Antibody-based method to identify, purify, and manipulate cell types and processes

A method of separating a target cell from a population of cells based on the target cell's glycosaminoglycan (GAG) glycotype, the method comprising:

• (a) contacting a mixture comprising the target cell and the population of cells with three or more anti-GAG motif antibodies or antigen-binding fragments thereof that bind to three or more GAG motifs on the surface of the target cell;
• and
• (b) separating the target cell from the population of cells, wherein:
• the target cell has a GAG glycotype that is different from the GAG glycotype for the population of cells;
• each of the anti-GAG motif antibodies or antigen-binding fragments thereof comprises a heavy variable chain comprising a CDR1H, CDR2H, and CDR3H;
• each of the anti-GAG motif antibodies or antigen-binding fragments thereof comprises a light variable chain comprising a CDR1L, CDR2L, and CDR3L;
• and
• the three or more anti-GAG motif antibodies or antigen-binding fragments thereof are selected from the group consisting of:
• (i) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SYAMS (SEQ ID NO:85), a CDR2H comprising AISGSGGSTYYADSVKG (SEQ ID NO:86), a CDR3H comprising SLRMNGWRAHQ (SEQ ID NO:43), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (ii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SYAMS (SEQ ID NO:85), a CDR2H comprising AISGSGGSTYYADSVKG (SEQ ID NO:86), a CDR3H comprising SISMNGVGVRIQ (SEQ ID NO:46), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (iii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising NAWMS (SEQ ID NO:90), a CDR2H comprising RIKSKTDGGTTDYAAPVKG (SEQ ID NO:91), a CDR3H comprising SGRQARQGRFPK (SEQ ID NO:49), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (iv) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising NAWMS (SEQ ID NO:90), a CDR2H comprising RIKSKTDGGTTDYAAPVKG (SEQ ID NO:91), a CDR3H comprising LRGTKMFRH (SEQ ID NO:59), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (v) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising NAWMS (SEQ ID NO:90), a CDR2H comprising RIKSKTDGGTTDYAAPVKG (SEQ ID NO:91), a CDR3H comprising GKVKLPN (SEQ ID NO:62), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (vi) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising NAWMS (SEQ ID NO:90), a CDR2H comprising RIKSKTDGGTTDYAAPVKG (SEQ ID NO:91), a CDR3H comprising GMRPRL (SEQ ID NO:64), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (vii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising NAWMS (SEQ ID NO:90), a CDR2H comprising RIKSKTDGGTTDYAAPVKG (SEQ ID NO:91), a CDR3H comprising GRRLKD (SEQ ID NO:68), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (viii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SYEMN (SEQ ID NO:92), a CDR2H comprising YISSSGSTIYYADSVKG (SEQ ID NO:93), a CDR3H comprising GMRPRL (SEQ ID NO:64), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (ix) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising NAWMS (SEQ ID NO:90), a CDR2H comprising RIKSKTDGGTTDYAAPVKG (SEQ ID NO:91), a CDR3H comprising HAPLRNTRTNT (SEQ ID NO:71), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (x) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising NAWMS (SEQ ID NO:90), a CDR2H comprising RIKSKTDGGTTDYAAPVKG (SEQ ID NO:91), a CDR3H comprising GSRSSR (SEQ ID NO:72), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• and
• (xi) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising DYGMS (SEQ ID NO:94), a CDR2H comprising GINWNGGSTGYADSVKG (SEQ ID NO:95), a CDR3H comprising RRYALDY (SEQ ID NO:75), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising NAWMS (SEQ ID NO:90), a CDR2H comprising RIKSKTDGGTTDYAAPVKG (SEQ ID NO:91), a CDR3H comprising GKMKLNR (SEQ ID NO:44), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xiii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SNYMS (SEQ ID NO:108), a CDR2H comprising VIYSGGSTYYADSVKG (SEQ ID NO:109), a CDR3H comprising GYRPRF (SEQ ID NO:45), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xiv) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising NAWMS (SEQ ID NO:90), a CDR2H comprising RIKSKTDGGTTDYAAPVKG (SEQ ID NO:91), a CDR3H comprising GRTVGRN (SEQ ID NO:47), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89),
• (xv) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising NAWMS (SEQ ID NO:90), a CDR2H comprising RIKSKTDGGTTDYAAPVKG (SEQ ID NO:91), a CDR3H comprising DRRNTQKTRYRT (SEQ ID NO:48), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xvi) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising NAWMS (SEQ ID NO:90), a CDR2H comprising RIKSKTDGGTTDYAAPVKG (SEQ ID NO:91), a CDR3H comprising GGTTRIRK (SEQ ID NO:50), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xvii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising GYYMH (SEQ ID NO:119), a CDR2H comprising WINPNSGGTNYAQKFQG (SEQ ID NO:110), a CDR3H comprising GTKLKMTK (SEQ ID NO:51), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xviii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising NAWMS (SEQ ID NO:90), a CDR2H comprising RIKSKTDGGTTDYAAPVKG (SEQ ID NO:91), a CDR3H comprising ERNTIRR (SEQ ID NO:52), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89),
• (xix) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SYAMH (SEQ ID NO:115), a CDR2H comprising AIGTGGGTYYADSVKG (SEQ ID NO:111), a CDR3H comprising GRLHLPRK (SEQ ID NO:53), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xx) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising GYYMH (SEQ ID NO:
• 119), a CDR2H comprising WINPNSGGTNYAQKFQ (SEQ ID NO:113), a CDR3H comprising SSSRHHRLHR (SEQ ID NO:54), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xxi) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SYAMH (SEQ ID NO:115), a CDR2H comprising WINAGNGNTKYSQKFQG (SEQ ID NO:114), a CDR3H comprising QRWKPAVTPKLV (SEQ ID NO:44), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xxii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SYAMH (SEQ ID NO:115), a CDR2H comprising AIGTGGGTYYADSVKG (SEQ ID NO:111), a CDR3H comprising ARMTGHVRNVMI (SEQ ID NO:56), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xxiii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SYAMH (SEQ ID NO:115), a CDR2H comprising AIGTGGGTYYADSVKG (SEQ ID NO:111), a CDR3H comprising PVSHRKWRVTV (SEQ ID NO:57), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xxiv) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising NAWMS (SEQ ID NO:90), a CDR2H comprising RIKSKTDGGTTDYAAPVKG (SEQ ID NO:91), a CDR3H comprising GRRHKLIR (SEQ ID NO:58), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xxv) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising DYYMH (SEQ ID NO:
• 118), a CDR2H comprising LVDPEDGETIYAEKFQG (SEQ ID NO:
• 112), a CDR3H comprising SRKTPKPFMRK (SEQ ID NO:60), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xxvi) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SNYMS (SEQ ID NO:108), a CDR2H comprising VIYSGGSTYYADSVKG (SEQ ID NO:109), a CDR3H comprising GARLKR (SEQ ID NO:61), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xxvii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SYAMH (SEQ ID NO:115), a CDR2H comprising AIGTGGGTYYADSVKG (SEQ ID NO:111), a CDR3H comprising GTKKLGK (SEQ ID NO:63), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xxviii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising DYYMH (SEQ ID NO:118), a CDR2H comprising LVDPEDGETIYAEKFQG (SEQ ID NO:112), a CDR3H comprising SRKTRKPFMRK (SEQ ID NO:65), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:892;
• (xxix) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising GYYMH (SEQ ID NO:119), a CDR2H comprising WINPNSGGTNYAQKFQG (SEQ ID NO:110), a CDR3H comprising YYHYKVN (SEQ ID NO:66), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xxx) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SGGYYWS (SEQ ID NO:120), a CDR2H comprising YIYYSGSTYYNPSLKS (SEQ ID NO:116), a CDR3H comprising WVTEP (SEQ ID NO:67), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xxxi) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SNYMS (SEQ ID NO:108), a CDR2H comprising VIYSGGSTYYADSVKG (SEQ ID NO:109), a CDR3H comprising SLRMNGCGAHQ (SEQ ID NO:70), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xxxii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SYAMS (SEQ ID NO:85), a CDR2H comprising AISGSGGSTYYADSVKG (SEQ ID NO:86), a CDR3H comprising QKKRPRF (SEQ ID NO:73), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89),
• (xxxiii) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SYWMH (SEQ ID NO:117), a CDR2H comprising RINSDGSSTTYADSVKG (SEQ ID NO:124), a CDR3H comprising SGRKGRMR (SEQ ID NO:74), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xxxiv) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SYYMH (SEQ ID NO:121), a CDR2H comprising IINPSGGSTSYAQKFQG (SEQ ID NO:122), a CDR3H comprising AMTQKKPRKLSL (SEQ ID NO:77), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• (xxxv) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising YRYLH (SEQ ID NO:125), a CDR2H comprising WITPFNGNTNYAQKFQD (SEQ ID NO:123), a CDR3H comprising SGRKYFRARDMN (SEQ ID NO:78), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89);
• and
• (xxxvi) an anti-GAG antibody or antigen-binding fragment thereof comprising a CDR1H comprising SYWMH (SEQ ID NO:117), a CDR2H comprising RINSDGSSTTYADSVKG (SEQ ID NO:124), a CDR3H comprising LKQQGIS (SEQ ID NO:76), a CDR1L comprising QGDSLRSYYAS (SEQ ID NO:87), a CDR2L comprising GKNNRPS (SEQ ID NO:88), and a CDR3L comprising NSRDSSGNHVV (SEQ ID NO:89).