Biology subjects

Liu, J. J.

Publications and source records attributed to Liu, J. J..

5 recordsLinked to original sources

bioRxiv2025

Calpain-4 Knockdown Modulates Cholesterol Metabolism and LXRα Nuclear Localization in Alcohol-Related Liver Disease

Background & AimsEthanol affects lipid metabolism through multiple pathways, leading to fatty liver development in most ALD patients. Recent studies have highlighted the role of calpain, a calcium-dependent protease, in liver inflammation and fibrosis. Calpain activity is regulated by its essential subunit, Capns1, (calpain-4, Capn4), which stabilizes and modulates the activity of its catalytic isoforms, calpain-1 and calpain-2. This study investigated calpains impact on lipid metabolism in ALD. Approach & ResultsSix-week-old C57Bl6/J mice were injected with rAAV8 vectors encoding Capn4 shRNA or control vectors. After four weeks, mice underwent a 10-day period of ad libitum ethanol consumption, followed by a single gavaged ethanol administration on day 11. Following Capn4 knockdown, microvesicular steatosis was attenuated. While triglycerides and free fatty acids levels showed no significant changes, cholesterol levels were significantly reduced in the ethanol (EtOH) group with Capn4 knockdown. Cpt1a expression increased significantly in the EtOH group with Capn4 knockdown. Western blot analysis revealed increased Cleaved-HMGCR to Pro-HMGCR ratio in Capn4 knockdown mice, suggesting reduced HMGCR activity and suppressed cholesterol biosynthesis. LXR expression was mainly increased in the cytoplasm in the EtOH group, and following Capn4 knockdown, it was relocalized to the nucleus via its activation. In addition, RNA sequencing analysis suggests that Capn4 knockdown contributes to the reprogramming of ethanol-induced disruptions in metabolic and homeostatic pathways, primarily those involving cholesterol metabolism. ConclusionsFurther investigation into the relationship between Capn4 and cholesterol biosynthesis proteins may provide insights into using calpain inhibitors as a therapeutic approach for alcohol-related hepatitis.

molecular biology↗

bioRxiv2024

Error rates in Q_ST--F_ST comparisons depend on genetic architecture and estimation procedures

Genetic and phenotypic variation among populations is one of the fundamental subjects of evolutionary genetics. One question that arises often in data on natural populations is whether differentiation among populations on a particular trait might be caused in part by natural selection. For the past several decades, researchers have used QST -FST approaches to compare the amount of trait differentiation among populations on one or more traits (measured by the statistic QST) with differentiation on genome-wide genetic variants (measured by FST). Theory says that under neutrality, FST and QST should be approximately equal in expectation, so QST values much larger than FST are consistent with local adaptation driving subpopulations trait values apart, and QST values much smaller than FST are consistent with stabilizing selection on similar optima. At the same time, investigators have differed in their definitions of genome-wide FST (such as "ratio of averages" vs. "average of ratios" versions of FST) and in their definitions of the variance components in QST . Here, we show that these details matter. Different versions of FST and QST have different interpretations in terms of coalescence time, and comparing incompatible statistics can lead to elevated type I error rates, with some choices leading to type I error rates near one when the nominal rate is 5%. We conduct simulations under varying genetic architectures and forms of population structure and show how they affect the distribution of QST . When many loci influence the trait, our simulations support procedures grounded in a coalescent-based framework for neutral phenotytpic differentiation.

evolutionary biology↗

bioRxiv2024

EasyAb: A High-Throughput Workflow for Antibody-Based PTM Peptide Enrichment Method Coupled to Mass Spectrometry

Reversible post-translational modification (PTMs) is a fundamental mechanism of cellular signal transduction. In vivo and ex vivo studies to profile PTMs have greatly advanced our understanding of the complexities of cellular signaling. However, apart from the most commonly studied PTMs, large-scale analysis is still very challenging, limiting our understanding of various cellular processes. PTM-bearing peptides often enriched by antibodies, followed by unbiased mass spectrometry (MS)-based readout of hundreds or thousands of sites. To extend the reach of this powerful technology to in vivo and ex vivo studies with small protein starting amounts, we here developed EasyAb, a streamlined and high throughput MS workflow for antibody-based PTM profiling. Using epidermal growth factor receptor (EGFR) signaling and acute myeloid leukemia (AML) cell systems, we demonstrate that EasyAb increases sensitivity and enables multiple large-scale systems-level studies. Furthermore, EasyAb resolves in vivo brain G protein-coupled receptor-mediated tyrosine kinase activation and reveals the long elusive hypothalamic neuron-specific leptin signaling architecture. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/620939v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@259537org.highwire.dtl.DTLVardef@1675a43org.highwire.dtl.DTLVardef@570b61org.highwire.dtl.DTLVardef@ac45df_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSEasyAb, a sensitive, rapid and high-throughput method to quantify post translationally modified peptides in diverse cell systems. EasyAb reveals differential tyrosine phosphorylation of mRNA splicing proteins in AML patient samples. Activation of KOR by "G-protein-biased" non-aversive agonist 6GNTI elicits Src kinase activity in mice. Elucidation of in vivo hypothalamic Leptin induced LEPRb-Jak2 phosphotyrosine signaling architecture.

biochemistry↗

bioRxiv2024

Single-cell genomics and regulatory networks for 388 human brains

Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized [~]250 disease-risk genes and drug targets with associated cell types. Summary Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/585576v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@70b24org.highwire.dtl.DTLVardef@6c9eddorg.highwire.dtl.DTLVardef@131fae2org.highwire.dtl.DTLVardef@4e0f1e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2020

Epithelial cell biomarkers are predictive of response to biologic agents in Crohn's disease

ObjectiveTherapeutic efficacy of biologics has remained at about 50% for 2 decades. In Crohns disease (CD) patients, we examined the predictive value of an epithelial cell biomarker, ileal microvillar length (MVL), for clinical response to ustekinumab (UST) and vedolizumab (VDZ), and its relationship to another biomarker, intestinal epithelial cell (IEC) pyroptosis with respect to response to VDZ. DesignIleal biopsies from the UNITI-2 randomized controlled trial were analyzed for MVL as a predictor of clinical response to UST. In a 5-center academic retrospective cohort of CD patients, ileal MVL was analyzed to determine its predictive value for response to VDZ. Correlation between ileal MVL and IEC pyroptosis was determined, and the discriminant ability of the combination of two biomarkers to VDZ was examined. ResultsClinical response in UST was significantly higher than placebo (65% vs. 39%, p=0.03), with patients with normal MVL (>1.7 {micro}m) having the greatest therapeutic effect: 85% vs. 20% (p=0.02). For VDZ, clinical response with MVL of 1.35-1.55 {micro}m was 82% vs. 44% (<1.35 {micro}m) and 40% (>1.55 {micro}m) (p=0.038). There was no correlation between ileal MVL and IEC pyroptosis. The combination criteria of ileal pyroptosis < 14 positive cells/1000 IECs or MVL of 1.35-1.55 {micro}m could identify 84% of responders and 67% of non-responders (p=0.001). ConclusionsIleal MVL was predictive of response to UST and VDZ in prospective and retrospective CD cohorts. It was independent of ileal IEC pyroptosis, combination of the two biomarkers enhanced the discriminate ability of responders from non-responders to VDZ.

cell biology↗