Methods and systems for predicting response to pd-1 axis directed therapeutics in colorectal tumors with deficient mismatch repair

A method of treating a subject having a dMMR and/or MSI-H colorectal tumor, the method comprising administering to the subject a PD-1 axis-directed therapy,

• (a) wherein the tumor has previously been determined to have an Predicted Response Score (PRS) indicative of response to the PD-1 axis-directed therapy and wherein the PRS is determined from a continuous scoring function incorporating a feature set comprising at least an average number of PD-1+ cells within 10 μm of a PD-L1 cell within the tumor region of a tissue section of the tumor;
• or
• (b) wherein the tumor has previously been determined to have a Predicted Response Score (PRS) indicative of response to the PD-1 axis directed therapy and wherein the PRS determined from a continuous scoring function incorporating a feature set comprising at least:
• (i) standard deviation of the distance of CD8+ cells from CD68+/PDL1+ cells within 10 μm in a stroma region of a tissue section of the tumor, and
• (ii) the mean distance of CD8+/PD-1+ cells from CD8+-PD-L1+ cells within 30 μm in a tumor region of a tissue section of the tumor;
• or
• (c) wherein the tumor has previously been determined to have a Predicted Response Score (PRS) indicative of response to the PD-1 axis-directed therapy and wherein the PRS determined from a continuous scoring function incorporating a feature set comprising at least:
• (i) standard deviation of the distance of CD8+ cells from CD68+/PDL1+ cells within 10 μm in a peritumor outside region of a tissue section of the tumor, and
• (ii) density of CD8+/epithelial marker− (EM−) cells within a tumor area;
• or
• (d) wherein the tumor has previously been determined to have a Predicted Response Score (PRS) indicative of response to the PD-1 axis-directed therapy and wherein the PRS determined from a continuous scoring function incorporating a feature set comprising at least:
• (i) median distance of CD8+ cells from epithelial marker+ (EM+) cells within 30 μm in a epithelial tumor region of a tissue section of the tumor,
• (ii) mean distance of CD8+ cells from PD-L1+/epithelial marker+ (EM+) cells within 10 μm a tumor stroma area,
• (iii) mean number CD8+/PD-1+ cells from CD8+/PD-L1+ cells within 10 μm in a tumor area, and
• (iv) mean distance of CD8+/PD-1+ cells from CD8+/PD-L1+ cells within 30 μm in a tumor area.

An image analysis system comprising a memory and a processor, wherein the processor implements a set of instructions stored on the memory, the set of instructions comprising extracting a Feature Set from one or more digital images of an affinity histochemically (AHC) labeled tissue sample from a colorectal tumor previously determined to be one or more of dMMR or MSI-H, wherein the Feature Set is selected from the group consisting of:

• (a) Feature Set 1, comprising:
• a standard deviation of the distance of CD8+ cells from CD68+/PDL1+ cells within 10 μm in a stroma region, and
• a mean distance of CD8+/PD-1+ cells from CD8+-PD-L1+ cells within 30 μm in a tumor region;
• (b) Feature Set 2, comprising:
• a standard deviation of the distance of CD8+ cells from CD68+/PDL1+ cells within 10 μm in a peritumor outside region, and
• a density of CD8+/epithelial marker− (EM−) cells within a tumor area;
• (c) Feature Set 3, comprising:
• a median distance of CD8+ cells from epithelial marker+ (EM+) cells within 30 μm in a epithelial tumor region of a tissue section of the tumor,
• a mean distance of CD8+ cells from PD-L1+/epithelial marker+ (EM+) cells within 10 μm a stroma area,
• a mean number CD8+/PD-1+ cells from CD8+/PD-L1+ cells within 10 μm in a tumor area, and
• a mean distance of CD8+/PD-1+ cells from CD8+/PD-L1+ cells within 30 μm in a tumor area, and
• (d) Feature Set 4, comprising a density of CD8+ cells in a tumor area;
• and
• (e) Feature Set 5, comprising an average number of PD-1+ cells within 10 μm of a PD-L1+ cell.

A biomarker-specific reagent panel for predicting response to a PD-1 axis-directed therapy, the panel selected from the group consisting:

• Panel A, comprising biomarker specific reagents specific for CD8, CD68, PD-L1, PD-1, and optionally epithelial marker (EM) proteins;
• Panel B, comprising biomarker specific reagents specific for CD8, CD68, PD-L1, and optionally EM proteins;
• Panel C, comprising biomarker specific reagents specific for CD8, EM, PD-L1, and PD-1 proteins;
• Panel D, comprising biomarker specific reagents specific for CD8 and EM proteins;
• Panel E, comprising biomarker specific reagents specific for CD8, PD-L1, PD-1, and optionally EM proteins;
• Panel F, comprising biomarker specific reagents specific for CD8, PD-L1, and EM proteins;
• and
• Panel G, comprising biomarker specific reagents specific for PD-1 and PD-L1.

A multiplex affinity histochemical (mAHC) assay-stained tissue section of a colorectal tumor previously determined to be one or more of dMMR or MSI-H, wherein the tissue section is differentially stained for a panel of biomarkers selected from the group consisting of:

• Panel A, wherein the AHC-stained tissue section is differentially stained for each of CD8, CD68, PD-L1, PD-1, and optionally epithelial marker (EM) proteins;
• Panel B, wherein the AHC-stained tissue section is differentially stained for each of CD8, CD68, PD-L1, and optionally EM proteins;
• Panel C, wherein the AHC-stained tissue section is differentially stained for each of CD8, EM, PD-L1, and PD-1 proteins;
• Panel D, wherein the AHC-stained tissue section is differentially stained for each of CD8 and EM proteins;
• Panel E, wherein the AHC-stained tissue section is differentially stained for each of CD8, PD-L1, PD-1, and optionally EM proteins;
• Panel F, wherein the AHC-stained tissue section is differentially stained for each of CD8, PD-L1, and EM proteins;
• and
• Panel G, wherein the AHC-stained tissue section is differentially stained for each of PD-1 and PD-L1 proteins.