Y. Lyu

optiPRM: A targeted immunopeptidomics LC-MS workflow with ultra-high sensitivity for the detection of mutation-derived tumor neoepitopes from limited input material

The paper introduces optiPRM, a targeted LC-MS workflow that enhances sensitivity for detecting mutation-derived neoepitopes from limited tumor samples.

Systemic delivery of murine SOD2 mRNA to experimental abdominal aortic aneurysm mitigates expansion and rupture

This study delivers SOD2 mRNA via nanoparticles to mice with abdominal aortic aneurysms, reducing aneurysm expansion and rupture by enhancing antioxidant activity and modulating inflammatory pathways.

An automated archival single-nucleus total RNA sequencing platform mapping integrative and retrospective cell atlas of gliomas

This paper introduces an automated single-nucleus RNA sequencing platform for analyzing archival glioma samples, revealing molecular characteristics and recurrence-related targets.

Widespread readthrough events in plants reveal unprecedented plasticity of stop codons

The paper identifies widespread stop codon readthrough events in plants and reveals the plasticity of stop codons in encoding amino acids.

Flexible and site-specific manipulation of histones in live animals

This paper introduces a method for site-specific histone manipulation in live animals, demonstrating its application in rodent neurons to study chromatin dynamics.

CDK4/6 inhibition enhances SHP2 inhibitor efficacy and is dependent upon restoration of RB function in malignant peripheral nerve sheath tumors

This study shows that combining SHP2 inhibitor TNO155 with CDK4/6 inhibitor enhances anti-tumor activity in MPNST by restoring RB function and overcoming resistance.

Low level of antioxidant capacity biomarkers but not target overexpression predicts vulnerability to ROS-inducing drugs

The paper identifies antioxidant-capacity biomarkers (ACBs) that predict susceptibility to ROS-inducing drugs in lung cancer cells, showing that low ACB expression correlates with nitric oxide levels, not ROS levels.

Increased public health threat of avian-origin H3N2 influenza virus during evolution in dogs

This study identifies how avian-origin H3N2 influenza viruses adapt to dogs, acquiring traits that increase their potential to infect humans.

Integrated single-cell sequencing analysis reveals peripheral immune landscape across the human lifespan

This study uses single-cell sequencing to analyze immune cell dynamics across human lifespan, identifying age-related changes in T cell function, cell interactions, and B cell subsets.

Ubiquitin-based pathway acts inside chloroplasts to regulate photosynthesis

The paper shows the ubiquitin-proteasome system targets proteins inside chloroplasts, including chloroplast-encoded photosynthesis subunits, via the CHLORAD pathway.

Ex vivo to in vivo model of malignant peripheral nerve sheath tumors for precision oncology

The paper develops an ex vivo 3D microtissue model of MPNST that captures genomic diversity and predicts in vivo drug response.

Interaction between spike protein of SARS-CoV-2 and human virus receptor ACE2 using two-color fluorescence cross-correlation spectroscopy

This study uses two-color fluorescence cross-correlation spectroscopy to analyze the interaction between SARS-CoV-2 S1 subunit and human ACE2, showing stronger binding of SARS-CoV-2 compared to SARS-CoV and one-to-one stoichiometry.

Proximity Biotin Labeling Reveals KSHV Interferon Regulatory Factor Networks

This paper uses proximity labeling to identify KSHV vIRF-1 and vIRF-4 interacting proteins, revealing their roles in viral reactivation and innate immune regulation.

RNAseq studies reveal distinct transcriptional response to vitamin A deficiency in small intestine versus colon, uncovering novel vitamin A-regulated genes

This study compares gene expression in the small intestine and colon of vitamin A deficient mice, identifying distinct transcriptional responses and novel VA-regulated genes.

High throughput small molecule screening reveals NRF2-dependent and -independent pathways of cellular stress resistance

This study identifies small molecules that induce cellular stress resistance against paraquat, cadmium, and methyl methanesulfonate, with some compounds activating Nrf2 signaling and others triggering inflammatory and AMPK pathways.

Structural variants, hemizygosity and clonal propagation in grapevines (Vitis vinifera)

The paper catalogs structural variants in grapevine genomes and shows their role in hemizygosity, phenotypic variation, and clonal propagation.

Perception of naturally dead conspecifics impairs health and longevity through serotonin signaling in Drosophila

This study shows that Drosophila perceives dead conspecifics, which affects health and longevity through serotonin signaling.