Deep learning facilitates multi-data type analysis and predictive biomarker discovery in cancer precision medicine.

Cancer progression is linked to gene-environment interactions that alter cellular homeostasis. The use of biomarkers as early indicators of disease manifestation and progression can substantially improve diagnosis and treatment. Large omics datasets generated by high-throughput profiling technologies, such as microarrays, RNA sequencing, whole-genome shotgun sequencing, nuclear magnetic resonance, and mass spectrometry, have enabled data-driven biomarker discoveries. The identification of differentially expressed traits as molecular markers has traditionally relied on statistical techniques that are often limited to linear parametric modeling. The heterogeneity, epigenetic changes, and high degree of polymorphism observed in oncogenes demand biomarker-assisted personalized medication schemes. Deep learning (DL), a major subunit of machine learning (ML), has been increasingly utilized in recent years to investigate various diseases. The combination of ML/DL approaches for performance optimization across multi-omics datasets produces robust ensemble-learning prediction models, which are becoming useful in precision medicine. This review focuses on the recent development of ML/DL methods to provide integrative solutions in discovering cancer-related biomarkers, and their utilization in precision medicine.

CRISP: a deep learning architecture for GC × GC-TOFMS contour ROI identification, simulation and analysis in imaging metabolomics.

Two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) provides a large amount of molecular information from biological samples. However, the lack of a comprehensive compound library or customizable bioinformatics tool is currently a challenge in GC × GC-TOFMS data analysis. We present an open-source deep learning (DL) software called contour regions of interest (ROI) identification, simulation and untargeted metabolomics profiler (CRISP). CRISP integrates multiple customizable deep neural network architectures for assisting the semi-automated identification of ROIs, contour synthesis, resolution enhancement and classification of GC × GC-TOFMS-based contour images. The approach includes the novel aggregate feature representative contour (AFRC) construction and stacked ROIs. This generates an unbiased contour image dataset that enhances the contrasting characteristics between different test groups and can be suitable for small sample sizes. The utility of the generative models and the accuracy and efficacy of the platform were demonstrated using a dataset of GC × GC-TOFMS contour images from patients with late-stage diabetic nephropathy and healthy control groups. CRISP successfully constructed AFRC images and identified over five ROIs to create a deepstacked dataset. The high fidelity, 512 × 512-pixels generative model was trained as a generator with a Fréchet inception distance of <47.00. The trained classifier achieved an AUROC of >0.96 and a classification accuracy of >95.00% for datasets with and without column bleed. Overall, CRISP demonstrates good potential as a DL-based approach for the rapid analysis of 4-D GC × GC-TOFMS untargeted metabolite profiles by directly implementing contour images. CRISP is available at https://github.com/vivekmathema/GCxGC-CRISP.

Predicting lupus membranous nephritis using reduced picolinic acid to tryptophan ratio as a urinary biomarker.

The current gold standard for classifying lupus nephritis (LN) progression is a renal biopsy, which is an invasive procedure. Undergoing a series of biopsies for monitoring disease progression and treatments is unlikely suitable for patients with LN. Thus, there is an urgent need for non-invasive alternative biomarkers that can facilitate LN class diagnosis. Such biomarkers will be very useful in guiding intervention strategies to mitigate or treat patients with LN. Urine samples were collected from two independent cohorts. Patients with LN were classified into proliferative (class III/IV) and membranous (class V) by kidney histopathology. Metabolomics was performed to identify potential metabolites, which could be specific for the classification of membranous LN. The ratio of picolinic acid (Pic) to tryptophan (Trp) ([Pic/Trp] ratio) was found to be a promising candidate for LN diagnostic and membranous classification. It has high potential as an alternative biomarker for the non-invasive diagnosis of LN.

Utility of Plasmodium falciparum DNA from rapid diagnostic test kits for molecular analysis and whole genome amplification.

BACKGROUND: Rapid diagnostic tests (RDTs) have become the most common diagnostic tool for detection of Plasmodium falciparum malaria, in particular in remote areas. RDT blood spots provide a source of parasite DNA for molecular analysis. In this study, the utility of RDTs for molecular analysis and the performance of different methods for whole genome amplification were investigated. METHODS: Positive P. falciparum RDTs were collected from Kayin, Myanmar from August 2014 to January 2016. The RDT samples were stored for 6 months, 9 months, 20 months, 21 months, and 32 months before DNA extraction and subsequent molecular analysis of P. falciparum kelch 13 (pfkelch13) mutations, P. falciparum multidrug resistance 1 (pfmdr1), and P. falciparum plasmepsin 2 (pfplasmepsin2) gene amplification. In addition, performance of four whole genome amplification (WGA) kits were compared, including REPLI-g®, MALBACTM, PicoPLEX®, and GenomePlex®, for which DNA quantity and quality were compared between original DNA and post-WGA products. RESULTS: The proportion of successful amplification of the different molecular markers was similar between blood spots analysed from RDTs stored for 6, 9, 20, 21, or 32 months. Successful amplification was dependent on the molecular markers fragment length (p value < 0.05): 18% for a 1245 bp fragment of pfkelch13, 71% for 364 bp of pfkelch13, 81% for 87 bp of pfmdr1, 81% for 108 bp of pfplasmepsin2. Comparison of the four WGA assay kits showed that REPLI-g®, MALBACTM, and PicoPLEX® increased the quantity of DNA 60 to 750-fold, whereas the ratio of parasite DNA amplification over human DNA was most favourable for MALBAC®. Sequencing results of pfkelch13, P. falciparum chloroquine resistance transporter (pfcrt), P. falciparum dihydrofolate reductase (pfdhfr) and six microsatellite markers assessed from the post-WGA product was the same as from the original DNA. CONCLUSIONS: Blood spots from RDTs are a good source for molecular analysis of P. falciparum, even after storage up to 32 months. WGA of RDT-derived parasite DNA reliably increase DNA quantity with sufficient quality for molecular analysis of resistance markers.

Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi.

Microsatellites can be utilized to explore genotypes, population structure, and other genomic features of eukaryotes. Systematic characterization of microsatellites has not been a focus for several species of Plasmodium, including P. malariae and P. ovale, as the majority of malaria elimination programs are focused on P. falciparum and to a lesser extent P. vivax. Here, five human malaria species (P. falciparum, P. vivax, P. malariae, P. ovale curtisi, and P. knowlesi) were investigated with the aim of conducting in-depth categorization of microsatellites for P. malariae and P. ovale curtisi. Investigation of reference genomes for microsatellites with unit motifs of 1-10 base pairs indicates high diversity among the five Plasmodium species. Plasmodium malariae, with the largest genome size, displays the second highest microsatellite density (1421 No./Mbp; 5% coverage) next to P. falciparum (3634 No./Mbp; 12% coverage). The lowest microsatellite density was observed in P. vivax (773 No./Mbp; 2% coverage). A, AT, and AAT are the most commonly repeated motifs in the Plasmodium species. For P. malariae and P. ovale curtisi, microsatellite-related sequences are observed in approximately 18-29% of coding sequences (CDS). Lysine, asparagine, and glutamic acids are most frequently coded by microsatellite-related CDS. The majority of these CDS could be related to the gene ontology terms "cell parts," "binding," "developmental processes," and "metabolic processes." The present study provides a comprehensive overview of microsatellite distribution and can assist in the planning and development of potentially useful genetic tools for further investigation of P. malariae and P. ovale curtisi epidemiology.

TITLE: Caractéristiques à l'échelle du génome des microsatellites de cinq espèces humaines de Plasmodium, spécialement Plasmodium malariae et P. ovale curtisi. ABSTRACT: Les microsatellites peuvent être utilisés pour explorer les génotypes, la structure de la population et d'autres caractéristiques génomiques des eucaryotes. La caractérisation systématique des microsatellites n'a pas été étudiée pour plusieurs espèces de Plasmodium, dont P. malariae et P. ovale, car la majorité des programmes d'élimination du paludisme se concentrent sur P. falciparum et, dans une moindre mesure, P. vivax. Dans cet article, cinq espèces causant le paludisme humain (P. falciparum, P. vivax, P. malariae, P. ovale curtisi et P. knowlesi) ont été étudiées dans le but de procéder à une catégorisation approfondie des microsatellites pour P. malariae et P. ovale curtisi. L'étude des génomes de référence pour les microsatellites avec des motifs unitaires de 1 à 10 paires de bases indique une grande diversité parmi les cinq espèces de Plasmodium. Plasmodium malariae, avec la plus grande taille de génome, affiche la deuxième densité de microsatellites la plus élevée (1421 No./Mpb ; 5 % de couverture) après P. falciparum (3634 No./Mpb ; 12 % de couverture). La plus faible densité de microsatellites a été observée chez P. vivax (773 No./Mpb ; 2 % de couverture). A, AT et AAT sont les motifs les plus fréquemment répétés chez les espèces de Plasmodium. Pour P. malariae et P. ovale curtisi, des séquences liées aux microsatellites sont observées dans environ 18 à 29 % des séquences codantes (CDS). La lysine, l'asparagine et les acides glutamiques sont les plus souvent codés par les CDS liés aux microsatellites. La majorité de ces CDS pourrait être liée aux termes d'ontologie génétique « parties cellulaires ¼, « liaison ¼, « processus de développement ¼ et « processus métaboliques ¼. Cette étude fournit un aperçu complet de la distribution des microsatellites et peut aider à la planification et au développement d'outils génétiques potentiellement utiles pour une étude plus approfondie de l'épidémiologie de P. malariae et P. ovale curtisi.

Molecular characterization of Plasmodium falciparum antifolate resistance markers in Thailand between 2008 and 2016.

BACKGROUND: Resistance to anti-malarials is a major threat to the control and elimination of malaria. Sulfadoxine-pyrimethamine (SP) anti-malarial treatment was used as a national policy for treatment of uncomplicated falciparum malaria in Thailand from 1973 to 1990. In order to determine whether withdrawal of this antifolate drug has led to restoration of SP sensitivity, the prevalence of genetic markers of SP resistance was assessed in historical Thai samples. METHODS: Plasmodium falciparum DNA was collected from the Thailand-Myanmar, Thailand-Malaysia and Thailand-Cambodia borders during 2008-2016 (N = 233). Semi-nested PCR and nucleotide sequencing were used to assess mutations in Plasmodium falciparum dihydrofolate reductase (pfdhfr), P. falciparum dihydropteroate synthase (pfdhps). Gene amplification of Plasmodium falcipaurm GTP cyclohydrolase-1 (pfgch1) was assessed by quantitative real-time PCR. The association between pfdhfr/pfdhps mutations and pfgch1 copy numbers were evaluated. RESULTS: Mutations in pfdhfr/pfdhsp and pfgch1 copy number fluctuated overtime through the study period. Altogether, 14 unique pfdhfr-pdfhps haplotypes collectively containing quadruple to octuple mutations were identified. High variation in pfdhfr-pfdhps haplotypes and a high proportion of pfgch1 multiple copy number (51% (73/146)) were observed on the Thailand-Myanmar border compared to other parts of Thailand. Overall, the prevalence of septuple mutations was observed for pfdhfr-pfdhps haplotypes. In particular, the prevalence of pfdhfr-pfdhps, septuple mutation was observed in the Thailand-Myanmar (50%, 73/146) and Thailand-Cambodia (65%, 26/40) border. In Thailand-Malaysia border, majority of the pfdhfr-pfdhps haplotypes transaction from quadruple (90%, 9/10) to quintuple (65%, 24/37) during 2008-2016. Within the pfdhfr-pfdhps haplotypes, during 2008-2013 the pfdhps A/S436F mutation was observed only in Thailand-Myanmar border (9%, 10/107), while it was not identified later. In general, significant correlation was observed between the prevalence of pfdhfr I164L (ϕ = 0.213, p-value = 0.001) or pfdhps K540E/N (ϕ = 0.399, p-value ≤ 0.001) mutations and pfgch1 gene amplification. CONCLUSIONS: Despite withdrawal of SP as anti-malarial treatment for 17 years, the border regions of Thailand continue to display high prevalence of antifolate and anti-sulfonamide resistance markers in falciparum malaria. Significant association between pfgch1 amplification and pfdhfr (I164L) or pfdhps (K540E) resistance markers were observed, suggesting a compensatory mutation.

Polymorphic markers for identification of parasite population in Plasmodium malariae.

BACKGROUND: Molecular genotyping in Plasmodium serves many aims including providing tools for studying parasite population genetics and distinguishing recrudescence from reinfection. Microsatellite typing, insertion-deletion (INDEL) and single nucleotide polymorphisms is used for genotyping, but only limited information is available for Plasmodium malariae, an important human malaria species. This study aimed to provide a set of genetic markers to facilitate the study of P. malariae population genetics. METHODS: Markers for microsatellite genotyping and pmmsp1 gene polymorphisms were developed and validated in symptomatic P. malariae field isolates from Myanmar (N = 37). Fragment analysis was used to determine allele sizes at each locus to calculate multiplicity of infections (MOI), linkage disequilibrium, heterozygosity and construct dendrograms. Nucleotide diversity (π), number of haplotypes, and genetic diversity (Hd) were assessed and a phylogenetic tree was constructed. Genome-wide microsatellite maps with annotated regions of newly identified markers were constructed. RESULTS: Six microsatellite markers were developed and tested in 37 P. malariae isolates which showed sufficient heterozygosity (0.530-0.922), and absence of linkage disequilibrium (IAS=0.03, p value > 0.05) (N = 37). In addition, a tandem repeat (VNTR)-based pmmsp1 INDEL polymorphisms marker was developed and assessed in 27 P. malariae isolates showing a nucleotide diversity of 0.0976, haplotype gene diversity of 0.698 and identified 14 unique variants. The size of VNTR consensus repeat unit adopted as allele was 27 base pairs. The markers Pm12_426 and pmmsp1 showed greatest diversity with heterozygosity scores of 0.920 and 0.835, respectively. Using six microsatellites markers, the likelihood that any two parasite strains would have the same microsatellite genotypes was 8.46 × 10-4 and was further reduced to 1.66 × 10-4 when pmmsp1 polymorphisms were included. CONCLUSIONS: Six novel microsatellites genotyping markers and a set of pmmsp1 VNTR-based INDEL polymorphisms markers for P. malariae were developed and validated. Each marker could be independently or in combination employed to access genotyping of the parasite. The newly developed markers may serve as a useful tool for investigating parasite diversity, population genetics, molecular epidemiology and for distinguishing recrudescence from reinfection in drug efficacy studies.

OSTRFPD: Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer.

Microsatellite mining is a common outcome of the in silico approach to genomic studies. The resulting short tandemly repeated DNA could be used as molecular markers for studying polymorphism, genotyping and forensics. The omni short tandem repeat finder and primer designer (OSTRFPD) is among the few versatile, platform-independent open-source tools written in Python that enables researchers to identify and analyse genome-wide short tandem repeats in both nucleic acids and protein sequences. OSTRFPD is designed to run either in a user-friendly fully featured graphical interface or in a command line interface mode for advanced users. OSTRFPD can detect both perfect and imperfect repeats of low complexity with customisable scores. Moreover, the software has built-in architecture to simultaneously filter selection of flanking regions in DNA and generate microsatellite-targeted primers implementing the Primer3 platform. The software has built-in motif-sequence generator engines and an additional option to use the dictionary mode for custom motif searches. The software generates search results including general statistics containing motif categorisation, repeat frequencies, densities, coverage, guanine-cytosine (GC) content, and simple text-based imperfect alignment visualisation. Thus, OSTRFPD presents users with a quick single-step solution package to assist development of microsatellite markers and categorise tandemly repeated amino acids in proteome databases. Practical implementation of OSTRFPD was demonstrated using publicly available whole-genome sequences of selected Plasmodium species. OSTRFPD is freely available and open-sourced for improvement and user-specific adaptation.

Polymorphisms in Pvkelch12 and gene amplification of Pvplasmepsin4 in Plasmodium vivax from Thailand, Lao PDR and Cambodia.

BACKGROUND: Mutations in Pfkelch13 and Pfplasmepsin2/3 gene amplification are well-established markers for artemisinin and piperaquine resistance in Plasmodium falciparum, a widespread problem in the Greater Mekong Subregion (GMS). The Plasmodium vivax parasite population has experienced varying drug pressure dependent on local drug policies. We investigated the correlation between drug pressure from artemisinins and piperaquine and mutations in the P. vivax orthologous genes Pvkelch12 and Pvplasmepsin4 (Pvpm4), as candidate resistance markers. METHODS: Blood samples from 734 P. vivax patients were obtained from Thailand (n = 399), Lao PDR (n = 296) and Cambodia (n = 39) between 2007 and 2017. Pvkelch12 and Pvpm4 was amplified and sequenced to assess gene mutations. To assess PvPM4 gene amplification, a Taqman® Real-Time PCR method was developed and validated. Selection of non-synonymous mutations was assessed by its ratio with synonymous mutations (Ka/Ks ratios). Mutation rates were compared to the estimated local drug pressure. RESULTS: Polymorphisms in Pvkelch12 were rare. Pvkelch12 mutations V552I, K151Q and M124I were observed in 1.0% (7/734) of P. vivax samples. V552I was the most common mutation with a frequency of 0.7% (5/734), most of which (4/5) observed in Ubon Ratchathani, Thailand. Polymorphisms in Pvpm4 were more common, with a frequency of 40.3% (123/305) in 305 samples from Thailand, Lao PDR and Cambodia, but this was not related to the estimated piperaquine drug pressure in these areas (Pearson's χ2 test, p = 0.50). Pvpm4 mutation V165I was most frequent in Tak, Thailand (40.2%, 43/107) followed by Pailin, Cambodia (43.5%, 37/85), Champasak, Lao PDR (40.4%, 23/57) and Ubon Ratchathani, Thailand (35.7%, 20/56). Pvpm4 amplification was not observed in 141 samples from Thailand and Cambodia. For both Pvkelch12 and Pvpm4, in all areas and at all time points, the Ka/Ks values were < 1, suggesting no purifying selection. CONCLUSIONS: A novel real-time PCR-based method to assess P. vivax Pvpm4 gene amplification was developed. Drug pressure with artemisinins and piperaquine in the GMS was not clearly related to signatures of selection for mutations in the P. vivax orthologous resistance genes Pvkelch12 and Pvpm4 in areas under investigation. Current resistance of P. vivax to these drugs is unlikely and additional observations including analysis of associated clinical data from these regions could further clarify current findings.

Regulatory roles of brain-specific angiogenesis inhibitor 1(BAI1) protein in inflammation, tumorigenesis and phagocytosis: A brief review.

Brain-specific angiogenesis inhibitor (BAI) family of proteins are basically putative G-protein-coupled receptors with wide spectrum of cellular activities. These BAIs exhibit intricate and complex nature of modulatory activities that researchers are only now beginning to understand. Here we mainly focus on the regulatory activities of a prominent member of BAI family, BAI1, with respect to its role in inflammation, tumorigenesis and phagocytosis. The emerging knowledge on cell- and site-specific function of BAI1 makes it both versatile and promising candidate for studies relating to cancer and host immune response. This review collectively specifies and comprehends important findings of BAI1 from several studies and provides latest insight to explore its properties for possible biomedical therapeutics.

A brief review on biomarkers and proteomic approach for malaria research.

Malaria remains as one of the significant health threat to people living in countries throughout tropical and subtropical zones. Proteomic studies of Plasmodium, the protozoan causing malaria, is essential for understanding its cellular structure, growth stage-specific expression of protein metabolites and complex interaction with host. In-depth knowledge of the pathogen is required for identification of novel biomarkers that can be utilized to develop diagnostic tests and therapeutic antimalarial drugs. The alarming rise in drug-resistant strains of Plasmodium has created an urgent need to identify new targets for drug development that can act by obstructing life cycle of this parasite. In the present review, we briefly discuss on role of various biomarkers including Plasmodium-associated aldolase, histidine-rich proteins and lactate dehydrogenase for diagnosis of malaria. Here we also summarize the present and future prospects of currently used techniques in proteomic approaches such as two dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) for diagnosis and potential identification of novel proteins for malaria research.

Current insights on cholangiocarcinoma research: a brief review.

Colangiocarcinoma (CCA) is a progressively fatal disease which generally occurs due to malignant transformation of hepatic biliary cholangiocytes. The incidence of CCA has been increasing worldwide and there is an urgent requirement for effective diagnosis and treatment strategies against this devastating disease. Different factors including liver-fluke infestation, viral hepatitis, exogenous nitrosamine-mediated DNA damage, and chronic inflammation have been linked to CCA genesis. However, the risk factors and underlying complex mechanisms leading to development of CCA are not sufficiently understood to devise an effective targeted treatment therapy. In this review, we summarize currently known epidemiological and pathological aspects of the disease and briefly describe various potential biomarkers and experimental anticancer phytochemicals related to CCA research. In addition, we also sum up recent findings that link chronic inflammation of hepatic biliary cholangiocytes with CCA. The collective information concisely presented in this article would provide useful insights into the current understanding of this cancer.

Octaphlorethol A inhibits the CpG-induced inflammatory response by attenuating the mitogen-activated protein kinase and NF-κB pathways.

Octaphlorethol A is a phenolic compound isolated from the marine alga Ishige foliacea. In the present study, we investigated the anti-inflammatory activity of octaphlorethol A in CpG-stimulated primary murine bone marrow-derived macrophages and dendritic cells. It exhibited anti-inflammatory activity by regulating the mitogen-activated protein kinase and NF-κB pathways.

Inhibitory effects of oleanane-type triterpenes and saponins from the stem bark of Kalopanax pictus on LPS-stimulated pro-inflammatory cytokine production in bone marrow-derived dendritic cells.

Kalopanax pictus (Araliaceae) is a deciduous tree distributed in Korea, Japan, and China. The stem bark of K. pictus has been functionally used as a traditional crude drug for the treatment of various inflammatory diseases. In the present study, we describe the inhibitory effects of oleanane-type triterpenes and saponins isolated from the stem bark of K. pictus on production of pro-inflammatory cytokines in LPS-stimulated bone marrow-derived dendritic cells. Of the compounds tested, 16,23,29-trihydroxy-3-oxo-olean-12-en-28-oic acid (1), 4,23,29-trihydroxy-3,4-seco-olean-12-en-3-oate-28-oic acid (2), 3ß,6ß,23-trihydroxyolean-12-en-28-oic acid 28-O-ß-D-glucopyranoside (3), nipponogenin E (6), 3ß,6ß,23-trihydroxyolean-12-en-28-oic acid (7), and caulophyllogenin (19) significantly inhibited the production of IL-12 p40 and IL-6 with IC50 values ranging from 3.3 to 9.1 µM. Compounds 2, 3, 7, and 19 significantly suppressed the secretion of TNF-α with IC50 ranging from 8.8 to 20.0 µM. These data provide scientific support for the use of K. pictus stem bark and its triterpene and saponin components in the inhibition of pro-inflammatory cytokine secretion, including IL-12 p40, IL-6, and TNF-α, and for prevention and treatment of inflammatory diseases.

Inhibition of cell death of bone marrow-derived macrophages infected with Ehrlichia muris.

Ehrlichia muris is a Gram-negative obligate intracellular bacterium belonging to the family Anaplasmataceae. It preferentially replicates inside macrophages by utilizing nutrients and processes of the host cell. In the present article, we studied the effects of E. muris infection on cell death of bone marrow-derived macrophages (BMDMs). Primary BMDMs were used for accessing E. muris-induced cell death, pro-inflammatory cytokine production and Western blot analysis. Human embryonic kidney cell line 293T (HEK293T) was used to access nuclear factor-kappaB (NF-κB) activity. BMDMs infected with E. muris showed significant inhibition of cell death when compared to uninfected cells. E. muris infection resulted in IκBα degradation, thus activation of NF-κB. In NF-κB reporter gene assay, the HEK293T cells infected with E. muris exhibited robust NF-κB-dependent luciferase activity in a bacterial dose-dependent manner. Furthermore, E. muris-induced inhibition of BMDMs cell death was abolished in the presence of MG132, a proteasome inhibitor that blocks NF-κB activation. Taken together, the results suggest that E. muris infection of BMDMs may have an inhibitory effect on cell death via a mechanism dependent on NF-κB activation.

Inhibitory effects of Carpinus tschonoskii leaves extract on CpG-stimulated pro-inflammatory cytokine production in murine bone marrow-derived macrophages and dendritic cells.

This report describes the anti-inflammatory effects of MeOH extract from leaves of Carpinus tschonoskii (CE) on primary bone marrow-derived macrophage (BMDMs) and dendritic cells (BMDCs). Primary BMDMs and BMDCs were used for pro-inflammatory cytokine production and Western blot analysis. Human embryonic kidney cell line 293 T (HEK293 T) was used to access NF-κB activity. In all cases, CpG DNA was used to stimulate the cells. The CE (0-150 µg/ml) was treated to BMDMs, BMDCs, and HEK293T cells. CE pre-treatment in CpG-stimulated BMDMs and BMDCs showed a dose-dependent inhibitory effect on pro-inflammatory cytokine (e.g., IL-12 p40, IL-6, and TNF-α) production as compared to non-treated controls. The CE pre-treatment had no significant inhibition on mitogen-activated protein kinases (MAPKs) phosphorylation but strongly inhibited IκBα degradation. In NF-κB reporter gene assay, the CE pre-treatment inhibited NF-κB-dependent luciferase activity in a dose-dependent manner. Taken together, these data suggest that CE has significant inhibitory effect on pro-inflammatory cytokine production and warrant further studies concerning potentials of CE for medicinal uses.

Labdane-type diterpenoids from the rhizomes of Hedychium coronarium inhibit lipopolysaccharide-stimulated production of pro-inflammatory cytokines in bone marrow-derived dendritic cells.

The rhizomes of Hedychium coronarium have been used for the treatment of inflammation, skin diseases, headache, and sharp pain due to rheumatism in traditional medicine. From this plant, two new labdanes, 15-methoxylabda-8(17),11E,13-trien-16,15-olide (1) and 16-methoxylabda-8(17),11E,13-trien-15,16-olide (3), named hedycoronens A and B, as well as four known, labda-8(17),11,13-trien-16,15-olide (2), 16-hydroxylabda-8(17),11,13-trien-15,16-olide (4), coronarin A (5), and corronarin E (6) were isolated. Their chemical structures were elucidated by mass, 1D- and 2D-nuclear magnetic resonance (NMR) spectroscopy. They were evaluated for inhibitory effects on the lipopolysaccharide (LPS)-stimulated production of pro-inflammatory cytokines in bone marrow-derived dendritic cells. Among of them, compounds 1-3 were potent inhibitors of LPS-stimulated interleukin-6 (IL-6) and IL-12 p40, with IC(50) ranging from 4.1±0.2 to 9.1±0.3 µM. Compounds 1 and 3 showed moderate inhibitory activity on the tumor necrosis factor-α (TNF-α) production with IC(50) values of 46.0±1.3 and 12.7±0.3 µM. The remains of compounds showed inactivity. These results warrant further studies concerning the potential anti-inflammatory benefits of labdane-diterpenes from H. coronarium.

Inhibitor of growth-4 mediates chromatin modification and has a suppressive effect on tumorigenesis and innate immunity.

Inhibitor of growth-4 (ING4) is a member of the ING family and acts as a tumor suppressor protein. ING4 is a promising candidate for cancer research due to its anti-angiogenic function and its role in the inhibition of cell migration, cell cycle, and induction of apoptosis. Interaction of this protein with the histone acetyl transferase complex plays a vital role in the regulation of multiple nuclear factor kappa light chain enhancer of activated B cells response elements and thus in the regulation of innate immunity. Splice variants of ING4 have different binding affinities to target sites, which results in the enhancement of its functional diversity. ING4 is among the few known regulatory proteins that can directly interact with chromatin as well as with transcription factors. The influence of ING4 on tumor necrosis factor-α, keratinocyte chemoattractant, interleukin (IL)-6, IL-8, matrix metalloproteinases, cyclooxygenase-2, and IκBα expression clearly demonstrates its critical role in the regulation of inflammatory mediators. Its interaction with liprin α1 and p53 contribute to mitigate cell spreading and induce apoptosis of cancer cells. Multiple factors including breast cancer melanoma suppressor-1 are upstream regulators of ING4 and are frequently deactivated in tumor cells. In the present review, the different properties of ING4 are discussed, and its activities are correlated with different aspects of cell physiology. Special emphasis is placed on our current understanding of ING4 with respect to its influence on chromatin modification, tumorigenesis, and innate immunity.

Parthenolide, a sesquiterpene lactone, expresses multiple anti-cancer and anti-inflammatory activities.

Parthenolide, a naturally occurring sesquiterpene lactone derived from feverfew (Tanacetum parthenium), exhibits exceptional anti-cancer and anti-inflammatory properties, making it a prominent candidate for further studies and drug development. In this review, we briefly investigate molecular events and cell-specific activities of this chemical in relation to cytochrome c, nuclear factor kappa-light-chain enhancer of activated B cells (NF-κB), signal transduction and activation of transcription (STAT), reactive oxygen species (ROS), TCP, HDACs, microtubules, and inflammasomes. This paper reports that parthenolide shows strong NF-κB- and STAT-inhibition-mediated transcriptional suppression of pro-apoptotic genes. This compound acts both at the transcriptional level and by direct inhibition of associated kinases (IKK-ß). Similarly, this review discusses parthenolide-induced ROS-mediated apoptosis of tumor cells via the intrinsic apoptotic signaling pathway. The unique ability of this compound to not harm normal cells but at the same time induce sensitization to extrinsic as well as intrinsic apoptosis signaling in cancer cells provides an important, novel therapeutic strategy for treatment of cancer and inflammation-related disorders.

Chemical constituents of the rhizomes of Hedychium coronarium and their inhibitory effect on the pro-inflammatory cytokines production LPS-stimulated in bone marrow-derived dendritic cells.

The rhizomes of Hedychium coronarium have been used for the treatment of inflammation, skin diseases, headache, and sharp pain due to rheumatism in traditional medicine. From this plant, three new labdane-type diterpenes 1-3, named coronarins G-I as well as seven known 4-10, coronarin D, coronarin D methyl ether, hedyforrestin C, (E)-nerolidol, ß-sitosterol, daucosterol, and stigmasterol were isolated. Their chemical structures were elucidated by mass, 1D- and 2D-nuclear magnetic resonance spectroscopy. They were evaluated for inhibitory effects on lipopolysaccharide-stimulated production of pro-inflammatory cytokines in bone marrow-derived dendritic cells. Among of them, compounds 1, 2, and 6 were significant inhibitors of LPS-stimulated TNF-α, IL-6, and IL-12 p40 productions with IC(50) ranging from 0.19±0.11 to 10.38±2.34 µM. The remains of compounds showed inactivity or due to cytotoxicity. These results warrant further studies concerning the potential anti-inflammatory benefits of labdane-type diterpenes from H. coronarium.