Nitrogen and phosphorus budget in an intensive irrigation area and effects on littoral water and groundwater (Yaqui Valley, Northwestern Mexico).

The Yaqui River Irrigation District is a region in Mexico with intensive agricultural production; thus, large quantities of fertilizers are used, and excess fertilizer can affect the quality of water bodies. The aim of this work was to estimate the water budget and nitrogen (N) and phosphorous (P) mass budgets to evaluate possible contamination of a littoral water body (Tóbari Bay) and leachates into an aquifer (Yaqui Valley aquifer). Wheat and corn crops were studied, climate information was compiled, and soil and water samples were collected for analysis. The water budget showed excess irrigation occurred due to the need for soil washing to prevent salinization. A total of 24% of all irrigation water was used for crops, 60% was discharged into the bay through runoff of the drainage system, and 16% corresponded to effective infiltration (aquifer recharge). The N budget showed that of the 100% N input, the highest percentage was used by plants (63%), and only minimal loss occurred through runoff (11%) and leachate into the aquifer (7%). The remaining N stayed in the soil (18%) or was volatilized (1%). These results indicate that the drainage system prevented large amounts of N from entering the aquifer; thus, the N concentrations in the groundwater did not exceed the regulated maximum limit for drinking water (10 mg N-NO3/L). In terms of the water pollution level in the bay, the presence of NO3- was minimal (concentrations below the quasintifiable limit). Of the 100% of P that was applied, 55% was used by the plants, and 40% remained in the soil; therefore, the P that was transported by runoff or was leached was minimal (3 and 2%, respectively). However, this minimal amount of P ranged from 0.1 to 0.2 mg/L in the bay, and these values exceeded the suggested values for the protection of aquatic life (0.01 mg/L). The administrators of the irrigation district must pay special attention to phosphate fertilizer management and implement irrigation techniques that increase water use efficiency.

Opening up the DNA methylome of dementia.

Dementia is a complex clinical condition characterized by several cognitive impairments that interfere with patient independence in executing everyday tasks. Various neurodegenerative disorders have dementia in common among their clinical manifestations. In addition, these diseases, such as Alzheimer's disease, Parkinson's disease, dementia with Lewy bodies and frontotemporal dementia, share molecular alterations at the neuropathological level. In recent years, the field of neuroepigenetics has expanded massively and it is now clear that epigenetic processes, such as DNA methylation, are mechanisms involved in both normal and pathological brain function. Despite the persistent methodological and conceptual caveats, it has been reported that several genes fundamental to the development of neurodegenerative disorders are deregulated by aberrant methylation patterns of their promoters, and even common epigenetic signatures for some dementia-associated pathologies have been identified. Therefore, understanding the epigenetic mechanisms that are altered in dementia, especially those associated with the initial phases, will allow us not only to understand the etiopathology of dementia and its progression but also to design effective therapies to reduce this global public health problem. This review provides an in-depth summary of our current knowledge about DNA methylation in dementia, focusing exclusively on the analyses performed in human brain.

Tumor MGMT promoter hypermethylation changes over time limit temozolomide efficacy in a phase II trial for metastatic colorectal cancer.

BACKGROUND: Objective response to dacarbazine, the intravenous form of temozolomide (TMZ), in metastatic colorectal cancer (mCRC) is confined to tumors harboring O(6)-methylguanine-DNA-methyltransferase (MGMT) promoter hypermethylation. We conducted a phase II study of TMZ enriched by MGMT hypermethylation in archival tumor (AT), exploring dynamic of this biomarker in baseline tumor (BT) biopsy and plasma (liquid biopsy). PATIENTS AND METHODS: We screened 150 mCRC patients for MGMT hypermethylation with methylation-specific PCR on AT from FFPE specimens. Eligible patients (n = 29) underwent BT biopsy and then received TMZ 200 mg/m(2) days 1-5 q28 until progression. A Fleming single-stage design was used to determine whether progression-free survival (PFS) rate at 12 weeks would be ≥35% [H0 ≤ 15%, type I error = 0.059 (one-sided), power = 0.849]. Exploratory analyses included comparison between MGMT hypermethylation in AT and BT, and MGMT methylation testing by MethylBEAMing in solid (AT, BT) and LB with regard to tumor response. RESULTS: The PFS rate at 12 weeks was 10.3% [90% confidence interval (CI) 2.9-24.6]. Objective response rate was 3.4% (90% CI 0.2-15.3), disease control rate 48.3% (90% CI 32.0-64.8), median OS 6.2 months (95% CI 3.8-7.6), and median PFS 2.6 months (95% CI 1.4-2.7). We observed the absence of MGMT hypermethylation in BT in 62.7% of tumors. CONCLUSION: Treatment of mCRC with TMZ driven by MGMT promoter hypermethylation in AT samples did not provide meaningful PFS rate at 12 weeks. This biomarker changed from AT to BT, indicating that testing BT biopsy or plasma is needed for refined target selection.

Digital PCR quantification of MGMT methylation refines prediction of clinical benefit from alkylating agents in glioblastoma and metastatic colorectal cancer.

BACKGROUND: O(6)-methyl-guanine-methyl-transferase (MGMT) silencing by promoter methylation may identify cancer patients responding to the alkylating agents dacarbazine or temozolomide. PATIENTS AND METHODS: We evaluated the prognostic and predictive value of MGMT methylation testing both in tumor and cell-free circulating DNA (cfDNA) from plasma samples using an ultra-sensitive two-step digital PCR technique (methyl-BEAMing). Results were compared with two established techniques, methylation-specific PCR (MSP) and Bs-pyrosequencing. RESULTS: Thresholds for MGMT methylated status for each technique were established in a training set of 98 glioblastoma (GBM) patients. The prognostic and the predictive value of MGMT methylated status was validated in a second cohort of 66 GBM patients treated with temozolomide in which methyl-BEAMing displayed a better specificity than the other techniques. Cutoff values of MGMT methylation specific for metastatic colorectal cancer (mCRC) tissue samples were established in a cohort of 60 patients treated with dacarbazine. In mCRC, both quantitative assays methyl-BEAMing and Bs-pyrosequencing outperformed MSP, providing better prediction of treatment response and improvement in progression-free survival (PFS) (P < 0.001). Ability of methyl-BEAMing to identify responding patients was validated in a cohort of 23 mCRC patients treated with temozolomide and preselected for MGMT methylated status according to MSP. In mCRC patients treated with dacarbazine, exploratory analysis of cfDNA by methyl-BEAMing showed that MGMT methylation was associated with better response and improved median PFS (P = 0.008). CONCLUSIONS: Methyl-BEAMing showed high reproducibility, specificity and sensitivity and was applicable to formalin-fixed paraffin-embedded tissues and cfDNA. This study supports the quantitative assessment of MGMT methylation for clinical purposes since it could refine prediction of response to alkylating agents.

Impacts of urbanization on groundwater hydrodynamics and hydrochemistry of the Toluca Valley aquifer (Mexico).

The Toluca Valley is located on the high plains of Mexico, where there are significant industrial zones and large populations. Water needs are almost exclusively met by groundwater, which has brought about intense exploitation of the aquifer and indication of some contamination. The present study investigates the effect of urbanization, related to industrialization of the region, on groundwater in the central portion of the Toluca Valley aquifer--a zone with high population density and where the largest industrial park is located. A general decline in the groundwater level has been found over the years, at a rate of as much as 2.5 m/year. The appearance of a large drawdown cone was identified, indicating changes in the direction of groundwater flow. Also identified was the presence of several ground fissures, the location of which coincided with the drawdown cone. In hydrochemical terms, the water type is sodium-magnesium bicarbonate and this characteristic has not changed over time, although it has been possible to detect the presence of larger quantities of sulfates (up to 117 mg/L) and nitrates (up to 47 mg/L) in recent years, likely associated with contamination from industrial and urban wastewater. Factor analysis made it possible to identify ions that would characterize natural processes involving the acquisition of salts (HCO3 (-), Na(+), Mg(2+), and Si), as well as anthropic activities (SO4 (2-), NO3 (-), Cl(-), Ca(2+), and K(+)).

Removal of groundwater arsenic using a household filter with iron spikes and stainless steel.

Arsenic (As) in groundwater for domestic use poses a worldwide threat to public health, most notably in rural areas. The aims of this study were: first, determine groundwater composition in a mining area in central Mexico (Huautla); second, assess As exposure through human groundwater consumption and; third, develop and test a household filter to obtain drinking water for these rural communities. From the 17th century through the 1990s, mines in the area produced Ag-galena and sphalerite from volcanic rock. Groundwater flooded the mines when they were abandoned due to low silver prices. Local households now use the water to meet domestic needs. Water from the mines was found to have high As content (0.04-0.26 mg L(-1)) and Fe, Mn, Pb and Cd were also above Mexican drinking water standards and WHO guidelines. All the population in the Huautla community was exposed to the metalloid through water used in food preparation. The best As removal was obtained with a filter using oxidized commercial fiber (HCl 2N as oxidant). Concentrations in the effluent were below Mexican drinking water standards (0.025 mg As L(-1) water) during the 105-day (2520 h) filter operation, with a maximum As removal efficiency of 95.4%. The household filter was simple, low-cost and may be very attractive for As removal in rural areas in developing countries.

Evaluation of hydrochemical changes due to intensive aquifer exploitation: case studies from Mexico.

The impact of intensive aquifer exploitation has been observed in numerous places around the world. Mexico is a representative example of this problem. In 2010, 101 out of the 653 aquifers recognized in the country, showed negative social, economic, and environmental effects related to intensive exploitation. The environmental effects include, among others, groundwater level decline, subsidence, attenuation, and drying up of springs, decreased river flow, and deterioration of water quality. This study aimed at determining the hydrochemical changes produced by intensive aquifer exploitation and highlighting water quality modifications, taking as example the Valle de Toluca, Salamanca, and San Luis Potosi aquifers in Mexico's highlands. There, elements such as fluoride, arsenic, iron, and manganese have been detected, resulting from the introduction of older groundwater with longer residence times and distinctive chemical composition (regional flows). High concentrations of other elements such as chloride, sulfate, nitrate, and vanadium, as well as pathogens, all related to anthropogenic pollution sources (wastewater infiltration, irrigation return flow, and atmospheric pollutants, among others) were also observed. Some of these elements (nitrate, fluoride, arsenic, iron, and manganese) have shown concentrations above Mexican and World Health Organization drinking water standards.

The chromatin remodeling factor CHD8 interacts with elongating RNA polymerase II and controls expression of the cyclin E2 gene.

CHD8 is a chromatin remodeling ATPase of the SNF2 family. We found that depletion of CHD8 impairs cell proliferation. In order to identify CHD8 target genes, we performed a transcriptomic analysis of CHD8-depleted cells, finding out that CHD8 controls the expression of cyclin E2 (CCNE2) and thymidylate synthetase (TYMS), two genes expressed in the G1/S transition of the cell cycle. CHD8 was also able to co-activate the CCNE2 promoter in transient transfection experiments. Chromatin immunoprecipitation experiments demonstrated that CHD8 binds directly to the 5' region of both CCNE2 and TYMS genes. Interestingly, both RNA polymerase II (RNAPII) and CHD8 bind constitutively to the 5' promoter-proximal region of CCNE2, regardless of the cell-cycle phase and, therefore, of the expression of CCNE2. The tandem chromodomains of CHD8 bind in vitro specifically to histone H3 di-methylated at lysine 4. However, CHD8 depletion does not affect the methylation levels of this residue. We also show that CHD8 associates with the elongating form of RNAPII, which is phosphorylated in its carboxy-terminal domain (CTD). Furthermore, CHD8-depleted cells are hypersensitive to drugs that inhibit RNAPII phosphorylation at serine 2, suggesting that CHD8 is required for an early step of the RNAPII transcription cycle.

Interaction of GB virus C/hepatitis G virus synthetic peptides with lipid langmuir monolayers and large unilamellar vesicles.

In this paper, we aimed to continue the previous study undertaken with one segment of E1 protein belonging to the GB virus C/hepatitis G virus (GBV-C/HGV), specifically between the 53-66 amino acids and their palmitoyl derivative peptide. The sequence selection has been made on the basis of different prediction algorithms of hydrophobicity and antigenicity. Their interactions between two different in vitro membrane models, lipid Langmuir monolayers and vesicles of different lipidic composition, have been evaluated. For this purpose, different lipids, varying the charge and the unsaturations of the hydrocarbon chain 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (sodium salt) (DPPG) and 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (sodium salt) (DOPG), have been selected. Miscibility and peptides/lipids interactions have been analyzed on the basis of surface pressure (pi)-mean molecular area (A) isotherms, which have been recorded for pure and mixed monolayers of different composition spread at the air/water interface. Furthermore, E1(53-66) sequence and PalmE1(53-66) have been labeled with a fluorescent group, succinimidyl 6-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)hexanoate (NBD succinimide), in order to study their behavior in the presence of vesicles. The obtained results are consistent with the existence of electrostatic (attractive) intermolecular interactions between the two positive net charges of the peptides and the polar heads of negative-charged lipids. However, both the lipidic membrane fluidity and the palmitic chain linked to the native peptide play an important role in the balance between the electrostatic forces established at the interface and the hydrophobic ones established inside the membrane. The fluorescence assays have demonstrated that electrostatic forces clearly predominate over the hydrophobic interactions only when the native sequence is retained at the polar interface of DPPG and DOPG vesicles. However, the palmitic tail linked to the peptide helped its penetration in the hydrophobic environment of the membrane, and this process was favored by decreasing the membrane fluidity.

Nitrate and phosphate leaching in a Phaeozem soil treated with biosolids, composted biosolids and inorganic fertilizers.

The use of organic wastes in agriculture may increase the production of crops by incorporating organic matter and nutrients into the soil, and by improving its physical characteristics; however, this use may cause environmental problems such as the leaching of certain ions. The objective of this study was to establish possible nitrogen and phosphorus leaching under real field conditions in Phaeozem soils. The experimental work was performed in a corn (Zea mays L.) field where three plots were conditioned with inorganic fertilizer, three plots with 4.5 Mgha(-1) of biosolids on dry basis, and three plots with the same amount of composted biosolids. The quality of biosolids and composted biosolids complied with the Mexican Official Standards. Soil water samples were collected with suction cups during two agricultural cycles and were analysed. Soil samples were also taken and analysed. The N-NO(3) concentrations in soil water fluctuated between 0.9 and 98mgL(-1) in the composted biosolid treatment, between 0.7 and 64 mgL(-1) in the biosolid treatment, and between 1 and 61 mgL(-1) in the inorganic fertilizer treatment. The maximum concentration of N-NO(2) and N-NH(3) in soil water was 1.02 and 2.65 mgL(-1), respectively. The greatest percentage of nitrogen leached is produced when inorganic fertilizer is used (37.4% and 24.0% N leached in the first and second years, respectively), followed by composted biosolids (17.1% and 13.5% N leached in the first and second years, respectively) and last by biosolids (11% for both years). This difference could be related to the form in which nitrogen is present in the fertilizers, while commercial fertilizer is as inorganic nitrogen, organic wastes are basically presented as organic nitrogen. The maximum PO(4)(3-) concentration in soil water was 1.9 mgL(-1) in the composted biosolid treatment, 1.7mgL(-1) in the biosolid treatment and 0.9 mgL(-1) in the inorganic fertilizer treatment. The estimated percentage of leached phosphorus was less than 1% for all treatments. The minimum leaching that occurred seemed to be due to a sorption-precipitation process.

Global DNA methylation: a common early event in oral cancer cases with exposure to environmental carcinogens or viral agents.

INTRODUCTION: Two separate molecular pathways have been proposed for the early carcinogenic events observed in the oral cavity and pharynx: one is associated with chemical etiological factors such as smoking and drinking, and the other one is associated with HPV insertion. OBJECTIVE: A proof-of-principle study was performed to ascertain if global DNA methylation could be used to distinguish between the early molecular changes in premalignant oral lesions. METHODS: Personal histories of tobacco and alcohol use were obtained by questionnaire. HPV insertion in tumor tissue was detected by polymerase chain reaction (PCR). Global DNA methylation levels were obtained using HPLC for fraction separation and mass spectrometry for quantification. Predictive simulations were performed to explore potential associations between different etiological factors and the global DNA methylation index. Significance of results was ascertained using Pearson's Chi-squared test. RESULTS: The global methylation index was found to be 4.28 (95% CI, 4.1, 4.4) in an oral cancer case series. Pearson's chi squared test showed no statistically significant difference between cases that had smoking (p = 0.21), drinking (p = 0.31) or HPV insertion (p = 0.34) as etiologic risk factors, when compared to cases that did not. An inverse significant association between smoking and DNA methylation was observed. As the smoking effect increases, the global methylation index decreases, In addition, no associations between the probability of DNA methylation and drinking, or DNA methylation and HPV insertion were observed in simulations. CONCLUSIONS: The global DNA methylation index was shown to vary for oral cancer cases with different etiologies. Smoking was inversely correlated with DNA methylation levels when generalized linear model simulations were performed. Future studies should look at global DNA methylation alterations associated to the progression from normal to premalignant oral epithelium tissue in a cohort of smokers and nonsmokers.

A lysimeter study under field conditions of nitrogen and phosphorus leaching in a turf grass crop amended with peat and hydrogel.

Golf courses represent an agricultural activity wherein grass is intensively cultivated using large quantities of fertilizers. In the present study, nitrogen and phosphorus leaching was analyzed over two years in an experimental green under actual field conditions. The green contained four plots with distinct amendments (P1: hydrogel + peat, P2: peat, P3: hydrogel, and P4: no amendment). The applied doses of nitrogen ranged from 5 to 103 kg/ha and of phosphorus from 9 to 31 kg/ha. The irrigation level varied as a function of the rainfall regime and the water requirements of grass; overall water intake varied from 1550 to 2080 mm/year. Daily, leached water volume was calculated, and samples were taken for chemical analysis. Nitrogen and phosphorus mass balances were calculated for different periods based on the collected data. The plot amended with peat and hydrogel (P1) had reduced water flow; the percentage of drainage water varied from 8.4 to 29%. As a result, the dissolution and leaching of nitrogen (N) and phosphorus (P) were the lowest in comparison to the other plots. According to the calculated mass balances, the lowest leaching values were also recorded in this plot (P1), ranging from 0.5 to 6.3% for N and from 0.8 to 20.9% for P. The plot without amendment (P4) drained the most water (25.9-44.8%) and leached the highest quantities of N and P, ranging from 9.1-45.7%, and 6-35.9%, respectively. The use of double amendments (hydrogel and peat) therefore represented optimal operating conditions for the green. Moreover, a relationship was found between increasing rates of fertilization and increasing percentages of N and P leaching as well as between higher irrigation levels and greater leaching.

Correction: CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer.

In the original article the authors have noted that the wrong image was used to illustrate the Uc.346 + Lu1-Lu2-Lu3 subpanel of Figure 5a. The correct image is now provided as Figure 1 in this article. This change does not affect the legend of the figure, the results, or conclusions reported in the manuscript. The authors apologize for the error, and regret any inconvenience this may have caused.

Specific hypermethylation of LINE-1 elements during abnormal overgrowth and differentiation of human placenta.

In human post-natal somatic cells, low global levels of DNA methylation have been associated with the hypomethylation of several repetitive elements, a feature that has been proposed to be a surrogate epigenetic marker. These data, mainly derived from the analysis of cancer cells, suggest a potential association between loss of cell-growth control and altered differentiation with hypomethylation of repetitive sequences. Partial hydatidiform moles (PHMs) can be used as an alternative model for investigating this association in a non-tumorigenic context. This gestational disease is characterized by abnormal overgrowth and differentiation of the placenta and spontaneous abortion. Here, we comprehensively analyse the DNA methylation of these trophoblastic tissues in both PHM and normal placenta at global and sequence-specific levels. Analysis of the global 5-methylcytosine content and immunohistochemistry indicate that PHM and normal placenta have identical global levels of DNA methylation. In contrast, bisulfite genomic sequencing shows that, whereas Alu, NBL2 and satellite 2 repetitive elements are equally methylated, LINE-1 sequences are hypermethylated in PHM tissues ( approximately 2-fold relative to normal placenta). Interestingly, altered demethylation is also found in triploid diandric embryos that originate from dispermic fertilization of an oocyte, a common event responsible for most PHMs. In conclusion, alterations of DNA methylation do not seem to be randomly distributed in PHM, as several repeated elements remain unaltered, whereas LINE-1 sequences are hypermethylated. In addition, our findings suggest that the hypomethylation of repetitive elements in cancer is directly linked to the neoplasic process and not a simple consequence of loss of growth control observed in most of the cancer cells.

Proteins that bind methylated DNA and human cancer: reading the wrong words.

DNA methylation and the machinery involved in epigenetic regulation are key elements in the maintenance of cellular homeostasis. Epigenetic mechanisms are involved in embryonic development and the establishment of tissue-specific expression, X-chromosome inactivation and imprinting patterns, and maintenance of chromosome stability. The balance between all the enzymes and factors involved in DNA methylation and its interpretation by different groups of nuclear factors is crucial for normal cell behaviour. In cancer and other diseases, misregulation of epigenetic marks is a common feature, also including DNA methylation and histone post-translational modifications. In this scenario, it is worth mentioning a family of proteins characterized by the presence of a methyl-CpG-binding domain (MBDs) that are involved in interpreting the information encoded by DNA methylation and the recruitment of the enzymes responsible for establishing a silenced state of the chromatin. The generation of novel aberrantly hypermethylated regions during cancer development and progression makes MBD proteins interesting targets for their biological and clinical implications.

Directing neuronal cell fate in vitro: Achievements and challenges.

Human pluripotent stem cell (PSC) technology and direct somatic cell reprogramming have opened up a promising new avenue in the field of neuroscience. These recent advances allow researchers to obtain virtually any cell type found in the human brain, making it possible to produce and study functional neurons in laboratory conditions for both scientific and medical purposes. Although distinct approaches have shown to be successful in directing neuronal cell fate in vitro, their refinement and optimization, as well as the search for alternative approaches, remains necessary to help realize the full potential of the eventually derived neuronal populations. Furthermore, we are currently limited in the number of neuronal subtypes whose induction is fully established, and different cultivation protocols for each subtype exist, making it challenging to increase the reproducibility and decrease the variances that are observed between different protocols. In this review, we summarize the progress that has been made in generating various neuronal subtypes from PSCs and somatic cells, with special emphasis on chemically defined systems, transcription factor-mediated reprogramming and epigenetic-based approaches. We also discuss the efforts that are being made to increase the efficiency of current protocols and address the potential for the use of these cells in disease modelling, drug discovery and regenerative medicine.

Epigenetic inactivation of the Wnt antagonist DICKKOPF-1 (DKK-1) gene in human colorectal cancer.

Colorectal cancer is a major cause of cancer death worldwide. A number of key oncogenes and tumor suppressor genes have been proposed to drive progression from healthy colonic epithelia to malignant tumors, including members of the Wnt/beta-catenin pathway. Recently, CpG island promoter hypermethylation was shown to cause inactivation of two extracellular Wnt inhibitors in colon cancer: secreted frizzled-related proteins (sFRPs) and Wnt inhibitory factor-1 (WIF-1). Here, we show for the first time that another extracellular Wnt inhibitor, the DICKKOPF-1 (DKK-1) gene, is transcriptionally silenced by CpG island promoter hypermethylation in colon cancer cell lines (n=9), whereas treatment with the DNA-demethylating agent 5-aza-2-deoxycytidine restored DKK-1 expression. Restoration of DKK-1 function in non-expressing cells bearing a truncated APC (Adenomatous Polyposis Coli) gene had no effect on beta-catenin/T-cell factor-dependent transcription, but induced tumor suppressor-like features such as reduced colony formation density and tumor growth inhibition in nude mice. These results suggest additional functions for DKK-1 other than inhibiting canonical Wnt signaling. In primary colorectal tumors, DKK-1 was found hypermethylated in 17% (nine of 54) of cases. Furthermore, while for both SFRP-1 and WIF-1 methylation-associated silencing occurred across the whole spectrum of colorectal tumorigenesis, DKK-1 promoter was selectively hypermethylated in advanced colorectal neoplasms (Duke's C and D tumors).

Sensitization of retinoids and corticoids to epigenetic drugs in MYC-activated lung cancers by antitumor reprogramming.

Components of the SWI/SNF chromatin remodeling complex, including BRG1 (also SMARCA4), are inactivated in cancer. Among other functions, SWI/SNF orchestrates the response to retinoid acid (RA) and glucocorticoids (GC) involving downregulation of MYC. The epigenetic drugs SAHA and azacytidine, as well as RA and GC, are currently being used to treat some malignancies but their therapeutic potential in lung cancer is not well established. Here we aimed to determine the possible therapeutic effects of azacytidine and SAHA (A/S) alone or in combination with GC plus RA (GC/RA) in lung cancers with either BRG1 inactivation or MYC amplification. In vitro, responses to GC/RA treatment were more effective in MYC-amplified cells. These effects were mediated by BRG1 and involved a reprogramming towards prodifferentiation gene expression signatures and downregulation of MYC. In MYC-amplified cells, administration of GC/RA enhanced the cell growth inhibitory effects of A/S which, in turn, accentuated the prodifferentiation features promoted by GC/RA. Finally, these treatments improved overall survival of mice orthotopically implanted with MYC-amplified, but not BRG1-mutant, cells and reduced tumor cell viability and proliferation. We propose that the combination of epigenetic treatments with retinoids and corticoids of MYC-driven lung tumors constitute a strategy for therapeutic intervention in this otherwise incurable disease.

DNA methylation signal has a major role in the response of human breast cancer cells to the microenvironment.

Breast cancer-associated fibroblasts (CAFs) have a crucial role in tumor initiation, metastasis and therapeutic resistance by secreting various growth factors, cytokines, protease and extracellular matrix components. Soluble factors secreted by CAFs are involved in many pathways including inflammation, metabolism, proliferation and epigenetic modulation, suggesting that CAF-dependent reprograming of cancer cells affects a large set of genes. This paracrine signaling has an important role in tumor progression, thus deciphering some of these processes could lead to relevant discoveries with subsequent clinical implications. Here, we investigated the mechanisms underlying the changes in gene expression patterns associated with the cross-talk between breast cancer cells and the stroma. From RNAseq data obtained from breast cancer cell lines grown in presence of CAF-secreted factors, we identified 372 upregulated genes, exhibiting an expression level positively correlated with the stromal content of breast cancer specimens. Furthermore, we observed that gene expression changes were not mediated through significant DNA methylation changes. Nevertheless, CAF-secreted factors but also stromal content of the tumors remarkably activated specific genes characterized by a DNA methylation pattern: hypermethylation at transcription start site and shore regions. Experimental approaches (inhibition of DNA methylation, knockdown of methyl-CpG-binding domain protein 2 and chromatin immunoprecipitation assays) indicated that this set of genes was epigenetically controlled. These data elucidate the importance of epigenetics marks in the cancer cell reprogramming induced by stromal cell and indicated that the interpreters of the DNA methylation signal have a major role in the response of the cancer cells to the microenvironment.

DNMT3A mutations mediate the epigenetic reactivation of the leukemogenic factor MEIS1 in acute myeloid leukemia.

This corrects the article DOI: 10.1038/onc.2015.359.