Artificial intelligence-powered spatial analysis of tumor infiltrating lymphocytes (TIL) to reflect target gene expressions of novel immuno-oncology agents.

Authors

null

Chan-Young Ock

Lunit Inc., Seoul, South Korea

Chan-Young Ock , Seunghwan Shin , Wonkyung Jung , Sangheon Ahn , Haejoon Kim , Chunggi Lee , Jaehong Aum , Daim Tak , Ahyoung Ryu , Taiwon Chung , Eunji Baek , Jisoo Shin , Seungje Lee , Jiwon Shin , Minuk Ma , Seonwook Park , Sergio Pereira , Jeongseok Kang , Donggeun Yoo , Kyunghyun Paeng

Organizations

Lunit Inc., Seoul, South Korea

Research Funding

Other
Lunit Inc

Background: Novel immuno-oncology (IO) agents are promising but showing their efficacy in early phase clinical trials has been challenging due to limited enrichment strategies using practical biomarker platforms. We hypothesize that an artificial intelligence (AI)-powered spatial analysis of TIL using practically feasible H&E slides, can reflect a specific target gene expression derived from RNA sequencing. This enhances its potential application in early development of novel IO agents. Methods: An AI-powered spatial TIL analyzer, namely Lunit SCOPE IO, was developed with data from 2.8 x 109 micrometer2 H&E-stained tissue regions and 5.9 x 106 TILs from 3,166 whole slide images of multiple cancer types, annotated by board-certified pathologists. Inflamed Score and Immune-Excluded Score was defined as the proportion of all tumor-containing 1 mm2-size tiles within a WSI classified as being of inflamed immune phenotype (high TIL density within cancer epithelium) and immune-excluded phenotype (low TIL density within cancer epithelium, but high TIL density within stroma), respectively. We used RNA sequencing data and H&E images from The Cancer Genome Atlas database, excluding those of mesenchymal origin (n = 7,467). Spearman's rank correlation between each gene expression and IS or IES, respectively, was calculated. Correlation coefficient > 0.2 and false discovery rate (FDR) < 1% was considered as a significant correlation. Results: In a total of 20,304 genes, 871 (4.3%) and 1,155 (5.7%) genes were significantly correlated with Inflamed Score (IS) and Immune-Excluded Score (IES), respectively. The IS was highly related to genes reflecting immune cytolytic activity and targets of approved immune checkpoint inhibitors (Table). Interestingly, it was also significantly correlated with target genes of novel IO such as TIGIT, LAG3, TIM3, IDO, Adenosine receptor A2A, OX40, ICOS, M-CSF, IL2, IL7, and IL12. Moreover, the IES was exclusively correlated with the target genes of CEACAM, TGFB, and IL1. Conclusions: Expression levels of novel I-O target genes are correlated with three scores derived from AI-powered TIL analysis using H&E slides, which can be easily applied to clinical research.

Gene
Pathway
Correlation coefficient (IS)
Gene
Pathway
Correlation coefficient (IS)
Gene
Pathway
Correlation coefficient (IS or IES)
CD8A
Cytolytic
0.490
TIGIT
TIGIT
0.424
IL2RB
IL2
0.437 (IS)
GZMA
Cytolytic
0.492
LAG3
LAG3
0.447
IL7R
IL7
0.228 (IS)
PRF1
Cytolytic
0.471
HAVCR2
TIM3
0.329
IL7
IL7
0.220 (IS)
CTLA4
CTLA4
0.371
IDO1
IDO1/2
0.395
IL12RB1
IL12
0.433 (IS)
CD86
CTLA4
0.325
IDO2
IDO1/2
0.319
IL12B
IL12
0.263 (IS)
PDCD1
PD(L)1/20.460
ADORA2A
A2AR
0.307
CEACAM5
CEACAM
0.356 (IES)
IFNG
PD(L)1/2
0.429
TNFRSF4
OX40
0.311
SERPINB5
TGFB
0.339 (IES)
PDCD1LG2
PD(L)1/2
0.313
ICOS
ICOS
0.387
IL1A
IL1
0.349 (IES)
CD274
PD(L)1/2
0.212
CSF1
M-CSF
0.257
IL1B
IL1
0.230 (IES)

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Abstract Details

Meeting

2021 ASCO Annual Meeting

Session Type

Publication Only

Session Title

Publication Only: Developmental Therapeutics—Immunotherapy

Track

Developmental Therapeutics—Immunotherapy

Sub Track

New Targets and New Technologies (IO)

Citation

J Clin Oncol 39, 2021 (suppl 15; abstr e14534)

DOI

10.1200/JCO.2021.39.15_suppl.e14534

Abstract #

e14534

Abstract Disclosures