/SAM adapter molecules and thus suggests a role in signaling pathways. We assume that SASH1 is a new tumor suppressor gene possibly involved in tumorigenesis of breast and other solid cancers. We were unable to find mutations in the coding region of the gene in primary breast cancers showing LOH within the critical region. We therefore hypothesize that other mechanisms as for instance methylation of the promoter region of SASH1 are responsible for the loss of expression of SASH1 in primary and metastatic breast cancer.


Assuntos
Neoplasias da Mama/genética , Cromossomos Humanos Par 6 , Regulação para Baixo , Genes Supressores de Tumor , Proteínas Supressoras de Tumor/genética , Neoplasias da Mama/metabolismo , Biologia Computacional , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Perda de Heterozigosidade , Repetições de Microssatélites , Proteínas Supressoras de Tumor/metabolismo
17.
Pancreatology ; 3(2): 169-78, 2003.
Artigo em Inglês | MEDLINE | ID: mdl-12748427

RESUMO

BACKGROUND: There is increasing knowledge about the genetic basis of pancreatic cancer (PaCa). Tumor suppressor genes (TSGs; e.g. p53 and DPC4) and oncogenes (e.g. K-ras) have been shown to be involved in the development of PaCa. However, the extent of chromosomal changes (gains and losses) implicates that many more genes may be involved in the multistep progression of PaCa. Identification of these genes is essential for understanding the molecular events in the development of PaCa. METHODS: We assembled public and proprietary libraries of more than 4 million expressed sequence tags using newly developed software tools. RESULTS: We identified a total of 249 genes with specific expression patterns in normal and cancerous tissue of the pancreas. Of these, 27 genes were found to be preferentially expressed in normal tissue of the pancreas, while 222 genes showed significant upregulation of expression in PaCa. Of the 249 genes, 232 (93.2%) were found to represent known human genes or putative human homologues of genes characterized previously in other species, while 17 (6.8%) represent putative new genes. CONCLUSION: These genes may represent a valuable source to identify novel TSGs and oncogenes involved in the carcinogenesis of PaCa.


Assuntos
Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Pâncreas/metabolismo , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/metabolismo , DNA Complementar/genética , DNA de Neoplasias/análise , Bases de Dados Factuais , Feminino , Biblioteca Gênica , Genoma Humano , Humanos , Masculino , RNA Neoplásico/análise
18.
FEBS Lett ; 527(1-3): 114-8, 2002 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-12220645

RESUMO

The human melanoma-associated chondroitin sulfate proteoglycan (MCSP) and its rat ortholog NG2 are thought to play important roles in angiogenesis-dependent processes like wound healing and tumor growth. Based on electron microscopy studies, the highly glycosylated ectodomain of NG2 has been subdivided into the globular N-terminus, a flexible rod-like central region and a C-terminal portion in globular conformation. We identified a novel repeat named CSPG in the central ectodomain of NG2, MCSP and other proteins from fly, worm, human, sea urchin and a cyanobacterium which shows similarity to cadherin repeats. As earlier electron microscopy studies indicate, the folding of the tandem repeats compresses the length of the proposed repeat region by a factor of approximately 10 compared to the fully extended peptide chain. We identified two conserved negatively charged residues which might govern the binding properties of CSPG repeats. The phyletic distribution of CSPG repeats suggests that horizontal gene transfer contributed to their evolutionary history.


Assuntos
Proteoglicanas de Sulfatos de Condroitina/química , Proteínas de Membrana/química , Sequências Repetitivas de Aminoácidos , Animais , Antígenos/química , Antígenos/metabolismo , Caderinas/química , Proteoglicanas de Sulfatos de Condroitina/metabolismo , Sequência Conservada , Bases de Dados de Proteínas , Humanos , Proteínas de Membrana/metabolismo , Filogenia , Proteoglicanas/química , Proteoglicanas/metabolismo , Ratos , Software
19.
Trends Biochem Sci ; 27(9): 441-4, 2002 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-12217514

RESUMO

Recent studies suggest that mutations in the LGI1/Epitempin gene cause autosomal dominant lateral temporal epilepsy. This gene encodes a protein of unknown function, which we postulate is secreted. The LGI1 protein has leucine-rich repeats in the N-terminal sequence and a tandem repeat (which we named EPTP) in its C-terminal region. A redefinition of the C-terminal repeat and the application of sensitive sequence analysis methods enabled us to define a new superfamily of proteins carrying varying numbers of the novel EPTP repeats in combination with various extracellular domains. Genes encoding proteins of this family are located in genomic regions associated with epilepsy and other neurological disorders.


Assuntos
Epilepsia do Lobo Temporal/genética , Proteínas/genética , Sequências de Repetição em Tandem , Sequência de Aminoácidos/genética , Animais , Epilepsia do Lobo Temporal/complicações , Humanos , Peptídeos e Proteínas de Sinalização Intracelular , Dados de Sequência Molecular , Sinais Direcionadores de Proteínas/genética , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Proteínas/metabolismo , Alinhamento de Sequência
20.
Gene ; 295(1): 27-32, 2002 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-12242008

RESUMO

Encephalopsin, also called Panopsin, is a recently discovered extraretinal photoreceptor, which may play a role in non-visual photic processes such as the entrainment of circadian rhythm or the regulation of pineal melatonin production. Based on RT-PCR data and comparative genomic sequence analysis, we show that the human OPN3 gene consists of six exons and expresses various splice variants, while the murine homologue contains four exons and produces just one splice form. Furthermore, the human OPN3 gene overlaps with the neighboring KMO gene on a genomic as well as on an RNA level, whereas the corresponding genes in mouse lie close together but do not overlap. This finding is of particular interest, since differences in gene organization between man and mouse, that have been reported so far, occur within gene clusters, i.e. the number of genes within a certain cluster may differ between man and mouse. OPN3 provides an exception to this rule, since it is positionally uncoupled from other genes of the opsin family.


Assuntos
Opsinas de Bastonetes/genética , Região 3'-Flanqueadora/genética , Processamento Alternativo , Sequência de Aminoácidos , Animais , Sequência de Bases , DNA/química , DNA/genética , Éxons , Perfilação da Expressão Gênica , Genes/genética , Homologia de Genes , Humanos , Íntrons , Quinurenina 3-Mono-Oxigenase , Camundongos , Oxigenases de Função Mista/genética , Dados de Sequência Molecular , Isoformas de Proteínas/genética , Alinhamento de Sequência , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...