Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features

Hitoshi Dejima,Shawna M Hubert,Jiexin Zhang,Alexandre Reuben,Xin Hu,J Jack Lee,Dan Su,Hoa H.n Pham ,P Andrew Futreal,Cara Haymaker,Jia Wu,Curtis Gumbs,Latasha Little,Humam Kadara,Myrna C.b Godoy ,Jie Ye,Dzifa Y Duose ,Junya Fujimoto,Marcos R.h Estécio ,Chi Wan Chow ,Ara A Vaporciyan,Edwin R Parra,Mara B Antonoff,Paul Scheet,Kazuhiro Tabata,Junya Fukuoka,Ying Liu ,Nicholas Mcgranahan,Runzhe Chen,Baili Zhang,Harvey I Pass,John V Heymach,Boris Sepesi,Carmen Behrens,Luisa M Solis,Ignacio I Wistuba

doi:10.1038/s41467-021-22890-x

Abstract

The mechanism by which anti-cancer immunity shapes early carcinogenesis of lung adenocarcinoma (ADC) is unknown. In this study, we characterize the immune contexture of invasive lung ADC and its precursors by transcriptomic immune profiling, T cell receptor (TCR) sequencing and multiplex immunofluorescence (mIF). Our results demonstrate that anti-tumor immunity evolved as a continuum from lung preneoplasia, to preinvasive ADC, minimally-invasive ADC and frankly invasive lung ADC with a gradually less effective and more intensively regulated immune response including down-regulation of immune-activation pathways, up-regulation of immunosuppressive pathways, lower infiltration of cytotoxic T cells (CTLs) and anti-tumor helper T cells (Th), higher infiltration of regulatory T cells (Tregs), decreased T cell clonality, and lower frequencies of top T cell clones in later-stages. Driver mutations, chromosomal copy number aberrations (CNAs) and aberrant DNA methylation may collectively impinge host immune responses and facilitate immune evasion, promoting the outgrowth of fit subclones in preneoplasia into dominant clones in invasive ADC.

Highlights

The mechanism by which anti-cancer immunity shapes early carcinogenesis of lung adenocarcinoma (ADC) is unknown
The classification of early-stage lung ADC and its precursors has been revised by several professional societies to include a spectrum from atypical adenomatous hyperplasia (AAH), the only recognized preneoplasia to lung ADC, to preinvasive adenocarcinoma in situ (AIS), to microinvasive lesions termed minimally invasive adenocarcinoma (MIA), and eventually frankly invasive ADC2–5
Examples of progressively increased genes included immune suppressive genes CD4710, CD27611 and CTLA412, while progressively decreased genes included ENTPD113, granzyme B (GZMB), and perforin 1 (PRF1)[14,15] (Supplementary Fig. 1)

Summary

Introduction

The mechanism by which anti-cancer immunity shapes early carcinogenesis of lung adenocarcinoma (ADC) is unknown. Early-stage lung ADCs and their precursors usually present as lung nodules with distinct radiologic features called ground glass opacity (GGO) These lung nodules are often referred to as indeterminate pulmonary nodules (IPNs) without histologic diagnosis, as the diagnostic yield from biopsy of GGO-predominant nodules is low and surgical resection is not the standard of care. Our pilot studies of gene expression and genomic profiling on lung ADC precursors have demonstrated distinct transcriptomic features[6] and progressive genomic evolution along the spectrum of AAH to AIS, MIA, and ADC7. We perform immune gene expression profiling, T cell receptor (TCR) sequencing and multiplex immunofluorescence (mIF) staining on a cohort of resected AAH, AIS, MIA and invasive ADC lesions and paired morphologically normal lung tissues (NL) to delineate the evolution of immune contexture, the T cell landscape, across different stages of early lung ADC pathogenesis. We further leverage whole exome sequencing (WES)[7] and methylation data[8] from the same cohort of IPNs to unravel the genomic and methylation alterations that may impinge on the immune contexture (Supplementary Data 1 and Fig. 1)

Methods

Results

Conclusion