Biology subjects

Pinamonti, V.

Publications and source records attributed to Pinamonti, V..

3 recordsLinked to original sources

bioRxiv2023

Boosting class II HLA epitope presentation to T cells with endoplasmic reticulum transmembrane domain fusion proteins

Antigen processing and presentation are crucial for T-cell receptor engagement and potent adaptive immune responses. While establishing an antigen presentation system to identify TCR-epitope pairs from large libraries of genetically templated, ectopically expressed antigens, we observed a longitudinal suppression of antigen processing in B cells, which we call antigen processing attenuation (APA). Beyond its potential role in regulating B cell-enforced peripheral tolerance, APA represents a bottleneck to sustained antigen presentation in screening and vaccination approaches. To overcome APA we screened several pathways which might enhance processing. Notably, we identified several sequences derived from transmembrane domains (TM) of endoplasmic reticulum-resident proteins which promote sustained minigene-encoded antigen presentation. In particular, the first TM domain of SYT6, a protein associated with synaptic vesicles, greatly enhances processing and ameliorates APA. These findings suggest a new entry point into antigen processing pathways, enabling the discovery of novel immune epitopes and improving T-cell based immunization strategies.

molecular biology↗

bioRxiv2023

T-FINDER: A highly sensitive, pan-HLA platform for functional T cell receptor and ligand discovery

Effective, unbiased, high-throughput methods to functionally identify both class II and class I HLA-presented T cell epitopes and their cognate T cell receptors (TCRs) are essential for and prerequisite to diagnostic and therapeutic applications, yet remain underdeveloped. Addressing this bottleneck, we established T-FINDER (T cell Functional Identification and (Neo)-antigen Discovery of Epitopes and Receptors), a platform that rapidly deconvolutes CD4 and CD8 TCR reactivities to targets physiologically processed and presented by an individuals unmanipulated, complete HLA haplotype. By using a highly sensitive TCR signaling reporter capable of detecting even low-affinity TCR:ligand interactions, T-FINDER not only robustly identifies unknown peptide:HLA ligands from complex antigen libraries, but also rapidly screens and functionally validates the specificity of complex TCR libraries against known or predicted targets. To demonstrate its pan-HLA presentation capacity, we apply the platform to multiple TCR-based applications, including glioma, celiac disease, and rheumatoid arthritis, providing unique biological insights and showcasing T-FINDERs potency and versatility.

immunology↗

bioRxiv2023

Neoepitope formation through the generation of RNA-derived "editopes"

Increasing the quantity and immunogenicity of neoantigens in tumors is essential for advancing immunotherapy. However, engineering neoantigens remains challenging due to the need for precise, tumor-specific antigen modification without affecting normal cells. To tackle this challenge, we developed Short Precise-Encodable ADAR Recruiting (SPEAR) ADAR-engagers, an approach that uses short guide RNAs to engage the endogenous RNA editor ADAR1 and direct it to regions of mRNA targets known to encode MHC-presented peptides. By precisely editing adenosine-to-inosine (A-to-I) in these contexts, we effectively mutate specific epitopes into neoepitopes (which we now term "editopes"). As proof of concept, we targeted the known antigen MART-1 (Melanoma-Associated Antigen Recognized by T cells-1), and demonstrated that guided ADAR1 editing can generate immunogenic epitopes that activate T cells and promote tumor cell elimination. Building on this concept, we developed a computational pipeline to identify tumor-specific somatic mutations suitable for SPEAR-mediated editing. This strategy enables selective neoantigen generation in cancer cells, effectively increasing their apparent tumor mutational burden and potentially enhancing their susceptibility to immunotherapy.

cancer biology↗