Systematic review and meta-analysis of multiparametric MRI clear cell likelihood scores for classification of small renal masses.

Purpose: To systematically assess the multiparametric MRI clear cell likelihood score (ccLS) algorithm for the classification of small renal masses (SRM). Methods: We conducted an electronic literature search on Web of Science, MEDLINE (Ovid and PubMed), Cochrane Library, EMBASE, and Google Scholar to identify relevant articles from 2017 up to June 30, 2022. We included studies reporting the diagnostic performance of the ccLS for characterization of solid SRM. The bivariate model and hierarchical summary receiver operating characteristic (HSROC) model were used to pool sensitivity, specificity, positive likelihood ratio (LR+), negative likelihood ratio (LR-), and diagnostic odds ratio (DOR). The quality evaluation was performed with the Quality Assessment of Diagnostic Accuracy Studies-2 tool. Results: A total of 6 studies with 825 renal masses (785 patients) were included in the current meta-analysis. The pooled sensitivity and specificity for cT1a renal masses were 0.80 (95% CI 0.75-0.85) and 0.74 (95% CI 0.65-0.81) at the threshold of ccLS ≥4, the pooled LR+, LR-, and DOR were 3.04 (95% CI 2.34-3.95), 0.27 (95% CI 0.22-0.33), and 11.4 (95% CI 8.2-15.9), respectively. The area under the HSROC curve was 0.84 (95% CI 0.81-0.87). For all cT1 renal masses, the pooled sensitivity and specificity were 0.80 (95% CI 0.74-0.85) and 0.76 (95% CI 0.67-0.83). Conclusions: The ccLS had moderate to high accuracy for identifying ccRCC from other RCC subtypes and with a moderate inter-reader agreement. However, its diagnostic performance remain needs multi-center, large cohort studies to validate in the future.

TRIP13 modulates protein deubiquitination and accelerates tumor development and progression of B cell malignancies.

Multiple myeloma (MM), a terminally differentiated B cell malignancy, remains difficult to cure. Understanding the molecular mechanisms underlying the progression of MM may identify therapeutic targets and lead to a fundamental shift in treatment of the disease. Deubiquitination, like ubiquitination, is a highly regulated process, implicated in almost every cellular process. Multiple deubiquitinating enzymes (DUBs) have been identified, but their regulation is poorly defined. Here, we determined that TRIP13 increases cellular deubiquitination. Overexpression of TRIP13 in mice and cultured cells resulted in excess cellular deubiquitination by enhancing the association of the DUB USP7 with its substrates. We show that TRIP13 is an oncogenic protein because it accelerates B cell tumor development in transgenic mice. TRIP13-induced resistance to proteasome inhibition can be overcome by a USP7 inhibitor in vitro and in vivo. These findings suggest that TRIP13 expression plays a critical role in B cell lymphoma and MM by regulating deubiquitination of critical oncogenic (NEK2) and tumor suppressor (PTEN, p53) proteins. High TRIP13 identifies a high-risk patient group amenable to adjuvant anti-USP7 therapy.

Molecular Dynamics Simulations of Mite Aquaporin DerfAQP1 from the Dust Mite Dermatophagoides farinae (Acariformes: Pyroglyphidae).

Aquaporins are a large family of transmembrane channel proteins that facilitate the passive but highly selective transport of water and other small solutes across biological membranes. House dust mite (Dermatophagoides farinae) is the major source of household immunogens, and we have recently reported six cDNA sequence encoding aquaporins from this mite species. To better understand the structure and role of mite aquaporin, we constructed a tertiary structure for DerfAQP1 by homology modeling from the X-ray structure of malaria aquaporin PfAQP (Protein Data Bank code No. 3C02) and conducted molecular dynamics simulation. The simulation arranged seven water molecules in a single file through the pores of the DerfAQP1. Further, two conserved Asn-Pro-Ala motifs were located on Asn203 and Asn77; residues Arg206, Trp57, Met190, Gly200, and Asp207 constituted an extracellular vestibule of the pore; and residues His75, Val80, Ile65, and Ile182 constituted the cytoplasmic portions. The overall free energy profile for water transport through DerfAQP1 revealed an energy barrier of ~2.5 kcal/mol. These results contribute to the understanding of mite physiology and pathology.

Identification of continuous immunoglobulin G epitopes of Dermatophagoides farinae allergens by peptide microarray immunoassay.

Dermatophagoides farinae, as a common house dust mite species, is one of the main sources of allergens in the world. At present, Dermatophagoides farinae is found to contain more than 30 groups of allergens. These allergens are used for allergen-specific immunotherapy (AIT) of allergic diseases. During the AIT process, immunoglobulin G (IgG) antibodies can block immunoglobulin E (IgE) antibody-induced allergic reactions in the human body. One of the mechanisms may be that IgG and IgE competitively bind to the same allergic protein, so it is necessary to explore the binding sites (epitopes) of IgG antibodies to allergens. In this study, peptide arrays were constructed to react with the serums from patients with allergic asthma to find the IgG epitopes of several allergens including major allergens (Der f 1, 2) and mid-tier allergens (Der f 4, 5, and 7), and then verified by enzyme-linked immunosorbent assay (ELISA) test. Relevant epitopic sequences were located on the tertiary structure of individual allergens, as reconstructed by homology modeling. One IgG epitope of Der f 1 (90-106aa, NVPSELDLRSLRTVTPI), five IgG epitopes of Der f 4 (61-77aa, ERYQPVSYDIHTRSGDE; 193-209aa, FRSDASTHQWPDDLRSI; 226-242aa, HPFIYHETIYYGGNGIN; 271-287aa, LRWLRNFGTEWGLVPSG; 352-368aa, NDWVGPPTDQHGNILSV), and one IgG epitope of Der f 5 (84-101aa, RYNVEIALKSNEILERDL) were identified. IgG epitopes of Der f 2, 7 were not found. There are overlaps between the IgG and IgE epitopes of Der f 1, 4, and 5. These findings not only reflect the practicality of peptide array and ELISA test in the allergen IgG epitope identification, but also provide more information for further understanding of the human immunological changes during AIT and the molecular mechanisms of IgG blocking IgE activity.

Expression of recombinant allergen, Der f 1, Der f 2 and Der f 4 using baculovirus-insect cell systems.

INTRODUCTION: Specific immunotherapy is critical for alleviating symptoms associated with house dust mite allergy, such as asthma and rhinitis. However, this approach relies on crude extracts, which are often not of sufficient quality or purity and are not standardized. The use of recombinant allergens may enable safer, more effective treatment. MATERIAL AND METHODS: Using our previously constructed plasmids pET28a(+)-Der f 1, pET28a(+)-Der f 2 and pET28b(+)-Der f 4 as templates, the gene fragments coding for the allergens Der f 1, Der f 2 and Der f 4, respectively, of the dust mite Dermatophagoides farinae were amplified by PCR. Next the PCR-amplified DNAs were recovered, cloned into pFastBacHT A, and transformed into Escherichia coli DH10Bac. The resulting vectors were co-transfected into Spodoptera frugiperda Sf9 cells for expression. The recombinant allergens were purified by Ni2+ affinity chromatography, and identified by SDS-PAGE and ELISA. RESULTS: The recombinant allergens were successfully expressed and purified from a baculovirus expression system introduced into Sf9 cells, which were verified as being of the correct predicted molecular weights by SDS-PAGE. Furthermore, the reactivity to recombinant allergens rDer f 1, rDer f 2, and rDer f 4 was 85.2%, 88.9%, and 44.4%, respectively, in 27 children with asthma and D. farinae allergy. CONCLUSIONS: Recombinant allergens from dust mites can be successfully generated using a baculovirus-insect expression system. Furthermore, these recombinant allergens can be used to detect mite sensitivity in sera, highlighting their utility in future work to understand and develop treatment for mite allergy.

Homology modeling and epitope prediction of Der f 33.

Dermatophagoides farinae (Der f), one of the main species of house dust mites, produces more than 30 allergens. A recently identified allergen belonging to the alpha-tubulin protein family, Der f 33, has not been characterized in detail. In this study, we used bioinformatics tools to construct the secondary and tertiary structures and predict the B and T cell epitopes of Der f 33. First, protein attribution, protein patterns, and physicochemical properties were predicted. Then, a reasonable tertiary structure was constructed by homology modeling. In addition, six B cell epitopes (amino acid positions 34-45, 63-67, 103-108, 224-230, 308-316, and 365-377) and four T cell epitopes (positions 178-186, 241-249, 335-343, and 402-410) were predicted. These results established a theoretical basis for further studies and eventual epitope-based vaccine design against Der f 33.

Homology modeling and prediction of B­cell and T­cell epitopes of the house dust mite allergen Der f 20.

House dust mite allergens can cause allergic diseases, including asthma, atopic dermatitis and rhinitis. Der f 20 is a novel allergen of Dermatophagoides farina (Der f), which is an arginine kinase. In the present study, the B­cell and T­cell epitopes of Der f 20 were predicted. The protein attribution, patterns, physicochemical properties and secondary structure of Der f 20 were also predicted. Der f 20 is a member of the ATP:guanido phosphotransferase family and contains a phosphagen kinase pattern. Using homology modeling, the present study constructed a reasonable tertiary structure of Der f 20. Using BcePred, ABCpred, BCPred and BPAP systems, B­cell epitopes at 20­25, 41­49, 111­118, 131­141, 170­174 and 312­321 were predicted. Using NetMHCIIpan­3.0 and NetMHCII­2.2, T­cell epitopes were predicted at 194­202, 239­247 and 274­282. These results provide a theoretical basis for the design off Der f 20 epitope­based vaccines.

Homology modeling and epitope prediction of Der f 33

Dermatophagoides farinae (Der f), one of the main species of house dust mites, produces more than 30 allergens. A recently identified allergen belonging to the alpha-tubulin protein family, Der f 33, has not been characterized in detail. In this study, we used bioinformatics tools to construct the secondary and tertiary structures and predict the B and T cell epitopes of Der f 33. First, protein attribution, protein patterns, and physicochemical properties were predicted. Then, a reasonable tertiary structure was constructed by homology modeling. In addition, six B cell epitopes (amino acid positions 34-45, 63-67, 103-108, 224-230, 308-316, and 365-377) and four T cell epitopes (positions 178-186, 241-249, 335-343, and 402-410) were predicted. These results established a theoretical basis for further studies and eventual epitope-based vaccine design against Der f 33.

Blocking beta 2-adrenergic receptor inhibits dendrite ramification in a mouse model of Alzheimer's disease.

Dendrite ramification affects synaptic strength and plays a crucial role in memory. Previous studies revealed a correlation between beta 2-adrenergic receptor dysfunction and Alzheimer's disease (AD), although the mechanism involved is still poorly understood. The current study investigated the potential effect of the selective ß2-adrenergic receptor antagonist, ICI 118551 (ICI), on Aß deposits and AD-related cognitive impairment. Morris water maze test results demonstrated that the performance of AD-transgenic (TG) mice treated with ICI (AD-TG/ICI) was significantly poorer compared with NaCl-treated AD-TG mice (AD-TG/NaCl), suggesting that ß2-adrenergic receptor blockage by ICI might reduce the learning and memory abilities of mice. Golgi staining and immunohistochemical staining revealed that blockage of the ß2-adrenergic receptor by ICI treatment decreased the number of dendritic branches, and ICI treatment in AD-TG mice decreased the expression of hippocampal synaptophysin and synapsin 1. Western blot assay results showed that the blockage of ß2-adrenergic receptor increased amyloid-ß accumulation by downregulating hippocampal α-secretase activity and increasing the phosphorylation of amyloid precursor protein. These findings suggest that blocking the ß2-adrenergic receptor inhibits dendrite ramification of hippocampal neurons in a mouse model of AD.

[Screening of specific IgE-binding epitopes of dust mite allergens using short peptide array].

Objective To screen the possible linear epitopes of major and mid-potency allergens in Dermatophagoides farinae (Der f1, Der f2, Der f4, Der f5 and Der f7). Methods Short peptides were synthesized on the basis of the amino acid sequences in active fraction of Der f1, Der f2, Der f4, Der f5 and Der f7. Each peptide had eight amino acids in length and seven of them were overlapped with each other. Put these peptides to the chip to build microarrays that would have immunoreaction with human serum IgE. Then the chips were scanned to analyze the data. Results A total of 1128 short peptides from the above five groups of allergens were synthesized, and the microarray chips were constructed. Six serum samples from children who were allergic to Dermatophagoides farinae were mixed and added to the microarray chips. The chips were scanned and analyzed, and the results showed that Der f1 had four epitopes (46-53aa, 71-78aa, 99-110aa and 179-186aa), that Der f2 had three epitopes (15-22aa, 80-89aa and 106-113aa), that Der f 4 had six epitopes (69-82aa, 107-116aa, 225-232aa, 261-268aa, 355-365aa and 483-496aa), that Der f5 had one epitope (102-109aa), and Der f7 had three epitopes (32-39aa, 52-64aa and 100-107aa). Conclusion We identified the linear epitopes of Der f1, Der f2, Der f4, Der f5 and Der f7.

Dermatophagoides farinae allergen Der f 9: Cloning, expression, purification, characterization and IgE-binding in children with atopic asthma.

BACKGROUND: The house dust mite species Dermatophagoides farinae releases allergens that cause allergies and asthma worldwide. This study sought to clone and express the full-length cDNA encoding the group 9 allergen of D. farinae (Der f 9). METHODS: The published sequence of Der f 9 was used to design primers for RT-PCR and RACE to obtain the full-length cDNA encoding Der f 9. After removal of signal peptide sequence, Der f 9 was then sub-cloned into plasmid pET-28b (+), and the plasmid was transformed into Escherichia coli BL21 (DE3) cells for expression. The recombinant protein was purified by Nickel affinity chromatography, identified by SDS-PAGE, Western blotting, dot blotting, and MALDI-TOF, and tested by ELISA for IgE reactivity with sera from children with asthma. Bioinformatics analyses were used to identify features of Der f 9. RESULTS: By RT-PCR, 3'-RACE, and 5'-RACE, the full-length sequence of Der f 9 was generated, which was confirmed by nucleotide sequencing. The mature Der f 9 was expressed successfully in E. coli, which was identified by SDS-PAGE. The recombinant allergen was purified by chromatography and confirmed by SDS-PAGE, Western blotting, dot blotting, and MALDI-TOF. Sera from 56.7% (17/30) of mite-allergic patients reacted with the purified recombinant Der f 9. CONCLUSIONS: The successful production of recombinant Der f 9 protein revealed the importance of Der f 9 in mite allergy, and provides a foundation for further study of this allergen in diagnosis and treatment of symptoms. Pediatr Pulmonol. 2017;52:282-292. © 2016 Wiley Periodicals, Inc.

Sequential epitopes of Dermatophagoides farinae allergens identified using peptide microarray-based immunoassay.

House dust mites produce over 30 proteins proposed to induce immunoglobulin E (IgE) antibody production in patients. Continued identification of IgE-binding epitopes of these allergens is critical to advancing diagnosis and treatment of allergic disease. To identify possible sequential IgE-binding epitopes of the major- and mid-potency allergens from the house dust mite Dermatophagoides farinae by peptide microarray-based immunoassay, nucleotide sequences of D. farinae allergens (Der f) 1, 2, 4, 5, and 7 were used to generate overlapping peptides covering the full protein sequences minus signal peptides. Short peptides were printed onto microarray chips. Because asthma occurs as a symptom of mite allergy more commonly among children than adults, the peptide chips were exposed to sera pooled from six serum-positive pediatric patients with D. farinae hypersensitivity and six serum-negative control children for screening sequential IgE-binding epitopes by IgE immunolabeling. Higher-than-average immunolabel signal intensity was observed for 21 short peptides in the serum-positive group (P < 0.01). Due to sequence overlap, these 21 signals represented four fragments of Der f 1 (amino acid positions 46-53, 71-78, 99-110, 179-186), three fragments of Der f 2 (15-22, 80-89, 106-113), six fragments of Der f 4 (69-82, 107-116, 225-232, 261-268, 355-365, 483-496), one fragment of Der f 5 (102-109), and three fragments of Der f 7 (32-39, 52-64, 100-107). These findings not only demonstrate the utility of a peptide microarray immunoassay in identifying epitopes for these allergens, but also provide a foundation for future exploration of specific immunotherapies. © 2016 IUBMB Life, 68(10):792-798, 2016.

Dust mite allergen Der f 4: Expression, characterization, and IgE binding in pediatric asthma.

BACKGROUND: House dust mite hypersensitivity affects millions of people worldwide, and although many allergens produced by house dust mite species have been identified, some of the less potent allergens remain to be studied. METHODS: The full-length cDNA encoding the group 4 allergen of the house dust mite species Dermatophagoides farinae (Der f 4) was generated through degenerate primer-based PCR, 5' RACE, and 3' RACE, and the cDNA fragment was cloned into an expression vector for nucleotide sequencing. Following codon optimization and removal of the signal peptide sequence, the mature gene fragment was subcloned into pET-28b (+) and transfected into E. coli BL21 cells for expression. The recombinant protein was purified by nickel affinity chromatography, identified by SDS-PAGE, Western blotting, and MALDI-TOF, and tested by ELISA for IgE reactivity with sera from individuals with asthma. Bioinformatics analyses were used to identify features of Der f 4. RESULTS: SDS-PAGE and Western blotting of the codon-optimized expression product showed a specific band. The mature recombinant Der f 4 was characterized as a stable and hydrophilic 57.9-kDa protein, and its secondary structure comprised alpha helix (25.3%), extended strand (22.51%), and random coils (52.19%). The structure of the recombinant protein was consistent with that of α-amylase. Among 27 pediatric asthma patients, 40.74% exhibited reactivity to rDer f 4 by ELISA. CONCLUSIONS: This initial cloning and characterization of the Der f 4 allergen serves as a foundation for future studies into the clinical importance and application of this protein for house dust mite allergy.

In silico structural analysis of group 3, 6 and 9 allergens from Dermatophagoides farinae.

Dermatophagoides farinae (Hughes; Acari: Pyroglyphidae) are the predominant source of dust mite allergens, which provoke allergic diseases, such as rhinitis, asthma and eczema. Of the 30 allergen groups produced by D. farinae, the Der f 3, Der f 6 and Der f 9 allergens are all trypsin­associated proteins, however little else is currently known about them. The present study used in silico tools to compare the amino acid sequences, and predict the secondary and tertiary structures of Der f 3, Der f 6 and Der f 9 allergens. Protein sequence alignment detected ~46% identity between Der f 3, Der f 6 and Der f 9. Furthermore, each protein was shown to contain three active sites and two highly conserved trypsin functional domains. Predictions of the secondary and tertiary structure identified α­helices, ß­sheets and random coils. The active sites of the three proteins appeared to fold onto each other in a three­dimensional model, constituting the active site of the enzyme. Epitope analysis demonstrated that Der f 3, Der f 6 and Der f 9 have 4­5 potential epitopes located in random coils, and the epitope sequences of Der f 3, Der f 6 and Der f 9 were shown to overlap in two domains (at amino acids 83­87 and 179­180); however the residues in these two domains were not identical. The present study aimed to conduct a biochemical and genetic analysis of these three allergens, and to potentially contribute to the development of vaccines for allergen­specific immunotherapy.

Expression, cloning, and IgE-binding of the full-length dust mite allergen Der f 8.

Dermatophagoides farinae, a domestic mite species, produces some of the most potent allergens that contribute to allergy in China and worldwide. We sought to clone and express the group 8 allergen of D. farinae (Der f 8) to investigate its IgE-binding reactivity. The full-length cDNA encoding Der f 8 was generated by using RT-PCR and 5' RACE, cloned into pCold-TF expression vector, confirmed by nucleotide sequencing, sub-cloned into pET-28b (+), and transfected into E. coli BL21 cells for expression. After purification by nickel affinity chromatography and identified by SDS-PAGE, the recombinant Der f 8 bound with sera from 40.9 % (9/22) of mite-allergic patients according to ELISA testing. Analysis of the recombinant DNA sequence revealed a 231 amino acid open reading frame encoding a protein with a derived molecular mass of 26.4 kDa and an isoelectric point of 6.84. The deduced amino acid sequence has nine phosphorylation sites, displaying strong homology with glutathione S-transferase, and its secondary structure comprises alpha helix (45.5 %), extended strand (11.3 %), and random coils (43.3 %). BLAST through the National Center for Biotechnology Information database and alignment identified similarity with group 8 allergens or glutathione S-transferases of Dermatophagoides pteronyssinus, Suidasia medanensis, Lepidoglyphus destructor, Glycyphagus domesticus, and Aleuroglyphus ovatus (64, 65, 53, 53, and 50 %, respectively). The first recombinant Der f 8 protein produced in full length successfully bound with patient IgE, demonstrating the importance of Der f 8 in mite allergy.

Cystathionine ß-synthase-derived hydrogen sulfide regulates lipopolysaccharide-induced apoptosis of the BRL rat hepatic cell line in vitro.

Hydrogen sulfide (H(2)S), is a member of the novel family of endogenous gaseous transmitters, termed "gasotransmitters exhibiting diverse physiological activities, and is generated in mammalian tissues mainly by cystathionine ß-synthase (CBS), cystathionine γ-lyase (CSE) and 3-mercaptopyruvate sulfurtransferase (3MST) in conjunction with cysteine (aspartate) aminotranferase (CAT). The distributions of these enzymes are species- and tissue-specific. The liver, as the main organ that generates H(2)S in vivo, functions in biotransformation and metabolism. However, the liver is vulnerable to damage from internal and external factors, including inflammatory mediators, drugs and poisons. The present study evaluated the endogenous CBS-H(2)S synthesis regulating lipopolysaccharide (LPS)-induced apoptosis of hepatic cells. The rat hepatic cell line, BRL, was incubated with LPS for various time periods to establish a cell-damage model. Incubation with LPS resulted in a significant increase in CBS expression and H(2)S production. It also stimulated apoptosis and decreased the mitochondrial membrane potential. Pretreatment with the CBS inhibitor aminooxyacetic acid (AOAA) or CBS small interfering RNA (siRNA) decreased LPS-enhanced H(2)S production. Notably, apoptosis increased for a short period and then decreased gradually, while the mitochondrial membrane potential demonstrated the opposite trend. These results showed that endogenous CBS-H(2)S synthesis demonstrated early anti-apoptotic activity and subsequent pro-apoptotic activity in LPS-induced apoptosis. These results suggest a new approach for developing novel drugs for this condition.

Effect of Fe(3)O(4)-magnetic nanoparticles on acute exercise enhanced KCNQ(1) expression in mouse cardiac muscle.

While the potential impact of magnetic nanoparticles (MNPs) has been widely explored in almost all medical fields, including cardiology, one question remains; that is whether MNPs interfere with cardiac physiological processes such as the expression and function of ion channels, especially in vivo. KCNQ(1) channels are richly expressed in cardiac myocytes and are critical to the repolarization of cardiac myocytes. In this study, we evaluated the effects of Fe(3)O(4)-magnetic nanoparticles (MNPs-Fe(3)O(4)) on the expression of KCNQ(1) in cardiac muscle of mice at rest and at different times following a single bout of swimming (SBS). Firstly, we demonstrated that the expression levels of KCNQ(1) channels are significantly up-regulated in mice following a SBS by means of reverse transcription polymerase chain reaction (RT-PCR) and western-blot. After treating mice with normal saline or pure MNPs-Fe(3)O(4) separately, we studied the potential effect of MNPs-Fe(3)O(4) on the expression profile of KCNQ(1) in mouse cardiac muscle following a SBS. A SBS increased the transcription of KCNQ(1) at 3 hours post exercise (3PE) 164% +/- 24% and at 12 hours post exercise (12PE) by 159% +/- 23% (P < 0.05), and up-regulated KCNQ(1) protein 161% +/- 27% at 12PE (P < 0.05) in saline mice. In MNPs-Fe(3)O(4) mice, KCNQ(1) mRNA increased by 151% +/- 14% and 147% +/- 12% at 3 and 12 PE, respectively (P <0.05). Meanwhile, an increase of 152% +/- 14% in KCNQ(1) protein was also detected at by 12PE. These results indicated that the administration of MNPs-Fe(3)O(4) did not cause any apparent effects on the expression profile of KCNQ(1) in rested or exercised mice cardiac muscle. Our studies suggest a novel path of KCNQ(1) current adaptations in the heart during physical exercise and in addition provide some useful information for the biomedical application of MNPs which are imperative to advance nanomedicine.