Biology subjects

Shen, J.

Publications and source records attributed to Shen, J..

At least 127 records · Page 7Linked to original sources

bioRxiv2023

Cell autonomous role of leucine-rich repeat kinase in protection of dopaminergic neuron survival

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of Parkinsons disease (PD), which is the leading neurodegenerative movement disorder characterized by the progressive loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc). However, whether LRRK2 mutations cause PD and degeneration of DA neurons via a toxic gain-of-function or a loss-of-function mechanism is unresolved and has pivotal implications for LRRK2-based PD therapies. In this study, we investigate whether LRRK2 and its functional homologue LRRK1 play an essential, intrinsic role in DA neuron survival through the development of DA neuron-specific LRRK conditional double knockout (cDKO) mice. We first generated and characterized floxed LRRK1 and LRRK2 mice and then confirmed that germline deletions of the floxed LRRK1 and LRRK2 alleles result in null mutations, as evidenced by the absence of LRRK1 and LRRK2 mRNA and protein in the respective homozygous deleted mutant mice. We further examined the specificity of Cre-mediated recombination driven by the dopamine transporter-Cre (DAT-Cre) knockin (KI) allele using a GFP reporter line and confirmed that DAT-Cre-mediated recombination is restricted to DA neurons in the SNpc. Crossing these validated floxed LRRK1 and LRRK2 mice with DAT-Cre KI mice, we then generated DA neuron-restricted LRRK cDKO mice and further showed that levels of LRRK1 and LRRK2 are reduced in dissected ventral midbrains of LRRK cDKO mice. While DA neuron-restricted LRRK cDKO mice of both sexes exhibit normal mortality and body weight, they develop age-dependent loss of DA neurons in the SNpc, as demonstrated by the progressive reduction of DA neurons in the SNpc of LRRK cDKO mice at the ages of 20 and 24 months but the unaffected number of DA neurons at the age of 15 months. Moreover, DA neurodegeneration is accompanied with increases of apoptosis and elevated microgliosis in the SNpc as well as decreases of DA terminals in the striatum, and is preceded by impaired motor coordination. Taken together, these findings provide the unequivocal evidence for the importance of LRRK in DA neurons and raise the possibility that LRRK2 mutations may impair its protection of DA neurons, leading to DA neurodegeneration in PD.

neuroscience↗

bioRxiv2023

Inhibiting Glutamine Metabolism Blocks Coronavirus Replication in Mammalian Cells

Developing therapeutic strategies against COVID-19 has gained widespread interest given the likelihood that new viral variants will continue to emerge. Here we describe one potential therapeutic strategy which involves targeting members of the glutaminase family of mitochondrial metabolic enzymes (GLS and GLS2), which catalyze the first step in glutamine metabolism, the hydrolysis of glutamine to glutamate. We show three examples where GLS expression increases during coronavirus infection of host cells, and another in which GLS2 is upregulated. The viruses hijack the metabolic machinery responsible for glutamine metabolism to generate the building blocks for biosynthetic processes and satisfy the bioenergetic requirements demanded by the glutamine addiction of virus-infected host cells. We demonstrate how genetic silencing of glutaminase enzymes reduces coronavirus infection and that newer members of two classes of small molecule allosteric inhibitors targeting these enzymes, designated as SU1, a pan-GLS/GLS2 inhibitor, and UP4, which is specific for GLS, block viral replication in mammalian epithelial cells. Overall, these findings highlight the importance of glutamine metabolism for coronavirus replication in human cells and show that glutaminase inhibitors can block coronavirus infection and thereby may represent a novel class of anti-viral drug candidates. TeaserInhibitors targeting glutaminase enzymes block coronavirus replication and may represent a new class of anti-viral drugs.

molecular biology↗

bioRxiv2023

A spatially mapped gene expression signature for intestinal stem-like cells identifies high-risk precursors of gastric cancer

ObjectiveGastric intestinal metaplasia (GIM) is a precancerous lesion that increases gastric cancer (GC) risk. The Operative Link on GIM (OLGIM) is a combined clinical-histopathologic system to risk-stratify patients with GIM. The identification of molecular biomarkers that are indicators for advanced OLGIM lesions may improve cancer prevention efforts. MethodsThis study was based on clinical and genomic data from four cohorts: 1) GAPS, a GIM cohort with detailed OLGIM severity scoring (N=303 samples); 2) the Cancer Genome Atlas (N=198); 3) a collation of in-house and publicly available scRNA-seq data (N=40), and 4) a spatial validation cohort (N=5) consisting of annotated histology slides of patients with either GC or advanced GIM. We used a multi-omics pipeline to identify, validate and sequentially parse a highly-refined signature of 26 genes which characterize high-risk GIM. ResultsUsing standard RNA-seq, we analyzed two separate, non-overlapping discovery (N=88) and validation (N=215) sets of GIM. In the discovery phase, we identified 105 upregulated genes specific for high-risk GIM (defined as OLGIM III-IV), of which 100 genes were independently confirmed in the validation set. Spatial transcriptomic profiling revealed 36 of these 100 genes to be expressed in metaplastic foci in GIM. Comparison with bulk GC sequencing data revealed 26 of these genes to be expressed in intestinal-type GC. Single-cell profiling resolved the 26-gene signature to both mature intestinal lineages (goblet cells, enterocytes) and immature intestinal lineages (stem-like cells). A subset of these genes was further validated using single-molecule multiplex fluorescence in situ hybridization. We found certain genes (TFF3 and ANPEP) to mark differentiated intestinal lineages, whereas others (OLFM4 and CPS1) localized to immature cells in the isthmic/crypt region of metaplastic glands, consistent with the findings from scRNAseq analysis. Conclusionsusing an integrated multi-omics approach, we identified a novel 26-gene expression signature for high-OLGIM precursors at increased risk for GC. We found this signature localizes to aberrant intestinal stem-like cells within the metaplastic microenvironment. These findings hold important translational significance for future prevention and early detection efforts.

cancer biology↗

bioRxiv2023

Identification of an osteopontin-derived peptide that binds neuropilin-1 and activates vascular cells

BackgroundThe osteopontin-derived peptide FOL-005 has been shown to stimulate hair growth. Using ligand-receptor glycocapture technology we identified neuropilin-1 (NRP-1), a known co-receptor for vascular endothelial growth factor (VEGF) receptors, as the most probable receptor for FOL-005. Considering that induction of perifollicular angiogenesis by VEGF is a critical step in activation of the anagen growth phase of hair follicles, we investigated the effect of the more stable FOL-005 analogue FOL-026 on vascular cells. MethodsX-ray diffraction and microscale thermophoresis analysis were used to determine receptor binding of FOL-peptides. Cultured human arterial smooth muscle cells were used for studies of cell proliferation, migration, intracellular signaling, and apoptosis. A Matrigel plug assay was used to study angiogenesis in vivo. RNA seq. was used to analyze changes in gene expression patterns. ResultsFOL-026 was found to share binding site with VEGF in the NRP-1 b1-subdomain. Stimulation of human umbilical vein endothelial cells with FOL-026 resulted in phosphorylation of AKT and ERK1/2, increased cell growth and migration, stimulation of endothelial tube formation and inhibition of apoptosis in vitro, as well as activation of angiogenesis in vivo. Down-regulation of NRP-1 by NRP-1-specific small interfering RNA blocked the stimulatory effects of FOL-026 on endothelial cells. RNA sequencing showed that FOL-026 activated pathways involved in tissue repair. Exposure of human coronary artery smooth muscle cells to FOL-026 stimulated cell proliferation, migration, inhibited apoptosis, and induced VEGF gene expression by an NRP-1-dependent mechanism. ConclusionsThese findings identify NRP-1 as the receptor for FOL-026 and show that its biological effects mimic that of growth factors binding to the VEGF receptor family. They also suggest that FOL-026 may have therapeutical potential in conditions that require vascular repair and / or enhanced angiogenesis. Clinical perspectiveO_LIInsufficient vascular repair increases the risk of acute cardiovascular events, something that is of particular importance in diabetes. C_LIO_LIA peptide derived from the extracellular matrix protein osteopontin (FOL-026) binds to the vascular endothelial growth factor (VEGF) co-receptor neuropilin-1 stimulating endothelial and vascular smooth muscle cell proliferation and migration as well as the formation of new vessels. C_LIO_LIBy mimicking the effects of VEGF FOL-026 may have therapeutical potential in conditions that require vascular repair and / or enhanced angiogenesis such as vascular complications to diabetes, peripheral artery disease and salvage of ischemic myocardium. C_LI

cell biology↗

bioRxiv2023

Interrogating Proteome-wide Cysteine Ligandabilities: Crystallography Meets Chemoproteomics Through Machine Learning

Machine learning (ML) identification of covalently ligandable sites may accelerate targeted covalent inhibitor design and help expand the druggable proteome space. Here we report the rigorous development and validation of the tree-based models and convolutional neural networks (CNNs) trained on a newly curated database (LigCys3D) of over 1,000 liganded cysteines in nearly 800 proteins represented by over 10,000 three-dimensional structures in the protein data bank. The unseen tests yielded 94% and 93% AUCs (area under the receiver operating characteristic curve) for the tree models and CNNs, respectively. Based on the AlphaFold2 predicted structures, the ML models recapitulated the newly liganded cysteines in the PDB with over 90% recall values. To assist the community of covalent drug discoveries, we report the predicted ligandable cysteines in 392 human kinases and their locations in the sequence-aligned kinase structure including the PH and SH2 domains. Furthermore, we disseminate a searchable online database LigCys3D (https://ligcys.computchem.org/) and a web prediction server DeepCys (https://deepcys.computchem.org/), both of which will be continuously updated and improved by including newly published experimental data. The present work represents a first step towards the ML-led integration of big genome data and structure models to annotate the human proteome space for the next-generation covalent drug discoveries.

bioinformatics↗

bioRxiv2023

Rapid and visual detection of Schistosoma japonicum circulating nucleic acids by CRISPR-Cas12a

BackgroundSchistosomiasis is the second most destructive parasitic disease globally. It poses a serious threat to human health if not diagnosed and treated promptly. However, the current detection methods have limitations due to their dependence on specialized equipments and personnel, and the long detection time, resulting in less-than-ideal detection outcomes. Therefore, more accurate and sensitive assays are required to aid in the control of schistosomiasis. This study aims to develop a rapid and practical method for detecting Schistosoma japonicum circulating nucleic acid by combining the Cas12a protein in the CRISPR (Clustered regularly interspaced short palindromic repeats) system with recombinase-mediated isothermal nucleic acid amplification technology. Methodology/Principal FindingsWe created a CRISPR-Cas12a detection method for Schistosomiasis. SjR2 and SjCHGCS19 genes with repetitive copies in the Schistosoma japonicum genome were targeted for detection. The CRISPR-Cas12a detection method can achieve a detection sensitivity of 1 cp/{micro}L, with no cross-reaction with the other three human-infecting trematode parasites. To vividly simulate clinical patients at different infection stages, we collected rabbits serums at 1 d, 3 d, 1 w, 3 w, 5 w, and 7 w post-infection. Circulating Schistosoma japonicum DNA in the serum can be detected as early as 3 days post-infection. The sample and positive rates of each stage were analyzed and the CRISPR-Cas12a detection method prevailed to Nested-PCR. Additionally, our assay offers flexible results readout options, including lateral test strips. Conclusions/SignificanceThis CRISPR-Cas12a detection method enables sensitive and specific detection of Schistosomiasis by detecting highly repetitive SjR2 and SjCHGCS19 genes. The method was fully validated with rabbits serums collected at different infection stages, which can be applied to monitoring the early infection of schistosomiasis in resource-limited regions. Author SummaryWith the development of schistosomiasis prevention and control efforts in recent years, the prevalence rate and infection intensity of schistosomiasis have decreased, making early and accurate diagnoses more challenging. Combining CRISPR-Cas12a protein with isothermal amplification technology, a detection method for the multi-copy sequences SjR2 and SjCHGCS19 in the genome of Schistosoma japonicum was developed in this study. The results demonstrated that the detection sensitivity of this method could reach 1 cp/{micro}L, with no cross reactivity with three other fluke-like human parasites. In this study, serum samples from 15 rabbits infected with Schistosoma japonicum were used to validate the method. The results demonstrated that rabbits could be identified as early as the third day after infection. CRISPR-Cas12a detection method has a higher positive rate than traditional Nested-PCR. In addition, lateral test strips enable direct observation of our assay results. The aforementioned research findings indicate that the CRISPR-Cas12a-based detection method can be utilized for the early diagnosis of schistosomiasis. In conjunction with the result reading method of the lateral test strips, it also provides a new method for the on-site diagnosis of schistosomiasis in environments with limited access to resources.

bioengineering↗

bioRxiv2023

Intrinsically disordered CsoS2 acts as a general molecular thread for α-carboxysome shell assembly

Carboxysomes are a paradigm of self-assembling proteinaceous organelles found in nature, offering compartmentalisation of enzymes and pathways to enhance carbon fixation. In -carboxysomes, the disordered linker protein CsoS2 plays an essential role in carboxysome assembly and Rubisco encapsulation. Its mechanism of action, however, is not fully understood. Here we synthetically engineered -carboxysome shells using minimal shell components and determined cryoEM structures of these to decipher the principle of shell assembly and encapsulation. The structures reveal that the intrinsically disordered CsoS2 C-terminus is well-structured and acts as a universal "molecular thread" stitching through multiple shell protein interfaces. We further uncovered in CsoS2 a remarkable highly conserved repetitive key interaction motif, [IV]TG, which is critical to the shell assembly and architecture. Our study provides a general mechanism for the CsoS2-govern carboxysome shell assembly and cargo encapsulation and further advances synthetic engineering of carboxysomes for diverse biotechnological applications.

microbiology↗

bioRxiv2023

Alternative splicing of a potato disease resistance gene maintains homeostasis between development and immunity, and functions as a novel process for pathogen surveillance

Plants possess a robust and sophisticated innate immune system against pathogens. The intracellular receptors with nucleotide-binding, leucine-rich repeat (NLR) motifs recognize pathogen-derived effector proteins to trigger the immune response. To balance plant growth and rapid pathogen detection, NLR expression is precisely controlled in multifaceted ways. The alternative splicing (AS) of introns in response to infection is recurrently observed but poorly understood. Here we report that the potato NLR gene RB undergoes AS of its intron, resulting in two transcriptional isoforms, which coordinately regulate plant immunity and growth homeostasis. During normal growth, RB predominantly exists as intron-retained isoform RB_IR, encoding a truncated protein containing only the N-terminus of the NLR. Upon late blight infection, the pathogen induces intron splicing of RB, increasing the abundance of RB_CDS, which encodes a full-length and active R protein. By deploying the RB splicing isoforms fused with a luciferase reporter system, we identified IPI-O1 (also known as Avrblb1), the RB cognate effector, as a facilitator of RB AS. IPI-O1 directly interacts with potato splicing factor StCWC15, resulting in altered localization of StCWC15 from the nucleoplasm to the nucleolus and nuclear speckles. Mutations in IPI-O1 that eliminate StCWC15 binding also disrupt StCWC15 re-localization and RB intron splicing. Thus, our study reveals that StCWC15 serves as a surveillance facilitator sensing the pathogen-secreted effector, and regulates the trade-off between RB-mediated plant immunity and growth, expanding our understanding of molecular plant-microbe interactions. One-sentence summaryPotato resistance gene RB balances plant growth and immunity through AS (alternative splicing), while pathogen-secreted effector IPI-O1 mediates AS of RB by targeting the conserved splicing factor StCWC15, further increasing the RB_CDS expression level to activate immunity.

plant biology↗

bioRxiv2023

A conserved and druggable pocket in class B G protein coupled receptors for orally active small molecule agonists

Class B G protein-coupled receptors (GPCRs), including glucagon-like receptor 1 (GLP-1R) and parathyroid hormone receptor 1 (PTH1R), are peptide hormone receptors and important drug targets. Injectable peptide drugs targeting class B GPCRs have been developed for the treatment of many diseases, including type 2 diabetes, obesity, and osteoporosis, but orally available small molecule drugs are hotly pursued in the field, especially small molecule agonists of GLP-1R and PTH1R. Here we report the first high-resolution structure of the human PTH1R in complex with the stimulatory G protein (Gs) and a small molecule agonist, PCO371, which reveals an unexpected binding mode of PCO371 at the interface of PTH1R and Gs. The binding site of PCO371 is totally different from all binding sites previously reported for small molecules or peptide ligands in GPCRs. Residues that make up the PCO371 binding pocket are mostly conserved in class B GPCRs and a single mutation in PTH type 2 receptor (PTH2R) and two residue mutations in GLP-1R convert these receptors to respond to PCO371 activation. Functional assays reveal that PCO371 is a G-protein biased agonist that is defective in promoting PTH1R-mediated arrestin signaling. Together, these results uncover a distinct binding site for designing small molecule agonists for PTH1R and possible other members of class B GPCRs and define a receptor conformation that is only specific for G protein activation but not arrestin signaling. These insights should facilitate the design of distinct types of class B GPCR small molecule agonists for various therapeutic indications.

biochemistry↗

bioRxiv2023

Molecular architecture and conservation of an immature human endogenous retrovirus

A significant part of the human genome consists of endogenous retroviruses sequences. Human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus, is activated and expressed in many cancers and amyotrophic lateral sclerosis and possibly contributes to the aging process. To understand the molecular architecture of endogenous retroviruses, we determined the structure of immature HERV-K from native virus-like particles (VLPs) using cryo-electron tomography and subtomogram averaging (cryoET STA). The HERV-K VLPs show a greater distance between the viral membrane and immature capsid lattice, correlating with the presence of additional peptides, SP1 and p15, between the capsid (CA) and matrix (MA) proteins compared to the other retroviruses. The resulting cryoET STA map of the immature HERV-K capsid at 3.2 [A] resolution shows a hexamer unit oligomerized through a 6-helix bundle which is further stabilized by a small molecule in the same way as the IP6 in immature HIV-1 capsid. The HERV-K immature CA hexamer assembles into the immature lattice via highly conserved dimmer and trimer interfaces, whose interactions were further detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the flexible linker between the N-terminal and the C-terminal domains of CA occurs between the immature and the mature HERV-K capsid protein, analogous to HIV-1. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time.

microbiology↗

bioRxiv2023

Single-chain fluorescent integrators for mapping G-protein-coupled receptor agonists

GPCRs transduce the effects of many neuromodulators including dopamine, serotonin, epinephrine, acetylcholine, and opioids. The localization of synthetic or endogenous GPCR agonists impacts their action on specific neuronal pathways. In this paper, we show a series of single-protein chain integrator sensors to determine GPCR agonist localization in the whole brain. We previously engineered integrator sensors for the mu and kappa opioid receptor agonists called M- and K-SPOTIT, respectively. Here, we show a new integrator sensor design platform called SPOTall that we used to engineer sensors for the beta-2-adrenergic receptor (B2AR), the dopamine receptor D1, and the cholinergic receptor muscarinic 2 agonists. For multiplexed imaging of SPOTIT and SPOTall, we engineered a red version of the SPOTIT sensors. Finally, we used M-SPOTIT and B2AR-SPOTall to detect morphine, isoproterenol, and epinephrine in the mouse brain. The SPOTIT and SPOTall sensor design platform can be used to design a variety of GPCR integrator sensors for unbiased agonist detection of many synthetic and endogenous neuromodulators across the whole brain.

bioengineering↗

bioRxiv2023

Mechanism of the Temperature-Dependent Self-Assembly and Polymorphism of Chitin

Chitin is the second most abundant natural biopolymer; its crystalline structures have been extensively studied; however, the mechanism of chitins self-assembly is unknown. Here we applied all-atom molecular dynamics to study chitins self-assembly process at different temperatures. Strikingly, at 278 K, an amorphous aggregate was formed, whereas at 300 K single-sheet and at 323 K both single- and multi-sheet nanofibril regions were formed. The nanofibrils contain antiparallel, parallel or mixed orientation chains, with antiparallel being slightly preferred, recapitulating chitins polymorphism observed in nature. The inverse temperature dependence is consistent with the recent experiment. The analysis suggested that the multi-sheet nanofibrils are assembled by stacking the single nanofibril sheets, which are formed through two types of pathways in which hydrophobic collapse either precedes or is concomitant with increasing number of interchain hydrogen bonds and solvent expulsion. Furthermore, the antiparallel and parallel chains are mediated by different interchain hydrogen bonds. The analysis also suggested that the inverse temperature dependence may be attributed to the hydrophobic effect reminiscent of the low critical solution temperature phase behavior. The present study provides a rich, atomic-level view of chitins polymorphic self-assembly process, paving the way for the rational design of chitin-derived novel materials.

bioengineering↗

bioRxiv2023

Carotenoid assembly regulates quinone diffusion and the Roseiflexus castenholzii reaction center-light harvesting complex architecture

Carotenoid (Car) pigments perform central roles in photosynthesis-related light harvesting (LH), photoprotection, and assembly of functional pigment-protein complexes. However, the relationships between Car depletion in the LH, assembly of the prokaryotic reaction center (RC)-LH complex, and quinone exchange are not fully understood. Here, we analyzed native RC-LH (nRC-LH) and Car-depleted RC-LH (dRC-LH) complexes in Roseiflexus castenholzii, a chlorosome-less filamentous anoxygenic phototroph that forms the deepest branch of photosynthetic bacteria. Newly identified exterior Cars functioned with the bacteriochlorophyll B800 to block the proposed quinone channel between LH{beta} subunits in the nRC-LH, forming a sealed LH ring that was disrupted by transmembrane helices from cytochrome c and subunit X to allow quinone shuttling. dRC-LH lacked subunit X, leading to an exposed LH ring with a larger opening, which together accelerated the quinone exchange rate. We also assigned amino acid sequences of subunit X and two hypothetical proteins Y and Z that functioned in forming the quinone channel and stabilizing the RC-LH interactions. This study reveals the structural basis by which Cars assembly regulates the architecture and quinone exchange of bacterial RC-LH complexes. These findings mark an important step forward in understanding the evolution and diversity of prokaryotic photosynthetic apparatus.

biochemistry↗

bioRxiv2023

Integration of microbial and chemical synthesis for the efficient production of plitidepsin, a promising anticancer and antiviral agent

Plitidepsin, a marine-derived anticancer medicine, is being tested in phase III clinical trials for treating COVID-19. However, the current supply of plitidepsin relies on laborious chemical synthesis processes. Here, we present a new approach that combines microbial and chemical synthesis to produce plitidepsin. We screened a Tistrella strain library to identify a high-yield didemnin B producer, and then introduced a second copy of the didemnin biosynthetic gene cluster into its genome, resulting in the highest yield of didemnin B reported in the literature. Next, we developed two straightforward chemical strategies to convert didemnin B to plitidepsin, one of which involved a one-step synthetic route giving over 90% overall yield. We also synthesized two new didemnin analogues and assessed their anticancer and antiviral activities. Our findings offer a practical and sustainable solution for producing plitidepsin and its derivatives, potentially expediting didemnin drug development.

synthetic biology↗

bioRxiv2023

Apolipoprotein B and Interleukin 1 Receptor Antagonist: Reversing the Risk of Coronary Heart Disease

BackgroundEpidemiological evidence for the link of interleukin 1 (IL-1) and its inhibition with coronary heart disease (CHD) remains controversial. We aim to investigate the cardiovascular effects of IL-1 receptor antagonist (IL-1Ra) and underlying mechanisms, as well as the potential interaction with lifestyle factors. MethodsA comprehensive multivariable Mendelian randomization study was performed. Genetic variants identified from a genome-wide association study involving 30,931 individuals were used as instrumental variables for the serum IL-1Ra concentrations. Genetic associations with CHD (60,801 cases and 123,504 controls) were extracted from the CARDIoGRAMplusC4D consortium. Inverse-variance weighted method was utilized to derive effect estimates, while supplementary analyses employing various statistical approaches. ResultsGenetically determined IL-1Ra level was associated with increased risk of CHD (odds ratio (OR), 1.07; 95% CI: 1.03-1.17) and myocardial infarction (OR, 1.13; 95% CI: 1.04-1.21). The main results remained consistent in supplementary analyses. Besides, IL-1Ra was associated with circulating levels of various lipoprotein lipids, apolipoproteins and fasting glucose. Interestingly, observed association pattern with CHD was reversed when adjusting for apolipoprotein B (OR, 0.84; 95%CI: 0.71-0.99) and slightly attenuated on accounting for other cardiometabolic risk factors. Appropriate lifestyle intervention was found to lower IL-1Ra concentration and mitigate the heightened CHD risk it posed. ConclusionsApolipoprotein B represents the key driver, and a potential target for reversal of the causal link between serum IL-1Ra and increased risk of CHD/MI. The combined therapy involving IL-1 inhibition and lipid-modifying treatment aimed at apolipoprotein B merit further exploration.

genetics↗

bioRxiv2023

Engineering GliaTrap: a biodegradable non-swelling hydrogel with tuned release of CXCL12 to attract migrating glioblastoma cells

Glioblastoma is the most aggressive type of brain cancer with an average overall survival of 15-21 months after first diagnosis. The relapse is mainly caused by migrating glioblastoma cells that diffuse away from the tumor mass into the brain parenchyma and retain cancer stem cell (GSC) properties. Current therapeutic options are ineffective and inevitably result in relapse, indicating a high unmet medical need for innovative therapies in the treatment of invasive glioblastoma. To address this challenge, we propose a new therapeutic modality: GliaTrap, a biodegradable non-swelling, injectable hydrogel with sustained release of a chemoattractant for GSCs that lures and traps the migrating cells back to the tumor resection cavity. We developed a biodegradable and injectable hyaluronan/collagen II-based (HA/Col) hydrogel that does not swell in vivo. The hydrogel is embedded with CXCL12 loaded liposomes and is tuned for sustained release of CXCL12. The safety profile of liposome-embedded HA/Col hydrogel was determined in-vivo after stereotactic implantation in the mouse brain. The efficacy of GliaTrap to attract GSCs was determined ex vivo using a 3D tumor spheroid model and in-vivo using 3D light-sheet microscopy in orthotopic human glioblastoma xenografts. Our findings suggest that GliaTrap could represent a safe and efficacious new therapeutic approach for glioblastoma and potentially serve as a drug delivery platform to locally deliver tumor-killing agents. One Sentence SummaryGliaTrap is a biodegradable non-swelling hydrogel with tuned release of a chemoattractant to attract invading glioma cells and serve as delivery platform for local therapeutics.

cancer biology↗

bioRxiv2023

Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences

Whole genome duplications (WGDs) are major events that drastically reshape genome architecture and are causally associated with organismal innovations and radiations1. The 2R Hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution2, 3. However, the veracity and timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved4-6 and whether these WGD events underlie vertebrate phenotypic diversification remains elusive7. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and the 2R event occurred in the gnathostome stem-lineage in the late Cambrian after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced two additional, independent genome duplications (herein CR1 and CR2). Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only after the 2R event, questioning the general expectation that WGDs lead to leaps of morphological complexity7.

genomics↗

bioRxiv2023

Free ferrous ions sustain activity of mammalian stearoyl-CoA desaturase-1

Mammalian stearoyl-CoA desaturase-1 (SCD1) introduces a double-bond to a saturated long-chain fatty acid and the reaction is catalyzed by a diiron center, which is well-coordinated by conserved histidine residues and is thought to remain with enzyme. However, we find that SCD1 progressively loses its activity during catalysis and becomes fully inactive after nine turnovers. Further studies show that the inactivation of SCD1 is due to the loss of an iron (Fe) ion in the diiron center, and that the addition of free ferrous ions (Fe2+) sustains the enzymatic activity. Using SCD1 labeled with Fe isotope, we further show that free Fe2+ is incorporated into the diiron center only during catalysis. We also discover that the diiron center in SCD1 has prominent electron paramagnetic resonance signals in its diferric state, indicative of distinct coupling between the two ferric ions. These results reveal that the diiron center in SCD1 is structurally dynamic during catalysis and that labile Fe2+ in cells could regulate SCD1 activity, and hence lipid metabolism.

biochemistry↗