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Ding LN, Yu YY, Ma CJ, Lei CJ, Zhang HB. SOX2-associated signaling pathways regulate biological phenotypes of cancers. Biomed Pharmacother 2023; 160:114336. [PMID: 36738502 DOI: 10.1016/j.biopha.2023.114336] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
SOX2 is a transcription factor involved in multiple stages of embryonic development. In related reports, SOX2 was found to be abnormally expressed in tumor tissues and correlated with clinical features such as TNM staging, tumor grade, and prognosis in patients with various cancer types. In most cancer types, SOX2 is a tumor-promoting factor that regulates tumor progression and metastasis primarily by maintaining the stemness of cancer cells. In addition, SOX2 also regulates the proliferation, apoptosis, invasion, migration, ferroptosis and drug resistance of cancer cells. However, SOX2 acts as a tumor suppressor in some cases in certain cancer types, such as gastric and lung cancer. These key regulatory functions of SOX2 involve complex regulatory networks, including protein-protein and protein-nucleic acid interactions through signaling pathways and noncoding RNA interactions, modulating SOX2 expression may be a potential therapeutic strategy for clinical cancer patients. Therefore, we sorted out the phenotypes related to SOX2 in cancer, hoping to provide a basis for further clinical translation.
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Affiliation(s)
- L N Ding
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Y Y Yu
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Oncology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - C J Ma
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Oncology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - C J Lei
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - H B Zhang
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Oncology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, China; Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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2
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Salas S, Ng N, Gerami-Naini B, Anchan RM. Induced Pluripotent Stem Cells from Ovarian Tissue. ACTA ACUST UNITED AC 2017; 95:21.10.1-21.10.22. [PMID: 29044473 DOI: 10.1002/cphg.47] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Yamanaka and colleagues revolutionized stem cell biology and regenerative medicine by observing that somatic cells can be reprogrammed into pluripotent stem cells. Evidence indicates that induced pluripotent stem (iPS) cells retain epigenetic memories that bias their spontaneous differentiation into the originating somatic cell type, therefore epigenetic memory may be exploited to improve tissue specific regeneration. We recently showed that iPS cells reprogrammed from ovarian granulosa cells using mouse and human tissue overwhelmingly differentiate homotypically into ovarian steroidogenic and primordial germ cells. Herein we detail a protocol for the culture of human ovarian granulosa cells. We review approaches for reprogramming human ovarian granulosa cells into iPS cells. Standard methods to induce pluripotency are outlined, concentrating on integrative retroviruses. Additionally, alternative protocols for lentivirus and Sendai virus are provided. Each approach has inherent limitations, such as reprogramming efficiency, insertional mutagenesis, and partial reprogramming. Major advances continue to be made in somatic cell reprogramming to identify an optimal approach and utilization in cell-based therapies. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Sophia Salas
- Department of Obstetrics, Gynecology and Reproductive Biology, Division of Reproductive Endocrinology and Infertility, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nicholas Ng
- Department of Obstetrics, Gynecology and Reproductive Biology, Division of Reproductive Endocrinology and Infertility, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Raymond M Anchan
- Department of Obstetrics, Gynecology and Reproductive Biology, Division of Reproductive Endocrinology and Infertility, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Harvard Stem Cell Institute, Cambridge, Massachusetts
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3
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Goeppert B, Roessler S, Becker N, Zucknick M, Vogel MN, Warth A, Pathil-Warth A, Mehrabi A, Schirmacher P, Mollenhauer J, Renner M. DMBT1 expression in biliary carcinogenesis with correlation of clinicopathological data. Histopathology 2017; 70:1064-1071. [PMID: 28130841 DOI: 10.1111/his.13175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 01/18/2017] [Accepted: 01/24/2017] [Indexed: 12/31/2022]
Abstract
AIMS Deleted in malignant brain tumours 1 (DMBT1) exerts functions in the regulation of epithelial differentiation and inflammation and has been proposed as a tumour suppressor. Because chronic inflammation is a hallmark of cholangiocarcinogenesis, the aim of this study was to investigate the expression of DMBT1 in biliary tract cancer (BTC) and to correlate this expression with clinicopathological data. METHODS AND RESULTS The expression of DMBT1 protein was examined immunohistochemically in 157 BTC patients [41 intrahepatic (ICC), 60 extrahepatic cholangiocarcinomas (ECC) and 56 adenocarcinomas of the gallbladder (GBAC)]. Additionally, 56 samples of high-grade biliary intraepithelial neoplasia (BilIN 3) and 92 corresponding samples of histological non-neoplastic biliary tract tissues were included. DMBT1 expression was increased significantly in BilIN 3 compared to normal tissue (P < 0.0001) and BTC (P < 0.0001). BTC showed no significant difference in DMBT1 expression compared to non-neoplastic biliary tissue (P = 0.315). Absent DMBT1 expression in non-neoplastic biliary tissue of BTC patients was associated with poorer survival (P = 0.027). DMBT1 expression was correlated significantly with patients' age (P < 0.001). CONCLUSION DMBT1 is expressed differently in cholangiocarcinogenesis and poorer patients' survival rates are associated with absent DMBT1 expression in non-neoplastic biliary tissue, suggesting a tumour-suppressive role of DMBT1 in early cholangiocarcinogenesis.
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Affiliation(s)
| | | | - Natalia Becker
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manuela Zucknick
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Oslo Center for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Monika N Vogel
- Diagnostic and Interventional Radiology, Thoraxklinik, University Hospital Heidelberg, Germany
| | - Arne Warth
- Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Anita Pathil-Warth
- Department of Internal Medicine IV, Gastroenterology and Hepatology, University Hospital Heidelberg, Germany
| | - Arianeb Mehrabi
- Department of General Visceral and Transplantation Surgery, University Hospital Heidelberg, Germany
| | | | - Jan Mollenhauer
- Molecular Oncology and Lundbeckfonden Center of Excellence NanoCAN, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Marcus Renner
- Institute of Pathology, University Hospital, Heidelberg, Germany
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4
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Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proc Natl Acad Sci U S A 2014; 111:E5643-50. [PMID: 25512504 DOI: 10.1073/pnas.1408993111] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We present single-cell clustering using bifurcation analysis (SCUBA), a novel computational method for extracting lineage relationships from single-cell gene expression data and modeling the dynamic changes associated with cell differentiation. SCUBA draws techniques from nonlinear dynamics and stochastic differential equation theories, providing a systematic framework for modeling complex processes involving multilineage specifications. By applying SCUBA to analyze two complementary, publicly available datasets we successfully reconstructed the cellular hierarchy during early development of mouse embryos, modeled the dynamic changes in gene expression patterns, and predicted the effects of perturbing key transcriptional regulators on inducing lineage biases. The results were robust with respect to experimental platform differences between RT-PCR and RNA sequencing. We selectively tested our predictions in Nanog mutants and found good agreement between SCUBA predictions and the experimental data. We further extended the utility of SCUBA by developing a method to reconstruct missing temporal-order information from a typical single-cell dataset. Analysis of a hematopoietic dataset suggests that our method is effective for reconstructing gene expression dynamics during human B-cell development. In summary, SCUBA provides a useful single-cell data analysis tool that is well-suited for the investigation of developmental processes.
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Abstract
The transcription factor Sox2 is a master regulator that maintains stemness in embryonic stem cells and neural stem cells. Using elegant lineage tracing strategies and genetic reporter mouse models, two studies (one of which is by Vanner and colleagues in this issue of Cancer Cell) now demonstrate that rare Sox2-expressing cells are the founding cancer stem cell population driving tumor initiation and therapy resistance.
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Affiliation(s)
- Wai Leong Tam
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; MIT Ludwig Center for Molecular Oncology, Cambridge, MA 02139, USA.
| | - Huck Hui Ng
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
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6
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Renner M, Wolf T, Meyer H, Hartmann W, Penzel R, Ulrich A, Lehner B, Hovestadt V, Czwan E, Egerer G, Schmitt T, Alldinger I, Renker EK, Ehemann V, Eils R, Wardelmann E, Büttner R, Lichter P, Brors B, Schirmacher P, Mechtersheimer G. Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas. Genome Biol 2013; 14:r137. [PMID: 24345474 PMCID: PMC4054884 DOI: 10.1186/gb-2013-14-12-r137] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 12/17/2013] [Indexed: 12/13/2022] Open
Abstract
Background High-grade soft tissue sarcomas are a heterogeneous, complex group of aggressive malignant tumors showing mesenchymal differentiation. Recently, soft tissue sarcomas have increasingly been classified on the basis of underlying genetic alterations; however, the role of aberrant DNA methylation in these tumors is not well understood and, consequently, the usefulness of methylation-based classification is unclear. Results We used the Infinium HumanMethylation27 platform to profile DNA methylation in 80 primary, untreated high-grade soft tissue sarcomas, representing eight relevant subtypes, two non-neoplastic fat samples and 14 representative sarcoma cell lines. The primary samples were partitioned into seven stable clusters. A classification algorithm identified 216 CpG sites, mapping to 246 genes, showing different degrees of DNA methylation between these seven groups. The differences between the clusters were best represented by a set of eight CpG sites located in the genes SPEG, NNAT, FBLN2, PYROXD2, ZNF217, COL14A1, DMRT2 and CDKN2A. By integrating DNA methylation and mRNA expression data, we identified 27 genes showing negative and three genes showing positive correlation. Compared with non-neoplastic fat, NNAT showed DNA hypomethylation and inverse gene expression in myxoid liposarcomas, and DNA hypermethylation and inverse gene expression in dedifferentiated and pleomorphic liposarcomas. Recovery of NNAT in a hypermethylated myxoid liposarcoma cell line decreased cell migration and viability. Conclusions Our analysis represents the first comprehensive integration of DNA methylation and transcriptional data in primary high-grade soft tissue sarcomas. We propose novel biomarkers and genes relevant for pathogenesis, including NNAT as a potential tumor suppressor in myxoid liposarcomas.
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Wierstra I. The transcription factor FOXM1 (Forkhead box M1): proliferation-specific expression, transcription factor function, target genes, mouse models, and normal biological roles. Adv Cancer Res 2013; 118:97-398. [PMID: 23768511 DOI: 10.1016/b978-0-12-407173-5.00004-2] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
FOXM1 (Forkhead box M1) is a typical proliferation-associated transcription factor, which stimulates cell proliferation and exhibits a proliferation-specific expression pattern. Accordingly, both the expression and the transcriptional activity of FOXM1 are increased by proliferation signals, but decreased by antiproliferation signals, including the positive and negative regulation by protooncoproteins or tumor suppressors, respectively. FOXM1 stimulates cell cycle progression by promoting the entry into S-phase and M-phase. Moreover, FOXM1 is required for proper execution of mitosis. Accordingly, FOXM1 regulates the expression of genes, whose products control G1/S-transition, S-phase progression, G2/M-transition, and M-phase progression. Additionally, FOXM1 target genes encode proteins with functions in the execution of DNA replication and mitosis. FOXM1 is a transcriptional activator with a forkhead domain as DNA binding domain and with a very strong acidic transactivation domain. However, wild-type FOXM1 is (almost) inactive because the transactivation domain is repressed by three inhibitory domains. Inactive FOXM1 can be converted into a very potent transactivator by activating signals, which release the transactivation domain from its inhibition by the inhibitory domains. FOXM1 is essential for embryonic development and the foxm1 knockout is embryonically lethal. In adults, FOXM1 is important for tissue repair after injury. FOXM1 prevents premature senescence and interferes with contact inhibition. FOXM1 plays a role for maintenance of stem cell pluripotency and for self-renewal capacity of stem cells. The functions of FOXM1 in prevention of polyploidy and aneuploidy and in homologous recombination repair of DNA-double-strand breaks suggest an importance of FOXM1 for the maintenance of genomic stability and chromosomal integrity.
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Binas B, Verfaillie CM. Concise review: Bone marrow meets blastocyst: lessons from an unlikely encounter. Stem Cells 2013; 31:620-6. [PMID: 23169605 DOI: 10.1002/stem.1287] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/28/2012] [Indexed: 12/17/2022]
Abstract
This article discusses the implications of the recent discovery that rat bone marrow-derived multipotent adult progenitor cells (rMAPCs), a cell type with broad somatic differentiation potential but of uncertain lineage identity, are similar to rat blastocyst-derived extraembryonic endoderm precursor (rXENP) cells, which appear to represent the committed extraembryonic endoderm precursor of the blastocyst. It was found that under rMAPC culture conditions, rXENP cells can be homogeneously cultured and similar cells, named rat hypoblast stem cells (rHypoSCs), can be derived from rat blastocysts more rapidly and directly. The detailed comparison of rHypoSCs, rXENP cells, and rMAPCs revealed highly similar gene expression profiles and developmental potentials. The significance of these findings for embryology, stem cell biology, and medicine is discussed. Specifically, the results assign a lineage identity to rMAPCs, indicate that rMAPCs originated by environmental reprogramming, and imply that HypoSCs, XENP cells, and MAPCs possess lineage plasticity. The MAPC-HypoSC relation also strengthens the consistency of rat and mouse embryology and consequently the idea that HypoSCs represent the committed extraembryonic endoderm precursor of the blastocyst. On this basis, it is argued that the direct comparison of HypoSCs (now available in pure form) with embryonic stem cells will be highly useful for the understanding of pluripotency and plasticity. Finally, the new findings suggest an explanation for an obscure observation on stem cell-induced transplantation tolerance. Thus, the HypoSC/XENP/MAPC phenotype provides a unique but broadly instructive model with which to study stem cell plasticity, reprogramming, and transplantation tolerance, all central themes in regenerative medicine.
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Affiliation(s)
- Bert Binas
- Division of Molecular and Life Science, Hanyang University, Kyeonggi-do, South Korea.
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Gonzales KAU, Ng HH. Driving pluripotency and reprogramming: nuclear receptors at the helm. Semin Cell Dev Biol 2013; 24:670-8. [PMID: 23916717 DOI: 10.1016/j.semcdb.2013.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 07/16/2013] [Accepted: 07/21/2013] [Indexed: 01/30/2023]
Abstract
The identity of a cell is determined by the concerted interplay of multiple molecular modulators such as transcription factors, chromatin modifiers and signalling mediators. Among these, the transcriptional circuitry holds great influence on the specification and maintenance of a cellular state, and its perturbation can trigger a transition to another cell state. This is particularly striking in the field of pluripotency, where tempering the expression levels of one or few transcription factors is sufficient to induce the loss or acquisition of the pluripotent state. Recently, nuclear receptors, a class of transcription factors, have emerged as major players in the molecular network governing pluripotency. In this review, we discuss the importance of nuclear receptors in embryonic stem cell self-renewal, differentiation and cellular reprogramming, highlighting recent discoveries as well as providing an outlook in stem cell and nuclear receptor research.
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Affiliation(s)
- Kevin Andrew Uy Gonzales
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore.
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Wierstra I. FOXM1 (Forkhead box M1) in tumorigenesis: overexpression in human cancer, implication in tumorigenesis, oncogenic functions, tumor-suppressive properties, and target of anticancer therapy. Adv Cancer Res 2013; 119:191-419. [PMID: 23870513 DOI: 10.1016/b978-0-12-407190-2.00016-2] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
FOXM1 (Forkhead box M1) is a typical proliferation-associated transcription factor and is also intimately involved in tumorigenesis. FOXM1 stimulates cell proliferation and cell cycle progression by promoting the entry into S-phase and M-phase. Additionally, FOXM1 is required for proper execution of mitosis. In accordance with its role in stimulation of cell proliferation, FOXM1 exhibits a proliferation-specific expression pattern and its expression is regulated by proliferation and anti-proliferation signals as well as by proto-oncoproteins and tumor suppressors. Since these factors are often mutated, overexpressed, or lost in human cancer, the normal control of the foxm1 expression by them provides the basis for deregulated FOXM1 expression in tumors. Accordingly, FOXM1 is overexpressed in many types of human cancer. FOXM1 is intimately involved in tumorigenesis, because it contributes to oncogenic transformation and participates in tumor initiation, growth, and progression, including positive effects on angiogenesis, migration, invasion, epithelial-mesenchymal transition, metastasis, recruitment of tumor-associated macrophages, tumor-associated lung inflammation, self-renewal capacity of cancer cells, prevention of premature cellular senescence, and chemotherapeutic drug resistance. However, in the context of urethane-induced lung tumorigenesis, FOXM1 has an unexpected tumor suppressor role in endothelial cells because it limits pulmonary inflammation and canonical Wnt signaling in epithelial lung cells, thereby restricting carcinogenesis. Accordingly, FOXM1 plays a role in homologous recombination repair of DNA double-strand breaks and maintenance of genomic stability, that is, prevention of polyploidy and aneuploidy. The implication of FOXM1 in tumorigenesis makes it an attractive target for anticancer therapy, and several antitumor drugs have been reported to decrease FOXM1 expression.
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Neumann O, Kesselmeier M, Geffers R, Pellegrino R, Radlwimmer B, Hoffmann K, Ehemann V, Schemmer P, Schirmacher P, Lorenzo Bermejo J, Longerich T. Methylome analysis and integrative profiling of human HCCs identify novel protumorigenic factors. Hepatology 2012; 56:1817-27. [PMID: 22689435 DOI: 10.1002/hep.25870] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/22/2012] [Indexed: 12/16/2022]
Abstract
UNLABELLED To identify new tumor-suppressor gene candidates relevant for human hepatocarcinogenesis, we performed genome-wide methylation profiling and vertical integration with array-based comparative genomic hybridization (aCGH), as well as expression data from a cohort of well-characterized human hepatocellular carcinomas (HCCs). Bisulfite-converted DNAs from 63 HCCs and 10 healthy control livers were analyzed for the methylation status of more than 14,000 genes. After defining the differentially methylated genes in HCCs, we integrated their DNA copy-number alterations as determined by aCGH data and correlated them with gene expression to identify genes potentially silenced by promoter hypermethylation. Aberrant methylation of candidates was further confirmed by pyrosequencing, and methylation dependency of silencing was determined by 5-aza-2'-deoxycytidine (5-aza-dC) treatment. Methylation profiling revealed 2,226 CpG sites that showed methylation differences between healthy control livers and HCCs. Of these, 537 CpG sites were hypermethylated in the tumor DNA, whereas 1,689 sites showed promoter hypomethylation. The hypermethylated set was enriched for genes known to be inactivated by the polycomb repressive complex 2, whereas the group of hypomethylated genes was enriched for imprinted genes. We identified three genes matching all of our selection criteria for a tumor-suppressor gene (period homolog 3 [PER3], insulin-like growth-factor-binding protein, acid labile subunit [IGFALS], and protein Z). PER3 was down-regulated in human HCCs, compared to peritumorous and healthy liver tissues. 5-aza-dC treatment restored PER3 expression in HCC cell lines, indicating that promoter hypermethylation was indeed responsible for gene silencing. Additionally, functional analysis supported a tumor-suppressive function for PER3 and IGFALS in vitro. CONCLUSION The present study illustrates that vertical integration of methylation data with high-resolution genomic and transcriptomic data facilitates the identification of new tumor-suppressor gene candidates in human HCC.
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Affiliation(s)
- Olaf Neumann
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
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Garcia-Bassets I, Wang D. Cistrome plasticity and mechanisms of cistrome reprogramming. Cell Cycle 2012; 11:3199-210. [PMID: 22895178 DOI: 10.4161/cc.21281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mammalian genomes contain thousands of cis-regulatory elements for each transcription factor (TF), but TFs only occupy a relatively small subset referred to as cistrome. Recent studies demonstrate that a TF cistrome might differ among different organisms, tissue types and individuals. In a cell, a TF cistrome might differ among different physiological states, pathological stages and between physiological and pathological conditions. It is, therefore, remarkable how highly plastic these binding profiles are, and how massively they can be reprogrammed in rapid response to intra/extracellular variations and during cell identity transitions and evolution. Biologically, cistrome reprogramming events tend to be followed by changes in transcriptional outputs, thus serving as transformative mechanisms to synchronically alter the biology of the cell. In this review, we discuss the molecular basis of cistrome plasticity and attempt to integrate the different mechanisms and biological conditions associated with cistrome reprogramming. Emerging data suggest that, when altered, these reprogramming events might be linked to tumor development and/or progression, which is a radical conceptual change in our mechanistic understanding of cancer and, potentially, other diseases.
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Affiliation(s)
- Ivan Garcia-Bassets
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
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Abstract
The forkhead box O (FoxO) family is involved in diverse cellular processes such as tumor suppression, stress response, and metabolism. In a recent Nature Cell Biology Letter, Zhang et al. (2011) uncover a novel role for FoxO proteins in regulating the identity of human ESCs.
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