SBIR-STTR Award

Newly developed immunotherapies have shown great promise for the management and treatment of various types of cancer. Among these new strategies, the development of T-cell Receptor engineered T-cells (TCR T- cells) targeting tumor specific neoantigens has arisen as a promising approach to improve efficacy, decrease toxicity and overcome acquired resistance. However, the multiplicity of mutations in cancer and the lack of high- throughput methods to identify neoantigen-specific TCRs is preventing the wide implementation of TCR T-cells therapies. Flexomics is developing an integrated platform harnessing recent advances in single cell genomics, immunoassays and microfluidics for the high-throughput characterization of antigen-specific TCRs. Our proprietary approach is designed to identify T-cell activation in response to specific antigen exposure at single cell level for 100,000s T-cells while simultaneously capturing phenotypic and genotypic information in the form of expression of key marker genes and full-length TCR sequence identification. To demonstrate the feasibility of our method we propose to: (1) track functional responses from single T-cells to cognate antigen-exposure by measuring their cytokine secretion in our novel high-density picowell plate that allows us to co-capture 100,000s pairs of Antigen Presenting Cell (APC) / T-cell, (2) retrieve and link TCR sequence and expression for 20 phenotypic markers to each individual T-cell thanks to our unique barcoding system, (3) demonstrate end-to-end workflow and recapitulate previously discovered antigen-specific TCR sequence for a well characterized neoantigen. At the end of our Phase I grant, we will have demonstrated a concrete example of how our platform allows the screening and characterization of antigen-TCR interactions at unprecedented scale. We will also have all processes in place to start screening other neoantigens and further refine our workflow. Screening and discovery of neoantigen-specific T-cell response and TCR is critical to the future progress of cancer immunotherapies. Our technology has been developed specifically to support and accelerate the development of personalized treatments by providing a rapid and cost-effective method to identify immunogenic neoantigens and characterize their associated antigen-specific TCRs.

Public Health Relevance Statement:
PROJECT NARRATIVE Identifying and characterizing neoantigen-specific TCR in a high-throughput manner is challenging. The proposed technology harnesses gold-standard immunoassays and cutting-edge single cell genomic technologies to meet this critical need and accelerate the development of personalized immunotherapies.

Project Terms:
Affinity; Antigen-Presenting Cells; antigen-specific T cells; Antigens; Bar Codes; base; Biological Assay; cancer immunotherapy; cancer type; Cell Lineage; Cell Proliferation; Cells; Clinical; Clone Cells; Cloning; Coculture Techniques; Complement; Consumption; cost effective; cytokine; Data; density; design; Development; Elements; engineered T cells; Engineering; Fluorescent Probes; Future; Genes; Genomics; Genotype; Goals; Gold; Grant; Human; Immune; Immunoassay; immunogenic; Immunotherapy; improved; Individual; innovation; Interferon Type II; Interleukin-2; Lead; Length; Link; Malignant Neoplasms; Measures; Methods; Microfluidics; Microscopy; miniaturize; Modeling; Monitor; Mutate; Mutation; neoantigens; next generation sequencing; novel; novel strategies; Nucleic Acids; Outcome; Patients; personalized cancer therapy; personalized immunotherapy; personalized medicine; Phase; Phenotype; phenotypic biomarker; phenotypic data; Population; prevent; Process; Property; Resistance; response; screening; single cell sequencing; Small Business Innovation Research Grant; System; T cell response; T cell therapy; T-Cell Activation; T-Cell Development; T-Cell Receptor; T-Lymphocyte; T-Lymphocyte Subsets; targeted sequencing; targeted treatment; TCR Activation; Technology; Testing; Therapeutic; Time; Toxic effect; TP53 gene; Transcript; transcriptome sequencing; tumor; Validation

Newly developed immunotherapies have shown great promise for the management and treatment of various types of cancer. Among these new strategies, the development of T-cell Receptor engineered T-cells (TCR T- cells) targeting tumor specific neoantigens has arisen as a promising approach to improve efficacy, decrease toxicity and overcome acquired resistance. However, the multiplicity of mutations in cancer and the lack of high- throughput methods to identify neoantigen-specific TCRs is preventing the wide implementation of TCR T-cells therapies. Flexomics is developing an integrated platform harnessing recent advances in single cell genomics, immunoassays and microfluidics for the high-throughput characterization of antigen-specific TCRs. Our proprietary approach is designed to identify T-cell activation in response to specific antigen exposure at single cell level for 100,000s T-cells while simultaneously capturing phenotypic and genotypic information in the form of expression of key marker genes and full-length TCR sequence identification. To demonstrate the feasibility of our method we propose to: (1) track functional responses from single T-cells to cognate antigen-exposure by measuring their cytokine secretion in our novel high-density picowell plate that allows us to co-capture 100,000s pairs of Antigen Presenting Cell (APC) / T-cell, (2) retrieve and link TCR sequence and expression for 20 phenotypic markers to each individual T-cell thanks to our unique barcoding system, (3) demonstrate end-to-end workflow and recapitulate previously discovered antigen-specific TCR sequence for a well characterized neoantigen. At the end of our Phase I grant, we will have demonstrated a concrete example of how our platform allows the screening and characterization of antigen-TCR interactions at unprecedented scale. We will also have all processes in place to start screening other neoantigens and further refine our workflow. Screening and discovery of neoantigen-specific T-cell response and TCR is critical to the future progress of cancer immunotherapies. Our technology has been developed specifically to support and accelerate the development of personalized treatments by providing a rapid and cost-effective method to identify immunogenic neoantigens and characterize their associated antigen-specific TCRs. Public Health Relevance Statement PROJECT NARRATIVE Identifying and characterizing neoantigen-specific TCR in a high-throughput manner is challenging. The proposed technology harnesses gold-standard immunoassays and cutting-edge single cell genomic technologies to meet this critical need and accelerate the development of personalized immunotherapies.