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PMC:7228307 / 46019-47486 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T2 118-124 https://glytoucan.org/Structures/Glycans/G82576YO denotes fucose
T3 154-160 https://glytoucan.org/Structures/Glycans/G82576YO denotes fucose
T4 1277-1283 https://glytoucan.org/Structures/Glycans/G82576YO denotes fucose

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
863 23-29 Chemical denotes glycan MESH:D011134
879 208-216 Gene denotes FcγRIIIa Gene:2214
880 221-229 Gene denotes FcγRIIIb Gene:2215
881 302-309 Gene denotes FcγRIIb Gene:2213
882 407-415 Gene denotes FcγRIIIa Gene:2214
883 512-516 Gene denotes HER2 Gene:2064
884 523-527 Gene denotes EGFR Gene:1956
885 669-676 Gene denotes FcγRIII Gene:2214
886 780-787 Gene denotes FcγRIII Gene:2214
887 924-932 Gene denotes FcγRIIIa Gene:2214
888 978-985 Gene denotes FcγRIIa Gene:2212
889 908-916 Gene denotes FcγRIIIb Gene:2215
890 50-65 Chemical denotes N‐linked glycan
891 118-124 Chemical denotes fucose MESH:D005643
892 154-160 Chemical denotes fucose MESH:D005643
893 478-483 Disease denotes tumor MESH:D009369
900 1247-1255 Species denotes patients Tax:9606
901 1128-1140 Chemical denotes obinutuzumab MESH:C543332
902 1277-1283 Chemical denotes fucose MESH:D005643
903 1295-1304 Chemical denotes rituximab MESH:D000069283
904 1378-1384 Chemical denotes glycan MESH:D011134
905 1218-1246 Disease denotes chronic lymphocytic leukemia MESH:D015451

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T376 118-124 Body_part denotes fucose http://purl.org/sig/ont/fma/fma82790
T377 128-138 Body_part denotes Antibodies http://purl.org/sig/ont/fma/fma62871
T378 154-160 Body_part denotes fucose http://purl.org/sig/ont/fma/fma82790
T379 832-839 Body_part denotes NK cell http://purl.org/sig/ont/fma/fma63147
T380 835-839 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T381 867-877 Body_part denotes neutrophil http://purl.org/sig/ont/fma/fma62860
T382 953-963 Body_part denotes neutrophil http://purl.org/sig/ont/fma/fma62860
T383 1226-1237 Body_part denotes lymphocytic http://purl.org/sig/ont/fma/fma62863
T384 1277-1283 Body_part denotes fucose http://purl.org/sig/ont/fma/fma82790

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T79 478-483 Disease denotes tumor http://purl.obolibrary.org/obo/MONDO_0005070
T80 849-853 Disease denotes ADCC http://purl.obolibrary.org/obo/MONDO_0008734
T81 1218-1246 Disease denotes chronic lymphocytic leukemia http://purl.obolibrary.org/obo/MONDO_0004948
T82 1226-1246 Disease denotes lymphocytic leukemia http://purl.obolibrary.org/obo/MONDO_0005402
T83 1238-1246 Disease denotes leukemia http://purl.obolibrary.org/obo/MONDO_0005059

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T802 20-22 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T803 111-112 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T804 208-210 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T805 221-223 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T806 302-304 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T807 407-409 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T808 615-616 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T809 669-671 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T810 780-782 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T811 832-839 http://purl.obolibrary.org/obo/CL_0000623 denotes NK cell
T812 908-910 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T813 924-926 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T814 978-980 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T815 1417-1419 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T235 118-124 Chemical denotes fucose http://purl.obolibrary.org/obo/CHEBI_33984
T236 154-160 Chemical denotes fucose http://purl.obolibrary.org/obo/CHEBI_33984
T237 796-804 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T238 1277-1283 Chemical denotes fucose http://purl.obolibrary.org/obo/CHEBI_33984
T239 1295-1304 Chemical denotes rituximab http://purl.obolibrary.org/obo/CHEBI_64357

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T221 835-839 http://purl.obolibrary.org/obo/CL_0000000 denotes cell
T222 964-973 http://purl.obolibrary.org/obo/BFO_0000034 denotes functions

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T48 118-124 Chemical denotes fucose http://purl.obolibrary.org/obo/CHEBI_33984
T49 154-160 Chemical denotes fucose http://purl.obolibrary.org/obo/CHEBI_33984
T50 1277-1283 Chemical denotes fucose http://purl.obolibrary.org/obo/CHEBI_33984

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
863 23-29 Chemical denotes glycan MESH:D011134
879 208-216 Gene denotes FcγRIIIa Gene:2214
880 221-229 Gene denotes FcγRIIIb Gene:2215
881 302-309 Gene denotes FcγRIIb Gene:2213
882 407-415 Gene denotes FcγRIIIa Gene:2214
883 512-516 Gene denotes HER2 Gene:2064
884 523-527 Gene denotes EGFR Gene:1956
885 669-676 Gene denotes FcγRIII Gene:2214
886 780-787 Gene denotes FcγRIII Gene:2214
887 924-932 Gene denotes FcγRIIIa Gene:2214
888 978-985 Gene denotes FcγRIIa Gene:2212
889 908-916 Gene denotes FcγRIIIb Gene:2215
890 50-65 Chemical denotes N‐linked glycan
891 118-124 Chemical denotes fucose MESH:D005643
892 154-160 Chemical denotes fucose MESH:D005643
893 478-483 Disease denotes tumor MESH:D009369
900 1247-1255 Species denotes patients Tax:9606
901 1128-1140 Chemical denotes obinutuzumab MESH:C543332
902 1277-1283 Chemical denotes fucose MESH:D005643
903 1295-1304 Chemical denotes rituximab MESH:D000069283
904 1378-1384 Chemical denotes glycan MESH:D011134
905 1218-1246 Disease denotes chronic lymphocytic leukemia MESH:D015451

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T268 0-29 Sentence denotes Modification of the Fc glycan
T269 30-310 Sentence denotes The typical complex N‐linked glycan attached to N297 of the heavy chain includes a core fucose.85 Antibodies that lack this fucose have approximately 50‐fold improved binding to FcγRIIIa and FcγRIIIb and importantly retain the weak, low‐affinity binding to the inhibitory FcγRIIb.
T270 311-685 Sentence denotes Furthermore, this glycoengineering increased binding affinity of the modified IgG1 mAb for both FcγRIIIa V158 and F158 allelotypes.86, 87, 88 Afucosyl versions of the tumor targeting mAbs such as anti‐HER2, anti‐EGFR and anti‐CD20 had greater antitumor effects and increased survival,68, 88, 89 which is a reflection of the greatly increased, and selective, FcγRIII binding.
T271 686-1011 Sentence denotes Compared with their unmodified counterparts, the afucosyl mAbs showed dramatic improvement of FcγRIII‐related effector responses such as stronger NK cell‐mediated ADCC, or enhanced neutrophil‐mediated phagocytosis through FcγRIIIb and/or FcγRIIIa.23 However, certain neutrophil functions via FcγRIIa may be compromised.90, 91
T272 1012-1116 Sentence denotes There are six afucosylated antibodies in late‐stage clinical trials or approved for treatment (Table 4).
T273 1117-1467 Sentence denotes Notable is obinutuzumab, an afucosyl anti‐CD20 mAb which nearly doubles progression‐free survival in chronic lymphocytic leukemia patients as compared with the fucose‐containing rituximab.68 This dramatic improvement in clinical utility reinforces the value of glycan engineering specifically and of Fc engineering generally in anticancer treatments.

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T582 537-541 Protein denotes CD20 https://www.uniprot.org/uniprot/Q3C2E2|https://www.uniprot.org/uniprot/Q13963|https://www.uniprot.org/uniprot/P19437|https://www.uniprot.org/uniprot/P11836|https://www.uniprot.org/uniprot/P08984|https://www.uniprot.org/uniprot/B4DT24|https://www.uniprot.org/uniprot/A6NMS4
T589 1159-1163 Protein denotes CD20 https://www.uniprot.org/uniprot/Q3C2E2|https://www.uniprot.org/uniprot/Q13963|https://www.uniprot.org/uniprot/P19437|https://www.uniprot.org/uniprot/P11836|https://www.uniprot.org/uniprot/P08984|https://www.uniprot.org/uniprot/B4DT24|https://www.uniprot.org/uniprot/A6NMS4

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T375 118-124 Body_part denotes fucose http://purl.org/sig/ont/fma/fma82790
T376 128-138 Body_part denotes Antibodies http://purl.org/sig/ont/fma/fma62871
T377 154-160 Body_part denotes fucose http://purl.org/sig/ont/fma/fma82790
T378 832-839 Body_part denotes NK cell http://purl.org/sig/ont/fma/fma63147
T379 835-839 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T380 867-877 Body_part denotes neutrophil http://purl.org/sig/ont/fma/fma62860
T381 953-963 Body_part denotes neutrophil http://purl.org/sig/ont/fma/fma62860
T382 1226-1237 Body_part denotes lymphocytic http://purl.org/sig/ont/fma/fma62863
T383 1277-1283 Body_part denotes fucose http://purl.org/sig/ont/fma/fma82790

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T107 523-527 http://purl.obolibrary.org/obo/GO_0005006 denotes EGFR
T108 849-853 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T109 887-899 http://purl.obolibrary.org/obo/GO_0006909 denotes phagocytosis

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T35 478-483 Disease denotes tumor http://purl.obolibrary.org/obo/MONDO_0005070
T36 1218-1246 Disease denotes chronic lymphocytic leukemia http://purl.obolibrary.org/obo/MONDO_0004948

LitCovid-sample-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T31 478-483 Phenotype denotes tumor http://purl.obolibrary.org/obo/HP_0002664
T32 1218-1246 Phenotype denotes chronic lymphocytic leukemia http://purl.obolibrary.org/obo/HP_0005550

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T107 523-527 http://purl.obolibrary.org/obo/GO_0005006 denotes EGFR
T108 849-853 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T109 887-899 http://purl.obolibrary.org/obo/GO_0006909 denotes phagocytosis

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T107 523-527 http://purl.obolibrary.org/obo/GO_0005006 denotes EGFR
T108 849-853 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T109 887-899 http://purl.obolibrary.org/obo/GO_0006909 denotes phagocytosis

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T268 0-29 Sentence denotes Modification of the Fc glycan
T269 30-310 Sentence denotes The typical complex N‐linked glycan attached to N297 of the heavy chain includes a core fucose.85 Antibodies that lack this fucose have approximately 50‐fold improved binding to FcγRIIIa and FcγRIIIb and importantly retain the weak, low‐affinity binding to the inhibitory FcγRIIb.
T270 311-685 Sentence denotes Furthermore, this glycoengineering increased binding affinity of the modified IgG1 mAb for both FcγRIIIa V158 and F158 allelotypes.86, 87, 88 Afucosyl versions of the tumor targeting mAbs such as anti‐HER2, anti‐EGFR and anti‐CD20 had greater antitumor effects and increased survival,68, 88, 89 which is a reflection of the greatly increased, and selective, FcγRIII binding.
T271 686-1011 Sentence denotes Compared with their unmodified counterparts, the afucosyl mAbs showed dramatic improvement of FcγRIII‐related effector responses such as stronger NK cell‐mediated ADCC, or enhanced neutrophil‐mediated phagocytosis through FcγRIIIb and/or FcγRIIIa.23 However, certain neutrophil functions via FcγRIIa may be compromised.90, 91
T272 1012-1116 Sentence denotes There are six afucosylated antibodies in late‐stage clinical trials or approved for treatment (Table 4).
T273 1117-1467 Sentence denotes Notable is obinutuzumab, an afucosyl anti‐CD20 mAb which nearly doubles progression‐free survival in chronic lymphocytic leukemia patients as compared with the fucose‐containing rituximab.68 This dramatic improvement in clinical utility reinforces the value of glycan engineering specifically and of Fc engineering generally in anticancer treatments.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T31 478-483 Phenotype denotes tumor http://purl.obolibrary.org/obo/HP_0002664
T32 1218-1246 Phenotype denotes chronic lymphocytic leukemia http://purl.obolibrary.org/obo/HP_0005550