Multiplex LAMP assay for detecting the prevalent species of dust mites Dermatophagoides farinae and Dermatophagoides pteronyssinus in the domestic environment.

Dermatophagoides farina (D. farinae) and Dermatophagoides pteronyssinus (D. pteronyssinus) are the prevalent kinds of house dust mites (HDMs). HDMs are common inhalant allergens that cause a range of allergic diseases, such as rhinitis, atopic dermatitis, and asthma. The epidemiology of these diseases is associated with exposure to mites. Therefore, in the present study, a method named multiplex loop-mediated isothermal amplification (LAMP) was developed to detect environmental dust mites. The multiplex LAMP assay allows amplification within a single tube and has an ITS plasmid detection limit as low as 40 fg/µL for both single dust mites and mixed dust mites (D. pteronyssinus and D. farinae), which is up to ten times more sensitive than classical PCR techniques. Furthermore, the multiplex LAMP method was applied to samples of single dust mites and clinical dust to confirm its validity. The multiplex LAMP assay exhibited higher sensitivity, simpler instrumentation, and visualization of test results, indicating that this method could be used as an alternative to traditional techniques for the detection of HDMs.

Genetic diversity and differentiation analysis reveals geographical structure characteristics of Dermatophagoides farinae (Acari: Pyroglyphidae).

Dermatophagoides farinae (Acari: Pyroglyphidae) has been reported as one of the major sources of indoor allergens that trigger allergic disease in humans. In this study, the genetic diversity and differentiation of nine geographic populations of D. farinae were investigated by analyzing mitochondrial and nuclear genes (COI, Cytb, COI+Cytb, and ITS). The results showed high genetic diversity across the D. farinae populations. The BX (Benxi) population showed the lowest genetic diversity, possibly due to climatic causes. Significant genetic differentiation was observed among D. farinae populations based on mitochondrial genes. The analysis of molecular variance (AMOVA) results elucidated that the contribution to the rate of variation was primarily from among populations. Phylogenetic analysis and haplotype network based on mitochondrial genes both indicated significant geographic structure among D. farinae populations. The nine geographic populations of D. farinae were divided into two groups with the Qinling Mountains-Huai River Line serving as the boundary for spatial analysis of molecular variance analysis (SAMOVA). However, the Mantel test analysis showed no association between genetic differentiation and geographic distance because of the high level of gene flow among some populations through the transportation of stored food. Overall, these results indicate both significant genetic differentiation among D. farinae populations, but also significant gene exchange between them. Results from the analysis of the nuclear gene ITS differed from the mitochondrial genes due to differences in molecular markers between mitochondrial genes and nuclear genes. These observations improve our understanding of the genetic diversity and structure of D. farinae populations.

Dermatophagoides farinae microRNAs released to external environments via exosomes regulate inflammation-related gene expression in human bronchial epithelial cells.

Background: Dermatophagoides farinae (DFA) is an important species of house dust mites (HDMs) that causes allergic diseases. Previous studies have focused on allergens with protein components to explain the allergic effect of HDMs; however, there is little knowledge on the role of microRNAs (miRNAs) in the allergic effect of HDMs. This study aimed to unravel the new mechanism of dust mite sensitization from the perspective of cross-species transport of extracellular vesicles-encapsulated miRNAs from HDMs. Methods: Small RNA (sRNA) sequencing was performed to detect miRNAs expression profiles from DFA, DFA-derived exosomes and DFA culture supernatants. A quantitative fluorescent real-time PCR (qPCR) assay was used to detect miRNAs expression in dust specimens. BEAS-2B cells endocytosed exosomes were modeled in vitro to detect miRNAs from DFA and the expression of related inflammatory factors. Representative dfa-miR-276-3p and dfa-novel-miR2 were transfected into BEAS-2B cells, and then differentially expressed genes (DEGs) were analyzed by RNA sequencing. Protein-protein interaction (PPI) network analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) terms enrichment analyses were performed on the first 300 nodes of DEGs. Results: sRNA sequencing identified 42 conserved miRNAs and 66 novel miRNAs in DFA, DFA-derived exosomes, and DFA culture supernatants. A homology analysis was performed on the top 18 conserved miRNAs with high expression levels. The presence of dust mites and miRNAs from HDMs in living environment were also validated. Following uptake of DFA-derived exosomes by BEAS-2B cells, exosomes transported miRNAs from DFA to target cells and produced pro-inflammatory effects in corresponding cells. RNA sequencing identified DEGs in dfa-miR-276-3p and dfa-novel-miR2 transfected BEAS-2B cells. GO and KEGG enrichment analyses revealed the role of exosomes with cross-species transporting of DFA miRNAs in inflammatory signaling pathways, such as JAK-STAT signaling pathway, PI3K/AKT signaling pathway and IL-6-mediated signaling pathway. Conclusion: Our findings demonstrate the miRNAs expression profiles in DFA for the first time. The DFA miRNAs are delivered into living environments via exosomes, and engulfed by human bronchial epithelial cells, and cross-species regulation may contribute to inflammation-related processes.

Exosomes Derived from Dermatophagoides farinae Induce Allergic Airway Inflammation.

House dust mites (HDMs) are a major source of indoor allergens that cause airway allergic disease. Dermatophagoides farinae, a predominant species of HDMs in China, has demonstrated pathogenic role in allergic disorders. Exosomes derived from human bronchoalveolar lavage fluid have been strongly associated with allergic respiratory diseases progression. However, the pathogenic role of D. farinae-derived exosomes in allergic airway inflammation has remained unclear until now. Here, D. farinae was stirred overnight in phosphate-buffered saline, and the supernatant was used to extract exosomes by ultracentrifugation. Then, shotgun liquid chromatography-tandem mass spectrometry and small RNA sequencing were performed to identify proteins and microRNAs contained in D. farinae exosomes. Immunoblotting, Western blotting, and enzyme-linked immunosorbent assay demonstrated the specific immunoreactivity of D. farinae-specific serum IgE antibody against D. farinae exosomes, and D. farinae exosomes were found to induce allergic airway inflammation in a mouse model. In addition, D. farinae exosomes invaded 16-HBE bronchial epithelial cells and NR8383 alveolar macrophages to release the inflammation-related cytokines interleukin-33 (IL-33), thymic stromal lymphopoietin, tumor necrosis factor alpha, and IL-6, and comparative transcriptomic analysis of 16-HBE and NR8383 cells revealed that immune pathways and immune cytokines/chemokines were involved in the sensitization of D. farinae exosomes. Taken together, our data demonstrate that D. farinae exosomes are immunogenic and may induce allergic airway inflammation via bronchial epithelial cells and alveolar macrophages. IMPORTANCE Dermatophagoides farinae, a predominant species of house dust mites in China, has displayed pathogenic role in allergic disorders, and exosomes derived from human bronchoalveolar lavage fluid have been strongly associated with allergic respiratory diseases progression. However, the pathogenic role of D. farinae-derived exosomes in allergic airway inflammation has remained unclear until now. This study, for the first time, extracted exosomes from D. farinae, and sequenced their protein cargo and microRNAs using shotgun liquid chromatography-tandem mass spectrometry and small RNA sequencing. D. farinae-derived exosomes trigger allergen-specific immune responses and present satisfactory immunogenicity, as revealed by immunoblotting, Western blotting, and enzyme-linked immunosorbent assay and may induce allergic airway inflammation via bronchial epithelial cells and alveolar macrophages. Our data provide insights into the mechanisms of allergic airway inflammation caused with D. farinae-derived exosomes and the treatment of house dust mite-induced allergic airway inflammation.

Establishment of purification method for prokaryotic expression of Serpin gene for Dermatophagoides farinae.

This study aimed to develop an effective method for the expression and purification of the Dermatophagoides farinae serpin protein and to establish an experimental foundation for elucidating its role in the temperature stress response. The total RNA of D. farinae was extracted, and specific primers were designed for serpin amplification. Serpin was joined with pET32a vector and transformed into BL21 (DE3) cells. Expression of recombinant proteins was induced. Proteins were extracted by enzymatic lysis or enzymatic lysis combined with ultrasonication. Recombinant proteins were purified by Ni-NTA method. SDS-PAGE was conducted to evaluate protein expression, extraction, and purification efficiency. Agarose gel electrophoresis and sequencing analysis showed that the amplified serpin open reading frame was 1284 bp, encoding a hydrophilic and stable protein with a relative molecular weight of 48.30 kD. SDS-PAGE demonstrated that there was a specific band at 55-70 kD, which was consistent with the predicted size of the recombinant pET32a-Serpin protein. Enzymatic lysis combined with 30% ultrasonic power promoted the release of soluble protein more effectively than enzymatic lysis alone. 16 °C for 4 h was optimal for inducing expression. The optimal imidazole concentrations for washing non-His-tagged protein and eluting His-tagged protein were determined to be 20 mM and 200 mM, respectively. In this study, A prokaryotic expression and purification system for the D. farinae serpin protein was successfully established, providing a technical reference for functional gene research in mites at the protein level.

[Bacterial community diversity in Dermatophagoides farinae using high-throughput sequencing].

OBJECTIVE: To investigate the bacterial community diversity in Dermatophagoides farinae. METHODS: Laboratory-cultured D. farinae was collected, and the composition of microbial communities was determined by sequence analyses of the V4 region in the bacterial 16S ribosomal RNA (16S rRNA) gene on an Illumina PE250 high-throughput sequencing platform. Following quality control and filtering of the raw sequence files, valid reads were obtained and subjected to operational taxonomic units (OTU) clustering and analysis of the composition of microbial communities and alpha diversity index using the Usearch software, Silva database, and Mothur software. RESULTS: A total of 187 616 valid reads were obtained, and 469 OTUs were clustered based on a sequence similarity of more than 97%. OTU annotation showed that the bacteria in D. farinae belonged to 26 phyla, 43 classes, 100 orders, 167 families and 284 genera. The bacteria in D. farinae were mainly annotated to five phyla of Proteobacteria, Firmicutes, Bacteroidota, Actinobacteriota, and Acidobacteriota, with Proteobacteria as the dominant phylum, and mainly annotated to five dominant genera of Ralstonia, norank-f-Mitochondria, Staphylococcus and Sphingomonas, with Wolbachia identified in the non-dominant genus. CONCLUSIONS: A high diversity is identified in the composition of the bacterial community in D. farinae, and there are differences in bacterial community diversity and abundance among D. farinae.

Pathogenic Mechanism of Der p 38 as a Novel Allergen Homologous to RipA and RipB Proteins in Atopic Dermatitis.

Atopic dermatitis (AD) is a chronic relapsing pruritic disease encompassing skin inflammation and barrier dysfunction. House dust mites are key allergens that augment the development of atopic dermatitis. We aimed to investigate the pathogenic mechanism of AD due to Der p 38, recently identified by us. The frequency of IgE reactivity to Der p 38 in AD subjects was 52.6% (10/19) in the skin prick test and 57.9% (11/19) in the dot blot assay. In human keratinocyte HaCaT cells, Der p 38 triggered the impairment of filaggrin expression and induced pro-inflammatory cytokines such as IL-6, IL-8 and MCP-1 through TLR4, PI3K, AKT, c-Jun N-terminal kinase (JNK) and NF-κB pathway. Supernatants from Der p 38-treated cells blocked filaggrin expression and neutrophil apoptosis. The anti-apoptotic effect of the Der p 38-released molecules on neutrophils was accomplished by inhibition of the caspase 9/3 pathway, and by increased MCL-1 expression and BCL-2/BAX expression ratio. In C57BL/6 wild type (WT) mice, Der p 38 induced a dose-dependent increase of AD-like skin lesions, with enhanced expressions of total and Der p 38-specific IgE. Der p 38 also diminished the expressions of skin barrier proteins and induced JNK activation. However, the AD-like features following cutaneous Der p 38 exposure were observed to be reduced in the TLR4 knockout (KO) group, as compared to the WT group. Skin infiltration of neutrophils, eosinophils and mast cells was increased in the WT mice, but was not portrayed in the TLR4 KO mice. These findings indicate that Der p 38 is a novel mite allergen that triggers AD by lowering skin barrier proteins and increasing inflammatory cells. Results of this study have thereby paved the way to unveil the pathogenic mechanisms of AD.

Temperature stress response: A novel important function of Dermatophagoides farinae allergens.

Dermatophagoides farinae, an important pathogen, has multiple allergens. However, their expression under physiological conditions are not understood. Our previous RNA-seq showed that allergens of D. farinae were up-regulated under temperature stress, implying that they may be involved in stress response. Here, we performed a comprehensive study. qRT-PCR detection indicated that 26 of the 34 allergens showed differential expression. Der f1 had the most abundant basic expression quantity. Der f 28.0201 (HSP70) and Der f3 had the same regulation pattern in 9 highly expressed transcripts, which only up-regulated at 41 °C and 43 °C, but Der f 28.0201 showed stronger regulation than Der f 3 (19.88-fold vs 6.02-fold). Whereas Der f 1, 2, 7, 21, 22, 27, and 30 were up-regulated under both heat and cold stress, and Der f 27 showed the strongest regulation ability among them. Der f 27 showed more significant up-regulation than Der f 28.0201 under heat stress (23.59-fold vs 19.88-fold), and Der f27 had more obvious up-regulation under cold than heat stress (30.70-fold vs 23.59-fold). The expression of Der f 27, 28.0201 and 1, and D. farinae survival rates significantly decreased following RNAi, indicating the upregulation of these allergens under temperature stress conferred thermo-tolerance or cold-tolerance to D. farinae. In this study, we described for the first time that these allergens have temperature-stress response functions. This new scientific discovery has important clinical value for revealing the more frequent and serious allergic diseases caused by D. farinae during the change of seasons.

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.

[Cloning and sequence analysis of leptin receptor overlapping transcript-like 1 gene from Dermatophagoides farinae].

OBJECTIVE: To obtain the leptin receptor overlapping transcript-like 1 encoding gene (LepROTL1 gene) from Dermatophagoides farina, investigate the molecular characteristics of the gene and construct a prokaryotic expression vector to express this gene. METHODS: The LepROTL1 gene-encoding sequence fragments were captured based on the transcriptome sequencing results, and the full-length gene fragments were amplified from total RNA of D. farinae using a RT-PCR assay, and used to construct the expression plasmid pET28a(+)-LepROTL1, followed by sequencing. The plasmid was transformed into E. coli BL21 (DE3) T1R for the induction of IPTG expression. The expression product was characterized by SDS-PAGE and Western blotting. Bioinformatics analyses were performed to analyze the sequence and the molecular characteristics of its encoded protein. RESULTS: The amplification products of the RT-PCR assay showed a clear band on agarose gel electrophoresis, and sequencing analysis of the pET28a(+)-LepROTL1 plasmid showed 417 bp in length of the coding gene from the start codon ATG to the termination codon TAA. Following the plasmid transformation into E. coli and induction with IPTG, a specific band was seen on SDS-PAGE, indicating successful expression. Bioinformatics analysis showed that the LepROTL1 gene-encoded protein was composed of 134 amino acids, and had a relative molecular weight of 14 378.13 Da, a hydrophilicity index of 1.149, and certain hydrophobicity. The secondary structure was composed of alpha-helix (19 aa, 14.18%), extended strand (48 aa, 35.82%) and random coil (67 aa, 50.00%). The deduced amino acid sequence was used to obtain homologous genes by BLAST, and the phylogenetic tree showed that D. farinae was clustered with D. pteronyssinus. CONCLUSIONS: The full-length sequences and expression plasmid of the LepROTL1 gene are obtained, and the molecular features of the gene are demonstrated using bioinformatics analyses, which provide insights into further studies on the gene.

Stress response and silencing verification of heat shock proteins in Dermatophagoides farinae under temperature stress.

Dermatophagoides farinae is a major exogenous allergen. Its ability to tolerate adverse external temperatures makes it responsible for widespread occurrence of allergies. Heat shock protein (HSP), a recognized temperature stress response gene, but its role in D. farinae remained unclear. Here, we performed a comprehensive study. First, we found that 25 °C was the optimal temperature, and all mites died at 48 or -20 °C for 1 h (LT100). Thus, 41 °C (LT15), 43 °C (LT25), 45 °C (LT45), and -10 °C (LT25) were selected as stress temperatures to perform de novo RNA-seq. Then, 17 main genes of the 47 differentially expressed HSP, were detected by qRT-PCR. Temperature and time gradient versus expression magnitude histogram revealed that HSP70, HSP83-1, HSP83-2, and HSP16-1 showed heat stress response only at 41-43 °C, while HSC71 and HSF played a regulatory role under both heat and cold stress, particularly HSF, with strong intensity, long duration, and quick upregulation at recovery for 10-20 min. Finally, gene expression and D. farinae survival rates significantly decreased following RNAi. These findings indicated that HSPs conferred thermo-tolerance or cold-tolerance to D. farinae. In conclusion, this was the first meaningful exploration that confirmed HSP and HSF playing an important role in temperature resistance of D. farinae.

Proteogenomics of the house dust mite, Dermatophagoides farinae: Allergen repertoire, accurate allergen identification, isoforms, and sex-biased proteome differences.

The allergen repertoire of the house dust mite, Dermatophagoides farinae, is incomplete despite most mite allergens having been described in this species. Using proteogenomics, we aimed to compare proteins and allergens between sexes and provide a foundation for the identification of novel allergens. Overall, 6297 protein hits were identified, and 2899 and 886 were male- and female-specific, respectively. Removal of trace results narrowed the dataset to 3478 hits, including 275 and 157 male- and female-specific hits, respectively. All 34 WHO/IUIS-approved D. farinae allergens (omitting Der f 17) were identified, and we also identified homologs of the yet undescribed Der f 9 and 38. Der f 27/serpin exhibited the largest sex-dependent difference and was dominant in females. Using official protein sequences, Der f 11, 14, 23, 28 and 30 were identified with low success. However, identification success of Der f 11 and 14 was greatly increased by using longer/complete sequences. Der f 30 is characterized by the same tryptic digests as the more abundant Der f 30 (isoform) identified here. Der f 23 appears to be of low abundance in mite bodies. Der f 28.0101 and Der f 28.0201 were detected at low abundance and in trace amounts, respectively. SIGNIFICANCE: In this work, we performed a proteogenomic annotation of the house dust mite, Dermatophagoides farinae, which is the most important source of house dust allergens. The proteogenomic analysis performed here provides a foundation for not only understanding the biology of the mite but also the identification of novel allergens. This study generated a robust proteomic dataset for D. farinae and reviewed existing and candidate allergens in this species. We stress some pitfalls of high-throughput analyses, especially that improper headers of allergen protein records provided in databases can lead to confusion. Using partial sequences in proteomic identification and quantification can lead to low identification success (low signal intensity or MS/MS counts). Thus, we individually curated the protein sequences for proper identification and quantification. The discovered sex differences can be one factor affecting allergen/immunogen variations in mite extracts. Overall, this work provides a benchmark for accurate identification of mite immunogenic proteins using proteomics.

Gene synthesizing, expression and immunogenicity characterization of recombinant translation elongation factor 2 from Dermatophagoides farinae.

House dust mite (HDM) hypersensitivity increasingly affects millions of individuals worldwide. Although numerous major allergens produced by HDM species have been characterized, some of the less potent allergens remain to be studied. The present study aimed to obtain the recombinant allergen of Translation Elongation Factor 2 (TEF 2) from the HDM Dermatophagoides farinae by synthesizing, and then expressing the recombinant TEF 2 to identify its immunogenicity. In the present study, the D. farinae TEF 2 (Der f TEF 2) was synthesized, expressed and purified. The molecular characteristics of Der f TEF 2 were analyzed using bioinformatics approaches. The recombinant protein was purified via affinity chromatography, and the allergenicity was assessed using immunoblotting, ELISAs and skin prick tests. The gene for TEF 2 consists of 2,535 bp and encodes an 844­amino acid protein. A positive response to recombinant Der f TEF 2 was detected in 16.2% of 37 patients with HDM allergies using skin prick tests. In addition, the immunoblotting indicated that the protein showed a high ability to bind serum IgE from patients allergic to HDMs, and that the recombinant TEF 2 was highly immunogenic. Bioinformatics analysis predicted 17 peptides as B cell epitopes (amino acids 29­35, 55­64, 92­99, 173­200, 259­272, 311­318, 360­365, 388­395, 422­428, 496­502, 512­518, 567­572, 580­586, 602­617, 785­790, 811­817 and 827­836) and 14 peptides as T cell epitopes (amino acids 1­15, 65­79, 120­134, 144­159, 236­250, 275­289, 404­418, 426­440, 463­477, 510­524, 644­658, 684­698, 716­730 and 816­830). The software DNAStar predicted the secondary structure of TEF 2, and showed that 27 α­helices and five ß­sheets were found in the protein. In conclusion, the present study cloned and expressed the Der f TEF 2 gene, and the recombinant protein exhibited immunogenicity, providing a theoretical bases, and references, for the diagnosis and treatment of allergic disease.

Screening of reference genes and quantitative real-time PCR detection and verification in Dermatophagoides farinae under temperature stress.

Dermatophagoides farinae is an important source of indoor allergens that shows strong tolerance to external temperatures. However, the regularity and mechanism of tolerance are still unclear. Based on our previous RNA-seq and annotation of D. farinae under temperature stress, it is planned to identify differentially expressed genes (DEGs) involved in the temperature stress response by quantitative real-time PCR (qRT-PCR). However, the lack of reference genes directly limited the detection and confirmation of DEGs. Accordingly, in this study, we have selected six candidates as reference genes in D. farinae: 60S RP L11, 60S RP L21, α tubulin, GAPDH, Der f Mal f 6, and calreticulin, and evaluated their expression stabilities as affected by heat and cold stresses, using geNorm, NormFinder, BestKeeper, comparative ΔCt and RefFinder methods. Then the expression level of 15 DEGs were detected and verified. geNorm analysis showed that α tubulin and calreticulin were the most stable reference genes under heat stress and cold stress of D. farinae. Similar evaluation results were obtained by NormFinder and BestKeeper, in which 60S RP L21 and α tubulin were the most stable reference genes. By comparative ΔCt method and a comprehensive evaluation of RefFinder, α tubulin was identified as the most ideal reference gene of D. farinae under heat and cold stresses. Furthermore, qRT-PCR detection results of 15 DEGs were almost identical to the RNA-seq results, indicating that α tubulin is stable as a reference gene. This study provided technical support for DEGs expression studies in D. farinae using qRT-PCR.

Function of heat shock protein 70 in the thermal stress response of Dermatophagoides farinae and establishment of an RNA interference method.

Dermatophagoides farinae are an important mite species that cause stored product deterioration and allergic diseases. They widely breed in human habitats because of their strong tolerance to extreme external temperatures. However, mechanisms underlying the stress response and tolerance of D. farinae are unclear. We hypothesized that heat shock protein 70 plays an important role in the heat stress response of D. farinae. In this study, we determined the survival rates of D. farinae at high temperatures (37 °C-45 °C) by performing temperature-gradient experiments in vitro and assessed the expression level of HSP70 by performing RT-qPCR. First, we confirmed that HSP70 regulated the heat stress response of D. farinae, with maximum heat stress regulation observed at 41 °C. Next, we confirmed the presence of a Dicer enzyme-mediated RNA interference (RNAi) pathway in D. farinae by searching the NCBI database and a Dicer site prediction website. Finally, we performed RNAi in D. farinae by using an immersion method with screened dsHSP70 fragments. Moreover, we performed concentration-gradient experiments to determine that 600 ng/µl was the minimal effective concentration of dsHSP70 for silencing HSP70. These results confirm that HSP70 regulates the heat stress response of D. farinae. The present study is the first to report the use of the non-invasive and highly sensitive immersion method for performing RNAi in D. farinae. The results of the present study provide a technical foundation for performing functional gene research and for developing molecular prevention and control strategies against medically important mites.

Transcriptomics-Based Identification of Aquaporin Diversity in the House Dust Mite Dermatophagoides farinae (Acariformes: Pyroglyphidae).

Aquaporin water channel proteins are highly conserved across many diverse species. Some evidence indicates that aquaporins in insects may contribute to insect-related mammalian diseases and inflammation, and thus these proteins may represent viable therapeutic targets. Here, we used RNA sequencing and bioinformatics to identify putative aquaporins from the house dust mite, Dermatophagoides farinae. Six putative aquaporins were identified based on sequence similarity with aquaporins from other species. These putative aquaporins, deposited in GenBank and named DerfAQP1-4 (KY231248, KY231249, KY231250, and KY231251, respectively), DerfAQP5.01, and DerfAQP5.02 (KY231252 and KY231253), were successfully cloned into a bacterial plasmid. The identification of full-length aquaporin sequences from D. farinae provides a foundation for future molecular and biochemical studies of these proteins in D. farinae and related species.

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.

lncRNA profiling in NCI-H292 cells after stimulation with Dermatophagoides farinae extracts.

Airway epithelium cells are the first line of defense against airborne allergens. When cultured, epithelial cells can be exposed to various allergens, providing an ideal model to investigate allergic disorders. This study sought to characterize the profile of long noncoding (lnc) RNAs, which can regulate gene expression and exert functions in diverse cellular processes, in airway epithelial cells exposed to house dust mite allergens. NCI-H292 cells were exposed to house dust mite extract for 24 h. RNA expression was profiled in exposed and unexposed cells. There were 270 lncRNAs that were differentially expressed (fold change ≥ 2, P < 0.05) in NCI-H292 cells after stimulation with Dermatophagoides farinae (house dust mite) extracts. Furthermore, 119 lncRNAs and 22 messenger RNAs were co-expressed. Gene Ontology analysis showed that these under-regulated and up-regulated lncRNAs were associated with biological process, cellular component, and molecular function. After bioinformatic analysis of significantly regulated signaling pathways, we found these lncRNAs may target 16 gene pathways, including glycolysis, axon guidance, ErbB signaling, and mitogen-activated protein kinases (MAPK) signaling. The identification of differentially regulated lncRNAs in NCI-H292 cells after stimulation with Dermatophagoides farinae extracts, as well as their target gene pathways, can provide insight to the etiology and pathogenesis of 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.