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1.
FASEB J ; 38(8): e23621, 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38651653

ABSTRACT

Denervated myofibers and senescent cells are hallmarks of skeletal muscle aging. However, sparse research has examined how resistance training affects these outcomes. We investigated the effects of unilateral leg extensor resistance training (2 days/week for 8 weeks) on denervated myofibers, senescent cells, and associated protein markers in apparently healthy middle-aged participants (MA, 55 ± 8 years old, 17 females, 9 males). We obtained dual-leg vastus lateralis (VL) muscle cross-sectional area (mCSA), VL biopsies, and strength assessments before and after training. Fiber cross-sectional area (fCSA), satellite cells (Pax7+), denervated myofibers (NCAM+), senescent cells (p16+ or p21+), proteins associated with denervation and senescence, and senescence-associated secretory phenotype (SASP) proteins were analyzed from biopsy specimens. Leg extensor peak torque increased after training (p < .001), while VL mCSA trended upward (interaction p = .082). No significant changes were observed for Type I/II fCSAs, NCAM+ myofibers, or senescent (p16+ or p21+) cells, albeit satellite cells increased after training (p = .037). While >90% satellite cells were not p16+ or p21+, most p16+ and p21+ cells were Pax7+ (>90% on average). Training altered 13 out of 46 proteins related to muscle-nerve communication (all upregulated, p < .05) and 10 out of 19 proteins related to cellular senescence (9 upregulated, p < .05). Only 1 out of 17 SASP protein increased with training (IGFBP-3, p = .031). In conclusion, resistance training upregulates proteins associated with muscle-nerve communication in MA participants but does not alter NCAM+ myofibers. Moreover, while training increased senescence-related proteins, this coincided with an increase in satellite cells but not alterations in senescent cell content or SASP proteins. These latter findings suggest shorter term resistance training is an unlikely inducer of cellular senescence in apparently healthy middle-aged participants. However, similar study designs are needed in older and diseased populations before definitive conclusions can be drawn.


Subject(s)
Cellular Senescence , Resistance Training , Humans , Resistance Training/methods , Male , Female , Middle Aged , Cellular Senescence/physiology , Muscle Fibers, Skeletal/metabolism , Muscle Fibers, Skeletal/physiology , Biomarkers/metabolism , Satellite Cells, Skeletal Muscle/metabolism , Muscle, Skeletal/metabolism , Muscle, Skeletal/physiology , PAX7 Transcription Factor/metabolism , Cyclin-Dependent Kinase Inhibitor p21/metabolism , Cyclin-Dependent Kinase Inhibitor p16/metabolism , Adult , Quadriceps Muscle/metabolism , Quadriceps Muscle/innervation
2.
Aging (Albany NY) ; 16(8): 6631-6651, 2024 04 19.
Article in English | MEDLINE | ID: mdl-38643460

ABSTRACT

The skeletal muscle proteome alterations to aging and resistance training have been reported in prior studies. However, conventional proteomics in skeletal muscle typically yields wide protein abundance ranges that mask the detection of lowly expressed proteins. Thus, we adopted a novel deep proteomics approach whereby myofibril (MyoF) and non-MyoF fractions were separately subjected to protein corona nanoparticle complex formation prior to digestion and Liquid Chromatography Mass Spectrometry (LC-MS). Specifically, we investigated MyoF and non-MyoF proteomic profiles of the vastus lateralis muscle of younger (Y, 22±2 years old; n=5) and middle-aged participants (MA, 56±8 years old; n=6). Additionally, MA muscle was analyzed following eight weeks of resistance training (RT, 2d/week). Across all participants, the number of non-MyoF proteins detected averaged to be 5,645±266 (range: 4,888-5,987) and the number of MyoF proteins detected averaged to be 2,611±326 (range: 1,944-3,101). Differences in the non-MyoF (8.4%) and MyoF (2.5%) proteomes were evident between age cohorts, and most differentially expressed non-MyoF proteins (447/543) were more enriched in MA versus Y. Biological processes in the non-MyoF fraction were predicted to be operative in MA versus Y including increased cellular stress, mRNA splicing, translation elongation, and ubiquitin-mediated proteolysis. RT in MA participants only altered ~0.3% of MyoF and ~1.0% of non-MyoF proteomes. In summary, aging and RT predominantly affect non-contractile proteins in skeletal muscle. Additionally, marginal proteome adaptations with RT suggest more rigorous training may stimulate more robust effects or that RT, regardless of age, subtly alters basal state skeletal muscle protein abundances.


Subject(s)
Aging , Muscle, Skeletal , Proteomics , Resistance Training , Humans , Aging/metabolism , Aging/genetics , Middle Aged , Proteomics/methods , Male , Young Adult , Muscle, Skeletal/metabolism , Proteome/metabolism , Muscle Proteins/metabolism , Muscle Proteins/genetics , Adult , Female
3.
bioRxiv ; 2023 Jul 05.
Article in English | MEDLINE | ID: mdl-37333259

ABSTRACT

We examined the myofibrillar (MyoF) and non-myofibrillar (non-MyoF) proteomic profiles of the vastus lateralis (VL) muscle of younger (Y, 22±2 years old; n=5) and middle-aged participants (MA, 56±8 years old; n=6), and MA following eight weeks of knee extensor resistance training (RT, 2d/week). Shotgun/bottom-up proteomics in skeletal muscle typically yields wide protein abundance ranges that mask lowly expressed proteins. Thus, we adopted a novel approach whereby the MyoF and non-MyoF fractions were separately subjected to protein corona nanoparticle complex formation prior to digestion and Liquid Chromatography Mass Spectrometry (LC-MS) analysis. A total of 10,866 proteins (4,421 MyoF and 6,445 non-MyoF) were identified. Across all participants, the number of non-MyoF proteins detected averaged to be 5,645±266 (range: 4,888-5,987) and the number of MyoF proteins detected averaged to be 2,611±326 (range: 1,944-3,101). Differences in the non-MyoF (8.4%) and MyoF (2.5%) proteome were evident between age cohorts. Further, most of these age-related non-MyoF proteins (447/543) were more enriched in MA versus Y. Several biological processes in the non-MyoF fraction were predicted to be operative in MA versus Y including (but not limited to) increased cellular stress, mRNA splicing, translation elongation, and ubiquitin-mediated proteolysis. Non-MyoF proteins associated with splicing and proteostasis were further interrogated, and in agreement with bioinformatics, alternative protein variants, spliceosome-associated proteins (snRNPs), and proteolysis-related targets were more abundant in MA versus Y. RT in MA non-significantly increased VL muscle cross-sectional area (+6.5%, p=0.066) and significantly increased knee extensor strength (+8.7%, p=0.048). However, RT modestly altered the MyoF (~0.3%, 11 upregulated and two downregulated proteins) and non-MyoF proteomes (~1.0%, 56 upregulated and eight downregulated proteins, p<0.01). Further, RT did not affect predicted biological processes in either fraction. Although participant numbers were limited, these preliminary results using a novel deep proteomic approach in skeletal muscle suggest that aging and RT predominantly affects protein abundances in the non-contractile protein pool. However, the marginal proteome adaptations occurring with RT suggest either: a) this may be an aging-associated phenomenon, b) more rigorous RT may stimulate more robust effects, or c) RT, regardless of age, subtly affects skeletal muscle protein abundances in the basal state.

4.
Mass Spectrom Rev ; 42(2): 822-843, 2023 03.
Article in English | MEDLINE | ID: mdl-34766650

ABSTRACT

Pancreatic ductal adenocarcinoma (PDAC) is the most common neoplastic disease of the pancreas, accounting for more than 90% of all pancreatic malignancies. As a highly lethal malignancy, PDAC is the fourth leading cause of cancer-related deaths worldwide with a 5-year overall survival of less than 8%. The efficacy and outcome of PDAC treatment largely depend on the stage of disease at the time of diagnosis. Surgical resection followed by adjuvant chemotherapy remains the only possibly curative therapy, yet 80%-90% of PDAC patients present with nonresectable PDAC stages at the time of clinical presentation. Despite our advancing knowledge of PDAC, the prognosis remains strikingly poor, which is primarily due to the difficulty of diagnosing PDAC at the early stages. Recent advances in glycoproteomics and glycomics based on mass spectrometry have shown that aberrations in protein glycosylation plays a critical role in carcinogenesis, tumor progression, metastasis, chemoresistance, and immuno-response of PDAC and other types of cancers. A growing interest has thus been placed upon protein glycosylation as a potential early detection biomarker for PDAC. We herein take stock of the advancements in the early detection of PDAC that were carried out with mass spectrometry, with special focus on protein glycosylation.


Subject(s)
Carcinoma, Pancreatic Ductal , Pancreatic Neoplasms , Humans , Pancreatic Neoplasms/diagnosis , Pancreatic Neoplasms/metabolism , Pancreatic Neoplasms/pathology , Carcinoma, Pancreatic Ductal/diagnosis , Carcinoma, Pancreatic Ductal/metabolism , Carcinoma, Pancreatic Ductal/pathology , Pancreas/metabolism , Pancreas/pathology , Prognosis , Glycoproteins/metabolism , Biomarkers, Tumor/metabolism
5.
Nat Commun ; 13(1): 3910, 2022 07 07.
Article in English | MEDLINE | ID: mdl-35798744

ABSTRACT

Core fucosylation of N-linked glycoproteins has been linked to the functions of glycoproteins in physiological and pathological processes. However, quantitative characterization of core fucosylation remains challenging due to the complexity and heterogeneity of N-linked glycosylation. Here we report a mass spectrometry-based method that employs sequential treatment of intact glycopeptides with enzymes (STAGE) to analyze site-specific core fucosylation of glycoproteins. The STAGE method utilizes Endo F3 followed by PNGase F treatment to generate mass signatures for glycosites that are formerly modified by core fucosylated N-linked glycans. We benchmark the STAGE method and use it to characterize site specific core fucosylation of glycoproteins from human hepatocellular carcinoma and pancreatic ductal adenocarcinoma, resulting in the identification of 1130 and 782 core fucosylated glycosites, respectively. These results indicate that our STAGE method enables quantitative characterization of core fucosylation events from complex protein mixtures, which may benefit our understanding of core fucosylation functions in various diseases.


Subject(s)
Glycopeptides , Liver Neoplasms , Fucose/metabolism , Glycopeptides/chemistry , Glycoproteins/metabolism , Glycosylation , Humans , Mass Spectrometry/methods
6.
ACS Omega ; 7(11): 9172-9180, 2022 Mar 22.
Article in English | MEDLINE | ID: mdl-35350332

ABSTRACT

Prostate cancer, bladder cancer, and renal cancers are major urogenital cancers. Of which, prostate cancer is the most commonly diagnosed and second leading cause of cancer death for men in the United States. For urogenital cancers, urine is considered as proximate body fluid to the tumor site for developing non-invasiveness tests. However, the specific molecular signatures from different urogenital cancers are needed to relate changes in urine to various cancer detections. Herein, we utilized a previously published C4-Tip and C18/MAX-Tip workflow for enrichment of glycopeptides from urine samples and evaluated urinary glycopeptides for its cancer specificity. We analyzed 66 urine samples from bladder cancer (n = 27), prostate cancer (n = 4), clear cell renal cell carcinoma (ccRCC, n = 3), and benign plastic hyperplasia (BPH, n = 32) and then compared them with a previous publication that reported glycopeptides associated with aggressive prostate cancer (Gleason score ≥ 8). We further demonstrated the cancer specificity of the glycopeptides associated with aggressive prostate cancer. In this study, a total of 33 glycopeptides were identified to be specifically differentially expressed in prostate cancer compared to other urogenital cancer types as well as BPH urines. By cross-comparison with our previous urinary glycoproteomic dataset for aggressive prostate cancer, we reported a total of four glycopeptides from glycoproteins DSC2, MGAM, PIK3IP1, and CD55, commonly identified to be prostate cancer-specific. Together, these results deepen our understanding of the urinary glycoproteins associated with urogenital cancer types and expand our knowledge of the cancer specificity of urinary glycoproteins among urogenital cancer progression.

7.
Anal Chem ; 93(41): 13774-13782, 2021 10 19.
Article in English | MEDLINE | ID: mdl-34622651

ABSTRACT

N-linked protein glycosylation is a key regulator in various biological functions. Previous studies have shown that aberrant glycosylation is associated with many diseases. Therefore, it is essential to elucidate protein modifications of glycosylation by quantitatively profiling intact N-linked glycopeptides. Data-independent acquisition (DIA) mass spectrometry (MS) is a cost-effective, flexible, and high-throughput method for global proteomics. However, substantial challenges are still present in the quantitative analysis of intact glycopeptides with high accuracy at high throughput. In this study, we have established a novel integrated platform for the DIA analysis of intact glycopeptides isolated from complex samples. The established analysis platform utilizes a well-designed DIA-MS method for raw data collection, a spectral library constructed specifically for intact glycopeptide quantification providing accurate results by the inclusion of Y ions for quantification and filtering of quantified intact glycopeptides with low-quality MS2 spectra automatically using a set of criteria. Intact glycopeptides isolated from human serum were used to evaluate the performance of the integrated platform. By utilizing 100 isolation windows for DIA data acquisition, a well-constructed human serum spectral library containing 1123 nonredundant intact glycopeptides with Y ions, and automated data inspection, 620 intact glycopeptides were quantified with high confidence from DIA-MS. In summary, our integrated platform can serve as a reliable quantitative tool for characterizing intact glycopeptides isolated from complex biological samples to assist our understanding of biological functions of N-linked glycosylation.


Subject(s)
Glycopeptides , Proteomics , Glycopeptides/metabolism , Glycosylation , Humans , Mass Spectrometry , Serum/metabolism
8.
Curr Protoc ; 1(7): e186, 2021 Jul.
Article in English | MEDLINE | ID: mdl-34232571

ABSTRACT

Protein glycosylation is one of the most common and diverse modifications. Aberrant protein glycosylation has been reported to associate with various diseases. High-throughput and comprehensive characterization of glycoproteins is crucial for structural and functional studies of altered glycosylation in biological, physiological, and pathological processes. In this protocol, we detail a workflow for comprehensive analyses of intact glycopeptides (IGPs), glycosylation sites, and glycans from N-linked glycoproteins. By utilizing liquid handling systems, our workflow could enrich IGPs in a high-throughput manner while reducing sample processing time and human error involved in traditional proteomics sample processing techniques. Together, our workflow enables a high-throughput enrichment of glycans, glycosites, and intact glycopeptides from complex biological or clinical samples. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Enzymatic digestion of glycoproteins using C4-tips Basic Protocol 2: Intact glycopeptide analysis using C18/MAX-tips Basic Protocol 3: Glycan and glycosite analysis.


Subject(s)
Glycopeptides , Tandem Mass Spectrometry , Glycopeptides/metabolism , Glycoproteins , Glycosylation , Humans , Polysaccharides
9.
J Proteome Res ; 20(7): 3590-3599, 2021 07 02.
Article in English | MEDLINE | ID: mdl-34106707

ABSTRACT

Recently, we have found that two urinary glycoproteins, prostatic acid phosphatase (ACPP) and clusterin (CLU), combined with serum prostate-specific antigen (PSA) can serve as a three-signature panel for detecting aggressive prostate cancer (PCa) based on a quantitative glycoproteomic study. To facilitate the translation of candidates into clinically applicable tests, robust and accurate targeted parallel reaction monitoring (PRM) assays that can be widely adopted in multiple labs were developed in this study. The developed PRM assays for the urinary glycopeptides, FLN*ESYK from ACPP and EDALN*ETR from CLU, demonstrated good repeatability and a sufficient working range covering three to four orders of magnitude, and their performance in differentiating aggressive PCa was assessed by the quantitative analysis of urine specimens collected from 69 nonaggressive (Gleason score = 6) and 73 aggressive (Gleason ≥ 8) PCa patients. When ACPP combined with CLU, the discrimination power was improved from an area under a curve (AUC) of 0.66 to 0.78. By combining ACPP, CLU, and serum PSA to form a three-signature panel, the AUC was further improved to 0.83 (sensitivity: 84.9%, specificity: 66.7%). Since the serum PSA test alone had an AUC of 0.68, our results demonstrated that the new urinary glycopeptide PRM assays can serve as an adjunct to the serum PSA test to achieve better predictive power toward aggressive PCa. In summary, our developed PRM assays for urinary glycopeptides were successfully applied to clinical PCa urine samples with a promising performance in aggressive PCa detection.


Subject(s)
Acid Phosphatase/urine , Clusterin/urine , Prostate-Specific Antigen , Prostatic Neoplasms , Biomarkers, Tumor , Glycoproteins/urine , Humans , Male , Prostate-Specific Antigen/blood , Prostatic Neoplasms/diagnosis
10.
J Hematol Oncol ; 13(1): 170, 2020 12 07.
Article in English | MEDLINE | ID: mdl-33287876

ABSTRACT

BACKGROUND: Proteomic characterization of cancers is essential for a comprehensive understanding of key molecular aberrations. However, proteomic profiling of a large cohort of cancer tissues is often limited by the conventional approaches. METHODS: We present a proteomic landscape of 16 major types of human cancer, based on the analysis of 126 treatment-naïve primary tumor tissues, 94 tumor-matched normal adjacent tissues, and 12 normal tissues, using mass spectrometry-based data-independent acquisition approach. RESULTS: In our study, a total of 8527 proteins were mapped to brain, head and neck, breast, lung (both small cell and non-small cell lung cancers), esophagus, stomach, pancreas, liver, colon, kidney, bladder, prostate, uterus and ovary cancers, including 2458 tissue-enriched proteins. Our DIA-based proteomic approach has characterized major human cancers and identified universally expressed proteins as well as tissue-type-specific and cancer-type-specific proteins. In addition, 1139 therapeutic targetable proteins and 21 cancer/testis (CT) antigens were observed. CONCLUSIONS: Our discoveries not only advance our understanding of human cancers, but also have implications for the design of future large-scale cancer proteomic studies to assist the development of diagnostic and/or therapeutic targets in multiple cancers.


Subject(s)
Neoplasms/pathology , Proteins/analysis , Drug Discovery , Humans , Molecular Targeted Therapy , Neoplasms/diagnosis , Neoplasms/drug therapy , Neoplasms/metabolism , Proteins/metabolism , Proteome/analysis , Proteome/metabolism , Proteomics
11.
Theranostics ; 10(26): 11892-11907, 2020.
Article in English | MEDLINE | ID: mdl-33204318

ABSTRACT

Background: There is an urgent need for the detection of aggressive prostate cancer. Glycoproteins play essential roles in cancer development, while urine is a noninvasive and easily obtainable biological fluid that contains secretory glycoproteins from the urogenital system. Therefore, here we aimed to identify urinary glycoproteins that are capable of differentiating aggressive from non-aggressive prostate cancer. Methods: Quantitative mass spectrometry data of glycopeptides from a discovery cohort comprised of 74 aggressive (Gleason score ≥8) and 68 non-aggressive (Gleason score = 6) prostate cancer urine specimens were acquired via a data independent acquisition approach. The glycopeptides showing distinct expression profiles in aggressive relative to non-aggressive prostate cancer were further evaluated for their performance in distinguishing the two groups either individually or in combination with others using repeated 5-fold cross validation with logistic regression to build predictive models. Predictive models showing good performance from the discovery cohort were further evaluated using a validation cohort. Results: Among the 20 candidate glycoproteins, urinary ACPP outperformed the other candidates. Urinary ACPP can also serve as an adjunct to serum PSA to further improve the discrimination power for aggressive prostate cancer (AUC= 0.82, 95% confidence interval 0.75 to 0.89). A three-signature panel including urinary ACPP, urinary CLU, and serum PSA displayed the ability to distinguish aggressive prostate cancer from non-aggressive prostate cancer with an AUC of 0.86 (95% confidence interval 0.8 to 0.92). Another three-signature panel containing urinary ACPP, urinary LOX, and serum PSA also demonstrated its ability in recognizing aggressive prostate cancer (AUC=0.82, 95% confidence interval 0.75 to 0.9). Moreover, consistent performance was observed from each panel when evaluated using a validation cohort. Conclusion: We have identified glycopeptides of urinary glycoproteins associated with aggressive prostate cancer using a quantitative mass spectrometry-based glycoproteomic approach and demonstrated their potential to serve as noninvasive urinary glycoprotein biomarkers worthy of further validation by a multi-center study.


Subject(s)
Biomarkers, Tumor/urine , Glycoproteins/urine , Prostatic Neoplasms/diagnosis , Adult , Aged , Biomarkers, Tumor/blood , Cohort Studies , Digital Rectal Examination , Feasibility Studies , Humans , Kallikreins/blood , Male , Middle Aged , Neoplasm Grading , Prostate-Specific Antigen/blood , Prostatic Neoplasms/blood , Prostatic Neoplasms/urine , ROC Curve
12.
Front Chem ; 8: 240, 2020.
Article in English | MEDLINE | ID: mdl-32363175

ABSTRACT

Recently, the glycoproteomic analysis of intact glycopeptides has emerged as an effective approach to decipher the glycan modifications of glycoproteins at the site-specific level. A rapid method to enrich intact glycopeptides is essential for the analysis of glycoproteins, especially for biopharmaceutical proteins. In this study, we established a one-step method for the rapid capture of intact glycopeptides for analysis by mass spectrometry. Compared to the conventional sequential enrichment method, the one-step intact glycopeptide enrichment method reduced the sample preparation time and improved the detection of intact glycopeptides with long sequences or non-polar amino acids. Moreover, an increased number of glycosite-containing peptides was identified by the one-step method compared with the sequential method. When we applied this method to the glycoproteomic analysis of glycoengineered Chinese hamster ovary (CHO)-K1 cells with α1,6-fucosyltransferase (FUT8) knockout, the results showed that the knockout of FUT8 altered the overall glycosylation profile of CHO-K1 cells with the elimination of core fucosylation and together with increases in high-mannose and sialylated N-glycans. Interestingly, the knockout of the FUT8 also appeared to regulate the expression of glycoproteins involved in several functions and pathways in CHO-K1 cells, such as the down-regulation of an intracellular lectin LMAN2 showing cellular adaptation to the alterations in FUT8 knockout cells. These findings indicate that the site-specific characterization of glycoproteins from glycoengineered CHO-K1 cells can be achieved rapidly using the one-step intact glycopeptide enrichment method, which could provide insights for bio-analysts and biotechnologists to better tailor therapeutic drugs.

13.
Anal Chem ; 92(2): 1680-1686, 2020 01 21.
Article in English | MEDLINE | ID: mdl-31859482

ABSTRACT

Aberrant glycosylation has been shown to associate with disease progression, and with glycoproteins representing the major protein component of biological fluids this makes them attractive targets for disease monitoring. Leveraging glycoproteomic analysis via mass spectrometry (MS) could provide the insight into the altered glycosylation patterns that relate to disease progression. However, investigation of large sample cohorts requires rapid, efficient, and highly reproducible sample preparation. To address the limitation, we developed a high-throughput method for characterizing glycans, glycosites, and intact glycopeptides (IGPs) derived from N-linked glycoproteins. We combined disparate peptide enrichment strategies (i.e., hydrophilic and hydrophobic) and a liquid handling platform allowing for a high throughput and rapid enrichment of IGP in a 96-well plate format. The C18/MAX-Tip workflow reduced sample processing time and facilitated the selective enrichment of IGPs from complex samples. Furthermore, our approach enabled the analysis of deglycosylated peptides and glycans from enriched IGPs following PNGase F digest. Following development and optimization of the C18/MAX-Tip methodology using the standard glycoprotein, fetuin, we investigated normal urine samples to obtain N-linked glycoprotein information. Together, our method enables a high-throughput enrichment of glycan, glycosites, and IGPs from biological samples.


Subject(s)
Glycopeptides/urine , Glycoproteins/chemistry , Polysaccharides/urine , Automation , Glycosylation , Humans , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Tandem Mass Spectrometry
14.
Anal Chem ; 92(2): 1842-1849, 2020 01 21.
Article in English | MEDLINE | ID: mdl-31859488

ABSTRACT

Recently, the rapid development and application of mass spectrometry (MS)-based technologies have markedly improved the comprehensive proteomic characterization of global proteome and protein post-translational modifications (PTMs). However, the current conventional approach for global proteomic analysis is often carried out separately from PTM analysis. In our study, we developed an integrated workflow for multiplex analysis of global, glyco-, and phospho-proteomics using breast cancer patient-derived xenograft (PDX) tumor samples. Our approach included the following steps: trypsin-digested tumor samples were enriched for phosphopeptides through immobilized metal ion affinity chromatography (IMAC), followed by enrichment of glycopeptides through mixed anion exchange (MAX) method, and then the flow-through peptides were analyzed for global proteomics. Our workflow demonstrated an increased identification of peptides and associated proteins in global proteome, as compared to those using the peptides without PTM depletion. In addition to global proteome, the workflow identified phosphopeptides and glycopeptides from the PTM enrichment. We also found a subset of glycans with unique distribution profiles in the IMAC flow-through, as compared to those enriched directly using the MAX method. Our integrated workflow provided an effective platform for simultaneous global proteomic and PTM analysis of biospecimens.


Subject(s)
Breast Neoplasms/chemistry , Glycopeptides/analysis , Phosphopeptides/analysis , Proteome/analysis , Proteomics/methods , Workflow , Animals , Chromatography, Liquid , Heterografts/chemistry , Humans , Mice , Proteolysis , Proteome/chemistry , Tandem Mass Spectrometry , Trypsin/chemistry
15.
Anal Chem ; 91(9): 5517-5522, 2019 05 07.
Article in English | MEDLINE | ID: mdl-30924636

ABSTRACT

Mass spectrometry-based urinary proteomics is one of the most attractive strategies to discover proteins for diagnosis, prognosis, monitoring, or prediction of therapeutic responses of urological diseases involving the kidney, prostate, and bladder; however, interfering compounds found in urine necessitate sample preparation strategies that are currently not suitable for urinary proteomics in the clinical setting. Herein, we describe the C4-tip method, comprising a simple, automated strategy utilizing a reverse-phase resin tip-based format and "on-tip" digestion to examine the urine proteome. We first determined the optimal conditions for protein isolation and protease digestion on the C4-tip using the standard protein bovine fetuin. Next, we applied the C4-tip method to urinary proteomics, identifying a total of 813 protein groups using LC-MS/MS, with identified proteins from the C4-tip method displaying a similar distribution of gene ontology (GO) cellular component assignments compared to identified proteins from an ultrafiltration preparation method. Finally, we assessed the reproducibility of the C4-tip method, revealing a high Spearman correlation R-value for shared proteins identified across all tips. Together, we have shown the C4-tip method to be a simple, robust method for high-throughput analysis of the urinary proteome by mass spectrometry in the clinical setting.


Subject(s)
Analytic Sample Preparation Methods/methods , Proteomics/methods , Urinalysis/methods , Workflow
16.
Biomater Sci ; 5(3): 523-531, 2017 Feb 28.
Article in English | MEDLINE | ID: mdl-28124034

ABSTRACT

Antifouling modification technology is developed for many biomedical applications such as blood-contact devices and biosensors. In this work, a photo-reactive polymer containing zwitterionic carboxybetaine groups was prepared by copolymerization of two kinds of methacrylic acids with carboxybetaine and azidoaniline. The carboxybetaine moiety is for low fouling and the azidophenyl moiety is for photo-crosslinking. The synthesized copolymers were coated onto polymeric substrates, and then covalently immobilized on the substrates by exposure to UV radiation. The poly(CBMA-co-AzMA) coating revealed that cell and platelet adhesion and protein adsorption to the substrates were reduced significantly compared to the untreated substrate. Furthermore, the direct immobilization of galactosamine was carried out on the polymer coating by EDC/NHS chemistry. The galactose-immobilized surface had the potential for selecting hepatocyte adhesion from the co-population of different cell types. In addition, the incorporation of photolithographic technology could make micropatterns of poly(CBMA-co-AzMA) coating for the cell co-culture of hepatocytes and fibroblasts. This work demonstrates that the reported technique is an economic and facile tool for layers of reduced adsorption of protein modification with functional groups in one step.


Subject(s)
Azides/chemistry , Betaine/chemistry , Coated Materials, Biocompatible/chemistry , Galactosamine/chemistry , Polymethacrylic Acids/chemistry , Adsorption , Cell Adhesion , Cell Line , Coculture Techniques/methods , Fibroblasts/cytology , Hepatocytes/cytology , Humans , Photochemical Processes , Platelet Adhesiveness , Surface Properties , Ultraviolet Rays
17.
J Mater Chem B ; 5(24): 4614-4622, 2017 Jun 28.
Article in English | MEDLINE | ID: mdl-32264304

ABSTRACT

Keratin has intrinsic biocompatibility and contains several peptide-binding motifs that support the attachment of a wide variety of cell types. We have previously shown that keratin extracted from human hair can promote cell adhesion and proliferation of 3T3 fibroblasts, MG63 osteoblasts, and human adipose stem cells (hASCs). Despite its bioactivity advantages, keratin possesses fragile mechanical properties that introduce challenges for tissue engineering. To remedy this, we examined the results of combining keratin with chitosan, a combination facilitated via induction of an azide functional group, which acted as a photocrosslinker, to improve mechanical strength. Analysis of the keratin/chitosan composite showed that films of this material demonstrated good adhesion and promoted the proliferation of human adipose stem cells. Most importantly, this biomaterial was shown to promote the osteogenic differentiation of hASCs, in terms of up-regulations in type I collagen, runt-related transcription factor 2, and alkaline phosphatase gene expression. We further demonstrated that lyophilizing the keratin/chitosan forms highly interconnected and porous scaffolds that might provide an ideal environment for tissue culture. We believe that keratin/chitosan composite biomaterials can be used in bioactive surface modification, and the crosslinkable properties can produce natural polymer 3D scaffolds for the application of tissue engineering research.

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