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viruses Article Comparative Proteomic Profiling: Cellular Metabolisms Are Mainly Affected in Senecavirus A-Inoculated Cells at an Early Stage of Infection Fuxiao Liu 1,† , Bo Ni 2,† and Rong Wei 2,* 1 College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China; [email protected] 2 Surveillance Laboratory of Livestock Diseases, China Animal Health and Epidemiology Center, Qingdao 266032, China; [email protected] * Correspondence: [email protected] † These authors contributed equally to this work. Abstract: Senecavirus A (SVA), also known as Seneca Valley virus, belongs to the genus Senecavirus in the family Picornaviridae. SVA can cause vesicular disease and epidemic transient neonatal losses in pigs. This virus efficiently propagates in some non-pig-derived cells, like the baby hamster kidney (BHK) cell line and its derivate (BSR-T7/5). Conventionally, a few proteins or only one protein is selected for exploiting a given mechanism concerning cellular regulation after SVA infection in vitro. Proteomics plays a vital role in the analysis of protein profiling, protein-protein interactions, and protein-directed metabolisms, among others. Tandem mass tag-labeled liquid chromatography- tandem mass spectrometry combined with the parallel reaction monitoring technique is increasingly used for proteomic research. In this study, this combined method was used to uncover separately proteomic profiles of SVA- and non-infected BSR-T7/5 cells. Furthermore, both proteomic profiles were compared with each other. The proteomic profiling showed that a total of 361 differentially Citation: Liu, F.; Ni, B.; Wei, R. expressed proteins were identified, out of which, 305 and 56 were upregulated and downregulated Comparative Proteomic Profiling: in SVA-infected cells at 12 h post-inoculation, respectively. GO (Gene Ontology) and KEGG (Kyoto Cellular Metabolisms Are Mainly Encyclopedia of Genes and Genomes) enrichment analyses showed that cellular metabolisms were Affected in Senecavirus A-Inoculated Cells at an Early Stage of Infection. affected mainly in SVA-inoculated cells at an early stage of infection. Therefore, an integrated Viruses 2021, 13, 1036. https:// metabolic atlas remains to be explored via metabolomic methods. doi.org/10.3390/v13061036 Keywords: Senecavirus A; proteomics; differentially expressed protein; enrichment analysis; Academic Editor: Petri Susi metabolism; pathway Received: 13 April 2021 Accepted: 18 May 2021 Published: 31 May 2021 1. Introduction Senecavirus A (SVA), previously known as Seneca Valley virus, is an emerging pathogen Publisher’s Note: MDPI stays neutral in China [1,2]. SVA infection is characterized by porcine vesicular lesions on coronary with regard to jurisdictional claims in bands as well as snout and oral cavities, clinically indistinguishable from those caused published maps and institutional affil- by foot-and-mouth disease virus, swine vesicular disease virus and vesicular stomati- iations. tis virus [3,4]. SVA is classified into the genus Senecavirus in the family Picornaviridae. Its genome is a positive-sense, single-stranded and nonsegmented RNA, approximately 7300 nucleotides in length, with a 30 poly (A) tail but without a 50 capped structure. The genome contains 50 and 30 untranslated regions and a single long open reading frame of Copyright: © 2021 by the authors. polyprotein precursor [5]. Morphologically, mature virion is a non-enveloped icosahedral Licensee MDPI, Basel, Switzerland. particle with a diameter of approximately 27 nm. Purified virion reveals a sphere-like This article is an open access article shape as evidenced by transmission electron microscopy [6]. Some pig-derived cells, such distributed under the terms and as testis (CRL-1746) and kidney (PK-15) cell lines, are susceptible to SVA infection. SVA conditions of the Creative Commons can also propagate efficiently in some non-pig-derived cells, like the baby hamster kidney Attribution (CC BY) license (https:// (BHK) cell line and its derivate (BSR-T7/5). Additionally, SVA is an oncolytic virus, with creativecommons.org/licenses/by/ 4.0/). selective tropism for some tumors with neuroendocrine characteristics [7–9]. Viruses 2021, 13, 1036. https://doi.org/10.3390/v13061036 https://www.mdpi.com/journal/viruses Viruses 2021, 13, 1036 2 of 14 SVA infection triggers a variety of metabolic and biochemical changes in its host cells through virus-specific or -nonspecific mechanisms [10–13]. For example, SVA has been demonstrated to have the ability to induce autophagy or (and) apoptosis of host cells. The SVA-induced autophagy was evidenced by detecting autophagosome formation, GFP-LC3 puncta and accumulation of LC3-II proteins in cultured PK-15 and BHK-21 cells [10]. The SVA-induced apoptosis resulted from the SVA 3C protease, by which the NF-κB-p65 was cleaved at the late stage of infection [13]. Additionally, the innate immune system plays an important role in SVA infection. Wen et al. (2019) demonstrated that SVA replication could induce the degradation of RIG-I in HEK-293T, SW620 and SK6 cells. Overexpression of RIG-I significantly inhibited SVA propagation. The viral 2C and 3C proteins notably reduced Sev- or RIG-I-induced interferon-β production [12]. According to conventional methods, a few host and (or) virus proteins are generally selected for exploiting a given mechanism of cellular regulation against viral infection. Integrated omics can assist in deciphering complex networks in vitro or in vivo and espe- cially in unveiling the interaction among related molecules to affect disease outcome [14]. Proteomic research plays a crucial role in analyzing protein-protein interactions, profiles and kinetics of protein expression, as well as complex regulatory mechanisms. Owing to its high-efficiency, -sensitivity and -throughput characteristics, the tandem mass tag (TMT)- labeled method has been broadly used for quantitative analysis of proteomics [15–17]. Parallel reaction monitoring (PRM) is a novel technique, is better than conventional methods to verify proteins, and provides reliable results of quantitative proteomics [18–20]. Additionally, with the development of bioinformatics, the efficiency of large-scale data processing has been greatly improved in the field of proteomic studies. The strategy, TMT-based quantitative analysis with PRM verification, has been gradually adopted for proteomic profiling [21–23]. We recently rescued a wild-type SVA (CH-LX-01-2016) from its cDNA clone using reverse genetics. The rescued virus could rapidly replicate in BSR-T7/5 cells and induced typical cytopathic effect (CPE) as early as 24 hpi, or even earlier [24]. In the present study, in order to uncover a proteomic profile of SVA-infected cells for further comparison to that of non-infected cells, the rescued SVA at passage 5 (P5) was used to inoculate BSR-T7/5 cells, subsequently subjected to a series of treatments for the proteomic analysis using TMT- labeled nano-liquid chromatography-tandem mass spectrometry (LC-MS/MS) followed by PRM verification. Comparative proteomic analysis showed that cellular metabolisms were affected mainly at the early stage of SVA infection. 2. Materials and Methods 2.1. Cell Line and Virus The BSR-T7/5 cells [25], derived from the BHK cell line, were cultured at 37 ◦C with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with 4% fetal bovine serum and containing penicillin (100 U/mL), streptomycin (100 µg/mL), amphotericin B (0.25 µg/mL) and G418 (500 µg/mL). The wild-type SVA was rescued previously from a cDNA clone [24], genetically derived from an isolate, CH-LX-01-2016 (Genbank access No.: KX751945) [26]. 2.2. Sample Preparation BSR-T7/5 cells were seeded into several T175 flasks for culture at 37 ◦C. Cell monolayers at 90% confluency were separately inoculated with the P5 SVA (MOI = 2.5), and the others served as non-infected controls. There were three SVA-infected samples (S1, S2 and S3) and three non-infected controls (C1, C2 and C3). At 12 h post-inoculation (hpi), SVA- and non-infected supernatants were removed from flasks. Cell monolayers were gently washed with D-PBS three times and then independently harvested into sterile 50 mL cen- trifuge tubes using cell scrapers. After centrifugation, cell pellets were suspended in 300 µL of SDT-lysis buffer (4% SDS, 100 mM DTT, 150 mM Tris-HCl pH 8.0), followed by boiling for 5 min, ultrasonic treatment for 2 min, and boiling for another 5 min. Undissolved Viruses 2021, 13, 1036 3 of 14 cellular debris was removed by centrifugation at 15,000× g for 20 min. The supernatants were collected and quantified with the BCA Protein Assay Kit (Bio-Rad, Richmond, VA, USA), followed by SDS-PAGE analysis. 2.3. Protein Digestion Digestion of protein (300 µg for each sample) was performed according to the pro- cedure of filter-aided sample preparation (FASP), as described previously [27]. Briefly, 300 µg of protein was added to DTT at a final concentration of 100 mM, boiled for 5 min, and then cooled to room temperature. The DTT and other low-molecular-weight compo- nents were removed using 200 µL of UA buffer (8 M urea, 150 mM Tris-HCl pH 8.0) by repeated ultrafiltration (Microcon units, 10 kD), facilitated by centrifugation at 12,000× g for 15 min. A total of 100 µL of IAA (50 mM iodoacetamide in UA buffer) was added to the concentrate, shaken at 600 rpm for 1 min, and incubated for 30 min in darkness, followed by centrifugation at 12,000× g for 10 min. A total of 100 µL of UA buffer was added to the concentrate, followed by centrifugation three times at 12,000× g for 10 min; then, 100 µL of TEAB buffer was added to the concentrate, followed by centrifugation three times at 14,000× g for 10 min. Forty µL of trypsin buffer (6 µg trypsin in 40 µL TEAB buffer) was added to the concentrate, subsequently shaken at 600 rpm for 1 min, and incubated at 37 ◦C for 16 h.

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