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US 2026/0286447 A1Published application
Screening for host-microbe interactions
AssigneeKanvas Biosciences, Inc.
InventorsPhilip S. Burnham, Matthew Cheng, Hao Shi, Prateek Sehgal, Gaetano Scuderi
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Abstract
Described herein are methods for screening potential live biotherapeutic products. In some embodiments, the method includes (i) providing a sample, a pathogen, at least one microbial strain, and at least one set of probes; (ii) performing an imaging assay; and (iii) quantifying the association between the at least one microbial strain and the sample as compared to the association between the pathogen and the sample, thereby determining the therapeutic potential of the at least one microbial strain to treat or prevent a disease caused by the pathogen.
Claims21
A screening method, comprising:
- (i) providing:
- (a) a sample;
- (b) a pathogen;
- (c) at least one microbial strain, and
- (d) at least one set of probes, wherein the at least one set of probes comprises at least one encoding probe and at least one emissive readout probe;
- (ii) performing an imaging assay, wherein the imagining assay comprises:
- (A) contacting the (a) sample with the (b) pathogen and the (c) at least one microbial strain to produce a first complex;
- (B) contacting the at least one encoding probe with the first complex to form a second complex, wherein the at least one encoding probe comprises a targeting sequence and a landing pad sequence,
- (C) contacting the at least one emissive readout probe with the second complex, wherein the at least one emissive readout probe comprises a label and a sequence complementary to the landing pad sequence;
- (D) acquiring one or more emission spectra from the at least one emissive readout probe;
- (E) repeating the aforementioned steps for at least one different encoding probe;
- (F.1) determining the spectra of “signal” and assigning them to a species of the at least one microbial strain;
- (F.2) determining the spectra of “signal” and assigning them to a species of the pathogen;
- (G) decoding the spectra into a single, targeted transcript through means of signal deconvolution, error correction, comparison to reference standards;
- and
- (iii) quantifying the association between the at least one microbial strain and the sample as compared to the association between the pathogen and the sample, thereby determining the therapeutic potential of the at least one microbial strain to treat or prevent a disease caused by the pathogen.
13 more elements
A screening method comprising:
- (i) providing:
- (a) a sample;
- (b) a pathogen;
- (c) at least one microbial strain, and
- (d) at least one set of probes, wherein the at least one set of probes comprises at least one encoding probe and at least one emissive readout probe;
- (ii) performing an imaging assay, wherein the imagining assay comprises:
- (A) contacting the (a) sample with the (b) pathogen and the (c) at least one microbial strain to produce a first complex;
- (B) contacting the at least one encoding probe with the first complex to form a second complex, wherein the at least one encoding probe comprises a targeting sequence and a landing pad sequence,
- (C) contacting the at least one emissive readout probe with the second complex, wherein the at least one emissive readout probe comprises a label and a sequence complementary to the landing pad sequence;
- (D) acquiring one or more emission spectra from the at least one emissive readout probe;
- (E) repeating the aforementioned steps for at least one different encoding probe;
- (F.1) determining the spectra of “signal” and assigning them to a species of the at least one microbial strain;
- (F.2) determining the spectra of “signal” and assigning them to a species of the pathogen;
- (G) decoding the spectra into a single, targeted transcript through means of signal deconvolution, error correction, comparison to reference standards;
- and
- (iii) quantifying the association between the at least one microbial strain and the sample as compared to the association between the pathogen and the sample, thereby determining the potential of the at least one microbial strain to be a live biotherapeutic product (LBP).
13 more elements
A library of constructs, each construct comprising:
- (a) a target cell;
- (b) a first plurality of encoding and readout probes, wherein each encoding probe comprises a targeting sequence that is a region of interest on a nucleotide of a pathogen and a landing pad sequence;
- and each readout probe comprises a label and a sequence complementary to the landing pad sequence;
- and
- (c) a second plurality of encoding and readout probes, wherein each encoding probe comprises a targeting sequence that is a region of interest on a nucleotide of a microbial strain and a landing pad sequence;
- and each readout probe comprises a label and a sequence complementary to the landing pad sequence.
3 more elements
A library of constructs, each construct comprising:
- (a) a target cell;
- (b) a first plurality of encoding and readout probes, wherein each encoding probe comprises a targeting sequence that is a region of interest on a nucleotide of a pathogen and a landing pad sequence;
- and each readout probe comprises a label and a sequence complementary to the landing pad sequence;
- and
- (c) a second plurality of encoding and readout probes, wherein each encoding probe comprises a targeting sequence that is a region of interest on a nucleotide of a bacterial strain and a landing pad sequence;
- and each readout probe comprises a label and a sequence complementary to the landing pad sequence.
3 more elements
A method for determining the spatial location of a complex, comprising:
- (i) providing:
- (a) a target cell;
- (b) a pathogen;
- (c) at least one microbial strain, and
- (d) at least one set of probes, wherein the at least one set of probes comprises at least one encoding probe and at least one emissive readout probe;
- (ii) performing an imaging assay, wherein the imagining assay comprises:
- (A) contacting the (a) target cell with the (b) pathogen and the (c) at least one microbial strain to produce a first complex;
- (B) contacting the at least one encoding probe with the first complex to form a second complex, wherein the at least one encoding probe comprises a targeting sequence and a landing pad sequence,
- (C) contacting the at least one emissive readout probe with the second complex, wherein the at least one emissive readout probe comprises a label and a sequence complementary to the landing pad sequence;
- (D) acquiring one or more emission spectra from the at least one emissive readout probe;
- (E) repeating the aforementioned steps for at least one different encoding probe;
- (F.1) determining the spectra of “signal” and assigning them to a species of the at least one microbial strain;
- (F.2) determining the spectra of “signal” and assigning them to a species of the pathogen;
- (G) decoding the spectra into a single, targeted transcript through means of signal deconvolution, error correction, comparison to reference standards;
- (H) performing a second assay to image the target cell;
- and
- (iii) quantify the abundance of the at least one microbial strain to the target cell and/or the association between the pathogen to the target cell, thereby determining the spatial location of the complex,
- wherein the complex is a target cell-microbial strain complex or a target cell-pathogen complex.
15 more elements
A method for determining the spatial location of a complex, comprising:
- (i) providing:
- (a) a target cell;
- (b) a pathogen;
- (c) at least one bacterial strain, and
- (d) at least one set of probes, wherein the at least one set of probes comprises at least one encoding probe and at least one emissive readout probe;
- (ii) performing an imaging assay, wherein the imagining assay comprises:
- (A) contacting the (a) target cell with the (b) pathogen and the (c) at least one bacterial strain to produce a first complex;
- (B) contacting the at least one encoding probe with the first complex to form a second complex, wherein the at least one encoding probe comprises a targeting sequence and a landing pad sequence,
- (C) contacting the at least one emissive readout probe with the second complex, wherein the at least one emissive readout probe comprises a label and a sequence complementary to the landing pad sequence;
- (D) acquiring one or more emission spectra from the at least one emissive readout probe;
- (E) repeating the aforementioned steps for at least one different encoding probe;
- (F.1) determining the spectra of “signal” and assigning them to a species of the at least one bacterial strain;
- (F.2) determining the spectra of “signal” and assigning them to a species of the pathogen;
- (G) decoding the spectra into a single, targeted transcript through means of signal deconvolution, error correction, comparison to reference standards;
- (H) performing a second assay to image the target cell;
- and
- (iii) quantify the abundance of the at least one bacterial strain to the target cell and/or the association between the pathogen to the target cell, thereby determining the spatial location of the complex,
- wherein the complex is a target cell-bacterial strain complex or a target cell-pathogen complex.
15 more elements
Dependencies are inferred from the claim text.