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AI-driven integration of multi-omics and multimodal data for precision medicine 认领 引用 被引量：1
1
作者 Heng-Rui Liu 《Medical Data Mining》 CAS 2026年第1期1-2,共2页
High-throughput transcriptomics has evolved from bulk RNA-seq to single-cell and spatial profiling,yet its clinical translation still depends on effective integration across diverse omics and data modalities.Emerging ... High-throughput transcriptomics has evolved from bulk RNA-seq to single-cell and spatial profiling,yet its clinical translation still depends on effective integration across diverse omics and data modalities.Emerging foundation models and multimodal learning frameworks are enabling scalable and transferable representations of cellular states,while advances in interpretability and real-world data integration are bridging the gap between discovery and clinical application.This paper outlines a concise roadmap for AI-driven,transcriptome-centered multi-omics integration in precision medicine(Figure 1). 展开更多
关键词 high throughput transcriptomics multi omics single cell multimodal learning frameworks foundation models omics data modalitiesemerging ai driven precision medicine
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Proteogenomics:decoding cancer in multiple dimensions 认领 引用
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作者 Qian Liu Yimin Chen Hu Zhou 《MedScience》 SCIE CAS CSCD 2026年第2期203-230,共28页
A key challenge in cancer precision oncology is the limited ability of genomic analyses to accurately predict changes in protein expression or function,even though proteins serve as the main targets of numerous modern... A key challenge in cancer precision oncology is the limited ability of genomic analyses to accurately predict changes in protein expression or function,even though proteins serve as the main targets of numerous modern therapies.Bridging this gap necessitates precise quantification of proteins and their post‑translational modifications(PTMs).Recent advances in mass spectrometry(MS)‑based proteomics now enable large‑scale,quantitative characterization of proteins and PTMs in tumor tissues.To link genomic aberrations to cancer phenotypes,the emerging field of proteogenomics integrates proteomic data,including PTMs,with genomic,epigenomic,and transcriptomic information.This comprehensive approach offers a deeper understanding of cancer biology at multiple levels.This review highlights recent advancements in MS‑based proteomics,key discoveries in cancer proteogenomics,and the transformative potential of this field in decoding the complexities of cancer across diverse dimensions. 展开更多
关键词 proteogenomics proteomics cancer precision oncology multi‑omics
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Immune decoding from a multi-omics perspective:Redefining pancreatic cancer tumor microenvironment 认领 引用
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作者 Enkui Zhang Yinmo Yang 《Chinese Journal of Cancer Research》 SCIE CAS CSCD 2026年第3期311-314,共4页
Pancreatic ductal adenocarcinoma(PDAC)has long been regarded as a prototypical immune-cold tumor because of its dense desmoplastic stroma,limited cytotoxic lymphocyte infiltration,and poor response to immunotherapy.Ho... Pancreatic ductal adenocarcinoma(PDAC)has long been regarded as a prototypical immune-cold tumor because of its dense desmoplastic stroma,limited cytotoxic lymphocyte infiltration,and poor response to immunotherapy.However,this definition is increasingly insufficient.Recent advances in single-cell sequencing,T-cell receptor(TCR)and B-cell receptor(BCR)repertoire profiling,single-cell immune receptor sequencing,three-dimensional(3D)genome technologies,spatial transcriptomics,spatial proteomics,and artificial intelligence(AI)-assisted data integration suggest that immune failure in PDAC is not merely a consequence of reduced immune effector cell abundance(1,2). 展开更多
关键词 transcriptomicsspatial proteomicsand cytotoxic lymphocyte immune decoding multi omics pancreatic ductal adenocarcinoma pdac pancreatic ductal adenocarcinoma artificial i desmoplastic stromalimited
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The application and prospects of spatial omics technologies in clinical medical research and molecular diagnostics 认领 引用
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作者 Xiaofeng Wu Weize Xu +4 位作者 Da Lin Leqiang Sun Lit-Hsin Loo Jinxia Dai Gang Cao 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2026年第2期181-196,共16页
While conventional FISH and IHC methods struggle to decode complex tissue heterogeneity and comprehensive molecular diagnosis due to low-throughput spatial information,spatial omics technologies enable high-throughput... While conventional FISH and IHC methods struggle to decode complex tissue heterogeneity and comprehensive molecular diagnosis due to low-throughput spatial information,spatial omics technologies enable high-throughput molecular mapping across tissue microenvironments.These technologies are emerging as transformative tools in molecular diagnostics and medical research.By integrating histopathological morphology with spatial multi-omics profiling(genome,transcriptome,epigenome,and proteome),spatial omics technologies open an avenue for understanding disease progression,therapeutic resistance mechanisms,and precise diagnosis.It particularly enhances tumor microenvironment analysis by mapping immune cell distributions and functional states,which may greatly facilitate tumor molecular subtyping,prognostic assessment,and prediction of the radiotherapy and chemotherapy efficacy.Despite the substantial advancements in spatial omics,the translation of spatial omics into clinical applications remains challenging due to robustness,efficacy,clinical validation,and cost constraints.In this review,we summarize the current progress and prospects of spatial omics technologies,particularly in medical research and diagnostic applications. 展开更多
关键词 Spatial omics Multi-omics Molecular diagnostics Clinical medical research Precise medicine
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From spatial maps to therapeutic targets:Next challenge for artificial intelligence in cancer spatial omics 认领 引用
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作者 Hui Xu Yuyuan Zhang +2 位作者 Yuqing Ren Peng Luo Haidong Zhu 《Chinese Journal of Cancer Research》 SCIE CAS CSCD 2026年第2期200-203,共4页
Recent advances in spatial omics have transformed cancer research by allowing tumors to be studied not as simple aggregates of malignant cells,but as spatially organized ecosystems.Within these ecosystems,tumor cells,... Recent advances in spatial omics have transformed cancer research by allowing tumors to be studied not as simple aggregates of malignant cells,but as spatially organized ecosystems.Within these ecosystems,tumor cells,immune populations,fibroblasts,vascular elements,and extracellular matrix components are arranged in structured local contexts that shape invasion,immune evasion,therapy resistance,and clinical outcome(1-4).Artificial intelligence(AI)has become the central analytical engine of this transformation.By integrating machine learning,computer vision,graph-based modeling,and multimodal analysis,AI has enabled the identification of cellular neighborhoods,the inference of local communication networks,and the linkage of tissue architecture to prognosis and therapeutic response(5-8).These advances have greatly expanded our ability to study cancer in situ,but they have also exposed a conceptual bottleneck.The field is increasingly adept at describing where biology happens,but remains far less capable of determining which spatially organized processes actively drive disease and therefore represent tractable therapeutic targets. 展开更多
关键词 cellular neighborhoods local communication networks tumor ecosystems analytical engine artificial intelligence cancer research spatial omics extracellular matrix components
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Integrated multi-omics dissects receptor-mediated phytomelatonin signaling 认领 引用
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作者 Ying Liu Shirui Jing +5 位作者 Yuhao Zheng Qiuyu He Chengcheng Shen Junxin Guo Yangdong Guo Na Zhang 《Horticultural Plant Journal》 SCIE CAS CSCD 2026年第2期485-488,共4页
Phytomelatonin,an emerging plant hormone,plays vital roles in plant growth,development,and stress adaptation(Arnao et al.,2022;Ullah et al.,2024).It acts both as a direct antioxidant and a signaling molecule,engaging ... Phytomelatonin,an emerging plant hormone,plays vital roles in plant growth,development,and stress adaptation(Arnao et al.,2022;Ullah et al.,2024).It acts both as a direct antioxidant and a signaling molecule,engaging complex networks and interacting with other phytohormones(Liu et al.,2022;Khan et al.,2023).Although phytomelatonin receptors(PMTRs)have been identified in many plants(Wei et al.,2018;Wang et al.,2022;Liu et al.,2025),the downstream signaling mechanisms,particularly receptor-mediated protein modifications and transcriptional regulation,remain poorly characterized. 展开更多
关键词 phytomelatonin receptors pmtrs transcriptional regulation signaling moleculeengaging complex networks integrated multi omics phytohormones protein modifications plant hormoneplays phytomelatonin signaling
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Single-cell multi-omics sequencing reveals cell-specific transcriptomic and chromatin accessibility profiles in gut microbiome metabolite butyrate-produced pain modulation 认领 引用
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作者 Ran Tao Sufang Liu +3 位作者 Joshua Crawford Phillip Kramer Steven Bender Feng Tao 《International Journal of Oral Science》 SCIE CAS CSCD 2026年第3期504-520,共17页
Pain is the most common symptom of temporomandibular joint(TMJ)disorders,which present significant clinical challenges due to their complexity and limited treatment options.Our previous study demonstrates that gut mic... Pain is the most common symptom of temporomandibular joint(TMJ)disorders,which present significant clinical challenges due to their complexity and limited treatment options.Our previous study demonstrates that gut microbiome-derived butyrate is critical for the modulation of TMJ pain.In this study,we investigated its underlying mechanisms,and we found that oral administration of tributyrin,a prodrug of butyrate,not only significantly alleviated TMJ pain but also reversed the reduction in histone acetylation in the spinal trigeminal nucleus caudalis(Sp5C)under the TMJ pain condition.Using single-cell multi-omics sequencing,we profiled gene expression and chromatin accessibility in the Sp5C cells at the single-cell resolution.Bioinformatics analysis revealed that TMJ pain disrupted both the expression and chromatin accessibility of Nop14,Matk,Idh3b,Ndst2,and Tomm6 across four cell types in the Sp5C,and these alterations were reversed by tributyrin treatment.Specifically,Nop14 exhibited increased chromatin accessibility at its promoter region under TMJ pain condition,and knockdown of Nop14 in the Sp5C restored histone acetylation and alleviated TMJ pain.Together,our findings reveal cell-type-specific gene regulation that underlies butyrate-mediated epigenetic regulation of TMJ pain,which suggesting that targeting gut microbiome metabolites could develop a non-opioid novel therapy for TMJ disorders. 展开更多
关键词 temporomandibular joint pain butyrate gut microbiome single cell multi omics sequencing epigenetic regulation nociceptive processing histone acetylation temporomandibular joint tmj disorderswhich
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Integration of pathomics and single-cell omics in pancreatic ductal adenocarcinoma:Applications and clinical translation prospects 认领 引用
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作者 Xin Yan Hong-Yu Xu +2 位作者 Jia-Wu Liu Zhi-Yong Yang Qian Zhu 《World Journal of Clinical Oncology》 2026年第5期61-80,共20页
Pancreatic ductal adenocarcinoma(PDAC),the predominant pathological subtype of pancreatic cancer,presents significant challenges in early diagnosis and treatment due to its high degree of heterogeneity.The emergence o... Pancreatic ductal adenocarcinoma(PDAC),the predominant pathological subtype of pancreatic cancer,presents significant challenges in early diagnosis and treatment due to its high degree of heterogeneity.The emergence of single-cell omics and pathomics are providing powerful new tools and insights that are advancing PDAC research.Single-cell omics elucidates the molecular profiles of malignant epithelial cells,immune cells,and stromal cells within the PDAC tumor microenvironment,uncovering key pathways and cellular subpopulations that drive PDAC progression and drug resistance.In contrast,pathomics quantitatively extracts subtle morphological features from digitized whole-slide images,employing machine and deep learning to build diagnostic and prognostic prediction models.The multi-omics integration based on single-cell and pathology data provides deeper insights into tumor microenvironment.This integrated approach not only enables the prediction of molecular subtypes and immune status from routine hematoxylin and eosin-stained images,providing a low-cost and rapid auxiliary diagnostic tool for clinical practice,but also accurately identifies therapeutic targets,predicts drug responses,and screens potential beneficiaries for immunotherapy.This minireview aims to dissect PDAC from a multi-omics perspective,with the objectives of fostering greater integration and exploration across these fields and thereby deepening the molecular and spatial understanding of PDAC and laying the groundwork for future precision medicine approaches. 展开更多
关键词 Pancreatic ductal adenocarcinoma Pathomics Single-cell omics Artificial intelligence Multimodal integration
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Cold exposure induces transcriptomic and metabolic reprogramming in the heart:An integrated multi-omics study 认领 引用
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作者 Jiaming Ju Zhengchao Wen +6 位作者 Jiayun Li Dandan Zhang Kejiao Zhang Haozhan Wang Roman E.Tokmachev Yang Li Yanan Jiang 《Frigid Zone Medicine》 2026年第2期97-108,I0067-I0118,共12页
Objective:Exposure to extreme cold temperatures may increase the risk of cardiovascular diseases.This study aimed to investigate the effects of cold exposure on the heart and its underlying mechanisms using an integra... Objective:Exposure to extreme cold temperatures may increase the risk of cardiovascular diseases.This study aimed to investigate the effects of cold exposure on the heart and its underlying mechanisms using an integrated transcriptomic and metabolomic approach.Methods:C57BL/6 mice were subjected to cold exposure at 4°C for 12 hours per day for 4 weeks.Transcriptomics and metabolomics profiles of the heart were analyzed.Differentially expressed genes(DEGs)and differentially expressed metabolites(DEMs)were identified,and mRNA expression levels were validated by qRT-PCR.Enrichment analyses were performed to identify significantly affected pathways.Transcriptomic and metabolomic data were then integrated to provide a comprehensive view of molecular alterations induced by cold exposure.To further evaluate the relationship between cold exposure and cardiovascular diseases,a myocardial infarction(MI)mouse model was established,and overlapping genes between cold exposure and MI were analyzed.Results:Cold exposure significantly altered both the transcriptomic and metabolomic profiles of mouse hearts.Pathway enrichment analyses based on DEGs and DEMs identified several signaling pathways affected by cold stress.Integrated transcriptomic and metabolomic analyses further highlighted potential metabolic and signaling pathways associated with cold exposure.By cross-referencing DEGs associated with cold exposure with those from the MI model in the GEO database(GSE223208),34 overlapping genes were identified.Integrated analyses implicated key genes(Tnfrsf12a and Nppb)in cold-aggravated cardiac remodeling,which were further validated in MI models.Conclusion:Cold exposure reprograms the cardiac transcriptome and metabolome in mice.Cold exposure and MI share a subset of DEGs,which may help illuminate the pathophysiological interplay between cold stress and MI,highlighting potential therapeutic targets for cold-exacerbated cardiovascular diseases. 展开更多
关键词 integrated omics transcriptomic reprogramming metabolomic reprogramming cardiovascular diseases gene expression metabolomics profiles integrated transcriptomic metabolomic approachmethods c bl cold exposure
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From innovation to application:Pioneering advances in mass spectrometry imaging for spatially resolved single-cell omics 认领 引用 被引量：1
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作者 Xiaopin Lai Hao Xu +2 位作者 Xing Chen Jiayi Ke Shu-Hai Lin 《Chinese Chemical Letters》 SCIE CAS CSCD 2026年第6期231-242,共12页
Mass spectrometry imaging(MSI)is a rapidly advancing field in omics research,offering spatially resolved localization of biomolecules such as metabolites,lipids,and proteins within tissue sections.Recent advancements ... Mass spectrometry imaging(MSI)is a rapidly advancing field in omics research,offering spatially resolved localization of biomolecules such as metabolites,lipids,and proteins within tissue sections.Recent advancements in high-resolution MSI instrumentation have significantly enhanced the visualization of cellular structures,enabling molecular mapping at the single-cell level.Current single-cell MSI techniques can be broadly categorized into label-free approaches and multiplexed antibody-based strategies,both of which are continuously evolving to support comprehensive molecular profiling with subcellular precision.These technologies have become particularly valuable in cancer and neurodegenerative disease research,where they facilitate the characterization of cellular heterogeneity,metabolic reprogramming,and microenvironmental changes associated with disease progression.To meet the increasing demands of high-content spatial biology,multiple single-cell MSI platforms have been employed to detect low-abundance molecules,distinguish phenotypically distinct cell populations,and uncover region-specific molecular alterations in complex tissues.Moreover,emerging capabilities such as three-dimensional MSI are further extending the potential of this technology to reconstruct tissue biochemical architecture and capture spatially resolved molecular dynamics.In this review,we highlight pioneering advancements in single-cell MSI techniques and their applications in cancer and neurodegenerative disease research,with a particular emphasis on their role in elucidating disease mechanisms at the cellular level.We also discuss current challenges and future perspectives for expanding the utility of single-cell MSI in subcellular imaging and deeper biological discoveries. 展开更多
关键词 Single-cell omics Mass spectrometry imaging Label-free detection Multiplexed imaging Tumor microenvironment Neurodegenerative disease
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A multi-omics technology to the study of lactic acid bacteria responses to environmental stress:the past,current and future trends 认领 引用 被引量：1
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作者 Yaqi Liu Jingxian Sun +3 位作者 Xiaowen Liu Mingpeng Zheng Wen Ma Gang Jin 《Food Science and Human Wellness》 SCIE CAS CSCD 2025年第7期2501-2513,共13页
Lactic acid bacteria and the fermentation environment interact to form an intertwined system.Lactic acid bacteria are constantly evolving to adapt to different fermentation environments,causing changes in their physio... Lactic acid bacteria and the fermentation environment interact to form an intertwined system.Lactic acid bacteria are constantly evolving to adapt to different fermentation environments,causing changes in their physiological processes.To achieve a targeted improvement of their adaptability to various environments,a detail analysis of their evolutionary physiological processes is required.While several studies have been carried out in the past by using single-omics techniques to investigate their response to environmental stress,most researchers are now using a multi-omics approach to explore more detail in the biological regulatory networks and molecular mechanisms of lactic acid bacteria in response to environmental stress,thereby overcoming the limitations of single-omics analysis.In this review,we describe the various single-omics approaches that have been used to study environmental stress in lactic acid bacteria,present the advantages of various multi-omics combined analysis approaches,and discuss the potential and practicality of applying emerging single-cell transcriptomics and single-cell metabolomics techniques to the molecular mechanism study of microbes response to environmental stress.Multi-omics approaches enable the accurate identification of complex microbial physiological processes in different environments,allow people to comprehensively reveal the molecular mechanisms of microbes response to stress from different perspectives.Single-cell omics techniques,analyze the targeted regulation of microbial functions in a multi-dimensional space,provides a new perspective on understanding microbes responses environment stress. 展开更多
关键词 Single-omics Multi-omics Single-cell omics technology Spatial multi-omics technology
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Machine learning uncovers tidal DOM transformations and keystone molecules via FT-ICR MS and reactomics for estuarine nutrient cycling 认领 引用
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作者 Guosheng Zhao Longfei Wang +3 位作者 Yi Li Jiaying Chen Lihua Niu Li Lin 《Journal of Environmental Sciences》 SCIE EI CAS CSCD 2026年第8期570-580,共11页
Tidal cycles in estuaries dynamically regulate the composition and transformation of dissolved organic matter(DOM).However,conventional methods exhibit inadequate capacity to decipher the molecular transformation path... Tidal cycles in estuaries dynamically regulate the composition and transformation of dissolved organic matter(DOM).However,conventional methods exhibit inadequate capacity to decipher the molecular transformation pathways,thereby limiting the understanding of nitrogen-sulfur biogeochemical cycles therein.This study employed Fourier transform ion cyclotron resonance mass spectrometry(FT-ICR MS),reaction omics based on paired mass distance(PMD)networks,and machine learning(ML)approaches to investigate tidal-driven DOM dynamics in the estuarine sediments of a representative mountainous river,i.e.,Mulan River.Results revealed that tidal cycling significantly enhanced the humification of DOM in sediments,with O/C ratio increased from 0.251 for shallow layer samples when tide receded to 0.395 in deep layer sample collected at high tide.Tide cycles also promoted the accumulation of nitrogen-containing and sulfur-containing compounds,i.e.,CHON and CHONS moieties,particularly in deeper sediments(proportion up to 37%).ML models,i.e.,XGBoost and LightGBM identified high molecular weight(>450 Da),elevated N/C(>0.05),and S/C(>0.025)ratios as key predictors of biodegradable DOM.PMD-based reaction networks uncovered microbially mediated transformations,including dealkylation,amide hydrolysis,and desulfonation,driving dominant fractions shifting from aliphatic/proteins to lignin/carboxyl-rich alicyclic molecules during tidal events.Network topology analysis disclosed that CHOS compounds,e.g.,C17H20O8S1,emerged as pivotal nodal regulators of sulfur cycling,serving as metabolic hubs bridging aerobic and anaerobic microbial communities.Putatively derived from cysteine/methionine biotransformation products,these sulfur-enriched molecules exhibited significantly enhanced betweenness centrality in post-tidal reaction networks,underscoring their role in maintaining functional resilience under oscillating redox regimes. 展开更多
关键词 Dissolved organic matter Tidal cycling FT-ICR MS Reaction omics Machine learning Estuarine biogeochemistry
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“Omics” in pharmaceutical research: overview, applications, challenges, and future perspectives 认领 引用 被引量：20
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作者 YAN Shi-Kai LIU Run-Hui +4 位作者 JIN Hui-Zi LIU Xin-Ru YE Ji SHAN Lei ZHANG Wei-Dong 《Chinese Journal of Natural Medicines》 SCIE CAS CSCD 2015年第1期3-21,共19页
In the post-genomic era, biological studies are characterized by the rapid development and wide application of a series of "omics" technologies, including genomics, proteomics, metabolomics, transcriptomics,... In the post-genomic era, biological studies are characterized by the rapid development and wide application of a series of "omics" technologies, including genomics, proteomics, metabolomics, transcriptomics, lipidomics, cytomics, metallomics, ionomics, interactomics, and phenomics. These "omics" are often based on global analyses of biological samples using high through-put analytical approaches and bioinformatics and may provide new insights into biological phenomena. In this paper, the development and advances in these omics made in the past decades are reviewed, especially genomics, transcriptomics, proteomics and metabolomics; the applications of omics technologies in pharmaceutical research are then summarized in the fields of drug target discovery, toxicity evaluation, personalized medicine, and traditional Chinese medicine; and finally, the limitations of omics are discussed, along with the future challenges associated with the multi-omics data processing, dynamics omics analysis, and analytical approaches, as well as amenable solutions and future prospects. 展开更多
关键词 Omics Genomics Transcriptomics Proteomics Metabolomics Target Discovery Toxicity Assessment PersonalizedMedicine Traditional Chinese Medicine
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Investigation of Brassica and its relative genomes in the post-genomics era 认领 引用 被引量：9
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作者 Jian Wu Jianli Liang +6 位作者 Runmao Lin Xu Cai Lei Zhang Xinlei Guo Tianpeng Wang Haixu Chen Xiaowu Wang 《Horticulture Research》 SCIE CSCD 2022年第1期3453-3465,共13页
The Brassicaceae family includes many economically important crop species,as well as cosmopolitan agricultural weed species.In addition,Arabidopsis thaliana,a member of this family,is used as a molecular model plant s... The Brassicaceae family includes many economically important crop species,as well as cosmopolitan agricultural weed species.In addition,Arabidopsis thaliana,a member of this family,is used as a molecular model plant species.The genus Brassica is mesopolyploid,and the genus comprises comparatively recently originated tetrapolyploid species.With these characteristics,Brassicas have achieved the commonly accepted status of model organisms for genomic studies.This paper reviews the rapid research progress in the Brassicaceae family from diverse omics studies,including genomics,transcriptomics,epigenomics,and three-dimensional(3D)genomics,with a focus on cultivated crops.The morphological plasticity of Brassicaceae crops is largely due to their highly variable genomes.The origin of several important Brassicaceae crops has been established.Genes or loci domesticated or contributing to important traits are summarized.Epigenetic alterations and 3D structures have been found to play roles in subgenome dominance,either in tetraploid Brassica species or their diploid ancestors.Based on this progress,we propose future directions and prospects for the genomic investigation of Brassicaceae crops. 展开更多
关键词 model organisms omics Brassica molecular model plant genomics transcriptomics epigenomics D genomics
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Current cutting-edge omics techniques on musculoskeletal tissues and diseases 认领 引用
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作者 Xiaofei Li Liang Fang +14 位作者 Renpeng Zhou Lutian Yao Sade W.Clayton Samantha Muscat Dakota R.Kamm Cuicui Wang Chuan-Ju Liu Ling Qin Robert J.Tower Courtney M.Karner Farshid Guilak Simon Y.Tang Alayna E.Loiselle Gretchen A.Meyer Jie Shen 《Bone Research》 SCIE CAS CSCD 2025年第4期761-790,共30页
Musculoskeletal disorders,including osteoarthritis,rheumatoid arthritis,osteoporosis,bone fracture,intervertebral disc degeneration,tendinopathy,and myopathy,are prevalent conditions that profoundly impact quality of ... Musculoskeletal disorders,including osteoarthritis,rheumatoid arthritis,osteoporosis,bone fracture,intervertebral disc degeneration,tendinopathy,and myopathy,are prevalent conditions that profoundly impact quality of life and place substantial economic burdens on healthcare systems.Traditional bulk transcriptomics,genomics,proteomics,and metabolomics have played a pivotal role in uncovering disease-associated alterations at the population level.However,these approaches are inherently limited in their ability to resolve cellular heterogeneity or to capture the spatial organization of cells within tissues,thus hindering a comprehensive understanding of the complex cellular and molecular mechanisms underlying these diseases.To address these limitations,advanced single-cell and spatial omics techniques have emerged in recent years,offering unparalleled resolution for investigating cellular diversity,tissue microenvironments,and biomolecular interactions within musculoskeletal tissues.These cutting-edge techniques enable the detailed mapping of the molecular landscapes in diseased tissues,providing transformative insights into pathophysiological processes at both the single-cell and spatial levels.This review presents a comprehensive overview of the latest omics technologies as applied to musculoskeletal research,with a particular focus on their potential to revolutionize our understanding of disease mechanisms.Additionally,we explore the power of multi-omics integration in identifying novel therapeutic targets and highlight key challenges that must be overcome to successfully translate these advancements into clinical applications. 展开更多
关键词 osteoarthritis spatial omics single cell omics musculoskeletal disordersincluding osteoarthritisrheumatoid arthritisosteoporosisbone musculoskeletal disorders rheumatoid arthritis osteoporosis
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Functional genomics in medicinal plants:achievements and future challenges 认领 引用
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作者 Yuping Li Xinghao Zhang +1 位作者 Ying Wang Xiaoman Yang 《Medicinal Plant Biology》 2025年第1期84-95,共12页
Medicinal plants synthesize abundant specialized metabolites that adapt to environmental stress,and these compounds are important for human health,from traditional medicine to industrial uses.Rapid advances in high-th... Medicinal plants synthesize abundant specialized metabolites that adapt to environmental stress,and these compounds are important for human health,from traditional medicine to industrial uses.Rapid advances in high-throughput sequencing technologies and declining costs have accelerated the generation of high-quality reference genomes for medicinal plants.Integrated multi-omics analysis,particularly transcriptomics,metabolomics,and epigenomics,are now essential for deciphering the genes,pathways,and regulatory networks underlying the biosynthesis of metabolites.While published research has explored hundreds of medicinal plant genomics,a comprehensive knowledge of secondary metabolism integrated via multi-omics strategies remains lacking.In this review,we bridge this gap by summarizing the distinctive features of medicinal plants'genomes and highlighting how integrated omics facilitate the discovery of biosynthetic mechanisms.We also explore some applications in molecular breeding and synthetic biology,demonstrating how genomic insights can drive the sustainable development and innovative utilization of medicinal plant resources. 展开更多
关键词 high throughput sequencing environmental stress integrated multi omics functional genomics medicinal plantsintegrated medicinal plants specialized metabolites reference genomes
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Whole brain lipid dyshomeostasis in depressive-like behavior young adult rats:Mapping by mass spectrometry imaging-based spatial omics 认领 引用
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作者 Chao Zhao Chenyu Gao +3 位作者 Zhiyi Yang Tianyou Cao Qian Luo Zhijun Zhang 《Chinese Chemical Letters》 SCIE CAS CSCD 2025年第10期545-550,共6页
There is growing evidence that lipid metabolism instability in depressive disorder may be a core early pathological event associated with numerous pathogenesis hypotheses.However,spatial distributions and quantitative... There is growing evidence that lipid metabolism instability in depressive disorder may be a core early pathological event associated with numerous pathogenesis hypotheses.However,spatial distributions and quantitative changes of lipids in specific brain regions associated with depressive disorder are far from elucidated.In the present study,lipid profiling characteristics of whole brain sections are systematically determined by using matrix-assisted laser desorption ionization-mass spectrometry imaging(MALDI-MSI)-combined with histomorphological analysis in rats with depressive-like behavior induced by multiple early life stress(mELS)and unstressed control.Lipid dyshomeostasis and different degrees of metabolic disturbance occur in the eight paired representative brain sections from micro-region and molecular level.More specifically,17 lipid molecules show the severe dyshomeostasis between intergroup(control and depressed rats)or intra-group(multiple emotion-regulation-related brain regions).Quite specially,phosphatidylcholine(PC)(39:6)expression in section 7 is significantly upregulated only in the amygdala of depressed rat relative to control rat,by contrast,up-regulated phosphatidylglycerol(PG)(34:2)in section 2 emerges in the medial prefrontal cortex,insular cortex,and nucleus accumbens simultaneously.Linking spatial distribution to quantitative variation of lipids from the whole brain sections contributes the uncovering of new insights in causal mechanism of lipid dyshomeostasis in depression investigation and related targeting interventions. 展开更多
关键词 Depressive disorder Lipid dyshomeostasis Mass spectrometry imaging Spatial omics Whole brain imaging Adolescent depression
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Integrated-omics analysis defines subtypes of hepatocellular carcinoma based on circadian rhythm 认领 引用
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作者 Xiao-jie Li Le Chang +8 位作者 Yang Mi Ge Zhang Shan-shan Zhu Yue-xiao Zhang Hao-yu Wang Yi-shuang Lu Ye-xuan Ping Peng-yuan Zheng Xia Xue 《Journal of Integrative Medicine》 SCIE CAS CSCD 2025年第4期445-456,共12页
Objective:Circadian rhythm disruption(CRD)is a risk factor that correlates with poor prognosis across multiple tumor types,including hepatocellular carcinoma(HCC).However,its mechanism remains unclear.This study aimed... Objective:Circadian rhythm disruption(CRD)is a risk factor that correlates with poor prognosis across multiple tumor types,including hepatocellular carcinoma(HCC).However,its mechanism remains unclear.This study aimed to define HCC subtypes based on CRD and explore their individual heterogeneity.Methods:To quantify CRD,the HCC CRD score(HCCcrds)was developed.Using machine learning algorithms,we identified CRD module genes and defined CRD-related HCC subtypes in The Cancer Genome Atlas liver HCC cohort(n=369),and the robustness of this method was validated.Furthermore,we used bioinformatics tools to investigate the cellular heterogeneity across these CRD subtypes.Results:We defined three distinct HCC subtypes that exhibit significant heterogeneity in prognosis.The CRD-related subtype with high HCCcrds was significantly correlated with worse prognosis,higher pathological grade,and advanced clinical stages,while the CRD-related subtype with low HCCcrds had better clinical outcomes.We also identified novel biomarkers for each subtype,such as nicotinamide nmethyltransferase and myristoylated alanine-rich protein kinase C substrate-like 1.Conclusion:We classify the HCC patients into three distinct groups based on circadian rhythm and identify their specific biomarkers.Within these groups greater HCCcrds was associated with worse prognosis.This approach has the potential to improve prediction of an individual’s prognosis,guide precision treatments,and assist clinical decision making for HCC patients. 展开更多
关键词 Circadian rhythm disruption Omics Hepatocellular carcinoma subtypes Personalized treatment Precise medicine
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Multi-omics analyses reveal the effects of layerage and grafting on flavonoid synthesis and accumulation in Citrus reticulata‘Chachi’ 认领 引用
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作者 Jianmu Su Mingmin Jiang +7 位作者 Huimin Pan Weitao Zhou Xueyan Cai Yukun Wang Wei Liu Desen Wang Mei Bai Hong Wu 《Horticulture Research》 SCIE CSCD 2025年第10期120-136,共17页
Guangdong Citri Reticulatae Pericarpium from the dry and mature peel of Citrus reticulata‘Chachi’(CRC)is a well-known medicinal and food material in Asia.The main propagation methods of CRC are layerage and grafting... Guangdong Citri Reticulatae Pericarpium from the dry and mature peel of Citrus reticulata‘Chachi’(CRC)is a well-known medicinal and food material in Asia.The main propagation methods of CRC are layerage and grafting.It is generally considered that the quality of CRC from layerage is superior to that obtained from plants propagated by grafting.Nevertheless,the effects of layerage and grafting on the biosynthesis of flavonoid(main bioactive ingredients)in the peel of CRC remain unknown.Here,metabolomic analyses revealed the effects of layerage,self-grafting,and heterografting(Citrus limonia as rootstock)on flavonoid biosynthesis in CRC from two main harvesting periods,CRCV(Citri Reticulatae Chachiensis Viride)and CRCR(Citri Reticulatae Chachiensis Reddish).Compared with CRCR,CRCV exhibited a higher content of flavonoids.Grafting CRC onto C.limonia exhibited a higher content of hesperidin,nobiletin,tangeretin,narirutin,demethylnobiletin,and sinensetin than layerage and self-grafting.This increase can be attributed to the upregulation of genes involved in flavonoid synthesis.Further,the transcription factor CrcMYBF1 was identified within the gene coexpression network and is confirmed to be significantly induced by methyl jasmonate(MeJA)and upregulate the expression of Crc1,6RhaT through interacting with its promoter region,thereby boosting the biosynthesis and accumulation of hesperidin.In summary,our findings provide mechanistic insights into the coordinated regulation of hesperidin biosynthesis via MeJA-inducing CrcMYBF1 in CRC.Our study is expected to provide a theoretical basis for CRC propagation and cultivation. 展开更多
关键词 medicinal food material flavonoid synthesis citrus reticulata chachi crc layerage multi omics analyses grafting propagation methods citri reticulatae
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Integrating explainable deep learning with multi-omics for screening progressive diagnostic biomarkers of hepatocellular carcinoma covering the“inflammation-cancer”transformation 认领 引用
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作者 Saiyu Li Yiwen Zhang +8 位作者 Lifang Guan Yijing Dong Mingzhe Zhang Qian Zhang Huarong Xu Wei Xiao Zhenzhong Wang Yan Cui Qing Li 《Journal of Pharmaceutical Analysis》 SCIE CAS CSCD 2025年第9期2199-2202,共4页
Chronic uncontrolled inflammation is a major risk factor driving the occurrence of hepatocellular carcinoma(HCC),with over half of global cases attributed to hepatitis B virus(HBV)infection.Persistent inflammation fre... Chronic uncontrolled inflammation is a major risk factor driving the occurrence of hepatocellular carcinoma(HCC),with over half of global cases attributed to hepatitis B virus(HBV)infection.Persistent inflammation frequently progresses to cirrhosis and,ultimately,malignancy[1].Monitoring the key risk factors involved in the inflammatory-to-cancerous transformation in HCC is crucial for enabling timely intervention and improving patient survival rates.To address this challenge,we analyzed plasma samples collected from healthy volunteers and patients at various stages of HCC progression,including hepatitis,cirrhosis,and HCC(Approval No.:2021-IRBQYYS-021)(Tables S1–S5). 展开更多
关键词 plasma samples chronic uncontrolled inflammation multi omics explainable deep learning hepatocellular carcinoma key risk factors inflammation cancer transformation hepatocellular carcinoma hcc
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