Novel fibro-inflammatory biomarkers associated with disease activity in patients with Crohn's disease.

INTRODUCTION: Crohn's disease (CD) is a complex disease, and assessing activity is challenging due to pathobiologic process e.g. ECM remodeling, mucosal damage, and intestinal fibrosis, which greatly limits current disease activity assessments through e.g. endoscopy and imaging techniques. AREAS COVERED: The review highlights the importance of novel biomarkers reflecting ECM remodeling and immune cell activity that accurately reflect CD activity and progression. Such biomarkers could include collagen formation and degradation fragments and a serum fragment of calprotectin, reflecting neutrophil activity. A new concept, fibro-inflammation, is also introduced in the review, in which all aspects of mucosal damage, such as inflammation, mucosal damage, tissue remodeling, intestinal fibrosis, and fibrosis resolution, should be assessed. PubMed searches performed from July 2022 - November 2022 provided the scientific information included in the review. EXPERT OPINION: Current data suggest intestinal fibrosis may sustain and exacerbate chronic inflammation, leading to non-response to anti-inflammatory treatments. Therefore, evaluating novel biomarkers reflecting different stages of fibro-inflammatory disease activity should be done in a clinical setting and considered for clinical trials. This approach will help accurately assess disease activity, leading to better management and treatment of CD.

Binding Characterization of Agonists and Antagonists by MCCS: A Case Study from Adenosine A2A Receptor.

Characterizing the structural basis of ligand recognition of adenosine A2A receptor (AA2AR) will facilitate its rational design and development of small molecules with high affinity and selectivity, as well as optimal therapeutic effects for pain, cancers, drug abuse disorders, etc. In the present work, we applied our reported algorithm, molecular complex characterizing system (MCCS), to characterize the binding features of AA2AR based on its reported 3D structures of protein-ligand complexes. First, we compared the binding score to the reported experimental binding affinities of each compound. Then, we calculated an output example of residue energy contribution using MCCS and compared the results with data obtained from MM/GBSA. The consistency in results indicated that MCCS is a powerful, fast, and accurate method. Sequentially, using a receptor-ligand data set of 57 crystallized structures of AA2ARs, we characterized the binding features of the binding pockets in AA2AR, summarized the key residues that distinguish antagonist from agonist, produced heatmaps of residue energy contribution for clustering various statuses of AA2ARs, explored the selectivity between AA2AR and AA1AR, etc. All the information provided new insights into the protein features of AA2AR and will facilitate its rational drug design.

An exploratory MALDI-TOF MS library based on SARAMIS superspectra for rapid identification of Aspergillus section Nigri.

Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is a broadly used technique for identification and typing of microorganisms. However, its application to filamentous fungi has been delayed. The objective of this study was to establish a data library for rapid identification of the genus Aspergillus sect. Nigri using MALDI-TOF MS. With respect to sample preparation, we compared the utility of using mature mycelia, including conidial structures, to accumulate a wider range of proteins versus the conventional method relying on young hyphae. Mass spectral datasets obtained for 61 strains of 17 species were subjected to cluster analysis and compared with a phylogenetic tree based on calmodulin gene sequences. Specific and frequent mass spectral peaks corresponding to each phylogenetic group were selected (superspectra for the SARAMIS system). Fifteen superspectra representing nine species were ultimately created. The percentage of correct identification for 217 spectra was improved from 36.41% to 86.64% using the revised library. Additionally, 2.76% of the spectra were assigned to candidates that comprised several related species, including the correct species.

MCCS, a novel characterization method for protein-ligand complex.

Delineating the fingerprint or feature vector of a receptor/protein will facilitate the structural and biological studies, as well as the rational design and development of drugs with high affinities and selectivity. However, protein is complicated by its different functional regions that can bind to some of its protein partner(s), substrate(s), orthosteric ligand(s) or allosteric modulator(s) where cogent methods like molecular fingerprints do not work well. We here elaborate a scoring-function-based computing protocol Molecular Complex Characterizing System to help characterize the binding feature of protein-ligand complexes. Based on the reported receptor-ligand interactions, we first quantitate the energy contribution of each individual residue which may be an alternative of MD-based energy decomposition. We then construct a vector for the energy contribution to represent the pattern of the ligand recognition at a receptor and qualitatively analyze the matching level with other receptors. Finally, the energy contribution vector is explored for extensive use in similarity and clustering. The present work provides a new approach to cluster proteins, a perspective counterpart for determining the protein characteristics in the binding, and an advanced screening technique where molecular docking is applicable.

Beyond Global Charge: Role of Amine Bulkiness and Protein Fingerprint on Nanoparticle-Cell Interaction.

Amino groups presented on the surface of nanoparticles are well-known to be a predominant factor in the formation of the protein corona and subsequent cellular uptake. However, the molecular mechanism underpinning this relationship is poorly defined. This study investigates how amine type and density affect the protein corona and cellular association of gold nanoparticles with cells in vitro. Four specific poly(vinyl alcohol-co-N-vinylamine) copolymers are synthesized containing primary, secondary, or tertiary amines. Particle cellular association (i.e., cellular uptake and surface adsorption), as well as protein corona composition, are then investigated. It is found that the protein corona (as a consequence of "amine bulkiness") and amine density are both important in dictating cellular association. By evaluating the nanoparticle surface chemistry and the protein fingerprint, proteins that are significant in mediating particle-cell association are identified. In particular, primary amines, when exposed on the polymer side chain, are strongly correlated with the presence of alpha-2-HS-glycoprotein, and promote nanoparticle cellular association.

Applications of a novel biodetection system to saliva using protein fingerprints with data processing.

A fundamental method has been developed focusing on a facile and rapid examination of periodontal disease. Periodontal disease is an oral disease thought to affect 80% of adults, and early detection with treatment is desirable for the improvement of the quality of life. Unfortunately conventional methods are not consistent as the disease is caused by a number of undefined bacteria and detection relies on the skills of the dentist. Thus an objective detection system is required. We have performed an experiment on saliva using a novel biodetection system, designated PepTenChip®. A disease model for saliva was prepared using a specimen from a healthy subject and a mixture of hemoglobin (f-Hb) and lactate dehydrogenase (LDH), which is used as a periodontal disease marker protein with healthy saliva. PepTenChip® is a peptide microarray in which fluorescent labelled structured peptides are immobilized on a novel amorphous carbon substrate. Since the peptides used as capture molecules are fluorescently labelled, labeling of analytes is not necessary. The fluorescence intensity change before and after application of analytes are detected rather than the ON/OFF detection common to conventional microarrays using a set of antigen-antibody. The fluorescence intensity value changes according to the concentration of captured protein allowing the generation of protein fingerprint (PFP) and dendrograms. The present method does not rely on a "one to one" interaction, unlike conventional biodetection, and advantages can be envisaged in the case of an undefined or unknown cause of disease. The statistical analyses, such as multivariate analyses, allow classification of the type of proteins added in saliva as mimetics of disease. PepTenChip® system is useful and convenient for examination of periodontal disease in health care.

Interrogation of an autofluorescence-based method for protein fingerprinting.

In the present study, we have designed a laser-induced fluorescence (LIF) based instrumentation and developed a sensitive methodology for the effective separation, visualization, identification and analysis of proteins on a single platform. In this method, intrinsic fluorescence spectra of proteins were detected after separation on 1 or 2 dimensional Sodium Dodecyl Sulfate-Tris(2-carboxyethyl)phosphine (SDS-TCEP) polyacrylamide gel electrophoresis (PAGE) and the data were analyzed. The MATLAB assisted software was designed for the development of PAGE fingerprint for the visualization of protein after 1- and 2-dimensional protein separation. These provided objective parameters of intrinsic fluorescence intensity, emission peak, molecular weight and isoelectric point using a single platform. Further, the current architecture could differentiate the overlapping proteins in the PAGE gels which otherwise were not identifiable by conventional staining, imaging and tagging methods. Categorization of the proteins based on the presence or absence of tyrosine or tryptophan residues and assigning the corresponding emission peaks (309-356 nm) with pseudo colors allowed the detection of proportion of proteins within the given spectrum. The present methodology doesn't use stains or tags, hence amenable to couple with mass spectroscopic measurements. This technique may have relevance in the field of proteomics that is used for innumerable applications.

Unique insight into microenvironmental changes in colorectal cancer: Ex vivo assessment of matrix metalloprotease-mediated molecular changes in human colorectal tumor tissue and corresponding non-neoplastic adjacent tissue.

Matrix metalloprotease (MMP)-mediated tissue remodeling is one of the malignant changes driving colorectal cancer. Measurement of altered MMP expression/activity is not sufficient to fully understand the effect of MMP-mediated tissue remodeling. Biomarkers are required that specifically reflect the dynamic processes of the MMP-mediated degradation of signature proteins from colorectal tissue. The aim of the present study was to profile and characterize the release of MMP-degraded type III collagen (C3M) and citrullinated and MMP-degraded vimentin (VICM) from tumor tissue and corresponding non-neoplastic adjacent tissue (NAT) in a human colorectal cancer ex vivo model. Colorectal tumor tissue and NAT biopsies from tissue removed during resection of colorectal cancer patients (n=13) were cut into pieces of 2 mm2 and cultured for 24 h in growth medium. C3M and VICM were evaluated by ELISA. As part of the characterization, C3M was determined subsequent to the tumor tissue being cleaved with recombinant MMP-2/-9 and trypsin. C3M was generated by MMP-2/-9, but not by trypsin. In addition, the level of C3M was significantly elevated in the conditioned medium from tumor tissues (3.7 ng/ml) compared with that observed in the conditioned medium from the NATs (2.2 ng/ml) and in the growth medium alone (1.9 ng/ml). The level of VICM was significantly elevated in the tumor tissues (0.51 ng/ml) and NATs (0.52 ng/ml) compared with that in the growth medium alone (0.03 ng/ml). No differences were detected between the tumor tissues and NATs. No correlation was observed between biomarker levels from the tumor tissue and corresponding NAT, and the biomarker levels did not correlate with tumor stage. In conclusion, the present study provided support of the concept that C3M and VICM are applicable as tools to investigate dynamic tissue changes of colorectal tumor tissue and corresponding NAT. By the assessment of these specific MMP-mediated molecular changes, the present study provides novel and relevant insight into the dynamic changes of colorectal tumor tissue and corresponding NAT.

Rhizosphere Bacterial Composition of the Sugar Beet Using SDS-PAGE Methodology

ABSTRACT The rhizosphere zone has been defined as the volume of soil directly influenced by the presence of living plant roots or soil compartment influenced by the root. During the growing season of 2014, the rhizobacteria of 23 sugar beet plants sampled from 12 sites in the west and north west of Iran were inventoried. Using a cultivation-dependent approach, a total of 217 bacteria were isolated from the rhizosphere. The bacterial isolates were tentatively grouped and documented based on polyacrylamide gel electrophoresis of whole-cell proteins and were found to represent 43 different protein electrotypes. The majority of the fingerprint types were found only on a single occasion. Fifty-nine percent of the strains belonged to the five bacterial species and identified as Stenotrophomonas maltophilia, Pseudomonas fluorescens, Pseudomonas aeruginosa, Stenotrophomonas rhizophila and Serratia marcescens. Minor occurring fingerprint types were identified as Flavobacterium spp, Erwinia spp, Acetobacter spp, Agrobacterium spp, Enterobacter spp, Aeromonas spp and Bacillus spp.

CRP and a biomarker of type I collagen degradation, C1M, can differentiate anti-inflammatory treatment response in ankylosing spondylitis.

AIM: To investigate if tissue turnover biomarkers were efficacy biomarkers in ankylosing spondylitis and if the biomarkers at baseline predicted a good outcome (BASDAI50). PATIENTS & METHODS: Twenty-two etanercept treated ankylosing spondylitis patients were investigated for inflammation (CRP, ESR, CRPM) and tissue turnover (C1M, C2M, C3M) during the first year of treatment. Biomarkers profiles and treatment response were investigated. RESULTS: ESR, CRP, BASDAI and C1M were decreased with treatment (p ≤ 0.04). C1M and CRP segregated patients into two populations predicting treatment efficacy. CONCLUSION: C1M and CRP were efficacy biomarkers and baseline biomarkers could select who benefited (by biomarkers) from treatment. C1M was not superior to CRP, but the biomarkers evaluate different pathologic events, indicating that C1M and CRP identify different events.

Clinical research of detection of thrombosis in patients with lung cancer by protein fingerprinting / 中国综合临床

Objective To investigate the changes of serum protein fingerprint in patients with lung cancer with deep venous thrombosis.Methods Eighteen case patients with lung cancer were selected,including 8 case of lung cancers with thrombosis and 10 cases of lung cancers with no thrombosis.Surface enhanced laser desorption ionization protein-time of flight mass spectrometry (SELDI-TOF-MS) was used to analyze serum protein content of two groups in the same mass to charge ratios(M/Z),then drew the protein peaks that content difference was statistically significant.Results The M/Z of lung cancer with thrombus group and control group were 5911,1216,4187,1019,4293,the protein peaks had significant differences between the two group (43.81±7.74,6.37±5.02,2.97±0.35,35.96± 12.10,9.65±4.37;15.35± 12.69,2.06±0.37,4.67± 1.35,15.94±6.47,14.65±8.80;t =5.334,4.800,2.981,4.639,4.596;P＜ 0.05).Compared with the control group,the decrease of protein peak M/Z were 5911,1019,1216,and the increase of protein peak M/Z were 4293,4187 in the deep venous thrombosis group.Conclusion In the serum of patients with tumors SELDI profiles M/Z are 5911,4293,4187,1019,1216 of SELDI protein fingerprinting can be considered in patients with thrombosis of tumor specific markers.

Dosakaya Juice Assuages Development of Sucrose Induced Impaired Glucose Tolerance and Imbalance in Antioxidant Defense.

OBJECTIVE: The objective was to explore the effect of Dosakaya (DK) (Cucumis melo var. chito) juice on sucrose induced dysglycemia and disturbances in antioxidant defense in rats. MATERIALS AND METHODS: Rats were preconditioned with DK juice before administration of sucrose beverage continuously for 1-month. Blood glucose tolerance test and glutathione (GSH) homeostasis pathways in kidney were analyzed in different group of animals at the end of the study. RESULTS: DK juice diffused (P < 0.001) hypertriglyceridemia inducing effect of sucrose and arrested sucrose induced weight gain. It improved glucose tolerance ability by significantly reducing (P < 0.05) first-hour glycemic excursion and decreasing 2 h glycemic load (P < 0.05) following oral glucose tolerance test in sucrose fed animals. Furthermore, disturbances in antioxidant defense mechanisms in terms of GSH homeostasis in kidney were restored due to juice feeding. DK juice administration checked reduction in GSH-S-transferase and glyoxalase-I activity, thus, significantly mitigated lipid peroxidation (P < 0.05), and formation of advanced glycation end-products (P < 0.001) in kidney and serum (P < 0.01). Quantitative analysis of juice found it a rich source of protein and polyphenols. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis revealed the presence of multiple protein bands in whole fruit juice. Therefore, SDS-PAGE protein fingerprint of DK juice may serve as a quality control tool for standardization of juice. CONCLUSION: The whole fruit juice of DK may become cost-effective, affordable health beverage in extenuating ill-health effects of sugar consumption. This is the first report identifying DK juice in preventing development dysglycemia, dyslipidemia, and oxidative stress induced due to chronic sucrose feeding in rats. SUMMARY: Chronic sucrose consumption induced development of dysglycemia and also impaired antioxidant defense mechanism in rats. The oral administration of Dosakaya juice prior to sucrose feeding however, mitigated the development of dysglycemia and impairment in antioxidant defense in rats.

Fingerprint analysis of serum protein in Xinjiang Uygurs and Han patients with thyroid cancer / 中华内分泌代谢杂志

Objective To compare serum protein fingerprint among Uygur patients with thyroid cancer and benign thyroid nodules, and Han patients with thyroid cancer, and to screen ethnic-specific protein markers of thyroid cancer. Methods Using the technology of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), the protein expression profiles of Uygur and Han patients with thyroid cancer and Uygur patients with thyroid nodules were established and compared by image analysis software between two groups. Liquid chromatography-mass spectrometry/mass spectrometry coupling techniques ( LC-MS/MS) were used to identify differential protein. The protein′s name, cellular localization and functional classification were searched in Swissport database. Results There are 11 differentially expressed proteins by comparison of sera in Uygur patients with benign thyroid nodules and thyroid cancer, in which complement C3 and C4b levels were down-regulated in the serums of Uygur patients with benign thyroid nodules, and 9 proteins such as heme-binding proteins etc were up-regulated. There are 7 differentially expressed proteins by comparison of serums in Uygur and Han patients with thyroid cancer, in which transferrin level was up-regulated in the serum of Uygur patients with thyroid cancer, and 6 proteins such as cytokeratin-1 etc were down-regulated in serum of Uygur patients with thyroid cancer. Conclusion Combined screening of multiple labelled proteins including heme-binding protein,α2-macroglobulin, and transferrin protein etc may provide the basis for the diagnosis of thyroid cancer in Uygurs and Hans.

Serum biomarkers reflecting specific tumor tissue remodeling processes are valuable diagnostic tools for lung cancer.

Extracellular matrix (ECM) proteins, such as collagen type I and elastin, and intermediate filament (IMF) proteins, such as vimentin are modified and dysregulated as part of the malignant changes leading to disruption of tissue homeostasis. Noninvasive biomarkers that reflect such changes may have a great potential for cancer. Levels of matrix metalloproteinase (MMP) generated fragments of type I collagen (C1M), of elastin (ELM), and of citrullinated vimentin (VICM) were measured in serum from patients with lung cancer (n = 40), gastrointestinal cancer (n = 25), prostate cancer (n = 14), malignant melanoma (n = 7), chronic obstructive pulmonary disease (COPD) (n = 13), and idiopathic pulmonary fibrosis (IPF) (n = 10), as well as in age-matched controls (n = 33). The area under the receiver operating characteristics (AUROC) was calculated and a diagnostic decision tree generated from specific cutoff values. C1M and VICM were significantly elevated in lung cancer patients as compared with healthy controls (AUROC = 0.98, P < 0.0001) and other cancers (AUROC = 0.83 P < 0.0001). A trend was detected when comparing lung cancer with COPD+IPF. No difference could be seen for ELM. Interestingly, C1M and VICM were able to identify patients with lung cancer with a positive predictive value of 0.9 and an odds ratio of 40 (95% CI = 8.7-186, P < 0.0001). Biomarkers specifically reflecting degradation of collagen type I and citrullinated vimentin are applicable for lung cancer patients. Our data indicate that biomarkers reflecting ECM and IMF protein dysregulation are highly applicable in the lung cancer setting. We speculate that these markers may aid in diagnosing and characterizing patients with lung cancer.

Rapid identification of four common bacteria by SELDI-TOF MS protein fingerprints / 中华微生物学和免疫学杂志

Objective To establish protein fingerprints of common bacteria in clinics and to lay a foundation for rapid identification of bacteria.Methods Strains of Escherichia coli,Klebsiella pneumoniae,Pseudomonas aeruginosa and Staphylococcus aureus were detected by surface enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF MS).Stable expression protein peaks were screened and the data was input into the self-constructed Fingerwave software for identification of target bacteria by protein fingerprint comparison.Two hundred and fifty-six clinical isolates,including E.coli,K.pneumoniae,P.aeruginosa and S.aureus were detected and the data was compared with constructed database to evaluate its diagnostic value.Results The protein fingerprints including four common bacteia was used to identify the target bacteria with identification rate of 93.1％ (54/58) for E.coli,87.2％ (75/86) for K.pneumoniae,96.2％ (60/63) for P.aeruginosa and 96.2％ (51/53) for S.aureus,respectively.Conclusion Common bacteria can be rapidly identified by using the protein fingerprint comparison,which provides a powerful tool for bacterial identification.

Application of Serum Protein Markers in Hirschsprung′s Disease / 实用儿科临床杂志

Objective To check serum protein of children′s Hirschsprung′s disease(HD) and sift specific protein marker which was used in constructing of HD screening and early diagnosis of serum protein fingerprint model.Methods Surface-enhanced laser desorption/ionization time of flight mass spectrometry(SELDI-TOF-MS) was applied to detect protein mass spectrometry of serum specimens in 82 cases(HD group 42 cases,20 cases of other types of obstruction,healthy control group 20 cases) and data were analyzed by bioinformatics methods(support vector machine).Results 1.For HD group and healthy control group:selected 3 M/Z in 3 221.7,5 639.2,6 884.2 protein markers were selected,HD early screening and diagnostic model was established,3 markers in HD low expression,the expressions of them in HD group and healthy control group were 378.29?273.34,295.65?159.38,444.13?254.06 and 1 428.18?1 192.61,1 039.60?785.64,1 115.72?680.48,respectively.There were significant differences in two groups(Pa0.05).Conclusions The establishment of serum protein fingerprint model of HD by SELDI-TOF-MS support vector machine could screen and diagnose HD early,which is a new method of better specificity,high sensitivity and is worthy of further research and application.