Biology subjects

Li, Y.-R.

Publications and source records attributed to Li, Y.-R..

4 recordsLinked to original sources

bioRxiv2025

A Nanovial-Based Platform for Functional Discovery of Antigen-Reactive TCRs from Unconventional T Cells

Unconventional T cells, such as mucosal-associated invariant T (MAIT) cells and invariant natural killer T (iNKT) cells, recognize non-peptide antigens presented by MR1 and CD1d, respectively, and play pivotal roles in immunity, allowing targeting of cells based on metabolic activity. Although components of the T cell receptors (TCRs) for these unconventional T cells are invariant, significant variability in the CDR3 regions still exist, opening questions as to how TCR sequence and function may be linked, and how to maximize the therapeutic potential of engineered unconventional T cells. Here, we develop a nanovial-based functional screening platform that enables high-throughput discovery of TCRs from unconventional T cells based on direct antigen recognition and cytokine secretion. By selectively labeling nanovials with MR1 and CD1d molecules displaying their cognate ligands, we achieve dose-dependent capture and activation of MAIT and iNKT cells from complex human PBMC samples comprising tens of millions of cells. Using oligonucleotide barcodes conjugated to nanovials encoding the antigen-presenting molecules and loading cytokine capture antibodies, we perform secretion-encoded single-cell sequencing to link TCR identity, gene expression, antigen specificity, and functional response. Applying this method, we isolate rare reactive T cells, recover their TCRs, and validate five novel MAIT TCRs. All five TCRs, when re-expressed in primary T cells, confer antigen-specific cytokine secretion and cytotoxicity. The top two TCRs were evaluated using an in vivo solid tumor model, demonstrating specific tumor homing and efficacy. This function-first strategy offers a powerful tool to uncover functional TCRs from unconventional T cells, yielding a 100% hit rate when secretion-based validation is included as part of the initial screen, unlocking new opportunities for cell-based immunotherapy.

bioengineering↗

bioRxiv2024

Discovery and Engineering of Retrons for Precise GenomeEditing

Retrons are promising gene editing tools because they can produce multi-copy single-stranded DNA in cells via self-primed reverse transcription. However, their potential for inserting genetic cargos in eukaryotes remains largely unexplored. Here we report the discovery and engineering of highly efficient retron-based gene editors for mammalian cells and vertebrates. Through bioinformatic analysis of metagenomic data and functional screening, we identified novel retron reverse transcriptases (RTs) that are highly active in mammalian cells. Rational design further improved the editing efficiency to levels comparable with conventional single-stranded oligodeoxynucleotide donors but from a genetically encoded cassette. Small molecule inhibitors of non-homologous end joining factors and Cas9-DNA repair protein fusions further increase homology-directed repair. Retron editors also exhibited robust activity with Cas12a nuclease and Cas9 nickase, expanding the genomic target scope and bypassing the need for a DNA double-stranded break. Using a rationally engineered retron editor, we incorporate a split GFP epitope tag for live cell imaging. Finally, we develop an all-RNA delivery strategy to enable DNA-free gene editing in cells and vertebrate embryos. This work establishes retron editors as a versatile and efficient tool for precise gene editing, offering new opportunities for biotechnology and biomedical research.

molecular biology↗

bioRxiv2023

Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes

mRNA translation relies on identifying translation initiation sites (TISs) in mRNAs. Alternative TISs are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear. Using ribosome profiling and machine learning, we developed models for predicting alternative TISs in Arabidopsis thaliana and tomato (Solanum lycopersicum). Distinct feature sets were predictive of AUG and non-AUG TISs in 5' untranslated regions and coding sequences, including a novel CU-rich sequence that promoted plant TIS activity, a translational enhancer found across dicots and monocots and also in humans and viruses. Our results elucidate the mechanistic and evolutionary basis of TIS recognition, whereby cis-regulatory RNA signatures affect start site selection. The TIS prediction model provides global estimates of TISs to discover neglected protein-coding genes across plant genomes. The prevalence of cis-regulatory signatures across eukaryotes and viruses suggests their broad, critical roles in reprogramming the translational landscape in the plant-virus arms race. TeaserNew insights into how plant ribosomes distinguish AUG and non-AUG triplets for protein synthesis via a conserved eukaryotic cis-regulatory strategy.

systems biology↗

bioRxiv2020

Trajectory Mapping of the Early Drosophila Germline Reveals Controls of Zygotic Activation and Sex Determination

Germ cells in D. melanogaster are specified maternally shortly after fertilization and are transcriptionally quiescent until their zygotic genome is activated to sustain further development. To understand the molecular basis of this process, we analyzed the progressing transcriptomes of early male and female germ cells at the single-cell level between germline specification and coalescence with somatic gonadal cells. Our data comprehensively covered zygotic activation in the germline genome, and analyses on genes that exhibit germline-restricted expression revealed that polymerase pausing and differential RNA stability are important mechanisms that establish gene expression differences between the germline and soma. In addition, we observed an immediate bifurcation between the male and female germ cells as zygotic transcription begins. The main difference between the two sexes is an elevation in X chromosome expression in females relative to males signifying incomplete dosage compensation with a few select genes exhibiting even higher expression increases. These indicate that the male program is the default mode in the germline that is driven to female development with a second X chromosome.

developmental biology↗