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1.  Mitochondrially targeted wild-type p53 induces apoptosis in a solid human tumor xenograft model 
Cell cycle (Georgetown, Tex.)  2008;7(16):2584-2590.
Classic but also novel roles of p53 are becoming increasingly well characterized. We previously showed that ex vivo retroviral transfer of mitochondrially targeted wild type p53 (mitop53) in the Eμ-myc mouse lymphoma model efficiently induces tumor cell killing in vivo. In an effort to further explore the therapeutic potential of mitop53 for its pro-apoptotic effect in solid tumors, we generated replication-deficient recombinant human Adenovirus type 5 vectors. We show here that adenoviral delivery of mitop53 by intratumoral injection into HCT116 human colon carcinoma xenograft tumors in nude mice is surprisingly effective, resulting in tumor cell death of comparable potency to conventional p53. These apoptotic effects in vivo were confirmed by Ad5-mitop53 mediated cell death of HCT116 cells in culture. Together, these data provide encouragement to further explore the potential for novel mitop53 proteins in cancer therapy to execute the shortest known circuitry of p53 death signaling.
PMCID: PMC3873818  PMID: 18719383
adenovirus; cancer; mitochondria; p53; therapy; xenograft
2.  A role of HAUSP in tumor suppression in a human colon carcinoma xenograft model 
Cell cycle (Georgetown, Tex.)  2008;7(9):1205-1213.
The protease HAUSP is a critical component of the p53-Mdm2 pathway and acts as a specific deubiquitinase for both p53 and Mdm2 and thus is important for p53 regulation. In knock-down and knock-out cellular systems it was observed that ablation of HAUSP induces profound stabilization of p53 due to enhanced degradation of Mdm2. Thus, inhibiting HAUSP by small compound interference has been proposed as a rational therapeutic strategy to activate p53 in p53 wild type tumors. However, HAUSP-mediated effects in the p53-Mdm2 axis are highly complex and non-linear and to date the role of HAUSP in tumor suppression in vivo remains unexplored.
Here we investigate the effect of HAUSP up and downregulation on cell proliferation, apoptosis and tumor growth in vitro and in a xenograft model in vivo, using an inducible isogenic human colon carcinoma cell system. Importantly, in the absence of stress, both HAUSP up and downregulation inhibit cell proliferation in vitro and tumor growth in vivo due to constitutively elevated p53 levels. Moreover, tumors with HAUSP up and downregulation respond to radiotherapy with further growth inhibition. However, HAUSP downregulation causes resistance to Camptothecin- and irradiation-induced apoptosis, which correlates with suppressed mitochondrial translocation of p53. Our data suggest that changes in HAUSP modulate tumor growth and apoptotic sensitivity in vivo.
PMCID: PMC3873824  PMID: 18418047
HAUSP; p53; ubiquitination; Mdm2; deubiquitination; mitochondrial translocation
3.  E2F1 plays a direct role in Rb stabilization and p53-independent tumor suppression 
Cell cycle (Georgetown, Tex.)  2008;7(12):1776-1781.
To better understand the role of E2F1 in tumor formation, we analyzed spontaneous tumorigenesis in p53−/−E2F1+/+ and p53−/−E2F1−/− mice. We show that the combined loss of p53 and E2F1 leads to an increased incidence of sarcomas and carcinomas compared to the loss of p53 alone. E2F1-deficient tumors show wide chromosomal variation, indicative of genomic instability. Consistent with this, p53−/−E2F1−/− primary fibroblasts have a reduced capacity to maintain genomic stability when exposed to S-phase inhibitors or genotoxic drugs. A major mechanism of E2F1’s contribution to genomic integrity lies in mediating stabilization and engagement of the Rb protein.
PMCID: PMC4012429  PMID: 18583939
Rb protein; p53; G2M checkpoint; DNA replication
4.  p53 further extends its reach 
Oncoimmunology  2013;2(5):e24959.
doi:10.4161/onci.24959
PMCID: PMC3829950  PMID: 24255806
5.  HSP90 inhibitor antagonizing MIF 
Oncoimmunology  2012;1(8):1425-1426.
Constitutively stabilized HSP90 client proteins are crucial for cancer cell survival and proliferation. Thus, despite—or perhaps because of—their pleiotropic effects on variety of critical oncoproteins, HSP90 inhibitors represent a promising new class of anticancer drugs. We identified MIF as an essential HSP90 client protein in a murine model of Her2-overexpressing breast cancer.
doi:10.4161/onci.21173
PMCID: PMC3518525  PMID: 23243616
CHIP; HSP90 inhibitors; MIF; breast cancer; client
6.  Inhibiting the HSP90 chaperone destabilizes macrophage migration inhibitory factor and thereby inhibits breast tumor progression 
In several human cancer cell lines, HSP90 inhibitors destabilize macrophage inhibitory factor protein; systemic treatment with an HSP90 inhibitor slows tumor growth and extends overall survival in a mouse model of HER2-positive human breast cancer.
Intracellular macrophage migration inhibitory factor (MIF) often becomes stabilized in human cancer cells. MIF can promote tumor cell survival, and elevated MIF protein correlates with tumor aggressiveness and poor prognosis. However, the molecular mechanism facilitating MIF stabilization in tumors is not understood. We show that the tumor-activated HSP90 chaperone complex protects MIF from degradation. Pharmacological inhibition of HSP90 activity, or siRNA-mediated knockdown of HSP90 or HDAC6, destabilizes MIF in a variety of human cancer cells. The HSP90-associated E3 ubiquitin ligase CHIP mediates the ensuing proteasome-dependent MIF degradation. Cancer cells contain constitutive endogenous MIF–HSP90 complexes. siRNA-mediated MIF knockdown inhibits proliferation and triggers apoptosis of cultured human cancer cells, whereas HSP90 inhibitor-induced apoptosis is overridden by ectopic MIF expression. In the ErbB2 transgenic model of human HER2-positive breast cancer, genetic ablation of MIF delays tumor progression and prolongs overall survival of mice. Systemic treatment with the HSP90 inhibitor 17AAG reduces MIF expression and blocks growth of MIF-expressing, but not MIF-deficient, tumors. Together, these findings identify MIF as a novel HSP90 client and suggest that HSP90 inhibitors inhibit ErbB2-driven breast tumor growth at least in part by destabilizing MIF.
doi:10.1084/jem.20111117
PMCID: PMC3280870  PMID: 22271573
7.  p53 opens the mitochondrial permeability transition pore to trigger necrosis 
Cell  2012;149(7):1536-1548.
Summary
Ischemia-associated oxidative damage leading to necrosis is a major cause of catastrophic tissue loss in human health. Elucidating its signaling mechanism is of paramount importance. p53 is a central stress sensor responding to multiple insults including oxidative stress to orchestrate apoptotic and autophagic types of cell death. Whether p53 can also activate oxidative stress-induced necrosis is unknown. Here we uncover a role of p53 in activating necrosis. In response to oxidative stress, p53 accumulates in the mitochondrial matrix and triggers mitochondrial permeability transition pore (PTP) opening and necrosis by physical interaction with the critical PTP regulator Cyclophilin D (CypD). Intriguingly, a robust p53-CypD complex forms during brain ischemia/reperfusion injury. In contrast, reduction of p53 levels or Cyclosporine A-pretreatment of mice prevents this complex and is associated with effective stroke protection. Our study identifies the mitochondrial p53-CypD axis as an important contributor to oxidative stress-induced necrosis and implicates this axis in stroke pathology.
doi:10.1016/j.cell.2012.05.014
PMCID: PMC3383624  PMID: 22726440
8.  Loss of p73 promotes dissemination of Myc-induced B cell lymphomas in mice 
The Journal of Clinical Investigation  2010;120(6):2070-2080.
Mice engineered to express c-Myc in B cells (Eμ-myc mice) develop lethal lymphomas in which the gene encoding the p53 tumor suppressor is frequently mutated. Whether the p53 homolog p73 also functions as a tumor suppressor in vivo remains controversial. Here we have shown that p73 loss does not substantially affect disease onset and mortality in Eμ-myc mice. However, it does alter the phenotype of the disease. Specifically, p73 loss decreased nodal disease and increased widespread extranodal dissemination. We further found that p53 acted as the dominant tumor suppressor during the onset of Eμ-myc–driven B cell lymphomagenesis, while p73 modulated tumor dissemination and extranodal growth. Immunophenotyping and expression profiling suggested that p73 loss allowed increased maturation of malignant B cells and deregulated genes involved in lymphocyte homing and dissemination of human lymphomas. Consistent with this, p73 expression was frequently downregulated in a large cohort of human mature aggressive B cell lymphomas, and both the incidence and degree of p73 downregulation in these tumors correlated with their extranodal dissemination status. These data indicate that p73 is a modifier of Myc-driven lymphomas in mice, favoring tumor dissemination, and suggest that p73 could be a biomarker for human B cell lymphoma dissemination, a notion that can now be tested in clinicopathologic correlation studies.
doi:10.1172/JCI40331
PMCID: PMC2877938  PMID: 20484818
9.  p53's mitochondrial translocation and MOMP action is independent of Puma and Bax and severely disrupts mitochondrial membrane integrity 
Cell research  2008;18(7):733-744.
p53's apoptotic program consists of transcription-dependent and transcription-independent pathways. In the latter, physical interactions between mitochondrial p53 and anti- and pro-apoptotic members of the Bcl2 family of mitochondrial permeability regulators are central. Using isogenic cell systems with defined deficiencies, we characterize in detail how mitochondrial p53 contributes to mitochondrial permeabilization, to what extent its action depends on other key Bcl2 family members and define its release activity. We show that mitochondrial p53 is highly efficient in inducing the release of soluble and insoluble apoptogenic factors by severely disrupting outer and inner mitochondrial membrane integrity. This action is associated with wild-type p53-induced oligomerization of Bax, Bak and VDAC and the formation of a stress-induced endogenous complex between p53 and cyclophilin D, normally located at the inner membrane. Tumor-derived p53 mutants are deficient in activating the Bax/Bak lipid pore. These actions are independent of Puma and Bax. Importantly, the latter distinguishes the mitochondrial from the cytosolic p53 death pathway.
doi:10.1038/cr.2008.62
PMCID: PMC2830652  PMID: 18504456
apoptosis; mitochondria; p53/Bcl2 family; Puma; Bax; Bak; VDAC; cyclophilin D
10.  The transcription-independent mitochondrial p53 program is a major contributor to nutlin-induced apoptosis in tumor cells 
Cell cycle (Georgetown, Tex.)  2009;8(11):1711-1719.
Strategies to induce p53 activation in tumors that retain wild-type p53 are promising for cancer therapy. Nutlin is a potent and selective pharmacological MDM2 inhibitor that competitively binds to its p53-binding pocket, thereby leading to non-genotoxic p53 stabilization and activation of growth arrest and apoptosis pathways. Nutlin-induced apoptosis is thought to occur via p53’s transcriptional program. Here we report that the transcription-independent mitochondrial p53 program plays an important role in Nutlin-induced p53-mediated tumor cell death. Aside from nuclear stabilization, Nutlin causes cytoplasmic p53 accumulation and translocation to mitochondria. Monoubiquitinated p53, originating from a distinct cytoplasmic pool, is the preferred p53 species that translocates to mitochondria in response to stress. Nutlin does not interfere with MDM2’s ability to monoubiquitinate p53, due to the fact that MDM2-p53 complexes are only partially disrupted and that Nutlin-stabilized MDM2 retains its E3 ubiquitin ligase activity. Nutlin-induced mitochondrial p53 translocation is rapid and associated with cytochrome C release that precedes induction of p53 target genes. Specific inhibition of mitochondrial p53 translocation by Pifithrin μ reduces the apoptotic Nutlin response by 2.5-fold, underlining the significance of p53’s mitochondrial program in Nutlin-induced apoptosis. Surprisingly, blocking the transcriptional arm of p53, either via α-Amanitin or the p53-specific transcriptional inhibitor Pifithrin α, not only fails to inhibit, but greatly potentiates Nutlin-induced apoptosis. In sum, the direct mitochondrial program is a major mechanism in Nutlin-induced p53-mediated apoptosis. Moreover, at least in some tumors the transcriptional p53 activities in net balance not only are dispensable for the apoptotic Nutlin response, but appear to actively block its therapeutic effect.
PMCID: PMC2823264  PMID: 19411846
nutlin; p53; MDM2; ubiquitination; mitochondria; apoptosis
11.  SAHA shows preferential cytotoxicity in mutant p53 cancer cells by destabilizing mutant p53 through inhibition of the HDAC6-Hsp90 chaperone axis 
Cell death and differentiation  2011;18(12):1904-1913.
Mutant p53 cancers are surprisingly dependent on their hyperstable mutp53 protein for survival, identifying mutp53 as a potentially significant clinical target. However, exploration of effective small molecule therapies targeting mutp53 has barely begun. Mutp53 hyperstabilization, a hallmark of p53 mutation, is cancer cell-specific and due to massive upregulation of the HSP90 chaperone machinery during malignant transformation. We recently showed that stable complex formation between HSP90 and its mutp53 client inhibits E3 ligases MDM2 and CHIP, causing mutp53 stabilization. HDAC inhibitors (HDACi) are a new class of promising anti-cancer drugs, hyperacetylating histone and non-histone targets. Currently, SAHA is the only FDA-approved HDACi. We show that SAHA exhibits preferential cytotoxicity for mutant, rather than wildtype and null p53 human cancer cells. Loss/gain-of-function experiments revealed that although able to exert multiple cellular effects, SAHA's cytotoxicity is caused to a significant degree by its ability to strongly destabilize mutp53 at the level of protein degradation. The underlying mechanism is SAHA's inhibition of HDAC6, an essential positive regulator of HSP90. This releases mutp53 and enables its MDM2- and CHIP-mediated degradation. SAHA also strongly chemosensitizes mutp53 cancer cells for chemotherapy due to its ability to degrade mutp53. This identifies a novel action of SAHA with the prospect of SAHA becoming a centerpiece in mutp53-specific anticancer strategies.
doi:10.1038/cdd.2011.71
PMCID: PMC3170683  PMID: 21637290
SAHA; mutant p53; HDAC6; activated Hsp90 chaperone; MDM2; CHIP
12.  Functional inactivation of endogenous MDM2 and CHIP by HSP90 causes aberrant stabilization of mutant p53 in human cancer cells 
Molecular cancer research : MCR  2011;9(5):577-588.
The tight control of wild-type (wt) p53 by mainly MDM2 in normal cells is permanently lost in tumors harboring mutant p53 (mutp53), which exhibit dramatic constitutive p53 hyperstabilization that far exceeds that of wtp53 tumors. Importantly, mutp53 hyperstabilization is critical for mutp53′s oncogenic gain-of function in vivo. Current insight into the mechanism of this dysregulation is fragmentary and largely derived from ectopically constructed cell systems. Importantly, mutp53 knockin mice established that normal mutp53 tissues have sufficient enzymatic reserves in MDM2 and other E3 ligases to maintain full control of mutp53.
We find that in human cancer cells endogenous mutant p53, despite its ability to interact with MDM2, suffers from a profound lack of ubiquitination as the root of its degradation defect. In contrast to wtp53, the many mutp53 proteins which are conformationally aberrant are engaged in complexes with the HSP90 chaperone machinery to prevent its aggregation. In contrast to wtp53 cancer cells, we show that in mutp53 cancer cells this HSP90 interaction blocks the endogenous MDM2 and CHIP E3 ligase activity. Interference with HSP90 either by RNAi against HSF1, the transcriptional regulator of the HSP90 pathway, or by direct knockdown of Hsp90 protein or by pharmacological inhibition of Hsp90 activity with 17AAG destroys the complex, liberates mutp53 and reactivates endogenous MDM2 and CHIP to degrade mutp53. Of note, 17AAG induces a stronger viability loss in mutp53 than in wtp53 cancer cells. Our data supports the rationale that suppression of mutp53 levels in vivo in established cancers might achieve clinically significant effects.
doi:10.1158/1541-7786.MCR-10-0534
PMCID: PMC3097033  PMID: 21478269
mutant p53; ubiquitination; MDM2; CHIP
13.  ΔNp73, A Dominant-Negative Inhibitor of Wild-type p53 and TAp73, Is Up-regulated in Human Tumors 
p73 has significant homology to p53. However, tumor-associated up-regulation of p73 and genetic data from human tumors and p73-deficient mice exclude a classical Knudson-type tumor suppressor role. We report that the human TP73 gene generates an NH2 terminally truncated isoform. ΔNp73 derives from an alternative promoter in intron 3 and lacks the transactivation domain of full-length TAp73. ΔNp73 is frequently overexpressed in a variety of human cancers, but not in normal tissues. ΔNp73 acts as a potent transdominant inhibitor of wild-type p53 and transactivation-competent TAp73. ΔNp73 efficiently counteracts transactivation function, apoptosis, and growth suppression mediated by wild-type p53 and TAp73, and confers drug resistance to wild-type p53 harboring tumor cells. Conversely, down-regulation of endogenous ΔNp73 levels by antisense methods alleviates its suppressive action and enhances p53- and TAp73-mediated apoptosis. ΔNp73 is complexed with wild-type p53, as demonstrated by coimmunoprecipitation from cultured cells and primary tumors. Thus, ΔNp73 mediates a novel inactivation mechanism of p53 and TAp73 via a dominant-negative family network. Deregulated expression of ΔNp73 can bestow oncogenic activity upon the TP73 gene by functionally inactivating the suppressor action of p53 and TAp73. This trait might be selected for in human cancers.
doi:10.1084/jem.20020179
PMCID: PMC2194062  PMID: 12235210
p73; ΔNp73; Ex2Del p73; apoptosis; deregulation in tumor
14.  Brdm2 – an aberrant hypomorphic p63 allele 
Cell death and differentiation  2010;17(1):184-186.
doi:10.1038/cdd.2009.158
PMCID: PMC2794917  PMID: 20161489
15.  p53-Responsive MicroRNAs 192 and 215 Are Capable of Inducing Cell Cycle Arrest 
Cancer research  2008;68(24):10094-10104.
microRNAs provide a novel layer of regulation for gene expression by interfering with the stability and/or translation of specific target mRNAs. Overall levels of microRNAs are frequently down-regulated in cancer cells, and reducing general microRNA processing increases cancerogenesis in transgenic models, suggesting that at least some microRNAs might act as effectors in tumor suppression. Accordingly, the tumor suppressor p53 up-regulates miR-34a, a microRNA that contributes to apoptosis and acute senescence. Here, we used array hybridization to find that p53 induces two additional, mutually related clusters of microRNAs, leading to the up-regulation of miR-192, miR-194, and miR-215. The same microRNAs were detected at high levels in normal colon tissue but were severely reduced in many colon cancer samples. On the other hand, miR-192 and its cousin miR-215 can each contribute to enhanced CDKN1A/p21 levels, colony suppression, cell cycle arrest, and cell detachment from a solid support. These effects were partially dependent on the presence of wild-type p53. Antagonizing endogenous miR-192 attenuated 5-fluorouracil–induced accumulation of p21. Hence, miR-192 and miR-215can act as effectors as well as regulators of p53; they seem to suppress cancerogenesis through p21 accumulation and cell cycle arrest.
doi:10.1158/0008-5472.CAN-08-1569
PMCID: PMC2836584  PMID: 19074875
16.  The mitochondrial p53 pathway 
Biochimica et biophysica acta  2008;1787(5):414.
p53 is one of the most mutated tumor suppressors in human cancers and as such has been intensively studied for a long time. p53 is a major orchestrator of the cellular response to a broad array of stress types by regulating apoptosis, cell cycle arrest, senescence, DNA repair and genetic stability. For a long time it was thought that these functions of p53 solely rely on its function as a transcription factor, and numerous p53 target genes have been identified [1]. In the last 8 years however, a novel transcription-independent proapoptotic function mediated by the cytoplasmic pool of p53 has been revealed. p53 participates directly in the intrinsic apoptosis pathway by interacting with the multidomain members of the Bcl-2 family to induce mitochondrial outer membrane permeabilization. Our review will discuss these studies, focusing on recent advances in the field.
doi:10.1016/j.bbabio.2008.10.005
PMCID: PMC2819081  PMID: 19007744
p53; Mitochondria; Apoptosis; Transcription; Bcl-2 family; Pathophysiology; Radiosensitivity; Ischemia
17.  The alpha/beta carboxyterminal domains of p63 are required for skin and limb development. New insights from the Brdm2 mouse which is not a complete p63 knockout but expresses p63 gamma-like proteins 
Cell death and differentiation  2009;16(8):1108-1117.
p63, an ancestral transcription factor of the p53 family, has three C-terminal isoforms whose relative in vivo functions are elusive. The p63 gene is essential for skin and limb development, as vividly shown by two independent global knockout mouse models. Both strains, although constructed differently, have identical and severe phenotypes, characterized by absent epidermis and hindlimbs and only rudimentary forelimbs at birth. Here we show that mice from one model, Brdm2, express normal levels of truncated p63 proteins that contain the DNA binding and oligomerization domain but lack the long carboxy-terminal SAM (sterile α-motif) and post-SAM domains that are specific for the α and β isoforms. As such, transcriptionally active p63 proteins from Brdm2 mice resemble the naturally occurring p63γ isoforms, which of all p63 isoforms most closely resemble p53. Thus, Brdm2 mice are p63α/β isoform-specific knockout mice, gaining unexpected new importance. Our studies identify that p63α/β but not p63γ are absolutely required for proper skin and limb development.
doi:10.1038/cdd.2009.25
PMCID: PMC2778344  PMID: 19300453
p63; p63 C-terminal isoforms; skin and limb development
18.  Regulation of autophagy by cytoplasmic p53 
Nature cell biology  2008;10(6):676-687.
Multiple cellular stressors, including activation of the tumour suppressor p53, can stimulate autophagy. Here we show that knockout, knockdown or pharmacological inhibition of p53 can induce autophagy in human, mouse and nematode cells. Enhanced autophagy improved the survival of p53-deficient cancer cells under conditions of hypoxia and nutrient depletion, allowing them to maintain high ATP levels. Inhibition of p53 led to autophagy in enucleated cells, and cytoplasmic, not nuclear, p53 was able to repress the enhanced autophagy of p53-/- cells. Many different inducers of autophagy (for example, starvation, rapamycin and toxins affecting the endoplasmic reticulum) stimulated proteasome-mediated degradation of p53 through a pathway relying on the E3 ubiquitin ligase HDM2. Inhibition of p53 degradation prevented the activation of autophagy in several cell lines, in response to several distinct stimuli. These results provide evidence of a key signalling pathway that links autophagy to the cancer-associated dysregulation of p53.
doi:10.1038/ncb1730
PMCID: PMC2676564  PMID: 18454141
19.  Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs 
Nucleic Acids Research  2004;32(15):4630-4645.
Nucleic acids are molecules of choice for both established and emerging nanoscale technologies. These technologies benefit from large functional densities of ‘DNA processing elements’ that can be readily manufactured. To achieve the desired functionality, polynucleotide sequences are currently designed by a process that involves tedious and laborious filtering of potential candidates against a series of requirements and parameters. Here, we present a complete novel methodology for the rapid rational design of large sets of DNA sequences. This method allows for the direct implementation of very complex and detailed requirements for the generated sequences, thus avoiding ‘brute force’ filtering. At the same time, these sequences have narrow distributions of melting temperatures. The molecular part of the design process can be done without computer assistance, using an efficient ‘human engineering’ approach by drawing a single blueprint graph that represents all generated sequences. Moreover, the method eliminates the necessity for extensive thermodynamic calculations. Melting temperature can be calculated only once (or not at all). In addition, the isostability of the sequences is independent of the selection of a particular set of thermodynamic parameters. Applications are presented for DNA sequence designs for microarrays, universal microarray zip sequences and electron transfer experiments.
doi:10.1093/nar/gkh802
PMCID: PMC516071  PMID: 15333695
20.  In Vivo Mitochondrial p53 Translocation Triggers a Rapid First Wave of Cell Death in Response to DNA Damage That Can Precede p53 Target Gene Activation 
Molecular and Cellular Biology  2004;24(15):6728-6741.
p53 promotes apoptosis in response to death stimuli by transactivation of target genes and by transcription-independent mechanisms. We recently showed that wild-type p53 rapidly translocates to mitochondria in response to multiple death stimuli in cultured cells. Mitochondrial p53 physically interacts with antiapoptotic Bcl proteins, induces Bak oligomerization, permeabilizes mitochondrial membranes, and rapidly induces cytochrome c release. Here we characterize the mitochondrial p53 response in vivo. Mice were subjected to γ irradiation or intravenous etoposide administration, followed by cell fractionation and immunofluorescence studies of various organs. Mitochondrial p53 accumulation occurred in radiosensitive organs like thymus, spleen, testis, and brain but not in liver and kidney. Of note, mitochondrial p53 translocation was rapid (detectable at 30 min in thymus and spleen) and triggered an early wave of marked caspase 3 activation and apoptosis. This caspase 3-mediated apoptosis was entirely p53 dependent, as shown by p53 null mice, and preceded p53 target gene activation. The transcriptional p53 program had a longer lag phase than the rapid mitochondrial p53 program. In thymus, the earliest apoptotic target gene products PUMA, Noxa, and Bax appeared at 2, 4, and 8 h, respectively, while Bid, Killer/DR5, and p53DinP1 remained uninduced even after 20 h. Target gene induction then led to further increase in active caspase 3. Similar biphasic kinetics was seen in cultured human cells. Our results suggest that in sensitive organs mitochondrial p53 accumulation in vivo occurs soon after a death stimulus, triggering a rapid first wave of apoptosis that is transcription independent and may precede a second slower wave that is transcription dependent.
doi:10.1128/MCB.24.15.6728-6741.2004
PMCID: PMC444865  PMID: 15254240
21.  Efficient RNA interference depends on global context of the target sequence: quantitative analysis of silencing efficiency using Eulerian graph representation of siRNA 
Nucleic Acids Research  2004;32(4):1469-1479.
Several aspects of gene silencing by small interfering RNA duplexes (siRNA) influence the efficiency of the silencing. They can be divided into two categories, one covering the cell-specific factors and the other covering molecular factors of the RNA interference (RNAi). A prerequisite for sequence-based siRNA design is that hybridization thermodynamics is the dominant factor. Our assumption is that cell-specific parameters (cell line, degradation, cross-hybridization, target conformation, etc.) can be pooled into an average cellular factor. Our hypothesis is that the molecular basis of the positional dependence of siRNA-induced gene silencing is the uniqueness of context of a corresponding target sequence segment relative to all other such segments along the attacked RNA. We encode this context into descriptors derived from Eulerian graph representation of siRNAs and show that the descriptor based upon the contextual similarity and predicted thermodynamic stability correlates with the experimentally observed silencing efficiency of human lamin A/C gene. We further show that information encoded in this regression function is generalizable and can be used as a predictor of siRNA efficiency in unrelated genes (CD54 and PTEN). In summary, our method represents an evolution of siRNA design from the currently used algorithms which are only qualitative in nature.
doi:10.1093/nar/gkh314
PMCID: PMC390352  PMID: 14993466
22.  ΔNp73 Facilitates Cell Immortalization and Cooperates with Oncogenic Ras in Cellular Transformation In Vivo 
Molecular and Cellular Biology  2003;23(16):5540-5555.
TP73, despite significant homology to TP53, is not a classic tumor suppressor gene, since it exhibits upregulation of nonmutated products in human tumors and lacks a tumor phenotype in p73-deficient mice. We recently reported that an N-terminally truncated isoform, ΔNp73, is upregulated in breast and gynecological cancers. We further showed that ΔNp73 is a potent transdominant inhibitor of wild-type p53 and TAp73 in cultured human tumor cells by efficiently counteracting their target gene transactivations, apoptosis, and growth suppression functions (A. I. Zaika et al., J. Exp. Med. 6:765-780, 2002). Although these data strongly suggest oncogenic properties of ΔNp73, this can only be directly shown in primary cells. We report here that ΔNp73 confers resistance to spontaneous replicative senescence of primary mouse embryo fibroblasts (MEFs) and immortalizes MEFs at a 1,000-fold-higher frequency than occurs spontaneously. ΔNp73 cooperates with cMyc and E1A in promoting primary cell proliferation and colony formation and compromises p53-dependent MEF apoptosis. Importantly, ΔNp73 rescues Ras-induced senescence. Moreover, ΔNp73 cooperates with oncogenic Ras in transforming primary fibroblasts in vitro and in inducing MEF-derived fibrosarcomas in vivo in nude mice. Wild-type p53 is likely a major target of ΔNp73 inhibition in primary fibroblasts since deletion of p53 or its requisite upstream activator ARF abrogates the growth-promoting effect of ΔNp73. Taken together, ΔNp73 behaves as an oncogene that targets p53 that might explain why ΔNp73 upregulation may be selected for during tumorigenesis of human cancers.
doi:10.1128/MCB.23.16.5540-5555.2003
PMCID: PMC166317  PMID: 12897129

Results 1-22 (22)