IP Library › Granted Patent US 12668644

Granted Patent B2

US 12668644 · App. 17/612,665 · Granted Jun 30, 2026

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

Inventors: Hannes E. Buelow (Bronx, NY); Ulrich G. Steidl (New Rochelle, NY); Steven C. Almo (Pelham, NY); Robert A. Townley (Shorewood, WI); Richard Pisczcaztowski (Rutherford, NJ); Ron Seidel, III (Bronx, NY); Sriram Sundaravel (Bronx, NY)

Assignee: Albert Einstein College of Medicine

C07K16/44 A61K47/6815 A61K47/6835 A61K49/0058 G01N33/56966 G01N2400/40

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Quick Facts

Patent No.: US 12668644
App. No.: 17/612,665
Granted: Jun 30, 2026
Kind: B2

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Abstract

This disclosure relates to compositions and methods of identifying, isolating, and modulating cells and tissues based on their cellular glycosaminoglycan pattern. In some aspects, provided are anti-GAG motif antibodies or antigen-binding fragments thereof and their use for determining a glycosaminoglycan (GAG) glycotype for a cell. Also provided are methods of isolating cells, identifying cells, detecting a disease or disorder, and/or treating a disease or disorder based on a cellular glycotype.

Claims (74)

1 . 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).

2 . The method according to claim 1 , wherein at least one of the one-three or more anti-GAG motif antibodies or antigen-binding fragments thereof comprises an affinity tag.

3 . The method according to claim 2 , the method further comprising a step of contacting the target cell bound to the one three or more anti-GAG motif antibodies or antigen binding fragments thereof with a medium that has a higher affinity for the affinity tag than the population of cells.

4 . The method according to claim 1 , wherein at least one of the three or more anti-GAG motif antibodies or antigen-binding fragments thereof is conjugated to a detectable moiety, an affinity tag, a magnetic moiety, or a combination thereof.

5 . The method according to claim 4 , wherein the detectable moiety is fluorescent.

6 . The method according to claim 1 , wherein at least one of the ene three or more anti-GAG motif antibodies or antigen-binding fragments thereof is conjugated to a Sortase motif.

7 . The method of claim 1 , wherein the three or more anti-GAG motif antibodies or antigen-binding fragments thereof are selected from the group consisting of:

8 . The method of claim 7 , wherein the three or more anti-GAG motif antibodies or antigen-binding fragments thereof are selected from the group consisting of:

(i) an anti-GAG motif antibody or antigen-binding fragment thereof comprising a heavy variable chain comprising SEQ ID NO:96 and a light variable chain comprising SEQ ID NO:97;

(ii) an anti-GAG motif antibody or antigen-binding fragment thereof comprising a heavy variable chain comprising SEQ ID NO:98 and a light variable chain comprising SEQ ID NO:97;

(iii) an anti-GAG motif antibody or antigen-binding fragment thereof comprising a heavy variable chain comprising SEQ ID NO:99 and a light variable chain comprising SEQ ID NO:97;

(iv) an anti-GAG motif antibody or antigen-binding fragment thereof comprising a heavy variable chain comprising SEQ ID NO:100 and a light variable chain comprising SEQ ID NO:97;

(v) an anti-GAG motif antibody or antigen-binding fragment thereof comprising a heavy variable chain comprising SEQ ID NO:101 and a light variable chain comprising SEQ ID NO:97;

(vi) an anti-GAG motif antibody or antigen-binding fragment thereof comprising a heavy variable chain comprising SEQ ID NO:102 and a light variable chain comprising SEQ ID NO:97;

(vii) an anti-GAG motif antibody or antigen-binding fragment thereof comprising a heavy variable chain comprising SEQ ID NO:103 and a light variable chain comprising SEQ ID NO:97;

(viii) an anti-GAG motif antibody or antigen-binding fragment thereof comprising a heavy variable chain comprising SEQ ID NO:104 and a light variable chain comprising SEQ ID NO:97;

(ix) an anti-GAG motif antibody or antigen-binding fragment thereof comprising a heavy variable chain comprising SEQ ID NO:105 and a light variable chain comprising SEQ ID NO:97;

(x) an anti-GAG motif antibody or antigen-binding fragment thereof comprising a heavy variable chain comprising SEQ ID NO:106 and a light variable chain comprising SEQ ID NO:97; and

(xi) an anti-GAG motif antibody or antigen-binding fragment thereof comprising a heavy variable chain comprising SEQ ID NO:107 and a light variable chain comprising SEQ ID NO:97.

9 . The method of claim 7 , wherein the three or more anti-GAG motif antibodies or antigen-binding fragments thereof are single chain fragments variable (scFv).

10 . The method of claim 8 , wherein the three or more anti-GAG motif antibodies or antigen-binding fragments thereof comprise a sequence selected from the group consisting of SEQ ID NOs:1, 4, 7, 17, 20, 22, 26, 27, 29, 30, or 33.