Immunogenomic determinants of response and resistance to neoadjuvant anti-PD-1 in resectable NSCLC

Summary More than 1.8 million people worldwide are diagnosed with non-small cell lung cancer (NSCLC) every year. Of these patients, 20% present with stage I or II disease. For these patients, neoadjuvant immune checkpoint blockade is now standard of care. However, even in apparently curative surgery, >40% of patients treated with this regimen will experience disease recurrence and will eventually die of the disease. Under the parent R37 award, we used whole exome sequencing, neoantigen predictions, functional assays, and single cell transcriptomics to identify transcriptional signatures of tumor-reactive TIL that were associated with response and resistance to neoadjuvant ICB. These signatures allowed us to develop a 3-gene score, called ‘MANAscore’, that can identify tumor-reactive TIL with high specificity and sensitivity from single cell transcriptomics alone, without the need for cumbersome functional assays. We also identified two dichotomous Treg subsets: a CCR5+ Th1-like subset that was associated with response, and a highly immunosuppressive subset, characterized by high OX40 expression, that was associated with resistance5. Intriguingly, tumor-reactive TIL expressed high levels of OX40L, thus hinting at the possibility of direct interaction between tumor-reactive TIL and this highly immunosuppressive Treg subset. However, this is not something that can be deciphered using single cell transcriptomics of live cell suspensions; it must be resolved spatially. Moreover, it is unclear if the underpinnings of pathological response that we identified in the parent award are the same mechanisms that promote long-term disease remission after surgical resection. In this R37 extension, using the same patient cohort, we will build on our discoveries from the parent award to optimize and apply MANAscore to spatial transcriptomics (sMANAscore) of resected lung tumors. This will allow us to discover and validate spatial interactions between pTRC and our Treg subsets of interest that are associated with disease recurrence after neoadjuvant ICB. Identification of targetable markers of disease relapse, development of novel bioinformatic approaches to analyze spatial transcriptomics data, and enumeration of immunogenomic determinants of disease relapse or remission are only some of the key outcomes of this study. Project Number: 4R37CA251447-06 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Kellie Smith | Institution: JOHNS HOPKINS UNIVERSITY, BALTIMORE, MD | Award Amount: $355,706 | Activity Code: R37 View on NIH RePORTER: https://reporter.nih.gov/project-details/11129236