scholarly journals Whole-Genome Differentially Hydroxymethylated DNA Regions among Twins Discordant for Cardiovascular Death

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1183
Author(s):  
Jun Dai ◽  
Ming Leung ◽  
Weihua Guan ◽  
Han‐Tian Guo ◽  
Ruth E. Krasnow ◽  
...  

Epigenetics is a mechanism underlying cardiovascular disease. It is unknown whether DNA hydroxymethylation is prospectively associated with the risk for cardiovascular death independent of germline and common environment. Male twin pairs middle-aged in 1969–1973 and discordant for cardiovascular death through December 31, 2014, were included. Hydroxymethylation was quantified in buffy coat DNA collected in 1986–1987. The 1893 differentially hydroxymethylated regions (DhMRs) were identified after controlling for blood leukocyte subtypes and age among 12 monozygotic (MZ) pairs (Benjamini–Hochberg False Discovery Rate < 0.01), of which the 102 DhMRs were confirmed with directionally consistent log2-fold changes and p < 0.01 among additional 7 MZ pairs. These signature 102 DhMRs, independent of the germline, were located on all chromosomes except for chromosome 21 and the Y chromosome, mainly within/overlapped with intergenic regions and introns, and predominantly hyper-hydroxymethylated. A binary linear classifier predicting cardiovascular death among 19 dizygotic pairs was identified and equivalent to that generated from MZ via the 2D transformation. Computational bioinformatics discovered pathways, phenotypes, and DNA motifs for these DhMRs or their subtypes, suggesting that hydroxymethylation was a pathophysiological mechanism underlying cardiovascular death that might be influenced by genetic factors and warranted further investigations of mechanisms of these signature regions in vivo and in vitro.

2021 ◽  
Vol 12 (4) ◽  
Author(s):  
Shourong Wang ◽  
Zixiang Wang ◽  
Jieyin Li ◽  
Junchao Qin ◽  
Jianping Song ◽  
...  

AbstractAberrant expression of splicing factors was found to promote tumorigenesis and the development of human malignant tumors. Nevertheless, the underlying mechanisms and functional relevance remain elusive. We here show that USP39, a component of the spliceosome, is frequently overexpressed in high-grade serous ovarian carcinoma (HGSOC) and that an elevated level of USP39 is associated with a poor prognosis. USP39 promotes proliferation/invasion in vitro and tumor growth in vivo. Importantly, USP39 was transcriptionally activated by the oncogene protein c-MYC in ovarian cancer cells. We further demonstrated that USP39 colocalizes with spliceosome components in nuclear speckles. Transcriptomic analysis revealed that USP39 deletion led to globally impaired splicing that is characterized by skipped exons and overrepresentation of introns and intergenic regions. Furthermore, RNA immunoprecipitation sequencing showed that USP39 preferentially binds to exon-intron regions near 5′ and 3′ splicing sites. In particular, USP39 facilitates efficient splicing of HMGA2 and thereby increases the malignancy of ovarian cancer cells. Taken together, our results indicate that USP39 functions as an oncogenic splicing factor in ovarian cancer and represents a potential target for ovarian cancer therapy.


2006 ◽  
Vol 80 (22) ◽  
pp. 11355-11361 ◽  
Author(s):  
Shirin Kordasti ◽  
Claudia Istrate ◽  
Mahanez Banasaz ◽  
Martin Rottenberg ◽  
Henrik Sjövall ◽  
...  

ABSTRACT In contrast to humans, adult but not infant small animals are resistant to rotavirus diarrhea. The pathophysiological mechanism behind this age-restricted diarrhea is currently unresolved, and this question was investigated by studying the secretory state of the small intestines of adult mice infected with rotavirus. Immunohistochemistry and histological examinations revealed that rotavirus (strain EDIM) infects all parts of the small intestines of adult mice, with significant numbers of infected cells in the ilea at 2 and 4 days postinfection. Furthermore, quantitative PCR revealed that 100-fold more viral RNA was produced in the ilea than in the jejuna or duodena of adult mice. In vitro perfusion experiments of the small intestine did not reveal any significant changes in net fluid secretion among mice infected for 3 days or 4 days or in those that were noninfected (37 ± 9 μl · h−1 · cm−1, 22 ± 13 μl · h−1 · cm−1, and 33 ± 6 μl · h−1 · cm−1, respectively) or in transmucosal potential difference (4.0 ± 0.3 mV versus 3.9 ± 0.4 mV), a marker for active chloride secretion, between control and rotavirus-infected mice. In vivo experiments also did not show any differences in potential difference between uninfected and infected small intestines. Furthermore, no significant differences in weight between infected and uninfected small intestines were found, nor were any differences in fecal output observed between infected and control mice. Altogether, these data suggest that rotavirus infection is not sufficient to stimulate chloride and water secretion from the small intestines of adult mice.


Open Medicine ◽  
2011 ◽  
Vol 6 (2) ◽  
pp. 181-184
Author(s):  
Miodrag Vucic ◽  
Ivan Tijanic ◽  
Nenad Govedarevic ◽  
Lana Macukanovic ◽  
Zoran Pavlovic

AbstractThe preparation of thrombocyte concentrates with filtration before storage (in-line) makes it possible to avoid the presence of mononuclear cells in the concentrate and proinflammatory cytokines. Therefore, this filtration may result with decreased activation of trombocyte receptors in vitro, which may improve therapeutic efficiancy. Methods. We compared two groups, each with 30 therapeutic doses of concentrated thrombocytes. We prepared the first group using the classic model from the buffy coat and the other with concentrated thrombocyte samples filtrated during sampling, so-called in-line, with the WBC filter Imuflex (Terumo). Mononuclear cells (MNC), thrombocyte, and erythrocyte counts in the units of concentrated thrombocytes were obtained on an automatic cell counter, and we used flow cytometry to measure the expression of surface thrombocyte receptors. The results demonstrated that the trombocytes prepared with pre-storage filtration contained a very low level of mononuclear cells and markedly reduced trombocyte receptors. Conclusion. The number of MNC and expression of surface thrombocyte receptors were markedly lower in the concentrated thrombocyte units prepared with in-line filtration. The thrombocytes prepared in this way contain fewer mononuclear cells, are of higher quality, are more functional, and may produce a better therapeutic effect in vivo.


2022 ◽  
Author(s):  
Siu Lung Ng ◽  
Sophia A. Kammann ◽  
Gabi Steinbach ◽  
Tobias Hoffmann ◽  
Peter J. Yunker ◽  
...  

Mutations in regulatory mechanisms that control gene expression contribute to phenotypic diversity and thus facilitate the adaptation of microbes to new niches. Regulatory architecture is often inferred from transcription factor identification and genome analysis using purely computational approaches. However, there are few examples of phenotypic divergence that arise from the rewiring of bacterial regulatory circuity by mutations in intergenic regions, because locating regulatory elements within regions of DNA that do not code for protein requires genomic and experimental data. We identify a single cis-acting single nucleotide polymorphism (SNP) dramatically alters control of the type VI secretion system (T6), a common weapon for inter-bacterial competition. Tight T6 regulatory control is necessary for adaptation of the waterborne pathogen Vibrio cholerae to in vivo conditions within the human gut, which we show can be altered by this single non-coding SNP that results in constitutive expression in vitro. Our results support a model of pathogen evolution through cis-regulatory mutation and preexisting, active transcription factors, thus conferring different fitness advantages to tightly regulated strains inside a human host and unfettered strains adapted to environmental niches.


Blood ◽  
1961 ◽  
Vol 17 (2) ◽  
pp. 139-165 ◽  
Author(s):  
T. E. BRITTINGHAM ◽  
HUGH CHAPLIN

Abstract 1. A leukoagglutinin was formed in the serum of a normal human subject who received 10 intravenous injections of blood from a single patient with chronic myelogenous leukemia over a period of 20 weeks. 2. Coincident with development of the leukoagglutinin, first detectable one week after the fifth injection of leukemic blood, the normal subject experienced progressively more severe febrile reactions to the infusions and exhibited a characteristic pattern of leukocyte response—namely, an immediate transient leukopenia, followed by a leukocytosis which reached its peak around 3 hours and subsided to normal within 12 hours. 3. During the early part of the investigation immature leukocytes, presumably from the leukemic donor, could be identified in the recipient’s circulation during the first hour immediately following injection, but none could be found following the tenth infusion of leukemic blood. 4. The leukoagglutinin which appeared in response to the injections of blood from the single leukemic donor was a typical iso-antibody, showing a broad pattern of reactivity against normal leukocytes from 127 of 129 donors, leukemic leukocytes from 5 of 5 patients with chronic myelocytic leukemia and 6 of 6 patients with chronic lymphocytic leukemia. No reactivity was observed against the recipient’s own leukocytes, and little or no reactivity was demonstrable against the immature leukocytes from 3 patients with acute leukemia. 5. Eighteen months after the last injection of leukemic blood, restimulation of a leukocyte iso-agglutinin in the previously immunized recipient was provoked within one week of commencing a series of intravenous infusions of blood from a single normal donor. 6. The volume of normal leukocytes employed for the restimulation was 1/10 to 1/100 the volume of leukemic leukocytes employed for the primary immunization. 7. The concept of antibody excess was demonstrable in the sensitized recipient. No evidence of in vivo absorption of leukoagglutinin activity was observed after transfusion of 500 ml. of blood from the normal donor. The severity of the recipient’s reaction to the transfused blood was clearly related to the dose of donor leukocytes administered, 0.47 billion cells causing no reaction but 4.16 billion causing a moderately severe reaction. 8. Fifteen months after completion of the injections of normal blood, reexposure of the normal subject to injections of blood from a second leukemic donor resulted in prompt restimulation of leukoagglutinin activity in the recipient’s serum. 9. The leukoagglutinin could be completely absorbed in vitro by incubation with donor leukocytes. 10. The leukoagglutinin was concentrated in the gamma globulin fraction of the recipient’s plasma. 11. The recipient exhibited typical symptomatic reactions and transient hematologic changes following the infusions of leukemic blood. 12. It was possible to correlate the severity of the recipient’s clinical reactions both with the strength of the recipient’s leukoagglutinin, as well as with the dose of donor leukocytes transfused. 13. Serologic observations, plus the results of fractionated transfusion studies, indicated that the recipient’s transfusion reactions were related to sensitivity to the donor’s buffy coat (Part II), and more specificially to donor leukocytes (Part III), rather than to donor plasma, platelets or erythrocytes. 14. Sustained stimulation of the recipient’s white cell count as a result of the injections of leukemic blood was not observed. 15. There has thus far been no evidence of transmission of leukemia to the recipient (now 6½ years after the first course of injections of leukemic blood and 2 years since completion of the present study).


2015 ◽  
Vol 25 (2-3) ◽  
pp. 143-153 ◽  
Author(s):  
Noa Gordon ◽  
Ronen Rosenblum ◽  
Anat Nussbaum-Shochat ◽  
Elad Eliahoo ◽  
Orna Amster-Choder

BglG/LicT-like proteins are transcriptional antiterminators that prevent termination of transcription at intrinsic terminators by binding to ribonucleic antiterminator (RAT) sites and stabilizing an RNA conformation which is mutually exclusive with the terminator structure. The known RAT sites, which are located in intergenic regions of sugar utilization operons, show low sequence conservation but significant structural analogy. To assess the prevalence of RATs in bacterial genomes, we employed bioinformatic tools that describe RNA motifs based on both sequence and structural constraints. Using descriptors with different stringency, we searched the genomes of <i>Escherichia</i><i>coli</i> K12, uropathogenic <i>E. coli</i> and <i>Bacillus subtilis</i> for putative RATs. Our search identified all known RATs and additional putative RAT elements. Surprisingly, most putative RATs do not overlap an intrinsic terminator and many reside within open reading frames (ORFs). The ability of one of the putative RATs, which is located within an antiterminator-encoding ORF and does not overlap a terminator, to bind to its cognate antiterminator protein in vitro and in vivo was confirmed experimentally. Our results suggest that the capacity of RAT elements has been exploited during evolution to mediate activities other than antitermination, for example control of transcription elongation or of RNA stability.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2339-2339 ◽  
Author(s):  
Mariasanta Napolitano ◽  
Lucio Lo Coco ◽  
Giorgia Saccullo ◽  
Piera Stefania Arfò ◽  
Giuseppe Tarantino ◽  
...  

Abstract Background: Cryopreservation of platelets (PLTs) at -80°C with dimethyl sulfoxide (DMSO) can extend their shelf life up to 2 years. Cryopreserved PLTs (CRY-PLTs) are reported to have a greater in vivo hemostatic effect than liquid-stored PLTs. Aims of this study were: i. to evaluate the thrombin generation potential of buffy coat derived cryopreserved PLTs (CRY- BC PLT) in comparison with fresh buffy coat derived platelets concentrates; ii. to determine the efficacy and safety of CRY-PLTs transfusion in hematological patients with severe thrombocytopenia. Materials and methods: BC PLTs were obtained from 5 buffy coats and pooled. The final PLTs concentrates were leukoreduced by filtration and transferred to a 650 mL patented cryopreservation kit (Promedical ®) which allowed mixing with DMSO 25% in a closed system and following removal of supernatant without further manipulations. BC-PLTs were washed prior freezing, suspended in homologous plasma from 1 of the 5 donors to a final concentration of 200 mL and frozen at - 80°. CRY- BC PLTs were preserved at -80°C with 6% DMSO. A system of 3 accessory bags directly connected to the mother bag was adopted for the in vitro study, to avoid repeated freezing/thawing of samples. In vitro assays were performed before freezing and at 3,6 and 9 months after thawing. Before assay, CRY-BC PLT were thawed at 37°C and diluted in plasma to adjust to 300× 109/L PLTs. Fresh BC PLTs underwent the same dilution to adjust to 300 ×109/L PLTs. Thrombin generation (TGA) was tested in CRY BC-PLTs and compared to TG potential of fresh BC PLTs. TGA was triggered by the addition of 0.5 pmol/L of recombinant human tissue factor. Endogenous thrombin potential (ETP) and peak height (PH) were determined. Flow Cytometry assays for PLTs activation markers and thromboelastography were also determined on each sample. CRY-BC PLTs, separately prepared according to the above described method for in vivo study, were infused in five hematological patients with acute leukemia (AL) and severe thrombocytopenia (PLTs <10 ×109/L) participating to the trial NCT02032134.CRY-BC PLTs were transfused to control epistaxis (n=2) and for prophylaxis (n=3). Patients were observed up to 7 days after infusion and the occurrence of any side effect was registered. An increase in PLTs count was observed only in one case, under prophylaxis, but bleeding was successfully controlled or prevented in all cases. Plasma from patients transfused with CRY-BC PLTs was tested for TGA pre-treatment and 24 hours after treatment Results Fourty nine BC-PLTs from 245 healthy volunteer donors (145 males and 100 females, mean age: 48.16.±18.91) were prepared, cryopreserved and analyzed up to 9 months after storage. Cryopreserved PLTs show a good thrombin generation potential that is stably maintained up to 9 months after cryopreservation [ETP (nM min): 529.25±98.64 at T0, 558.82±114.67 at T3, at 548.57±93.38 T6 and 533.04±103.15 at T9 months, respectively; PH(nM): 132.77±44.9 at T0, 103.4±44.9 at T3, 108.0±36.7 at T6 and 132.0±44.6 at T9 months, respectively]. At TGA, fresh BC-PLTs (n=35) had a mean ETP of 760.13±130.11, PH was 138.9±40.2. Thrombin generation of CRY-BC PLTs is comparable to fresh BC-PLTs, even if slightly decreased. Infusion of CRY-BC PLT (1U) was effective in controlling mucosal bleeding (epistaxis) in two patients with AL and severe thrombocytopenia. CRY-PLT were also effective when administered for prophylaxis in 3 patients with very low platelets count secondary to chemotherapy. In vivo, thrombin generation is stably maintained up to 24 hours after infusion of 1 Unit of CRY-BC PLTs, without any adverse effect (mean ETP pre-treatment was: 414.13±160.60, 24 hours after transfusion: 326.95±152.54). CRY-BC PLTs were safe and they did not determine any thrombotic event. At flow-cytometry, CRY-BC PLTs expressed higher activation markers (CD62P,CD63) than fresh BC PLTs. CRY-BC PLTs are able to significantly decrease the time to clot formation and clot strength, as measured also by thromboelastography. CRY-BCPLTs activation/deterioration is accompanied by an effective hemostatic in vivo function. Conclusions: Cryopreserved PLTs have an enhanced hemostatic activity and a good thrombin generation potential. They are effective and safe in preventing and controlling bleeding, being available in emergency/urgency settings also for patients with acute leukemia and severe thrombocytopenia. Disclosures Reina: Promedical: Consultancy.


2003 ◽  
Vol 77 (20) ◽  
pp. 10731-10739 ◽  
Author(s):  
Kristin M. Rogers ◽  
Katie A. Ealey ◽  
Jerry W. Ritchey ◽  
Darla H. Black ◽  
R. Eberle

ABSTRACT In comparisons of the pathogenicity of simian alphaherpesviruses in mice, two isolates of the baboon virus HVP2 were nearly as lethal as monkey B virus, a biological safety level 4 agent (J. W. Ritchey, K. A. Ealey, M. Payton, and R. Eberle, J. Comp. Pathol. 127:150-161, 2002). To confirm these results, mice were inoculated intramuscularly with 105 PFU of HVP2 isolates obtained from different baboon subspecies and primate centers. Some of the HVP2 isolates (6 of 13) caused paralysis and death in the mice, while 7 of 13 HVP2 isolates produced no clinical signs of disease. The apathogenic HVP2 isolates (HVP2ap) induced only low levels of serum antiviral immunoglobulin G relative to levels observed in sera from mice infected with the neurovirulent isolates of HVP2 (HVP2nv). Histological examination of tissues from mice inoculated with HVP2nv isolates showed extensive neural tissue destruction, while mice infected with HVP2ap isolates showed no lesions. Tissue samples collected at 48-h intervals postinfection suggested that HVP2ap isolates failed to replicate at the site of inoculation. There was no significant difference in the in vitro replication, plaque size, or cytopathic effect morphology of HVP2ap versus HVP2nv isolates. While HVP2 isolates replicated better in Vero monkey kidney cells than in murine L cells, plaquing efficiency of individual isolates did not correlate with the dichotomous pathogenic properties seen in mice. Phylogenetic analyses of both coding and intergenic regions (US4-6) of the HVP2 genome separated isolates into two distinct clades that correlated with the two in vivo virulence phenotypes. Taken together, these results demonstrate that two subtypes of HVP2 exist that are very closely related but differ dramatically in their ability to cause disease in a murine model.


1985 ◽  
Vol 10 (2-3) ◽  
pp. 245-252 ◽  
Author(s):  
J.F. Guelfi ◽  
M.K. Courdouhji ◽  
M. Alvinerie ◽  
P.L. Toutain

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