Abstract 2426: Liquid biopsy for a predictive biomarker of resistance to immunotherapy
Authors: Sinkoe Andrew , Gulley James L. 
Published: March 2024

Immunotherapy has become a mainstay for cancer treatment. However, immune editing is a well-known resistance paradigm that limits the efficacy of immunotherapy in many patients. One type of immune editing that occurs in 1/6 of all cancer patients, with prevalence over 40% in some cancer types, is human leukocyte antigen loss of heterozygosity (HLA LOH). Liquid biopsies provide a non-invasive and inexpensive way of guiding treatment decision-making. We have developed a liquid biopsy assay for detecting HLA LOH in cancer patients, with the goal of utilizing the assay for deciding whether immunotherapy is the right course of treatment for a given patient.

The assay was tested utilizing sample sets from cancer patients, where each sample set from a patient included a solid tumor biopsy, a liquid biopsy plasma sample, and PBMC sample for control. Tumor HLA LOH results were used for ground truth, and HLA LOH results from the liquid biopsy sample were compared to those from the tumor sample from the same patient. Whole exome sequencing (WES) was performed on tumor DNA, cell-free DNA (cfDNA) from plasma, and germline DNA from PBMCs, and we ran our novel liquid biopsy HLA LOH detection algorithm on the plasma WES data. Standard copy number variant (CNV) calling tools were utilized for calling HLA LOH from the tumor sequencing data. In both cases - tumor and plasma - germline PBMC DNA was used as control.

We tested the liquid biopsy HLA LOH detection method on sample sets from 2 HPV-negative primary head and neck cancer patients, 14 castration-resistant prostate cancer patients, and 27 metastatic breast cancer patients. The samples from the head and neck cancer patients were obtained from patients on clinical trials at NCI, while WES data from prostate cancer patient samples and breast cancer patient samples were downloaded from NCBI Database of Genotypes and Phenotypes (dbGaP) after applying for access to dataset phs001417.v1.p1 (Adalsteinsson, et al., Nature Communications, 2017). The method for liquid biopsy HLA LOH detection utilizes a novel mathematical framework that takes into account biological and experimental variables to generate allele-specific HLA LOH information from sequencing data.

In the first two cohorts tested - the head and neck cancer cohort and the prostate cancer cohort - the method was 100% consistent when comparing liquid biopsy HLA LOH results from our method to CNV calling results from matched tumors (4 true positives and 36 true negatives; 0 false negatives and 0 false positives). In the breast cancer cohort, some false negatives and false positives were observed (6 true positives and 48 true negatives; 5 false negatives and 8 false positives). Experiments are ongoing in a CLIA lab to establish sensitivity, specificity, and limit of detection (LoD) for the assay. Upon improvements and validation of the assay, the goal is to utilize the liquid biopsy HLA LOH detection method in the clinic for treatment selection in the context of immunotherapy.

Citation Format: Andrew Sinkoe, James L. Gulley. Liquid biopsy for a predictive biomarker of resistance to immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2426.