Intrahepatic homeobox protein MSX-1 is a novel host restriction factor of hepatitis B virus.

Chronic hepatitis B virus (HBV) infection (CHB) is a risk factor for the development of liver fibrosis, cirrhosis, and hepatocellular carcinoma. Covalently closed circular DNA serves as the sole transcription template for all viral RNAs and viral transcription is driven and enhanced by viral promoter and enhancer elements, respectively. Interactions between transcription factors and these cis-elements regulate their activities and change the production levels of viral RNAs. Here, we report the identification of homeobox protein MSX-1 (MSX1) as a novel host restriction factor of HBV in liver. In both HBV-transfected and HBV-infected cells, MSX1 suppresses viral gene expression and genome replication. Mechanistically, MSX1 downregulates enhancer II/core promoter (EnII/Cp) activity via direct binding to an MSX1 responsive element within EnII/Cp, and such binding competes with hepatocyte nuclear factor 4α binding to EnII/Cp due to partial overlap between their respective binding sites. Furthermore, CHB patients in immune active phase express higher levels of intrahepatic MSX1 but relatively lower levels of serum and intrahepatic HBV markers compared to those in immune tolerant phase. Finally, MSX1 was demonstrated to induce viral clearance in two mouse models of HBV persistence, suggesting possible therapeutic potential for CHB.IMPORTANCECovalently closed circular DNA plays a key role for the persistence of hepatitis B virus (HBV) since it serves as the template for viral transcription. Identification of transcription factors that regulate HBV transcription not only provides insights into molecular mechanisms of viral life cycle regulation but may also provide potential antiviral targets. In this work, we identified host MSX1 as a novel restriction factor of HBV transcription. Meanwhile, we observed higher intrahepatic MSX1 expression in chronic hepatitis B virus (CHB) patients in immune active phase compared to those in immune tolerant phase, suggesting possible involvement of MSX1 in the regulation of HBV activity by the host. Lastly, intrahepatic overexpression of MSX1 delivered by recombinant adenoviruses into two mouse models of HBV persistence demonstrated MSX1-mediated repression of HBV in vivo, and MSX1-induced clearance of intrahepatic HBV DNA in treated mice suggested its potential as a therapeutic target for the treatment of CHB.

Recent Progress in Modular Electrochemical Synthesis of Hydrogen and High-Value-added Chemicals based on Solid Redox Mediator.

Electrochemical synthesis of H2 and high-value-added chemicals is an efficient and cost-effective approach that can be powered using renewable electricity. Compared to a conventional electrochemical production system, the modular electrochemical production system (MEPS) based on a solid redox mediator (SRM) can separate the anodic and cathodic reactions in time and space. The MEPS can avoid the use of membranes and formation of useless products, as well as eliminate the mutual dependence of production rates at anode and cathode. The SRM can temporarily store or release electrons and ions to pair with cathodic and anodic reactions, respectively, in MEPS. Designing of SRMs with large charge capacity and good cyclability is of great significance for constructing a high-performance MEPS. This work summarizes the design principles, recent advances in MEPS based on SRM, and application in redox flow cells. Moreover, structure design strategies as well as in situ characterization techniques and theoretical calculations for SRM is also proposed. It is expected to promote the vigorous development of MEPS based on SRM. Finally, the challenges and perspectives of MEPS based on SRM are discussed.

Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling.

Protein-DNA interactions (PDIs) mediate a broad range of functions essential for cellular differentiation, function, and survival. However, it is still a daunting task to comprehensively identify and profile sequence-specific PDIs in complex genomes. Here, we have used a combined bioinformatics and protein microarray-based strategy to systematically characterize the human protein-DNA interactome. We identified 17,718 PDIs between 460 DNA motifs predicted to regulate transcription and 4,191 human proteins of various functional classes. Among them, we recovered many known PDIs for transcription factors (TFs). We identified a large number of unanticipated PDIs for known TFs, as well as for previously uncharacterized TFs. We also found that over three hundred unconventional DNA-binding proteins (uDBPs)--which include RNA-binding proteins, mitochondrial proteins, and protein kinases--showed sequence-specific PDIs. One such uDBP, ERK2, acts as a transcriptional repressor for interferon gamma-induced genes, suggesting important biological roles for such proteins.

Decreased frequency of a novel T-lymphocyte subset, CD3+ CD4- CD7+ CD57- T cells, in hepatitis B virus-related end-stage liver disease might contribute to disease progression.

CD7 and CD57 are related to the differentiation and functional stages of CD8+ T cells. However, the role of their combined presence in CD8+ T cells in patients with chronic hepatitis B virus (HBV) infection, especially those with end-stage liver disease, remains unclear. Blood samples from healthy volunteers and patients with chronic hepatitis B were analyzed via Luminex assay and ELISA to measure plasma cytokine levels. Further, recombinant IL-22 was used to stimulate peripheral blood mononuclear cells from healthy volunteers, and the frequency of CD3+ CD4- CD7+ CD57- T cells and apoptosis rates were investigated via flow cytometry. Patients with end-stage liver disease, particularly those with acute to chronic liver failure, showed decreased CD3+ CD4- CD7+ CD57- T cell frequency. Furthermore, the prevalence of CD3+ CD4- CD7+ CD57- T cells was negatively correlated with disease severity, prognosis, and complications (ascites). We also observed that IL-22 promoted apoptosis and brought about a decrease in the number of CD3+ CD4- CD7+ CD57- T cells in a dose-dependent manner. CD3+ CD4- CD7+ CD57- T cells displayed a B and T lymphocyte attenuator (BTLA)high CD25high CD127high immunosuppressive phenotype and showed low interferon-γ, tumor necrosis factor-α, granzyme A, and perforin expression levels. The present findings will elucidate the pathogenesis of HBV-related end-stage liver disease and aid the identification of novel drug targets.

Induction of IL-32 in the immune response of keratinocytes to Mycobacterium marinum infection.

Keratinocytes are the predominant cell type in the skin epidermis, and they not only protect the skin from the influence of external physical factors but also function as an immune barrier against microbial invasion. However, little is known regarding the immune defence mechanisms of keratinocytes against mycobacteria. Here, we performed single-cell RNA sequencing (scRNA-seq) on skin biopsy samples from patients with Mycobacterium marinum infection and bulk RNA sequencing (bRNA-seq) on M. marinum-infected keratinocytes in vitro. The combined analysis of scRNA-seq and bRNA-seq data revealed that several genes were upregulated in M. marinum-infected keratinocytes. Further in vitro validation of these genes by quantitative polymerase chain reaction and western blotting assay confirmed the induction of IL-32 in the immune response of keratinocytes to M. marinum infection. Immunohistochemistry also showed the high expression of IL-32 in patients' lesions. These findings suggest that IL-32 induction is a possible mechanism through which keratinocytes defend against M. marinum infection; this could provide new targets for the immunotherapy of chronic cutaneous mycobacterial infections.

Autophagy in Intracerebral Hemorrhage: From Mechanism to Regulation.

Intracerebral hemorrhage (ICH) is the most lethal type of stroke. Secondary injury from ICH determines the recovery, but there is still a lack of effective treatment. The identification of new therapeutic targets may address the current dilemma. The process of autophagy is mediated through the lysosomal pathway and is used to maintain cell homeostasis. Recent studies have advanced our knowledge of autophagy, and in particular its involvement in cell physiology and pathology. Autophagy involves multiple targets and signaling pathways and occurs in many brain cells. It also regulates oxidative stress and inflammation after ICH, both of which are important factors in secondary brain injury. An appropriate level of autophagy is protective in ICH, whereas excessive autophagy may be detrimental. In this review, we discuss the signaling pathways for autophagy in ICH and related factors that provide a theoretical basis for the discovery of new treatment targets.

Bifunctional Al-Doped Cobalt Ferrocyanide Nanocube Array for Energy-Saving Hydrogen Production via Urea Electrolysis.

The very slow anodic oxygen evolution reaction (OER) greatly limits the development of large-scale hydrogen production via water electrolysis. By replacing OER with an easier urea oxidation reaction (UOR), developing an HER/UOR coupling electrolysis system for hydrogen production could save a significant amount of energy and money. An Al-doped cobalt ferrocyanide (Al-Co2Fe(CN)6) nanocube array was in situ grown on nickel foam (Al-Co2Fe(CN)6/NF). Due to the unique nanocube array structure and regulated electronic structure of Al-Co2Fe(CN)6, the as-prepared Al-Co2Fe(CN)6/NF electrode exhibited outstanding catalytic activities and long-term stability to both UOR and HER. The Al-Co2Fe(CN)6/NF electrode needed potentials of 0.169 V and 1.118 V (vs. a reversible hydrogen electrode) to drive 10 mA cm-2 for HER and UOR, respectively, in alkaline conditions. Applying the Al-Co2Fe(CN)6/NF to a whole-urea electrolysis system, 10 mA cm-2 was achieved at a cell voltage of 1.357 V, which saved 11.2% electricity energy compared to that of traditional water splitting. Density functional theory calculations demonstrated that the boosted UOR activity comes from Co sites with Al-doped electronic environments. This promoted and balanced the adsorption/desorption of the main intermediates in the UOR process. This work indicates that Co-based materials as efficient catalysts have great prospects for application in urea electrolysis systems and are expected to achieve low-cost and energy-saving H2 production.

Hepatitis B e antigen induces the expansion of monocytic myeloid-derived suppressor cells to dampen T-cell function in chronic hepatitis B virus infection.

Chronic hepatitis B virus (HBV) infection is associated with functionally impaired virus-specific T cell responses. Although the myeloid-derived suppressor cells (MDSCs) are known to play a critical role in impairing antiviral T cell responses, viral factors responsible for the expansion of MDSCs in chronic hepatitis B (CHB) remain obscure. In order to elucidate the mechanism of monocytic MDSCs (mMDSCs) expansion and T cell function suppression during persistent HBV infection, we analyzed the circulation frequency of mMDSCs in 164 CHB patients and 70 healthy donors, and found that the proportion of mMDSCs in HBeAg (+) CHB patients was significantly increased compared to that in HBeAg (-) patients, which positively correlated with the level of HBeAg. Furthermore, exposure of peripheral blood mononuclear cells (PBMCs) isolated from healthy donors to HBeAg led to mMDSCs expansion and significant upregulation of IL-1ß, IL-6 and indoleamine-2, 3-dioxygenase (IDO), and depletion of the cytokines abrogated HBeAg-induced mMDSCs expansion. Moreover, HBeAg-induced mMDSCs suppressed the autologous T-cell proliferation in vitro, and the purified mMDSCs from HBeAg (+) subjects markedly reduced the proliferation of CD4+ and CD8+ T cells and IFN-γ production, which could be efficiently restored by inhibiting IDO. In summary, HBeAg-induced mMDSCs expansion impairs T cell function through IDO pathway and favors the establishment of a persistent HBV infection, suggesting a mechanism behind the development of HBeAg-induced immune tolerance.

A neutrophil-to-lymphocyte ratio-based prognostic model to predict mortality in patients with HBV-related acute-on-chronic liver failure.

BACKGROUND: Although the Asian Pacific Association for the Study of the Liver acute-on-chronic liver failure (ACLF) research consortium (AARC) ACLF score is easy to use in patients with hepatitis b virus-related ACLF (HBV-ACLF), serum lactate is not routinely tested in primary hospitals, and its value may be affected by some interference factors. Neutrophil-to-lymphocyte ratio (NLR) is used to assess the status of bacterial infection (BI) or outcomes in patients with various diseases. We developed an NLR-based AARC ACLF score and compared it with the existing model. METHODS: A total of 494 HBV-ACLF patients, enrolled in four tertiary academic hospitals in China with 90-day follow-up, were analysed. Prognostic performance of baseline NLR and lactate were compared between cirrhotic and non-cirrhotic subgroups via the receiver operating curve and Kaplan-Meier analyses. A modified AARC ACLF (mAARC ACLF) score using NLR as a replacement for lactate was developed (n = 290) and validated (n = 204). RESULTS: There were significantly higher baseline values of NLR in non-survivors, patients with admission BI, and those with higher grades of ACLF compared with the control groups. Compared with lactate, NLR better reflected BI status in the cirrhotic subgroup, and was more significantly correlated with CTP, MELD, MELD-Na, and the AARC score. NLR was an independent predictor of 90-day mortality, and was categorized into three risk grades (< 3.10, 3.10-4.78, and > 4.78) with 90-day cumulative mortalities of 8%, 21.2%, and 77.5% in the derivation cohort, respectively. The mAARC ACLF score, using the three grades of NLR instead of corresponding levels of lactate, was superior to the other four scores in predicting 90-day mortality in the derivation (AUROC 0.906, 95% CI 0.872-0.940, average P < 0.001) and validation cohorts (AUROC 0.913, 95% CI 0.876-0.950, average P < 0.01), with a considerable performance in predicting 28-day mortality in the two cohorts. CONCLUSIONS: The prognostic value of NLR is superior to that of lactate in predicting short-term mortality risk in cirrhotic and non-cirrhotic patients with HBV-ACLF. NLR can be incorporated into the AARC ACLF scoring system for improving its prognostic accuracy and facilitating the management guidance in patients with HBV-ACLF in primary hospitals.

Oxygen doped MoS2 quantum dots for efficient electrocatalytic hydrogen generation.

In this study, we report an oxygen-doped MoS2 quantum dot (O-MoS2 QD) hybrid electrocatalyst for the hydrogen evolution reaction (HER). The O-MoS2 QDs were prepared with a one-pot microwave method by hydrazine-mediated oxygen-doping. The synthetic method is straightforward, time-saving, and can be applied in large scale preparation. Ultra-small O-MoS2 QDs with the average size of 5.83 nm and 1-4 layers can be uniformly distributed on the surface of reduced graphene oxide (RGO). Benefited from the unique structure and the doping effect of oxygen in the MoS2 QDs and the great number of active sites, the O-MoS2 QD hybrid displayed outstanding electrocatalytic performance toward HER. A low overpotential of 76 mV at 10 mA/cm2 and a Tafel slope of 58 mV/dec were obtained in an acidic solution toward HER. Additionally, the resultant O-MoS2 QD hybrid also exhibited excellent stability and durability toward HER, displaying negligible current density loss after 1000 cycles of cyclic voltammetry. The design and synthesis of the electrocatalyst in this work open up a prospective route to prepare active and stable electrocatalysts toward substituting precious metals for hydrogen generation.

Exonuclease I and III improve the detection efficacy of hepatitis B virus covalently closed circular DNA.

BACKGROUND: Hepatitis B virus covalently closed circular DNA (HBV cccDNA) is an important biomarker of hepatitis B virus infection. However, the current methods are not specific and sensitive. The present study aimed to develop a specific and sensitive assay method for the quantification of HBV cccDNA. METHODS: Exonuclease I (Exo I) & Exonuclease III (Exo III) and specific primer probes are used in real-time PCR. The virus particles isolated from peripheral blood mononuclear cells were used as negative control and HBV1.3 recombinant plasmid 3.2 kb circular DNA fragment was used as positive control. The methods of cccDNA detection were evaluated in cell lines, plasmid, animal model, patient serum and liver biopsies. RESULTS: A linear range of 101-107 copies/assay using specific primers for HBV cccDNA was established. HBV cccDNA were only detected in cell lines, animal model and liver tissue. It cannot be detected in serum samples. Intrahepatic HBV cccDNA level had good correlation with intrahepatic total HBV DNA level (r = 0.765, P < 0.001). CONCLUSIONS: The real-time quantitative PCR is an effective and feasible method for sensitive and specific detection of low copy number of cccDNA. The novel detection method is fast, provides high sensitivity and specificity and can be used in clinical practice.

Differentially Expressed Intrahepatic Genes Contribute to Control of Hepatitis B Virus Replication in the Inactive Carrier Phase.

Background: The natural history of chronic hepatitis B virus (HBV) infection was divided into 4 phases. Patients in the inactive carrier (IC) status and immune tolerant (IT) phase had normal alanine aminotransferase levels but huge different viral loads. The mechanism underlying low viral replication status in IC phase is unknown. Methods: We determined the intrahepatic transcriptomes of 83 chronic hepatitis B patients by microarray analysis of liver biopsies, and screened the effect of differentially regulated genes on HBV replication using specific small interfering RNAs in vitro. Results: The gene profile distinguishing active chronic hepatitis from IT and IC was predominantly composed of immune-related genes. The liver transcriptomes between the IT and IC phase were largely similar, and 109 expressed genes were significantly different. By performing systematic screening, 5 candidate genes including EVA1A, which were expressed at a relative higher level in IC phase than IT, were identified to regulate HBV replication and gene expression in cellular models. Conclusions: The immune-related pathways were up-regulated in the active chronic hepatitis phase but not in the IT and IC phase. A number of intrahepatic genes highly expressed in the IC phase may participate in the control of HBV replication and determine the inactive status of HBV infection.

Mitophagy, a potential therapeutic target for stroke.

Mitochondria autophagy, termed as mitophagy, is a mechanism of specific autophagic elimination of mitochondria. Mitophagy controls the quality and the number of mitochondria, eliminating dysfunctional or excessive mitochondria that can generate reactive oxygen species (ROS) and cause cell death. Mitochondria are centrally implicated in neuron and tissue injury after stroke, due to the function of supplying adenosine triphosphate (ATP) to the tissue, regulating oxidative metabolism during the pathologic process, and contribution to apoptotic cell death after stroke. As a catabolic mechanism, mitophagy links numbers of a complex network of mitochondria, and affects mitochondrial dynamic process, fusion and fission, reducing mitochondrial production of ROS, mediated by the mitochondrial permeability transition pore (MPTP). The precise nature of mitophagy's involvement in stroke, and its underlying molecular mechanisms, have yet to be fully clarified. This review aims to provide a comprehensive overview of the integration of mitochondria with mitophagy, also to introduce and discuss recent advances in the understanding of the potential role, and possible signaling pathway, of mitophagy in the pathological processes of both hemorrhagic and ischemic stroke. The author also provides evidence to explain the dual role of mitophagy in stroke.

Validation and comparison of seventeen noninvasive models for evaluating liver fibrosis in Chinese hepatitis B patients.

BACKGROUND & AIMS: To avoid liver biopsy, many noninvasive models comprised of serum markers for liver fibrosis assessment have been developed. Given that most of them were developed in hepatitis C cohorts and few of them have been validated in Chinese hepatitis B patients, we aim to conduct this validation and compare their diagnostic accuracies in such a population. METHODS: A total of 937 HBV-infected patients who underwent liver biopsy were included in this single-centre retrospective study. The diagnostic accuracies of the 17 noninvasive models were assessed by areas under the receiver-operating characteristic curves (AUROCs), using histologically evaluated fibrotic stages of the biopsy specimens as standards. To compare efficiencies of the models, a grading system based on AUROC levels was developed. RESULTS: For discriminating significant fibrosis in all patients, the best three noninvasive models were King's score (AUROC = 0.756), Virahep-C model (AUROC = 0.756) and GPR (AUROC = 0.744); and for diagnosing cirrhosis, Lok index (AUROC = 0.832), FI (AUROC = 0.820) and FIB-4 (AUROC = 0.818) got the first three places. AUROCs in HBeAg-positive group were generally higher than those in HBeAg-negative group. In addition, based on the grading system, Virahep-C and GPR outstood others in evaluating liver fibrosis in all patients. CONCLUSIONS: In Chinese HBV-infected patients, Virahep-C models and GPR had high accuracies in diagnosing liver fibrosis and cirrhosis, while the most discussed models like APRI and FIB-4 did not outstand. Assessment should take into account the HBeAg sero-status, since these noninvasive models were more appropriate for HBeAg-positive patients than HBeAg-negative ones.

Role of quantitative hepatitis B core antibody levels in predicting significant liver inflammation in chronic hepatitis B patients with normal or near-normal alanine aminotransferase levels.

AIM: Chronic hepatitis B (CHB) patients with normal alanine aminotransferase (ALT) levels are not free from significant hepatic lesions. Recently, there has been an improved understanding of the clinical significance of quantitative hepatitis B core antibody levels (qAnti-HBc) during CHB management. In this cross-sectional study, we evaluated the utility of qAnti-HBc in identifying significant liver inflammation in CHB patients. METHODS: A total of 469 patients (training set, n = 363; validation set, n = 106) who underwent liver biopsy (LB) were included. The qAnti-HBc levels were quantified and the relationship between histology and serum markers was systematically analyzed. RESULTS: In the training set, qAnti-HBc levels were found to have significant diagnostic value for moderate to severe liver inflammation (≥G2) in all patients (area under the receiver operating characteristic curve [AUROC] = 0.768; 95% confidence interval [CI], 0.721-0.810; P < 0.001) and in patients with normal or near-normal ALT levels (AUROC = 0.767; 95% CI, 0.697-0.828; P < 0.001). Our novel index (AC index) for the identification of ≥G2 inflammation, which combined the qAnti-HBc and ALT levels, significantly improved diagnostic performance (AUROC = 0.813; 95% CI, 0.768-0.852) compared to the use of ALT alone (AUROC = 0.779; 95% CI, 0.732-0.821) in all patients. In the validation set, the AC index showed an improved AUROC of 0.890 (95% CI, 0.814-0.942) and 0.867 (95% CI, 0.749-0.943) in all patients and patients with normal ALT levels, respectively. CONCLUSIONS: The qAnti-HBc level predicts significant liver inflammation well, even in patients with normal or near-normal ALT levels. Compared with the conventional ALT level, the AC index is a more reliable non-invasive biomarker for significant liver inflammation in CHB patients.

Effects of konjac glucomannan and acetylated distarch phosphate on the gel properties of pork meat myofibrillar proteins.

The effects of konjac glucomannan (KGM) and acetylated distarch phosphate (ADSP) on properties of pork meat myofibrillar protein (MP) were investigated using rotary rheometer, colorimeter, texture analyzer, Fourier transform infrared spectroscopy (FTIR), scanning electron microscope (SEM) and confocal laser scanning microscope (CLSM). The addition of KGM and ADSP resulted in increase in both storage modulus (G') and water holding capacity. Whiteness of MP gels was not influenced by the addition of KGM or ADSP, but the texture of MP gels changed apparently with the incorporation of KGM or ADSP. The temperature sweep showed that the increase in G' was associated with the gelatinization of ADSP and its synergistic effect with KGM. The FTIR indicated that the addition of KGM and ADSP enhanced the hydrogen bond in the gel system. The addition of KGM and ADSP changed the microstructures of MP gels, indicating the possible interactions among KGM, ADSP and MP. The images of CLSM showed that starch granules filled in the gap in the protein network, meanwhile the KGM evenly dispersed in the protein network structure.

A strategy for evaluating pathway analysis methods.

BACKGROUND: Researchers have previously developed a multitude of methods designed to identify biological pathways associated with specific clinical or experimental conditions of interest, with the aim of facilitating biological interpretation of high-throughput data. Before practically applying such pathway analysis (PA) methods, we must first evaluate their performance and reliability, using datasets where the pathways perturbed by the conditions of interest have been well characterized in advance. However, such 'ground truths' (or gold standards) are often unavailable. Furthermore, previous evaluation strategies that have focused on defining 'true answers' are unable to systematically and objectively assess PA methods under a wide range of conditions. RESULTS: In this work, we propose a novel strategy for evaluating PA methods independently of any gold standard, either established or assumed. The strategy involves the use of two mutually complementary metrics, recall and discrimination. Recall measures the consistency of the perturbed pathways identified by applying a particular analysis method to an original large dataset and those identified by the same method to a sub-dataset of the original dataset. In contrast, discrimination measures specificity-the degree to which the perturbed pathways identified by a particular method to a dataset from one experiment differ from those identifying by the same method to a dataset from a different experiment. We used these metrics and 24 datasets to evaluate six widely used PA methods. The results highlighted the common challenge in reliably identifying significant pathways from small datasets. Importantly, we confirmed the effectiveness of our proposed dual-metric strategy by showing that previous comparative studies corroborate the performance evaluations of the six methods obtained by our strategy. CONCLUSIONS: Unlike any previously proposed strategy for evaluating the performance of PA methods, our dual-metric strategy does not rely on any ground truth, either established or assumed, of the pathways perturbed by a specific clinical or experimental condition. As such, our strategy allows researchers to systematically and objectively evaluate pathway analysis methods by employing any number of datasets for a variety of conditions.

Using Chemical-Induced Gene Expression in Cultured Human Cells to Predict Chemical Toxicity.

Chemical toxicity is conventionally evaluated in animal models. However, animal models are resource intensive; moreover, they face ethical and scientific challenges because the outcomes obtained by animal testing may not correlate with human responses. To develop an alternative method for assessing chemical toxicity, we investigated the feasibility of using chemical-induced genome-wide expression changes in cultured human cells to predict the potential of a chemical to cause specific organ injuries in humans. We first created signatures of chemical-induced gene expression in a vertebral-cancer of the prostate cell line for ∼15,000 chemicals tested in the US National Institutes of Health Library of Integrated Network-Based Cellular Signatures program. We then used the signatures to create naïve Bayesian prediction models for chemical-induced human liver cholestasis, interstitial nephritis, and long QT syndrome. Detailed cross-validation analyses indicated that the models were robust with respect to false positives and false negatives in the samples we used to train the models and could predict the likelihood that chemicals would cause specific organ injuries. In addition, we performed a literature search for drugs and dietary supplements, not formally categorized as causing organ injuries in humans but predicted by our models to be most likely to do so. We found a high percentage of these compounds associated with case reports of relevant organ injuries, lending support to the idea that in vitro cell-based experiments can be used to predict the toxic potential of chemicals. We believe that this approach, combined with a robust technique to model human exposure to chemicals, may serve as a promising alternative to animal-based chemical toxicity assessment.

A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury.

The multifactorial nature of traumatic brain injury (TBI), especially the complex secondary tissue injury involving intertwined networks of molecular pathways that mediate cellular behavior, has confounded attempts to elucidate the pathology underlying the progression of TBI. Here, systems biology strategies are exploited to identify novel molecular mechanisms and protein indicators of brain injury. To this end, we performed a meta-analysis of four distinct high-throughput gene expression studies involving different animal models of TBI. By using canonical pathways and a large human protein-interaction network as a scaffold, we separately overlaid the gene expression data from each study to identify molecular signatures that were conserved across the different studies. At 24 hr after injury, the significantly activated molecular signatures were nonspecific to TBI, whereas the significantly suppressed molecular signatures were specific to the nervous system. In particular, we identified a suppressed subnetwork consisting of 58 highly interacting, coregulated proteins associated with synaptic function. We selected three proteins from this subnetwork, postsynaptic density protein 95, nitric oxide synthase 1, and disrupted in schizophrenia 1, and hypothesized that their abundance would be significantly reduced after TBI. In a penetrating ballistic-like brain injury rat model of severe TBI, Western blot analysis confirmed our hypothesis. In addition, our analysis recovered 12 previously identified protein biomarkers of TBI. The results suggest that systems biology may provide an efficient, high-yield approach to generate testable hypotheses that can be experimentally validated to identify novel mechanisms of action and molecular indicators of TBI.