Accelerating Proteomics Using Broad Specificity Proteases.

Trypsin is the gold-standard protease in bottom-up proteomics, but many sequence stretches of the proteome are inaccessible to trypsin and standard LC-MS approaches. Thus, multienzyme strategies are used to maximize sequence coverage in post-translational modification profiling. We present fast and robust SP3- and STRAP-based protocols for the broad-specificity proteases subtilisin, proteinase K, and thermolysin. All three enzymes are remarkably fast, producing near-complete digests in 1-5 min, and cost 200-1000× less than proteomics-grade trypsin. Using FragPipe resolved a major challenge by drastically reducing the duration of the required "unspecific" searches. In-depth analyses of proteinase K, subtilisin, and thermolysin Jurkat digests identified 7374, 8178, and 8753 unique proteins with average sequence coverages of 21, 29, and 37%, including 10,000s of amino acids not reported in PeptideAtlas' >2400 experiments. While we could not identify distinct cleavage patterns, machine learning could distinguish true protease products from random cleavages, potentially enabling the prediction of cleavage products. Finally, proteinase K, subtilisin, and thermolysin enabled label-free quantitation of 3111, 3659, and 4196 unique Jurkat proteins, which in our hands is comparable to trypsin. Our data demonstrate that broad-specificity proteases enable quantitative proteomics of uncharted areas of the proteome. Their fast kinetics may allow "on-the-fly" digestion of samples in the future.

Population pharmacokinetics of mycophenolic acid and dose optimisation in adult Chinese kidney transplant recipients.

1. This study aimed to establish a population pharmacokinetic (PPK) model of mycophenolic acid (MPA), quantify the effect of clinical factors and pharmacogenomics of MPA, and optimise the dosage for adult kidney transplant recipients.2. One-hundred and four adult renal transplant patients were enrolled. The PPK model was established using the Phoenix® NMLE software and the stepwise methods were filtered for significant covariates. Monte Carlo simulations were performed to optimise the dosage regimen.3. A two-compartment model with first-order absorption and elimination (including lag time) provided a more accurate description of MPA pharmacokinetics. Serum albumin (ALB) significantly affected the central apparent clearance (CL/F), whereas post-transplant time and creatinine clearance were associated with a central apparent volume of distribution (V/F). The estimated population values obtained by the final model were 17.5 L/h and 93.97 L for CL/F and V/F, respectively. Simulation results revealed that larger mycophenolate mofetil doses are required as the ALB concentration decreases. This study established a PPK model of MPA and validated it using various methods. ALB significantly affected CL/F and recommended optimal dose strategies were given based on the final model. These results provide a reference for the personalised therapy of MPA for kidney transplant patients.

Improved Coverage of the N-Terminome by Combining ChaFRADIC with Alternative Proteases.

Many proteolytic cleavage events cannot be covered with conventional trypsin-based N-terminomics workflows. These typically involve the derivatization of protein N-termini and Lys residues as an initial step, such that trypsin will cleave C-terminal of arginine but not lysine residues (ArgC-like cleavage). From 20,422 reviewed human protein sequences in Uniprot, 3597 have known N-terminal signal peptides. An in silico ArgC-like digestion of the corresponding 3597 mature protein sequences reveals that-even for these well-known and well-studied proteolytic events-trypsin-based N-terminomics workflows may miss up to 50% of signaling cleavage events as the corresponding neo-N-terminal peptides will have an unfavorable length of <7 (875 peptides) or >30 (911 peptides) amino acids. In this chapter, we provide a protocol that can be applied to all kinds of samples to improve access to this "inaccessible" N-terminome, by making use of the alternative, broad-specificity protease subtilisin for fast and reproducible digestion of proteins.

Gene polymorphisms affect postoperative imatinib plasma levels and edema in adults with gastrointestinal stromal tumor.

Aim: To assess the role of genetic polymorphisms in postoperative imatinib concentrations and edema in patients with gastrointestinal stromal tumor. Methods: The relationships between genetic polymorphisms, imatinib concentrations and edema were explored. Results: Carriers of the rs683369 G-allele and rs2231142 T-allele had significantly higher imatinib concentrations. Grade ≥2 periorbital edemas were related to the carriership of two C-alleles in rs2072454 with an adjusted odds ratio of 2.85, two T-alleles in rs1867351 with an adjusted odds ratio of 3.42 and two A-alleles in rs11636419 with an adjusted odds ratio of 3.15. Conclusion: rs683369 and rs2231142 affect the metabolism of imatinib; rs2072454, rs1867351 and rs11636419 are related to grade ≥2 periorbital edemas.

Personalized Dose of Adjuvant Imatinib in Patients with Gastrointestinal Stromal Tumors: Results from a Population Pharmacokinetic Analysis.

Purpose: Imatinib is the first-line treatment for patients with gastrointestinal stromal tumors (GIST) after surgery. However, its pharmacokinetic profile varies remarkably between individuals and has not been well characterized in postoperative Chinese patients with GIST. Therefore, this study aimed to develop a population pharmacokinetic (PPK) model and recommend appropriate doses for different patients to achieve the target trough concentration in such a population. Patients and Methods: A total of 110 surgically treated GIST patients were enrolled, of which 85 were applied to conduct a PPK analysis with a nonlinear mixed-effect model and 25 for external validation of the model. Demographic and biomedical covariates, as well as six single nucleotide polymorphisms were tested to explore the sources of variation in pharmacokinetic parameters of imatinib. Monte Carlo simulations were performed to establish the initial dosing regimens. Results: A one-compartment model was established in postoperative GIST patients. The red blood cell count (RBC) and ABCG2 rs2231142 were observed to have a significant effect on the clearance of imatinib. The typical values estimated by the final model were 9.72 L/h for clearance (CL/F) and 229 L for volume of distribution (V/F). Different from the fixed dose regimen of 400 mg each day, patients carrying rs2231142 heterozygous type and with a lower level of RBC (2.9 × 1012/L), 300 mg imatinib daily is enough to achieve the target trough concentration. When RBC rises to 4.9 × 1012/L, 500 mg daily is recommended. For patients with rs2231142 GG genotype, 500 mg a day is required at RBCs of 3.9 × 1012/L and 4.9 × 1012/L. Conclusion: RBC and rs2231142 contribute to the pharmacokinetic variation of imatinib and personalized dose recommendations based on patient characteristics may be necessary.

Hematologic toxicities of sunitinib in patients with gastrointestinal stromal tumors: a systematic review and meta-analysis.

PURPOSE: Sunitinib offers a significant survival benefit to patients with imatinib-resistant gastrointestinal stromal tumors (GIST). However, the incidence and risk of sunitinib-induced hematologic toxicities in such a population are often overlooked and have not been well characterized. This meta-analysis was performed to assess the summary incidence and risk of hematologic toxicities secondary to sunitinib in patients with GIST. METHODS: Searches were performed in PubMed, Embase, Cochrane Library, and Web of Science as well as ClinicalTrials.gov to identify relevant studies up to April 2022. Studies with adequate safety profile, including anemia, neutropenia, and thrombocytopenia, were included to calculate the pooled incidence, relative risk (RR), and corresponding 95% confidence intervals (CIs). This study was registered with PROSPERO under number CRD42022328202. RESULTS: A total of 2593 patients from 13 studies were included in the present meta-analysis. For patients with GIST assigned to sunitinib, the overall incidences of all-grade anemia, neutropenia, and thrombocytopenia were 26.2% (95% CI, 14.9-39.4%), 41.8% (95% CI, 29.0-55.1%), and 36.4% (95% CI, 22.8-51.1%), respectively. Regarding high-grade (grades 3 and 4) events, there were 4.7% (95% CI, 3.8-5.6%) for anemia, 9.3% (95% CI, 5.6-13.7%) for neutropenia and 5.0% (95% CI, 2.9-7.3%) for thrombocytopenia. Compared to placebo arms, sunitinib was related to an increased risk of high-grade neutropenia with an RR of 10.39 (95% CI, 1.53-70.72; p = 0.017). CONCLUSIONS: Sunitinib carries a relatively high incidence of hematologic toxicities and a substantial increased risk of high-grade neutropenia in patients with GIST. Appropriate prevention and management seem to be inevitable.

The ion channel TRPV1 gain-of-function reprograms the immune microenvironment to facilitate colorectal tumorigenesis.

Transient receptor potential vanilloid 1 (TRPV1) is a Ca2+-permeable ion channel that acts as cellular sensor and is implicated in the tumor microenvironment cross talk. However, the functional role of TRPV1 in colorectal cancer (CRC) is still controversial. By using a TRPV1 gain-of-function model, we previously reported that hyperfunctional TRPV1 exacerbated experimental colitis by modulating mucosal immunity. Here, we found that TRPV1 gain-of-function significantly promoted tumor initiation and progression in colitis-associated cancer, as evidenced by the increase in the number and size of tumor. Systemic TRPV1 hyperactivation fostered a tumor permissive microenvironment through altering macrophage activation status and shifting the Th1/Th2 balance towards Th2 phenotype. Mechanistically, TRPV1 gain-of-function directly potentiated M1 cytokine production in macrophage and enhanced Th2 immune response by promoting Calcineurin/nuclear factor of activated T cells (NFATc2) signaling activation. In patients with CRC, TRPV1 expression was increased in tumor immune infiltrating cells. TRPV1 level was associated with CRC progression and could impact clinical outcome. Our study reveals an important role for TRPV1 in regulating the immune microenvironment during colorectal tumorigenesis. TRPV1 might be a potential target for CRC immunotherapy.

A novel SoxB2 gene is required for maturation of sperm nucleus during spermiogenesis in the Chinese mitten crab, Eriocheir sinensis.

SRY-related HMG box (Sox) genes are characterized by the presence of a DNA-binding HMG domain and involved in a diverse range of developmental processes. In this study, we identified a novel Sox gene, designated as EsSoxB2-1, from the Chinese mitten crab Eriocheir sinensis. The EsSoxB2-1 encodes a protein of 259 amino acids, sharing the highest identity with the beetle Tribolium castaneum SOX21b. Unlike insect Sox21b, however, EsSoxB2-1 is intronless and exhibits a gonad-specific expression pattern at both mRNA and protein level. Two core promoters in 5' flanking region were demonstrated to be essential for inducing transcriptional regulatory activity. The transcription of EsSoxB2-1 mRNA begins in spermatogonia stage, while the translation of EsSOXB2-1 protein initiates at spermiogenesis stage. Interestingly, EsSOXB2-1 protein was exclusively localized in the nucleus of spermatid and spermatozoa even at the end of acrosome reaction, and was bound to the uncondensed chromatin in nucleoplasm of mature spermatozoa. Knockdown of EsSoxB2-1 by RNAi leads to abnormal transformation of the nucleus during spermiogenesis. Together, these findings demonstrated the requirement of EsSoxB2-1 for the spermatozoa nucleus maturation and also suggested that EsSoxB2-1 would be delivered into fertilized eggs along with chromatins as a paternal transcription factor for regulating early embryonic development.

[Determination of 20 Trace Elements in the Blood Collection Tubes with ICP-MS].

To investigate the contamination of blood collection tubes, 20 trace elements (Al, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Mo, Cd, Sn, Sb, Ba, W, Hg, Tl, Pb) in 13 different types of blood collection tube were studied with ICP-MS method. The lixivium of H(2)O and 10% HNO(3) were measured with ICP-MS, and then the contamination coming from the blood collection tube is specified. According to the concentration range of human blood, plasma and serum from recently published literature, this report presents a detailed analysis of capable trace elements for each blood collection tube. The results showed that, tube No.1 is capable to analyze 18 trace elements in the human serum; tube No.6 is capable to analyze 15 trace elements in the human plasma; tube No. 13 is capable to analyze 17 trace elements in the human blood. But we still should be aware that, the elements Sb and W in tube No.1, the elements V, Cr, Ni, and Sb in tube No.6, and the elements Al, Sb and W in tube No.13, are in the same magnitude of the normal trace element concentration range in the human serum, plasma and blood. They might affect the testing results. The serum collected from the same volunteer by tube No.1 and tube No.3 were compared here, the results show that, almost each trace element concentration of human serum from tube No.1 is lower than from tube No.3, especially for elements Al, V, Cr, Mn, As, Sn, and Sb. The results indicate that the blood collection tubes show great impact on determination of trace element.

Effects of surfactants on graphene oxide nanoparticles transport in saturated porous media.

Transport behaviors of graphene oxide nanoparticles (GONPs) in saturated porous media were examined as a function of the presence and concentration of anionic surfactant (SDBS) and non-ionic surfactant (Triton X-100) under different ionic strength (IS). The results showed that the GONPs were retained obviously in the sand columns at both IS of 50 and 200mmol/L, and they were more mobile at lower IS. The presence and concentration of surfactants could enhance the GONP transport, particularly as observed at higher IS. It was interesting to see that the GONP transport was surfactant type dependent, and SDBS was more effective to facilitate GONP transport than Triton X-100 in our experimental conditions. The advection-dispersion-retention numerical modeling followed this trend and depicted the difference quantitatively. Derjaguin-Landau-Verwey-Overbeek (DLVO) interaction calculations also were performed to interpret these effects, indicating that secondary minimum deposition was critical in this study.

[Research on optimization of mathematical model of flow injection-hydride generation-atomic fluorescence spectrometry].

Flow injection-hydride generation-atomic fluorescence spectrometry was a widely used method in the industries of health, environmental, geological and metallurgical fields for the merit of high sensitivity, wide measurement range and fast analytical speed. However, optimization of this method was too difficult as there exist so many parameters affecting the sensitivity and broadening. Generally, the optimal conditions were sought through several experiments. The present paper proposed a mathematical model between the parameters and sensitivity/broadening coefficients using the law of conservation of mass according to the characteristics of hydride chemical reaction and the composition of the system, which was proved to be accurate as comparing the theoretical simulation and experimental results through the test of arsanilic acid standard solution. Finally, this paper has put a relation map between the parameters and sensitivity/broadening coefficients, and summarized that GLS volume, carrier solution flow rate and sample loop volume were the most factors affecting sensitivity and broadening coefficients. Optimizing these three factors with this relation map, the relative sensitivity was advanced by 2.9 times and relative broadening was reduced by 0.76 times. This model can provide a theoretical guidance for the optimization of the experimental conditions.

Female-only sex-linked amplified fragment length polymorphism markers support ZW/ZZ sex determination in the giant freshwater prawn Macrobrachium rosenbergii.

Sex determination mechanisms in many crustacean species are complex and poorly documented. In the giant freshwater prawn, Macrobrachium rosenbergii, a ZW/ZZ sex determination system was previously proposed based on sex ratio data obtained by crosses of sex-reversed females (neomales). To provide molecular evidence for the proposed system, novel sex-linked molecular markers were isolated in this species. Amplified fragment length polymorphism (AFLP) using 64 primer combinations was employed to screen prawn genomes for DNA markers linked with sex loci. Approximately 8400 legible fragments were produced, 13 of which were uniquely identified in female prawns with no indication of corresponding male-specific markers. These AFLP fragments were reamplified, cloned and sequenced, producing two reliable female-specific sequence characterized amplified region (SCAR) markers. Additional individuals from two unrelated geographic populations were used to verify these findings, confirming female-specific amplification of single bands. Detection of internal polymorphic sites was conducted by designing new primer pairs based on these internal fragments. The internal SCAR fragments also displayed specificity in females, indicating high levels of variation between female and male specimens. The distinctive feature of female-linked SCAR markers can be applied for rapid detection of prawn gender. These sex-specific SCAR markers and sex-associated AFLP candidates unique to female specimens support a sex determination system consistent with female heterogamety (ZW) and male homogamety (ZZ).

The influence of Typhoon Khanun on the return migration of Nilaparvata lugens (Stål) in eastern China.

Migratory insects adapt to and exploit the atmospheric environment to complete their migration and maintain their population. However, little is known about the mechanism of insect migration under the influence of extreme weather conditions such as typhoons. A case study was conducted to investigate the effect of typhoon Khanun, which made landfall in the eastern China in Sept. 2005, on the migration of brown planthopper, Nilaparvata lugens (Stål). The migration pathways of N. lugens were reconstructed for the period under the influence of the typhoon by calculating trajectories using the MM5, a mesoscale numerical weather prediction model, and migration events were examined in 7 counties of the Yangtze River Delta region with ancillary information. The light trap catches and field observations indicated that the migration peak of N. lugens coincided with the period when the typhoon made landfall in this region. The trajectory analyses revealed that most emigrations from this region during this period were hampered or ended in short distances. The sources of the light-trap catches were mainly located the nearby regions of each station (i.e. mostly less than 100 km away, with a few exceeding 200 km but all less than 300 km). This disrupted emigration was very different from the usual N. lugens migration which would bring them to Hunan, Jiangxi, and southern Anhui from this region at this time of year. This study revealed that the return migration of N. lugens was suppressed by the typhoon Khanun, leading to populations remaining high in the Yangtze River Delta and exacerbating later outbreaks.

The effect of various S-alkylating agents on the chromatographic behavior of cysteine-containing peptides in reversed-phase chromatography.

We investigate the influence of various alkylation chemistries on the reversed phase (RP) HPLC behavior of Cys-containing peptides under the most popular RP-HPLC conditions used in proteomics: C18 phases with trifluoroacetic acid (TFA) or formic acid (FA) as the ion pairing modifiers, and separation at pH 10. Akylating agents studied are iodoacetamide (IAM), iodoacetic acid (IAA), 4-vinylpyridine (4-VP), acrylamide (AA) and methyl methanethiosulfonate (MMTS). These were compared against the retention of identical peptides without alkylation, i.e. free cysteines. The intrinsic hydrophobicity values of the Cys residue under formic acid conditions for these modifications were found to increase in the following order: 4-VP