Biology subjects

Sun, Y.-F.

Publications and source records attributed to Sun, Y.-F..

4 recordsLinked to original sources

bioRxiv2025

LadybirdBase: a comprehensive biology, ecology and omics resource for ladybird beetles (Coccinellidae)

Ladybird beetles (Coleoptera: Coccinellidae) represent a highly diverse insect group comprising over 6000 species. Recently, an increasing amount of omics data on ladybirds has accumulated. To better understand their roles and adaptations in biological control, we developed LadybirdBase (http://www.ladybirdbase.com/), a comprehensive database that compiles both published and self-collected data on ladybird beetles. It contains five main modules that encompass: (1) the Biology Module summarizing information on over 6000 species, including their classification, morphology, diet, distribution, and omics data; (2) the Ecology Module offering diet and distribution records; (3) the Genomics Module integrating published and unpublished resources such as genomes, transcriptomes, mitogenomes, orthogroups, and variance; (4) the Microbiomics Module presenting 16S rRNA, ITS, and metagenome data; and (5) the Lab Test Module covering diet ranges, life histories under different treatments, and stress tolerance. Additionally, LadybirdBase offers analysis tools for species detection using morphology or barcodes, BLAST searches against the genome resources, differential gene expression analysis, and PCR primer search. LadybirdBase can greatly simplify species identification, enhance the efficiency of omics studies, and provide a theoretical foundation for the use of ladybirds in biological control.

bioinformatics↗

bioRxiv2024

PhyloAln: a convenient reference-based tool to align sequences and high-throughput reads for phylogeny and evolution in the omic era

The current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, traditional methods typically involve intricate and time-consuming procedures prior to core analyses. These procedures encompass assembly from high-throughput reads, decontamination, gene prediction, homology search, orthology assignment, multiple alignment, and matrix trimming. Such processes significantly impede the efficiency of research when dealing with extensive datasets. In this study, we present PhyloAln, a convenient reference-based tool capable of directly aligning high-throughput reads or complete sequences with existing alignments as reference for phylogenetic and evolutionary analyses. Through testing with both simulated and authentic datasets, PhyloAln demonstrates consistently robust performance in terms of alignment completeness and identity when compared to other reference-based tools. Additionally, we validate the tools adeptness in managing foreign and cross-contamination issues prevalent in sequencing data, which are often overlooked by other tools. Moreover, we showcase the broad applicability of PhyloAln by generating alignments and reconstructing phylogenies from transcriptomes of ladybird beetles, plastid genes of peppers, and ultraconserved elements of turtles. These results underscore the versatility of our tool. Leveraging these advantages, PhyloAln stands poised to expedite phylogenetic and evolutionary analyses in the omic era. The tool is accessible at https://github.com/huangyh45/PhyloAln.

bioinformatics↗

bioRxiv2022

Galectin-8 is a major ligand of LILRB4 prompting MDSC functions in the tumor microenvironment

The LILRB4 myeloid receptor has been implicated in an immunosuppressive microenvironment, with specific antibodies under preclinical or clinical development for tumor immunotherapy. However, it remains largely unknown which natural ligand may trigger LILRB4 to expand myeloid derived suppressive cells (MDSC), and the relevant downstream signaling pathways are also under debate. Here we show that Galectin-8 is a high-affinity functional ligand of LILRB4, and its ligation induces MDSC by activating STAT3 as well as inhibiting NF-{kappa}B. Importantly, Galectin-8 but not APOE could induce MDSC, and both ligands bind LILRB4 in a non-competitive manner. Antibodies recognizing a defined epitope on LILRB4 could efficiently block Galectin-8 binding and neutralize its effects on MDSC induction and relevant signaling pathways. Galectin-8 expression promoted B16 tumor growth in mice, and knockout of LILRB4 attenuated tumor growth in this context. The LILRB4-specific Galectin-8 blocking antibody efficiently suppressed MDSC expansion and tumor growth in vivo. These results identify Galectin-8 as a functionally important ligand of LILRB4, highlighting the blockade of LILRB4-Galectin-8 interaction as a promising strategy for cancer immunotherapy.

immunology↗

bioRxiv2022

The ITPRIPL1- CD3ϵ axis: a novel immune checkpoint controlling T cells activation

The immune system is critical to fighting infections and disease. The molecular recognition of harmful entities takes place when antigen-presenting cells (APC) harboring major histocompatibility complex (MHC) molecules bound to peptides derived from harmful antigens (ligand) dock on specific T cell receptor (TCR)-CD3 complex (receptor) at the surface of CD8+ T cells. The discovery of a general immune checkpoint mechanism to avoid the harmful impact of T cell hyperactivation provoked a paradigm shift. The clinical relevance of this mechanism is highlighted by the fact that PD-1 and PD-L1 inhibitors are very effective at boosting immune reactions. Still, immune evasion frequently happens. The observation that some PD-1/PD-L1 negative tumors have a poor immune response opens the door to identifying a novel immune checkpoint mechanism. Here, we discovered that ITPRIPL1, a gene with unknown function, impairs T cell activation. Surprisingly, we found that CD3{varepsilon} is the direct receptor of ITPRIPL1. This novel immune checkpoint was validated as a drug target using ITPRIPL1 KO mice and monoclonal antibodies. Thus, targeting the ITPRIPL1-CD3e axis, especially in PD-1 - PDL-1 negative patients, is a promising therapeutic strategy to reduce immune evasion.

immunology↗