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  1. Article: Janus kinase inhibitors modify the fatty acid profile of extracellular vesicles and modulate the immune response.

    Daza Zapata, Ana María / Álvarez, Karen / Vásquez Duque, Gloria / Palacio, Juliana / Rojas López, Mauricio

    Heliyon

    2024  Volume 10, Issue 3, Page(s) e24710

    Abstract: ... EVs were isolated from monocytes (M) and lymphocytes (L) of healthy individuals, as well as from U937 ... The neutrophil respiratory burst was attenuated in greater extent by M-EVs than by L-EVs. Autologous ITA ... cell proliferation induced by BARI-L/M-EVs could explain the lymphocytosis observed in patients treated with BARI ...

    Abstract Background: Janus kinase inhibitors (jakinibs) are immunomodulators used for treating malignancies, autoimmune diseases, and immunodeficiencies. However, they induce adverse effects such as thrombosis, lymphocytosis, and neutropenia that could be mediated by extracellular vesicles (EVs). These particles are cell membrane-derived structures that transport cellular and environmental molecules and participate in intercellular communication. Jakinibs can modify the content of EVs and enable them to modulate the activity of different components of the immune response.
    Objective: to evaluate the interactions between immune system components of healthy individuals and EVs derived from monocytic and lymphoid lineage cells generated in the presence of baricitinib (BARI) and itacitinib (ITA) and their possible effects.
    Methods: EVs were isolated from monocytes (M) and lymphocytes (L) of healthy individuals, as well as from U937 (U) and Jurkat (J) cells exposed to non-cytotoxic concentrations of BARI, ITA, and dimethyl sulfoxide (DMSO; vehicle control). The binding to and engulfment of EVs by peripheral blood leukocytes of healthy individuals were analyzed by flow cytometry using CFSE-stained EVs and anti-CD45-PeCy7 mAb-labeled whole blood. The effect of EVs on respiratory burst, T-cell activation and proliferation, cytokine synthesis, and platelet aggregation was evaluated. Respiratory burst was assessed in PMA-stimulated neutrophils by the dihydrorhodamine (DHR) test and flow cytometry. T-cell activation and proliferation and cytokine production were assessed in CFSE-stained PBMC cultures stimulated with PHA; expression of the T-cell activation markers CD25 and CD69 and T-cell proliferation were analyzed by flow cytometry, and the cytokine levels were quantified in culture supernatants by Luminex assays. Platelet aggregation was analyzed in platelet-rich plasma (PRP) samples by light transmission aggregometry. The EVs' fatty acid (FA) profile was analyzed using methyl ester derivatization followed by gas chromatography.
    Results: ITA exposure during the generation of EVs modified the size of the EVs released; however, treatment with DMSO and BARI did not alter the size of EVs generated from U937 and Jurkat cells. Circulating neutrophils, lymphocytes, and monocytes showed a 2-fold greater tendency to internalize ITA-U-EVs than their respective DMSO control. The neutrophil respiratory burst was attenuated in greater extent by M-EVs than by L-EVs. Autologous ITA-
    Conclusions: Cellular origin and jakinib exposure modify the FA profile of EVs, enabling them, in turn, to modulate neutrophil respiratory burst, T-cell proliferation, and platelet aggregation. The increased T-cell proliferation induced by BARI-L/M-EVs could explain the lymphocytosis observed in patients treated with BARI. The higher proportion of arachidonic acid in the FA content of ITA-L/M-EVs could be related to the thrombosis described in patients treated with ITA. EVs also induced a decrease in the respiratory burst of neutrophils.
    Language English
    Publishing date 2024-01-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2024.e24710
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Dynamic alternative DNA structures in biology and disease.

    Wang, Guliang / Vasquez, Karen M

    Nature reviews. Genetics

    2022  Volume 24, Issue 4, Page(s) 211–234

    Abstract: Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four- ... ...

    Abstract Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.
    MeSH term(s) Humans ; DNA/genetics ; DNA/chemistry ; G-Quadruplexes ; DNA Replication ; Genome, Human ; Biology
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2022-10-31
    Publishing country England
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 2035157-4
    ISSN 1471-0064 ; 1471-0056
    ISSN (online) 1471-0064
    ISSN 1471-0056
    DOI 10.1038/s41576-022-00539-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Methods to Study Z-DNA-Induced Genetic Instability.

    Wang, Guliang / Christensen, Laura / Vasquez, Karen M

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

    2023  Volume 2651, Page(s) 227–240

    Abstract: Alternative DNA structures that differ from the canonical B-DNA double helix, including Z-DNA, have received much attention recently due to their impact on DNA metabolic processes, including replication, transcription, and genome maintenance. Non-B-DNA- ... ...

    Abstract Alternative DNA structures that differ from the canonical B-DNA double helix, including Z-DNA, have received much attention recently due to their impact on DNA metabolic processes, including replication, transcription, and genome maintenance. Non-B-DNA-forming sequences can also stimulate genetic instability associated with disease development and evolution. Z-DNA can stimulate different types of genetic instability events in different species, and several different assays have been established to detect Z-DNA-induced DNA strand breaks and mutagenesis in prokaryotic and eukaryotic systems. In this chapter, we will introduce some of these methods including Z-DNA-induced mutation screening and detection of Z-DNA-induced strand breaks in mammalian cells, yeast, and mammalian cell extracts. Results from these assays should provide better insight into the mechanisms of Z-DNA-related genetic instability in different eukaryotic model systems.
    MeSH term(s) Animals ; DNA, Z-Form ; DNA Repair ; DNA/genetics ; DNA/chemistry ; DNA Damage ; Mutagenesis ; Genomic Instability ; Mammals/genetics
    Chemical Substances DNA, Z-Form ; DNA (9007-49-2)
    Language English
    Publishing date 2023-03-09
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3084-6_16
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Targeting Chromosomal Architectural HMGB Proteins Could Be the Next Frontier in Cancer Therapy.

    Mukherjee, Anirban / Vasquez, Karen M

    Cancer research

    2020  Volume 80, Issue 11, Page(s) 2075–2082

    Abstract: Chromatin-associated architectural proteins are part of a fundamental support system for cellular DNA-dependent processes and can maintain/modulate the efficiency of DNA replication, transcription, and DNA repair. Interestingly, prognostic outcomes of ... ...

    Abstract Chromatin-associated architectural proteins are part of a fundamental support system for cellular DNA-dependent processes and can maintain/modulate the efficiency of DNA replication, transcription, and DNA repair. Interestingly, prognostic outcomes of many cancer types have been linked with the expression levels of several of these architectural proteins. The high mobility group box (HMGB) architectural protein family has been well studied in this regard. The differential expression levels of HMGB proteins and/or mRNAs and their implications in cancer etiology and prognosis present the potential of novel targets that can be explored to increase the efficacy of existing cancer therapies. HMGB1, the most studied member of the HMGB protein family, has pleiotropic roles in cells including an association with nucleotide excision repair, base excision repair, mismatch repair, and DNA double-strand break repair. Moreover, the HMGB proteins have been identified in regulating DNA damage responses and cell survival following treatment with DNA-damaging agents and, as such, may play roles in modulating the efficacy of chemotherapeutic drugs by modulating DNA repair pathways. Here, we discuss the functions of HMGB proteins in DNA damage processing and their potential roles in cancer etiology, prognosis, and therapeutics.
    MeSH term(s) Animals ; Chromosomes ; DNA Damage ; DNA Repair ; HMGB Proteins/genetics ; HMGB Proteins/metabolism ; Humans ; Molecular Targeted Therapy ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/therapy
    Chemical Substances HMGB Proteins
    Language English
    Publishing date 2020-03-09
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 1432-1
    ISSN 1538-7445 ; 0008-5472
    ISSN (online) 1538-7445
    ISSN 0008-5472
    DOI 10.1158/0008-5472.CAN-19-3066
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: MoCoLo: a testing framework for motif co-localization.

    Xu, Qi / Del Mundo, Imee M A / Zewail-Foote, Maha / Luke, Brian T / Vasquez, Karen M / Kowalski, Jeanne

    Briefings in bioinformatics

    2024  Volume 25, Issue 2

    Abstract: Sequence-level data offers insights into biological processes through the interaction of two or more genomic features from the same or different molecular data types. Within motifs, this interaction is often explored via the co-occurrence of feature ... ...

    Abstract Sequence-level data offers insights into biological processes through the interaction of two or more genomic features from the same or different molecular data types. Within motifs, this interaction is often explored via the co-occurrence of feature genomic tracks using fixed-segments or analytical tests that respectively require window size determination and risk of false positives from over-simplified models. Moreover, methods for robustly examining the co-localization of genomic features, and thereby understanding their spatial interaction, have been elusive. We present a new analytical method for examining feature interaction by introducing the notion of reciprocal co-occurrence, define statistics to estimate it and hypotheses to test for it. Our approach leverages conditional motif co-occurrence events between features to infer their co-localization. Using reverse conditional probabilities and introducing a novel simulation approach that retains motif properties (e.g. length, guanine-content), our method further accounts for potential confounders in testing. As a proof-of-concept, motif co-localization (MoCoLo) confirmed the co-occurrence of histone markers in a breast cancer cell line. As a novel analysis, MoCoLo identified significant co-localization of oxidative DNA damage within non-B DNA-forming regions that significantly differed between non-B DNA structures. Altogether, these findings demonstrate the potential utility of MoCoLo for testing spatial interactions between genomic features via their co-localization.
    MeSH term(s) Genomics ; Computer Simulation ; DNA
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2024-03-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbae019
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Obesity and cancer: A mechanistic overview of metabolic changes in obesity that impact genetic instability.

    Kompella, Pallavi / Vasquez, Karen M

    Molecular carcinogenesis

    2019  Volume 58, Issue 9, Page(s) 1531–1550

    Abstract: Obesity, defined as a state of positive energy balance with a body mass index exceeding 30 kg/m ...

    Abstract Obesity, defined as a state of positive energy balance with a body mass index exceeding 30 kg/m
    MeSH term(s) Adipose Tissue/metabolism ; Animals ; DNA Damage/genetics ; DNA Repair/genetics ; Energy Metabolism/genetics ; Epigenesis, Genetic/genetics ; Genomic Instability/genetics ; Humans ; Neoplasms/genetics ; Neoplasms/metabolism ; Obesity/genetics ; Obesity/metabolism ; Oxidative Stress/genetics
    Language English
    Publishing date 2019-06-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 1004029-8
    ISSN 1098-2744 ; 0899-1987
    ISSN (online) 1098-2744
    ISSN 0899-1987
    DOI 10.1002/mc.23048
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  7. Article ; Online: The multifaceted roles of DNA repair and replication proteins in aging and obesity.

    D'Amico, Alexandra M / Vasquez, Karen M

    DNA repair

    2021  Volume 99, Page(s) 103049

    Abstract: Efficient mechanisms for genomic maintenance (i.e., DNA repair and DNA replication) are crucial for cell survival. Aging and obesity can lead to the dysregulation of genomic maintenance proteins/pathways and are significant risk factors for the ... ...

    Abstract Efficient mechanisms for genomic maintenance (i.e., DNA repair and DNA replication) are crucial for cell survival. Aging and obesity can lead to the dysregulation of genomic maintenance proteins/pathways and are significant risk factors for the development of cancer, metabolic disorders, and other genetic diseases. Mutations in genes that code for proteins involved in DNA repair and DNA replication can also exacerbate aging- and obesity-related disorders and lead to the development of progeroid diseases. In this review, we will discuss the roles of various DNA repair and replication proteins in aging and obesity as well as investigate the possible mechanisms by which aging and obesity can lead to the dysregulation of these proteins and pathways.
    MeSH term(s) Aging/genetics ; Aging/metabolism ; Animals ; DNA Repair ; DNA Replication ; Genomic Instability ; Humans ; Obesity/genetics ; Obesity/metabolism
    Language English
    Publishing date 2021-01-21
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2071608-4
    ISSN 1568-7856 ; 1568-7864
    ISSN (online) 1568-7856
    ISSN 1568-7864
    DOI 10.1016/j.dnarep.2021.103049
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Interactions of high mobility group box protein 1 (HMGB1) with nucleic acids: Implications in DNA repair and immune responses.

    Mandke, Pooja / Vasquez, Karen M

    DNA repair

    2019  Volume 83, Page(s) 102701

    Abstract: High mobility group box protein 1 (HMGB1) is a highly versatile, abundant, and ubiquitously expressed, non-histone chromosomal protein, which belongs to the HMGB family of proteins. These proteins form an integral part of the architectural protein ... ...

    Abstract High mobility group box protein 1 (HMGB1) is a highly versatile, abundant, and ubiquitously expressed, non-histone chromosomal protein, which belongs to the HMGB family of proteins. These proteins form an integral part of the architectural protein repertoire to support chromatin structure in the nucleus. In the nucleus, the role of HMGB1 is attributed to its ability to bind to undamaged DNA, damaged DNA, and alternative (i.e. non-B) DNA structures with high affinity and subsequently induce bending of the DNA substrates. Due to its binding to DNA, HMGB1 has been implicated in critical biological processes, such as DNA transcription, replication, repair, and recombination. In addition to its intracellular functions, HMGB1 can also be released in the extracellular space where it elicits immunological responses. HMGB1 associates with many different molecules, including DNA, RNA, proteins, and lipopolysaccharides to modulate a variety of processes in both DNA metabolism and in innate immunity. In this review, we will focus on the implications of the interactions of HMGB1 with nucleic acids in DNA repair and immune responses. We report on the roles of HMGB1 in nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR) and DNA double-strand break repair (DSBR). We also report on its roles in immune responses via its potential effects on antigen receptor diversity generation [V(D)J recombination] and interactions with foreign and self-nucleic acids. HMGB1 expression is altered in a variety of cancers and immunological disorders. However, due to the diversity and complexity of the biological processes influenced by HMGB1 (and its family members), a detailed understanding of the intracellular and extracellular roles of HMGB1 in DNA damage repair and immune responses is warranted to ensure the development of effective HMGB1-related therapies.
    MeSH term(s) Animals ; DNA/genetics ; DNA/metabolism ; DNA Repair ; HMGB1 Protein/metabolism ; Humans ; Immunity ; Protein Binding
    Chemical Substances HMGB1 Protein ; DNA (9007-49-2)
    Language English
    Publishing date 2019-09-16
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2071608-4
    ISSN 1568-7856 ; 1568-7864
    ISSN (online) 1568-7856
    ISSN 1568-7864
    DOI 10.1016/j.dnarep.2019.102701
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  9. Article: Distinct mechanisms of mutagenic processing of alternative DNA structures by repair proteins.

    McKinney, Jennifer A / Wang, Guliang / Vasquez, Karen M

    Molecular & cellular oncology

    2020  Volume 7, Issue 3, Page(s) 1743807

    Abstract: Repetitive sequences can form a variety of alternative DNA structures (non-B DNA) that can modulate transcription, replication, and repair. However, non-B DNA-forming sequences can also stimulate mutagenesis, and are enriched at mutation hotspots in ... ...

    Abstract Repetitive sequences can form a variety of alternative DNA structures (non-B DNA) that can modulate transcription, replication, and repair. However, non-B DNA-forming sequences can also stimulate mutagenesis, and are enriched at mutation hotspots in human cancer genomes. Interestingly, different types of non-B DNA stimulate mutagenesis via distinct repair processing mechanisms.
    Language English
    Publishing date 2020-04-02
    Publishing country United States
    Document type Journal Article
    ISSN 2372-3556
    ISSN 2372-3556
    DOI 10.1080/23723556.2020.1743807
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Activation-induced marker assays for identification of Trypanosoma cruzi-specific CD4 or CD8 T cells in chronic Chagas disease patients.

    Ferragut, Fátima / Cruz, Karen M / Gallardo, Juan P / Fernández, Marisa / Hernández Vasquez, Yolanda / Gómez, Karina A

    Immunology

    2023  Volume 169, Issue 2, Page(s) 185–203

    Abstract: Antigen-specific T cells are central to the adaptive immune response against T. cruzi infection and underpin the efficacy of on-going vaccine strategies. In this context, the present study focuses on T-cell assays that define the parasite-specificity on ... ...

    Abstract Antigen-specific T cells are central to the adaptive immune response against T. cruzi infection and underpin the efficacy of on-going vaccine strategies. In this context, the present study focuses on T-cell assays that define the parasite-specificity on the basis of upregulation of TCR stimulation-induced surface markers. For this purpose, we tested different dual marker combinations (OX40, CD25, CD40L, CD137, CD69, PD-L1, CD11a, CD49d, HLA-DR, CD38) to reliably identify activated CD4
    MeSH term(s) Humans ; Trypanosoma cruzi ; CD8-Positive T-Lymphocytes ; B7-H1 Antigen ; CD40 Ligand ; Chagas Disease/diagnosis
    Chemical Substances B7-H1 Antigen ; CD40 Ligand (147205-72-9)
    Language English
    Publishing date 2023-01-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 80124-0
    ISSN 1365-2567 ; 0019-2805 ; 0953-4954
    ISSN (online) 1365-2567
    ISSN 0019-2805 ; 0953-4954
    DOI 10.1111/imm.13622
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