Biology subjects

Jing, Y.

Publications and source records attributed to Jing, Y..

45 records · Page 3Linked to original sources

bioRxiv2021

Polycystin-2 is upregulated in fibrotic kidneys and inhibition of plycystin-2 by triptolide attenuates renal fibrosis

Mutations in PKD1 (encoding polycystin-1) or PKD2 (encoding polycystin-2) gene cause autosomal dominant polycystic kidney disease (ADPKD), however high levels of polycystins are detected in renal tissues of ADPKD patients. Animal studies showed that loss and gain of function of polycystins are both pathogenic and can induce cystic phenotype in the kidney, which are associated with enhanced renal fibrosis. Recent studies showed that increased expression of polycystins contributes to organ fibrosis. However, the role of polycystins in renal tubulointerstitial fibrosis remains unclear. In this study, we demonstrated that polycystin-1 or polycystin-2 was highly expressed in the kidney of two different fibrotic mouse models and positively correlated with expression of collagen-I. Pharmaceutical inhibition of polycystin-2 with triptolide or genetic knockout of polycystin-2 reduced the expression of epithelial-mesenchymal transition (EMT) markers and deposition of extracellular matrix proteins in fibrotic kidneys. Similarly, conditional knockout of Pkd1 gene also attenuated renal fibrosis in mouse models. Thus, we further hypothesized that inhibition of polycystins delays cyst growth by mitigating renal fibrosis. Here, we showed that polycystin-1 or polycystin-2 was up-regulated in Pkd2 or Pkd1 mice respectively and tightly correlated with the growth of renal cysts and fibrosis development. Genetic deletion of both polycystin-1 and polycystin-2 retarded cyst growth in Pkd1 or Pkd2 mice. Finally, we deleted pkd1 gene in a fibrosis triggered adult ADPKD mouse model at different time point before or after the fibrotic injury. We showed that early and long-term inactivation of Pkd1 delayed fibrosis triggered renal cyst growth in adult Pkd1 mice as compared with mice with late and short-term inactivation of Pkd1 gene. We conclude that tubular obstruction induced polycystin up-regulation is pro-fibrotic and accelerates cyst growth through enhancing renal interstitial fibrosis in ADPKD mice. Our study indicates that ADPKD is caused by both loss and gain function of polycystins. Reduction of the aberrant upregulation of polycystins in cystic kidneys is a therapeutic option for ADPKD patients. Research highlightsO_LIPolycystin1 and polycystin-2 are up-regulated in fibrotic kidneys C_LIO_LIInhibition or deletion of polycystins inhibits EMT and attenuates renal tubulointerstitial fibrosis C_LIO_LIUpregulation of polycystin1 or polycystin-2 is positively correlated with fibrosis progression and renal cyst growth in ADPKD mice C_LIO_LIDouble knockout of Pkd1 and Pkd2 gene inhibits renal cyst growth in ADPKD mice C_LIO_LILong-term deletion of Pkd1 gene delayed fibrosis triggered renal cyst growth in ADPKD mice C_LI

pathology↗

bioRxiv2021

Three bacterium-plasmid golden combinations facilitate the spread of ST11/CG258 carbapenemase-producing Klebsiella pneumoniae in China

Carbapenemase-producing Klebsiella pneumoniae (cpKP) poses serious threats to public health. Previous studies showed that only ST11/CG258-cpKP successfully disseminated in China, however, the underlying genetic bases are still unknown. We conducted a comprehensive genomic-epidemiology analysis on 420 cpKP isolates from 70 hospitals in 24 Chinese provinces during 2009-2017 based on short-/long-reads sequencing. Three golden combinations of host--blaKPC-carrying plasmids (Clade 3.1+3.2--IncFIIpHN7A8, Clade 3.1+3.2--IncFIIpHN7A8:IncR, Clade 3.3--IncFIIpHN7A8:IncpA1763-KPC) endowed cpKP with advantages both in genotypes (strong-correlation/co-evolution) and phenotypes (resistance/growth/competition), thereby facilitating nationwide spread of ST11/CG258-cpKP. Intriguingly, Bayesian skyline illustrated that the three golden combinations might directly lead to the strong population expansion during 2007-2008 and subsequent maintenance of the dissemination of ST11/CG258-cpKP after 2008. We tested drug-resistance profiles and proposed combination treatment regimens for CG258/non-CG258 cpKP. Our findings systematically revealed the molecular-epidemiology and genetic-basis for dissemination of Chinese ST11/CG258 cpKP and reminded us to monitor the golden combinations of cpKP- plasmid closely.

microbiology↗

bioRxiv2020

Harnessing Ionic Selectivity In Acetyltransferase Chemoproteomic Probes

Chemical proteomics provides a powerful strategy for the high-throughput assignment of enzyme function or inhibitor selectivity. However, identifying optimized probes for an enzyme family member of interest and differentiating signal from background remain persistent challenges in the field. To address this obstacle, here we report a physiochemical discernment strategy for optimizing chemical proteomics based on the Coenzyme A (CoA) cofactor. First, we synthesize a pair of CoA-based Sepharose pulldown resins differentiated by a single negatively charged residue, and find this change alters their capture properties in gel-based profiling experiments. Next, we integrate these probes with quantitative proteomics and benchmark analysis of probe selectivity versus traditional competitive chemical proteomics. This reveals the former is well-suited for the identification of optimized pulldown probes for specific enzyme family members, while the latter may have advantages in discovery applications. Finally, we apply our anionic CoA pulldown probe to evaluate the selectivity of a recently reported small molecule N-terminal acetyltransferase inhibitor. These studies further validate the use of physical discriminant strategies in chemoproteomic hit identification and demonstrate how CoA-based chemoproteomic probes can be used to evaluate the selectivity of small molecule protein acetyltransferase inhibitors, an emerging class of pre-clinical therapeutic agents.

biochemistry↗

bioRxiv2020

Synthesis and Evaluation of a Stable Isostere of Malonyllysine

Lysine malonylation is a recently characterized posttranslational modification involved in the regulation of energy metabolism and gene expression. Two unique features of this posttranslational modification are its negative charge and potential susceptibility to decarboxylation, both of which pose possible challenges to its study. As a step towards addressing these challenges, here we report the synthesis and evaluation of a stable isostere of malonyllysine. First, we find that synthetic substitution of the malonyl group with a tetrazole isostere results in amino acids resistant to thermal decarboxylation. Next, we demonstrate that protected variants of this amino acid are readily incorporated into peptides. Finally, we show that tetrazole isosteres of malonyllysine can be recognized by anti-malonyllysine antibodies, validating their ability to mimic features of the endogenous lysine modification. Overall, this study establishes a new chemical strategy for stably mimicking a metabolite-derived posttranslational modification, providing a foothold for tool development and functional analyses.

biochemistry↗

bioRxiv2020

Identification of sulfenylated cysteines in Arabidopsis thaliana proteins using a disulfide-linked peptide reporter

In proteins, hydrogen peroxide (H2O2) reacts with redox-sensitive cysteines to form cysteine sulfenic acid, also known as S-sulfenylation. These cysteine oxidation events can steer diverse cellular processes by altering protein interactions, trafficking, conformation, and function. Previously, we had identified S-sulfenylated proteins by using a tagged proteinaceous probe based on the yeast AP-1-like (Yap1) transcription factor that specifically reacts with sulfenic acids and traps them through a mixed disulfide bond. However, the identity of the S-sulfenylated amino acid residues remained enigmatic. Here, we present a technological advancement to identify in situ sulfenylated cysteines directly by means of the transgenic Yap1 probe. In Arabidopsis thaliana cells, after an initial affinity purification and a tryptic digestion, we further enriched the mixed disulfide-linked peptides with an antibody targeting the YAP1C-derived peptide (C598SEIWDR) that entails the redox-active cysteine. Subsequent mass spectrometry analysis with pLink 2 identified 1,745 YAP1C cross-linked peptides, indicating sulfenylated cysteines in over 1,000 proteins. Approximately 55% of these YAP1C-linked cysteines had previously been reported as redox-sensitive cysteines (S-sulfenylation, S-nitrosylation, and reversibly oxidized cysteines). The presented methodology provides a noninvasive approach to identify sulfenylated cysteines in any species that can be genetically modified.

plant biology↗

bioRxiv2018

Comparative Transcriptomes Analysis of Taenia pisiformis at Different Development Stages

To understand the characteristics of the transcriptional group of Taenia pisiformis at different developmental stages, and to lay the foundation for the screening of vaccine antigens and drug target genes, the transcriptomes of adult and larva of T. pisiformis were assembled and analyzed using bioinformatic tools. A total of 36,951 unigenes with a mean length of 950bp were formed, among which 12,665, 8,188, 7,577, and 6,293 unigenes have been annotated respectively by sequence similarity analysis with four databases (NR, Swiss-Prot, KOG, and KEGG). It should be noted there are 5,662 unigenes that share good similarity with the four databases and get a relatively perfect functional annotation. Besides, a total of 10,247 differentially expressed genes were screened. To be specific, 6,910 unigenes were up-regulated in the larva stage while 3,337 were down-regulated in the adult stage. To sum up, this study sequenced and analyzed the transcriptomes of the larval and adult stages of T. pisiformis. The results of differentially expressed genes in these two stages could provide basis for functional genomics, immunology and gene expression profiles of T. pisiformis.

molecular biology↗

bioRxiv2018

Gut Microbiota in male patients with chronic traumatic complete spinal cord injury

This study examined the diversity and structure of gut microbiota in healthy adults and chronic traumatic complete spinal cord injury (SCI) patients, documented neurogenic bowel management of SCI patients. The V3-V4 region of 16S rRNA gene from DNA of 91 fecal samples of 48 healthy and 43 diseased subjects was amplified and sequenced. There was difference in gut microbiota between healthy adult males and females. Neurogenic bowel dysfunction (NBD) was common in patients with chronic traumatic complete SCI, patients with quadriplegia have longer time to defecate than paraplegic patients, with higher NBD scores and heavier neurogenic bowel symptoms. Gut microbiota dysbiosis existed in SCI patients. The abundance of Veillonellaceae and Prevotellaceae increased while Bacteroidaceae and Bacteroides decreased in SCI group. The abundance of Bacteroidaceae, Bacteroides in quadriplegia group and Acidaminococcaceae, Blautia in paraplegia group were significant high than the health male group. Serum biomarkers GLU, HDL, CR and NBD symptoms defecation time, COURSE had significant correlation with microbial community structure. This study presents a comprehensive landscape of gut microbiota in adult male patients with chronic traumatic complete SCI and documents their neurogenic bowel management. The gut microbiota dysbiosis of SCI patients was correlation with serum biomarkers and NBD symptoms.\n\nIMPORTANCENeurogenic bowel dysfunction is a major physical and psychological problem in patients with spinal cord injury, which can seriously affect the quality life of them. Gut dysbiosis are highly likely to occur in spinal cord injury patients There are few studies on intestinal microecology after spinal cord injury, and the clinical studies are fewer. It is importance to document their neurogenic bowel management and present a landscape of gut microbiota in them. We found the gut microbiota dysbiosis of spinal cord injury patients was correlation with serum biomarkers and neurogenic bowel dysfunction symptoms. These results may have implications in the next study about metagenomics and precision treatment of neurogenic bowel dysfunction in spinal cord injury patients.

neuroscience↗

bioRxiv2018

Apigenin relaxes rat intrarenal arteries: involvement of Cl- channels and K+ channels

The vasodilator effect of apigenin (API) was demonstrated in a number of vascular beds. We aimed to characterize the vasospasmolytic and electrophysiological effects of apigenin (API) in intrarenal arteries (IRAs). The vascular tone of male rat isolated IRAs was recorded with a myograph. Transmembrane Cl- currents through Ca2+-activated Cl- channels (CaCCs), K+ currents through voltage-gated K+ (Kv) channels and inwardly rectifier K+ (Kir) channels were recorded with patch clamp in the freshly isolated arterial smooth muscle cells (ASMCs). Preincubation with API (10-100 M) concentration-dependently depressed the contractions induced by KCl, 9,11-dideoxy-9,11-methanoepoxy prostaglandin F2 (U46619), phenylephrine and vasopressin without significant preference and the IC50 values were 13.27-26.26 M. Acute application of API elicited instant relaxations in the IRAs precontracted with these vasoconstrictors and the RC50 values were 5.80-24.33 M. API relaxation was attenuated by chloride deprivation, CaCC blockers, Kv blocker and nitric oxide synthase inhibitor, but not by Kir blocker and cyclooxygenase inhibitor. At 10-100 M, API depressed CaCC currents and Kir currents while enhanced Kv currents of IRA ASMCs. The present results demonstrate that API counteracts various vasoconstrictors noncompetitively and nonspecifically and suggest that modulation of CaCCs, Kv and Kir channels of IRA ASMCs is involved in its vasospasmolytic effects.

pharmacology and toxicology↗

bioRxiv2018

MITA couples with PI3K to regulate actin reorganization during BCR activation

As an adaptor protein, MITA has been extensively studied in innate immunity. However, its role in adaptive immunity as well as its underlying mechanism are not completely understood. We used MITA KO mice to study the effect of MITA deficiency on B cell development and differentiation, BCR signaling during BCR activation and humoral immune response. We found that MITA deficiency promotes the differentiation of marginal zone B cells, which is linked to the lupus-like autoimmune disease that develops in MITA KO mice. MITA is involved in BCR activation and negatively regulates the activation of CD19 and Btk and positively regulates the activation of SHIP. Interestingly, we found that the activation of WASP and accumulation of F-actin is enhanced in MITA KO B cells upon stimulation. Mechanistically, we found that MITA uses PI3K mediated by the CD19-Btk axis as a central hub to control the actin remodeling that, in turn, offers feedback to BCR signaling. Overall, our study has provided a new mechanism on how MITA regulates BCR signaling via feedback from actin reorganization, which may contribute to the effects of MITA on the humoral immune response.

immunology↗