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  1. Article ; Online: CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy.

    Salgado-Albarrán, Marisol / Späth, Julian / González-Barrios, Rodrigo / Baumbach, Jan / Soto-Reyes, Ernesto

    NPJ systems biology and applications

    2022  Volume 8, Issue 1, Page(s) 5

    Abstract: High-grade serous ovarian carcinoma (HGSC) is the most lethal gynecologic malignancy due to the lack of reliable biomarkers, effective treatment, and chemoresistance. Improving the diagnosis and the development of targeted therapies is still needed. The ... ...

    Abstract High-grade serous ovarian carcinoma (HGSC) is the most lethal gynecologic malignancy due to the lack of reliable biomarkers, effective treatment, and chemoresistance. Improving the diagnosis and the development of targeted therapies is still needed. The molecular pathomechanisms driving HGSC progression are not fully understood though crucial for effective diagnosis and identification of novel targeted therapy options. The oncogene CTCFL (BORIS), the paralog of CTCF, is a transcriptional factor highly expressed in ovarian cancer (but in rarely any other tissue in females) with cancer-specific characteristics and therapeutic potential. In this work, we seek to understand the regulatory functions of CTCFL to unravel new target genes with clinical relevance. We used in vitro models to evaluate the transcriptional changes due to the presence of CTCFL, followed by a selection of gene candidates using de novo network enrichment analysis. The resulting mechanistic candidates were further assessed regarding their prognostic potential and druggability. We show that CTCFL-driven genes are involved in cytoplasmic membrane functions; in particular, the PI3K-Akt initiators EGFR1 and VEGFA, as well as ITGB3 and ITGB6 are potential drug targets. Finally, we identified the CTCFL targets ACTBL2, MALT1 and PCDH7 as mechanistic biomarkers to predict survival in HGSC. Finally, we elucidated the value of CTCFL in combination with its targets as a prognostic marker profile for HGSC progression and as putative drug targets.
    MeSH term(s) DNA-Binding Proteins/genetics ; Female ; Humans ; Ovarian Neoplasms/drug therapy ; Ovarian Neoplasms/genetics ; Ovarian Neoplasms/metabolism ; Phosphatidylinositol 3-Kinases/genetics ; Proto-Oncogene Proteins c-akt/genetics ; Signal Transduction ; Transcription Factors
    Chemical Substances CTCFL protein, human ; DNA-Binding Proteins ; Transcription Factors ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1)
    Language English
    Publishing date 2022-02-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2056-7189
    ISSN (online) 2056-7189
    DOI 10.1038/s41540-022-00214-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: CTCF and Its Multi-Partner Network for Chromatin Regulation.

    Del Moral-Morales, Aylin / Salgado-Albarrán, Marisol / Sánchez-Pérez, Yesennia / Wenke, Nina Kerstin / Baumbach, Jan / Soto-Reyes, Ernesto

    Cells

    2023  Volume 12, Issue 10

    Abstract: Architectural proteins are essential epigenetic regulators that play a critical role in organizing chromatin and controlling gene expression. CTCF (CCCTC-binding factor) is a key architectural protein responsible for maintaining the intricate 3D ... ...

    Abstract Architectural proteins are essential epigenetic regulators that play a critical role in organizing chromatin and controlling gene expression. CTCF (CCCTC-binding factor) is a key architectural protein responsible for maintaining the intricate 3D structure of chromatin. Because of its multivalent properties and plasticity to bind various sequences, CTCF is similar to a Swiss knife for genome organization. Despite the importance of this protein, its mechanisms of action are not fully elucidated. It has been hypothesized that its versatility is achieved through interaction with multiple partners, forming a complex network that regulates chromatin folding within the nucleus. In this review, we delve into CTCF's interactions with other molecules involved in epigenetic processes, particularly histone and DNA demethylases, as well as several long non-coding RNAs (lncRNAs) that are able to recruit CTCF. Our review highlights the importance of CTCF partners to shed light on chromatin regulation and pave the way for future exploration of the mechanisms that enable the finely-tuned role of CTCF as a master regulator of chromatin.
    MeSH term(s) CCCTC-Binding Factor/genetics ; Chromatin ; DNA/metabolism ; Cell Nucleus/metabolism ; Genome
    Chemical Substances CCCTC-Binding Factor ; Chromatin ; DNA (9007-49-2)
    Language English
    Publishing date 2023-05-10
    Publishing country Switzerland
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells12101357
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy

    Marisol Salgado-Albarrán / Julian Späth / Rodrigo González-Barrios / Jan Baumbach / Ernesto Soto-Reyes

    npj Systems Biology and Applications, Vol 8, Iss 1, Pp 1-

    2022  Volume 10

    Abstract: Abstract High-grade serous ovarian carcinoma (HGSC) is the most lethal gynecologic malignancy due to the lack of reliable biomarkers, effective treatment, and chemoresistance. Improving the diagnosis and the development of targeted therapies is still ... ...

    Abstract Abstract High-grade serous ovarian carcinoma (HGSC) is the most lethal gynecologic malignancy due to the lack of reliable biomarkers, effective treatment, and chemoresistance. Improving the diagnosis and the development of targeted therapies is still needed. The molecular pathomechanisms driving HGSC progression are not fully understood though crucial for effective diagnosis and identification of novel targeted therapy options. The oncogene CTCFL (BORIS), the paralog of CTCF, is a transcriptional factor highly expressed in ovarian cancer (but in rarely any other tissue in females) with cancer-specific characteristics and therapeutic potential. In this work, we seek to understand the regulatory functions of CTCFL to unravel new target genes with clinical relevance. We used in vitro models to evaluate the transcriptional changes due to the presence of CTCFL, followed by a selection of gene candidates using de novo network enrichment analysis. The resulting mechanistic candidates were further assessed regarding their prognostic potential and druggability. We show that CTCFL-driven genes are involved in cytoplasmic membrane functions; in particular, the PI3K-Akt initiators EGFR1 and VEGFA, as well as ITGB3 and ITGB6 are potential drug targets. Finally, we identified the CTCFL targets ACTBL2, MALT1 and PCDH7 as mechanistic biomarkers to predict survival in HGSC. Finally, we elucidated the value of CTCFL in combination with its targets as a prognostic marker profile for HGSC progression and as putative drug targets.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Transcriptomic and Drug Discovery Analyses Reveal Natural Compounds Targeting the KDM4 Subfamily as Promising Adjuvant Treatments in Cancer.

    Del Moral-Morales, Aylin / Salgado-Albarrán, Marisol / Ortiz-Gutiérrez, Elizabeth / Pérez-Hernández, Gerardo / Soto-Reyes, Ernesto

    Frontiers in genetics

    2022  Volume 13, Page(s) 860924

    Abstract: KDM4 proteins are a subfamily of histone demethylases that target the trimethylation of lysines 9 and 36 of histone H3, which are associated with transcriptional repression and elongation respectively. Their deregulation in cancer may lead to chromatin ... ...

    Abstract KDM4 proteins are a subfamily of histone demethylases that target the trimethylation of lysines 9 and 36 of histone H3, which are associated with transcriptional repression and elongation respectively. Their deregulation in cancer may lead to chromatin structure alteration and transcriptional defects that could promote malignancy. Despite that KDM4 proteins are promising drug targets in cancer therapy, only a few drugs have been described as inhibitors of these enzymes, while studies on natural compounds as possible inhibitors are still needed. Natural compounds are a major source of biologically active substances and many are known to target epigenetic processes such as DNA methylation and histone deacetylation, making them a rich source for the discovery of new histone demethylase inhibitors. Here, using transcriptomic analyses we determined that the KDM4 family is deregulated and associated with a poor prognosis in multiple neoplastic tissues. Also, by molecular docking and molecular dynamics approaches, we screened the COCONUT database to search for inhibitors of natural origin compared to FDA-approved drugs and DrugBank databases. We found that molecules from natural products presented the best scores in the FRED docking analysis. Molecules with sugars, aromatic rings, and the presence of OH or O- groups favor the interaction with the active site of KDM4 subfamily proteins. Finally, we integrated a protein-protein interaction network to correlate data from transcriptomic analysis and docking screenings to propose FDA-approved drugs that could be used as multitarget therapies or in combination with the potential natural inhibitors of KDM4 enzymes. This study highlights the relevance of the KDM4 family in cancer and proposes natural compounds that could be used as potential therapies.
    Language English
    Publishing date 2022-04-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2022.860924
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Individuating Possibly Repurposable Drugs and Drug Targets for COVID-19 Treatment Through Hypothesis-Driven Systems Medicine Using CoVex.

    Matschinske, Julian / Salgado-Albarrán, Marisol / Sadegh, Sepideh / Bongiovanni, Dario / Baumbach, Jan / Blumenthal, David B

    Assay and drug development technologies

    2020  Volume 18, Issue 8, Page(s) 348–355

    Abstract: Coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 virus, has developed into a pandemic causing major disruptions and hundreds of thousands of deaths in wide parts of the world. As of July 3, 2020, neither vaccines nor approved drugs for ... ...

    Abstract Coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 virus, has developed into a pandemic causing major disruptions and hundreds of thousands of deaths in wide parts of the world. As of July 3, 2020, neither vaccines nor approved drugs for effective treatment are available. In this article, we showcase how to individuate drug targets and potentially repurposable drugs
    MeSH term(s) Algorithms ; Antiviral Agents ; Computational Biology ; Computer Simulation ; Drug Delivery Systems ; Drug Repositioning/trends ; Humans ; Molecular Docking Simulation ; Proteomics ; COVID-19 Drug Treatment
    Chemical Substances Antiviral Agents
    Keywords covid19
    Language English
    Publishing date 2020-11-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ISSN 1557-8127
    ISSN (online) 1557-8127
    DOI 10.1089/adt.2020.1010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Lessons from the COVID-19 pandemic for advancing computational drug repurposing strategies.

    Galindez, Gihanna / Matschinske, Julian / Rose, Tim Daniel / Sadegh, Sepideh / Salgado-Albarrán, Marisol / Späth, Julian / Baumbach, Jan / Pauling, Josch Konstantin

    Nature computational science

    2021  Volume 1, Issue 1, Page(s) 33–41

    Abstract: Responding quickly to unknown pathogens is crucial to stop uncontrolled spread of diseases that lead to epidemics, such as the novel coronavirus, and to keep protective measures at a level that causes as little social and economic harm as possible. This ... ...

    Abstract Responding quickly to unknown pathogens is crucial to stop uncontrolled spread of diseases that lead to epidemics, such as the novel coronavirus, and to keep protective measures at a level that causes as little social and economic harm as possible. This can be achieved through computational approaches that significantly speed up drug discovery. A powerful approach is to restrict the search to existing drugs through drug repurposing, which can vastly accelerate the usually long approval process. In this Review, we examine a representative set of currently used computational approaches to identify repurposable drugs for COVID-19, as well as their underlying data resources. Furthermore, we compare drug candidates predicted by computational methods to drugs being assessed by clinical trials. Finally, we discuss lessons learned from the reviewed research efforts, including how to successfully connect computational approaches with experimental studies, and propose a unified drug repurposing strategy for better preparedness in the case of future outbreaks.
    Language English
    Publishing date 2021-01-14
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2662-8457
    ISSN (online) 2662-8457
    DOI 10.1038/s43588-020-00007-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Transcriptomic and Drug Discovery Analyses Reveal Natural Compounds Targeting the KDM4 Subfamily as Promising Adjuvant Treatments in Cancer

    Aylin del Moral-Morales / Marisol Salgado-Albarrán / Elizabeth Ortiz-Gutiérrez / Gerardo Pérez-Hernández / Ernesto Soto-Reyes

    Frontiers in Genetics, Vol

    2022  Volume 13

    Abstract: KDM4 proteins are a subfamily of histone demethylases that target the trimethylation of lysines 9 and 36 of histone H3, which are associated with transcriptional repression and elongation respectively. Their deregulation in cancer may lead to chromatin ... ...

    Abstract KDM4 proteins are a subfamily of histone demethylases that target the trimethylation of lysines 9 and 36 of histone H3, which are associated with transcriptional repression and elongation respectively. Their deregulation in cancer may lead to chromatin structure alteration and transcriptional defects that could promote malignancy. Despite that KDM4 proteins are promising drug targets in cancer therapy, only a few drugs have been described as inhibitors of these enzymes, while studies on natural compounds as possible inhibitors are still needed. Natural compounds are a major source of biologically active substances and many are known to target epigenetic processes such as DNA methylation and histone deacetylation, making them a rich source for the discovery of new histone demethylase inhibitors. Here, using transcriptomic analyses we determined that the KDM4 family is deregulated and associated with a poor prognosis in multiple neoplastic tissues. Also, by molecular docking and molecular dynamics approaches, we screened the COCONUT database to search for inhibitors of natural origin compared to FDA-approved drugs and DrugBank databases. We found that molecules from natural products presented the best scores in the FRED docking analysis. Molecules with sugars, aromatic rings, and the presence of OH or O- groups favor the interaction with the active site of KDM4 subfamily proteins. Finally, we integrated a protein-protein interaction network to correlate data from transcriptomic analysis and docking screenings to propose FDA-approved drugs that could be used as multitarget therapies or in combination with the potential natural inhibitors of KDM4 enzymes. This study highlights the relevance of the KDM4 family in cancer and proposes natural compounds that could be used as potential therapies.
    Keywords epigenetics (chromatin remodeling) ; KDM4 inhibitor ; cancer ; natural compounds ; drug discovery ; structural biology ; Genetics ; QH426-470
    Subject code 540
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: The Transcriptional Regulatory Network of

    Parise, Doglas / Teixeira Dornelles Parise, Mariana / Pinto Gomide, Anne Cybelle / Figueira Aburjaile, Flávia / Bentes Kato, Rodrigo / Salgado-Albarrán, Marisol / Tauch, Andreas / Ariston de Carvalho Azevedo, Vasco / Baumbach, Jan

    Microorganisms

    2021  Volume 9, Issue 2

    Abstract: Corynebacterium ... ...

    Abstract Corynebacterium pseudotuberculosis
    Language English
    Publishing date 2021-02-17
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms9020415
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Individuating Possibly Repurposable Drugs and Drug Targets for COVID-19 Treatment through Hypothesis-Driven Systems Medicine Using CoVex

    Matschinske, Julian / Salgado-Albarrán, Marisol / Sadegh, Sepideh / Bongiovanni, Dario / Baumbach, Jan / Blumenthal, David B

    Abstract: Coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 virus, has developed into a pandemic causing major disruptions and hundreds of thousands of deaths in wide parts of the world. As of July 3, 2020, neither vaccines nor approved drugs for ... ...

    Abstract Coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 virus, has developed into a pandemic causing major disruptions and hundreds of thousands of deaths in wide parts of the world. As of July 3, 2020, neither vaccines nor approved drugs for effective treatment are available. In this article, we showcase how to individuate drug targets and potentially repurposable drugs in silico using CoVex a recently presented systems medicine platform for COVID-19 drug repurposing. Starting from initial hypotheses, CoVex leverages network algorithms to individuate host proteins involved in COVID-19 disease mechanisms, as well as existing drugs targeting these potential drug targets. Our analysis reveals GLA, PLAT, and GGCX as potential drug targets, and urokinase, argatroban, dabigatran etexilate, betrixaban, ximelagatran and anisindione as potentially repurposable drugs.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #915847
    Database COVID19

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  10. Article: The Regulatory Roles of Non-coding RNAs in Angiogenesis and Neovascularization From an Epigenetic Perspective.

    Hernández-Romero, Itzel Alejandra / Guerra-Calderas, Lissania / Salgado-Albarrán, Marisol / Maldonado-Huerta, Tatiana / Soto-Reyes, Ernesto

    Frontiers in oncology

    2019  Volume 9, Page(s) 1091

    Abstract: Angiogenesis is a crucial process for organ morphogenesis and growth during development, and it is especially relevant during the repair of wounded tissue in adults. It is coordinated by an equilibrium of pro- and anti-angiogenic factors; nevertheless, ... ...

    Abstract Angiogenesis is a crucial process for organ morphogenesis and growth during development, and it is especially relevant during the repair of wounded tissue in adults. It is coordinated by an equilibrium of pro- and anti-angiogenic factors; nevertheless, when affected, it promotes several diseases. Lately, a growing body of evidence is indicating that non-coding RNAs (ncRNAs), such as miRNAs, circRNAs, and lncRNAs, play critical roles in angiogenesis. These ncRNAs can act
    Language English
    Publishing date 2019-10-24
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2649216-7
    ISSN 2234-943X
    ISSN 2234-943X
    DOI 10.3389/fonc.2019.01091
    Database MEDical Literature Analysis and Retrieval System OnLINE

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