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  1. AU="Procopio, Francesco A"
  2. AU="Nagata, Kosei"
  3. AU="Kevin Pottie"
  4. AU=Das Tandrila AU=Das Tandrila
  5. AU="Couto Souza, Paulo Henrique"
  6. AU="Morris, Zachary"

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  1. Artikel ; Online: TILDA: Tat/Rev Induced Limiting Dilution Assay.

    Lungu, Cynthia / Procopio, Francesco A

    Methods in molecular biology (Clifton, N.J.)

    2022  Band 2407, Seite(n) 365–372

    Abstract: Recently the Tat/rev Induced Limiting Dilution Assay, or TILDA, has been proposed as a possible alternative method to quantify the HIV-1 reservoir. TILDA estimates the frequency of latently infected cells by probing, in a limiting dilution format, the ... ...

    Abstract Recently the Tat/rev Induced Limiting Dilution Assay, or TILDA, has been proposed as a possible alternative method to quantify the HIV-1 reservoir. TILDA estimates the frequency of latently infected cells by probing, in a limiting dilution format, the presence or inducibility of tat and rev multiply spliced HIV-1 RNA. In doing so, TILDA reduces overestimation of reservoir size compared to HIV-1 DNA measurements because multiply spliced HIV-1 RNA is less likely to be transcribed from dysfunctional genomes with replication defects. TILDA is easy to perform, requires a very low input number of cells and has a fast turnaround time, making it ideal for use in clinical settings. Here we describe the execution of TILDA with particular emphasis on cell preparation and the limiting dilution scheme.
    Mesh-Begriff(e) CD4-Positive T-Lymphocytes ; HIV Infections ; HIV-1/genetics ; Humans ; RNA, Viral/genetics ; Virus Latency ; Virus Replication ; tat Gene Products, Human Immunodeficiency Virus/genetics
    Chemische Substanzen RNA, Viral ; tat Gene Products, Human Immunodeficiency Virus
    Sprache Englisch
    Erscheinungsdatum 2022-01-05
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1871-4_24
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel: Inducible HIV-1 Reservoir Quantification: Clinical Relevance, Applications and Advancements of TILDA.

    Lungu, Cynthia / Banga, Riddhima / Gruters, Rob A / Procopio, Francesco A

    Frontiers in microbiology

    2021  Band 12, Seite(n) 686690

    Abstract: The presence of a stable HIV-1 reservoir persisting over time despite effective antiretroviral suppression therapy precludes a cure for HIV-1. Characterizing and quantifying this residual reservoir is considered an essential prerequisite to develop and ... ...

    Abstract The presence of a stable HIV-1 reservoir persisting over time despite effective antiretroviral suppression therapy precludes a cure for HIV-1. Characterizing and quantifying this residual reservoir is considered an essential prerequisite to develop and validate curative strategies. However, a sensitive, reproducible, cost-effective, and easily executable test is still needed. The quantitative viral outgrowth assay is considered the gold standard approach to quantify the reservoir in HIV-1-infected patients on suppressive ART, but it has several limitations. An alternative method to quantify the viral reservoir following the reactivation of latent HIV-1 provirus detects multiply-spliced
    Sprache Englisch
    Erscheinungsdatum 2021-06-15
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.686690
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Current approaches to assess HIV-1 persistence.

    Banga, Riddhima / Procopio, Francesco A / Perreau, Matthieu

    Current opinion in HIV and AIDS

    2016  Band 11, Heft 4, Seite(n) 424–431

    Abstract: Purpose of review: The persistence of HIV within long-lived HIV-infected CD4 T cells is the primary obstacle towards HIV eradication and numerous strategies are currently being evaluated to target and kill HIV-infected cells to ultimately find a cure. ... ...

    Abstract Purpose of review: The persistence of HIV within long-lived HIV-infected CD4 T cells is the primary obstacle towards HIV eradication and numerous strategies are currently being evaluated to target and kill HIV-infected cells to ultimately find a cure. HIV reservoirs are classically quantified by standard methods such as integrated HIV DNA (Alu PCR) and/or quantitative viral outgrowth assay; however, recent technical advances may offer new opportunities to comprehensively assess the impact of clinical interventions.
    Recent findings: Digital droplet PCR, tat/rev-induced limiting dilution analysis, enhanced quantitative viral outgrowth assay, and whole genome sequencing technologies offer increased precision and/or higher sensitivity to quantify and characterize HIV reservoirs in antiretroviral therapy-treated HIV-infected patients.
    Summary: The objective of this review is to highlight the characteristics and limits of recent technical advances that may help to monitor the impact of clinical interventions in antiretroviral therapy-treated patients.
    Mesh-Begriff(e) Anti-Retroviral Agents/therapeutic use ; CD4-Positive T-Lymphocytes/virology ; HIV Infections/drug therapy ; HIV Infections/virology ; Humans ; Viral Load/methods ; Viral Load/trends ; Virus Latency
    Chemische Substanzen Anti-Retroviral Agents
    Sprache Englisch
    Erscheinungsdatum 2016-07
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Review
    ZDB-ID 2502511-9
    ISSN 1746-6318 ; 1746-630X
    ISSN (online) 1746-6318
    ISSN 1746-630X
    DOI 10.1097/COH.0000000000000282
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  4. Artikel ; Online: Comparative analysis and generation of a robust HIV-1 DNA quantification assay.

    Thomas, Jordan / Ruggiero, Alessandra / Procopio, Francesco A / Pantaleo, Giuseppe / Paxton, William A / Pollakis, Georgios

    Journal of virological methods

    2018  Band 263, Seite(n) 24–31

    Abstract: HIV-1 infection cannot be cured due to the presence of the latent reservoir (LR). Novel cure or treatment strategies, such as "shock and kill" or therapeutic vaccination, aim to reduce or eradicate the LR. Cure strategies utilise robust DNA ... ...

    Abstract HIV-1 infection cannot be cured due to the presence of the latent reservoir (LR). Novel cure or treatment strategies, such as "shock and kill" or therapeutic vaccination, aim to reduce or eradicate the LR. Cure strategies utilise robust DNA quantification assays to measure the change in the LR in low copy scenarios. No standard assay exists, which impedes the reliable comparison of results from different therapy and vaccine trials and HIV-1 total DNA quantification methods have not been previously compared. The HIV-1 long terminal repeat (LTR) has been shown to be the best target for DNA quantification. We have analysed two HIV-1 quantification assays, both able to differentiate between the variant HIV-1 DNA forms via the use of pre-amplification and primers targeting LTR. We identify a strong correlation (r=0.9759, P<0.0001) between assays which is conserved in low copy samples (r=0.8220, P<0.0001) indicating that these assays may be used interchangeably. The RvS assay performed significantly (P=0.0021) better than the CV assay when quantifying HIV-1 total DNA in patient CD4+ T lymphocytes. Sequence analysis demonstrated that viral diversity can limit DNA quantification, however in silico analysis of the primers indicated that within the target region nucleotide miss-matches appear infrequently. Further in silico analysis using up to-date sequence information led to the improvement of primers and enabled us to establish a more broadly specific assay with significantly higher HIV-1 DNA quantification capacity in patient samples (p=0.0057, n=17).
    Mesh-Begriff(e) CD4-Positive T-Lymphocytes/virology ; Cell Line ; DNA, Viral/analysis ; DNA, Viral/genetics ; Genetic Variation ; HIV Infections/virology ; HIV Long Terminal Repeat/genetics ; HIV-1/genetics ; HIV-1/isolation & purification ; Humans ; Polymerase Chain Reaction ; Viral Load/methods
    Chemische Substanzen DNA, Viral
    Sprache Englisch
    Erscheinungsdatum 2018-10-13
    Erscheinungsland Netherlands
    Dokumenttyp Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 8013-5
    ISSN 1879-0984 ; 0166-0934
    ISSN (online) 1879-0984
    ISSN 0166-0934
    DOI 10.1016/j.jviromet.2018.10.010
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: The deficiency in Th2-like Tfh cells affects the maturation and quality of HIV-specific B cell response in viremic infection.

    Noto, Alessandra / Suffiotti, Madeleine / Joo, Victor / Mancarella, Antonio / Procopio, Francesco A / Cavet, Guy / Leung, Yvonne / Corpataux, Jean-Marc / Cavassini, Matthias / Riva, Agostino / Stamatatos, Leonidas / Gottardo, Raphael / McDermott, Adrian B / Koup, Richard A / Fenwick, Craig / Perreau, Matthieu / Pantaleo, Giuseppe

    Frontiers in immunology

    2022  Band 13, Seite(n) 960120

    Abstract: Optimal T follicular helper (Tfh) cells function is important to promote the development of germinal centers and maturation of high affinity antigen-specific B cells. We have found that the expression of CXCR3 defines distinct Tfh subsets: ... ...

    Abstract Optimal T follicular helper (Tfh) cells function is important to promote the development of germinal centers and maturation of high affinity antigen-specific B cells. We have found that the expression of CXCR3 defines distinct Tfh subsets: CXCR3
    Mesh-Begriff(e) Cytokines/metabolism ; Germinal Center/metabolism ; HIV Infections/metabolism ; Humans ; Interleukin-4/metabolism ; T Follicular Helper Cells ; Viremia
    Chemische Substanzen Cytokines ; Interleukin-4 (207137-56-2)
    Sprache Englisch
    Erscheinungsdatum 2022-08-24
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2022.960120
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  6. Artikel ; Online: Detection of Human Immunodeficiency Virus Type 1 (HIV-1) Antisense Protein (ASP) RNA Transcripts in Patients by Strand-Specific RT-PCR.

    Mancarella, Antonio / Procopio, Francesco A / Achsel, Tilmann / De Crignis, Elisa / Foley, Brian T / Corradin, Giampietro / Bagni, Claudia / Pantaleo, Giuseppe / Graziosi, Cecilia

    Journal of visualized experiments : JoVE

    2019  , Heft 153

    Abstract: In retroviruses, antisense transcription has been described in both human immunodeficiency virus type 1 (HIV-1) and human T-lymphotropic virus 1 (HTLV-1). In HIV-1, the antisense protein ASP gene is located on the negative strand of env, in the reading ... ...

    Abstract In retroviruses, antisense transcription has been described in both human immunodeficiency virus type 1 (HIV-1) and human T-lymphotropic virus 1 (HTLV-1). In HIV-1, the antisense protein ASP gene is located on the negative strand of env, in the reading frame -2, spanning the junction gp120/gp41. In the sense orientation, the 3' end of the ASP open reading frame overlaps with gp120 hypervariable regions V4 and V5. The study of ASP RNA has been thwarted by a phenomenon known as RT-self-priming, whereby RNA secondary structures have the ability to prime RT in absence of the specific primer, generating non-specific cDNAs. The combined use of high RNA denaturation with biotinylated reverse primers in the RT reaction, together with affinity purification of the cDNA onto streptavidin-coated magnetic beads, has allowed us to selectively amplify ASP RNA in CD4+ T cells derived from individuals infected with HIV-1. Our method is relatively low-cost, simple to perform, highly reliable, and easily reproducible. In this respect, it represents a powerful tool for the study of antisense transcription not only in HIV-1 but also in other biological systems.
    Mesh-Begriff(e) Adult ; HIV-1/genetics ; Humans ; Male ; Middle Aged ; Open Reading Frames/genetics ; RNA, Antisense/genetics ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Young Adult
    Chemische Substanzen RNA, Antisense
    Sprache Englisch
    Erscheinungsdatum 2019-11-27
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Video-Audio Media
    ZDB-ID 2259946-0
    ISSN 1940-087X ; 1940-087X
    ISSN (online) 1940-087X
    ISSN 1940-087X
    DOI 10.3791/60511
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: Detection of antisense protein (ASP) RNA transcripts in individuals infected with human immunodeficiency virus type 1 (HIV-1).

    Mancarella, Antonio / Procopio, Francesco A / Achsel, Tilmann / De Crignis, Elisa / Foley, Brian T / Corradin, Giampietro / Bagni, Claudia / Pantaleo, Giuseppe / Graziosi, Cecilia

    The Journal of general virology

    2019  Band 100, Heft 5, Seite(n) 863–876

    Abstract: The detection of antisense RNA is hampered by reverse transcription (RT) non-specific priming, due to the ability of RNA secondary structures to prime RT in the absence of specific primers. The detection of antisense RNA by conventional RT-PCR does not ... ...

    Abstract The detection of antisense RNA is hampered by reverse transcription (RT) non-specific priming, due to the ability of RNA secondary structures to prime RT in the absence of specific primers. The detection of antisense RNA by conventional RT-PCR does not allow assessment of the polarity of the initial RNA template, causing the amplification of non-specific cDNAs. In this study we have developed a modified protocol for the detection of human immunodeficiency virus type 1 (HIV-1) antisense protein (ASP) RNA. Using this approach, we have identified ASP transcripts in CD4+ T cells isolated from five HIV-infected individuals, either untreated or under suppressive therapy. We show that ASP RNA can be detected in stimulated CD4+ T cells from both groups of patients, but not in unstimulated cells. We also show that in untreated patients, the patterns of expression of ASP and env are very similar, with the levels of ASP RNA being markedly lower than those of env. Treatment of cells from one viraemic patient with α-amanitin greatly reduces the rate of ASP RNA synthesis, suggesting that it is associated with RNA polymerase II, the central enzyme in the transcription of protein-coding genes. Our data represent the first nucleotide sequences obtained in patients for ASP, demonstrating that its transcription indeed occurs in those HIV-1 lineages in which the ASP open reading frame is present.
    Mesh-Begriff(e) Adult ; Base Sequence/genetics ; CD4-Positive T-Lymphocytes/virology ; Gene Expression Regulation, Viral/genetics ; HIV Infections/virology ; HIV-1/genetics ; Humans ; Male ; Middle Aged ; Open Reading Frames/genetics ; RNA, Antisense/genetics ; RNA, Viral/genetics ; Virus Replication/genetics ; Young Adult
    Chemische Substanzen RNA, Antisense ; RNA, Viral
    Sprache Englisch
    Erscheinungsdatum 2019-03-21
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 219316-4
    ISSN 1465-2099 ; 0022-1317
    ISSN (online) 1465-2099
    ISSN 0022-1317
    DOI 10.1099/jgv.0.001244
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: Differential Production of Midkine and Pleiotrophin by Innate APCs upon Stimulation through Nucleic Acid-Sensing TLRs.

    Said, Elias A / Al-Dughaishi, Sumaya / Al-Hatmi, Wadha / Al-Reesi, Iman / Al-Balushi, Mohammed S / Al-Bimani, Atika / Al-Busaidi, Juma Z / Al-Riyami, Marwa / Al-Khabori, Murtadha / Al-Kindi, Salam / Procopio, Francesco A / Al-Sinawi, Shadia / Al-Ansari, Aliyaa / Koh, Crystal Y / Al-Naamani, Khalid / Al-Jabri, Ali A

    Journal of immunology research

    2023  Band 2023, Seite(n) 7944102

    Abstract: Midkine (MK) and pleiotrophin (PTN) belong to the same family of cytokines. They have similar sequences and functions. Both have important roles in cellular proliferation, tumors, and diseases. They regulate and are expressed by some immune cells. We ... ...

    Abstract Midkine (MK) and pleiotrophin (PTN) belong to the same family of cytokines. They have similar sequences and functions. Both have important roles in cellular proliferation, tumors, and diseases. They regulate and are expressed by some immune cells. We have recently demonstrated MK production by some human innate antigen-presenting cells (iAPCs), i.e., monocyte-derived dendritic cells (MDDCs) and macrophages stimulated through Toll-like receptor (TLR)-4, and plasmacytoid dendritic cells (pDCs) stimulated through TLR 7. While PTN production was only documented in tissue macrophages. TLRs 3, 7, 8, and 9 are nucleic acid sensing (NAS) TLRs that detect nucleic acids from cell damage and infection and induce iAPC responses. We investigated whether NAS TLRs can induce MK and PTN production by human iAPCs, namely monocytes, macrophages, MDDCs, myeloid dendritic cells (mDCs), and pDCs. Our results demonstrated for the first time that PTN is produced by all iAPCs upon TLR triggering (
    Mesh-Begriff(e) Humans ; Cytokines ; Dendritic Cells ; Midkine ; Neoplasms
    Chemische Substanzen Cytokines ; Midkine (137497-38-2) ; pleiotrophin (134034-50-7) ; MDK protein, human
    Sprache Englisch
    Erscheinungsdatum 2023-10-09
    Erscheinungsland Egypt
    Dokumenttyp Journal Article
    ZDB-ID 2817541-4
    ISSN 2314-7156 ; 2314-7156
    ISSN (online) 2314-7156
    ISSN 2314-7156
    DOI 10.1155/2023/7944102
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel: Detection of human immunodeficiency virus type 1 (hiv-1) antisense protein (asp) rna transcripts in patients by strand-specific rt-pcr

    Mancarella, Antonio / Procopio, Francesco A / Achsel, Tilmann / De Crignis, Elisa / Foley, Brian T / Corradin, Giampietro / Bagni, Claudia / Pantaleo, Giuseppe / Graziosi, Cecilia

    Journal of visualized experiments. 2019 Nov. 27, , no. 153

    2019  

    Abstract: In retroviruses, antisense transcription has been described in both human immunodeficiency virus type 1 (HIV-1) and human T-lymphotropic virus 1 (HTLV-1). In HIV-1, the antisense protein ASP gene is located on the negative strand of env, in the reading ... ...

    Abstract In retroviruses, antisense transcription has been described in both human immunodeficiency virus type 1 (HIV-1) and human T-lymphotropic virus 1 (HTLV-1). In HIV-1, the antisense protein ASP gene is located on the negative strand of env, in the reading frame -2, spanning the junction gp120/gp41. In the sense orientation, the 3' end of the ASP open reading frame overlaps with gp120 hypervariable regions V4 and V5. The study of ASP RNA has been thwarted by a phenomenon known as RT-self-priming, whereby RNA secondary structures have the ability to prime RT in absence of the specific primer, generating non-specific cDNAs. The combined use of high RNA denaturation with biotinylated reverse primers in the RT reaction, together with affinity purification of the cDNA onto streptavidin-coated magnetic beads, has allowed us to selectively amplify ASP RNA in CD4+ T cells derived from individuals infected with HIV-1. Our method is relatively low-cost, simple to perform, highly reliable, and easily reproducible. In this respect, it represents a powerful tool for the study of antisense transcription not only in HIV-1 but also in other biological systems.
    Schlagwörter CD4-positive T-lymphocytes ; Human immunodeficiency virus 1 ; Primate T-lymphotropic virus 1 ; complementary DNA ; denaturation ; genes ; magnetism ; messenger RNA ; open reading frames ; patients
    Sprache Englisch
    Erscheinungsverlauf 2019-1127
    Umfang p. e60511.
    Erscheinungsort Journal of Visualized Experiments
    Dokumenttyp Artikel
    ZDB-ID 2259946-0
    ISSN 1940-087X
    ISSN 1940-087X
    DOI 10.3791/60511
    Datenquelle NAL Katalog (AGRICOLA)

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  10. Artikel ; Online: Human macrophages and monocyte-derived dendritic cells stimulate the proliferation of endothelial cells through midkine production.

    Said, Elias A / Al-Dughaishi, Sumaya / Al-Hatmi, Wadha / Al-Reesi, Iman / Al-Riyami, Marwa / Al-Balushi, Mohammed S / Al-Bimani, Atika / Al-Busaidi, Juma Z / Al-Khabori, Murtadha / Al-Kindi, Salam / Procopio, Francesco A / Al-Rashdi, Afrah / Al-Ansari, Aliyaa / Babiker, Hamza / Koh, Crystal Y / Al-Naamani, Khalid / Pantaleo, Giuseppe / Al-Jabri, Ali A

    PloS one

    2022  Band 17, Heft 4, Seite(n) e0267662

    Abstract: The cytokine midkine (MK) is a growth factor that is involved in different physiological processes including tissue repair, inflammation, the development of different types of cancer and the proliferation of endothelial cells. The production of MK by ... ...

    Abstract The cytokine midkine (MK) is a growth factor that is involved in different physiological processes including tissue repair, inflammation, the development of different types of cancer and the proliferation of endothelial cells. The production of MK by primary human macrophages and monocyte-derived dendritic cells (MDDCs) was never described. We investigated whether MK is produced by primary human monocytes, macrophages and MDDCs and the capacity of macrophages and MDDCs to modulate the proliferation of endothelial cells through MK production. The TLR stimulation of human monocytes, macrophages and MDDCs induced an average of ≈200-fold increase in MK mRNA and the production of an average of 78.2, 62, 179 pg/ml MK by monocytes, macrophages and MDDCs respectively (p < 0.05). MK production was supported by its detection in CD11c+ cells, CLEC4C+ cells and CD68+ cells in biopsies of human tonsils showing reactive lymphoid follicular hyperplasia. JSH-23, which selectively inhibits NF-κB activity, decreased the TLR-induced production of MK in PMBCs, macrophages and MDDCs compared to the control (p < 0.05). The inhibition of MK production by macrophages and MDDCs using anti-MK siRNA decreased the capacity of their supernatants to stimulate the proliferation of endothelial cells (p = 0.01 and 0.04 respectively). This is the first study demonstrating that the cytokine MK is produced by primary human macrophages and MDDCs upon TLR triggering, and that these cells can stimulate endothelial cell proliferation through MK production. Our results also suggest that NF-κB plays a potential role in the production of MK in macrophages and MDDCs upon TLR stimulation. The production of MK by macrophages and MDDCs and the fact that these cells can enhance the proliferation of endothelial cells by producing MK are novel immunological phenomena that have potentially important therapeutic implications.
    Mesh-Begriff(e) Cell Proliferation ; Cytokines/metabolism ; Dendritic Cells ; Endothelial Cells ; Humans ; Lectins, C-Type/metabolism ; Macrophages ; Membrane Glycoproteins/metabolism ; Midkine/metabolism ; Monocytes ; NF-kappa B/metabolism ; Receptors, Immunologic/metabolism
    Chemische Substanzen CLEC4C protein, human ; Cytokines ; Lectins, C-Type ; Membrane Glycoproteins ; NF-kappa B ; Receptors, Immunologic ; Midkine (137497-38-2)
    Sprache Englisch
    Erscheinungsdatum 2022-04-27
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0267662
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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