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  1. Article ; Online: ELAC2 is a functional prostate cancer risk allele.

    Blinka, Steven / Mishra, Rashmi / Hsieh, Andrew C

    Trends in molecular medicine

    2023  Volume 29, Issue 8, Page(s) 586–588

    Abstract: Stentenbach and colleagues have unveiled a functional role of a human germline mutation found in the ribonuclease (RNase) Z enzyme, ELAC2, in prostate cancer. Here, we discuss the importance of these findings in enhancing our understanding of how risk ... ...

    Abstract Stentenbach and colleagues have unveiled a functional role of a human germline mutation found in the ribonuclease (RNase) Z enzyme, ELAC2, in prostate cancer. Here, we discuss the importance of these findings in enhancing our understanding of how risk variants enable prostate cancer progression and the post-transcriptional mechanisms underlying oncogenesis.
    MeSH term(s) Male ; Humans ; Alleles ; Prostatic Neoplasms/genetics ; Genetic Predisposition to Disease ; Neoplasm Proteins/genetics
    Chemical Substances ELAC2 protein, human ; Neoplasm Proteins
    Language English
    Publishing date 2023-06-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 2036490-8
    ISSN 1471-499X ; 1471-4914
    ISSN (online) 1471-499X
    ISSN 1471-4914
    DOI 10.1016/j.molmed.2023.06.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Citron Kinase Is a Druggable Target in Treatment-Resistant Prostate Cancer.

    Mishra, Rashmi / Blinka, Steven / Hsieh, Andrew C

    Cancer research

    2023  Volume 83, Issue 24, Page(s) 4008–4009

    Abstract: Prolonged treatment with androgen deprivation therapy (ADT) inevitably leads to castration-resistant prostate cancer (CRPC). Development of novel androgen-targeting agents and chemo/radiotherapies has resulted in improved survival. However, metastatic ... ...

    Abstract Prolonged treatment with androgen deprivation therapy (ADT) inevitably leads to castration-resistant prostate cancer (CRPC). Development of novel androgen-targeting agents and chemo/radiotherapies has resulted in improved survival. However, metastatic CRPC remains incurable. New therapeutics are greatly needed, and exploration of novel pathways such as the mechanisms underlying prostate cancer cell proliferation could potentially augment the natural course of CRPC. In the latest issue of Cancer Research, Rawat and colleagues delved deeply into the mechanistic role of citron kinase (CIT) in orchestrating prostate cancer proliferation and revealed its catalytic activity as a druggable target for treatment-resistant prostate cancer. The researchers utilized in vitro and in vivo methodologies to elucidate the function of CIT in mediating uncontrolled interphase progression and prostate cancer growth. Furthermore, the authors employed both androgen receptor-dependent and independent models to validate the significance of CIT kinase activity as a crucial factor in driving treatment-resistant prostate cancer growth. At a mechanistic level they determined that the E2F2-Skp2-p27 axis regulates CIT expression. Finally, they defined the landscape of CIT substrates in prostate cancer that encompasses a spectrum of cellular functions that spans key proliferation regulators to alternative splicing events. This comprehensive work provides insights into CIT as a potential biomarker for prostate cancer treatment resistance and disease progression and establishes the CIT kinase domain as a druggable target in CRPC. See related article by Rawat et al., p. 4142.
    MeSH term(s) Male ; Humans ; Prostatic Neoplasms, Castration-Resistant/metabolism ; Androgens ; Androgen Antagonists ; Receptors, Androgen/metabolism ; Prostate/pathology ; Cell Line, Tumor
    Chemical Substances Androgens ; Androgen Antagonists ; Receptors, Androgen
    Language English
    Publishing date 2023-12-15
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 1432-1
    ISSN 1538-7445 ; 0008-5472
    ISSN (online) 1538-7445
    ISSN 0008-5472
    DOI 10.1158/0008-5472.CAN-23-2858
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Nanog Expression in Embryonic Stem Cells - An Ideal Model System to Dissect Enhancer Function.

    Blinka, Steven / Rao, Sridhar

    BioEssays : news and reviews in molecular, cellular and developmental biology

    2017  Volume 39, Issue 12

    Abstract: Embryonic stem cells (ESCs) are derived from the preimplantation embryo and can differentiate into virtually any other cell type (termed pluripotency), which is governed by lineage specific transcriptions factors (TFs) binding to cis regulatory elements ( ...

    Abstract Embryonic stem cells (ESCs) are derived from the preimplantation embryo and can differentiate into virtually any other cell type (termed pluripotency), which is governed by lineage specific transcriptions factors (TFs) binding to cis regulatory elements (CREs) to mediate changes in gene expression. The reliance on transcriptional regulation to maintain pluripotency makes ESCs a valuable model to study the role of distal CREs such as enhancers in modulating gene expression to affect cell fate decisions. This review will highlight recent advance on transcriptional enhancers, focusing on studies performed in ESCs. In addition, we argue that the Nanog locus, which encodes for an ESC-critical TF, is particularly informative because it contains multiple co-regulated genes and enhancers in close proximity to one another. The unique landscape at Nanog permits the study of ongoing questions including whether multiple enhancers function additively versus synergistically, determinants of gene specificity, and cell-to-cell variability in gene expression.
    MeSH term(s) Animals ; Cell Differentiation ; Enhancer Elements, Genetic ; Epigenesis, Genetic ; Gene Expression Regulation, Developmental ; Genetic Loci ; Genome ; Histones/genetics ; Histones/metabolism ; Mice ; Models, Genetic ; Mouse Embryonic Stem Cells/cytology ; Mouse Embryonic Stem Cells/metabolism ; Nanog Homeobox Protein/genetics ; Nanog Homeobox Protein/metabolism ; Octamer Transcription Factor-3/genetics ; Octamer Transcription Factor-3/metabolism ; Pluripotent Stem Cells/cytology ; Pluripotent Stem Cells/metabolism ; SOXB1 Transcription Factors/genetics ; SOXB1 Transcription Factors/metabolism ; Transcription, Genetic
    Chemical Substances Histones ; Nanog Homeobox Protein ; Nanog protein, mouse ; Octamer Transcription Factor-3 ; Pou5f1 protein, mouse ; SOXB1 Transcription Factors ; Sox2 protein, mouse
    Language English
    Publishing date 2017-10-04
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.201700086
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Nanog Expression in Embryonic Stem Cells – An Ideal Model System to Dissect Enhancer Function

    Blinka, Steven / Sridhar Rao

    BioEssays. 2017 Dec., v. 39, no. 12

    2017  

    Abstract: Embryonic stem cells (ESCs) are derived from the preimplantation embryo and can differentiate into virtually any other cell type (termed pluripotency), which is governed by lineage specific transcriptions factors (TFs) binding to cis regulatory elements ( ...

    Abstract Embryonic stem cells (ESCs) are derived from the preimplantation embryo and can differentiate into virtually any other cell type (termed pluripotency), which is governed by lineage specific transcriptions factors (TFs) binding to cis regulatory elements (CREs) to mediate changes in gene expression. The reliance on transcriptional regulation to maintain pluripotency makes ESCs a valuable model to study the role of distal CREs such as enhancers in modulating gene expression to affect cell fate decisions. This review will highlight recent advance on transcriptional enhancers, focusing on studies performed in ESCs. In addition, we argue that the Nanog locus, which encodes for an ESC‐critical TF, is particularly informative because it contains multiple co‐regulated genes and enhancers in close proximity to one another. The unique landscape at Nanog permits the study of ongoing questions including whether multiple enhancers function additively versus synergistically, determinants of gene specificity, and cell‐to‐cell variability in gene expression.
    Keywords embryonic stem cells ; gene expression ; gene expression regulation ; genes ; landscapes ; loci ; models ; regulatory sequences ; transcription (genetics)
    Language English
    Dates of publication 2017-12
    Size p. .
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note REVIEW
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.201700086
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Genome editing demonstrates that the -5 kb Nanog enhancer regulates Nanog expression by modulating RNAPII initiation and/or recruitment.

    Agrawal, Puja / Blinka, Steven / Pulakanti, Kirthi / Reimer, Michael H / Stelloh, Cary / Meyer, Alison E / Rao, Sridhar

    The Journal of biological chemistry

    2020  Volume 296, Page(s) 100189

    Abstract: Transcriptional enhancers have been defined by their ability to operate independent of distance and orientation in plasmid-based reporter assays of gene expression. At present, histone marks are used to identify and define enhancers but do not consider ... ...

    Abstract Transcriptional enhancers have been defined by their ability to operate independent of distance and orientation in plasmid-based reporter assays of gene expression. At present, histone marks are used to identify and define enhancers but do not consider the endogenous role of an enhancer in the context of native chromatin. We employed a combination of genomic editing, single cell analyses, and sequencing approaches to investigate a Nanog-associated cis-regulatory element, which has been reported by others to be either an alternative promoter or a super-enhancer. We first demonstrate both distance and orientation independence in native chromatin, eliminating the issues raised with plasmid-based approaches. We next demonstrate that the dominant super-enhancer modulates Nanog globally and operates by recruiting and/or initiating RNA Polymerase II. Our studies have important implications to how transcriptional enhancers are defined and how they regulate gene expression.
    MeSH term(s) Animals ; CRISPR-Cas Systems ; Cell Line ; Enhancer Elements, Genetic ; Gene Editing ; Gene Expression Regulation ; Mice ; Mouse Embryonic Stem Cells/cytology ; Mouse Embryonic Stem Cells/metabolism ; Nanog Homeobox Protein/genetics ; RNA Polymerase II/genetics ; Transcriptional Activation
    Chemical Substances Nanog Homeobox Protein ; Nanog protein, mouse ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2020-12-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.RA120.015152
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes.

    Blinka, Steven / Reimer, Michael H / Pulakanti, Kirthi / Rao, Sridhar

    Cell reports

    2016  Volume 17, Issue 1, Page(s) 19–28

    Abstract: Super-enhancers are tissue-specific cis-regulatory elements that drive expression of genes associated with cell identity and malignancy. A cardinal feature of super-enhancers is that they are transcribed to produce enhancer-derived RNAs (eRNAs). It ... ...

    Abstract Super-enhancers are tissue-specific cis-regulatory elements that drive expression of genes associated with cell identity and malignancy. A cardinal feature of super-enhancers is that they are transcribed to produce enhancer-derived RNAs (eRNAs). It remains unclear whether super-enhancers robustly activate genes in situ and whether their functions are attributable to eRNAs or the DNA element. CRISPR/Cas9 was used to systematically delete three discrete super-enhancers at the Nanog locus in embryonic stem cells, revealing functional differences in Nanog transcriptional regulation. One distal super-enhancer 45 kb upstream of Nanog (-45 enhancer) regulates both nearest neighbor genes, Nanog and Dppa3. Interestingly, eRNAs produced at the -45 enhancer specifically regulate Dppa3 expression by stabilizing looping of the -45 enhancer and Dppa3. Our work illustrates that genomic editing is required to determine enhancer function and points to a method to selectively target a subset of super-enhancer-regulated genes by depleting eRNAs.
    MeSH term(s) Animals ; CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; Endonucleases/genetics ; Endonucleases/metabolism ; Enhancer Elements, Genetic ; Gene Editing ; Gene Expression Regulation ; Human Embryonic Stem Cells/cytology ; Human Embryonic Stem Cells/metabolism ; Humans ; Mice ; NIH 3T3 Cells ; Nanog Homeobox Protein/genetics ; Nanog Homeobox Protein/metabolism ; Pluripotent Stem Cells/cytology ; Pluripotent Stem Cells/metabolism ; Primary Cell Culture ; Proteins/genetics ; Proteins/metabolism ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; Transcription, Genetic
    Chemical Substances DPPA3 protein, human ; NANOG protein, human ; Nanog Homeobox Protein ; Proteins ; RNA, Long Noncoding ; Endonucleases (EC 3.1.-)
    Language English
    Publishing date 2016-09-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2016.09.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing.

    Blinka, Steven / Reimer, Michael H / Pulakanti, Kirthi / Pinello, Luca / Yuan, Guo-Cheng / Rao, Sridhar

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

    2017  Volume 1468, Page(s) 91–109

    Abstract: Recent work has shown that RNA polymerase II-mediated transcription at distal cis-regulatory elements serves as a mark of highly active enhancers. Production of noncoding RNAs at enhancers, termed eRNAs, correlates with higher expression of genes that ... ...

    Abstract Recent work has shown that RNA polymerase II-mediated transcription at distal cis-regulatory elements serves as a mark of highly active enhancers. Production of noncoding RNAs at enhancers, termed eRNAs, correlates with higher expression of genes that the enhancer interacts with; hence, eRNAs provide a new tool to model gene activity in normal and disease tissues. Moreover, this unique class of noncoding RNA has diverse roles in transcriptional regulation. Transcribed enhancers can be identified by a common signature of epigenetic marks by overlaying a series of genome-wide chromatin immunoprecipitation and RNA sequencing datasets. A computational approach to filter non-enhancer elements and other classes of noncoding RNAs is essential to not cloud downstream analysis. Here we present a protocol that combines wet and dry bench methods to accurately identify transcribed enhancers genome-wide as well as an experimental procedure to validate these datasets.
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-4035-6_8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Transcriptional-translational conflict is a barrier to cellular transformation and cancer progression.

    Jana, Sujata / Brahma, Sandipan / Arora, Sonali / Wladyka, Cynthia L / Hoang, Patrick / Blinka, Steven / Hough, Rowan / Horn, Jessie L / Liu, Yuzhen / Wang, Li-Jie / Depeille, Philippe / Smith, Eric / Montgomery, Robert B / Lee, John K / Haffner, Michael C / Vakar-Lopez, Funda / Grivas, Petros / Wright, Jonathan L / Lam, Hung-Ming /
    Black, Peter C / Roose, Jeroen P / Ryazanov, Alexey G / Subramaniam, Arvind R / Henikoff, Steven / Hsieh, Andrew C

    Cancer cell

    2023  Volume 41, Issue 5, Page(s) 853–870.e13

    Abstract: We uncover a tumor-suppressive process in urothelium called transcriptional-translational conflict caused by deregulation of the central chromatin remodeling component ARID1A. Loss of Arid1a triggers an increase in a nexus of pro-proliferation ... ...

    Abstract We uncover a tumor-suppressive process in urothelium called transcriptional-translational conflict caused by deregulation of the central chromatin remodeling component ARID1A. Loss of Arid1a triggers an increase in a nexus of pro-proliferation transcripts, but a simultaneous inhibition of the eukaryotic elongation factor 2 (eEF2), which results in tumor suppression. Resolution of this conflict through enhancing translation elongation speed enables the efficient and precise synthesis of a network of poised mRNAs resulting in uncontrolled proliferation, clonogenic growth, and bladder cancer progression. We observe a similar phenomenon in patients with ARID1A-low tumors, which also exhibit increased translation elongation activity through eEF2. These findings have important clinical implications because ARID1A-deficient, but not ARID1A-proficient, tumors are sensitive to pharmacologic inhibition of protein synthesis. These discoveries reveal an oncogenic stress created by transcriptional-translational conflict and provide a unified gene expression model that unveils the importance of the crosstalk between transcription and translation in promoting cancer.
    MeSH term(s) Humans ; Chromatin ; Urinary Bladder Neoplasms/genetics
    Chemical Substances Chromatin
    Language English
    Publishing date 2023-04-20
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078448-X
    ISSN 1878-3686 ; 1535-6108
    ISSN (online) 1878-3686
    ISSN 1535-6108
    DOI 10.1016/j.ccell.2023.03.021
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes

    Steven Blinka / Michael H. Reimer Jr. / Kirthi Pulakanti / Sridhar Rao

    Cell Reports, Vol 17, Iss 1, Pp 19-

    2016  Volume 28

    Abstract: Super-enhancers are tissue-specific cis-regulatory elements that drive expression of genes associated with cell identity and malignancy. A cardinal feature of super-enhancers is that they are transcribed to produce enhancer-derived RNAs (eRNAs). It ... ...

    Abstract Super-enhancers are tissue-specific cis-regulatory elements that drive expression of genes associated with cell identity and malignancy. A cardinal feature of super-enhancers is that they are transcribed to produce enhancer-derived RNAs (eRNAs). It remains unclear whether super-enhancers robustly activate genes in situ and whether their functions are attributable to eRNAs or the DNA element. CRISPR/Cas9 was used to systematically delete three discrete super-enhancers at the Nanog locus in embryonic stem cells, revealing functional differences in Nanog transcriptional regulation. One distal super-enhancer 45 kb upstream of Nanog (−45 enhancer) regulates both nearest neighbor genes, Nanog and Dppa3. Interestingly, eRNAs produced at the −45 enhancer specifically regulate Dppa3 expression by stabilizing looping of the −45 enhancer and Dppa3. Our work illustrates that genomic editing is required to determine enhancer function and points to a method to selectively target a subset of super-enhancer-regulated genes by depleting eRNAs.
    Keywords embryonic stem cells ; transcriptional regulation ; super-enhancers ; eRNAs ; long non-coding RNAs ; Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2016-09-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Activin-A and Bmp4 levels modulate cell type specification during CHIR-induced cardiomyogenesis.

    Kim, Min-Su / Horst, Audrey / Blinka, Steven / Stamm, Karl / Mahnke, Donna / Schuman, James / Gundry, Rebekah / Tomita-Mitchell, Aoy / Lough, John

    PloS one

    2015  Volume 10, Issue 2, Page(s) e0118670

    Abstract: The use of human pluripotent cell progeny for cardiac disease modeling, drug testing and therapeutics requires the ability to efficiently induce pluripotent cells into the cardiomyogenic lineage. Although direct activation of the Activin-A and/or Bmp ... ...

    Abstract The use of human pluripotent cell progeny for cardiac disease modeling, drug testing and therapeutics requires the ability to efficiently induce pluripotent cells into the cardiomyogenic lineage. Although direct activation of the Activin-A and/or Bmp pathways with growth factors yields context-dependent success, recent studies have shown that induction of Wnt signaling using low molecular weight molecules such as CHIR, which in turn induces the Activin-A and Bmp pathways, is widely effective. To further enhance the reproducibility of CHIR-induced cardiomyogenesis, and to ultimately promote myocyte maturation, we are using exogenous growth factors to optimize cardiomyogenic signaling downstream of CHIR induction. As indicated by RNA-seq, induction with CHIR during Day 1 (Days 0-1) was followed by immediate expression of Nodal ligands and receptors, followed later by Bmp ligands and receptors. Co-induction with CHIR and high levels of the Nodal mimetic Activin-A (50-100 ng/ml) during Day 0-1 efficiently induced definitive endoderm, whereas CHIR supplemented with Activin-A at low levels (10 ng/ml) consistently improved cardiomyogenic efficiency, even when CHIR alone was ineffective. Moreover, co-induction using CHIR and low levels of Activin-A apparently increased the rate of cardiomyogenesis, as indicated by the initial appearance of rhythmically beating cells by Day 6 instead of Day 8. By contrast, co-induction with CHIR plus low levels (3-10 ng/ml) of Bmp4 during Day 0-1 consistently and strongly inhibited cardiomyogenesis. These findings, which demonstrate that cardiomyogenic efficacy is improved by optimizing levels of CHIR-induced growth factors when applied in accord with their sequence of endogenous expression, are consistent with the idea that Nodal (Activin-A) levels toggle the entry of cells into the endodermal or mesodermal lineages, while Bmp levels regulate subsequent allocation into mesodermal cell types.
    MeSH term(s) Activins/physiology ; Bone Morphogenetic Protein 4/physiology ; Cell Differentiation ; Embryonic Stem Cells/cytology ; Humans ; Myocytes, Cardiac/cytology ; Sequence Analysis, RNA
    Chemical Substances Bone Morphogenetic Protein 4 ; activin A ; Activins (104625-48-1)
    Language English
    Publishing date 2015
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0118670
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