Qadir, D. | Search bioRxiv

bioRxiv2025

LINE-1 ORF1p is a shared and immunogenic antigen in cancer

BackgroundRecent clinical trials are beginning to show the potential for therapeutic cancer vaccines directed against tumor associated antigens. However, there is a limited set of well-defined antigens that are shared across tumors. Noncanonical coding elements in the genome that are usually silenced in normal cells potentially represent a rich source of "dark" antigens when expressed and presented to the immune system. LINE-1 elements are repetitive, virus-like genomic sequences that can copy themselves to new genomic loci, and which are reactivated in many cancers. In this study, we explore ORF1p, a protein encoded by LINE-1 elements, as a potential shared cancer vaccine antigen. MethodsWe assessed the tumor specificity of LINE-1 expression in large scale public RNA-seq data sets and in a curated database of public immunopeptidomics studies. We validated these findings using cell line and tissue data and performed an in vitro vaccination assay using healthy donor PBMCs to test the immunogenicity of ORF1p. ResultsWe found widespread RNA expression of LINE-1 across many tumor types with esophageal cancer showing the most highly elevated expression. We also found widespread MHC class I presentation of ORF1p-derived peptides in a range of tumor types, including esophageal cancer. We validated the tumor specific protein expression of ORF1p in a small set of 5 tumor, 5 matched normal, and 5 healthy esophageal samples. Finally, we demonstrated that dendritic cells pulsed with ORF1p peptides were able to induce interferon gamma production in healthy donor human T cells after repeated stimulation in vitro. ConclusionsWe present data demonstrating that dark antigens derived from LINE-1 elements are 1) expressed in a cancer tissue-specific manner, 2) detected in immunopeptidomics data (both publicly available and newly generated for this study) and 3) immunogenic in vitro. The tumor specificity and immunogenicity of ORF1p peptides point to their potential as a cancer vaccine antigen.

cancer biology↗

bioRxiv2019

Partial FMRP expression is sufficient to normalize neuronal hyperactivity in Fragile X neurons

Fragile X Syndrome (FXS) is the most common genetic form of intellectual disability caused by a CGG repeat expansion in the 5-UTR of the Fragile X mental retardation gene FMR1, triggering epigenetic silencing and the subsequent absence of the protein, FMRP. Reactivation of FMR1 represents an attractive therapeutic strategy targeting the genetic root cause of FXS. However, largely missing in the FXS field is an understanding of how much FMR1 reactivation is required to rescue FMRP-dependent mutant phenotypes. Here, we utilize FXS patient derived excitatory neurons to model FXS in vitro and confirm that the absence of FMRP leads to neuronal hyperactivity. We further determined the levels of FMRP and the percentage of FMRP positive cells necessary to correct this phenotype utilizing a mixed and mosaic neuronal culture system and a combination of CRISPR, antisense and expression technologies to titrate FMRP in FXS and WT neurons. Our data demonstrate that restoration of greater than 5% of overall FMRP expression levels or greater than 20% FMRP expressing neurons in a mosaic pattern is sufficient to normalize a FMRP-dependent, hyperactive phenotype in FXS iPSC-derived neurons.\n\nHighlightsO_LICRISPR gene editing to generate FMRP KO and CGG-deleted isogenic iPSCs\nC_LIO_LIMEA as an approach to identify FMR1 dependent phenotype in NGN2 neurons derived from FXS and FMRP KO iPSCs\nC_LIO_LICell mixing paradigm as mosaicism in a dish to rescue phenotype\nC_LIO_LIMinimal level of FMRP determined by FMR1 mRNA and targeted demethylation of CGG repeats to correct the hyperactive phenotype in FXS neurons\nC_LIO_LIASO titration-validated partial expression of FMRP is sufficient to normalize increased neuronal activity\nC_LI

neuroscience↗