scholarly journals Architecture of a multi-cellular polygenic network governing immune homeostasis

2018 ◽  
Author(s):  
Tania Dubovik ◽  
Elina Starosvetsky ◽  
Benjamin LeRoy ◽  
Rachelly Normand ◽  
Yasmin Admon ◽  
...  
Keyword(s):  
Network Architecture ◽  
Cellular Network ◽  
Cell Types ◽  
Mouse Strains ◽  
Clinical Implications ◽  
Mass Cytometry ◽  
Cell Synchronization ◽  
High Heritability ◽  
Environmentally Sensitive ◽  
Shed Light

SummaryComplex physiological functionality is often the outcome of multiple interacting cell-types, yet mechanistically how a large number of trait-associated genes yield a single multi-cellular network governing the phenotype has not been well defined. Individuals’ immune-cellular profiles at homeostasis show high heritability and inter-individual variation with functional and clinical implications. We profiled immune cellular variation by mass-cytometry in 55 genetically diverse mouse strains. We identify 788 genes associated with cellular homeostasis, supporting a polygenic model where 52% of genes correspond to core homeostatic functions whose genetic variants suffice to predict phenotype. Trait genes form a multi-cellular network architecture showing increased functional complexity over evolutionary timescales for shared regulation to all cells, specialized cell-specific programs, and between-cell synchronization. Contrasting to human studies suggests the regulatory network expands with environmental exposure history. Our findings shed light on the origin of immune-cellular variation and regulatory architectures that may generalize to other environmentally sensitive systems.

scholarly journals Mast Cell-Specific Expression of Human Siglec-8 in Conditional Knock-in Mice

2018 ◽  
Vol 20 (1) ◽  
pp. 19 ◽  
Author(s):  
Yadong Wei ◽  
Krishan Chhiba ◽  
Fengrui Zhang ◽  
Xujun Ye ◽  
Lihui Wang ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Mast Cell ◽  
Mast Cells ◽  
Es Cells ◽  
Embryonic Stem ◽  
Surface Protein ◽  
Cell Types ◽  
Mouse Strains ◽  
Specific Expression

Sialic acid-binding Ig-like lectin 8 (Siglec-8) is expressed on the surface of human eosinophils, mast cells, and basophils—cells that participate in allergic and other diseases. Ligation of Siglec-8 by specific glycan ligands or antibodies triggers eosinophil death and inhibits mast cell degranulation; consequences that could be leveraged as treatment. However, Siglec-8 is not expressed in murine and most other species, thus limiting preclinical studies in vivo. Based on a ROSA26 knock-in vector, a construct was generated that contains the CAG promoter, a LoxP-floxed-Neo-STOP fragment, and full-length Siglec-8 cDNA. Through homologous recombination, this Siglec-8 construct was targeted into the mouse genome of C57BL/6 embryonic stem (ES) cells, and chimeric mice carrying the ROSA26-Siglec-8 gene were generated. After cross-breeding to mast cell-selective Cre-recombinase transgenic lines (CPA3-Cre, and Mcpt5-Cre), the expression of Siglec-8 in different cell types was determined by RT-PCR and flow cytometry. Peritoneal mast cells (dual FcεRI+ and c-Kit+) showed the strongest levels of surface Siglec-8 expression by multicolor flow cytometry compared to expression levels on tissue-derived mast cells. Siglec-8 was seen on a small percentage of peritoneal basophils, but not other leukocytes from CPA3-Siglec-8 mice. Siglec-8 mRNA and surface protein were also detected on bone marrow-derived mast cells. Transgenic expression of Siglec-8 in mice did not affect endogenous numbers of mast cells when quantified from multiple tissues. Thus, we generated two novel mouse strains, in which human Siglec-8 is selectively expressed on mast cells. These mice may enable the study of Siglec-8 biology in mast cells and its therapeutic targeting in vivo.

scholarly journals Action detection using a neural network elucidates the genetics of mouse grooming behavior

2020 ◽  
Author(s):  
Brian Q. Geuther ◽  
Asaf Peer ◽  
Hao He ◽  
Gautam Sabnis ◽  
Vivek M. Philip ◽  
...  
Keyword(s):  
Neural Network ◽  
Network Architecture ◽  
Stereotyped Behavior ◽  
General Purpose ◽  
Training Data ◽  
Mouse Strains ◽  
Human Observer ◽  
Grooming Behavior ◽  
Action Detection ◽  
Visual Diversity

AbstractAutomated detection of complex animal behaviors remains a challenging problem in neuroscience, particularly for behaviors that consist of disparate sequential motions. Grooming, a prototypical stereotyped behavior, is often used as an endophenotype in psychiatric genetics. Using mouse grooming behavior as an example, we develop a general purpose neural network architecture capable of dynamic action detection at human observer-level performance and operate across dozens of mouse strains with high visual diversity. We provide insights into the amount of human annotated training data that are needed to achieve such performance. We survey grooming behavior in the open field in 2500 mice across 62 strains, determine its heritable components, conduct GWAS to outline its genetic architecture, and perform PheWAS to link human psychiatric traits through shared underlying genetics. Our general machine learning solution that automatically classifies complex behaviors in large datasets will facilitate systematic studies of mechanisms underlying these behaviors.

scholarly journals Single-cell RNA counting at allele- and isoform-resolution using Smart-seq3

2019 ◽  
Author(s):  
Michael Hagemann-Jensen ◽  
Christoph Ziegenhain ◽  
Ping Chen ◽  
Daniel Ramsköld ◽  
Gert-Jan Hendriks ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Cell Types ◽  
Mouse Strains ◽  
Rna Molecules ◽  
Counting Strategy ◽  
Long Read ◽  
Sequencing Strategy ◽  
Transcriptome Coverage ◽  
Scale Characterization

AbstractLarge-scale sequencing of RNAs from individual cells can reveal patterns of gene, isoform and allelic expression across cell types and states1. However, current single-cell RNA-sequencing (scRNA-seq) methods have limited ability to count RNAs at allele- and isoform resolution, and long-read sequencing techniques lack the depth required for large-scale applications across cells2,3. Here, we introduce Smart-seq3 that combines full-length transcriptome coverage with a 5’ unique molecular identifier (UMI) RNA counting strategy that enabled in silico reconstruction of thousands of RNA molecules per cell. Importantly, a large portion of counted and reconstructed RNA molecules could be directly assigned to specific isoforms and allelic origin, and we identified significant transcript isoform regulation in mouse strains and human cell types. Moreover, Smart-seq3 showed a dramatic increase in sensitivity and typically detected thousands more genes per cell than Smart-seq2. Altogether, we developed a short-read sequencing strategy for single-cell RNA counting at isoform and allele-resolution applicable to large-scale characterization of cell types and states across tissues and organisms.

Fluorescent phospholipids preferentially accumulate in sub-tegumental cells of schistosomula of Schistosoma mansoni

1992 ◽  
Vol 103 (3) ◽  
pp. 823-830 ◽  
Author(s):  
S.T. Furlong ◽  
K.S. Thibault ◽  
R.A. Rogers
Keyword(s):  
Cellular Network ◽  
Biochemical Analysis ◽  
Phosphatidyl Ethanolamine ◽  
De Novo ◽  
Cell Types ◽  
Host Immunity ◽  
Epifluorescence Microscopy ◽  
Specific Cell ◽  
Back Exchange ◽  
Intact Molecule

Schistosomes do not make sterols or fatty acids de novo and thus require host lipids for survival. The acquisition of host lipids may also be an important factor in the schistosome's defense from host immunity; however, little is known about the regulation of this process. Here we have examined binding of radiolabeled and fluorescently labeled liposomes to schistosomula, and followed incorporation of fluorescent phospholipids into the worm by both morphological and biochemical methods. Saturable binding of radiolabeled phosphatidylcholine containing liposomes was observed and epifluorescence microscopy showed binding of C6-NBD-phosphatidylcholine (C6-NBD-PC), C12-NBD-phosphatidylcholine (C12-NBD-PC) and C6-NBD-phosphatidyl-ethanolamine (C6-NBD-PE) containing liposomes on the surface of the parasite. Following back-exchange with unlabeled liposomes, NBD-PC and NBD-PE were observed to be preferentially incorporated into specific cell types within the worm. Furthermore, cells which had accumulated the fluorescent lipid formed an interconnecting cellular network immediately below the tegument, identified as cytons. By contrast, fluorescein-PE was found only on the surface of the parasite and in the gut but not in the cytons. Biochemical analysis demonstrated that > 90% of the C6-NBD-PC and C12-NBD-PC remained as the intact molecule after a one hour incubation with the parasite, but that greater than 70% of the NBD-PE was converted to other lipids. These studies demonstrate that incorporation of phospholipid analogs into schistosomula can be followed morphologically and biochemically. As there was little localization of NBD-PE or NBD-PC in the gut, these analogs must be assimilated by crossing the tegument.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals Comparison of the Opn-CreER and Ck19-CreER Drivers in Bile Ducts of Normal and Injured Mouse Livers

Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 380 ◽  
Author(s):  
Lesaffer ◽  
Verboven ◽  
Van Huffel ◽  
Moya ◽  
van Grunsven ◽  
...  
Keyword(s):  
Bile Ducts ◽  
Cell Lineage ◽  
Cell Types ◽  
Lineage Tracing ◽  
Tamoxifen Treatment ◽  
Mouse Strains ◽  
Recombination Efficiency ◽  
Cre Recombination ◽  
Low Efficiency ◽  
Toxic Liver Injury

Inducible cyclization recombinase (Cre) transgenic mouse strains are powerful tools for cell lineage tracing and tissue-specific knockout experiments. However, low efficiency or leaky expression can be important pitfalls. Here, we compared the efficiency and specificity of two commonly used cholangiocyte-specific Cre drivers, the Opn-iCreERT2 and Ck19-CreERT drivers, using a tdTomato reporter strain. We found that Opn-iCreERT2 triggered recombination of the tdTomato reporter in 99.9% of all cholangiocytes while Ck19-CreERT only had 32% recombination efficiency after tamoxifen injection. In the absence of tamoxifen, recombination was also induced in 2% of cholangiocytes for the Opn-iCreERT2 driver and in 13% for the Ck19-CreERT driver. For both drivers, Cre recombination was highly specific for cholangiocytes since recombination was rare in other liver cell types. Toxic liver injury ectopically activated Opn-iCreERT2 but not Ck19-CreERT expression in hepatocytes. However, ectopic recombination in hepatocytes could be avoided by applying a three-day long wash-out period between tamoxifen treatment and toxin injection. Therefore, the Opn-iCreERT2 driver is best suited for the generation of mutant bile ducts, while the Ck19-CreERT driver has near absolute specificity for bile duct cells and is therefore favorable for lineage tracing experiments.

scholarly journals Prion Protein Expression Differences in Microglia and Astroglia Influence Scrapie-Induced Neurodegeneration in the Retina and Brain of Transgenic Mice

2007 ◽  
Vol 81 (19) ◽  
pp. 10340-10351 ◽  
Author(s):  
Lisa Kercher ◽  
Cynthia Favara ◽  
James F. Striebel ◽  
Rachel LaCasse ◽  
Bruce Chesebro
Keyword(s):  
Transgenic Mice ◽  
Prion Protein ◽  
Microglial Activation ◽  
Prion Diseases ◽  
Cell Types ◽  
Mouse Strains ◽  
Activation Markers ◽  
Activated Microglia ◽  
Morphological Criteria ◽  
Scrapie Infection

ABSTRACT Activated microglia and astroglia are known to be involved in a variety of neurodegenerative diseases, including prion diseases. In the present experiments, we studied activation of astroglia and microglia after intraocular scrapie infection in transgenic mice expressing prion protein (PrP) in multiple cell types (tg7 mice) or in neurons only (tgNSE mice). In this model, scrapie infection and protease-resistant PrP deposition occurs in the retinas of both strains of mice, but retinal degeneration is observed only in tg7 mice. Our results showed that the retinas of tg7 and tgNSE mice both had astroglial activation with increased chemokine expression during the course of infection. However, only tg7 retinas exhibited strong microglial activation compared to tgNSE retinas, which showed little microglial activation by biochemical or morphological criteria. Therefore, microglial PrP expression might be required for scrapie-induced retinal microglial activation and damage. Furthermore, microglial activation preceded retinal neurodegeneration in tg7 mice, suggesting that activated microglia might contribute to the degenerative process, rather than being a response to the damage. Surprisingly, brain differed from retina in that an altered profile of microglial activation markers was upregulated, and the profiles in the two mouse strains were indistinguishable. Microglial activation in the brain was associated with severe brain vacuolation and neurodegeneration, leading to death. Thus, retinal and brain microglia appeared to differ in their requirements for activation, suggesting that different activation pathways occur in the two tissues.

scholarly journals Facets of Autophagy Based Unconventional Protein Secretion–The Road Less Traveled

2020 ◽  
Vol 7 ◽  
Author(s):  
Sreedevi Padmanabhan ◽  
Ravi Manjithaya
Keyword(s):  
Endoplasmic Reticulum ◽  
Protein Secretion ◽  
Cell Types ◽  
Recycling Process ◽  
Physiological Conditions ◽  
The Road ◽  
Secretory Autophagy ◽  
Shed Light

Unconventional protein secretion (UCPS) of leaderless proteins bypasses the conventional endoplasmic reticulum (ER)-Golgi route. The proportion of UCPS in the secretome varies tremendously across eukaryotes. Interestingly, macroautophagy, an intracellular recycling process that is generally involved in cargo degradation, also participates in UCPS. This emerging field of secretory mode of autophagy is underexplored and has several unanswered questions regarding the composition of players, cargo, and the mechanisms that drive it. As secretomes vary considerably across cell types and physiological conditions, the contribution of secretory autophagy in healthy and pathophysiological states remain to be elucidated. Recent studies have begun to shed light on this enigmatic process.

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