AIM： To study the genes responsible for retinitis pigmentosa.METHODS： A total of 15 Chinese families with retinitis pigmentosa, containing 94 sporadically afflicted cases, were recruited. The targeted sequences were...AIM： To study the genes responsible for retinitis pigmentosa.METHODS： A total of 15 Chinese families with retinitis pigmentosa, containing 94 sporadically afflicted cases, were recruited. The targeted sequences were captured using the Target_Eye_365_V3 chip and sequenced using the BGISEQ-500 sequencer, according to the manufacturer＇s instructions. Data were aligned to UCSC Genome Browser build hg19, using the Burroughs Wheeler Aligner MEM algorithm. Local realignment was performed with the Genome Analysis Toolkit（GATK v.3.3.0） Indel Realigner, and variants were called with the Genome Analysis Toolkit Haplotypecaller, without any use of imputation. Variants were filtered against a panel derived from 1000 Genomes Project, 1000 G_ASN, ESP6500, Ex AC and db SNP138. In all members of Family ONE and Family TWO with available DNA samples, the genetic variant was validated using Sanger sequencing.RESULTS： A novel, pathogenic variant of retinitis pigmentosa, c.357_358 del AA（p.Ser119 Serfs X5） was identified in PRPF31 in 2 of 15 autosomal-dominant retinitis pigmentosa（ADRP） families, as well as in one, sporadic case. Sanger sequencing was performed uponprobands, as well as upon other family members. This novel, pathogenic genotype co-segregated with retinitis pigmentosa phenotype in these two families. CONCLUSION： ADRP is a subtype of retinitis pigmentosa, defined by its genotype, which accounts for 20%-40% of the retinitis pigmentosa patients. Our study thus expands the spectrum of PRPF31 mutations known to occur in ADRP, and provides further demonstration of the applicability of the BGISEQ500 sequencer for genomics research.展开更多
Dear Editor,Rift Valley fever(RVF)is an anthropozoonosis caused by Rift Valley fever virus(RVFV).RVFV belongs to the Phlebovirus genus in the family Bunyaviridae,which is circulating among ruminants.Human infection wi...Dear Editor,Rift Valley fever(RVF)is an anthropozoonosis caused by Rift Valley fever virus(RVFV).RVFV belongs to the Phlebovirus genus in the family Bunyaviridae,which is circulating among ruminants.Human infection with RVFV is generally asymptomatic,however,minority of patients develop severe RVF diseases like encephalitis展开更多
Parkinson's disease(PD)is a neurodegenerative disease,leading to the impairment of movement execution.PD pathogenesis has been largely investigated,either limited to bulk transcriptomic levels or at certain cell t...Parkinson's disease(PD)is a neurodegenerative disease,leading to the impairment of movement execution.PD pathogenesis has been largely investigated,either limited to bulk transcriptomic levels or at certain cell types,which failed to capture the cellular heterogeneity and intrinsic interplays among distinct cell types.Here,we report the application of single-nucleus RNA-seq on midbrain,striatum,and cerebellum of theα-syn-A53 T mouse,a well-established PD mouse model,and matched controls,generating the first single cell transcriptomic atlas for the PD model mouse brain composed of 46,174 individual cells.Additionally,we comprehensively depicte the dysfunctions in PD pathology,covering the elevation of NF-k B activity,the alteration of ion channel components,the perturbation of protein homeostasis network,and the dysregulation of glutamatergic signaling.Notably,we identify a variety of cell types closely associated with PD risk genes.Taken together,our study provides valuable resources to systematically dissect the molecular mechanism of PD pathogenesis at the single-cell resolution,which facilitates the development of novel approaches for diagnosis and therapies against PD.展开更多
Objective:Neoantigens arising from gene mutations in tumors can induce specific immune responses,and neoantigen-based immunotherapies have been tested in clinical trials.Here,we characterized the efficacy of altered n...Objective:Neoantigens arising from gene mutations in tumors can induce specific immune responses,and neoantigen-based immunotherapies have been tested in clinical trials.Here,we characterized the efficacy of altered neoepitopes in improving immunogenicity against gastric cancer.Methods:Raw data of whole-exome sequencing derived from a patient with gastric cancer were analyzed using bioinformatics methods to identify neoepitopes.Neoepitopes were modified by P1Y(the first amino acid was replaced by tyrosine)and P2L(the second amino acid was replaced by leucine).T2 binding and stability assays were used to detect the affinities between the neoepitopes and the HLA molecules,as well as the stabilities of complexes.Dendritic cells(DCs)presented with neoepitopes stimulated naïve CD8+T cells to induce specific cytotoxic T lymphocytes.ELISA and carboxyfluorescein succinimidyl ester were used to detect IFN-γand TNF-αlevels,and T cell proliferation.Perforin was detected by flow cytometry.The cytotoxicity of T cells was determined using the lactate dehydrogenase assay.Results:Bioinformatics analysis,T2 binding,and stability assays indicated that residue substitution increased the affinity between neoepitopes and HLA molecules,as well as the stabilities of complexes.DCs presented with altered neoepitopes stimulated CD8+T cells to release more IFN-γand had a greater effect on promoting proliferation than wild-type neoepitopes.CD8+T cells stimulated with altered neoepitopes killed more wild-type neoepitope-pulsed T2 cells than those stimulated with wild-type neoepitopes,by secreting more IFN-γ,TNF-α,and perforin.Conclusions:Altered neoepitopes exhibited greater immunogenicity than wild-type neoepitopes.Residue substitution could be used as a new strategy for immunotherapy to target neoantigens.展开更多
Dear Editor,In recent years,the incidence of human infections caused by emerging or re-emerging pathogens has rapidly increased.Diseases that were once regional now have the ability to spread globally in a short amoun...Dear Editor,In recent years,the incidence of human infections caused by emerging or re-emerging pathogens has rapidly increased.Diseases that were once regional now have the ability to spread globally in a short amount of time and pose a wider threat to public health(Weaver et al.2018).Yellow fever virus(YFV,family Flaviviridae,genus Flavivirus)is a mosquito-borne flavivirus that causes yellow fever in humans and has been endemic in Africa and Latin America for many years(Domingo et al.2018).展开更多
Olfaction,the sense of smell,is a fundamental trait crucial to many species.The olfactory bulb(OB)plays pivotal roles in processing and transmitting odor information from the environment to the brain.The cellular hete...Olfaction,the sense of smell,is a fundamental trait crucial to many species.The olfactory bulb(OB)plays pivotal roles in processing and transmitting odor information from the environment to the brain.The cellular heterogeneity of the mouse OB has been studied using single-cell RNA sequencing.However,the epigenetic landscape of the m OB remains mostly unexplored.Herein,we apply single-cell assay for transposaseaccessible chromatin sequencing to profile the genome-wide chromatin accessibility of 9,549 single cells from the m OB.Based on single-cell epigenetic signatures,m OB cells are classified into 21 clusters corresponding to 11 cell types.We identify distinct sets of putative regulatory elements specific to each cell cluster from which putative target genes and enriched potential functions are inferred.In addition,the transcription factor motifs enriched in each cell cluster are determined to indicate the developmental fate of each cell lineage.Our study provides a valuable epigenetic data set for the m OB at single-cell resolution,and the results can enhance our understanding of regulatory circuits and the therapeutic capacity of the OB at the single-cell level.展开更多
The Dianchi golden-line barbel,Sinocyclocheilus grahami(Regan,1904),is one of the“Four Famous Fishes”of Yunnan Province,China.Given its economic value,this species has been artificially bred successfully since 2007,...The Dianchi golden-line barbel,Sinocyclocheilus grahami(Regan,1904),is one of the“Four Famous Fishes”of Yunnan Province,China.Given its economic value,this species has been artificially bred successfully since 2007,with a nationally selected breed(“S.grahami,Bayou No.1”)certified in 2018.For the future utilization of this species,its growth rate,disease resistance,and wild adaptability need to be improved,which could be achieved with the help of molecular markerassisted selection(MAS).In the current study,we constructed the first chromosome-level genome of S.grahami,assembled 48 pseudo-chromosomes,and obtained a genome size of 1.49 Gb.We also performed QTL-seq analysis of S.grahami using the highest and lowest bulks(i.e.,largest and smallest size)in both a sibling and random population.We screened two quantitative trait loci(QTLs)(Chr3,14.9-39.1 Mb and Chr17,4.1-27.4 Mb)as major growth-related locations.Several candidate genes(e.g.,map2k5,stat1,phf21a,sox6,and smad6)were also identified,with functions related to growth,such as cell differentiation,neuronal development,skeletal muscle development,chondrogenesis,and immunity.These results built a solid foundation for in-depth MAS studies on the growth traits of S.grahami.展开更多
Powdery mildew(PM),caused by the fungus Microsphaera diffusa,causes severe yield losses in soybean[Glycine max(L.)Merr.]under suitable environmental conditions.Identifying resistance genes and developing resistant cul...Powdery mildew(PM),caused by the fungus Microsphaera diffusa,causes severe yield losses in soybean[Glycine max(L.)Merr.]under suitable environmental conditions.Identifying resistance genes and developing resistant cultivars may prevent soybean PM damage.In this study,analysis of F_(1),F_(2),and F8:11 recombinant inbred line(RIL)populations derived from the cross between Zhonghuang 24(ZH24)and Huaxia 3(HX3)indicated that adult-plant resistance(APR)to powdery mildew in the soybean cultivar(cv.)ZH24 was controlled by a single dominant locus.A high-density genetic linkage map of the RIL population was used for fine mapping.The APR locus in ZH24 was mapped to a 281-kb genomic region on chromosome 16.Using 283 susceptible plants of another F2 population,the candidate region was finemapped to a 32.8-kb genomic interval flanked by the markers InDel14 and Gm16_428.The interval harbored five genes,including four disease resistance(R)-like genes,according to the Williams 82.a2.v1 reference genome.Quantitative real-time PCR assays of candidate genes revealed that the expression levels of Glyma.16g214300 and Glyma.16g214500 were changed by M.diffusa infection and might be involved in disease defense.Rmd_B13 showed all-stage resistance(ASR)to PM in soybean cv.B13.An allelism test in the F2 segregating population from the cross of ZH24 × B13 suggested that the APR locus Rmd_ZH24 and the ASR locus Rmd_B13 may be allelic or tightly linked.These results provide a reference marker-assisted selection in breeding programs.展开更多
Pattern recognition receptors(PRRs) play important roles in innate immunity system and trigger the specific pathogen recognition by detecting the pathogen-associated molecular patterns. The main four PRRs components i...Pattern recognition receptors(PRRs) play important roles in innate immunity system and trigger the specific pathogen recognition by detecting the pathogen-associated molecular patterns. The main four PRRs components including Toll-like receptors(TLRs), RIG-I-like receptors(RLRs), NOD-like receptors(NLRs) and C-type lectin receptors(CLRs) were surveyed in the five genomes of non-teleost ray-finned fishes(NTR) including bichir(Polypterus senegalus), American paddlefish(Polyodon spathula), alligator gar(Atractosteus spatula), spotted gar(Lepisosteus oculatus) and bowfin(Amia calva), representing all the four major basal groups of ray-finned fishes. The result indicates that all the four PRRs components have been well established in these NTR fishes. In the RLR-MAVS signal pathway, which detects intracellular RNA ligands to induce production of type I interferons(IFNs), the MAVS was lost in bichir particularly. Also, the essential genes of recognition of Lipopolysaccharide(LPS) commonly in mammals like MD2, LY96 and LBP could not be identified in NTR fishes. It is speculated that TLR4 in NTR fishes may act as a cooperator with other PRRs and has a different pathway of recognizing LPS compared with that in mammals. In addition, we provide a survey of NLR and CLR in NTR fishes. The CLRs results suggest that Group V receptors are absent in fishes and Group II and VI receptors are well established in the early vertebrate evolution. Our comprehensive research of PRRs involving NTR fishes provides a new insight into PRR evolution in primitive vertebrate.展开更多
Astragalus and Angelica decoction(A&A)has been clinically used as a classical traditional Chinese medicine(TCM)formula in China for many years for the treatment of kidney diseases,especially renal interstitial fib...Astragalus and Angelica decoction(A&A)has been clinically used as a classical traditional Chinese medicine(TCM)formula in China for many years for the treatment of kidney diseases,especially renal interstitial fibrosis(RIF).However,the mechanisms underlying the therapeutic effects of A&A on RIF remains poorly understood.In the present study,systematic network pharmacology and effective experimental verification were utilized for the first time to elucidate the pharmacological efficacy and potential mechanism.The outcomes indicated that 22 active components and 87 target genes of A&A were identified and cross-referenced with RIF-associated genes,contributing to confirmation of 74 target genes of A&A for RIF.Pathway and functional enrichment analyses revealed that A&A had substantial effects on MAPK,PI3K-Akt and TNF signaling pathways.In addition,seven core targets with relatively higher betweenness and degree were identified in the constructed Chinese medicine material-chemical component-target-signal pathway network.Moreover,we verified the potential therapeutic effect of A&A in vivo(using a mouse model of RIF),confirming that A&A could effectively protect the kidney by regulating these target genes.The therapeutic effect of A&A on RIF could be attributed to its role in regulating the cell cycle,limiting the apoptosis,and inhibiting the inflammation.展开更多
The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of o...The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study （GWAS） on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restriction-site associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms （SNPs） were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including adgrb2, csnkzal, cers5, co122al, creb5, dndl, dzankl, dnail, npy2r, fat3, lrrk2, lrp5, map3k9, and so on. Among these candidate genes, npy2r （neuropeptide Y receptor Y2） was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers.展开更多
The vagina contains at least a billion microbial cells,dominated by lactobacilli.Here we perform metagenomic shotgun sequencing on cervical and fecal samples from a cohort of 516 Chinese women of reproductive age,as w...The vagina contains at least a billion microbial cells,dominated by lactobacilli.Here we perform metagenomic shotgun sequencing on cervical and fecal samples from a cohort of 516 Chinese women of reproductive age,as well as cervical,fecal,and salivary samples from a second cohort of 632 women.Factors such as pregnancy history,delivery history,cesarean section,and breastfeeding were all more important than menstrual cycle in shaping the microbiome,and such information would be necessary before trying to interpret differences between vagino-cervical microbiome data.Greater proportion of Bifidobacterium breve was seen with older age at sexual debut.The relative abundance of lactobacilli especially Lactobacillus crispatus was negatively associated with pregnancy history.Potential markers for lack of menstrual regularity,heavy flow,dysmenorrhea,and contraceptives were also identified.Lactobacilli were rare during breastfeeding or post-menopause.Other features such as mood fluctuations and facial speckles could potentially be predicted from the vagino-cervical microbiome.Gut and salivary microbiomes,plasma vitamins,metals,amino acids,and hormones showed associations with the vagino-cervical microbiome.Our results offer an unprecedented glimpse into the microbiota of the female reproductive tract and call for international collaborations to better understand its long-term health impact other than in the settings of infection or pre-term birth.展开更多
Rapidly spreading coronavirus disease 2019(COVID-19)is currently affecting the world.Specifically,cytokine storms are a key feature in a substantial num ber of COVID-19 patients,1 and studies from our group and others...Rapidly spreading coronavirus disease 2019(COVID-19)is currently affecting the world.Specifically,cytokine storms are a key feature in a substantial num ber of COVID-19 patients,1 and studies from our group and others suggest that the IL-6/IL-6R cascade plays a dom inant role in symptom-correlated cytokine storms.展开更多
Single-cell genomics provides substantial resources for dissecting cellular heterogeneity and cancer evolution.Unfortunately,classical DNA amplification-based methods have low throughput and introduce coverage bias du...Single-cell genomics provides substantial resources for dissecting cellular heterogeneity and cancer evolution.Unfortunately,classical DNA amplification-based methods have low throughput and introduce coverage bias during sample preamplification.We developed a single-cell DNA library preparation method without preamplification in nanolitre scale(scDPN)to address these issues.The method achieved a throughput of up to 1800 cells per run for copy number variation(CNV)detection.Also,our approach demonstrated a lower level of amplification bias and noise than the multiple displacement amplification(MDA)method and showed high sensitivity and accuracy for cell line and tumor tissue evaluation.We used this approach to profile the tumor clones in paired primary and relapsed tumor samples of hepatocellular carcinoma(HCC).We identified three clonal subpopulations with a multitude of aneuploid alterations across the genome.Furthermore,we observed that a minor clone of the primary tumor containing additional alterations in chromosomes 1q,10q,and 14q developed into the dominant clone in the recurrent tumor,indicating clonal selection during recurrence in HCC.Overall,this approach provides a comprehensive and scalable solution to understand genome heterogeneity and evolution.展开更多
Understanding the mechanisms,structuring microbial communities in oligotrophic ocean surface waters remains a major ecological endeavor.Functional redundancy and metabolic tuning are two mechanisms that have been prop...Understanding the mechanisms,structuring microbial communities in oligotrophic ocean surface waters remains a major ecological endeavor.Functional redundancy and metabolic tuning are two mechanisms that have been proposed to shape microbial response to environmental forcing.However,little is known about their roles in the oligotrophic surface ocean due to less integrative characterization of community taxonomy and function.Here,we applied an integrated meta-omics-based approach,from genes to proteins,to investigate the microbial community of the oligotrophic northern Indian Ocean.Insignificant spatial variabilities of both genomic and proteomic compositions indicated a stable microbial community that was dominated by Prochlorococcus,Synechococcus,and SAR11.However,fine tuning of some metabolic functions that are mainly driven by salinity and temperature was observed.Intriguingly,a tuning divergence occurred between metabolic potential and activity in response to different environmental perturbations.Our results indicate that metabolic tuning is an important mechanism for sustaining the stability of microbial communities in oligotrophic oceans.In addition,integrated meta-omics provides a powerful tool to comprehensively understand microbial behavior and function in the ocean.展开更多
Dear Editor,The axolotl,Ambystoma mexicanum,has extraordinary capability to fully recover multiple tissues after lost,whereas such capability has disappeared in mammals.Thus,deci-phering detailed mechanisms underlying...Dear Editor,The axolotl,Ambystoma mexicanum,has extraordinary capability to fully recover multiple tissues after lost,whereas such capability has disappeared in mammals.Thus,deci-phering detailed mechanisms underlying axolotl regenera-tion could provide valuable lessons for regenerative medicine.However,many questions,such as the origin of essential progenitor cells and key responses of individual types of cells for regeneration remain elusive(Haas and Whited,2017).Newly developed single-cell RNA sequenc-ing(scRNA-seq)method enables researchers to observe cellular and molecular dynamics in axolotl regeneration at the single-cell resolution(Gerber et al.,2018;Leigh et al.,2018),but the reported transcriptome landscapes are only for certain cell types or in certain regenerative stages.A complete overview of the regeneration process for all cell types is still lacking.展开更多
There is a worldwide pandemic of COVID-19 caused by SARS-CoV-2.1 By January 28,2021,more than 100 million cases had been diagnosed,and more than 2 million deaths had been reported(https://coronavirus.jhu.edu/map.html)...There is a worldwide pandemic of COVID-19 caused by SARS-CoV-2.1 By January 28,2021,more than 100 million cases had been diagnosed,and more than 2 million deaths had been reported(https://coronavirus.jhu.edu/map.html).The comprehensive and in-depth elucidation of SARS-CoV-2-specific IgG responses will help us to better understand COVID-19 immunity and facilitate the precise development of neutralizing antibodies and vaccines.展开更多
CRISPR/Cas9 is an adaptive immunity system in bacteria and most archaea(Koonin and Makarova,2009;Horvath and Barrangou,2010).The CRISPR/Cas9 gene editing system is comprised of two key components,a small guide RNA(gRN...CRISPR/Cas9 is an adaptive immunity system in bacteria and most archaea(Koonin and Makarova,2009;Horvath and Barrangou,2010).The CRISPR/Cas9 gene editing system is comprised of two key components,a small guide RNA(gRNA)and a Cas9 endonuclease(Deltcheva etal.,2011;Jineketal.,2012).展开更多
T lymphocytes are crucial for antiviral responses and provide a promising repertoire for potential therapies of viral diseases such as cytomegalovirus(CMV)infection1 and the ongoing COVID-19 pandemic caused by SARS-Co...T lymphocytes are crucial for antiviral responses and provide a promising repertoire for potential therapies of viral diseases such as cytomegalovirus(CMV)infection1 and the ongoing COVID-19 pandemic caused by SARS-CoV-2.^(2) CMV-related diseases occur once the host immune system is impaired or lacks a protective repertoire of virus-specific T lymphocytes.3 Adoptive transfer of T-cell receptor(TCR)-engineered T cells(TCR-Ts)provides an encouraging alternative treatment option for patients with CMV reactivation.^(4) However,generating TCR-Ts requires the identification of epitope-specific and functional TCR pairs.Modern single-cell sequencing techniques open up the ability to unravel TCR repertoires,^(5 )which offers a potential opportunity to screen functional TCR pairs for TCR-T therapy.Here,we report an efficient approach that combines ex vivo CD8+T-cell stimulation with single-cell RNA and TCR V(D)J sequencing to identify CMV-specific TCRs for generating TCR-Ts.展开更多
Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has been redetected after discharge in some coronavirus disease 2019(COVID-19)patients.The reason for the recurrent positivity of the test and the potential p...Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has been redetected after discharge in some coronavirus disease 2019(COVID-19)patients.The reason for the recurrent positivity of the test and the potential public health concern due to this occurrence are still unknown.Here,we analyzed the viral data and clinical manifestations of 289 domestic Chinese COVID-19 patients and found that 21 individuals(7.3%)were readmitted for hospitalization after detection of SARS-CoV-2 after discharge.First,we experimentally confirmed that the virus was involved in the initial infection and was not a secondary infection.In positive retests,the virus was usually found in anal samples(15 of 21,71.4%).Through analysis of the intracellular viral subgenomic messenger RNA(sgmRNA),we verified that positive retest patients had active viral replication in their gastrointestinal tracts(3 of 16 patients,18.7%)but not in their respiratory tracts.Then,we found that viral persistence was not associated with high viral titers,delayed viral clearance,old age,or more severe clinical symptoms during the first hospitalization.In contrast,viral rebound was associated with significantly lower levels of and slower generation of viral receptor-binding domain(RBD)-specific IgA and IgG antibodies.Our study demonstrated that the positive retest patients failed to create a robust protective humoral immune response,which might result in SARS-CoV-2 persistence in the gastrointestinal tract and possibly in active viral shedding.Further exploration of the mechanism underlying the rebound in SARS-CoV-2 in this population will be crucial for preventing virus spread and developing effective vaccines.展开更多
文摘AIM： To study the genes responsible for retinitis pigmentosa.METHODS： A total of 15 Chinese families with retinitis pigmentosa, containing 94 sporadically afflicted cases, were recruited. The targeted sequences were captured using the Target_Eye_365_V3 chip and sequenced using the BGISEQ-500 sequencer, according to the manufacturer＇s instructions. Data were aligned to UCSC Genome Browser build hg19, using the Burroughs Wheeler Aligner MEM algorithm. Local realignment was performed with the Genome Analysis Toolkit（GATK v.3.3.0） Indel Realigner, and variants were called with the Genome Analysis Toolkit Haplotypecaller, without any use of imputation. Variants were filtered against a panel derived from 1000 Genomes Project, 1000 G_ASN, ESP6500, Ex AC and db SNP138. In all members of Family ONE and Family TWO with available DNA samples, the genetic variant was validated using Sanger sequencing.RESULTS： A novel, pathogenic variant of retinitis pigmentosa, c.357_358 del AA（p.Ser119 Serfs X5） was identified in PRPF31 in 2 of 15 autosomal-dominant retinitis pigmentosa（ADRP） families, as well as in one, sporadic case. Sanger sequencing was performed uponprobands, as well as upon other family members. This novel, pathogenic genotype co-segregated with retinitis pigmentosa phenotype in these two families. CONCLUSION： ADRP is a subtype of retinitis pigmentosa, defined by its genotype, which accounts for 20%-40% of the retinitis pigmentosa patients. Our study thus expands the spectrum of PRPF31 mutations known to occur in ADRP, and provides further demonstration of the applicability of the BGISEQ500 sequencer for genomics research.
基金funded by the Science andTechnology Planning Project of Guangdong province(Grant No.2015A020213007)the Science and Technology Planning Project of General Administration of Quality Supervision,Inspection and Quarantine of China(Grant No.2015IK066)
文摘Dear Editor,Rift Valley fever(RVF)is an anthropozoonosis caused by Rift Valley fever virus(RVFV).RVFV belongs to the Phlebovirus genus in the family Bunyaviridae,which is circulating among ruminants.Human infection with RVFV is generally asymptomatic,however,minority of patients develop severe RVF diseases like encephalitis
基金supported by the National Natural Science Foundation of China(31702074 and 31872309)Sanming Project of Medicine in Shenzhen(SZSM202011012)Science,Technology and Innovation Commission of Shenzhen Municipality(JCYJ20170412153100794)。
文摘Parkinson's disease(PD)is a neurodegenerative disease,leading to the impairment of movement execution.PD pathogenesis has been largely investigated,either limited to bulk transcriptomic levels or at certain cell types,which failed to capture the cellular heterogeneity and intrinsic interplays among distinct cell types.Here,we report the application of single-nucleus RNA-seq on midbrain,striatum,and cerebellum of theα-syn-A53 T mouse,a well-established PD mouse model,and matched controls,generating the first single cell transcriptomic atlas for the PD model mouse brain composed of 46,174 individual cells.Additionally,we comprehensively depicte the dysfunctions in PD pathology,covering the elevation of NF-k B activity,the alteration of ion channel components,the perturbation of protein homeostasis network,and the dysregulation of glutamatergic signaling.Notably,we identify a variety of cell types closely associated with PD risk genes.Taken together,our study provides valuable resources to systematically dissect the molecular mechanism of PD pathogenesis at the single-cell resolution,which facilitates the development of novel approaches for diagnosis and therapies against PD.
基金This work was supported by grants from the Science and Technology Project in Fujian Province of China(Grant No.2018I0004)Joint Funds for the innovation of Science and Technology,Fujian Province of China(Grant No.2018Y9108).
文摘Objective:Neoantigens arising from gene mutations in tumors can induce specific immune responses,and neoantigen-based immunotherapies have been tested in clinical trials.Here,we characterized the efficacy of altered neoepitopes in improving immunogenicity against gastric cancer.Methods:Raw data of whole-exome sequencing derived from a patient with gastric cancer were analyzed using bioinformatics methods to identify neoepitopes.Neoepitopes were modified by P1Y(the first amino acid was replaced by tyrosine)and P2L(the second amino acid was replaced by leucine).T2 binding and stability assays were used to detect the affinities between the neoepitopes and the HLA molecules,as well as the stabilities of complexes.Dendritic cells(DCs)presented with neoepitopes stimulated naïve CD8+T cells to induce specific cytotoxic T lymphocytes.ELISA and carboxyfluorescein succinimidyl ester were used to detect IFN-γand TNF-αlevels,and T cell proliferation.Perforin was detected by flow cytometry.The cytotoxicity of T cells was determined using the lactate dehydrogenase assay.Results:Bioinformatics analysis,T2 binding,and stability assays indicated that residue substitution increased the affinity between neoepitopes and HLA molecules,as well as the stabilities of complexes.DCs presented with altered neoepitopes stimulated CD8+T cells to release more IFN-γand had a greater effect on promoting proliferation than wild-type neoepitopes.CD8+T cells stimulated with altered neoepitopes killed more wild-type neoepitope-pulsed T2 cells than those stimulated with wild-type neoepitopes,by secreting more IFN-γ,TNF-α,and perforin.Conclusions:Altered neoepitopes exhibited greater immunogenicity than wild-type neoepitopes.Residue substitution could be used as a new strategy for immunotherapy to target neoantigens.
基金supported by grants from the National Science and Technology Major Project of China (2016ZX10004222 and 2016YFC1200800)Strategic Priority Research Program of the Chinese Academy of Sciences (XDB29010102)+5 种基金Sanming Project of Medicine in Shenzhen (SZSM201412003)Shenzhen Municipal Government of China (JCYJ20160427151920801)Beijing Municipal Science & Technology Commission (Z161100000116049)the National Natural Science Foundation of China (NSFC) International Cooperation and Exchange Program (816110193)supported by the NSFC Outstanding Young Scholars (31822055)Youth Innovation Promotion Association of Chinese Academy of Sciences (CAS) (2017122)
文摘Dear Editor,In recent years,the incidence of human infections caused by emerging or re-emerging pathogens has rapidly increased.Diseases that were once regional now have the ability to spread globally in a short amount of time and pose a wider threat to public health(Weaver et al.2018).Yellow fever virus(YFV,family Flaviviridae,genus Flavivirus)is a mosquito-borne flavivirus that causes yellow fever in humans and has been endemic in Africa and Latin America for many years(Domingo et al.2018).
基金supported by Shenzhen Sanming Engineering Project(SZSM202011012)Shenzhen Innovation Science and Technology Committee(JCYJ20180228175358223)National Natural Science Foundation of China(31670742)。
文摘Olfaction,the sense of smell,is a fundamental trait crucial to many species.The olfactory bulb(OB)plays pivotal roles in processing and transmitting odor information from the environment to the brain.The cellular heterogeneity of the mouse OB has been studied using single-cell RNA sequencing.However,the epigenetic landscape of the m OB remains mostly unexplored.Herein,we apply single-cell assay for transposaseaccessible chromatin sequencing to profile the genome-wide chromatin accessibility of 9,549 single cells from the m OB.Based on single-cell epigenetic signatures,m OB cells are classified into 21 clusters corresponding to 11 cell types.We identify distinct sets of putative regulatory elements specific to each cell cluster from which putative target genes and enriched potential functions are inferred.In addition,the transcription factor motifs enriched in each cell cluster are determined to indicate the developmental fate of each cell lineage.Our study provides a valuable epigenetic data set for the m OB at single-cell resolution,and the results can enhance our understanding of regulatory circuits and the therapeutic capacity of the OB at the single-cell level.
基金This study was supported by the National Natural Science Foundation of China(31672282,U1702233,U1902202)Program of the Chinese Academy of Sciences(XDA24030505,XDA23080500,KFJ-STS-QYZD-101)Program of Yunnan Provincial Science and Technology Department(202003AD150017,2018FY001-007)。
文摘The Dianchi golden-line barbel,Sinocyclocheilus grahami(Regan,1904),is one of the“Four Famous Fishes”of Yunnan Province,China.Given its economic value,this species has been artificially bred successfully since 2007,with a nationally selected breed(“S.grahami,Bayou No.1”)certified in 2018.For the future utilization of this species,its growth rate,disease resistance,and wild adaptability need to be improved,which could be achieved with the help of molecular markerassisted selection(MAS).In the current study,we constructed the first chromosome-level genome of S.grahami,assembled 48 pseudo-chromosomes,and obtained a genome size of 1.49 Gb.We also performed QTL-seq analysis of S.grahami using the highest and lowest bulks(i.e.,largest and smallest size)in both a sibling and random population.We screened two quantitative trait loci(QTLs)(Chr3,14.9-39.1 Mb and Chr17,4.1-27.4 Mb)as major growth-related locations.Several candidate genes(e.g.,map2k5,stat1,phf21a,sox6,and smad6)were also identified,with functions related to growth,such as cell differentiation,neuronal development,skeletal muscle development,chondrogenesis,and immunity.These results built a solid foundation for in-depth MAS studies on the growth traits of S.grahami.
基金supported by the National Natural Science Foundation of China(31971966)the Key-Areas Research and Development Program of Guangdong Province(2020B020220008)the China Agriculture Research System(CARS-04-PS09).
文摘Powdery mildew(PM),caused by the fungus Microsphaera diffusa,causes severe yield losses in soybean[Glycine max(L.)Merr.]under suitable environmental conditions.Identifying resistance genes and developing resistant cultivars may prevent soybean PM damage.In this study,analysis of F_(1),F_(2),and F8:11 recombinant inbred line(RIL)populations derived from the cross between Zhonghuang 24(ZH24)and Huaxia 3(HX3)indicated that adult-plant resistance(APR)to powdery mildew in the soybean cultivar(cv.)ZH24 was controlled by a single dominant locus.A high-density genetic linkage map of the RIL population was used for fine mapping.The APR locus in ZH24 was mapped to a 281-kb genomic region on chromosome 16.Using 283 susceptible plants of another F2 population,the candidate region was finemapped to a 32.8-kb genomic interval flanked by the markers InDel14 and Gm16_428.The interval harbored five genes,including four disease resistance(R)-like genes,according to the Williams 82.a2.v1 reference genome.Quantitative real-time PCR assays of candidate genes revealed that the expression levels of Glyma.16g214300 and Glyma.16g214500 were changed by M.diffusa infection and might be involved in disease defense.Rmd_B13 showed all-stage resistance(ASR)to PM in soybean cv.B13.An allelism test in the F2 segregating population from the cross of ZH24 × B13 suggested that the APR locus Rmd_ZH24 and the ASR locus Rmd_B13 may be allelic or tightly linked.These results provide a reference marker-assisted selection in breeding programs.
基金supported by the National Natural Science Foundation of China(31372190)
文摘Pattern recognition receptors(PRRs) play important roles in innate immunity system and trigger the specific pathogen recognition by detecting the pathogen-associated molecular patterns. The main four PRRs components including Toll-like receptors(TLRs), RIG-I-like receptors(RLRs), NOD-like receptors(NLRs) and C-type lectin receptors(CLRs) were surveyed in the five genomes of non-teleost ray-finned fishes(NTR) including bichir(Polypterus senegalus), American paddlefish(Polyodon spathula), alligator gar(Atractosteus spatula), spotted gar(Lepisosteus oculatus) and bowfin(Amia calva), representing all the four major basal groups of ray-finned fishes. The result indicates that all the four PRRs components have been well established in these NTR fishes. In the RLR-MAVS signal pathway, which detects intracellular RNA ligands to induce production of type I interferons(IFNs), the MAVS was lost in bichir particularly. Also, the essential genes of recognition of Lipopolysaccharide(LPS) commonly in mammals like MD2, LY96 and LBP could not be identified in NTR fishes. It is speculated that TLR4 in NTR fishes may act as a cooperator with other PRRs and has a different pathway of recognizing LPS compared with that in mammals. In addition, we provide a survey of NLR and CLR in NTR fishes. The CLRs results suggest that Group V receptors are absent in fishes and Group II and VI receptors are well established in the early vertebrate evolution. Our comprehensive research of PRRs involving NTR fishes provides a new insight into PRR evolution in primitive vertebrate.
基金The work was supported by the grants from National Natural Science Foundation of China(No.81773959 to C.F.Yuan and No.81974528 to C.F.Yuan)Open Foundation for Tumor Microenvironment and Immunotherapy Key Laboratory of Hubei province in China(No.2019KZL09 to C.F.Yuan)Health commission of Hubei Province scientific research project in China(No.WJ2019H527 to C.F.Yuan).
文摘Astragalus and Angelica decoction(A&A)has been clinically used as a classical traditional Chinese medicine(TCM)formula in China for many years for the treatment of kidney diseases,especially renal interstitial fibrosis(RIF).However,the mechanisms underlying the therapeutic effects of A&A on RIF remains poorly understood.In the present study,systematic network pharmacology and effective experimental verification were utilized for the first time to elucidate the pharmacological efficacy and potential mechanism.The outcomes indicated that 22 active components and 87 target genes of A&A were identified and cross-referenced with RIF-associated genes,contributing to confirmation of 74 target genes of A&A for RIF.Pathway and functional enrichment analyses revealed that A&A had substantial effects on MAPK,PI3K-Akt and TNF signaling pathways.In addition,seven core targets with relatively higher betweenness and degree were identified in the constructed Chinese medicine material-chemical component-target-signal pathway network.Moreover,we verified the potential therapeutic effect of A&A in vivo(using a mouse model of RIF),confirming that A&A could effectively protect the kidney by regulating these target genes.The therapeutic effect of A&A on RIF could be attributed to its role in regulating the cell cycle,limiting the apoptosis,and inhibiting the inflammation.
基金supported by National Natural Science Foundation of China (31370047)Shenzhen Scientific R&D Grant (GJHS20160331150703934)Shenzhen Dapeng Special Program for Industrial Development (KY20160102, KY20170205)
文摘The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study （GWAS） on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restriction-site associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms （SNPs） were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including adgrb2, csnkzal, cers5, co122al, creb5, dndl, dzankl, dnail, npy2r, fat3, lrrk2, lrp5, map3k9, and so on. Among these candidate genes, npy2r （neuropeptide Y receptor Y2） was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers.
文摘The vagina contains at least a billion microbial cells,dominated by lactobacilli.Here we perform metagenomic shotgun sequencing on cervical and fecal samples from a cohort of 516 Chinese women of reproductive age,as well as cervical,fecal,and salivary samples from a second cohort of 632 women.Factors such as pregnancy history,delivery history,cesarean section,and breastfeeding were all more important than menstrual cycle in shaping the microbiome,and such information would be necessary before trying to interpret differences between vagino-cervical microbiome data.Greater proportion of Bifidobacterium breve was seen with older age at sexual debut.The relative abundance of lactobacilli especially Lactobacillus crispatus was negatively associated with pregnancy history.Potential markers for lack of menstrual regularity,heavy flow,dysmenorrhea,and contraceptives were also identified.Lactobacilli were rare during breastfeeding or post-menopause.Other features such as mood fluctuations and facial speckles could potentially be predicted from the vagino-cervical microbiome.Gut and salivary microbiomes,plasma vitamins,metals,amino acids,and hormones showed associations with the vagino-cervical microbiome.Our results offer an unprecedented glimpse into the microbiota of the female reproductive tract and call for international collaborations to better understand its long-term health impact other than in the settings of infection or pre-term birth.
基金supported by CAMS Research Units of Adaptive Evolution and Control of Emerging Viruses(2018RU009)Beijing New-star Plan of Science and Technology(Z181100006218080)+3 种基金supported by the Excellent Young Scientist Program of the National Natural Science Foundation of China(81822040)the National Youth Talent Support Programfunded by the National Natural Science Foundation of China(31900466)funded by the China Postdoctoral Science Foundation(2020T130080ZX).
文摘Rapidly spreading coronavirus disease 2019(COVID-19)is currently affecting the world.Specifically,cytokine storms are a key feature in a substantial num ber of COVID-19 patients,1 and studies from our group and others suggest that the IL-6/IL-6R cascade plays a dom inant role in symptom-correlated cytokine storms.
基金This work was supported by the Technology and Innovation Commission of Shenzhen Municipality,China(Grant No.GJHZ20180419190827179)the Science,Technology and Innovation Commission of Shenzhen Municipality,China(Grant No.JCYJ20170303151334808).
文摘Single-cell genomics provides substantial resources for dissecting cellular heterogeneity and cancer evolution.Unfortunately,classical DNA amplification-based methods have low throughput and introduce coverage bias during sample preamplification.We developed a single-cell DNA library preparation method without preamplification in nanolitre scale(scDPN)to address these issues.The method achieved a throughput of up to 1800 cells per run for copy number variation(CNV)detection.Also,our approach demonstrated a lower level of amplification bias and noise than the multiple displacement amplification(MDA)method and showed high sensitivity and accuracy for cell line and tumor tissue evaluation.We used this approach to profile the tumor clones in paired primary and relapsed tumor samples of hepatocellular carcinoma(HCC).We identified three clonal subpopulations with a multitude of aneuploid alterations across the genome.Furthermore,we observed that a minor clone of the primary tumor containing additional alterations in chromosomes 1q,10q,and 14q developed into the dominant clone in the recurrent tumor,indicating clonal selection during recurrence in HCC.Overall,this approach provides a comprehensive and scalable solution to understand genome heterogeneity and evolution.
基金supported by research grants from the National Natural Science Foundation of China(Project No.41425021)the Ministry of Science and Technology(Project No.2015CB954003)+1 种基金COMRA program(No.DY125-15-R-01)Dayang Yihao 26th cruise program of COMRA.DZW was also supported by the‘Ten Thousand Talents Program’for leading talents in science and technological innovation.
文摘Understanding the mechanisms,structuring microbial communities in oligotrophic ocean surface waters remains a major ecological endeavor.Functional redundancy and metabolic tuning are two mechanisms that have been proposed to shape microbial response to environmental forcing.However,little is known about their roles in the oligotrophic surface ocean due to less integrative characterization of community taxonomy and function.Here,we applied an integrated meta-omics-based approach,from genes to proteins,to investigate the microbial community of the oligotrophic northern Indian Ocean.Insignificant spatial variabilities of both genomic and proteomic compositions indicated a stable microbial community that was dominated by Prochlorococcus,Synechococcus,and SAR11.However,fine tuning of some metabolic functions that are mainly driven by salinity and temperature was observed.Intriguingly,a tuning divergence occurred between metabolic potential and activity in response to different environmental perturbations.Our results indicate that metabolic tuning is an important mechanism for sustaining the stability of microbial communities in oligotrophic oceans.In addition,integrated meta-omics provides a powerful tool to comprehensively understand microbial behavior and function in the ocean.
文摘Dear Editor,The axolotl,Ambystoma mexicanum,has extraordinary capability to fully recover multiple tissues after lost,whereas such capability has disappeared in mammals.Thus,deci-phering detailed mechanisms underlying axolotl regenera-tion could provide valuable lessons for regenerative medicine.However,many questions,such as the origin of essential progenitor cells and key responses of individual types of cells for regeneration remain elusive(Haas and Whited,2017).Newly developed single-cell RNA sequenc-ing(scRNA-seq)method enables researchers to observe cellular and molecular dynamics in axolotl regeneration at the single-cell resolution(Gerber et al.,2018;Leigh et al.,2018),but the reported transcriptome landscapes are only for certain cell types or in certain regenerative stages.A complete overview of the regeneration process for all cell types is still lacking.
基金partially supported by National Key Research and Developm ent Program of China Grant(No.2016YFA0500600)National Natural Science Foundation of China(Nos.31970130,31670831,31370813,and 31501054)Open Foundation of Key Laboratory of Systems Biomedicine(No.KLSB2020QN-05).
文摘There is a worldwide pandemic of COVID-19 caused by SARS-CoV-2.1 By January 28,2021,more than 100 million cases had been diagnosed,and more than 2 million deaths had been reported(https://coronavirus.jhu.edu/map.html).The comprehensive and in-depth elucidation of SARS-CoV-2-specific IgG responses will help us to better understand COVID-19 immunity and facilitate the precise development of neutralizing antibodies and vaccines.
基金This work was supported by the Lundbeck Foundation(R219-2016-1375 and R173-2014-1105)the Danish Research Council for Independent Research(DFF-1337-00128 and 9041-00317B)+4 种基金the Sapere Aude Young Research Talent Prize(DFF-1335-00763A)the Innovation Fund Denmark(BrainStem)Aarhus University Strategic Grant(AU-iCRISPR)the Sanming Project of Medicine in Shenzhen(SZ5M201612074)BGIResearch,and Guangdong Provincial Key Laboratory of Genome Read and Write(2017B030301011)。
文摘CRISPR/Cas9 is an adaptive immunity system in bacteria and most archaea(Koonin and Makarova,2009;Horvath and Barrangou,2010).The CRISPR/Cas9 gene editing system is comprised of two key components,a small guide RNA(gRNA)and a Cas9 endonuclease(Deltcheva etal.,2011;Jineketal.,2012).
基金supported by the Science,Technology and Innovation Commission of Shenzhen Municipality under grant No.JCYJ20170303151334808 and grant No.JSGG20180508152912700The first author would like to acknowledge financial support from the China Scholarship Council(CSC)(grant No.201904910476).
文摘T lymphocytes are crucial for antiviral responses and provide a promising repertoire for potential therapies of viral diseases such as cytomegalovirus(CMV)infection1 and the ongoing COVID-19 pandemic caused by SARS-CoV-2.^(2) CMV-related diseases occur once the host immune system is impaired or lacks a protective repertoire of virus-specific T lymphocytes.3 Adoptive transfer of T-cell receptor(TCR)-engineered T cells(TCR-Ts)provides an encouraging alternative treatment option for patients with CMV reactivation.^(4) However,generating TCR-Ts requires the identification of epitope-specific and functional TCR pairs.Modern single-cell sequencing techniques open up the ability to unravel TCR repertoires,^(5 )which offers a potential opportunity to screen functional TCR pairs for TCR-T therapy.Here,we report an efficient approach that combines ex vivo CD8+T-cell stimulation with single-cell RNA and TCR V(D)J sequencing to identify CMV-specific TCRs for generating TCR-Ts.
基金supported by the National Natural Science Foundation of China(Nos.81670536 and 81770593)the National Grand Program on Key Infectious Disease Control(2017ZX10202203-004-002 and 2018ZX10301404-003-002).
文摘Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has been redetected after discharge in some coronavirus disease 2019(COVID-19)patients.The reason for the recurrent positivity of the test and the potential public health concern due to this occurrence are still unknown.Here,we analyzed the viral data and clinical manifestations of 289 domestic Chinese COVID-19 patients and found that 21 individuals(7.3%)were readmitted for hospitalization after detection of SARS-CoV-2 after discharge.First,we experimentally confirmed that the virus was involved in the initial infection and was not a secondary infection.In positive retests,the virus was usually found in anal samples(15 of 21,71.4%).Through analysis of the intracellular viral subgenomic messenger RNA(sgmRNA),we verified that positive retest patients had active viral replication in their gastrointestinal tracts(3 of 16 patients,18.7%)but not in their respiratory tracts.Then,we found that viral persistence was not associated with high viral titers,delayed viral clearance,old age,or more severe clinical symptoms during the first hospitalization.In contrast,viral rebound was associated with significantly lower levels of and slower generation of viral receptor-binding domain(RBD)-specific IgA and IgG antibodies.Our study demonstrated that the positive retest patients failed to create a robust protective humoral immune response,which might result in SARS-CoV-2 persistence in the gastrointestinal tract and possibly in active viral shedding.Further exploration of the mechanism underlying the rebound in SARS-CoV-2 in this population will be crucial for preventing virus spread and developing effective vaccines.
