1
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Malone HA, Roberts CWM. Chromatin remodellers as therapeutic targets. Nat Rev Drug Discov 2024:10.1038/s41573-024-00978-5. [PMID: 39014081 DOI: 10.1038/s41573-024-00978-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2024] [Indexed: 07/18/2024]
Abstract
Large-scale cancer genome sequencing studies have revealed that chromatin regulators are frequently mutated in cancer. In particular, more than 20% of cancers harbour mutations in genes that encode subunits of SWI/SNF (BAF) chromatin remodelling complexes. Additional links of SWI/SNF complexes to disease have emerged with the findings that some oncogenes drive transformation by co-opting SWI/SNF function and that germline mutations in select SWI/SNF subunits are the basis of several neurodevelopmental disorders. Other chromatin remodellers, including members of the ISWI, CHD and INO80/SWR complexes, have also been linked to cancer and developmental disorders. Consequently, therapeutic manipulation of SWI/SNF and other remodelling complexes has become of great interest, and drugs that target SWI/SNF subunits have entered clinical trials. Genome-wide perturbation screens in cancer cell lines with SWI/SNF mutations have identified additional synthetic lethal targets and led to further compounds in clinical trials, including one that has progressed to FDA approval. Here, we review the progress in understanding the structure and function of SWI/SNF and other chromatin remodelling complexes, mechanisms by which SWI/SNF mutations cause cancer and neurological diseases, vulnerabilities that arise because of these mutations and efforts to target SWI/SNF complexes and synthetic lethal targets for therapeutic benefit.
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Affiliation(s)
- Hayden A Malone
- Division of Molecular Oncology, Department of Oncology, and Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
- St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Division of Molecular Oncology, Department of Oncology, and Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA.
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2
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Shen Z, Wu Y, Manna A, Yi C, Cairns BR, Evason KJ, Chandrasekharan MB, Tantin D. Oct4 redox sensitivity potentiates reprogramming and differentiation. Genes Dev 2024; 38:308-321. [PMID: 38719541 PMCID: PMC11146590 DOI: 10.1101/gad.351411.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/17/2024] [Indexed: 05/21/2024]
Abstract
The transcription factor Oct4/Pou5f1 is a component of the regulatory circuitry governing pluripotency and is widely used to induce pluripotency from somatic cells. Here we used domain swapping and mutagenesis to study Oct4's reprogramming ability, identifying a redox-sensitive DNA binding domain, cysteine residue (Cys48), as a key determinant of reprogramming and differentiation. Oct4 Cys48 sensitizes the protein to oxidative inhibition of DNA binding activity and promotes oxidation-mediated protein ubiquitylation. Pou5f1 C48S point mutation has little effect on undifferentiated embryonic stem cells (ESCs) but upon retinoic acid (RA) treatment causes retention of Oct4 expression, deregulated gene expression, and aberrant differentiation. Pou5f1 C48S ESCs also form less differentiated teratomas and contribute poorly to adult somatic tissues. Finally, we describe Pou5f1 C48S (Janky) mice, which in the homozygous condition are severely developmentally restricted after E4.5. Rare animals bypassing this restriction appear normal at birth but are sterile. Collectively, these findings uncover a novel Oct4 redox mechanism involved in both entry into and exit from pluripotency.
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Affiliation(s)
- Zuolian Shen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Yifan Wu
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Asit Manna
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Chongil Yi
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Bradley R Cairns
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Kimberley J Evason
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Mahesh B Chandrasekharan
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA;
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
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3
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Gourisankar S, Krokhotin A, Wenderski W, Crabtree GR. Context-specific functions of chromatin remodellers in development and disease. Nat Rev Genet 2024; 25:340-361. [PMID: 38001317 DOI: 10.1038/s41576-023-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 11/26/2023]
Abstract
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.
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Affiliation(s)
- Sai Gourisankar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Andrey Krokhotin
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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4
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Shen Z, Wu Y, Mana A, Yi C, Cairns B, Evason KJ, Chandrasekharan MB, Tantin D. Oct4 redox sensitivity potentiates reprogramming and differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.21.529404. [PMID: 36865286 PMCID: PMC9980064 DOI: 10.1101/2023.02.21.529404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The transcription factor Oct4/Pou5f1 is a component of the regulatory circuitry governing pluripotency and is widely used to induce pluripotency from somatic cells. Here we use domain swapping and mutagenesis to study Oct4s reprogramming ability, identifying a redox-sensitive DNA binding domain cysteine residue (Cys48) as a key determinant of reprogramming and differentiation. Oct4 Cys48 sensitizes the protein to oxidative inhibition of DNA binding activity and promotes oxidation-mediated protein ubiquitylation. Pou5f1C48S point mutation has little effect on undifferentiated embryonic stem cells (ESCs), but upon retinoic acid (RA) treatment causes retention of Oct4 expression, deregulated gene expression and aberrant differentiation. Pou5f1C48S ESCs also form less differentiated teratomas and contribute poorly to adult somatic tissues. Finally, we describe Pou5f1C48S (Janky) mice, which in the homozygous condition are severely developmentally restricted after E4.5. Rare animals bypassing this restriction appear normal at birth but are sterile. Collectively, these findings uncover a novel Oct4 redox mechanism involved in both entry into and exit from pluripotency.
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5
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MacCarthy CM, Wu G, Malik V, Menuchin-Lasowski Y, Velychko T, Keshet G, Fan R, Bedzhov I, Church GM, Jauch R, Cojocaru V, Schöler HR, Velychko S. Highly cooperative chimeric super-SOX induces naive pluripotency across species. Cell Stem Cell 2024; 31:127-147.e9. [PMID: 38141611 DOI: 10.1016/j.stem.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 09/02/2023] [Accepted: 11/20/2023] [Indexed: 12/25/2023]
Abstract
Our understanding of pluripotency remains limited: iPSC generation has only been established for a few model species, pluripotent stem cell lines exhibit inconsistent developmental potential, and germline transmission has only been demonstrated for mice and rats. By swapping structural elements between Sox2 and Sox17, we built a chimeric super-SOX factor, Sox2-17, that enhanced iPSC generation in five tested species: mouse, human, cynomolgus monkey, cow, and pig. A swap of alanine to valine at the interface between Sox2 and Oct4 delivered a gain of function by stabilizing Sox2/Oct4 dimerization on DNA, enabling generation of high-quality OSKM iPSCs capable of supporting the development of healthy all-iPSC mice. Sox2/Oct4 dimerization emerged as the core driver of naive pluripotency with its levels diminished upon priming. Transient overexpression of the SK cocktail (Sox+Klf4) restored the dimerization and boosted the developmental potential of pluripotent stem cells across species, providing a universal method for naive reset in mammals.
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Affiliation(s)
| | - Guangming Wu
- Max Planck Institute for Molecular Biomedicine, Münster, Germany; International Bio Island, Guangzhou, China; MingCeler Biotech, Guangzhou, China
| | - Vikas Malik
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Taras Velychko
- Max Planck Institute for Molecular Biomedicine, Münster, Germany; Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Gal Keshet
- Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rui Fan
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ivan Bedzhov
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Wyss Institute, Harvard University, Boston, MA, USA
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Centre for Translational Stem Cell Biology, Hong Kong SAR, China
| | - Vlad Cojocaru
- Max Planck Institute for Molecular Biomedicine, Münster, Germany; University of Utrecht, Utrecht, the Netherlands; STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Münster, Germany.
| | - Sergiy Velychko
- Max Planck Institute for Molecular Biomedicine, Münster, Germany; Department of Genetics, Harvard Medical School, Boston, MA, USA; Wyss Institute, Harvard University, Boston, MA, USA.
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6
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Riesle AJ, Gao M, Rosenblatt M, Hermes J, Hass H, Gebhard A, Veil M, Grüning B, Timmer J, Onichtchouk D. Activator-blocker model of transcriptional regulation by pioneer-like factors. Nat Commun 2023; 14:5677. [PMID: 37709752 PMCID: PMC10502082 DOI: 10.1038/s41467-023-41507-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023] Open
Abstract
Zygotic genome activation (ZGA) in the development of flies, fish, frogs and mammals depends on pioneer-like transcription factors (TFs). Those TFs create open chromatin regions, promote histone acetylation on enhancers, and activate transcription. Here, we use the panel of single, double and triple mutants for zebrafish genome activators Pou5f3, Sox19b and Nanog, multi-omics and mathematical modeling to investigate the combinatorial mechanisms of genome activation. We show that Pou5f3 and Nanog act differently on synergistic and antagonistic enhancer types. Pou5f3 and Nanog both bind as pioneer-like TFs on synergistic enhancers, promote histone acetylation and activate transcription. Antagonistic enhancers are activated by binding of one of these factors. The other TF binds as non-pioneer-like TF, competes with the activator and blocks all its effects, partially or completely. This activator-blocker mechanism mutually restricts widespread transcriptional activation by Pou5f3 and Nanog and prevents premature expression of late developmental regulators in the early embryo.
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Affiliation(s)
- Aileen Julia Riesle
- Department of Developmental Biology, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015, Monterotondo, RM, Italy
| | - Meijiang Gao
- Department of Developmental Biology, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
- Signalling Research centers BIOSS and CIBSS, 79104, Freiburg, Germany
| | - Marcus Rosenblatt
- Institute of Physics, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
- Freiburg Center for Data Analysis and Modelling (FDM), 79104, Freiburg, Germany
| | - Jacques Hermes
- Institute of Physics, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
- Freiburg Center for Data Analysis and Modelling (FDM), 79104, Freiburg, Germany
| | - Helge Hass
- Institute of Physics, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
- Freiburg Center for Data Analysis and Modelling (FDM), 79104, Freiburg, Germany
| | - Anna Gebhard
- Department of Developmental Biology, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
| | - Marina Veil
- Department of Developmental Biology, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
| | - Björn Grüning
- Department of Computer Science, University of Freiburg, 79110, Freiburg, Germany
- Center for Biological Systems Analysis (ZBSA), University of Freiburg, 79104, Freiburg, Germany
| | - Jens Timmer
- Signalling Research centers BIOSS and CIBSS, 79104, Freiburg, Germany.
- Institute of Physics, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany.
- Freiburg Center for Data Analysis and Modelling (FDM), 79104, Freiburg, Germany.
| | - Daria Onichtchouk
- Department of Developmental Biology, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany.
- Signalling Research centers BIOSS and CIBSS, 79104, Freiburg, Germany.
- Institute of Developmental Biology RAS, 119991, Moscow, Russia.
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7
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Obernikhin SS, Yaglova NV, Timokhina EP, Nazimova SV, Yaglov VV. Regulation of Morphogenetic Processes during Postnatal Development and Physiological Regeneration of the Adrenal Medulla. Bull Exp Biol Med 2023; 175:549-556. [PMID: 37776400 DOI: 10.1007/s10517-023-05903-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Indexed: 10/02/2023]
Abstract
Regulation of morphogenetic processes during postnatal development of the rat adrenal medulla was studied. Termination of the adrenal medulla growth was found to be associated with decreased chromaffin cell proliferation, activation of canonical Wnt-signaling pathway, and enhanced expression of Sonic Hedgehog ligand. Analysis of transcription factors associated with pluripotency revealed increased percentage of Oct4-expressing cells by the end of medulla growth and no signs of Sox2 expression. All the cells demonstrating activation of Wnt-signaling and expression of Oct4 and Sonic Hedgehog were found to be highly differentiated chromaffin cells actively producing tyrosine hydroxylase. These findings allow considering the formation of the cell pools for dedifferentiation as a putative mechanism for physiological regeneration of the adrenal medulla.
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Affiliation(s)
- S S Obernikhin
- Laboratory of Endocrine System Development, A. P. Avtsyn Research Institute of Human Morphology, A. P. Petrovsky Russian Research Center of Surgery, Moscow, Russia
| | - N V Yaglova
- Laboratory of Endocrine System Development, A. P. Avtsyn Research Institute of Human Morphology, A. P. Petrovsky Russian Research Center of Surgery, Moscow, Russia
| | - E P Timokhina
- Laboratory of Endocrine System Development, A. P. Avtsyn Research Institute of Human Morphology, A. P. Petrovsky Russian Research Center of Surgery, Moscow, Russia
| | - S V Nazimova
- Laboratory of Endocrine System Development, A. P. Avtsyn Research Institute of Human Morphology, A. P. Petrovsky Russian Research Center of Surgery, Moscow, Russia
| | - V V Yaglov
- Laboratory of Endocrine System Development, A. P. Avtsyn Research Institute of Human Morphology, A. P. Petrovsky Russian Research Center of Surgery, Moscow, Russia.
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8
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Sinha KK, Bilokapic S, Du Y, Malik D, Halic M. Histone modifications regulate pioneer transcription factor cooperativity. Nature 2023; 619:378-384. [PMID: 37225990 PMCID: PMC10338341 DOI: 10.1038/s41586-023-06112-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 04/21/2023] [Indexed: 05/26/2023]
Abstract
Pioneer transcription factors have the ability to access DNA in compacted chromatin1. Multiple transcription factors can bind together to a regulatory element in a cooperative way, and cooperation between the pioneer transcription factors OCT4 (also known as POU5F1) and SOX2 is important for pluripotency and reprogramming2-4. However, the molecular mechanisms by which pioneer transcription factors function and cooperate on chromatin remain unclear. Here we present cryo-electron microscopy structures of human OCT4 bound to a nucleosome containing human LIN28B or nMATN1 DNA sequences, both of which bear multiple binding sites for OCT4. Our structural and biochemistry data reveal that binding of OCT4 induces changes to the nucleosome structure, repositions the nucleosomal DNA and facilitates cooperative binding of additional OCT4 and of SOX2 to their internal binding sites. The flexible activation domain of OCT4 contacts the N-terminal tail of histone H4, altering its conformation and thus promoting chromatin decompaction. Moreover, the DNA-binding domain of OCT4 engages with the N-terminal tail of histone H3, and post-translational modifications at H3K27 modulate DNA positioning and affect transcription factor cooperativity. Thus, our findings suggest that the epigenetic landscape could regulate OCT4 activity to ensure proper cell programming.
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Affiliation(s)
- Kalyan K Sinha
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Silvija Bilokapic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yongming Du
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Deepshikha Malik
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mario Halic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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9
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Guan R, Lian T, Zhou BR, Wheeler D, Bai Y. Structural mechanism of LIN28B nucleosome targeting by OCT4. Mol Cell 2023; 83:1970-1982.e6. [PMID: 37327775 PMCID: PMC10276192 DOI: 10.1016/j.molcel.2023.05.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/31/2023] [Accepted: 05/19/2023] [Indexed: 06/18/2023]
Abstract
Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the in vivo nucleosomal DNA targets is unknown. Here, we determine the high-resolution structures of the nucleosome containing human LIN28B DNA and its complexes with the OCT4 DNA binding region. Three OCT4s bind the pre-positioned nucleosome by recognizing non-canonical DNA sequences. Two use their POUS domains while the other uses the POUS-loop-POUHD region; POUHD serves as a wedge to unwrap ∼25 base pair DNA. Our analysis of previous genomic data and determination of the ESRRB-nucleosome-OCT4 structure confirmed the generality of these structural features. Moreover, biochemical studies suggest that multiple OCT4s cooperatively open the H1-condensed nucleosome array containing the LIN28B nucleosome. Thus, our study suggests a mechanism of how OCT4 can target the nucleosome and open closed chromatin.
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Affiliation(s)
- Ruifang Guan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tengfei Lian
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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10
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Sinha K, Bilokapic S, Du Y, Malik D, Halic M. Histone modifications regulate pioneer transcription factor binding and cooperativity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532583. [PMID: 36993452 PMCID: PMC10055048 DOI: 10.1101/2023.03.14.532583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Pioneer transcription factors have the ability to access DNA in compacted chromatin. Multiple transcription factors can bind together to a regulatory element in a cooperative way and cooperation between pioneer transcription factors Oct4 and Sox2 is important for pluripotency and reprogramming. However, the molecular mechanisms by which pioneer transcription factors function and cooperate remain unclear. Here we present cryo-EM structures of human Oct4 bound to a nucleosome containing human Lin28B and nMatn1 DNA sequences, which bear multiple binding sites for Oct4. Our structural and biochemistry data reveal that Oct4 binding induces changes to the nucleosome structure, repositions the nucleosomal DNA and facilitates cooperative binding of additional Oct4 and of Sox2 to their internal binding sites. The flexible activation domain of Oct4 contacts the histone H4 N-terminal tail, altering its conformation and thus promoting chromatin decompaction. Moreover, the DNA binding domain of Oct4 engages with histone H3 N-terminal tail, and posttranslational modifications at H3K27 modulate DNA positioning and affect transcription factor cooperativity. Thus, our data show that the epigenetic landscape can regulate Oct4 activity to ensure proper cell reprogramming.
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Affiliation(s)
- Kalyan Sinha
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Silvija Bilokapic
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yongming Du
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Deepshikha Malik
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Mario Halic
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Corresponding author:
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11
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Mafi A, Rezaee M, Hedayati N, Hogan SD, Reiter RJ, Aarabi MH, Asemi Z. Melatonin and 5-fluorouracil combination chemotherapy: opportunities and efficacy in cancer therapy. Cell Commun Signal 2023; 21:33. [PMID: 36759799 PMCID: PMC9912526 DOI: 10.1186/s12964-023-01047-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/14/2023] [Indexed: 02/11/2023] Open
Abstract
Combined chemotherapy is a treatment method based on the simultaneous use of two or more therapeutic agents; it is frequently necessary to produce a more effective treatment for cancer patients. Such combined treatments often improve the outcomes over that of the monotherapy approach, as the drugs synergistically target critical cell signaling pathways or work independently at different oncostatic sites. A better prognosis has been reported in patients treated with combination therapy than in patients treated with single drug chemotherapy. In recent decades, 5-fluorouracil (5-FU) has become one of the most widely used chemotherapy agents in cancer treatment. This medication, which is soluble in water, is used as the first line of anti-neoplastic agent in the treatment of several cancer types including breast, head and neck, stomach and colon cancer. Within the last three decades, many studies have investigated melatonin as an anti-cancer agent; this molecule exhibits various functions in controlling the behavior of cancer cells, such as inhibiting cell growth, inducing apoptosis, and inhibiting invasion. The aim of this review is to comprehensively evaluate the role of melatonin as a complementary agent with 5-FU-based chemotherapy for cancers. Additionally, we identify the potential common signaling pathways by which melatonin and 5-FU interact to enhance the efficacy of the combined therapy. Video abstract.
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Affiliation(s)
- Alireza Mafi
- grid.411036.10000 0001 1498 685XDepartment of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Malihe Rezaee
- grid.411600.2School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran ,grid.411705.60000 0001 0166 0922Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Islamic Republic of Iran
| | - Neda Hedayati
- grid.411746.10000 0004 4911 7066School of Medicine, Iran University of Medical Science, Tehran, Islamic Republic of Iran
| | - Sara Diana Hogan
- grid.8993.b0000 0004 1936 9457Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Russel J. Reiter
- grid.43582.380000 0000 9852 649XDepartment of Cell Systems and Anatomy, UT Health. Long School of Medicine, San Antonio, TX USA
| | - Mohammad-Hossein Aarabi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran.
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran.
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12
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Tan DS, Cheung SL, Gao Y, Weinbuch M, Hu H, Shi L, Ti SC, Hutchins AP, Cojocaru V, Jauch R. The homeodomain of Oct4 is a dimeric binder of methylated CpG elements. Nucleic Acids Res 2023; 51:1120-1138. [PMID: 36631980 PMCID: PMC9943670 DOI: 10.1093/nar/gkac1262] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023] Open
Abstract
Oct4 is essential to maintain pluripotency and has a pivotal role in establishing the germline. Its DNA-binding POU domain was recently found to bind motifs with methylated CpG elements normally associated with epigenetic silencing. However, the mode of binding and the consequences of this capability has remained unclear. Here, we show that Oct4 binds to a compact palindromic DNA element with a methylated CpG core (CpGpal) in alternative states of pluripotency and during cellular reprogramming towards induced pluripotent stem cells (iPSCs). During cellular reprogramming, typical Oct4 bound enhancers are uniformly demethylated, with the prominent exception of the CpGpal sites where DNA methylation is often maintained. We demonstrate that Oct4 cooperatively binds the CpGpal element as a homodimer, which contrasts with the ectoderm-expressed POU factor Brn2. Indeed, binding to CpGpal is Oct4-specific as other POU factors expressed in somatic cells avoid this element. Binding assays combined with structural analyses and molecular dynamic simulations show that dimeric Oct4-binding to CpGpal is driven by the POU-homeodomain whilst the POU-specific domain is detached from DNA. Collectively, we report that Oct4 exerts parts of its regulatory function in the context of methylated DNA through a DNA recognition mechanism that solely relies on its homeodomain.
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Affiliation(s)
- Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shun Lai Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ya Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Maike Weinbuch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China,Institute for Molecular Medicine, Ulm University, Ulm, Germany
| | - Haoqing Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Liyang Shi
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shih-Chieh Ti
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Andrew P Hutchins
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Vlad Cojocaru
- STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania,Computational Structural Biology Group, Utrecht University, The Netherlands,Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ralf Jauch
- To whom correspondence should be addressed. Tel: +852 3917 9511; Fax: +852 28559730;
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13
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Lo JHH, Edwards M, Langerman J, Sridharan R, Plath K, Smale ST. Oct4:Sox2 binding is essential for establishing but not maintaining active and silent states of dynamically regulated genes in pluripotent cells. Genes Dev 2022; 36:1079-1095. [PMID: 36418052 PMCID: PMC9744233 DOI: 10.1101/gad.350113.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022]
Abstract
Much has been learned about the mechanisms of action of pluripotency factors Oct4 and Sox2. However, as with other regulators of cell identity, little is known about the impact of disrupting their binding motifs in a native environment or the characteristics of genes they regulate. By quantitatively examining dynamic ranges of gene expression instead of focusing on conventional measures of differential expression, we found that Oct4 and Sox2 enhancer binding is strongly enriched near genes subject to large dynamic ranges of expression among cell types, with binding sites near these genes usually within superenhancers. Mutagenesis of representative Oct4:Sox2 motifs near such active, dynamically regulated genes revealed critical roles in transcriptional activation during reprogramming, with more limited roles in transcriptional maintenance in the pluripotent state. Furthermore, representative motifs near silent genes were critical for establishing but not maintaining the fully silent state, while genes whose transcript levels varied by smaller magnitudes among cell types were unaffected by nearby Oct4:Sox2 motifs. These results suggest that Oct4 and Sox2 directly establish both active and silent transcriptional states in pluripotent cells at a large number of genes subject to dynamic regulation during mammalian development, but are less important than expected for maintaining transcriptional states.
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Affiliation(s)
- Jerry Hung-Hao Lo
- Molecular Biology Institute, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Broad Stem Cell Research Center, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Miguel Edwards
- Molecular Biology Institute, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Broad Stem Cell Research Center, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Justin Langerman
- Molecular Biology Institute, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Broad Stem Cell Research Center, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
| | - Kathrin Plath
- Molecular Biology Institute, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Broad Stem Cell Research Center, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Stephen T Smale
- Molecular Biology Institute, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Broad Stem Cell Research Center, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
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14
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MacCarthy CM, Huertas J, Ortmeier C, Vom Bruch H, Tan DS, Reinke D, Sander A, Bergbrede T, Jauch R, Schöler HR, Cojocaru V. OCT4 interprets and enhances nucleosome flexibility. Nucleic Acids Res 2022; 50:10311-10327. [PMID: 36130732 PMCID: PMC9561370 DOI: 10.1093/nar/gkac755] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 01/06/2023] Open
Abstract
Pioneer transcription factors are proteins that induce cellular identity transitions by binding to inaccessible regions of DNA in nuclear chromatin. They contribute to chromatin opening and recruit other factors to regulatory DNA elements. The structural features and dynamics modulating their interaction with nucleosomes are still unresolved. From a combination of experiments and molecular simulations, we reveal here how the pioneer factor and master regulator of pluripotency, Oct4, interprets and enhances nucleosome structural flexibility. The magnitude of Oct4’s impact on nucleosome dynamics depends on the binding site position and the mobility of the unstructured tails of nucleosomal histone proteins. Oct4 uses both its DNA binding domains to propagate and stabilize open nucleosome conformations, one for specific sequence recognition and the other for nonspecific interactions with nearby regions of DNA. Our findings provide a structural basis for the versatility of transcription factors in engaging with nucleosomes and have implications for understanding how pioneer factors induce chromatin dynamics.
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Affiliation(s)
- Caitlin M MacCarthy
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Jan Huertas
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Yusuf Hamied Department of Chemistry, University of Cambridge, UK
| | - Claudia Ortmeier
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Hermann Vom Bruch
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Deike Reinke
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Astrid Sander
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Hans R Schöler
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Medical Faculty, University of Münster, Germany
| | - Vlad Cojocaru
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Computational Structural Biology Group, University of Utrecht, The Netherlands.,STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania
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15
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Sukparangsi W, Morganti E, Lowndes M, Mayeur H, Weisser M, Hammachi F, Peradziryi H, Roske F, Hölzenspies J, Livigni A, Godard BG, Sugahara F, Kuratani S, Montoya G, Frankenberg SR, Mazan S, Brickman JM. Evolutionary origin of vertebrate OCT4/POU5 functions in supporting pluripotency. Nat Commun 2022; 13:5537. [PMID: 36130934 PMCID: PMC9492771 DOI: 10.1038/s41467-022-32481-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 07/30/2022] [Indexed: 12/31/2022] Open
Abstract
The support of pluripotent cells over time is an essential feature of development. In eutherian embryos, pluripotency is maintained from naïve states in peri-implantation to primed pluripotency at gastrulation. To understand how these states emerged, we reconstruct the evolutionary trajectory of the Pou5 gene family, which contains the central pluripotency factor OCT4. By coupling evolutionary sequence analysis with functional studies in mouse embryonic stem cells, we find that the ability of POU5 proteins to support pluripotency originated in the gnathostome lineage, prior to the generation of two paralogues, Pou5f1 and Pou5f3 via gene duplication. In osteichthyans, retaining both genes, the paralogues differ in their support of naïve and primed pluripotency. The specialization of these duplicates enables the diversification of function in self-renewal and differentiation. By integrating sequence evolution, cell phenotypes, developmental contexts and structural modelling, we pinpoint OCT4 regions sufficient for naïve pluripotency and describe their adaptation over evolutionary time.
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Affiliation(s)
- Woranop Sukparangsi
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark.,Department of Biology, Faculty of Science, Burapha University, Chon Buri, Thailand
| | - Elena Morganti
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Molly Lowndes
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Hélène Mayeur
- CNRS, Sorbonne Université, Biologie Intégrative des Organismes Marins, UMR7232, F-66650, Banyuls sur Mer, France
| | - Melanie Weisser
- Structural Molecular Biology Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Fella Hammachi
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, 5 Little France Drive, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Hanna Peradziryi
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Fabian Roske
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Jurriaan Hölzenspies
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Alessandra Livigni
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, 5 Little France Drive, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Benoit Gilbert Godard
- CNRS, Sorbonne Université, UPMC Univ Paris 06, FR2424, Development and Evolution of Vertebrates Group, Station Biologique, F-29688, Roscoff, France.,CNRS, Sorbonne Université, Laboratoire de Biologie du Développement de Villefranche, UMR7009, F-06234, Villefranche sur Mer, France
| | - Fumiaki Sugahara
- Division of Biology, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | | | - Sylvie Mazan
- CNRS, Sorbonne Université, Biologie Intégrative des Organismes Marins, UMR7232, F-66650, Banyuls sur Mer, France.
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark.
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16
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Haldavnekar R, Venkatakrishnan K, Tan B. Cancer Stem Cell Derived Extracellular Vesicles with Self-Functionalized 3D Nanosensor for Real-Time Cancer Diagnosis: Eliminating the Roadblocks in Liquid Biopsy. ACS NANO 2022; 16:12226-12243. [PMID: 35968931 DOI: 10.1021/acsnano.2c02971] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Liquid biopsy for determining the presence of cancer and the underlying tissue of origin is crucial to overcome the limitations of existing tissue biopsy and imaging-based techniques by capturing critical information from the dynamic tumor heterogeneity. A newly emerging liquid biopsy with extracellular vesicles (EVs) is gaining momentum, but its clinical relevance is in question due to the biological and technical challenges posed by existing technologies. The biological barriers of existing technologies include the inability to generate fundamental details of molecular structure, chemical composition as well as functional variations in EVs by gathering simultaneous information on multiple intra-EV molecules, unavailability of holistic qualitative analysis, in addition to the inability to identify tissue of origin. Technological barriers include reliance on EV isolation with a few labeled biomarkers, resulting in the inability to generate comprehensive information on the disease. A more favorable approach would be to generate holistic information on the disease without the use of labels. Such a marker-free diagnosis is impossible with the existing liquid biopsy due to the unavailability clinically validated cancer stem cells (CSC)-specific markers and dependence of existing technologies on EV isolation, undermining the clinical relevance of EV-based liquid biopsy. Here, CSC EVs were employed as an independent liquid biopsy modality. We hypothesize that tracking the signals of CSCs in peripheral blood with CSC EVs will provide a reliable solution for accurate cancer diagnosis, as CSC are the originators of tumor contributing to tumor heterogeneity. We report nanoengineered 3D sensors of extremely small nano-scaled probes self-functionalized for SERS, enabling integrative molecular and functional profiling of otherwise undetectable CSC EVs. A substantially enhanced SERS and ultralow limit of detection (10 EVs per 10 μL) were achieved. This was attributed to the efficient probe-EV interaction due to the 3D networks of nanoprobes, ensuring simultaneous detection of multiple EV signals. We experimentally demonstrate the crucial role of CSC EVs in cancer diagnosis. We then completed a pilot validation of this modality for cancer detection as well as for identification of the tissue of origin. An artificial neural network distinguished cancer from noncancer with 100% sensitivity and 100% specificity for three hard to detect cancers (breast, lung, and colorectal cancer). Binary classification to distinguish one tissue of origin against all other achieved 100% accuracy, while simultaneous identification of all three tissues of origin with multiclass classification achieved up to 79% accuracy. This noninvasive tool may complement existing cancer diagnostics, treatment monitoring as well as longitudinal disease monitoring by validation with a large cohort of clinical samples.
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Affiliation(s)
- Rupa Haldavnekar
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Ryerson University and St. Michael's Hospital, Toronto, Ontario M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nanocharacterization Laboratory, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano-Bio Interface Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Krishnan Venkatakrishnan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nanocharacterization Laboratory, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano-Bio Interface Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Bo Tan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario M5B 1W8, Canada
- Nanocharacterization Laboratory, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
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17
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OCT4-mediated transcription confers oncogenic advantage for a subset of gastric tumors with poor clinical outcome. Funct Integr Genomics 2022; 22:1345-1360. [DOI: 10.1007/s10142-022-00894-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/26/2022]
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18
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Xiong L, Tolen EA, Choi J, Velychko S, Caizzi L, Velychko T, Adachi K, MacCarthy CM, Lidschreiber M, Cramer P, Schöler HR. Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells. eLife 2022; 11:71533. [PMID: 35621159 PMCID: PMC9142147 DOI: 10.7554/elife.71533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 05/17/2022] [Indexed: 12/21/2022] Open
Abstract
The transcription factor Oct4 is essential for the maintenance and induction of stem cell pluripotency, but its functional roles are not fully understood. Here, we investigate the functions of Oct4 by depleting and subsequently recovering it in mouse embryonic stem cells (ESCs) and conducting a time-resolved multiomics analysis. Oct4 depletion leads to an immediate loss of its binding to enhancers, accompanied by a decrease in mRNA synthesis from its target genes that are part of the transcriptional network that maintains pluripotency. Gradual decrease of Oct4 binding to enhancers does not immediately change the chromatin accessibility but reduces transcription of enhancers. Conversely, partial recovery of Oct4 expression results in a rapid increase in chromatin accessibility, whereas enhancer transcription does not fully recover. These results indicate different concentration-dependent activities of Oct4. Whereas normal ESC levels of Oct4 are required for transcription of pluripotency enhancers, low levels of Oct4 are sufficient to retain chromatin accessibility, likely together with other factors such as Sox2.
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Affiliation(s)
- Le Xiong
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Erik A Tolen
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Jinmi Choi
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Sergiy Velychko
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Livia Caizzi
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Taras Velychko
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Kenjiro Adachi
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Caitlin M MacCarthy
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Michael Lidschreiber
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
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19
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Haldavnekar R, Ganesh S, Venkatakrishnan K, Tan B. Cancer Stem Cell DNA Enabled Real-Time Genotyping with Self-Functionalized Quantum Superstructures-Overcoming the Barriers of Noninvasive cfDNA Cancer Diagnostics. SMALL METHODS 2022; 6:e2101467. [PMID: 35247038 DOI: 10.1002/smtd.202101467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Cancer diagnosis and determining its tissue of origin are crucial for clinical implementation of personalized medicine. Conventional diagnostic techniques such as imaging and tissue biopsy are unable to capture the dynamic tumor landscape. Although circulating tumor DNA (ctDNA) shows promise for diagnosis, the clinical relevance of ctDNA remains largely undetermined due to several biological and technical complexities. Here, cancer stem cell-ctDNA is used to overcome the biological complexities like the inability for molecular analysis of ctDNA and dependence on ctDNA concentration rather than the molecular profile. Ultrasensitive quantum superstructures overcome the technical complexities of trace-level detection and rapid diagnosis to detect ctDNA within its short half-life. Activation of multiple surface enhanced Raman scattering mechanisms of the quantum superstructures achieved a very high enhancement factor (1.35 × 1011 ) and detection at ultralow concentration (10-15 M) with very high reliability (RSD: 3-12%). Pilot validation with clinical plasma samples from an independent validation cohort achieved a diagnosis sensitivity of ≈95% and specificity of 83%. Quantum superstructures identified the tissue of origin with ≈75-86% sensitivity and ≈92-96% specificity. With large scale clinical validation, the technology can develop into a clinically useful liquid biopsy tool improving cancer diagnostics.
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Affiliation(s)
- Rupa Haldavnekar
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Ryerson University and St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, Toronto, ON, M5B 2K3, Canada
- Nanocharacterization Laboratory, Faculty of Engineering and Architectural Sciences, Ryerson University, Toronto, ON, M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Ryerson University, Toronto, ON, M5B 2K3, Canada
| | - Swarna Ganesh
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Ryerson University and St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, Toronto, ON, M5B 2K3, Canada
- Nanocharacterization Laboratory, Faculty of Engineering and Architectural Sciences, Ryerson University, Toronto, ON, M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Ryerson University, Toronto, ON, M5B 2K3, Canada
| | - Krishnan Venkatakrishnan
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Ryerson University and St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, Toronto, ON, M5B 2K3, Canada
- Nanocharacterization Laboratory, Faculty of Engineering and Architectural Sciences, Ryerson University, Toronto, ON, M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Ryerson University, Toronto, ON, M5B 2K3, Canada
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON, M5B 1W8, Canada
| | - Bo Tan
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Ryerson University and St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
- Nanocharacterization Laboratory, Faculty of Engineering and Architectural Sciences, Ryerson University, Toronto, ON, M5B 2K3, Canada
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON, M5B 1W8, Canada
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20
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Han D, Wu G, Chen R, Drexler HCA, MacCarthy CM, Kim KP, Adachi K, Gerovska D, Mavrommatis L, Bedzhov I, Araúzo-Bravo MJ, Schöler HR. A balanced Oct4 interactome is crucial for maintaining pluripotency. SCIENCE ADVANCES 2022; 8:eabe4375. [PMID: 35171666 PMCID: PMC8849292 DOI: 10.1126/sciadv.abe4375] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Oct4 collaborates primarily with other transcriptional factors or coregulators to maintain pluripotency. However, how Oct4 exerts its function is still unclear. Here, we show that the Oct4 linker interface mediates competing yet balanced Oct4 protein interactions that are crucial for maintaining pluripotency. Oct4 linker mutant embryonic stem cells (ESCs) show decreased expression of self-renewal genes and increased expression of differentiation genes, resulting in impaired ESC self-renewal and early embryonic development. The linker mutation interrupts the balanced Oct4 interactome. In mutant ESCs, the interaction between Oct4 and Klf5 is decreased. In contrast, interactions between Oct4 and Cbx1, Ctr9, and Cdc73 are increased, disrupting the epigenetic state of ESCs. Control of the expression level of Klf5, Cbx1, or Cdc73 rebalances the Oct4 interactome and rescues the pluripotency of linker mutant ESCs, indicating that such factors interact with Oct4 competitively. Thus, we provide previously unidentified molecular insights into how Oct4 maintains pluripotency.
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Affiliation(s)
- Dong Han
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Guangming Wu
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, 6 Luoxuan Avenue, Haizhu District, 510320 Guangzhou, P. R. China
| | - Rui Chen
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Hannes C. A. Drexler
- Bioanalytical Mass Spectrometry, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Caitlin M. MacCarthy
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Kee-Pyo Kim
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul 06591, Republic of Korea
| | - Kenjiro Adachi
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Daniela Gerovska
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastian 20014, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao 48011, Spain
| | - Lampros Mavrommatis
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Ivan Bedzhov
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Marcos J. Araúzo-Bravo
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastian 20014, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao 48011, Spain
| | - Hans R. Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
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21
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Rafiee MR, Zagalak JA, Sidorov S, Steinhauser S, Davey K, Ule J, Luscombe NM. Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs. Nucleic Acids Res 2021; 49:13092-13107. [PMID: 34871434 PMCID: PMC8682780 DOI: 10.1093/nar/gkab1180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/05/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
RNA-binding proteins (RBPs) play diverse roles in regulating co-transcriptional RNA-processing and chromatin functions, but our knowledge of the repertoire of chromatin-associated RBPs (caRBPs) and their interactions with chromatin remains limited. Here, we developed SPACE (Silica Particle Assisted Chromatin Enrichment) to isolate global and regional chromatin components with high specificity and sensitivity, and SPACEmap to identify the chromatin-contact regions in proteins. Applied to mouse embryonic stem cells, SPACE identified 1459 chromatin-associated proteins, ∼48% of which are annotated as RBPs, indicating their dual roles in chromatin and RNA-binding. Additionally, SPACEmap stringently verified chromatin-binding of 403 RBPs and identified their chromatin-contact regions. Notably, SPACEmap showed that about 40% of the caRBPs bind chromatin by intrinsically disordered regions (IDRs). Studying SPACE and total proteome dynamics from mES cells grown in 2iL and serum medium indicates significant correlation (R = 0.62). One of the most dynamic caRBPs is Dazl, which we find co-localized with PRC2 at transcription start sites of genes that are distinct from Dazl mRNA binding. Dazl and other PRC2-colocalised caRBPs are rich in intrinsically disordered regions (IDRs), which could contribute to the formation and regulation of phase-separated PRC condensates. Together, our approach provides an unprecedented insight into IDR-mediated interactions and caRBPs with moonlighting functions in native chromatin.
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Affiliation(s)
| | - Julian A Zagalak
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | | | | | - Karen Davey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK.,National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK.,UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK.,Okinawa Institute of Science & Technology Graduate University, Okinawa 904-0495, Japan
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22
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Bakhmet EI, Tomilin AN. Key features of the POU transcription factor Oct4 from an evolutionary perspective. Cell Mol Life Sci 2021; 78:7339-7353. [PMID: 34698883 PMCID: PMC11072838 DOI: 10.1007/s00018-021-03975-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/16/2021] [Accepted: 10/12/2021] [Indexed: 01/06/2023]
Abstract
Oct4, a class V POU-domain protein that is encoded by the Pou5f1 gene, is thought to be a key transcription factor in the early development of mammals. This transcription factor plays indispensable roles in pluripotent stem cells as well as in the acquisition of pluripotency during somatic cell reprogramming. Oct4 has also been shown to play a role as a pioneer transcription factor during zygotic genome activation (ZGA) from zebrafish to human. However, during the past decade, several studies have brought these conclusions into question. It was clearly shown that the first steps in mouse development are not affected by the loss of Oct4. Subsequently, the role of Oct4 as a genome activator was brought into doubt. It was also found that the reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) could proceed without Oct4. In this review, we summarize recent findings, reassess the role of Oct4 in reprogramming and ZGA, and point to structural features that may underlie this role. We speculate that pluripotent stem cells resemble neural stem cells more closely than previously thought. Oct4 orthologs within the POUV class hold key roles in genome activation during early development of species with late ZGA. However, in Placentalia, eutherian-specific proteins such as Dux overtake Oct4 in ZGA and endow them with the formation of an evolutionary new tissue-the placenta.
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Affiliation(s)
- Evgeny I Bakhmet
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.
| | - Alexey N Tomilin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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23
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Nayak C, Singh SK. In silico identification of natural product inhibitors against Octamer-binding transcription factor 4 (Oct4) to impede the mechanism of glioma stem cells. PLoS One 2021; 16:e0255803. [PMID: 34613998 PMCID: PMC8494328 DOI: 10.1371/journal.pone.0255803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 07/23/2021] [Indexed: 02/07/2023] Open
Abstract
Octamer-binding transcription factor 4 (Oct4) is a core regulator in the retention of stemness, invasive, and self-renewal properties in glioma initiating cells (GSCs) and its overexpression inhibits the differentiation of glioma cells promoting tumor cell proliferation. The Pit-Oct-Unc (POU) domain comprising POU-specific domain (POUS) and POU-type homeodomain (POUHD) subdomains is the most critical part of the Oct4 for the generation of induced pluripotent stem cells from somatic cells that lead to tumor initiation, invasion, posttreatment relapse, and therapeutic resistance. Therefore, the present investigation hunts for natural product inhibitors (NPIs) against the POUHD domain of Oct4 by employing receptor-based virtual screening (RBVS) followed by binding free energy calculation and molecular dynamics simulation (MDS). RBVS provided 13 compounds with acceptable ranges of pharmacokinetic properties and good docking scores having key interactions with the POUHD domain. More Specifically, conformational and interaction stability analysis of 13 compounds through MDS unveiled two compounds ZINC02145000 and ZINC32124203 which stabilized the backbone of protein even in the presence of linker and POUS domain. Additionally, ZINC02145000 and ZINC32124203 exhibited stable and strong interactions with key residues W277, R242, and R234 of the POUHD domain even in dynamic conditions. Interestingly, ZINC02145000 and ZINC32124203 established communication not only with the POUHD domain but also with the POUS domain indicating their incredible potency toward thwarting the function of Oct4. ZINC02145000 and ZINC32124203 also reduced the flexibility and escalated the correlations between the amino acid residues of Oct4 evidenced by PCA and DCCM analysis. Finally, our examination proposed two NPIs that can impede the Oct4 function and may help to improve overall survival, diminish tumor relapse, and achieve a cure not only in deadly disease GBM but also in other cancers with minimal side effects.
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Affiliation(s)
- Chirasmita Nayak
- Computer-Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer-Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi Tamil Nadu, India
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24
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Roberts GA, Ozkan B, Gachulincová I, O'Dwyer MR, Hall-Ponsele E, Saxena M, Robinson PJ, Soufi A. Dissecting OCT4 defines the role of nucleosome binding in pluripotency. Nat Cell Biol 2021; 23:834-845. [PMID: 34354236 PMCID: PMC7611526 DOI: 10.1038/s41556-021-00727-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 07/01/2021] [Indexed: 12/19/2022]
Abstract
Pioneer transcription factors such as OCT4 can target silent genes embedded in nucleosome-dense regions. How nucleosome interaction enables transcription factors to target chromatin and determine cell identity remains elusive. Here, we systematically dissect OCT4 to show that nucleosome binding is encoded within the DNA-binding domain and yet can be uncoupled from free-DNA binding. Furthermore, accelerating the binding kinetics of OCT4 to DNA enhances nucleosome binding. In cells, uncoupling nucleosome binding diminishes the ability of OCT4 to individually access closed chromatin, while more dynamic nucleosome binding results in expansive genome scanning within closed chromatin. However, both uncoupling and enhancing nucleosome binding are detrimental to inducing pluripotency from differentiated cells. Remarkably, stable interactions between OCT4 and nucleosomes are continuously required for maintaining the accessibility of pluripotency enhancers in stem cells. Our findings reveal how the affinity and residence time of OCT4-nucleosome complexes modulate chromatin accessibility during cell fate changes and maintenance.
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Affiliation(s)
- Gareth A Roberts
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute of Stem Cell Research, University of Edinburgh, Edinburgh, UK
| | - Burak Ozkan
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute of Stem Cell Research, University of Edinburgh, Edinburgh, UK
| | - Ivana Gachulincová
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute of Stem Cell Research, University of Edinburgh, Edinburgh, UK
| | - Michael R O'Dwyer
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute of Stem Cell Research, University of Edinburgh, Edinburgh, UK
| | - Elisa Hall-Ponsele
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute of Stem Cell Research, University of Edinburgh, Edinburgh, UK
| | - Manoj Saxena
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
| | - Philip J Robinson
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
| | - Abdenour Soufi
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute of Stem Cell Research, University of Edinburgh, Edinburgh, UK.
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25
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Biological importance of OCT transcription factors in reprogramming and development. Exp Mol Med 2021; 53:1018-1028. [PMID: 34117345 PMCID: PMC8257633 DOI: 10.1038/s12276-021-00637-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
Ectopic expression of Oct4, Sox2, Klf4 and c-Myc can reprogram somatic cells into induced pluripotent stem cells (iPSCs). Attempts to identify genes or chemicals that can functionally replace each of these four reprogramming factors have revealed that exogenous Oct4 is not necessary for reprogramming under certain conditions or in the presence of alternative factors that can regulate endogenous Oct4 expression. For example, polycistronic expression of Sox2, Klf4 and c-Myc can elicit reprogramming by activating endogenous Oct4 expression indirectly. Experiments in which the reprogramming competence of all other Oct family members tested and also in different species have led to the decisive conclusion that Oct proteins display different reprogramming competences and species-dependent reprogramming activity despite their profound sequence conservation. We discuss the roles of the structural components of Oct proteins in reprogramming and how donor cell epigenomes endow Oct proteins with different reprogramming competences. Cells can be reprogrammed into induced pluripotent stem cells (iPSCs), embryonic-like stem cells that can turn into any cell type and have extensive potential medical uses, without adding the transcription factor OCT4. Although other nearly identical OCT family members had been tried, only OCT4 could induce reprogramming and was previously thought to be indispensable. However, it now appears that the reprogramming can be induced by multiple pathways, as detailed in a review by Hans Schöler, Max Planck Institute for Biomolecular Medicine, Münster, and Johnny Kim, Max Planck Institute for Heart and Lung Research, Bad Nauheim, in Germany. They report that any factors that trigger cells to activate endogeous OCT4 can produce iPSCs without exogeously admistration of OCT4. The mechanisms for producing iPSCs can differ between species. These results illuminate the complex mechanisms of reprogramming.
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26
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Dan S, Song Y, Duan X, Pan X, Chen C, She S, Su T, Li J, Chen X, Zhou Y, Chen W, Zhang X, Pan X, Wang YJ, Kang B. LSD1-mediated demethylation of OCT4 safeguards pluripotent stem cells by maintaining the transcription of PORE-motif-containing genes. Sci Rep 2021; 11:10285. [PMID: 33986438 PMCID: PMC8119428 DOI: 10.1038/s41598-021-89734-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 04/30/2021] [Indexed: 11/09/2022] Open
Abstract
Reversible lysine methylation is essential for regulating histones and emerges to critically regulate non-histone proteins as well. Here we show that the master transcription factor OCT4 in pluripotent stem cells (PSCs) was methylated at multiple lysine residues. LSD1 that is highly expressed in PSCs can directly interact with and demethylate OCT4 at lysine 222 (K222) in the flexible linker region. Reduced LSD1 activity led to the methylation of OCT4-K222 that diminished the differentiation potential of PSCs while facilitating proteasome-independent degradation of OCT4 proteins. Furthermore, site-specifically replacing K222 with phenylalanine to mimic the constitutively methylated lysine promoted the 'locked-in' mode engagement of the OCT4 PORE-homodimers that tightly bind to and block the transcription of multiple PORE-motif-containing target genes regulating cell fate determination and cell junction organization, and thereby reducing the pluripotency of PSCs. Thus, LSD1-mediated demethylation of OCT4 plays a crucial role in restricting the 'locked-in' mode binding of OCT4 PORE-homodimers to the PORE-motif-containing genes and thereby maintaining their transcription to safeguard the pluripotency of PSCs.
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Affiliation(s)
- Songsong Dan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Yuelin Song
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Xiaotao Duan
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xiao Pan
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Cheng Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Shiqi She
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Tong Su
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Jingchao Li
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Xinyu Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Yanwen Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Wenjie Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Xiaobing Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Xiaoyun Pan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Ying-Jie Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China.
| | - Bo Kang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China.
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27
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Generation of biologically active recombinant human OCT4 protein from E. coli. 3 Biotech 2021; 11:207. [PMID: 33927995 DOI: 10.1007/s13205-021-02758-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 03/27/2021] [Indexed: 02/06/2023] Open
Abstract
Octamer-binding transcription factor 4 (OCT4) is vital for early embryonic development and is a master regulator of pluripotency in embryonic stem cells. Notably, OCT4 is a key reprogramming factor to derive induced pluripotent stem cells, which have tremendous prospects in regenerative medicine. In the current study, we report heterologous expression and purification of human OCT4 in E. coli to produce pure recombinant protein under native conditions. To achieve this, the 1083 bp coding sequence of the human OCT4 gene was codon-optimized for heterologous expression in E. coli. The codon-optimized sequence was fused with fusion tags, namely a cell-penetrating peptide sequence for intracellular delivery, a nuclear localization sequence for intranuclear delivery, and a His-tag for affinity purification. Subsequently, the codon-optimized sequence and the fusion tags were cloned in the protein expression vector, pET28a(+), and transformed into E. coli strain BL21(DE3) for expression. The recombinant OCT4 protein was purified from the soluble fraction under native conditions using immobilized metal ion affinity chromatography in a facile manner, and its identity was confirmed by Western blotting and mass spectrometry. Furthermore, the secondary structure of the recombinant protein was analyzed using far ultraviolet circular dichroism spectroscopy, which confirmed that the purified fusion protein maintained a secondary structure conformation, and it predominantly composed of α-helices. Next, the recombinant OCT4 protein was applied to human cells, and was found that it was able to enter the cells and translocate to the nucleus. Furthermore, the biological activity of the transduced OCT4 protein was also demonstrated on human cells. This recombinant tool can substitute for genetic and viral forms of OCT4 to enable the derivation of integration-free pluripotent cells. It can also be used to elucidate its biological role in various cellular processes and diseases and for structural and biochemical studies. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02758-z.
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28
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Pourbagher R, Ghorbani H, Akhavan-Niaki H, Jorsaraei SGA, Fattahi S, Ghooran S, Abedian Z, Ghasemi M, Saeedi F, Jafari N, Kalali B, Mostafazadeh A. Downregulation of Stemness Genes and Induction of Necrosis in Rat LA7 Cancer Stem Cells Induced Tumors Treated with Starved Fibroblasts Culture Supernatant. Rep Biochem Mol Biol 2021; 10:105-118. [PMID: 34277874 PMCID: PMC8279721 DOI: 10.52547/rbmb.10.1.105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/11/2020] [Indexed: 04/11/2023]
Abstract
BACKGROUND Stem cell differentiation therapy is a promising strategy in cancer treatment. we show that protein cocktail prepared from serum starved fibroblasts has therapeutic potential based on this strategy. METHODS The condition medium was prepared from foreskin isolated fibroblasts and analyzed by Liquid chromatography electrospray ionization mass spectrometry-mass spectrometry (LC-ESI-MS/MS). LA7 mammary gland cancer stem cells originated tumors were induced in Sprague Dawley rats. The rats treated subcutaneously with DMEM (group A), condition medium (group B), or normal saline (group C) once daily for 7 days. Then the tumors were removed and divided into the two parts, one part was used to quantify gene expression by stem-loop RT-qPCR assay and the other part was used for Hematoxylin & Eosin (H & E), Giemsa, and immunohistochemistry (IHC) staining. RESULTS All induced tumors appeared as sarcomatoid carcinoma (SC). Immunohistochemistry staining confirmed this conclusion by recognizing the tumor as Ki67+, cytokeratin+, vimentine+, and estrogen receptor negative SC. RT-qPCR analysis revealed that Oct4-, Sox-2, Nanog- gene expression was much reduced in the condition medium treated tumors versus proper controls (p< 0.05). Tissue necrosis was more prevalent in this group while tumors volume was diminished almost by 40%. The LC-ESI-MS/MS analysis unrevealed the stemness reducing and the cell death inducing proteins such as, pigment epithelium-derived factor (PEDF), insulin like growth factor binding protein-5 (IGFBP-5) and -7 (IGFBP-7) in the condition medium. CONCLUSION This study showed that the substances released from starved human fibroblasts were able to down-regulate the stemness-related genes and induce necrosis in LA7 derived tumors.
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Affiliation(s)
- Roghayeh Pourbagher
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
| | - Hossein Ghorbani
- Department of Pathology, Rohani Hospital, Babol University of Medical Sciences, Babol, Iran.
| | - Haleh Akhavan-Niaki
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
| | - Seyed Gholam Ali Jorsaraei
- Fatemeh Zahra Infertility and Reproductive Health Research Centre, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
| | - Sadegh Fattahi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
| | - Sahar Ghooran
- Department of Pathology, Rohani Hospital, Babol University of Medical Sciences, Babol, Iran.
| | - Zeinab Abedian
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.
- Dental Materials Research Center, Dental Faculty, Babol University of Medical Sciences, Babol, Iran.
| | - Masoumeh Ghasemi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
| | - Fatemeh Saeedi
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
| | - Negar Jafari
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
| | - Behnam Kalali
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany.
| | - Amrollah Mostafazadeh
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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29
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Understanding transcription across scales: From base pairs to chromosomes. Mol Cell 2021; 81:1601-1616. [PMID: 33770487 DOI: 10.1016/j.molcel.2021.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
The influence of genome organization on transcription is central to our understanding of cell type specification. Higher-order genome organization is established through short- and long-range DNA interactions. Coordination of these interactions, from single atoms to entire chromosomes, plays a fundamental role in transcriptional control of gene expression. Loss of this coupling can result in disease. Analysis of transcriptional regulation typically involves disparate experimental approaches, from structural studies that define angstrom-level interactions to cell-biological and genomic approaches that assess mesoscale relationships. Thus, to fully understand the mechanisms that regulate gene expression, it is critical to integrate the findings gained across these distinct size scales. In this review, I illustrate fundamental ways in which cells regulate transcription in the context of genome organization.
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30
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Tan DS, Chen Y, Gao Y, Bednarz A, Wei Y, Malik V, Ho DHH, Weng M, Ho SY, Srivastava Y, Velychko S, Yang X, Fan L, Kim J, Graumann J, Stormo GD, Braun T, Yan J, Schöler HR, Jauch R. Directed Evolution of an Enhanced POU Reprogramming Factor for Cell Fate Engineering. Mol Biol Evol 2021; 38:2854-2868. [PMID: 33720298 PMCID: PMC8233511 DOI: 10.1093/molbev/msab075] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcription factor-driven cell fate engineering in pluripotency induction, transdifferentiation, and forward reprogramming requires efficiency, speed, and maturity for widespread adoption and clinical translation. Here, we used Oct4, Sox2, Klf4, and c-Myc driven pluripotency reprogramming to evaluate methods for enhancing and tailoring cell fate transitions, through directed evolution with iterative screening of pooled mutant libraries and phenotypic selection. We identified an artificially evolved and enhanced POU factor (ePOU) that substantially outperforms wild-type Oct4 in terms of reprogramming speed and efficiency. In contrast to Oct4, not only can ePOU induce pluripotency with Sox2 alone, but it can also do so in the absence of Sox2 in a three-factor ePOU/Klf4/c-Myc cocktail. Biochemical assays combined with genome-wide analyses showed that ePOU possesses a new preference to dimerize on palindromic DNA elements. Yet, the moderate capacity of Oct4 to function as a pioneer factor, its preference to bind octamer DNA and its capability to dimerize with Sox2 and Sox17 proteins remain unchanged in ePOU. Compared with Oct4, ePOU is thermodynamically stabilized and persists longer in reprogramming cells. In consequence, ePOU: 1) differentially activates several genes hitherto not implicated in reprogramming, 2) reveals an unappreciated role of thyrotropin-releasing hormone signaling, and 3) binds a distinct class of retrotransposons. Collectively, these features enable ePOU to accelerate the establishment of the pluripotency network. This demonstrates that the phenotypic selection of novel factor variants from mammalian cells with desired properties is key to advancing cell fate conversions with artificially evolved biomolecules.
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Affiliation(s)
- Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yanpu Chen
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ya Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Anastasia Bednarz
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.,Department of Biology, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Yuanjie Wei
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Vikas Malik
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Derek Hoi-Hang Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mingxi Weng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sik Yin Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yogesh Srivastava
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sergiy Velychko
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Xiaoxiao Yang
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ligang Fan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China.,School of Medicine, Northwest University, Xi'an, China
| | - Johnny Kim
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Johannes Graumann
- Max Planck Institute for Heart and Lung Research, Mass Spectrometry Service Group, Bad Nauheim, Germany
| | - Gary D Stormo
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Thomas Braun
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jian Yan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China.,School of Medicine, Northwest University, Xi'an, China
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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31
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Nasimi M, Jorsaraei SGA, Fattahi E, Tabari MG, Neyshaburi EZ. SCF Improves In Vitro Differentiation of SSCs Through Transcriptionally Up-regulating PRTM1, STRA8, c-KIT, PIWIL2, and OCT4 Genes. Reprod Sci 2021; 28:963-972. [PMID: 33492648 DOI: 10.1007/s43032-020-00326-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022]
Abstract
Several lines of evidence strongly suggest that retinoic acid (RA) and stem cell factor (SCF)/c-Kit signal transduction pathways are involved in the differentiation of spermatogonial stem cells (SSCs). This study was aimed to investigate the effect of RA and SCF on in vitro differentiation of SSCs via evaluation of the mRNA expression of meiosis-specific genes in cultured testicular tissues. Testicular tissue samples were obtained from bilaterally vasectomized rats and also healthy adult rats and then were cultured for 25, 30, and 35 days on different conditions. The cultured testicular pieces were sectioned and stained with PAS to histological analysis. The total RNA was extracted from cultured testicular samples, and the expression of ACR, PRTM1, SYCP3, STRA8, c-KIT, PIWIL2, and OCT4 genes at mRNA level was quantified using real-time polymerase chain reaction (qPCR) procedure. After 1-month surgery, bilateral testicular weight showed a significant decrease in vasectomized adult rats compared with healthy adult rats (P < 0.05). Reduction in the diameter of the seminiferous tubules and depletion of advanced germinal elements in vasectomized rats compared with healthy adult rats were also observed. Our findings also demonstrated that the mRNA expression level of PRTM1, STRA8, c-KIT, PIWIL2, and OCT4 genes in cultured testicular tissues significantly up-regulated in experimental group II compared with the control group (P < 0.001). Our findings lead us to conclude that SCF improves in vitro differentiation of SSCs in the OA rats, at least partially, by transcriptionally upregulating PRTM1, STRA8, c-KIT, PIWIL2, and OCT4 genes.
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Affiliation(s)
- Mahnaz Nasimi
- Department of Biology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Seyed Gholam Ali Jorsaraei
- Department of Anatomy and Embryology, Infertility and Health Reproductive Research Center, Babol University of Medical Sciences, P.O. Box: 4136747176, Babol, Iran.
| | - Esmail Fattahi
- Department of Biology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | | | - Ebrahim Zabihi Neyshaburi
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran.,Department of Pharmacology and Toxicology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
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32
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Wu Y, Zhang W. The Role of E3s in Regulating Pluripotency of Embryonic Stem Cells and Induced Pluripotent Stem Cells. Int J Mol Sci 2021; 22:1168. [PMID: 33503896 PMCID: PMC7865285 DOI: 10.3390/ijms22031168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/14/2022] Open
Abstract
Pluripotent embryonic stem cells (ESCs) are derived from early embryos and can differentiate into any type of cells in living organisms. Induced pluripotent stem cells (iPSCs) resemble ESCs, both of which serve as excellent sources to study early embryonic development and realize cell replacement therapies for age-related degenerative diseases and other cell dysfunction-related illnesses. To achieve these valuable applications, comprehensively understanding of the mechanisms underlying pluripotency maintenance and acquisition is critical. Ubiquitination modifies proteins with Ubiquitin (Ub) at the post-translational level to monitor protein stability and activity. It is extensively involved in pluripotency-specific regulatory networks in ESCs and iPSCs. Ubiquitination is achieved by sequential actions of the Ub-activating enzyme E1, Ub-conjugating enzyme E2, and Ub ligase E3. Compared with E1s and E2s, E3s are most abundant, responsible for substrate selectivity and functional diversity. In this review, we focus on E3 ligases to discuss recent progresses in understanding how they regulate pluripotency and somatic cell reprogramming through ubiquitinating core ESC regulators.
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Affiliation(s)
| | - Weiwei Zhang
- College of Life Sciences, Capital Normal University, Beijing 100048, China;
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33
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The Role of Cellular Prion Protein in Promoting Stemness and Differentiation in Cancer. Cancers (Basel) 2021; 13:cancers13020170. [PMID: 33418999 PMCID: PMC7825291 DOI: 10.3390/cancers13020170] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Aside from its well-established role in prion disorders, in the last decades the significance of cellular prion protein (PrPC) expression in human cancers has attracted great attention. An extensive body of work provided evidence that PrPC contributes to tumorigenesis by regulating tumor growth, differentiation, and resistance to conventional therapies. In particular, PrPC over-expression has been related to the acquisition of a malignant phenotype of cancer stem cells (CSCs) in a variety of solid tumors, encompassing pancreatic ductal adenocarcinoma, osteosarcoma, breast, gastric, and colorectal cancers, and primary brain tumors as well. According to consensus, increased levels of PrPC endow CSCs with self-renewal, proliferative, migratory, and invasive capacities, along with increased resistance to anti-cancer agents. In addition, increasing evidence demonstrates that PrPc also participates in multi-protein complexes to modulate the oncogenic properties of CSCs, thus sustaining tumorigenesis. Therefore, strategies aimed at targeting PrPC and/or PrPC-organized complexes could be a promising approach for anti-cancer therapy. Abstract Cellular prion protein (PrPC) is seminal to modulate a variety of baseline cell functions to grant homeostasis. The classic role of such a protein was defined as a chaperone-like molecule being able to rescue cell survival. Nonetheless, PrPC also represents the precursor of the deleterious misfolded variant known as scrapie prion protein (PrPSc). This variant is detrimental in a variety of prion disorders. This multi-faceted role of PrP is greatly increased by recent findings showing how PrPC in its folded conformation may foster tumor progression by acting at multiple levels. The present review focuses on such a cancer-promoting effect. The manuscript analyzes recent findings on the occurrence of PrPC in various cancers and discusses the multiple effects, which sustain cancer progression. Within this frame, the effects of PrPC on stemness and differentiation are discussed. A special emphasis is provided on the spreading of PrPC and the epigenetic effects, which are induced in neighboring cells to activate cancer-related genes. These detrimental effects are further discussed in relation to the aberrancy of its physiological and beneficial role on cell homeostasis. A specific paragraph is dedicated to the role of PrPC beyond its effects in the biology of cancer to represent a potential biomarker in the follow up of patients following surgical resection.
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34
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Su YH, Tang LP, Zhao XY, Zhang XS. Plant cell totipotency: Insights into cellular reprogramming. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:228-243. [PMID: 32437079 DOI: 10.1111/jipb.12972] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Plant cells have a powerful capacity in their propagation to adapt to environmental change, given that a single plant cell can give rise to a whole plant via somatic embryogenesis without the need for fertilization. The reprogramming of somatic cells into totipotent cells is a critical step in somatic embryogenesis. This process can be induced by stimuli such as plant hormones, transcriptional regulators and stress. Here, we review current knowledge on how the identity of totipotent cells is determined and the stimuli required for reprogramming of somatic cells into totipotent cells. We highlight key molecular regulators and associated networks that control cell fate transition from somatic to totipotent cells. Finally, we pose several outstanding questions that should be addressed to enhance our understanding of the mechanisms underlying plant cell totipotency.
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Affiliation(s)
- Ying Hua Su
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Li Ping Tang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
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35
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Kim KP, Choi J, Yoon J, Bruder JM, Shin B, Kim J, Arauzo-Bravo MJ, Han D, Wu G, Han DW, Kim J, Cramer P, Schöler HR. Permissive epigenomes endow reprogramming competence to transcriptional regulators. Nat Chem Biol 2021; 17:47-56. [PMID: 32807969 DOI: 10.1038/s41589-020-0618-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 07/08/2020] [Indexed: 01/09/2023]
Abstract
Identifying molecular and cellular processes that regulate reprogramming competence of transcription factors broadens our understanding of reprogramming mechanisms. In the present study, by a chemical screen targeting major epigenetic pathways in human reprogramming, we discovered that inhibiting specific epigenetic roadblocks including disruptor of telomeric silencing 1-like (DOT1L)-mediated H3K79/K27 methylation, but also other epigenetic pathways, catalyzed by lysine-specific histone demethylase 1A, DNA methyltransferases and histone deacetylases, allows induced pluripotent stem cell generation with almost all OCT factors. We found that simultaneous inhibition of these pathways not only dramatically enhances reprogramming competence of most OCT factors, but in fact enables dismantling of species-dependent reprogramming competence of OCT6, NR5A1, NR5A2, TET1 and GATA3. Harnessing these induced permissive epigenetic states, we performed an additional screen with 98 candidate genes. Thereby, we identified 25 transcriptional regulators (OTX2, SIX3, and so on) that can functionally replace OCT4 in inducing pluripotency. Our findings provide a conceptual framework for understanding how transcription factors elicit reprogramming in dependency of the donor cell epigenome that differs across species.
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Affiliation(s)
- Kee-Pyo Kim
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Jinmi Choi
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Juyong Yoon
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Department of Early Discovery, Ksilink, Strasbourg, France
| | - Jan M Bruder
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Borami Shin
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Jonghun Kim
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, Republic of Korea
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Marcos J Arauzo-Bravo
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Dong Han
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Guangming Wu
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Dong Wook Han
- School of Biotechnology and Healthcare, Wuyi University, Jiangmen, China
| | - Johnny Kim
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.
- Medical Faculty, University of Münster, Münster, Germany.
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36
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In Silico Estimation of the Abundance and Phylogenetic Significance of the Composite Oct4-Sox2 Binding Motifs within a Wide Range of Species. DATA 2020. [DOI: 10.3390/data5040111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
High-throughput sequencing technologies have greatly accelerated the progress of genomics, transcriptomics, and metagenomics. Currently, a large amount of genomic data from various organisms is being generated, the volume of which is increasing every year. Therefore, the development of methods that allow the rapid search and analysis of DNA sequences is urgent. Here, we present a novel motif-based high-throughput sequence scoring method that generates genome information. We found and identified Utf1-like, Fgf4-like, and Hoxb1-like motifs, which are cis-regulatory elements for the pluripotency transcription factors Sox2 and Oct4 within the genomes of different eukaryotic organisms. The genome-wide analysis of these motifs was performed to understand the impact of their diversification on mammalian genome evolution. Utf1-like, Fgf4-like, and Hoxb1-like motif diversity was evaluated across genomes from multiple species.
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37
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Kap1 regulates the self-renewal of embryonic stem cells and cellular reprogramming by modulating Oct4 protein stability. Cell Death Differ 2020; 28:685-699. [PMID: 32895487 DOI: 10.1038/s41418-020-00613-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 08/15/2020] [Accepted: 08/25/2020] [Indexed: 12/27/2022] Open
Abstract
Oct4 plays a crucial role in the regulation of self-renewal of embryonic stem cells (ESCs) and reprogramming of somatic cells to induced pluripotent stem cells. However, the molecular mechanisms underlying posttranslational regulation and protein stability of Oct4 remain unclear. Using affinity purification and mass spectrometry analysis, we identified Kap1 as an Oct4-binding protein. Silencing of Kap1 reduced the protein levels of Oct4 in ESCs, whereas the overexpression of Kap1 stimulated the levels of Oct4. In addition, Kap1 overexpression stimulated the self-renewal of ESCs and attenuated the spontaneous differentiation of ESCs in response to LIF withdrawal. Kap1 overexpression increased the stability of Oct4 by inhibiting the Itch-mediated ubiquitination of Oct4. Silencing of Kap1 augmented Itch-mediated ubiquitination and inhibited the stability of Oct4. We identified the lysine 133 (K133) residue in Oct4 as a ubiquitination site responsible for the Kap1-Itch-dependent regulation of Oct4 stability. Preventing ubiquitination at the lysine residue by mutation to arginine augmented the reprogramming of mouse embryonic fibroblasts to induced pluripotent stem cells. These results suggest that Kap1 plays a crucial role in the regulation of the pluripotency of ESCs and somatic cell reprogramming by preventing Itch-mediated ubiquitination and the subsequent degradation of Oct4.
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38
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Kim KP, Wu Y, Yoon J, Adachi K, Wu G, Velychko S, MacCarthy CM, Shin B, Röpke A, Arauzo-Bravo MJ, Stehling M, Han DW, Gao Y, Kim J, Gao S, Schöler HR. Reprogramming competence of OCT factors is determined by transactivation domains. SCIENCE ADVANCES 2020; 6:6/36/eaaz7364. [PMID: 32917606 PMCID: PMC7467702 DOI: 10.1126/sciadv.aaz7364] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
OCT4 (also known as POU5F1) plays an essential role in reprogramming. It is the only member of the POU (Pit-Oct-Unc) family of transcription factors that can induce pluripotency despite sharing high structural similarities to all other members. Here, we discover that OCT6 (also known as POU3F1) can elicit reprogramming specifically in human cells. OCT6-based reprogramming does not alter the mesenchymal-epithelial transition but is attenuated through the delayed activation of the pluripotency network in comparison with OCT4-based reprogramming. Creating a series of reciprocal domain-swapped chimeras and mutants across all OCT factors, we clearly delineate essential elements of OCT4/OCT6-dependent reprogramming and, conversely, identify the features that prevent induction of pluripotency by other OCT factors. With this strategy, we further discover various chimeric proteins that are superior to OCT4 in reprogramming. Our findings clarify how reprogramming competences of OCT factors are conferred through their structural components.
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Affiliation(s)
- Kee-Pyo Kim
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - You Wu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Juyong Yoon
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Kenjiro Adachi
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Guangming Wu
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Sergiy Velychko
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Caitlin M MacCarthy
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Borami Shin
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Albrecht Röpke
- Institute of Human Genetics, University of Münster, Vesaliusweg 12-14, Münster 48149, Germany
| | - Marcos J Arauzo-Bravo
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastian 20014, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao 48011, Spain
| | - Martin Stehling
- Flow Cytometry Unit, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Dong Wook Han
- School of Biotechnology and Healthcare, Wuyi University, Jiangmen 529020, China
| | - Yawei Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Johnny Kim
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany.
- University of Münster, Medical Faculty, Domagkstrasse 3, Münster 48149, Germany
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39
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Nucleosome binding by the pioneer transcription factor OCT4. Sci Rep 2020; 10:11832. [PMID: 32678275 PMCID: PMC7367260 DOI: 10.1038/s41598-020-68850-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/24/2020] [Indexed: 11/22/2022] Open
Abstract
Transcription factor binding to genomic DNA is generally prevented by nucleosome formation, in which the DNA is tightly wrapped around the histone octamer. In contrast, pioneer transcription factors efficiently bind their target DNA sequences within the nucleosome. OCT4 has been identified as a pioneer transcription factor required for stem cell pluripotency. To study the nucleosome binding by OCT4, we prepared human OCT4 as a recombinant protein, and biochemically analyzed its interactions with the nucleosome containing a natural OCT4 target, the LIN28B distal enhancer DNA sequence, which contains three potential OCT4 target sequences. By a combination of chemical mapping and cryo-electron microscopy single-particle analysis, we mapped the positions of the three target sequences within the nucleosome. A mutational analysis revealed that OCT4 preferentially binds its target DNA sequence located near the entry/exit site of the nucleosome. Crosslinking mass spectrometry consistently showed that OCT4 binds the nucleosome in the proximity of the histone H3 N-terminal region, which is close to the entry/exit site of the nucleosome. We also found that the linker histone H1 competes with OCT4 for the nucleosome binding. These findings provide important information for understanding the molecular mechanism by which OCT4 binds its target DNA in chromatin.
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40
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Shanak S, Helms V. DNA methylation and the core pluripotency network. Dev Biol 2020; 464:145-160. [PMID: 32562758 DOI: 10.1016/j.ydbio.2020.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/01/2020] [Accepted: 06/04/2020] [Indexed: 01/06/2023]
Abstract
From the onset of fertilization, the genome undergoes cell division and differentiation. All of these developmental transitions and differentiation processes include cell-specific signatures and gradual changes of the epigenome. Understanding what keeps stem cells in the pluripotent state and what leads to differentiation are fascinating and biomedically highly important issues. Numerous studies have identified genes, proteins, microRNAs and small molecules that exert essential effects. Notably, there exists a core pluripotency network that consists of several transcription factors and accessory proteins. Three eminent transcription factors, OCT4, SOX2 and NANOG, serve as hubs in this core pluripotency network. They bind to the enhancer regions of their target genes and modulate, among others, the expression levels of genes that are associated with Gene Ontology terms related to differentiation and self-renewal. Also, much has been learned about the epigenetic rewiring processes during these changes of cell fate. For example, DNA methylation dynamics is pivotal during embryonic development. The main goal of this review is to highlight an intricate interplay of (a) DNA methyltransferases controlling the expression levels of core pluripotency factors by modulation of the DNA methylation levels in their enhancer regions, and of (b) the core pluripotency factors controlling the transcriptional regulation of DNA methyltransferases. We discuss these processes both at the global level and in atomistic detail based on information from structural studies and from computer simulations.
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Affiliation(s)
- Siba Shanak
- Faculty of Science, Arab-American University, Jenin, Palestine; Center for Bioinformatics, Saarland University, Saarbruecken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany.
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41
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Patra SK. Roles of OCT4 in pathways of embryonic development and cancer progression. Mech Ageing Dev 2020; 189:111286. [PMID: 32531293 DOI: 10.1016/j.mad.2020.111286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/08/2020] [Accepted: 06/06/2020] [Indexed: 12/11/2022]
Abstract
Somatic cells may be reprogrammed to pluripotent state by ectopic expression of certain transcription factors; namely, OCT4, SOX2, KLF4 and c-MYC. However, the molecular and cellular mechanisms are not adequately understood, especially for human embryonic development. Studies during the last five years implicated importance of OCT4 in human zygotic genome activation (ZGA), patterns of OCT4 protein folding and role of specialized sequences in binding to DNA for modulation of gene expression during development. Epigenetic modulation of OCT4 gene and post translational modifications of OCT4 protein activity in the context of multiple cancers are important issues. A consensus is emerging that chromatin organization and epigenetic landscape play crucial roles for the interactions of transcription factors, including OCT4 with the promoters and/or regulatory sequences of genes associated with human embryonic development (ZGA through lineage specification) and that when the epigenome niche is deregulated OCT4 helps in cancer progression, and how OCT4 silencing in somatic cells of adult organisms may impact ageing.
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Affiliation(s)
- Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
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42
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Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schübeler D, Thomä NH. Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science 2020; 368:1460-1465. [PMID: 32327602 DOI: 10.1126/science.abb0074] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022]
Abstract
Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors OCT4 and SOX2 in mouse embryonic stem cells. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling structure determination by cryo-electron microscopy at two preferred positions. Depending on motif location, OCT4 and SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from histone H2A and histone H3; however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA-binding domains to engage DNA in both structures, reading out a partial motif. These findings explain site-specific nucleosome engagement by the pluripotency factors OCT4 and SOX2, and they reveal how TFs distort nucleosomes to access chromatinized motifs.
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Affiliation(s)
- Alicia K Michael
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Zuzanna Kozicka
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,Faculty of Science, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Richard D Bunker
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Andreas D Schenk
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Alexandra Graff-Meyer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Ganesh R Pathare
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Joscha Weiss
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Syota Matsumoto
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland. .,Faculty of Science, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
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43
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Targeting cancer stem cells by melatonin: Effective therapy for cancer treatment. Pathol Res Pract 2020; 216:152919. [PMID: 32171553 DOI: 10.1016/j.prp.2020.152919] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/21/2020] [Accepted: 03/07/2020] [Indexed: 12/15/2022]
Abstract
Melatonin is a physiological hormone produced by the pineal gland. In recent decades, enormous investigations showed that melatonin can prompt apoptosis in cancer cells and inhibit tumor metastasis and angiogenesis in variety of malignancies such as ovarian, melanoma, colon, and breast cancer; therefore, its possible therapeutic usage in cancer treatment was confirmed. CSCs, which has received much attention from researchers in past decades, are major challenges in the treatment of cancer. Because CSCs are resistant to chemotherapeutic drugs and cause recurrence of cancer and also have the ability to be regenerated; they can cause serious problems in the treatment of various cancers. For these reasons, the researchers are trying to find a solution to destroy these cells within the tumor mass. In recent years, the effect of melatonin on CSCs has been investigated in some cancers. Given the importance of CSCs in the process of cancer treatment, this article reviewed the studies conducted on the effect of melatonin on CSCs as a solution to the problems caused by CSCs in the treatment of various cancers.
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Wu E, Vastenhouw NL. From mother to embryo: A molecular perspective on zygotic genome activation. Curr Top Dev Biol 2020; 140:209-254. [PMID: 32591075 DOI: 10.1016/bs.ctdb.2020.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In animals, the early embryo is mostly transcriptionally silent and development is fueled by maternally supplied mRNAs and proteins. These maternal products are important not only for survival, but also to gear up the zygote's genome for activation. Over the last three decades, research with different model organisms and experimental approaches has identified molecular factors and proposed mechanisms for how the embryo transitions from being transcriptionally silent to transcriptionally competent. In this chapter, we discuss the molecular players that shape the molecular landscape of ZGA and provide insights into their mode of action in activating the transcription program in the developing embryo.
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Affiliation(s)
- Edlyn Wu
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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45
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Pádua D, Barros R, Luísa Amaral A, Mesquita P, Filipa Freire A, Sousa M, Filipe Maia A, Caiado I, Fernandes H, Pombinho A, Filipe Pereira C, Almeida R. A SOX2 Reporter System Identifies Gastric Cancer Stem-Like Cells Sensitive to Monensin. Cancers (Basel) 2020; 12:E495. [PMID: 32093282 PMCID: PMC7072720 DOI: 10.3390/cancers12020495] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/12/2020] [Accepted: 02/15/2020] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer remains a serious health burden with few therapeutic options. Therefore, the recognition of cancer stem cells (CSCs) as seeds of the tumorigenic process makes them a prime therapeutic target. Knowing that the transcription factors SOX2 and OCT4 promote stemness, our approach was to isolate stem-like cells in human gastric cancer cell lines using a traceable reporter system based on SOX2/OCT4 activity (SORE6-GFP). Cells transduced with the SORE6-GFP reporter system were sorted into SORE6+ and SORE6- cell populations, and their biological behavior characterized. SORE6+ cells were enriched for SOX2 and exhibited CSC features, including a greater ability to proliferate and form gastrospheres in non-adherent conditions, a larger in vivo tumor initiating capability, and increased resistance to 5-fluorouracil (5-FU) treatment. The overexpression and knockdown of SOX2 revealed a crucial role of SOX2 in cell proliferation and drug resistance. By combining the reporter system with a high-throughput screening of pharmacologically active small molecules we identified monensin, an ionophore antibiotic, displaying selective toxicity to SORE6+ cells. The ability of SORE6-GFP reporter system to recognize cancer stem-like cells facilitates our understanding of gastric CSC biology and serves as a platform for the identification of powerful therapeutics for targeting gastric CSCs.
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Affiliation(s)
- Diana Pádua
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (D.P.); (R.B.); (A.L.A.); (P.M.); (A.F.F.); (M.S.); (A.F.M.); (A.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-465 Porto, Portugal
| | - Rita Barros
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (D.P.); (R.B.); (A.L.A.); (P.M.); (A.F.F.); (M.S.); (A.F.M.); (A.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-465 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Ana Luísa Amaral
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (D.P.); (R.B.); (A.L.A.); (P.M.); (A.F.F.); (M.S.); (A.F.M.); (A.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-465 Porto, Portugal
| | - Patrícia Mesquita
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (D.P.); (R.B.); (A.L.A.); (P.M.); (A.F.F.); (M.S.); (A.F.M.); (A.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-465 Porto, Portugal
| | - Ana Filipa Freire
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (D.P.); (R.B.); (A.L.A.); (P.M.); (A.F.F.); (M.S.); (A.F.M.); (A.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-465 Porto, Portugal
| | - Mafalda Sousa
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (D.P.); (R.B.); (A.L.A.); (P.M.); (A.F.F.); (M.S.); (A.F.M.); (A.P.)
- IBMC—Institute of Molecular and Cell Biology, University of Porto, 4200-135 Porto, Portugal
| | - André Filipe Maia
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (D.P.); (R.B.); (A.L.A.); (P.M.); (A.F.F.); (M.S.); (A.F.M.); (A.P.)
- IBMC—Institute of Molecular and Cell Biology, University of Porto, 4200-135 Porto, Portugal
| | - Inês Caiado
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; (I.C.); (H.F.); (C.F.P.)
- Cell Reprogramming in Hematopoiesis and Immunity laboratory, Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, 221 84 Lund, Sweden
| | - Hugo Fernandes
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; (I.C.); (H.F.); (C.F.P.)
- Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - António Pombinho
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (D.P.); (R.B.); (A.L.A.); (P.M.); (A.F.F.); (M.S.); (A.F.M.); (A.P.)
- IBMC—Institute of Molecular and Cell Biology, University of Porto, 4200-135 Porto, Portugal
| | - Carlos Filipe Pereira
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; (I.C.); (H.F.); (C.F.P.)
- Cell Reprogramming in Hematopoiesis and Immunity laboratory, Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, 221 84 Lund, Sweden
| | - Raquel Almeida
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (D.P.); (R.B.); (A.L.A.); (P.M.); (A.F.F.); (M.S.); (A.F.M.); (A.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-465 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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46
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Pourbagher R, Akhavan-Niaki H, Jorsaraei SGA, Fattahi S, Sabour D, Zabihi E, Abedian Z, Ghasemi M, Golpour M, Mostafazadeh A. Targeting LA7 breast cancer stem cells of rat through repressing the genes of stemness-related transcription factors using three different biological fluids. Gene 2020; 734:144381. [PMID: 31978510 DOI: 10.1016/j.gene.2020.144381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
Abstract
Down-regulation of stemness genes expression is important in differentiation therapy against cancer stem cells (CSCs). The aim of this study was to evaluate the Oct4 , Sox2, Nanog, and C-myc expression in rat breast cancer stem cells (LA7) which treated with human ovarian follicular fluid (FF), replicative senescent fibroblast culture supernatant (P14), and 16 h serum starved fibroblast supernatant (16 h-SFS). The cells were exposed to these biological fluids for 24 h, 72 h, and 7 days. Stem-loop RT-qPCR assay was used to quantify the expression of above mentioned genes. Results showed that FF had the least cytotoxic effect on the LA7 cells. Except for Nanog gene, exposure of LA7 cell line to 16 h-SFS and P14 decreased significantly expression of the three other genes after 24 h (P < 0.05). Nanog and Sox2 genes expression was also decreased in LA7 cells which have been already treated with FF for 24 h. Moreover, compared to the control solution, the expression of Oct4 increased significantly after 7 days exposure to FF (P < 0.05). Annexin V-PE /7-AAD-, acridine orange/ethidium bromide staining and doubling time assays revealed apoptosis and necrosis induction by these biological fluids in LA7 cells. Moreover, in an in vitro model of metastasis assay, i.e., scratch test, these fluids exhibited anti-LA7 migration activity which culminated in 16 h-SFS treated cells. Generally, this study showed that FF, 16 h-SFS, and P14 have positive effects on down-regulation of Nanog, Oct4, Sox2 and C-myc expression, and consequently can increase the differentiation of breast cancer stem cells. For the first time, this study provided some evidence indicating that some biological fluids have potential to differentiate the CSCs, show anti- survival, growth-, and cell migration activity.
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Affiliation(s)
- Roghayeh Pourbagher
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran; Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Haleh Akhavan-Niaki
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Seyed Gholam Ali Jorsaraei
- Fatemeh Zahra Infertility and Reproductive Health Research Centre, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Sadegh Fattahi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Davood Sabour
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Ebrahim Zabihi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Zeinab Abedian
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran; Dental Materials Research Center, Dental Faculty, Babol University of Medical Sciences, Babol, Iran
| | - Masoumeh Ghasemi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Monireh Golpour
- Molecular and Cell Biology Research Center, Student Research Committee, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Amrollah Mostafazadeh
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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47
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Huertas J, MacCarthy CM, Schöler HR, Cojocaru V. Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding. Biophys J 2020; 118:2280-2296. [PMID: 32027821 PMCID: PMC7202942 DOI: 10.1016/j.bpj.2019.12.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/04/2019] [Accepted: 12/23/2019] [Indexed: 01/16/2023] Open
Abstract
Transcription factor (TF) proteins bind to DNA to regulate gene expression. Normally, accessibility to DNA is required for their function. However, in the nucleus, the DNA is often inaccessible, wrapped around histone proteins in nucleosomes forming the chromatin. Pioneer TFs are thought to induce chromatin opening by recognizing their DNA binding sites on nucleosomes. For example, Oct4, a master regulator and inducer of stem cell pluripotency, binds to DNA in nucleosomes in a sequence-specific manner. Here, we reveal the structural dynamics of nucleosomes that mediate Oct4 binding from molecular dynamics simulations. Nucleosome flexibility and the amplitude of nucleosome motions such as breathing and twisting are enhanced in nucleosomes with multiple TF binding sites. Moreover, the regions around the binding sites display higher local structural flexibility. Probing different structures of Oct4-nucleosome complexes, we show that alternative configurations in which Oct4 recognizes partial binding sites display stable TF-DNA interactions similar to those observed in complexes with free DNA and compatible with the DNA curvature and DNA-histone interactions. Therefore, we propose a structural basis for nucleosome recognition by a pioneer TF that is essential for understanding how chromatin is unraveled during cell fate conversions.
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Affiliation(s)
- Jan Huertas
- In Silico Biomolecular Structure and Dynamics Group, Hubrecht Institute, Utrecht, the Netherlands; Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster, Germany; and
| | - Caitlin M MacCarthy
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Hans R Schöler
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Medical Faculty, University of Münster, Münster, Germany
| | - Vlad Cojocaru
- In Silico Biomolecular Structure and Dynamics Group, Hubrecht Institute, Utrecht, the Netherlands; Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster, Germany; and.
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48
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In Vivo Quantitative Estimation of DNA-Dependent Interaction of Sox2 and Oct4 Using BirA-Catalyzed Site-Specific Biotinylation. Biomolecules 2020; 10:biom10010142. [PMID: 31963153 PMCID: PMC7022529 DOI: 10.3390/biom10010142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/03/2020] [Accepted: 01/09/2020] [Indexed: 11/25/2022] Open
Abstract
Protein–protein interactions of core pluripotency transcription factors play an important role during cell reprogramming. Cell identity is controlled by a trio of transcription factors: Sox2, Oct4, and Nanog. Thus, methods that help to quantify protein–protein interactions may be useful for understanding the mechanisms of pluripotency at the molecular level. Here, a detailed protocol for the detection and quantitative analysis of in vivo protein–protein proximity of Sox2 and Oct4 using the proximity-utilizing biotinylation (PUB) method is described. The method is based on the coexpression of two proteins of interest fused to a biotin acceptor peptide (BAP)in one case and a biotin ligase enzyme (BirA) in the other. The proximity between the two proteins leads to more efficient biotinylation of the BAP, which can be either detected by Western blotting or quantified using proteomics approaches, such as a multiple reaction monitoring (MRM) analysis. Coexpression of the fusion proteins BAP-X and BirA-Y revealed strong biotinylation of the target proteins when X and Y were, alternatively, the pluripotency transcription factors Sox2 and Oct4, compared with the negative control where X or Y was green fluorescent protein (GFP), which strongly suggests that Sox2 and Oct4 come in close proximity to each other and interact.
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49
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Chen K, Long Q, Xing G, Wang T, Wu Y, Li L, Qi J, Zhou Y, Ma B, Schöler HR, Nie J, Pei D, Liu X. Heterochromatin loosening by the Oct4 linker region facilitates Klf4 binding and iPSC reprogramming. EMBO J 2020; 39:e99165. [PMID: 31571238 PMCID: PMC6939195 DOI: 10.15252/embj.201899165] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 01/13/2023] Open
Abstract
The success of Yamanaka factor reprogramming of somatic cells into induced pluripotent stem cells suggests that some factor(s) must remodel the nuclei from a condensed state to a relaxed state. How factor-dependent chromatin opening occurs remains unclear. Using FRAP and ATAC-seq, we found that Oct4 acts as a pioneer factor that loosens heterochromatin and facilitates the binding of Klf4 and the expression of epithelial genes in early reprogramming, leading to enhanced mesenchymal-to-epithelial transition. A mutation in the Oct4 linker, L80A, which shows impaired interaction with the BAF complex component Brg1, is inactive in heterochromatin loosening. Oct4-L80A also blocks the binding of Klf4 and retards MET. Finally, vitamin C or Gadd45a could rescue the reprogramming deficiency of Oct4-L80A by enhancing chromatin opening and Klf4 binding. These studies reveal a cooperation between Oct4 and Klf4 at the chromatin level that facilitates MET at the cellular level and shed light into the research of multiple factors in cell fate determination.
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Affiliation(s)
- Keshi Chen
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Qi Long
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Guangsuo Xing
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
- Institute of Physical Science and Information TechnologyAnhui UniversityHefeiChina
| | - Tianyu Wang
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Yi Wu
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Linpeng Li
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Juntao Qi
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Yanshuang Zhou
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Bochao Ma
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Hans R Schöler
- Department for Cell and Developmental BiologyMax Planck Institute for Molecular BiomedicineMünsterGermany
| | - Jinfu Nie
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
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50
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Pálfy M, Schulze G, Valen E, Vastenhouw NL. Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation. PLoS Genet 2020; 16:e1008546. [PMID: 31940339 PMCID: PMC6986763 DOI: 10.1371/journal.pgen.1008546] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 01/28/2020] [Accepted: 12/02/2019] [Indexed: 12/12/2022] Open
Abstract
In many organisms, early embryonic development is driven by maternally provided factors until the controlled onset of transcription during zygotic genome activation. The regulation of chromatin accessibility and its relationship to gene activity during this transition remain poorly understood. Here, we generated chromatin accessibility maps with ATAC-seq from genome activation until the onset of lineage specification. During this period, chromatin accessibility increases at regulatory elements. This increase is independent of RNA polymerase II-mediated transcription, with the exception of the hypertranscribed miR-430 locus. Instead, accessibility often precedes the transcription of associated genes. Loss of the maternal transcription factors Pou5f3, Sox19b, and Nanog, which are known to be required for zebrafish genome activation, results in decreased accessibility at regulatory elements. Importantly, the accessibility of regulatory regions, especially when established by Pou5f3, Sox19b and Nanog, is predictive for future transcription. Our results show that the maternally provided transcription factors Pou5f3, Sox19b, and Nanog open up chromatin and prime genes for activity during zygotic genome activation in zebrafish.
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Affiliation(s)
- Máté Pálfy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Gunnar Schulze
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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