Reduced non-CpG methylation is a potential epigenetic target after spinal cord injury

DNA methylation is a critical epigenetic regulator in the occurrence and development of diseases and is closely related to various functional responses in relation to spinal cord injury.To investigate the role of DNA methylation in spinal cord injury,we constructed a library with reduced-representation bisulfite sequencing data obtained at various time points(day 0-42)after spinal cord injury in mice.Global DNA methylation levels,specifically non-CpG(CHG and CHH)methylation levels,decreased modestly following spinal cord injury.Stages post-spinal cord injury were classified as early(day 0-3),intermediate(day7-14),and late(day 28-42)based on similarity and hie rarchical cluste ring of global DNA methylation patterns.The non-CpG methylation level,which included CHG and CHH methylation levels,was markedly reduced despite accounting for a minor proportion of total methylation abundance.At multiple genomic sites,including the 5’untranslated regions,promoter,exon,intron,and 3’untranslated regions,the non-CpG methylation level was markedly decreased following spinal cord injury,whereas the CpG methylation level remained unchanged at these locations.Approximately one-half of the differentially methylated regions were located in intergenic areas;the other differentially methylated regions in both CpG and non-CpG regions were cluste red in intron regions,where the DNA methylation level was highest.The function of genes associated with differentially methylated regions in promoter regions was also investigated.From Gene Ontology analysis results,DNA methylation was implicated in a number of essential functional responses to spinal cord injury,including neuronal synaptic connection creation and axon regeneration.Notably,neither CpG methylation nor non-CpG methylation was implicated in the functional response of glial or inflammatory cells.In summary,our work elucidated the dynamic pattern of DNA methylation in the spinal co rd following injury and identified reduced nonCpG methylation as an epigenetic target after spinal cord injury in mice.

Spinal cord injury:molecular mechanisms and therapeutic interventions

Spinal cord injury(SCI)remains a severe condition with an extremely high disability rate.The challenges of SCI repair include its complex pathological mechanisms and the difficulties of neural regeneration in the central nervous system.In the past few decades,researchers have attempted to completely elucidate the pathological mechanism of SCI and identify effective strategies to promote axon regeneration and neural circuit remodeling.

Temporal and spatial cellular and molecular pathological alterations with single-cell resolution in the adult spinal cord after injury

Spinal cord injury(SCI)involves diverse injury responses in different cell types in a temporally and spatially specific manner.Here,using single-cell transcriptomic analyses combined with classic anatomical,behavioral,electrophysiological analyses,we report,with single-cell resolution,temporal molecular and cellular changes in crush-injured adult mouse spinal cord.Data revealed pathological changes of 12 different major cell types,three of which infiltrated into the spinal cord at distinct times post-injury.We discovered novel microglia and astrocyte subtypes in the uninjured spinal cord,and their dynamic conversions into additional stage-specific subtypes/states.Most dynamic changes occur at 3-days post-injury and by day-14 the second wave of microglial activation emerged,accompanied with changes in various cell types including neurons,indicative of the second round of attacks.By day-38,major cell types are still substantially deviated from uninjured states,demonstrating prolonged alterations.This study provides a comprehensive mapping of cellular/molecular pathological changes along the temporal axis after SCI,which may facilitate the development of novel therapeutic strategies,including those targeting microglia.

Breakthrough of extracellular vesicles in pathogenesis, diagnosis and treatment of osteoarthritis

Osteoarthritis(OA)is a highly prevalent whole-joint disease that causes disability and pain and affects a patient’s quality of life.However,currently,there is a lack of effective early diagnosis and treatment.Although stem cells can promote cartilage repair and treat OA,problems such as immune rejection and tumorigenicity persist.Extracellular vesicles(EVs)can transmit genetic information from donor cells and mediate intercellular communication,which is considered a functional paracrine factor of stem cells.Increasing evidences suggest that EVs may play an essential and complex role in the pathogenesis,diagnosis,and treatment of OA.Here,we introduced the role of EVs in OA progression by influencing inflammation,metabolism,and aging.Next,we discussed EVs from the blood,synovial fluid,and joint-related cells for diagnosis.Moreover,we outlined the potential of modified and unmodified EVs and their combination with biomaterials for OA therapy.Finally,we discuss the deficiencies and put forward the prospects and challenges related to the application of EVs in the field of OA.

Modified constraint-induced movement therapy alters synaptic plasticity of rat contralateral hippocampus following middle cerebral artery occlusion

Modified constraint-induced movement therapy is an effective treatment for neurological and motor impairments in patients with stroke by increasing the use of their affected limb and limiting the contralateral limb.However,the molecular mechanism underlying its efficacy remains unclear.In this study,a middle cerebral artery occlusion(MCAO)rat model was produced by the suture method.Rats received modified constraint-induced movement therapy 1 hour a day for 14 consecutive days,starting from the 7^th day after middle cerebral artery occlusion.Day 1 of treatment lasted for 10 minutes at 2r/min,day 2 for 20 minutes at 2 r/min,and from day 3 onward for 20 minutes at 4 r/min.CatWalk gait analysis,adhesive removal test,and Y-maze test were used to investigate motor function,sensory function as well as cognitive function in rodent animals from the 1st day before MCAO to the 21^st day after MCAO.On the 21^st day after MCAO,the neurotransmitter receptor-related genes from both contralateral and ipsilateral hippocampi were tested by micro-array and then verified by western blot assay.The glutamate related receptor was shown by transmission electron microscopy and the glutamate content was determined by high-performance liquid chromatography.The results of behavior tests showed that modified constraint-induced movement therapy promoted motor and sensory functional recovery in the middle cerebral artery-occluded rats,but had no effect on cognitive function.The modified constraint-induced movement therapy upregulated the expression of glutamate ionotropic receptor AMPA type subunit 3(Gria3)in the hippocampus and downregulated the expression of the beta3-adrenergic receptor gene Adrb3 and arginine vasopressin receptor 1 A,Avprla in the middle cerebral artery-occluded rats.In the ipsilateral hippocampus,only Adra2 a was downregulated,and there was no significant change in Gria3.Transmission electron microscopy revealed a denser distribution the more distribution of postsynaptic glutamate receptor 2/3,which is an a-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptor,within 240 nm of the postsynaptic density in the contralateral cornu ammonis 3 region.The size and distribution of the synaptic vesicles within 100 nm of the presynaptic active zone were unchanged.Western blot analysis showed that modified constraint-induced movement therapy also increased the expression of glutamate receptor 2/3 and brain-derived neurotrophic factor in the hippocampus of rats with middle cerebral artery occlusion,but had no effect on Synapsin I levels.Besides,we also found modified constraint-induced movement therapy effectively reduced glutamate content in the contralateral hippocampus.This study demonstrated that modified constraint-induced movement therapy is an effective rehabilitation therapy in middle cerebral artery-occluded rats,and suggests that these positive effects occur via the upregulation of the postsynaptic membrane a-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptor expression.This study was approved by the Institutional Animal Care and Use Committee of Fudan University,China(approval No.201802173 S)on March 3,2018.

Privacy-preserving integration of multiple institutional data for single-cell type identification with scPrivacy

The rapid accumulation of large-scale single-cell RNA-seq datasets from multiple institutions presents remarkable opportunities for automatically cell annotations through integrative analyses.However,the privacy issue has existed but being ignored,since we are limited to access and utilize all the reference datasets distributed in different institutions globally due to the prohibited data transmission across institutions by data regulation laws.To this end,we present scPrivacy,which is the first and generalized automatically single-cell type identification prototype to facilitate single cell annotations in a data privacy-preserving collaboration manner.We evaluated scPrivacy on a comprehensive set of publicly available benchmark datasets for single-cell type identification to stimulate the scenario that the reference datasets are rapidly generated and distributed in multiple institutions,while they are prohibited to be integrated directly or exposed to each other due to the data privacy regulations,demonstrating its effectiveness,time efficiency and robustness for privacy-preserving integration of multiple institutional datasets in single cell annotations.

Autophagy mediates osteoporotic bone regeneration induced by micro-/nano-structured modification on hydroxyapatite bioceramics

Osteoporosis(OP)is an age-related disease of bone metabolism,characterized by bone mass loss and bone mi-croarchitecture deterioration,the poor osteogenesis microenvironment of OP caused hardly repairing of the bone defects.As a dynamic process to fuel cellular renovation,autophagy has been proved to play a vital role in regulating cell differentiation and maintaining bone homeostasis.Traditional bone repairing biomaterials are hardly repairing the bone defects under OP pathological microenvironment.Therefore,it is essential to develop-ment novel biomaterials to improve osteoporotic osteogenesis.Compared to biochemical cues,biophysical cues exhibited more advantages in biocompatible and side effects.Herein,inspired by the importance of enhanced au-tophagic response in osteoporotic environment,we intend to utilize the micro-/nano-structured hydroxyapatite(mnHA)bioceramics as the mimic structure of natural bone tissue to regulate autophagic activity in ovariectomy bone mesenchymal stem cells(OVX-BMSCs),finally promote to bone regeneration in OP condition.The results indicated that mnHA bioceramics promoted cell adhesion and osteogenesis of OVX-BMSCs,and enhanced au-tophagy level in OVX-BMSCs.In the calvarial defects of OVX-rats,the mnHA scaffold acquired excellent bone repair effect.According to the current findings,regulating the level of autophagy could be a promising strategy for improve osteoporotic osteogenesis in the future.

Extracellular vesicles,from the pathogenesis to the therapy of neurodegenerative diseases

Extracellular vesicles(EVs)are small bilipid layer-enclosed vesicles that can be secreted by all tested types of brain cells.Being a key intercellular communicator,EVs have emerged as a key contributor to the pathogenesis of various neurodegenerative diseases(NDs)including Alzheimer’s disease,Parkinson’s disease,amyotrophic lateral sclerosis,and Huntington’s disease through delivery of bioactive cargos within the central nervous system(CNS).Importantly,CNS cell-derived EVs can be purified via immunoprecipitation,and EV cargos with altered levels have been identified as potential biomarkers for the diagnosis and prognosis of NDs.Given the essential impact of EVs on the pathogenesis of NDs,pathological EVs have been considered as therapeutic targets and EVs with therapeutic effects have been utilized as potential therapeutic agents or drug delivery platforms for the treatment of NDs.In this review,we focus on recent research progress on the pathological roles of EVs released from CNS cells in the pathogenesis of NDs,summarize findings that identify CNS-derived EV cargos as potential biomarkers to diagnose NDs,and comprehensively discuss promising potential of EVs as therapeutic targets,agents,and drug delivery systems in treating NDs,together with current concerns and challenges for basic research and clinical applications of EVs regarding NDs.

DrSim: Similarity Learning for Transcriptional Phenotypic Drug Discovery

Transcriptional phenotypic drug discovery has achieved great success,and various compound perturbation-based data resources,such as connectivity map(CMap)and library of integrated network-based cellular signatures(LINCS),have been presented.Computational strategies fully mining these resources for phenotypic drug discovery have been proposed.Among them,the fundamental issue is to define the proper similarity between transcriptional profiles.Traditionally,such similarity has been defined in an unsupervised way.However,due to the high dimensionality and the existence of high noise in high-throughput data,similarity defined in the traditional way lacks robustness and has limited performance.To this end,we present Dr Sim,which is a learning-based framework that automatically infers similarity rather than defining it.We evaluated Dr Sim on publicly available in vitro and in vivo datasets in drug annotation and repositioning.The results indicated that Dr Sim outperforms the existing methods.In conclusion,by learning transcriptional similarity,Dr Sim facilitates the broad utility of high-throughput transcriptional perturbation data for phenotypic drug discovery.The source code and manual of Dr Sim are available at https://github.com/bm2-lab/Dr Sim/.