Identification of Tea Plant Purple Acid Phosphatase Genes and Their Expression Responses to Excess Iron.

Purple acid phosphatase (PAP) encoding genes are a multigene family. PAPs require iron (Fe) to exert their functions that are involved in diverse biological roles including Fe homeostasis. However, the possible roles of PAPs in response to excess Fe remain unknown. In this study, we attempted to understand the regulation of PAPs by excess Fe in tea plant (Camellia sinensis). A genome-wide investigation of PAP encoding genes identified 19 CsPAP members based on the conserved motifs. The phylogenetic analysis showed that PAPs could be clustered into four groups, of which group II contained two specific cysteine-containing motifs "GGECGV" and "YERTC". To explore the expression patterns of CsPAP genes in response to excessive Fe supply, RNA-sequencing (RNA-seq) analyses were performed to compare their transcript abundances between tea plants that are grown under normal and high iron conditions, respectively. 17 members were shown to be transcribed in both roots and leaves. When supplied with a high amount of iron, the expression levels of four genes were significantly changed. Of which, CsPAP15a, CsPAP23 and CsPAP27c were shown as downregulated, while the highly expressed CsPAP10a was upregulated. Moreover, CsPAP23 was found to be alternatively spliced, suggesting its post-transcriptional regulation. The present work implicates that some CsPAP genes could be associated with the responses of tea plants to the iron regime, which may offer a new direction towards a further understanding of iron homeostasis and provide the potential approaches for crop improvement in terms of iron biofortification.

Glycoproteomic Alterations in Drug-Resistant Nonsmall Cell Lung Cancer Cells Revealed by Lectin Magnetic Nanoprobe-Based Mass Spectrometry.

Understanding the functional role of glycosylation-mediated pathogenesis requires deep characterization of glycoproteome, which remains extremely challenging due to the inherently complex nature of glycoproteins. We demonstrate the utility of lectin-magnetic nanoprobe (MNP@lectin) coupled to Orbitrap HCD-CID-MS/MS for complementary glycotope-specific enrichment and site-specific glycosylation analysis of the glycoproteome. By three nanoprobes, MNP@ConA, MNP@AAL, and MNP@SNA, our results revealed the first large-scale glycoproteome of nonsmall cell lung cancer (NSCLC) with 2290 and 2767 nonredundant glycopeptides confidently identified (Byonic score ≥100) in EGFR-TKI-sensitive PC9 and -resistant PC9-IR cells, respectively, especially with more fucosylated and sialylated glycopeptides in PC9-IR cells. The complementary enrichment was demonstrated with only five glycopeptides commonly enriched in three MNP@lectins. Glycotope specificity of 79 and 62% for enrichment was achieved using MNP@AAL and MNP@SNA, respectively. Label-free quantitation revealed predominant fucosylation in PC9-IR cells, suggesting its potential role associated with NSCLC resistance. Moreover, without immunoprecipitation, this multilectin nanoprobe allows the sensitive identification of 51 glycopeptides from 10 of 12 reported sites from onco-protein EGFR. Our results not only demonstrated a sensitive approach to study the vastly under-represented N-glycoprotome but also may pave the way for a glycoproteomic atlas to further explore the site-specific function of glycoproteins associated with drug resistance in NSCLC.

Functional Characterization of Thyrostimulin in Amphioxus Suggests an Ancestral Origin of the TH Signaling Pathway.

Thyrostimulin, consisting of GpA2 and GpB5 subunits, has been identified in amphioxus, but to date, little is known about the roles of GPA2/GPB5‒type hormone in this evolutionarily important animal. We showed here that amphioxus GpA2, GpB5, and TSH receptor (TSHR) represent the archetypes of vertebrate TSHα, TSHß, and TSHR, respectively, and both gpa2 and gpb5 were coexpressed in the Hatschek pit, a homolog of the vertebrate pituitary, in amphioxus. We also showed that recombinant amphioxus GpA2 and GpB5, like zebrafish TSHα and TSHß, bound to both amphioxus and zebrafish TSHR and that tethered amphioxus thyrostimulin activated both protein kinase A and protein kinase C pathways in the cells expressing amphioxus TSHR. Moreover, we demonstrated that recombinant amphioxus thyrostimulin induced the production of thyroid hormone (TH) T4. Because genuine TSH is absent in amphioxus and thyrostimulin is the only and sole glycoprotein hormone, our data likely provide evidence that amphioxus thyrostimulin is a functional glycoprotein hormone that plays a role as TSH does in vertebrates. The data also suggest that the TH signaling pathway evolved in the basal chordate more than 500 million years ago.

Identification of glycoproteins in mucous cells of the gill epithelium of Colossoma macropomum after exposure to organophosphate / Identificação das glicoproteínas nas células mucosas do epitélio branquial de Colossoma macropomum após exposição ao organofosforado

The use of organophosphates has been recommended for fish, especially the trichlorfon to control parasites. Colossoma macropomum were exposed to trichlorfon during 96 hours and of total number of mucous cells decreased in the number of cells when compared to the control group. Glycoproteins acid, acid sulphated and neutral was identified in the gill epithelium. Neutra glycoprotein had a significant decrease between control and the sublethal concentration. Acid glycoprotein didn't have any significant difference between the groups exposed to the trichlorfon, compared to the control group. Sulfated acidic glycoprotein in the group exposed to the trichlorfon was noticed a reduction in number of mucosal cells acidic sulphated. The differences between density cell and production glycoprotein was a response of these cells after exposure to xenobiotic. The reduction of neutral, acid and sulphated acid glycoprotein in the MC of the gill epithelium Colossoma macropomum may affect gills epithelial surface protection by reducing the formation of an unstirred layer and enhance the ion loss.(AU)

A utilização de organofosforados tem sido recomendada em pisciculturas, principalmente o trichlorfon, para o controle de parasitoses. Colossoma macropomum foram expostos ao trichlorfon durante 96 horas, e o número total de células mucosas diminuiu no número de células quando comparado com o grupo controle. Glicoproteínas ácida, ácida sulfatada e neutra foram identificadas no epitélio branquial. Glicoproteína neutra teve uma diminuição significativa entre o controle e a concentração subletal. Glicoproteína ácida não apresentou diferença significativa entre os grupos expostos ao triclorfon, em comparação com o grupo controle. Glicoproteína ácida sulfatada no grupo exposto ao triclorfon teve uma redução no número de células da mucosa ácida sulfatada. As diferenças entre a densidade celular e a produção de glicoproteína foi uma resposta dessas células após exposição aos xenobióticos. A redução das glicoproteínas neutra, ácida e ácida sulfatada no epitélio branquial de Colossoma macropomum pode afetar a proteção da superfície, reduzindo a formação de uma camada de muco, e aumentar a perda de íons.(AU)

Comparative proteomics of a model MCF10A-KRasG12V cell line reveals a distinct molecular signature of the KRasG12V cell surface.

Oncogenic Ras mutants play a major role in the etiology of most aggressive and deadly carcinomas in humans. In spite of continuous efforts, effective pharmacological treatments targeting oncogenic Ras isoforms have not been developed. Cell-surface proteins represent top therapeutic targets primarily due to their accessibility and susceptibility to different modes of cancer therapy. To expand the treatment options of cancers driven by oncogenic Ras, new targets need to be identified and characterized at the surface of cancer cells expressing oncogenic Ras mutants. Here, we describe a mass spectrometry-based method for molecular profiling of the cell surface using KRasG12V transfected MCF10A (MCF10A-KRasG12V) as a model cell line of constitutively activated KRas and native MCF10A cells transduced with an empty vector (EV) as control. An extensive molecular map of the KRas surface was achieved by applying, in parallel, targeted hydrazide-based cell-surface capturing technology and global shotgun membrane proteomics to identify the proteins on the KRasG12V surface. This method allowed for integrated proteomic analysis that identified more than 500 cell-surface proteins found unique or upregulated on the surface of MCF10A-KRasG12V cells. Multistep bioinformatic processing was employed to elucidate and prioritize targets for cross-validation. Scanning electron microscopy and phenotypic cancer cell assays revealed changes at the cell surface consistent with malignant epithelial-to-mesenchymal transformation secondary to KRasG12V activation. Taken together, this dataset significantly expands the map of the KRasG12V surface and uncovers potential targets involved primarily in cell motility, cellular protrusion formation, and metastasis.

New Perspectives on Ebola Virus Evolution.

Since the recent devastating outbreak of Ebola virus disease in western Africa, there has been significant effort to understand the evolution of the deadly virus that caused the outbreak. There has been a considerable investment in sequencing Ebola virus (EBOV) isolates, and the results paint an important picture of how the virus has spread in western Africa. EBOV evolution cannot be understood outside the context of previous outbreaks, however. We have focused this study on the evolution of the EBOV glycoprotein gene (GP) because one of its products, the spike glycoprotein (GP1,2), is central to the host immune response and because it contains a large amount of the phylogenetic signal for this virus. We inferred the maximum likelihood phylogeny of 96 nonredundant GP gene sequences representing each of the outbreaks since 1976 up to the end of 2014. We tested for positive selection and considered the placement of adaptive amino acid substitutions along the phylogeny and within the protein structure of GP1,2. We conclude that: 1) the common practice of rooting the phylogeny of EBOV between the first known outbreak in 1976 and the next outbreak in 1995 provides a misleading view of EBOV evolution that ignores the fact that there is a non-human EBOV host between outbreaks; 2) the N-terminus of GP1 may be constrained from evolving in response to the host immune system by the highly expressed, secreted glycoprotein, which is encoded by the same region of the GP gene; 3) although the mucin-like domain of GP1 is essential for EBOV in vivo, it evolves rapidly without losing its twin functions: providing O-linked glycosylation sites and a flexible surface.

Vertebrate TFPI-2 C-terminal peptides exert therapeutic applications against Gram-negative infections.

BACKGROUND: Tissue factor pathway inhibitor-2 (TFPI-2) is a serine protease inhibitor that exerts multiple physiological and patho-physiological activities involving the modulation of coagulation, angiogenesis, tumor invasion, and apoptosis. In previous studies we reported a novel role of human TFPI-2 in innate immunity by serving as a precursor for host defense peptides. Here we employed a number of TFPI-2 derived peptides from different vertebrate species and found that their antibacterial activity is evolutionary conserved although the amino acid sequence is not well conserved. We further studied the theraputic potential of one selected TFPI-2 derived peptide (mouse) in a murine sepsis model. RESULTS: Hydrophobicity and net charge of many peptides play a important role in their host defence to invading bacterial pathogens. In vertebrates, the C-terminal portion of TFPI-2 consists of a highly conserved cluster of positively charged amino acids which may point to an antimicrobial activity. Thus a number of selected C-terminal TFPI-2 derived peptides from different species were synthesized and it was found that all of them exert antimicrobial activity against E. coli and P. aeruginosa. The peptide-mediated killing of E. coli was enhanced in human plasma, suggesting an involvement of the classical pathway of the complement. Under in vitro conditions the peptides displayed anti-coagulant activity by modulating the intrinsic pathway of coagulation and in vivo treatment with the mouse derived VKG24 peptide protects mice from an otherwise lethal LPS shock model. CONCLUSIONS: Our results suggest that the evolutionary conserved C-terminal part of TFPI-2 is an interesting agent for the development of novel antimicrobial therapies.

Convergent evolution of pregnancy-specific glycoproteins in human and horse.

Pregnancy-specific glycoproteins (PSGs) are members of the carcinoembryonic antigen cell adhesion molecule (CEACAM) family that are secreted by trophoblast cells. PSGs may modulate immune, angiogenic and platelet responses during pregnancy. Until now, PSGs are only found in species that have a highly invasive (hemochorial) placentation including humans, mice and rats. Surprisingly, analyzing the CEACAM gene family of the horse, which has a non-invasive epitheliochorial placenta, with the exception of the transient endometrial cups, we identified equine CEACAM family members that seem to be related to PSGs of rodents and primates. We identified seven genes that encode secreted PSG-like CEACAMs Phylogenetic analyses indicate that they evolved independently from an equine CEACAM1-like ancestor rather than from a common PSG-like ancestor with rodents and primates. Significantly, expression of PSG-like genes (CEACAM44, CEACAM48, CEACAM49 and CEACAM55) was found in non-invasive as well as invasive trophoblast cells such as purified chorionic girdle cells and endometrial cup cells. Chorionic girdle cells are highly invasive trophoblast cells that invade the endometrium of the mare where they form endometrial cups and are in close contact with maternal immune cells. Therefore, the microenvironment of invasive equine trophoblast cells has striking similarities to the microenvironment of trophoblast cells in hemochorial placentas, suggesting that equine PSG-like CEACAMs and rodent and primate PSGs have undergone convergent evolution. This is supported by our finding that equine PSG-like CEACAM49 exhibits similar activity to certain rodent and human PSGs in a functional assay of platelet-fibrinogen binding. Our results have implications for understanding the evolution of PSGs and their functions in maternal-fetal interactions.

Differential retention and expansion of the ancestral genes associated with the paleopolyploidies in modern rosid plants, as revealed by analysis of the extensins super-gene family.

BACKGROUND: All modern rosids originated from a common hexapolyploid ancestor, and the genomes of some rosids have undergone one or more cycles of paleopolyploidy. After the duplication of the ancient genome, wholesale gene loss and gene subfunctionalization has occurred. Using the extensin super-gene family as an example, we tracked the differential retention and expansion of ancestral extensin genes in four modern rosids, Arabidopsis, Populus, Vitis and Carica, using several analytical methods. RESULTS: The majority of extensin genes in each of the modern rosids were found to originate from different ancestral genes. In Arabidopsis and Populus, almost half of the extensins were paralogous duplicates within the genome of each species. By contrast, no paralogous extensins were detected in Vitis and Carica, which have only undergone the common γ-triplication event. It was noteworthy that a group of extensins containing the IPR006706 domain had actively duplicated in Arabidopsis, giving rise to a neo-extensin around every 3 million years. However, such extensins were absent from, or rare in, the other three rosids. A detailed examination revealed that this group of extensins had proliferated significantly in the genomes of a number of species in the Brassicaceae. We propose that this group of extensins might play important roles in the biology and in the evolution of the Brassicaceae. Our analyses also revealed that nearly all of the paralogous and orthologous extensin-pairs have been under strong purifying selection, leading to the strong conservation of the function of extensins duplicated from the same ancestral gene. CONCLUSIONS: Our analyses show that extensins originating from a common ancestor have been differentially retained and expanded among four modern rosids. Our findings suggest that, if Arabidopsis is used as the model plant, we can only learn a limited amount about the functions of a particular gene family. These results also provide an example of how it is essential to learn the origination of a gene when analyzing its function across different plant species.

Targeting deeper the human serum fucome by a liquid-phase multicolumn platform in combination with combinatorial peptide ligand libraries.

Combinatorial peptide ligand library (CPLL) was evaluated as an off line step to narrow the differences of protein concentration in human serum prior to the capturing of human fucome from disease-free and breast cancer sera by a multicolumn platform via lectin affinity chromatography (LAC) followed by the fractionation of the captured glycoproteins by reversed phase chromatography (RPC). Two monolithic lectin columns specific to fucose, namely Aleuria aurantia lectin (AAL) and Lotus tetragonolobus agglutinin (LTA) columns were utilized to capture the fucome, which was subsequently fractionated by RPC yielding desalted fractions in volatile acetonitrile-rich mobile phase, which after vacuum evaporation were subjected to tryptic digestion prior to LC-MS/MS analysis. AAL has a strong affinity towards core fucosylated N-glycans and has a weak binding towards fucose in the outer arm while LTA can bind to glycans having fucose present in the outer arm. The combined strategy consisting of the CPLL, multicolumn platform and LC-MS/MS analysis permitted the identification of the differentially expressed proteins (DEPs) in breast cancer serum yielding 58 DEPs in both the LTA and AAL fractions with 6 DEPs common to both lectins. 17 DEPs were of the low abundance type, 16 DEPs of the borderline abundance type, 4 DEPs of the medium abundance type and 15 DEPs of the high abundance type. The remaining 6 DEPs are of unknown concentration. Only proteins exhibiting 99.9% protein identification probability, 95% peptide identification probability, and a minimum of 5 unique peptides were considered in finding the DEPs via scatterplots.

Moving pieces in a venomic puzzle: unveiling post-translationally modified toxins from Tityus serrulatus.

Besides being a public health problem, scorpion venoms have a potential biotechnological application since they contain peptides that may be used as drug leads and/or to reveal novel pharmacological targets. A comprehensive Tityus serrulatus venom proteome study with emphasis on the phosphoproteome and N-glycoproteome was performed to improve our knowledge on the molecular diversity of the proteinaceous toxins. We combined two peptide identification methodologies, i.e., database search and de novo sequencing, to achieve a more comprehensive overview of the molecular diversity of the venoms. A total of 147 proteins were identified, including neurotoxins, enzymes, bradykinin-potentiating peptides, and molecules with antimicrobial and diuretic activities. Among those, three proteins were found to be phosphorylated, and one N-glycosylated. Finally, cleavage of toxin polypeptide chains seems to be a common post-translational modification in the venom since 80% of the identified molecules were, in fact, products of toxins proteolysis.

Development of global consensus sequence of HCV glycoproteins involved in viral entry.

BACKGROUND: HCV affects>170 million people worldwide and is a leading cause of liver diseases such as hepatocellular carcinoma. Each year, Pakistan reports hundreds of cases and now it has become a serious health issue. HCV has two transmembrane glycoproteins (E1 and E2) that are involved in virus entry through viral attachment, but because of their hypervariable nature they have become difficult targets for vaccine development. METHODS: A total of 150 protein sequences of E1 and E2 belonging to genotypes 3a and 1a were retrieved from the NCBI protein database and were subjected to conservation and variation analysis using the multiple sequence alignment feature of the CLC workbench. A consensus sequence of each genotype of E1 and E2 was obtained and these consensus sequences were further analyzed to construct a global consensus sequence, which was used to design potentially conserved peptides. RESULTS: From the sequence conservation analysis, highly conserved residues were identified and were used to design peptides. Only two peptides were found to be conserved in the E1 protein of genotypes 3a and 1a and a total of nine conserved peptides were designed for the HCV E2 protein of those genotypes. These designed peptides could serve as useful targets in developing new inhibitory compounds. CONCLUSION: This study was designed to perform conservation and variability analysis of HCV glycoproteins and to find potentially conserved peptides among genotypes 3a and 1a (the most prevalent genotypes in Pakistan) that could serve as useful targets in the development of novel inhibitory compounds, thus reducing the threat of HCV infection in Pakistan.

Repeated evolution of identical domain architecture in metazoan netrin domain-containing proteins.

The majority of proteins in eukaryotes are composed of multiple domains, and the number and order of these domains is an important determinant of protein function. Although multidomain proteins with a particular domain architecture were initially considered to have a common evolutionary origin, recent comparative studies of protein families or whole genomes have reported that a minority of multidomain proteins could have appeared multiple times independently. Here, we test this scenario in detail for the signaling molecules netrin and secreted frizzled-related proteins (sFRPs), two groups of netrin domain-containing proteins with essential roles in animal development. Our primary phylogenetic analyses suggest that the particular domain architectures of each of these proteins were present in the eumetazoan ancestor and evolved a second time independently within the metazoan lineage from laminin and frizzled proteins, respectively. Using an array of phylogenetic methods, statistical tests, and character sorting analyses, we show that the polyphyly of netrin and sFRP is well supported and cannot be explained by classical phylogenetic reconstruction artifacts. Despite their independent origins, the two groups of netrins and of sFRPs have the same protein interaction partners (Deleted in Colorectal Cancer/neogenin and Unc5 for netrins and Wnts for sFRPs) and similar developmental functions. Thus, these cases of convergent evolution emphasize the importance of domain architecture for protein function by uncoupling shared domain architecture from shared evolutionary history. Therefore, we propose the terms merology to describe the repeated evolution of proteins with similar domain architecture and discuss the potential of merologous proteins to help understanding protein evolution.

Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers.

We used a lectin chromatography/MS-based approach to screen conditioned medium from a panel of luminal (less aggressive) and triple negative (more aggressive) breast cancer cell lines (n=5/subtype). The samples were fractionated using the lectins Aleuria aurantia (AAL) and Sambucus nigra agglutinin (SNA), which recognize fucose and sialic acid, respectively. The bound fractions were enzymatically N-deglycosylated and analyzed by LC-MS/MS. In total, we identified 533 glycoproteins, ∼90% of which were components of the cell surface or extracellular matrix. We observed 1011 glycosites, 100 of which were solely detected in ≥3 triple negative lines. Statistical analyses suggested that a number of these glycosites were triple negative-specific and thus potential biomarkers for this tumor subtype. An analysis of RNaseq data revealed that approximately half of the mRNAs encoding the protein scaffolds that carried potential biomarker glycosites were up-regulated in triple negative vs luminal cell lines, and that a number of genes encoding fucosyl- or sialyltransferases were differentially expressed between the two subtypes, suggesting that alterations in glycosylation may also drive candidate identification. Notably, the glycoproteins from which these putative biomarker candidates were derived are involved in cancer-related processes. Thus, they may represent novel therapeutic targets for this aggressive tumor subtype.

Genetic variation of the 8-kDa glycoprotein family from Echinococcus granulosus, Taenia multiceps and Taenia hydatigena.

BACKGROUND: Echinococcosis, coenurosis and cysticercosis are debilitating diseases which prevail in China. Immunological diagnosis of metacestodosis is important in disease control. The 8-kDa glycoproteins from taeniid cestodes have successfully been used for diagnosis of human cysticercosis in immunological assays. The aim of the present study was to investigate genetic variations and phylogenetic relationships of the 8-kDa proteins for evaluating the possibility of utilizing these proteins as diagnostic antigens for other metacestode infections. METHODS: The genes and complementary DNAs (cDNAs) encoding the 8-kDa proteins from Echinococcus (E.) granulosus, Taenia (T.) multiceps and T. hydatigena were amplified using PCR method. Their amplicons were cloned into the vector pMD18 and the positive clones were sequenced. Sequence data were analyzed with the SeqMan program, and sequence homology searches were performed using the BLAST program. Alignments were conducted using the ClustalX program, and the phylogenetic analyses were performed with the Protein Sequences Program and the Puzzle Program using the Neighbor-joining method. RESULTS: Fifteen, 18 and 22 different genomic DNA sequences were identified as members of the 8-kDa protein gene family from E. granulosus, T. multiceps and T. hydatigena, respectively. Eight, four and six different cDNA clones respectively from E. granulosus, T. multiceps and T. hydatigena were characterized. Analysis of these sequences revealed 54 unique 8-kDa protein sequences. Phylogenetic trees demonstrated that the taeniid 8-kDa proteins are clustered into eight clades at least: Ts18, Ts14, TsRS1, TsRS2, T8kDa-1, T8kDa-2, T8kDa-3 and T8kDa-4. CONCLUSION: We found that the gene family encoding for the taeniid 8-kDa antigens is comprised of many members with high diversity, which will provide molecular evidence for cross-reaction or specific reaction among metacestode infections and may contribute to the development of promising immunological methods for diagnosis of metacestodosis.

Human stanniocalcin-1 interacts with nuclear and cytoplasmic proteins and acts as a SUMO E3 ligase.

Human stanniocalcin-1 (STC1) is a glycoprotein that has been implicated in different physiological process, including angiogenesis, apoptosis and carcinogenesis. Here we identified STC1 as a putative molecular marker for the leukemic bone marrow microenvironment and identified new interacting protein partners for STC1. Seven selected interactions retrieved from yeast two-hybrid screens were confirmed by GST-pull down assays in vitro. The N-terminal region was mapped to be the region that mediates the interaction with cytoplasmic, mitochondrial and nuclear proteins. STC1 interacts with SUMO-1 and several proteins that have been shown to be SUMOylated and localized to SUMOylation related nuclear bodies. Although STC1 interacts with SUMO-1 and has a high theoretical prediction score for a SUMOylation site, endogenous co-immunoprecipitation and in vitro SUMOylation assays with the purified recombinant protein could not detect STC1 SUMOylation. However, when we tested STC1 for SUMO E3 ligase activity, we found in an in vitro assay, that it significantly increases the SUMOylation of two other proteins. Confocal microscopic subcellular localization studies using both transfected cells and specific antibodies for endogenous STC1 revealed a cytoplasmic and nuclear deposition, the latter in the form of some specific dot-like substructure resembling SUMOylation related nuclear bodies. Together, these findings suggest a new role for STC1 in SUMOylation pathways, in nuclear bodies.

Lung cancer serum biomarker discovery using glycoprotein capture and liquid chromatography mass spectrometry.

Targeted glycoproteomics represents an attractive approach for conducting peripheral blood based cancer biomarker discovery due to the well-known altered pattern of protein glycosylation in cancer and the reduced complexity of the resultant glycoproteome. Here we report its application to a set of pooled nonsmall cell lung cancer (NSCLC) case sera (9 adenocarcinoma and 6 squamous cell carcinoma pools from 54 patients) and matched controls pools, including 8 clinical control pools with computed tomography detected nodules but being nonmalignant as determined by biopsy from 54 patients, and 8 matched healthy control pools from 106 cancer-free subjects. The goal of the study is to discover biomarkers that may enable improved early detection and diagnosis of lung cancer. Immunoaffinity subtraction was used to first deplete the topmost abundant serum proteins; the remaining serum proteins were then subjected to hydrazide chemistry based glycoprotein capture and enrichment. Hydrazide resin in situ trypsin digestion was used to release nonglycosylated peptides. Formerly N-linked glycosylated peptides were released by peptide-N-glycosidase F (PNGase F) treatment and were subsequently analyzed by liquid chromatography (LC)-tandem mass spectrometry (MS/MS). A MATLAB based in-house tool was developed to facilitate retention time alignment across different LC-MS/MS runs, determination of precursor ion m/z values and elution profiles, and the integration of mass chromatograms based on determined parameters for identified peptides. A total of 38 glycopeptides from 22 different proteins were significantly differentially abundant across the case/control pools (P < 0.01, Student's t test) and their abundances led to a near complete separation of case and control pools based on hierarchical clustering. The differential abundances of three of these candidate proteins were verified by commercially available ELISAs applied in the pools. Strong positive correlations between glycopeptide mass chromatograms and ELISA-measured protein abundance was observed for all of the selected glycoproteins.

Quantitative analyses of CD133 expression facilitate researches on tumor stem cells.

CD133 is regarded as a marker of tumor initiating cells in many tumors, including colorectal cancer. O'Brien and Ricci et al. have proved that in primary colorectal tumors there are colorectal tumor stem cells (initiating cells) which are marked by CD133 antigen. Using a genetic knockin lacZ reporter mouse model, Shmelkov et al. challenged this increasingly influential viewpoint and drew two important conclusions that challenge former opinions. First, CD133 is widely distributed throughout the full range of tumor epithelial cells in the colon as opposed to being limited to a few cells. Second, CD133 negative cells of colon tumors are also tumorigenic, and are more inclined to metastasize. Based on these two opinions, we hypothesize that the expression of CD133 is different among tumor cells, and that quantitative but not qualitative analyses of CD133 abundance are necessary to determine the relationship between CD133 expression and tumor stem cell characteristics. To verify this hypothesis, colorectal cancer cell line SW620 was cultured and sorted into CD133(Hi), CD133(Mid) and CD133(Low) subgroups using magnetic microbeads to compare their xenograft biological characteristics. The results showed that the CD133(Hi) subgroup of SW620 is more close to the tumor initiating cells in terms of biological characteristics than CD133(Mid) and CD133(low) subgroups, but the CD133(low) subgroup still maintains the ability of tumorigenicity. It supported that tumor initiating cells are more correlated to the abundance of CD133.

Coevolution of activating and inhibitory receptors within mammalian carcinoembryonic antigen families.

BACKGROUND: Most rapidly evolving gene families are involved in immune responses and reproduction, two biological functions which have been assigned to the carcinoembryonic antigen (CEA) gene family. To gain insights into evolutionary forces shaping the CEA gene family we have analysed this gene family in 27 mammalian species including monotreme and marsupial lineages. RESULTS: Phylogenetic analysis provided convincing evidence that the primordial CEA gene family in mammals consisted of five genes, including the immune inhibitory receptor-encoding CEACAM1 (CEA-related cell adhesion molecule) ancestor. Our analysis of the substitution rates within the nucleotide sequence which codes for the ligand binding domain of CEACAM1 indicates that the selection for diversification is, perhaps, a consequence of the exploitation of CEACAM1 by a variety of viral and bacterial pathogens as their cellular receptor. Depending on the extent of the amplification of an ancestral CEACAM1, the number of CEACAM1-related genes varies considerably between mammalian species from less than five in lagomorphs to more than 100 in bats. In most analysed species, ITAM (immunoreceptor tyrosine-based activation motifs) or ITAM-like motif-containing proteins exist which contain Ig-V-like, ligand binding domains closely related to that of CEACAM1. Human CEACAM3 is one such protein which can function as a CEACAM1 decoy receptor in granulocytes by mediating the uptake and destruction of specific bacterial pathogens via its ITAM-like motif. The close relationship between CEACAM1 and its ITAM-encoding relatives appears to be maintained by gene conversion and reciprocal recombination. Surprisingly, secreted CEACAMs resembling immunomodulatory CEACAM1-related trophoblast-specific pregnancy-specific glycoproteins (PSGs) found in humans and rodents evolved only in a limited set of mammals. The appearance of PSG-like genes correlates with invasive trophoblast growth in these species. CONCLUSIONS: These phylogenetic studies provide evidence that pathogen/host coevolution and a possible participation in fetal-maternal conflict processes led to a highly species-specific diversity of mammalian CEA gene families.

Both CD133+ and CD133- subpopulations of A549 and H446 cells contain cancer-initiating cells.

Tumors have been known to contain a small population of cancer stem cells that initiate tumor growth and promote tumor spreading. CD133 alone or in combination with other markers is currently being used for identification and isolation of the putative cancer stem cell population from malignant tumors. To determine whether the CD133+ cells constitute the stem cell populations of lung cancer cells A549 and H446, CD133+ and CD133- subpopulations were sorted from A549 and H446 cells by magnetic cell separation and characterized for their in vitro stem cell-like properties. Interestingly, both the CD133+ and CD133- cells displayed similar abilities of colony formation, self-renewal, proliferation, differentiation, and invasion, as well as resistance to chemotherapy drugs. Furthermore, colony formation assays showed that more than 40% of cells in both the CD133+ cells and CD133- subpopulations could form large colonies capable of regenerating the unsorted populations and forming tumors in nude mice. These results suggest that CD133 alone cannot be used as a stem cell marker for the lung cancer cells A549 and H446, and both the CD133+ and CD133- subpopulations contain similar numbers of cancer stem cells.