In this paper,a standardized analysis method is established for identifying meat quality-related genes in Ordos finewool sheep using transcriptome sequencing data.A meticulously standardized approach is utilized to in...In this paper,a standardized analysis method is established for identifying meat quality-related genes in Ordos finewool sheep using transcriptome sequencing data.A meticulously standardized approach is utilized to investigate the genetic determinants of meat quality in Ordos fine-wool sheep through transcriptome sequencing analysis.Muscle samples from the longissimus dorsi of one-year-old sheep are collected under controlled conditions,and key texture properties—hardness,elasticity,and chewiness—are measured to categorize samples into high-and low-textural-value groups.Genes significantly associated with meat quality traits are identified through standardized RNA extraction,high-throughput sequencing,and differential gene expression analysis.Functional enrichment analysis reveals their involvement in biological processes such as extracellular matrix organization and metabolic pathways.The findings underscore the pivotal role of standardization in meat quality research,laying a solid scientific foundation for future research on meat quality improvement and molecular breeding.展开更多
Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocyt...Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocytes,microglia,and oligodendrocytes in the central nervous system,and satellite glial cells and Schwann cells in the peripheral nervous system.Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models,few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord.Here,we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes,microglia,and oligodendrocytes in the human spinal cord.To explore the conservation and divergence across species,we compared these findings with those from mice.In the human spinal cord,astrocytes,microglia,and oligodendrocytes were each divided into six distinct transcriptomic subclusters.In the mouse spinal cord,astrocytes,microglia,and oligodendrocytes were divided into five,four,and five distinct transcriptomic subclusters,respectively.The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice.Additionally,we detected sex differences in gene expression in human spinal cord glial cells.Specifically,in all astrocyte subtypes,the levels of NEAT1 and CHI3L1 were higher in males than in females,whereas the levels of CST3 were lower in males than in females.In all microglial subtypes,all differentially expressed genes were located on the sex chromosomes.In addition to sex-specific gene differences,the levels of MT-ND4,MT2A,MT-ATP6,MT-CO3,MT-ND2,MT-ND3,and MT-CO_(2) in all spinal cord oligodendrocyte subtypes were higher in females than in males.Collectively,the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cordrelated illnesses,including chronic pain,amyotrophic lateral sclerosis,and multiple sclerosis.展开更多
BACKGROUND Hemorrhoids,a prevalent chronic condition globally,significantly impact patients'quality of life.While various surgical interventions,such as external stripping and internal ligation,procedure for prola...BACKGROUND Hemorrhoids,a prevalent chronic condition globally,significantly impact patients'quality of life.While various surgical interventions,such as external stripping and internal ligation,procedure for prolapse and hemorrhoids,and tissue selecting technique,are employed for treatment,they are often associated with postoperative complications,including unsatisfactory defecation,bleeding,and anal stenosis.In contrast,Xiaozhiling injection,a traditional Chinese medicine-based therapy,has emerged as a minimally invasive and effective alternative for internal hemorrhoids.This treatment offers distinct advantages,such as reduced dietary restrictions,broad applicability,and minimal induction of systemic inflammatory responses.Additionally,Xiaozhiling injection effectively eliminates hemorrhoid nuclei,prevents local tissue necrosis,preserves anal cushion integrity,and mitigates postoperative complications,including bleeding and prolapse.Despite its clinical efficacy,the molecular mechanisms underlying its therapeutic effects remain poorly understood,warranting further investigation.AIM To investigate the molecular mechanism underlying the therapeutic effect of Xiaozhiling injection in the treatment of internal hemorrhoids.METHODS An internal hemorrhoid model was established in rats,and the rats were randomly divided into a modeling group[control group(CK group)]and a treatment group.One week after injection,Stereo-seq and electron microscopy were used to study the changes in gene expression and subcellular structures in fibroblasts.RESULTS Single-cell sequencing revealed differences in the expression and transcript levels of the genes collagen 3 alpha 1,decorin,and actin alpha 2 in fibroblasts between the CK group and the treatment group.Spatial transcriptome analysis revealed that genes of the sphingosine kinase 1(Sphk1)/sphingosine-1-phosphate(S1P)pathway spatially overlapped with key genes of the transforming growth factor beta 1 pathway,namely,Sphk1,S1P receptor,and transforming growth factor beta 1,in the treatment group.The proportion of fibroblasts was lower in the treatment group than in the CK group,and Xiaozhiling treatment had a significant effect on the proportion of fibroblasts in hemorrhoidal tissue.Immunohistochemistry revealed a significant increase in the expression of a fibroblast marker.Electron microscopy showed that the endoplasmic reticulum of fibroblasts contained a large amount of glycogen,indicating cell activation.Fibroblast activation and the expression of key genes of the Sphk1-S1P pathway could be observed at the injection site,suggesting that after Xiaozhiling intervention,the Sphk1-S1P pathway could be activated to promote fibrosis.CONCLUSION Xiaozhiling injection exerts its therapeutic effects on internal hemorrhoids by promoting collagen synthesis and secretion in fibroblasts.After Xiaozhiling intervention,the Sphk1-S1P pathway can be activated to promote fibrosis.展开更多
OBJECTIVE: To corroborate the efficacy of Jintiange capsules(JTGs)( 金天格胶囊) in the treatment of osteoarthritis(OA) by exploring the potential mechanism of action of synovial mesenchymal stem cell exosomes(SMSC-Exo...OBJECTIVE: To corroborate the efficacy of Jintiange capsules(JTGs)( 金天格胶囊) in the treatment of osteoarthritis(OA) by exploring the potential mechanism of action of synovial mesenchymal stem cell exosomes(SMSC-Exos) and articular chondrocytes(ACs) through transcriptome sequencing(RNA-seq). METHODS: Type Ⅱ collagenase was used to induce OA in rats. The efficacy of JTGs was confirmed by macroscopic observation of articular cartilage, micro-CT observation, and safranin fast green staining. After SMSC-Exos and ACs were qualified, RNA-seq was used to screen differentially expressed mi RNAs and m RNAs. The target genes of differentially expressed mi RNAs in Synovial mesenchymal stem cells(SMSCs) were predicted based on the multi Mi R R package. The codifferentially expressed genes of SMSC-Exos and ACs were obtained by venny 2.1.0. The mi RNA-m RNA regulatory network was constructed by Cytoscape software. Based on the Omic Share platform, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis was performed on the m RNA regulated by key mi RNAs. Expression trend analysis was performed for co-differentially expressed genes. Correlation analysis was performed on micro-CT efficacy indicators, co-differentially expressed genes mRNA and miRNA. RESULTS: The efficacy of each administration group of JTGs was significant compared with the model group. SMSC-Exos and ACs were identified by their characteristics. The expression of rno-mi R-23a-3p, rnomi R-342-3p, rno-miR-146b-5p, rno-miR-501-3p, rnomiR-214-3p was down-regulated in OA pathological state, and the expression of rno-mi R-222-3p, rno-mi R-30e-3p, rno-mi R-676, and rno-miR-192-5p expression was upregulated, and the expression of all these mi RNAs was reversed after the intervention with JTGs containing serum. The co-differentially expressed genes were enriched in the interleukin 17 signaling pathway, tumor necrosis factor signaling pathway, transforming growth factor-β signaling pathway, etc. The expression trends of Ccl7, Akap12, Grem2, Egln3, Arhgdib, Ccl20, Mmp12, Pla2g2a, and Nr4a1 were significant. There was a correlation between micro-CT pharmacodynamic index, m RNA, and mi RNA. CONCLUSION: JTGs can improve the degeneration of joint cartilage and achieve the purpose of cartilage protection, which can be used for the treatment of OA. SMSCs-related mi RNA expression profiles were significantly altered after the intervention with JTGs containing serum. The 9 co-differentially expressed genes may be the key targets for the efficacy of JTGs in the treatment of OA rats, which can be used for subsequent validation.展开更多
BACKGROUND Esophageal squamous cell carcinoma(ESCC)is one of the most common malignancies worldwide,and its development comprises a multistep process from intraepithelial neoplasia(IN)to carcinoma(CA).However,the crit...BACKGROUND Esophageal squamous cell carcinoma(ESCC)is one of the most common malignancies worldwide,and its development comprises a multistep process from intraepithelial neoplasia(IN)to carcinoma(CA).However,the critical regulators and underlying molecular mechanisms remain largely unknown.AIM To explore the genes and infiltrating immune cells in the microenvironment that are associated with the multistage progression of ESCC to facilitate diagnosis and early intervention.METHODS A mouse model mimicking the multistage development of ESCC was established by providing warter containing 4-nitroquinoline 1-oxide(4NQO)to C57BL/6 mice.Moreover,we established a control group without 4NQO treatment of mice.Then,transcriptome sequencing was performed for esophageal tissues from patients with different pathological statuses,including low-grade IN(LGIN),high-grade IN(HGIN),and CA,and controlled normal tissue(NOR)samples.Differentially expressed genes(DEGs)were identified in the LGIN,HGIN,and CA groups,and the biological functions of the DEGs were analyzed via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses.The CIBERSORT algorithm was used to detect the pattern of immune cell infilt-ration.Immunohistochemistry(IHC)was also conducted to validate our results.Finally,the Luminex multiplex cytokine analysis was utilized to measure the serum cytokine levels in the mice.RESULTS Compared with those in the NOR group,a total of 681541,and 840 DEGs were obtained in the LGIN,HGIN,and CA groups,respectively.Using the intersection of the three sets of DEGs,we identified 86 genes as key genes involved in the development of ESCC.Enrichment analysis revealed that these genes were enriched mainly in the keratinization,epidermal cell differentiation,and interleukin(IL)-17 signaling pathways.CIBERSORT analysis revealed that,compared with those in the NOR group,M0 and M1 macrophages in the 4NQO group showed stronger infiltration,which was validated by IHC.Serum cytokine analysis revealed that,compared with those in the NOR group,IL-1βand IL-6 were upregulated,while IL-10 was downregulated in the LGIN,HGIN,and CA groups.Moreover,the expression of the representative key genes,such as S100a8 and Krt6b,was verified in external human samples,and the results of immunohistochemical staining were consistent with the findings in mice.CONCLUSION We identified a set of key genes represented by S100a8 and Krt6b and investigated their potential biological functions.In addition,we found that macrophage infiltration and abnormal alterations in the levels of inflam-mation-associated cytokines,such as IL-1β,IL-6,and IL-10,in the peripheral blood may be closely associated with the development of ESCC.展开更多
Nanopore direct RNA sequencing(DRS)provides the direct access to native RNA strands with full-length information,shedding light on rich qualitative and quantitative properties of gene expression profiles.Here with Nan...Nanopore direct RNA sequencing(DRS)provides the direct access to native RNA strands with full-length information,shedding light on rich qualitative and quantitative properties of gene expression profiles.Here with NanoTrans,we present an integrated computational framework that comprehensively covers all major DRS-based application scopes,including isoform clustering and quantification,poly(A)tail length estimation,RNA modification profiling,and fusion gene detection.In addition to its merit in providing such a streamlined one-stop solution,NanoTrans also shines in its workflow-orientated modular design,batch processing capability,all-in-one tabular and graphic report output,as well as automatic installation and configuration supports.Finally,by applying NanoTrans to real DRS datasets of yeast,Arabidopsis,as well as human embryonic kidney and cancer cell lines,we further demonstrate its utility,effectiveness,and efficacy across a wide range of DRS-based application settings.展开更多
High fish predation pressure can trigger"induced defense"in Daphnia species,resulting in phenotypic plasticity in morphology,behavior,or life-history traits.The molecular mechanisms of defense morphogenesis(...High fish predation pressure can trigger"induced defense"in Daphnia species,resulting in phenotypic plasticity in morphology,behavior,or life-history traits.The molecular mechanisms of defense morphogenesis(e.g.,the tail spine and helmet)in Daphnia remain unclear.In the pres-ent study,the tail spine,helmet,and body of Daphnia galeata under fish and non-fish kairomones conditions were collected for transcriptome analysis.A total of 24 candidate genes related to the morphological defense of D.galeata were identified,including 2 trypsin,one cuticle protein,1 C1qDC protein,and 2 ferritin genes.The function of the Dagcut gene(D.galeata cuticle protein gene)in relation to tail spine morphology was assessed using RNA interference(RNAi).Compared with the EGFP(Enhanced green fluorescent protein)treatment,after RNAi,the expression levels of the Dagcut gene(D.galeata cuticle protein gene)showed a significant decrease.Correspondingly,the tail spines of the offspring pro-duced by D.galeata after RNAi of the Dagcut gene appeared curved during the experiment.In whole-mount in situ hybridization,a clear signal site was detected on the tail spine of D.galeata before RNAi which disappeared after RNAi.Our results suggest that the Dagcut gene may play an important role in tail spine formation of D.galeata,and will provide a theoretical basis for studying the molecular mechanisms of the morpho-logical plasticityin cladocera inthefuture.展开更多
BACKGROUND Mesenchymal stem cells(MSCs)modulated by various exogenous signals have been applied extensively in regenerative medicine research.Notably,nanosecond pulsed electric fields(nsPEFs),characterized by short du...BACKGROUND Mesenchymal stem cells(MSCs)modulated by various exogenous signals have been applied extensively in regenerative medicine research.Notably,nanosecond pulsed electric fields(nsPEFs),characterized by short duration and high strength,significantly influence cell phenotypes and regulate MSCs differentiation via multiple pathways.Consequently,we used transcriptomics to study changes in messenger RNA(mRNA),long noncoding RNA(lncRNA),microRNA(miRNA),and circular RNA expression during nsPEFs application.AIM To explore gene expression profiles and potential transcriptional regulatory mechanisms in MSCs pretreated with nsPEFs.METHODS The impact of nsPEFs on the MSCs transcriptome was investigated through whole transcriptome sequencing.MSCs were pretreated with 5-pulse nsPEFs(100 ns at 10 kV/cm,1 Hz),followed by total RNA isolation.Each transcript was normalized by fragments per kilobase per million.Fold change and difference significance were applied to screen the differentially expressed genes(DEGs).Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to elucidate gene functions,complemented by quantitative polymerase chain reaction verification.RESULTS In total,263 DEGs were discovered,with 92 upregulated and 171 downregulated.DEGs were predominantly enriched in epithelial cell proliferation,osteoblast differentiation,mesenchymal cell differentiation,nuclear division,and wound healing.Regarding cellular components,DEGs are primarily involved in condensed chromosome,chromosomal region,actin cytoskeleton,and kinetochore.From aspect of molecular functions,DEGs are mainly involved in glycosaminoglycan binding,integrin binding,nuclear steroid receptor activity,cytoskeletal motor activity,and steroid binding.Quantitative real-time polymerase chain reaction confirmed targeted transcript regulation.CONCLUSION Our systematic investigation of the wide-ranging transcriptional pattern modulated by nsPEFs revealed the differential expression of 263 mRNAs,2 miRNAs,and 65 lncRNAs.Our study demonstrates that nsPEFs may affect stem cells through several signaling pathways,which are involved in vesicular transport,calcium ion transport,cytoskeleton,and cell differentiation.展开更多
The calpain system is ubiquitous in cells, mainly comprising calpains and calpain inhibitors, and is a widespread calcium-dependent cysteine protease in organisms that is involved in many cellular processes such as mu...The calpain system is ubiquitous in cells, mainly comprising calpains and calpain inhibitors, and is a widespread calcium-dependent cysteine protease in organisms that is involved in many cellular processes such as muscle degradation in vivo and affects the tenderness of meat after animal slaughter. The study found 128 DEGs that probably regulated tenderness traits were selected from 16 significantly enriched GO terms by transcriptome sequencing analysis, and found that the developmental changes in the expression levels of the CAPN1 gene in the pectoral and leg muscles were significantly positively correlated ( P <0.05) with the cumulative growth values of live weight and comb weight. The developmental changes in the expression levels of the CAST gene in the pectoral and leg muscles were not significantly correlated with the cumulative growth values of live weight and comb weight. Our results helped demonstrate the potential molecular mechanisms of tenderness in chickens and provide valuable information for chicken breeding.展开更多
Single-cell transcriptome sequencing has been a rapidly developing and powerful biological tool in recent years,and it plays a vital role in describing tissue development,cell heterogeneity,stress response,etc.Cerebro...Single-cell transcriptome sequencing has been a rapidly developing and powerful biological tool in recent years,and it plays a vital role in describing tissue development,cell heterogeneity,stress response,etc.Cerebrovascular disease is one of the leading causes affecting human health in the world.Thus,it is important to understand the characteristics of cerebrovascular structure,function,and environmental response.Notably,single-cell transcriptome sequencing provides deeper insights into cerebrovascular research in health and disease states.This article will briefly introduce the basic structure and function of cerebrovascular endothelial cells(ECs),summarize the current research and new findings on cerebrovascular ECs at the single-cell transcriptome level,and discuss the challenges in this field.展开更多
Oviductus Ranae is the dried oviduct of female Rana tem-poraria chensinensis （David）, distributed mainly in North- eastern China. Oviductus Ranae is one of the best-known and highly valued oriental foods and medicin...Oviductus Ranae is the dried oviduct of female Rana tem-poraria chensinensis （David）, distributed mainly in North- eastern China. Oviductus Ranae is one of the best-known and highly valued oriental foods and medicines. Traditional Chinese medicine holds that Oviductus Ranae can nourish yin, moisten lung and replenish the kidney essence. Meanwhile, activities of Oviductus Ranae such as anti-aging, anti-lipemic, anti-oxidation and anti-fatigue have also been demonstrated by modern phar-macological studies. Previous studies have shown that Oviductus Ranae is mainly composed of proteins, which are up to 50% or more.展开更多
Derris fordii and Derris elliptica belong to the Derris genus of the Fabaceae family, distinguished by their high isoflavonoid content, particularly rotenoids, which hold significance in pharmaceuticals and agricultur...Derris fordii and Derris elliptica belong to the Derris genus of the Fabaceae family, distinguished by their high isoflavonoid content, particularly rotenoids, which hold significance in pharmaceuticals and agriculture. Rotenone, as a prominent rotenoid, has a longstanding history of use in pesticides, veterinary applications, medicine, and medical research. The accumulation of rotenoids within Derris plants adheres to species-specific and tissue-specific patterns and is also influenced by environmental factors. Current research predominantly addresses extraction techniques, pharmacological applications, and pesticide formulations, whereas investigations into the biosynthesis pathway and regulatory mechanism of rotenoids remain relatively scarce. In this study, we observed notable differences in rotenone content across the roots, stems, and leaves of D. fordii, as well as within the roots of D. elliptica. Utilizing RNA sequencing (RNA-seq), we analyzed the transcriptomes and expression profiles of unigenes from these four tissues, identifying a total of 121,576 unigenes. Differentially expressed genes (DEGs) across four comparison groups demonstrated significant enrichment in the phenylpropanoid and flavonoid biosynthesis pathways. Key unigenes implicated in the rotenoid biosynthesis pathway were identified, with PAL, C4H, CHS, CHI, IFS, and HI4OMT playing critical roles in D. fordii, while IFS and HI4OMT were determined to be essential for rotenoid biosynthesis in D. elliptica. These findings enhance our understanding of the biosynthesis mechanism of rotenoids in Derris species. The unigenes identified in this study represent promising candidates for future investigations aimed at validating their roles in rotenoid biosynthesis.展开更多
Meniscus injuries are widespread and the available treatments do not offer enough healing potential.Here,we provide critical support for using pigs as a biological model for meniscal degeneration and the development o...Meniscus injuries are widespread and the available treatments do not offer enough healing potential.Here,we provide critical support for using pigs as a biological model for meniscal degeneration and the development of cutting-edge therapies in orthopedics.We present a single-cell transcriptome atlas of the meniscus,consisting of cell clusters corresponding to four major cell types:chondrocytes,endothelial cells,smooth muscle cells,and immune cells.Five distinct chondrocyte subclusters(CH0–CH4)were annotated,of which only one was widespread in both the red and white zones,indicating a major difference in the cellular makeup of the zones.Subclusters distinct to the white zone appear responsible for cartilage-specific matrix deposition and protection against adverse microenvironmental factors,while those in the red zone exhibit characteristics of mesenchymal stem cells and are more likely to proliferate and migrate.Additionally,they induce remodeling actions in other chondrocyte subclusters and promote the proliferation and maturation of endothelial cells,inducing healing and vascularization processes.Considering that they have substantial remodeling capabilities,these subclusters should be of great interest for tissue engineering studies.We also show that the cellular makeup of the pig meniscus is comparable to that of humans,which supports the use of pigs as a model in orthopedic therapy development.展开更多
Gastric cancer(GC)remains one of the leading causes of cancer-related morbidity and mortality globally.Although significant progress has been made in treatment options,the survival rates for GC patients continue to be...Gastric cancer(GC)remains one of the leading causes of cancer-related morbidity and mortality globally.Although significant progress has been made in treatment options,the survival rates for GC patients continue to be low.This is primarily attributed to the intricate and insufficiently understood mechanisms of disease progression,as well as the considerable challenges associated with tumor hetero-geneity.The recent study by Tang et al provides a detailed single-cell RNA se-quencing analysis of GC across different stages,revealing dynamic changes in the tumor microenvironment and key immune responses.We aim to offer a compre-hensive interpretation of the study’s findings and propose several innovative directions for future academic research in gastric cancer.These include exploring advanced multi-omics approaches,leveraging spatial transcriptomics,integrating artificial intelligence for clinical applications,and developing novel immuno-therapy strategies.We further emphasize the importance of personalized medi-cine,early detection,and novel drug discovery techniques in improving GC treatment outcomes.展开更多
Head and neck cutaneous squamous cell carcinoma(HNCSCC)remains underexplored compared to oropharyngeal squamous cell carcinoma,particularly in relation to human papillomavirus(HPV)and molecular markers such as p16 and...Head and neck cutaneous squamous cell carcinoma(HNCSCC)remains underexplored compared to oropharyngeal squamous cell carcinoma,particularly in relation to human papillomavirus(HPV)and molecular markers such as p16 and p53.While p16 is a well-established surrogate for HPV in oropharyngeal cancer,our review highlights its unreliable role in HNCSCC,where positivity is instead associated with recurrence and metastasis.Similarly,p53 illustrates a dual role-wild-type as a genomic safeguard,mutated as an oncogenic driver-complicating prognostication.Methodological considerations,including the limitations of immunohistochemistry for HPV detection,underscore the need for multi-method and molecular validation in future studies.Ultraviolet radiation is posited as a key modifier of p16 function,decoupling expression from tumor suppression.To contextualize these findings,we draw parallels to glioblastoma(GBM),where subclonal evolution,p53 dysfunction,and intratumoral heterogeneity drive relapse despite aggressive multimodal therapies.GBM exemplifies how bulk-level biomarker generalizations often obscure dynamic cellular ecosystems,reinforcing the necessity of single-cell and spatial approaches.Multi-omics integration-encompassing genome,transcriptome,proteome,and tumor microenvironment mapping-coupled with single-cell RNA sequencing and spatial transcriptomics,offers a path forward for resolving subclonal dynamics in both HNCSCC and GBM.These technologies provide the resolution needed to track tumor-immunestromal co-evolution,identify therapy-resistant clones,and anticipate recurrence.We argue for a N-of-1,patient-and cell-centric paradigm that reframes biomarkers not as static surrogates but as dynamic readouts of cancer evolution across time and tissue contexts.Conceptually,we propose kinetic and microenvironmental frameworks(e.g.,“load-and-lock”barriers;dormancy and immunesynapse stabilization)as hypothesis-generating avenues to stall clonal handoffs and improve outcome prediction.Together,these perspectives argue for revised biomarker frameworks in HNCSCC and ethically inclusive,mechanism-anchored studies that bridge discovery with individualized care.By bridging insights from HNCSCC with the lessons of GBM,this review underscores the need for ethically inclusive,mechanistically informed frameworks that integrate subclonal evolution,biomarker re-interpretation,and precision-personalized hybrid models.Such an approach will be essential for advancing from one-size-fits-all strategies to individualized lifetime cancer care.展开更多
Over the past decade, there has been a growing realization that studying the small RNA transcriptome is essential for understanding the complexity of transcriptional regulation. With an increased throughput and a redu...Over the past decade, there has been a growing realization that studying the small RNA transcriptome is essential for understanding the complexity of transcriptional regulation. With an increased throughput and a reduced cost, next-generation sequencing technology has provided an unprecedented opportunity to measure the extent and complexity of small RNA transcriptome. Meanwhile, the large amount of obtained data and varied technology platforms have also posed multiple challenges for effective data analysis and mining. To provide some insight into the small RNA transcriptome investigation, this review describes the major small RNA classes, experimental methods to identify small RNAs, and available bioinformatics tools and databases.展开更多
A total of 8375 genic simple sequence repeat（SSR） loci were discovered from a unigene set assembled from 116282 transcriptomic unigenes in this study.Dinucleotide repeat motifs were the most common with a frequency ...A total of 8375 genic simple sequence repeat（SSR） loci were discovered from a unigene set assembled from 116282 transcriptomic unigenes in this study.Dinucleotide repeat motifs were the most common with a frequency of 65.11%,followed by trinucleotide（32.81%）.A total of 4100 primer pairs were designed from the SSR loci.Of these,343 primer pairs（repeat length≥15 bp） were synthesized with an M13 tail and tested for stable amplification and polymorphism in four Pyrus accessions.After the preliminary test,104 polymorphic genic SSR markers were developed; dinucleotide and trinucleotide repeats represented 97.11%（101） of these.Twenty-eight polymorphic genic SSR markers were selected randomly to further validate genetic diversity among 28 Pyrus accessions.These markers displayed a high level of polymorphism.The number of alleles at these SSR loci ranged from 2 to 17,with a mean of 9.43 alleles per locus,and the polymorphism information content（PIC） values ranged from 0.26 to 0.91.The UPGMA（unweighted pair-group method with arithmetic average） cluster analysis grouped the 28 Pyrus accessions into two groups： Oriental pears and Occidental pears,which are congruent to the traditional taxonomy,demonstrating their effectiveness in analyzing Pyrus phylogenetic relationships,enriching rare Pyrus EST-SSR resources,and confirming the potential value of a pear transcriptome database for the development of new SSR markers.展开更多
BACKGROUND Cardiac tumors are rare and complex entities.Surgery represents the cornerstone of therapy,while the role of adjuvant treatment remains unclear and,in case of relapse or metastatic disease,the prognosis is ...BACKGROUND Cardiac tumors are rare and complex entities.Surgery represents the cornerstone of therapy,while the role of adjuvant treatment remains unclear and,in case of relapse or metastatic disease,the prognosis is very poor.Lack of prospective,randomized clinical trials hinders the generation of high level evidence for the optimal diagnostic workup and multimodal treatment of cardiac sarcomas.Herein,we describe the multidisciplinary clinical management and molecular characterization of a rare case of cardiac myxofibrosarcoma in an elderly woman.CASE SUMMARY A 73-year-old woman presented signs and symptoms of acute left-sided heart failure.Imaging examination revealed a large,left atrial mass.With suspicion of a myxoma,she underwent surgery,and symptoms were promptly relieved.Histology showed a cardiac myxofibrosarcoma,a rare histotype of cardiac sarcoma.Eight months later,disease unfortunately relapsed,and after a multidisciplinary discussion,a chemotherapy with doxorubicin and then gemcitabine was started,achieving partial radiologic and complete metabolic response,which was maintained up to 2 years and is still present.This report is focused on the entire clinical path of our patient from diagnosis to follow-up,through surgery and strategies adopted at relapse.Moreover,due to their rarity,very little is known about the molecular landscape of myxofibrosarcomas.Thus,we also performed and described preliminary genome analysis of the tumor tissue to get further insight on mechanisms involved in tumor growth,and to possibly unveil new clinically actionable targets.CONCLUSION We report a case of cardiac myxofibrosarcoma that achieved a very good prognosis due to an integrated surgical,cardiac and oncologic treatment strategy.展开更多
A programme of functional genomics research is underway at the University of Greenwich,UK,to develop and apply genomics technologies to characterise an economically-important but under-researched Bemisia tabaci（Hemip...A programme of functional genomics research is underway at the University of Greenwich,UK,to develop and apply genomics technologies to characterise an economically-important but under-researched Bemisia tabaci（Hemiptera：Aleyrodidae）,the Asia 1 mtCOI phylogenetic group.A comparison of this putative species from India with other important B.tabaci populations and insect species may provide targets for the development of more effective whitefly control strategies.As a first step,next-generation sequencing（NGS）has been used to survey the transcriptome of adult female whitefly,with high quality RNA preparations being used to generate cDNA libraries for NGS using the Roche 454 Titanium DNA sequencing platform.Contig assemblies constructed from the resultant sequences（301 094 reads）using the software program CLC Genomics Workbench generated 3 821 core contigs.Comparison of a selection of these contigs with related sequences from other B.tabaci genetic groups has revealed good alignment for some genes（e.g.,HSP90）but misassemblies in other datasets（e.g.,the vitellogenin gene family）,highlighting the need for manual curation as well as collaborative international efforts to obtain accurate assemblies from the existing next generation sequence datasets.Nevertheless,data emerging from the NGS has facilitated the development of accurate and reliable methods for analysing gene expression based on quantitative real-time RT-PCR,illustrating the power of this approach to enable rapid expression analyses in an organism for which a complete genome sequence is currently lacking.展开更多
The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown. In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure a...The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown. In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure and function. This study investigated the role that CSRP3 plays in chicken skeletal muscle. First, the antibody against chicken CSRP3 protein was prepared, and the expression levels of the mRNA and protein of the CSRP3 gene in four chicken skeletal muscles with different myofiber compositions were compared. Then the effects of CSRP3 silencing on the expression profile of chicken myoblast transcriptomes were analyzed. The results showed that the expression levels of the mRNA and protein of the CSRP3 gene were both associated with the composition of fiber types in chicken skeletal muscles. A total of 650 genes with at least 1.5-fold differences(Q<0.05) were identified, of which 255 genes were upregulated and 395 genes were downregulated by CSRP3 silencing. Functional enrichment showed that several pathways, including adrenergic signaling in cardiomyocytes, adipocytokine signaling pathway and apelin signaling pathway, were significantly(P<0.05) enriched both in differentially expressed genes and all expressed genes. The co-expressed gene network suggested that CSRP3 silencing caused a compensatory upregulation(Q<0.05) of genes related to the assembly of myofibrils, muscle differentiation, and contraction. Meanwhile, two fast myosin heavy chain genes(MyH1B and MyH1E)were upregulated(Q<0.05) upon CSRP3 silencing. These results suggested that CSRP3 plays a crucial role in chicken myofiber composition, and affects the distribution of chicken myofiber types, probably by regulating the expression of MyH1B and MyH1E.展开更多
基金funded by the 2023 Inner Mongolia Public Institution High-Level Talent Introduction Scientific Research Support Project,and the Ordos Municipal Science and Technology Major Special Project(Grant No.2022EEDSKJZDZX021).
文摘In this paper,a standardized analysis method is established for identifying meat quality-related genes in Ordos finewool sheep using transcriptome sequencing data.A meticulously standardized approach is utilized to investigate the genetic determinants of meat quality in Ordos fine-wool sheep through transcriptome sequencing analysis.Muscle samples from the longissimus dorsi of one-year-old sheep are collected under controlled conditions,and key texture properties—hardness,elasticity,and chewiness—are measured to categorize samples into high-and low-textural-value groups.Genes significantly associated with meat quality traits are identified through standardized RNA extraction,high-throughput sequencing,and differential gene expression analysis.Functional enrichment analysis reveals their involvement in biological processes such as extracellular matrix organization and metabolic pathways.The findings underscore the pivotal role of standardization in meat quality research,laying a solid scientific foundation for future research on meat quality improvement and molecular breeding.
基金supported by the National Natural Science Foundation of China,No.82301403(to DZ)。
文摘Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocytes,microglia,and oligodendrocytes in the central nervous system,and satellite glial cells and Schwann cells in the peripheral nervous system.Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models,few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord.Here,we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes,microglia,and oligodendrocytes in the human spinal cord.To explore the conservation and divergence across species,we compared these findings with those from mice.In the human spinal cord,astrocytes,microglia,and oligodendrocytes were each divided into six distinct transcriptomic subclusters.In the mouse spinal cord,astrocytes,microglia,and oligodendrocytes were divided into five,four,and five distinct transcriptomic subclusters,respectively.The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice.Additionally,we detected sex differences in gene expression in human spinal cord glial cells.Specifically,in all astrocyte subtypes,the levels of NEAT1 and CHI3L1 were higher in males than in females,whereas the levels of CST3 were lower in males than in females.In all microglial subtypes,all differentially expressed genes were located on the sex chromosomes.In addition to sex-specific gene differences,the levels of MT-ND4,MT2A,MT-ATP6,MT-CO3,MT-ND2,MT-ND3,and MT-CO_(2) in all spinal cord oligodendrocyte subtypes were higher in females than in males.Collectively,the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cordrelated illnesses,including chronic pain,amyotrophic lateral sclerosis,and multiple sclerosis.
基金Supported by the National Natural Science Foundation of China,No.81774118the Foreign Cooperation Project of Science and Technology Department of Fujian Province,No.2023I0021the Medical Innovation Project of Fujian Province,No.2024CXB013.
文摘BACKGROUND Hemorrhoids,a prevalent chronic condition globally,significantly impact patients'quality of life.While various surgical interventions,such as external stripping and internal ligation,procedure for prolapse and hemorrhoids,and tissue selecting technique,are employed for treatment,they are often associated with postoperative complications,including unsatisfactory defecation,bleeding,and anal stenosis.In contrast,Xiaozhiling injection,a traditional Chinese medicine-based therapy,has emerged as a minimally invasive and effective alternative for internal hemorrhoids.This treatment offers distinct advantages,such as reduced dietary restrictions,broad applicability,and minimal induction of systemic inflammatory responses.Additionally,Xiaozhiling injection effectively eliminates hemorrhoid nuclei,prevents local tissue necrosis,preserves anal cushion integrity,and mitigates postoperative complications,including bleeding and prolapse.Despite its clinical efficacy,the molecular mechanisms underlying its therapeutic effects remain poorly understood,warranting further investigation.AIM To investigate the molecular mechanism underlying the therapeutic effect of Xiaozhiling injection in the treatment of internal hemorrhoids.METHODS An internal hemorrhoid model was established in rats,and the rats were randomly divided into a modeling group[control group(CK group)]and a treatment group.One week after injection,Stereo-seq and electron microscopy were used to study the changes in gene expression and subcellular structures in fibroblasts.RESULTS Single-cell sequencing revealed differences in the expression and transcript levels of the genes collagen 3 alpha 1,decorin,and actin alpha 2 in fibroblasts between the CK group and the treatment group.Spatial transcriptome analysis revealed that genes of the sphingosine kinase 1(Sphk1)/sphingosine-1-phosphate(S1P)pathway spatially overlapped with key genes of the transforming growth factor beta 1 pathway,namely,Sphk1,S1P receptor,and transforming growth factor beta 1,in the treatment group.The proportion of fibroblasts was lower in the treatment group than in the CK group,and Xiaozhiling treatment had a significant effect on the proportion of fibroblasts in hemorrhoidal tissue.Immunohistochemistry revealed a significant increase in the expression of a fibroblast marker.Electron microscopy showed that the endoplasmic reticulum of fibroblasts contained a large amount of glycogen,indicating cell activation.Fibroblast activation and the expression of key genes of the Sphk1-S1P pathway could be observed at the injection site,suggesting that after Xiaozhiling intervention,the Sphk1-S1P pathway could be activated to promote fibrosis.CONCLUSION Xiaozhiling injection exerts its therapeutic effects on internal hemorrhoids by promoting collagen synthesis and secretion in fibroblasts.After Xiaozhiling intervention,the Sphk1-S1P pathway can be activated to promote fibrosis.
基金Shaanxi Province Key R&D Program (2022SF-238)Chinese Medicine Pharmaceutical Key Discipline of Shaanxi province (303061107)+1 种基金Discipline Innovation team Project of Shaanxi University of Chinese Medicine (2019-YL11)Shaanxi Province Key subject of pharmacy engineering of Shaanxi Provincial Traditional Chinese Medicine administration (2017001)。
文摘OBJECTIVE: To corroborate the efficacy of Jintiange capsules(JTGs)( 金天格胶囊) in the treatment of osteoarthritis(OA) by exploring the potential mechanism of action of synovial mesenchymal stem cell exosomes(SMSC-Exos) and articular chondrocytes(ACs) through transcriptome sequencing(RNA-seq). METHODS: Type Ⅱ collagenase was used to induce OA in rats. The efficacy of JTGs was confirmed by macroscopic observation of articular cartilage, micro-CT observation, and safranin fast green staining. After SMSC-Exos and ACs were qualified, RNA-seq was used to screen differentially expressed mi RNAs and m RNAs. The target genes of differentially expressed mi RNAs in Synovial mesenchymal stem cells(SMSCs) were predicted based on the multi Mi R R package. The codifferentially expressed genes of SMSC-Exos and ACs were obtained by venny 2.1.0. The mi RNA-m RNA regulatory network was constructed by Cytoscape software. Based on the Omic Share platform, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis was performed on the m RNA regulated by key mi RNAs. Expression trend analysis was performed for co-differentially expressed genes. Correlation analysis was performed on micro-CT efficacy indicators, co-differentially expressed genes mRNA and miRNA. RESULTS: The efficacy of each administration group of JTGs was significant compared with the model group. SMSC-Exos and ACs were identified by their characteristics. The expression of rno-mi R-23a-3p, rnomi R-342-3p, rno-miR-146b-5p, rno-miR-501-3p, rnomiR-214-3p was down-regulated in OA pathological state, and the expression of rno-mi R-222-3p, rno-mi R-30e-3p, rno-mi R-676, and rno-miR-192-5p expression was upregulated, and the expression of all these mi RNAs was reversed after the intervention with JTGs containing serum. The co-differentially expressed genes were enriched in the interleukin 17 signaling pathway, tumor necrosis factor signaling pathway, transforming growth factor-β signaling pathway, etc. The expression trends of Ccl7, Akap12, Grem2, Egln3, Arhgdib, Ccl20, Mmp12, Pla2g2a, and Nr4a1 were significant. There was a correlation between micro-CT pharmacodynamic index, m RNA, and mi RNA. CONCLUSION: JTGs can improve the degeneration of joint cartilage and achieve the purpose of cartilage protection, which can be used for the treatment of OA. SMSCs-related mi RNA expression profiles were significantly altered after the intervention with JTGs containing serum. The 9 co-differentially expressed genes may be the key targets for the efficacy of JTGs in the treatment of OA rats, which can be used for subsequent validation.
基金Supported by National Natural Foundation of China,No.821742232019 Chinese and Western Medicine Clinical Collaborative Capacity Building Project for Major Difficult Diseases,No.2019-ZX-005。
文摘BACKGROUND Esophageal squamous cell carcinoma(ESCC)is one of the most common malignancies worldwide,and its development comprises a multistep process from intraepithelial neoplasia(IN)to carcinoma(CA).However,the critical regulators and underlying molecular mechanisms remain largely unknown.AIM To explore the genes and infiltrating immune cells in the microenvironment that are associated with the multistage progression of ESCC to facilitate diagnosis and early intervention.METHODS A mouse model mimicking the multistage development of ESCC was established by providing warter containing 4-nitroquinoline 1-oxide(4NQO)to C57BL/6 mice.Moreover,we established a control group without 4NQO treatment of mice.Then,transcriptome sequencing was performed for esophageal tissues from patients with different pathological statuses,including low-grade IN(LGIN),high-grade IN(HGIN),and CA,and controlled normal tissue(NOR)samples.Differentially expressed genes(DEGs)were identified in the LGIN,HGIN,and CA groups,and the biological functions of the DEGs were analyzed via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses.The CIBERSORT algorithm was used to detect the pattern of immune cell infilt-ration.Immunohistochemistry(IHC)was also conducted to validate our results.Finally,the Luminex multiplex cytokine analysis was utilized to measure the serum cytokine levels in the mice.RESULTS Compared with those in the NOR group,a total of 681541,and 840 DEGs were obtained in the LGIN,HGIN,and CA groups,respectively.Using the intersection of the three sets of DEGs,we identified 86 genes as key genes involved in the development of ESCC.Enrichment analysis revealed that these genes were enriched mainly in the keratinization,epidermal cell differentiation,and interleukin(IL)-17 signaling pathways.CIBERSORT analysis revealed that,compared with those in the NOR group,M0 and M1 macrophages in the 4NQO group showed stronger infiltration,which was validated by IHC.Serum cytokine analysis revealed that,compared with those in the NOR group,IL-1βand IL-6 were upregulated,while IL-10 was downregulated in the LGIN,HGIN,and CA groups.Moreover,the expression of the representative key genes,such as S100a8 and Krt6b,was verified in external human samples,and the results of immunohistochemical staining were consistent with the findings in mice.CONCLUSION We identified a set of key genes represented by S100a8 and Krt6b and investigated their potential biological functions.In addition,we found that macrophage infiltration and abnormal alterations in the levels of inflam-mation-associated cytokines,such as IL-1β,IL-6,and IL-10,in the peripheral blood may be closely associated with the development of ESCC.
基金facility support from the Single-Molecule Sequencing Platform at Sun Yat-sen University Cancer Center.This work is supported by the National Natural Science Foundation of China(32070592 to JXY,32000395 to JL,82272789 to LZ)Guangdong Basic and Applied Basic Research Foundation(2022A1515010717 and 2019A1515110762 to JXY and 2022A1515011873 to JL)+2 种基金Guangdong Pearl River Talents Program(2019QN01Y183 to JXY,2021QN02Y168 to JL)Guangzhou Municipal Science and Technology Bureau(202102020938 to JL)Young Talents Program of Sun Yat-sen University Cancer Center(YTP-SYSUCC-0042 to JXY and YTP-SYSUCC-0040 to JL)。
文摘Nanopore direct RNA sequencing(DRS)provides the direct access to native RNA strands with full-length information,shedding light on rich qualitative and quantitative properties of gene expression profiles.Here with NanoTrans,we present an integrated computational framework that comprehensively covers all major DRS-based application scopes,including isoform clustering and quantification,poly(A)tail length estimation,RNA modification profiling,and fusion gene detection.In addition to its merit in providing such a streamlined one-stop solution,NanoTrans also shines in its workflow-orientated modular design,batch processing capability,all-in-one tabular and graphic report output,as well as automatic installation and configuration supports.Finally,by applying NanoTrans to real DRS datasets of yeast,Arabidopsis,as well as human embryonic kidney and cancer cell lines,we further demonstrate its utility,effectiveness,and efficacy across a wide range of DRS-based application settings.
基金supported by National Natural Science Foundation of China(No.31870451,31370470 and 32001155)the State Key Laboratory of Lake Science and Environment Foundation(2022SKL011).
文摘High fish predation pressure can trigger"induced defense"in Daphnia species,resulting in phenotypic plasticity in morphology,behavior,or life-history traits.The molecular mechanisms of defense morphogenesis(e.g.,the tail spine and helmet)in Daphnia remain unclear.In the pres-ent study,the tail spine,helmet,and body of Daphnia galeata under fish and non-fish kairomones conditions were collected for transcriptome analysis.A total of 24 candidate genes related to the morphological defense of D.galeata were identified,including 2 trypsin,one cuticle protein,1 C1qDC protein,and 2 ferritin genes.The function of the Dagcut gene(D.galeata cuticle protein gene)in relation to tail spine morphology was assessed using RNA interference(RNAi).Compared with the EGFP(Enhanced green fluorescent protein)treatment,after RNAi,the expression levels of the Dagcut gene(D.galeata cuticle protein gene)showed a significant decrease.Correspondingly,the tail spines of the offspring pro-duced by D.galeata after RNAi of the Dagcut gene appeared curved during the experiment.In whole-mount in situ hybridization,a clear signal site was detected on the tail spine of D.galeata before RNAi which disappeared after RNAi.Our results suggest that the Dagcut gene may play an important role in tail spine formation of D.galeata,and will provide a theoretical basis for studying the molecular mechanisms of the morpho-logical plasticityin cladocera inthefuture.
基金Supported by the National Natural Science Foundation,China,No.82272568,81902247,and 32201013Natural Science Foundation of Shandong Province,China,No.ZR2021QH275+1 种基金Natural Science Foundation of Jinan City,China,No.202225070Guangdong Basic and Applied Basic Research Foundation,China,No.2022A1515220056.
文摘BACKGROUND Mesenchymal stem cells(MSCs)modulated by various exogenous signals have been applied extensively in regenerative medicine research.Notably,nanosecond pulsed electric fields(nsPEFs),characterized by short duration and high strength,significantly influence cell phenotypes and regulate MSCs differentiation via multiple pathways.Consequently,we used transcriptomics to study changes in messenger RNA(mRNA),long noncoding RNA(lncRNA),microRNA(miRNA),and circular RNA expression during nsPEFs application.AIM To explore gene expression profiles and potential transcriptional regulatory mechanisms in MSCs pretreated with nsPEFs.METHODS The impact of nsPEFs on the MSCs transcriptome was investigated through whole transcriptome sequencing.MSCs were pretreated with 5-pulse nsPEFs(100 ns at 10 kV/cm,1 Hz),followed by total RNA isolation.Each transcript was normalized by fragments per kilobase per million.Fold change and difference significance were applied to screen the differentially expressed genes(DEGs).Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to elucidate gene functions,complemented by quantitative polymerase chain reaction verification.RESULTS In total,263 DEGs were discovered,with 92 upregulated and 171 downregulated.DEGs were predominantly enriched in epithelial cell proliferation,osteoblast differentiation,mesenchymal cell differentiation,nuclear division,and wound healing.Regarding cellular components,DEGs are primarily involved in condensed chromosome,chromosomal region,actin cytoskeleton,and kinetochore.From aspect of molecular functions,DEGs are mainly involved in glycosaminoglycan binding,integrin binding,nuclear steroid receptor activity,cytoskeletal motor activity,and steroid binding.Quantitative real-time polymerase chain reaction confirmed targeted transcript regulation.CONCLUSION Our systematic investigation of the wide-ranging transcriptional pattern modulated by nsPEFs revealed the differential expression of 263 mRNAs,2 miRNAs,and 65 lncRNAs.Our study demonstrates that nsPEFs may affect stem cells through several signaling pathways,which are involved in vesicular transport,calcium ion transport,cytoskeleton,and cell differentiation.
基金Supported by Science and Technology Support Planning Project of Sichuan Province(2021YFYZ0031SASA2024CZYX002)National Modern Agricultural Technology System Construction of China(CARS-41-G07)。
文摘The calpain system is ubiquitous in cells, mainly comprising calpains and calpain inhibitors, and is a widespread calcium-dependent cysteine protease in organisms that is involved in many cellular processes such as muscle degradation in vivo and affects the tenderness of meat after animal slaughter. The study found 128 DEGs that probably regulated tenderness traits were selected from 16 significantly enriched GO terms by transcriptome sequencing analysis, and found that the developmental changes in the expression levels of the CAPN1 gene in the pectoral and leg muscles were significantly positively correlated ( P <0.05) with the cumulative growth values of live weight and comb weight. The developmental changes in the expression levels of the CAST gene in the pectoral and leg muscles were not significantly correlated with the cumulative growth values of live weight and comb weight. Our results helped demonstrate the potential molecular mechanisms of tenderness in chickens and provide valuable information for chicken breeding.
文摘Single-cell transcriptome sequencing has been a rapidly developing and powerful biological tool in recent years,and it plays a vital role in describing tissue development,cell heterogeneity,stress response,etc.Cerebrovascular disease is one of the leading causes affecting human health in the world.Thus,it is important to understand the characteristics of cerebrovascular structure,function,and environmental response.Notably,single-cell transcriptome sequencing provides deeper insights into cerebrovascular research in health and disease states.This article will briefly introduce the basic structure and function of cerebrovascular endothelial cells(ECs),summarize the current research and new findings on cerebrovascular ECs at the single-cell transcriptome level,and discuss the challenges in this field.
基金supported by the National Key Technology Research and Development Program of the Ministry of Science and Technology of China (No. 2011BAI03B00)the National Science and Technology Major Project of the Ministry of Science and Technology of China (No. 2011ZX09401-305)
文摘Oviductus Ranae is the dried oviduct of female Rana tem-poraria chensinensis （David）, distributed mainly in North- eastern China. Oviductus Ranae is one of the best-known and highly valued oriental foods and medicines. Traditional Chinese medicine holds that Oviductus Ranae can nourish yin, moisten lung and replenish the kidney essence. Meanwhile, activities of Oviductus Ranae such as anti-aging, anti-lipemic, anti-oxidation and anti-fatigue have also been demonstrated by modern phar-macological studies. Previous studies have shown that Oviductus Ranae is mainly composed of proteins, which are up to 50% or more.
基金Guangxi Science and Technology Base and Talent Special Fund,Project No.AD21220130Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain,Project No.20-065-7Guangxi Institute of Botany Fund,Project No.21014.
文摘Derris fordii and Derris elliptica belong to the Derris genus of the Fabaceae family, distinguished by their high isoflavonoid content, particularly rotenoids, which hold significance in pharmaceuticals and agriculture. Rotenone, as a prominent rotenoid, has a longstanding history of use in pesticides, veterinary applications, medicine, and medical research. The accumulation of rotenoids within Derris plants adheres to species-specific and tissue-specific patterns and is also influenced by environmental factors. Current research predominantly addresses extraction techniques, pharmacological applications, and pesticide formulations, whereas investigations into the biosynthesis pathway and regulatory mechanism of rotenoids remain relatively scarce. In this study, we observed notable differences in rotenone content across the roots, stems, and leaves of D. fordii, as well as within the roots of D. elliptica. Utilizing RNA sequencing (RNA-seq), we analyzed the transcriptomes and expression profiles of unigenes from these four tissues, identifying a total of 121,576 unigenes. Differentially expressed genes (DEGs) across four comparison groups demonstrated significant enrichment in the phenylpropanoid and flavonoid biosynthesis pathways. Key unigenes implicated in the rotenoid biosynthesis pathway were identified, with PAL, C4H, CHS, CHI, IFS, and HI4OMT playing critical roles in D. fordii, while IFS and HI4OMT were determined to be essential for rotenoid biosynthesis in D. elliptica. These findings enhance our understanding of the biosynthesis mechanism of rotenoids in Derris species. The unigenes identified in this study represent promising candidates for future investigations aimed at validating their roles in rotenoid biosynthesis.
基金supported by the National Centre for Research and Development TECHMATSTRATEG-Ⅲ/0027/2019,POWR.03.02.00-00-I006/17the IDUB UAM。
文摘Meniscus injuries are widespread and the available treatments do not offer enough healing potential.Here,we provide critical support for using pigs as a biological model for meniscal degeneration and the development of cutting-edge therapies in orthopedics.We present a single-cell transcriptome atlas of the meniscus,consisting of cell clusters corresponding to four major cell types:chondrocytes,endothelial cells,smooth muscle cells,and immune cells.Five distinct chondrocyte subclusters(CH0–CH4)were annotated,of which only one was widespread in both the red and white zones,indicating a major difference in the cellular makeup of the zones.Subclusters distinct to the white zone appear responsible for cartilage-specific matrix deposition and protection against adverse microenvironmental factors,while those in the red zone exhibit characteristics of mesenchymal stem cells and are more likely to proliferate and migrate.Additionally,they induce remodeling actions in other chondrocyte subclusters and promote the proliferation and maturation of endothelial cells,inducing healing and vascularization processes.Considering that they have substantial remodeling capabilities,these subclusters should be of great interest for tissue engineering studies.We also show that the cellular makeup of the pig meniscus is comparable to that of humans,which supports the use of pigs as a model in orthopedic therapy development.
基金Supported by Scientific Research Project of Putian University,No.2022059Special Project for Outstanding Young Talents of Putian University,No.2024072Natural Science Foundation of Fujian Province,No.2023J01160.
文摘Gastric cancer(GC)remains one of the leading causes of cancer-related morbidity and mortality globally.Although significant progress has been made in treatment options,the survival rates for GC patients continue to be low.This is primarily attributed to the intricate and insufficiently understood mechanisms of disease progression,as well as the considerable challenges associated with tumor hetero-geneity.The recent study by Tang et al provides a detailed single-cell RNA se-quencing analysis of GC across different stages,revealing dynamic changes in the tumor microenvironment and key immune responses.We aim to offer a compre-hensive interpretation of the study’s findings and propose several innovative directions for future academic research in gastric cancer.These include exploring advanced multi-omics approaches,leveraging spatial transcriptomics,integrating artificial intelligence for clinical applications,and developing novel immuno-therapy strategies.We further emphasize the importance of personalized medi-cine,early detection,and novel drug discovery techniques in improving GC treatment outcomes.
文摘Head and neck cutaneous squamous cell carcinoma(HNCSCC)remains underexplored compared to oropharyngeal squamous cell carcinoma,particularly in relation to human papillomavirus(HPV)and molecular markers such as p16 and p53.While p16 is a well-established surrogate for HPV in oropharyngeal cancer,our review highlights its unreliable role in HNCSCC,where positivity is instead associated with recurrence and metastasis.Similarly,p53 illustrates a dual role-wild-type as a genomic safeguard,mutated as an oncogenic driver-complicating prognostication.Methodological considerations,including the limitations of immunohistochemistry for HPV detection,underscore the need for multi-method and molecular validation in future studies.Ultraviolet radiation is posited as a key modifier of p16 function,decoupling expression from tumor suppression.To contextualize these findings,we draw parallels to glioblastoma(GBM),where subclonal evolution,p53 dysfunction,and intratumoral heterogeneity drive relapse despite aggressive multimodal therapies.GBM exemplifies how bulk-level biomarker generalizations often obscure dynamic cellular ecosystems,reinforcing the necessity of single-cell and spatial approaches.Multi-omics integration-encompassing genome,transcriptome,proteome,and tumor microenvironment mapping-coupled with single-cell RNA sequencing and spatial transcriptomics,offers a path forward for resolving subclonal dynamics in both HNCSCC and GBM.These technologies provide the resolution needed to track tumor-immunestromal co-evolution,identify therapy-resistant clones,and anticipate recurrence.We argue for a N-of-1,patient-and cell-centric paradigm that reframes biomarkers not as static surrogates but as dynamic readouts of cancer evolution across time and tissue contexts.Conceptually,we propose kinetic and microenvironmental frameworks(e.g.,“load-and-lock”barriers;dormancy and immunesynapse stabilization)as hypothesis-generating avenues to stall clonal handoffs and improve outcome prediction.Together,these perspectives argue for revised biomarker frameworks in HNCSCC and ethically inclusive,mechanism-anchored studies that bridge discovery with individualized care.By bridging insights from HNCSCC with the lessons of GBM,this review underscores the need for ethically inclusive,mechanistically informed frameworks that integrate subclonal evolution,biomarker re-interpretation,and precision-personalized hybrid models.Such an approach will be essential for advancing from one-size-fits-all strategies to individualized lifetime cancer care.
基金supported by the National High Technology Research and Development Program of China(No. 2006AA02A304)Major State Basic Research Development Program of China(No.2007CB512302)
文摘Over the past decade, there has been a growing realization that studying the small RNA transcriptome is essential for understanding the complexity of transcriptional regulation. With an increased throughput and a reduced cost, next-generation sequencing technology has provided an unprecedented opportunity to measure the extent and complexity of small RNA transcriptome. Meanwhile, the large amount of obtained data and varied technology platforms have also posed multiple challenges for effective data analysis and mining. To provide some insight into the small RNA transcriptome investigation, this review describes the major small RNA classes, experimental methods to identify small RNAs, and available bioinformatics tools and databases.
基金supported by the National Natural Science Foundation of China(No.31201592)the Modern Agro-industry Technology Research System(No.nycytx-29-14)the Doctoral Program of Higher Education(No.20110101110091),China
文摘A total of 8375 genic simple sequence repeat（SSR） loci were discovered from a unigene set assembled from 116282 transcriptomic unigenes in this study.Dinucleotide repeat motifs were the most common with a frequency of 65.11%,followed by trinucleotide（32.81%）.A total of 4100 primer pairs were designed from the SSR loci.Of these,343 primer pairs（repeat length≥15 bp） were synthesized with an M13 tail and tested for stable amplification and polymorphism in four Pyrus accessions.After the preliminary test,104 polymorphic genic SSR markers were developed; dinucleotide and trinucleotide repeats represented 97.11%（101） of these.Twenty-eight polymorphic genic SSR markers were selected randomly to further validate genetic diversity among 28 Pyrus accessions.These markers displayed a high level of polymorphism.The number of alleles at these SSR loci ranged from 2 to 17,with a mean of 9.43 alleles per locus,and the polymorphism information content（PIC） values ranged from 0.26 to 0.91.The UPGMA（unweighted pair-group method with arithmetic average） cluster analysis grouped the 28 Pyrus accessions into two groups： Oriental pears and Occidental pears,which are congruent to the traditional taxonomy,demonstrating their effectiveness in analyzing Pyrus phylogenetic relationships,enriching rare Pyrus EST-SSR resources,and confirming the potential value of a pear transcriptome database for the development of new SSR markers.
文摘BACKGROUND Cardiac tumors are rare and complex entities.Surgery represents the cornerstone of therapy,while the role of adjuvant treatment remains unclear and,in case of relapse or metastatic disease,the prognosis is very poor.Lack of prospective,randomized clinical trials hinders the generation of high level evidence for the optimal diagnostic workup and multimodal treatment of cardiac sarcomas.Herein,we describe the multidisciplinary clinical management and molecular characterization of a rare case of cardiac myxofibrosarcoma in an elderly woman.CASE SUMMARY A 73-year-old woman presented signs and symptoms of acute left-sided heart failure.Imaging examination revealed a large,left atrial mass.With suspicion of a myxoma,she underwent surgery,and symptoms were promptly relieved.Histology showed a cardiac myxofibrosarcoma,a rare histotype of cardiac sarcoma.Eight months later,disease unfortunately relapsed,and after a multidisciplinary discussion,a chemotherapy with doxorubicin and then gemcitabine was started,achieving partial radiologic and complete metabolic response,which was maintained up to 2 years and is still present.This report is focused on the entire clinical path of our patient from diagnosis to follow-up,through surgery and strategies adopted at relapse.Moreover,due to their rarity,very little is known about the molecular landscape of myxofibrosarcomas.Thus,we also performed and described preliminary genome analysis of the tumor tissue to get further insight on mechanisms involved in tumor growth,and to possibly unveil new clinically actionable targets.CONCLUSION We report a case of cardiac myxofibrosarcoma that achieved a very good prognosis due to an integrated surgical,cardiac and oncologic treatment strategy.
基金Funding for the studies described was provided by the University of Greenwich Proof of Concept and Research Funds,UK(E0162/RAE-NRI-009/09and K0070)
文摘A programme of functional genomics research is underway at the University of Greenwich,UK,to develop and apply genomics technologies to characterise an economically-important but under-researched Bemisia tabaci（Hemiptera：Aleyrodidae）,the Asia 1 mtCOI phylogenetic group.A comparison of this putative species from India with other important B.tabaci populations and insect species may provide targets for the development of more effective whitefly control strategies.As a first step,next-generation sequencing（NGS）has been used to survey the transcriptome of adult female whitefly,with high quality RNA preparations being used to generate cDNA libraries for NGS using the Roche 454 Titanium DNA sequencing platform.Contig assemblies constructed from the resultant sequences（301 094 reads）using the software program CLC Genomics Workbench generated 3 821 core contigs.Comparison of a selection of these contigs with related sequences from other B.tabaci genetic groups has revealed good alignment for some genes（e.g.,HSP90）but misassemblies in other datasets（e.g.,the vitellogenin gene family）,highlighting the need for manual curation as well as collaborative international efforts to obtain accurate assemblies from the existing next generation sequence datasets.Nevertheless,data emerging from the NGS has facilitated the development of accurate and reliable methods for analysing gene expression based on quantitative real-time RT-PCR,illustrating the power of this approach to enable rapid expression analyses in an organism for which a complete genome sequence is currently lacking.
基金supported by the earmarked fund for China Agriculture Research System (CARS-41)the earmarked fund for Jiangsu Agricultural Industry Technology System, China (JATS[2021]396)+6 种基金the Special Fund for Major Breeding Programs in Jiangsu Province (PZCZ201728)the Natural Science Foundation of Jiangsu Province (BK20161322, BK20211121, and BK20210955)the Projects of Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province (JQLAB-ZZ-201703)the Open Project Program of Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, China (JILAR-KF202020)the Yangzhou Science and Technology Support Program for Modem Agriculture (YZ2021029)the Jiangsu Provincal Agricultural Independent Innovation Fund Project (CX(21)2011-1)the Independent Scientific Foundation of Public Welfare Scientific Institutes of Jiangsu Province (BM2018026)。
文摘The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown. In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure and function. This study investigated the role that CSRP3 plays in chicken skeletal muscle. First, the antibody against chicken CSRP3 protein was prepared, and the expression levels of the mRNA and protein of the CSRP3 gene in four chicken skeletal muscles with different myofiber compositions were compared. Then the effects of CSRP3 silencing on the expression profile of chicken myoblast transcriptomes were analyzed. The results showed that the expression levels of the mRNA and protein of the CSRP3 gene were both associated with the composition of fiber types in chicken skeletal muscles. A total of 650 genes with at least 1.5-fold differences(Q<0.05) were identified, of which 255 genes were upregulated and 395 genes were downregulated by CSRP3 silencing. Functional enrichment showed that several pathways, including adrenergic signaling in cardiomyocytes, adipocytokine signaling pathway and apelin signaling pathway, were significantly(P<0.05) enriched both in differentially expressed genes and all expressed genes. The co-expressed gene network suggested that CSRP3 silencing caused a compensatory upregulation(Q<0.05) of genes related to the assembly of myofibrils, muscle differentiation, and contraction. Meanwhile, two fast myosin heavy chain genes(MyH1B and MyH1E)were upregulated(Q<0.05) upon CSRP3 silencing. These results suggested that CSRP3 plays a crucial role in chicken myofiber composition, and affects the distribution of chicken myofiber types, probably by regulating the expression of MyH1B and MyH1E.
