Tumor immunity portrait: An AI-driven molecular predictor combining tumor microenvironment and tumor mutational burden for immune checkpoint inhibitor response prediction.

Authors

null

Polina Shilo

BostonGene, Corp., Waltham, MA

Polina Shilo , Artem Tarasov , Anna Filatova , Konstantin Danilov , Ivan Valiev , Nikita Kotlov , Jessica H. Brown , Anna Ogloblina , Alexander Bagaev , Nathan Fowler

Organizations

BostonGene, Corp., Waltham, MA

Research Funding

No funding received
None.

Background: Low response rates and toxicities from immune checkpoint inhibitors (ICI) highlight the need for improved ICI response prediction tools. Increasing evidence shows the tumor microenvironment (TME) plays a critical role in therapy response; however, current ICI response prediction methods often use a single tumor characteristic (i.e., tumor mutational burden [TMB]). Here, we present the BostonGene Tumor Immunity Portrait, an AI-driven molecular predictor based on the TME subtype combined with TMB status to identify ICI responders in non-small cell lung cancer (NSCLC), melanoma, and gastric cancer (GC). Methods: We collected a meta cohort from 26 publicly available datasets (n = 2,077) composed of NSCLC, melanoma, and GC patients that received ICI therapy. A transcriptomic-based TME subtyping approach was used to classify the TME as fibrotic (F), immune-enriched, fibrotic (IE/F), immune-enriched (IE), or desert (D) (Bagaev, Cancer Cell, 2021). TMB status (low < 10; high > 10) was determined by whole exome sequencing. A logistic regression model was used to generate a score of 0, 1, 2, or 3 based on the sum of points assigned to the TME subtype (F = 0 points, IE/F and D = 1 point, IE = 2 points) and to the TMB status (high = 1 point and low = 0 points). Each score corresponded to one of four Tumor Immunity Portrait types: 0 - Immunosuppressive; 1 - Resistant; 2 - Neutral; 3 - Immune Primed. Results: Tumor Immunity Portrait types were associated with increasing ICI response rates in each cancer type. Immune Primed type (IE + TMB-High) response rates in melanoma and GC were 76.2% and 100%, respectively. Immunosuppressive type (F + TMB-Low) was associated with ICI non-response in melanoma (p = 0.003) and NSCLC (p < 0.001). The Tumor Immunity Portrait accurately predicted ICI non-response, shown by the negative predictive value (NPV) of the Immunosuppressive type (F + TMB-Low) for NSCLC (100%), melanoma (92.3%), and GC (96.1%). Conclusions: Using an integrated approach combining the tumor’s characteristics and TME, the BostonGene Tumor Immunity Portrait provides accurate prediction of ICI non-response in 3 cancer types, warranting further validation for use in personalized treatment decision making.

Tumor Immunity Portrait type response rates (RR) and binary classification results.
Tumor Immunity Portrait
(TME subtype and TMB status)
NSCLC
(n=27)
RR (%)
Gastric Cancer (n=55)
RR (%)
Melanoma (n=1,995)
RR (%)
Immunosuppressive
(Score 0)
F + TMB-Low07.713.9
Resistant
(Score 1)
IE/F + TMB-Low
F + TMB-High
D + TMB-Low
207.136.0
Neutral
(Score 2)
IE + TMB-Low
IE/F + TMB-High
D+ TMB-High
5054.545.6
Immune Primed
(Score 3)
IE + TMB-HighNA10076.2
Binary classification (%)10096.192.3
Binary classification odds ratio [95% CI], P value0.000 [0.000 - ∞]
p < 0.001
0.136 [0.016-1.199]
p = 0.072
0.223 [0.084-0.592]
p = 0.003

Disclaimer

This material on this page is ©2024 American Society of Clinical Oncology, all rights reserved. Licensing available upon request. For more information, please contact licensing@asco.org

Abstract Details

Meeting

2023 ASCO Annual Meeting

Session Type

Publication Only

Session Title

Publication Only: Developmental Therapeutics—Immunotherapy

Track

Developmental Therapeutics—Immunotherapy

Sub Track

Other IO-Related Topics

Citation

J Clin Oncol 41, 2023 (suppl 16; abstr e14691)

DOI

10.1200/JCO.2023.41.16_suppl.e14691

Abstract #

e14691

Abstract Disclosures