Influenza A virus (IAV) infection activates the caspases that cleave host and viral proteins, which, in turn, have pro- and antiviral functions. By employing inhibitors, RNA interference, site-directed mutagenesis, and western blotting and RT-qPCR techniques, caspases in infected mammalian cells that cleave host cortactin and histone deacetylases were identified.
Caspases, a family of cysteine proteases, orchestrate programmed cell death in response to various stimuli, including microbial infections. Initially described to occur by apoptosis, programmed cell death is now known to encompass three interconnected pathways: pyroptosis, apoptosis, and necroptosis, together coined as one process, PANoptosis. Influence A virus (IAV) infection induces PANoptosis in mammalian cells by inducing the activation of different caspases, which, in turn, cleave various host as well as viral proteins, leading to processes like the activation of the host innate antiviral response or the degradation of antagonistic host proteins. In this regard, caspase 3-mediated cleavage of host cortactin, histone deacetylase 4 (HDAC4), and histone deacetylase 6 (HDAC6) has been discovered in both animal and human epithelial cells in response to the IAV infection. To demonstrate this, inhibitors, RNA interference, and site-directed mutagenesis were employed, and, subsequently, the cleavage or resistance to cleavage and the recovery of cortactin, HDAC4, and HDAC6 polypeptides were measured by western blotting. These methods, in conjunction with RT-qPCR, form a simple yet effective strategy to identify the host as well as viral proteins undergoing caspase-mediated cleavage during an infection of IAV or other human and animal viruses. The present protocol elaborates the representative results of this strategy, and the ways to make it more effective are also discussed.
Influenza A virus (IAV) is the prototypic member of the Orthomyxoviridae family and is known to cause global epidemics and unpredictable pandemics. IAV causes human respiratory disease, influenza, commonly known as "flu". The flu is an acute disease that results in the induction of host pro- and anti-inflammatory innate immune responses and the death of epithelial cells in the human respiratory tract. Both processes are governed by a phenomenon called programmed cell death1. The signaling for programmed cell death is induced as soon as various pathogen recognition receptors sense the incoming virus particles in host cells. This leads to the programming of the death of infected cells and signaling to the neighboring healthy cells by three interconnected pathways called pyroptosis, apoptosis, and necroptosis-recently coined as one process, PANoptosis1.
PANoptosis involves the proteolytic processing of many host and viral proteins from induction to execution. Such processing of proteins is primarily spearheaded by a family of cysteine proteases called caspases1,2. Up to 18 caspases (from caspase 1 to caspase 18) are known3. Most caspases are expressed as pro-caspases and activated by undergoing their own proteolytic processing either by autocatalysis or other caspases4 in response to a stimulus like a virus infection. The PANoptosis of IAV-infected cells was thought to be a host defense mechanism, but IAV has evolved ways to evade and exploit it to facilitate its replication1,2,5,6. One of them is to antagonize the host factors via caspase-mediated cleavage or degradation that are either inherently antiviral or interfere with one of the steps of the IAV life cycle. To this end, host factors, cortactin, HDAC4, and HDAC6 have been discovered to undergo caspase-mediated cleavage or degradation in IAV-infected epithelial cells7,8,9. The HDAC4 and HDAC6 are anti-IAV factors8,10, and cortactin interferes with IAV replication at a later stage of infection, potentially during viral assembly and budding11.
In addition, various caspases are also activated, which, in turn, cleave multiple proteins to activate the host inflammatory response during IAV infection1,2. Furthermore, nucleoprotein (NP), ion-channel M2 protein of IAV12,13,14, and various proteins of other viruses3,15,16 also undergo caspase-mediated cleavage during infection, which influences viral pathogenesis. Therefore, there is a continuous need to study caspase-mediated cleavage or degradation of host and viral proteins during IAV and other virus infections to understand the molecular basis of viral pathogenesis. Herein, the methods are presented to (1) assess the cleavage or degradation of such proteins by caspases, (2) identify those caspases, and (3) locate the cleavage sites.
Regulatory approvals were obtained from the University of Otago Institutional Biological Safety Committee to work with the IAV and mammalian cells. Madin-Darby Canine Kidney (MDCK) or human lung alveolar epithelial A549 cells and IAV H1N1 subtypes were used for the present study. IAV was grown in chicken eggs, as described elsewhere17. Sterile and aseptic conditions were used to work with mammalian cells, and a Biosafety Level 2 (or Physical Containment 2) facility and Class II biosafety cabinet were used to work with IAV subtypes.
1. Assessing the cleavage or degradation of proteins in IAV-infected cells by caspases
2. Confirmation of caspase-mediated cleavage or degradation of proteins in IAV-infected cells by RNA interference
3. Site-directed mutagenesis for locating the caspase cleavage site(s) in the polypeptide
Treatment with caspase 3 inhibitor
It has been discovered that host cortactin, HDAC4, and HDAC6 polypeptides undergo degradation in response to IAV infection in both canine (MDCK) and human (A549, NHBE) cells7,8,9. By using the above approaches, it was uncovered that IAV-induced host caspases, particularly caspase 3, cause their degradation7,8,9. The cortactin was degraded in an infection dose- and time-dependent manner and a host cell- and IAV strain-independent manner7. Similar results were obtained for HDAC48 and HDAC69. Interestingly, the degradation of all three host proteins coincided with the cleavage of viral NP7,8,9, which is known to undergo caspase-mediated cleavage14. Thus, it was hypothesized that cortactin, HDAC4, and HDAC6 also undergo caspase-mediated cleavage and subsequent degradation. To test this, first, the IAV-infected cells were treated with a caspase 3 inhibitor, and the rescue of cortactin, HDAC4, and HDAC6 polypeptides was analyzed by western blotting. All three polypeptides (as well as viral NP) recovered from the IAV infection-induced degradation after caspase 3 inhibitor treatment7,8,9. The representative data7 for cortactin are shown in Figure 1A. This recovery was quantified by measuring the intensity of protein bands and normalizing the value of the cortactin band by the value of the corresponding actin (loading control) band. Subsequently, the normalized value of cortactin in the corresponding uninfected samples was considered 100% to determine its value in the infected samples. This quantitation method accounted the recovery of cortactin polypeptide in caspase 3 inhibitor-treated infected cells as 78.8% from 20.7% in untreated infected cells7 (Figure 1B).
RNA interference-mediated knockdown of caspase 3 expression
Next, a genetic tool, RNA interference (RNAi), was employed, followed by western blotting to confirm the role of caspases in IAV infection-induced degradation of cortactin11 and HDAC48. In caspase 3-depleted cells (Figure 2C)11, both cortactin (Figure 2A)11 and HDAC48 polypeptides recovered from the IAV infection-induced degradation. However, in caspase 6- or caspase 7-depleted cells (Figure 2C)11, no significant recovery in cortactin polypeptide levels was observed (Figure 2A)11. Specifically, when quantified and compared to their levels in corresponding uninfected cells as mentioned above, the cortactin polypeptide level in infected cells with depleted caspase 3 expression recovered to 83% from 28.6% in infected cells with normal caspase 3 expression (Figure 2B)11.
Caspase cleavage motifs in cortactin and HDAC6 polypeptides
Finally, the amino acid sequence in cortactin and HDAC6 polypeptides were screened and, in putative caspase cleavage motifs, the aspartic acid at the P1 position was mutated to glutamic acid9,11. This approach identified the aspartic acid 116 in cortactin polypeptide11 and the aspartic acid 1088 in HDAC6 polypeptide9 as a caspase cleavage site. The mutation of both aspartic acid residues to glutamic acid rendered the cortactin (Figure 3A)11 and HDAC69 polypeptides resistant to IAV infection-induced degradation. Specifically, when quantified and compared to their levels in corresponding uninfected cells as mentioned above, the level of plasmid-expressed mutant cortactin polypeptide in infected cells was 77.9%, whereas the level of plasmid-expressed wild-type cortactin polypeptide in infected cells was 23.6% (Figure 3B)11.
Figure 1: Cortactin polypeptide undergoes caspase 3-mediated degradation in IAV-infected cells. (A) MDCK cells were infected with influenza virus A/New Caledonia/20/1999/H1N1 strain at an MOI of 0.5 and subsequently treated as mock or with caspase 3 inhibitor (Cas3-I, 40 µM). After 24 h, the cortactin, viral NP, and actin polypeptides were detected in total cell lysates by western blotting. UNI, uninfected; INF, infected. Arrows point to the full-length and cleaved NP. (B) The intensity of cortactin and actin bands was quantified. Then, the value of cortactin was normalized with the value of actin. The normalized amount of cortactin in UNI samples was considered 100% to determine its amount in the corresponding INF samples. Data presented are means ± SE of three biological replicates. ***P = 0.0006, calculated using two-way ANOVA. ns, not significant. This figure has been modified from Chen et al.7. Please click here to view a larger version of this figure.
Figure 2: Knockdown of caspase 3 expression rescued cortactin polypeptide degradation in IAV-infected cells. (A) A549 cells were transfected in duplicates with 10 nM of control (Ctrl), caspase 3 (Cas3), caspase 6 (Cas6), or caspase 7 (Cas7) siRNA. After 72 h, the cells in one replicate were harvested and processed to extract total RNA. The cells in the other replicate were infected with influenza virus A/WSN/1933/H1N1 subtype at an MOI of 3.0. After 24 h, the cortactin, viral NP, and actin polypeptides were detected by western blotting. UNI, uninfected; INF, infected. (B) The intensity of cortactin and actin bands was quantified, and the value of cortactin was normalized with the value of actin. Then, the normalized amount of cortactin in the UNI samples was considered 100% to determine its amount in the corresponding INF samples. Data presented are means ± SE of three biological replicates. ****P < 0.0001, ***P = 0.0007, ***P = 0.0002, calculated using two-way ANOVA. ns, not significant. (C) Total RNA extracted above was converted to cDNA, which was then used as a template to detect caspase 3, caspase 6, caspase 7, and actin mRNA levels by RT-qPCR. The actin mRNA level was used as a reference, and the mRNA level of each caspase in control siRNA (Ctrl) and respective caspase siRNA (Cas) transfected cells was calculated using the standard 2−ΔΔCT method. ****P < 0.0001, calculated using two-way ANOVA. This figure has been modified from Chen et al.11. Please click here to view a larger version of this figure.
Figure 3: Mutation of aspartic acid 116 to glutamic acid rendered the cortactin polypeptide resistant to IAV infection-induced degradation. (A) MDCK cells were transfected with a plasmid expressing the wild-type (WT) or mutated (D116E) GFP-cortactin fusion. After 48 h, cells were infected with influenza virus A/WSN/1933/H1N1 subtype at an MOI of 3.0. After 24 h, the GFP-cortactin, viral NP, and actin polypeptides were detected by western blotting. UNI, uninfected; INF, infected. (B) The intensity of cortactin and actin bands was quantified, and the value of cortactin was normalized with the value of actin. Then, the normalized amount of cortactin in UNI samples was considered 100% to determine its amount in the corresponding INF samples. Data presented are means ± SE of three biological replicates. **P = 0.001, calculated using two-way ANOVA. ns, not significant. This figure has been modified from Chen et al.11. Please click here to view a larger version of this figure.
It is established that viruses tailor the host factors and pathways to their benefit. In turn, the host cells resist that by employing various strategies. One of those strategies is PANoptosis, which host cells use as an antiviral strategy against virus infections. However, viruses like IAV have evolved their own strategies to counter PANoptosis and exploit it to their advantage1,3,6. This interplay involves the cleavage of various host and viral proteins by caspases. Identifying those caspases and their cleavage sites in substrate proteins are important to elucidate the mechanisms and significance of such interplay.
To this end, standard biochemical and molecular methods were used to identify the caspases and their cleavage sites in host cortactin, HDAC4, and HDAC67,8,9,11. The protocols described above can be used for such studies involving influenza viruses, other mammalian viruses, other microbes, and external stimuli like toxins and chemicals. Furthermore, these methods can be replicated in a standard molecular biology laboratory with pertinent skills and do not require specialized equipment and software training. The 12-well cell culture plate format was successfully adapted for these and similar studies to generate sufficient sample amounts for downstream analyses by western blotting and RT-qPCR. Nevertheless, as needed, this format can be downscaled or upscaled accordingly. When doing an experiment involving a caspase inhibitor for the first time, using a pan-caspase inhibitor (Z-VAD-FMK) alongside a lysosome and proteasome inhibitor is suggested to assess whether the protein of interest undergoes caspase-mediated degradation. Further, in addition to NH4Cl and MG132, other lysosome and proteasome inhibitors like Bafilomycin A and Epoxomicin, respectively, can be used. After positive results with a pan-caspase inhibitor, either specific inhibitors of individual caspases can be used, or RNA interference can be employed. For the former, it is important to optimize the effective inhibitory concentrations to avoid toxicity to the target cell type and non-specific results.
A genetic tool like RNA interference or CRISPR must be employed next to confirm the involvement of caspases because inhibitors do cross-react. Alternatively, an RNA interference or CRISPR screen individually targeting all known caspases can be carried out. The siRNA, gRNA, and RT-qPCR primer pairs to all known caspases could be procured as pre-designed or designed using online tools. In addition, two or more caspases can be depleted simultaneously to assess the sequential or cooperative cleavage of polypeptides (this strategy was recently used in a yet-to-be-published study). RNA interference is believed to be an ideal tool for virus-host cell interaction research. The latter requires a controlled manipulation of host gene expression so that the host cells remain relatively viable for virus infection and completion of the life cycle to display the phenotype of that manipulation. However, optimizing an effective siRNA concentration and siRNA-transfection reagent combination is needed for each cell type for an optimal knockdown and viability ratio for subsequent infection.
To locate the putative caspase cleavage motifs, many databases such as CASBAH18, CaspDB19, CutDB20, DegraBase21, MEROPS22, and TopFIND23,24 have been developed. A visual screening was performed to locate these motifs on HDAC6 polypetide9, but for cortactin11, the CaspDB was used (though the CaspDB website has been inaccessible lately). Those motifs were successfully confirmed as caspase cleavage sites by mutating the P1 aspartic acid to glutamic acid. However, mutating the aspartic acid to a non-polar amino acid-like alanine or valine first is suggested because some caspases can cleave after P1 glutamic acid4. This exercise may promptly result in the identification of caspase cleavage site(s) but could require generating tens of mutants if the target polypeptide is rich in aspartic acids and the putative target motifs are non-canonical. For the delivery of plasmids (and siRNA) to cells, forward, instead of reverse, transfection can be carried out. Further, the infection dose and time kinetics should be performed using a 4%-20% gradient SDS-PAGE for western blotting to assess the degradation kinetics of the polypeptides and identify any smaller-sized cleavage products. Finally, to confirm the protein of interest as a direct caspase substrate, in vitro biochemical assays containing purified caspases and target proteins (WT or mutant) and any cofactors could be developed.
The authors have nothing to disclose.
The author acknowledges Jennifer Tipper, Bilan Li, Jesse vanWestrienen, Kevin Harrod, Da-Yuan Chen, Farjana Ahmed, Sonya Mros, Kenneth Yamada, Richard Webby, the BEI Resources (NIAID), the Health Research Council of New Zealand, the Maurice and Phyllis Paykel Trust (New Zealand), the H.S. and J.C. Anderson Trust (Dunedin), and the Department of Microbiology and Immunology and School of Biomedical Sciences (University of Otago).
A549 cells | ATCC | CRM-CCL-185 | Human, epithelial, lung |
Ammonium chloride | Sigma-Aldrich | A9434 | |
Caspase 3 Inhibitor | Sigma-Aldrich | 264156-M | Also known as 'InSolution Caspase-3 Inhibitor II – Calbiochem' |
cOmplete, Mini Protease Inhibitor Cocktail | Roche | 11836153001 | |
Goat anti-NP antibody | Gift from Richard Webby (St Jude Children’s Research Hospital, Memphis, USA) to MH | ||
Lipofectamine 2000 Transfection Reagent | ThermoFisher Scientific | 31985062 | |
Lipofectamine RNAiMAX Transfection Reagent | ThermoFisher Scientific | 13778150 | |
MDCK cells | ATCC | CCL-34 | Dog, epithelial, kidney |
MG132 | Sigma-Aldrich | M7449 | |
Minimum Essential Medium (MEM) | ThermoFisher Scientific | 11095080 | Add L-glutamine, antibiotics or other supplements as required |
MISSION siRNA Universal Negative Control #1 | Sigma-Aldrich | SIC001 | |
Odyssey Fc imager with Image Studio Lite software 5.2 | LI-COR | Odyssey Fc has been replaced with Odyssey XF and Image Studio Lite software has been replaced with Empiria Studio software. | |
Pierce BCA Protein Assay Kit | ThermoFisher Scientific | 23225 | |
Plasmid expressing human cortactin-GFP fusion | Addgene | 50728 | Gift from Kenneth Yamada to Addgene |
Pre-designed small interferring RNA (siRNA) to caspase 3 | Sigma-Aldrich | NM_004346 | siRNA ID: SASI_Hs01_00139105 |
Pre-designed small interferring RNA to caspase 6 | Sigma-Aldrich | NM_001226 | siRNA ID: SASI_Hs01_00019062 |
Pre-designed small interferring RNA to caspase 7 | Sigma-Aldrich | NM_001227 | siRNA ID: SASI_Hs01_00128361 |
Pre-designed SYBR Green RT-qPCR Primer pairs | Sigma-Aldrich | KSPQ12012 | Primer Pair IDs: H_CASP3_1; H_CASP6_1; H_CASP7_1 |
Protran Premium nitrocellulose membrane | Cytiva (Fomerly GE Healthcare) | 10600003 | |
Rabbit anti-actin antibody | Abcam | ab8227 | |
Rabbit anti-cortactin antibody | Cell Signaling | 3502 | |
Rabbit anti-GFP antibody | Takara | 632592 | |
SeeBlue Pre-stained Protein Standard | ThermoFisher Scientific | LC5625 | |
Transfection medium, Opti-MEM | ThermoFisher Scientific | 11668019 | |
Tris-HCl, NaCl, SDS, Sodium Deoxycholate, Triton X-100 | Merck | ||
Trypsin, TPCK-Treated | Sigma-Aldrich | 4370285 |