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Chu, Q.

Publications and source records attributed to Chu, Q..

At least 19 recordsLinked to original sources

A FIT2-BLTP1 module sustains lipid droplet phosphatidic acid and restrains overgrowth

Lipid droplets (LDs) are assembled at discrete endoplasmic reticulum (ER) subdomains whose local phospholipid composition, rather than their protein content alone, determines whether a LD nucleates and how large it grows. Phosphatidic acid (PA) is the pivotal lipid of this environment, yet how PA reaches a forming LD has remained unknown. Here we show that the bridge-like lipid transfer protein BLTP1 is required to maintain PA in LD-associated membranes. BLTP1 depletion impaired LD formation and produced fewer but enlarged LDs across mammalian cell types, and lowered LD accumulation during adipogenic differentiation. At the ER, BLTP1 engaged the LD emergence factor FIT2 through its N-terminal transmembrane segment, an interaction that strengthened upon induction of LD formation and was strongly reduced by the disease-associated FIT2 G232R substitution. Co-depletion of FIT2 relieved the LD overgrowth caused by loss of BLTP1. Wild-type BLTP1, but neither a FIT2-binding-defective chimera nor a lipid-transfer-groove mutant, rescued LD formation in BLTP1-depleted cells. Lipidomics of purified LDs showed that BLTP1 loss most strongly lowered PA, most prominently the species PA 36:2, whereas PA and the major phospholipid classes of bulk ER membranes were unchanged. Collectively, we propose that local PA supply by BLTP1 coordinates LD assembly and growth.

cell biology↗

Metabolic responses to physiological stressors assessed using continuous glucose monitoring integrated with indirect calorimetry in mice

Continuous glucose monitoring (CGM) in rodents has provided unprecedented temporal resolution of glycemic dynamics in vivo. Even in the absence of deliberate perturbation, glucose levels in mice are dynamic, fluctuating in response to the timing and duration of feeding events, changes in neurological and hormonal states, physical activity, and photoperiod. To obtain a comprehensive view of metabolic adaptations under common experimental conditions, we monitored freely moving mice simultaneously using CGM and indirect calorimetry to quantify glucose, food intake, physical activity and metabolic rate. We characterized glycemic and metabolic responses to routine laboratory interventions, including short-term and overnight fasting, refeeding, tail blood sampling during glucose tolerance tests, changes in ambient temperature to cold or thermoneutral conditions, and access to running wheels. We found that food removal induced a robust, transient stress response characterized by increased blood glucose, body temperature, energy expenditure, and physical activity. However, prolonged fasting ultimately led to hypoglycemia and torpor. The magnitude and variability of glycemic responses to insulin tolerance tests were strongly influenced by fasting duration, and tail-tip blood collection itself elicited substantial hyperglycemia. In contrast to prolonged fasting, refeeding produced relatively modest and transient effects on glucose and energy expenditure. Cold exposure elicited increased energy expenditure along with a sustained hyperglycemic response. Voluntary wheel running induced transient increases in glucose and metabolic activity and promoted a shift toward increased fatty acid oxidation. Together, these findings demonstrate that common laboratory manipulations exert dynamic, often substantial effects on glycemia and whole-body metabolism that are readily revealed by CGM and indirect calorimetry.

physiology↗

Somatic-to-germline transmission of horizontally acquired extrachromosomal circular DNA in Brassica graft chimeras

Whether somatically acquired traits can contribute to heritable variation has remained an open question in plant biology for over a century. Here, using graft-induced periclinal chimeras between Brassica juncea and Brassica oleracea, we identified extrachromosomal circular DNA (eccDNA) as mobile genetic elements capable of crossing histological boundaries and entering the germline. We demonstrated that grafting could promote the horizontal transfer of eccDNA between somatic cell layers, enabling its stable maintenance in recipient tissues and permitting transmission through sexual reproduction across multiple generations. We found that transmitted eccDNA is non-randomly distributed across the genome, preferentially originating from gene-dense regions, and enriched for features associated with molecular persistence, such as inverted repeats, hairpin-forming sequences, and autonomously replicating sequence (ARS) consensus motifs. These genetic regions conferred replication competence, as evidenced by autonomous propagation in an ARS-less heterologous yeast system. Sexual progeny carrying graft-acquired eccDNA exhibited reproducible and lineage-dependent alterations in leaf morphology and drought tolerance, accompanied by coordinated transcriptional reprogramming. Notably, a subset of inherited eccDNA remained transcriptionally active in progeny, producing transcripts absent from self-grafted controls. Our findings establish eccDNA as heritable extrachromosomal elements that link graft-mediated somatic genetic transfer with stable germline transmission, thereby expanding the molecular scope of heritable variation in plants and providing a conceptual framework for graft-based trait transmission.

plant biology↗

Automatic binding of basic sensory features requires consciousness

Conscious awareness requires establishing coherent percepts. Yet, whether consciousness is necessary for initiating the integration of basic sensory features remains unclear. Competing theories implicate distinct functional regimes of consciousness in the process of feature binding and creating conscious percepts. We used a novel multi-feature oddball paradigm with intracranial stereo-electroencephalography (sEEG) recordings in awake and anesthetized states to investigate the functional boundary of consciousness. In the awake state, the auditory attributes of loudness and tone, as well as the binding of the two features, were automatically encoded without attention to the stimuli in a functionally localized sensory cortical network. In the anesthetized state, the cortical registration of single attributes was preserved, whereas the binding was abolished. Moreover, anesthesia mostly influenced later cortical processes after stimuli offset. These results reveal the borderline of exertion of consciousness between the encoding and manipulation of basic sensory features in local cortical circuits - the functional boundary of consciousness constrains the feedforward binding and recurrent process directly at local rather than global level computations.

neuroscience↗

Competitive catabolism in systemic mammalian metabolic homeostasis

Systemic metabolic homeostasis maintains circulating nutrient concentrations within physiological ranges. Insulin is central to this process, lowering circulating levels of glucose, free fatty acids, and ketones. Yet, how simultaneous homeostasis of these nutrients is achieved remains unclear. Here we develop a differential equation model of fasting metabolic homeostasis. Grounded in mass action kinetics, this multi-nutrient model reveals how a fixed energy demand naturally leads to competition between major circulating nutrients for oxidation ( competitive catabolism). Perturbative nutrient infusions confirm this emergent behavior. The multi-nutrient model predicts that insulin promotes fasting glucose homeostasis primarily indirectly by slowing lipolysis. It further identifies a physiological circuit by which obesity causes diabetes: Increased fat mass promotes lipolysis, releasing fatty acids into circulation that compete with glucose for oxidation, elevating glucose. Resulting hyperinsulinemia restores proper lipid catabolic flux but not euglycemia. Thus, quantitative modeling reveals a physiological homeostatic circuit through which obesity causes type 2 diabetes.

physiology↗

BLTP1-dependent phospholipid efflux prevents mitochondrial lipid overload and apoptosis at FKBP8-tethered ER-mitochondrial contact

Maintenance of mitochondrial phospholipid homeostasis is critical for organellar function and cell survival, yet mechanisms enabling phospholipid efflux from mitochondria remain undefined. We identify BLTP1 as a phospholipid transporter that exports phospholipids from mitochondria to maintain lipid homeostasis. The outer mitochondrial membrane protein FKBP8 recruits BLTP1 to ER-mitochondrial contact sites, establishing a dedicated lipid export pathway. BLTP1 deficiency triggers pathological accumulation of phosphatidic acid (PA), phosphatidylglycerol (PG), and cardiolipin (CL) within mitochondria. This lipid overload is associated with elevation of mitochondrial reactive oxygen species (ROS), bioenergetic dysfunction, and apoptosis. Critically, depleting intramitochondrial lipid transfer proteins (e.g., PRELID1) or enzymes in the CL synthesis pathway (e.g., PTPMT1, CRLS1) prevents apoptosis caused by BLTP1 deficiency. Our findings defines a BLTP1-FKBP8-dependent mechanism for mitochondrial phospholipid efflux that is essential for mitochondrial function and cell survival.

cell biology↗

Influence of Macrocyclization Strategies on DNA-Encoded Cyclic Peptide Libraries

Discovery of cyclic peptide hits using DNA-encoded libraries (DELs) has recently been extensively researched, with significant efforts directed toward developing DEL-compatible macrocyclization methods. To investigate how different cyclic linkers influence DEL selection outcomes, we constructed eight distinct sub-libraries and screened them against two protein targets, MDM2 and GIT1, resulting in two representative yet contrasting scenarios. Validation studies for MDM2 revealed that structural similarity patterns observed across multiple sub-libraries could enhance confidence in the authenticity of identified hits. Notably, cmp-10 demonstrated potent inhibitory activity, exhibiting an inhibition constant of 11 nM. In contrast, selections against GIT1 produced discrete enrichment patterns. From these outcomes, two exemplary compounds were selected and validated through both on-DNA and off-DNA modes. cmp-17 was confirmed to bind specifically to the desired binding pocket, displaying a dissociation constant of 1.22 M. Furthermore, ITC experiments using mutant GIT1 proteins (GIT1L271A/L279A and GIT1L271L/L279L) provided additional insights into the mechanism by which cmp-17 disrupts the interaction between GIT1 and {beta}-Pix.

biochemistry↗

Sub-clustering, marker identification and multi-omics integration influenced by protoplasting in plant scRNA -seq data analysis

Single-cell RNA sequencing (scRNA-seq) technology is a powerful tool for exploring cell heterogeneity and lineage dynamics, revealing complex mechanisms driving tissue function and development. However, plant cells rigid cell walls require a protoplasing step, an enzymatic process that can introduce biases. The impact of protoplasting on plant scRNA-seq data remains poorly understood. In this study, we analyzed gene expression patterns from bulk RNA-seq of various plant tissues before and after protoplasting. Cell-type specific protoplasting effects were discovered in different plant tissues. Protoplasting-related biases were found to distort clustering, marker gene identification, and multi-omics integration. By calculating protoplasted scores based on gene expression, we identified and mitigated protoplasting effects, enabling the accurate clustering and annotation of tobacco BY-2 cells and identification of cell-cycle-related genes. Our findings underscore the importance of assessing and correcting for protoplasting biases in plant scRNA-seq data analysis, offering new insights for more accurate data interpretation and biological discovery.

bioinformatics↗

Off-target depletion of plasma tryptophan by allosteric inhibitors of BCKDK

The activation of branched chain amino acid (BCAA) catabolism has garnered interest as a potential therapeutic approach to improve insulin sensitivity, enhance recovery from heart failure, and blunt tumor growth. Evidence for this interest relies in part on BT2, a small molecule that promotes BCAA oxidation and is protective in mouse models of these pathologies. BT2 and other analogs allosterically inhibit branched chain ketoacid dehydrogenase kinase (BCKDK) to promote BCAA oxidation, which is presumed to underlie the salutary effects of BT2. Potential "off-target" effects of BT2 have not been considered, however. We therefore tested for metabolic off-target effects of BT2 in Bckdk-/- animals. As expected, BT2 failed to activate BCAA oxidation in these animals. Surprisingly, however, BT2 strongly reduced plasma tryptophan levels and promoted catabolism of tryptophan to kynurenine in both control and Bckdk-/- mice. Mechanistic studies revealed that none of the principal tryptophan catabolic or kynurenine-producing/consuming enzymes (TDO, IDO1, IDO2, or KATs) were required for BT2-mediated lowering of plasma tryptophan. Instead, using equilibrium dialysis assays and mice lacking albumin, we show that BT2 avidly binds plasma albumin and displaces tryptophan, releasing it for catabolism. These data confirm that BT2 activates BCAA oxidation via inhibition of BCKDK but also reveal a robust off-target effect on tryptophan metabolism via displacement from serum albumin. The data highlight a potential confounding effect for pharmaceutical compounds that compete for binding with albumin-bound tryptophan.

pharmacology and toxicology↗

Proteomic Stratification of Prognosis and Treatment Options for Small Cell Lung Cancer

Small cell lung cancer (SCLC) is a highly malignant and heterogeneous cancer with limited therapeutic options and prognosis prediction models. Here, we analyzed formalin-fixed, paraffin-embedded (FFPE) samples of surgical resections by proteomic profiling, and stratified SCLC into three proteomic subtypes (S-I, S-II, and S-III) with distinct clinical outcomes and chemotherapy responses. The proteomic subtyping was an independent prognostic factor and performed better than current TNM or Veterans Administration Lung Study Group (VALG) staging methods. The subtyping results could be further validated using FFPE biopsy samples from an independent center, extending the analysis to both surgical and biopsy samples. The signatures of the S-II subtype in particular suggest potential benefits from immunotherapy. Differentially overexpressed proteins in S-III, the worst prognostic subtype, allowed us to nominate potential therapeutic targets, indicating that patient selection may bring new hope for previously failed clinical trials. Finally, analysis of an independent cohort of SCLC patients who had received immunotherapy validated the prediction that the S-II patients had better Progression Free Survival (PFS) and Overall Survival (OS) after first-line immunotherapy. Collectively, our study provides the rationale for future clinical investigations to validate the current findings for more accurate prognosis prediction and precise treatments.

cancer biology↗

The complete chloroplast genome sequence of Akebia trifoliata and a comparative analysis within the Ranales clade

The complete nucleotide sequence of the Akebia trifoliata chloroplast (cp) genome was reported and characterized in this study. The cp genome is a closed circular molecule of 157 949 bp, composed of a pair of IR regions of 26 149 bp, one LSC region of 86 595 bp, and one SSC region of 19 056 bp. The GC contents of the LSC, SSC, and IR regions, and the whole cp genome are 37.11%, 33.62%, 43.08% and 38.66%, respectively. The cp genome contains 130 predicted functional genes, including 85 PCGs of 79 107 bp, 37 tRNA and 8 rRNA genes of 11 851 bp. 168 SSRs and 23 long repeats were identified in the cp genome. The results revealed that 21 891 codons characterize the coding capacity of 85 protein-coding genes in Akebia trifoliata, 10.84% and 1.20% of the codons coded for leucine and cysteine respectively. The usage of the start codon exhibited no bias in the A. trifoliata cp genome. Phylogenetic analysis suggest that A. trifoliata is most closely related to S. japonica, which then formed a cluster with N. dormestica and M. saniculifolia to form subgroup of Ranunculales. Our study provides information on mangrove plant species in coastal intertidal zones.

plant biology↗

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed by computational detection tools. During the last decade, a plethora of such tools have been developed, but a systematic comparison with orthogonal validation is missing. Here, we set up a circRNA detection tool benchmarking study, in which 16 tools were used and detected over 315,000 unique circRNAs in three deeply sequenced human cell types. Next, 1,516 predicted circRNAs were empirically validated using three orthogonal methods. Generally, tool-specific precision values are high and similar (median of 98.8%, 96.3%, and 95.5% for qPCR, RNase R, and amplicon sequencing, respectively) whereas the sensitivity and number of predicted circRNAs (ranging from 1,372 to 58,032) are the most significant tool differentiators. Furthermore, we demonstrate the complementarity of tools through the increase in detection sensitivity by considering the union of highly-precise tool combinations while keeping the number of false discoveries low. Finally, based on the benchmarking results, recommendations are put forward for circRNA detection and validation.

genomics↗

SEN1 is responsible for molybdate transport into nodule symbiosomes for nitrogen fixation in Lotus japonicus

Symbiotic nitrogen fixation (SNF) in legume root nodules requires a steady supply of molybdenum (Mo) for synthesis of the iron-Mo cofactor for nitrogenase in bacteroids. For this nutrient to be exported by the host plant it must cross the peribacteroid membrane (PBM), however, the molybdate transporter responsible has not yet been identified. A Lotus japonicus symbiotic mutant, sen1, forms nodules that do not fix nitrogen; it has nodule defects and bacteroid degradation. The biochemical function and subcellular localization of SEN1 protein remains to be elucidated. Here, we found a new phenotype in which the SEN1 mutation resulted in increased Mo accumulation in the nodule host fractions but decreased Mo accumulation in the bacteroids at 10 days post inoculation. We identified the molybdate efflux transport activity of SEN1 via heterologous expression in yeast. SEN1 was expressed exclusively in nodules, and its expression was stable in response to varying Mo supply in nutrient solution. In situ immunostaining verified that the SEN1 protein is localized, in part, to the PBM in the rhizobium-infected cells. Taken together, these results confirmed that SEN1 is responsible for mediating molybdate efflux from the cytosol of nodule host cells to the symbiosomes for SNF. Furthermore, SEN1 mutation reduced the expression of nifD and nifK, suggesting that SEN1 may be pertinent to iron-Mo-cofactor assembly. This work fills the knowledge gap regarding how molybdate is allocated from the host plant to the bacteroids; such knowledge is critical for developing new SNF biological systems in non-legume plants. One-sentence summarySEN1 is localized partly in the peribacteroid membrane of nodule cells and mediates the molybdate exportation from the host plant cytosol to the symbiosomes for symbiotic nitrogen fixation.

plant biology↗

A complex containing RhoBTB3-SHIP164-Vps26B promotes the biogenesis of early endosome buds at Golgi-endosome contacts

Early endosomes (EEs) are central hubs for cargo sorting in vesicular trafficking. Cargoes destined for degradation retain in EEs that are eventually delivered to lysosomes, while recycled cargo destined for the plasma membrane (PM) or to the Golgi are segregated into EE buds, a specialized membrane structure transiently generated on EEs during cargo sorting. Until now, the molecular basis of the membrane expansion during the biogenesis of EE buds is completely elusive. Here, we identify a protein complex containing a Vps13 domain-containing lipid transporter SHIP164, ATPase RhoBTB3 and retromer component Vps26B, promotes the membrane expansion in the biogenesis of EE buds at Golgi-EE contacts. SHIP164 depletion specifically reduces the size and number of EE buds marked by Vps26B and actin, and results in less but enlarged EEs, which can be substantially rescued by wild type SHIP164 other than lipid transfer-defective mutants, suggesting a role of lipid transfer of SHIP164 in the process. SHIP164 and RhoBTB3 interact with enzymes for phospholipid synthesis on motile Golgi vesicles, that frequently contact EEs. Functionally, SHIP164 depletion substantially reduces the trafficking of sphingomyelin to the PM, and impairs cell growth. Together, we propose a lipid transport-dependent route from the Golgi to EEs at the contacts required for EE bud biogenesis.

cell biology↗

Dual-stream cortical feedbacks mediate sensory prediction

Predictions are constantly generated from diverse sources to optimize cognitive functions in the ever-changing environment. However, the neural origin and generation process of top-down induced prediction remain elusive. We hypothesized that motor-based and memory-based predictions are mediated by distinct feedback networks from motor and memory systems to the sensory cortices. Using fMRI and a dual imagery paradigm, we showed that motor and memory upstream systems excited the auditory cortex in a content-specific manner. Moreover, the inferior and posterior parts of the parietal lobe differentially relayed predictive signals in motor-to-sensory and memory-to-sensory networks. Our results reveal the functionally distinct neural networks that mediate top-down sensory prediction and ground the neurocomputational basis of predictive processing.

neuroscience↗

NAD precursors cycle between host tissues and the gut microbiome

Nicotinamide adenine dinucleotide (NAD) is an essential redox cofactor in both mammals and microbes. Here we use isotope tracing to investigate the precursors supporting NAD synthesis in the gut microbiome. We find that preferred dietary NAD precursors are absorbed in the proximal part of the gastrointestinal tract and not available to microbes in the distal gut. Instead, circulating host nicotinamide enters the gut lumen and supports gut microbiome NAD synthesis. In addition, the microbiome converts nicotinamide, originating from the host circulation, into nicotinic acid. Host tissues uptake and utilize this microbiome-derived nicotinic acid for NAD synthesis, maintaining circulating nicotinic acid levels even in the absence of dietary consumption. Moreover, the main route from oral nicotinamide riboside, a widely used nutraceutical, to host NAD is via conversion into nicotinic acid by the gut microbiome. Thus, NAD precursors cycle between the host and gut microbiome to maintain NAD homeostasis.

physiology↗

The genomic landscape of intrinsic and acquired resistance to cyclin-dependent kinase 4/6 inhibitors in patients with hormone receptor positive metastatic breast cancer

Clinical resistance mechanisms to CDK4/6 inhibitors in HR+ breast cancer have not been clearly defined. Whole exome sequencing of 59 tumors with CDK4/6i exposure revealed multiple candidate resistance mechanisms including RB1 loss, activating alterations in AKT1, RAS, AURKA, CCNE2, ERBB2, and FGFR2, and loss of ER expression. In vitro experiments confirmed that these alterations conferred CDK4/6i resistance. Cancer cells cultured to resistance with CDK4/6i also acquired RB1, KRAS, AURKA, or CCNE2 alterations, which conferred sensitivity to AURKA, ERK, or CHEK1 inhibition. Besides inactivation of RB1, which accounts for [~]5% of resistance, seven of these mechanisms have not been previously identified as clinical mediators of resistance to CDK4/6 inhibitors in patients. Three of these--RAS activation, AKT activation, and AURKA activation--have not to our knowledge been previously demonstrated preclinically. Together, these eight mechanisms were present in 80% of resistant tumors profiled and may define therapeutic opportunities in patients. SignificanceWe identified eight distinct mechanisms of resistance to CDK4/6 inhibitors present in 80% of resistant tumors profiled. Most of these have a therapeutic strategy to overcome or prevent resistance in these tumors. Taken together, these findings have critical implications related to the potential utility of precision-based approaches to overcome resistance in many patients with HR+ MBC.

cancer biology↗

A novel role for Myosin-Va in mitochondrial fission

In cancer cells metabolic changes and mitochondrial morphology are coupled. It is known that the cytoskeleton and molecular motors are directly involved in regulating mitochondrial morphology. Here we show that myosin-Va, an actin-based molecular motor, is required for the malignant properties of melanoma cells and localizes to mitochondria in these cells. Knockdown of myosin-Va increases cellular respiration rates and ROS production and decreases glucose uptake and lactate secretion. In addition, knockdown of myosin-Va results in reduced mitochondrial fission and correspondingly elongated mitochondria. We show that myosin-Va interacts with the mitochondrial outer membrane protein Spire1C, an actin-regulatory protein implicated in mitochondrial fission, and that Spire1C recruits myosin-Va to mitochondria. Finally, we show that during mitochondrial fission myosin-Va localization to mitochondria increases, and that myosin-Va localizes to mitochondrial fission sites immediately adjacent to Drp1 punctae. We conclude that myosin-Va facilitates mitochondrial fission. These data implicate myosin-Va as a target for the Warburg effect in melanoma cells.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC=\"FIGDIR/small/655803v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@1130e72org.highwire.dtl.DTLVardef@196619org.highwire.dtl.DTLVardef@17e09edorg.highwire.dtl.DTLVardef@1bdc311_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗