Platform for discovery and analysis of therapeutic agents

Patent metadata

Field	Value
Publication number	US-12559864-B2
Application number	US-202519028468-A
Country	US
Kind code	B2
Filing date	Jan 17, 2025
Priority date	May 11, 2015
Publication date	Feb 24, 2026
Grant date	Feb 24, 2026

Abstract

A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.

First claim

What is claimed is:

1 . A method of characterizing a plurality of cells, comprising:
(a) contacting a substrate with a plurality of cells to form an array of cells, wherein the substrate is a component of a flow cell; (b) contacting the array of cells with one or more reporter molecules; (c) detecting the one or more reporter molecules using a nucleic acid sequencing device comprising imaging optics; (d) identifying a phenotypic cellular characteristic of a cell within the array of cells based on the detecting of the one or more reporter molecules, wherein the phenotypic cellular characteristic is an optically detectable characteristic; (e) synthesizing at least one nucleic acid complementary to one or more nucleic acid tags associated with the cell within the array of cells, wherein the synthesizing comprises a plurality of cycles in which one or more types of nucleotides contact the one or more nucleic acid tags; (f) detecting, over the plurality of cycles, the one or more types of nucleotides contacting the one or more nucleic acid tags using the imaging optics of the nucleic acid sequencing device; (g) determining a nucleic acid sequence of the one or more nucleic acid tags based on the detecting of the one or more types of nucleotides; and (h) characterizing the cell within the array of cells based on the phenotypic cellular characteristic and the nucleic acid sequence of the one or more nucleic acid tags, wherein the characterizing comprises determining a cellular behavior.

2 . The method of claim 1 , wherein the plurality of cells are selected from the group consisting of natural cells isolated from a multicellular organism, natural cells that comprise single cell organisms, genetically engineered cells, and cultured cells.

3 . The method of claim 2 , wherein the plurality of cells are stem cells or immune cells.

4 . The method of claim 1 , wherein the plurality of cells are live cells.

5 . The method of claim 4 , further comprising culturing the plurality of cells on the substrate.

6 . The method of claim 1 , wherein detecting the one or more reporter molecules comprises detecting a luminescent signal.

7 . The method of claim 6 , wherein the one or more reporter molecules interact with the cell within the array of cells by attachment to a plasma membrane lipid, a fatty acid, or a protein on a cell surface.

8 . The method of claim 1 , wherein step (a) further comprises spatially resolving the array of cells on the substrate.

9 . The method of claim 1 , wherein the array of cells are arranged on the substrate in a grid.

10 . The method of claim 1 , wherein the array of cells are arranged on the substrate in an irregular pattern.

11 . The method of claim 10 , wherein the array of cells are arranged on the substrate in a non-repeating pattern.

12 . The method of claim 1 , wherein the one or more nucleic acid tags comprises an antibody or a nucleic acid having specific binding affinity for a cellular component.

13 . The method of claim 12 , wherein the one or more nucleic acid tags is attached to the cell of the array of cells by interacting with a protein or component in a plasma membrane lipid of the cell.

14 . The method of claim 1 , wherein the one or more nucleic acid tags comprises a universal primer binding sequence capable of being sequenced.

15 . The method of claim 1 , wherein the method comprises:
(i) acquiring optical signals emitted from the one or more reporter molecules at several time points; (ii) acquiring sequencing information of the one or more nucleic acid tags at several time points; or (iii) both (i) and (ii), wherein a change in the optical signals or the sequencing information is detected over time.

16 . The method of claim 1 , further comprising amplifying the one or more nucleic acid tags to produce amplicons of the one or more nucleic acid tags.

17 . The method of claim 16 , wherein synthesizing the at least one nucleic acid complementary to the one or more nucleic acid tags comprises synthesizing nucleic acids complementary to the amplicons of the one or more nucleic acid tags.

18 . The method of claim 17 , further comprising attaching the amplicons of the one or more nucleic acid tags to the substrate prior to sequencing.

19 . The method of claim 18 , wherein the amplicons of the one or more nucleic acid tags can be spatially resolved during sequencing on the substrate.

20 . The method of claim 1 , wherein the detecting of the one or more types of nucleotides comprises detecting optical signals indicative of the one or more types of nucleotides.

21 . The method of claim 1 , wherein the method further comprises contacting the array of cells with a stimulus.

22 . The method of claim 21 , wherein the array of cells are characterized before and after contacting the cells with the stimulus.

23 . The method of claim 22 , wherein the method comprises:
(i) acquiring optical signals emitted from the one or more reporter molecules at one or more time points before and one or more time points after contacting the array of cells with the stimulus; and (ii) comparing the optical signal acquired at the one or more time points before contacting the array of cells with the stimulus to the optical signal acquired at the one or more time points after the array of cells is contacted with the stimulus.

24 . The method of claim 1 , wherein the detecting of step (f) is by sequencing by synthesis.

Assignees

• Illumina Inc

Inventors

• He Molly
• Previte Michael
• Golynskiy Misha
• Kellinger Matthew William
• Peisajovich Sergio
• Boutell Jonathan Mark

Classifications

• C12N15/1068

  Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis · CPC title

• C12N15/1075

  by coupling phenotype to genotype, not provided for in other groups of this subclass · CPC title

• C12N15/1065

  Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags · CPC title

• C12N15/1062

  mRNA-Display, e.g. polypeptide and encoding template are connected covalently · CPC title

• B01J2219/00743

  Cells · CPC title