scholarly journals Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution

2016 ◽  
Author(s):  
Amit Blumberg ◽  
Edward J. Rice ◽  
Anshul Kundaje ◽  
Charles G. Danko ◽  
Dan Mishmar
Keyword(s):  
Cell Lines ◽  
Human Cell ◽  
Transcription Initiation ◽  
De Novo ◽  
Cell Types ◽  
Reference Sequence ◽  
Sequence Motif ◽  
Mtdna Sequence ◽  
Mtdna Transcription

AbstractMitochondrial DNA (mtDNA) genes are long known to be co-transcribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. To this end we used deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organisms. Surprisingly, accurate detection of human mtDNA transcription initiation sites (TIS) in the heavy and light strands revealed a novel conserved transcription pausing site near the light strand TIS, upstream to the transcription-replication transition region. This pausing site correlated with the presence of a bacterial pausing sequence motif, yet the transcription pausing index varied quantitatively among the cell lines. Analysis of non-human organisms enabled de novo mtDNA sequence assembly, as well as detection of previously unknown mtDNA TIS, pausing, and transcription termination sites with unprecedented accuracy. Whereas mammals (chimpanzee, rhesus macaque, rat, and mouse) showed a human-like mtDNA transcription pattern, the invertebrate pattern (Drosophila and C. elegans) profoundly diverged. Our approach paves the path towards in vivo, quantitative, reference sequence-free analysis of mtDNA transcription in all eukaryotes.

scholarly journals Analysis of Mitochondrial DNA Polymorphisms in the Human Cell Lines HepaRG and SJCRH30

2019 ◽  
Vol 20 (13) ◽  
pp. 3245 ◽  
Author(s):  
Matthew J. Young ◽  
Anitha D. Jayaprakash ◽  
Carolyn K. J. Young
Keyword(s):  
Mitochondrial Dna ◽  
Cell Lines ◽  
Human Cell ◽  
Cell Types ◽  
Dna Polymorphisms ◽  
Reference Sequence ◽  
Sequencing Analysis ◽  
Human Cell Lines ◽  
Mtdna Sequences ◽  
Mtdna Variants

The mitochondrial DNA (mtDNA) sequences of two commonly used human cell lines, HepaRG and SJCRH30, were determined. HepaRG originates from a liver tumor obtained from a patient with hepatocarcinoma and hepatitis C while SJCRH30 originates from a rhabdomyosarcoma patient tumor. In comparison to the revised Cambridge Reference Sequence, HepaRG and SJCRH30 mtDNA each contain 14 nucleotide variations. In addition to an insertion of a cytosine at position 315 (315insC), the mtDNA sequences from both cell types share six common polymorphisms. Heteroplasmic variants were identified in both cell types and included the identification of the 315insC mtDNA variant at 42 and 75% heteroplasmy in HepaRG and SJCRH30, respectively. Additionally, a novel heteroplasmic G13633A substitution in the HepaRG ND5 gene was detected at 33%. Previously reported cancer-associated mtDNA variants T195C and T16519C were identified in SJCRH30, both at homoplasmy (100%), while HepaRG mtDNA harbors a known prostate cancer-associated T6253C substitution at near homoplasmy, 95%. Based on our sequencing analysis, HepaRG mtDNA is predicted to lie within haplogroup branch H15a1 while SJCRH30 mtDNA is predicted to localize to H27c. The catalog of polymorphisms and heteroplasmy reported here should prove useful for future investigations of mtDNA maintenance in HepaRG and SJCRH30 cell lines.

scholarly journals Enhanced Cellular Uptake of H-Chain Human Ferritin Containing Gold Nanoparticles

Pharmaceutics ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1966
Author(s):  
Italo Moglia ◽  
Margarita Santiago ◽  
Simon Guerrero ◽  
Mónica Soler ◽  
Alvaro Olivera-Nappa ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Cell Lines ◽  
Cellular Uptake ◽  
Human Cell ◽  
Animal Experiments ◽  
Cell Types ◽  
Biological Properties ◽  
Human Cell Lines ◽  
Theranostic Agents

Gold nanoparticles (AuNP) capped with biocompatible layers have functional optical, chemical, and biological properties as theranostic agents in biomedicine. The ferritin protein containing in situ synthesized AuNPs has been successfully used as an effective and completely biocompatible nanocarrier for AuNPs in human cell lines and animal experiments in vivo. Ferritin can be uptaken by different cell types through receptor-mediated endocytosis. Despite these advantages, few efforts have been made to evaluate the toxicity and cellular internalization of AuNP-containing ferritin nanocages. In this work, we study the potential of human heavy-chain (H) and light-chain (L) ferritin homopolymers as nanoreactors to synthesize AuNPs and their cytotoxicity and cellular uptake in different cell lines. The results show very low toxicity of ferritin-encapsulated AuNPs on different human cell lines and demonstrate that efficient cellular ferritin uptake depends on the specific H or L protein chains forming the ferritin protein cage and the presence or absence of metallic cargo. Cargo-devoid apoferritin is poorly internalized in all cell lines, and the highest ferritin uptake was achieved with AuNP-loaded H-ferritin homopolymers in transferrin-receptor-rich cell lines, showing more than seven times more uptake than apoferritin.

scholarly journals Infection, dissemination, and transmission efficiencies of Zika virus in Aedes aegypti after serial passage in mosquito or mammalian cell lines or alternating passage in both cell types

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Lourdes G. Talavera-Aguilar ◽  
Reyes A. Murrieta ◽  
Sungmin Kiem ◽  
Rosa C. Cetina-Trejo ◽  
Carlos M. Baak-Baak ◽  
...  
Keyword(s):  
Aedes Aegypti ◽  
Cell Lines ◽  
Zika Virus ◽  
Cell Types ◽  
Mosquito Cell ◽  
Cell Passage ◽  
Genetic Changes ◽  
Synonymous Substitutions ◽  
Vertebrate Cell

Abstract Background Zika virus (ZIKV) is an arthropod-borne virus (arbovirus) with an urban transmission cycle that primarily involves humans and Aedes aegypti. Evidence suggests that the evolution of some arboviruses is constrained by their dependency on alternating between disparate (vertebrate and invertebrate) hosts. The goals of this study are to compare the genetic changes that occur in ZIKV after serial passaging in mosquito or vertebrate cell lines or alternate passaging in both cell types and to compare the replication, dissemination, and transmission efficiencies of the cell culture-derived viruses in Ae. aegypti. Methods An isolate of ZIKV originally acquired from a febrile patient in Yucatan, Mexico, was serially passaged six times in African green monkey kidney (Vero) cells or Aedes albopictus (C6/36) cells or both cell types by alternating passage. A colony of Ae. aegypti from Yucatan was established, and mosquitoes were challenged with the cell-adapted viruses. Midguts, Malpighian tubules, ovaries, salivary glands, wings/legs and saliva were collected at various times after challenge and tested for evidence of virus infection. Results Genome sequencing revealed the presence of two non-synonymous substitutions in the premembrane and NS1 regions of the mosquito cell-adapted virus and two non-synonymous substitutions in the capsid and NS2A regions of both the vertebrate cell-adapted and alternate-passaged viruses. Additional genetic changes were identified by intrahost variant frequency analysis. Virus maintained by continuous C6/36 cell passage was significantly more infectious in Ae. aegypti than viruses maintained by alternating passage and consecutive Vero cell passage. Conclusions Mosquito cell-adapted ZIKV displayed greater in vivo fitness in Ae. aegypti compared to the other viruses, indicating that obligate cycling between disparate hosts carries a fitness cost. These data increase our understanding of the factors that drive ZIKV adaptation and evolution and underscore the important need to consider the in vivo passage histories of flaviviruses to be evaluated in vector competence studies. Graphic abstract "Image missing"

scholarly journals Epithelial argininosuccinate synthetase is dispensable for intestinal regeneration and tumorigenesis

2021 ◽  
Vol 12 (10) ◽  
Author(s):  
Jonathan H. M. van der Meer ◽  
Ruben J. de Boer ◽  
Bartolomeus J. Meijer ◽  
Wouter L. Smit ◽  
Jacqueline L. M. Vermeulen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Intestinal Epithelium ◽  
De Novo ◽  
Cell Types ◽  
Intestinal Epithelial ◽  
Argininosuccinate Synthetase ◽  
Important Amino Acid ◽  
Tissue Specimens ◽  
Colorectal Cancer Patients

AbstractThe epithelial signaling pathways involved in damage and regeneration, and neoplastic transformation are known to be similar. We noted upregulation of argininosuccinate synthetase (ASS1) in hyperproliferative intestinal epithelium. Since ASS1 leads to de novo synthesis of arginine, an important amino acid for the growth of intestinal epithelial cells, its upregulation can contribute to epithelial proliferation necessary to be sustained during oncogenic transformation and regeneration. Here we investigated the function of ASS1 in the gut epithelium during tissue regeneration and tumorigenesis, using intestinal epithelial conditional Ass1 knockout mice and organoids, and tissue specimens from colorectal cancer patients. We demonstrate that ASS1 is strongly expressed in the regenerating and Apc-mutated intestinal epithelium. Furthermore, we observe an arrest in amino acid flux of the urea cycle, which leads to an accumulation of intracellular arginine. However, loss of epithelial Ass1 does not lead to a reduction in proliferation or increase in apoptosis in vivo, also in mice fed an arginine-free diet. Epithelial loss of Ass1 seems to be compensated by altered arginine metabolism in other cell types and the liver.

Abstract 897: Alliance of Blood Derived Endothelial Cells and Adipose Stromal Cells in Human Vasculogenesis

Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Dmitry O Traktuev ◽  
Daniel N Prater ◽  
Aravind R Sanjeevaiah ◽  
Stephanie Merfeld-Clauss ◽  
Brian H Johnstone ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Stromal Cells ◽  
De Novo ◽  
Functional Integration ◽  
Cell Types ◽  
Specific Marker ◽  
Pronounced Difference ◽  
Adipose Stromal Cells ◽  
Small Vessels

Introduction Both Endothelial progenitor cells (EPC) and adipose stromal cells (ASC) are under investigation as therapies for cardiovascular diseases. Both cell types are capable of modulating vascular assembly and are, thereby, capable of directly promoting revascularization of ischemic tissues. We have shown that EPC differentiate into endothelial cells to form small vessels, whereas ASC have pericytic properties and naturally stabilize vessels. In this study we tested the possibility that ASC would interact with EPC to assemble de novo vessels in collagen in an in vivo chimeric implant. Methods and Results Collagen implants embedded with either umbilical cord blood EPC or adult ASC or a 4:1 mixture of both (2x10 6 cells/ml) were implanted subcutaneously into NOD/SCID mice. After 14 d implants were harvested and evaluated by immunohistochemistry. There was a pronounced difference among the groups in vascular network assembly. The majority of vessels formed in the EPC and ASC monocultures were small capillaries bounded by a single endothelial layer. Conversely, 100% of the plugs embedded with both cell types were highly invaded with multilayered arteriolar vessels. The density of the CD31 + vessels in the EPC and co-culture plugs was 26.6 ± 5.8 and 122.4 ± 9.8 per mm 2 , respectively. No CD31 + cells of human origin were detected in the ASC monocultures, indicating that ASC, which do not express this EC-specific marker, engage murine EC or form pseudovessels in this system. The density of α-SMA + vessels with lumens per mm 2 was 13.1 ± 3.6 (EPC), 10.2 ± 3.5 (ASC) and 124.7 ± 19.7 (co-culture). The total overlap of CD31 + and SMA + vessels demonstrates that mature, multilayered conduits were formed with the co-culture. Moreover, the majority of these vessels were filled with erythrocytes (92.5 ± 16.2 per mm 2 ), indicating inosculation with the native vasculature, which was confirmed by ultrasound with echogenic microbubbles and persisted to at least 4 months. Conclusion This study is the first to demonstrate that non-transformed human EPC and ASC cooperatively form mature and stable vasculature with subsequent functional integration into a host vasculature system.

Cytokine-mediated PGE2expression in human colonic fibroblasts

1998 ◽  
Vol 275 (4) ◽  
pp. C988-C994 ◽  
Author(s):  
Edward C. Kim ◽  
Yingting Zhu ◽  
Valerie Andersen ◽  
Daniela Sciaky ◽  
H. James Cao ◽  
...  
Keyword(s):  
Epithelial Cell ◽  
Cell Lines ◽  
Shape Change ◽  
Cell Types ◽  
Mrna Levels ◽  
Primary Fibroblast ◽  
Fibroblast Cultures ◽  
Epithelial Cell Lines ◽  
Factor Α

We investigated prostanoid biogenesis in human colonic fibroblasts (CCD-18Co and 5 primary fibroblast cultures) and epithelial cell lines (NCM460, T84, HT-29, and LS 174T) and the effect of PGE2 on fibroblast morphology. Cytokine-stimulated PGE2production was measured. PGH synthase-1 and -2 (PGHS-1 and -2) protein and mRNA expression were evaluated. Basal PGE2 levels were low in all cell types (0.15–6.47 ng/mg protein). Treatment for 24 h with interleukin-1β (IL-1β; 10 ng/ml) or tumor necrosis factor-α (50 ng/ml), respectively, elicited maximal 25- and 6-fold inductions of PGE2 synthesis in CCD-18Co cultures and similar results in primary fibroblast cultures; maximal inductions with IL-1β in colonic epithelial cell lines were from zero to fivefold. Treatment of CCD-18Co fibroblasts with IL-1β caused maximal 21- and 53-fold increases, respectively, in PGHS-2 protein and mRNA levels without altering PGHS-1 expression. PGE2 (0.1 μmol/l) elicited a dramatic shape change in selected fibroblasts. Colonic fibroblasts are potentially important as cytokine targets and a source of and target for colonic prostanoids in vivo.

scholarly journals Corrigendum: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution

2019 ◽  
Vol 29 (4) ◽  
pp. 710.1-710.1
Author(s):  
Amit Blumberg ◽  
Edward J. Rice ◽  
Anshul Kundaje ◽  
Charles G. Danko ◽  
Dan Mishmar
Keyword(s):  
Human Cell ◽  
Cell Types ◽  
Mtdna Transcription

scholarly journals Viral Cross-Class Serpin Inhibits Vascular Inflammation and T Lymphocyte Fratricide; A Study in Rodent Models In Vivo and Human Cell Lines In Vitro

PLoS ONE ◽  
2012 ◽  
Vol 7 (9) ◽  
pp. e44694 ◽  
Author(s):  
Kasinath Viswanathan ◽  
Ilze Bot ◽  
Liying Liu ◽  
Erbin Dai ◽  
Peter C. Turner ◽  
...  
Keyword(s):  
Cell Lines ◽  
T Lymphocyte ◽  
Human Cell ◽  
Vascular Inflammation ◽  
Rodent Models ◽  
Human Cell Lines

Methylation and expression of the Myo D1 determination gene

1990 ◽  
Vol 326 (1235) ◽  
pp. 277-284 ◽  
Keyword(s):  
De Novo ◽  
Cell Types ◽  
Model System ◽  
Parental Line ◽  
Molecular Control ◽  
Embryo Cells ◽  
End Stage ◽  
Derivatives Of

Mouse embryo cells induced to differentiate with the demethylating agent 5- azacytidine represent an excellent model system to investigate the molecular control of development. Clonal derivatives of 10T1/2 cells that have become determined to the myogenic or adipogenic lineages can be isolated from the multipotential parental line after drug treatment. These determined derivatives can be cultured indefinitely and will differentiate into end-stage phenotypes on appropriate stimulation. A gene called Myo D1, recently isolated from such a myoblast line, will confer myogenesis when expressed in 10T1/2 or other cell types (Davis et al. 1987). The cDNA for Myo D1 contains a large number of CpG sequences and the gene is relatively methylated in 10T1/2 cells and an adipocyte derivative, but is demethylated in myogenic derivatives. Myo D1 may therefore be subject to methylation control in vitro . On the other hand, preliminary observations suggest that Myo D1 is not methylated at CCGG sites in vivo so that a de novo methylation event may have occurred in vitro . These observations may have significance in the establishment of immortal cell lines and tumours.

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