Integration of the Transcriptome and Glycome for Identification of Glycan Cell Signatures
[['Glycosylation , a broad term covering the addition of oligosaccharides ( glycans ) to proteins and lipids followed by their subsequent modification during transit through the secretory apparatus , is an intricate intracellular process whose complexity hinders ready interpretation from mass spectral and other data sets .', 'Nonetheless , three decades of research has made it clear that the glycosylation of healthy and diseased cells often diverges resulting in glycan changes that contribute to pathological progression [1] , [2] , [3] , [4] , [5] .', 'A prime example of the contribution of glycan analysis to the understanding of a pathological process and the development of clinically relevant biomarkers is provided by prostate specific antigen ( PSA ) [6] , [7] , [8] , [9] , [10] .', 'Changes in the glycosylation status of this widely used biomarker for prostate cancer screening have been useful in improving its specificity and ability to distinguish benign forms of this disease from highly malignant cancer [11] , [12] .', 'While considerable progress has been made from decades of painstaking research focused on PSA , efforts to identify additional glycan markers of disease suffer from the difficulties in identifying specific glycosylation changes .', 'However , with the current proliferation of high throughput ‘omics’ approaches , opportunities are at hand to develop and implement methodologies that analyze the resulting large data sets in order to provide critical glycan signatures of disease; for example to expand analyses from PSA to additional prostate cancer biomarkers and , more broadly , from prostate cancer to the numerous cancers and diseases known to have abnormalities in glycosylation .', 'Unfortunately , the disparate sets of data needed to fully characterize glycosylation –including expression profiles of the enzymes involved in glycosylation , the activities of the resulting enzymes , and finally the large number of glycans actually produced by these enzymes – cannot be directly compared and there is yet no facile way to integrate the data to generate meaningful biological insights .', 'Transcriptional profiling of mRNA allows quantitative global assessment of the many genes involved in glycan biosynthesis i . e . glycosyltransferases , the enzymes responsible for generating glycans .', 'A wealth of data is also becoming available from the detailed assessment of the glycans using mass spectrometric techniques [13] .', 'Despite progress on both ‘omics’ fronts , useful bioinformatics tools to identify glycan structural data and also to link these findings with transcriptional profiles of the enzymes that produce these sugars have lagged .', 'For example , a common approach for mass spectrometry-based glycoprofiling involves a one-to-one data base matching of particular mass spectrometry measurements to specific glycans from a known glycan library in order to annotate the mass spectra [14] , [15] .', 'Statistical database-driven approaches have attempted to relate gene expression levels to the abundance of specific glycan linkages [16] , [17] , [18]; however these approaches do not provide quantitative predictions of detailed glycan distributions .', 'As a consequence , there is no clear understanding of how mRNA levels relate to the actual amount and distribution of glycans found within a healthy or diseased cell .', 'In addition , current bioinformatic techniques only consider each mass spectral peak in isolation and do not consider other relevant peaks when making an identification or quantification .', 'In this work , we address this void with a novel systems biology model that interconnects glycan structural data obtained from mass spectrometry with changes in gene expression obtained from mRNA profiling of the relevant glycan processing enzymes .', 'The glycobioinformatics approach interprets mass spectral data in terms of the activity of glycan-processing enzymes and then compares these values to those indicated from gene expression profile .', 'The model identifies a number of unrecognized glycan structures and their abundances from mass spectral peaks by analyzing the entire mass spectrum in concert instead of considering each mass peak in isolation .', 'The model can also process the relative enzyme transcript gene expression levels , and translates them into a synthetic mass spectrum and a quantitative glycan profile .', 'This model approach has been applied to uncover subtle differences in the glycan signatures between two sets of cancer cells , specifically low and high passage , androgen dependent and independent ( respectively ) LNCaP prostate cancer cells .', 'This effort has yielded insights into glycan-specific changes associated with malignant progression in this disease .', 'In addition , this model approach enables a comparison of the result from the two ‘omics’ platforms and enables identification of consistent and inconsistent patterns across the two media .', 'Moreover , this systems biology methodology allows users to gain insights into the complex multi-step cellular glycosylation process from disparate data sets and will serve as a critical step along the path towards the identification of key glycan biomarkers and therapeutic disease targets .'], ['In previous publications we applied a comprehensive mathematical model that incorporates a kinetic network for enzyme processing of N-glycans to interpret mass spectral and other glycan analytical data ( HPLC ) in terms of detailed glycan structures as well as specific enzyme activities [19] , [20] .', 'This analysis was useful for screening differences in glycan profiles and enzyme activities between different cell types .', 'In this study we present an integrative glycan systems modeling approach that considers mRNA gene expression profiles for the glycosyltransferases and other enzymes involved in glycan synthesis together with matching MALDI TOF ( Matrix assisted laser desorption ionization time of flight ) mass spectral data .', 'This data integrative modeling approach provides a thorough characterization of the changes in the glycan structural profile and abundances through the mass spectra .', 'Model sizes used in this study are typically limited to about 10 , 000 to 25 , 000 glycan structures based on the implementation of a molecular mass cutoff and a network pruning method .', 'This allows prediction of the complete glycan profile and its abundances for any set of assumed enzyme concentrations and reaction rate parameters .', 'A schematic representation and explanation of how the model integration of mass spectrometric and gene expression data works is shown in Figure 1 ( for more details see Materials and Methods ) .', 'High and low passage LNCaP cells provide a model for cancer progression from the androgen-dependent to the androgen-independent state [21] .', 'The MALDI TOF mass spectrometry data for the low and high passage human prostate LNCaP cells are available at the Consortium of Functional Glycomics ( CFG ) database [22] and under supplementary material in Dataset S1 and Dataset S2 .', 'The C-33 cells , or low passage cells , include cells between passages 25 and 35 and serve as a model for androgen-dependent cells .', 'The C-81 cells or high passage type were derived from the low passage cell line and have diverged into an androgen non-responsive state; they include cells between passages 81 and 125 [21] .', 'The comparison of model generated synthetic mass spectra to experimental MALDI TOF mass spectra ( Figure 2 and Figure 3 ) requires processing of the raw mass spectra , including baseline correction , mass calibration adjustment , peak integration and filtering of isolated spikes ( individual peaks without isotopic satellites ) , software development for that end is described in Materials and Methods .', 'Fitting of both MALDI TOF experimental data sets to synthetic mass spectra obtained through solving our N-glycosylation computational model as described in Figure 1 generates a set of glycan structures and abundances .', 'The parity plot in Figure 2 gives the agreement of the calculated and measured experimental mass spectrometric data in the range of 1400–4000 for both high and low passage LNCaP cells .', 'Peaks in agreement are located on the parity line; in general , a good fit is obtained for many of the glycans .', 'The experimental mass spectrum extends to 5000; however , for this set of data few molecular masses are significant in the 4000 to 5000 range and thus the model was limited to the 4000 range .', 'This model approach can be readily implemented to assign a group of glycans with specific details on their associated structures and abundances to each peak in the MALDI TOF mass spectra of diverse mammalian cell types .', 'For example , the good agreement obtained between the measured and synthetic mass spectra obtained from the model as indicated in Figure 2 for both LNCaP cell lines , is translated in Figure 3 as a close alignment of the experimental mass spectral levels ( blue line ) with the model predictions ( red line ) for most of the peaks .', 'Overall , in Figure 3 , we present a selected portion of the mass spectra for the low and high passage cell lines in the range of 2150 to 2750 with the dominant glycan structures producing each peak indicated by schematic structural diagrams .', 'The comparative glycoprofiling of both cell lines is discussed in the next section and the complete set of glycans annotated across the 1500–4000 MS range is provided in Figure S1 .', 'High and low passage LNCaP cells that provide a model of cancer progression from the androgen-dependent to androgen-independent state exhibited considerable similarity in N-glycan patterns ( Figure 3 ) ; this result was expected because both cell lines come from the same progenitor and only differ in the number of passages .', 'However , the comparative glycoprofiling shown in Figure 3 establishes that there are also several differences between the two cell lines .', 'For example , at the peak envelope starting at a monoisotopic mass of 2418 . 21 ( the lowest mass of the isotope group ) , the high passage cells have about twice the signal of the low passage cells , partially due to the appearance of a structure containing the blood group H ( II ) epitope ( Fucα1 , 2Galβ1 , 4GlcNAcβ ) in the high passage glycans ( See Figure 4 for N-glycan processing diagram ) .', 'Another peak envelope starting at a mass of 2592 . 30 is about four times higher for the high-passage cells , due to the increased abundance of terminal fucose groups ( Fucα1 , 2Galβ ) .', 'Predictions of the abundances of glycans based on the model analysis of the complete mass spectral data is shown in terms of types of glycans in Figure 5 and glycan moieties associated into blood group categories in Figure 6 .', 'The mass spectra for both high and low passage prostate cancer LNCaP cells are most abundant in high mannose glycoforms ( Figure 5 ) .', 'Indeed , prostate-specific membrane antigen ( PMSA ) protein derived from LNCaP cells was found to contain high mannose structures [23] which indicates the generation of these structures from this cell line .', 'In addition , a series of complex glycans with tetraantennary structures being the most abundant followed by biantennary and triantennary glycans are observed in both low and high passage cell lines ( Figure 5 ) and were reported in [24] .', 'Here we see that the more metastatic high passage cells have higher levels of hybrid glycans and lower levels of complex glycans , especially tetraantennary .', 'Nearly 70%–80% of the hybrid and complex glycan structures ( % based on hybrid and complex not total glycans ) in both low and high passage LNCaP cells are core fucosylated ( Figure 5 ) .', 'Indeed , previous studies have reported core fucosylated glycan structures as characteristic of PSA from LNCaP cells [8] , [10] , [25] .', 'Complex glycans are mostly identified as non sialic acid capped complexes of the bi , tri and tetraantennary type .', 'However , limited levels of monosialylated , bisected glycans structures and lactosamine repeats ( Galβ1–4GlcNAc ) are predicted .', 'Glycan moieties of type II are predominant in both cell lines ( Figure 5 and Figure 4 ) .', 'Note that a single glycan can contain more than one of a particular glycan moiety , so the abundances of some moieties can exceed 100% of the total number of glycans , used as the basis for this percentage .', 'In terms of blood group structures which include antigens A , B , Lea , Leb , Ley , Lex and H in Figure 4 , the H ( II ) and the Ley epitopes , containing α1 , 2-fucose linkages , are predicted in these types of prostate cancer cells , with greater abundance in high passage LNCaP cells ( Figure 5 ) .', 'Indeed , these epitopes have been reported as characteristic markers for prostate cancer [7] , [10] , [26] , [27] , [28] , [29] , [30] .', 'The concentrations of the glycan-processing enzymes were adjusted in the computational model until satisfactory agreement was obtained between the in silico mass spectral profile with the experimental mass spectral profile for both data sets .', 'Shown in Table 1 ( columns 4 and 5 ) are the adjusted enzyme activities that provided the best fit with both experimental mass spectral data sets and produced the glycan abundances in Figure 5 and 6 .', 'A comparison of the observed changes in the enzyme levels between high and low passage LNCaP cells provides a succinct way of interpreting the differences in glycan structural profiles between these LNCaP cells lines .', 'In general we observe that model predicted enzyme activities are in qualitative agreement with available published enzyme values in terms of increasing and decreasing levels between cases .', 'A description of some of the trends that were observed in the enzymatic activities corresponding to the resulting glycan profiles for the two LNCaP cell lines are described in following sections .', 'Mapping of model enzymes Table 1 ( column 1 ) to gene probes ( columns 6 and 7 ) on the Consortium of Functional Glycomics ( CFG ) Glycogene microarray ( Glycochip version 3 , CFG ) was performed for both low and high passage human prostate LNCaP cell line data available at the Consortium of Functional Glycomics website ( MAEXP_291_040606 ) and also included in Dataset S3 [22] .', 'Listed in columns 8 and 9 of Table 1 are the observed changes in expression levels of these genes as determined from mRNA analysis of microarrays for the low passage and high passage LNCaP cells .', 'These expression signals were obtained by averaging three replicate samples for each glycogene in the microarray and represent the average relative abundance of a transcript .', 'The glycogenes were assigned calls by CFG of present ( P ) , marginal ( M ) or absent ( A ) ( more information on the classification criteria is found in Materials and Methods ) .', 'In Table 1 the marginal or absent calls are indicated with numbers in bold .', 'Note that more than one gene can encode the same type of enzyme activity .', 'In addition to the genes for N-Glycan processing as discussed for Table 1 , the glycochip version 3 includes genes for many other glycosylation-related genes .', 'However , in some cases not all the genes that encode for a given enzyme are included on the CFG version 3 microarray .', 'Interestingly , the largest shifts in gene expression observed between the two types of prostate cancer cell types from the glycochip are those that encode for the enzyme glucuronosyltransferase ( EC 2 . 4 . 1 . 17 ) , which is involved in androgen/estrogen metabolism but has no effect on N-glycan structure [36] , [37] , [38] .', 'In general transcript expression levels from the microarray are consistent with the enzyme activities resulting from the model , at least in terms of the presence or absence of enzymes in the model and on the gene expression array .', 'Enzymes whose genes are classified as marginal or absent in the microarray data include GnTIII , a6SiaT , GalTB and GalNacT-A ( Table 1 columns 8 and 9 in bold ) .', 'Interestingly , enzymatic activity levels for this same collection of enzymes were also predicted by the model to be low or zero independently based on fits of the mass spectral data ( Table 1 columns 4 and 5 ) .', 'The most significant percentage shift in enzyme activity that differentiates high and low passage LNCaP cells was increased FucTH activity in high passage or androgen independent LNCaP cells .', 'Although the model based solely on mass spectrometry measurements deduced this finding of increased FucTH activity , the uptick in FucTH expression was also correlated with mRNA microarray expression data for the FUT1 gene ( Table 1 columns 8 and 9 ) .', 'The FUT1 gene has been experimentally identified in LNCaP cells and prostate cancer tissues as responsible for production of the H ( II ) epitope [10] , [28] .', 'In addition model-fitted mass spectra data indicate a lower capacity for generating type I glycans relative to type II glycans as b3GalT activity is lower than b4GalT activity in Table 1 .', 'This finding also correlated with the relative gene expression data in that the expression of b3GalT genes encoded by B3GALT1 , B3GALT2 , and B3GALT5 are marginal in both data sets from both cell lines ( Table 1 columns 8 and 9 ) .', 'In contrast , gene expression levels for the B4GALT1 , B4GALT2 , B4GALT3 and B4GALT5 ( Table 1 columns 8 and 9 ) encoding b4GalT activity for type II glycans is robust in both cell lines as it is the generation of type II glycans as indicated by the model fitting of mass spectral data and predicted b4GalT enzymatic activity .', 'While there were many consistencies between model interpretation of mass spectrometry and gene expression profiles , there were also some disagreements between the model-calculated enzyme levels and the expression levels obtained from mRNA , such as for GnTV , a3SialT and FucTLe .', 'For some enzymes , these differences can be attributed to shortcomings in the mRNA profiling chips .', 'A case in point is that the inactivity of a probe set for MGAT5 ( one of two genes encoding GnTV activity ) in the glycochip version 3 from CFG led to a reported lack of expression of this gene despite the presence of GnTV activity in the results modeled from the mass spectral data ( Table 1 column 4 and 5 ) .', 'Interestingly , by reviewing all experimental cases run with the glycochip version 3 for all cell lines posted on the CFG we found that the probe set for MGAT5 gene was inactive .', 'Furthermore , the presence of GnTV indicated by the model interpretations of the mass spectral data agrees with a previous experimental study that reports positive GnTV enzymatic activity using a zymography assay and active expression of MGAT5 through RT-PCR in LNCaP cell lines [32] .', 'Results from model testing of this proposed deficiency in the glycochip version 3 are discussed in Text S2 , Figure S2 , and Figure S3 .', 'These findings support the interpretation that the inactivity of the GnTV in the microarray data is due to a defect in this specific probe on the microarray .', 'For other enzymes , the lack of model agreement with gene expression data is likely due to the scope of the current model .', 'For example , the microarray data indicates significant levels of α3SiaT mRNA for both LNCaP cell passages , although the enzymatic model interpretation from MALDI TOF indicated that LNCaP cells have low a3SialT activity .', 'Interestingly , analysis of expression of genes associated with sialic acid biosynthesis , a feature not included in the current model , indicates that the transcript levels for the GNE gene ( that encodes the bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase ) for both cell lines are interpreted as absent .', 'Bifunctional GNE catalyzes two critical steps involving sequential reactions in the biosynthesis of the sugar nucleotide CMP-Neu5Ac ( CMP-sialic acid ) ( Figure S4 , Text S3 ) , which is the co-substrate for a3SiaT .', 'The α2 , 3- or α2 , 6-linked sialylated N-glycans are generated by the transfer of the sialic acid ( Neu5Ac ) group from the nucleotide donor sugar CMP-Neu5Ac onto the oligosaccharide acceptor ending in a galactose ( Gal ) residue .', 'Thus , the formation of a limited number of sialylated glycoforms may be due to low levels of the nucleotide sugar substrate , CMP-Neu5Ac , rather than due to a limitation in the a3SiaT activity as currently manifested in the model .', 'While the current model has focused on glycosyltransferase activities , it can be readily expanded to include other metabolic reactions such as the generation of sugar nucleotides including CMP-Neu5Ac and others .', 'For the FucTLe enzyme , the model predictions show lack of activity , while the microarray data shows gene expression signal for FucTLe .', 'Both FucTLe and a3FucT enzymes catalyze the addition of α-3 fucose to GlcNAc residues on type II chains as shown in Figure 4 .', 'They only differ on Type I chains , in the generation of Lea and Leb structures .', 'The lack of these Le structures makes it difficult for the model to separate the two enzyme activities and at least part of the activity the model shows for a3FucT may be due to FucTLe .', 'As an alternative predictive approach , the potential also exists for using gene expression profiles to estimate changes in enzyme activities .', 'Appreciating that mRNA levels do not always reflect enzyme levels directly , we assumed shifts in gene expression data were related to shifts in enzyme levels .', 'These shifts in gene expression were then used to predict the corresponding shifts in glycan profile and abundances for high and low passage LNCaP cells .', 'To get the transcript expression level of the enzymes in the model , the average of all mRNA-microarray gene signals corresponding to each enzyme was used .', 'Next the ratios of average signals ( high/low passages ) for each enzyme were used as inputs to the N-glycosylation model based on the assumption that they are estimates of the relative enzyme levels for high and low passage LNCaP cells .', 'The implementation of this methodology into the model also required adjusting the enzyme levels in the model to match the experimental mass spectra data for one case ( low passage for this study ) while maintaining the enzyme activity ratios to be equal to the experimental values obtained from the microarray data ( Table S1 ) .', 'The ratios of expression levels of high to low passage cells were then used to predict the enzyme levels for the high passage case and the resulting glycan profile predicted .', 'No constraint was placed on the concentrations of GnTV or ManI in the model as these enzymes have either a probe defect ( GnTV ) or are missing in the glycochip version 3 ( Man I ) .', 'The results of keeping the enzyme ratios constant and equal to the microarray ratios are shown in Figure 7 , which show the abundances of different categories of glycans .', 'The percentage of different structures predicted by the model using MALDI-TOF mass spectral data alone ( green bars ) are compared to the abundances obtained after fixing the gene expression mRNA ratios ( orange bars ) .', 'Predictions for the low passage , androgen dependent LNCaP cells are indicated by light green bars for mass spectral data and light orange bars for mRNA data .', 'Similarly , predictions for high passage , androgen independent LNCaP cells are indicated by dark green bars for mass spectra data and dark orange bars for mRNA data .', 'This approach allows the model to predict changes in glycan structure profile and glycan abundances based on comparative N- glycosylation enzyme gene expression data .', 'Although constraining model fitting to fixed gene expression ratios resulted in a higher RMS error ( lower model agreement ) with respect to the model fitting to the mass spectra data alone ( as would be expected for additional model constraints ) , the trends in glycan structures and abundances are comparable in both cases with a few minor exceptions .', 'In general , glycan structure prediction from both data sets ( gene expression and mass spectra vs . mass spectra alone ) show consistency in terms of presence , absence and increased or decreased abundances of glycans in high passage with respect to low passage LNCaP cells .', 'For example , both model predictions with mass spectra and gene expression data suggest an increase in abundance of hybrid and biantennary structures in the high passage cells and a corresponding decrease in the tetraantennary structures .', 'Both mRNA data and models predict high levels of type II chains in both low and high passage LNCaP cells , reaffirming that these cell lines contain predominantly type II glycans .', 'The model based on gene expression data suggested lack of type I glycans , principally due to imposing a strict restriction on b3GalT which in reality may not be as strict as the mRNA data for the genes encoding this enzyme are classified as either marginal or absent .'], ['In this study , a systems biology computational model that connects diverse experimental data sets was used to evaluate N-glycan data from MALDI-TOF mass spectra and mRNA expression arrays for androgen independent , high passage LNCaP cells , and androgen dependent , low passage , LNCaP cells .', 'Most significantly , insights into the N-glycosylation processing for LNCaP high and low passage cells were found based on model predictions of enzyme activities , glycan structures and gene expression profiles .', 'The model was also useful for identifying consistencies as well as incongruities between glycan structural information and gene expression data .', 'The N-glycosylation model identified and quantified glycan structural details not typically derived from single-stage mass spectral or gene expression data , such as the type of fucosylation ( Fuc-α1 , 2-Gal vs . Fuc-α1 , 3-GlcNAc and Fuc-α1 , 6-GlcNAc ) , the predominance of Type II chains ( Gal-β1 , 4-GlcNAc ) versus Type I chains ( Gal-β1 , 3-GlcNAc ) or the number of antennae .', 'This is possible by analyzing the total mass spectrum in terms of the underlying processing events and enzyme activities that generate both the individual structures and the assemblage of structures resulting in the complete mass spectrum .', 'For example , Fuc-α1 , 2-Gal can be differentiated from Fuc-α1 , 3-GlcNAc because they include the different molecular weight linked sugars of Gal and GlcNAc .', 'More relevant to the current modeling approach , Fuc-α1 , 3-GlcNAc and Fuc-α1 , 6-GlcNAc can be differentiated because , even though both include the same molecular weight linkages , Fuc-α1 , 6-GlcNAc is added to the glycan core early in processing , while the Fuc-α1 , 3 is only added later to GlcNAc on one of the N-glycan branch extensions .', 'The presence of a collection of mass spec peaks provides a fingerprint that the model can interpret to indicate whether this fucose is added earlier ( Fuc-α1 , 6-GlcNAc ) or later ( Fuc-α1 , 3-GlcNAc ) in the N-glycan processing pathway .', 'Thus the model creates a picture of the complete N-glycan processing , including enzyme activity levels acting sequentially through the secretory apparatus that is consistent with the entire collection of glycan peaks across the molecular weight spectrum .', 'Comparison of the underlying enzyme activities derived by the model from the mass spectral data with changes in gene expression levels measured by the CFG glycogene microarray show them to be consistent for most enzymes , which tends to verify that the model-derived shifts are meaningful .', 'The agreement also suggests that the model could be used to predict shifts in glycan structure from a well-defined base case based on changes in microarray expression data when MS data for other cases is not available .', 'It is important to note that aberrant N- and O-glycosylation are important features of cancer cells .', 'Indeed a number of the genes included in the model act on both N-glycans and O-glycans , while the model infers changes in the total enzyme activities based only on the observed shifts in N-glycan structures .', 'Thus if the levels of O-glycan structures that compete with N-glycan structures for a number of enzymes changes significantly , the fraction of those enzymes activities that are available for N-glycan processing could also change , distorting the comparison between model predicted enzyme activities and enzyme gene expression levels .', 'While our N-glycosylation model gave very good agreement between the model-predicted and measured mass spectra , it is expected that the incorporation of O-glycosylation together with N-glycosylation will improve the model predictability .', 'In addition , these competing reactions will be better modulated in the model .', 'Implementation of O-glycosylation in the current model framework is possible since kinetic parameters for the corresponding O-glycan enzymes as well as experimental data are available to tune the model .', 'Of course , processing larger data sets including O-glycans may very well elucidate limitations in the model that will need to be addressed through appropriate modification of model parameters .', 'Interestingly , the most significant difference found between high and low passage prostate cancer cell lines was the increase in expression of α1 , 2-Fuc-transferase ( FucTH ) enzyme in the high passage LNCaP cells , as predicted by the model based on mass spectrometry and verified by the gene expression data .', 'The microarray data indicates that the FUT1 gene is predominant in high passage LNCaP cells with respect to low passage LNCaP cells .', 'The FUT1 gene has been experimentally identified in LNCaP cells and prostate cancer tissues and associated to the H ( II ) epitope ( Fucα1 , 2Galβ1–4GlcNAc ) [28] .', 'Moreover , the presence of Fucα1-2Gal residues that results from the enzymatic action of FuTH has been reported in PSA from LNCaP cells [10] , [28] , [31] , [35] .', 'The high passage LNCaP cells in this work were obtained from low passage LNCaP cells ( androgen dependent ) after successive passages and they have diverged into an androgen independent state .', 'Our finding that high passage LNCaP prostate cancer cells ( androgen independent ) have increased levels of the enzyme FucTH ( FUT1 gene ) responsible for α1 , 2-fucosylation and the H ( II ) and Ley epitopes with respect to low passage LNCaP cells may represent a potential marker of higher malignancy or androgen refractory prostate cancer cells and may be relevant in diagnosing prostate cancer stage .', 'For example it may be possible to compare glycan mass spectra of PSA concentrated from blood serum , presumably originating in cancer cells , to PSA from semen samples , derived mostly from normal prostate cells , to evaluate the stage of the cancer .', 'Our results also indicate that b4GalT is present in both high and low passage LNCaP cells .', 'The most expressed member of the family is the B4GALT1 gene followed by the B4GALT3 gene .', 'Evidence of b4GalT in prostatic cancer samples is found by detection of Galβ1 , 4GlcNAc ( Type II ) structure with the Erithrina cristagalli lectin ( ECL ) in PSA from prostate cancer serum and PSA from LNCaP medium as compared to seminal plasma ( normal control ) [25] .', 'This type II structure was also detected with a set of lectin-immobilized columns together with enzyme-linked immunosorbent assays ( ELISA ) on prostate cancer serum PSA and LNCaP cells PSA as compared to benign prostate hyperplasia ( BHP ) serum PSA [31] .', 'Interestingly , screened experimental data on prostate cancer predominantly reports the presence of Galβ1 , 4GlcNAc ( Type II ) glycans and some of its derivatives and almost no information is found for Galβ1 , 3GlcNAc ( type I ) glycans .', 'In agreement with that , the model predicted the presence of H type II ( Fuc1 , 2Galβ1 , 4GlcNAc ) and Ley- ( Fuc1 , 2Galβ1 , 4GlcNAc Fuc1-3 ) glycans and also increased levels of these epitopes in the more metastatic high passage LNCaP cells .', 'Importantly , several previous studies have reported type II based epitopes H [10] , [26] , [27] , [28] and Ley as blood group antigens as characteristic of prostate cancer [7] , [29] , [30] , [39] .', 'For example , lectin histochemistry comparisons between normal human prostate and prostatic carcinoma tissues show increased expression of galactose ( using DSA lectin suggesting presence of Galβ1 , 4GlcNAc ) , and fucose [6] ( using UEA-I , a marker for the H antigen ) .', 'Also , investigations 
['Introduction', 'Results', 'Discussion', 'Materials and Methods']
['Abnormalities in glycan biosynthesis have been conclusively linked to many diseases but the complexity of glycosylation has hindered the analysis of glycan data in order to identify glycoforms contributing to disease .', 'To overcome this limitation , we developed a quantitative N-glycosylation model that interprets and integrates mass spectral and transcriptomic data by incorporating key glycosylation enzyme activities .', 'Using the cancer progression model of androgen-dependent to androgen-independent Lymph Node Carcinoma of the Prostate ( LNCaP ) cells , the N-glycosylation model identified and quantified glycan structural details not typically derived from single-stage mass spectral or gene expression data .', 'Differences between the cell types uncovered include increases in H ( II ) and Ley epitopes , corresponding to greater activity of α2-Fuc-transferase ( FUT1 ) in the androgen-independent cells .', 'The model further elucidated limitations in the two analytical platforms including a defect in the microarray for detecting the GnTV ( MGAT5 ) enzyme .', 'Our results demonstrate the potential of systems glycobiology tools for elucidating key glycan biomarkers and potential therapeutic targets .', 'The integration of multiple data sets represents an important application of systems biology for understanding complex cellular processes .']
['Glycans are the sugar attachments that are found on proteins and lipids .', 'These highly variable and structurally diverse sugar chains confer distinctive characteristics to the cell surface .', 'Recent research has revealed that these glycan profiles can represent important signatures of disease states and thus understanding glycan processing and structures in cells is an important systems biology goal .', 'Glycan structures are often characterized through mass spectral analysis while their glycosylation processing enzymes are characterized using gene expression profiling .', 'Unfortunately , due to the complexity of glycosylational processing , it has been difficult to relate these disparate data sets until now .', 'In this paper we demonstrate for the first time the ability of a systems glycobiology model to link glycan structural data obtained from mass spectral analysis with mRNA expression data in terms of enzyme activities catalyzing the glycosylation reactions in the cells .', 'We show that such a systems biology model enables identification of distinctive and subtle glycan fingerprints differences between prostate cancer cell stages ( androgen-dependent and more metastatic androgen independent ) .', 'This systems approach will enable us to use high throughput glycomics and gene expression data sets in order to specify glycan-based signatures as important diagnostic markers of disease and potential therapeutic targets .']
['systems biology', 'biology', 'genetics and genomics']