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Single-cell profiling of the pig cecum at various developmental stages

Zoological Research 2024年第1期45卷 55-68页

作者： Yan-Yuan Xiao Qing Zhang Fei Huang Lin Rao Tian-Xiong Yao Si-Yu Yang Lei Xie Xiao-Xiao Zou Li-Ping Cai Jia-Wen Yang Bin Yang Lu-Sheng Huang National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation Ministry of Science and Technology of ChinaJiangxi Agricultural UniversityNanchangJiangxi 330045China

The gastrointestinal tract is essential for food digestion,nutrient absorption,waste elimination,and microbial defense.Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding of cellular diversity,functional heterogeneity,and their importance in intestinal tract development and disease.Although such profiling has been extensively conducted in humans and mice,the single-cell gene expression landscape of the pig cecum remains unexplored.Here,single-cell RNA sequencing was performed on 45572 cells obtained from seven cecal samples in pigs at four different developmental stages(days(D)30,42,150,and 730).Analysis revealed 12 major cell types and 38 subtypes,as well as their distinctive genes,transcription factors,and regulons,many of which were conserved in humans.An increase in the relative proportions of CD8^(+)T and Granzyme A(low expression)natural killer T cells(GZMA^(low)NKT)cells and a decrease in the relative proportions of epithelial stem cells,Tregs,RHEX^(+)T cells,and plasmacytoid dendritic cells(pDCs)were noted across the developmental stages.Moreover,the post-weaning period exhibited an up-regulation in mitochondrial genes,COX2 and ND2,as well as genes involved in immune activation in multiple cell types.Cell-cell crosstalk analysis indicated that IBP6^(+)fibroblasts were the main signal senders at D30,whereas IBP6^(−)fibroblasts assumed this role at the other stages.NKT cells established interactions with epithelial cells and IBP6^(+)fibroblasts in the D730 cecum through mediation of GZMA-F2RL1/F2RL2 pairs.This study provides valuable insights into cellular heterogeneity and function in the pig cecum at different development stages.

关键词： Single-cell RNA-seq Cecum Bama Xiang pigs Various developmental stages cellular heterogeneity

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Food nutrition and toxicology targeting on specific organs in the era of single-cell sequencing

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Food Science and Human Wellness 2024年第1期13卷 75-89页

作者： Xiaofei Wang Xiaowen Cheng Huiling Liu Xiaohuan Mu Hao Zheng National Engineering Technology Research Center for Fruit and Vegetable Processing Key Open Laboratory of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural AffairsBeijing Key Laboratory of Food Non-Thermal ProcessingCollege of Food Science and Nutritional EngineeringChina Agricultural UniversityBeijing 100083China

Due to the complex natures of dietary food components,it is difficult to elucidate how the compounds affect host health.Dietary food often selectively presents its mechanism of action on different cell types,and participates in the modulation of targeted cells and their microenvironments within organs.However,the limitations of traditional in vitro assays or in vivo animal experiments cannot comprehensively examine cellular heterogeneity and the tissue-biased influences.Single-cell RNA sequencing(sc RNA-seq)has emerged as an indispensable methodology to decompose tissues into different cell types for the demonstration of transcriptional profiles of individual cells.Sc RNA-seq applications has been summarized on three typical organs(brain,liver,kidney),and two representative immune-and tumor related health problems.The everincreasing role of sc RNA-seq in dietary food research with further improvement can provide sub-cellular information and the coupling between other cellular modalities.In this review,we propose utilizing sc RNAseq to more effectively capture the subtle and complex effects of food chemicals,and how they may lead to health problems at single-cell resolution.This novel technique will be valuable to elucidate the underlying mechanism of both the health benefits of food nutrients and the detrimental consequences food toxicants at the cellular level.

关键词： Dietary food cellular heterogeneity Single-cell RNA sequencing Food nutrients Food toxicants

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Decoding Human Biology and Disease Using Single-cell Omics Technologies

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Genomics, Proteomics & Bioinformatics 2023年第5期21卷 926-949页

作者： Qiang Shi Xueyan Chen Zemin Zhang Biomedical Pioneering Innovation Center School of Life SciencesPeking UniversityBeijing 100871China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871China Changping Laboratory Beijing 102206China

Over the past decade,advances in single-cell omics(SCO)technologies have enabled the investigation of cellular heterogeneity at an unprecedented resolution and scale,opening a new avenue for understanding human biology and disease.In this review,we summarize the developments of sequencing-based SCO technologies and computational methods,and focus on considerable insights acquired from SCO sequencing studies to understand normal and diseased properties,with a particular emphasis on cancer research.We also discuss the technological improvements of SCO and its possible contribution to fundamental research of the human,as well as its great potential in clinical diagnoses and personalized therapies of human disease.

关键词： Single-cell omics Computational method cellular heterogeneity Disease Cancer research

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Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development

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Genomics, Proteomics & Bioinformatics 2023年第5期21卷 950-961页

作者： Lin-Fang Ju Heng-Ji Xu Yun-Gui Yang Ying Yang Sino-Danish College University of Chinese Academy of SciencesBeijing 100049China University of Chinese Academy of Sciences Beijing 100049China CAS Key Laboratory of Genomic and Precision Medicine Collaborative Innovation Center of Genetics and DevelopmentBeijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China Institute of Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China

During mammalian preimplantation development,a totipotent zygote undergoes several cell cleavages and two rounds of cell fate determination,ultimately forming a mature blastocyst.Along with compaction,the establishment of apicobasal cell polarity breaks the symmetry of an embryo and guides subsequent cell fate choice.Although the lineage segregation of the inner cell mass(ICM)and trophectoderm(TE)is the first symbol of cell differentiation,several molecules have been shown to bias the early cell fate through their inter-cellular variations at much earlier stages,including the 2-and 4-cell stages.The underlying mechanisms of early cell fate determination have long been an important research topic.In this review,we summarize the molecular events that occur during early embryogenesis,as well as the current understanding of their regulatory roles in cell fate decisions.Moreover,as powerful tools for early embryogenesis research,single-cell omics techniques have been applied to both mouse and human preimplantation embryos and have contributed to the discovery of cell fate regulators.Here,we summarize their applications in the research of preimplantation embryos,and provide new insights and perspectives on cell fate regulation.

关键词： Cell fate determination cellular heterogeneity Cell polarity Single-cell omics Mammalian preimplantation embryo

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A Single-cell Transcriptome Atlas of Cashmere Goat Hair Follicle Morphogenesis

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Genomics, Proteomics & Bioinformatics 2021年第3期19卷 437-451页

作者： Wei Ge Weidong Zhang Yuelang Zhang Yujie Zheng Fang Li Shanhe Wang Jinwang Liu Shaojing Tan Zihui Yan Lu Wang Wei Shen Lei Qu Xin Wang Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China College of Animal Science&Technology Yangzhou UniversityYangzhou 225000China Life Science Research Center Yulin UniversityYulin 719000China College of Life Sciences Qingdao Agricultural UniversityQingdao 266109China

Cashmere,also known as soft gold,is produced from the secondary hair follicles(SHFs)of cashmere goats.The number of SHFs determines the yield and quality of cashmere;therefore,it is of interest to investigate the transcriptional profiles present during cashmere goat hair follicle development.However,mechanisms underlying this development process remain largely unexplored,and studies regarding hair follicle development mostly use a murine research model.In this study,to provide a comprehensive understanding of cellular heterogeneity and cell fate decisions,single-cell RNA sequencing was performed on 19,705 single cells of the dorsal skin from cashmere goat fetuses at induction(embryonic day 60;E60),organogenesis(E90),and cytodifferentiation(E120)stages.For the first time,unsupervised clustering analysis identified 16 cell clusters,and their corresponding cell types were also characterized.Based on lineage inference,a detailed molecular landscape was revealed along the dermal and epidermal cell lineage developmental pathways.Notably,our current data also confirmed the heterogeneity of dermal papillae from different hair follicle types,which was further validated by immunofluorescence analysis.The current study identifies different biomarkers during cashmere goat hair follicle development and has implications for cashmere goat breeding in the future.

关键词： Single-cell transcriptome Cashmere goat cellular heterogeneity Developmental trajectory Hair follicle morphogenesis

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