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Biomedical subjects

Gregory J Hannon

Publications and source records attributed to Gregory J Hannon.

17 recordsLinked to original sources
PubMed2026

Virtual Tumors Enable Prediction of Personalized Therapeutic Combinations for Non-Small Cell Lung Cancer.

UNLABELLED: The disease burden from non-small cell lung cancer (NSCLC) adenocarcinoma is substantial, with a million new cases diagnosed globally each year and a 5-year survival rate of less than 20%. The lack of therapeutic options personalized to individual patients leads to high variation in survival. The combination of patient stratification with personalized treatment has the potential to improve outcomes; however, the variation in mutations found in patients with NSCLC adenocarcinoma makes experimentally determining treatment combinations time-consuming and expensive. In this study, we developed an interpretable mechanistic model to decipher complex signaling interplay and guide personalized therapy in NSCLC adenocarcinoma. This "virtual tumor" model encompassed key tumor-intrinsic oncogenic signaling pathways for efficiently predicting rational drug-drug and drug-radiotherapy combination therapies in NSCLC. Diverse genetic profiles were simulated for testing more than 10,000 therapeutic strategies to identify optimal approaches to overcome resistance mechanisms specific to genetic profiles and p53 status. The virtual tumor model reproduced drug additivity screens, predicted radiosensitizing genes validated in a CRISPR screen, and identified 53BP1 as a potential drug target that improved the therapeutic window during radiotherapy. A 19-gene signature derived from the virtual tumor framework stratified patients most likely to benefit from radiotherapy, which was validated using The Cancer Genome Atlas (TCGA) data. These results show the utility of virtual tumors to predict effective therapeutic combinations and present a computational resource for large-scale screening of personalized therapies to guide clinical decision-making in patients with NSCLC. SIGNIFICANCE: A computational framework that simulates thousands of personalized treatment strategies offers a scalable, cost-effective way to tailor therapies and improve outcomes for patients with genetically diverse NSCLC.

Humans↗
PubMed2003

Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence.

Cellular senescence is an extremely stable form of cell cycle arrest that limits the proliferation of damaged cells and may act as a natural barrier to cancer progression. In this study, we describe a distinct heterochromatic structure that accumulates in senescent human fibroblasts, which we designated senescence-associated heterochromatic foci (SAHF). SAHF formation coincides with the recruitment of heterochromatin proteins and the retinoblastoma (Rb) tumor suppressor to E2F-responsive promoters and is associated with the stable repression of E2F target genes. Notably, both SAHF formation and the silencing of E2F target genes depend on the integrity of the Rb pathway and do not occur in reversibly arrested cells. These results provide a molecular explanation for the stability of the senescent state, as well as new insights into the action of Rb as a tumor suppressor.

Binding Sites↗
PubMed2003

An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo.

The application of RNA interference (RNAi) to mammalian systems has the potential to revolutionize genetics and produce novel therapies. Here we investigate whether RNAi applied to a well-characterized gene can stably suppress gene expression in hematopoietic stem cells and produce detectable phenotypes in mice. Deletion of the Trp53 tumor suppressor gene greatly accelerates Myc-induced lymphomagenesis, resulting in highly disseminated disease. To determine whether RNAi suppression of Trp53 could produce a similar phenotype, we introduced several Trp53 short hairpin RNAs (shRNAs) into hematopoietic stem cells derived from E(mu)-Myc transgenic mice, and monitored tumor onset and overall pathology in lethally irradiated recipients. Different Trp53 shRNAs produced distinct phenotypes in vivo, ranging from benign lymphoid hyperplasias to highly disseminated lymphomas that paralleled Trp53-/- lymphomagenesis in the E(mu)-Myc mouse. In all cases, the severity and type of disease correlated with the extent to which specific shRNAs inhibited p53 activity. Therefore, RNAi can stably suppress gene expression in stem cells and reconstituted organs derived from those cells. In addition, intrinsic differences between individual shRNA expression vectors targeting the same gene can be used to create an 'epi-allelic series' for dissecting gene function in vivo.

Alleles↗
PubMed2003

RNAi: an ever-growing puzzle.

In recent years, sequence-specific gene silencing has been an area of increasing focus, both because of its interesting biology and because of its power as an experimental tool. A growing understanding of one such phenomenon, RNA interference (RNAi), has provided clues that many homology-dependent gene-silencing mechanisms share a common trigger, double-stranded RNA. Recent findings that RNAi and related pathways are involved not only in the response to exogenous pathogenic and endogenous parasitic nucleic acids but also in basic cellular processes, such as gene regulation and heterochromatin formation, have further fueled interest in this rapidly expanding field.

Animals↗
PubMed2003

siRNAs and shRNAs: skeleton keys to the human genome.

The use of RNA interference (RNAi) to evoke gene silencing in mammalian cell systems is rapidly becoming a standard laboratory technique. Recent experiments have also proven the utility of RNAi in animals. The next few years will bear witness to the first RNAi-based genome-wide screens in mammals, breaking the barrier to the use of mammalian cells as a genetic system. In this review, some of the key features of RNAi in mammalian systems are discussed.

Animals↗
PubMed2002

The centrosomal kinase Aurora-A/STK15 interacts with a putative tumor suppressor NM23-H1.

Alterations in the activity of the centrosomal kinase, Aurora-A/STK15, have been implicated in centrosome amplification, genome instability and cellular transformation. How STK15 participates in all of these processes remains largely mysterious. The activity of STK15 is regulated by phosphorylation and ubiquitin-mediated degradation, and physically interacts with protein phosphatase 1 (PP1) and CDC20. However, the precise roles of these modifications and interactions have yet to be fully appreciated. Here we show that STK15 associates with a putative tumor and metastasis suppressor, NM23-H1. STK15 and NM23 were initially found to interact in yeast in a two-hybrid assay. Association of these proteins in human cells was confirmed by co-immunoprecipitation from cell lysates and biochemical fractionation indicating that STK15 and NM23-H1 are present in a stable, physical complex. Notably, SKT15 and NM23 both localize to centrosomes throughout the cell cycle irrespective of the integrity of the microtubule network in normal human fibroblasts.

Aurora Kinase A↗
PubMed2002

Fragile X-related protein and VIG associate with the RNA interference machinery.

RNA interference (RNAi) is a flexible gene silencing mechanism that responds to double-stranded RNA by suppressing homologous genes. Here, we report the characterization of RNAi effector complexes (RISCs) that contain small interfering RNAs and microRNAs (miRNAs). We identify two putative RNA-binding proteins, the Drosophila homolog of the fragile X mental retardation protein (FMRP), dFXR, and VIG (Vasa intronic gene), through their association with RISC. FMRP, the product of the human fragile X locus, regulates the expression of numerous mRNAs via an unknown mechanism. The possibility that dFXR, and potentially FMRP, use, at least in part, an RNAi-related mechanism for target recognition suggests a potentially important link between RNAi and human disease.

Amino Acid Sequence↗
PubMed2002

RNA interference.

A conserved biological response to double-stranded RNA, known variously as RNA interference (RNAi) or post-transcriptional gene silencing, mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes. RNAi has been cultivated as a means to manipulate gene expression experimentally and to probe gene function on a whole-genome scale.

Animals↗
PubMed2002

RNA interference in adult mice.

RNA interference is an evolutionarily conserved surveillance mechanism that responds to double-stranded RNA by sequence-specific silencing of homologous genes. Here we show that transgene expression can be suppressed in adult mice by synthetic small interfering RNAs and by small-hairpin RNAs transcribed in vivo from DNA templates. We also show the therapeutic potential of this technique by demonstrating effective targeting of a sequence from hepatitis C virus by RNA interference in vivo.

Aging↗
PubMed2002

Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells.

RNA interference (RNAi) was first recognized in Caenorhabditis elegans as a biological response to exogenous double-stranded RNA (dsRNA), which induces sequence-specific gene silencing. RNAi represents a conserved regulatory motif, which is present in a wide range of eukaryotic organisms. Recently, we and others have shown that endogenously encoded triggers of gene silencing act through elements of the RNAi machinery to regulate the expression of protein-coding genes. These small temporal RNAs (stRNAs) are transcribed as short hairpin precursors (approximately 70 nt), processed into active, 21-nt RNAs by Dicer, and recognize target mRNAs via base-pairing interactions. Here, we show that short hairpin RNAs (shRNAs) can be engineered to suppress the expression of desired genes in cultured Drosophila and mammalian cells. shRNAs can be synthesized exogenously or can be transcribed from RNA polymerase III promoters in vivo, thus permitting the construction of continuous cell lines or transgenic animals in which RNAi enforces stable and heritable gene silencing.

3T3 Cells↗
PubMed2002

Stable suppression of gene expression by RNAi in mammalian cells.

In a diverse group of organisms including plants, Caenorhabditis elegans, Drosophila, and trypanosomes, double-stranded RNA (dsRNA) is a potent trigger of gene silencing. In several model systems, this natural response has been developed into a powerful tool for the investigation of gene function. Use of RNA interference (RNAi) as a genetic tool has recently been extended to mammalian cells, being inducible by treatment with small, approximately 22-nt RNAs that mimic those produced in the first step of the silencing process. Here, we show that some cultured murine cells specifically silence gene expression upon treatment with long dsRNAs (approximately 500 nt). This response shows hallmarks of conventional RNAi including silencing at the posttranscriptional level and the endogenous production of approximately 22-nt small RNAs. Furthermore, enforced expression of long, hairpin dsRNAs induced stable gene silencing. The ability to create stable "knock-down" cell lines expands the utility of RNAi in mammalian cells by enabling examination of phenotypes that develop over long time periods and lays the groundwork for by using RNAi in phenotype-based, forward genetic selections.

Animals↗
PubMed2002

RNA interference: the new somatic cell genetics?

RNAi is evolving into a powerful tool for manipulating gene expression in mammalian cells with potential utility for investigating gene function, for high-throughput, function-based genetic screens and potentially for development as a therapeutic tool.

Animals↗
PubMed2002

Transformation of normal human cells in the absence of telomerase activation.

Our knowledge of the transformation process has emerged largely from studies of primary rodent cells and animal models. However, numerous attempts to transform human cells using oncogene combinations that are effective in rodents have proven unsuccessful. These findings strongly argue for the study of homologous experimental systems. Here we report that the combined expression of adenovirus E1A, Ha-RasV12, and MDM2 is sufficient to convert a normal human cell into a cancer cell. Notably, transformation did not require telomerase activation. Therefore, we provide evidence that activation of telomere maintenance strategies is not an obligate characteristic of tumorigenic human cells.

Animals↗
PubMed2002

Oncogenic ras and p53 cooperate to induce cellular senescence.

Oncogenic activation of the mitogen-activated protein (MAP) kinase cascade in murine fibroblasts initiates a senescence-like cell cycle arrest that depends on the ARF/p53 tumor suppressor pathway. To investigate whether p53 is sufficient to induce senescence, we introduced a conditional murine p53 allele (p53(val135)) into p53-null mouse embryonic fibroblasts and examined cell proliferation and senescence in cells expressing p53, oncogenic Ras, or both gene products. Conditional p53 activation efficiently induced a reversible cell cycle arrest but was unable to induce features of senescence. In contrast, coexpression of oncogenic ras or activated mek1 with p53 enhanced both p53 levels and activity relative to that observed for p53 alone and produced an irreversible cell cycle arrest that displayed features of cellular senescence. p19(ARF) was required for this effect, since p53(-/-) ARF(-/-) double-null cells were unable to undergo senescence following coexpression of oncogenic Ras and p53. Although the levels of exogenous p53 achieved in ARF-null cells were relatively low, the stabilizing effects of p19(ARF) on p53 could not explain the cooperation between oncogenic Ras and p53 in promoting senescence. Hence, enforced p53 expression without oncogenic ras in p53(-/-) mdm2(-/-) double-null cells produced extremely high p53 levels but did not induce senescence. Taken together, our results indicate that oncogenic activation of the MAP kinase pathway in murine fibroblasts converts p53 into a senescence inducer through both quantitative and qualitative mechanisms.

Animals↗