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Zuo Z, Roux ME, Dagdas YF, Rodriguez E, Petersen M. PAT mRNA decapping factors are required for proper development in Arabidopsis. FEBS Lett 2024; 598:1008-1021. [PMID: 38605280 DOI: 10.1002/1873-3468.14872] [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: 02/27/2024] [Revised: 04/10/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
Evolutionarily conserved protein associated with topoisomerase II (PAT1) proteins activate mRNA decay through binding mRNA and recruiting decapping factors to optimize posttranscriptional reprogramming. Here, we generated multiple mutants of pat1, pat1 homolog 1 (path1), and pat1 homolog 2 (path2) and discovered that pat triple mutants exhibit extremely stunted growth and all mutants with pat1 exhibit leaf serration while mutants with pat1 and path1 display short petioles. All three PATs can be found localized to processing bodies and all PATs can target ASYMMETRIC LEAVES 2-LIKE 9 transcripts for decay to finely regulate apical hook and lateral root development. In conclusion, PATs exhibit both specific and redundant functions during different plant growth stages and our observations underpin the selective regulation of the mRNA decay machinery for proper development.
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Affiliation(s)
- Zhangli Zuo
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
| | - Milena Edna Roux
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
| | - Yasin F Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Austria
| | - Eleazar Rodriguez
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
| | - Morten Petersen
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
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2
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Žukauskaitė D, Zentelytė A, Girniūtė E, Navakauskienė R. The outcome of tissue cryopreservation on the cellular, molecular and epigenetic characteristics of endometrial tissue and stromal cells. Reprod Biomed Online 2024; 49:103990. [PMID: 38824763 DOI: 10.1016/j.rbmo.2024.103990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 06/04/2024]
Abstract
RESEARCH QUESTION What impact does the cryopreservation of endometrial tissue have on cell characteristics and molecular and epigenetic profile changes in endometrial tissue and stromal cells? DESIGN Cellular properties, such as proliferation efficiency, surface marker expression and the differentiation potency of endometrial stromal cells (ESC) isolated from fresh (Native) and cryopreserved (Cryo) tissue were compared. Moreover, changes in the expression of genes associated with pluripotency, endometrial function and epigenetic regulation and microRNA (miRNA, miR) were assessed, as were levels of DNA methylation and histone modifications. RESULTS Native and Cryo cells exhibit very similar profiles including cell surface marker expression, differentiation potency and histone modifications, except for a decrease in proliferative potency and cell surface marker SUSD2 expression in Cryo cells. It was demonstrated that endometrial tissue cryopreservation led to an up-regulated expression of genes associated with pluripotency (NANOG, OCT4 [also known as POU5F1]). This confirms that despite being recovered from cryopreserved differentiated tissue, cells retained their stemness properties. In addition, alterations in DNA methyltransferase (DNMT1, DNMT3A, DNMT3B) gene regulation were observed, along with a down-regulation of hsa-miR145-5p in Cryo ESC. CONCLUSIONS These findings contribute to a deeper understanding of the complex effects of endometrial tissue cryopreservation, providing insights for both medical and basic research applications. Since different tissues possess unique characteristics, it is essential to select the most suitable cryopreservation method for each tissue individually. Furthermore, the study findings indicate the potential utility of slow-cooling cryopreservation for both normal and pathological endometrial tissue samples, with the purpose of isolating stromal cell cultures.
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Affiliation(s)
- Deimantė Žukauskaitė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania..
| | - Aistė Zentelytė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Erika Girniūtė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rūta Navakauskienė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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3
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Hiew VV, Teoh PL. Differential gene expression of Wharton's jelly-derived mesenchymal cells mediated by graphene oxide in basal and osteo-induced media. Mol Biol Rep 2024; 51:383. [PMID: 38433142 DOI: 10.1007/s11033-024-09324-9] [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: 07/20/2023] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Graphene oxide (GO) is widespread in scaffold engineering owing to its extraordinary properties such as multiple oxygen functional groups, high hydrophilicity ability and biocompatibility. It is known to promote differentiation in mesenchymal stem cells, but concomitant comparison of its modulation on the expression profiles of Wharton's jelly (WJ)-MSC surface markers, lineage differentiation, and epigenetic regulatory genes in basal and induced condition are still lacking. Unraveling the fundamental mechanisms is essential for the effective utilization of WJ-MSCs incorporated with GO in therapy. This study aims to explore the unique gene expression profiles and epigenetic characteristics of WJ-MSCs influenced by GO. METHODS AND RESULTS The characterized GO-coated coverslip served as a substrate for culturing WJ-MSCs. In addition to investigating the impact of GO on cell proliferation and differentiation, we conducted a gene expression study using PCR array, while epigenetic control was assessed through bisulfite sequencing and Western blot analysis. Our findings indicate that the presence of GO maintained the proliferation and survival of WJ-MSCs. In the absence of induction, GO led to minor lipid and glycosaminoglycan deposition in WJ-MSCs. This was evidenced by the sustained expression of pluripotency and lineage-specific genes, demethylation at the OCT4 promoter, and a decrease in H3K9 methylation. In osteo-induced condition, the occurrence of osteogenesis appeared to be guided by BMP/TGF and ERK pathway activation, accompanied by the upregulation of osteogenic-related genes and downregulation of DNMT3b. CONCLUSIONS GO in osteo-induced condition create a favorable microenvironment that promotes the osteogenesis of WJ-MSCs by influencing genetic and epigenetic controls. This helps in advancing our knowledge on the use of GO as priming platform and WJ-MSCs an alternate source for bone repair and regeneration.
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Affiliation(s)
- Vun Vun Hiew
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Peik Lin Teoh
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.
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4
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Yücel AD, Gladyshev VN. The long and winding road of reprogramming-induced rejuvenation. Nat Commun 2024; 15:1941. [PMID: 38431638 PMCID: PMC10908844 DOI: 10.1038/s41467-024-46020-5] [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: 07/22/2023] [Accepted: 02/12/2024] [Indexed: 03/05/2024] Open
Abstract
Organismal aging is inherently connected to the aging of its constituent cells and systems. Reducing the biological age of the organism may be assisted by reducing the age of its cells - an approach exemplified by partial cell reprogramming through the expression of Yamanaka factors or exposure to chemical cocktails. It is crucial to protect cell type identity during partial reprogramming, as cells need to retain or rapidly regain their functions following the treatment. Another critical issue is the ability to quantify biological age as reprogrammed older cells acquire younger states. We discuss recent advances in reprogramming-induced rejuvenation and offer a critical review of this procedure and its relationship to the fundamental nature of aging. We further comparatively analyze partial reprogramming, full reprogramming and transdifferentiation approaches, assess safety concerns and emphasize the importance of distinguishing rejuvenation from dedifferentiation. Finally, we highlight translational opportunities that the reprogramming-induced rejuvenation approach offers.
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Affiliation(s)
- Ali Doğa Yücel
- Department of Molecular Biology and Genetics, Koc University, Istanbul, 34450, Turkey
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Vadim N Gladyshev
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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5
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Petersen M, Ebstrup E, Rodriguez E. Going through changes - the role of autophagy during reprogramming and differentiation. J Cell Sci 2024; 137:jcs261655. [PMID: 38393817 DOI: 10.1242/jcs.261655] [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] [Indexed: 02/25/2024] Open
Abstract
Somatic cell reprogramming is a complex feature that allows differentiated cells to undergo fate changes into different cell types. This process, which is conserved between plants and animals, is often achieved via dedifferentiation into pluripotent stem cells, which have the ability to generate all other types of cells and tissues of a given organism. Cellular reprogramming is thus a complex process that requires extensive modification at the epigenetic and transcriptional level, unlocking cellular programs that allow cells to acquire pluripotency. In addition to alterations in the gene expression profile, cellular reprogramming requires rearrangement of the proteome, organelles and metabolism, but these changes are comparatively less studied. In this context, autophagy, a cellular catabolic process that participates in the recycling of intracellular constituents, has the capacity to affect different aspects of cellular reprogramming, including the removal of protein signatures that might hamper reprogramming, mitophagy associated with metabolic reprogramming, and the supply of energy and metabolic building blocks to cells that undergo fate changes. In this Review, we discuss advances in our understanding of the role of autophagy during cellular reprogramming by drawing comparisons between plant and animal studies, as well as highlighting aspects of the topic that warrant further research.
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Affiliation(s)
- Morten Petersen
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Elise Ebstrup
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Eleazar Rodriguez
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
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6
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Iordache F, Petcu A(I, Pisoschi AM, Stanca L, Geicu OI, Bilteanu L, Curuțiu C, Amuzescu B, Serban AI. PCR Array Profiling of miRNA Expression Involved in the Differentiation of Amniotic Fluid Stem Cells toward Endothelial and Smooth Muscle Progenitor Cells. Int J Mol Sci 2023; 25:302. [PMID: 38203477 PMCID: PMC10779355 DOI: 10.3390/ijms25010302] [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: 11/08/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Differentiation of amniotic fluid stem cells (AFSCs) into multiple lineages is controlled by epigenetic modifications, which include DNA methylation, modifications of histones, and the activity of small noncoding RNAs. The present study investigates the role of miRNAs in the differentiation of AFSCs and addresses how their unique signatures contribute to lineage-specific differentiation. The miRNA profile was assessed in AFSCs after 4 weeks of endothelial and muscular differentiation. Our results showed decreased expression of five miRNAs (miR-18a-5p, miR-125b-5p, miR-137, miR-21-5p, and let-7a) and increased expression of twelve miRNAs (miR-134-5p, miR-103a-3p, let-7i-5p, miR-214-3p, let-7c-5p, miR-129-5p, miR-210-3p, let-7d-5p, miR-375, miR-181-5p, miR-125a-5p, and hsa-let-7e-5p) in endothelial progenitor cells (EPCs) compared with undifferentiated AFSCs. AFSC differentiation into smooth muscle revealed notable changes in nine out of the 84 tested miRNAs. Among these, three miRNAs (miR-18a-5p, miR-137, and sa-miR-21-5p) were downregulated, while six miRNAs (miR-155-5p, miR-20a-5p, let-7i-5p, hsa-miR-134-5p, hsa-miR-214-3p, and hsa-miR-375) exhibited upregulation. Insights from miRNA networks promise future advancements in understanding and manipulating endothelial and muscle cell dynamics. This knowledge has the potential to drive innovation in areas like homeostasis, growth, differentiation, and vascular function, leading to breakthroughs in biomedical applications and therapies.
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Affiliation(s)
- Florin Iordache
- Department of Preclinical Sciences, Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 105 Blvd. Splaiul Independentei, 050097 Bucharest, Romania; (A.P.); (A.M.P.); (L.S.); (O.I.G.); (L.B.); (A.I.S.)
- S.C. Personal Genetics S.R.L. Genetic Medical Center, 010987 Bucharest, Romania
| | - Adriana (Ionescu) Petcu
- Department of Preclinical Sciences, Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 105 Blvd. Splaiul Independentei, 050097 Bucharest, Romania; (A.P.); (A.M.P.); (L.S.); (O.I.G.); (L.B.); (A.I.S.)
| | - Aurelia Magdalena Pisoschi
- Department of Preclinical Sciences, Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 105 Blvd. Splaiul Independentei, 050097 Bucharest, Romania; (A.P.); (A.M.P.); (L.S.); (O.I.G.); (L.B.); (A.I.S.)
| | - Loredana Stanca
- Department of Preclinical Sciences, Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 105 Blvd. Splaiul Independentei, 050097 Bucharest, Romania; (A.P.); (A.M.P.); (L.S.); (O.I.G.); (L.B.); (A.I.S.)
| | - Ovidiu Ionut Geicu
- Department of Preclinical Sciences, Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 105 Blvd. Splaiul Independentei, 050097 Bucharest, Romania; (A.P.); (A.M.P.); (L.S.); (O.I.G.); (L.B.); (A.I.S.)
| | - Liviu Bilteanu
- Department of Preclinical Sciences, Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 105 Blvd. Splaiul Independentei, 050097 Bucharest, Romania; (A.P.); (A.M.P.); (L.S.); (O.I.G.); (L.B.); (A.I.S.)
| | - Carmen Curuțiu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independentei, 050095 Bucharest, Romania;
| | - Bogdan Amuzescu
- Department of Biophysics and Physiology, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independentei, 050095 Bucharest, Romania;
| | - Andreea Iren Serban
- Department of Preclinical Sciences, Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 105 Blvd. Splaiul Independentei, 050097 Bucharest, Romania; (A.P.); (A.M.P.); (L.S.); (O.I.G.); (L.B.); (A.I.S.)
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7
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Ong ALC, Kokaji T, Kishi A, Takihara Y, Shinozuka T, Shimamoto R, Isotani A, Shirai M, Sasai N. Acquisition of neural fate by combination of BMP blockade and chromatin modification. iScience 2023; 26:107887. [PMID: 37771660 PMCID: PMC10522999 DOI: 10.1016/j.isci.2023.107887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/07/2023] [Accepted: 09/07/2023] [Indexed: 09/30/2023] Open
Abstract
Neural induction is a process where naive cells are converted into committed cells with neural characteristics, and it occurs at the earliest step during embryogenesis. Although the signaling molecules and chromatin remodeling for neural induction have been identified, the mutual relationships between these molecules are yet to be fully understood. By taking advantage of the neural differentiation system of mouse embryonic stem (ES) cells, we discovered that the BMP signal regulates the expression of several polycomb repressor complex (PRC) component genes. We particularly focused on Polyhomeotic Homolog 1 (Phc1) and established Phc1-knockout (Phc1-KO) ES cells. We found that Phc1-KO failed to acquire the neural fate, and the cells remained in pluripotent or primitive non-neural states. Chromatin accessibility analysis suggests that Phc1 is essential for chromatin packing. Aberrant upregulation of the BMP signal was confirmed in the Phc1 homozygotic mutant embryos. Taken together, Phc1 is required for neural differentiation through epigenetic modification.
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Affiliation(s)
- Agnes Lee Chen Ong
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Toshiya Kokaji
- Data-driven biology, NAIST Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Arisa Kishi
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Yoshihiro Takihara
- Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima 734-0037, Japan
| | - Takuma Shinozuka
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ren Shimamoto
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ayako Isotani
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Manabu Shirai
- Omics Research Center (ORC), National Cerebral and Cardiovascular Center, 6-1 Kishibe Shinmachi, Suita, Osaka 564-8565, Japan
| | - Noriaki Sasai
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
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8
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Zuo Z, Roux ME, Chevalier JR, Dagdas YF, Yamashino T, Højgaard SD, Knight E, Østergaard L, Rodriguez E, Petersen M. The mRNA decapping machinery targets LBD3/ASL9 to mediate apical hook and lateral root development. Life Sci Alliance 2023; 6:e202302090. [PMID: 37385753 PMCID: PMC10310928 DOI: 10.26508/lsa.202302090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023] Open
Abstract
Multicellular organisms perceive and transduce multiple cues to optimize development. Key transcription factors drive developmental changes, but RNA processing also contributes to tissue development. Here, we report that multiple decapping deficient mutants share developmental defects in apical hook, primary and lateral root growth. More specifically, LATERAL ORGAN BOUNDARIES DOMAIN 3 (LBD3)/ASYMMETRIC LEAVES 2-LIKE 9 (ASL9) transcripts accumulate in decapping deficient plants and can be found in complexes with decapping components. Accumulation of ASL9 inhibits apical hook and lateral root formation. Interestingly, exogenous auxin application restores lateral roots formation in both ASL9 over-expressors and mRNA decay-deficient mutants. Likewise, mutations in the cytokinin transcription factors type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs) ARR10 and ARR12 restore the developmental defects caused by over-accumulation of capped ASL9 transcript upon ASL9 overexpression. Most importantly, loss-of-function of asl9 partially restores apical hook and lateral root formation in both dcp5-1 and pat triple decapping deficient mutants. Thus, the mRNA decay machinery directly targets ASL9 transcripts for decay, possibly to interfere with cytokinin/auxin responses, during development.
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Affiliation(s)
- Zhangli Zuo
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Milena E Roux
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan R Chevalier
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Yasin F Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Takafumi Yamashino
- Laboratory of Molecular Microbiology, School of Agriculture, Nagoya University, Nagoya, Japan
| | - Søren D Højgaard
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Emilie Knight
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Lars Østergaard
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Eleazar Rodriguez
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Morten Petersen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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9
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Luo Q, Maity AK, Teschendorff AE. Distance covariance entropy reveals primed states and bifurcation dynamics in single-cell RNA-Seq data. iScience 2022; 25:105709. [PMID: 36578319 PMCID: PMC9791356 DOI: 10.1016/j.isci.2022.105709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/08/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Cell-fate transitions are fundamental to development and differentiation. Studying them with single-cell omic data is important to advance our understanding of the cell-fate commitment process, yet this remains challenging. Here we present a computational method called DICE, which analyzes the entropy of expression covariation patterns and which is applicable to static and dynamically changing cell populations. Using only single-cell RNA-Seq data, DICE is able to predict multipotent primed states and their regulatory factors, which we subsequently validate with single-cell epigenomic data. DICE reveals that primed states are often defined by epigenetic regulators or pioneer factors alongside lineage-specific transcription factors. In developmental time course single-cell RNA-Seq datasets, DICE can pinpoint the timing of bifurcations more precisely than lineage-trajectory inference algorithms or competing variance-based methods. In summary, by studying the dynamic changes of expression covariation entropy, DICE can help elucidate primed states and bifurcation dynamics without the need for single-cell epigenomic data.
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Affiliation(s)
- Qi Luo
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Alok K. Maity
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China,Corresponding author
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10
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Duddu AS, Majumdar SS, Sahoo S, Jhunjhunwala S, Jolly MK. Emergent dynamics of a three-node regulatory network explain phenotypic switching and heterogeneity: a case study of Th1/Th2/Th17 cell differentiation. Mol Biol Cell 2022; 33:ar46. [PMID: 35353012 PMCID: PMC9265159 DOI: 10.1091/mbc.e21-10-0521] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Naïve helper (CD4+) T-cells can differentiate into distinct functional subsets including Th1, Th2, and Th17 phenotypes. Each of these phenotypes has a 'master regulator' - T-bet (Th1), GATA3 (Th2) and RORγT (Th17) - that inhibits the other two master regulators. Such mutual repression among them at a transcriptional level can enable multistability, giving rise to six experimentally observed phenotypes - Th1, Th2, Th17, hybrid Th/Th2, hybrid Th2/Th17 and hybrid Th1/Th17. However, the dynamics of switching among these phenotypes, particularly in the case of epigenetic influence, remains unclear. Here, through mathematical modeling, we investigated the coupled transcription-epigenetic dynamics in a three-node mutually repressing network to elucidate how epigenetic changes mediated by any 'master regulator' can influence the transition rates among different cellular phenotypes. We show that the degree of plasticity exhibited by one phenotype depends on relative strength and duration of mutual epigenetic repression mediated among the master regulators in a three-node network. Further, our model predictions can offer putative mechanisms underlying relatively higher plasticity of Th17 phenotype as observed in vitro and in vivo. Together, our modeling framework characterizes phenotypic plasticity and heterogeneity as an outcome of emergent dynamics of a three-node regulatory network, such as the one mediated by T-bet/GATA3/RORγT.
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Affiliation(s)
- Atchuta Srinivas Duddu
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sauma Suvra Majumdar
- epartment of Biotechnology, National Institute of Technology, Durgapur 713216, India
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Siddharth Jhunjhunwala
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
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11
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Jia W, Jolly MK, Levine H. NRF2-dependent Epigenetic Regulation can Promote the Hybrid Epithelial/Mesenchymal Phenotype. Front Cell Dev Biol 2022; 9:828250. [PMID: 35118079 PMCID: PMC8803900 DOI: 10.3389/fcell.2021.828250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/28/2021] [Indexed: 11/17/2022] Open
Abstract
The epithelial-mesenchymal transition (EMT) is a cellular process critical for wound healing, cancer metastasis and embryonic development. Recent efforts have identified the role of hybrid epithelial/mesenchymal states, having both epithelial and mesehncymal traits, in enabling cancer metastasis and resistance to various therapies. Also, previous work has suggested that NRF2 can act as phenotypic stability factor to help stablize such hybrid states. Here, we incorporate a phenomenological epigenetic feedback effect into our previous computational model for EMT signaling. We show that this type of feedback can stabilize the hybrid state as compared to the fully mesenchymal phenotype if NRF2 can influence SNAIL at an epigenetic level, as this link makes transitions out of hybrid state more difficult. However, epigenetic regulation on other NRF2-related links do not significantly change the EMT dynamics. Finally, we considered possible cell division effects in our epigenetic regulation model, and our results indicate that the degree of epigenetic inheritance does not appear to be a critical factor for the hybrid E/M state stabilizing behavior of NRF2.
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Affiliation(s)
- Wen Jia
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, United States
- Department of Physics and Astronomy, Rice University, Houston, TX, United States
- Department of Physics, Northeastern University, Boston, MA, United States
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- *Correspondence: Mohit Kumar Jolly, ; Herbert Levine,
| | - Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, United States
- Department of Physics, Northeastern University, Boston, MA, United States
- Department of Bioengineering, Northeastern University, Boston, MA, United States
- *Correspondence: Mohit Kumar Jolly, ; Herbert Levine,
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12
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Subbalakshmi AR, Sahoo S, McMullen I, Saxena AN, Venugopal SK, Somarelli JA, Jolly MK. KLF4 Induces Mesenchymal-Epithelial Transition (MET) by Suppressing Multiple EMT-Inducing Transcription Factors. Cancers (Basel) 2021; 13:5135. [PMID: 34680284 PMCID: PMC8533753 DOI: 10.3390/cancers13205135] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022] Open
Abstract
Epithelial-Mesenchymal Plasticity (EMP) refers to reversible dynamic processes where cells can transition from epithelial to mesenchymal (EMT) or from mesenchymal to epithelial (MET) phenotypes. Both these processes are modulated by multiple transcription factors acting in concert. While EMT-inducing transcription factors (TFs)-TWIST1/2, ZEB1/2, SNAIL1/2/3, GSC, and FOXC2-are well-characterized, the MET-inducing TFs are relatively poorly understood (OVOL1/2 and GRHL1/2). Here, using mechanism-based mathematical modeling, we show that transcription factor KLF4 can delay the onset of EMT by suppressing multiple EMT-TFs. Our simulations suggest that KLF4 overexpression can promote a phenotypic shift toward a more epithelial state, an observation suggested by the negative correlation of KLF4 with EMT-TFs and with transcriptomic-based EMT scoring metrics in cancer cell lines. We also show that the influence of KLF4 in modulating the EMT dynamics can be strengthened by its ability to inhibit cell-state transitions at the epigenetic level. Thus, KLF4 can inhibit EMT through multiple parallel paths and can act as a putative MET-TF. KLF4 associates with the patient survival metrics across multiple cancers in a context-specific manner, highlighting the complex association of EMP with patient survival.
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Affiliation(s)
- Ayalur Raghu Subbalakshmi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (A.R.S.); (S.S.); (S.K.V.)
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (A.R.S.); (S.S.); (S.K.V.)
| | | | | | - Sudhanva Kalasapura Venugopal
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (A.R.S.); (S.S.); (S.K.V.)
| | - Jason A. Somarelli
- Department of Medicine, Duke University, Durham, NC 27708, USA;
- Duke Cancer Institute, Duke University, Durham, NC 27708, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (A.R.S.); (S.S.); (S.K.V.)
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13
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Kim MH, Thanuthanakhun N, Fujimoto S, Kino-Oka M. Effect of initial seeding density on cell behavior-driven epigenetic memory and preferential lineage differentiation of human iPSCs. Stem Cell Res 2021; 56:102534. [PMID: 34530397 DOI: 10.1016/j.scr.2021.102534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/22/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022] Open
Abstract
Understanding the cellular behavioral mechanisms underlying memory formation and maintenance in human induced pluripotent stem cell (hiPSC) culture provides key strategies for achieving stability and robustness of cell differentiation. Here, we show that changes in cell behavior-driven epigenetic memory of hiPSC cultures alter their pluripotent state and subsequent differentiation. Interestingly, pluripotency-associated genes were activated during the entire cell growth phases along with increased active modifications and decreased repressive modifications. This memory effect can last several days in the long-term stationary phase and was sustained in the aspect of cell behavioral changes after subculture. Further, changes in growth-related cell behavior were found to induce nucleoskeletal reorganization and active versus repressive modifications, thereby enabling hiPSCs to change their differentiation potential. Overall, we discuss the cell behavior-driven epigenetic memory induced by the culture environment, and the effect of previous memory on cell lineage specification in the process of hiPSC differentiation.
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Affiliation(s)
- Mee-Hae Kim
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Naruchit Thanuthanakhun
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shun Fujimoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahiro Kino-Oka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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14
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Saini A, Gallo JM. Epigenetic instability may alter cell state transitions and anticancer drug resistance. PLoS Comput Biol 2021; 17:e1009307. [PMID: 34424912 PMCID: PMC8412323 DOI: 10.1371/journal.pcbi.1009307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 09/02/2021] [Accepted: 07/26/2021] [Indexed: 01/22/2023] Open
Abstract
Drug resistance is a significant obstacle to successful and durable anti-cancer therapy. Targeted therapy is often effective during early phases of treatment; however, eventually cancer cells adapt and transition to drug-resistant cells states rendering the treatment ineffective. It is proposed that cell state can be a determinant of drug efficacy and manipulated to affect the development of anticancer drug resistance. In this work, we developed two stochastic cell state models and an integrated stochastic-deterministic model referenced to brain tumors. The stochastic cell state models included transcriptionally-permissive and -restrictive states based on the underlying hypothesis that epigenetic instability mitigates lock-in of drug-resistant states. When moderate epigenetic instability was implemented the drug-resistant cell populations were reduced, on average, by 60%, whereas a high level of epigenetic disruption reduced them by about 90%. The stochastic-deterministic model utilized the stochastic cell state model to drive the dynamics of the DNA repair enzyme, methylguanine-methyltransferase (MGMT), that repairs temozolomide (TMZ)-induced O6-methylguanine (O6mG) adducts. In the presence of epigenetic instability, the production of MGMT decreased that coincided with an increase of O6mG adducts following a multiple-dose regimen of TMZ. Generation of epigenetic instability via epigenetic modifier therapy could be a viable strategy to mitigate anticancer drug resistance.
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Affiliation(s)
- Anshul Saini
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - James M. Gallo
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, New York, United States of America
- * E-mail:
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15
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Wadkin LE, Orozco-Fuentes S, Neganova I, Lako M, Parker NG, Shukurov A. A mathematical modelling framework for the regulation of intra-cellular OCT4 in human pluripotent stem cells. PLoS One 2021; 16:e0254991. [PMID: 34347824 PMCID: PMC8336844 DOI: 10.1371/journal.pone.0254991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/07/2021] [Indexed: 12/04/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) have the potential to differentiate into all cell types, a property known as pluripotency. A deeper understanding of how pluripotency is regulated is required to assist in controlling pluripotency and differentiation trajectories experimentally. Mathematical modelling provides a non-invasive tool through which to explore, characterise and replicate the regulation of pluripotency and the consequences on cell fate. Here we use experimental data of the expression of the pluripotency transcription factor OCT4 in a growing hPSC colony to develop and evaluate mathematical models for temporal pluripotency regulation. We consider fractional Brownian motion and the stochastic logistic equation and explore the effects of both additive and multiplicative noise. We illustrate the use of time-dependent carrying capacities and the introduction of Allee effects to the stochastic logistic equation to describe cell differentiation. We conclude both methods adequately capture the decline in OCT4 upon differentiation, but the Allee effect model has the advantage of allowing differentiation to occur stochastically in a sub-set of cells. This mathematical framework for describing intra-cellular OCT4 regulation can be extended to other transcription factors and developed into predictive models.
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Affiliation(s)
- L E Wadkin
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - S Orozco-Fuentes
- Department of Mathematics, Physics and Electrical Engineering, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - I Neganova
- Institute of Cytology, RAS St Petersburg, Novosibirsk, Russia
| | - M Lako
- Bioscience Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - N G Parker
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - A Shukurov
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, United Kingdom
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16
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Abstract
AbstractIn this work, we explore the properties of a control mechanism exerted on random Boolean networks that takes inspiration from the methylation mechanisms in cell differentiation and consists in progressively freezing (i.e. clamping to 0) some nodes of the network. We study the main dynamical properties of this mechanism both theoretically and in simulation. In particular, we show that when applied to random Boolean networks, it makes it possible to attain dynamics and path dependence typical of biological cells undergoing differentiation.
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17
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Guillemin A, Stumpf MPH. Noise and the molecular processes underlying cell fate decision-making. Phys Biol 2021; 18:011002. [PMID: 33181489 DOI: 10.1088/1478-3975/abc9d1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cell fate decision-making events involve the interplay of many molecular processes, ranging from signal transduction to genetic regulation, as well as a set of molecular and physiological feedback loops. Each aspect offers a rich field of investigation in its own right, but to understand the whole process, even in simple terms, we need to consider them together. Here we attempt to characterise this process by focussing on the roles of noise during cell fate decisions. We use a range of recent results to develop a view of the sequence of events by which a cell progresses from a pluripotent or multipotent to a differentiated state: chromatin organisation, transcription factor stoichiometry, and cellular signalling all change during this progression, and all shape cellular variability, which becomes maximal at the transition state.
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Affiliation(s)
- Anissa Guillemin
- School of BioSciences, University of Melbourne, Parkville, Australia
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18
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Feng Y, Wang Y, Wang X, He X, Yang C, Naseri A, Pederson T, Zheng J, Zhang S, Xiao X, Xie W, Ma H. Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription. Genome Biol 2020; 21:296. [PMID: 33292531 PMCID: PMC7722448 DOI: 10.1186/s13059-020-02201-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Despite the long-observed correlation between H3K9me3, chromatin architecture, and transcriptional repression, how H3K9me3 regulates genome higher-order organization and transcriptional activity in living cells remains unclear. RESULT Here, we develop EpiGo (Epigenetic perturbation induced Genome organization)-KRAB to introduce H3K9me3 at hundreds of loci spanning megabases on human chromosome 19 and simultaneously track genome organization. EpiGo-KRAB is sufficient to induce genomic clustering and de novo heterochromatin-like domain formation, which requires SETDB1, a methyltransferase of H3K9me3. Unexpectedly, EpiGo-KRAB-induced heterochromatin-like domain does not result in widespread gene repression except a small set of genes with concurrent loss of H3K4me3 and H3K27ac. Ectopic H3K9me3 appears to spread in inactive regions but is largely restricted from transcriptional initiation sites in active regions. Finally, Hi-C analysis showed that EpiGo-KRAB reshapes existing compartments mainly at compartment boundaries. CONCLUSIONS These results reveal the role of H3K9me3 in genome organization could be partially separated from its function in gene repression.
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Affiliation(s)
- Ying Feng
- School of Biotechnology, East China University of Science and Technology, Shanghai, China; School of Life Science and Technology, ShanghaiTech University,, Shanghai, China
| | - Yao Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xiangnan Wang
- School of Life Science and Technology, ShanghaiTech University,, Beijing, China
| | - Xiaohui He
- School of Life Science and Technology, ShanghaiTech University,, Beijing, China
| | - Chen Yang
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ardalan Naseri
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Thoru Pederson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jing Zheng
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Xiao Xiao
- School of Biotechnology, East China University of Science and Technology,, Shanghai, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
| | - Hanhui Ma
- School of Life Science and Technology, ShanghaiTech University,, Beijing, China.
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19
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Chen T, Ali Al-Radhawi M, Sontag ED. A mathematical model exhibiting the effect of DNA methylation on the stability boundary in cell-fate networks. Epigenetics 2020; 16:436-457. [PMID: 32842865 DOI: 10.1080/15592294.2020.1805686] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cell-fate networks are traditionally studied within the framework of gene regulatory networks. This paradigm considers only interactions of genes through expressed transcription factors and does not incorporate chromatin modification processes. This paper introduces a mathematical model that seamlessly combines gene regulatory networks and DNA methylation (DNAm), with the goal of quantitatively characterizing the contribution of epigenetic regulation to gene silencing. The 'Basin of Attraction percentage' is introduced as a metric to quantify gene silencing abilities. As a case study, a computational and theoretical analysis is carried out for a model of the pluripotent stem cell circuit as well as a simplified self-activating gene model. The results confirm that the methodology quantitatively captures the key role that DNAm plays in enhancing the stability of the silenced gene state.
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Affiliation(s)
- Tianchi Chen
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - M Ali Al-Radhawi
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA
| | - Eduardo D Sontag
- Department of Bioengineering, Northeastern University, Boston, MA, USA.,Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA.,Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
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20
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Alba G, Martínez R, Postigo-Corrales F, López S, Santa-María C, Jiménez J, Cahuana GM, Soria B, Bedoya FJ, Tejedo JR. AICAR Stimulates the Pluripotency Transcriptional Complex in Embryonic Stem Cells Mediated by PI3K, GSK3β, and β-Catenin. ACS OMEGA 2020; 5:20270-20282. [PMID: 32832780 PMCID: PMC7439381 DOI: 10.1021/acsomega.0c02137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/23/2020] [Indexed: 05/03/2023]
Abstract
Pluripotent stem cells maintain the property of self-renewal and differentiate into all cell types under clear environments. Though the gene regulatory mechanism for pluripotency has been investigated in recent years, it is still not completely understood. Here, we show several signaling pathways involved in the maintenance of pluripotency. To investigate whether AMPK is involved in maintaining the pluripotency in mouse embryonic stem cells (mESCs) and elucidating the possible molecular mechanisms, implicated D3 and R1/E mESC lines were used in this study. Cells were cultured in the absence or presence of LIF and treated with 1 mM and 0.5 mM 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranoside (AICAR), 2 mM metformin, compound C, and the PI3K inhibitor LY294002 for 24, 72, and 120 h. The levels of Nanog, Oct3/4, and REX1 and Brachyury, Notch2, and Gata4 mRNAs and Nanog or OCT3/4 protein levels were analyzed. Alkaline phosphatase and the cellular cycle were determined. The pGSK3β, GSK3β, p-β-catenin, and β-catenin protein levels were also investigated. We found that AMPK activators such as AICAR and metformin increase mRNA expression of pluripotency markers and decrease mRNA expression of differentiation markers in R1/E and D3 ES cells. AICAR increases phosphatase activity and arrests the cellular cycle in the G1 phase in these cells. We describe that AICAR effects were mediated by AMPK activation using a chemical inhibitor or by silencing this gene. AICAR effects were also mediated by PI3K, GSK3β, and β-catenin in R1/E ES cells. According to our findings, we provide a mechanism by which AICAR increases and maintains a pluripotency state through enhanced Nanog expression, involving AMPK/PI3K and p-GSK3β Ser21/9 pathways backing up the AICAR function as a potential target for this drug controlling pluripotency. The highlights of this study are that AICAR (5-aminoimidazole-4-carboxamied-1-b-riboside), an AMP protein kinase (AMPK) activator, blocks the ESC differentiation and AMPK is a key enzyme for pluripotency and shows valuable data to clarify the molecular pluripotency mechanism.
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Affiliation(s)
- Gonzalo Alba
- Department
of Medical Biochemistry and Molecular Biology, Universidad de Sevilla, Seville 41009, Spain
- . Telephone: +34-955421044. Fax: +34-954907048
| | - Raquel Martínez
- Department
of Regeneration and Cell Therapy, Andalusian Center for Molecular
Biology and Regenerative Medicine-CABIMER, Universidad Pablo de Olavide-University of Seville-CSIC, Seville 41013, Spain
| | - Fátima Postigo-Corrales
- Department
of Regeneration and Cell Therapy, Andalusian Center for Molecular
Biology and Regenerative Medicine-CABIMER, Universidad Pablo de Olavide-University of Seville-CSIC, Seville 41013, Spain
| | - Soledad López
- Department
of Medical Biochemistry and Molecular Biology, Universidad de Sevilla, Seville 41009, Spain
| | - Consuelo Santa-María
- Department
of Biochemistry and Molecular Biology, Universidad
de Sevilla, Seville 41009, Spain
| | - Juan Jiménez
- Department
of Medical Biochemistry and Molecular Biology, Universidad de Sevilla, Seville 41009, Spain
| | - Gladys M. Cahuana
- Department
of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville 41013, Spain
- Biomedical
Research Network for Diabetes and Related Metabolic Diseases-CIBERDEM,
Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Bernat Soria
- Department
of Regeneration and Cell Therapy, Andalusian Center for Molecular
Biology and Regenerative Medicine-CABIMER, Universidad Pablo de Olavide-University of Seville-CSIC, Seville 41013, Spain
- Biomedical
Research Network for Diabetes and Related Metabolic Diseases-CIBERDEM,
Instituto de Salud Carlos III, Madrid 28029, Spain
- Cell
Therapy
Network, Madrid (RED-TERCEL), Instituto
de Salud Carlos III, Madrid 28029, Spain
- Universidad
Miguel Hernández, Alicante 03550, Spain
| | - Francisco J. Bedoya
- Department
of Regeneration and Cell Therapy, Andalusian Center for Molecular
Biology and Regenerative Medicine-CABIMER, Universidad Pablo de Olavide-University of Seville-CSIC, Seville 41013, Spain
- Department
of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville 41013, Spain
- Biomedical
Research Network for Diabetes and Related Metabolic Diseases-CIBERDEM,
Instituto de Salud Carlos III, Madrid 28029, Spain
- Cell
Therapy
Network, Madrid (RED-TERCEL), Instituto
de Salud Carlos III, Madrid 28029, Spain
| | - Juan R. Tejedo
- Department
of Regeneration and Cell Therapy, Andalusian Center for Molecular
Biology and Regenerative Medicine-CABIMER, Universidad Pablo de Olavide-University of Seville-CSIC, Seville 41013, Spain
- Department
of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville 41013, Spain
- Biomedical
Research Network for Diabetes and Related Metabolic Diseases-CIBERDEM,
Instituto de Salud Carlos III, Madrid 28029, Spain
- Cell
Therapy
Network, Madrid (RED-TERCEL), Instituto
de Salud Carlos III, Madrid 28029, Spain
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21
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Huang D, Wang R. Exploring the mechanisms of cell reprogramming and transdifferentiation via intercellular communication. Phys Rev E 2020; 102:012406. [PMID: 32795030 DOI: 10.1103/physreve.102.012406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 07/02/2020] [Indexed: 11/07/2022]
Abstract
In the past years, the mechanisms of cell reprogramming and transdifferentiation via the way of gene regulation, stochastic fluctuations, or chemical induction to realize cell type transitions from the perspectives of single cells were explored. In multicellular organisms, intercellular communication plays crucial roles in cell fate decisions. However, the importance of intercellular communication to the processes of cell reprogramming and transdifferentiation is often neglected. In this paper, the mechanisms of cell reprogramming and transdifferentiation by intercellular communication are investigated. A two-gene circuit with mutual inhibition and self-activation as a basic model is selected. Then, a coupling mechanism via intercellular communication by introducing a specific signaling molecule into the gene circuit is considered. Finally, the influence of coupling intensity on the dynamics of the coupled system of two cells is analyzed. Moreover, when the coupling intensity changes with respect to the cell number in a discrete way, the effects of coupling intensity on cell reprogramming and transdifferentiation are discussed. Some theoretical analysis of stability and bifurcation of the systems are also given. Our research shows that cells can realize cell reprogramming and transdifferentiation via intercellular interaction at opportune coupling intensity. These results not only further enrich previous studies but also are beneficial to understand the mechanisms of cell reprogramming and transdifferentiation via intercellular communication in the growth and development of multicellular organisms.
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Affiliation(s)
- Dasong Huang
- Department of Mathematics, Shanghai University, Shanghai 200436, China
| | - Ruiqi Wang
- Department of Mathematics, Shanghai University, Shanghai 200436, China
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22
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Jia W, Tripathi S, Chakraborty P, Chedere A, Rangarajan A, Levine H, Jolly MK. Epigenetic feedback and stochastic partitioning during cell division can drive resistance to EMT. Oncotarget 2020; 11:2611-2624. [PMID: 32676163 PMCID: PMC7343638 DOI: 10.18632/oncotarget.27651] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) and its reverse process mesenchymal-epithelial transition (MET) are central to metastatic aggressiveness and therapy resistance in solid tumors. While molecular determinants of both processes have been extensively characterized, the heterogeneity in the response of tumor cells to EMT and MET inducers has come into focus recently, and has been implicated in the failure of anti-cancer therapies. Recent experimental studies have shown that some cells can undergo an irreversible EMT depending on the duration of exposure to EMT-inducing signals. While the irreversibility of MET, or equivalently, resistance to EMT, has not been studied in as much detail, evidence supporting such behavior is slowly emerging. Here, we identify two possible mechanisms that can underlie resistance of cells to undergo EMT: epigenetic feedback in ZEB1/GRHL2 feedback loop and stochastic partitioning of biomolecules during cell division. Identifying the ZEB1/GRHL2 axis as a key determinant of epithelial-mesenchymal plasticity across many cancer types, we use mechanistic mathematical models to show how GRHL2 can be involved in both the abovementioned processes, thus driving an irreversible MET. Our study highlights how an isogenic population may contain subpopulation with varying degrees of susceptibility or resistance to EMT, and proposes a next set of questions for detailed experimental studies characterizing the irreversibility of MET/resistance to EMT.
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Affiliation(s)
- Wen Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Physics and Astronomy, Rice University, Houston, TX, USA
| | - Shubham Tripathi
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Priyanka Chakraborty
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Adithya Chedere
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Annapoorni Rangarajan
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
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23
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Tripathi S, Levine H, Jolly MK. The Physics of Cellular Decision Making During Epithelial-Mesenchymal Transition. Annu Rev Biophys 2020; 49:1-18. [PMID: 31913665 DOI: 10.1146/annurev-biophys-121219-081557] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The epithelial-mesenchymal transition (EMT) is a process by which cells lose epithelial traits, such as cell-cell adhesion and apico-basal polarity, and acquire migratory and invasive traits. EMT is crucial to embryonic development and wound healing. Misregulated EMT has been implicated in processes associated with cancer aggressiveness, including metastasis. Recent experimental advances such as single-cell analysis and temporal phenotypic characterization have established that EMT is a multistable process wherein cells exhibit and switch among multiple phenotypic states. This is in contrast to the classical perception of EMT as leading to a binary choice. Mathematical modeling has been at the forefront of this transformation for the field, not only providing a conceptual framework to integrate and analyze experimental data, but also making testable predictions. In this article, we review the key features and characteristics of EMT dynamics, with a focus on the mathematical modeling approaches that have been instrumental to obtaining various useful insights.
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Affiliation(s)
- Shubham Tripathi
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, USA.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA; .,Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA; .,Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India;
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24
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Jia W, Deshmukh A, Mani SA, Jolly MK, Levine H. A possible role for epigenetic feedback regulation in the dynamics of the epithelial-mesenchymal transition (EMT). Phys Biol 2019; 16:066004. [PMID: 31342918 DOI: 10.1088/1478-3975/ab34df] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The epithelial-mesenchymal transition (EMT) often plays a critical role in cancer metastasis and chemoresistance, and decoding its dynamics is crucial to design effective therapeutics. EMT is regulated at multiple levels-transcriptional, translational, protein stability and epigenetics; the mechanisms by which epigenetic regulation can alter the dynamics of EMT remain elusive. Here, to identify the possible effects of epigenetic regulation in EMT, we incorporate a feedback term in our previously proposed model of EMT regulation of the miR-200/ZEB/miR-34/SNAIL circuit. This epigenetic feedback that stabilizes long-term transcriptional activity can alter the relative stability and distribution of states in a given cell population, particularly when incorporated in the inhibitory effect on miR-200 from ZEB. This feedback can stabilize the mesenchymal state, thus making transitions out of that state difficult. Conversely, epigenetic regulation of the self-activation of ZEB has only minor effects. Our model predicts that this effect could be seen in experiments, when epithelial cells are treated with an external EMT-inducing signal for a sufficiently long period of time and then allowed to recover. Our preliminary experimental data indicates that a chronic TGF-β exposure gives rise to irreveversible EMT state; i.e. unable to reverse back to the epithelial state. Thus, this integrated theoretical-experimental approach yields insights into how an epigenetic feedback may alter the dynamics of EMT.
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Affiliation(s)
- Wen Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States of America. Department of Physics and Astronomy, Rice University, Houston, TX 77005, United States of America. These authors contributed equally
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Sun Z, Yu S, Chen S, Liu H, Chen Z. SP1 regulates KLF4 via SP1 binding motif governed by DNA methylation during odontoblastic differentiation of human dental pulp cells. J Cell Biochem 2019; 120:14688-14699. [PMID: 31009133 PMCID: PMC8895433 DOI: 10.1002/jcb.28730] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/14/2019] [Accepted: 04/01/2019] [Indexed: 12/16/2022]
Abstract
OBJECTIVE DNA methylation is a critical epigenetic modulation in regulating gene expression in cell differentiation process, however, its detailed molecular mechanism during odontoblastic differentiation remains elusive. We aimed to study the global effect of DNA methylation on odontoblastic differentiation and how DNA methylation affects the transactivation of transcription factor (TF) on its target gene. METHODS DNA methyltransferase (DNMTs) inhibition assay and following odontoblastic differentiation assay were performed to evaluate the effect of DNA methylation inhibition on odontoblastic differentiation. Promoter DNA methylation microarray and motif enrichment assay were performed to predict the most DNA-methylation-affected TF motifs during odontoblastic differentiation. The enriched target sites and motifs were further analyzed by methylation-specific polymerase chain reaction (MS-PCR) and sequencing. The functional target sites were validated in vitro with Luciferase assay. The regulatory effect of DNA methylation on the enriched target sites in primary human dental pulp cells and motifs were confirmed by in vitro methylation assay. RESULTS Inhibition of DNMTs in preodontoblast cells increased the expression level of Klf4 as well as marker genes of odontoblastic differentiation including Dmp1 and Dspp, and enhanced the efficiency of odontoblastic differentiation. SP1/KLF4 binding motifs were found to be highly enriched in the promoter regions and showed demethylation during odontoblastic differentiation. Mutation of SP1 binding site at -75 within KLF4's promoter region significantly decreased the luciferase activity. The in vitro methylation of KLF4's promoter decreased the transactivation of SP1 on KLF4. CONCLUSION We confirmed that SP1 regulates KLF4 through binding site lying in a CpG island in KLF4's promoter region which demethylated during odontoblastic differentiation thus enhancing the efficiency of SP1's binding and transcriptional regulation on KLF4.
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Affiliation(s)
- Zheyi Sun
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Shuaitong Yu
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Shuo Chen
- Department of Developmental Dentistry, University of Texas Health Science Center, San Antonio, Texas
| | - Huan Liu
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Periodontology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Zhi Chen
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
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Hamaneh MB, Yu YK. Exploring induced pluripotency in human fibroblasts via construction, validation, and application of a gene regulatory network. PLoS One 2019; 14:e0220742. [PMID: 31374103 PMCID: PMC6677386 DOI: 10.1371/journal.pone.0220742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/21/2019] [Indexed: 12/31/2022] Open
Abstract
Reprogramming of somatic cells to induced pluripotent stem cells, by overexpressing certain factors referred to as the reprogramming factors, can revolutionize regenerative medicine. To provide a coherent description of induced pluripotency from the gene regulation perspective, we use 35 microarray datasets to construct a reprogramming gene regulatory network. Comprising 276 nodes and 4471 links, the resulting network is, to the best of our knowledge, the largest gene regulatory network constructed for human fibroblast reprogramming and it is the only one built using a large number of experimental datasets. To build the network, a model that relates the expression profiles of the initial (fibroblast) and final (induced pluripotent stem cell) states is proposed and the model parameters (link strengths) are fitted using the experimental data. Twenty nine additional experimental datasets are collectively used to test the model/network, and good agreement between experimental and predicted gene expression profiles is found. We show that the model in conjunction with the constructed network can make useful predictions. For example, we demonstrate that our approach can incorporate the effect of reprogramming factor stoichiometry and that its predictions are consistent with the experimentally observed trends in reprogramming efficiency when the stoichiometric ratios vary. Using our model/network, we also suggest new (not used in training of the model) candidate sets of reprogramming factors, many of which have already been experimentally verified. These results suggest our model/network can potentially be used in devising new recipes for induced pluripotency with higher efficiencies. Additionally, we classify the links of the network into three classes of different importance, prioritizing them for experimental verification. We show that many of the links in the top ranked class are experimentally known to be important in reprogramming. Finally, comparing with other methods, we show that using our model is advantageous.
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Affiliation(s)
- Mehdi B. Hamaneh
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yi-Kuo Yu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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27
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Akhmetzhanov AR, Kim JW, Sullivan R, Beckman RA, Tamayo P, Yeang CH. Modelling bistable tumour population dynamics to design effective treatment strategies. J Theor Biol 2019; 474:88-102. [DOI: 10.1016/j.jtbi.2019.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 12/16/2022]
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Shparberg RA, Glover HJ, Morris MB. Modeling Mammalian Commitment to the Neural Lineage Using Embryos and Embryonic Stem Cells. Front Physiol 2019; 10:705. [PMID: 31354503 PMCID: PMC6637848 DOI: 10.3389/fphys.2019.00705] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/20/2019] [Indexed: 12/21/2022] Open
Abstract
Early mammalian embryogenesis relies on a large range of cellular and molecular mechanisms to guide cell fate. In this highly complex interacting system, molecular circuitry tightly controls emergent properties, including cell differentiation, proliferation, morphology, migration, and communication. These molecular circuits include those responsible for the control of gene and protein expression, as well as metabolism and epigenetics. Due to the complexity of this circuitry and the relative inaccessibility of the mammalian embryo in utero, mammalian neural commitment remains one of the most challenging and poorly understood areas of developmental biology. In order to generate the nervous system, the embryo first produces two pluripotent populations, the inner cell mass and then the primitive ectoderm. The latter is the cellular substrate for gastrulation from which the three multipotent germ layers form. The germ layer definitive ectoderm, in turn, is the substrate for multipotent neurectoderm (neural plate and neural tube) formation, representing the first morphological signs of nervous system development. Subsequent patterning of the neural tube is then responsible for the formation of most of the central and peripheral nervous systems. While a large number of studies have assessed how a competent neurectoderm produces mature neural cells, less is known about the molecular signatures of definitive ectoderm and neurectoderm and the key molecular mechanisms driving their formation. Using pluripotent stem cells as a model, we will discuss the current understanding of how the pluripotent inner cell mass transitions to pluripotent primitive ectoderm and sequentially to the multipotent definitive ectoderm and neurectoderm. We will focus on the integration of cell signaling, gene activation, and epigenetic control that govern these developmental steps, and provide insight into the novel growth factor-like role that specific amino acids, such as L-proline, play in this process.
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Affiliation(s)
| | | | - Michael B. Morris
- Embryonic Stem Cell Laboratory, Discipline of Physiology, School of Medical Sciences, Bosch Institute, University of Sydney, Sydney, NSW, Australia
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Parey E, Crombach A. Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins. Genome Biol Evol 2019; 11:660-677. [PMID: 30689829 PMCID: PMC6411481 DOI: 10.1093/gbe/evz019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2019] [Indexed: 12/30/2022] Open
Abstract
In the nucleus of eukaryotic cells, genomic DNA associates with numerous protein complexes and RNAs, forming the chromatin landscape. Through a genome-wide study of chromatin-associated proteins in Drosophila cells, five major chromatin types were identified as a refinement of the traditional binary division into hetero- and euchromatin. These five types were given color names in reference to the Greek word chroma. They are defined by distinct but overlapping combinations of proteins and differ in biological and biochemical properties, including transcriptional activity, replication timing, and histone modifications. In this work, we assess the evolutionary relationships of chromatin-associated proteins and present an integrated view of the evolution and conservation of the fruit fly Drosophila melanogaster chromatin landscape. We combine homology prediction across a wide range of species with gene age inference methods to determine the origin of each chromatin-associated protein. This provides insight into the evolution of the different chromatin types. Our results indicate that for the euchromatic types, YELLOW and RED, young associated proteins are more specialized than old ones; and for genes found in either chromatin type, intron/exon structure is lineage-specific. Next, we provide evidence that a subset of GREEN-associated proteins is involved in a centromere drive in D. melanogaster. Our results on BLUE chromatin support the hypothesis that the emergence of Polycomb Group proteins is linked to eukaryotic multicellularity. In light of these results, we discuss how the regulatory complexification of chromatin links to the origins of eukaryotic multicellularity.
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Affiliation(s)
- Elise Parey
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Université Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Anton Crombach
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Université Paris, France.,Inria, Antenne Lyon La Doua, Villeurbanne, France.,Université de Lyon, INSA-Lyon, LIRIS, UMR 5205, Villeurbanne, France
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30
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Pasipoularides A. Clinical-pathological correlations of BAV and the attendant thoracic aortopathies. Part 2: Pluridisciplinary perspective on their genetic and molecular origins. J Mol Cell Cardiol 2019; 133:233-246. [PMID: 31175858 DOI: 10.1016/j.yjmcc.2019.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/10/2019] [Accepted: 05/27/2019] [Indexed: 12/30/2022]
Abstract
Bicuspid aortic valve (BAV) arises during valvulogenesis when 2 leaflets/cusps of the aortic valve (AOV) are fused together. Its clinical manifestations pertain to faulty AOV function, the associated aortopathy, and other complications surveyed in Part 1 of the present bipartite-series. Part 2 examines mainly genetic and epigenetic causes of BAV and BAV-associated aortopathies (BAVAs) and disease syndromes (BAVD). Part 1 explored the heterogeneity among subsets of patients with BAV and BAVA/BAVD, and investigated abnormal fluid dynamic stress and strain patterns sustained by the cusps. Specific BAV morphologies engender systolic outflow asymmetries, associated with abnormal aortic regional wall-shear-stress distributions and the expression/localization of BAVAs. Understanding fluid dynamic factors besides the developmental mechanisms and underlying genetics governing these congenital anomalies is necessary to explain patient predisposition to aortopathy and phenotypic heterogeneity. BAV aortopathy entails complex/multifactorial pathophysiology, involving alterations in genetics, epigenetics, hemodynamics, and in cellular and molecular pathways. There is always an interdependence between organismic developmental signals and genes-no systemic signals, no gene-expression; no active gene, no next step. An apposite signal induces the expression of the next developmental gene, which needs be expressed to trigger the next signal, and so on. Hence, embryonic, then post-partum, AOV and thoracic aortic development comprise cascades of developmental genes and their regulation. Interdependencies between them arise, entailing reciprocal/cyclical mutual interactions and adaptive feedback loops, by which developmental morphogenetic processes self-correct responding to environmental inputs/reactions. This Survey can serve as a reference point and driver for further pluridisciplinary BAV/BAVD studies and their clinical translation.
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Affiliation(s)
- Ares Pasipoularides
- Duke/NSF Center for Emerging Cardiovascular Technologies, Emeritus Faculty of Surgery and of Biomedical Engineering, Duke University School of Medicine and Graduate School, Durham, NC, USA.
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31
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Mahmoudian RA, Bahadori B, Rad A, Abbaszadegan MR, Forghanifard MM. MEIS1 knockdown may promote differentiation of esophageal squamous carcinoma cell line KYSE-30. Mol Genet Genomic Med 2019; 7:e00746. [PMID: 31090196 PMCID: PMC6625128 DOI: 10.1002/mgg3.746] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 04/01/2019] [Accepted: 04/27/2019] [Indexed: 12/11/2022] Open
Abstract
Background MEIS1 (Myeloid ecotropic viral integration site 1), as a homeobox (HOX) transcription factor, has a dual function in different types of cancer. Although numerous roles are proposed for MEIS1 in differentiation, stem cell function, gastrointestinal development and tumorigenesis, the involved molecular mechanisms are poor understood. Our aim in this study was to elucidate the functional correlation between MEIS1, as regulator of differentiation process, and the involved genes in cell differentiation in human esophageal squamous carcinoma (ESC) cell line KYSE‐30. Methods The KYSE‐30 cells were transduced using recombinant retroviral particles containing specific shRNA sequence against MEIS1 to knockdown MEIS1 gene expression. Following RNA extraction and cDNA synthesis, mRNA expression of MEIS1 and the selected genes including TWIST1, EGF, CDX2, and KRT4 was examined using relative comparative real‐time PCR. Results Retroviral transduction caused a significant underexpression of MEIS1 in GFP‐hMEIS1 compared to control GFP cells approximately 5.5‐fold. While knockdown of MEIS1 expression caused a significant decrease in EGF and TWIST1 mRNA expression, nearly ‐8‐ and ‐12‐fold respectively, it caused a significant increase in mRNA expression of differentiation markers including KRT4 and CDX2, approximately 34‐ and 1.14‐fold, correspondingly. Conclusion MEIS1 gene silencing in KYSE‐30 cells increased expression of epithelial markers and decreased expression of epithelial‐mesenchymal transition (EMT) marker TWIST1. It may highlight the role of MEIS1 in differentiation process of KYSE‐30 cells. These results may confirm that MEIS1 silencing promotes differentiation and decreases EMT capability of ESC cell line KYSE‐30.
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Affiliation(s)
| | - Bahareh Bahadori
- Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
| | - Abolfazl Rad
- Cellular and Molecular Research center, Sabzevar Univeristy of Medical Sciences, Sabzevar, Iran
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Rauch A, Haakonsson AK, Madsen JGS, Larsen M, Forss I, Madsen MR, Van Hauwaert EL, Wiwie C, Jespersen NZ, Tencerova M, Nielsen R, Larsen BD, Röttger R, Baumbach J, Scheele C, Kassem M, Mandrup S. Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis. Nat Genet 2019; 51:716-727. [PMID: 30833796 DOI: 10.1038/s41588-019-0359-1] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 01/22/2019] [Indexed: 12/19/2022]
Abstract
Mesenchymal (stromal) stem cells (MSCs) constitute populations of mesodermal multipotent cells involved in tissue regeneration and homeostasis in many different organs. Here we performed comprehensive characterization of the transcriptional and epigenomic changes associated with osteoblast and adipocyte differentiation of human MSCs. We demonstrate that adipogenesis is driven by considerable remodeling of the chromatin landscape and de novo activation of enhancers, whereas osteogenesis involves activation of preestablished enhancers. Using machine learning algorithms for in silico modeling of transcriptional regulation, we identify a large and diverse transcriptional network of pro-osteogenic and antiadipogenic transcription factors. Intriguingly, binding motifs for these factors overlap with SNPs related to bone and fat formation in humans, and knockdown of single members of this network is sufficient to modulate differentiation in both directions, thus indicating that lineage determination is a delicate balance between the activities of many different transcription factors.
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Affiliation(s)
- Alexander Rauch
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Anders K Haakonsson
- Molecular Endocrinology and Stem Cell Research Unit (KMEB), Department of Endocrinology and Metabolism, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jesper G S Madsen
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mette Larsen
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Isabel Forss
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Martin R Madsen
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Elvira L Van Hauwaert
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christian Wiwie
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Naja Z Jespersen
- Centre of Inflammation and Metabolism and Centre for Physical Activity Research, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Danish Diabetes Academy, Odense University Hospital, Odense, Denmark
| | - Michaela Tencerova
- Molecular Endocrinology and Stem Cell Research Unit (KMEB), Department of Endocrinology and Metabolism, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Ronni Nielsen
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Bjørk D Larsen
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.,Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Camilla Scheele
- Centre of Inflammation and Metabolism and Centre for Physical Activity Research, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Moustapha Kassem
- Molecular Endocrinology and Stem Cell Research Unit (KMEB), Department of Endocrinology and Metabolism, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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Liu J, An L, Wang J, Liu Z, Dai Y, Liu Y, Yang L, Du F. Dynamic patterns of H3K4me3, H3K27me3, and Nanog during rabbit embryo development. Am J Transl Res 2019; 11:430-441. [PMID: 30787999 PMCID: PMC6357316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/14/2018] [Indexed: 06/09/2023]
Abstract
Epigenetic modification and expression of key pluripotent factors are critical for development, cell fate determination, and differentiation in early embryos. In this study, we systematically examined the dynamic patterns of histone modifications (H3K4me3 and H3K27me3) and Nanog expression during the development of preimplantation rabbit embryos. Rabbit oocytes, 1-, 2-, 4-, 8-, and 16-cell embryos, morulae, and blastocysts were collected at specific time points following superovulation and assessed for nuclear H3K4me3, H3K27me3, and Nanog expression by immunofluorescence microscopy. The frequency of H3K4me3-positive nuclear staining was highest in oocytes through 4-cell embryos (100%), decreased in 8-cell (97.2%) and 16-cell (94.4%) embryos (P > 0.05), declined dramatically in morulae (86.7%) (1- through 8-cell embryos vs morulae, P < 0.05), and was the lowest in blastocysts (76.2%) (P < 0.05). Nuclear staining of H3K27me3 was negative in oocytes and embryos through the 16-cell stage but was positive in 25.9% of morulae and 34.2% of blastocyst (P < 0.05). Similarly, rabbit oocytes and embryos through the 16-cell stage did not express Nanog, but Nanog was expressed in 24.9% of morulae and 36.5% of blastocysts (P < 0.05). The observed decrease in H3K4me3 and increase in H3K27me3 as development progressed in preimplantation rabbit embryos, together with late Nanog expression, indicates a correlation of these factors with early embryonic cell fate determination and differentiation. Our study provides a specific and dynamic profile of histone modifications and gene expression that will be important for the derivation of rabbit embryonic stem cells and improving rabbit cloning by somatic cell nuclear transfer.
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Affiliation(s)
- Jiao Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
| | - Liyou An
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
| | - Jiqiang Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
| | - Zhihui Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
| | - Yujian Dai
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
| | - Yanhong Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
| | - Lan Yang
- Lannuo Biotechnologies Wuxi Inc.Wuxi 214000, PR China
| | - Fuliang Du
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
- Lannuo Biotechnologies Wuxi Inc.Wuxi 214000, PR China
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The Impact of Epigenetic Signatures on Amniotic Fluid Stem Cell Fate. Stem Cells Int 2018; 2018:4274518. [PMID: 30627172 PMCID: PMC6304862 DOI: 10.1155/2018/4274518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/04/2018] [Indexed: 02/07/2023] Open
Abstract
Epigenetic modifications play a significant role in determining the fate of stem cells and in directing the differentiation into multiple lineages. Current evidence indicates that mechanisms involved in chromatin regulation are essential for maintaining stable cell identities. There is a tight correlation among DNA methylation, histone modifications, and small noncoding RNAs during the epigenetic control of stem cells' differentiation; however, to date, the precise mechanism is still not clear. In this context, amniotic fluid stem cells (AFSCs) represent an interesting model due to their unique features and the possible advantages of their use in regenerative medicine. Recent studies have elucidated epigenetic profiles involved in AFSCs' lineage commitment and differentiation. In order to use these cells effectively for therapeutic purposes, it is necessary to understand the basis of multiple-lineage potential and elaborate in detail how cell fate decisions are made and memorized. The present review summarizes the most recent findings on epigenetic mechanisms of AFSCs with a focus on DNA methylation, histone modifications, and microRNAs (miRNAs) and addresses how their unique signatures contribute to lineage-specific differentiation.
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35
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Tyrovola JB. The "mechanostat" principle in cell differentiation. The osteochondroprogenitor paradigm. J Cell Biochem 2018; 120:37-44. [PMID: 30144147 DOI: 10.1002/jcb.27509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/25/2018] [Indexed: 12/13/2022]
Abstract
The "mechanostat" principle may be depicted as an oscillating signal of a signaling molecule, in which the amplitude, frequency, cumulative level, delay, and duration of the curve encode the information for concrete cellular responses and biological activities. When the oscillating signal is kept sustained (present delay), cell exit may be performed, whereas when the oscillating signal remains robust, cell proliferation may take place. B-catenin-Wnt signaling pathway has a key role in the differentiation of osteochondroprogenitor cells. Sustained downregulation of the β-catenin-Wnt pathway forces osteochondroprogenitors to a chondrogenic fate instead of an osteoblastic one. Other signaling, for example, bone morphogenetic protein and Notch signaling pathways interact with the Wnt pathway. The crosstalk between biochemical and mechanical stimuli produces the final information that leads to the final cell fate decisions, through the "mechanostat" principle.
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Li L, Miu KK, Gu S, Cheung HH, Chan WY. Comparison of multi-lineage differentiation of hiPSCs reveals novel miRNAs that regulate lineage specification. Sci Rep 2018; 8:9630. [PMID: 29941943 PMCID: PMC6018499 DOI: 10.1038/s41598-018-27719-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/07/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are known to be crucial players in governing the differentiation of human induced pluripotent stem cells (hiPSCs). Despite their utter importance, identifying key lineage specifiers among the myriads of expressed miRNAs remains challenging. We believe that the current practice in mining miRNA specifiers via delineating dynamic fold-changes only is inadequate. Our study, therefore, provides evidence to pronounce "lineage specificity" as another important attribute to qualify for these lineage specifiers. Adopted hiPSCs were differentiated into representative lineages (hepatic, nephric and neuronal) over all three germ layers whilst the depicted miRNA expression changes compiled into an integrated atlas. We demonstrated inter-lineage analysis shall aid in the identification of key miRNAs with lineage-specificity, while these shortlisted candidates were collectively known as "lineage-specific miRNAs". Subsequently, we followed through the fold-changes along differentiation via computational analysis to identify miR-192 and miR-372-3p, respectively, as representative candidate key miRNAs for the hepatic and nephric lineages. Indeed, functional characterization validated that miR-192 and miR-372-3p regulate lineage differentiation via modulation of the expressions of lineage-specific genes. In summary, our presented miRNA atlas is a resourceful ore for the mining of key miRNAs responsible for lineage specification.
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Affiliation(s)
- Lu Li
- CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine, School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
- School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Kai-Kei Miu
- CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine, School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Shen Gu
- CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine, School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
- M&H Genetics/Baylor Genetics Laboratories, Baylor College of Medicine, Houston, TX, USA
| | - Hoi-Hung Cheung
- CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine, School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR.
| | - Wai-Yee Chan
- CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine, School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR.
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Akberdin IR, Omelyanchuk NA, Fadeev SI, Leskova NE, Oschepkova EA, Kazantsev FV, Matushkin YG, Afonnikov DA, Kolchanov NA. Pluripotency gene network dynamics: System views from parametric analysis. PLoS One 2018; 13:e0194464. [PMID: 29596533 PMCID: PMC5875786 DOI: 10.1371/journal.pone.0194464] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/02/2018] [Indexed: 01/06/2023] Open
Abstract
Multiple experimental data demonstrated that the core gene network orchestrating self-renewal and differentiation of mouse embryonic stem cells involves activity of Oct4, Sox2 and Nanog genes by means of a number of positive feedback loops among them. However, recent studies indicated that the architecture of the core gene network should also incorporate negative Nanog autoregulation and might not include positive feedbacks from Nanog to Oct4 and Sox2. Thorough parametric analysis of the mathematical model based on this revisited core regulatory circuit identified that there are substantial changes in model dynamics occurred depending on the strength of Oct4 and Sox2 activation and molecular complexity of Nanog autorepression. The analysis showed the existence of four dynamical domains with different numbers of stable and unstable steady states. We hypothesize that these domains can constitute the checkpoints in a developmental progression from naïve to primed pluripotency and vice versa. During this transition, parametric conditions exist, which generate an oscillatory behavior of the system explaining heterogeneity in expression of pluripotent and differentiation factors in serum ESC cultures. Eventually, simulations showed that addition of positive feedbacks from Nanog to Oct4 and Sox2 leads mainly to increase of the parametric space for the naïve ESC state, in which pluripotency factors are strongly expressed while differentiation ones are repressed.
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Affiliation(s)
- Ilya R. Akberdin
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- San Diego State University, San Diego, CA, United States of America
| | - Nadezda A. Omelyanchuk
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Stanislav I. Fadeev
- Novosibirsk State University, Novosibirsk, Russia
- Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
| | - Natalya E. Leskova
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Evgeniya A. Oschepkova
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Fedor V. Kazantsev
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Yury G. Matushkin
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Dmitry A. Afonnikov
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Nikolay A. Kolchanov
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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Spitalieri P, Talarico RV, Caioli S, Murdocca M, Serafino A, Girasole M, Dinarelli S, Longo G, Pucci S, Botta A, Novelli G, Zona C, Mango R, Sangiuolo F. Modelling the pathogenesis of Myotonic Dystrophy type 1 cardiac phenotype through human iPSC-derived cardiomyocytes. J Mol Cell Cardiol 2018; 118:95-109. [PMID: 29551391 DOI: 10.1016/j.yjmcc.2018.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/12/2018] [Accepted: 03/14/2018] [Indexed: 12/20/2022]
Abstract
Myotonic Dystrophy type 1 (DM1) is a multisystemic disease, autosomal dominant, caused by a CTG repeat expansion in DMPK gene. We assessed the appropriateness of patient-specific induced pluripotent stem cell-derived cardiomyocytes (CMs) as a model to recapitulate some aspects of the pathogenetic mechanism involving cardiac manifestations in DM1 patients. Once obtained in vitro, CMs have been characterized for their morphology and their functionality. CMs DM1 show intranuclear foci and transcript markers abnormally spliced respect to WT ones, as well as several irregularities in nuclear morphology, probably caused by an unbalanced lamin A/C ratio. Electrophysiological characterization evidences an abnormal profile only in CMs DM1 such that the administration of antiarrythmic drugs to these cells highlights even more the functional defect linked to the disease. Finally, Atomic Force Measurements reveal differences in the biomechanical behaviour of CMs DM1, in terms of frequencies and synchronicity of the beats. Altogether the complex phenotype described in this work, strongly reproduces some aspects of the human DM1 cardiac phenotype. Therefore, the present study provides an in vitro model suggesting novel insights into the mechanisms leading to the development of arrhythmogenesis and dilatative cardiomyopathy to consider when approaching to DM1 patients, especially for the risk assessment of sudden cardiac death (SCD). These data could be also useful in identifying novel biomarkers effective in clinical settings and patient-tailored therapies.
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Affiliation(s)
- Paola Spitalieri
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Rosa V Talarico
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | | | - Michela Murdocca
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | | | | | | | | | - Sabina Pucci
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Annalisa Botta
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Giuseppe Novelli
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Cristina Zona
- I.R.C.C.S. S. Lucia, Rome, Italy; Dept of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | - Federica Sangiuolo
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy.
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39
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Ferreira AF, Calin GA, Picanço-Castro V, Kashima S, Covas DT, de Castro FA. Hematopoietic stem cells from induced pluripotent stem cells - considering the role of microRNA as a cell differentiation regulator. J Cell Sci 2018; 131:131/4/jcs203018. [PMID: 29467236 DOI: 10.1242/jcs.203018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although hematopoietic stem cell (HSC) therapy for hematological diseases can lead to a good outcome from the clinical point of view, the limited number of ideal donors, the comorbidity of patients and the increasing number of elderly patients may limit the application of this therapy. HSCs can be generated from induced pluripotent stem cells (iPSCs), which requires the understanding of the bone marrow and liver niches components and function in vivo iPSCs have been extensively applied in several studies involving disease models, drug screening and cellular replacement therapies. However, the somatic reprogramming by transcription factors is a low-efficiency process. Moreover, the reprogramming process is also regulated by microRNAs (miRNAs), which modulate the expression of the transcription factors OCT-4 (also known as POU5F1), SOX-2, KLF-4 and MYC, leading somatic cells to a pluripotent state. In this Review, we present an overview of the challenges of cell reprogramming protocols with regard to HSC generation from iPSCs, and highlight the potential role of miRNAs in cell reprogramming and in the differentiation of induced pluripotent stem cells.
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Affiliation(s)
- Aline F Ferreira
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences, University of São Paulo (USP), Ribeirão Preto, São Paulo 14040-903, Brazil
| | - George A Calin
- Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Virgínia Picanço-Castro
- Center of Cell Therapy, Regional Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo 14051-140, Brazil
| | - Simone Kashima
- Center of Cell Therapy, Regional Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo 14051-140, Brazil
| | - Dimas T Covas
- Center of Cell Therapy, Regional Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo 14051-140, Brazil.,Department of Internal Medicine, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Fabiola A de Castro
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences, University of São Paulo (USP), Ribeirão Preto, São Paulo 14040-903, Brazil
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40
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Lee K, Park OS, Seo PJ. Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation. Sci Signal 2017; 10:10/507/eaan0316. [PMID: 29184030 DOI: 10.1126/scisignal.aan0316] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular dedifferentiation, the transition of differentiated somatic cells to pluripotent stem cells, ensures developmental plasticity and contributes to wound healing in plants. Wounding induces cells to form a mass of unorganized pluripotent cells called callus at the wound site. Explanted cells can also form callus tissues in vitro. Reversible cellular differentiation-dedifferentiation processes in higher eukaryotes are controlled mainly by chromatin modifications. We demonstrate that ARABIDOPSIS TRITHORAX-RELATED 2 (ATXR2), a histone lysine methyltransferase that promotes the accumulation of histone H3 proteins that are trimethylated on lysine 36 (H3K36me3) during callus formation, promotes early stages of cellular dedifferentiation through activation of LATERAL ORGAN BOUNDARIES DOMAIN (LBD) genes. The LBD genes of Arabidopsis thaliana are activated during cellular dedifferentiation to enhance the formation of callus. Leaf explants from Arabidopsis atxr2 mutants exhibited a reduced ability to form callus and a substantial reduction in LBD gene expression. ATXR2 bound to the promoters of LBD genes and was required for the deposition of H3K36me3 at these promoters. ATXR2 was recruited to LBD promoters by the transcription factors AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19. Leaf explants from arf7-1arf19-2 double mutants were defective in callus formation and showed reduced H3K36me3 accumulation at LBD promoters. Genetic analysis provided further support that ARF7 and ARF19 were required for the ability of ATXR2 to promote the expression of LBD genes. These observations indicate that the ATXR2-ARF-LBD axis is key for the epigenetic regulation of callus formation in Arabidopsis.
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Affiliation(s)
- Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ok-Sun Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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41
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Sala L, Bellin M, Mummery CL. Integrating cardiomyocytes from human pluripotent stem cells in safety pharmacology: has the time come? Br J Pharmacol 2017; 174:3749-3765. [PMID: 27641943 PMCID: PMC5647193 DOI: 10.1111/bph.13577] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 07/27/2016] [Accepted: 08/11/2016] [Indexed: 12/20/2022] Open
Abstract
Cardiotoxicity is a severe side effect of drugs that induce structural or electrophysiological changes in heart muscle cells. As a result, the heart undergoes failure and potentially lethal arrhythmias. It is still a major reason for drug failure in preclinical and clinical phases of drug discovery. Current methods for predicting cardiotoxicity are based on guidelines that combine electrophysiological analysis of cell lines expressing ion channels ectopically in vitro with animal models and clinical trials. Although no new cases of drugs linked to lethal arrhythmias have been reported since the introduction of these guidelines in 2005, their limited predictive power likely means that potentially valuable drugs may not reach clinical practice. Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are now emerging as potentially more predictive alternatives, particularly for the early phases of preclinical research. However, these cells are phenotypically immature and culture and assay methods not standardized, which could be a hurdle to the development of predictive computational models and their implementation into the drug discovery pipeline, in contrast to the ambitions of the comprehensive pro-arrhythmia in vitro assay (CiPA) initiative. Here, we review present and future preclinical cardiotoxicity screening and suggest possible hPSC-CM-based strategies that may help to move the field forward. Coordinated efforts by basic scientists, companies and hPSC banks to standardize experimental conditions for generating reliable and reproducible safety indices will be helpful not only for cardiotoxicity prediction but also for precision medicine. LINKED ARTICLES This article is part of a themed section on New Insights into Cardiotoxicity Caused by Chemotherapeutic Agents. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.21/issuetoc.
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Affiliation(s)
- Luca Sala
- Department of Anatomy and EmbryologyLeiden University Medical CenterLeidenZAThe Netherlands
| | - Milena Bellin
- Department of Anatomy and EmbryologyLeiden University Medical CenterLeidenZAThe Netherlands
| | - Christine L Mummery
- Department of Anatomy and EmbryologyLeiden University Medical CenterLeidenZAThe Netherlands
- Department of Applied Stem Cell TechnologiesUniversity of TwenteEnschedeThe Netherlands
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42
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Vaghjiani V, Cain JE, Lee W, Vaithilingam V, Tuch BE, St John JC. Modulation of Mitochondrial DNA Copy Number to Induce Hepatocytic Differentiation of Human Amniotic Epithelial Cells. Stem Cells Dev 2017; 26:1505-1519. [PMID: 28756741 DOI: 10.1089/scd.2017.0041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial deoxyribonucleic acid (mtDNA) copy number is tightly regulated during pluripotency and differentiation. There is increased demand of cellular adenosine triphosphate (ATP) during differentiation for energy-intensive cell types such as hepatocytes and neurons to meet the cell's functional requirements. During hepatocyte differentiation, mtDNA copy number should be synchronously increased to generate sufficient ATP through oxidative phosphorylation. Unlike bone marrow mesenchymal cells, mtDNA copy number failed to increase by 28 days of differentiation of human amniotic epithelial cells (hAEC) into hepatocyte-like cells (HLC) despite their expression of some end-stage hepatic markers. This was due to higher levels of DNA methylation at exon 2 of POLGA, the mtDNA-specific replication factor. Treatment with a DNA demethylation agent, 5-azacytidine, resulted in increased mtDNA copy number, reduced DNA methylation at exon 2 of POLGA, and reduced hepatic gene expression. Depletion of mtDNA followed by subsequent differentiation did not increase mtDNA copy number, but reduced DNA methylation at exon 2 of POLGA and increased expression of hepatic and pluripotency genes. We encapsulated hAEC in barium alginate microcapsules and subsequently differentiated them into HLC. Encapsulation resulted in no net increase of mtDNA copy number but a significant reduction in DNA methylation of POLGA. RNAseq analysis showed that differentiated HLC express hepatocyte-specific genes but also increased expression of inflammatory interferon genes. Differentiation in encapsulated cells showed suppression of inflammatory genes as well as increased expression of genes associated with hepatocyte function pathways and networks. This study demonstrates that an increase in classical hepatic gene expression can be achieved in HLC through encapsulation, although they fail to effectively regulate mtDNA copy number.
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Affiliation(s)
- Vijesh Vaghjiani
- 1 Centre for Genetic Diseases, Hudson Institute of Medical Research , Clayton, Australia .,2 Department of Molecular and Translational Science, Monash University , Clayton, Australia
| | - Jason E Cain
- 2 Department of Molecular and Translational Science, Monash University , Clayton, Australia .,3 Centre for Cancer Research, Hudson Institute of Medical Research , Clayton, Australia
| | - William Lee
- 1 Centre for Genetic Diseases, Hudson Institute of Medical Research , Clayton, Australia .,2 Department of Molecular and Translational Science, Monash University , Clayton, Australia
| | - Vijayaganapathy Vaithilingam
- 4 Future Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation , North Ryde, Australia
| | - Bernard E Tuch
- 4 Future Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation , North Ryde, Australia .,5 School of Biomedical Science, Discipline Physiology, University of Sydney , Sydney, Australia
| | - Justin C St John
- 1 Centre for Genetic Diseases, Hudson Institute of Medical Research , Clayton, Australia .,2 Department of Molecular and Translational Science, Monash University , Clayton, Australia
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43
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HPV16-E2 protein modifies self-renewal and differentiation rate in progenitor cells of human immortalized keratinocytes. Virol J 2017; 14:65. [PMID: 28372578 PMCID: PMC5376701 DOI: 10.1186/s12985-017-0736-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/23/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Cervical cancer is the fourth cause of death worldwide by cancer in women and is a disease associated to persistent infection with human papillomavirus (HPV), particularly from two high-risk types HPV16 and 18. The virus initiates its replicative cycle infecting cells located in the basal layer of the epithelium, where a small population of epithelial stem cells is located performing important functions of renewal and maintenance of the tissue. Viral E2 gene is one of the first expressed after infection and plays relevant roles in the replicative cycle of the virus, modifying fundamental processes in the infected cells. Thus, the aim of the present study was to demonstrate the presence of hierarchic subpopulations in HaCaT cell line and evaluate the effect of HPV16-E2 expression, on their biological processes. METHODS HaCaT-HPV16-E2 cells were generated by transduction of HaCaT cell line with a lentiviral vector. The α6-integrin-CD71 expression profile was established by immunostaining and flow cytometric analysis. After sorting, cell subpopulations were analyzed in biological assays for self-renewal, clonogenicity and expression of stemness factors (RT-qPCR). RESULTS We identified in HaCaT cell line three different subpopulations that correspond to early differentiated cells (α6-integrindim), transitory amplifying cells (α6-integrinbri/CD71bri) and progenitor cells (α6-integrinbri/CD71dim). The last subpopulation showed stem cell characteristics, such as self-renewal ability, clonogenicity and expression of the well-known stem cell factors SOX2, OCT4 and NANOG, suggesting they are stem-like cells. Interestingly, the expression of HPV16-E2 in HaCaT cells changed its α6-integrin-CD71 immunophenotype modifying the relative abundance of the cell subpopulations, reducing significantly the percentage of α6-integrinbri/CD71dim cells. Moreover, the expression of the stem cell markers was also modified, increasing the expression of SOX2 and NANOG, but decreasing notably the expression of OCT4. CONCLUSIONS Our data demonstrated the presence of a small subpopulation with epithelial "progenitor cells" characteristics in the HaCaT cell line, and that HPV16-E2 expression on these cells induces early differentiation.
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44
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Liu L. Linking Telomere Regulation to Stem Cell Pluripotency. Trends Genet 2016; 33:16-33. [PMID: 27889084 DOI: 10.1016/j.tig.2016.10.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 10/18/2016] [Accepted: 10/31/2016] [Indexed: 12/31/2022]
Abstract
Embryonic stem cells (ESCs), somatic cell nuclear transfer ESCs, and induced pluripotent stem cells (iPSCs) represent the most studied group of PSCs. Unlimited self-renewal without incurring chromosomal instability and pluripotency are essential for the potential use of PSCs in regenerative therapy. Telomere length maintenance is critical for the unlimited self-renewal, pluripotency, and chromosomal stability of PSCs. While telomerase has a primary role in telomere maintenance, alternative lengthening of telomere pathways involving recombination and epigenetic modifications are also required for telomere length regulation, notably in mouse PSCs. Telomere rejuvenation is part of epigenetic reprogramming to pluripotency. Insights into telomere reprogramming and maintenance in PSCs may have implications for understanding of aging and tumorigenesis. Here, I discuss the link between telomere elongation and homeostasis to the acquisition and maintenance of stem cell pluripotency, and their regulatory mechanisms by epigenetic modifications.
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Affiliation(s)
- Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Sciences, Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin 300071, China.
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45
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Cho KH, Joo JI, Shin D, Kim D, Park SM. The reverse control of irreversible biological processes. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2016; 8:366-77. [PMID: 27327189 PMCID: PMC5094504 DOI: 10.1002/wsbm.1346] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/16/2016] [Accepted: 04/28/2016] [Indexed: 12/17/2022]
Abstract
Most biological processes have been considered to be irreversible for a long time, but some recent studies have shown the possibility of their reversion at a cellular level. How can we then understand the reversion of such biological processes? We introduce a unified conceptual framework based on the attractor landscape, a molecular phase portrait describing the dynamics of a molecular regulatory network, and the phenotype landscape, a map of phenotypes determined by the steady states of particular output molecules in the attractor landscape. In this framework, irreversible processes involve reshaping of the phenotype landscape, and the landscape reshaping causes the irreversibility of processes. We suggest reverse control by network rewiring which changes network dynamics with constant perturbation, resulting in the restoration of the original phenotype landscape. The proposed framework provides a conceptual basis for the reverse control of irreversible biological processes through network rewiring. WIREs Syst Biol Med 2016, 8:366–377. doi: 10.1002/wsbm.1346 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Kwang-Hyun Cho
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jae Il Joo
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Dongkwan Shin
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Dongsan Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sang-Min Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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46
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Pfeuty B, Kaneko K. Requirements for efficient cell-type proportioning: regulatory timescales, stochasticity and lateral inhibition. Phys Biol 2016; 13:026007. [PMID: 27172110 DOI: 10.1088/1478-3975/13/2/026007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell types. This developmental differentiation process typically involves intracellular regulatory and stochastic mechanisms to generate cell-fate diversity as well as intercellular signaling mechanisms to coordinate cell-fate decisions at tissue level. We thus surmise that key insights about the developmental regulation of cell-type proportion can be captured by the modeling study of clustering dynamics in population of inhibitory-coupled noisy bistable systems. This general class of dynamical system is shown to exhibit a very stable two-cluster state, but also metastability, collective oscillations or noise-induced state hopping, which can prevent from timely and reliably reaching a robust and well-proportioned clustered state. To circumvent these obstacles or to avoid fine-tuning, we highlight a general strategy based on dual-time positive feedback loops, such as mediated through transcriptional versus epigenetic mechanisms, which improves proportion regulation by coordinating early and flexible lineage priming with late and firm commitment. This result sheds new light on the respective and cooperative roles of multiple regulatory feedback, stochasticity and lateral inhibition in developmental dynamics.
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Affiliation(s)
- B Pfeuty
- Université de Lille, CNRS, Laboratoire de Physique des Lasers, Atomes, et Molécules, F-59000, Lille, France
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47
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Zhao X, Ouyang Q, Wang H. Designing a stochastic genetic switch by coupling chaos and bistability. CHAOS (WOODBURY, N.Y.) 2015; 25:113112. [PMID: 26627572 DOI: 10.1063/1.4936087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In stem cell differentiation, a pluripotent stem cell becomes progressively specialized and generates specific cell types through a series of epigenetic processes. How cells can precisely determine their fate in a fluctuating environment is a currently unsolved problem. In this paper, we suggest an abstract gene regulatory network to describe mathematically the differentiation phenomenon featuring stochasticity, divergent cell fates, and robustness. The network consists of three functional motifs: an upstream chaotic motif, a buffering motif of incoherent feed forward loop capable of generating a pulse, and a downstream motif which is bistable. The dynamic behavior is typically a transient chaos with fractal basin boundaries. The trajectories take transiently chaotic journeys before divergently settling down to the bistable states. The ratio of the probability that the high state is achieved to the probability that the low state is reached can maintain a constant in a population of cells with varied molecular fluctuations. The ratio can be turned up or down when proper parameters are adjusted. The model suggests a possible mechanism for the robustness against fluctuations that is prominently featured in pluripotent cell differentiations and developmental phenomena.
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Affiliation(s)
- Xiang Zhao
- State Key Laboratory for Mesoscopic Physics and School of Physics, Peking University, Beijing 100871, China
| | - Qi Ouyang
- State Key Laboratory for Mesoscopic Physics and School of Physics, Peking University, Beijing 100871, China
| | - Hongli Wang
- State Key Laboratory for Mesoscopic Physics and School of Physics, Peking University, Beijing 100871, China
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