Biology subjects

Zhang, Y.-g.

Publications and source records attributed to Zhang, Y.-g..

9 recordsLinked to original sources

bioRxiv2025

Disrupted tRNA modification leads to intestinal mitochondrial dysfunction and microbial dysbiosis

Background and aimsTransfer RNA (tRNA) modifications determine translation fidelity and efficiency. It occurs through the action of specific enzymes that modify the nucleotides within the tRNA molecule. Our previous study demonstrated tRNA modopathies and altered queuine-related metabolites in inflammatory bowel diseases. Queuine tRNA-ribosyltransferase catalytic subunit 1 (QTRT1) and QTRT 2 co-localize in mitochondria and form a heterodimeric TGT participating in tRNA Queuosine (tRNA-Q) modification. Human body acquires Queuine/Vitamin Q from intestinal microbiota or from diet. However, the roles of tRNA-Q modifications in the maintenance of intestinal mitochondrial homeostasis and microbiome are still unclear. MethodsWe used publicly available human IBD datasets, QTRT1 knockout (KO) mice, QTRT1 intestinal epithelial conditional KO (QTRT1{Delta}IEC) mice, cultured cell lines with QTRT1-specific siRNA, and organoids from patients with IBD to investigate the mechanism of tRNA-Q modifications in intestinal mitochondrial homeostasis and therapeutic potential in anti-inflammation. ResultsIn single cell RNA sequencing datasets of human IBD, we identified significant reduced intestinal epithelial QTRT1 expression in the patients with Crohns Disease. Using publicly available datasets, we identified significantly changes of Vitamin Q-associated bacteria in human IBD, compared to the healthy control. Qtrt1-/- mice had significant reduction of Q-associated bacteria, e.g., Bacteroides. Alcian Blue and Mucin-2 staining revealed mucosal barrier damage and disrupted homeostasis, with reduced colonic cell proliferation. Intestinal tight junction integrity was impaired in QTRT1-KO mice, as evidenced by reduced ZO-1 and increased Claudin-10 expression. QTRT1{Delta}IEC mice also showed dysbiosis and disrupted TJs. ATP synthesis was significantly decreased in the colon of QTRT1-KO mice, accompanied by severe mitochondrial dysfunction: reduced mitochondrial quality, Cytochrome-C release, and mitochondrial DNA (mtDNA) leakage. Mitochondrial dysfunction contributed to colonic cell death, as shown by elevated expressions of Cleaved Caspase-3 and Cleaved Caspase-1, increased BAX/Bcl-2 ratio, and positive TUNEL signals. Elevated CDC42, CD14, and CD4 levels in QTRT1-KO colon suggested mucosal immune activation and tissue repair responses. QTRT1-deficient CaCO2-BBE cells showed mitochondrial dysfunction. Cytochrome-C and mito-DNA release leading to cell death characterized by elevated expressions of Cleaved Caspase-3 and Caspase-1, increased BAX/Bcl-2 ratio, and higher apoptosis rate. Organoids isolated from patients with IBD showed reduced levels of QTRT1 and dysfunctional mitochondria. Restoring mitochondrial function leads to enhanced QTRT1. ConclusionsThese findings underscore the critical role of QTRT1/Q-tRNA modification in maintaining intestinal and microbial homeostasis. Mechanistically, QTRT1 loss impacts mitochondrial integrity and mucosal homeostasis. Our study highlights the novel roles of tRNA-Q modification in maintaining mucosal barriers and innate immunity in intestinal health. What is already known about this subject?O_LIEukaryotes acquire queuine (q), also known as Vitamin Q, as a micronutrient factor from intestinal microbiota or from diet. C_LIO_LIVitamin Q is needed for queuosine (Q) modification of tRNAs for the protein translation rate and fidelity. C_LIO_LIQueuine tRNA-ribosyltransferase catalytic subunit 1 (QTRT1) is reduced in human IBD. C_LIO_LIHowever, health consequences of disturbed availability of queuine and altered Q-tRNA modification in digestive diseases remain to be investigated. C_LI What are the new findings?O_LIQTRT1 deficiency leads to altered microbiome and reduced Vitamin Q-associated bacteria in human IBD and a QTRT1 KO animal model. C_LIO_LIQTRT1 protects the host against losing intestinal integrity during inflammation. C_LIO_LIQTRT1 localizes in mitochondria and plays novel functions by maintaining intestinal mitochondrial function. QTRT1 loss impacts tRNA modification in the intestine, linking to mitochondrial integrity and mucosal homeostasis. C_LIO_LIHuman IBD showed reduced levels of QTRT1 and dysfunctional mitochondria. Restoring mitochondrial function leads to enhanced QTRT1. C_LI How might it impact on clinical practice in the foreseeable future?Targeting tRNA-Q modification in enhancing mitochondrial function will be a novel method to maintain intestinal health.

cell biology↗

bioRxiv2025

Loss of intestinal endosome associated protein sorting nexin 27 disrupts epithelial barrier and promotes inflammation

Backgrounds and aimsSNX27, member of the sorting nexin (SNX) family, carries a unique PDZ domain and mediates recycling of endocytosed transmembrane proteins. SNX27 is critical for neurodevelopmental processes, however its role in intestine remains unexplored. We aim to determine the previously unknown roles of SNX27 in regulating intestinal homeostasis, epithelial barrier integrity, and inflammatory responses. MethodsWe used available datasets to analyze SNX27 expression in human IBD. We generated a novel mouse model of SNX27 conditional deletion from intestinal epithelial cells (SNX27{Delta}IEC) and challenged these mice with Dextran Sulfate Sodium (DSS). ResultsSNX27 expression was significantly lower in human IBD, including UC and CD. SNX27{Delta}IEC mice had significantly lower bodyweight and exhibited increased proliferation and poor differentiation of secretory Paneth and Goblet cells. We found reduced mucin layer and downregulation of crucial epithelial barrier proteins {Delta}-catenin, E-cadherin, ZO-1, and Claudin10 in SNX27{Delta}IEC mice. SNX27{Delta}IEC mice showed high intestinal permeability and spontaneously developed intestinal inflammation. Moreover, SNX27{Delta}IEC mice were more susceptible towards DSS-induced colitis, compared to the SNX27Loxp mice. ConclusionOverall, deletion of intestinal epithelial SNX27 weakens barrier functions and promotes inflammation. Our results indicate a novel role of SNX27 in regulating intestinal physiology and protecting against intestinal disorders. Thus, understanding the mechanisms of SNX27 downregulation in IBD will provide insights into new prevention and targets against chronic inflammation. SynopsisO_LISNX27 recycles internalized transmembrane proteins in the endocytic pathway. Human IBD showed reduced levels of SNX27. C_LIO_LISNX27 plays novel functions by maintaining intestinal homeostasis and inhibiting inflammation. C_LIO_LISNX27 protects the host against losing intestinal integrity during inflammation. C_LI

physiology↗

bioRxiv2022

Extraintestinal roles of intestinal vitamin D receptor in protecting against dysbiosis and tumorigenesis in breast cancer

The microbiota play critical roles in regulating the function and health of intestine and extraintestinal organs. A fundamental question is whether there is an intestinal-microbiome-breast axis during the development of breast cancer. If yes, what are the roles of host factors? Vitamin D receptor (VDR) involves host factors and the human microbiome. Vdr gene variation shapes the human microbiome and VDR deficiency leads to dysbiosis. We hypothesized that intestinal VDR protects hosts against tumorigenesis in breast. Reduced VDR mRNA expression was observed in patients with breast cancer. We used a 7,12-dimethylbenzanthracene (DMBA)-induced breast cancer model in intestinal epithelial VDR knockout (VDR{Delta}IEC) mice. We reported that VDR{Delta}IEC mice with dysbiosis are more susceptible to breast cancer induced by DMBA. Intestinal and breast microbiota analysis showed that lacking VDR leads to bacterial profile shift from normal to susceptible carcinogenesis. We found enhanced bacterial staining within breast tumors. At the molecular and cellular levels, we identified the mechanisms by which intestinal epithelial VDR deficiency led to increased gut permeability, disrupted tight junctions, microbial translocation, and enhanced inflammation, thus increasing the tumor size and number in breast. Furthermore, treatment with beneficial bacterial metabolite butyrate or probiotic Lactobacillus plantarum reduced the breast tumors, enhanced the tight junctions, and inhibited inflammation in the VDR{Delta}IEC mice. Gut microbiome contribute to the pathogenesis of diseases, not only in the intestine, but also in the breast. Our study provides new insights into the mechanism by which intestinal VDR dysfunction and gut dysbiosis led to high risk of extraintestinal tumorigenesis. Gut-tumor-microbiome interactions indicate a new target in the prevention and treatment of breast cancer. O_FIG O_LINKSMALLFIG WIDTH=165 HEIGHT=200 SRC="FIGDIR/small/492300v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@7e354eorg.highwire.dtl.DTLVardef@1dd9b50org.highwire.dtl.DTLVardef@1ffe2c5org.highwire.dtl.DTLVardef@810b1a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

Dysfunction of transfer RNA modifications in inflammatory bowel disease

Backgrounds and aimsTransfer RNA (tRNA) is the most extensively modified RNA in cells. Queuosine (Q)-modification is a fundamental process for fidelity and efficiency of translation from RNA to proteins. In eukaryotes, tRNA-Q-modification relies on the intestinal microbial product queuine. However, the roles and potential mechanisms of Q-tRNA modifications in IBD are unknown. MethodsWe explored the Q-tRNA modifications and expression of Q tRNA ribosyltransferase catalytic subunit 1 (QTRT1) in patients with IBD by investigating human biopsies and reanalyzing datasets. We used colitis models, organoids, and cultured cells for loss- and gain-of-function studies to investigate the molecular mechanisms of Q-tRNA modifications in intestinal inflammation. ResultsQTRT1 expression was significantly downregulated in ulcerative colitis and Crohns disease patients. The four Q-tRNA-related tRNA synthetases (asparaginyl-aspartyl-, histidyl-, and tyrosyl-tRNA synthetase) were decreased in IBD patients. This reduction was further confirmed in DSS-induced colitis and IL10-deficient mice. Reduced QTRT1 was significantly correlated with cell proliferation and intestinal junctions, including downregulated {beta}-catenin and Claudin-5 and upregulated Claudin-2. These alterations were confirmed in vitro by deleting QTRT1 from cells. Queuine treatment significantly enhanced cell proliferation and junction functions in cell lines and human colonoids. Queuine treatment also reduced inflammation in epithelial cells. Moreover, altered QTRT1-related metabolites were found in human IBD. ConclusiontRNA modifications play an unexplored novel role in the pathogenesis of intestinal inflammation by altering epithelial proliferation and junctions. Investigations on tRNA modification will uncover novel molecular mechanisms for potential prevention and therapy for IBD.

cell biology↗

bioRxiv2022

Dietary butyrate treatment enhances healthy metabolites by longitudinal untargeted metabolomic analysis in amyotrophic lateral sclerosis mice

Microbial metabolites affect the neuron system and muscle cell functions. Amyotrophic Lateral Sclerosis (ALS) is a multifactorial neuromuscular disease. Our previous study has demonstrated elevated intestinal inflammation and dysfunctional microbiome in ALS patients and an ALS mouse model (human-SOD1G93A transgenic mice). However, the metabolites in ALS progression are unknown. Using an unbiased global metabolomic measurement and targeted measurement, we investigated the longitudinal changes of fecal metabolites in the SOD1G93A mice over the course of 13 weeks. We compared the changes of metabolites and inflammatory response in age-matched WT and SOD1G93A mice treated with bacterial product butyrate. We found changes in carbohydrate levels, amino acid metabolism, and formation of gamma-glutamyl amino acids. Shifts in several microbially-contributed catabolites of aromatic amino acids agree with butyrate-induced changes in composition of gut microbiome. Declines in gamma-glutamyl amino acids in feces may stem from differential expression of GGT in response to butyrate administration. Due to signaling nature of amino acid-derived metabolites, these changes indicate changes in inflammation (e.g. histamine) and contribute to differences in systemic levels of neurotransmitters (e.g. GABA, glutamate). Butyrate treatment was able to restore some of the healthy metabolites in ALS mice. Moreover, microglia in the spinal cord were measured by the IBA1 staining. Butyrate treatment significantly suppressed the IBA1 level in the SOD1G93A mice. The serum IL-17 and LPS were significantly reduced in the butyrate treated SOD1G93A mice. We have demonstrated an inter-organ communications link among metabolites, inflammation, and ALS progression, suggesting the potential to use metabolites as ALS hallmarks and for treatment. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/476456v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@16d3e4dorg.highwire.dtl.DTLVardef@1155c05org.highwire.dtl.DTLVardef@14c6155org.highwire.dtl.DTLVardef@18a30d6_HPS_FORMAT_FIGEXP M_FIG We compared the changes of metabolites and inflammatory response in age-matched WT and SOD1G93A mice treated with bacterial product butyrate. Butyrate treatment was able to restore some of the healthy metabolites in ALS mice. Due to signaling nature of amino acid-derived metabolites, these changes indicate changes in inflammation and contribute to differences in systemic levels of neurotransmitters (e.g. GABA, glutamate). Moreover, butyrate treatment significantly suppressed the microglia IBA1 level and aggregated SOD1G93A in the SOD1G93A mice. The inflammatory cytokine, e.g serum IL-17, was significantly reduced in the butyrate treated SOD1G93A mice. We have demonstrated an inter-organ communications link among metabolites, inflammation, and ALS progression, suggesting the potential to use metabolites as ALS hallmarks and for treatment. C_FIG

physiology↗

bioRxiv2021

Aberrant enteric neuromuscular system and dysbiosis in amyotrophic lateral sclerosis

BackgroundEmerging evidence has demonstrated that microbiota directly affects the enteric neuron system (ENS) and smooth muscle cell functions via metabolic products or endogenous bacterial components. Amyotrophic Lateral Sclerosis is a neuromuscular disease characterized by the progressive death of motor neurons and muscle atrophy. The GI symptoms in patients were largely ignored or underestimated, especially before the diagnosis of ALS. The relationship between enteric neuromuscular system and microbiome in ALS progression is unknown. MethodsWe performed longitudinal studies on the ENS and microbiome in the ALS human-SOD1G93A transgenic G93A mice. We treated age-matched wild-type and ALS mice with bacterial product butyrate or antibiotics to investigate microbiome and neuromuscular functions. Intestinal motility, microbiome, an ENS marker GFAP, a smooth muscle marker (SMMHC), and human colonoids have been examined. The distribution of human-G93A-SOD1 (Superoxide Dismutase 1) protein was tested as an indicator of ALS progression. ResultsAt 2-month-old before ALS onset, G93A mice had significant lower intestinal motility, decreased grip strength, and reduced time in the rotarod. We observed increased GFAP and decreased SMMHC expression. These changes correlated with consistent increased aggregation of mutated SOD1G93A in the colon, small intestine, and spinal cord. Butyrate and antibiotic treatment showed a significantly longer latency to fall in the rotarod test, reduced SOD1G93A aggregation, and enhanced ENS and muscle function. Feces from 2-month-old SOD1G93A mice significantly enhanced SOD1G93A aggregation in human colonoids transfected with a SOD1G93A-GFP plasmid. Longitudinal studies of microbiome data further showed the altered bacterial community related with autoimmunity (e.g., Clostridium sp. ASF502, Lachnospiraceae bacterium A4), inflammation (e.g., Enterohabdus Muris,), and metabolism (e.g., Desulfovibrio fairfieldensis) at 1- and 2-month-old SOD1G93A mice, suggesting the early microbial contribution to the pathological changes. ConclusionsWe have demonstrated a novel link between microbiome, hSOD1G93A aggregation, and intestinal mobility. Dysbiosis occurred at the early stage of the ALS mice before observed mutated-SOD1 aggregation, slow intestinal motility, and dysfunction of ENS. Manipulating the microbiome improves the muscle performance of SOD1G93A mice. Our study provides insights into fundamentals of intestinal neuromuscular structure/function and microbiome in ALS.

physiology↗

bioRxiv2021

Vitamin D Receptor Upregulates Tight Junction Protein Claudin-5 against Tumorigenesis

Background/ObjectiveTight junctions (TJs) are essential for barrier integrity, inflammation, and cancer. The TJ protein Claudin-5 in the epithelia forms paracellular barriers and pores for permeability. Vitamin D and the vitamin D receptor (VDR) play important roles in various cancers. Although VDR and Claudin-5 are all involved in colorectal cancer (CRC), it remains unclear if they are closely related or function independently. DesignUsing the human CRC database, we explored the correlation between VDR and Claudin-5. We then investigated the VDR regulation of Claudin-5 using VDR knockout (VDR-/-) and intestinal epithelial VDR knockout mice (VDR{Delta}IEC) with chemical-induced colon cancer and an epithelial VDR overexpression model. Human samples, organoids, and intestinal epithelial cells were used to determine the underlying mechanisms. ResultsIn human colon cancer, colonic VDR expression was low and was significantly correlated with a reduction of Claudin-5 mRNA and protein. In the colon of VDR-/- and VDR{Delta}IEC mice, deletion of VDR led to lower protein and mRNA levels of Claudin-5. Intestine permeability was increased in the AOM-DSS-induced VDR-/- colon cancer model. Lack of VDR and a reduction of Claudin-5 are associated with an increased number of tumors in the VDR-/- and VDR{Delta}IEC mice. Furthermore, gain and loss of function studies have identified CLDN-5 as a downstream target of the VDR signaling pathway. Epithelial VDR overexpression protected against the loss of Claudin 5 in response to intestinal inflammation ConclusionThis study advances the understanding of how VDR regulates intestinal barrier functions in tumorigenesis as a biomarker and potential treatment. A short summaryO_LIWhat is already known about this subject? O_LITight junction structures are essential for intestinal barrier integrity, inflammation, and cancer. C_LIO_LIVitamin D deficiency and the vitamin D receptor (VDR) play important roles in the development of colon cancer. C_LI C_LIO_LIWhat are the new findings? O_LIOur study is the first to link barrier function, a specific tight junction protein, and genetic susceptibility through intestinal epithelial VDR in human colorectal cancer. C_LIO_LIOur study fills an existing gap by characterizing the mechanism of intestinal epithelial VDR in regulating barrier functions through alterations in TJs in tumorigenesis. VDR is important for the maintenance of the physiological level of the TJ protein Claudin-5 in the colon. The CLDN-5 gene is a downstream target of the VDR signaling pathway. Lack of VDR led to a reduction of Claudin-5 in tumors, whereas enhancing VDR increased Claudin-5 to protect the intestinal epithelial cells from tumorigenesis. C_LIO_LIWe report fecal VDR reduction in a colon cancer model. This introduces the possibility for the identification of new biomarkers and therapeutic targets to restore VDR-dependent functions in CRC. C_LI C_LIO_LIHow might it impact on clinical practice in the foreseeable future O_LIDiagnosis of CRC considering VDR status C_LIO_LIBarrier: direct, indirect biomarkers C_LIO_LIIntestinal barriers in cancer prevention and treatment C_LI C_LI Barrier function and VDR are not only essential for the maintenance of intestinal homeostasis, but they are also critical for the development of chronic mucosal inflammation and cancer. This knowledge can be immediately used to develop intestinal VDR and Claudin-5 as clinical biomarkers for identifying patients who may benefit from currently available interventions and could also be used for the eventual development of novel strategies for the prevention and treatment of human CRC.

cancer biology↗

bioRxiv2020

Vitamin D receptor protects against dysbiosis and tumorigenesis via the JAK/STAT pathway in intestine

BackgroundVitamin D exerts regulatory roles via vitamin D receptor (VDR) in mucosal immunity, host defense, and inflammation involving host factors and microbiome. Human Vdr gene variation shapes the microbiome and VDR deletion leads to dysbiosis. Low VDR expression and diminished vitamin D/VDR signaling are observed in colon cancer. Nevertheless, how intestinal epithelial VDR is involved in tumorigenesis through gut microbiota remains unknown. We hypothesized that intestinal VDR protects mice against dysbiosis via modulating the JAK/STAT pathway in tumorigenesis. To test our hypothesis, we used an azoxymethane/Dextran Sulfate Sodium-induced cancer model in intestinal VDR conditional knockout (VDR{Delta}IEC) mice, cell cultures, stem-cell derived colonoids, and human colon cancer samples. ResultsVDR{Delta}IEC mice have higher numbers of tumors with location shifted from distal to proximal colon. Fecal microbiota analysis showed that VDR deletion leads to bacterial profile shift from normal to susceptible carcinogenesis. We found enhanced bacterial staining in mouse and human tumors. Microbial metabolites from VDR{Delta}IEC mice showed elevated secondary bile acids, consistent with the observations in human CRC. We further identified that VDR protein bound to the Jak2 promoter, suggesting that VDR transcriptionally regulated Jak2. The JAK/STAT pathway is critical in intestinal and microbial homeostasis. Fecal samples from VDR{Delta}IEC mice activate the STAT3 activation in human and mouse organoids. Lack of VDR led to hyperfunction of Jak2 in respond to intestinal dysbiosis. A JAK/STAT inhibitor abolished the microbiome-induced activation of STAT3. ConclusionWe provide insights into the mechanism of VDR dysfunction leading to dysbiosis and tumorigenesis. It indicates a new target -- microbiome and VDR for prevention of cancer.

cancer biology↗

bioRxiv2020

Salmonella Enteritidis Effector AvrA suppresses autophagy by reducing Beclin-1 protein

Autophagy is a cellular process to clear pathogens. Salmonella enterica serovar Enteritidis (S.E) has emerged as one of the most important food-borne pathogens. However, major studies still focus on Salmonella enterica serovar Typhimurium. Here, we reported that AvrA, a S. Enteritidis effector, inhibited autophagy to promote bacterial survival in the host. We found that AvrA regulates the conversion of LC3 I into LC3 II and the enrichment of lysosomes. Beclin-1, a key molecular regulator of autophagy, was decreased after AvrA expressed strain colonization. In S.E-AvrA--infected cells, we found the increases of protein levels of p-JNK and p-c-Jun and the transcription level of AP-1. AvrA-reduction of Beclin-1 protein expression is through the JNK pathway. The JNK inhibitor abolished the AvrA-reduced Beclin-1 protein expression. Moreover, we identified that the AvrA mutation C186A abolished its regulation of Beclin-1 expression. In addition, AvrA protein interacted with Beclin-1. In organoids and infected mice, we explored the physiologically related effects and mechanism of AvrA in reducing Beclin-1 through the JNK pathway, thus attenuating autophagic responses. ImportanceSalmonella Enteritidis is an important pathogen with a public health concern and farm production risk, yet the host-pathogen interactions that govern the survival of S. Enteritidis infections are incompletely understood. Anti-bacterial autophagy provides potent cell-autonomous immunity against bacterial colonization. Here, we report that a new role for effector AvrA of S. Enteritidis in the reduction of Beclin-1 protein expression through the JNK pathway and the attenuation of the autophagic response in intestinal epithelial cells. This finding not only indicates an important role of S. Enteritidis effector in reducing host protein as a strategy to suppress autophagy, but also suggests manipulating autophagy as a new strategy to treat infectious diseases.

microbiology↗