Biology subjects

Cao, Y.

Publications and source records attributed to Cao, Y..

At least 253 records · Page 14Linked to original sources

bioRxiv2022

Modeling the Cell Cycle Response to Carbon and Nitrogen deprivation in Caulobacter Populations

Caulobacter crescentus inhabits a wide range of aquatic ecosystems, including environments with poor nutrients. It undergoes an asymmetrical cell division cycle, generating a pair of daughter cells with distinct motility and replicative potentials. Caulobacter populations have the flexibility to save energy by halting chromosome replication and reduce intraspecific competition by settling in different places in environments. The control mechanisms underlying Caulobacter cell development have been well studied under nutrient-rich conditions, however, its mechanism of response to stressful changes is not fully understood. Here we present a mathematical model to analyze the starvation responses in Caulobacter. We investigate several known starvation signaling pathways to study how these pathways influence cell cycle development and explain experimental observations of starved Caulobacter populations. We also apply a new parameterization strategy to mathematical modeling of biological systems, whose diverse communities have to be robust with many parameter variations, while still having accurate control to maintain regular cell cycle dynamics. Our model demonstrates that the guanine-based second messenger, c-di-GMP (cdG), plays important roles to immediately arrest the cell cycle of Caulobacter under nutrient deprivation; however, it is not sufficient to cause the robust arrest. Our model suggests there should be unknown pathway(s) reducing the levels of CtrA under starvation condition, which results in a significant delay in cytokinesis of starved stalked Caulobacter cells.

bioinformatics↗

bioRxiv2022

Neutralizing antibody evasion and receptor binding features of SARS-CoV-2 Omicron BA.2.75

Recently emerged SARS-CoV-2 Omicron subvariant, BA.2.75, displayed a local growth advantage over BA.2.38, BA.2.76 and BA.5 in India. The underlying mechanism of BA.2.75s enhanced infectivity, especially compared to BA.5, remains unclear. Here, we show that BA.2.75 exhibits substantially higher ACE2-binding affinity than BA.5. Also, BA.2.75 spike shows decreased thermostability and increased "up" RBD conformation in acidic conditions, suggesting enhanced low-pH-endosomal cell-entry pathway utilization. BA.2.75 is less humoral immune evasive than BA.4/BA.5 in BA.1/BA.2 breakthrough-infection convalescents; however, BA.2.75 shows heavier neutralization evasion in Delta breakthrough-infection convalescents. Importantly, plasma from BA.5 breakthrough infection exhibit significantly weaker neutralization against BA.2.75 than BA.5, mainly due to BA.2.75s distinct RBD and NTD-targeting antibody escaping pattern from BA.4/BA.5. Additionally, Evusheld and Bebtelovimab remain effective against BA.2.75, and Sotrovimab recovered RBD-binding affinity. Together, our results suggest BA.2.75 may prevail after the global BA.4/BA.5 wave, and its increased receptor-binding capability could allow further incorporation of immune-evasive mutations.

immunology↗

bioRxiv2022

Hi-TrAC reveals fractal nesting of super-enhancers

Eukaryotic genome spatial folding plays a key role in genome function. Decoding the principles and dynamics of 3D genome organization depends on improving technologies to achieve higher resolution. Chromatin domains have been suggested as regulatory micro-environments, whose identification is crucial to understand the genome architecture. We report here that our recently developed method, Hi-TrAC, which specializes in detecting chromatin loops among genomic accessible regulatory regions, allows us to examine active domains with limited sequencing depths at a high resolution. Hi-TrAC can detect active sub-TADs with a median size of 100kb, most of which harbor one or two cell specifically expressed genes and regulatory elements such as super-enhancers organized into nested interaction domains. These active sub-TADs are characterized by highly enriched signals of histone mark H3K4me1 and chromatin-binding proteins, including Cohesin complex. We show that knocking down core subunit of the Cohesin complex using shRNAs in human cells or decreasing the H3K4me1 modification by deleting the H3K4 methyltransferase Mll4 gene in mouse Th17 cells disrupted the sub-TADs structure. In summary, Hi-TrAC serves as a compatible and highly responsive approach to studying dynamic changes of active sub-TADs, allowing us more explicit insights into delicate genome structures and functions. Highlights- Hi-TrAC detects active sub-TADs with a median size of 100 kb. - Hi-TrAC reveals a block-to-block interaction pattern between super-enhancers, and fractal structures within super-enhancers. - Active sub-TADs are disrupted by the knockdown of RAD21. - Active sub-TADs interaction densities are decreased by the knockout of Mll4.

genomics↗

bioRxiv2022

Metformin protects trabecular meshwork against oxidative injury via activating integrin/ROCK signals

BackgroundThis study aimed to investigate the protective effect of metformin on the trabecular meshwork (TM) and explore its molecular mechanisms in vivo and in vitro. MethodsOcular hypertension (OHT) mouse models were induced with dexamethasone (DEX) and further treated with metformin to determine its IOP lowering effect. Cultured human TM cells (HTMC) were pre-stimulated with tert-butyl hydroperoxide (tBHP) to induce oxidative damage and then supplemented with metformin for another 24 h. The expression of fibrotic markers and integrin/ROCK signals, including -SMA, TGF-{beta}, fibronectin, F-actin, integrin beta 1, Rho-associated kinase (ROCK)1/2, AMP-activated protein kinase (AMPK), myosin light chain 1 (MLC 1), and F-actin were determined by western blotting (WB) and immunofluorescence (IF). Reactive oxygen species (ROS) content was analysed using flow cytometry (FCM). ResultsAdministration of metformin reduced the elevated IOP and alleviated the fibrotic activity of aqueous humour outflow in OHT models. Additionally, metformin rearranged the disordered cytoskeleton in the TM both in vivo and in vitro. Furthermore, metformin significantly inhibited ROS production and activated integrin/ROCK signalling induced by tBHP in HTMC. ConclusionMetformin reduced the elevated IOP in steroid-induced OHT mouse models and exerted its protective effects against oxidative injury by regulating cytoskeleton remodelling through the integrin/ROCK pathway. This study provides new insights into metformin use and preclinical evidence for the potential treatment of primary open-angle glaucoma.

pharmacology and toxicology↗

bioRxiv2022

PRPF31 interacts with PRPH2 confirmed by co-immunoprecipitation and co-localization

PurposeTo investigate the potential interaction between PRPF31 and PRPH2. MethodsHEK293T and human retinal pigment epithelial cells 19 (APRE-19) were used for our experiments. eGFP and mCherry reporter expression vectors were constructed for PRPF31 and PRPH2, respectively. Immunoblotting and co-immunoprecipitation (Co-IP) were used for gene expression validation and protein interaction. Immunofluorescence staining assay was used to test the co-localization analysis of PRPF31 and PRPH2. ResultsPRPF31-eGFP and PRPH2-mcherry were highly expressed in HEK293T and APRE-19 cells on fluorescence microscopy and western blot. Co-IP experiments showed that PRPF31 could be pulled down with an anti-PRPH2 antibody. There was co-localization between PRPF31 and PRPH2 in HEK293T, APRE-19 and mouse retina. ConclusionCo-IP and co-localization experiments suggest that PRPF31 interacted with PRPH2.

genetics↗

bioRxiv2022

Rad51 and Dmc1 have similar tolerance for mismatches in yeast meiosis

In many eukaryotes, including both budding yeast and mammals, repair of double-strand breaks (DSBs) is carried out by different apparatus in somatic and meiotic cells. In mitotic cells, Rad51 recombinase, acting with Rad54, facilitates the search for homology and DNA strand exchange. In meiosis, Rad51 is inhibited by Hed1 and plays only an effector role, while strand exchange is driven by Rad51s homolog, Dmc1, acting with Rad54s homolog, Rdh54/Tid1. To directly compare the activities of Rad51 and Dmc1 and especially their tolerance for recombination between divergent sequences, we created diploids in which a site-specific DSB was created by HO endonuclease, either under control of a galactose-inducible promoter or a meiosis-specific SPO13 promoter. Homologous recombination was measured by an ectopic break-induced replication (BIR) assay in which a 108-bp homologous sequence shared between the DSB end and the donor sequence could be easily modified. As previously shown for a haploid mitotic strain, BIR efficiency decreased with increasing divergence between donor and recipient, but repair occurred even when every 6th base pair was mismatched. There was little difference in the tolerance of mismatches in mitotic haploids or meiotic diploids; however, there were notable differences in meiotic diploids when recombination was facilitated by Dmc1 or when Rad51 took over from Dmc1 in both hed1{Delta} and dmc1{Delta} hed1{Delta} mutants. We found that Dmc1 and Rad51 are similarly tolerant of mismatches during meiotic recombination in budding yeast. Surveillance of mismatches by the Msh2 mismatch repair protein proved to be Dmc1-specific. In all cases, assimilation of mismatches into the BIR product was dependent on the 3 to 5 exonuclease activity of DNA polymerase {delta}. Author SummaryIn many eukaryotes, including both budding yeast and mammals, repair of double-strand breaks (DSBs) is carried out by different apparatus in somatic and meiotic cells. In mitotic cells, Rad51 recombinase, acting with Rad54, facilitates the search for homology and DNA strand exchange. In budding yeast meiosis, Rad51 is inhibited by Hed1 and plays only an effector role, while strand exchange is driven by Rad51s homolog, Dmc1, acting with Rad54s homolog, Rdh54/Tid1. To directly compare the activities of Rad51 and Dmc1 and especially their tolerance for recombination between divergent sequences, we created diploids in which a site-specific DSB was created by HO endonuclease. Homologous recombination was measured by an ectopic break-induced replication (BIR) assay in which recombination occurred between a 108-bp homologous sequence shared between the DSB end and the donor sequence. The donor sequence could be easily modified to introduce different arrangements of mismatches. BIR efficiency decreased with increasing divergence between donor and recipient, but repair occurred even when every 6th base pair was mismatched. There was little difference in the tolerance of mismatches in mitotic or meiotic diploids; however, there were notable differences in meiotic diploids when recombination was facilitated by Dmc1 or when Dmc1 was deleted and Rad51 was activated. We found that Dmc1 and Rad51 are similarly tolerant of mismatches during meiotic recombination. Surveillance of mismatches by the Msh2 mismatch repair protein proved to be Dmc1-specific. As in mitotic cells, the assimilation of mismatches into the BIR product was dependent on the 3 to 5 exonuclease activity of DNA polymerase {delta}.

genetics↗

bioRxiv2022

TANGO2 deficient iPSC-differentiated cardiomyocyte and dermal fibroblasts have normal mitochondrial OXPHOS function

Bi-allelic loss-of-function mutations in TANGO2 (Transport and Golgi Organization protein 2) cause a rare multiorgan genetic disorder. Despite normal cardiac function at baseline, patients may experience lethal cardiac arrhythmias during "crises" often associated with metabolic stresses such as fasting, viral illness and fever. The molecular function of TANGO2 remains largely unknown. Previous studies have suggested a functional association with the mitochondrion, however definitive evidence is lacking. Further, functional impact of TANGO2 deficiency on mitochondrial function has not been investigated in a cardiac model. In this study, we utilized a recently developed patient-derived induced pluripotent stem cell differentiated cardiomyocytes (iPSC-CM) model by our group, along with patient-derived dermal fibroblast model, to interrogate whether loss of TANGO2 function leads to defective mitochondrial function. Both baseline and fasting condition were investigated. Oxygen consumption rate (OCR) was measured in Seahorse assays to assess mitochondrial function in vitro. The results showed both TANGO2 deficient dermal fibroblasts and iPSC-CM had no apparent defects in mitochondrial oxidative phosphorylation (OXPHOS) function under either baseline or fasting condition. Based on our study, we conclude that the lethal cardiac arrhythmias in TANGO2 patients are unlikely to be related to impaired mitochondrial OXPHOS function in the cardiomyocytes.

cell biology↗

bioRxiv2022

Clean-PIE: a novel strategy for efficiently constructing precise circRNA with thoroughly minimized immunogenicity to direct potent and durable protein expression

Translatable circular RNAs (circRNAs) are emerging as a crucial molecular format for transient protein expression, with high potential to be an alternative for linear mRNA to reshape the landscape of mRNA pharmaceutical industry. Canonical Anabaena permuted intron-exon (Ana PIE) format that developed by ORNA is an efficient method for RNA circularization, and the engineered circRNAs direct supreme protein expression in eukaryotic cells. However, recent studies revealed that this method may unavoidably result in a remain of immunogenicity in the circRNA products, albeit after thorough RNA purification. In the current study, we develop a novel strategy for efficient generation of circRNA, via the permuted T4Td introns mediated autocatalytically ribozymatic reaction mediated ligation of the flanking segment sequences that concealing in ORF or translation initiation sequence (normally equal to IRES). This strategy universally realizes around 90% circularization effectivity, and the circRNA products can be purified to around 90% purity by our new purification method, and presented thoroughly minimized immunogenicity, thus is termed "Clean-PIE". The purified circRNAs are found to direct potent and durable expression of various proteins in vitro and in vivo. The partly purified Fluc circRNA by HPLC-SEC was found to direct Fluc expression in muscle for no less than 20 days. The highly purified circRNA exhibits much stronger protein expression in vitro and in vivo, and presumed a longer duration. Additionally, the scale-up of RNA circularization with the RNA precursors from 1 L transcription revealed high circularization effectivity (around 90%) and a high productivity of the final circRNA products. Collectively, Clean-PIE is a novel circRNA platform that possesses high circularization effectivity, enabled high RNA purity and thoroughly minimized immunogenicity, as well as scaling-up accessibility and directing extreme durability of protein expression, thus has the potential to develop advanced RNA vaccines and therapeutics in pharmaceutical industrial scale.

molecular biology↗

bioRxiv2022

Molecular insights into intrinsic transducer-coupling bias in the CXCR4-CXCR7 system

Chemokine receptors constitute an important subfamily of G protein-coupled receptors (GPCRs), and they are critically involved in a broad range of immune response mechanisms. Ligand promiscuity among these receptors makes them an interesting target to explore novel aspects of biased agonism. Here, we comprehensively characterize two chemokine receptors namely, CXCR4 and CXCR7, which share a common chemokine agonist (CXCL12), in terms of their G-protein coupling, {beta}-arrestin ({beta}arr) recruitment, contribution of GRKs, and ERK1/2 MAP kinase activation. We observe that CXCR7 lacks G-protein coupling while maintaining robust {beta}arr recruitment with a major contribution of GRK5/6. On the other hand, CXCR4 displays robust G-protein activation as expected, however, it exhibits significantly reduced {beta}arr-coupling compared to CXCR7 in response to their shared natural agonist, CXCL12. These two receptors induce distinct {beta}arr conformations even when activated by the same agonist, and CXCR7, unlike CXCR4, fails to activate ERK1/2 MAP kinase. We further determine the crystal structure of {beta}arr2 in complex with a carboxyl-terminal phosphopeptide derived from CXCR7, which reveals a smaller interdomain rotation than observed previously for activated {beta}arrs. Importantly, structure-guided cellular experiments reveal a key contribution of a single phosphorylation site in CXCR7 on {beta}arr recruitment and endosomal trafficking. Taken together, our study provides molecular insights into intrinsic bias encoded in the CXCR4-CXCR7 system, and it has broad implications for therapeutically important framework of biased agonism.

biochemistry↗

bioRxiv2022

Hi-TrAC reveals fine-scale chromatin structures organized by transcription factors

The three-dimensional genomic structure plays a critical role in gene expression, cellular differentiation, and pathological conditions. It is pivotal to elucidate fine-scale chromatin architectures, especially interactions of regulatory elements, to understand the temporospatial regulation of gene expression. In this study, we report Hi-TrAC as a proximity ligation free, robust, and sensitive technique to profile genome-wide chromatin interactions at high-resolution among accessible regulatory elements. Hi-TrAC detects chromatin looping among accessible chromatin regions at single nucleosome resolution. With almost half-million identified loops, we constructed a comprehensive interaction network of regulatory elements across the genome. After integrating chromatin binding profiles of transcription factors, we discovered that cohesin complex and CTCF are responsible for organizing long-range chromatin loops, related to domain formation; whereas ZNF143 and HCFC1 are involved in structuring short-range chromatin loops between regulatory elements, which directly regulate gene expression. Thus, we developed a new methodology to identify a delicate and comprehensive network of cis-regulatory elements, revealing the complexity and a division of labor of TFs in chromatin looping for genome organization and gene expression.

genomics↗

bioRxiv2022

Genome-wide identification of microsatellite markers and their application in genetic studies of wolfberry (Lycium barbarum)

The wolfberry (Lycium barbarum) has been an important traditional Chinese food and medicine for hundreds of years. However, few microsatellite markers have been developed for assessing the genetic diversity and genetic linkage maps among Lycium species in genetic research. In the present study, a total of 397,558 microsatellite loci were identified from whole wolfberry genome sequences with an overall density of 212.1 Mb/SSRs. Dinucleotide microsatellites were the most abundant type, representing 58.26% of the total microsatellite loci, followed by tri-, penta-, hexa-, and tetranucleotide. The AT motifs were the most abundant of all nucleotide repeat motifs, accounting for 44.52%. A set of 600 primer pairs were synthesized and preliminarily screened among four wolfberry accessions. Of these, 277 primer pairs were selected as polymorphic markers. In total, 22 highly polymorphic SSR markers were selected for the characterization of genetic diversity among 37 wolfberry accessions. A total of 323 alleles were detected with an average of 14.7 alleles per marker. The polymorphic information content (PIC) values ranged from 0.612 to 0.911. The dendrogram revealed that the phylogenetic relationships among these wolfberry accessions were consistent with their genetic background. Thus, the large number of genome-wide microsatellite markers developed from the wolfberry genome provides a valuable resource for genetic diversity, genetic map construction, quantitative trait locus (QTL) mapping, and marker-assisted selection breeding in Lycium species.

molecular biology↗

bioRxiv2022

A Cdh3-Lam332 signaling axis in a leader cell subpopulation controls protrusion dynamics and tumor organoid collective migration

Carcinoma dissemination can occur when heterogeneous tumor and tumor stromal cells clusters migrate together via collective migration. Cells at the front lead and direct collective migration, yet how these leader cells form and interact with the microenvironment to direct migration are not fully appreciated. From live videos of primary mouse and human breast tumor organoids in a 3D microfluidic system that mimics the native breast tumor microenvironment, we developed 3D computational models which hypothesize that leader cells generate high protrusive forces and overcome extracellular matrix (ECM) resistance. Using single cell sequencing, we reveal leader cells are heterogeneous, and identify and isolate a unique Cadherin-3 (Cdh3) positive leader cell subpopulation that is necessary and sufficient to lead migration. Cdh3 controls leader cell protrusion dynamics through the local production of Laminin-332 which is required for integrin/focal adhesion function. Our findings highlight how a subset of leader cells interact with the microenvironment to direct collective migration. TeaserHigher protrusions of Cdh3+ leader cells polarize tumor organoids that then invade collagen via Lam332 adhesion feedback.

cancer biology↗

bioRxiv2022

Validation of tWO novel primers for THE promising amplification of the mitogenomic Cytochrome c Oxidase subunit I (COI) barcoding region in Artemia aff. sinica (Branchiopoda, Anostraca)

Due to the lack of a taxonomic key for the identification of Artemia species, molecular markers have been increasingly used for phylogenetic studies. The mtCOI marker is a regularly considered marker for the molecular systematics of Artemia populations. The proposed universal and specific primers have mostly failed to amplify the Artemia aff. sinica mtCOI marker, and on the whole, the successfully amplified products of the PCR were inefficient, primarily through the representation of poly-peak or incomplete sequences. We presumed that if a forward primer could be developed regarding the joint regions of the last part of the previous gene (tRNATyr) and the beginning of the target gene mtCOI, the sequence could be relevant to the target-sequence of mtCOI. Thus, here, we describe a new set of primers, which could be used to amplify the mtCOI barcoding region of Artemia aff. sinica Cai, 1989, with a high performance of sequencing. The new primer set worked well also for other Artemia bisexual species, as well as for parthenogenetic populations. It is recommended that joint regions between the previous/next gene(s) and the target marker, could be aimed at when designing specific primers for other markers and taxa.

zoology↗

bioRxiv2022

Human variation impacting MCOLN2 restricts Salmonella Typhi replication by magnesium deprivation

Human genetic diversity can reveal critical factors in host-pathogen interactions. This is especially useful for human-restricted pathogens like Salmonella enterica serovar Typhi (S. Typhi), the cause of Typhoid fever. One key dynamic during infection is competition for nutrients: host cells attempt to restrict intracellular replication by depriving bacteria of key nutrients or delivering toxic metabolites in a process called nutritional immunity. Here, a cellular genome-wide association study of intracellular replication by S. Typhi in nearly a thousand cell lines from around the world--and extensive follow-up using intracellular S. Typhi transcriptomics and manipulation of magnesium concentrations--demonstrates that the divalent cation channel mucolipin-2 (MCOLN2) restricts S. Typhi intracellular replication through magnesium deprivation. Our results reveal natural diversity in Mg2+ limitation as a key component of nutritional immunity against S. Typhi. One-Sentence SummaryHuman immune cells genetically vary in their ability to use magnesium deprivation to restrict growth of the typhoid fever bacterium.

genetics↗

bioRxiv2022

Visualizing cell-cell interactions between immune effector and tumor cells induced by antibodies using a proximity-dependent biosensor system

Background and PurposeDespite the promising results of therapeutic antibodies in engaging the immune system to eliminate malignant cells, many aspects of the complex interplay between immune cells and cancer cells during antibody therapy remain incompletely understood. This study aimed to develop a biosensor system that can evaluate direct cell-cell contact and interactions between immune effector and target cells induced by therapeutic antibodies in physiologically relevant environments. Experimental ApproachThe system uses two structural complementary luciferase units (SmBit and LgBit) expressed on the respective membranes of immune effector and target cells. Upon cell-cell contact, the two subunits form active NanoLuc, generating a luminescent signal, allowing for real-time monitoring of cell-cell interactions and quantitatively assessing the pharmacological effects of therapeutic antibodies. Key ResultsWe optimized the system to ensure selectivity by adjusting the spacer lengths between two luciferase units to minimize interference from nonspecific intercellular contact. The system was able to quantitatively and longitudinally monitor cell-cell interactions between NK and target cells induced by rituximab and between T and target cells induced by blinatumomab in a three-dimensional cell culture system. The observation that NK cells exhibited faster interactions with target cells compared to T cells is intriguing and suggests potential differences in the mechanisms or kinetics of cell-cell interactions between different types of effector cells and tumor cells. Conclusions and ImplicationsThe biosensor system has the potential for broad applications to optimize antibody pharmacology and efficacy in various therapeutic areas through a deeper understanding of antibody-mediated cell-cell interactions. What is already knownO_LITherapeutic antibodies can activate the immune system to elicit cytotoxicity through inducing cell-cell interactions between immune and tumor cells. C_LIO_LIApproaches for longitudinally evaluating cell-cell interaction induced by therapeutic antibodies remain limited. C_LI What does this study addO_LIThis study develops a biosensor system for detecting cell-cell interactions induced by therapeutic antibodies in a longitudinal manner. C_LIO_LIThe system is able to monitor cell-cell interactions between NK and target cells, as well as between T and target cells, in a three-dimensional cell culture system. C_LI What is the clinical significanceO_LIThe biosensor system has the potential for broad applications in the field of antibody pharmacology by providing a deeper understanding of antibody-mediated cell-cell interactions and their dynamics. C_LI

pharmacology and toxicology↗

bioRxiv2022

Immunological Synapse Dynamics Induced by Bispecific T-cell Engagers Predict Clinical Pharmacodynamics and Tumor Evolution across Anatomical Sites

Effector T cells form immunological synapses (IS) with recognized target cells to elicit cytolytic effects. Facilitating IS formation is the principal pharmacological action of most T cell-based cancer immunotherapies. However, the dynamics of IS formation at the cell population level, the primary driver of the pharmacodynamics of many cancer immunotherapies, remains poorly defined. With classic immunotherapy CD3/CD19 bispecific T cell engager (BiTE) as a model system, we integrate experimental and theoretical approaches to investigate the population dynamics of IS formation and their relevance to clinical pharmacodynamics and treatment resistance. Our models produce experimentally consistent predictions when defining IS formation as a series of spatiotemporally coordinated events driven by molecular and cellular interactions. The models predict tumor-killing pharmacodynamics in patients and reveal trajectories of tumor evolution across anatomical sites under BiTE immunotherapy. Our model highlight the bone marrow may serve as a sanctuary site permitting tumor evolution and antigen escape. The models also suggest the optimal dosing regimens as a function of tumor growth and patient T cell abundance that confer adequate tumor control with minimal disease evolution. This work has implications for developing more effective T cell-based cancer immunotherapies.

pharmacology and toxicology↗

bioRxiv2022

The specific roles of renal macrophages in monitoring and clearing off intratubular particles

During the filtrate of the glomerulus flows though the renal tubular system, a variety of microscopic sediment particles, including mineral crystals resulting from urine concentration, are generated. Dislodging these particles in the intratubular compartment is critical to ensure free flow of filtrate and the final formation of urine. However, the underlying mechanism for the clearance is unclear. Here, using high-resolution microscopy, we uncovered that the juxtatubular macrophages in the medulla constitutively formed transepithelial protrusions and were "sampling" urine contents. These behaviors were strengthened in the development of nephrolithiasis. In particular, the juxtatubular macrophages were efficient in sequestering and phagocytosing intraluminal sediment particles, and occasionally making transmigration to the tubule lumen to escort the excretion of urine particles. Specific depletion of renal macrophages precipitated kidney stone formation and aggravated the accompanied inflammation upon hyperoxaluria challenge. Thus, renal macrophages undertake a specific role in maintaining the tubular system unobstructed.

immunology↗

bioRxiv2022

A conserved mechanism regulates reversible amyloids via pH-sensing regions

Amyloids were long viewed as irreversible, pathological aggregates, often associated with neurodegenerative diseases1. However, recent insights challenge this view, providing evidence that reversible amyloids can form upon stress conditions and fulfil crucial cellular functions2. Yet, the molecular mechanisms regulating functional amyloids and the differences to their pathological counterparts remain poorly understood. Here we investigate the conserved principles of amyloid reversibility by studying the essential metabolic enzyme pyruvate kinase (PK) in yeast and human cells. We demonstrate that PK forms stress-dependent reversible amyloids through a pH-sensitive amyloid core. Stress- induced cytosolic acidification promotes aggregate formation via protonation of specific glutamate (in yeast) or histidine (in human) residues within the amyloid core. Our work thus unravels a conserved and potentially widespread mechanism underlying amyloid functionality and reversibility, fine-tuned to the respective physiological cellular pH range.

cell biology↗