Genome-wide transcriptional analysis of apoptosis-related genes and pathways regulated by H2AX in lung cancer A549 cells

Endogenous retrotransposons cause catastrophic deoxyribonucleic acid damage in human trophoblasts

OBJECTIVE

To determine the mechanistic role of mobile genetic elements in causing widespread DNA damage in primary human trophoblasts.

DESIGN

Experimental ex vivo study.

SETTING

Hospital-affiliated University.

PATIENT(S)

Trophoblasts from a patient with unexplained recurrent pregnancy loss and patients with spontaneous and elective abortions (n = 10).

INTERVENTION(S)

Biochemical and genetic analysis and modification of primary human trophoblasts.

MAIN OUTCOME MEASURE(S)

To phenotype and systematically evaluate the underlying pathogenic mechanism for elevated DNA damage observed in trophoblasts derived from a patient with unexplained recurrent pregnancy loss, transcervical embryoscopy, G-band karyotyping, RNA sequencing, quantitative polymerase chain reaction, immunoblotting, biochemical and siRNA assays, and whole-genome sequencing were performed.

RESULT(S)

Transcervical embryoscopy revealed a severely dysmorphic embryo that was euploid on G-band karyotyping. RNA sequencing was notable for markedly elevated LINE-1 expression, confirmed with quantitative polymerase chain reaction, and that resulted in elevated expression of LINE-1-encoded proteins, as shown by immunoblotting. Immunofluorescence, biochemical and genetic approaches demonstrated that overexpression of LINE-1 caused reversible widespread genomic damage and apoptosis.

CONCLUSION(S)

Derepression of LINE-1 elements in early trophoblasts results in reversible but widespread DNA damage.

Vitamin D3 and Salinomycin synergy in MCF-7 cells cause cell death via endoplasmic reticulum stress in monolayer and 3D cell culture

1α, 25, dihydroxyvitamin D₃ (1,25D), the active form of vitamin D₃, has antitumor properties in several cancer cell lines in vitro. Salinomycin (Sal) has anticancer activity against cancer cell lines. This study aims to examine the cytotoxic and antiproliferative effect of Sal associated with 1,25D on MCF-7 breast carcinoma cell line cultured in monolayer (2D) and three-dimensional models (mammospheres). We also aim to evaluate the molecular mechanism of Sal and 1,25D-mediated effects. We report that Sal and 1,25D act synergistically in MCF-7 mammospheres and monolayer causing G1 cell cycle arrest, reduction of mitochondrial membrane potential (MMP), and reactive oxygen species (ROS) overproduction with a long-lasting cytotoxic response represented by clonogenic and mammosphere assay. We observed the induction of cell death by apoptosis with upregulation in mRNA levels of apoptosis-related genes (CASP7, CASP9, and BBC3). Extensive cytoplasmic vacuolization, a morphological characteristic found in paraptosis, was also seen and could be triggered by endoplasmic reticulum stress (ER) as we found transcriptional upregulation of genes related to ER stress (ATF6, GADD153, GADD45G, EIF2AK3, and HSPA5). Overall, Sal and 1,25D act synergistically, inhibiting cell proliferation by activating simultaneously multiple death pathways and may be a novel and promising luminal A breast cancer therapy strategy.

Feiyanning Formula Induces Apoptosis of Lung Adenocarcinoma Cells by Activating the Mitochondrial Pathway

Feiyanning formula (FYN) is a traditional Chinese medicine (TCM) prescription used for more than 20 years in the treatment of lung cancer. FYN is composed of Astragalus membranaceus, Polygonatum sibiricum, Atractylodes macrocephala, Cornus officinalis, Paris polyphylla, and Polistes olivaceous, etc. All of them have been proved to have anti-tumor effect. In this study, we used the TCM network pharmacological analysis to perform the collection of compound and disease target, the prediction of compound target and biological signal and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. It was found that the activation of mitochondrial pathway might be the molecular mechanism of the anti-lung cancer effect of FYN. The experimental results showed that FYN had an inhibitory effect on the growth of lung cancer cells in a dose-dependent and time-dependent manner. Moreover, FYN induced G₂/M cell cycle arrest and apoptotic cell death as early as 6 h after treatment. In addition, FYN significantly induced mitochondrial membrane depolarization and increased calreticulin expression. Metabolomics analysis showed the increase of ATP utilization (assessed by a significant increase of the AMP/ATP and ADP/ATP ratio, necessary for apoptosis induction) and decrease of polyamines (that reflects growth potential). Taken together, our study suggested that FYN induced apoptosis of lung adenocarcinoma cells by promoting metabolism and changing the mitochondrial membrane potential, further supporting the validity of network pharmacological prediction.

Nano-Al2O3 can mediate transduction-like transformation of antibiotic resistance genes in water

The prevalence of various antibiotic resistance genes (ARGs) and resistant bacteria has caused global public health risks. The carrier transport mediated by phages or membrane vesicles is an important way for horizontal transfer of ARGs. Nano metal oxide particles (NMOPs), which can enter cell through the cell membrane, may be used as the carriers of genes. However, whether they can be used as transmembrane delivery vectors for the horizontal ARG transfer remains unknown. Here, we set up a model of MONPs-mediated transfer of ARGs, and demonstrate that NMOPs, especially for nano-Al₂O₃, can act as carriers mediating the transduction-like ARG transformation in water. The highest transfer rate mediated by nano-Al₂O₃ is 4.53 × 10⁴ cfu/mmol, and it is 10⁴ times higher than that of control. Nano-Al₂O₃ can combine with plasmid coding for ARGs to form high-density package and prevent ARGs from degradation by endonuclease. The results of superresolution fluorescence microscopy and transmission electron microscopy show that nano-Al₂O₃ can carry ARGs for transmembrane transport. Genome-wide transcription microarray and qPCR indicate that SOS response was closely related to transduction-like ARG transformation mediated by nano-Al₂O₃. This study is the first to demonstrate that as a new transmembrane carrier, nano-Al₂O₃ can also cause ARGs diffusion in water.

TAK1-AMPK Pathway in Macrophages Regulates Hypothyroid Atherosclerosis

PURPOSE

Hypothyroidism (HT) is associated with accelerated atherosclerosis (AS). The efficacy of traditional strategies of hypothyroid AS remains controversial. Here, we aimed to deepen the understanding of the HT-induced acceleration of AS, to decrease the residual risk of coronary artery disease (CAD) and to find a new therapeutic target.

METHODS

We collected peripheral venous blood samples from 20 patients and divided them into 4 groups, namely, the normal group, the HT group, the CAD group and the HT + CAD group. Then we performed mRNA microarray analysis and bioinformatics analysis to screen the differentially expressed genes and pathways, and we also conducted validations on ApoE knockout mice models and Raw264.7 cell models.

RESULTS

In short, (1) in the analysis between the CAD group and the HT + CAD group, we found a total of 1218 differentially expressed genes, 11 upregulated pathways and 40 downregulated pathways. (2) We validated that patients with HT and CAD had a significantly decreased expression of MAP3K7 (encoding transforming growth factor-β-activated kinase 1, TAK1) gene than normal subjects. (3) In animal and cell experiments, we found the decreased expression of TAK1 and the reduced phosphorylation of AMP-activated protein kinase (AMPK) under the hypothyroid and atherosclerotic condition. (4) Changes in the expressions of TAK1 may affect the progression of AS.

CONCLUSION

Taken together, these data suggest that the accelerated AS in hypothyroid patients may be due to the suppression of TAK1-AMPK pathway in macrophages. This new finding may become a novel therapeutic target in hypothyroid AS.

Identification of Common and Subtype-Specific Mutated Sub-Pathways for a Cancer

The heterogeneity of cancer is a big obstacle for cancer diagnosis and treatment. Prioritizing combinations of driver genes that mutate in most patients of a specific cancer or a subtype of this cancer is a promising way to tackle this problem. Here, we developed an empirical algorithm, named PathMG, to identify common and subtype-specific mutated sub-pathways for a cancer. By analyzing mutation data of 408 samples (Lung-data1) for lung cancer, three sub-pathways each covering at least 90% of samples were identified as the common sub-pathways of lung cancer. These sub-pathways were enriched with mutated cancer genes and drug targets and were validated in two independent datasets (Lung-data2 and Lung-data3). Especially, applying PathMG to analyze two major subtypes of lung cancer, lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LSCC), we identified 13 subtype-specific sub-pathways with at least 0.25 mutation frequency difference between LUAD and LSCC samples in Lung-data1, and 12 of the 13 sub-pathways were reproducible in Lung-data2 and Lung-data3. Similar analyses were done for colorectal cancer. Together, PathMG provides us a novel tool to identify potential common and subtype-specific sub-pathways for a cancer, which can provide candidates for cancer diagnoses and sub-pathway targeted treatments.

The therapeutic role of inhibition of miR-328 on pulmonary carcinoma induced by chlamydia pneumoniae through targeting histone H2AX

Lung cancer represents a major healthy concern due to high incidence and morality. Increasing evidences showed critical regulatory role of microRNA (miR) in cell growth, differentiation and apoptosis. It has been indicated that the level of miR-328 is abnormally up regulated in lung cancer cell line, which is correlated with cell apoptosis. An in vitro lung cancer model was established through induction of chlamydia pneumonia. Western blot and real-time quantitative PCR were used to measure miR-328 level and its effects on histone H2AX expression. Bioinformatics analysis and luciferase reporter gene assay were to determine if H2AX was the direct target of miR-328. TUNEL assay, AV-PI staining and Caspase-3 activity assay measured the effect of the decrease of miR-328 on lung cancer cell apoptosis at both in vivo and in vitro level. Bioinformatics analysis predicted histone H2AX as the target of miR-328 during the regulation of lung cancer. Both in vivo and in vitro knockdown of miR-328 up-regulated H2AX expression and elevated TUNEL-positive cell number. In vivo down-regulation of miR-328 decreased incidence of lung cancer induced by chlamydia pneumoniae, suppressed tumor volume, increased caspase 3 activity, and facilitated tumor cell apoptosis. Histone protein H2AX serves as the target of miR-328 and participates in lung cancer regulation. Suppression of miR-328 level promotes lung cancer tissue apoptosis, which provides novel target for lung cancer therapy.

Genome-wide Transcriptional Analysis of Oxidative Stress-related Genes and Pathways Induced by CdTe aqQDs in Mice

Objective: Quantum dots (QDs) has widely applied in the field of science, whose potential toxic effect has increasingly become a focus concern we need pay attention to in public health. The purpose of this article was to explore the toxicity mechanism with oxidative damage from treatment with QDs at the molecular level through a gene microarray.

Methods: Mice were administered aqueously synthesized cadmium telluride QDs (CdTe aqQDs) via intravenous tail injection of a 2 µmol/kg solution (based on the molar mass of Cd), and their kidneys were collected at 1 day in strict accordance with the programs used for treated mice. We determined the hierarchical clustering of expression ratios, enriched gene ontology (GO) terms and signaling pathways through gene microarray analysis and bioinformatics analysis in kidney tissue and screened the key enzyme genes, which were verified by real-time quantitative polymerase chain reaction (real-time qPCR).

Results: Compared to control group, 459 lncRNAs (197 down-regulated and 262 up-regulated) and 256 mRNAs (103 down-regulated and 153 up-regulated) were differentially expressed. According to biological processes in enriched GO terms, the response to a redox state played a significant role in the biological processes involved altered genes. Pathway analysis showed that the signaling pathways that involved cytochrome P450 (CYP450) enzymes had a close relationship with QDs. Among these signaling pathways, gene expression profiling revealed that selected differentially expressed mRNAs (CYP19A1, CYP1B1, CYP11A1, CYP11B2, and CYP17A1 in the kidney and CYP19A1 and CYP1B1 in the liver) were validated by real-time qPCR, resulting in expression levels of CYP11A1, CYP11B2 and CYP17A1 in the kidney and CYP19A1 and CYP1B1 in the liver that were significantly increased, however in expression levels of CYP19A1 and CYP1B1 compared with control group in the kidney, there was no significant difference.

Conclusions: Our results provide a foundation for and potential insight into the role of CYP450-related genes in QD-induced oxidative stress. QDs may produce a great deal of reactive oxygen species (ROS) by promoting high expression of CYP450 enzymes and accumulating steroid hormones, which may be an important toxicity mechanism for mediating oxidative stress and tissue damage.

MicroRNA-3196 is inhibited by H2AX phosphorylation and attenuates lung cancer cell apoptosis by downregulating PUMA

Histone H2AX is a tumor suppressor protein that plays an important role in apoptosis. However, the mechanism underlying the association of H2AX with apoptosis in cancer cells remains elusive. Here, we showed that H2AX knockdown in lung cancer A549 cells affected the expression of 16 microRNAs (miRNAs), resulting in the downregulation of 1 and the upregulation of 15 miRNAs. MicroRNA-3196 (miR-3196) was identified as a target of H2AX and shown to inhibit apoptosis in lung cancer cells by targeting p53 upregulated modulator of apoptosis (PUMA). Phosphorylated H2AX (γH2AX) was shown to bind to the promoter of miR-3196 and regulate its expression. In addition, H2AX phosphorylation increased H3K27 trimethylation in the promoter region of miR-3196 and inhibited the binding of RNA polymerase II to the promoter of miR-3196, leading to the inhibition of miR-3196 transcription. Taken together, these results indicated that H2AX phosphorylation regulates apoptosis in lung cancer cells via the miR-3196/PUMA pathway.

Self-defense of Escherichia coli against damages caused by nanoalumina

Although studies showed effects of nanoalumina (nano-Al₂O₃) on Escherichia coli, no study completely provides understanding on how bacterial cells respond to damages, especially on how they initiate self-defense. In this study, we showed three types of responses of E. coli to damages caused by nano-Al₂O₃. Live, dead, and injured, bacteria showed improved survival rates reaching 104%, 116%, and 104% after exposure to 0.1, 1, and 10mmol/L of nano-Al₂O₃ respectively. Survival rates improved from 100% to 114%, corresponding to an exposure time of 0-9h, and from 100% to 127%, corresponding to 0-1000μg/L Al³⁺. Improvements were noted in survival rates of E. coli K12 MG1655, HB101, DH5α, and K12 MG1655 △lexA treated by nano-Al₂O₃ in Luria-Bertani (LB) exposure system or K12 MG1655 in LB, normal saline(NS) and H₂O exposure system. Bacterial cells transformed from long rods to ellipsoidal or nearly spherical as form of self-preservation mechanism; this phenomenon may be related to changes in membrane potential induced by free Al³⁺ released from nano-Al₂O₃ particles. Molecular mechanism of this response involved inhibited gene expression of sythesis and metabolism of carbohydrates, lipids and proteins. Findings presented in this study may improve understanding of potential danger of nanomaterials and control their spread to environmen.

Comprehensive understanding of PM2.5 on gene and microRNA expression patterns in zebrafish (Danio rerio) model

PM_2.5 is a major public health concern and some severe diseases have been attributed to exposure to PM_2.5. However, a comprehensive understanding of gene and microRNA expression patterns induced by PM_2.5 is missing. The objective of this study was to evaluate the toxicity of PM_2.5 via genome-wide transcriptional analysis in the model teleost fish, zebrafish (Danio rerio). Gene ontology analysis revealed that the most impact gene functional categories induced by PM_2.5 included oxidation-reduction process, transport, response to xenobiotic stimulus, response to chemical stimulus and metabolic process. Pathway and Signal-net analysis showed that the critical pathway involved in the response to exposure to PM_2.5 was the metabolism of xenobiotics by cytochrome P450. Results from verification experiments also demonstrated that the key genes with degree higher than 10 induced by PM_2.5 were related to metabolism of xenobiotics by cytochrome P450, including cyp3a65, mgst2, gstp1, gsto2, gsto1, cyp1a, ehx1, gstal and aldh3b1. The differential expression of 8 microRNAs corresponding to those in the human genome, revealed that PM_2.5 could up-regulate let-7b, miR-153b-3p, miR-122, miR-24 and down-regulate let-7i, miR-19a-3p, miR-19b-3p and miR-7a, which suggested PM_2.5 had multiple means through which it induced toxicity in living organisms, such as suppression of adaptive immune responses, autophagy, deregulation of metabolism, impaired vasorelaxation, progression of cancers, as well as hypertension, atherosclerosis and myocardial infarction.

Genome-wide transcriptional analysis of silica nanoparticle-induced toxicity in zebrafish embryos

Although silica nanoparticles (SiNPs) have a promising application in biomedical fields, there is still a lack of comprehensive understanding of genome-wide transcriptional analysis. This study aims to clarify the toxic effect and molecular mechanisms of SiNPs in zebrafish embryos based on microarray analysis and bioinformatics analysis. Microarray data analysis demonstrated that SiNP-induced toxicity in zebrafish embryos affected expression of 2515 genes, including 1107 genes that were up-regulated and 1408 genes that were down-regulated. These differentially expressed genes were subjected to bioinformatics analysis for exploring the biological processes triggered by SiNPs in zebrafish embryos. Gene ontology analysis showed that SiNPs caused significant changes in gene expression patterns related to many important functions, including response to stimuli, immune response, cellular processes, and embryonic development. In addition, pathway analysis and Signal-net analysis indicated that the gap junction, vascular smooth muscle contraction, and metabolic pathways, apoptosis, the MAPK signaling pathway, the calcium signaling pathway and the JAK-STAT signaling pathway were the most prominent significant pathways in SiNP-induced toxicity in zebrafish embryos. In addition, the results from qRT-PCR and western blot analysis showed that the IL-6 dependent JAK1/STAT3 signaling pathway was activated by SiNPs in zebrafish embryos. In summary, our data will provide compelling clues for further exploration of SiNP-induced toxicity in zebrafish embryos.

Enhanced immunotherapy of SM5-1 in hepatocellular carcinoma by conjugating with gold nanoparticles and its in vivo bioluminescence tomographic evaluation

SM5-1 is a humanized mouse monoclonal antibody, targeting an over-expressed membrane protein of approximately 230 kDa in hepatocellular carcinoma (HCC). SM5-1 can be used for target therapy in hepatocellular carinoma due to its ability of inhibiting cell growth and inducing apoptosis. However, the tumor inhibition efficacy of SM5-1 in HCC cancer treatment remains low. In this study, we synthesized SM5-1-conjugated gold nanoparticles (Au-SM5-1 NPs) and investigated their anticancer efficacy in HCC both in vitro and in vivo. The tumor inhibition rates of Au-SM5-1 NPs for subcutaneous tumor mice were 40.10% ± 4.34%, 31.37% ± 5.12%, and 30.63% ± 4.87% on day 12, 18, and 24 post-treatment as determined by bioluminescent intensity. In addition, we investigated the antitumor efficacy of Au-SM5-1 NPs in orthotopic HCC tumor models. The results showed that the inhibition rates of Au-SM5-1 NPs can reach up to 39.64% ± 4.87% on day 31 post-treatment determined by the bioluminescent intensity of the abdomen in tumor-bearing mice. Furthermore, three-dimensional reconstruction results of the orthotopic tumor revealed that Au-SM5-1 NPs significantly inhibited tumor growth compared with SM5-1 alone. Our results suggested that the developed Au-SM5-1 NPs has great potential as an antibody-based nano-drug for HCC therapy.

Resveratrol induces apoptosis of human chronic myelogenous leukemia cells in vitro through p38 and JNK-regulated H2AX phosphorylation

AIM

The phosphorylation of histone H2AX, a novel tumor suppressor protein, is involved in regulation of cancer cell apoptosis. The aim of this study was to examine whether H2AX phosphorylation was required for resveratrol-induced apoptosis of human chronic myelogenous leukemia (CML) cells in vitro.

METHODS

K562 cells were tested. Cell apoptosis was analyzed using flow cytometry, and the phosphorylation of H2AX and other signaling proteins was examined with Western blotting. To analyze the signaling pathways, the cells were transfected with lentiviral vectors encoding H2AX-wt or specific siRNAs.

RESULTS

Treatment of K562 cells with resveratrol (20-100 μmol/L) induced apoptosis and phosphorylation of H2AX at Ser139 in time- and dose-dependent manners, but reduced phosphorylation of histone H3 at Ser10. Resveratrol treatment activated two MAPK family members p38 and JNK, and blocked the activation of another MAPK family member ERK. Pretreatment with the p38 inhibitor SB202190 or the JNK inhibitor SP600125 dose-dependently reduced resveratrol-induced phosphorylation of H2AX, which were also observed when the cells were transfected with p38- or JNK-specific siRNAs. Overexpression of H2AX in K562 cells markedly increased resveratrol-induced apoptosis, whereas overexpression of H2AX-139m (Ser139 was mutated to block phosphorylation) inhibited resveratrol-induced apoptosis. K562 cells transfected with H2AX-specific siRNAs were resistant to resveratrol-induced apoptosis.

CONCLUSION

H2AX phosphorylation at Ser139 in human CML cells, which is regulated by p38 and JNK, is essential for resveratrol-induced apoptosis.

H2AX phosphorylation regulated by p38 is involved in Bim expression and apoptosis in chronic myelogenous leukemia cells induced by imatinib

Increasing evidence suggests that histone H2AX plays a critical role in regulation of tumor cell apoptosis and acts as a novel human tumor suppressor protein. However, the action of H2AX in chronic myelogenous leukemia (CML) cells is unknown. The detailed mechanism and epigenetic regulation by H2AX remain elusive in cancer cells. Here, we report that H2AX was involved in apoptosis of CML cells. Overexpression of H2AX increased apoptotic sensitivity of CML cells (K562) induced by imatinib. However, overexpression of Ser139-mutated H2AX (blocking phosphorylation) decreased sensitivity of K562 cells to apoptosis. Similarly, knockdown of H2AX made K562 cells resistant to apoptotic induction. These results revealed that the function of H2AX involved in apoptosis is strictly related to its phosphorylation (Ser139). Our data further indicated that imatinib may stimulate mitogen-activated protein kinase (MAPK) family member p38, and H2AX phosphorylation followed a similar time course, suggesting a parallel response. H2AX phosphorylation can be blocked by p38 siRNA or its inhibitor. These data demonstrated that H2AX phosphorylation was regulated by p38 MAPK pathway in K562 cells. However, the p38 MAPK downstream, mitogen- and stress-activated protein kinase-1 and -2, which phosphorylated histone H3, were not required for H2AX phosphorylation during apoptosis. Finally, we provided epigenetic evidence that H2AX phosphorylation regulated apoptosis-related gene Bim expression. Blocking of H2AX phosphorylation inhibited Bim gene expression. Taken together, these data demonstrated that H2AX phosphorylation regulated by p38 is involved in Bim expression and apoptosis in CML cells induced by imatinib.

Genes responsive to elevated CO2 concentrations in triploid white poplar and integrated gene network analysis

BACKGROUND

The atmospheric CO2 concentration increases every year. While the effects of elevated CO2 on plant growth, physiology and metabolism have been studied, there is now a pressing need to understand the molecular mechanisms of how plants will respond to future increases in CO2 concentration using genomic techniques.

PRINCIPAL FINDINGS

Gene expression in triploid white poplar ((Populus tomentosa ×P. bolleana) ×P. tomentosa) leaves was investigated using the Affymetrix poplar genome gene chip, after three months of growth in controlled environment chambers under three CO2 concentrations. Our physiological findings showed the growth, assessed as stem diameter, was significantly increased, and the net photosynthetic rate was decreased in elevated CO2 concentrations. The concentrations of four major endogenous hormones appeared to actively promote plant development. Leaf tissues under elevated CO2 concentrations had 5,127 genes with different expression patterns in comparison to leaves under the ambient CO2 concentration. Among these, 8 genes were finally selected for further investigation by using randomized variance model corrective ANOVA analysis, dynamic gene expression profiling, gene network construction, and quantitative real-time PCR validation. Among the 8 genes in the network, aldehyde dehydrogenase and pyruvate kinase were situated in the core and had interconnections with other genes.

CONCLUSIONS

Under elevated CO2 concentrations, 8 significantly changed key genes involved in metabolism and responding to stimulus of external environment were identified. These genes play crucial roles in the signal transduction network and show strong correlations with elevated CO2 exposure. This study provides several target genes, further investigation of which could provide an initial step for better understanding the molecular mechanisms of plant acclimation and evolution in future rising CO2 concentrations.

Integrating omics technologies to study pulmonary physiology and pathology at the systems level

Assimilation and integration of "omics" technologies, including genomics, epigenomics, proteomics, and metabolomics has readily altered the landscape of medical research in the last decade. The vast and complex nature of omics data can only be interpreted by linking molecular information at the organismic level, forming the foundation of systems biology. Research in pulmonary biology/medicine has necessitated integration of omics, network, systems and computational biology data to differentially diagnose, interpret, and prognosticate pulmonary diseases, facilitating improvement in therapy and treatment modalities. This review describes how to leverage this emerging technology in understanding pulmonary diseases at the systems level -called a "systomic" approach. Considering the operational wholeness of cellular and organ systems, diseased genome, proteome, and the metabolome needs to be conceptualized at the systems level to understand disease pathogenesis and progression. Currently available omics technology and resources require a certain degree of training and proficiency in addition to dedicated hardware and applications, making them relatively less user friendly for the pulmonary biologist and clinicians. Herein, we discuss the various strategies, computational tools and approaches required to study pulmonary diseases at the systems level for biomedical scientists and clinical researchers.

Epstein-Barr virus essential antigen EBNA3C attenuates H2AX expression

Epstein-Barr virus (EBV) latent antigen EBNA3C is implicated in B-cell immortalization and linked to several B-cell malignancies. Deregulation of H2AX can induce genomic instability with increased chromosomal aberrations, which ultimately leads to tumorigenesis. Here we demonstrated that EBNA3C can attenuate H2AX expression at the transcript and protein levels. A reduction of total H2AX levels was clearly observed upon infection of primary B cells with wild-type EBV but not with EBNA3C knockout recombinant EBV. H2AX also interacted with EBNA3C through its N-terminal domain (residues 1 to 100). Furthermore, H2AX mutated at Ser139 failed to interact with EBNA3C. Luciferase-based reporter assays also revealed that the binding domain of EBNA3C is sufficient for transcriptional inhibition of the H2AX promoter. EBNA3C also facilitated H2AX degradation through recruitment of components of the ubiquitin proteasome pathway. We further demonstrated that knockdown of H2AX in lymphoblastoid cell lines (LCLs) led to the upregulation of the Bub1 oncoprotein and downregulated expression of p53. Overall, our study provides additional insights into EBV-associated B-cell lymphomas, which are linked to the regulation of the DNA damage response system in infected cells. The importance of these insights are as follows: (i) EBNA3C downregulates H2AX expression at the protein and transcript levels in epithelial cells, B cells, and EBV-transformed LCLs, (ii) EBNA3C binds with wild-type H2AX but not with the Ser139 mutant of H2AX, (iii) the N terminus (residues 1 to 100) of EBNA3C is critical for binding to H2AX, (iv) localization of H2AX is predominantly nuclear in the presence of EBNA3C, and (v) H2AX knocked down in LCLs led to enhanced expression of Bub1 and downregulation of the tumor suppressor p53, which are both important for driving the oncogenic process.