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Resampling approaches for the quantitative analysis of spatially distributed cells

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Data Intelligence 2024年第1期6卷 104-119页

作者： Giorgio Bertolazzi Michele Tumminello Gaia Morello Beatrice belmonte Claudio Tripodo Department of Economics Business and StatisticsUniversity of PalermoPalermoItaly Tumor Immunology Unit Department of Health SciencesUniversity of PalermoPalermoItaly Histopathology Unit Institute of Molecular Oncology Foundation(IFOM)ETS-The AIRC Institute of Molecular OncologyMilanItaly

Image segmentation is a crucial step in various image analysis pipelines and constitutes one of the cutting-edge areas of digital *** advent of quantitative analysis has enabled the evaluation of millions of individual cells in tissues,allowing for the combined assessment of morphological features,biomarker expression,and spatial *** recorded cells can be described as a point pattern ***,the classical statistical approaches to point pattern processes prove unreliable in this context due to the presence of multiple irregularly-shaped interstitial cell-devoid spaces in the domain,which correspond to anatomical features(***,lipid vacuoles,glandular lumina)or tissue artefacts(*** fractures),and whose coordinates are *** interstitial spaces impede the accurate calculation of the domain area,resulting in biased clustering ***,the mistaken inclusion of empty regions of the domain can directly impact the results of hypothesis *** literature currently lacks any introduced bias correction method to address interstitial cell-devoid *** address this gap,we propose novel resampling methods for testing spatial randomness and evaluating relationships among different cell *** methods obviate the need for domain area estimation and provide non-biased clustering *** created the SpaceR software(https://***/GBertolazzi/SpaceR)to enhance the accessibility of our methodologies.

关键词： Digital pathology spatial cytometry spatial clustering spatial randomness resampling

Transcriptome landscape of the early Brassica napus seed

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journal of Integrative Plant Biology 2019年第5期61卷 639-650页

作者： Dylan j.Ziegler Deirdre Khan jenna L.Kalichuk Michael G.Becker Mark F.belmonte University of Manitoba

Brassica napus L.(canola) is one of the world’s most economically important oilseeds. Despite our growing knowledge of Brassica genetics, we still know little about the genes and gene regulatory networks underlying early seed development. In this work, we use laser microdissection coupled with RNA sequencing to profile gene activity of both the maternal and filial subregions of the globular seed. We find subregions of the chalazal end including the chalazal endosperm, chalazal proliferating tissue, and chalazal seed coat, have unique transcriptome profiles associated with hormone biosynthesis and polysaccharide metabolism. We confirm that the chalazal seed coat is uniquely enriched for sucrose biosynthesis and transport, and that the chalazal endosperm may function as an important regulator of the maternal region through brassinosteroid synthesis. The chalazal proliferating tissue,a poorly understood subregion, was specifically enriched in transcripts associated with megasporogenesis and trehalose biosynthesis, suggesting this ephemeral structure plays an important role in both sporophytic development and carbon nutrient balance, respectively. Finally, compartmentalization of transcription factors and their regulatory circuits has uncovered previously unknown roles for the chalazal pole in early seed development.

关键词： Brassica napus L.(canola) understood subregion

Effect of Long-Term Soil Management on the Mutual Interaction Among Soil Organic Matter, Microbial Activity and Aggregate Stability in a Vineyard

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Pedosphere 2018年第2期28卷 288-298页

作者： Sergio A.belmonte Luisella CELI Ruby j.STAHEL Eleonora BONIFACIO Vittorino NOVELLO Ermanno ZANINI Kerri L.STEENWERTH Department of Agricultural Forest and Food Sciences Turin University USDA-ARS Crops Pathology and Genetics Research Unit

Vineyard management practices to enhance soil conservation principally focus on increasing carbon(C)input,whereas mitigating impacts of disturbance through reduced tillage has been rarely ***,information is lacking on the effects of soil management practices adopted in the under-vine zone on soil *** this work,we evaluated the long-term effects(22 years)of alley with a sown cover crop and no-tillage(S+NT),alley with a sown cover crop and tillage(S+T),and under-vine zone with no vegetation and tillage(UV)on soil organic matter(SOM),microbial activity,aggregate stability,and their mutual interactions in a California vineyard in *** biomass,microbial biomass and activity,organic C and nitrogen(N)pools,and SOM size fractionation and aggregate stability were *** characteristics only partially reflected the differences in vegetation biomass *** C and N pools and microbial biomass/activity in S+NT were higher than those in S+T,while the values in UV were intermediate between the other two ***,S+NT also exhibited higher particulate organic matter C in *** differences were found in POM C between S+T and UV,but the POM fraction in S+T was characterized by fresher *** stability was decreased in the order:S+NT>UV>S+***,even if shallow and performed infrequently,had a negative effect on organic C and N pools and aggregate ***,the combination of a sown cover crop and reduced tillage still limited SOM accumulation and reduced aggregate stability in the surface soil layer of vineyards,suggesting relatively lower resistance of soils to erosion compared to no-till systems.

关键词： loamy Ultisol microbial biomass permanent grass soil organic matter fractionation soil respiration tillage vegetationbiomass

Periosteum derived stem cells for regenerative medicine proposals: boosting current knowledge

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World journal of Stem Cells 2014年第3期6卷 266-277页

作者： Concetta Ferretti Monica Mattioli-belmonte Department of Clinical and Molecular Sciences School of Medicine Università Politecnica delle Marche

Periosteum is a thin fibrous layer that covers most bones. It resides in a dynamic mechanically loaded environment and provides a niche for pluripotent cells and a source for molecular factors that modulate cell behaviour. Elucidating periosteum regenerative poten-tial has become a hot topic in orthopaedics. This review discusses the state of the art of osteochondral tissue engineering rested on periosteum derived progenitor cells(PDPCs) and suggests upcoming research direc-tions. Periosteal cells isolation, characterization and migration in the site of injury, as well as their differen-tiation, are analysed. Moreover, the role of cell mecha-nosensing and its contribution to matrix organization, bone microarchitecture and bone stenght is examined. In this regard the role of periostin and its upregulation under mechanical stress in order to preserve PDPC sur-vival and bone tissue integrity is contemplated. The re-view also summarized the role of the periosteum in the field of dentistry and maxillofacial reconstruction. The involvement of microRNAs in osteoblast differentiation and in endogenous tissue repair is explored as well. Fi-nally the novel concept of a guided bone regenerationbased on the use of periosteum itself as a smart mate-rial and the realization of constructs able to mimic the extracellular matrix features is talked out. Additionally, since periosteum can differentiate into insulin produc-ing cells it could be a suitable source in allogenic trans-plantations. That innovative applications would takeadvantage from investigations aimed to assess PDPCimmune privilege.

关键词： Periosteum Mesenchymal stem cells Mi-croRNA Bone tissue engineering Bone turn-over

A single-cell transcriptomic atlas of primate pancreatic islet aging

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National Science Review 2021年第2期8卷 17-31页

作者： jingyi Li Yuxuan Zheng Pengze Yan Moshi Song Si Wang Liang Sun Zunpeng Liu Shuai Ma juan Carlos Izpisua belmonte Piu Chan Qi Zhou Weiqi Zhang Guang-Hui Liu Fuchou Tang jing Qu State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of Sciences National Laboratory of Biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences Beijing Institute for Brain Disorders Advanced Innovation Center for Human Brain ProtectionNational Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical University University of Chinese Academy of Sciences Beijing Advanced Innovation Center for Genomics Biomedical Pioneering Innovation CenterCollege of Life SciencesPeking University Ministry of Education Key Laboratory of Cell Proliferation and Differentiation Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesPeking University Institute for Stem Cell and Regeneration Chinese Academy of Sciences The MOH Key Laboratory of Geriatrics Beijing HospitalNational Center of Gerontology State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of Sciences Gene Expression Laboratory Salk Institute for Biological Studies CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences China National Center for Bioinformation

Aging-related degeneration of pancreatic islet cells contributes to impaired glucose tolerance and *** cells age heterogeneously, complicating the efforts to unravel the molecular drivers underlying endocrine aging. To overcome these obstacles, we undertook single-cell RNA sequencing of pancreatic islet cells obtained from young and aged non-diabetic cynomolgus monkeys. Despite sex differences and increased transcriptional variations, aged β-cells showed increased unfolded protein response(UPR) along with the accumulation of protein aggregates. We observed transcriptomic dysregulation of UPR components linked to canonical ATF6 and IRE1 signaling pathways, comprising adaptive UPR during pancreatic aging. Notably, we found aging-related β-cell-specific upregulation of HSP90 B1, an endoplasmic reticulum-located chaperone, impeded high glucose-induced insulin secretion. Our work decodes aging-associated transcriptomic changes that underlie pancreatic islet functional decay at single-cell resolution and indicates that targeting UPR components may prevent loss of proteostasis,suggesting an avenue to delaying β-cell aging and preventing aging-related diabetes.

关键词： islet β-cell aging single-cell RNA sequencing primate

Modeling CADASIL vascular pathologies with patient-derived induced pluripotent stem cells

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Protein & Cell 2019年第4期10卷 249-271页

作者： Chen Ling Zunpeng Liu Moshi Song Weiqi Zhang Si Wang Xiaoqian Liu Shuai Ma Shuhui Sun Lina Fu Qun Chu juan Carlos Izpisua belmonte Zhaoxia Wang jing Qu Yun Yuan Guang-Hui Liu Advanced Innovation Center for Human Brain Protection National Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China Beijing Institute for Brain Disorders Capital Medical UniversityBeijing 100069China Department of Neurology Peking University First HospitalBeijing 100034China National Laboratory of Biomacromolecules CAS Center for Excellenee in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Gene Expression Laboratory Salk Institute for Biological Studies10010 North Torrey Pines RoadLa JollaCA 92037USA Institute for Stem cell and Regeneration CASBeijing 100101China Key Laboratory of Regenerative Medicine of Ministry of Education Institute of Aging and Regenerative MedicineJinan UniversityGuangzhou 510632China

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy(CADASIL)is a rare hereditary cerebrovascular disease caused by a NOTCH3 ***,the underlying cellular and molecular mechanisms remain ***,we generated non-integrative induced pluripotent stem cells(iPSCs)from fibroblasts of a CADASIL patient harboring a heterozygous NOTCH3 mutation(c.3226C>T,p.R1076C).Vascular smooth muscle cells(VSMCs)differentiated from CADASIL-specific iPSCs showed gene expression changes associated with disease phenotypes,including activation of the NOTCH and NF-kB signaling pathway,cytoskeleton disorganization,and excessive cell *** comparison,these abnormalities were not observed in vascular endothelial cells(VECs)derived from the patients ***,the abnormal upregulation of NF-kB target genes in CADASIL VSMCs was diminished by a NOTCH pathway inhibitor,providing a potential therapeutic strategy for ***,using this iPSCbased disease model,our study identified clues for studying the pathogenic mechanisms of CADASIL and developing treatment strategies for this disease.

关键词： CADASIL iPSC NOTCH NF-kB vascular smooth muscle

A human circulating immune cell landscape in aging and COVID-19

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Protein & Cell 2020年第10期11卷 740-770页

作者： Yingfeng Zheng Xiuxing Liu Wenqing Le Lihui Xie He Li Wen Wen Si Wang Shuai Ma Zhaohao Huang jinguo Ye Wen Shi Yanxia Ye Zunpeng Liu Moshi Song Weiqi Zhang jing-Dong j.Han juan Carlos lzpisua belmonte Chuanle Xiao jing Qu Hongyang Wang Guang-Hui Liu Wenru Su State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat-sen UniversityGuangzhou 510060China State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeiing 100101China National Center for Liver Cancer Second Military Medical UniversityShanghai 200433China Department of Critical Care Wuhan Hankou HospitalWuhan 430012China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Institute for Stem Cell and Regeneration CASBejjing 100101China University of Chinese Academy of Sciences Beijing 100049China Advanced Innovation Center for Human Brain Protection National Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China China National Center for Bioinformation Beijing 100101China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China Gene Expression Laboratory Salk Institute for Biological StudiesLa JollaCAUSA

Age-associated changes in immune cells have been linked to an increased risk for ***,a global and detailed characterization of the changes that human circulating immune cells undergo with age is ***,we combined scRNA-seq,mass cytometry and sCATAC-seq to compare immune cell types in peripheral blood collected from young and old subjects and patients with *** found that the immune cell landscape was reprogrammed with age and was characterized by T cell polarization from naive and memory cells to effector,cytotoxic,exhausted and reg-ulatory cells,along with increased late natural killer cells,age-associated B cells,inflammatory monocytes and age-associated dendritic *** addition,the expression of genes,which were implicated in coron-avirus susceptibility,was upregulated in a cell subtype-specific manner with ***,COVID-19 promoted age-induced immune cell polarization and gene expression related to inflammation and cellular ***,these findings suggest that a dysreg-ulated immune system and increased gene expression associated with SARS-CoV-2 susceptibility may at least partially account for COVID-19 vulnerability in the elderly.

关键词： aging single-cell sequencing blood COVID-19 immune cells

Modeling xeroderma pigmentosum associated neurological pathologies with patients-derived iPSCs

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Protein & Cell 2016年第3期7卷 210-221页

作者： Lina Fu Xiuling Xu Ruotong Ren jun Wu Weiqi Zhang jiping Yang Xiaoqing Ren Si Wang Yang Zhao Liang Sun Yang Yu Zhaoxia Wang Ze Yang Yun Yuan jie Qiao juan Carlos Izpisua belmonte jing Qu Guang-Hui Liu National Laboratory of Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China FSU-CAS Innovation Institute Foshan University Foshan 528000 China State Key Laboratory of Stem Cell and Reproductive Biology Institute of Zoology Chinese Academy of Sciences Beijing 100101 China Gene Expression Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla CA 92037 USA Universidad Cato1ica San Antonio de Murcia (UCAIVI) Campus de los jer6nimos N° 135 Guadalupe 30107 Murcia Spain Beijing Hospital of the Ministry of Health Beijing 100730 China Department of Gynecology and Obstetrics Peking University Third Hospital Beijing 100191 China Department of Neurology Peking University First Hospital Beijing 100034 China Beijing Institute for Brain Disorders Capital Medical University Beijing 100069 China University of Chinese Academy of Sciences Beijing 100049 China

Xeroderma pigmentosum （XP） is a group of genetic disorders caused by mutations of XP-associated genes, resulting in impairment of DNA repair. XP patients frequently exhibit neurological degeneration, but the underlying mechanism is unknown, in part due to lack of proper disease models. Here, we generated patientspecific induced pluripotent stem cells （iPSCs） harboring mutations in five different XP genes including XPA, XPB, XPC, XPG, and XPV. These iPSCs were further differentiated to neural cells, and their susceptibility to DNA damage stress was investigated. Mutation of XPA in either neural stem cells （NSCs） or neurons resulted in severe DNA damage repair defects, and these neural cells with mutant XPA were hyper-sensitive to DNA damage-induced apoptosis. Thus, XP-mutant neural cells represent valuable tools to clari the molecular mechanisms of neurological abnormalities in the XP patients.

关键词： xeroderma pigmentosum iPSC disease model neural stem cell. neuron

Single-nucleus transcriptomic landscape of primate hippocampal aging

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Protein & Cell 2021年第9期12卷 695-716页

作者： Hui Zhang jiaming Li jie Ren Shuhui Sun Shuai Ma Weiqi Zhang Yang Yu Yusheng Cai Kaowen Yan Wei Li Baoyang Hu Piu Chan Guo-Guang Zhao juan Carlos Izpisua belmonte Qi Zhou jing Qu Si Wang Guang-Hui Liu State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Advanced Innovation Center for Human Brain Protection National Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China China National Center for Bioinformation Beijing 100101China Aging Translational Medicine Center Xuanwu HospitalCapital Medical UniversityBeijing 100053China Department of Neurosurgery Xuanwu HospitalCapital Medical UniversityBeijing 100053China Sino Danish CollegeUniversity of Chinese Academy of SciencesBeijing 101408China Sino Danish Center for Education and ResearchBeijing 101408China Department of Obstetrics and Gynecology Center for Reproductive MedicinePeking University Third HospitalBeijing 100191China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China Stem Cell Research Center Peking University Third HospitalBeijing 100191China Gene Expression Laboratory Salk Institute for Biological StudiesLa JollaCAUSA

The hippocampus plays a crucial role in learning and memory,and its progressive deterioration with age is functionally linked to a variety of human neurodegenerative *** a systematic profiling of the aging effects on various hippocampal cell types in primates is still ***,we reported a variety of new aging-associated phenotypic changes of the primate *** include,in particular,increased DNA damage and heterochromatin erosion with time,alongside loss of proteostasis and elevated *** understand their cellular and molecular causes,we established the first single-nucleus transcriptomic atlas of primate hippocampal *** the 12 identified cell types,neural transiently amplifying progenitor cell(TAPC)and microglia were most affected by ***-depth dissection of gene-expression dynamics revealed impaired TAPC division and compromised neuronal function along the neurogenesis trajectory;additionally elevated pro-inflammatory responses in the aged microglia and oligodendrocyte,as well as dysregulated coagulation pathways in the aged endothelial cells may contribute to a hostile microenvironment for *** rich resource for understanding primate hippocampal aging may provide potential diagnostic biomarkers and therapeutic interventions against age-related neurodegenerative diseases.

关键词： aging hippocampus primate single-cell RNA sequencing