ABSTRACT
Variation in gene expression levels is pervasive among individuals and races or varieties, and has substantial agronomic consequences, for example, by contributing to hybrid vigor. Gene expression level variation results from mutations in regulatory sequences (cis) and/or transcription factor (TF) activity (trans), but the mechanisms underlying cis- and/or trans-regulatory variation of complex phenotypes remain largely unknown. Here, we investigated gene expression variation mechanisms underlying the differential accumulation of the insecticidal compounds maysin and chlorogenic acid in silks of widely used maize (Zea mays) inbreds, B73 and A632. By combining transcriptomics and cistromics, we identified 1,338 silk direct targets of the maize R2R3-MYB TF Pericarp color1 (P1), consistent with it being a regulator of maysin and chlorogenic acid biosynthesis. Among these P1 targets, 464 showed allele-specific expression (ASE) between B73 and A632 silks. Allelic DNA-affinity purification sequencing identified 34 examples in which P1 allelic specific binding (ASB) correlated with cis-expression variation. From previous yeast one-hybrid studies, we identified 9 TFs potentially implicated in the control of P1 targets, with ASB to 83 out of 464 ASE genes (cis) and differential expression of 4 out of 9 TFs between B73 and A632 silks (trans). These results provide a molecular framework for understanding universal mechanisms underlying natural variation of gene expression levels, and how the regulation of metabolic diversity is established.
Subject(s)
Gene Expression Regulation, Plant , Plant Proteins , Zea mays , Zea mays/genetics , Zea mays/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Transcription Factors/metabolism , Transcription Factors/genetics , Alleles , Chlorogenic Acid/metabolism , Phenotype , Genetic VariationABSTRACT
Basic helix-loop-helix (bHLH) proteins are one of the largest families of transcription factor (TF) in eukaryotes, and ~30% of all flowering plants' bHLH TFs contain the aspartate kinase, chorismate mutase, and TyrA (ACT)-like domain at variable distances C-terminal from the bHLH. However, the evolutionary history and functional consequences of the bHLH/ACT-like domain association remain unknown. Here, we show that this domain association is unique to the plantae kingdom with green algae (chlorophytes) harboring a small number of bHLH genes with variable frequency of ACT-like domain's presence. bHLH-associated ACT-like domains form a monophyletic group, indicating a common origin. Indeed, phylogenetic analysis results suggest that the association of ACT-like and bHLH domains occurred early in Plantae by recruitment of an ACT-like domain in a common ancestor with widely distributed ACT DOMAIN REPEAT (ACR) genes by an ancestral bHLH gene. We determined the functional significance of this association by showing that Chlamydomonas reinhardtii ACT-like domains mediate homodimer formation and negatively affect DNA binding of the associated bHLH domains. We show that, while ACT-like domains have experienced faster selection than the associated bHLH domain, their rates of evolution are strongly and positively correlated, suggesting that the evolution of the ACT-like domains was constrained by the bHLH domains. This study proposes an evolutionary trajectory for the association of ACT-like and bHLH domains with the experimental characterization of the functional consequence in the regulation of plant-specific processes, highlighting the impacts of functional domain coevolution.
Subject(s)
Basic Helix-Loop-Helix Transcription Factors , Plants , Basic Helix-Loop-Helix Transcription Factors/metabolism , Phylogeny , Plants/genetics , Transcription Factors/metabolism , Helix-Loop-Helix MotifsABSTRACT
Plants respond to wounding stress by changing gene expression patterns and inducing the production of hormones including jasmonic acid. This wounding transcriptional response activates specialized metabolism pathways such as the glucosinolate pathways in Arabidopsis thaliana. While the regulatory factors and sequences controlling a subset of wound-response genes are known, it remains unclear how wound response is regulated globally. Here, we how these responses are regulated by incorporating putative cis-regulatory elements, known transcription factor binding sites, in vitro DNA affinity purification sequencing, and DNase I hypersensitive sites to predict genes with different wound-response patterns using machine learning. We observed that regulatory sites and regions of open chromatin differed between genes upregulated at early and late wounding time-points as well as between genes induced by jasmonic acid and those not induced. Expanding on what we currently know, we identified cis-elements that improved model predictions of expression clusters over known binding sites. Using a combination of genome editing, in vitro DNA-binding assays, and transient expression assays using native and mutated cis-regulatory elements, we experimentally validated four of the predicted elements, three of which were not previously known to function in wound-response regulation. Our study provides a global model predictive of wound response and identifies new regulatory sequences important for wounding without requiring prior knowledge of the transcriptional regulators.
Subject(s)
Arabidopsis/physiology , Gene Expression Regulation, Plant , Plant Growth Regulators/physiology , Arabidopsis/drug effects , Arabidopsis/genetics , Cyclopentanes/pharmacology , Metabolic Networks and Pathways , Models, Biological , Oxylipins/pharmacology , Plant Growth Regulators/pharmacology , Plants, Genetically Modified , Regulatory Sequences, Nucleic Acid , Reproducibility of Results , Transcription Factors/geneticsABSTRACT
Camelina (Camelina sativa) is an annual oilseed plant that is gaining momentum as a biofuel cover crop. Understanding gene regulatory networks is essential to deciphering plant metabolic pathways, including lipid metabolism. Here, we take advantage of a growing collection of gene expression datasets to predict transcription factors (TFs) associated with the control of Camelina lipid metabolism. We identified approximately 350 TFs highly co-expressed with lipid-related genes (LRGs). These TFs are highly represented in the MYB, AP2/ERF, bZIP, and bHLH families, including a significant number of homologs of well-known Arabidopsis lipid and seed developmental regulators. After prioritizing the top 22 TFs for further validation, we identified DNA-binding sites and predicted target genes for 16 out of the 22 TFs tested using DNA affinity purification followed by sequencing (DAP-seq). Enrichment analyses of targets supported the co-expression prediction for most TF candidates, and the comparison to Arabidopsis revealed some common themes, but also aspects unique to Camelina. Within the top potential lipid regulators, we identified CsaMYB1, CsaABI3AVP1-2, CsaHB1, CsaNAC2, CsaMYB3, and CsaNAC1 as likely involved in the control of seed fatty acid elongation and CsaABI3AVP1-2 and CsabZIP1 as potential regulators of the synthesis and degradation of triacylglycerols (TAGs), respectively. Altogether, the integration of co-expression data and DNA-binding assays permitted us to generate a high-confidence and short list of Camelina TFs involved in the control of lipid metabolism during seed development.
Subject(s)
Arabidopsis , Brassicaceae , Arabidopsis/genetics , Brassicaceae/genetics , Humans , Lipid Metabolism/genetics , Seeds/metabolism , Triglycerides/metabolismABSTRACT
About a third of the plant basic helix-loop-helix (bHLH) transcription factors harbor a C-terminal aspartate kinase, chorismate mutase, and TyrA (ACT)-like domain, which was originally identified in the maize R regulator of anthocyanin biosynthesis, where it modulates the ability of the bHLH to dimerize and bind DNA. Characterization of other bHLH ACT-like domains, such as the one in the Arabidopsis R ortholog, GL3, has not definitively confirmed dimerization, raising the question of the overall role of this potential regulatory domain. To learn more, we compared the dimerization of the ACT-like domains of R (RACT) and GL3 (GL3ACT). We show that RACT dimerizes with a dissociation constant around 100 nM, over an order of magnitude stronger than GL3ACT. Structural predictions combined with mutational analyses demonstrated that V568, located in a hydrophobic pocket in RACT, is important: when mutated to the Ser residue present in GL3ACT, dimerization affinity dropped by almost an order of magnitude. The converse S595V mutation in GL3ACT significantly increased the dimerization strength. We cloned and assayed dimerization for all identified maize ACT-like domains and determined that 12 of 42 formed heterodimers in yeast two-hybrid assays, irrespective of whether they harbored V568, which was often replaced by other aliphatic amino acids. Moreover, we determined that the presence of polar residues at that position occurs only in a small subset of anthocyanin regulators. The combined results provide new insights into possibly regulatory mechanisms and suggest that many of the other plant ACT-like domains associate to modulate fundamental cellular processes.
Subject(s)
Arabidopsis Proteins/chemistry , Arabidopsis Proteins/metabolism , Basic Helix-Loop-Helix Transcription Factors/chemistry , Basic Helix-Loop-Helix Transcription Factors/metabolism , Hydrophobic and Hydrophilic Interactions , Protein Multimerization , Arabidopsis , Models, Molecular , Protein Domains , Protein Stability , Protein Structure, QuaternaryABSTRACT
BACKGROUND: Pancreatic cancer has highly aggressive features, such as local recurrence that leads to significantly high morbidity and mortality and recurrence after successful tumour resection. Intraoperative radiation therapy (IORT), which delivers targeted radiation to a tumour bed, is known to reduce local recurrence by directly killing tumour cells and modifying the tumour microenvironment. METHODS: Among 30 patients diagnosed with pancreatic cancer, 17 patients received IORT immediately after surgical resection. We investigated changes in the immune response induced by IORT by analysing the peritoneal fluid (PF) and blood of patients with and without IORT treatment after pancreatic cancer surgery. Further, we treated three pancreatic cell lines with PF to observe proliferation and activity changes. RESULTS: Levels of cytokines involved in the PI3K/SMAD pathway were increased in the PF of IORT-treated patients. Moreover, IORT-treated PF inhibited the growth, migration, and invasiveness of pancreatic cancer cells. Changes in lymphocyte populations in the blood of IORT-treated patients indicated an increased immune response. CONCLUSIONS: Based on the characterisation and quantification of immune cells in the blood and cytokine levels in the PF, we conclude that IORT induced an anti-tumour effect by activating the immune response, which may prevent pancreatic cancer recurrence. CLINICAL TRIAL REGISTRATION: NCT03273374 .
Subject(s)
Immunity, Cellular/radiation effects , Intraoperative Care , Neoplasm Recurrence, Local/prevention & control , Pancreatic Neoplasms/radiotherapy , Pancreatic Neoplasms/surgery , Ascitic Fluid/chemistry , Ascitic Fluid/metabolism , Ascitic Fluid/radiation effects , Cell Line, Tumor , Cell Movement/radiation effects , Cell Proliferation/radiation effects , Cytokines/analysis , Humans , Lymphocytes/cytology , Neoplasm Invasiveness , Pancreatic Neoplasms/blood , Pancreatic Neoplasms/immunology , Phosphatidylinositol 3-Kinase/metabolism , Prospective Studies , Smad Proteins/metabolism , Tumor Microenvironment/radiation effectsABSTRACT
Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production and complicated genome structure that hamper its study. Here, we unveil the genomic architecture of tetraploid P. ginseng by de novo genome assembly, representing 2.98 Gbp with 59 352 annotated genes. Resequencing data indicated that diploid Panax species diverged in association with global warming in Southern Asia, and two North American species evolved via two intercontinental migrations. Two whole genome duplications (WGD) occurred in the family Araliaceae (including Panax) after divergence with the Apiaceae, the more recent one contributing to the ability of P. ginseng to overwinter, enabling it to spread broadly through the Northern Hemisphere. Functional and evolutionary analyses suggest that production of pharmacologically important dammarane-type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots; that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance; and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light. A genome-scale metabolic network provides a holistic view of Panax ginsenoside biosynthesis. This study provides valuable resources for improving medicinal values of ginseng either through genomics-assisted breeding or metabolic engineering.
Subject(s)
Genome, Plant/genetics , Panax/genetics , Adaptation, Biological/genetics , Biological Evolution , Diploidy , Genes, Chloroplast/genetics , Genes, Plant/genetics , Ginsenosides/biosynthesis , Panax/metabolism , TetraploidyABSTRACT
The anticancer effects of Src kinase inhibitors are controversial. This study found an association between alterations in the TP53 gene and the synergy score for combination treatment with doxorubicin and an Src kinase inhibitor using human osteosarcoma cell lines (MG63 and U2OS) and human colon cancer cell line. Doxorubicin was found to activate signal transducer and activator of transcription 3 via Src kinase in cancer cells harboring alterations in TP53. A drug combination study using patient-derived cells confirmed that an Src kinase inhibitor synergizes with doxorubicin in cancer cells harboring alterations in TP53, while antagonizing its effect in cancer cells expressing wild-type TP53. Our findings suggest that genetic alterations in TP53 are a critical factor in determining the use of a combination treatment of doxorubicin and Src inhibitors.
Subject(s)
Doxorubicin/pharmacology , Genes, p53/drug effects , Protein Kinase Inhibitors/pharmacology , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism , src-Family Kinases/antagonists & inhibitors , A549 Cells , Animals , Cell Line, Tumor , Colonic Neoplasms/diet therapy , Colonic Neoplasms/genetics , Colonic Neoplasms/metabolism , Female , HCT116 Cells , Hep G2 Cells , Humans , MCF-7 Cells , Mice , Mice, Inbred BALB C , Mice, Nude , Osteosarcoma/drug therapy , Osteosarcoma/genetics , Osteosarcoma/metabolism , Signal Transduction/drug effectsABSTRACT
The anticancer effect of doxorubicin is closely related to the generation of reactive oxygen species. On the contrary, doxorubicin-induced reactive oxygen species induces heart failure, a critical side effect of doxorubicin. Antioxidant supplementation has been proposed to reduce the side effects. However, the use of antioxidants may hamper the anticancer effect of doxorubicin. In this study, doxorubicin-induced reactive oxygen species was shown to differentially affect cancer cells based on their TP53 genetic status; doxorubicin-induced apoptosis was attenuated by an antioxidant, N-acetylcysteine, in TP53 wild cells; however, N-acetylcysteine caused a synergistic increase in the apoptosis rate in TP53-altered cells. N-acetylcysteine prevented phosphorylation of P53 protein that had been induced by doxorubicin. However, N-acetylcysteine increased the cleavage of poly (ADP-ribose) polymerase in the presence of doxorubicin. Synergy score of 26 patient-derived cells were evaluated after the combination treatment of doxorubicin and N-acetylcysteine. The synergy score was significantly higher in TP53-altered group compared with those in TP53 wild group. In conclusion, TP53 genetic alteration is a critical factor that determines the use of antioxidant supplements during doxorubicin treatment.
Subject(s)
Acetylcysteine/administration & dosage , Drug Synergism , Heart Failure/drug therapy , Neoplasms/drug therapy , Tumor Suppressor Protein p53/genetics , A549 Cells , Antioxidants/administration & dosage , Apoptosis/drug effects , Cell Proliferation/drug effects , Doxorubicin/administration & dosage , Doxorubicin/adverse effects , Heart Failure/chemically induced , Heart Failure/pathology , Humans , MCF-7 Cells , Neoplasms/pathology , Phosphorylation , Reactive Oxygen Species/metabolismABSTRACT
RRP12 (ribosomal RNA processing 12 homolog), a nucleolar protein, plays important roles in cell cycle progression and the response to deoxyribonucleic acid (DNA) damage in yeast cells. However, its role has not been investigated in mammalian cells that possess p53, which has close functional association to nucleolus. We explored the role of RRP12 in nucleolar stress condition using an osteosarcoma cell line, U2OS. To induce DNA damage and nucleolar disruption, two cytotoxic drugs, doxorubicin and actinomycin D were used. Cytotoxic stress resulted nucleolar disruption induced cell cycle arrest and apoptosis in U2OS cells. However, RRP12 overexpression promoted resistance to cytotoxic stress. In contrast, RRP12 silencing enhanced susceptibility to cytotoxic stress. During drug treatment, p53 activity and cell death were suppressed by RRP12 overexpression but promoted by RRP12 silencing. This study demonstrated that RRP12 was crucial for cell survival during cytotoxic stress via the repression of p53 stability. Thus, targeting RRP12 may enhance chemotherapeutic effect in cancers.
Subject(s)
Cell Nucleolus/genetics , Nuclear Proteins/genetics , Osteosarcoma/genetics , Tumor Suppressor Protein p53/biosynthesis , Apoptosis/drug effects , Cell Line, Tumor , Cell Survival/drug effects , DNA Damage/drug effects , Dactinomycin/administration & dosage , Doxorubicin/administration & dosage , Humans , Nuclear Proteins/antagonists & inhibitors , Nuclear Proteins/biosynthesis , Osteosarcoma/drug therapy , Osteosarcoma/pathology , Tumor Suppressor Protein p53/geneticsABSTRACT
BACKGROUND: The production of metabolites via in vitro culture is promoted by the availability of fully defined metabolic pathways. Withanolides, the major bioactive phytochemicals of Withania somnifera, have been well studied for their pharmacological activities. However, only a few attempts have been made to identify key candidate genes involved in withanolide biosynthesis. Understanding the steps involved in withanolide biosynthesis is essential for metabolic engineering of this plant to increase withanolide production. RESULTS: Transcriptome sequencing was performed on in vitro adventitious root and leaf tissues using the Illumina platform. We obtained a total of 177,156 assembled transcripts with an average unigene length of 1,033 bp. About 13% of the transcripts were unique to in vitro adventitious roots but no unique transcripts were observed in in vitro-grown leaves. A putative withanolide biosynthetic pathway was deduced by mapping the assembled transcripts to the KEGG database, and the expression of candidate withanolide biosynthesis genes -were validated by qRT PCR. The accumulation pattern of withaferin A and withanolide A varied according to the type of tissue and the culture period. Further, we demonstrated that in vitro leaf extracts exhibit anticancer activity against human gastric adenocarcinoma cell lines at sub G1 phase. CONCLUSIONS: We report here a validated large-scale transcriptome data set and the potential biological activity of in vitro cultures of W. somnifera. This study provides important information to enhance tissue-specific expression and accumulation of secondary metabolites, paving the way for industrialization of in vitro cultures of W. somnifera.
Subject(s)
Transcriptome , Withania/metabolism , Withanolides/metabolism , Antioxidants/metabolism , Cell Cycle Checkpoints/drug effects , Cell Line, Tumor , Cell Proliferation/drug effects , Cell Survival/drug effects , Expressed Sequence Tags , Humans , Microsatellite Repeats/genetics , Plant Leaves/cytology , Plant Leaves/genetics , Plant Leaves/metabolism , Plant Roots/cytology , Plant Roots/genetics , Plant Roots/metabolism , Sequence Analysis, RNA , Withania/genetics , Withanolides/isolation & purification , Withanolides/toxicityABSTRACT
BACKGROUND: Korean ginseng (Panax ginseng C.A. Meyer) is a highly effective medicinal plant containing ginsenosides with various pharmacological activities, whose roots are produced commercially for crude drugs. RESULTS: Here, we used the Illumina platform to generate over 232 million RNA sequencing reads from four root samples, including whole roots from one-year-old plants and three types of root tissue from six-year-old plants (i.e., main root bodies, rhizomes, and lateral roots). Through de novo assembly and reference-assisted selection, we obtained a non-redundant unigene set consisting of 55,949 transcripts with an average length of 1,250 bp. Among transcripts in the unigene set, 94 % were functionally annotated via similarity searches against protein databases. Approximately 28.6 % of the transcripts represent novel gene sequences that have not previously been reported for P. ginseng. Digital expression profiling revealed 364 genes showing differential expression patterns among the four root samples. Additionally, 32 were uniquely expressed in one-year-old roots, while seven were uniquely expressed in six-year-old root tissues. We identified 38 transcripts encoding enzymes involved in ginsenoside biosynthesis pathways and 189 encoding UDP-glycosyltransferases. CONCLUSION: Our analysis provides new insights into the role of the root transcriptome in development and secondary metabolite biosynthesis in P. ginseng.
Subject(s)
Panax/genetics , Plant Roots/genetics , Transcriptome/genetics , Gene Expression Profiling , Gene Expression Regulation, Plant , Gene Ontology , Genetic Association Studies , Ginsenosides/biosynthesis , Molecular Sequence Annotation , RNA, Messenger/genetics , RNA, Messenger/metabolism , Sequence Analysis, RNAABSTRACT
BACKGROUND: The roe deer, Capreolus sp., is one of the most widespread meso-mammals of Palearctic distribution, and includes two species, the European roe deer, C. capreolus inhabiting mainly Europe, and the Siberian roe deer, C. pygargus, distributed throughout continental Asia. Although there are a number of genetic studies concerning European roe deer, the Siberian roe deer has been studied less, and none of these studies use microsatellite markers. Natural processes have led to genetic structuring in wild populations. To understand how these factors have affected genetic structure and connectivity of Siberian roe deer, we investigated variability at 12 microsatellite loci for Siberian roe deer from ten localities in Asia. RESULTS: Moderate levels of genetic diversity (H(E) = 0.522 to 0.628) were found in all populations except in Jeju Island, South Korea, where the diversity was lowest (H(E) = 0.386). Western populations showed relatively low genetic diversity and higher degrees of genetic differentiation compared with eastern populations (mean Ar = 3.54 (east), 2.81 (west), mean F(ST) = 0.122). Bayesian-based clustering analysis revealed the existence of three genetically distinct groups (clusters) for Siberian roe deer, which comprise of the Southeastern group (Mainland Korea, Russian Far East, Trans-Baikal region and Northern part of Mongolia), Northwestern group (Western Siberia and Ural in Russia) and Jeju Island population. Genetic analyses including AMOVA (F(RT) = 0.200), Barrier and PCA also supported genetic differentiation among regions separated primarily by major mountain ridges, suggesting that mountains played a role in the genetic differentiation of Siberian roe deer. On the other hand, genetic evidence also suggests an ongoing migration that may facilitate genetic admixture at the border areas between two groups. CONCLUSIONS: Our results reveal an apparent pattern of genetic differentiation among populations inhabiting Asia, showing moderate levels of genetic diversity with an east-west gradient. The results suggest at least three distinct management units of roe deer in continental Asia, although genetic admixture is evident in some border areas. The insights obtained from this study shed light on management of Siberian roe deer in Asia and may be applied in conservation of local populations of Siberian roe deer.
Subject(s)
Deer/genetics , Genetic Variation , Genetics, Population , Animals , Cluster Analysis , Evolution, Molecular , Gene Flow , Geography , Microsatellite Repeats/genetics , SiberiaABSTRACT
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare aggressive hematologic malignancy primarily found in adults, often carrying a poor prognosis. There are only 33 reported pediatric cases of BPDCN in the literature. Although standard treatment is not yet established for children, current literature recommends the use of high-risk acute lymphoblastic leukemia (ALL)-type chemotherapy. Recent studies, however, have explored the benefits of combining chemotherapy with stem-cell transplantation. Here, the authors present 2 cases of pediatric BPDCN treated with different modalities. The first case is a 13-year-old girl who presented with a 3-month history of an initially asymptomatic firm nodule on her left shin. The second case is a 15-year-old boy who presented with a 4-month history of an enlarging subcutaneous nodule on the lower leg. Immunohistochemical staining of both patients was positive for markers consistent with BPDCN. The latter patient received ALL-type therapy alone, whereas the former received ALL-type chemotherapy and stem-cell transplantation. Since initial treatment, both patients remain disease-free. These cases contribute to the limited number of pediatric BPDCN cases, thus helping to advance our knowledge toward an optimal treatment protocol for clinical remission.
Subject(s)
Dendritic Cells/pathology , Hematologic Neoplasms/therapy , Adolescent , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Bone Marrow Transplantation , Female , Hematopoietic Stem Cell Transplantation , Humans , Male , Treatment OutcomeABSTRACT
S100A9 and S100A8 are called damage-associated molecular pattern (DAMP) molecules because of their pro-inflammatory properties. Few studies have evaluated S100A9 and S100A8 function as DAMP molecules in atopic dermatitis (AD). We investigated how house-dust mites affect S100A9 and S100A8 expression in Th2 cytokine- and Th17 cytokine-treated keratinocytes, and how secretion of these molecules affects keratinocyte-derived cytokines. Finally, we evaluated expression of these DAMP molecules in AD patients. S100A9 expression and S100A8 expression were strongly induced in IL-17A- and Dermatophagoides (D.) farinae-treated keratinocytes, respectively. Furthermore, co-treatment with D. farinae and IL-17A strongly increased expression of S100A9 and S100A8 compared with D. farinae-Th2 cytokine co-treatment. The IL-33 mRNA level increased in a dose-dependent manner in S100A9-treated keratinocytes, but TSLP expression did not change. S100A8/A9 levels were also higher in the lesional skin and serum of AD patients, and correlated with disease severity. Taken together, S100A9 and S100A8 may be involved in inducing DAMP-mediated inflammation in AD triggered by IL-17A and house-dust mites.
Subject(s)
Calgranulin A/metabolism , Calgranulin B/metabolism , Dermatitis, Atopic/immunology , Dermatophagoides farinae/immunology , Interleukin-17/metabolism , Animals , Cell Line , Cytokines/metabolism , Dermatitis, Atopic/etiology , Dermatitis, Atopic/genetics , Dermatophagoides farinae/pathogenicity , Humans , Immunity, Innate , Interleukin-33 , Interleukins/biosynthesis , Interleukins/genetics , Keratinocytes/immunology , RNA, Messenger/genetics , RNA, Messenger/metabolism , Th17 Cells/immunology , Th2 Cells/immunology , Up-RegulationABSTRACT
Transcription factors (TFs) provide potentially powerful tools for plant metabolic engineering as they often control multiple genes in a metabolic pathway. However, selecting the best TF for a particular pathway has been challenging, and the selection often relies significantly on phylogenetic relationships. Here, we offer examples where evolutionary relationships have facilitated the selection of the suitable TFs, alongside situations where such relationships are misleading from the perspective of metabolic engineering. We argue that the evolutionary trajectory of a particular TF might be a better indicator than protein sequence homology alone in helping decide the best targets for plant metabolic engineering efforts. This article is part of the theme issue 'The evolution of plant metabolism'.
Subject(s)
Evolution, Molecular , Metabolic Engineering , Plants , Transcription Factors , Transcription Factors/metabolism , Transcription Factors/genetics , Plants/genetics , Plants/metabolism , Phylogeny , Plant Proteins/genetics , Plant Proteins/metabolismABSTRACT
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive solid malignancies. A specific mechanism of its metastasis has not been established. In this study, we investigated whether Neural Wiskott-Aldrich syndrome protein (N-WASP) plays a role in distant metastasis of PDAC. We found that N-WASP is markedly expressed in clinical patients with PDAC. Clinical analysis showed a notably more distant metastatic pattern in the N-WASP-high group compared to the N-WASP-low group. N-WASP was noted to be a novel mediator of epithelial-mesenchymal transition (EMT) via gene expression profile studies. Knockdown of N-WASP in pancreatic cancer cells significantly inhibited cell invasion, migration, and EMT. We also observed positive association of lysyl oxidase-like 2 (LOXL2) and focal adhesion kinase (FAK) with the N-WASP-mediated response, wherein EMT and invadopodia function were modulated. Both N-WASP and LOXL2 depletion significantly reduced the incidence of liver and lung metastatic lesions in orthotopic mouse models of pancreatic cancer. These results elucidate a novel role for N-WASP signaling associated with LOXL2 in EMT and invadopodia function, with respect to regulation of intercellular communication in tumor cells for promoting pancreatic cancer metastasis. These findings may aid in the development of therapeutic strategies against pancreatic cancer.
Subject(s)
Carcinoma, Pancreatic Ductal , Pancreatic Neoplasms , Animals , Humans , Mice , Amino Acid Oxidoreductases/genetics , Amino Acid Oxidoreductases/metabolism , Carcinoma, Pancreatic Ductal/pathology , Cell Line, Tumor , Cell Movement/genetics , Epithelial-Mesenchymal Transition/genetics , Focal Adhesion Protein-Tyrosine Kinases/metabolism , Pancreatic Neoplasms/pathology , Signal Transduction , Wiskott-Aldrich Syndrome Protein/metabolismABSTRACT
Atopic dermatitis (AD) is a highly pruritic, chronic relapsing inflammatory skin disease characterized by innate and adaptive immune reactions. In AD, innate immune mechanisms such as pattern recognition receptors and antimicrobial peptides have been investigated in detail, but recently, epidermis-derived cytokines, namely thymic stromal lymphopoietin (TSLP), IL-25 and IL-33, were shown to participate in innate immune reactions independently of adaptive immunity. In addition to conventional innate cells, such as mast cells, basophils and eosinophils, Th2 cytokine-producing invariant natural killer T (iNKT) cells, innate lymphoid cells (ILCs) and Th17/Th22 cytokine-producing innate cells - iNKT cells and natural killer (NK)-like cells - can participate in innate immune modulation in AD. Accordingly, early control of innate immune responses in AD before activation of adaptive immune responses by conventional T and B cells that perpetuate chronic skin inflammation may adequately alleviate acute exacerbations of AD. Therefore, we hypothesized that select immune modulators targeting the innate immune response could potentially be used for individualized treatment of AD.
Subject(s)
Cytokines/metabolism , Dermatitis, Atopic/immunology , Immunity, Innate , Lymphocytes/metabolism , Humans , Natural Killer T-Cells/immunologyABSTRACT
Sixty peony root training samples of the same age were collected from various regions in Korea and China, and their genetic diversity was investigated for 23 chloroplast intergenic space regions. All samples were genetically indistinguishable, indicating that the DNA-based techniques employed were not appropriate for determining the samples' regions of origin. In contrast, (1)H-nuclear magnetic resonance ((1)H-NMR) spectroscopy-based metabolomics coupled with multivariate statistical analysis revealed a clear difference between the metabolic profiles of the Korean and Chinese samples. Orthogonal projections on the latent structure-discrimination analysis allowed the identification of potential metabolite markers, including γ-aminobutyric acid, arginine, alanine, paeoniflorin, and albiflorin, that could be useful for classifying the samples' regions of origin. The validity of the discrimination model was tested using the response permutation test and blind prediction test for internal and external validations, respectively. Metabolomic data of 21 blended samples consisting of Korean and Chinese samples mixed at various proportions were also acquired by (1)H-NMR analysis. After data preprocessing which was designed to eliminate uncontrolled deviations in the spectral data between the testing and training sets, a new statistical procedure for estimating the mixing proportions of blended samples was established using the constrained least squares method for the first time. The predictive procedure exhibited relatively good predictability (adjusted R (2) = 0.7669), and thus has the potential to be used in the quality control of peony root by providing correct indications for a sample's geographical origins.
Subject(s)
Chloroplasts/chemistry , Metabolomics/statistics & numerical data , Paeonia/chemistry , Phylogeny , Plant Roots/chemistry , Alanine/analysis , Alanine/metabolism , Arginine/analysis , Arginine/metabolism , Biomarkers/analysis , Biomarkers/metabolism , Bridged-Ring Compounds/analysis , Bridged-Ring Compounds/metabolism , China , Chloroplasts/metabolism , DNA, Intergenic/genetics , DNA, Plant/genetics , Glucosides/analysis , Glucosides/metabolism , Magnetic Resonance Spectroscopy , Monoterpenes/analysis , Monoterpenes/metabolism , Multivariate Analysis , Paeonia/classification , Paeonia/genetics , Paeonia/metabolism , Phylogeography , Plant Roots/genetics , Plant Roots/metabolism , Quality Control , Republic of Korea , gamma-Aminobutyric Acid/analysis , gamma-Aminobutyric Acid/metabolismABSTRACT
BACKGROUND: Although office-based dermatologic procedures are generally considered safe, there is a lack of prospective data on the rate of adverse events (AEs) associated with these procedures. OBJECTIVE: To determine the frequency of AEs after dermatologic surgery and to characterize the most commonly encountered AEs. METHODS: A web-based interface was designed to track AEs with the input of four dermatologic surgeons. Patient demographic and operative data were collected at the time of the dermatologic surgery procedure. AEs occurring at any time during the data collection period were logged according to an a priori categorization scheme. RESULTS: The AE rate was 2.0% in this series of 2,418 subjects undergoing dermatologic surgery from February 1 through December 14, 2010. The most commonly reported AEs were suspicion of infection (64%), postoperative hemorrhage (20%), and wound dehiscence (8%). Suspicion of infection was slightly less frequent in subjects who received prophylactic preoperative antibiotics (0.4%) than in those who did not (1.5%, p = .07). There were no serious AEs and no deaths. CONCLUSION: AEs are uncommon after office-based dermatologic surgery procedures. Preoperative antibiotics may further decrease the infection rate after dermatologic surgery, but the risks and benefits must be weighed given the already low AE rate.