Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood

Abstract

SUMMARYNeoantigen-specific T cells are increasingly viewed as important immunotherapy effectors, but physically isolating these rare cell populations is challenging. Here, we describe a sensitive method for the enumeration and isolation of neoantigen-specific CD8+ T cells from small samples of patient tumor or blood. The method relies on magnetic nanoparticles that present neoantigen-loaded major histocompatibility complex (MHC) tetramers at high avidity by barcoded DNA linkers. The magnetic particles provide a convenient handle to isolate the desired cell populations, and the barcoded DNA enables multiplexed analysis. The method exhibits superior recovery of antigen-specific T cell populations relative to literature approaches. We applied the method to profile neoantigen-specific T cell populations in the tumor and blood of patients with metastatic melanoma over the course of anti-PD1 checkpoint inhibitor therapy. We show that the method has value for monitoring clinical responses to cancer immunotherapy and might help guide the development of personalized mutational neoantigen-specific T cell therapies and cancer vaccines.

The miRNAs Role in Melanoma and in Its Resistance to Therapy

“…These molecules are new to the immune system and may trigger an immune response. It has been reported that in patients with melanoma, a personalized treatment vaccine generated a robust immune response against the cancer and may have helped to prevent it from returning [66]. Although this clinical trial is in the I phase, the studies confirm the potential of neo-antigen vaccines to treat cancer and should lead to larger trials in the future in order to help address such challenges for effective cancer immunotherapy.…”

Towards new horizons: characterization, classification and implications of the tumour antigenic repertoire

“…Of note, all mutated TSAs detected using these methods are restricted to individual tumours. Shared mutated TSAs that can be detected in more than one patient are currently elusive 58,59 . The reasons why TSAs seem to be so difficult to detect have yet to be completely elucidated but might reflect technical limitations of the employed detection and/or discovery methodologies (TAbLe 2), as well as immunoediting by the patient's initial antitumour immune response, leading to elimination of the most antigenic tumour clones.…”

“…Furthermore, T cell recognition of TSAs might lead to the upregulation of inhibitory ligands, such as PD-L1, and contribute to the development of an immunosuppressive tumour microenvironment, both of which might impede the expansion and response of antigen-specific T cells 60,61 . In summary, antigen-specific T cells against a specific mutated TSA can frequently be detected in the absence of a robust antitumour immune response 35,49,50,59,62 , and thus the antigen either must have previously been present, but has been removed by immunoediting 59 , or still prevails but remains undetectable by MS/MS. Exonic variants potentially leading to mutated TSAs (fIg.…”

Neoantigen-Specific Adoptive Cell Therapies for Cancer: Making T-Cell Products More Personal

“…As a result, up to thousands of unique specificities can be potentially identified simultaneously, paving the way for high-throughput platforms and downstream applications such as TCR redirected T-cell therapy ( 60 , 61 ). Of note, state-of-the-art microfluidic devices can help with potential sample size limitation by allowing on-chip detection and manipulation of multimer-sorted neoantigen-specific T cells for downstream analysis and applications ( 38 ).…”

“…In this regard, Cohen et al ( 22 ) first provided a simplified and noninvasive blood-based strategy as an alternative to current TIL production by demonstrating that neoantigen and self-antigen reactive T-cells can be reliably isolated from the peripheral blood of melanoma patients. Detection of neoantigen-specific CD8 + and CD4 + lymphocytes from peripheral blood has been subsequently described in patients with relatively low tumor mutation burden, such as ovarian and gastrointesinal cancers ( 20 , 38 – 40 ). However, circulating neoantigen-specific T-cells share with their infiltrating counterpart very low detection frequencies (ranging from 0.5 to 0.002%) ( 20 , 22 , 37 , 41 , 42 ), hence the need for specific enrichment strategies.…”