RESUMO
Gene co-expression network analysis is an effective method for predicting gene functions and disease biomarkers. However, few studies have systematically identified co-expressed genes involved in the molecular origin and development of various types of tumors. In this study, we used a network mining algorithm to identify tightly connected gene co-expression networks that are frequently present in microarray datasets from 33 types of cancer which were derived from 16 organs/tissues. We compared the results with networks found in multiple normal tissue types and discovered 18 tightly connected frequent networks in cancers, with highly enriched functions on cancer-related activities. Most networks identified also formed physically interacting networks. In contrast, only 6 networks were found in normal tissues, which were highly enriched for housekeeping functions. The largest cancer network contained many genes with genome stability maintenance functions. We tested 13 selected genes from this network for their involvement in genome maintenance using two cell-based assays. Among them, 10 were shown to be involved in either homology-directed DNA repair or centrosome duplication control including the well-known cancer marker MKI67. Our results suggest that the commonly recognized characteristics of cancers are supported by highly coordinated transcriptomic activities. This study also demonstrated that the co-expression network directed approach provides a powerful tool for understanding cancer physiology, predicting new gene functions, as well as providing new target candidates for cancer therapeutics.
Assuntos
Expressão Gênica , Instabilidade Genômica , Algoritmos , Redes Reguladoras de Genes , Humanos , Análise de Sequência com Séries de Oligonucleotídeos , Interferência de RNARESUMO
BRCA1/2 proteins function in homologous recombination (HR)-mediated DNA repair and cooperate with Fanconi anemia (FA) proteins to maintain genomic integrity through replication fork stabilization. Loss of BRCA1/2 proteins results in DNA repair deficiency and replicative stress, leading to genomic instability and enhanced sensitivity to DNA-damaging agents. Recent studies have shown that BRCA1/2-deficient tumors upregulate Polθ-mediated alternative end-joining (alt-EJ) repair as a survival mechanism. Whether other mechanisms maintain genomic integrity upon loss of BRCA1/2 proteins is currently unknown. Here we show that BRCA1/2-deficient tumors also upregulate FANCD2 activity. FANCD2 is required for fork protection and fork restart in BRCA1/2-deficient tumors. Moreover, FANCD2 promotes Polθ recruitment at sites of damage and alt-EJ repair. Finally, loss of FANCD2 in BRCA1/2-deficient tumors enhances cell death. These results reveal a synthetic lethal relationship between FANCD2 and BRCA1/2, and they identify FANCD2 as a central player orchestrating DNA repair pathway choice at the replication fork.
Assuntos
Proteína BRCA1/deficiência , Proteína BRCA2/deficiência , Reparo do DNA por Junção de Extremidades , Replicação do DNA , Proteína do Grupo de Complementação D2 da Anemia de Fanconi/metabolismo , Neoplasias/genética , Neoplasias/patologia , Animais , Proteína BRCA1/metabolismo , Proteína BRCA2/metabolismo , Proteínas de Transporte/metabolismo , Linhagem Celular Tumoral , Sobrevivência Celular , Reparo do DNA por Junção de Extremidades/genética , Replicação do DNA/genética , DNA Polimerase Dirigida por DNA/metabolismo , Endodesoxirribonucleases , Instabilidade Genômica , Humanos , Camundongos Nus , Mutação/genética , Proteínas Nucleares/metabolismo , Poli(ADP-Ribose) Polimerases/metabolismo , Ubiquitinação , Regulação para Cima/genética , DNA Polimerase tetaRESUMO
To find genes and proteins that collaborate with BRCA1 or BRCA2 in the pathogenesis of breast cancer, we used an informatics approach and found a candidate BRCA interactor, KIAA0101, to function like BRCA1 in exerting a powerful control over centrosome number. The effect of KIAA0101 on centrosomes is likely direct, as its depletion does not affect the cell cycle, KIAA0101 localizes to regions coincident with the centrosomes, and KIAA0101 binds to BRCA1. We analyzed whether KIAA0101 protein is overexpressed in breast cancer tumor samples in tissue microarrays, and we found that overexpression of KIAA0101 correlated with positive Ki67 staining, a biomarker associated with increased disease severity. Furthermore, overexpression of the KIAA0101 gene in breast tumors was found to be associated with significantly decreased survival time. This study identifies KIAA0101 as a protein important for breast tumorigenesis, and as this factor has been reported as a UV repair factor, it may link the UV damage response to centrosome control.
Assuntos
Proteína BRCA1/metabolismo , Biomarcadores Tumorais/metabolismo , Neoplasias da Mama/metabolismo , Proteínas de Transporte/metabolismo , Centrossomo/metabolismo , Proteína BRCA1/genética , Neoplasias da Mama/patologia , Proteínas de Transporte/genética , Dano ao DNA , Proteínas de Ligação a DNA , Proteínas da Matriz Extracelular/metabolismo , Feminino , Regulação Neoplásica da Expressão Gênica , Instabilidade Genômica , Células HeLa , Recombinação Homóloga/genética , Humanos , Receptores de Hialuronatos/metabolismo , Antígeno Ki-67/análise , RNA Interferente Pequeno/genéticaRESUMO
Centrosomes are the organelles that organize microtubule networks and establish the bipolar mitotic spindle, which is essential for the segregation of chromosomes during cell division. Proper duplication of centrosomes is necessary to prevent genetic instability, thus control of this organelle is important in the suppression of tumorigenesis. The BRCA1 dependent ubiquitination activity regulates centrosome number in breast derived cell lines and this activity is likely critical for the tumor suppression activity of BRCA1. This review will focus on the importance of controlling centrosome number and on the effect of BRCA1 on the centrosome duplication cycle in mammary cells.