Cooperative control of tumor suppressor genes by a network of oncogenic microRNAs

Individual microRNAs (miRNAs) have been implicated as oncogenes in experimental cancer models and their expression may affect clinical outcomes. To gain a more comprehensive view of miRNA action in leukemia, we analyzed miRNA expression patters in T-cell leukemia ALL (T-ALL) and cross-referenced the results with an unbiased genetic screen and computational analyses.1 We found that multiple microRNAs contribute to leukmogenesis and act as multi-targeted regulators of several tumor suppressor genes. The oncomirs form a network of overlapping and partially redundant interactions that stabilize the malignant phenotype though coordinate repression of cellular failsafe programs. The emerging network pattern of oncomir action is distinct from the notion of single oncogenic 'driver' mutation. We will discuss experimental, diagnostic and therapeutic implications of this concept of miRNA action in cancer.     

Functional integration of microRNAs into oncogenic and tumor suppressor pathways

A large body of evidence has documented abnormal microRNA (miRNA) expression patterns in diverse human malignancies. Given that miRNA expression is tightly regulated during development and cellular differentiation, aberrant miRNA expression in cancer cells is likely to be in part a consequence of the loss of normal cellular identity that accompanies malignant transformation. Nevertheless, it is now clear that miRNAs function as critical effectors of several canonical oncogenic and tumor suppressor pathways, including those controlled by Myc and p53. Gain- and loss-of-function of these factors in cancer cells contributes to miRNA dysregulation, directly influencing neoplastic phenotypes including cellular proliferation and apoptosis.     

Population genetics of tumor suppressor genes

Cancer emerges when a single cell receives multiple mutations. For example, the inactivation of both alleles of a tumor suppressor gene (TSG) can imply a net reproductive advantage of the cell and might lead to clonal expansion. In this paper, we calculate the probability as a function of time that a population of cells has generated at least one cell with two inactivated alleles of a TSG. Different kinetic laws hold for small and large populations. The inactivation of the first allele can either be neutral or lead to a selective advantage or disadvantage. The inactivation of the first and of the second allele can occur at equal or different rates. Our calculations provide insights into basic aspects of population genetics determining cancer initiation and progression.     

TSGDB: a database system for tumor suppressor genes

A Web-based database system was constructed and implemented that contains 174 tumor suppressor genes. The database homepage was created to accommodate these genes in a pull-down window so that each gene can be viewed individually in a separate Web page. Information displayed on each page includes gene name, aliases, source organism, chromosome location, expression cells/tissues, gene structure, protein size, gene functions and major reference sources. Queries to the database can be conducted through a user-friendly interface, and query results are returned in the HTML format on dynamically generated web pages. AVAILABILITY: The database is available at http://www.cise.ufl.edu/~yy1/HTML-TSGDB/Homepage.html (data files also at http://www.patcar.org/Databases/Tumor_Suppressor_Genes)     

Akt versus p53 in a network of oncogenes and tumor suppressor genes regulating cell survival and death

The tumor suppressor protein, p53, and the oncoprotein, Akt, are involved in a cross talk that could be at the core of a cell's control machinery for switching between survival and death. This cross talk is a combination of reciprocally antagonistic pathways emanating from p53 and Akt, and also involves another tumor suppressor gene, PTEN, and another oncogene, Mdm2; such a connected network of cancer-relevant genes must be significant and demands a critical study. The p53-Akt network is shown in this report to possess the potential to exhibit bistability, a phenomenon in which two stable steady states of the system coexist for a fixed set of control parameter values. A hierarchy of qualitative networks and abstract kinetic models are analyzed and simulated on a computer to demonstrate the robustness of the bistable behavior, which, as argued in this study, is a likely candidate mechanism for a cellular survival-death switch. The analysis applies to cells that are neither p53-null nor Akt-null. The models presented here offer experimental predictions on the identity of control parameters of apoptotic thresholds and on network perturbations (including DNA damage and Akt inhibition) that are sufficient to generate switching between pro-survival and pro-death cellular states.     

Histone deacetylases induce angiogenesis by negative regulation of tumor suppressor genes

Low oxygen tension influences tumor progression by enhancing angiogenesis; and histone deacetylases (HDAC) are implicated in alteration of chromatin assembly and tumorigenesis. Here we show induction of HDAC under hypoxia and elucidate a role for HDAC in the regulation of hypoxia-induced angiogenesis. Overexpressed wild-type HDAC1 downregulated expression of p53 and von Hippel-Lindau tumor suppressor genes and stimulated angiogenesis of human endothelial cells. A specific HDAC inhibitor, trichostatin A (TSA), upregulated p53 and von Hippel-Lindau expression and downregulated hypoxia-inducible factor-1alpha and vascular endothelial growth factor. TSA also blocked angiogenesis in vitro and in vivo. TSA specifically inhibited hypoxia-induced angiogenesis in the Lewis lung carcinoma model. These results indicate that hypoxia enhances HDAC function and that HDAC is closely involved in angiogenesis through suppression of hypoxia-responsive tumor suppressor genes.     

ErbB2-intronic MicroRNA-4728: a novel tumor suppressor and antagonist of oncogenic MAPK signaling

Although the role of the ErbB2/HER2 oncogene in cancers has been extensively studied, how ErbB2 is regulated remains poorly understood. A novel microRNA, mir-4728, was recently found within an intron of the ErbB2 gene. However, the function and clinical relevance of this intronic miRNA are completely unknown. Here, we demonstrate that mir-4728 is a negative regulator of MAPK signaling through directly targeting the ERK upstream kinase MST4 and exerts numerous tumor-suppressive properties in vitro and in animal models. Importantly, our patient sample study shows that mir-4728 was under-expressed in breast tumors compared with normal tissue, and loss of mir-4728 correlated with worse overall patient survival. These results strongly suggest that mir-4728 is a tumor-suppressive miRNA that controls MAPK signaling through targeting MST4, revealing mir-4728''s significance as a potential prognostic factor and target for therapeutic intervention in cancer. Moreover, this study represents a conceptual advance by providing strong evidence that a tumor-suppressive miRNA can antagonize the canonical signaling of its host oncogene.Breast cancer is a major health problem in the United States, accounting for over 232 000 new diagnoses and nearly 40 000 fatalities in 2013.¹ Deregulation of microRNAs (miRNAs) has been implicated in the progression of breast cancer.² MiRNAs are small, non-coding RNA molecules capable of silencing gene expression by binding with complementary targets to cause translational repression or direct mRNA degradation. Therefore, depending on their target genes, miRNAs can play tumor-suppressive or oncogenic roles.The human epidermal growth factor receptor 2 gene (ErbB2/HER2, hereafter called ErbB2), encodes a 185-kDa transmembrane protein that belongs to the epidermal growth factor receptor family.^{3, 4} Through its downstream signaling pathways, such as the mitogen-activated protein kinase (MAPK) pathway, ErbB2 regulates several important cell functions in cancer development and progression, such as growth, differentiation, and apoptosis.⁵ The ErbB2 gene is amplified or overexpressed in approximately 25% of human breast carcinomas and plays a role in many other human malignancies.^{6, 7}Introns, originally thought to be nonsense spacing elements in gene structure, have received attention in recent years owing to the discovery of important functions for these sequences. However, the mechanisms by which intronic miRNAs regulate oncogenes or tumor-suppressor genes and the roles of intronic miRNAs in cancer development and progression are poorly understood. In 2011, by next-generation sequencing techniques, mir-4728 was found to be encoded within an intron of the ErbB2 gene.⁸ The discovery of mir-4728 within an intron of ErbB2 has led to new questions regarding the regulation of ErbB2 signaling. Therefore, it is important to determine what role this miRNA plays in human cancers.In this study, we investigated the role of mir-4728 in breast cancer and its underlying mechanism. We demonstrated a critical role of mir-4728 in the regulation of MAPK signaling and breast cancer tumorigenesis. Our results indicate that mir-4728 is a novel tumor-suppressive miRNA in breast cancer that can not only potentially serve as a biomarker for breast cancer progression and as a future target for therapeutic intervention, but also represents a novel class of antagonistic intronic miRNAs that has remained elusive to researchers.     

microRNAs在肿瘤免疫中的调控作用

microRNAs（miRNAs）是一类转录后调控基因表达的内源性非编码微小RNA。愈来愈多的研究显示,miRNAs在肿瘤免疫应答中发挥重要调控作用。一方面,miRNAs通过转录后调控ICAM（intercellular adhesion molecule）、B7（CD80／86）和HLA—G（human leucocyte antigen—G）等肿瘤表面分子的表达,影响肿瘤的免疫原性;另一方面,miRNAs通过平衡肿瘤局部的细胞因子微环境或调控肿瘤免疫相关细胞的分化、发育及功能发挥,调节机体抗肿瘤免疫应答。为后续深入研究肿瘤与宿主的相互作用机制,以及发展更有效的肿瘤生物治疗手段,就目前miRNAs在肿瘤免疫中的调控作用的研究进展做一综述。     

A densely interconnected genome-wide network of microRNAs and oncogenic pathways revealed using gene expression signatures

MicroRNAs (miRNAs) are important components of cellular signaling pathways, acting either as pathway regulators or pathway targets. Currently, only a limited number of miRNAs have been functionally linked to specific signaling pathways. Here, we explored if gene expression signatures could be used to represent miRNA activities and integrated with genomic signatures of oncogenic pathway activity to identify connections between miRNAs and oncogenic pathways on a high-throughput, genome-wide scale. Mapping >300 gene expression signatures to >700 primary tumor profiles, we constructed a genome-wide miRNA-pathway network predicting the associations of 276 human miRNAs to 26 oncogenic pathways. The miRNA-pathway network confirmed a host of previously reported miRNA/pathway associations and uncovered several novel associations that were subsequently experimentally validated. Globally, the miRNA-pathway network demonstrates a small-world, but not scale-free, organization characterized by multiple distinct, tightly knit modules each exhibiting a high density of connections. However, unlike genetic or metabolic networks typified by only a few highly connected nodes ("hubs"), most nodes in the miRNA-pathway network are highly connected. Sequence-based computational analysis confirmed that highly-interconnected miRNAs are likely to be regulated by common pathways to target similar sets of downstream genes, suggesting a pervasive and high level of functional redundancy among coexpressed miRNAs. We conclude that gene expression signatures can be used as surrogates of miRNA activity. Our strategy facilitates the task of discovering novel miRNA-pathway connections, since gene expression data for multiple normal and disease conditions are abundantly available.     

DNA damage tumor suppressor genes and genomic instability

Disruption of the mechanisms that regulate cell-cycle checkpoints, DNA repair, and apoptosis results in genomic instability and the development of cancer in multicellular organisms. The protein kinases ATM and ATR, as well as their downstream substrates Chk1 and Chk2, are central players in checkpoint activation in response to DNA damage. Histone H2AX, ATRIP, as well as the BRCT-motif-containing molecules 53BP1, MDC1, and BRCA1 function as molecular adapters or mediators in the recruitment of ATM or ATR and their targets to sites of DNA damage. The increased chromosomal instability and tumor susceptibility apparent in mutant mice deficient in both p53 and either histone H2AX or proteins that contribute to the nonhomologous end-joining mechanism of DNA repair indicate that DNA damage checkpoints play a pivotal role in tumor suppression.     

Merlin, a tumor suppressor, interacts with transactivation-responsive RNA-binding protein and inhibits its oncogenic activity

The neurofibromatosis type 2 gene-encoded protein, merlin, is related to the ERM (ezrin, radixin, and moesin) family of membrane-cytoskeleton-associated proteins. Recent studies suggest that the loss of neurofibromatosis type 2 function contributes to tumor development and metastasis. Although the cellular functions of merlin as a tumor suppressor are relatively well characterized, the cellular mechanism whereby merlin controls cell proliferation from membrane locations is still poorly understood. During our efforts to find potential merlin modulators through protein-protein interactions, we identified transactivation-responsive RNA-binding protein (TRBP) as a merlin-binding protein in a yeast two-hybrid screen. The interaction between TRBP and merlin was confirmed by glutathione S-transferase pull-down assays, co-immunoprecipitation, and co-localization experiments. The carboxyl-terminal regions of each protein were responsible for their interaction. Cells overexpressing TRBP showed enhanced cell growth in cell proliferation assays and also exhibited transformed phenotypes, such as anchorage-independent cell growth and tumor development in mouse xenografts. Merlin efficiently inhibited these oncogenic activities of TRBP in our experiments. These results provide the first clue to the functional interaction between TRBP and merlin and suggest a novel mechanism for the tumor suppressor function of merlin both in vitro and in vivo.     

Mapping of two tumor suppressor genes in the pig

Mutations in the breast cancer 1, early onset (BRCA1) gene confer an increased risk of breast and ovarian cancer in humans. The human MAD (mothers against decapentaplegic, Drosophila) homolog 4 (MADH4) locus is a target for deletion in pancreatic and other cancers. Given the role of the pig in biomedical studies, pig orthologs of BRCA1 and MADH4 were identified and localized in the porcine genome.     

The menin tumor suppressor protein is an essential oncogenic cofactor for MLL-associated leukemogenesis

The Mixed-Lineage Leukemia (MLL) protein is a histone methyltransferase that is mutated in clinically and biologically distinctive subsets of acute leukemia. MLL normally associates with a cohort of highly conserved cofactors to form a macromolecular complex that includes menin, a product of the MEN1 tumor suppressor gene, which is mutated in heritable and sporadic endocrine tumors. We demonstrate here that oncogenic MLL fusion proteins retain an ability to stably associate with menin through a high-affinity, amino-terminal, conserved binding motif and that this interaction is required for the initiation of MLL-mediated leukemogenesis. Furthermore, menin is essential for maintenance of MLL-associated but not other oncogene induced myeloid transformation. Acute genetic ablation of menin reverses aberrant Hox gene expression mediated by MLL-menin promoter-associated complexes, and specifically abrogates the differentiation arrest and oncogenic properties of MLL-transformed leukemic blasts. These results demonstrate that a human oncoprotein is critically dependent on direct physical interaction with a tumor suppressor protein for its oncogenic activity, validate a potential target for molecular therapy, and suggest central roles for menin in altered epigenetic functions underlying the pathogenesis of hematopoietic cancers.