CORD-19-Sentences  

CORD-19:ff6bd29c8ecd325c4edddb2b050d5f4919db6112 JSONTXT 8 Projects

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Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-133 Sentence denotes Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals 1 a proviral role for CEACAM1 2 3
TextSentencer_T1 0-133 Sentence denotes Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals 1 a proviral role for CEACAM1 2 3
TextSentencer_T2 135-143 Sentence denotes Abstract
TextSentencer_T2 135-143 Sentence denotes Abstract
TextSentencer_T3 144-264 Sentence denotes 15 Current prophylactic and therapeutic strategies targeting human influenza viruses include 16 vaccines and antivirals.
TextSentencer_T3 144-264 Sentence denotes 15 Current prophylactic and therapeutic strategies targeting human influenza viruses include 16 vaccines and antivirals.
TextSentencer_T4 265-408 Sentence denotes Given variable rates of vaccine efficacy and antiviral resistance, 17 alternative strategies are urgently required to improve disease outcomes.
TextSentencer_T4 265-408 Sentence denotes Given variable rates of vaccine efficacy and antiviral resistance, 17 alternative strategies are urgently required to improve disease outcomes.
TextSentencer_T5 409-607 Sentence denotes Here we describe the 18 use of HiSeq deep sequencing to analyze host gene expression in primary human alveolar 19 epithelial type II cells infected with highly pathogenic avian influenza H5N1 virus.
TextSentencer_T5 409-607 Sentence denotes Here we describe the 18 use of HiSeq deep sequencing to analyze host gene expression in primary human alveolar 19 epithelial type II cells infected with highly pathogenic avian influenza H5N1 virus.
TextSentencer_T6 608-735 Sentence denotes At 24 hours 20 post-infection, 623 host genes were significantly up-regulated, including the cell adhesion 21 molecule CEACAM1.
TextSentencer_T6 608-735 Sentence denotes At 24 hours 20 post-infection, 623 host genes were significantly up-regulated, including the cell adhesion 21 molecule CEACAM1.
TextSentencer_T7 736-847 Sentence denotes The up-regulation of CEACAM1 was blocked in the presence of the 22 reactive oxygen species inhibitor, apocynin.
TextSentencer_T7 736-847 Sentence denotes The up-regulation of CEACAM1 was blocked in the presence of the 22 reactive oxygen species inhibitor, apocynin.
TextSentencer_T8 848-1049 Sentence denotes H5N1 virus infection stimulated significantly higher 23 CEACAM1 protein expression when compared to low pathogenic PR8 H1N1 virus, suggesting a 24 key role for CEACAM1 in influenza virus pathogenicity.
TextSentencer_T8 848-1049 Sentence denotes H5N1 virus infection stimulated significantly higher 23 CEACAM1 protein expression when compared to low pathogenic PR8 H1N1 virus, suggesting a 24 key role for CEACAM1 in influenza virus pathogenicity.
TextSentencer_T9 1050-1250 Sentence denotes Furthermore, silencing of endogenous 25 CEACAM1 resulted in reduced levels of proinflammatory cytokine/chemokine production, as 26 well as reduced levels of virus replication following H5N1 infection.
TextSentencer_T9 1050-1250 Sentence denotes Furthermore, silencing of endogenous 25 CEACAM1 resulted in reduced levels of proinflammatory cytokine/chemokine production, as 26 well as reduced levels of virus replication following H5N1 infection.
TextSentencer_T10 1251-1437 Sentence denotes Our study provides 27 evidence for the involvement of CEACAM1 in a clinically relevant model of H5N1 infection and 28 may assist in the development of host-oriented antiviral strategies.
TextSentencer_T10 1251-1437 Sentence denotes Our study provides 27 evidence for the involvement of CEACAM1 in a clinically relevant model of H5N1 infection and 28 may assist in the development of host-oriented antiviral strategies.
TextSentencer_T11 1438-1457 Sentence denotes 29 30 IMPORTANCE 31
TextSentencer_T11 1438-1457 Sentence denotes 29 30 IMPORTANCE 31
TextSentencer_T12 1458-1552 Sentence denotes Highly pathogenic avian H5N1 influenza virus continues to pose a potential pandemic 32 threat.
TextSentencer_T12 1458-1552 Sentence denotes Highly pathogenic avian H5N1 influenza virus continues to pose a potential pandemic 32 threat.
TextSentencer_T13 1553-1684 Sentence denotes Therapeutic strategies that enhance host immune responses to promote clearance of 33 influenza virus infection are urgently needed.
TextSentencer_T13 1553-1684 Sentence denotes Therapeutic strategies that enhance host immune responses to promote clearance of 33 influenza virus infection are urgently needed.
TextSentencer_T14 1685-1797 Sentence denotes CEACAM1 was significantly up-regulated in 34 primary alveolar epithelial type II cells infected with H5N1 virus.
TextSentencer_T14 1685-1797 Sentence denotes CEACAM1 was significantly up-regulated in 34 primary alveolar epithelial type II cells infected with H5N1 virus.
TextSentencer_T15 1798-1930 Sentence denotes It was one of 623 human genes 35 identified using HiSeq deep sequencing analysis that were up-regulated following H5N1 36 infection.
TextSentencer_T15 1798-1930 Sentence denotes It was one of 623 human genes 35 identified using HiSeq deep sequencing analysis that were up-regulated following H5N1 36 infection.
TextSentencer_T16 1931-2061 Sentence denotes Although CEACAM1 is known for its multifaceted immune regulatory role, little is 37 known about its contribution to host immunity.
TextSentencer_T16 1931-2061 Sentence denotes Although CEACAM1 is known for its multifaceted immune regulatory role, little is 37 known about its contribution to host immunity.
TextSentencer_T17 2062-2130 Sentence denotes The results presented here show that CEACAM1 38 All rights reserved.
TextSentencer_T17 2062-2130 Sentence denotes The results presented here show that CEACAM1 38 All rights reserved.
TextSentencer_T18 2131-2167 Sentence denotes No reuse allowed without permission.
TextSentencer_T18 2131-2167 Sentence denotes No reuse allowed without permission.
TextSentencer_T19 2169-2273 Sentence denotes regulates the innate immune response in a clinically relevant in vitro human model of H5N1 39 infection.
TextSentencer_T19 2169-2273 Sentence denotes regulates the innate immune response in a clinically relevant in vitro human model of H5N1 39 infection.
TextSentencer_T20 2274-2276 Sentence denotes 40
TextSentencer_T20 2274-2276 Sentence denotes 40
TextSentencer_T21 2277-2379 Sentence denotes Influenza viruses cause acute and highly contagious seasonal respiratory disease in all age 43 groups.
TextSentencer_T21 2277-2379 Sentence denotes Influenza viruses cause acute and highly contagious seasonal respiratory disease in all age 43 groups.
TextSentencer_T22 2380-2472 Sentence denotes Between 3-5 million cases of severe influenza-related illness and over 250 000 deaths are 44
TextSentencer_T22 2380-2472 Sentence denotes Between 3-5 million cases of severe influenza-related illness and over 250 000 deaths are 44
TextSentencer_T23 2473-2493 Sentence denotes reported every year.
TextSentencer_T23 2473-2493 Sentence denotes reported every year.
TextSentencer_T24 2494-2738 Sentence denotes In addition to constant seasonal outbreaks, highly pathogenic avian influenza 45 (HPAI) strains, such as H5N1, remain an ongoing pandemic threat with recent WHO figures showing 46 454 confirmed laboratory infections and a mortality rate of 53%.
TextSentencer_T24 2494-2738 Sentence denotes In addition to constant seasonal outbreaks, highly pathogenic avian influenza 45 (HPAI) strains, such as H5N1, remain an ongoing pandemic threat with recent WHO figures showing 46 454 confirmed laboratory infections and a mortality rate of 53%.
TextSentencer_T25 2739-2855 Sentence denotes It is important to note that humans 47 have very little pre-existing immunity towards avian influenza virus strains.
TextSentencer_T25 2739-2855 Sentence denotes It is important to note that humans 47 have very little pre-existing immunity towards avian influenza virus strains.
TextSentencer_T26 2856-2923 Sentence denotes Moreover, there is no 48 commercially available human H5N1 vaccine.
TextSentencer_T26 2856-2923 Sentence denotes Moreover, there is no 48 commercially available human H5N1 vaccine.
TextSentencer_T27 2924-3129 Sentence denotes Given the potential for H5N1 viruses to trigger a 49 pandemic (1, 2), there is an urgent need to develop novel therapeutic interventions to combat known 50 deficiencies in our ability to control outbreaks.
TextSentencer_T27 2924-3129 Sentence denotes Given the potential for H5N1 viruses to trigger a 49 pandemic (1, 2), there is an urgent need to develop novel therapeutic interventions to combat known 50 deficiencies in our ability to control outbreaks.
TextSentencer_T28 3130-3252 Sentence denotes Current seasonal influenza virus prophylactic and 51 therapeutic strategies involve the use of vaccination and antivirals.
TextSentencer_T28 3130-3252 Sentence denotes Current seasonal influenza virus prophylactic and 51 therapeutic strategies involve the use of vaccination and antivirals.
TextSentencer_T29 3253-3463 Sentence denotes Vaccine efficacy is highly variable 52 as evidenced by a particularly severe 2017/18 epidemic and frequent re-formulation of the vaccine is 53 required to combat ongoing mutations in the influenza virus genome.
TextSentencer_T29 3253-3463 Sentence denotes Vaccine efficacy is highly variable 52 as evidenced by a particularly severe 2017/18 epidemic and frequent re-formulation of the vaccine is 53 required to combat ongoing mutations in the influenza virus genome.
TextSentencer_T30 3464-3622 Sentence denotes In addition, antiviral resistance 54 has been reported for many circulating strains, including the avian influenza H7N9 virus that emerged 55 in 2013 (3, 4) .
TextSentencer_T30 3464-3622 Sentence denotes In addition, antiviral resistance 54 has been reported for many circulating strains, including the avian influenza H7N9 virus that emerged 55 in 2013 (3, 4) .
TextSentencer_T31 3623-3763 Sentence denotes Influenza A viruses have also been shown to target and hijack multiple host cellular 56 pathways to promote survival and replication (5, 6).
TextSentencer_T31 3623-3763 Sentence denotes Influenza A viruses have also been shown to target and hijack multiple host cellular 56 pathways to promote survival and replication (5, 6).
TextSentencer_T32 3764-3926 Sentence denotes As such, there is increasing evidence to suggest 57 that targeting host pathways will influence virus replication, inflammation, immunity and pathology (6, 58 7).
TextSentencer_T32 3764-3926 Sentence denotes As such, there is increasing evidence to suggest 57 that targeting host pathways will influence virus replication, inflammation, immunity and pathology (6, 58 7).
TextSentencer_T33 3927-4086 Sentence denotes Alternative intervention strategies based on modulation of the host response could be used to 59 supplement the current prophylactic and therapeutic protocols.
TextSentencer_T33 3927-4086 Sentence denotes Alternative intervention strategies based on modulation of the host response could be used to 59 supplement the current prophylactic and therapeutic protocols.
TextSentencer_T34 4087-4089 Sentence denotes 60
TextSentencer_T34 4087-4089 Sentence denotes 60
TextSentencer_T35 4090-4347 Sentence denotes While the impact of influenza virus infection has been relatively well studied in animal models 61 (8, 9) , the human cellular responses are poorly defined due to the lack of available human autopsy 62 material, especially from HPAI virus-infected patients.
TextSentencer_T35 4090-4347 Sentence denotes While the impact of influenza virus infection has been relatively well studied in animal models 61 (8, 9) , the human cellular responses are poorly defined due to the lack of available human autopsy 62 material, especially from HPAI virus-infected patients.
TextSentencer_T36 4348-4562 Sentence denotes In the present study, we characterized influenza 63 virus infection of primary human alveolar epithelial type II (ATII) cells isolated from normal human 64 lung tissue donated by patients undergoing lung resection.
TextSentencer_T36 4348-4562 Sentence denotes In the present study, we characterized influenza 63 virus infection of primary human alveolar epithelial type II (ATII) cells isolated from normal human 64 lung tissue donated by patients undergoing lung resection.
TextSentencer_T37 4563-4719 Sentence denotes ATII cells are a physiologically relevant 65 infection model as they are a major target for influenza A viruses when entering the respiratory tract 66 (10).
TextSentencer_T37 4563-4719 Sentence denotes ATII cells are a physiologically relevant 65 infection model as they are a major target for influenza A viruses when entering the respiratory tract 66 (10).
TextSentencer_T38 4720-4886 Sentence denotes Human host gene expression following HPAI H5N1 virus (A/Chicken/Vietnam/0008/04) 67 infection of primary ATII cells was analyzed using Illumina HiSeq deep sequencing.
TextSentencer_T38 4720-4886 Sentence denotes Human host gene expression following HPAI H5N1 virus (A/Chicken/Vietnam/0008/04) 67 infection of primary ATII cells was analyzed using Illumina HiSeq deep sequencing.
TextSentencer_T39 4887-5254 Sentence denotes In order to gain a 68 better understanding of the mechanisms underlying modulation of host immunity in an anti-69 inflammatory environment, we also analyzed changes in gene expression following HPAI H5N1 70 infection in the presence of the reactive oxygen species inhibitor (ROS), apocynin, a compound known 71 to interfere with NADPH oxidase subunit assembly (5, 6).
TextSentencer_T39 4887-5254 Sentence denotes In order to gain a 68 better understanding of the mechanisms underlying modulation of host immunity in an anti-69 inflammatory environment, we also analyzed changes in gene expression following HPAI H5N1 70 infection in the presence of the reactive oxygen species inhibitor (ROS), apocynin, a compound known 71 to interfere with NADPH oxidase subunit assembly (5, 6).
TextSentencer_T40 5255-5257 Sentence denotes 72
TextSentencer_T40 5255-5257 Sentence denotes 72
TextSentencer_T41 5258-5482 Sentence denotes Our HiSeq analysis described herein focused on differentially regulated genes following H5N1 73 infection and identified carcinoembryonic-antigen (CEA)-related cell adhesion molecule 1 74 (CEACAM1) as a key gene of interest.
TextSentencer_T41 5258-5482 Sentence denotes Our HiSeq analysis described herein focused on differentially regulated genes following H5N1 73 infection and identified carcinoembryonic-antigen (CEA)-related cell adhesion molecule 1 74 (CEACAM1) as a key gene of interest.
TextSentencer_T42 5483-5686 Sentence denotes CEACAM1 (also known as BGP or CD66) is expressed on 75 epithelial and endothelial cells (11), as well as B cells, T cells, neutrophils, NK cells, macrophages and 76 dendritic cells (DCs) (12) (13) (14) .
TextSentencer_T42 5483-5686 Sentence denotes CEACAM1 (also known as BGP or CD66) is expressed on 75 epithelial and endothelial cells (11), as well as B cells, T cells, neutrophils, NK cells, macrophages and 76 dendritic cells (DCs) (12) (13) (14) .
TextSentencer_T43 5687-5949 Sentence denotes Human CEACAM1 has been shown to act as a receptor for several 77 human bacterial and fungal pathogens, including Haemophilus influenza, Escherichia coli, Salmonella 78 typhi and Candida albicans, but has not as yet been implicated in virus entry (15) (16) (17) .
TextSentencer_T43 5687-5949 Sentence denotes Human CEACAM1 has been shown to act as a receptor for several 77 human bacterial and fungal pathogens, including Haemophilus influenza, Escherichia coli, Salmonella 78 typhi and Candida albicans, but has not as yet been implicated in virus entry (15) (16) (17) .
TextSentencer_T44 5950-6229 Sentence denotes There is however 79 emerging evidence to suggest that CEACAM1 is involved in host immunity as enhanced lymphocyte 80 expression was detected in pregnant women infected with cytomegalovirus (18) and in cervical tissue 81 isolated from patients with papillomavirus infection (19) .
TextSentencer_T44 5950-6229 Sentence denotes There is however 79 emerging evidence to suggest that CEACAM1 is involved in host immunity as enhanced lymphocyte 80 expression was detected in pregnant women infected with cytomegalovirus (18) and in cervical tissue 81 isolated from patients with papillomavirus infection (19) .
TextSentencer_T45 6230-6232 Sentence denotes 82
TextSentencer_T45 6230-6232 Sentence denotes 82
TextSentencer_T46 6233-6298 Sentence denotes Eleven CEACAM1 splice variants have been reported in humans (20).
TextSentencer_T46 6233-6298 Sentence denotes Eleven CEACAM1 splice variants have been reported in humans (20).
TextSentencer_T47 6299-6540 Sentence denotes CEACAM1 isoforms 83 (Uniprot P13688-1 to -11) can differ in the number of immunoglobulin-like domains present, in the 84 presence or absence of a transmembrane domain and/or the length of their cytoplasmic tail (i.e. L, long 85 or S, short).
TextSentencer_T47 6299-6540 Sentence denotes CEACAM1 isoforms 83 (Uniprot P13688-1 to -11) can differ in the number of immunoglobulin-like domains present, in the 84 presence or absence of a transmembrane domain and/or the length of their cytoplasmic tail (i.e. L, long 85 or S, short).
TextSentencer_T48 6541-6839 Sentence denotes The full-length human CEACAM1 protein (CEACAM1-4L) consists of four extracellular 86 domains (one extracellular immunoglobulin variable-region-like (IgV-like) domain and three 87 immunoglobulin constant region 2-like (IgC2-like) domains), a transmembrane domain, and a long (L) 88 cytoplasmic tail.
TextSentencer_T48 6541-6839 Sentence denotes The full-length human CEACAM1 protein (CEACAM1-4L) consists of four extracellular 86 domains (one extracellular immunoglobulin variable-region-like (IgV-like) domain and three 87 immunoglobulin constant region 2-like (IgC2-like) domains), a transmembrane domain, and a long (L) 88 cytoplasmic tail.
TextSentencer_T49 6840-6988 Sentence denotes The long cytoplasmic tail contains two immunoreceptor tyrosine-based inhibitory 89 motifs (ITIMs) that are absent in the short form (20) Table S1 ).
TextSentencer_T49 6840-6988 Sentence denotes The long cytoplasmic tail contains two immunoreceptor tyrosine-based inhibitory 89 motifs (ITIMs) that are absent in the short form (20) Table S1 ).
TextSentencer_T50 6989-7243 Sentence denotes HPAI H5N1 infection of ATII cells 124 activated an antiviral state as evidenced by the up-regulation of numerous interferon-induced genes, 125 genes associated with pathogen defense, cell proliferation, apoptosis, and metabolism (Table 1; Table 126 S2).
TextSentencer_T50 6989-7243 Sentence denotes HPAI H5N1 infection of ATII cells 124 activated an antiviral state as evidenced by the up-regulation of numerous interferon-induced genes, 125 genes associated with pathogen defense, cell proliferation, apoptosis, and metabolism (Table 1; Table 126 S2).
TextSentencer_T51 7244-7446 Sentence denotes In the apocynin alone-treated (HA) group, a large number of genes were also significantly up-127 regulated (509 genes) or down-regulated (782 genes) ( Fig. 1A ; Table S1 ) relative to the control group.
TextSentencer_T51 7244-7446 Sentence denotes In the apocynin alone-treated (HA) group, a large number of genes were also significantly up-127 regulated (509 genes) or down-regulated (782 genes) ( Fig. 1A ; Table S1 ) relative to the control group.
TextSentencer_T52 7447-7450 Sentence denotes 128
TextSentencer_T52 7447-7450 Sentence denotes 128
TextSentencer_T53 7451-7686 Sentence denotes Whilst a subset of genes was differentially expressed in both the HD and HA groups, a majority of 129 Genes down-regulated by apocynin include those that are involved in cell adhesion (GO:0007155), 135 regulation of cell migration (GO:
TextSentencer_T53 7451-7686 Sentence denotes Whilst a subset of genes was differentially expressed in both the HD and HA groups, a majority of 129 Genes down-regulated by apocynin include those that are involved in cell adhesion (GO:0007155), 135 regulation of cell migration (GO:
TextSentencer_T54 7687-7772 Sentence denotes 0030334), regulation of cell proliferation (GO:0042127), signal 136 transduction (GO:
TextSentencer_T54 7687-7772 Sentence denotes 0030334), regulation of cell proliferation (GO:0042127), signal 136 transduction (GO:
TextSentencer_T55 7773-7885 Sentence denotes 0007165) and oxidation-reduction processes (GO:0055114) (Table S2 , "ND vs HA 137 Down"; Down, down-regulation).
TextSentencer_T55 7773-7885 Sentence denotes 0007165) and oxidation-reduction processes (GO:0055114) (Table S2 , "ND vs HA 137 Down"; Down, down-regulation).
TextSentencer_T56 7886-7980 Sentence denotes 138 A total of 623 genes were up-regulated following H5N1 infection ("ND vs HD Up", Fig. 1D ).
TextSentencer_T56 7886-7980 Sentence denotes 138 A total of 623 genes were up-regulated following H5N1 infection ("ND vs HD Up", Fig. 1D ).
TextSentencer_T57 7981-7984 Sentence denotes 139
TextSentencer_T57 7981-7984 Sentence denotes 139
TextSentencer_T58 7985-8148 Sentence denotes By overlapping the two lists of genes from "ND vs HD Up" and "HD vs HA Down", 245 genes were 140 shown to be down-regulated in the presence of apocynin (Fig. 1D ).
TextSentencer_T58 7985-8148 Sentence denotes By overlapping the two lists of genes from "ND vs HD Up" and "HD vs HA Down", 245 genes were 140 shown to be down-regulated in the presence of apocynin (Fig. 1D ).
TextSentencer_T59 8149-8479 Sentence denotes By overlapping three lists of genes 141 from "ND vs HD Up", "HD vs HA Down" and "ND vs HA Up", 55 genes out of the 245 genes were 142 present in all three lists (Fig. 1E ), indicating that these 55 genes were significantly inhibited by 143 apocynin but to a level that was still significantly higher than that in uninfected cells.
TextSentencer_T59 8149-8479 Sentence denotes By overlapping three lists of genes 141 from "ND vs HD Up", "HD vs HA Down" and "ND vs HA Up", 55 genes out of the 245 genes were 142 present in all three lists (Fig. 1E ), indicating that these 55 genes were significantly inhibited by 143 apocynin but to a level that was still significantly higher than that in uninfected cells.
TextSentencer_T60 8480-8837 Sentence denotes The 55 genes 144 include those involved in influenza A immunity (hsa05164; DDX58, IFIH1, IFNB1, MYD88, PML, 145 STAT2), Jak-STAT signaling (hsa04630; IFNB1, IL15RA, IL22RA1, STAT2), cytokine-cytokine 146 receptor interaction (hsa04060; CX3CL1, IFNB1, IL15RA, IL22RA1) and RIG-I-like receptor 147 signaling (hsa04622; DDX58, IFIH1, IFNB1) (Table S3 and S4) .
TextSentencer_T60 8480-8837 Sentence denotes The 55 genes 144 include those involved in influenza A immunity (hsa05164; DDX58, IFIH1, IFNB1, MYD88, PML, 145 STAT2), Jak-STAT signaling (hsa04630; IFNB1, IL15RA, IL22RA1, STAT2), cytokine-cytokine 146 receptor interaction (hsa04060; CX3CL1, IFNB1, IL15RA, IL22RA1) and RIG-I-like receptor 147 signaling (hsa04622; DDX58, IFIH1, IFNB1) (Table S3 and S4) .
TextSentencer_T61 8838-8959 Sentence denotes Therefore, critical immune responses 148 induced following H5N1 infection were not dampened following apocynin treatment.
TextSentencer_T61 8838-8959 Sentence denotes Therefore, critical immune responses 148 induced following H5N1 infection were not dampened following apocynin treatment.
TextSentencer_T62 8960-9150 Sentence denotes The remaining 149 190 of 245 genes excluded from the "ND vs HA Up" list were those significantly inhibited by apocynin 150 to a level that was similar to uninfected control cells (Fig. 1E ).
TextSentencer_T62 8960-9150 Sentence denotes The remaining 149 190 of 245 genes excluded from the "ND vs HA Up" list were those significantly inhibited by apocynin 150 to a level that was similar to uninfected control cells (Fig. 1E ).
TextSentencer_T63 9151-9651 Sentence denotes The 190 genes that were reduced by 151 apocynin to basal levels were those involved in PI3K-Akt signaling (hsa04151; CCND1, GNB4, 152 IL2RG, IL6, ITGA2, JAK2, LAMA1, MYC, IPK3AP1, TLR2, VEGFC), cytokine-cytokine receptor 153 interaction (hsa04060; VEGFC, IL6, CCL2, CXCL5, CXCL16, IL2RG, CD40, CCL5, CCL7, IL1A), 154 TNF signaling (hsa04668; CASP10, CCL2, CCL5, CFLAR, CXCL5, END1, IL6, TRAF1, VEGFC) 155 and apoptosis (hsa04210; BAK1, CASP10, CFLAR, CTSO, CTSS, PARP3, TRAF1) (Table S3 and 156 S4) .
TextSentencer_T63 9151-9651 Sentence denotes The 190 genes that were reduced by 151 apocynin to basal levels were those involved in PI3K-Akt signaling (hsa04151; CCND1, GNB4, 152 IL2RG, IL6, ITGA2, JAK2, LAMA1, MYC, IPK3AP1, TLR2, VEGFC), cytokine-cytokine receptor 153 interaction (hsa04060; VEGFC, IL6, CCL2, CXCL5, CXCL16, IL2RG, CD40, CCL5, CCL7, IL1A), 154 TNF signaling (hsa04668; CASP10, CCL2, CCL5, CFLAR, CXCL5, END1, IL6, TRAF1, VEGFC) 155 and apoptosis (hsa04210; BAK1, CASP10, CFLAR, CTSO, CTSS, PARP3, TRAF1) (Table S3 and 156 S4) .
TextSentencer_T64 9652-9741 Sentence denotes This is consistent with the role of apocynin in reducing inflammation and apoptosis (29).
TextSentencer_T64 9652-9741 Sentence denotes This is consistent with the role of apocynin in reducing inflammation and apoptosis (29).
TextSentencer_T65 9742-9892 Sentence denotes By overlapping the three lists of genes from "ND vs HD Up", "HD vs HA Down" and "ND vs 158 HA Down", eleven genes were found in all three comparisons.
TextSentencer_T65 9742-9892 Sentence denotes By overlapping the three lists of genes from "ND vs HD Up", "HD vs HA Down" and "ND vs 158 HA Down", eleven genes were found in all three comparisons.
TextSentencer_T66 9893-10103 Sentence denotes This suggests that these 11 genes are 159 upregulated following H5N1 infection and are significantly reduced by apocynin treatment to a level 160 lower than that observed in uninfected control cells (Fig. 1F ).
TextSentencer_T66 9893-10103 Sentence denotes This suggests that these 11 genes are 159 upregulated following H5N1 infection and are significantly reduced by apocynin treatment to a level 160 lower than that observed in uninfected control cells (Fig. 1F ).
TextSentencer_T67 10104-10354 Sentence denotes Among these were inflammatory 161 cytokines/chemokines genes, including CXCL5, IL1A, AXL (a member of the TAM receptor family of 162 receptor tyrosine kinases) and TMEM173/STING (Stimulator of IFN Genes) ( Table S4) . and qRT-PCR analysis (Fig. 2E ).
TextSentencer_T67 10104-10354 Sentence denotes Among these were inflammatory 161 cytokines/chemokines genes, including CXCL5, IL1A, AXL (a member of the TAM receptor family of 162 receptor tyrosine kinases) and TMEM173/STING (Stimulator of IFN Genes) ( Table S4) . and qRT-PCR analysis (Fig. 2E ).
TextSentencer_T68 10355-10429 Sentence denotes Apocynin treatment further increased SOCS1 mRNA expression (Fig. 172 2E) .
TextSentencer_T68 10355-10429 Sentence denotes Apocynin treatment further increased SOCS1 mRNA expression (Fig. 172 2E) .
TextSentencer_T69 10430-10676 Sentence denotes Although HiSeq analysis did not detect a statistically significant increase of SOCS1 following 173 apocynin treatment, the Log2 fold-changes in SOCS1 gene expression were similar between the HD 174 and HA groups (4.8-fold vs 4.0-fold) (Fig. 2E) .
TextSentencer_T69 10430-10676 Sentence denotes Although HiSeq analysis did not detect a statistically significant increase of SOCS1 following 173 apocynin treatment, the Log2 fold-changes in SOCS1 gene expression were similar between the HD 174 and HA groups (4.8-fold vs 4.0-fold) (Fig. 2E) .
TextSentencer_T70 10677-10868 Sentence denotes SOCS3 transcription was also found to be significantly 175 increased following H5N1 infection alone following HiSeq analysis and was further increased after 176 apocynin treatment (Fig. 2F ).
TextSentencer_T70 10677-10868 Sentence denotes SOCS3 transcription was also found to be significantly 175 increased following H5N1 infection alone following HiSeq analysis and was further increased after 176 apocynin treatment (Fig. 2F ).
TextSentencer_T71 10869-10974 Sentence denotes In contrast, SOCS3 mRNA was only slightly increased when samples 177 were analyzed by qRT-PCR (Fig. 2F) .
TextSentencer_T71 10869-10974 Sentence denotes In contrast, SOCS3 mRNA was only slightly increased when samples 177 were analyzed by qRT-PCR (Fig. 2F) .
TextSentencer_T72 10975-10978 Sentence denotes 178
TextSentencer_T72 10975-10978 Sentence denotes 178
TextSentencer_T73 10979-11123 Sentence denotes Apocynin, a compound that inhibits expression of ROS, has been shown to influence influenza-179 specific responses in vitro (5) and in vivo (6).
TextSentencer_T73 10979-11123 Sentence denotes Apocynin, a compound that inhibits expression of ROS, has been shown to influence influenza-179 specific responses in vitro (5) and in vivo (6).
TextSentencer_T74 11124-11308 Sentence denotes Although virus titers are not affected by apocynin 180 treatment in vitro (5), some anti-viral activity is observed in vivo when mice have been infected with a 181 All rights reserved.
TextSentencer_T74 11124-11308 Sentence denotes Although virus titers are not affected by apocynin 180 treatment in vitro (5), some anti-viral activity is observed in vivo when mice have been infected with a 181 All rights reserved.
TextSentencer_T75 11309-11345 Sentence denotes No reuse allowed without permission.
TextSentencer_T75 11309-11345 Sentence denotes No reuse allowed without permission.
TextSentencer_T76 11346-11537 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint low pathogenic A/HongKong/X31 H3N2 virus (6).
TextSentencer_T76 11346-11537 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint low pathogenic A/HongKong/X31 H3N2 virus (6).
TextSentencer_T77 11538-11816 Sentence denotes Our HiSeq analysis of HPAI H5N1 virus gene 182 transcription ( Fig. 2G ) showed that although there was a trend for increased influenza virus gene 183 expression following apocynin treatment, with only influenza non-structural (NS) gene expression 184 statistically significant.
TextSentencer_T77 11538-11816 Sentence denotes Our HiSeq analysis of HPAI H5N1 virus gene 182 transcription ( Fig. 2G ) showed that although there was a trend for increased influenza virus gene 183 expression following apocynin treatment, with only influenza non-structural (NS) gene expression 184 statistically significant.
TextSentencer_T78 11817-11908 Sentence denotes 185 186 Enrichment of antiviral and immune response genes in HPAI H5N1-infected ATII cells.
TextSentencer_T78 11817-11908 Sentence denotes 185 186 Enrichment of antiviral and immune response genes in HPAI H5N1-infected ATII cells.
TextSentencer_T79 11909-12122 Sentence denotes 187 GO enrichment analysis was performed on genes that were significantly upregulated following HPAI 188 H5N1 infection in ATII cells in the presence or absence of apocynin to identify over-presented GO 189 terms.
TextSentencer_T79 11909-12122 Sentence denotes 187 GO enrichment analysis was performed on genes that were significantly upregulated following HPAI 188 H5N1 infection in ATII cells in the presence or absence of apocynin to identify over-presented GO 189 terms.
TextSentencer_T80 12123-12439 Sentence denotes Many of the H5N1-upregulated genes were broadly involved in defense response 190 (GO:0006952), response to external biotic stimulus (GO:0043207), immune system processes 191 (GO:0002376), cytokine-mediated signaling pathway (GO:0019221) and type I interferon signaling 192 pathway (GO:0060337) ( Table 1; Table S2 ).
TextSentencer_T80 12123-12439 Sentence denotes Many of the H5N1-upregulated genes were broadly involved in defense response 190 (GO:0006952), response to external biotic stimulus (GO:0043207), immune system processes 191 (GO:0002376), cytokine-mediated signaling pathway (GO:0019221) and type I interferon signaling 192 pathway (GO:0060337) ( Table 1; Table S2 ).
TextSentencer_T81 12440-12685 Sentence denotes In addition, many of the H5N1-upregulated genes mapped 193 to metabolic pathways (hsa01100), cytokine-cytokine receptor interaction (hsa04060), Influenza A 194 (hsa05164), TNF signaling (hsa04668) or to Jak-STAT signaling (hsa04630) (Table S3 ).
TextSentencer_T81 12440-12685 Sentence denotes In addition, many of the H5N1-upregulated genes mapped 193 to metabolic pathways (hsa01100), cytokine-cytokine receptor interaction (hsa04060), Influenza A 194 (hsa05164), TNF signaling (hsa04668) or to Jak-STAT signaling (hsa04630) (Table S3 ).
TextSentencer_T82 12686-12879 Sentence denotes However, not 195 all the H5N1-upregulated genes in these pathways were inhibited by apocynin treatment as mentioned 196 above ( Table 2; CEACAM5, were not affected by H5N1 infection (Fig. 3B ).
TextSentencer_T82 12686-12879 Sentence denotes However, not 195 all the H5N1-upregulated genes in these pathways were inhibited by apocynin treatment as mentioned 196 above ( Table 2; CEACAM5, were not affected by H5N1 infection (Fig. 3B ).
TextSentencer_T83 12880-13118 Sentence denotes It is also worth noting that more reads were 203 obtained for CEACAM5 (>1000 FPKM) than CEACAM1 (~ 7 FPKM) in uninfected ATII cells (Fig. 3A 204 and B), which is consistent with their normal expression patterns in human lung tissue (30).
TextSentencer_T83 12880-13118 Sentence denotes It is also worth noting that more reads were 203 obtained for CEACAM5 (>1000 FPKM) than CEACAM1 (~ 7 FPKM) in uninfected ATII cells (Fig. 3A 204 and B), which is consistent with their normal expression patterns in human lung tissue (30).
TextSentencer_T84 13119-13152 Sentence denotes Although 205 All rights reserved.
TextSentencer_T84 13119-13152 Sentence denotes Although 205 All rights reserved.
TextSentencer_T85 13153-13189 Sentence denotes No reuse allowed without permission.
TextSentencer_T85 13153-13189 Sentence denotes No reuse allowed without permission.
TextSentencer_T86 13190-13504 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint CEACAM1 forms heterodimers with CEACAM5 (23), the higher basal expression of CEACAM5 in 206 ATII cells may explain why its expression was not altered by H5N1 infection.
TextSentencer_T86 13190-13504 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint CEACAM1 forms heterodimers with CEACAM5 (23), the higher basal expression of CEACAM5 in 206 ATII cells may explain why its expression was not altered by H5N1 infection.
TextSentencer_T87 13505-13620 Sentence denotes Apocynin treatment 207 significantly reduced transcription levels of both CEACAM1 (Fig. 3A) and CEACAM5 (Fig. 3B ).
TextSentencer_T87 13505-13620 Sentence denotes Apocynin treatment 207 significantly reduced transcription levels of both CEACAM1 (Fig. 3A) and CEACAM5 (Fig. 3B ).
TextSentencer_T88 13621-13624 Sentence denotes 208
TextSentencer_T88 13621-13624 Sentence denotes 208
TextSentencer_T89 13625-13994 Sentence denotes Expression of 11 CEACAM1 variants in ATII and/or A549 cells was further characterized using qRT-209 PCR using primer pairs designed to specifically detect each variant (Table S5) difference in CEACAM1 protein levels were observed at various MOIs (2, 5 or 10), CEACAM1 222 protein expression at 48 hpi was significantly higher than that at observed at 24 hpi (Fig. 3E) .
TextSentencer_T89 13625-13994 Sentence denotes Expression of 11 CEACAM1 variants in ATII and/or A549 cells was further characterized using qRT-209 PCR using primer pairs designed to specifically detect each variant (Table S5) difference in CEACAM1 protein levels were observed at various MOIs (2, 5 or 10), CEACAM1 222 protein expression at 48 hpi was significantly higher than that at observed at 24 hpi (Fig. 3E) .
TextSentencer_T90 13995-13998 Sentence denotes 223
TextSentencer_T90 13995-13998 Sentence denotes 223
TextSentencer_T91 13999-14284 Sentence denotes After confirming the upregulation of CEACAM1 protein expression following infection with 224 the low pathogenic PR8 virus in A549 cells, CEACAM1 protein expression was then examined in 225 primary human ATII cells infected with HPAI H5N1 and compared to PR8 virus infection (Fig. 3F) .
TextSentencer_T91 13999-14284 Sentence denotes After confirming the upregulation of CEACAM1 protein expression following infection with 224 the low pathogenic PR8 virus in A549 cells, CEACAM1 protein expression was then examined in 225 primary human ATII cells infected with HPAI H5N1 and compared to PR8 virus infection (Fig. 3F) .
TextSentencer_T92 14285-14288 Sentence denotes 226
TextSentencer_T92 14285-14288 Sentence denotes 226
TextSentencer_T93 14289-14407 Sentence denotes Lower MOIs of 0.5, 1 and 2 HPAI H5N1 were tested due to the strong cytopathogenic effect it causes 227 at higher MOIs.
TextSentencer_T93 14289-14407 Sentence denotes Lower MOIs of 0.5, 1 and 2 HPAI H5N1 were tested due to the strong cytopathogenic effect it causes 227 at higher MOIs.
TextSentencer_T94 14408-14527 Sentence denotes Endogenous CEACAM1 protein levels were significantly elevated in H5N1-infected 228 ATII cells at all three MOIs tested.
TextSentencer_T94 14408-14527 Sentence denotes Endogenous CEACAM1 protein levels were significantly elevated in H5N1-infected 228 ATII cells at all three MOIs tested.
TextSentencer_T95 14528-14614 Sentence denotes Similar levels of CEACAM1 protein expression were observed at 229 All rights reserved.
TextSentencer_T95 14528-14614 Sentence denotes Similar levels of CEACAM1 protein expression were observed at 229 All rights reserved.
TextSentencer_T96 14615-14651 Sentence denotes No reuse allowed without permission.
TextSentencer_T96 14615-14651 Sentence denotes No reuse allowed without permission.
TextSentencer_T97 14652-14877 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint MOIs of 0.5 and 1 and were higher at 48 hpi when compared to 24 hpi (Fig. 3F ).
TextSentencer_T97 14652-14877 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint MOIs of 0.5 and 1 and were higher at 48 hpi when compared to 24 hpi (Fig. 3F ).
TextSentencer_T98 14878-15290 Sentence denotes HPAI H5N1 virus 230 infection at MOIs of 0.5, 1 and 2 stimulated higher endogenous levels of CEACAM1 protein 231 expression when compared to low pathogenic PR8 H1N1 virus infection at a MOI of 2 (a maximum 232 23-fold increase induced by H5N1 at MOIs of 0.5 and 1, 48 hpi when compared to PR8 at MOI of 2), 233 suggesting a possible role for CEACAM1 in influenza virus pathogenicity (Fig. 3F) . (data not shown).
TextSentencer_T98 14878-15290 Sentence denotes HPAI H5N1 virus 230 infection at MOIs of 0.5, 1 and 2 stimulated higher endogenous levels of CEACAM1 protein 231 expression when compared to low pathogenic PR8 H1N1 virus infection at a MOI of 2 (a maximum 232 23-fold increase induced by H5N1 at MOIs of 0.5 and 1, 48 hpi when compared to PR8 at MOI of 2), 233 suggesting a possible role for CEACAM1 in influenza virus pathogenicity (Fig. 3F) . (data not shown).
TextSentencer_T99 15291-15470 Sentence denotes CEACAM1 protein expression was reduced by approximately 50% in both ATII and 250 A549 cells following siCEACAM1 transfection when compared with siNeg-transfected cells (Fig. 4C) .
TextSentencer_T99 15291-15470 Sentence denotes CEACAM1 protein expression was reduced by approximately 50% in both ATII and 250 A549 cells following siCEACAM1 transfection when compared with siNeg-transfected cells (Fig. 4C) .
TextSentencer_T100 15471-15474 Sentence denotes 251
TextSentencer_T100 15471-15474 Sentence denotes 251
TextSentencer_T101 15475-15605 Sentence denotes It is important to note that the anti-CEACAM1 antibody only detects L isoforms based on 252 epitope information provided by Abcam.
TextSentencer_T101 15475-15605 Sentence denotes It is important to note that the anti-CEACAM1 antibody only detects L isoforms based on 252 epitope information provided by Abcam.
TextSentencer_T102 15606-15680 Sentence denotes Therefore, observed reductions in CEACAM1 protein 253 All rights reserved.
TextSentencer_T102 15606-15680 Sentence denotes Therefore, observed reductions in CEACAM1 protein 253 All rights reserved.
TextSentencer_T103 15681-15717 Sentence denotes No reuse allowed without permission.
TextSentencer_T103 15681-15717 Sentence denotes No reuse allowed without permission.
TextSentencer_T104 15718-15941 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint expression can be attributed mainly to the abolishment of CEACAM1-4L isoform.
TextSentencer_T104 15718-15941 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint expression can be attributed mainly to the abolishment of CEACAM1-4L isoform.
TextSentencer_T105 15942-16072 Sentence denotes Increasing doses of 254 siCEACAM1 (10, 15 and 20 pmol) did not further down-regulate CEACAM1 protein expression in 255 A549 cells.
TextSentencer_T105 15942-16072 Sentence denotes Increasing doses of 254 siCEACAM1 (10, 15 and 20 pmol) did not further down-regulate CEACAM1 protein expression in 255 A549 cells.
TextSentencer_T106 16073-16190 Sentence denotes As such, 15 pmol of siCEACAM1 was chosen for subsequent knockdown studies in both 256 ATII and A549 cells (Fig. 4C) .
TextSentencer_T106 16073-16190 Sentence denotes As such, 15 pmol of siCEACAM1 was chosen for subsequent knockdown studies in both 256 ATII and A549 cells (Fig. 4C) .
TextSentencer_T107 16191-16194 Sentence denotes 257
TextSentencer_T107 16191-16194 Sentence denotes 257
TextSentencer_T108 16195-16315 Sentence denotes The functional consequences of CEACAM1 knockdown were then examined in ATII and A549 258 cells following H5N1 infection.
TextSentencer_T108 16195-16315 Sentence denotes The functional consequences of CEACAM1 knockdown were then examined in ATII and A549 258 cells following H5N1 infection.
TextSentencer_T109 16316-16430 Sentence denotes IL-6, IFN-β, CXCL10, CCL5, and TNF production was analyzed in 259 H5N1-infected A549 and ATII cells using qRT-PCR.
TextSentencer_T109 16316-16430 Sentence denotes IL-6, IFN-β, CXCL10, CCL5, and TNF production was analyzed in 259 H5N1-infected A549 and ATII cells using qRT-PCR.
TextSentencer_T110 16431-16799 Sentence denotes ATII (Fig. 5A ) and A549 cells ( The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint modulation of reactive oxygen species (ROS) to reduce inflammation (5) and inhibition of NFκB and 278 mitogenic Raf/MEK/ERK kinase cascade activation to suppress viral replication (34, 35).
TextSentencer_T110 16431-16799 Sentence denotes ATII (Fig. 5A ) and A549 cells ( The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint modulation of reactive oxygen species (ROS) to reduce inflammation (5) and inhibition of NFκB and 278 mitogenic Raf/MEK/ERK kinase cascade activation to suppress viral replication (34, 35).
TextSentencer_T111 16800-16931 Sentence denotes These host 279 targeting strategies will offer an alternative to current interventions that are focused on targeting the 280 virus.
TextSentencer_T111 16800-16931 Sentence denotes These host 279 targeting strategies will offer an alternative to current interventions that are focused on targeting the 280 virus.
TextSentencer_T112 16932-17080 Sentence denotes In the present study, we analyzed human host gene expression profiles following HPAI H5N1 281 infection and treatment with the antioxidant apocynin.
TextSentencer_T112 16932-17080 Sentence denotes In the present study, we analyzed human host gene expression profiles following HPAI H5N1 281 infection and treatment with the antioxidant apocynin.
TextSentencer_T113 17081-17260 Sentence denotes As expected, genes that were significantly 282 upregulated following H5N1 infection were involved in biological processes including cytokine 283 signaling, immunity and apoptosis.
TextSentencer_T113 17081-17260 Sentence denotes As expected, genes that were significantly 282 upregulated following H5N1 infection were involved in biological processes including cytokine 283 signaling, immunity and apoptosis.
TextSentencer_T114 17261-17476 Sentence denotes In addition, H5N1-upregulated genes were also involved in 284 regulation of protein phosphorylation, cellular metabolism and cell proliferation, which are thought to 285 be exploited by viruses for replication (36).
TextSentencer_T114 17261-17476 Sentence denotes In addition, H5N1-upregulated genes were also involved in 284 regulation of protein phosphorylation, cellular metabolism and cell proliferation, which are thought to 285 be exploited by viruses for replication (36).
TextSentencer_T115 17477-17725 Sentence denotes Apocynin treatment had both anti-viral (Table S2 , S3, S4) 286 (6) and pro-viral impact (Fig. 2G) , which is not surprising as ROS are potent microbicidal agents, as 287 well as important immune signaling molecules at different concentrations (37).
TextSentencer_T115 17477-17725 Sentence denotes Apocynin treatment had both anti-viral (Table S2 , S3, S4) 286 (6) and pro-viral impact (Fig. 2G) , which is not surprising as ROS are potent microbicidal agents, as 287 well as important immune signaling molecules at different concentrations (37).
TextSentencer_T116 17726-17910 Sentence denotes In our hands, apocynin 288 treatment reduced H5N1-induced inflammation, but unavoidably impacted the cellular defense 289 response, cytokine production and cytokine-mediated signaling.
TextSentencer_T116 17726-17910 Sentence denotes In our hands, apocynin 288 treatment reduced H5N1-induced inflammation, but unavoidably impacted the cellular defense 289 response, cytokine production and cytokine-mediated signaling.
TextSentencer_T117 17911-17956 Sentence denotes Importantly, critical antiviral responses 290
TextSentencer_T117 17911-17956 Sentence denotes Importantly, critical antiviral responses 290
TextSentencer_T118 17957-18112 Sentence denotes were not compromised, i.e. the expression of pattern recognition receptors (e.g. DDX58 (RIG-I), TLRs, 291 IFIH1 (MDA5)) was not down-regulated (Table S1 ).
TextSentencer_T118 17957-18112 Sentence denotes were not compromised, i.e. the expression of pattern recognition receptors (e.g. DDX58 (RIG-I), TLRs, 291 IFIH1 (MDA5)) was not down-regulated (Table S1 ).
TextSentencer_T119 18113-18258 Sentence denotes Given the significant interference of influenza 292 viruses on host immunity, we focused our attention on key regulators of the immune responses.
TextSentencer_T119 18113-18258 Sentence denotes Given the significant interference of influenza 292 viruses on host immunity, we focused our attention on key regulators of the immune responses.
TextSentencer_T120 18259-18262 Sentence denotes 293
TextSentencer_T120 18259-18262 Sentence denotes 293
TextSentencer_T121 18263-18376 Sentence denotes Through HiSeq analysis, we identified the cell adhesion molecule CEACAM1 as a critical regulator of 294 immunity.
TextSentencer_T121 18263-18376 Sentence denotes Through HiSeq analysis, we identified the cell adhesion molecule CEACAM1 as a critical regulator of 294 immunity.
TextSentencer_T122 18377-18526 Sentence denotes Knockdown of endogenous CEACAM1 not only reduced H5N1-stimulated inflammatory 295 cytokine/chemokine production but also inhibited virus replication.
TextSentencer_T122 18377-18526 Sentence denotes Knockdown of endogenous CEACAM1 not only reduced H5N1-stimulated inflammatory 295 cytokine/chemokine production but also inhibited virus replication.
TextSentencer_T123 18527-18795 Sentence denotes 296 H5N1 infection resulted in significant upregulation of a number of inflammatory 297 cytokines/chemokines genes, including AXL and STING, which were significantly reduced by 298 apocynin treatment to a level lower than that observed in uninfected cells (Table S4 ).
TextSentencer_T123 18527-18795 Sentence denotes 296 H5N1 infection resulted in significant upregulation of a number of inflammatory 297 cytokines/chemokines genes, including AXL and STING, which were significantly reduced by 298 apocynin treatment to a level lower than that observed in uninfected cells (Table S4 ).
TextSentencer_T124 18796-18966 Sentence denotes It has been 299 previously demonstrated that treatment of PR8 H1N1-infected mice with anti-AXL antibody 300 significantly reduces lung inflammation and virus titers (38).
TextSentencer_T124 18796-18966 Sentence denotes It has been 299 previously demonstrated that treatment of PR8 H1N1-infected mice with anti-AXL antibody 300 significantly reduces lung inflammation and virus titers (38).
TextSentencer_T125 18967-19028 Sentence denotes STING has been shown to be important 301 All rights reserved.
TextSentencer_T125 18967-19028 Sentence denotes STING has been shown to be important 301 All rights reserved.
TextSentencer_T126 19029-19065 Sentence denotes No reuse allowed without permission.
TextSentencer_T126 19029-19065 Sentence denotes No reuse allowed without permission.
TextSentencer_T127 19066-19349 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint for promoting anti-viral responses, as STING-knockout THP-1 cells produce less type I IFN following 302 influenza A virus infection (39).
TextSentencer_T127 19066-19349 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint for promoting anti-viral responses, as STING-knockout THP-1 cells produce less type I IFN following 302 influenza A virus infection (39).
TextSentencer_T128 19350-19646 Sentence denotes Reduction of STING gene expression or other anti-viral factors (e.g. 303 IFNB1, MX1, ISG15; Table S1 ) by apocynin, may in part, explain the slight increase of the 304 transcription levels of all influenza genes (NS gene was significantly upregulated) following apocynin 305 treatment (Fig. 2G) .
TextSentencer_T128 19350-19646 Sentence denotes Reduction of STING gene expression or other anti-viral factors (e.g. 303 IFNB1, MX1, ISG15; Table S1 ) by apocynin, may in part, explain the slight increase of the 304 transcription levels of all influenza genes (NS gene was significantly upregulated) following apocynin 305 treatment (Fig. 2G) .
TextSentencer_T129 19647-19753 Sentence denotes These results also suggest that apocynin treatment may reduce H5N1-induced 306 inflammation and apoptosis.
TextSentencer_T129 19647-19753 Sentence denotes These results also suggest that apocynin treatment may reduce H5N1-induced 306 inflammation and apoptosis.
TextSentencer_T130 19754-20095 Sentence denotes Indeed, the anti-inflammatory and anti-apoptotic effects of apocynin have 307 been shown previously in a number of disease models, including diabetes mellitus (40) could suggest the possibility that upregulation of CEACAM1 (to inhibit NK activity) may be a novel 324 and uncharacterized immune evasion strategy employed by influenza viruses.
TextSentencer_T130 19754-20095 Sentence denotes Indeed, the anti-inflammatory and anti-apoptotic effects of apocynin have 307 been shown previously in a number of disease models, including diabetes mellitus (40) could suggest the possibility that upregulation of CEACAM1 (to inhibit NK activity) may be a novel 324 and uncharacterized immune evasion strategy employed by influenza viruses.
TextSentencer_T131 20096-20142 Sentence denotes Our laboratory is now 325 All rights reserved.
TextSentencer_T131 20096-20142 Sentence denotes Our laboratory is now 325 All rights reserved.
TextSentencer_T132 20143-20179 Sentence denotes No reuse allowed without permission.
TextSentencer_T132 20143-20179 Sentence denotes No reuse allowed without permission.
TextSentencer_T133 20180-20270 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.
TextSentencer_T133 20180-20270 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.
TextSentencer_T134 20271-20518 Sentence denotes In support of this notion, we did not observe a difference in apoptosis of PR8-infected A549 cells 338 following transfection with siCEACAM1, siNeg, or mock-transfected cells using flow cytometry-based 339 Annexin V/7AAD staining (data not shown).
TextSentencer_T134 20271-20518 Sentence denotes In support of this notion, we did not observe a difference in apoptosis of PR8-infected A549 cells 338 following transfection with siCEACAM1, siNeg, or mock-transfected cells using flow cytometry-based 339 Annexin V/7AAD staining (data not shown).
TextSentencer_T135 20519-20647 Sentence denotes Our study, together with the CEACAM6 findings, serve 340 to highlight the emerging role of CEACAMs in influenza virus infection.
TextSentencer_T135 20519-20647 Sentence denotes Our study, together with the CEACAM6 findings, serve 340 to highlight the emerging role of CEACAMs in influenza virus infection.
TextSentencer_T136 20648-20651 Sentence denotes 341
TextSentencer_T136 20648-20651 Sentence denotes 341
TextSentencer_T137 20652-20983 Sentence denotes The molecular mechanism of CEACAM1 action following infection has also been explored in 342 A549 cells using the low pathogenic PR8 virus (51) (18) and 359 papillomavirus (19), it will be important to determine whether a common mechanism of action can be 360 attributed to CEACAM1 in order to determine its functional significance.
TextSentencer_T137 20652-20983 Sentence denotes The molecular mechanism of CEACAM1 action following infection has also been explored in 342 A549 cells using the low pathogenic PR8 virus (51) (18) and 359 papillomavirus (19), it will be important to determine whether a common mechanism of action can be 360 attributed to CEACAM1 in order to determine its functional significance.
TextSentencer_T138 20984-21095 Sentence denotes If this can be established, 361 CEACAM1 could be used as a target for the development of a pan-antiviral agent.
TextSentencer_T138 20984-21095 Sentence denotes If this can be established, 361 CEACAM1 could be used as a target for the development of a pan-antiviral agent.
TextSentencer_T139 21096-21292 Sentence denotes Furthermore, it has 362 been shown that CEACAM1-S isoforms and soluble isoforms (CEACAM1-4C1, -3, -3C2) also have 363 regulatory effects (stimulatory or inhibitory) on CEACAM1-L isoforms (20, 52).
TextSentencer_T139 21096-21292 Sentence denotes Furthermore, it has 362 been shown that CEACAM1-S isoforms and soluble isoforms (CEACAM1-4C1, -3, -3C2) also have 363 regulatory effects (stimulatory or inhibitory) on CEACAM1-L isoforms (20, 52).
TextSentencer_T140 21293-21554 Sentence denotes Although 364 CEACAM1-Ls are the dominate isoforms, the involvement of other CEACAM1 isoforms in influenza 365 immunity should also be further investigated, especially as H5N1 infection increased mRNA 366 expression levels of several CEACAM1 variants (Fig. 3C) .
TextSentencer_T140 21293-21554 Sentence denotes Although 364 CEACAM1-Ls are the dominate isoforms, the involvement of other CEACAM1 isoforms in influenza 365 immunity should also be further investigated, especially as H5N1 infection increased mRNA 366 expression levels of several CEACAM1 variants (Fig. 3C) .
TextSentencer_T141 21555-21558 Sentence denotes 367
TextSentencer_T141 21555-21558 Sentence denotes 367
TextSentencer_T142 21559-21766 Sentence denotes In summary, molecules on the cell surface such as CEACAM1 are particularly attractive 368 candidates for therapeutic development, as drugs do not need to cross the cell membrane in order to be 369 effective.
TextSentencer_T142 21559-21766 Sentence denotes In summary, molecules on the cell surface such as CEACAM1 are particularly attractive 368 candidates for therapeutic development, as drugs do not need to cross the cell membrane in order to be 369 effective.
TextSentencer_T143 21767-21946 Sentence denotes Targeting of host-encoded genes in combination with current antivirals and vaccines may be 370 a way of reducing morbidity and mortality associated with influenza virus infection.
TextSentencer_T143 21767-21946 Sentence denotes Targeting of host-encoded genes in combination with current antivirals and vaccines may be 370 a way of reducing morbidity and mortality associated with influenza virus infection.
TextSentencer_T144 21947-22113 Sentence denotes Our study clearly 371 demonstrates that increased CEACAM1 expression is observed in primary human ATII cells infected 372 with highly pathogenic H5N1 influenza virus.
TextSentencer_T144 21947-22113 Sentence denotes Our study clearly 371 demonstrates that increased CEACAM1 expression is observed in primary human ATII cells infected 372 with highly pathogenic H5N1 influenza virus.
TextSentencer_T145 22114-22183 Sentence denotes Importantly, knockdown of CEACAM1 expression 373 All rights reserved.
TextSentencer_T145 22114-22183 Sentence denotes Importantly, knockdown of CEACAM1 expression 373 All rights reserved.
TextSentencer_T146 22184-22220 Sentence denotes No reuse allowed without permission.
TextSentencer_T146 22184-22220 Sentence denotes No reuse allowed without permission.
TextSentencer_T147 22221-22311 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.
TextSentencer_T147 22221-22311 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.
TextSentencer_T148 22312-22370 Sentence denotes DNase I (0.5 mg/mL; Roche Diagnostics) for 60 min at 37°C.
TextSentencer_T148 22312-22370 Sentence denotes DNase I (0.5 mg/mL; Roche Diagnostics) for 60 min at 37°C.
TextSentencer_T149 22371-22690 Sentence denotes Single cell suspensions were obtained by 389 filtration through a 40 μm cell strainer and cells were allowed to attach to a petri dish in a 1:1 mixture 390 of DMEM/F12 medium (Gibco) and small airway growth medium (SAGM) medium (Lonza) 391 containing 5% fetal calf serum (FCS) and 0.5 mg/mL DNase I for 2 hours at 37°C.
TextSentencer_T149 22371-22690 Sentence denotes Single cell suspensions were obtained by 389 filtration through a 40 μm cell strainer and cells were allowed to attach to a petri dish in a 1:1 mixture 390 of DMEM/F12 medium (Gibco) and small airway growth medium (SAGM) medium (Lonza) 391 containing 5% fetal calf serum (FCS) and 0.5 mg/mL DNase I for 2 hours at 37°C.
TextSentencer_T150 22691-22879 Sentence denotes The non-adherent 392 cells, including ATII cells, were collected and subjected to centrifugation at 300 g for 20 min on a 393 discontinuous Percoll density gradient (1.089 and 1.040 g/mL).
TextSentencer_T150 22691-22879 Sentence denotes The non-adherent 392 cells, including ATII cells, were collected and subjected to centrifugation at 300 g for 20 min on a 393 discontinuous Percoll density gradient (1.089 and 1.040 g/mL).
TextSentencer_T151 22880-23235 Sentence denotes Purified ATII cells from the interface 394 of two density gradients was collected, washed in HBSS, and re-suspended in SAGM media 395 supplemented with 1% charcoal-filtered FCS (Gibco) and 100 units/mL penicillin and 100 µg/mL 396 streptomycin (Gibco), prior to plating on polyester Transwell inserts (0.4 μm pore; Corning) coated 397 All rights reserved.
TextSentencer_T151 22880-23235 Sentence denotes Purified ATII cells from the interface 394 of two density gradients was collected, washed in HBSS, and re-suspended in SAGM media 395 supplemented with 1% charcoal-filtered FCS (Gibco) and 100 units/mL penicillin and 100 µg/mL 396 streptomycin (Gibco), prior to plating on polyester Transwell inserts (0.4 μm pore; Corning) coated 397 All rights reserved.
TextSentencer_T152 23236-23272 Sentence denotes No reuse allowed without permission.
TextSentencer_T152 23236-23272 Sentence denotes No reuse allowed without permission.
TextSentencer_T153 23273-23499 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint with type IV human placenta collagen (0.05 mg/mL; Sigma) at 300,000 cells/cm 2 .
TextSentencer_T153 23273-23499 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint with type IV human placenta collagen (0.05 mg/mL; Sigma) at 300,000 cells/cm 2 .
TextSentencer_T154 23500-23653 Sentence denotes Cells were then 398 cultured under liquid-covered conditions in a humidified incubator (5% CO 2 , 37°C) and growth 399 medium was changed every 48 hours.
TextSentencer_T154 23500-23653 Sentence denotes Cells were then 398 cultured under liquid-covered conditions in a humidified incubator (5% CO 2 , 37°C) and growth 399 medium was changed every 48 hours.
TextSentencer_T155 23654-23845 Sentence denotes These culture conditions encourage ATII cells to grow and 400 differentiate into alveolar epithelial cells. trypsin (Worthington) was included in media post-inoculation to assist replication.
TextSentencer_T155 23654-23845 Sentence denotes These culture conditions encourage ATII cells to grow and 400 differentiate into alveolar epithelial cells. trypsin (Worthington) was included in media post-inoculation to assist replication.
TextSentencer_T156 23846-23954 Sentence denotes Virus titers were 420 determined using standard plaque assays using MDCK cells as previously described (56).
TextSentencer_T156 23846-23954 Sentence denotes Virus titers were 420 determined using standard plaque assays using MDCK cells as previously described (56).
TextSentencer_T157 23955-23979 Sentence denotes 421 All rights reserved.
TextSentencer_T157 23955-23979 Sentence denotes 421 All rights reserved.
TextSentencer_T158 23980-24016 Sentence denotes No reuse allowed without permission.
TextSentencer_T158 23980-24016 Sentence denotes No reuse allowed without permission.
TextSentencer_T159 24017-24219 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint RNA extraction, quality control (QC) and HiSeq analysis.
TextSentencer_T159 24017-24219 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint RNA extraction, quality control (QC) and HiSeq analysis.
TextSentencer_T160 24220-24293 Sentence denotes ATII cells from three individual 422 donors were used for HiSeq analysis.
TextSentencer_T160 24220-24293 Sentence denotes ATII cells from three individual 422 donors were used for HiSeq analysis.
TextSentencer_T161 24294-24366 Sentence denotes Total RNA was extracted from cells using a RNeasy Mini kit 423 (Qiagen).
TextSentencer_T161 24294-24366 Sentence denotes Total RNA was extracted from cells using a RNeasy Mini kit 423 (Qiagen).
TextSentencer_T162 24367-24515 Sentence denotes Influenza-infected cells were washed with PBS three times and cells lysed with RLT buffer 424 supplemented with β-mercaptoethanol (10 μL/mL; Gibco).
TextSentencer_T162 24367-24515 Sentence denotes Influenza-infected cells were washed with PBS three times and cells lysed with RLT buffer 424 supplemented with β-mercaptoethanol (10 μL/mL; Gibco).
TextSentencer_T163 24516-24554 Sentence denotes Cell lysates were homogenized with 425
TextSentencer_T163 24516-24554 Sentence denotes Cell lysates were homogenized with 425
TextSentencer_T164 24555-24714 Sentence denotes QIAshredder columns followed by on-column DNA digestion with the RNase-Free DNase Set 426 (Qiagen), and RNA extracted according to manufacturer's instructions.
TextSentencer_T164 24555-24714 Sentence denotes QIAshredder columns followed by on-column DNA digestion with the RNase-Free DNase Set 426 (Qiagen), and RNA extracted according to manufacturer's instructions.
TextSentencer_T165 24715-25090 Sentence denotes Initial QC was conducted to 427 ensure that the quantity and quality of RNA samples for HiSeq analysis met the following criteria; 1) 428 RNA samples had OD260/280 ratios between 1.8 and 2.0 as measured with NanoDrop TM 429 Spectrophotometer (Thermo Scientific); 2) Sample concentrations were at a minimum of 100 ng/μl; 3) 430 RNA was analyzed by agarose gel electrophoresis.
TextSentencer_T165 24715-25090 Sentence denotes Initial QC was conducted to 427 ensure that the quantity and quality of RNA samples for HiSeq analysis met the following criteria; 1) 428 RNA samples had OD260/280 ratios between 1.8 and 2.0 as measured with NanoDrop TM 429 Spectrophotometer (Thermo Scientific); 2) Sample concentrations were at a minimum of 100 ng/μl; 3) 430 RNA was analyzed by agarose gel electrophoresis.
TextSentencer_T166 25091-25295 Sentence denotes RNA integrity and quality were validated by the 431 presence of the sharp clear bands of 28S and 18S ribosomal RNA, with a 28S:18S ratio of 2:1, along 432 with the absence of genomic DNA and degraded RNA.
TextSentencer_T166 25091-25295 Sentence denotes RNA integrity and quality were validated by the 431 presence of the sharp clear bands of 28S and 18S ribosomal RNA, with a 28S:18S ratio of 2:1, along 432 with the absence of genomic DNA and degraded RNA.
TextSentencer_T167 25296-25694 Sentence denotes As part of the initial QC and as an indication of 433 consistent H5N1 infection, parallel quantitative real-time reverse transcriptase PCR (qRT-PCR) was 434 performed as previously described (5) to measure mRNA expression of IL-6, CXCL10, CCL5, 435 suppressor of cytokine signaling (SOCS) 1 and SOCS3 (Fig. 2) , which is known to be up-regulated 436 following HPAI H5N1 infection of A549 cells (5).
TextSentencer_T167 25296-25694 Sentence denotes As part of the initial QC and as an indication of 433 consistent H5N1 infection, parallel quantitative real-time reverse transcriptase PCR (qRT-PCR) was 434 performed as previously described (5) to measure mRNA expression of IL-6, CXCL10, CCL5, 435 suppressor of cytokine signaling (SOCS) 1 and SOCS3 (Fig. 2) , which is known to be up-regulated 436 following HPAI H5N1 infection of A549 cells (5).
TextSentencer_T168 25695-25901 Sentence denotes RNA samples were stored in 0.1 volumes of 3 M 437 Sodium Acetate (pH7.5 in DEPC-treated water) and 2 volumes of 100% Ethanol and submitted to 438 Macrogen Inc. (Seoul, Republic of Korea) for HiSeq analysis.
TextSentencer_T168 25695-25901 Sentence denotes RNA samples were stored in 0.1 volumes of 3 M 437 Sodium Acetate (pH7.5 in DEPC-treated water) and 2 volumes of 100% Ethanol and submitted to 438 Macrogen Inc. (Seoul, Republic of Korea) for HiSeq analysis.
TextSentencer_T169 25902-25905 Sentence denotes 439
TextSentencer_T169 25902-25905 Sentence denotes 439
TextSentencer_T170 25906-25941 Sentence denotes Sequencing analysis and annotation.
TextSentencer_T170 25906-25941 Sentence denotes Sequencing analysis and annotation.
TextSentencer_T171 25942-26184 Sentence denotes After confirming checksums and assessing raw data 440 quality of the FASTQ files with FASTQC, RNA-Seq reads were processed according to standard 441 Tuxedo pipeline protocols (57), using the annotated human genome (GRCh37, downloaded from 442
TextSentencer_T171 25942-26184 Sentence denotes After confirming checksums and assessing raw data 440 quality of the FASTQ files with FASTQC, RNA-Seq reads were processed according to standard 441 Tuxedo pipeline protocols (57), using the annotated human genome (GRCh37, downloaded from 442
TextSentencer_T172 26185-26219 Sentence denotes Illumina iGenomes) as a reference.
TextSentencer_T172 26185-26219 Sentence denotes Illumina iGenomes) as a reference.
TextSentencer_T173 26220-26415 Sentence denotes Briefly, raw reads for each sample were mapped to the human 443 genome using TopHat2, sorted and converted to SAM format using Samtools and then assembled into 444 transcriptomes using Cufflinks.
TextSentencer_T173 26220-26415 Sentence denotes Briefly, raw reads for each sample were mapped to the human 443 genome using TopHat2, sorted and converted to SAM format using Samtools and then assembled into 444 transcriptomes using Cufflinks.
TextSentencer_T174 26416-26509 Sentence denotes Cuffmerge was used to combine transcript annotations from individual 445 All rights reserved.
TextSentencer_T174 26416-26509 Sentence denotes Cuffmerge was used to combine transcript annotations from individual 445 All rights reserved.
TextSentencer_T175 26510-26546 Sentence denotes No reuse allowed without permission.
TextSentencer_T175 26510-26546 Sentence denotes No reuse allowed without permission.
TextSentencer_T176 26547-26800 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint samples into a single reference transcriptome, and Cuffquant was used to obtain per-sample read 446 counts.
TextSentencer_T176 26547-26800 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint samples into a single reference transcriptome, and Cuffquant was used to obtain per-sample read 446 counts.
TextSentencer_T177 26801-26868 Sentence denotes Cuffdiff was then used to conduct differential expression analysis.
TextSentencer_T177 26801-26868 Sentence denotes Cuffdiff was then used to conduct differential expression analysis.
TextSentencer_T178 26869-27136 Sentence denotes All programs were run using 447 recommended parameters, however the reference gtf file provided to cuffmerge was first edited using a 448 custom python script to exclude lines containing features other than exon/cds, and contigs other than 449 chromosomes 1-22, X, Y.
TextSentencer_T178 26869-27136 Sentence denotes All programs were run using 447 recommended parameters, however the reference gtf file provided to cuffmerge was first edited using a 448 custom python script to exclude lines containing features other than exon/cds, and contigs other than 449 chromosomes 1-22, X, Y.
TextSentencer_T179 27137-27140 Sentence denotes 450
TextSentencer_T179 27137-27140 Sentence denotes 450
TextSentencer_T180 27141-27180 Sentence denotes Gene ontology (GO) and KEGG enrichment.
TextSentencer_T180 27141-27180 Sentence denotes Gene ontology (GO) and KEGG enrichment.
TextSentencer_T181 27181-27361 Sentence denotes Official gene IDs for transcripts that were 451 differentially modulated following HPAI H5N1 infection with or without apocynin treatment were 452 compiled into three target lists.
TextSentencer_T181 27181-27361 Sentence denotes Official gene IDs for transcripts that were 451 differentially modulated following HPAI H5N1 infection with or without apocynin treatment were 452 compiled into three target lists.
TextSentencer_T182 27362-27518 Sentence denotes Statistically significant differentially expressed transcripts were defined 453 as having ≥ 2-fold change with a Benjamini-Hochberg adjusted P value < 0.01.
TextSentencer_T182 27362-27518 Sentence denotes Statistically significant differentially expressed transcripts were defined 453 as having ≥ 2-fold change with a Benjamini-Hochberg adjusted P value < 0.01.
TextSentencer_T183 27519-27651 Sentence denotes A background list of 454 genes was compiled by retrieving all gene IDs identified from the present HiSeq analysis with FPKM > 455 1.
TextSentencer_T183 27519-27651 Sentence denotes A background list of 454 genes was compiled by retrieving all gene IDs identified from the present HiSeq analysis with FPKM > 455 1.
TextSentencer_T184 27652-27823 Sentence denotes Biological process GO enrichment was performed using GOrilla comparing unranked background 456 and target lists (58) and redundant GO terms were removed using REVIGO (59).
TextSentencer_T184 27652-27823 Sentence denotes Biological process GO enrichment was performed using GOrilla comparing unranked background 456 and target lists (58) and redundant GO terms were removed using REVIGO (59).
TextSentencer_T185 27824-28124 Sentence denotes The target lists were 457 also subjected to KEGG pathway analysis using a basic KEGG pathway mapper (60). (Table S5 ) were designed to estimate the expression of CEACAM1 467 variants in ATII and A549 cells using iTaq Universal SYBR Green Supermix (BioRad) according to 468 manufacturer's instruction.
TextSentencer_T185 27824-28124 Sentence denotes The target lists were 457 also subjected to KEGG pathway analysis using a basic KEGG pathway mapper (60). (Table S5 ) were designed to estimate the expression of CEACAM1 467 variants in ATII and A549 cells using iTaq Universal SYBR Green Supermix (BioRad) according to 468 manufacturer's instruction.
TextSentencer_T186 28125-28219 Sentence denotes The absence of nonspecific amplification was confirmed by agarose gel 469 All rights reserved.
TextSentencer_T186 28125-28219 Sentence denotes The absence of nonspecific amplification was confirmed by agarose gel 469 All rights reserved.
TextSentencer_T187 28220-28256 Sentence denotes No reuse allowed without permission.
TextSentencer_T187 28220-28256 Sentence denotes No reuse allowed without permission.
TextSentencer_T188 28257-28447 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint electrophoresis of qRT-PCR products (15 μL).
TextSentencer_T188 28257-28447 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint electrophoresis of qRT-PCR products (15 μL).
TextSentencer_T189 28448-28601 Sentence denotes Gene expression was normalized to β-actin mRNA 470 using the 2 -ΔΔCT method where expression levels were determined relative to uninfected cell controls.
TextSentencer_T189 28448-28601 Sentence denotes Gene expression was normalized to β-actin mRNA 470 using the 2 -ΔΔCT method where expression levels were determined relative to uninfected cell controls.
TextSentencer_T190 28602-28843 Sentence denotes 471 qRT-PCR primers and primer pairs used to identify each CEACAM1 variant are listed in Table S5 cell adhesion molecule of the immunoglobulin superfamily, on human lymphocytes: structure, 555 expression and involvement in T cell activation.
TextSentencer_T190 28602-28843 Sentence denotes 471 qRT-PCR primers and primer pairs used to identify each CEACAM1 variant are listed in Table S5 cell adhesion molecule of the immunoglobulin superfamily, on human lymphocytes: structure, 555 expression and involvement in T cell activation.
TextSentencer_T191 28844-28871 Sentence denotes Eur J Immunol 28:3664-3674.
TextSentencer_T191 28844-28871 Sentence denotes Eur J Immunol 28:3664-3674.
TextSentencer_T192 28872-28896 Sentence denotes 556 All rights reserved.
TextSentencer_T192 28872-28896 Sentence denotes 556 All rights reserved.
TextSentencer_T193 28897-28933 Sentence denotes No reuse allowed without permission.
TextSentencer_T193 28897-28933 Sentence denotes No reuse allowed without permission.
TextSentencer_T194 28934-29217 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint and chemokine production in response to H5N1 infection (MOI of 0.01, 24 hpi) by qRT-PCR com-775 pared to siNeg-transfected control cells.
TextSentencer_T194 28934-29217 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint and chemokine production in response to H5N1 infection (MOI of 0.01, 24 hpi) by qRT-PCR com-775 pared to siNeg-transfected control cells.
TextSentencer_T195 29218-29331 Sentence denotes One sample t test compared to siNeg-transfected cells that 776 have a fold-change of 1, *p < 0.05 and **p < 0.01.
TextSentencer_T195 29218-29331 Sentence denotes One sample t test compared to siNeg-transfected cells that 776 have a fold-change of 1, *p < 0.05 and **p < 0.01.
TextSentencer_T196 29332-29498 Sentence denotes Plaque assay of H5N1 virus titres in ATII (C) and 777 A549 (D) that were either mock-transfected or transfected with siCEACAM1 or siNeg. *p < 0.05 and 778 **p < 0.01.
TextSentencer_T196 29332-29498 Sentence denotes Plaque assay of H5N1 virus titres in ATII (C) and 777 A549 (D) that were either mock-transfected or transfected with siCEACAM1 or siNeg. *p < 0.05 and 778 **p < 0.01.
TextSentencer_T197 29499-29502 Sentence denotes 779
TextSentencer_T197 29499-29502 Sentence denotes 779
TextSentencer_T198 29503-29523 Sentence denotes All rights reserved.
TextSentencer_T198 29503-29523 Sentence denotes All rights reserved.
TextSentencer_T199 29524-29560 Sentence denotes No reuse allowed without permission.
TextSentencer_T199 29524-29560 Sentence denotes No reuse allowed without permission.
TextSentencer_T200 29561-29715 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint TABLE 2.
TextSentencer_T200 29561-29715 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/324723 doi: bioRxiv preprint TABLE 2.
TextSentencer_T201 29716-29900 Sentence denotes Representatives of over-represented KEGG pathways and the number of genes contributing 784 to each pathway that is significantly up-regulated following H5N1 infection ("ND vs. HD Up").
TextSentencer_T201 29716-29900 Sentence denotes Representatives of over-represented KEGG pathways and the number of genes contributing 784 to each pathway that is significantly up-regulated following H5N1 infection ("ND vs. HD Up").
TextSentencer_T202 29901-30068 Sentence denotes The 785 number of genes in the same pathway expressed at a significantly lower level in the HA group are also 786 listed (Fig. 1D , "ND vs. HD Up and HD vs. HA Down").
TextSentencer_T202 29901-30068 Sentence denotes The 785 number of genes in the same pathway expressed at a significantly lower level in the HA group are also 786 listed (Fig. 1D , "ND vs. HD Up and HD vs. HA Down").
TextSentencer_T203 30069-30199 Sentence denotes The full list of over-represented KEGG 787 pathways is presented in Table S3 . hsa04622 RIG-I-like receptor signaling pathway 11 5
TextSentencer_T203 30069-30199 Sentence denotes The full list of over-represented KEGG 787 pathways is presented in Table S3 . hsa04622 RIG-I-like receptor signaling pathway 11 5
TextSentencer_T204 30200-30244 Sentence denotes hsa04514 Cell adhesion molecules (CAMs) 11 4
TextSentencer_T204 30200-30244 Sentence denotes hsa04514 Cell adhesion molecules (CAMs) 11 4
TextSentencer_T205 30245-30265 Sentence denotes All rights reserved.
TextSentencer_T205 30245-30265 Sentence denotes All rights reserved.
TextSentencer_T206 30266-30302 Sentence denotes No reuse allowed without permission.
TextSentencer_T206 30266-30302 Sentence denotes No reuse allowed without permission.
TextSentencer_T207 30303-30393 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.
TextSentencer_T207 30303-30393 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.