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Multi-omics Analysis of Primary Cell Culture Models Reveals Genetic and Epigenetic Basis of Intratumoral Phenotypic Diversity

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Genomics, Proteomics & Bioinformatics 2019年第6期17卷 576-589页

作者： Sixue Liu Zuyu Yang Guanghao Li Chunyan Li Yanting Luo Qiang Gong Xin Wu Tao Li Zhiqian Zhang Baocai Xing Xiaolan Xu Xuemei Lu CAS Key Laboratory of Genomics and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Invasive Pathogens Laboratory Institute of Environmental Science and ResearchPorirua 5022WellingtonNew Zealand Department of Cell Biology Key Laboratory of Carcinogenesis and Translational ResearchCenter for Molecular and Translational MedicinePeking University Cancer Hospital and InstituteBeijing 100142China Department of Hepatobiliary Surgery I Peking University Cancer Hospital and InstituteBeijing 100142China National Key Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of SciencesBeijing 100101China CAS Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

Uncovering the functionally essential variations related to tumorigenesis and tumor progression from cancer genomics data is still challenging due to the genetic diversity among patients,and extensive inter-and intra-tumoral heterogeneity at different levels of gene expression regulation,including but not limited to the genomic, epigenomic, and transcriptional levels. To minimize the impact of germline genetic heterogeneities, in this study, we establish multiple primary cultures from the primary and recurrent tumors of a single patient with hepatocellular carcinoma(HCC). Multiomics sequencing was performed for these cultures that encompass the diversity of tumor cells from the same patient. Variations in the genome sequence, epigenetic modification, and gene expression are used to infer the phylogenetic relationships of these cell cultures. We find the discrepancy among the relationships revealed by single nucleotide variations(SNVs) and transcriptional/epigenomic profiles from the cell cultures. We fail to find overlap between sample-specific mutated genes and differentially expressed genes(DEGs), suggesting that most of the heterogeneous SNVs among tumor stages or lineages of the patient are functionally insignificant. Moreover, copy number alterations(CNAs) and DNA methylation variation within gene bodies, rather than promoters, are significantly correlated with gene expression variability among these cell cultures. Pathway analysis of CNA/DNA methylation-related genes indicates that a single cell clone from the recurrent tumor exhibits distinct cellular characteristics and tumorigenicity, and such an observation is further confirmed by cellular experiments both in vitro and in vivo. Our systematic analysis reveals that CNAs and epigenomic changes, rather than SNVs, are more likely to contribute to the Phenotypic diversity among subpopulations in the tumor. These findings suggest that new therapeutic strategies targeting gene dosage and epigenetic modification should be considered in personalized cancer medic

关键词： Intra-individual tumor heterogeneity Parallel primary culture Multi-omics Functional Phenotypic diversity

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The role of DNA methylation in the maintenance of Phenotypic variation induced by grafting chimerism in Brassica

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Horticulture Research 2023年第3期10卷 164-175页

作者： Ke Liu Tingjin Wang Duohong Xiao Bin Liu Yang Yang Kexin Xu Zhenyu Qi Yan Wang Junxing Li Xun Xiang Lu Yuan Liping Chen Department of Horticulture College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China Agricultural Experiment Station Zhejiang UniversityHangzhou 310058China

Grafting facilitates the interaction between heterologous cells with different genomes,resulting in abundant Phenotypic variation,which provides opportunities for crop improvement.However,how grafting-induced variation occurs and is transmitted to progeny remains elusive.A graft chimera,especially a periclinal chimera,which has genetically distinct cell layers throughout the plant,is an excellent model to probe the molecular mechanisms of grafting-induced variation maintenance.Here we regenerated a plant from the T-cell layer of a periclinal chimera,TCC(where the apical meristem was artificially divided into three cell layers–from outside to inside,L1,L2,and L3;T=Tuber mustard,C=red Cabbage),named rTTT0(r=regenerated).Compared with the control(rsTTT,s=self-grafted),rTTT0 had multiple Phenotypic variations,especially leaf shape variation,which could be maintained in sexual progeny.Transcriptomes were analyzed and 58 Phenotypic variation-associated genes were identified.Whole-genome bisulfite sequencing analyses revealed that the methylome of rTTT0 was changed,and the CG methylation level was significantly increased by 8.74%.In rTTT0,the coding gene bodies are hypermethylated in the CG context,while their promoter regions are hypomethylated in the non-CG context.DNA methylation changes in the leaf shape variation-associated coding genes,ARF10,IAA20,ROF1,and TPR2,were maintained for five generations of rTTT0.Interestingly,grafting chimerism also affected transcription of the microRNA gene(MIR),among which the DNA methylation levels of the promoters of three MIRs associated with leaf shape variation were changed in rTTT0,and the DNA methylation modification of MIR319 was maintained to the fifth generation of selfed progeny of rTTT0(rTTT5).These findings demonstrate that DNA methylation of coding and non-coding genes plays an important role in heterologous cell interaction-induced variation formation and its transgenerational inheritance.

关键词： Phenotypic maintained grafting

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Phenotypic plasticity of Artemisia ordosica seedlings in response to different levels of calcium carbonate in soil

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Journal of Arid Land 2019年第1期11卷 58-65页

作者： XUE Pingping ZHAO Xuelai GAO Yubao HE Xingdong College of Life Sciences Nankai University

Plant Phenotypic plasticity is a common feature that is crucial for explaining interspecific competition, dynamics and biological evolution of plant communities. In this study, we tested the effects of soil CaCO_3(calcium carbonate) on the Phenotypic plasticity of a psammophyte, Artemisia ordosica, an important plant species on sandy lands in arid and semi-arid areas of China, by performing pot experiments under different CaCO_3 contents with a two-factor randomized block design and two orthogonal designs. We analyzed the growth responses(including plant height, root length, shoot-leaf biomass and root biomass) of A. ordosica seedlings to different soil CaCO_3 contents. The results revealed that, with a greater soil CaCO_3 content, A. ordosica seedlings gradually grew more slowly, with their relative growth rates of plant height, root length, shoot-leaf biomass and root biomass all decreasing significantly. Root N/P ratios showed significant negative correlations with the relative growth rates of plant height, shoot-leaf biomass and root length of A. ordosica seedlings; however, the relative growth rate of root length increased significantly with the root P concentration increased, showing a positive correlation. These results demonstrate that soil CaCO_3 reduces the local P availability in soil, which produces a non-adaptive Phenotypic plasticity to A. ordosica seedlings. This study should prove useful for planning and promoting the restoration of damaged/degraded vegetation in arid and semi-arid areas of China.

关键词： Artemisia ordosica N/P ratio Phenotypic plasticity relative growth rate soil CaCO3 soil P availability arid and semi-arid areas

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Phenotypic diversity in Ethiopian durum wheat(Triticum turgidum var.durum)landraces

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The Crop Journal 2015年第3期3卷 190-199页

作者： Dejene K.Mengistu Afeworki Y.Kiros Mario E.Pè Department of Dryland Crop and Horticultural Sciences Mekelle University P.O.Box 231 Mekelle Ethiopia Scuola Superiore Sant'Anna (SSSUP) Pizza Martiri Liberà 33 – 56127 Pisa Italy

The Phenotypic diversity of 274 Ethiopian durum wheat accessions was analyzed, taking their geographic origins into account. The aim was to assess the extent and patterns of agronomically important Phenotypic variation across districts of origin and altitude classes for major qualitative traits using diversity index and multivariate methods. Eight qualitative and three quantitative traits were scored for 2740 plants and analyzed for diversity. The Shannon–Weaver diversity(H′) index was used to estimate Phenotypic diversity. The estimated H′ ranged from monomorphic for glume hairiness to highly polymorphic for other traits. The highest(0.86) H′ was obtained for seed degree of shriveling, possibly indicating the differential responses of the genotypes to water deficit during later growth stages. With respect to district of origin, the highest(0.72) and lowest(0.44) H′ values were obtained for the Bale and SNNP districts, respectively. With respect to altitude, the highest(0.76) and lowest(0.62) H′ values were recorded for altitudes 1600–2000and > 3000 m above sea levels, respectively. Principal components analysis explained substantial variation contributed by district of origin and altitude range. Genotypes were clustered into three groups by districts of origin and altitude class, with relatively strong bootstrap values of 57 and 62 for the former and latter, respectively. It could be concluded that Ethiopian durum wheat landraces are very diverse both within and among districts of origin and altitude classes. This wealth of genetic diversity should be exploited for wheat improvement of yield and for resistance to biotic and abiotic stresses, particularly terminal drought.

关键词： Phenotypic diversity Diversity index Landraces Districts of origin Altitude Ethiopia

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Phylogenetic relationship and Phenotypic comparison of Psychrobacter species isolated from polar oceans

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Progress in Natural Science:Materials International 2007年第1期17卷 44-48页

作者： ZENG Yinxin, LI Huirong, YU Yong and CHEN Bo (Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai 200136, China) Key Laboratory for Polar Science of State Oceanic Administration Polar Research Institute of China Shanghai 200136 China

To investigate the phylogenetic relationship and biogeography of bacterioplankton in polar oceans, four Psychrobacter strains, BSw10170, BSw20352, BSw20370, and BSw20461, isolated from seawater of the Beijing Sea, the Chukchi Sea, and the Prydz Bay, were characterized by 16S rDNA sequencing and physiological and biochemical testing. Results demonstrated that close relationships existed between the Arctic and Antarctic strains with sequence similarities higher than 97 %. These four Psychrobacter strains not only showed almost identical Phenotypic characteristics among them, but also shared a lot of similarities with those related Psychrobacter species, indicating that psychrotolerance and halotolerance of Psychrobacter strains may be among the reasons for their bipolar, even global distribution in marine environments at the genus level.

关键词： Psychrobacter phylogenetic Phenotypic Arctic Antarctic.

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Phenotypic and Genotypic Antibiotic Resistant Diarrheagenic Escherichia coli Isolated from Patients with Diarrhea in Ouagadougou, Burkina Faso

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Advances in Microbiology 2023年第7期13卷 347-359页

作者： Haoua Cissé Assèta Kagambèga Soutongnooma Caroline Bouda Abdallah Sawadogo Nicolas Barro Laboratoire de Biologie Molé culaire d’Epid&eacutemiologie et de Surveillance des agents Transmissibles par les Aliments (LaBESTA) Universit&eacute Joseph KI-Zerbo Ouagadougou Burkina Faso Ecole Normale Supé rieure (ENS) Ouagadougou Burkina Faso

Background: The emergence and spread of multidrug-resistant bacteria have become a major public health problem worldwide, particularly in developing countries such as Burkina Faso. This study aims to determine Phenotypic and genotypic antibiotic resistant diarrheagenic Escherichia coli (DEC) from patients with diarrhea in Ouagadougou, Burkina Faso. Methodology: Microbiological and biochemical analysis were done to detect two hundred and ninety-two (292) strains. The susceptibility of the strains to antibiotics was determined by the agar disc diffusion method. 16-plex-PCR assays were carried out to detect both virulence and resistance genes encoding betalactams, quinolones, phenicols, tetracyclines and virulence gene of DEC. Results: Diarrheagenic Escherichia coli was detected in 8% (23/292) of patients with diarrhea using the 16-plex-PCR and 39.1% (9/23) of the DEC detected carry at least one resistance gene. Resistance rate in disc diffusion test was 86.96% to tetracycline, 65.23% to cotrimoxazole, 17.4% to nalidixic acid, 17.4% to norfloxacin, 17.4% to ciprofloxacin, 13.04% to ceftriaxone, 13.04% to cefotaxime, 8.7% to gentamicin, 8.7% to Chloramphenicol, 0% to netilmicin. The prevalence of different resistance genes in the studied strains varied from 44.4% to 5.5%. The gene Tet coding for resistance to tetracycline was found in 8 strains (44.4%). The CatA gene coding for resistance to Chloramphenicol was detected in 38.9% of isolates. The qnrS, blaSHV and blaOXA genes were each detected in 5.5% of isolates. No strain hosts the qnrA, qnrB and blaTEM genes. Conclusion: This study identified β-lactams, quinolones, phenicols and tetracyclines resistance genes in DEC isolates from patients with diarrhea in Ouagadougou, Burkina Faso. These results indicate the need for a surveillance program to reduce the prevalence of resistance to Enterobacteriaceae strains in hospitals.

关键词： Diarrheagenic Escherichia coli Phenotypic Genotypic Resistance Ouagadougou

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Phenotypic and Genotypic Characterization of Extended Spectrum Beta-Lactamases Producing Bacteria Causing Urinary Tract Infections among Expectant Women Attending Antenatal Clinic at Ruiru Sub County Hospital, Kenya

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Advances in Microbiology 2023年第12期13卷 571-587页

作者： Eunice Maingi Andrew Nyerere Celestine Makobe Department of Medical Microbiology College of Health Science Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya

Background: Urinary tract infection (UTI) is a bacterial infection affecting males and females but is more prevalent in expectant women. ESBLs are bacteria with enzymes that make them resistant to many antibiotics, posing a significant health challenge. This study aims to determine the characteristics of ESBL-producing bacteria causing UTIs in expectant women. Methodology: A self-administered survey was carried out;300 expectant women were recruited using a random sampling method. A questionnaire was used to collect socio-demographic information. Urine samples were collected in sterile universal bottles and processed at the JKUAT Zoology laboratory. Urine samples were analyzed using urinalysis, microscopy, culture, and sensitivity testing. ESBL-producing bacteria were identified Phenotypically using the double-disc synergy test (DDST) and genotyped for specific resistant genes using PCR. Results: UTI prevalence was 32.7% (98/300). UTI was significantly associated with the history of previous UTI (OR = 0.84, p = 0.02) and multigravida (OR = 0.14 p = 0.01). UTI was common in women aged between 28-37 years in their second trimester. Bacteria isolated were E. coli 57.1% (56/98), S. aureus 21.4% (21/98) K. pneumonia 11.2% (11/98) and Proteus spp 10.4% (10/98). Bacteria antibiotic resistance patterns were E. coli-tetracycline (91.1%), sulfamethoxazole (55.4%), cefotaxime (53.4%) and augmentin (53.4%). S. aureus-sulfamethozaxole (100%) and augmentin (71.4%), K. pneumoniae-sulfame-thoxazole (72.2%) cefotaxime (63.6%), chloramphenicol and tetracycline (54.5%). Proteus spp: tetracycline (100%), nitrofurantoin (90%), cefotaxime and chloramphenicol (50%). The proportion of ESBLs bacterial producers was 37.6% (29/77) and 44.8% (13/29) possessed ESBLs resistant genes;Bla CTX-M 53.8% (7/13), Bla SHV and Bla TEM 23.1% (3/13) each, Bla OXA (0%) was not detected. Conclusion: The study revealed a high proportion of ESBLs producing bacteria responsible for UTI in expectant women. ESBLs screening, routine culture and sensitivity test

关键词： Urinary Tract Infections Resistant Genes Genotypic Phenotypic Extended Spectrum Beta Lactamases

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Phenotypic analysis of the medullary-type CD4^-CD8^+ thymocytes in mice

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Chinese Science Bulletin 2000年第3期45卷 232-237页

作者： TIAN Tian WANG Hongfang FENG Meifu CHEN Weifeng Department of Immunology Beijing Medical UniversityBeijing 100083China Institute of Zoology Chinese Academy of SciencesBeijing 100080China

Phenotypic analysis of the medullary-type CD4 CD8+ (CD8SP) thymocytes has revealed Phenotypic heterogeneity within this cell population. The phenotype of mature peripheral CD8+T cells is TCRαβ+CD3+Qa-2+HSA3G11 6C10 , whereas in the medullary-type CD8SP thymocytes, 20% are Qa-2+; 33%, HAS ; 30%, 3G11 ; and 70% are 6C10 . The disparate expression patterns of these four cell surface markers suggest that medullary-type CD8SP thymocytes may undergo Phenotypic maturation process. According to the distribution of these four celi surface markers, six subgroups of CD8SP thymocytes have been identified. The precursor-progeny relationship along with developmental pathway is postulated as follows: 6C10+HSA+3G11 Qa-2 - 6C10+HSA+ 3G11+Qa-2 6C10 HSA+3G11+Qa-2 -6C10 HSA 3G11 +Qa-2 -6C10 HSA 3G11 Qa-2 -6C10 HA S 3G11 Qa-2+, the cells inthe last subgroup exit the thymus and home into periphery.

关键词： CD^4 CD8^+ medullary-type thymocytes cell phenotype Phenotypic differentiation.

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Reply to “Phenotypic and Genotypic Peculiarities in Chinese Patients with Leigh Syndrome”

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Chinese Medical Journal 2019年第5期132卷 628-629页

作者： Xiao-Lin Yu Yu-Ying Zhao Department of Geriatrics Medicine Qilu Hospital Shandong University Jinan Shandong 250012 China Department of Neurology Research Institute of Neuromuscular and Neurodegenerative Diseases Qilu Hospital Shandong UniversityJinan Shandong 250012 China

To the Editor: We really appreciate the readers5 interest and comments about our article, and to have the opportunity to make an explanation[1].

关键词： Phenotypic Genotypic Peculiarities Chinese Patients with Leigh Syndrome

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Comparison of Phenotypic markers and neural differentiation potential of multipotent adult progenitor cells and mesenchymal stem cells

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World Journal of Stem Cells 2013年第2期5卷 53-60页

作者： Saurabh Pratap Singh Naresh Kumar Tripathy Soniya Nityanand Stem Cell Research Facility Department of Hematology Sanjay Gandhi Post-Graduate Institute of Medical SciencesLucknow 226014 India

AIM: To compare the Phenotypic and neural differentiation potential of human bone marrow derived multipotent adult progenitor cells (MAPC) and mesenchymal stem cells (MSC). METHODS: Cultures of MAPC and MSC were established in parallel from same samples of human bone marrow (n = 5). Both stem cell types were evaluated for expression of pluripotency markers including Oct-4 and Nanog by immunocytochemistry and reversetranscription polymerase chain reaction (RT-PCR) and expression of standard mesenchymal markers including CD14, CD34, CD44, CD45, CD73, CD90, CD105 andhuman leukocyte antigen (HLA)-ABC by flow cytometry. After treatment with neural induction medium both MAPC and MSC were evaluated for expression of neural proteins [neuronal filament-200 (NF-200) and glial fibrillar acidic protein (GFAP)] by immunocytochemistry and Western blotting and neural genes [NF-200, GFAP, Tau, microtubule-associated protein (MAP)-1B, MAP-2, neuron-specific enolase (NSE) and oligodendrocyte-1 (Olig-1)] by quantitative real-time-PCR. RESULTS: MAPC had small trigonal shaped while MSC had elongated spindle-shaped morphology. The MAPC expressed Oct-4 and Nanog both at gene and protein levels, whereas MSC were negative for these pluripotent markers. MAPC were negative for HLA-ABC while MSC had high expression of HLA-ABC. In addition, MAPC as compared to MSC had significantly lower expression of CD44 (36.56% ± 1.92% vs 98.23% ± 0.51%), CD73 (15.11% ± 2.24% vs 98.53% ± 2.22%) and CD105 (13.81% ± 3.82%vs 95.12% ± 5.65%) (P < 0.001, for all) MAPC cultures compared to MSC cultures treated with neural induction medium had significantly higher fold change expression of NF-200 (0.64), GFAP (0.52), Tau (0.59), MAP-2 (0.72), Olig-1 (0.18) and NSE (0.29) proteins (P < 0.01 for Olig-1 and P < 0.001 for rest) as well as higher fold change expression of genes of NF-200 (1.34),GFAP (1.12),Tau (1.08),MAP-1B (0.92), MAP-2 (1.14) andNSE (0.4) (P < 0.001 for all). CONCLUSION: MAPC can be differentially characterized from MSC as Oct-4 and Nanog positive

关键词： Bone marrow Human multipotent adult progenitor cells Human mesenchymal Stem cells Phenotypic markers Neural differentiation

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