Building a translational cancer dependency map for The Cancer Genome Atlas.

Cancer dependency maps have accelerated the discovery of tumor vulnerabilities that can be exploited as drug targets when translatable to patients. The Cancer Genome Atlas (TCGA) is a compendium of 'maps' detailing the genetic, epigenetic and molecular changes that occur during the pathogenesis of cancer, yet it lacks a dependency map to translate gene essentiality in patient tumors. Here, we used machine learning to build translational dependency maps for patient tumors, which identified tumor vulnerabilities that predict drug responses and disease outcomes. A similar approach was used to map gene tolerability in healthy tissues to prioritize tumor vulnerabilities with the best therapeutic windows. A subset of patient-translatable synthetic lethalities were experimentally tested, including PAPSS1/PAPSS12 and CNOT7/CNOT78, which were validated in vitro and in vivo. Notably, PAPSS1 synthetic lethality was driven by collateral deletion of PAPSS2 with PTEN and was correlated with patient survival. Finally, the translational dependency map is provided as a web-based application for exploring tumor vulnerabilities.

Effects of intratracheal exposure of 2-chloroethyl ethyl sulfide (CEES) on the activation of CCAAT-enhancer-binding protein (C/EBP) and its protection by antioxidant liposome.

Exposure of 2-chloroethyl ethyl sulfide (CEES) to guinea pigs causes lung injury by infiltration of neutrophils in interstitial lung spaces. A unique MAPK-regulated transcription factor, C/EBP (CCAAT-enhancer-binding protein), regulates the expression of intracellular adhesion molecule-1 (ICAM-1), involved in recruiting neutrophils in lung. The present study was to determine if CEES exposure causes activation of C/EBP, in particular the predominant ß-isoform and if so whether it can be prevented by intratracheal delivery of an antioxidant liposome containing N-acetyl cysteine and tocopherols. Lung injury was developed in guinea pigs by intratracheal exposure of CEES (0.5 mg/kg). The antioxidant liposome was given intratracheally 5 min after CEES exposure, and the animals were sacrificed after 30 days. CEES exposure caused a 2.3-fold increase in the activation of C/EBP accompanied with a 45% and 121% increase in the protein level of C/EBP ß and ICAM-1, respectively, and this effect was counteracted by the antioxidant liposome.

SOX2, OCT3/4 and NANOG expression and cellular plasticity in rare human somatic cells requires CD73.

Endogenous Plastic Somatic (ePS) cells isolated from adult human tissues exhibit extensive lineage plasticity in vitro and in vivo. Here we visualize these rare ePS cells in a latent state, i.e. lacking SOX2, OCT3/4 and NANOG (SON) expression, in non-diseased breast specimens through immunohistochemical analysis of previously identified ePS-specific biomarkers (CD73+, EpCAM+ and CD90-). We also report a novel mechanism by which these latent ePS cells acquire SON expression and plasticity in vitro. Four extracellular factors are necessary for the acquisition of SON expression and lineage plasticity in ePS cells: adenosine (which is produced by the 5' ecto-nucleotidase CD73 and activates in turn the PKA-dependent IL6/STAT3 pathway through the adenosine receptor ADORA2b), IL6, FGF2 and ACTIVIN A. Blocking any pathway component renders ePS cells incapable of SON expression and lineage plasticity. Notably, hESCs do not use adenosine or IL6 nor they express CD73 or ADORA2b and inhibition of adenosine signaling does not ablate their plasticity. Therefore, the data presented here delineate novel circuitry and physiological signals for accessing SON expression in rare, undifferentiated human cells.

Protection Against Dimethylbenz[a] Anthracene-Induced Breast Cancer in Female Rats by α-Lactalbumin.

Consumption of α-lactalbumin as dietary protein offers a beneficial effect on breast cancer development. Breast cancer was developed by gavage administration of single dose of dimethylbenz(a)anthracene (DMBA) in female rats, maintained on AIN-76A diet with either 20% casein or α-lactalbumin (a component of whey protein). All tumors were detected by palpation. After approximately 130 days of DMBA administration, the animals were euthanized. There was a delay in the development of breast tumor in the α-lactalbumin group in comparison to the casein group. The number of tumors per rat was less in the α-lactalbumin group than that in the casein group at any time point up to 130 days after DMBA administration. Also the incidence of tumors and tumor volume was less in the α-lactalbumin group than those in the casein group. The casein group had a mixture of grade I, grade II and grade III tumors whereas the α-lactalbumin group had mostly grade I tumor. Furthermore, the proliferative index was significantly lower in the α-lactalbumin group than that in the casein group.

Lung retinoid metabolism and signaling in chronic obstructive pulmonary disease.

There are a number of sites that are required for the production and/or action of all-trans retinoic acid (ATRA). In particular, interruption of different components of the chain of trafficking and metabolism has been associated with cancers arising in numerous organs of the body. Preliminary work suggests that such interruptions may be a factor in lung disorders induced by the smoke exposure. The active metabolite of retinoid, ATRA offers a therapeutic strategy to protect against functional abnormality in the lung, including chronic obstructive pulmonary disease (COPD). This review deals with the lung retinoid metabolism and mediators of retinoid trafficking and signaling with special emphasis on their roles in health and disease.

Rare somatic cells from human breast tissue exhibit extensive lineage plasticity.

We identified cell surface markers associated with repression of p16(INK4a)/cyclin-dependent kinase inhibitor 2A(CDKN2A), a critical determinant in the acquisition of a plastic state. These cell surface markers allowed direct isolation of rare cells from healthy human breast tissue that exhibit extensive lineage plasticity. This subpopulation is poised to transcribe plasticity markers, OCT3/4, SOX2, and NANOG, at levels similar to those measured in human embryonic stem cells and to acquire a plastic state sensitive to environmental programming. In vitro, in vivo, and teratoma assays demonstrated that either a directly sorted (uncultured) or a single-cell (clonogenic) cell population from primary tissue can differentiate into functional derivatives of each germ layer, ectodermal, endodermal, and mesodermal. In contrast to other cells that express OCT3/4, SOX2, and NANOG, these human endogenous plastic somatic cells are mortal, express low telomerase activity, expand for an extensive but finite number of population doublings, and maintain a diploid karyotype before arresting in G1.

Comparative effects of histone deacetylase inhibitors on p53 target gene expression, cell cycle and apoptosis in MCF-7 breast cancer cells.

Histone deacetylase inhibitors are currently being evaluated for their therapeutic potential and have shown considerable promise as adjuvant therapies for a number of cancers. This study compared the effects of 2 hydroxamic acid based inhibitors, CG-1521 and SAHA, on gene expression, cell cycle and cell death in MCF-7 human breast cancer cells. Both compounds show a dose- and time-dependent effect on cell number (evaluated using crystal violet), however CG-1521 exerts its effects significantly earlier than SAHA, and CG-1521 induces apoptosis (assessed by Apo-BrdU staining and flow cytometry) more rapidly than SAHA. qPCR of cell cycle regulatory and apoptotic genes shows that CG-1521 and SAHA modulate similar cohorts of p53-responsive genes, however, the levels of induction and the timing of the induction differs significantly between the 2 inhibitors. In particular SAHA downregulates cell cycle-associated genes that modulate the G1/S transition (including cyclin D1 and cdc25a) and the G2/M transition [cyclin B1, Plk1, Stk6 (serine-threonine kinase 6, Aurora kinase A) and Kntc2] more significantly than CG-1521. In contrast, CG-1521 significantly induces the expression of several p53 target genes associated with apoptosis including Bnip3/Bnip3L, p21/p21B and Gdf15. The differential levels of gene induction provide molecular evidence of both cell cycle arrest and apoptosis, and suggest a molecular mechanism that explains the difference in the biological effects of the 2 histone deacetylase inhibitors.

Uptake of all-trans retinoic acid-containing aerosol by inhalation to lungs in a guinea pig model system--a pilot study.

Systemic therapies with retinoic acid (RA) can result in toxic side effects without yielding biologically effective levels in target tissues such as lung. The authors adapted a PARI LC Star nebulizer to create a tubular system for short-term inhalation treatment of guinea pigs using a water-miscible formulation of all-trans RA (ATRA) or vehicle. Based on the initial average weight, animals received an estimated average ATRA doses of either 0.32 mg·kg(-1) (low dose, 1.4 mM), or 0.62 mg·kg(-1) (medium dose, 2.8 mM), or 1.26 mg·kg(-1) (high dose, 5.6 mM) 20 minutes per day for 6 consecutive days. This system led to a rise of ATRA levels in lung, but not liver or plasma. Cellular lung levels of retinol, retinyl palmitate, and retinyl stearate also appeared to be unaffected (245.6 ± 10.7, 47.4 ± 3.4, and 132.8 ± 7.7 ng·g(-1) wet weight, respectively). The application of this aerosolized ATRA also induced a dose-dependent protein expression of the cellular retinol-binding protein 1 (CRBP-1) in lung, without apparent harmful side effects.

Qualitative and quantitative analysis of retinol, retinyl esters, tocopherols and selected carotenoids out of various internal organs form different species by HPLC.

We report the validation of a reversed-phase gradient HPLC method allowing simultaneous quantification of retinol, retinyl esters, tocopherols and selected carotenoids in lung, liver and plasma of mouse, rat and guinea pig (gp) using a diode array detector. A significant species difference was observed regarding the distribution of retinol and retinyl esters. The levels of total retinol in lung, liver and plasma were in the following order: mouse >> rat > gp; rat >mouse > gp; and gp >> rat > mouse, respectively. Furthermore, comparison studies revealed similarities between the vitamin A profiles of human and gp lung samples.

Breast cancer is associated with an increase in the activity and expression of cholinephosphotransferase in rats.

AIM: The present study aims to establish that cholinephosphotransferase (CPT), the terminal enzyme for the de novo biosynthesis of phosphatidylcholine (PC), can be used as a biomarker for breast cancer in an animal model. MAIN METHODS: Breast cancer was induced by intragastric administration of dimethylbenz(a)anthracene (DMBA) in rats. The activity and expression of CPT were compared between normal breast tissues and breast tumors. To establish possible mechanistic model, we looked into other enzymes of PC biosynthesis as well as c-fos protein expression and DNA binding. KEY FINDINGS: CPT enzyme activity and its expression were significantly higher in breast cancer tissues relative to normal breast tissues. Corresponding to the increase in the CPT activity and its expression, c-fos activity and its expression were also increased in breast tumors. SIGNIFICANCE: The present study suggests that increased CPT activity and expression is associated with DMBA-induced breast cancer development.

Identification of lutein, a dietary antioxidant carotenoid in guinea pig tissues.

Lutein, a dietary carotenoid, is a well known antioxidant. The major source of this carotenoid in humans is diet. We report here the presence of lutein, a dietary carotenoid in several guinea pig tissues (in decreasing order: liver>spleen>lung>>testis>kidney>plasma>eye but not in white adipose tissue). The presence of lutein in lung and other tissues may be significant in term of its antioxidant capacity of these organs.

Array-based analysis of the effects of trichostatin A and CG-1521 on cell cycle and cell death in LNCaP prostate cancer cells.

Previous studies comparing the effects of two histone deacetylase (HDAC) inhibitors, trichostatin A (TSA) and CG-1521, have shown that these compounds selectively inhibit HDAC and induce differentially acetylated p53 isoforms and assembly of mutually exclusive transcriptional complexes on the p21 promoter. To determine whether the differential transcriptional regulation seen in p21 gene is unique or whether it is representative of the genome-wide effects of these two HDAC inhibitors, we have used microarray and Ingenuity pathway analysis to compare the effects of TSA and CG-1521 on gene expression on LNCaP cells. Gene array analysis confirmed by quantitative real-time PCR shows that CG-1521 modulates the expression of a highly circumscribed group of genes involved in cell cycle progression and cell death. In contrast, TSA appears to induce widespread transrepression of many genes and does not modulate the expression of the same cohort as CG-1521. These data show that the selective effects of CG-1521 and TSA on the assembly of transcription complexes are not unique to the p21 gene and suggest that selective inhibition of HDAC can lead to significant changes in gene expression through the acetylation of transcription factors including but not limited to p53.

Site-specific acetylation of p53 directs selective transcription complex assembly.

Histone deacetylase (HDAC) inhibitors are being investigated as possible adjuvant therapies for a number of diseases, including cancer. In addition to stabilization of acetylated histones, HDAC inhibitors stabilize the acetylation of a number of transcription factors, including p53. This study investigates the action of two HDAC inhibitors, CG-1521 and trichostatin A, which stabilize Ac-Lys-373 p53 and Ac-Lys-382 p53, respectively, in LNCaP prostate cancer cells. Real-time PCR demonstrates that CG-1521 induces p21 transcription whereas trichostatin A does not alter the steady state level of p21 mRNA. Co-immunoprecipitation demonstrates that the selective acetylation of p53 directs the recruitment of mutually exclusive coactivator complexes on the p53 response elements in the p21 promoter. Furthermore, the co-activator complexes initiate the recruitment of the components of the basal transcription apparatus to the basal promoter with markedly different outcomes because only Ac-Lys-373 p53 promotes the assembly of the basal transcriptional apparatus on the p21 promoter. These data highlight the profound effects of post-translational modification, including acetylation, on the function of p53. The data also suggest a novel and critically important role for protein acetylation/deacetylation in the assembly of active transcription processes that may be as important as classical phosphorylation/dephosphorylation.

Inhibition of cholinephosphotransferase activity in lung injury induced by 2-chloroethyl ethyl sulfide, a mustard analog.

Exposure to mustard gas causes inflammatory lung diseases including acute respiratory distress syndrome (ARDS). A defect in the lung surfactant system has been implicated as a cause of ARDS. A major component of lung surfactant is dipalmitoyl phosphatidylcholine (DPPC) and the major pathway for its synthesis is the cytidine diphosphocholine (CDP-choline) pathway. It is not known whether the ARDS induced by mustard gas is mediated by its direct effects on some of the enzymes in the CDP-choline pathway. In the present study we investigated whether mustard gas exposure modulates the activity of cholinephosphotransferase (CPT) the terminal enzyme by CDP-choline pathway. Adult guinea pigs were intratracheally infused with single doses of 2-chloroethyl ethyl sulfide (CEES) (0.5 mg/kg b.wt. in ethanol). Control animals were injected with vehicles only. The animals were sacrificed at different time and the lungs were removed after perfusion with physiological saline. CPT activity increased steadily up to 4 h and then decreased at 6 h and stabilized at 7 days in both mitochondria and microsomes. To determine the dose-dependent effect of CEES on CPT activity we varied the doses of CEES (0.5-6.0 mg/kg b.wt.) and sacrificed the animals at 1 h and 4 h. CPT activity showed a dose-dependent increase of up to 2.0 mg/kg b.wt. of CEES in both mitochondria and microsomes then decreased at 4.0 mg/kg b.wt. For further studies we used a fixed single dose of CEES (2.0 mg/kg b.wt.) and fixed exposure time (7 days). Lung injury was determined by measuring the leakage of iodinated-bovine serum albumin into lung tissue and expressed as the permeability index. CEES exposure (2.0 mg/kg b.wt. for 7 days) caused a significant decrease of both CPT gene expression (approximately 1.7-fold) and activity (approximately 1.5-fold) in the lung. This decrease in CPT activity was not associated with any mutation of the CPT gene. Previously we reported that CEES infusion increased the production of ceramides which are known to modulate PC synthesis. To determine whether ceramides affect microsomal CPT activity the lung microsomal fraction was incubated with different concentrations of C(2)-ceramide prior to CPT assay. CPT activity decreased significantly with increasing dose and time. The present study indicates that CEES causes lung injury and significantly decreases CPT gene expression and activity. This decrease in CPT activity was not associated with any mutation of the CPT gene is probably mediated by accumulation of ceramides. CEES induced ceramide accumulation may thus play an important role in the development of ARDS by modulating CPT enzyme.

Modulation of cholinephosphotransferase activity in breast cancer cell lines by Ro5-4864, a peripheral benzodiazepine receptor agonist.

Changes in phospholipid and fatty acid profile are hallmarks of cancer progression. Increase in peripheral benzodiazepine receptor expression has been implicated in breast cancer. The benzodiazepine, Ro5-4864, increases cell proliferation in some breast cancer cell lines. Biosynthesis of phosphatidylcholine (PC) has been identified as a marker for cells proliferating at high rates. Cholinephosphotransferase (CPT) is the terminal enzyme for the de novo biosynthesis of PC. We have addressed here whether Ro5-4864 facilitates some cancer causing mechanisms in breast cancer. We report that cell proliferation increases exponentially in aggressive breast cancer cell lines 11-9-1-4 and BT-549 when treated with nanomolar concentrations of Ro5-4864. This increase is seen within 24 h of treatment, consistent with the cell doubling time in these cells. Ro5-4864 also upregulates c-fos expression in breast cancer cell lines 11-9-1-4 and BT-549, while expression in non-tumorigenic cell line MCF-12A was either basal or slightly downregulated. We further examined the expression of the CPT gene in breast cancer (11-9-1-4, BT-549) and non-tumorigenic cell lines (MCF-12A, MCF-12F). We found that the CPT gene is overexpressed in breast cancer cell lines compared to the non-tumorigenic cell lines. Furthermore, the activity of CPT in forming PC is increased in the breast cancer cell lines cultured for 24 h. Additionally, we examined the CPT activity in the presence of nanomolar concentrations of Ro5-4864. Biosynthesis of PC was increased in breast cancer cell lines upon treatment. We therefore propose that Ro5-4864 facilitates PC formation, a process important in membrane biogenesis for proliferating cells.

Differential effect of cadmium on cholinephosphotransferase activity in normal and cancerous human mammary epithelial cell lines.

Cadmium (Cd) is an ubiquitous environmental carcinogen. Membrane phospholipids as well as fatty acid profile of membrane phospholipids are known to be altered in tumorigenicity and malignancy. Synthesis of cellular phosphatidylcholine (PC) has been used as a marker for membrane proliferation in the neoplastic mammary gland tissue. Cholinephosphotransferase (CPT), the terminal enzyme in de novo synthesis of PC, has an important role in regulating the acyl group of PC in mammalian cells. Our previous studies have shown that CPT is expressed differentially in the normal and cancerous mammary epithelial cell lines. In this study, we examined the effect of cadmium on CPT activity using normal (MCF-12A and MCF-12F) and cancerous (MCF-7, BT-549, and 11-9-1-4) human mammary epithelial cell lines. There was no consistent pattern of CPT activity in response to different doses of cadmium. The activity did not show a time-dependent variation at 5 micro M concentration, except in MCF-7 and 11-9-1-4. CPT gene expression increased with cadmium as evident from slot blots. Mutation in the nucleotide sequence was also observed as the result of cadmium but this did not result into amino acid sequence changes.