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We have performed a genome-wide analysis of copy number changes in breast and colorectal tumors using approaches that can reliably detect homozygous deletions and amplifications. We found that the number of genes altered by major copy number changes, deletion of all copies or amplification to at least 12 copies per cell, averaged 17 per tumor. We have integrated these data with previous mutation analyses of the Reference Sequence genes in these same tumor types and have identified genes and cellular pathways affected by both copy number changes and point alterations. Pathways enriched for genetic alterations included those controlling cell adhesion, intracellular signaling, DNA topological change, and cell cycle control. These analyses provide an integrated view of copy number and sequencing alterations on a genome-wide scale and identify genes and pathways that could prove useful for cancer diagnosis and therapy.

Although the sequencing of the human genome has been completed, the number and identity of genes contained within it remains to be fully determined. We used LongSAGE to analyze 660,357 human transcripts from human brain mRNA and identified expression of 17,409 known genes and >15,000 different transcripts that were not annotated in genome databases. Analysis of a subset of these unannotated transcripts suggests that 85% were differentially expressed in various tissue types and that fewer than 20% would have been detected by ab initio gene predictions. These studies suggest that the human genome contains on the order of twice as many transcribed regions as are currently annotated and that experimental approaches will be required to fully elucidate the novel genes corresponding to these transcripts.

GSTP1 is a member of the glutathione S-transferase enzyme superfamily, which catalyzes the conjugation of electrophiles with glutathione in the process of detoxification. GSTP1 is widely overexpressed in colorectal cancer, from aberrant crypt foci to advanced carcinomas. Increased expression of GSTP1 is associated with multidrug resistance and a worse clinical prognosis. However, GSTP1-null mice have an increased risk of tumor formation. Thus, the biological function of GSTP1 in colorectal cancer biology remains speculative. In an effort to gain further insights into the role of GSTP1 in tumorigenesis, we disrupted the GSTP1 gene in HCT116 human colorectal cancer cells using targeted homologous recombination. We find that loss of GSTP1 resulted in impaired clonogenic survival and proliferation. Specifically, under growth-limiting conditions, (a) GSTP1 protected HCT116 cells from oxidative stress and associated apoptosis and (b) promoted mitogen-activated protein kinase-extracellular signal-regulated kinase kinase/extracellular signal-regulated kinase–mediated G1-S cell cycle progression. In vivo, GSTP1 was critical for engraftment and growth of HCT116 tumor xenografts. These studies directly show that GSTP1 promotes clonogenic survival and proliferation in HCT116 human colon cancer cells.

Through digital karyotyping of permanent medulloblastoma cell lines, we found that the homeobox gene OTX2 was amplified more than 10-fold in three cell lines. Gene expression analyses showed that OTX2 transcripts were present at high levels in 14 of 15 (93%) medulloblastomas with anaplastic histopathologic features. Knockdown of OTX2 expression by siRNAs inhibited medulloblastoma cell growth in vitro, whereas pharmacologic doses of all-trans retinoic acid repressed OTX2 expression and induced apoptosis only in medulloblastoma cell lines that expressed OTX2. These observations suggest that OTX2 is essential for the pathogenesis of anaplastic medulloblastomas and that these tumors may be amenable to therapy with all-trans-retinoic acid.

p53 ubiquitination is the principal mechanism by which p53 levels are regulated in the cell. HAUSP (also known as USP7) has been proposed to serve as a substrate-specific deubiquitinase of p53, and an increase in p53 levels was reported upon overexpression of HAUSP. We have disrupted the HAUSP genomic locus by homologous recombination and shown that HAUSP ablation results in a phenotype opposite to that predicted. Rather than decreasing p53 levels associated with increased p53 ubiquitination, the absence of HAUSP resulted in p53 accumulation accompanied by decreased p53 ubiquitination. The p53 protein in HAUSP-deficient cells was active, as assessed by the induction of its transcriptional targets and growth arrest. The basis for this phenotype was traced to the increased ubiquitination of MDM2, a negative regulator of p53 levels. These results demonstrate that MDM2, rather than p53, is the substrate for HAUSP under physiologic conditions and document a fascinating and unexpected twist to the regulation of the p53/MDM2 axis.

The key step in the manufacturing process for the HIV reverse transcriptase inhibitor efavirenz (Sustiva) involves addition of the 2:2 tetrameric complex 6 [formed from lithium cyclopropylacetylide (5) and lithium (1R,2S)-N-pyrrolidinylnorephedrate (4)] to ketone 2, to give 3 in 95% yield and 98% enantioselectivity. Studies of acetylide-alkoxide complexes in solution by NMR spectroscopy and in the solid state by X-ray crystallography are described. Studies of the asymmetric addition reaction involving 2:2 tetramer 6 using low-temperature NMR spectroscopy provide conclusive evidence for formation of 2:1:1 tetramer 9 containing the product alkoxide 3. Observation of this reaction intermediate strongly supports the proposed reaction mechanism involving the tetramer 6 in the stereo-determining step.

Products derived from the homolysis of the aromatic CI bond of ortho -iodobenzophenones by photolysis or tributyltin radicals indicate 1,5-hydrogen migration. The reactions include iodine migration, hydrogen abstraction and arylation.

A simple vinyl group is sufficient to induce a stepwise mechanism for the ring expansion of cyclopropylcarbenes.

Decomposition of a naphtho-fused cyclopropyldiazomethane leads to benzocyclooctatetraene, 1-vinylnaphthalene, 2-vinylnaphthalene, and small amounts of benzobarrelene. Diradical intermediates are postulated.

Although the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) has been shown to play an important role in the immunosurveillance of neoplasia, apoptotic factors that modulate the sensitivity of cancer cells to TRAIL are poorly understood. The inhibitor of apoptosis proteins (IAPs) have generated considerable interest as potential targets for cancer therapy, but the lack of a phenotype in X-linked IAP (XIAP) knockout mice has generated speculation that IAP function may be redundant. Using gene targeting technology, we show that disruption of the gene encoding XIAP in human cancer cells did not interfere with basal proliferation, but caused a remarkable sensitivity to TRAIL. These results demonstrate that XIAP is a nonredundant modulator of TRAIL-mediated apoptosis and provide a rationale for XIAP as a therapeutic target.

A simple vinyl group is sufficient to induce a stepwise mechanism for the ring expansion of cyclopropylcarbenes.

Background Microorganisms have been associated with many types of human diseases; however, a significant number of clinically important microbial pathogens remain to be discovered. Methods We have developed a genome-wide approach, called Digital Karyotyping Microbe Identification (DK-MICROBE), to identify genomic DNA of bacteria and viruses in human disease tissues. This method involves the generation of an experimental DNA tag library through Digital Karyotyping (DK) followed by analysis of the tag sequences for the presence of microbial DNA content using a compiled microbial DNA virtual tag library. Results To validate this technology and to identify pathogens that may be associated with human cancer pathogenesis, we used DK-MICROBE to determine the presence of microbial DNA in 58 human tumor samples, including brain, ovarian, and colorectal cancers. We detected DNA from Human herpesvirus 6 (HHV-6) in a DK library of a colorectal cancer liver metastasis and in normal tissue from the same patient. Conclusion DK-MICROBE can identify previously unknown infectious agents in human tumors, and is now available for further applications for the identification of pathogen DNA in human cancer and other diseases.

microRNAs (miRNAs) are abundant, approximately 21-nucleotide, noncoding regulatory RNAs. Each miRNA may regulate hundreds of mRNA targets, but the identities of these targets and the processes they regulate are poorly understood. Here we have explored the use of microarray profiling and functional screening to identify targets and biological processes triggered by the transfection of human cells with miRNAs. We demonstrate that a family of miRNAs sharing sequence identity with miRNA-16 (miR-16) negatively regulates cellular growth and cell cycle progression. miR-16-down-regulated transcripts were enriched with genes whose silencing by small interfering RNAs causes an accumulation of cells in G(0)/G(1). Simultaneous silencing of these genes was more effective at blocking cell cycle progression than disruption of the individual genes. Thus, miR-16 coordinately regulates targets that may act in concert to control cell cycle progression.

Skin cancer has become the most common neoplasm in the United States. With early diagnosis and appropriate management, most skin cancers have an overall 5-year survival rate of 95%. Cutaneous malignant melanoma (CMM), however, has a significantly higher morbidity and mortality, resulting in 65% of all skin cancer deaths. Although the long-term survival rate for patients with metastatic melanoma is only 5%, early detection of CMM carries an excellent prognosis, with surgical excision often being curative. Primary care physicians can play a critical role in reducing morbidity and mortality from CMM by recognizing patients at risk, encouraging the adoption of risk-reducing behaviors, and becoming adept at identifying suspicious lesions.

MicroRNAs (miRNAs) are a class of small noncoding RNAs that have important regulatory roles in multicellular organisms. The public miRNA database contains 321 human miRNA sequences, 234 of which have been experimentally verified. To explore the possibility that additional miRNAs are present in the human genome, we have developed an experimental approach called miRNA serial analysis of gene expression (miRAGE) and used it to perform the largest experimental analysis of human miRNAs to date. Sequence analysis of 273,966 small RNA tags from human colorectal cells allowed us to identify 200 known mature miRNAs, 133 novel miRNA candidates, and 112 previously uncharacterized miRNA* forms. To aid in the evaluation of candidate miRNAs, we disrupted the Dicer locus in three human colorectal cancer cell lines and examined known and novel miRNAs in these cells. These studies suggest that the human genome contains many more miRNAs than currently identified and provide an approach for the large-scale experimental cloning of novel human miRNAs in human tissues.

Hypoxia-inducible factor-1α (HIF-1α) is a transcription factor that directly transactivates genes important for the growth and metabolism of solid tumors. HIF-1α is overexpressed in cancer, and its level of expression is correlated with patient mortality. Increased synthesis or stability of HIF-1α can be induced by hypoxia-dependent or hypoxia-independent factors. Thus, HIF-1α is expressed in both nonhypoxic and hypoxic cancer cells. The role of HIF-1α in nonhypoxia-mediated cancer cell proliferation remains speculative. We have disrupted HIF-1α by targeted homologous recombination in HCT116 and RKO human colon cancer cells. Loss of HIF-1α significantly reduced nonhypoxia-mediated cell proliferation in vitro and in vivo. Paradoxically, loss of HIF-1α expression did not grossly affect the hypoxic compartments within tumor xenografts in vivo, although HIF-1α promoted cell proliferation and survival under hypoxia in vitro. To further test the role of HIF-1α within tumor compartments, we generated cells with combined disruptions of both HIF-1α and vascular endothelial growth factor (VEGF). In all xenografts, disruption of VEGF led to marked expansion of the hypoxic compartments and growth delay. Nonetheless, the presence or absence of HIF-1α did not grossly affect these expanded hypoxic compartments. These data provide compelling evidence that, in a subset of colon cancers, (a) HIF-1α is a positive factor for nonhypoxia-mediated cell proliferation in vitro and in vivo and (b) HIF-1α is a positive factor for cell proliferation and survival under hypoxic conditions in vitro, but does not grossly contribute to the tumor hypoxic compartments in vivo. (Cancer Res 2006; 66(3): 1684-93)

Although most colorectal cancers are chromosomally unstable, the basis for this instability has not been defined. To determine whether genes shown to cause chromosomal instability in model systems were mutated in colorectal cancers, we identified their human homologues and determined their sequence in a panel of colorectal cancers. We found 19 somatic mutations in five genes representing three distinct instability pathways. Seven mutations were found in MRE11, whose product is involved in double-strand break repair. Four mutations were found among hZw10, hZwilch/FLJ10036, and hRod/KNTC, whose products bind to one another in a complex that localizes to kinetochores and controls chromosome segregation. Eight mutations were found in Ding, a previously uncharacterized gene with sequence similarity to the Saccharomyces cerevisiae Pds1, whose product is essential for proper chromosome disjunction. This analysis buttresses the evidence that chromosomal instability has a genetic basis and provides clues to the mechanistic basis of instability in cancers.

p53 ubiquitination is the principal mechanism by which p53 levels are regulated in the cell. HAUSP (also known as USP7) has been proposed to serve as a substrate-specific deubiquitinase of p53, and an increase in p53 levels was reported upon overexpression of HAUSP. We have disrupted the HAUSP genomic locus by homologous recombination and shown that HAUSP ablation results in a phenotype opposite to that predicted. Rather than decreasing p53 levels associated with increased p53 ubiquitination, the absence of HAUSP resulted in p53 accumulation accompanied by decreased p53 ubiquitination. The p53 protein in HAUSP-deficient cells was active, as assessed by the induction of its transcriptional targets and growth arrest. The basis for this phenotype was traced to the increased ubiquitination of MDM2, a negative regulator of p53 levels. These results demonstrate that MDM2, rather than p53, is the substrate for HAUSP under physiologic conditions and document a fascinating and unexpected twist to the regulation of the p53/MDM2 axis.

[reaction: see text] Experiments show that free radical hydrogen shift is significant in the Pschorr cyclization of diphenyl ethers (X = O) and thioethers (X = S) and does not take place with sufoxides (X = SO) and sulfones (X = SO(2)). DFT calculations of the product ratios, activation energies, rate constants for H-transfers, and ring-closings at the UB3PW91/6-31G(d,p) level are in excellent agreement with the experimental results reported here and elsewhere in the literature.

Arising from: Li, M. et al. Nature 416, 648–653 (2002) Ubiquitination of p53 is the principal mechanism through which p53 concentrations in the cell are regulated1,2 in order to maintain its effects on tumori-genesis and normal cell growth. The protein HAUSP (also known as USP7) is a ubiquitin-specific protease (deubiquitinase)3,4 that has been shown by Li et al. to bind to p53 (ref. 5); in overexpression experiments, Li et al. showed that p53 could be stabilized as a result of deubiquitination by HAUSP and suggested that HAUSP may thereby act as a tumour suppressor5,6. Here we use a different approach to investigate the relationship between HAUSP and p53 stability, in which we disrupt the HAUSP gene in human cells by targeted homologous recombination. Instead of the expected increase in ubiquitinated p53 and destabilization of p53, we find that disruption of HAUSP results in the opposite phenotype, leading to stabilization and functional activation of p53 in our system. It may be that HAUSP can deubiquitinate other proteins such as MDM2, another regulator of p53, and that the balance between the deubiquitination of the different targets of HAUSP determines the steady-state level of p53.

Protein kinases are enzymes that are important for controlling cellular growth and invasion, and their malfunction is implicated in the development of some tumours. We analysed human colorectal cancers for genetic mutations in 340 serine/threonine kinases and found mutations in eight genes, including in three members of the phosphatidylinositol-3-OH kinase (PI(3)K) pathway. The discovery of this mutational activation of a key cell-signalling pathway may provide new targets for therapeutic intervention.

SummaryPIK3CA is mutated in diverse human cancers, but the functional effects of these mutations have not been defined. To evaluate the consequences of PIK3CA alterations, the two most common mutations were inactivated by gene targeting in colorectal cancer (CRC) cells. Biochemical analyses of these cells showed that mutant PIK3CA selectively regulated the phosphorylation of AKT and the forkhead transcription factors FKHR and FKHRL1. PIK3CA mutations had little effect on growth under standard conditions, but reduced cellular dependence on growth factors. PIK3CA mutations resulted in attenuation of apoptosis and facilitated tumor invasion. Treatment with the PI3K inhibitor LY294002 abrogated PIK3CA signaling and preferentially inhibited growth of PIK3CA mutant cells. These data have important implications for therapy of cancers harboring PIK3CA alterations.