1  Introduction
Porcine deltacoronavirus (PDCoV) is enveloped and has a single-stranded, positive-sense RNA genome, which is classified in the genus Deltacoronavirus within the Coronaviridae family.1 Although PDCoV was initially identified in rectal swabs of pigs during a molecular epidemiological investigation conducted in Hong Kong, China in 2012,2 diarrheal diseases in pigs associated with PDCoV infection were first recorded in the U.S. in 2014.3 Since then, the virus has been detected in many other countries, including Canada, mainland China, South Korea, Thailand, Laos, Vietnam, Japan, Mexico, and so on.4,5 Clinically, PDCoV-infected pigs often present with diarrhea and/or vomiting, dehydration, and death of neonatal piglets.6 The outbreak of PDCoV infection in numerous countries has resulted in considerable economic losses to the global swine industry.7
PDCoV has an obvious enteropathogenic characteristic in pigs.1,6 The small intestine of pigs, in particular the jejunum and ileum, are the primary target organs of PDCoV, and porcine small intestinal epithelial cells (IPEC) are the main sites of PDCoV replication in vivo.1,8,9 Histopathologic analyses showed that PDCoV infection not only causes villus atrophy and fall-off but also leads to necrosis of small intestinal enterocytes in infected pigs.1,6 Currently, an immortalized, nontumorigenic IPEC-J2 cell line, originally established using the jejunum of a newborn unsuckled piglet,10 has been shown to exhibit high similarities to porcine intestinal primary epithelial cells,11 and thus can better simulate the porcine physiological state than any other cell lines. At present, IPEC-J2 cells have been successfully utilized as an ideal in vitro model system for investigating the interactions between epithelial cells and porcine enteric viruses, such as porcine rotavirus,12 porcine endemic diarrhea virus (PEDV),13 and transmissible gastroenteritis virus (TGEV).14 Recently, Jung and colleagues demonstrated that IPEC-J2 cells are quite susceptible to PDCoV infection in vitro.8
As a newly emerged swine enteropathogenic coronavirus, the pathogenic mechanisms of PDCoV are still poorly documented and warrant further exploration.1 It is well-known that when a virus invades a host cell, complex interactions between the host cell and the virus will occur. On the one hand, the invading virus subverts some of the cellular biological functions in favor of the replication of the virus itself; on the other, the cells adopt various defense strategies to fight against the invading virus.15 The whole process of virus–cell interactions is usually accompanied by changes of genomics, transcriptomics, and proteomics.16 Recently, a systematic transcriptome analysis of PDCoV-infected PK-15 cells was conducted using high-throughput RNA sequencing, and 3762 differentially expressed genes were identified, most of which participate in the innate immunity and the corresponding signal transduction pathways.17 As of yet, however, no proteomic data are currently available for PDCoV-infected cells.
Proteomics is an effective tool for the comprehensive analysis of host cellular responses to viral infections, which is conducive to elucidating the underlying pathogenesis of the virus.18 The currently available proteomics techniques include two-dimensional gel electrophoresis,15 two-dimensional difference gel electrophoresis,19 stable isotope labeling by amino acids in cell culture,20,21 isobaric tags for relative and absolute quantitation (iTRAQ),22 and label-free proteomic techniques.23 Among all these mentioned techniques, iTRAQ coupled with liquid chromatography–tandem mass spectrometry (LC-MS/MS) analysis has shown several comparative advantages over its counterparts, for instance, high sensitivity, high throughput, high separating capacity, and high accuracy, and thus emerged as a robust quantitative proteomics technique for the comprehensive analysis of differentially expressed proteins (DEPs). To date, this technique has been successfully applied to numerous studies involved in virus-host interactions, examples of which include TGEV,22 PEDV,24 foot-and-mouth disease virus (FMDV),25 porcine circovirus type 2 (PCV2), and classical swine fever virus (CSFV).26 These studies have given a good overview of the dynamic interactions between the virus and its host, and provide important clues for a better understanding of the viral pathogenesis. For PDCoV, there has been no proteomic study on the virus so far. In the present study, we coupled iTRAQ with LC-MS/MS to quantitatively analyze the DEPs of IPEC-J2 cells in response to PDCoV infection. The identified DEPs were subsequently analyzed by comprehensive bioinformatics analyses.