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Ward, Todd J., Lisa Gorski, Monica K. Borucki, Robert E. Mandrell, Jan Hutchins et Kitty Pupedis. « Intraspecific Phylogeny and Lineage Group Identification Based on the prfA Virulence Gene Cluster of Listeria monocytogenes† ». Journal of Bacteriology 186, no 15 (1 août 2004) : 4994–5002. http://dx.doi.org/10.1128/jb.186.15.4994-5002.2004.
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ABSTRACT Listeria monocytogenes is a serious food-borne pathogen that can cause invasive disease in humans and other animals and has been the leading cause of food recalls due to microbiological concerns in recent years. In order to test hypotheses regarding L. monocytogenes lineage composition, evolution, ecology, and taxonomy, a robust intraspecific phylogeny was developed based on prfA virulence gene cluster sequences from 113 L. monocytogenes isolates. The results of the multigene phylogenetic analyses confirm that L. monocytogenes comprises at least three evolutionary lineages, demonstrate that lineages most frequently (lineage 1) and least frequently (lineage 3) associated with human listeriosis are sister-groups, and reveal for the first time that the human epidemic associated serotype 4b is prevalent among strains from lineage 1 and lineage 3. In addition, a PCR-based test for lineage identification was developed and used in a survey of food products demonstrating that the low frequency of association between lineage 3 isolates and human listeriosis cases likely reflects rarity of exposure and not reduced virulence for humans as has been previously suggested. However, prevalence data do suggest lineage 3 isolates may be better adapted to the animal production environment than the food-processing environment. Finally, analyses of haplotype diversity indicate that lineage 1 has experienced a purge of genetic variation that was not observed in the other lineages, suggesting that the three L. monocytogenes lineages may represent distinct species within the framework of the cohesion species concept.
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Drissen, Roy, Supat Thongjuea, Kim Theilgaard-Mönch et Claus Nerlov. « Identification of two distinct pathways of human myelopoiesis ». Science Immunology 4, no 35 (24 mai 2019) : eaau7148. http://dx.doi.org/10.1126/sciimmunol.aau7148.
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Human myelopoiesis has been proposed to occur through oligopotent common myeloid progenitor (CMP) and lymphoid-primed multipotent progenitor (LMPP) populations. However, other studies have proposed direct commitment of multipotent cells to unilineage fates, without specific intermediary lineage cosegregation patterns. We here show that distinct human myeloid progenitor populations generate the neutrophil/monocyte and mast cell/basophil/eosinophil lineages as previously shown in mouse. Moreover, we find that neutrophil/monocyte potential selectively cosegregates with lymphoid lineage and mast cell/basophil/eosinophil potentials with megakaryocyte/erythroid potential early during lineage commitment. Furthermore, after this initial commitment step, mast cell/basophil/eosinophil and megakaryocyte/erythroid potentials colocalize at the single-cell level in restricted oligopotent progenitors. These results show that human myeloid lineages are generated through two distinct cellular pathways defined by complementary oligopotent cell populations.
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He, Zhisong, Ashley Maynard, Akanksha Jain, Tobias Gerber, Rebecca Petri, Hsiu-Chuan Lin, Malgorzata Santel et al. « Lineage recording in human cerebral organoids ». Nature Methods 19, no 1 (30 décembre 2021) : 90–99. http://dx.doi.org/10.1038/s41592-021-01344-8.
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AbstractInduced pluripotent stem cell (iPSC)-derived organoids provide models to study human organ development. Single-cell transcriptomics enable highly resolved descriptions of cell states within these systems; however, approaches are needed to directly measure lineage relationships. Here we establish iTracer, a lineage recorder that combines reporter barcodes with inducible CRISPR–Cas9 scarring and is compatible with single-cell and spatial transcriptomics. We apply iTracer to explore clonality and lineage dynamics during cerebral organoid development and identify a time window of fate restriction as well as variation in neurogenic dynamics between progenitor neuron families. We also establish long-term four-dimensional light-sheet microscopy for spatial lineage recording in cerebral organoids and confirm regional clonality in the developing neuroepithelium. We incorporate gene perturbation (iTracer-perturb) and assess the effect of mosaic TSC2 mutations on cerebral organoid development. Our data shed light on how lineages and fates are established during cerebral organoid formation. More broadly, our techniques can be adapted in any iPSC-derived culture system to dissect lineage alterations during normal or perturbed development.
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House, L. Caroline, Amer Hasan, Andi Asnayanti, Adnan A. K. Alrubaye, Jeff Pummill et Douglas Rhoads. « Phylogenomic Analyses of Three Distinct Lineages Uniting Staphylococcus cohnii and Staphylococcus urealyticus from Diverse Hosts ». Microorganisms 12, no 8 (29 juillet 2024) : 1549. http://dx.doi.org/10.3390/microorganisms12081549.
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We sequenced and assembled genomes for 17 isolates of Staphylococcus cohnii isolated from osteomyelitis lesions in young broilers from two separate experiments where we induced lameness using a hybrid wire-litter flooring system. Whole genome comparisons using three different methods support a close relationship of genomes from both S. cohnii and Staphylococcus urealyticus. The data support three different lineages, which we designated as Lineage 1, Lineage 2, and Lineage 3, uniting these two species within an evolving complex. We present evidence for horizontal transfer between lineages of genomic regions from 50–440 kbp. The transfer of a 186 kbp region from Lineage 1 to Lineage 2 appears to have generated Lineage 3. Human-associated isolates appear to be limited to Lineages 2 and 3 but Lineage 2 appears to contain a higher number of human pathogenic isolates. The chicken isolates from our lameness trials included genomically diverse isolates from both Lineage 1 and 2, and isolates from both lineages were obtained from osteomyelitis lesions of individual birds. Our results expand the diversity of Staphylococci associated with osteomyelitis in poultry and suggest a high diversity in the microbiome of day-old chicks. Our data also support a reevaluation and unification of the taxonomic classifications of S. cohnii and S. urealyticus.
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Yoshizato, Tetsuichi, Christer Nilsson, Francesca Grasso, Kari Högstrand, Stefania Mazzi, Axel Winroth, Madeleine Lehander et al. « Stable Contribution of Lineage-Restricted Stem Cells to Steady-State Aged Human Hematopoiesis ». Blood 144, Supplement 1 (5 novembre 2024) : 27. https://doi.org/10.1182/blood-2024-204105.
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Background Multipotent self-renewing hematopoietic stem cells (HSCs) possess the potential to replenish all mature blood cell lineages, playing a critical role in safeguarding life-long replenishment of millions of short-lived blood cells every second during steady-state hematopoiesis and in response to hematopoietic challenges. Our knowledge of the functional properties and roles of mammalian HSCs is largely based on studies in mice. Studies of steady-state replenishment of blood cell lineages by individual human HSC clones have been hampered by the large number of active HSCs in adult hematopoiesis. Moreover, while the dynamic contribution of HSC clones to different lineages can only be assessed by tracing the same individual HSC clones over time, steady-state contribution from individual HSCs has only been investigated at a single time point, both in mice and in humans. Results We assessed blood lineage contribution for 51 driver and 10 non-driver mutations in clonal hematopoiesis related genes, derived from 33 healthy aged volunteers (age 70-84) with normal blood parameters, with ≥2% and ≥1% mutant cell fractions (MCFs), respectively. Of these 61 clonal mutations, 3 showed involvement exclusively in the T cell lineage, and not in any other blood cell lineages or HSCs, which is consistent with reflecting long-lived T cells. Of the remaining 58 mutations, all but one could be traced back to HSCs. These 57 HSC clones were evaluated for multilineage contribution, including platelets (P), erythrocytes (E), myeloid cells (M), and B (B) and T (T) lymphocytes. In addition to the 22 HSCs replenishing all five lineages, we identified HSCs replenishing all lineages except T lymphocytes (n=30), and all three myeloid lineages (PEM) but no lymphoid cells (n=5). No further lineage restriction patterns were reproducibly observed. In addition to the HSCs displaying PEM- and PEMB-restricted lineage replenishment patterns, other HSC clones showed distinct PEM (and PEMB) lineage bias (contributions to all PEM lineages >5 times higher than both B and T lymphocytes). Collectively, PEMB-restricted/biased (n=26) or PEM-restricted/biased (n=12) HSC replenishment was more frequent than balanced PEMBT lineage replenishment (n=15). Clonal assessment in pro-B cells in the bone marrow revealed that the steady-state B cell contribution from individual HSC clones reflects ongoing B lymphopoiesis. The PEMBT pattern was almost exclusively observed in HSC clones with DNMT3A mutations. In contrast, PEMB- and PEM-restricted/biased HSC clones showed no significant bias for mutations in specific genes and included HSC clones marked by non-driver mutations, supporting that PEMB- and PEM-restriction/biases occur independently of the mutations. Analysis of 22 HSC clones through serially collected bone marrow samples from 11 healthy individuals up to 41 months after the first analysis revealed that the observed patterns of lineage replenishment were remarkably stable over time, whether representing balanced PEMBT, PEMB-restricted/biased, or PEM-restricted/biased HSCs. This stability was also observed upon transplantation into immune-deficient mice, suggesting that these patterns are HSC intrinsically programmed. Phylogenetic analysis using single colony whole-genome sequencing of hematopoietic stem/progenitor cells combined with lineage contribution patterns of the identified clades in 7 donors revealed novel insights into the hierarchical relationships of HSC clones with different lineage patterns, in that PEMBT HSC clones gave rise to PEMB clones which could give rise to PEM HSC clones, but not vice versa, establishing a unidirectional hierarchical relationship between increasingly lineage-restricted/biased HSC clones. Conclusions Utilizing somatically acquired mutations as natural barcodes, we revealed the existence of distinct human HSC clones with stable multilineage as well as myeloid-restricted and -biased contributions to steady-state human hematopoiesis. Whether replenishing hematopoiesis in a balanced multilineage or lineage-restricted manner, individual HSCs invariably showed a remarkably stable lineage contribution pattern and clonal size over years of observation. Phylogenetic analysis demonstrated that aging leads to myeloid-biased and even myeloid-restricted production from HSCs that originally replenished hematopoiesis in a fully multipotent manner.
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Baryshnikova, D. V., A. V. Mordyk et L. V. Puzyreva. « Human cytopenia variants at diverse HIV infection stages ». Russian Journal of Infection and Immunity 12, no 1 (22 novembre 2021) : 179–84. http://dx.doi.org/10.15789/2220-7619-hcv-1652.
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Over decades, HIV infection and its complications have been one of the most debated problems in the world. The human immunodeficiency virus not only weaken the immune system, but also disrupts normal hematopoiesis manifested as cytopenia (anemia, thrombocytopenia and neutropenia). Materials and methods. A retrospective analysis of cases of combined HIV infection and inhibited hematopoiesis was carried out according to hemogram data of patients admitted for treatment at the Infectious Clinical Hospital No. 1 named after D. Dalmatov, Omsk. The inclusion criteria were cytopenia during hospitalization detected in detailed blood test (by calculating hemoglobin level, counts of erythrocytes, leukocytes, platelets). The age of the patients included in the study differed: from 20 to 29 years — 27 patients (24.6%), from 30 to 39 years — 69 patients (62.7%), from 40 to 49 years — 13 patients (11.8%), over 50 years old 1 patient (0.9%). All patients had suppression of at least one hematopoietic cell lineage. Anemia was considered as decreased hemoglobin level below than 130 g/l in men and 120 g/l in women. Erythrocytopenia was considered as decreased erythrocyte count below 4.76 × 1012/L. Leukopenia was defined as decreased total count of leukocytes below 4.0 × 109/L, while a decrease in the absolute count of neutrophils below 1000 cells/μL was considered as neutropenia. Thrombocytopenia was determined as decreased platelet count below 150 × 109/L. Results. All patients had suppression of at least one hematopoietic cell lineage. 6 patients with stage 2 had one-cell lineage cytopenias, 7 — two-cell lineages. While analyzing the data obtained, it can be concluded that in patients with stage 2 HIV, inhibition of erythroid and platelet cell lineage predominates, whereas thrombocytopenia reached grade IV. At stage 3 HIV, all 7 patients had inhibition of only one cell lineage. In this group, the inhibition of hematopoiesis had a lighter degree in all hematopoietic cell lineages. In 46 patients with stage 4, there were various oppression of one of the hematopoietic cell lineages, in 44 patients there were two-cell lineage cytopenias. For patients with a more advanced stage of HIV, a decrease in the number of all cellular elements of the blood in the hemogram is characteristic; these disorders are more severe and persistent.
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DOWD, SCOT E., et JASON B. WILLIAMS. « Comparison of Shiga-Like Toxin II Expression between Two Genetically Diverse Lineages of Escherichia coli O157:H7 ». Journal of Food Protection 71, no 8 (1 août 2008) : 1673–78. http://dx.doi.org/10.4315/0362-028x-71.8.1673.
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The existence of two separate lineages of Escherichia coli O157:H7 has previously been reported, and research indicates that one of these lineages (lineage I) might be more pathogenic toward human hosts. We postulated that the lineage more pathogenic expresses higher levels of Shiga toxin 2 (Stx2) than do the nonpathogenic lineage II. A comprehensive set of methodologies were used to investigate the difference in Stx2 protein and mRNA expression between the two lineages. An initial Stx2-specific enzyme-linked immunosorbent assay was conducted, and lineage I overall demonstrated significantly more toxin proteins expressed (P < 0.01). Gene expression analyses all showed significantly higher stx2 gene expression in lineage I (P = 0.02). PCR mapping revealed a possible explanation for decreased amounts of stx2 transcripts in the potentially nonpathogenic lineage II isolates, suggesting that genomic changes have modified the toxin-encoding region of the phage. This study provides additional data to support the existence of two diverse lineages of E. coli O157:H7, one of which may have lower pathogenic potential in relation to human hosts. The PCR described also provides a possible screening tool for E. coli O157 populations to differentiate these lineages. This study provides useful information on the ecology of E. coli O157, with broad implications within the clinical, scientific, and livestock industries.
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Roberts, Angela, Kendra Nightingale, Greg Jeffers, Esther Fortes, Jose Marcelino Kongo et Martin Wiedmann. « Genetic and phenotypic characterization of Listeria monocytogenes lineage III ». Microbiology 152, no 3 (1 mars 2006) : 685–93. http://dx.doi.org/10.1099/mic.0.28503-0.
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Listeria monocytogenes has been previously grouped into three evolutionary groups, termed lineages I, II and III. While lineages I and II are commonly isolated from various sources, lineage III isolates are rare and have several atypical and unique phenotypic characteristics. Relative to their prevalence in other sources, lineage III strains are overrepresented among isolates from food-production animals, and underrepresented among isolates from human clinical cases and foods. This work describes an extensive genotypic and phenotypic characterization of 46 lineage III isolates. Phylogenetic analyses of partial sigB and actA sequences showed that lineage III represents three distinct subgroups, which were termed IIIA, IIIB and IIIC. Each of these lineage III subgroups is characterized by differentiating genotypic and phenotypic characteristics. Unlike typical L. monocytogenes, all subgroup IIIB and IIIC isolates lack the ability to ferment rhamnose. While all IIIC and most IIIB isolates carry the putative virulence gene lmaA, the majority of subgroup IIIA isolates lack this gene. All three lineage III subgroups contain isolates from human clinical cases as well as isolates that are cytopathogenic in a cell culture plaque assay, indicating that lineage III isolates have the potential to cause human disease. The identification of specific genotypic and phenotypic characteristics among the three lineage III subgroups suggests that these subgroups may occupy different ecological niches and, therefore, may be transmitted by different pathways.
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Liu, Liyun, Liyun Qin, Shuai Hao, Ruiting Lan, Baohong Xu, Yumei Guo, Ruiping Jiang et al. « Lineage, Antimicrobial Resistance and Virulence of Citrobacter spp ». Pathogens 9, no 3 (6 mars 2020) : 195. http://dx.doi.org/10.3390/pathogens9030195.
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Citrobacter spp. are opportunistic human pathogens which can cause nosocomial infections, sporadic infections and outbreaks. In order to determine the genetic diversity, in vitro virulence properties and antimicrobial resistance profiles of Citrobacter spp., 128 Citrobacter isolates obtained from human diarrheal patients, foods and environment were assessed by multilocus sequence typing (MLST), antimicrobial susceptibility testing and adhesion and cytotoxicity testing to HEp-2 cells. The 128 Citrobacter isolates were typed into 123 sequence types (STs) of which 101 were novel STs, and these STs were divided into five lineages. Lineages I and II contained C. freundii isolates; Lineage III contained all C. braakii isolates, while Lineage IV and V contained C. youngae isolates. Lineages II and V contained more adhesive and cytotoxic isolates than Lineages I, III, and IV. Fifty-one of the 128 isolates were found to be multidrug-resistant (MDR, ≥3) and mainly distributed in Lineages I, II, and III. The prevalence of quinolone resistance varied with Lineage III (C. braakii) having the highest proportion of resistant isolates (52.6%), followed by Lineage I (C. freundii) with 23.7%. Seven qnrB variants, including two new alleles (qnrB93 and qnrB94) were found with Lineage I being the main reservoir. In summary, highly cytotoxic MDR isolates from diarrheal patients may increase the risk of severe disease.
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Burgess, Darren J. « Human cell-lineage imbalances ». Nature Reviews Genetics 22, no 5 (30 mars 2021) : 266–67. http://dx.doi.org/10.1038/s41576-021-00358-4.
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Payne, Kimberly J., et Gay M. Crooks. « Human hematopoietic lineage commitment ». Immunological Reviews 187, no 1 (septembre 2002) : 48–64. http://dx.doi.org/10.1034/j.1600-065x.2002.18705.x.
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Cheng, Keren, Taku Moriwaki, Yasunari Seita et Kotaro Sasaki. « OR04-1 The Developmental Origin and the Specification of the Adrenal Cortex in Humans and Cynomolgus Monkeys ». Journal of the Endocrine Society 6, Supplement_1 (1 novembre 2022) : A79—A80. http://dx.doi.org/10.1210/jendso/bvac150.165.
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Abstract The adrenal cortex and gonads are the two major endocrine hubs that participate in the hormonal regulation of vital aspects of mammalian homeostasis. Accordingly, their developmental aberrancies drive various congenital and adult-onset diseases. Lineage tracing studies in mice reveal that the adrenal cortex and gonads originate from a common progenitor, the adrenogonadal primordium. However, the specification pathways of the adrenal cortex and gonads and their lineage relationship remain poorly understood in humans. Here, we conduct the high resolution spatial and temporal lineage trajectory mapping of early human adrenal and gonadal lineages using single cell transcriptomics and histologic profiling on human embryos at 3-8 week post fertilization. We find that in humans, the adrenocortical lineage originates in a temporally and spatially distinct fashion from the gonadal lineage, arising earlier and more anteriorly within the coelomic epithelium. The adrenal primordium arises from adrenogenic coelomic epithelium via an epithelial-to-mesenchymal-like transition, which then progresses into the steroidogenic fetal zone via both direct and indirect routes. Notably, we find that adrenocortical and gonadal lineages exhibit distinct HOX codes, suggesting distinct anterior-posterior regionalization. Together, our assessment of the early divergence of these lineages challenges the paradigm established in rodents and present evidence that the specification programs directing the formation of adrenal glands and gonads differ between rodents and humans. The molecular details of early lineage diversification of human adrenals and gonads will serve as both a framework for understanding the molecular pathology of human disorders. Presentation: Saturday, June 11, 2022 11:30 a.m. - 11:45 a.m.
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Martins, Luís Felipe Leite, Miguel Ângelo Martins Moreira, Rodrigo Alves Pinto, Neilane Bertoni dos Reis, Shayany Pinto Felix, João Paulo Castello Branco Vidal, Leuridan Cavalcante Torres, Ariani Impieri Souza et Liz Maria de Almeida. « Human Papillomavirus 16 Lineage D is Associated with High Risk of Cervical Cancer in the Brazilian Northeast Region ». Revista Brasileira de Ginecologia e Obstetrícia / RBGO Gynecology and Obstetrics 45, no 08 (août 2023) : e474-e479. http://dx.doi.org/10.1055/s-0043-1772180.
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Abstract Objective Similar to Human Papillomavirus (HPV) genotypes, different lineages of a genotype also have different carcinogenic capabilities. Studies have shown that specific genotype lineages of oncogenic HPV are associated with variable risks for the development of cervical intraepithelial neoplasia (CIN2/CIN3) and cervical cancer. The present study aimed to analyze the genetic diversity of the HPV16 genotype in women with CIN2/CIN3 and cervical cancer, from the northeast region of Brazil. Methods A cross-sectional multicenter study was conducted in the northeast region of Brazil, from 2014 to 2016. This study included 196 cases of HPV16 variants (59 and 137 cases of CIN2/CIN3 and cervical cancer, respectively). The difference of proportion test was used to compare patients with CIN2/CIN3 and cervical cancer, based on the prevalent HPV16 lineage (p < 0.05). Results According to the histopathological diagnosis, the percentage of lineage frequencies revealed a marginal difference in the prevalence of lineage A in CIN2/CIN3, compared with that in cervical cancer (p = 0.053). For lineage D, the proportion was higher in cancer cases (32.8%), than in CIN2/CIN3 cases (16.9%), with p = 0.023. Conclusion HPV16 lineage A was the most frequent lineage in both CIN2/CIN3 and cervical cancer samples, while lineage D was predominant in cervical cancer, suggesting a possible association between HPV16 lineage D and cervical cancer.
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Wright, Nicholas A. « Aspects of the biology of regeneration and repair in the human gastrointestinal tract ». Philosophical Transactions of the Royal Society of London. Series B : Biological Sciences 353, no 1370 (29 juin 1998) : 925–33. http://dx.doi.org/10.1098/rstb.1998.0257.
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The main pathways of epithelial differentiation in the intestine, Paneth, mucous, endocrine and columnar cell lineages are well recognized. However, in abnormal circumstances, for example in mucosal ulceration, a cell lineage with features distinct from these emerges, which has often been dismissed in the past as ‘pyloric’ metaplasia, because of its morphological resemblance to the pyloric mucosa in the stomach. However, we can conclude that this cell lineage has a defined phenotype unique in gastrointestinal epithelia, has a histogenesis that resembles that of Brunner's glands, but acquires a proliferative organization similar to that of the gastric gland. It expresses several peptides of particular interest, including epidermal growth factor, the trefoil peptides TFF1, TFF2, TFF3, lysozyme and PSTI. The presence of this lineage also appears to cause altered gene expression in adjacent indigenous cell lineages. We propose that this cell lineage is induced in gastrointestinal stem cells as a result of chronic mucosal ulceration, and plays an important part in ulcer healing; it should therefore be added to the repertoire of gastrointestinal stem cells.
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Doulatov, Sergei, Faiyaz Notta et John E. Dick. « Clonal Analysis of the Human Hematopoietic Hierarchy Reveals An Early Lymphoid Progenitor with Extensive Monocytic Potential. » Blood 114, no 22 (20 novembre 2009) : 1503. http://dx.doi.org/10.1182/blood.v114.22.1503.1503.
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Abstract Abstract 1503 Poster Board I-526 The classical model of hematopoiesis posits the segregation of lymphoid and myeloid lineages as the earliest fate decision. Although the validity of this model in the mouse has recently been questioned, its status in human hematopoiesis is unclear, since little is known concerning lineage potential of human progenitors at the clonal level. We isolated and clonally mapped the developmental potential of each major progenitor class from neonatal cord blood and adult bone marrow providing the first comprehensive analysis of the human hematopoietic hierarchy. Human myeloid commitment follows the classical pattern of lineage restriction, however lymphoid development is initiated by a novel cell type, termed lympho-myeloid progenitor (LMP), which displays extensive monocytic potential. However, this myeloid capacity is lost following B- or T/NK-cell lineage commitment. The myeloid potential of LMPs is sensitive to extrinsic signals and can be directed towards differentiation into dendritic cells (DCs). Thus, human lymphoid development does not follow a rigid model of segregation of myeloid-lymphoid lineages, but proceeds through LMPs. LMPs can be massively expanded and differentiated into mature T-cells and DCs that are functionally indistinguishable from DCs derived from peripheral blood monocytes. The prospective isolation and elucidation of clonal lineage potential of human progenitors provides the basis for novel cellular therapeutics and a powerful means to uncover the cellular and molecular regulators that govern human lineage commitment. Disclosures: Dick: Roche: Research Funding; CSL Ltd: Research Funding.
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Xie, Stephanie Zhi-Juan, Kerstin Kaufmann, Olga I. Gan, Sasan Zandi, Naoya Takayama et John E. Dick. « Sphingolipids Regulate Myeloid-Erythroid Fate Determination in Human Hematopoiesis ». Blood 128, no 22 (2 décembre 2016) : 3865. http://dx.doi.org/10.1182/blood.v128.22.3865.3865.
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Abstract The established model of hematopoiesis posits mature blood lineages are derived through successive stages of progenitors that become increasingly lineage-restricted. Whereas the master transcriptional regulators of myeloid-erythroid fate specification such a in Pu.1, Gata1 and CEBPalpha are well studied, the signaling networks that link extrinsic niche signals to lineage commitment is ill-defined. Sphingosine-1-phosphate (S1P) is a bioactive lipid produced from sphingolipid metabolism that in mice has been implicated in HSC egress, lymphocyte trafficking and lymphocyte lineage determination, mainly through the receptor S1PR1. However, the role of sphingolipid biology in human lineage specification is unknown. Gene expression profiling of 11 highly resolved populations of human stem, progenitor and lineage commited cells was undertaken to gain insight into the transcriptional signatures that define each cell population and the changes that occur during lineage commitment. We previously established that sphingolipid metabolism is transcriptionally distinct between HSC and progenitors (Xie et al In prep). Unbiased clustering of RNA-seq data of 46 sphingolipid genes was sufficient to segregate mature human erythroid, lymphoid, and myeloid cells suggesting that tight regulation of S1P signaling is required for lineage commitment. Myeloid cells have the highest transcriptional expression of S1P receptors among mature lineages whereas erythroid cells have little to no expression predicting that S1P signaling may be important in governing myeloid-erythroid fate. We found that manipulating S1P transport via overexpression of the S1P transporter SPNS2 in cord blood was sufficient to limit erythropoiesis as assayed by single cell in vitro assays and in vivo xenotransplantation. S1P signals through a family of 5 G-protein coupled S1P receptors, with S1PR3 expression being myeloid-specific. S1PR3 protein expression is restricted in the primitive human hematopoietic hierarchy to only a subset of granulocyte-macrophage progenitors. Enforced expression of S1PR3 in HSC, MPP (multipotent progenitors) and CMP (common myeloid progenitors) is sufficient to inhibit erythropoiesis and upregulate myelopoiesis in single cell stromal-based assays suggesting S1PR3 has a unique role in myeloid-erythroid fate specification. Flow cytometry analysis shows S1PR3 protein is highly overexpressed in primary AML relative to normal blood cells, suggesting S1P biology is dysregulated in AML. Collectively, our studies provide the first direct evidence that the S1P pathway governs fate determination along myeloid-erythroid lineage commitment. Future studies will need to be undertaken to determine how this new mechanism of lineage commitment is linked to the transcription factor network. Our studies also suggest that this pathway may play a role in AML biology raising the possibility of a new therapeutic direction for AML. Disclosures No relevant conflicts of interest to declare.
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Herfst, Sander, Vicente Mas, Lorena S. Ver, Rutger J. Wierda, Albert D. M. E. Osterhaus, Ron A. M. Fouchier et José A. Melero. « Low-pH-Induced Membrane Fusion Mediated by Human Metapneumovirus F Protein Is a Rare, Strain-Dependent Phenomenon ». Journal of Virology 82, no 17 (2 juillet 2008) : 8891–95. http://dx.doi.org/10.1128/jvi.00472-08.
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ABSTRACT Membrane fusion promoted by human metapneumovirus (HMPV) fusion (F) protein was suggested to require low pH (R. M. Schowalter, S. E. Smith, and R. E. Dutch, J. Virol. 80:10931-10941, 2006). Using prototype F proteins representing the four HMPV genetic lineages, we detected low-pH-dependent fusion only with some lineage A proteins and not with lineage B proteins. A glycine at position 294 was found responsible for the low-pH requirement in lineage A proteins. Only 6% of all HMPV lineage A F sequences have 294G, and none of the lineage B sequences have 294G. Thus, acidic pH is not a general trigger of HMPV F proteins for activity.
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Garraway, Levi A., et William R. Sellers. « Lineage dependency and lineage-survival oncogenes in human cancer ». Nature Reviews Cancer 6, no 8 (1 août 2006) : 593–602. http://dx.doi.org/10.1038/nrc1947.
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Abyzov, Alexej, et Flora M. Vaccarino. « Cell Lineage Tracing and Cellular Diversity in Humans ». Annual Review of Genomics and Human Genetics 21, no 1 (31 août 2020) : 101–16. http://dx.doi.org/10.1146/annurev-genom-083118-015241.
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Tracing cell lineages is fundamental for understanding the rules governing development in multicellular organisms and delineating complex biological processes involving the differentiation of multiple cell types with distinct lineage hierarchies. In humans, experimental lineage tracing is unethical, and one has to rely on natural-mutation markers that are created within cells as they proliferate and age. Recent studies have demonstrated that it is now possible to trace lineages in normal, noncancerous cells with a variety of data types using natural variations in the nuclear and mitochondrial DNA as well as variations in DNA methylation status. It is also apparent that the scientific community is on the verge of being able to make a comprehensive and detailed cell lineage map of human embryonic and fetal development. In this review, we discuss the advantages and disadvantages of different approaches and markers for lineage tracing. We also describe the general conceptual design for how to derive a lineage map for humans.
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Mori, Yasuo, James Y. Chen, John V. Pluvinage, Jun Seita et Irving L. Weissman. « Prospective isolation of human erythroid lineage-committed progenitors ». Proceedings of the National Academy of Sciences 112, no 31 (20 juillet 2015) : 9638–43. http://dx.doi.org/10.1073/pnas.1512076112.
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Determining the developmental pathway leading to erythrocytes and being able to isolate their progenitors are crucial to understanding and treating disorders of red cell imbalance such as anemia, myelodysplastic syndrome, and polycythemia vera. Here we show that the human erythrocyte progenitor (hEP) can be prospectively isolated from adult bone marrow. We found three subfractions that possessed different expression patterns of CD105 and CD71 within the previously defined human megakaryocyte/erythrocyte progenitor (hMEP; Lineage− CD34+ CD38+ IL-3Rα− CD45RA−) population. Both CD71− CD105− and CD71+ CD105− MEPs, at least in vitro, still retained bipotency for the megakaryocyte (MegK) and erythrocyte (E) lineages, although the latter subpopulation is skewed in differentiation toward the erythroid lineage. Notably, the proliferative and differentiation output of the CD71intermediate(int)/+ CD105+ subset of cells within the MEP population was completely restricted to the erythroid lineage with the loss of MegK potential. CD71+ CD105− MEPs are erythrocyte-biased MEPs (E-MEPs) and CD71int/+ CD105+ cells are EPs. These previously unclassified populations may facilitate further understanding of the molecular mechanisms governing human erythroid development and serve as potential therapeutic targets in disorders of the erythroid lineage.
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Six, Emmanuelle, Agathe Guilloux, Adeline Denis, Arnaud Lecoules, Alessandra Magnani, Romain Vilette, Frances Male et al. « Clonal tracking in gene therapy patients reveals a diversity of human hematopoietic differentiation programs ». Blood 135, no 15 (9 avril 2020) : 1219–31. http://dx.doi.org/10.1182/blood.2019002350.
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Abstract In gene therapy with human hematopoietic stem and progenitor cells (HSPCs), each gene-corrected cell and its progeny are marked in a unique way by the integrating vector. This feature enables lineages to be tracked by sampling blood cells and using DNA sequencing to identify the vector integration sites. Here, we studied 5 cell lineages (granulocytes, monocytes, T cells, B cells, and natural killer cells) in patients having undergone HSPC gene therapy for Wiskott-Aldrich syndrome or β hemoglobinopathies. We found that the estimated minimum number of active, repopulating HSPCs (which ranged from 2000 to 50 000) was correlated with the number of HSPCs per kilogram infused. We sought to quantify the lineage output and dynamics of gene-modified clones; this is usually challenging because of sparse sampling of the various cell types during the analytical procedure, contamination during cell isolation, and different levels of vector marking in the various lineages. We therefore measured the residual contamination and corrected our statistical models accordingly to provide a rigorous analysis of the HSPC lineage output. A cluster analysis of the HSPC lineage output highlighted the existence of several stable, distinct differentiation programs, including myeloid-dominant, lymphoid-dominant, and balanced cell subsets. Our study evidenced the heterogeneous nature of the cell lineage output from HSPCs and provided methods for analyzing these complex data.
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Liu, Wei, Junhua Li, Hongli Du et Zhihua Ou. « Mutation Profiles, Glycosylation Site Distribution and Codon Usage Bias of Human Papillomavirus Type 16 ». Viruses 13, no 7 (30 juin 2021) : 1281. http://dx.doi.org/10.3390/v13071281.
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Human papillomavirus type 16 (HPV16) is the most prevalent HPV type causing cervical cancers. Herein, using 1597 full genomes, we systemically investigated the mutation profiles, surface protein glycosylation sites and the codon usage bias (CUB) of HPV16 from different lineages and sublineages. Multiple lineage- or sublineage-conserved mutation sites were identified. Glycosylation analysis showed that HPV16 lineage D contained the highest number of different glycosylation sites from lineage A in both L1 and L2 capsid proteins, which might lead to their antigenic distances between the two lineages. CUB analysis showed that the HPV16 open reading frames (ORFs) preferred codons ending with A/T. The CUB of HPV16 ORFs was mainly affected by natural selection except for E1, E5 and L2. HPV16 only shared some of the preferred codons with humans, which might help reduce competition in translational resources. These findings increase our understanding of the heterogeneity between HPV16 lineages and sublineages, and the adaptation mechanism of HPV in human cells. In summary, this study might facilitate HPV classification and improve vaccine development and application.
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de Figueiredo, Fábio Vidal, Gerusinete Rodrigues Bastos dos Santos, Flávia Castello Branco Vidal, Marcos Antonio Custódio Neto da Silva, Rodrigo Lopes da Silva, Zulmira da Silva Batista, Marcelo Souza de Andrade et al. « Impact of HPV-16 Lineages Infection in Response to Radio-Chemotherapy in Cervical Cancer ». Biomedicines 11, no 7 (23 juillet 2023) : 2069. http://dx.doi.org/10.3390/biomedicines11072069.
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Background: HPV is strongly related to cervical cancer. HPV lineages can contribute to a response to cervical cancer therapy. The aim of this research was to estimate the frequency of human papillomavirus (HPV)-16 lineages in specimens of cervical cancer, relate the pathological factors in these variants, and assess their response to treatment with radical chemoradiotherapy. Methods: Samples of cervical cancer were collected from women who were referred to a reference cancer hospital to test the presence of human papillomavirus-type DNA. The standard protocol of this service consisted of cisplatin-based chemotherapy of 40 mg/m2, plus conventional pelvic irradiation in doses of 45–50.4 Gy and high dose-rate brachytherapy of 28–30 Gy to Point A. The response to chemotherapy was evaluated after three months in patients with the HPV-16 lineage. Results: HPV DNA was detected in 104 (88.1%) of the 118 patients. HPV-16 was present in 63 patients (53%). Lineages of HPV-16 were identified in 57 patients and comprised 33 instances of (57.8%) lineage A, 2 instances of lineage B (3.5%), 2 instances of lineage C (3.5%), and 20 instances of (35.0%) lineage D. The median age of the patients was 48.4 years (range 25–85 years). Squamous cell carcinoma was detected 48 times (84.2%). Adenocarcinoma was more likely to occur in lineage D, as three of the four cases occurred in this lineage. A total of 11 patients with the HPV-16 variant were treated with chemoradiotherapy. After three months, it was observed that nine of the eleven patients (81.8%) achieved a complete response, five with the lineage A type, two with the lineage C type, and two with the lineage D type. The two cases of partial response and disease progression, one of each, occurred in lineage A. Conclusions: In addition to the small number of patients and HPV variants, we noticed a better response in patients with the HPV-16 lineage A. Increasing the sample size could be helpful to better assess the impact of HPV variants on cervical cancer treatment.
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Wang, Xin, Li Yang, Yan-Chun Wang, Zi-Ran Xu, Ye Feng, Jing Zhang, Yi Wang et Cheng-Ran Xu. « Comparative analysis of cell lineage differentiation during hepatogenesis in humans and mice at the single-cell transcriptome level ». Cell Research 30, no 12 (20 juillet 2020) : 1109–26. http://dx.doi.org/10.1038/s41422-020-0378-6.
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AbstractDuring embryogenesis, the liver is the site of hepatogenesis and hematopoiesis and contains many cell lineages derived from the endoderm and mesoderm. However, the characteristics and developmental programs of many of these cell lineages remain unclear, especially in humans. Here, we performed single-cell RNA sequencing of whole human and mouse fetal livers throughout development. We identified four cell lineage families of endoderm-derived, erythroid, non-erythroid hematopoietic, and mesoderm-derived non-hematopoietic cells, and defined the developmental pathways of the major cell lineage families. In both humans and mice, we identified novel markers of hepatic lineages and an ID3+ subpopulation of hepatoblasts as well as verified that hepatoblast differentiation follows the “default-directed” model. Additionally, we found that human but not mouse fetal hepatocytes display heterogeneity associated with expression of metabolism-related genes. We described the developmental process of erythroid progenitor cells during human and mouse hematopoiesis. Moreover, despite the general conservation of cell differentiation programs between species, we observed different cell lineage compositions during hematopoiesis in the human and mouse fetal livers. Taken together, these results reveal the dynamic cell landscape of fetal liver development and illustrate the similarities and differences in liver development between species, providing an extensive resource for inducing various liver cell lineages in vitro.
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Yang, Zhijie, Joy Kovar, Jaehyoung Kim, Joseph Nietfeldt, David R. Smith, Rodney A. Moxley, Michael E. Olson, Paul D. Fey et Andrew K. Benson. « Identification of Common Subpopulations of Non-Sorbitol-Fermenting, β-Glucuronidase-Negative Escherichia coli O157:H7 from Bovine Production Environments and Human Clinical Samples ». Applied and Environmental Microbiology 70, no 11 (novembre 2004) : 6846–54. http://dx.doi.org/10.1128/aem.70.11.6846-6854.2004.
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ABSTRACT Non-sorbitol-fermenting, β-glucuronidase-negative Escherichia coli O157:H7 strains are regarded as a clone complex, and populations from different geographical locations are believed to share a recent common ancestor. Despite their relatedness, high-resolution genotyping methods can detect significant genome variation among different populations. Phylogenetic analysis of high-resolution genotyping data from these strains has shown that subpopulations from geographically unlinked continents can be divided into two primary phylogenetic lineages, termed lineage I and lineage II, and limited studies of the distribution of these lineages suggest there could be differences in their propensity to cause disease in humans or to be transmitted to humans. Because the genotyping methods necessary to discriminate the two lineages are tedious and subjective, these methods are not particularly suited for studying the large sets of strains that are required to systematically evaluate the ecology and transmission characteristics of these lineages. To overcome this limitation, we have developed a lineage-specific polymorphism assay (LSPA) that can readily distinguish between the lineage I and lineage II subpopulations. In the studies reported here, we describe the development of a six-marker test (LSPA-6) and its validation in a side-by-side comparison with octamer-based genome scanning. Analysis of over 1,400 O157:H7 strains with the LSPA-6 demonstrated that five genotypes comprise over 91% of the strains, suggesting that these subpopulations may be widespread.
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Radtke, Stefan, Yan-Yi Chan, Morgan A. Giese, Zachary K. Norgaard, Lauren E. Schefter, Jennifer E. Adair et Hans-Peter Kiem. « Conserved Lineage Development in Human and Nonhuman Primate Hematopoiesis ». Blood 128, no 22 (2 décembre 2016) : 2646. http://dx.doi.org/10.1182/blood.v128.22.2646.2646.
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Abstract For more than 30 years, hematopoietic stem cell (HSC) research has been performed according to the classical model of human hematopoiesis suggesting an early segregation of lymphoid and erythro-myeloid potentials. However, several studies have recently proposed a great variety of models for the human blood hierarchy showing alternative lineage relationships and read-outs for multipotent HSCs. While the debate about hematopoietic lineage relationships is still ongoing, consequences of these findings and the challenges they pose for the development of treatment strategies for hematological diseases and malignancies are rarely discussed. A critical factor for the development of stem cell therapies is the availability of a reliable and robust read-out for multipotent HSCs/MPPs (multipotent progenitor cells) supporting the development of all blood cell lineages. Unfortunately, the current gold standard, NOD/SCID mouse xenograft repopulation assay does not support erythrocyte and megakaryocyte development and, thus, does not fully read-out multi-lineage potential of human HSCs/MPP. In addition, development of therapeutic approaches in the mouse model is not possible due to differences in cell surface marker expression, physiology, life span, and the demand on stem cell self-renewal and differentiation compared to humans. The pigtail macaque (PM; Macaca nemestrina) and the rhesus macaque (RM: Macaca mulatta) share a close evolutionary relationship with humans and have been used as a pre-clinical model system to study basic HSC biology or to develop specific HSC gene therapy approaches. Surprisingly, however, a comparison of hematopoietic subpopulations and the hierarchical organization of defined lineages has not been performed between NHPs and humans. This will be a critical factor for a better understanding of the newly defined blood lineage associations and hierarchies, as well as the development of treatment approaches based on these lineages. Here, we comprehensively analyzed all known markers of human hematopoiesis in the NHP to identify subpopulations of candidate NHP hematopoietic stem and progenitor cells (HSPCs) and then validated HSPC phenotypes of these fractions with functional in vitro read outs. We further evaluated and compared lineage relationships between these subpopulations to recently proposed models of human hematopoiesis to determine whether conservation of hematopoiesis exists with the goal of informing studies evaluating treatments for hematological diseases in the NHP model. We show for the first time a phenotypic mapping strategy in NHP hematopoietic cells predicting a revised model of hematopoiesis. Similar to humans, NHP HSCs give rise to multipotent progenitors (MPPs), followed by a segregation of lympho-myeloid, erythro-myeloid, and megakaryocytic lineages (see figure). Conservation of hematopoietic lineage relationships was confirmed by RNA expression analysis of corresponding subpopulations. In summary, we identified corresponding human and NHP hematopoietic subpopulations, which share phenotypical, functional and transcriptional properties in both species, validating the NHP as an excellent pre-clinical model system for HSC biology and the development of novel HSC-based treatment approaches. Figure Figure. Disclosures Adair: Rocket Pharmaceuticals: Consultancy, Equity Ownership. Kiem:Rocket Pharmaceuticals: Consultancy, Equity Ownership, Research Funding.
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Oliver, H. F., R. H. Orsi, M. Wiedmann et K. J. Boor. « Listeria monocytogenes σB Has a Small Core Regulon and a Conserved Role in Virulence but Makes Differential Contributions to Stress Tolerance across a Diverse Collection of Strains ». Applied and Environmental Microbiology 76, no 13 (7 mai 2010) : 4216–32. http://dx.doi.org/10.1128/aem.00031-10.
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ABSTRACT Listeria monocytogenes strains are classified in at least three distinct phylogenetic lineages. There are correlations between lineage classification and source of bacterial isolation; e.g., human clinical and food isolates usually are classified in either lineage I or II. However, human clinical isolates are overrepresented in lineage I, while food isolates are overrepresented in lineage II. σB, a transcriptional regulator previously demonstrated to contribute to environmental stress responses and virulence in L. monocytogenes lineage II strains, was hypothesized to provide differential abilities for L. monocytogenes survival in various niches (e.g., food and human clinical niches). To determine if the contributions of σB to stress response and virulence differ across diverse L. monocytogenes strains, ΔsigB mutations were created in strains belonging to lineages I, II, IIIA, and IIIB. Paired parent and ΔsigB mutant strains were tested for survival under acid and oxidative stress conditions, Caco-2 cell invasion efficiency, and virulence using the guinea pig listeriosis infection model. Parent and ΔsigB mutant strain transcriptomes were compared using whole-genome expression microarrays. σB contributed to virulence in each strain. However, while σB contributed significantly to survival under acid and oxidative stress conditions and Caco-2 cell invasion in lineage I, II, and IIIB strains, the contributions of σB were not significant for these phenotypes in the lineage IIIA strain. A core set of 63 genes was positively regulated by σB in all four strains; different total numbers of genes were positively regulated by σB in the strains. Our results suggest that σB universally contributes to L. monocytogenes virulence but specific σB-regulated stress response phenotypes vary among strains.
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Garraway, Levi A., et William R. Sellers. « Erratum : Lineage dependency and lineage-survival oncogenes in human cancer ». Nature Reviews Cancer 6, no 9 (septembre 2006) : 742. http://dx.doi.org/10.1038/nrc1972.
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Cela-Conde, C. J., et F. J. Ayala. « Genera of the human lineage ». Proceedings of the National Academy of Sciences 100, no 13 (6 juin 2003) : 7684–89. http://dx.doi.org/10.1073/pnas.0832372100.
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Steele, Marina, Kim Ziebell, Yongxiang Zhang, Andrew Benson, Roger Johnson, Chad Laing, Eduardo Taboada et Victor Gannon. « Genomic Regions Conserved in Lineage II Escherichia coli O157:H7 Strains ». Applied and Environmental Microbiology 75, no 10 (27 mars 2009) : 3271–80. http://dx.doi.org/10.1128/aem.02123-08.
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ABSTRACT Populations of the food- and waterborne pathogen Escherichia coli O157:H7 are comprised of two major lineages. Recent studies have shown that specific genotypes within these lineages differ substantially in the frequencies with which they are associated with human clinical disease. While the nucleotide sequences of the genomes of lineage I strains E. coli O157 Sakai and EDL9333 have been determined, much less is known about the genomes of lineage II strains. In this study, suppression subtractive hybridization (SSH) was used to identify genomic features that define lineage II populations. Three SSH experiments were performed, yielding 1,085 genomic fragments consisting of 811 contigs. Bacteriophage sequences were identified in 11.3% of the contigs, 9% showed insertions and 2.3% deletions with respect to E. coli O157:H7 Sakai, and 23.2% did not have significant identity to annotated sequences in GenBank. In order to test for the presence of these novel loci in lineage I and II strains, 27 PCR primer sets were designed based on sequences from these contigs. All but two of these PCR targets were found in the majority (51.9% to 100%) of 27 lineage II strains but in no more than one (<6%) of the 17 lineage I strains. Several of these linage II-related fragments contain insertions/deletions that may play an important role in virulence. These lineage II-related loci were also shown to be useful markers for genotyping of E. coli O157:H7 strains isolated from human and animal sources.
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Limaye, Sanket, Anant Shelke, Mohan M. Kale, Urmila Kulkarni-Kale et Suresh V. Kuchipudi. « IDV Typer : An Automated Tool for Lineage Typing of Influenza D Viruses Based on Return Time Distribution ». Viruses 16, no 3 (28 février 2024) : 373. http://dx.doi.org/10.3390/v16030373.
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Influenza D virus (IDV) is the most recent addition to the Orthomyxoviridae family and cattle serve as the primary reservoir. IDV has been implicated in Bovine Respiratory Disease Complex (BRDC), and there is serological evidence of human infection of IDV. Evolutionary changes in the IDV genome have resulted in the expansion of genetic diversity and the emergence of multiple lineages that might expand the host tropism and potentially increase the pathogenicity to animals and humans. Therefore, there is an urgent need for automated, accurate and rapid typing tools for IDV lineage typing. Currently, IDV lineage typing is carried out using BLAST-based searches and alignment-based molecular phylogeny of the hemagglutinin-esterase fusion (HEF) gene sequences, and lineage is assigned to query sequences based on sequence similarity (BLAST search) and proximity to the reference lineages in the tree topology, respectively. To minimize human intervention and lineage typing time, we developed IDV Typer server, implementing alignment-free method based on return time distribution (RTD) of k-mers. Lineages are assigned using HEF gene sequences. The server performs with 100% sensitivity and specificity. The IDV Typer server is the first application of an RTD-based alignment-free method for typing animal viruses.
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Steele, Marina, Kim Ziebell, Yongxiang Zhang, Andrew Benson, Paulina Konczy, Roger Johnson et Victor Gannon. « Identification of Escherichia coli O157:H7 Genomic Regions Conserved in Strains with a Genotype Associated with Human Infection ». Applied and Environmental Microbiology 73, no 1 (20 octobre 2006) : 22–31. http://dx.doi.org/10.1128/aem.00982-06.
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ABSTRACT Beta-glucuronidase-negative, sorbitol-nonfermenting isolates of Shiga toxin-producing Escherichia coli O157 comprise part of a clone complex of related enterohemorrhagic E. coli isolates. High-resolution genotyping shows that the O157 populations have diverged into two different lineages that appear to have different ecologies. To identify genomic regions unique to the most common human-associated genotype, suppression subtractive hybridization was used to identify DNA sequences present in two clinical strains representing the human lineage I O157:H7 strains but absent from two bovine-derived lineage II strains. PCR assays were then used to test for the presence of these regions in 10 lineage I strains and 20 lineage II strains. Twelve conserved regions of genomic difference for lineage I (CRDI) were identified that were each present in at least seven of the lineage I strains but absent in most of the lineage II strains tested. The boundaries of the lineage I conserved regions were further delimited by PCR. Eleven of these CRDI were associated with E. coli Sakai S-loops 14, 16, 69, 72, 78, 82, 83, 91 to 93, 153, and 286, and the final CRDI was located on the pO157 virulence plasmid. Several potential virulence factors were identified within these regions, including a putative hemolysin-activating protein, an iron transport system, and several possible regulatory genes. Cluster analysis based on lineage I conserved regions showed that the presence/absence of these regions was congruent with the inferred phylogeny of the strains.
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Eppinger, Mark, Mark K. Mammel, Joseph E. LeClerc, Jacques Ravel et Thomas A. Cebula. « Genome Signatures of Escherichia coli O157:H7 Isolates from the Bovine Host Reservoir ». Applied and Environmental Microbiology 77, no 9 (18 mars 2011) : 2916–25. http://dx.doi.org/10.1128/aem.02554-10.
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ABSTRACTCattle comprise a main reservoir of Shiga toxin-producingEscherichia coliO157:H7 (STEC). The significant differences in host prevalence, transmissibility, and virulence phenotypes among strains from bovine and human sources are of major interest to the public health community and livestock industry. Genomic analysis revealed divergence into three lineages: lineage I and lineage I/II strains are commonly associated with human disease, while lineage II strains are overrepresented in the asymptomatic bovine host reservoir. Growing evidence suggests that genotypic differences between these lineages, such as polymorphisms in Shiga toxin subtypes and synergistically acting virulence factors, are correlated with phenotypic differences in virulence, host ecology, and epidemiology. To assess the genomic plasticity on a genome-wide scale, we have sequenced the whole genome of strain EC869, a bovine-associatedE. coliO157:H7 isolate. Comparative phylogenomic analysis of this key isolate enabled us to place accurately bovine lineage II strains within the genetically homogenousE. coliO157:H7 clade. Identification of polymorphic loci that are anchored both in the chromosomal backbone and horizontally acquired regions allowed us to associate bovine genotypes with altered virulence phenotypes and host prevalence. This study catalogued numerous novel lineage II-specific genome signatures, some of which appear to be associated intimately with the altered pathogenic potential and niche adaptation within the bovine rumen. The presented extended list of polymorphic markers is valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies of this emerging human pathogen.
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Parvez, Rehnuma, Paluru Vijayachari, Mrinmoy Kumar Saha, Lipika Biswas, Jawahar Ramasamy, Alwin Vins, Nisha Beniwal et al. « Distribution of Human Papillomavirus Genotypes among the Women of South Andaman Island, India ». Diagnostics 13, no 17 (25 août 2023) : 2765. http://dx.doi.org/10.3390/diagnostics13172765.
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Background: Human Papillomavirus (HPV) causes various types of cancer in both men and women. Woman with HPV infection has a risk of developing invasive cervical cancer. Globally, HPV 16 and 18 were predominant. This study aims to find the distribution of various HPV types in South Andaman. Methods: A cross-sectional study was conducted among women in South Andaman, where cervical scrapes were collected after collecting written informed consent. Detection of HPV genotypes was carried out by using a PCR assay. Further, sequencing analysis was performed using MEGA11 to identify various genotypes in this territory. Result: Of these 1000 samples, 32 were positive for HR-HPV 16, and four were positive for HR-HPV 18. Fifteen HPV genotypes were detected using molecular evolutionary analysis. Six cases were identified with multiple genotypes. The most prevalent genotype is HPV 16 which belongs to Lineage-A and sub-lineage A2. HPV 18 identified in South Andaman belonged to the lineage A1 to A5. Discussion: Various HPV types were identified among women in South Andaman. Global burden of cervical cancer associated with various HPV sub-lineages. HPV-16 A1 sub-lineage was globally widespread, whereas sub-lineages A1, A2 and D1 prevailed in South Andaman. Conclusions: HR-HPV identified in this study enlightens the importance of HPV vaccination among women in remote places. These findings will help to strengthen public health awareness programs and prevention strategies for women in remote areas.
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Nakhaei-Nejad, Maryam, Luke Trinity, Hosna Jabbari, Manijeh Pasdar et Nadia Jahroudi. « In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells ». Journal of Clinical Medicine 10, no 18 (15 septembre 2021) : 4161. http://dx.doi.org/10.3390/jcm10184161.
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Despite a major interest in understanding how the endothelial cell phenotype is established, the underlying molecular basis of this process is not yet fully understood. We have previously reported the generation of induced pluripotent stem cells (iPS) from human umbilical vein endothelial cells and differentiation of the resulting HiPS back to endothelial cells (Ec-Diff), as well as neural (Nn-Diff) cell lineage that contained both neurons and astrocytes. Furthermore, the identities of these cell lineages were established by gene array analysis. Here, we explored the same arrays to gain insight into the gene alteration processes that accompany the establishment of endothelial vs. non-endothelial neural cell phenotypes. We compared the expression of genes that code for transcription factors and epigenetic regulators when HiPS is differentiated into these endothelial and non-endothelial lineages. Our in silico analyses have identified cohorts of genes that are similarly up- or downregulated in both lineages, as well as those that exhibit lineage-specific alterations. Based on these results, we propose that genes that are similarly altered in both lineages participate in priming the stem cell for differentiation in a lineage-independent manner, whereas those that are differentially altered in endothelial compared to neural cells participate in a lineage-specific differentiation process. Specific GATA family members and their cofactors and epigenetic regulators (DNMT3B, PRDM14, HELLS) with a major role in regulating DNA methylation were among participants in priming HiPS for lineage-independent differentiation. In addition, we identified distinct cohorts of transcription factors and epigenetic regulators whose alterations correlated specifically with the establishment of endothelial vs. non-endothelial neural lineages.
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Bondre, Vijay P., R. S. Jadi, A. C. Mishra, P. N. Yergolkar et V. A. Arankalle. « West Nile virus isolates from India : evidence for a distinct genetic lineage ». Journal of General Virology 88, no 3 (1 mars 2007) : 875–84. http://dx.doi.org/10.1099/vir.0.82403-0.
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The complete genomic sequence of one human isolate of West Nile virus (WNV) and the partial genomic sequences of 14 other strains from India isolated in the period 1955–1982 from different hosts and geographical areas were determined. Phylogenetic analyses based on complete and partial genomic sequences (921 nt of the C–prM–E region) revealed that WNV could be classified into five distinct groups that differed from each other by 20–25 % at the complete genome level and by 20–26 % using partial sequences. Of the Indian isolates, 13 formed a distinct genetic lineage, lineage 5, whereas two isolates, one from a human patient (1967) and another from a bat (1968), were related closely to lineage 1 strains. The complete genomic sequence of the Indian isolate, 804994, showed 20–22 % genetic divergence from the previously proposed lineage 1 and 2 strains and 24–25 % divergence from isolates of the newly proposed lineages 3 (Rabensburg isolate 97-103 of 1997) and 4 (Russian isolate LEIV-Krnd88-190 of 1998). Similarly, the partial genomic sequences of the Indian isolates showed 21–26 % divergence from lineage 1 and 2 strains and from the Rabensburg (97-103) and Russian (LEIV-Krnd88-190) isolates. Cross-neutralization using strain-specific polyclonal antibodies against lineage 1 strain Eg-101 and representative Indian strains suggests substantial antigenic variation. This study documents circulation of WNV strains typical to India for 27 years and the introduction of lineage 1 strains during 1967–1968. These results indicate strongly that WNV should be classified into five genetic lineages, with Indian viruses constituting the distinct genetic lineage 5.
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Sene, Ousseynou, Samba Niang Sagne, Ndeye Sakha Bob, Moundhir Mhamadi, Idrissa Dieng, Aboubacry Gaye, Haoua Ba et al. « Re-Emergence of Rift Valley Fever Virus Lineage H in Senegal in 2022 : In Vitro Characterization and Impact on its Global Emergence in West Africa ». Viruses 16, no 7 (25 juin 2024) : 1018. http://dx.doi.org/10.3390/v16071018.
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Rift Valley fever (RVF) is a re-emerging vector-borne zoonosis with a high public health and veterinary impact. In West Africa, many lineages were previously detected, but since 2020, lineage H from South Africa has been the main cause of the outbreaks. In this study, clinical samples collected through national surveillance were screened for RVF virus (RVFV) acute infection by RT-PCR and IgM ELISA tests. Sequencing, genome mapping and in vitro phenotypic characterization in mammal cells were performed on RT-PCR positive samples in comparison with other epidemic lineages (G and C). Four RVFV human cases were detected in Senegal and the sequence analyses revealed that the strains belonged to lineage H. The in vitro kinetics and genome mapping showed different replication efficiency profiles for the tested RVFV lineages and non-conservative mutations, which were more common to lineage G or specific to lineage H. Our findings showed the re-emergence of lineage H in Senegal in 2022, its high viral replication efficiency in vitro and support the findings that genetic diversity affects viral replication. This study gives new insights into the biological properties of lineage H and calls for deeper studies to better assess its potential to cause a future threat in Senegal.
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Norton, Dawn M., Janet M. Scarlett, Kelly Horton, David Sue, Joanne Thimothe, Kathryn J. Boor et Martin Wiedmann. « Characterization and Pathogenic Potential of Listeria monocytogenes Isolates from the Smoked Fish Industry ». Applied and Environmental Microbiology 67, no 2 (1 février 2001) : 646–53. http://dx.doi.org/10.1128/aem.67.2.646-653.2001.
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ABSTRACT This study was designed to evaluate the hypothesis that some of theListeria monocytogenes subtypes associated with foods, specifically smoked fish, may have an attenuated ability to cause human disease. We tested this hypothesis by using two different approaches: (i) comparison of molecular subtypes found among 117 isolates from smoked fish, raw materials, fish in process, and processing environments with subtypes found among a collection of 275 human clinical isolates and (ii) the evaluation of the cytopathogenicity of industrial isolates. Ribotyping and PCR-restriction fragment length polymorphism typing of the hlyA and actA genes differentiated 23 subtypes among the industrial isolates and allowed classification of the isolates into three genetic lineages. A significantly higher proportion of human isolates (69.1%) than industrial isolates (36.8%) were classified as lineage I, which contains human sporadic isolates and all epidemic isolates. All other industrial isolates (63.2%) were classified as lineage II, which contains only human sporadic isolates. Lineage I ribotypes DUP-1038B and DUP-1042B represented a significantly higher proportion of the human isolates than industrial isolates (5.1%). Lineage II ribotypes DUP-1039C, DUP-1042C, and DUP-1045, shown previously to persist in the smoked fish processing environment, represented nearly 50% of the industrial isolates, compared to 7.6% of the human isolates. Representatives of each subtype were evaluated with a tissue culture plaque assay. Lineage I isolates formed plaques that were significantly larger than those formed by lineage II isolates. Isolates from the smoked fish industry representing three ribotypes formed no plaques or small plaques, indicating that they had an impaired ability to infect mammalian cells. While L. monocytogenes clonal groups linked to human listeriosis cases and outbreaks were isolated, our data also suggest that at least some L. monocytogenes subtypes present in ready-to-eat foods may have limited human-pathogenic potential.
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Pinheiro, Maisa, Ariana Harari, Mark Schiffman, Gary M. Clifford, Zigui Chen, Meredith Yeager, Michael Cullen et al. « Phylogenomic Analysis of Human Papillomavirus Type 31 and Cervical Carcinogenesis : A Study of 2093 Viral Genomes ». Viruses 13, no 10 (28 septembre 2021) : 1948. http://dx.doi.org/10.3390/v13101948.
Texte intégralRésumé :
Human papillomavirus (HPV) type 31 (HPV31) is closely related to the most carcinogenic type, HPV16, but only accounts for 4% of cervical cancer cases worldwide. Viral genetic and epigenetic variations have been associated with carcinogenesis for other high-risk HPV types, but little is known about HPV31. We sequenced 2093 HPV31 viral whole genomes from two large studies, one from the U.S. and one international. In addition, we investigated CpG methylation in a subset of 175 samples. We evaluated the association of HPV31 lineages/sublineages, single nucleotide polymorphisms (SNPs) and viral methylation with cervical carcinogenesis. HPV31 A/B clade was >1.8-fold more associated with cervical intraepithelial neoplasia grade 3 and cancer (CIN3+) compared to the most common C lineage. Lineage/sublineage distribution varied by race/ethnicity and geographic region. A viral genome-wide association analysis identified SNPs within the A/B clade associated with CIN3+, including H23Y (C626T) (odds ratio = 1.60, confidence intervals = 1.17–2.19) located in the pRb CR2 binding-site within the E7 oncogene. Viral CpG methylation was higher in lineage B, compared to the other lineages, and was most elevated in CIN3+. In conclusion, these data support the increased oncogenicity of the A/B lineages and suggest variation of E7 as a contributing risk factor.
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Ameke, Selassie, Prince Asare, Samuel Yaw Aboagye, Isaac Darko Otchere, Stephen Osei-Wusu, Dorothy Yeboah-Manu et Adwoa Asante-Poku. « Molecular epidemiology of Mycobacterium tuberculosis complex in the Volta Region of Ghana ». PLOS ONE 16, no 3 (17 mars 2021) : e0238898. http://dx.doi.org/10.1371/journal.pone.0238898.
Texte intégralRésumé :
Context Available molecular epidemiological data from recent studies suggest significant genetic variation between the different lineages of Mycobacterium tuberculosis complex (MTBC) and the MTBC lineages might have adapted to different human populations. Aim This study sought to determine the population structure of clinical MTBC isolates from the Volta Region of Ghana. Methods The MTBC isolates obtained from collected sputum samples were identified by PCR detecting of IS6110 and genotyped using spoligotyping. Non-tuberculous mycobacterial isolates were characterized by amplification of the heat shock protein 65 (hsp65) gene and sequencing. The drug susceptibility profiles of the MTBCs determined using GenoType MTBDRplus. Results One hundred and seventeen (117, 93.6%) out of 125 mycobacterial positive isolates were characterized as members of the MTBC of which M. tuberculosis sensu stricto (MTBss) and M. africanum (MAF) were respectively 94 (80.3%) and 23 (19.7%). In all, 39 distinct spoligotype patterns were obtained; 26 for MTBss and 13 for MAF lineages. Spoligotyping identified 89 (76%) Lineage 4, 16 (13.6%) Lineage 5, 7 (6.0%) Lineage 6, 3 (2.6%) Lineage 2, 1(0.9%) Lineage 3 and 1 (0.9%) Lineage 1. Among the Lineage 4 isolates, 62/89 (69.7%) belonged to Cameroon sub-lineage, 13 (14.7%) Ghana, 8 (9.0%) Haarlem, 2 (2.2%) LAM, 1 (1.1%) Uganda I, 1 (1.1%) X and the remaining two (2.2%) were orphan. Significant localization of MAF was found within the Ho municipality (n = 13, 29.5%) compared to the more cosmopolitan Ketu-South/Aflao (n = 3, 8.3%) (p-value = 0.017). Eight (8) non-tuberculous mycobacteria were characterized as M. abscessus (7) and M. fortuitum (1). Conclusion We confirmed the importance of M. africanum lineages as a cause of TB in the Volta region of Ghana.
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Gan, Lu, Ying Liu, Dixin Cui, Yue Pan, Liwei Zheng et Mian Wan. « Dental Tissue-Derived Human Mesenchymal Stem Cells and Their Potential in Therapeutic Application ». Stem Cells International 2020 (1 septembre 2020) : 1–17. http://dx.doi.org/10.1155/2020/8864572.
Texte intégralRésumé :
Human mesenchymal stem cells (hMSCs) are multipotent cells, which exhibit plastic adherence, express specific cell surface marker spectrum, and have multi-lineage differentiation potential. These cells can be obtained from multiple tissues. Dental tissue-derived hMSCs (dental MSCs) possess the ability to give rise to mesodermal lineage (osteocytes, adipocytes, and chondrocytes), ectodermal lineage (neurocytes), and endodermal lineages (hepatocytes). Dental MSCs were first isolated from dental pulp of the extracted third molar and till now they have been purified from various dental tissues, including pulp tissue of permanent teeth and exfoliated deciduous teeth, apical papilla, periodontal ligament, gingiva, dental follicle, tooth germ, and alveolar bone. Dental MSCs are not only easily accessible but are also expandable in vitro with relative genomic stability for a long period of time. Moreover, dental MSCs have exhibited immunomodulatory properties by secreting cytokines. Easy accessibility, multi-lineage differentiation potential, and immunomodulatory effects make dental MSCs distinct from the other hMSCs and an effective tool in stem cell-based therapy. Several preclinical studies and clinical trials have been performed using dental MSCs in the treatment of multiple ailments, ranging from dental diseases to nondental diseases. The present review has summarized dental MSC sources, multi-lineage differentiation capacities, immunomodulatory features, its potential in the treatment of diseases, and its application in both preclinical studies and clinical trials. The regenerative therapeutic strategies in dental medicine have also been discussed.
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SAUDERS, BRIAN D., YNTE SCHUKKEN, LAURA KORNSTEIN, VASUDHA REDDY, TAMMY BANNERMAN, ELLEN SALEHI, NELLIE DUMAS, BRIDGET J. ANDERSON, JEFFREY P. MASSEY et MARTIN WIEDMANN. « Molecular Epidemiology and Cluster Analysis of Human Listeriosis Cases in Three U.S. States ». Journal of Food Protection 69, no 7 (1 juillet 2006) : 1680–89. http://dx.doi.org/10.4315/0362-028x-69.7.1680.
Texte intégralRésumé :
To better understand the transmission and epidemiology of human listeriosis, 647 Listeria monocytogenes isolates obtained from human listeriosis cases in four U.S. locations (Michigan, Ohio, New York State, and New York City) over 61 months (1998 to 2003) were characterized by automated EcoRI ribotyping. A total of 65 ribotypes were differentiated among the characterized isolates; 393, 227, and 24 isolates were classified into lineages I, II, and III, respectively, and 3 isolates were not classified to lineage. The three most common ribotypes (responsible for 39% of all cases) represented L. monocytogenes epidemic clones, each of which had previously been linked to at least two human listeriosis outbreaks. Categorical analyses revealed that ribotypes and lineages were nonrandomly distributed among the four locations. Temporal cluster analysis of cases identified 13 statistically significant temporal subtype clusters, which represented 26% of all cases. Three of these clusters matched previously described human listeriosis outbreaks. Isolates involved in clusters belonged to nine ribotypes. Four, eight, and one cluster were caused by lineages I, II, and III, respectively. The two largest clusters were both caused by the epidemic clone representing ribotype DUP-1044A. Categorical analyses revealed no significant associations between lineage or ribotype and clinical manifestation (central nervous system infection, septicemia, fetal infection, or other infection) or disease outcome (fatal or not fatal). Although human listeriosis cases are caused by isolates belonging to a diversity of EcoRI ribotypes, specific lineage I epidemic clones cause a large number of human listeriosis cases. Many human listeriosis cases can be grouped into statistically significant temporal clusters, including widely distributed and region-specific clusters associated with isolates of various ribotypes. L. monocytogenes lineages and EcoRI ribotypes do not appear to differ in their likelihood of causing different clinical manifestations or mortality.
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Lowe, Ross M. S., Danica Baines, L. Brent Selinger, James E. Thomas, Tim A. McAllister et Ranjana Sharma. « Escherichia coli O157:H7 Strain Origin, Lineage, and Shiga Toxin 2 Expression Affect Colonization of Cattle ». Applied and Environmental Microbiology 75, no 15 (12 juin 2009) : 5074–81. http://dx.doi.org/10.1128/aem.00391-09.
Texte intégralRésumé :
ABSTRACT Enterohemorrhagic Escherichia coli O157:H7 has evolved into an important human pathogen with cattle as the main reservoir. The recent discovery of E. coli O157:H7-induced pathologies in challenged cattle has suggested that previously discounted bacterial virulence factors may contribute to the colonization of cattle. The objective of the present study was to examine the impact of lineage type, cytotoxin activity, and cytotoxin expression on the amount of E. coli O157:H7 colonization of cattle tissue and cells in vitro. Using selected bovine- and human-origin strains, we determined that lineage type predicted the amount of E. coli O157:H7 strain colonization: lineage I > intermediate lineages > lineage II. All E. coli O157:H7 strain colonization was dose dependent, with threshold colonization at 103 to 105 CFU and maximum colonization at 107 CFU. We also determined that an as-yet-unknown factor of strain origin was the most dominant predictor of the amount of strain colonization in vitro. The amount of E. coli O157:H7 colonization was also influenced by strain cytotoxin activity and the inclusion of cytotoxins from lineage I or intermediate lineage strains increased colonization of a lineage II strain. There was a higher level of expression of the Shiga toxin 1 gene (stx 1) in human-origin strains than in bovine-origin strains. In addition, lineage I strains expressed higher levels of the Shiga toxin 2 gene (stx 2). The present study supports a role for strain origin, lineage type, cytotoxin activity, and stx 2 expression in modulating the amount of E. coli O157:H7 colonization of cattle.
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Uckun, FM, KJ Gajl-Peczalska, AJ Provisor et NA Heerema. « Immunophenotype-karyotype associations in human acute lymphoblastic leukemia ». Blood 73, no 1 (1 janvier 1989) : 271–80. http://dx.doi.org/10.1182/blood.v73.1.271.271.
Texte intégralRésumé :
Abstract The present study is a detailed analysis of the cytogenetic features of leukemic cells from 104 immunologically classified acute lymphoblastic leukemia (ALL) (78 B lineage and 26 T lineage) cases. Clonal chromosomal abnormalities were found in marrow blasts from 77 of 104 (74%) cases. Hyperdiploidy was much more frequent in B-lineage ALL cases, whereas normal diploidy was more common in T-lineage ALL cases. Fifty-nine of 104 cases (46 of 78 B-lineage ALL and 13 of 26 T-lineage ALL cases) had structural chromosomal abnormalities. Structural abnormalities involving 2p11, 7p13, 7p22, proximal q arm of 7 (7q11 or 7q22), 11q23–24, and translocations involving 12p11–13 appeared to be B- lineage specific. By comparison, structural abnormalities involving 7p15, 7q32, and 14q11 displayed T-lineage specificity. Structural abnormalities involving 9p22-p23 or 14q32, del (6)(q21-q23), del (12)(p11-p13), and the Philadelphia chromosome were found in B-lineage as well as T-lineage ALL cases. This study expands the current knowledge about immunophenotype-karyotype associations in ALL.
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Uckun, FM, KJ Gajl-Peczalska, AJ Provisor et NA Heerema. « Immunophenotype-karyotype associations in human acute lymphoblastic leukemia ». Blood 73, no 1 (1 janvier 1989) : 271–80. http://dx.doi.org/10.1182/blood.v73.1.271.bloodjournal731271.
Texte intégralRésumé :
The present study is a detailed analysis of the cytogenetic features of leukemic cells from 104 immunologically classified acute lymphoblastic leukemia (ALL) (78 B lineage and 26 T lineage) cases. Clonal chromosomal abnormalities were found in marrow blasts from 77 of 104 (74%) cases. Hyperdiploidy was much more frequent in B-lineage ALL cases, whereas normal diploidy was more common in T-lineage ALL cases. Fifty-nine of 104 cases (46 of 78 B-lineage ALL and 13 of 26 T-lineage ALL cases) had structural chromosomal abnormalities. Structural abnormalities involving 2p11, 7p13, 7p22, proximal q arm of 7 (7q11 or 7q22), 11q23–24, and translocations involving 12p11–13 appeared to be B- lineage specific. By comparison, structural abnormalities involving 7p15, 7q32, and 14q11 displayed T-lineage specificity. Structural abnormalities involving 9p22-p23 or 14q32, del (6)(q21-q23), del (12)(p11-p13), and the Philadelphia chromosome were found in B-lineage as well as T-lineage ALL cases. This study expands the current knowledge about immunophenotype-karyotype associations in ALL.
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Christopher, Grace A., Rebecca J. Noort et Jessica L. Esseltine. « Connexin 43 Gene Ablation Does Not Alter Human Pluripotent Stem Cell Germ Lineage Specification ». Biomolecules 12, no 1 (22 décembre 2021) : 15. http://dx.doi.org/10.3390/biom12010015.
Texte intégralRésumé :
During embryonic germ layer development, cells communicate with each other and their environment to ensure proper lineage specification and tissue development. Connexin (Cx) proteins facilitate direct cell–cell communication through gap junction channels. While previous reports suggest that gap junctional intercellular communication may contribute to germ layer formation, there have been limited comprehensive expression analyses or genetic ablation studies on Cxs during human pluripotent stem cell (PSC) germ lineage specification. We screened the mRNA profile and protein expression patterns of select human Cx isoforms in undifferentiated human induced pluripotent stem cells (iPSCs), and after directed differentiation into the three embryonic germ lineages: ectoderm, definitive endoderm, and mesoderm. Transcript analyses by qPCR revealed upregulation of Cx45 and Cx62 in iPSC-derived ectoderm; Cx45 in mesoderm; and Cx30.3, Cx31, Cx32, Cx36, Cx37, and Cx40 in endoderm relative to control human iPSCs. Generated Cx43 (GJA1) CRISPR-Cas9 knockout iPSCs successfully differentiated into cells of all three germ layers, suggesting that Cx43 is dispensable during directed iPSC lineage specification. Furthermore, qPCR screening of select Cx transcripts in our GJA1-/- iPSCs showed no significant Cx upregulation in response to the loss of Cx43 protein. Future studies will reveal possible compensation by additional Cxs, suggesting targets for future CRISPR-Cas9 ablation studies in human iPSC lineage specification.
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Katagiri, Takamasa, Hiroshi Kawamoto, Takashi Nakakuki, Mariko Okada, Shigeki Ohtake et Shinji Nakao. « Individual Hematopoietic Stem Cells in Human Bone Marrow Stably Give Rise to Limited Cell Lineages »,. Blood 118, no 21 (18 novembre 2011) : 3410. http://dx.doi.org/10.1182/blood.v118.21.3410.3410.
Texte intégralRésumé :
Abstract Abstract 3410 Background: To sustain hematopoiesis, hematopoietic stem cells (HSCs) must, on the one hand, replenish themselves by self-renewal and on the other hand produce differentiating progenitor cells. However, it has been difficult to address the actual dynamics of hematopoiesis due to the lack of appropriate experimental systems, regardless of animal species. In the case of humans, however, we were lead to consider one “experiment of nature” that makes it possible to track the progeny of a HSC; i.e. by detecting blood cells deficient in glycosylphosphatidylinositol-anchored proteins (GPI-APs) using flow cytometry. These cells are known to be derived from HSCs with a mutation in the phosphatidylinositol N-acetylglucosaminyltransferase subunit A (PIG-A) gene, which have properties similar to normal HSCs. We recently found that GPI-APs− cells in patients with aplastic anemia (AA) and myelodysplastic syndrome (MDS) frequently show various patterns in the proportion of granulocytes and erythrocytes and that the individual patterns of the two lineage combinations can persist for many years. GPI-APs− cells were rather frequently found in patients with less severe bone marrow (BM) failure. We thus reasoned that the dynamics of HSCs visualized in these cases might reflect those occurring during normal hematopoiesis. Objectives/Methods: We determined the proportion of GPI-APs− cells in six major lineages, namely granulocytes (G), monocytes (M), erythrocytes (E), T cells (T), NK cells (NK) and B cells (B), in peripheral blood cells from 601 BM failure patients using a highly sensitivity flow cytometric analysis and classified the lineage combinations of GPI-APs− cells in patients possessing GPI-APs− cells. We have attempted to test our idea of hematopoiesis by modeling and simulation. Results: Of 601 patients with BM failure, GPI-APs− cells cells were detected in at least one lineage of cells of 250 patients (42%) and the lineage combinations of GPI-APs− cells were classified into 16 different patterns such as GEM, GEMTBNK and GE. Of special interest was our finding that in all 250 cases, the same combinations of lineages were detected regardless of the interval between the first and second analysis and there was a clear trend toward the pattern of the higher the percentage of GPI-APs− granulocytes in patients, the greater the number of GPI-APs− cell lineages. It was clear from our studies that most of the small clones contain only limited lineage cells and even in the case of larger clones, e.g. clones of 1–3% that might be maintained with more than two HSCs, the majority (81%) were non-full-lineage clones. Based on these results indicating that most individual human HSCs only give rise to a limited range of hematopoietic progeny, we proposed a new idea that the observed patterns could be explained by assuming the presence of mosaic-like hematopoietic environments that could simultaneously support the “commitment” of early multipotent progenitors to a certain lineage. We have attempted to test this idea by modeling and simulation and assumed that a self-renewing HSC is located in a particular location in BM and that uncommitted progenitors derived from this HSC can reach to a certain defined area (Figure), which we termed the “commitment sphere”. If the BM microenvironment is mosaic in terms of function in the commitment of progenitors towards a certain lineage, and the size of such mosaic is as large as commitment sphere, then production of progenitors of limited lineages can occur. Indeed, by simulation of many virtual HSCs in a certain type of mosaic environment, formation of similar clone types was recapitulated. We also performed simulations of many virtual HSCs in the same mosaic environment while changing clone size (i.e. changing the size of the commitment sphere). The relationship between clone size and number of lineages in each clone in vivo was quite similar to that of the simulation model. Thus, these simulations provide a reasonable explanation for the observed in vivo findings. Conclusions: Individual HSCs in humans produce only restricted lineages of blood cells. The paradoxical phenomenon can be explained by a model in which the BM microenvironment is mosaic in supporting commitment of progenitors towards distinct lineages. Disclosures: No relevant conflicts of interest to declare.
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Zhou, Xiaohui, Xinan Jiao et Martin Wiedmann. « Listeria monocytogenes in the Chinese food system : strain characterization through partial actA sequencing and tissue-culture pathogenicity assays ». Journal of Medical Microbiology 54, no 3 (1 mars 2005) : 217–24. http://dx.doi.org/10.1099/jmm.0.45882-0.
Texte intégralRésumé :
Human listeriosis is generally caused by consumption of ready-to-eat (RTE) foods that are stored for extended periods of time at refrigeration temperatures and that permit the growth of the causative agent, Listeria monocytogenes. Food-consumption patterns in China are undergoing rapid changes and more regular consumption of refrigerated-storage RTE foods may increase the risk of human listeriosis. In total, 40 L. monocytogenes isolates were obtained from food (n = 32) and sewage (n = 6) samples and from two human listeriosis cases that occurred in China. All isolates were characterized into molecular subtypes by DNA sequencing of the 597 bp 3′-terminal region of the virulence gene actA. Sequence data were used to classify the 40 Chinese L. monocytogenes isolates into sequence types and phylogenetic lineages, and to compare the sequence types of the Chinese isolates with those of isolates from the USA. Phylogenetic analyses showed that the Chinese isolates could be separated into two genetic lineages, with 14 and 26 isolates belonging to lineages I and II, respectively. Lineage II could be subdivided further into two clusters, IIA and IIB. Lineages I and II were identical to the two lineages described previously among US L. monocytogenes isolates. In total, 14 actA sequence types could be differentiated among the 40 Chinese L. monocytogenes isolates; two specific actA sequence types were found among both Chinese and US isolates. Isolates belonging to lineage II showed a significantly lower ability to invade and multiply within human intestinal epithelial Caco-2 cells than lineage I isolates. It was concluded that DNA sequencing of the 3′-terminal region of actA appears to be an effective method for rapid subtype and lineage classification of L. monocytogenes. As strains belonging to lineages I and II have previously been found among isolates from Europe and North America, these results show that L. monocytogenes clonal groups found in China are very similar to those found in the USA. Many L. monocytogenes strains may thus represent globally distributed clonal types. Together with the first description of two human listeriosis cases in China, these data indicate that changes in food-distribution and -consumption patterns in China and other countries will probably lead to the emergence of human listeriosis as a food-safety issue, as virulent strains of this pathogen appear to be present in the Chinese food supply.
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Keinanen, M., S. Knuutila, CD Bloomfield, E. Elonen et A. de la Chapelle. « The proportion of mitoses in different cell lineages changes during short-term culture of normal human bone marrow ». Blood 67, no 5 (1 mai 1986) : 1240–43. http://dx.doi.org/10.1182/blood.v67.5.1240.1240.
Texte intégralRésumé :
Abstract To determine the hematopoietic cell lineage of mitotic cells in human bone marrow on direct examination and after 24-hour culture, marrow mitoses from four healthy individuals were studied, using a new technique that allows analysis of karyotypes in cells whose cell membrane and cytoplasm have been preserved. Mitoses were identified as being of erythroid lineage by immunofluorescent staining for surface glycophorin A and as being of granulocytic lineage by cytoplasmic staining for Sudan black B. On direct marrow examination without prior culture, the great majority of mitoses (74% to 90%) were of erythroid lineage; only a few (0% to 10%) were granulocytic. After 24-hour culture, the percentage of erythroid mitoses (15% to 40%) decreased, while the percentage of granulocytic mitoses (58% to 87%) increased strikingly. These data indicate that mitotic cells of different hematopoietic cell lineages predominate in marrow at different culture times and offer a plausible explanation for the high frequency of normal karyotypes in acute myeloid leukemia after direct marrow cytogenetic evaluation.
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Keinanen, M., S. Knuutila, CD Bloomfield, E. Elonen et A. de la Chapelle. « The proportion of mitoses in different cell lineages changes during short-term culture of normal human bone marrow ». Blood 67, no 5 (1 mai 1986) : 1240–43. http://dx.doi.org/10.1182/blood.v67.5.1240.bloodjournal6751240.
Texte intégralRésumé :
To determine the hematopoietic cell lineage of mitotic cells in human bone marrow on direct examination and after 24-hour culture, marrow mitoses from four healthy individuals were studied, using a new technique that allows analysis of karyotypes in cells whose cell membrane and cytoplasm have been preserved. Mitoses were identified as being of erythroid lineage by immunofluorescent staining for surface glycophorin A and as being of granulocytic lineage by cytoplasmic staining for Sudan black B. On direct marrow examination without prior culture, the great majority of mitoses (74% to 90%) were of erythroid lineage; only a few (0% to 10%) were granulocytic. After 24-hour culture, the percentage of erythroid mitoses (15% to 40%) decreased, while the percentage of granulocytic mitoses (58% to 87%) increased strikingly. These data indicate that mitotic cells of different hematopoietic cell lineages predominate in marrow at different culture times and offer a plausible explanation for the high frequency of normal karyotypes in acute myeloid leukemia after direct marrow cytogenetic evaluation.