IP Library › Granted Patent US 12,461,007
Granted Patent B2
US 12,461,007 · App. 18/817,528 · Granted Nov 4, 2025

CD34 stem cell mimics

Inventors: Jeffrey Kim (Berkeley, CA); Anh Tuan Nguyen (San Francisco, CA); Subhanip Biswas (Emeryville, CA); Kanwal Palla (Oakland, CA)
Assignee: Slingshot Biosciences, Inc.
G01N15/1012G01N33/582G01N2015/1014G01N2333/70589G01N2333/70596
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Quick Facts
Patent No.
US 12,461,007
App. No.
18/817,528
Filed
Aug 28, 2024
Granted
Nov 4, 2025
Kind
B2
Art Unit
1634
USPC
435/29
Abstract

Hydrogel beads with quantifiable attached biomolecules and their use as cell mimics in cytometric applications are described. The cell mimics described herein are selectively tunable to have at least one optical property substantially similar to the at least one optical property of a target cell (e.g., CD34+ stem cell). The disclosure further relates to methods of using the disclosed cell mimics as enrichment controls in cytometric applications.

Claims (56)

1 . A composition comprising a first population of hydrogel beads comprising:

a) a polymerized monomer and a bifunctional monomer; and

b) a cell surface biomarker profile comprising:

i) a CD34 extracellular domain and a CD45 extracellular domain,

wherein the CD34 extracellular domain comprises a sequence comprising at least 90% identity with SEQ ID NO: 1, and the CD45 extracellular domain comprises a sequence comprising at least 90% identity with SEQ ID NO: 10.

2 . The composition of claim 1 , comprising a second population of hydrogel beads comprising:

c) a polymerized monomer and a bifunctional monomer; and

d) a cell surface biomarker profile comprising:

i) the CD45 extracellular domain, but lacking the CD34 extracellular domain.

3 . The composition of claim 1 , comprising a second population of hydrogel beads comprising:

c) a polymerized monomer and a bifunctional monomer; and

d) a cell surface biomarker profile comprising:

i) the CD45 extracellular domain,

wherein the second population of hydrogel beads comprises no more than 10% of a median number of the CD34 extracellular domain comprised in the first population of hydrogel beads.

4 . The composition of claim 3 , wherein the second population of hydrogel beads comprises no more than 1% of the median number of the CD34 extracellular domain comprised in the first population of hydrogel beads.

5 . The composition of claim 3 , wherein the second population hydrogel beads comprises (i) between about 10% and about 400% of an amount of the CD45 extracellular domain present on the cell surface of a target cell, and (ii) no more than 10% of an amount of the CD34 extracellular domain present on the cell surface of the target cell.

6 . The composition of claim 3 , wherein the first population of hydrogel beads or second population of hydrogel beads has a mean bead diameter of between about 1 μm and about 40 μm.

7 . The composition of claim 3 , wherein an active portion of the composition comprises or consists of the first and second population of hydrogel beads.

8 . The composition of claim 3 :

wherein a number of hydrogel beads of the first population of hydrogel beads is between 1-3% of a total number of hydrogel beads in the composition; and

wherein a number of hydrogel beads of the second population of hydrogel beads is between 97-99% of the total number of hydrogel beads in the composition.

9 . A kit comprising:

a first container, comprising a first composition comprising:

a) a first population of hydrogel beads, comprising:

i) a polymerized monomer and a bifunctional monomer; and

ii) a cell surface biomarker profile comprising a CD34 extracellular domain and a CD45 extracellular domain, wherein the CD34 extracellular domain comprises a sequence comprising at least 90% identity with SEQ ID NO: 1,and the CD45 extracellular domain comprises a sequence comprising at least 90% identity with SEQ ID NO: 10;

b) a second population of hydrogel beads comprising:

i) a polymerized monomer and a bifunctional monomer; and

ii) a cell surface biomarker profile comprising the CD45 extracellular domain,

wherein the second population of hydrogel beads comprises no more than 10% of a median number of the CD34 extracellular domain comprised in the first population of hydrogel beads, wherein a number of hydrogel beads of the first population of hydrogel beads in the first composition is between 1-3% of a total number of hydrogel beads in the first composition; and a number of hydrogel beads of the second population of hydrogel beads in the first composition is between 97-99% of the total number of hydrogel beads in the first composition; and

a second container, comprising a second composition, comprising the first population of hydrogel beads and the second population of hydrogel beads, wherein a number of hydrogel beads of the first population of hydrogel beads in the second composition is between 80-95% of a total number of hydrogel beads in the second composition, and wherein a number of hydrogel beads of the second population of hydrogel beads in the second composition is between 5-20% of the total number of hydrogel beads in the second composition.

10 . The kit of claim 9 , wherein the first container comprises about 5×10 5 to about 2×10 6 beads and the second container comprises about 1×10 5 to about 4×10 5 beads.

11 . The composition of claim 3 :

wherein the first population comprises between 80-95% of a number of hydrogel beads in an active portion of the composition; and

wherein the second population comprises between 5-20% of the number of hydrogel beads in the active portion of the composition.

12 . The composition of claim 3 , wherein the ratio of a number of hydrogel beads of the first population of hydrogel beads to a number of hydrogel beads of the second population of hydrogel beads is between about 0.0183 and about 0.0142.

13 . The composition of claim 3 , wherein the ratio of a number of hydrogel beads of the first population of hydrogel beads to a number of hydrogel beads of the second population of hydrogel beads is between about 9 and about 19.

14 . The composition of claim 1 , wherein the first population of hydrogel beads comprises (i) between about 10% and about 400% of an amount of the CD45 extracellular domain present on the cell surface of a target cell, and (ii) between about 10% and about 400% of an amount of the CD34 extracellular domain present on the cell surface of the target cell.

15 . The composition of claim 14 , wherein the amount of the CD34 extracellular domain or the CD45 extracellular domain present on the cell surface of the target cell is a median amount of the CD34 extracellular domain or the CD45 extracellular domain present on cell surface of cells in a leukopack enriched in CD34+ cells using regimen H treatment.

16 . The composition of claim 14 , wherein the target cell is a CD45dim-positive (CD45dim+) and CD34-positive (CD34+) stem cell.

17 . The composition of claim 14 , wherein the amount of the CD45 extracellular domain or the CD34 extracellular domain present in the hydrogel beads or on the cell surface is measured based on a fluorescence intensity using flow cytometry.

18 . The composition of claim 17 , wherein the fluorescence intensity of the CD45 extracellular domain is measured using a fluorophore labeled CD45-specific binding molecule, or wherein the fluorescence intensity of the CD34 extracellular domain is measured using a fluorophore labeled CD34-specific binding molecule, wherein the fluorophore labeled CD45-specific binding molecule or the fluorophore labeled CD34-specific binding molecule comprises a monoclonal antibody or antigen binding fragment thereof.

19 . The composition of claim 18 , wherein the fluorophore labeled CD34-specific binding molecule is selected from: a phycoerythrin (PE) labeled anti-CD34 antibody clone 8G12, a phycoerythrin (PE) labeled anti-CD34 antibody clone AC136, an allophycocyanin (APC) labeled anti-CD34 antibody clone 4H11, and a BV421 labeled anti-CD34 antibody clone 581, and wherein the CD45-specific binding molecule is selected from: a fluorescein isothiocyanate (FITC) labeled anti-CD45 antibody clone 2D1, a PerCP-Cy5.5 labeled anti-CD45 antibody clone 2D1, a phycoerythrin (PE) labeled anti-CD45 antibody clone MEM-28, and a V500 labeled anti-CD45 antibody clone HI30.

20 . The composition of claim 19 , wherein the combination of the CD34-specific binding molecule and the CD45-specific binding molecule are selected from:

(a) the fluorophore labeled CD34-specific binding molecule is anti-CD34-PE clone 8G12 and the fluorophore labeled CD45-specific binding molecule is anti-CD45-FITC clone 2D1;

(b) the fluorophore labeled CD34-specific binding molecule is anti-CD34-PE clone AC136 and the fluorophore labeled CD45-specific binding molecule is anti-CD45-PerCPCy5.5 clone 2D1;

(c) the fluorophore labeled CD34-specific binding molecule is anti-CD34-APC clone 4H11 and the fluorophore labeled CD45-specific binding molecule is anti-CD45-PE clone MEM-28; or

(d) the fluorophore labeled CD34-specific binding molecule is anti-CD34-BV421 clone 581 and the fluorophore labeled CD45-specific binding molecule is anti-CD45-V500 clone HI30.

21 . The composition of claim 1 , wherein one or more biomarkers of the cell surface biomarker proile are covalently attached to a matrix of a hydrogel bead of the first population of hydrogel beads.

22 . The composition of claim 1 , wherein the CD34 extracellular domain and the CD45 extracellular domain each comprises a different fluorophore.

23 . The composition of claim 1 , wherein the first population of hydrogel beads exhibits at least one optical property that is substantially similar to a corresponding optical property of a target cell, wherein the at least one optical property comprises side scatter or forward scatter, and wherein the target cell is a hematopoietic stem cell or a lymphocyte cell.

24 . A method of calibrating a cytometer for detection of a CD34-expressing or CD45-expressing cell in a population of cells, comprising sampling the composition of claim 3 , and calibrating the cytometer based on at least one optical property of the hydrogel beads of the composition.

25 . The method of claim 24 , further comprising sampling the population of cells and obtaining a cell comprising the at least one optical property, wherein the at least one optical property comprises median fluorescence intensity (MFI) of CD45, MFI of CD34, or a combination thereof.

26 . The method of claim 24 , wherein the method comprises forming a gating scheme based on the at least one optical property, wherein the at least one optical property comprises median fluorescence intensity (MFI) of CD45, MFI of CD34, or a combination thereof.

27 . The method of claim 24 , wherein the CD34-expressing cell expresses a diminished amount of CD45.

28 . A method of enriching a population of CD34-expressing cells, comprising sampling the composition of claim 3 and forming a gating scheme based on at least one optical property of the hydrogel beads of the composition, and selecting the population of CD34-expressing cells in a population of cells based on the gating scheme, wherein the at least one optical property comprises median fluorescence intensity (MFI) of CD45, MFI of CD34, or a combination thereof.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Sep 27, 2024
From: KIM, JEFFREY; NGUYEN, ANH TUAN; BISWAS, SUBHANIP; PALLA, KANWAL
To: SLINGSHOT BIOSCIENCES, INC.
Reel/Frame 068725/0914 →
Continuity (2)
Provisional Application 63535233 · Aug 29, 2023
Related Publication 20250076175A1 · Mar 6, 2025
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