Biology subjects

Chen, Y.-X.

Publications and source records attributed to Chen, Y.-X..

12 recordsLinked to original sources

bioRxiv2026

Proteostatic significance of helix O alanine residues in CLC channels

The voltage-gated chloride channels ClC-1 and ClC-2 are homodimeric structures essential for maintaining muscle excitability and tissue fluid homeostasis, respectively. Mutations in these channels disrupt protein homeostasis (proteostasis), leading to hereditary disorders such as myotonia congenita and leukodystrophy. Specifically, the substitution of highly conserved alanine residues within the transmembrane helix O, exemplified by ClC-1 (A531V) and ClC-2 (A500V), results in severe proteostatic defects characterized by reduced protein stability and impaired surface trafficking. However, the precise role of helix O in these pathological processes remains poorly understood. In this study, we investigated these conserved residues using biochemical and functional approaches. Our findings demonstrate that even subtle structural alterations at these critical sites significantly interfere with channel stability and membrane expression. This study highlights the critical contribution of helix O to proper CLC channel folding and endoplasmic reticulum (ER) quality control, providing deeper insights into the molecular mechanisms of CLC-related channelopathies.

cell biology↗

bioRxiv2024

Male Mice Have no Sugar-preference Behavior

Sugar-preference behavior is considered to be universally innate among humans and animals. Current research on the detection and mechanisms of sugar-preference behavior largely adopts the "two-bottle choice assay", and most experiments use male mice as the model, which has serious methodological flaws, leading to questionable conclusions. As expected, through adopting our improved experimental method, we discovered distinct sugar preferences between male and female mice: females possess an innate preference, while males do not. However, the innate sugar preference in female mice can be lost due to their long-term normal diet. Even after "training" with high-sugar food for a long time, the results still show differences between males and females. Female mice retain a significant preference for sugar, while male mice are not influenced by the training of high-sugar food and still do not evolve a sugar preference. From this, we conclude that gender determines the emergence and development of sugar preference in mice. Our results can provide researchers with a new understanding of sugar preference, which will help them fill in or even correct the gaps in the original experimental design methods to obtain more reliable conclusions.

animal behavior and cognition↗

bioRxiv2022

Mechanical morphotype switching as an adaptive response in mycobacteria

Invading microbes face a myriad of cidal mechanisms of phagocytes that inflict physical damage to microbial structures. How intracellular bacterial pathogens adapt to these stresses is not fully understood. Here, we report a new virulence mechanism by which mycobacteria alter the mechanical stiffness of their cell surface to become refractory to killing during infection. Long-Term Time-Lapse Atomic Force Microscopy was used to reveal a process of "mechanical morphotype switching" in mycobacteria exposed to host intracellular stress. A "soft" mechanical morphotype switch enhances tolerance to intracellular macrophage stress, including cathelicidin. Genetic manipulation, by deletion of uvrA, or pharmacological treatment, with bedaquiline, locked mycobacteria into a "soft" mechanical morphotype state, enhancing survival in macrophages. Our study proposes microbial mechanical adaptation as a new axis for surviving host-mediated stressors. One-Sentence SummaryBacteria alter their cell surface mechanical properties to increase survival during macrophage infection.

microbiology↗

bioRxiv2020

Study on β-Chitosan against the binding of SARS-CoV-2S-RBD/ACE2

SARS-CoV-2 invades human respiratory epithelial cells via an interaction between its spike RBD protein (SARS-CoV-2 S-RBD) and the host cell receptor angiotensin converting enzyme II (ACE2). Blocking this interaction provides a potent approach to preventing and controlling SARS-CoV-2 infection. In this work, the ability of {beta}-chitosan to block the binding interaction between SARS-CoV-2 S-RBD and ACE2 was investigated. The inhibitory effect of {beta}-chitosan on inflammation induced by the SARS-CoV-2 S-RBD was also studied. Native-PAGE analysis indicated that {beta}-chitosan could bind with ACE2 and the SARS-CoV-2 S-RBD and a conjugate of {beta}-chitosan and ACE2 could no longer bind with the SARS-CoV-2 S-RBD. HPLC analysis suggested that a conjugate of {beta}-chitosan and the SARS-CoV-2 S-RBD displayed high binding affinity without dissociation under high pressure (40 MPa) compared with that of {beta}-chitosan and ACE2. Furthermore, immunofluorescent staining of Vero E6 cells and lungs from hACE2 mice showed that the presence of {beta}-chitosan prevented SARS-CoV-2 S-RBD from binding to ACE2. Meanwhile, {beta}-chitosan could dramatically suppress the inflammation caused by the presence of the SARS-CoV-2 S-RBD both in vitro and vivo. Moreover, the decreased expression of ACE2 caused by {beta}-chitosan treatment was restored by addition of TAPI-1, an inhibitor of the transmembrane protease ADAM17. Our findings demonstrated that {beta}-chitosan displays an antibody-like function capable of neutralizing the SARS-CoV-2 S-RBD and effectively preventing the binding of the SARS-CoV-2 S-RBD to ACE2. Moreover, ADAM17 activation induced by {beta}-chitosan treatment can enhance the cleavage of the extracellular domain of ACE2, releasing the active ectodomain into the extracellular environment, which can prevent the binding, internalization, and degradation of ACE2 bound to the SARS-CoV-2 S-RBD and thus diminish inflammation. Our study provides an alternative avenue for preventing SARS-CoV-2 infection using {beta}-chitosan.

cell biology↗

bioRxiv2020

Adopting STING agonist cyclic dinucleotides as a potential adjuvant for SARS-CoV-2 vaccine

A novel STING agonist CDGSF unilaterally modified with phosphorothioate and fluorine was synthesized. CDGSF displayed better STING activity over dithio CDG. Immunization of SARS-CoV-2 Spike protein with CDGSF as an adjuvant elicited an exceptional high antibody titer and a robust T cell response, which were better than the group using aluminium hydroxide as a adjuvant. These results highlighted the adjuvant potential of STING agonist in SARS-CoV-2 vaccine preparation for the first time.

immunology↗

bioRxiv2020

Heat Shock Protein 27 versus Estrogen Therapy for Post-Menopausal Atherosclerosis: Rethinking Mechanisms of Cholesterol Lowering

Aims The estrogen-inducible protein Heat Shock Protein 27 (HSP27) as well as anti-HSP27 antibodies are elevated in healthy subjects compared to cardiovascular disease patients. Vaccination of ApoE-/- mice with recombinant HSP25 (rHSP25, the murine ortholog), boosts anti-HSP25 levels and attenuates atherogenesis. As estrogens promote HSP27 synthesis, cellular release and blood levels, we hypothesize that menopause will result in loss of HSP27 atheroprotection. Hence, we now compare the efficacy of rHSP25 vaccination vs. estradiol (E2) therapy for the prevention of post-menopausal atherogenesis.Methods and Results ApoE-/- mice subjected to ovariectomy (OVX) showed a 65% increase atherosclerotic burden compared to sham mice after 5 weeks of a high fat diet. Relative to vaccination with rC1, a truncated HSP27 control peptide, atherogenesis was reduced by 5-weekly rHSP25 vaccinations (−43%), a subcutaneous E2 slow release pellet (−52%) or a combination thereof (−82%). Plasma cholesterol levels declined in parallel with the reductions in atherogenesis, but relative to rC1/OVX mice plasma PCSK9 levels were 52% higher in E2/OVX and 41% lower in rHSP25/OVX mice (p<0.0001 for both). Hepatic LDLR mRNA levels did not change with E2 treatment but increased markedly with rHSP25 vaccination. Conversely, hepatic PCSK9 mRNA increased 148% with E2 treatment vs. rC1/OVX but did not change with rHSP25 vaccination. In human HepG2 hepatocytes E2 increased PCSK9 promoter activity 303%, while the combination of [rHSP27 + PAb] decreased PCSK9 promoter activity by 64%.Conclusion The reduction in post-OVX atherogenesis and cholesterol levels with rHSP25 vaccination is associated with increased LDLR but not PCSK9 expression. Surprisingly, E2 therapy attenuates atherogenesis and cholesterol levels post-OVX without altering LDLR but increases PCSK9 expression and promoter activity. This is the first documentation of increased PCSK9 expression with E2 therapy and raises questions about balancing physiological estrogenic / PCSK9 homeostasis and targeting PCSK9 in women – are there effects beyond cholesterol?Competing Interest StatementEOB and YXC are inventors on US patents 8343915B2 and 8343916B2; EOB, CS and YXC are inventors on US patent application PCT/CA2016/051018; EOB is the inventor on US patent application 63/031,6402020; all intellectual property pertains to HSP27 diagnostics / therapeutics. EOB is the Scientific Co-Founder of Pemi31 Therapeutics Inc., a startup company that controls the aforementioned intellectual property. EOB, CS and YXC have equity interests in Pemi31 Therapeutics Inc.AbbreviationsAAbanti-HSP27 (or anti-HSP25) antibodiesApoE-/-apolipoprotein E nulla.u.absorbance unitsE217β estradiolHFDhigh fat dietHPRThypoxanthine-phosphoribosyltransferaseHSP27Heat Shock Protein 27HSP27o/eHSP27 over-expressingLDL-Clow density lipoprotein cholesterolLDLRlow density lipoprotein receptorMPmenopausemRNAmessenger RNANF-κBnuclear factor kappa light chain enhancer of activated B cellsONovernightOVXovariectomyPAbpolyclonal anti-HSP27 IgG antibodyPBSphosphate buffered salinePCSK9Proprotein Convertase Subtilisin/Kexin type 9rC1recombinant C-terminal truncation of HSP27 spanning amino acids 90-205rHSP27recombinant HSP27SDS-PAGEsodium dodecyl sulfate and polyacrylamide gelWBWestern BlotView Full Text

pathology↗

bioRxiv2020

Heat Shock Protein 27 Immune Complex Altered Signaling and Transport (ICAST): Novel Mechanisms of Attenuating Inflammation

Blood levels of heat shock protein (HSP27) and natural IgG auto-antibodies to HSP27 (AAbs) are higher in healthy controls compared to cardiovascular disease patients. Vaccination of mice with recombinant HSP25 (rHSP25, murine ortholog of human rHSP27) increased AAb levels, attenuated atherogenesis and reduced plaque inflammation and cholesterol content. We sought to determine if the HSP27 immune complex (IC) altered MΦ inflammation signaling (Toll Like Receptor 4; TLR4), and scavenger receptors involved in cholesterol uptake (SR-AI, CD-36). Combining a validated polyclonal IgG anti-HSP27 antibody (PAb) with rHSP27 enhanced binding to THP-1 MΦ cell membranes and activation of NF-κB signaling via TLR4, competing away LPS and effecting an anti-inflammatory cytokine profile. Similarly, adding the PAb with rHSP27 enhanced binding to SR-AI and CD-36, as well as lowered oxLDL binding in HEK293 cells separately transfected with SR-AI and CD-36, or THP-1 MΦ. Finally, the PAb enhanced the uptake and internalization of rHSP27 in THP-1 MΦ. Thus, the HSP27 IC potentiates HSP27 cell membrane signaling with receptors involved in modulating inflammation and cholesterol uptake, as well as HSP27 internalization. Going forward, we will explore HSP27 Immune Complex Altered Signaling and Transport (ICAST) as a new anti-inflammatory therapeutic strategy in vivo.Competing Interest StatementEOB is the inventor on US Provisional Patent Application (serial number: 63/031,640). EOB is the Scientific Co-Founder of Pemi31 Therapeutics Inc., a startup company that controls the aforementioned intellectual property. EOB, CS and YXC have equity interests in Pemi31 Therapeutics Inc.Nonstandard AbbreviationsAAbanti-HSP27 (or anti-HSP25) antibodiesApoE-/-apolipoprotein E nulla.u.absorbance unitsBSAbovine serum albuminHSPheat shock proteinHSP27Heat Shock Protein 27IL-10interleukin-10IL-1βinterleukin-1 betaLDLlow density lipoprotein cholesterolLDLRlow density lipoprotein receptorNF-κBnuclear factor kappa light chain enhancer of activated B cellsONovernightoxLDLoxidized LDLPBSphosphate buffered salinePBSTPBS tweenrC1recombinant C-terminal truncation of HSP27 spanning amino acids 90-205rHSP27recombinant HSP27Strep-HRTstreptavidin-horse radish peroxidaseTLR-4toll-like receptor 4TMB3,3′,5,5′-tetramethylbenzidineView Full Text

pathology↗

bioRxiv2020

3D chromatin organization changes modulate adipogenesis and osteogenesis

Human mesenchymal stem cells (hMSCs) can be differentiated into adipocytes and osteoblasts. While the transcriptomic and epigenomic changes during adipogenesis and osteogenesis have been characterized, what happens to the chromatin loops is hardly known. Here we induced hMSCs to adipogenic and osteogenic differentiation, and performed 2 kb resolution Hi-C experiments for loop detection and generated RNA-seq, histone modification ChIP-seq and ATAC-seq data for integrative analysis before and after differentiation. We quantitatively identified differential contact loops and unique loops. After integrating with multi-omics data, we demonstrate that strengthened loops after differentiation are associated with gene expression activation. Specially, unique loops are linked with cell fate determination. We also proposed loop-mediated regulatory networks and identified IRS2 and RUNX2 as being activated by cell-specific loops to facilitate adipocytes and osteoblasts commitment, respectively. These results are expected to help better understand the long-range regulation in controlling hMSC differentiation, and provide novel targets for studying adipocytes and osteoblasts determination.

genetics↗

bioRxiv2020

Heat Shock Protein 27 Immune Complex Upregulates LDLR Expression Thereby Reducing Plasma Cholesterol and Atherogenesis

Elevated Heat Shock Protein 27 levels predict relative freedom from cardiovascular events. In ApoE-/- mice HSP27 over-expression or twice daily subcutaneous injections reduce blood and plaque cholesterol levels, inflammation and atherogenesis. While natural antibodies to HSP27 are present in human blood their role is unknown. Here, we show that blood levels of both HSP27 and anti-HSP27 IgG antibodies are elevated in healthy controls compared to patients with cardiovascular disease. ApoE-/- mice vaccinated with recombinant HSP25 (murine ortholog) develop elevated anti-HSP25 IgG antibodies and reduced levels of cholesterol, inflammation and atherosclerosis. The effects on cholesterol metabolism were divergent: increased hepatic LDLR expression and reduced plasma PCSK9 levels. In vitro, a polyclonal anti-HSP27 IgG antibody combined with rHSP27 to upregulate hepatocyte LDLR expression via an NF-kB-dependent pathway that is independent of SREBP2 expression and intracellular cholesterol levels. HSP27 immunotherapy represents a novel means of lowering not only cholesterol but also PCSK9.Competing Interest StatementEOB and YXC are inventors on US patents 8343915B2 and 8343916B2 and EOB, CS and YXC are inventors on US patent application PCT/CA2016/051018, all pertaining to HSP27 diagnostics / therapeutics. EOB is the Scientific Co-Founder of Pemi31 Therapeutics Inc., a startup company that controls the aforementioned intellectual property. EOB, CS and YXC have equity interests in Pemi31 Therapeutics Inc.View Full Text

pathology↗

bioRxiv2019

Multifaceted diversity traits of crucial microbial groups in biological soil crusts promote soil multifunctionality

AbstractsMicrobial diversity is one of the most important drivers on ecosystem to maintain the simultaneous performance of functions (multifunctionality, MF) under climatic oscillation. However, existing studies typically consider taxonomic richness or Shannon index at the community level in which relations between diversity and functioning are not highly consistent. To disentangle the underlying linkages in real-world ecosystems, we conducted field investigation on biological soil crusts of Tibetan Plateau and evaluated multiple diversity facets (i.e., richness, evenness, and phylogeny-related trait dissimilarity) of carbon- and nitrogen-fixing functional groups (FGs). Seven crucial variables of soil functioning were also identified to calculate MF. We found that the integrated index, invoking multiple diversity components, was a stronger predictor on MF than richness. Moreover, the divergent performance of different diversity facets determined the idiosyncratic diversity effect of each FG on the MF. Namely, richness was the dominant factor for diazotrophs to maximize MF, whereas phylogenetic dissimilarity was the most important one for phototrophs. The heterogeneity among the focal FGs derived from the significant differentiation of the extent of multifunctional redundancy. Collectively, we speculated that the multifaceted diversity pattern depicts the response ability of crucial FGs by which biocrusts stabilize MF under environmental perturbation. Taken together, our results provided a perspective to bridge the gap between taxonomic and trait-based approaches for elucidating the biodiversity-ecosystem functioning relationship, and could ultimately help to boost the practices of dryland management against global change.

ecology↗

bioRxiv2019

Selective translation by alternative bacterial ribosomes

Alternative ribosome subunit proteins are prevalent in the genomes of diverse bacterial species but their functional significance is controversial. Attempts to study microbial ribosomal heterogeneity have mostly relied on comparing wild-type strains with mutants in which subunits have been deleted, but this approach does not allow direct comparison of alternate ribosome isoforms isolated from identical cellular contexts. Here, by simultaneously purifying canonical and alternative RpsR ribosomes from Mycobacterium smegmatis, we show that alternative ribosomes have distinct translational features compared with their canonical counterparts. Both alternative and canonical ribosomes actively take part in gene translation, although they translate a subset of genes with differential efficiency as measured by ribosome profiling. We also show that alternative ribosomes have a relative defect in initiation complex formation. Our work convincingly confirms the distinct and non-redundant contribution of alternative bacterial ribosomes for adaptation to hostile environments.\n\nSignificance StatementMany organisms, including most bacteria code for multiple paralogues of some ribosomal protein subunits. The relative contribution of these alternative subunits to ribosome function and gene translation is unknown and controversial. Furthermore, many studies on alternative ribosomes have been confounded by isolation of alternative and canonical ribosomes from different strains and/ or different growth conditions, potentially confounding results. Here, we show unequivocally that one form of alternative ribosome from Mycobacterium smegmatis actively engages in gene translation, but its translational profile from an identical cellular context is subtly different from canonical ribosomes. Given the prevalence of alternative ribosomal genes in diverse organisms, our study suggests that alternative ribosomes may represent a further layer of regulation of gene translation.

microbiology↗

bioRxiv2018

Modeling circRNAs expression pattern with integrated sequence and epigenetic features identifies H3K79me2 as regulators for circRNAs expression

Circular RNAs (circRNAs) are an abundant class of noncoding RNAs with widespread, cell/tissue specific pattern. Because of their involvement in the pathogenesis of multiple disease, they are receiving increasing attention. Previous work suggested that epigenetic features might be related to circRNA expression. However, current algorithms for circRNAs prediction neglect these features, leading to constant results across different cells.\n\nHere we built a machine learning framework named CIRCScan, to predict expression status and expression levels of circRNAs in various cell lines based on sequence and epigenetic features. Both expression status and expression levels can be accurately predicted by different groups of features. For expression status, the top features were similar in different cells. However, the top features for predicting expression levels were different in different cells. Noteworthy, the importance of H3K79me2 ranked high in predicting both circRNAs expression status and levels across different cells, indicating its important role in regulating circRNAs expression. Further validation experiment in K562 confirmed that knock down of H3K79me2 did result in reduction of circRNA production.\n\nOur study offers new insights into the regulation of circRNAs by incorporating epigenetic features in prediction models in different cellular contexts.

bioinformatics↗