scholarly journals Porcine colonoids and enteroids keep the memory of their origin during regeneration.

Author(s):  
Alicia M. Barnett ◽  
Jane A. Mullaney ◽  
Charlotte Hendriks ◽  
Lisa Le Borgne ◽  
Warren C. McNabb ◽  
...  

The development of alternative in vitro culture methods has increased in the last decade as three-dimensional organoids of various tissues, including those of the small and large intestines. Due to their multicellular composition, organoids offer advantages over traditionally used immortalized or primary cell lines. However, organoids must be accurate models of their tissues of origin. This study compared gene expression profiles with respect to markers of specific cell-types (stem-cells, enterocytes, goblet and enteroendocrine cells) and barrier maturation (tight junctions) of colonoid and enteroid cultures with their tissues of origin, and colonoids with enteroids. Colonoids derived from three healthy pigs formed multi-lobed structures with a monolayer of cells similar to the crypt structures in colonic tissue. Colonoid and enteroid gene expression signatures were more similar to those found for the tissues of their origin than to each other. However, relative to their derived tissues, organoids had increased gene expression levels of stem-cell markers Sox9 and Lgr5 encoding Sex determining region Y-box 9 and leucine-rich repeat-containing G-protein coupled rector 5, respectively. In contrast, expression levels of Occl and Zo1 encoding occludin and zonula occludens 1 respectively, were decreased. Expression levels of the cell lineage markers Atoh1, Cga and Muc2 encoding atonal homolog 1, chromogranin A and mucin 2 respectively, were decreased in colonoids, while Sglt1 and Apn encoding sodium-glucose transporter 1 and aminopeptidase A respectively, were decreased in enteroids. These results indicate colonoid and enteroid cultures were predominantly comprised of undifferentiated cell-types with decreased barrier maturation relative to their tissues of origin.

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wiruntita Chankeaw ◽  
Sandra Lignier ◽  
Christophe Richard ◽  
Theodoros Ntallaris ◽  
Mariam Raliou ◽  
...  

Abstract Background A number of studies have examined mRNA expression profiles of bovine endometrium at estrus and around the peri-implantation period of pregnancy. However, to date, these studies have been performed on the whole endometrium which is a complex tissue. Consequently, the knowledge of cell-specific gene expression, when analysis performed with whole endometrium, is still weak and obviously limits the relevance of the results of gene expression studies. Thus, the aim of this study was to characterize specific transcriptome of the three main cell-types of the bovine endometrium at day-15 of the estrus cycle. Results In the RNA-Seq analysis, the number of expressed genes detected over 10 transcripts per million was 6622, 7814 and 8242 for LE, GE and ST respectively. ST expressed exclusively 1236 genes while only 551 transcripts were specific to the GE and 330 specific to LE. For ST, over-represented biological processes included many regulation processes and response to stimulus, cell communication and cell adhesion, extracellular matrix organization as well as developmental process. For GE, cilium organization, cilium movement, protein localization to cilium and microtubule-based process were the only four main biological processes enriched. For LE, over-represented biological processes were enzyme linked receptor protein signaling pathway, cell-substrate adhesion and circulatory system process. Conclusion The data show that each endometrial cell-type has a distinct molecular signature and provide a significantly improved overview on the biological process supported by specific cell-types. The most interesting result is that stromal cells express more genes than the two epithelial types and are associated with a greater number of pathways and ontology terms.


2019 ◽  
Author(s):  
Arnav Moudgil ◽  
Michael N. Wilkinson ◽  
Xuhua Chen ◽  
June He ◽  
Alex J. Cammack ◽  
...  

AbstractIn situ measurements of transcription factor (TF) binding are confounded by cellular heterogeneity and represent averaged profiles in complex tissues. Single cell RNA-seq (scRNA-seq) is capable of resolving different cell types based on gene expression profiles, but no technology exists to directly link specific cell types to the binding pattern of TFs in those cell types. Here, we present self-reporting transposons (SRTs) and their use in single cell calling cards (scCC), a novel assay for simultaneously capturing gene expression profiles and mapping TF binding sites in single cells. First, we show how the genomic locations of SRTs can be recovered from mRNA. Next, we demonstrate that SRTs deposited by the piggyBac transposase can be used to map the genome-wide localization of the TFs SP1, through a direct fusion of the two proteins, and BRD4, through its native affinity for piggyBac. We then present the scCC method, which maps SRTs from scRNA-seq libraries, thus enabling concomitant identification of cell types and TF binding sites in those same cells. As a proof-of-concept, we show recovery of cell type-specific BRD4 and SP1 binding sites from cultured cells. Finally, we map Brd4 binding sites in the mouse cortex at single cell resolution, thus establishing a new technique for studying TF biology in situ.


2019 ◽  
Author(s):  
Chen-Hao Chen ◽  
Rongbin Zheng ◽  
Jingyu Fan ◽  
Myles Brown ◽  
Jun S. Liu ◽  
...  

AbstractTo characterize the genomic distances over which transcription factors (TFs) influence gene expression, we examined thousands of TF and histone modification ChIP-seq datasets and thousands of gene expression profiles. A model integrating these data revealed two classes of TF: one with short-range regulatory influence, the other with long-range regulatory influence. The two TF classes also had distinct chromatin-binding preferences and auto-regulatory properties. The regulatory range of a single TF bound within different topologically associating domains (TADs) depended on intrinsic TAD properties such as local gene density and G/C content, but also on the TAD chromatin state in specific cell types. Our results provide evidence that most TFs belong to one of these two functional classes, and that the regulatory range of long-range TFs is chromatin-state dependent. Thus, consideration of TF type, distance-to-target, and chromatin context is likely important in identifying TF regulatory targets and interpreting GWAS and eQTL SNPs.


2006 ◽  
Vol 18 (2) ◽  
pp. 134
Author(s):  
S. Kurosaka ◽  
N. A. Leu ◽  
K. J. McLaughlin

Mammalian somatic cell clones frequently exhibit abnormal gene expression that presumably results from errors in reprogramming of the transplanted genome. In the mouse, aggregation of 4-cell stage clones with each other improves reprogramming with respect to Oct-4 expression in blastocysts and an increase in term development (Boiani et al. 2003 EMBO J. 22, 5304-5312). To determine if clone-clone aggregation has a similar beneficial effect in the bovine, we aggregated 8-16 cell bovine clones with each other and profiled gene expression levels in bovine clones and clone-clone aggregates at the blastocyst stage. Clone embryos were produced from fibroblasts and cultured in vitro in SOF supplemented with fetal bovine serum at 39�C in an atmosphere of 5% CO2, 5% O2, and 90% N2. For aggregation of embryos, we first removed the zonae pepellucidae by treatment with 0.5% pronase at the 8-16 cell stage and then placed two zona-free embryos per well into deep microwells produced on the bottom of a culture dish by pressing a heated darning needle onto the surface. Seven to 10 microwells in close proximity were covered by a culture 50-�L drop of culture medium, and embryos were cultured until Day 7. Real-time RT-PCR analysis for Oct-4, DNA methyltransferase 1 (Dnmt1), Dnmt3, glucose transporter 1 (Glut1), Glut3, and Poly(A) polymerase (PolyA) was performed on reusable Dynabead Oligo (dT)25-cDNA libraries synthesized from individual blastocysts at Day 7. In vitro-fertilized embryos were used as controls. To compare the variation of gene expression in each embryo within the group, the coefficient of variation (COV; standard deviation/mean) was calculated. Although spatial distribution of Oct-4 transcript is normal in bovine blastocyst stage clones (Kurosaka et al. 2004 Reprod. Fertil. Dev. 16, 147), we detected disturbances in the level of Oct-4 expression in clones: 44.4% (8 of 18) of clones expressed Oct-4 within a range of 0.5- and 1.5-fold of the average level of expression in IVF embryos, compared to 81.8% (9 of 11) of IVF embryos. Only 22.2% (4 of 18) of clones expressed all genes examined within a range of 0.5- and 2.0-fold of the average level of IVF embryos, versus 45.5% (5 of 11) of IVF embryos. Clone-clone aggregation did not increase the proportion of clones with normal expression levels but did reduce the coefficient of variation of gene expression levels between individual clones for the genes Oct-4, Dnmt1, Dnmt3a and PolyA, but not for Glut1 and Glut3. Interestingly, bovine clone-clone aggregates (n = 25) had less variation between individual embryos compared to IVF aggregates (n = 11) for all genes except Glut1 and Glut3, although variation of single clones was larger than that of single IVF embryos. Analysis of Oct-4 and �-Actin transcripts in mouse clone blastocysts indicated a similar decrease in gene expression variation subsequent to aggregation of mouse clones. These results demonstrate that bovine pre-implantation stage clones exhibit a high degree of variation in gene expression levels and suggest that aggregation of clones is beneficial in reducing the variation in expression of some genes.


2012 ◽  
Vol 24 (1) ◽  
pp. 121
Author(s):  
L. S. A. Camargo ◽  
M. M. Pereira ◽  
S. Wohlres-Viana ◽  
C. R. C. Quintão ◽  
L. T. Iguma ◽  
...  

Trichostatin A is a histone deacetylase inhibitor that improves histone acetylation and chromatin remodeling of somatic cell nuclear-transferred embryos (Iager et al. 2008 Cloning Stem Cells 10, 371–379; Maalouf et al. 2009 BMC Dev. Biol. 9, 11). We have previously observed that it also improves quality of bovine cloned embryos, which may increase pregnancy rates. This study aimed to evaluate the effect of trichostatin A treatment of zygotes on relative abundance of 9 transcripts in bovine nuclear-transferred blastocysts. In vitro matured oocytes were enucleated, fused to somatic cells and activated with ionomycin (Camargo et al. 2011 Reprod. Fertil. Dev. 23, 122). After activation, putative zygotes were randomly separated into 2 groups: NT-TRICHO, zygotes were cultured for 4 h in 6-DMAP followed by 7 h in CR2 aa medium plus with 2.5% fetal calf serum (FCS; Nutricell, Campinas, Brazil), both supplemented with 50 nM trichostatin A (Sigma); NT-CONT, zygotes were cultured in the same described conditions without thichostatin A supplementation. In vitro-fertilized embryos (IVF group) were used as a calibrator for relative transcript quantification. Embryos from the 3 groups were cultured in CR2 aa supplemented with 2.5% FCS under 5% CO2, 5% O2 and 90% N2 at 38.5°C. At 168 h postactivation, the embryos were rapidly frozen in liquid nitrogen. Pools of 10 blastocysts for each group were subject to RNA extraction and reverse transcription, in which cDNA was amplified by real-time PCR using the β-actin and GAPDH genes as endogenous references. The transcripts analysed encode high mobility group N1 (HMGN1), peroxiredoxin 1 (PRDX1), octamer-binding protein 4 (OCT4), insulin-like growth factor 1 and 2 receptors (IGF1r and IGF2r), glucose transporter 1 and 5 (GLUT1 and GLUT5), histone acetyltransferase (HAT) and heat shock protein 70.1 (HSP70) genes. Results were analysed by a pair-wise fixed reallocation randomization test using the REST software v.2. Data from NT-TRICHO and NT-CONT were compared with the IVF group and between themselves. The relative abundance of HSP70, PRDX1, IGF2r and HMGN1 transcripts was higher (P < 0.05) in NT-TRICHO compared with the IVF group and no difference was detected for the other transcripts. In the NT-CONT group, the relative abundance of IGF2r and HAT was higher (P < 0.05), whereas IGF1r and OCT4 were lower (P < 0.05) compared with IVF embryos. When data from NT-TRICHO and NT-CONT were compared, a higher amount (P < 0.05) of stress-associated transcripts (HSP70 and PRDX1) were found in NT-TRICO blastocysts. These results suggest that although trichostatin A may improve chromatin remodeling, alterations on gene expression still persist in bovine somatic cell nuclear-transferred blastocysts in comparison with IVF embryos. Financial support: Embrapa Project 01.07.01.002, CNPq 403019/2008–7 and Fapemig.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 1183-1183
Author(s):  
Davorka Messmer ◽  
Tomoyuki Endo ◽  
Bradley T. Messmer ◽  
Danelle James ◽  
Nathan J. Zvaifler ◽  
...  

Abstract When CD14+ blood mononuclear cells are cultured with chronic lymphocytic leukemia (CLL) B cells they can differentiate into “nurselike” cells (NLCs), which in turn can support the survival of CLL B cells in vitro and possibly in vivo. While factors that contribute to NLC-mediated support of CLL B cell survival have been identified, it is not clear how this cell type relates to other cell types that also can differentiate from CD14+ blood cells, such as monocyte-derived dendritic cells (DCs). Prior studies have identified some phenotypic differences between NLCs, DCs, and other CD14+ blood mononuclear cells. Thus we hypothesized that these cell types may have different gene expression patterns that may relate to distinctive functional properties. To resolve this we examined the genes expressed by monocytes, NLCs, and immature DCs using Affymetrix U133 microarray analyses. Gene expression profiles were generated from the CD14+ monocyte progenitors, NLC, and DC from three different individuals. The expression profiles of DCs and NLCs differed from the CD14+ progenitors by the expression of many thousands of genes and NLC were distinguished from DCs by the expression of several hundred genes. Some of the genes expressed at higher levels in DCs relative to NLCs encode accessory molecules involved in antigen presentation. Consistent with this, we found that immature DCs were 10 times more effective than NLCs in presenting antigen to allogeneic T cells. DCs express toll like receptors (TLR) on their cell surface that recognize pathogen components and upon exposure to TLR ligands DCs undergo a maturation process, whereby they upregulate surface molecules and gain increased T cell stimulatory capacity. The expression of TLR2, 4, and 9 was analyzed in DCs and NLCs by RT PCR. Both DCs and NLCs were found to express mRNA for TLR2 and 4, but only NLCs expressed TLR9. In concordance with this, NLCs but not DCs unregulated MHC-II after exposure to nonmethylated CpG oligodeoxinucleotides (ODN), a TLR9 agonist, whereas both cell types upregulated MHC-II after exposure to lipopolysaccharide. Given the propensity of CD14+ cells to differentiate down a NLC pathway when co-cultured with leukemic B cells in vitro, we speculate that differentiation of CD14+ cells into NLCs may be favored in patients with CLL over differentiation into DCs. Given the relative differences in APC function of these two cell types, this may account in part for the acquired immune deficiency often observed in patients with this disease. On the other hand a stimulus like CpG ODN, might increase the ability of NLCs to activate T cells and decrease their ability to support CLL B cells survival.


2019 ◽  
Vol 40 (4) ◽  
pp. 747-759 ◽  
Author(s):  
Yan Wang ◽  
Ying Luo ◽  
Yang Yao ◽  
Yuhua Ji ◽  
Liangshu Feng ◽  
...  

Long noncoding RNAs (lncRNA) expression profiles change in the ischemic brain after stroke, but their roles in specific cell types after stroke have not been studied. We tested the hypothesis that lncRNA modulates brain injury by altering macrophage functions. Using RNA deep sequencing, we identified 73 lncRNAs that were differentially expressed in monocyte-derived macrophages (MoDMs) and microglia-derived macrophages (MiDMs) isolated in the ischemic brain three days after stroke. Among these, the lncRNA, GM15628, is highly expressed in pro-inflammatory MoDMs but not in MiDMs, and are functionally related to its neighbor gene, lymphocyte cytosolic protein 1 (LCP1), which plays a role in maintaining cell shape and cell migration. We termed this lncRNA as Macrophage contained LCP1 related pro-inflammatory lncRNA, Maclpil. Using cultured macrophages polarized by LPS, M(LPS), we found that downregulation of Maclpil in M(LPS) decreased pro-inflammatory gene expression while promoting anti-inflammatory gene expression. Maclpil inhibition also reduced the migration and phagocytosis ability of MoDMs by inhibiting LCP1. Furthermore, adoptive transfer of Maclpil silenced M(LPS), reduced ischemic brain infarction, improved behavioral performance and attenuated penetration of MoDMs in the ischemic hemisphere. We conclude that by blocking macrophage, Maclpil protects against acute ischemic stroke by inhibiting neuroinflammation.


2016 ◽  
Vol 22 (6) ◽  
pp. 579-592 ◽  
Author(s):  
Xiaomin Dong ◽  
Yanan You ◽  
Jia Qian Wu

The composition and function of the central nervous system (CNS) is extremely complex. In addition to hundreds of subtypes of neurons, other cell types, including glia (astrocytes, oligodendrocytes, and microglia) and vascular cells (endothelial cells and pericytes) also play important roles in CNS function. Such heterogeneity makes the study of gene transcription in CNS challenging. Transcriptomic studies, namely the analyses of the expression levels and structures of all genes, are essential for interpreting the functional elements and understanding the molecular constituents of the CNS. Microarray has been a predominant method for large-scale gene expression profiling in the past. However, RNA-sequencing (RNA-Seq) technology developed in recent years has many advantages over microarrays, and has enabled building more quantitative, accurate, and comprehensive transcriptomes of the CNS and other systems. The discovery of novel genes, diverse alternative splicing events, and noncoding RNAs has remarkably expanded the complexity of gene expression profiles and will help us to understand intricate neural circuits. Here, we discuss the procedures and advantages of RNA-Seq technology in mammalian CNS transcriptome construction, and review the approaches of sample collection as well as recent progress in building RNA-Seq-based transcriptomes from tissue samples and specific cell types.


Blood ◽  
2005 ◽  
Vol 105 (12) ◽  
pp. 4613-4619 ◽  
Author(s):  
Falk Martin ◽  
Tobias Linden ◽  
Dörthe M. Katschinski ◽  
Felix Oehme ◽  
Ingo Flamme ◽  
...  

Abstract Cellular oxygen partial pressure is sensed by a family of prolyl-4-hydroxylase domain (PHD) enzymes that modify hypoxia-inducible factor (HIF)α subunits. Upon hydroxylation under normoxic conditions, HIFα is bound by the von Hippel-Lindau tumor suppressor protein and targeted for proteasomal destruction. Since PHD activity is dependent on oxygen and ferrous iron, HIF-1 mediates not only oxygen- but also iron-regulated transcriptional gene expression. Here we show that copper (CuCl2) stabilizes nuclear HIF-1α under normoxic conditions, resulting in hypoxia-response element (HRE)-dependent reporter gene expression. In in vitro hydroxylation assays CuCl2 inhibited prolyl-4-hydroxylation independently of the iron concentration. Ceruloplasmin, the main copper transport protein in the plasma and a known HIF-1 target in vitro, was also induced in vivo in the liver of hypoxic mice. Both hypoxia and CuCl2 increased ceruloplasmin (as well as vascular endothelial growth factor [VEGF] and glucose transporter 1 [Glut-1]) mRNA levels in hepatoma cells, which was due to transcriptional induction of the ceruloplasmin gene (CP) promoter. In conclusion, our data suggest that PHD/HIF/HRE-dependent gene regulation can serve as a sensory system not only for oxygen and iron but also for copper metabolism, regulating the oxygen-, iron- and copper-binding transport proteins hemoglobin, transferrin, and ceruloplasmin, respectively. (Blood. 2005;105:4613-4619)


Parasitology ◽  
2005 ◽  
Vol 132 (1) ◽  
pp. 83-94 ◽  
Author(s):  
J. MATSUMOTO ◽  
N. MÜLLER ◽  
A. HEMPHILL ◽  
Y. OKU ◽  
M. KAMIYA ◽  
...  

The present study aimed to search for and characterize parasite molecules, whose expression levels correlate with the viability and growth activity of Echinococcus multilocularis metacestodes. We focused on the expression profiles of 2 parasite-derived genes, 14-3-3 and II/3-10, as putative molecular markers for viability and growth activity of the larval parasite. In experiments in vivo, gene expression levels of 14-3-3 and II/3-10 were relatively quantified by real-time reverse transcription-PCR using a housekeeping gene, beta-actin, as a reference reaction. All three reactions were compared with growth activity of the parasite developing in permissive nu/nu and in non-permissive wild type BALB/c mice. At 2 months p.i., the transcription level of 14-3-3 was significantly higher in parasites actively proliferating in nu/nu mice compared to parasites moderately growing in wild type mice. Immunoblotting experiments confirmed at the protein level that 14-3-3 was over-expressed in parasites derived from nu/nu mice at 2 months p.i. In vitro treatment of E. multilocularis with an anti-echinococcal drug nitazoxanide resulted in a significant decrease of both 14-3-3 and II/3-10 transcription levels found after 8 days of treatment, which correlated with the kinetics of a housekeeping gene, beta-actin. The conclusion is that 14-3-3, combined with II/3-10, exhibits good potential as a molecular marker to assess viability and growth activity of the parasite.


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