Biology subjects

Huang, J.

Publications and source records attributed to Huang, J..

At least 307 records · Page 17Linked to original sources

bioRxiv2023

Nerve Growth Factor Receptor Limits Inflammation to Promote Remodeling and Repair of Osteoarthritic Joints

Osteoarthritis (OA) is a painful, incurable disease affecting over 500 million people. The need for relieving OA pain is paramount but inadequately addressed, partly due to limited understandings of how pain signaling regulates non-neural tissues. Here we report that nerve growth factor receptor (NGFR) is upregulated in skeletal cells during OA and plays an essential role in the remodeling and repair of osteoarthritic joints. Specifically, NGFR is expressed in osteochondral cells but not in skeletal progenitor cells and induced by TNF to attenuate NF-{kappa}B activation, maintaining proper BMP-SMAD1 signaling and suppressing RANKL expression. NGFR deficiency hyper-activates NF-{kappa}B in murine osteoarthritic joints, which impairs bone formation and enhances bone resorption as exemplified by a reduction in subchondral bone and osteophytes. In human OA cartilage, NGFR is also negatively associated with NF-{kappa}B activation. Together, this study uncovers a role of NGFR in limiting inflammation for repair of diseased skeletal tissues.

cell biology↗

bioRxiv2023

Evolution of resistance to KRASG12C inhibitor in a non-small cell lung cancer responder

Despite initial therapeutic successes, most patients with non-small cell lung cancer (NSCLC) who carry the KRASG12C mutation ultimately exhibit resistance to targeted treatments. To improve our comprehension of how acquired resistance develops, we present an unprecedented longitudinal case study profiling the transcriptome of peripheral blood mononuclear cells (PBMCs) over 5 months from an NSCLC patient with the KRASG12C mutation and initial response to sotorasib followed by resistance and death. Single-cell RNA sequencing analysis uncovered notable fluctuations in immune cell populations throughout treatment with sotorasib. Specifically, we observed a decline in circulating CD8+CD161hi T cells correlating with periods of therapeutic response, followed by a resurgence during phases of nonresponse. This study established a high-resolution atlas detailing the evolutionary trajectory of resistance to sotorasib and characterizes a CD8+CD161hi T cells population in KRASG12C mutation patient.

cancer biology↗

bioRxiv2023

Improved bladder cancer antitumor efficacy with a recombinant BCG that releases a STING agonist

Despite the introduction of several new agents for the treatment of bladder cancer (BC), intravesical BCG remains a first line agent for the management of non-muscle invasive bladder cancer. In this study we evaluated the antitumor efficacy in animal models of BC of a recombinant BCG known as BCG-disA-OE that releases the small molecule STING agonist c-di-AMP. We found that compared to wild-type BCG (BCG-WT), in both the orthotopic, carcinogen-induced rat MNU model and the heterotopic syngeneic mouse MB-49 model BCG-disA-OE afforded improved antitumor efficacy. A mouse safety evaluation further revealed that BCG-disA-OE proliferated to lesser degree than BCG-WT in BALB/c mice and displayed reduced lethality in SCID mice. To probe the mechanisms that may underlie these effects, we found that BCG-disA-OE was more potent than BCG-WT in eliciting IFN-{beta} release by exposed macrophages, in reprogramming myeloid cell subsets towards an M1-like proinflammatory phenotypes, inducing epigenetic activation marks in proinflammatory cytokine promoters, and in shifting monocyte metabolomic profiles towards glycolysis. Many of the parameters elevated in cells exposed to BCG-disA-OE are associated with BCG-mediated trained innate immunity suggesting that STING agonist overexpression may enhance trained immunity. These results indicate that modifying BCG to release high levels of proinflammatory PAMP molecules such as the STING agonist c-di-AMP can enhance antitumor efficacy in bladder cancer.

cancer biology↗

bioRxiv2023

The Arabidopsis PPR protein EMB1006 interacts with both EMB1270 and CFM2 to facilitate plastid clpP1 intron2 splicing

Plastid intron splicing is an essential step for gene expression. Although many nucleus-encoded splicing factors have been identified for plastid intron splicing, how these proteins coordinately regulate intron splicing is unclear. Here we found that EMB1006, an Arabidopsis P-type PPR protein, is required for splicing several plastid introns including clpP1 intron 2 by analyzing the level of intron retention in its knockdown lines and RIP-qPCR (RNA immunoprecipitation and quantitative PCR) assay. In addition, RNA electrophoretic mobility shift assay (REMSA) showed that EMB1006 specifically binds to the sequence UUACCAAACGU close to the 3 end of clpP1 exon 2 in vitro. Furthermore, yeast two hybrid (Y2H), split luciferase complementation (Split-LUC) and semi-in vivo pull-down assays showed that EMB1006 interacts with both EMB1270 and CFM2, which also interact each other. Taken together, our data indicate that EMB1006 forms a complex with EMB1270 and CFM2 to facilitate clpP1 intron 2 splicing in chloroplasts.

plant biology↗

bioRxiv2023

Sord deficient rats develop a motor-predominant peripheral neuropathy unveiling novel pathophysiological insights

Biallelic SORD mutations cause one of the most frequent forms of recessive hereditary neuropathy, estimated to affect approximately 10,000 patients in North America and Europe alone. Pathogenic SORD loss-of-function changes in the encoded enzyme sorbitol dehydrogenase result in abnormally high sorbitol levels in cells and serum. How sorbitol accumulation leads to peripheral neuropathy remains to be elucidated. A reproducible animal model for SORD neuropathy is essential to illuminate the pathogenesis of SORD deficiency and for preclinical studies of potential therapies. Therefore, we have generated a Sord knockout (KO), Sord-/-, Sprague Dawley rat, to model the human disease and to investigate the pathophysiology underlying SORD deficiency. We have characterized the phenotype in these rats with a battery of behavioral tests as well as biochemical, physiological, and comprehensive histological examinations. Sord-/- rats had remarkably increased levels of sorbitol in serum, cerebral spinal fluid (CSF), and peripheral nerve. Moreover, serum from Sord-/- rats contained significantly increased levels of neurofilament light chain, NfL, an established biomarker for axonal degeneration. Motor performance significantly declined in Sord-/- animals starting at [~]7 months of age. Gait analysis evaluated with video motion tracking confirmed abnormal gait patterns in the hindlimbs. Motor nerve conduction velocities of the tibial nerves were slowed. Light and electron microscopy of the peripheral nervous system revealed degenerating myelinated axons, de- and remyelinated axons, and a likely pathognomonic finding - enlarged "ballooned" myelin sheaths. These findings mainly affected myelinated motor axons; myelinated sensory axons were largely spared. In summary, Sord-/- rats develop a motor-predominant neuropathy that closely resembles the human phenotype. Our studies revealed novel significant aspects of SORD deficiency, and this model will lead to an improved understanding of the pathophysiology and the therapeutic options for SORD neuropathy.

neuroscience↗

bioRxiv2023

pan-MHC and cross-Species Prediction of T Cell Receptor-Antigen Binding

Profiling the binding of T cell receptors (TCRs) of T cells to antigenic peptides presented by MHC proteins is one of the most important unsolved problems in modern immunology. Experimental methods to probe TCR-antigen interactions are slow, labor-intensive, costly, and yield moderate throughput. To address this problem, we developed pMTnet-omni, an Artificial Intelligence (AI) system based on hybrid protein sequence and structure information, to predict the pairing of TCRs of {beta} T cells with peptide-MHC complexes (pMHCs). pMTnet-omni is capable of handling peptides presented by both class I and II pMHCs, and capable of handling both human and mouse TCR-pMHC pairs, through information sharing enabled this hybrid design. pMTnet-omni achieves a high overall Area Under the Curve of Receiver Operator Characteristics (AUROC) of 0.888, which surpasses competing tools by a large margin. We showed that pMTnet-omni can distinguish binding affinity of TCRs with similar sequences. Across a range of datasets from various biological contexts, pMTnet-omni characterized the longitudinal evolution and spatial heterogeneity of TCR-pMHC interactions and their functional impact. We successfully developed a biomarker based on pMTnet-omni for predicting immune-related adverse events of immune checkpoint inhibitor (ICI) treatment in a cohort of 57 ICI-treated patients. pMTnet-omni represents a major advance towards developing a clinically usable AI system for TCR-pMHC pairing prediction that can aid the design and implementation of TCR-based immunotherapeutics.

immunology↗

bioRxiv2023

Expansion of human hematopoietic stem cells by inhibiting translation

Hematopoietic stem cell (HSC) transplantation using umbilical cord blood (UCB) is a potentially life-saving treatment for leukemia and bone marrow failure but is limited by the low number of HSCs in UCB. The loss of HSCs after ex vivo manipulation is also a major obstacle to gene editing for inherited blood disorders. HSCs require a low rate of translation to maintain their capacity for self-renewal, but hematopoietic cytokines used to expand HSCs stimulate protein synthesis and impair long-term self-renewal. We previously described cytokine-free conditions that maintain but do not expand human and mouse HSCs ex vivo. Here we performed a high throughput screen and identified translation inhibitors that allow ex vivo expansion of human HSCs while minimizing cytokine exposure. Transplantation assays show a [~]5-fold expansion of long-term HSCs from UCB after one week of culture in low cytokine conditions. Single cell transcriptomic analysis demonstrates maintenance of HSCs expressing mediators of the unfolded protein stress response, further supporting the importance of regulated proteostasis in HSC maintenance and expansion. These culture conditions maintain adult HSCs after CRISPR/Cas9 editing of the BCL11A+58 enhancer, overcoming a major obstacle to ex vivo gene correction for human hemoglobinopathies. SignificanceO_LIWe report ex vivo expansion of human hematopoietic stem cells from umbilical cord blood using low cytokines and small molecule inhibitors of GSK-3, mTORC1, and the translation initiation factor eIF4E. C_LIO_LIOur method maintains human HSCs ex vivo after gene editing with conventional CRISPR/Cas9, lipid nanoparticle delivery, and base editing approaches, overcoming a major obstacle to gene editing for inherited blood disorders. C_LI

cell biology↗

bioRxiv2023

Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04

Drug resistance poses a significant challenge in the development of effective therapies against SARS-CoV-2. Here, we identified two double mutations, M49K/M165V and M49K/S301P, in the 3C-like protease (3CLpro) that confer resistance to a novel non-covalent inhibitor, WU-04. Crystallographic analysis indicates that the M49K mutation destabilizes the WU-04 binding pocket, impacting the binding of WU-04 more significantly than the binding of 3CLpro substrates. The M165V mutation directly interferes with WU-04 binding. The S301P mutation, which is far from the WU-04 binding pocket, indirectly affects WU-04 binding by restricting the rotation of 3CLpros C-terminal tail and impeding 3CLpro dimerization. We further explored 3CLpro mutations that confer resistance to two clinically used inhibitors: ensitrelvir and nirmatrelvir, and revealed a trade-off between the catalytic activity, thermostability, and drug resistance of 3CLpro. We found that mutations at the same residue (M49) can have distinct effects on the 3CLpro inhibitors, highlighting the importance of developing multiple antiviral agents with different skeletons for fighting SARS-CoV-2. These findings enhance our understanding of SARS-CoV-2 resistance mechanisms and inform the development of effective therapeutics.

microbiology↗

bioRxiv2023

WTAP is Transcriptionally Regulated by p65 and Promotes Inflammation through m6A Modification and Phase Separation

Emerging evidence has linked dysregulation of N6-methyladenosine (m6A) to inflammation and inflammatory diseases, but the underlying mechanism still needs investigation. Here, we found that high m6A modification in a variety of hyperinflammatory states is p65-dependent, because Wilms tumor 1 associated protein (WTAP), a key component of the writer complex, is transcriptionally regulated by p65 and its overexpression can lead to higher m6A modification. Mechanistically, upregulated WTAP is more prone to phase separation to facilitate the aggregation of "writer" complex to nuclear speckles and the deposition of m6A marks onto transcriptionally active inflammatory transcripts, thereby accelerating proinflammatory response. Furthermore, myeloid deficiency of WTAP attenuates the severity of LPS-induced sepsis and DSS-induced IBD. Thus, the proinflammatory effect of WTAP is a general risk-increasing mechanism, and interrupting the assembly of m6A writer complex by targeting the phase separation of WTAP to reduce the global m6A level may be a potential and promising therapeutic strategy for alleviating hyperinflammation.

immunology↗

bioRxiv2023

The laminar pattern of proprioceptive activation in human primary motor cortex

The primary motor cortex (M1) has traditionally been viewed as a motor output generator. However, its vital role in proprioceptive somatosensation is increasingly being recognized. Yet, our understanding of proprioceptive somatosensation in M1 at the laminar scale is limited, largely due to methodological challenges. Empirical findings in primates and rodents suggest a pronounced role of superficial cortical layers, but the involvement of deep layers has yet to be examined in humans. Submillimeter resolution fMRI has emerged in recent years, paving the way for the study of layer-dependent activity in humans (laminar fMRI). In the present study, laminar fMRI was employed to investigate the laminar pattern of proprioceptive somatosensation on M1 deep layer activation using passive finger movements as proprioceptive stimulation. Significant M1 deep layer activation was observed in response to proprioceptive stimulation across 10 healthy subjects using vascular space occupancy (VASO) at 7T. For further validation, two additional subjects were scanned using a balanced steady-state free precession (bSSFP) sequence with ultrahigh (0.3 mm) in-plane resolution, yielding converging results. These results were interpreted in the light of previous laminar fMRI studies and the active inference account of motor control. We suggest that a considerable proportion of M1 deep layer activation is due to proprioceptive influence and that deep layers of M1 constitute a key component in proprioceptive circuits.

neuroscience↗

bioRxiv2023

Theranostic multifunctional lipid nanoparticles containing curcumin for integrated imaging and stabilizing vulnerable atherosclerotic plaques through an "eat-me" signal

BACKGROUNDCurcumin has emerged as a promising candidate capable of polarization of macrophages, which promote the stability of atherosclerotic plaque. Nevertheless, a notable limitation lies in the non-specific nature of curcumins targeting. The present study endeavors to harness multifunctional lipid nanoparticles (MLNPs), which could both facilitate imaging and achieve targeted delivery of curcumin specifically to inflammatory macrophages, to effectively counteract vulnerable plaque and mitigate the risk of ischemic events. METHODSThe term "MLNPs", for targeted delivery of curcumin using multimodal imaging techniques including single photon emission computed tomography (SPECT) and magnetic resonance imaging (MRI), refers to a new type of nanoparticle designed to specifically target and modulate macrophages with phagocytic function. These nanoparticles are cholesteryl-9-carboxynonanoate-(125I-iron oxide nanoparticle/Cur)-lipid-coated nanoparticles [9-CCN-(125I-ION/Cur)-LNPs], which carry hybrid imaging agents. These agents are combinations of 125I-ION and lipids that contain phagocytic "eat-me" signals, which induces macrophages to swallow MLNPs. RESULTSThe accumulation of the devised 9-CCN-(125I-ION/Cur)-LNPs on the unstable plaque of animal models in vivo was accurately reflected and lesions were highlighted by both SPECT and MRI. The intense radioactive signals on SPECT images facilitated the identification and quantification of the target lesion, while MRI based on ION particles facilitated the visualization of the focal localization and volumetry of atherosclerotic plaque. The targeted distribution of the unstable plaque in the rabbit aorta was further confirmed by ex vivo planar images of nuclide and Prussian blue staining for ION. Additionally, 9-CCN-(125I-ION/Cur)-LNPs were found to specifically and effectively bind to the pro-inflammatory M1 macrophages present in the unstable plaque, resulting in the accumulation of radionuclide and hypointensity on T2W images. CONCLUSIONSThe 9-CCN-(125I-ION/Cur)-LNPs demonstrated remarkable capability in the delivery of both 125I-ION and curcumin to macrophages, ultimately resulting in M1-M2 macrophage polarization, which may offer valuable insights into addressing unstable atherosclerotic plaque.

neuroscience↗

bioRxiv2023

Decoupling of the Onset of Anharmonicity between a Protein and Its Surface Water around 200 K

The protein dynamical transition at [~] 200 K, where the biomolecule transforms from a harmonic, non-functional form to an anharmonic, functional state, has been thought to be slaved to the thermal activation of dynamics in its surface hydration water. Here, by selectively probing the dynamics of protein and hydration water using elastic neutron scattering and isotopic labelling, we found that the onset of anharmonicity in the two components around 200 K are decoupled. The one in protein is an intrinsic transition, whose characteristic temperature is independent of the instrumental resolution time, but varies with the biomolecular structure and the amount of hydration, while the one of water is merely a resolution effect.

biophysics↗

bioRxiv2023

Rolling 2D Bioelectronic film into 1D: a Suturable Long-term Implantable Soft Microfiber

Long-term implantable bioelectronics can efficiently evaluate the function of the nervous system. 1D fiber-shaped devices require small surgical incisions significantly benefiting long-term biocompatibility. We report a strategy of rolling to reduce the dimension of bioelectronic devices from 2D film to 1D microfiber. The soft and stretchable multifunctional microfiber accommodates more than 60-channel longitudinally-distributed electrodes for bio-electric and -mechanical monitoring. It can be sutured into muscle with tiny incision for 8-month bio-electrical monitoring in rats. Importantly, after 13-month implantation, the fibroblast encapsulation around the fiber is negligible. Moreover, it can wander inside a brain under magnetic field. This strategy not only opens up the study of multi-channel and -function soft and stretchable fiber-shaped sensors but offers a platform for minimally-invasive implantable bioelectronics. One-Sentence SummaryThe rolling enables stretchable electrode array along one single microfiber and multimodal long-term in-vivo monitoring.

neuroscience↗

bioRxiv2023

DP/MM: A Hybrid Model for Zinc-Protein Interactions in Molecular Dynamics

Zinc-containing proteins are essential to a variety of biological processes, yet accurately modeling them using classical force fields is hindered by complicated polarization and charge transfer effects. This study introduces DP/MM, a hybrid force field model that combines ab initio accuracy with MM-level efficiency for modeling zinc-protein interactions. The DP/MM scheme utilizes a deep potential model to correct the atomic forces of zinc ions and their coordinated atoms, elevating them from MM to QM levels of accuracy. The model is trained on the difference in atomic forces between MM and QM calculations across diverse zinc coordination groups. Simulations on a variety of zinccontaining proteins demonstrate that DP/MM faithfully reproduces their coordination geometry and structural characteristics, for example, the tetrahedral coordination structures for the Cys4 and the Cys3His1 groups. Furthermore, DP/MM is capable of handling exchangeable water molecules in the zinc coordination environment. With its unique blend of accuracy, efficiency, flexibility, and transferability, DP/MM not only serves as a valuable tool for studying zinc-containing proteins but also represents a pioneering approach that augments the growing landscape of machine learning potentials in molecular modeling.

biophysics↗

bioRxiv2023

Disease-specific selective vulnerability and neuroimmune pathways in dementia revealed by single cellgenomics

Summary/AbstractThe development of successful therapeutics for dementias requires an understanding of their shared and distinct molecular features in the human brain. We performed single-nuclear RNAseq and ATACseq in Alzheimer disease (AD), Frontotemporal degeneration (FTD), and Progressive Supranuclear Palsy (PSP), analyzing 40 participants, yielding over 1.4M cells from three brain regions ranging in vulnerability and pathological burden. We identify 35 shared disease-associated cell types and 14 that are disease-specific, replicating those previously identified in AD. Disease-specific cell states represent molecular features of disease-specific glial-immune mechanisms and neuronal vulnerability in each disorder, layer 4/5 intra-telencephalic neurons in AD, layer 2/3 intra-telencephalic neurons in FTD, and layer 5/6 near-projection neurons in PSP. We infer intrinsic disease-associated gene regulatory networks, which we empirically validate by chromatin footprinting. We find that causal genetic risk acts in specific neuronal and glial cells that differ across disorders, primarily non-neuronal cells in AD and specific neuronal subtypes in FTD and PSP. These data illustrate the heterogeneous spectrum of glial and neuronal composition and gene expression alterations in different dementias and identify new therapeutic targets by revealing shared and disease-specific cell states.

neuroscience↗

bioRxiv2023

Conditioned Protein Structure Prediction

Deep learning based protein structure prediction has facilitated major breakthroughs in biological sciences. However, current methods struggle with alternative conformation prediction and offer limited integration of expert knowledge on protein dynamics. We introduce AFEXplorer, a generic approach that tailors AlphaFold predictions to user-defined constraints in coarse coordinate spaces by optimizing embedding features. Its effectiveness in generating functional protein conformations in accordance with predefined conditions were demonstrated through comprehensive examples. AFEXplorer serves as a versatile platform for conditioned protein structure prediction, bridging the gap between automated models and domain-specific insights.

bioinformatics↗

bioRxiv2023

The apoptotic splicing regulators RBM5 and RBM10 are subunits of the U2 snRNP engaged with intron branch sites on chromatin

Understanding the mechanisms of pre-mRNA splicing and spliceosome assembly is limited by technical challenges to examining spliceosomes in vivo. Here we report the isolation of RNP complexes derived from precatalytic A or B-like spliceosomes solubilized from the chromatin pellet of lysed nuclei. We found that these complexes contain U2 snRNP proteins and a portion of the U2 snRNA, bound with intronic branch sites prior to the first catalytic step of splicing. Sequencing these pre-mRNA fragments allowed the transcriptome-wide mapping of branch sites with high sensitivity. In addition to known U2 snRNP proteins, these complexes contained the proteins RBM5 and RBM10. RBM5 and RBM10 are alternative splicing regulators that control exons affecting apoptosis and cell proliferation in cancer, but were not previously shown to associate with the U2 snRNP or to play roles in branch site selection. We delineate a common segment of RBM5 and RBM10, separate from their known functional domains, that is required for their interaction with the U2 snRNP. We identify a large set of splicing events regulated by RBM5 and RBM10 and find that they predominantly act as splicing silencers. Disruption of their U2 interaction renders the proteins inactive for repression of many alternative exons. We further find that these proteins assemble on branch sites of nearly all exons across the transcriptome, including those whose splicing is not altered by them. We propose a model where RBM5 and RBM10 act as components of the U2 snRNP complex. From within this complex, they sense structural features of branchpoint recognition to either allow progression to functional spliceosome or rejection of the complex to inhibit splicing.

molecular biology↗

bioRxiv2023

Using recurrent neural networks to detect supernumerary chromosomes in fungal strains causing blast diseases

The genomes of the fungus Magnaporthe oryzae that causes blast diseases on diverse grass species, including major crop plants, have indispensable core-chromosomes and may contain one or more additional supernumerary chromosomes, also known as mini-chromosomes. The mini-chromosome is speculated to play a role in fungal biology, provide effector gene mobility, and may transfer between strains. To understand and study the biological function of mini-chromosomes, it is crucial to be able to identify whether a given strain of M. oryzae possesses a mini-chromosome. In this study, we applied recurrent neural network models, more specifically, Bidirectional Long Short-Term Models (Bi-LSTM), for classifying DNA sequences as core-or mini-chromosomes. The models were trained with sequences from multiple available core- and mini-chromosome assemblies. The trained model was then used to predict the presence of the mini-chromosome in a global collection of M. oryzae isolates using short-read DNA sequences. The model predicted that the mini-chromosome was prevalent in M. oryzae isolates, including those isolated from rice, wheat, Lolium and many other grass species. Interestingly, 23 recent wheat strains collected since 2005 all carried the mini-chromosome, but none of nine early strains collected before 1991 had the mini-chromosome, indicating the preferential selection for strains carrying the mini-chromosome in recent years. Based on the limited sample size, we found the presence of the mini-chromosome in isolates of pathotype Eleusine was not as high as isolates of other pathotypes. The deep learning model was also used to identify assembled sequence contigs that were derived from the mini-chromosome and partial regions on core-chromosomes potentially translocated from a mini-chromosome. In summary, our study has developed a reliable method for categorizing DNA sequences and showcases an application of recurrent neural networks in the field of predictive genomics.

genomics↗