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Abstract
Male and female differ genetically by their respective sex chromosome composition, that is, XY as male and XX as female. Although both X and Y chromosomes evolved from the same ancestor pair of autosomes, the Y chromosome harbors male-specific genes, which play pivotal roles in male sex determination, germ cell differentiation, and masculinization of various tissues. Deletions or translocation of the sex-determining gene, SRY, from the Y chromosome causes disorders of sex development (previously termed as an intersex condition) with dysgenic gonads. Failure of gonadal development results not only in infertility, but also in increased risks of germ cell tumor (GCT), such as gonadoblastoma and various types of testicular GCT. Recent studies demonstrate that either loss of Y chromosome or ectopic expression of Y chromosome genes is closely associated with various male-biased diseases, including selected somatic cancers. These observations suggest that the Y-linked genes are involved in male health and diseases in more frequently than expected. Although only a small number of protein-coding genes are present in the male-specific region of Y chromosome, the impacts of Y chromosome genes on human diseases are still largely unknown, due to lack of in vivo models and differences between the Y chromosomes of human and rodents. In this review, we highlight the involvement of selected Y chromosome genes in cancer development in men.
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Affiliation(s)
| | - Yun-Fai Chris Lau
- Division of Cell and Developmental Genetics, Department of Medicine, Veterans Affairs Medical Center, Institute for Human Genetics, University of California, San Francisco, California 94121, USA
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102
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Li HL, Wei JF, Fan LY, Wang SH, Zhu L, Li TP, Lin G, Sun Y, Sun ZJ, Ding J, Liang XL, Li J, Han Q, Zhao RCH. miR-302 regulates pluripotency, teratoma formation and differentiation in stem cells via an AKT1/OCT4-dependent manner. Cell Death Dis 2016; 7:e2078. [PMID: 26821070 PMCID: PMC4816169 DOI: 10.1038/cddis.2015.383] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/20/2015] [Accepted: 11/20/2015] [Indexed: 12/12/2022]
Abstract
Pluripotency makes human pluripotent stem cells (hPSCs) promising for regenerative medicine, but the teratoma formation has been considered to be a major obstacle for their clinical applications. Here, we determined that the downregulation of miR-302 suppresses the teratoma formation, hampers the self-renewal and pluripotency, and promotes hPSC differentiation. The underlying mechanism is that the high endogenous expression of miR-302 suppresses the AKT1 expression by directly targeting its 3'UTR and subsequently maintains the pluripotent factor OCT4 at high level. Our findings reveal that miR-302 regulates OCT4 by suppressing AKT1, which provides hPSCs two characteristics related to their potential for clinical applications: the benefit of pluripotency and the hindrance of teratoma formation. More importantly, we demonstrate that miR-302 upregulation cannot lead OCT4 negative human adult mesenchymal stem cells (hMSCs) to acquire the teratoma formation in vivo. Whether miR-302 upregulation can drive hMSCs to acquire a higher differentiation potential is worthy of deep investigation.
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Affiliation(s)
- H-L Li
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - J-F Wei
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China.,Department of Histology and Embryology, School of Basic Medical Sciences, Xuzhou Medical University, Xuzhou, China
| | - L-Y Fan
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - S-H Wang
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - L Zhu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
| | - T-P Li
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - G Lin
- Institute of Reproductive and Stem Cell Engineering, Key Laboratory of Stem Cells and Reproductive Engineering, Ministry of Health, Central South University, Changsha, China
| | - Y Sun
- Department of Nuclear Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Z-J Sun
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
| | - J Ding
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
| | - X-L Liang
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - J Li
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - Q Han
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - R-C-H Zhao
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China.,Peking Union Medical College Hospital, Beijing, China
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103
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Matic I, Antunovic M, Brkic S, Josipovic P, Mihalic KC, Karlak I, Ivkovic A, Marijanovic I. Expression of OCT-4 and SOX-2 in Bone Marrow-Derived Human Mesenchymal Stem Cells during Osteogenic Differentiation. Open Access Maced J Med Sci 2016; 4:9-16. [PMID: 27275321 PMCID: PMC4884261 DOI: 10.3889/oamjms.2016.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 11/17/2022] Open
Abstract
AIM: Determine the levels of expression of pluripotency genes OCT-4 and SOX-2 before and after osteogenic differentiation of human mesenchymal stem cells (hMSCs). METHODS: Human MSCs were derived from the bone marrow and differentiated into osteoblasts. The analyses were performed on days 0 and 14 of the cell culture. In vitro differentiation was evaluated due to bone markers – alkaline phosphatase (AP) activity and the messenger RNA (mRNA) expression of AP and bone sialoprotein (BSP). The OCT-4 and SOX-2 expression was evaluated at mRNA level by real-time qPCR and at protein level by immunocytochemistry. RESULTS: In vitro cultures on day 14 showed an increase in AP activity and upregulation of AP and BSP gene expression. OCT-4 and SOX-2 in undifferentiated hMSCs on day 0 is detectable and very low compared to tumor cell lines as a positive control. Immunocytochemistry detected OCT-4 in the cell nuclei prior (day 0) and post differentiation (day 14). On the same time points, cultures were negative for SOX-2 protein. CONCLUSION: Messenger RNA for pluripotency markers OCT-4 and SOX-2 isolated from hMSCs was less present, while OCT-4 protein was detected in cell nuclei prior and post differentiation into osteoblast lineage.
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Affiliation(s)
- Igor Matic
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Maja Antunovic
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Sime Brkic
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Pavle Josipovic
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Katarina Caput Mihalic
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivan Karlak
- Department of Traumatology, University Hospital Sestre Milosrdnice, Zagreb, Croatia
| | | | - Inga Marijanovic
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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104
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Asprer JST, Lakshmipathy U. Current methods and challenges in the comprehensive characterization of human pluripotent stem cells. Stem Cell Rev Rep 2016; 11:357-72. [PMID: 25504379 DOI: 10.1007/s12015-014-9580-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Pluripotent stem cells (PSCs) are powerful tools for basic scientific research and promising agents for drug discovery and regenerative medicine. Technological advances have made it increasingly easy to generate PSCs but the various lines generated may differ in their characteristics based on their origin, derivation, number of passages, and culture conditions. In order to confirm the pluripotency, quality, identity, and safety of pluripotent cell lines as they are derived and maintained, it is critical to perform a panel of characterization assays. Functional pluripotency is determined using tests that rely on the expression of specific markers in the undifferentiated and differentiated states; tests for quality, identity and safety are less specialized. This article provides a comprehensive review of current practices in PSC characterization and explores challenges in the field, from the selection of markers to the development of simple and scalable methods. It also delves into emerging trends like the adoption of alternative assays that could be used to supplement or replace traditional methods, specifically the use of in silico assays for determining pluripotency.
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Affiliation(s)
- Joanna S T Asprer
- Cell Biology, Life Sciences Solutions, Thermo Fisher Scientific, 5781 Van Allen Way, Carlsbad, CA, 92008, USA
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105
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Putiri EL, Tiedemann RL, Liu C, Choi JH, Robertson KD. Impact of human MLL/COMPASS and polycomb complexes on the DNA methylome. Oncotarget 2015; 5:6338-52. [PMID: 25071008 PMCID: PMC4171634 DOI: 10.18632/oncotarget.2215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The correlation between DNA methylation and a subset of histone post-translational modifications (positive and negative) has hinted at an underlying regulatory crosstalk between histone marks and DNA methylation in patterning the human DNA methylome, an idea further supported by corresponding alterations to both histone marks and DNA methylation during malignant transformation. This study investigated the framework by which histone marks influence DNA methylation at a genome-wide level. Using RNAi in a pluripotent human embryonic carcinoma cell line we depleted essential components of the MLL/COMPASS, polycomb repressive complex 2 (PRC2), and PRC1 histone modifying complexes that establish, respectively, the post-translational modifications H3K4me3, H3K27me3, and H2AK119ub, and assayed the impact of the subsequent depletion of these marks on the DNA methylome. Absence of H2AK119ub resulted predominantly in hypomethylation across the genome. Depletion of H3K4me3 and, surprisingly, H3K27me3 caused CpG island hypermethylation at a subset of loci. Intriguingly, many promoters were co-regulated by all three histone marks, becoming hypermethylated with loss of H3K4me3 or H3K27me3 and hypomethylated with depletion of H2AK119ub, and many of these co-regulated loci were among those commonly targeted for aberrant hypermethylation in cancer. Taken together, our results elucidate novel roles for polycomb and MLL/COMPASS in regulating DNA methylation and define targets of this regulation.
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Affiliation(s)
- Emily L Putiri
- Department of Molecular Pharmacology and Experimental Therapeutics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Rochelle L Tiedemann
- Department of Molecular Pharmacology and Experimental Therapeutics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Cancer Center, Georgia Regents University, Augusta, GA
| | - Chunsheng Liu
- Department of Molecular Pharmacology and Experimental Therapeutics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Jeong-Hyeon Choi
- Department of Molecular Pharmacology and Experimental Therapeutics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Cancer Center, Georgia Regents University, Augusta, GA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN
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106
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Hoff AM, Alagaratnam S, Zhao S, Bruun J, Andrews PW, Lothe RA, Skotheim RI. Identification of Novel Fusion Genes in Testicular Germ Cell Tumors. Cancer Res 2015; 76:108-16. [PMID: 26659575 DOI: 10.1158/0008-5472.can-15-1790] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/01/2015] [Indexed: 11/16/2022]
Abstract
Testicular germ cell tumors (TGCT) are the most frequently diagnosed solid tumors in young men ages 15 to 44 years. Embryonal carcinomas (EC) comprise a subset of TGCTs that exhibit pluripotent characteristics similar to embryonic stem (ES) cells, but the genetic drivers underlying malignant transformation of ECs are unknown. To elucidate the abnormal genetic events potentially contributing to TGCT malignancy, such as the existence of fusion genes or aberrant fusion transcript expression, we performed RNA sequencing of EC cell lines and their nonmalignant ES cell line counterparts. We identified eight novel fusion transcripts and one gene with alternative promoter usage, ETV6. Four out of nine transcripts were found recurrently expressed in an extended panel of primary TGCTs and additional EC cell lines, but not in normal parenchyma of the testis, implying tumor-specific expression. Two of the recurrent transcripts involved an intrachromosomal fusion between RCC1 and HENMT1 located 80 Mbp apart and an interchromosomal fusion between RCC1 and ABHD12B. RCC1-ABHD12B and the ETV6 transcript variant were found to be preferentially expressed in the more undifferentiated TGCT subtypes. In vitro differentiation of the NTERA2 EC cell line resulted in significantly reduced expression of both fusion transcripts involving RCC1 and the ETV6 transcript variant, indicating that they are markers of pluripotency in a malignant setting. In conclusion, we identified eight novel fusion transcripts that, to our knowledge, are the first fusion genes described in TGCT and may therefore potentially serve as genomic biomarkers of malignant progression.
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Affiliation(s)
- Andreas M Hoff
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway. Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Sharmini Alagaratnam
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway. Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Sen Zhao
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway. Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway. Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Peter W Andrews
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, United Kingdom. Centre for Stem Cell Biology, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway. Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway. Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway.
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107
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Yuan J, Li M, Torres YR, Galle CS, Meier JL. Differentiation-Coupled Induction of Human Cytomegalovirus Replication by Union of the Major Enhancer Retinoic Acid, Cyclic AMP, and NF-κB Response Elements. J Virol 2015; 89:12284-98. [PMID: 26423948 PMCID: PMC4665231 DOI: 10.1128/jvi.00965-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 09/08/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Triggers and regulatory pathways that effectively link human cytomegalovirus (HCMV) major immediate early (MIE) latent-lytic switch activation with progeny production are incompletely understood. In the quiescently infected human NTera2 cell model of primitive neural stem cells, we found that costimulation with vasoactive intestinal peptide (V) and phorbol ester (P) synergistically activated viral infection, but this effect waned over time. Coupling retinoic acid (R), an inducer of neuronal differentiation, to VP pulse stimulation attenuated the decline in viral activity and promoted the spread of the active infection through concentric layers of neighboring cells as cellular differentiation progressed. R stimulation alone was unable to activate the infection. The MIE enhancer cis-regulatory mechanisms responsible for this result were characterized by a strategy of combinatorial mutagenesis of five cis-acting element types (retinoic acid receptor binding elements [RARE], cyclic AMP [cAMP] response elements [CRE], NF-κB binding sites [kB], serum response element, and ETS/ELK-1 binding site) and multiple methods of assessment. We found that the CRE and kB combination sets the preinduction enhancer tone, is the major initiator and amplifier of RVP-induced MIE gene expression, and cooperates with RARE during cellular differentiation to enhance viral spread. In predifferentiated NTera2, we also found that the CRE-kB combination functions as initiator and amplifier of unstimulated HCMV MIE gene expression and cooperatively interacts with RARE to enhance viral spread. We conclude that RVP-stimulated signaling cascades and cellular differentiation operate through the enhancer CRE-kB-RARE core in strengthening induction of HCMV MIE gene expression in linkage with viral propagation. IMPORTANCE Cytomegalovirus-seropositive persons commonly lack detectable levels of cytomegalovirus replication, even when profoundly immunocompromised. In a human NTera2 cell model of primitive neural stem cells carrying resting cytomegalovirus genomes, we show that costimulation of protein kinase A and C-delta signaling cascades in conjunction with retinoic acid-induced neuronal differentiation brings about progeny virus propagation. Iterated DNA binding sites for retinoic acid receptor, CREB, and NF-κB family members in the cytomegalovirus major enhancer are at the crux in the pathway to HCMV activation. The stimulated CREB and NF-κB binding site combination vigorously initiates and amplifies the active cytomegalovirus infection and cooperates with activated retinoic acid receptor binding sites to further promote viral proliferation and spread between differentiated cells. These results support a paradigm in which a specific combination of stimuli coupled with cellular differentiation satisfies a core cis-activating code that unlocks enhancer silence to repower the cycle of cytomegalovirus propagation.
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Affiliation(s)
- Jinxiang Yuan
- University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Ming Li
- University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | | | - Courtney S Galle
- University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Jeffery L Meier
- Iowa City Veterans Affairs Medical Center, Iowa City, Iowa, USA University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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108
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Zeira E, Abramovitch R, Meir K, Ram SE, Gil Y, Bulvik B, Bromberg Z, Levkovitch O, Nahmansson N, Adar R, Reubinoff B, Galun E, Gropp M. The knockdown of H19lncRNA reveals its regulatory role in pluripotency and tumorigenesis of human embryonic carcinoma cells. Oncotarget 2015; 6:34691-703. [PMID: 26415227 PMCID: PMC4741483 DOI: 10.18632/oncotarget.5787] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 08/31/2015] [Indexed: 12/27/2022] Open
Abstract
The function of imprinted H19 long non-coding RNA is still controversial. It is highly expressed in early embryogenesis and decreases after birth and re-expressed in cancer. To study the role of H19 in oncogenesis and pluripotency, we down-regulated H19 expression in vitro and in vivo in pluripotent human embryonic carcinoma (hEC) and embryonic stem (hES) cells. H19 knockdown resulted in a decrease in the expression of the pluripotency markers Oct4, Nanog, TRA-1-60 and TRA-1-81, and in the up-regulation of SSEA1; it further attenuated cell proliferation, decreased cell-matrix attachment, and up-regulated E-Cadherin expression. SCID-Beige mice transplanted with H19 down-regulated hEC cells exhibited slower kinetics of tumor formation, resulting in an increased animal survival. Tumors derived from H19 down-regulated cells showed a decrease in the expression of pluripotency markers and up-regulation of SSEA-1 and E-cadherin. Our results suggest that H19 oncogenicity in hEC cells is mediated through the regulation of the pluripotency state.
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Affiliation(s)
- Evelyne Zeira
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Rinat Abramovitch
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Karen Meir
- The Department of Pathology, Hadassah University Hospital, Jerusalem, Israel
| | - Sharona Even Ram
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- The Sydney and Judy Swartz Human Embryonic Stem Cell Research Center, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Yaniv Gil
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- The Sydney and Judy Swartz Human Embryonic Stem Cell Research Center, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Baruch Bulvik
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Zohar Bromberg
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Or Levkovitch
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Nathalie Nahmansson
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Revital Adar
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Benjamin Reubinoff
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- The Sydney and Judy Swartz Human Embryonic Stem Cell Research Center, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eithan Galun
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Michal Gropp
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- The Sydney and Judy Swartz Human Embryonic Stem Cell Research Center, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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109
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Nong W, Xie TS, Li LY, Lu AG, Mo J, Gou YF, Lan G, Jiang H, Len J, Li MM, Jiang QY, Huang B. Qualitative Analyses of Protein Phosphorylation in Bovine Pluripotent Stem Cells Generated from Embryonic Fibroblasts. Reprod Domest Anim 2015; 50:989-98. [DOI: 10.1111/rda.12619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 09/07/2015] [Indexed: 12/19/2022]
Affiliation(s)
- W Nong
- College of Animal Science and Technology; Guangxi University; Nanning China
- Guangxi University of Chinese Medicine; Nanning China
| | - TS Xie
- College of Animal Science and Technology; Guangxi University; Nanning China
- Nanning Languang Biotechnology Inc.; Nanning China
| | - LY Li
- College of Animal Science and Technology; Guangxi University; Nanning China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources; Guangxi University; Nanning China
| | - AG Lu
- College of Animal Science and Technology; Guangxi University; Nanning China
- Guangxi Analysis and Testing Center; Nanning China
| | - J Mo
- Guangxi Analysis and Testing Center; Nanning China
| | - YF Gou
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - G Lan
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - H Jiang
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - J Len
- Guangxi University of Chinese Medicine; Nanning China
| | - MM Li
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - QY Jiang
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - B Huang
- College of Animal Science and Technology; Guangxi University; Nanning China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources; Guangxi University; Nanning China
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110
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Schraufstatter IU, Khaldoyanidi SK, DiScipio RG. Complement activation in the context of stem cells and tissue repair. World J Stem Cells 2015; 7:1090-1108. [PMID: 26435769 PMCID: PMC4591784 DOI: 10.4252/wjsc.v7.i8.1090] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 07/27/2015] [Indexed: 02/06/2023] Open
Abstract
The complement pathway is best known for its role in immune surveillance and inflammation. However, its ability of opsonizing and removing not only pathogens, but also necrotic and apoptotic cells, is a phylogenetically ancient means of initiating tissue repair. The means and mechanisms of complement-mediated tissue repair are discussed in this review. There is increasing evidence that complement activation contributes to tissue repair at several levels. These range from the chemo-attraction of stem and progenitor cells to areas of complement activation, to increased survival of various cell types in the presence of split products of complement, and to the production of trophic factors by cells activated by the anaphylatoxins C3a and C5a. This repair aspect of complement biology has not found sufficient appreciation until recently. The following will examine this aspect of complement biology with an emphasis on the anaphylatoxins C3a and C5a.
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111
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Kushwaha R, Jagadish N, Kustagi M, Tomishima MJ, Mendiratta G, Bansal M, Kim HR, Sumazin P, Alvarez MJ, Lefebvre C, Villagrasa-Gonzalez P, Viale A, Korkola JE, Houldsworth J, Feldman DR, Bosl GJ, Califano A, Chaganti RSK. Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency. Stem Cells 2015; 33:367-77. [PMID: 25336442 DOI: 10.1002/stem.1870] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 09/03/2014] [Accepted: 09/12/2014] [Indexed: 01/01/2023]
Abstract
The predominant view of pluripotency regulation proposes a stable ground state with coordinated expression of key transcription factors (TFs) that prohibit differentiation. Another perspective suggests a more complexly regulated state involving competition between multiple lineage-specifying TFs that define pluripotency. These contrasting views were developed from extensive analyses of TFs in pluripotent cells in vitro. An experimentally validated, genome-wide repertoire of the regulatory interactions that control pluripotency within the in vivo cellular contexts is yet to be developed. To address this limitation, we assembled a TF interactome of adult human male germ cell tumors (GCTs) using the Algorithm for the Accurate Reconstruction of Cellular Pathways (ARACNe) to analyze gene expression profiles of 141 tumors comprising pluripotent and differentiated subsets. The network (GCT(Net)) comprised 1,305 TFs, and its ingenuity pathway analysis identified pluripotency and embryonal development as the top functional pathways. We experimentally validated GCT(Net) by functional (silencing) and biochemical (ChIP-seq) analysis of the core pluripotency regulatory TFs POU5F1, NANOG, and SOX2 in relation to their targets predicted by ARACNe. To define the extent of the in vivo pluripotency network in this system, we ranked all TFs in the GCT(Net) according to sharing of ARACNe-predicted targets with those of POU5F1 and NANOG using an odds-ratio analysis method. To validate this network, we silenced the top 10 TFs in the network in H9 embryonic stem cells. Silencing of each led to downregulation of pluripotency and induction of lineage; 7 of the 10 TFs were identified as pluripotency regulators for the first time.
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Affiliation(s)
- Ritu Kushwaha
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
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Shah SM, Saini N, Ashraf S, Zandi M, Manik RS, Singla SK, Palta P, Chauhan MS. Development, Characterization, and Pluripotency Analysis of Buffalo (Bubalus bubalis) Embryonic Stem Cell Lines Derived from In Vitro-Fertilized, Hand-Guided Cloned, and Parthenogenetic Embryos. Cell Reprogram 2015; 17:306-22. [PMID: 26168169 DOI: 10.1089/cell.2014.0098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We present the derivation, characterization, and pluripotency analysis of three buffalo embryonic stem cell (buESC) lines, from in vitro-fertilized, somatic cell nuclear-transferred, and parthenogenetic blastocysts. These cell lines were developed for later differentiation into germ lineage cells and elucidation of the signaling pathways involved. The cell lines were established from inner cell masses (ICMs) that were isolated manually from the in vitro-produced blastocysts. Most of the ICMs (45-55%) resulted in formation of primary colonies that were subcultured after 8-10 days, leading subsequently to the formation of three buESC lines, one from each blastocyst type. All the cell lines expressed stem cell markers, such as Alkaline Phosphatase, OCT4, NANOG, SSEA1, SSEA4, TRA-1-60, TRA-1-81, SOX2, REX1, CD-90, STAT3, and TELOMERASE. They differentiated into all three germ layers as determined by ectodermal, mesodermal, and endodermal RNA and protein markers. All of the cell lines showed equal expression of pluripotency markers as well as equivalent differentiation potential into all the three germ layers. The static suspension culture-derived embryoid bodies (EBs) showed greater expression of all the three germ layer markers as compared to hanging drop culture-derived EBs. When analyzed for germ layer marker expression, EBs derived from 15% fetal bovine serum (FBS)-based spontaneous differentiation medium showed greater differentiation across all the three germ layers as compared to those derived from Knock-Out Serum Replacement (KoSR)-based differentiation medium.
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Affiliation(s)
- Syed Mohmad Shah
- Animal Biotechnology Centre, National Dairy Research Institute , Karnal 132001, Haryana, India
| | - Neha Saini
- Animal Biotechnology Centre, National Dairy Research Institute , Karnal 132001, Haryana, India
| | - Syma Ashraf
- Animal Biotechnology Centre, National Dairy Research Institute , Karnal 132001, Haryana, India
| | - Mohammad Zandi
- Animal Biotechnology Centre, National Dairy Research Institute , Karnal 132001, Haryana, India
| | - Radhey Sham Manik
- Animal Biotechnology Centre, National Dairy Research Institute , Karnal 132001, Haryana, India
| | - Suresh Kumar Singla
- Animal Biotechnology Centre, National Dairy Research Institute , Karnal 132001, Haryana, India
| | - Prabhat Palta
- Animal Biotechnology Centre, National Dairy Research Institute , Karnal 132001, Haryana, India
| | - Manmohan Singh Chauhan
- Animal Biotechnology Centre, National Dairy Research Institute , Karnal 132001, Haryana, India
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113
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Fluoxetine-induced regulation of heat shock protein 90 and 14-3-3ε in human embryonic carcinoma cells. Neuroreport 2015; 25:1399-404. [PMID: 25353280 DOI: 10.1097/wnr.0000000000000284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Fluoxetine, a serotonin-selective reuptake inhibitor, exerts antidepressant and antianxiety effects on major depressive and anxiety disorders. Previous studies suggest that treatment with fluoxetine influences the expression of various proteins that are involved in proliferation, differentiation, and apoptosis in the neuronal cells of the brain. However, many aspects of the molecular pathways that modulate antidepressant action are not well understood. Here, with the aim of identifying proteins involved in antidepressant action, we examined the protein expression profile of human embryonic carcinoma (NCCIT) cells in response to fluoxetine treatment using proteomic techniques such as two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). We found several upregulated and downregulated proteins in fluoxetine-treated NCCIT cells, and then biochemically confirmed the increased expression of heat shock protein 90 and 14-3-3ε, which play an essential role in many cellular mechanisms including cell cycle control and other signaling pathways. Our data suggest that the regulated expression of heat shock protein 90, 14-3-3ε, and other identified proteins may be associated with the therapeutic action of fluoxetine.
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114
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Nettersheim D, Jostes S, Sharma R, Schneider S, Hofmann A, Ferreira HJ, Hoffmann P, Kristiansen G, Esteller MB, Schorle H. BMP Inhibition in Seminomas Initiates Acquisition of Pluripotency via NODAL Signaling Resulting in Reprogramming to an Embryonal Carcinoma. PLoS Genet 2015; 11:e1005415. [PMID: 26226633 PMCID: PMC4520454 DOI: 10.1371/journal.pgen.1005415] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/02/2015] [Indexed: 12/18/2022] Open
Abstract
Type II germ cell cancers (GCC) can be subdivided into seminomas and non-seminomas. Seminomas are similar to carcinoma in situ (CIS) cells, the common precursor of type II GCCs, with regard to epigenetics and expression, while embryonal carcinomas (EC) are totipotent and differentiate into teratomas, yolk-sac tumors and choriocarcinomas. GCCs can present as seminomas with a non-seminoma component, raising the question if a CIS gives rise to seminomas and ECs at the same time or whether seminomas can be reprogrammed to ECs. In this study, we utilized the seminoma cell line TCam-2 that acquires an EC-like status after xenografting into the murine flank as a model for a seminoma to EC transition and screened for factors initiating and driving this process. Analysis of expression and DNA methylation dynamics during transition of TCam-2 revealed that many pluripotency- and reprogramming-associated genes were upregulated while seminoma-markers were downregulated. Changes in expression level of 53 genes inversely correlated to changes in DNA methylation. Interestingly, after xenotransplantation 6 genes (GDF3, NODAL, DNMT3B, DPPA3, GAL, AK3L1) were rapidly induced, followed by demethylation of their genomic loci, suggesting that these 6 genes are poised for expression driving the reprogramming. We demonstrate that inhibition of BMP signaling is the initial event in reprogramming, resulting in activation of the pluripotency-associated genes and NODAL signaling. We propose that reprogramming of seminomas to ECs is a multi-step process. Initially, the microenvironment causes inhibition of BMP signaling, leading to induction of NODAL signaling. During a maturation phase, a fast acting NODAL loop stimulates its own activity and temporarily inhibits BMP signaling. During the stabilization phase, a slow acting NODAL loop, involving WNTs re-establishes BMP signaling and the pluripotency circuitry. In parallel, DNMT3B-driven de novo methylation silences seminoma-associated genes and epigenetically fixes the EC state.
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Affiliation(s)
- Daniel Nettersheim
- Institute of Pathology, Department of Developmental Pathology, University Medical School, Bonn, Germany
| | - Sina Jostes
- Institute of Pathology, Department of Developmental Pathology, University Medical School, Bonn, Germany
| | - Rakesh Sharma
- Institute of Pathology, Department of Developmental Pathology, University Medical School, Bonn, Germany
| | - Simon Schneider
- Institute of Pathology, Department of Developmental Pathology, University Medical School, Bonn, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, University Medical School, Bonn, Germany
| | - Humberto J Ferreira
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Per Hoffmann
- Institute of Human Genetics, University Medical School, Bonn, Germany
| | - Glen Kristiansen
- Institute of Pathology, University Medical School, Bonn, Germany
| | - Manel B Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Hubert Schorle
- Institute of Pathology, Department of Developmental Pathology, University Medical School, Bonn, Germany
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115
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An Inducible Caspase-9 Suicide Gene to Improve the Safety of Therapy Using Human Induced Pluripotent Stem Cells. Mol Ther 2015; 23:1475-85. [PMID: 26022733 DOI: 10.1038/mt.2015.100] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/25/2015] [Indexed: 12/22/2022] Open
Abstract
Human induced pluripotent stem cells (hiPSC) hold promise for regenerative therapies, though there are several safety concerns including the risk of oncogenic transformation or unwanted adverse effects associated with hiPSC or their differentiated progeny. Introduction of the inducible caspase-9 (iC9) suicide gene, which is activated by a specific chemical inducer of dimerization (CID), is one of the most appealing safety strategies for cell therapies and is currently being tested in multicenter clinical trials. Here, we show that the iC9 suicide gene with a human EF1α promoter can be introduced into hiPSC by lentiviral transduction. The transduced hiPSC maintain their pluripotency, including their capacity for unlimited self-renewal and the potential to differentiate into three germ layer tissues. Transduced hiPSC are eliminated within 24 hours of exposure to pharmacological levels of CID in vitro, with induction of apoptosis in 94-99% of the cells. Importantly, the iC9 suicide gene can eradicate tumors derived from hiPSC in vivo. In conclusion, we have developed a direct and efficient hiPSC killing system that provides a necessary safety mechanism for therapies using hiPSC. We believe that our iC9 suicide gene will be of value in clinical applications of hiPSC-based therapy.
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116
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Pinto JP, Kalathur RK, Oliveira DV, Barata T, Machado RSR, Machado S, Pacheco-Leyva I, Duarte I, Futschik ME. StemChecker: a web-based tool to discover and explore stemness signatures in gene sets. Nucleic Acids Res 2015; 43:W72-7. [PMID: 26007653 PMCID: PMC4489266 DOI: 10.1093/nar/gkv529] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/10/2015] [Indexed: 11/25/2022] Open
Abstract
Stem cells present unique regenerative abilities, offering great potential for treatment of prevalent pathologies such as diabetes, neurodegenerative and heart diseases. Various research groups dedicated significant effort to identify sets of genes—so-called stemness signatures—considered essential to define stem cells. However, their usage has been hindered by the lack of comprehensive resources and easy-to-use tools. For this we developed StemChecker, a novel stemness analysis tool, based on the curation of nearly fifty published stemness signatures defined by gene expression, RNAi screens, Transcription Factor (TF) binding sites, literature reviews and computational approaches. StemChecker allows researchers to explore the presence of stemness signatures in user-defined gene sets, without carrying-out lengthy literature curation or data processing. To assist in exploring underlying regulatory mechanisms, we collected over 80 target gene sets of TFs associated with pluri- or multipotency. StemChecker presents an intuitive graphical display, as well as detailed statistical results in table format, which helps revealing transcriptionally regulatory programs, indicating the putative involvement of stemness-associated processes in diseases like cancer. Overall, StemChecker substantially expands the available repertoire of online tools, designed to assist the stem cell biology, developmental biology, regenerative medicine and human disease research community. StemChecker is freely accessible at http://stemchecker.sysbiolab.eu.
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Affiliation(s)
- José P Pinto
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Ravi K Kalathur
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal Experimental and Clinical Cell Therapy Institute, Spinal Cord and Tissue Regeneration Center Salzburg, Paracelsus Medizinische Privatuniversität, Salzburg, A-5020, Austria
| | - Daniel V Oliveira
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Tânia Barata
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Rui S R Machado
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Susana Machado
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Ivette Pacheco-Leyva
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Isabel Duarte
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal
| | - Matthias E Futschik
- Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Algarve, 8005-139, Portugal
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117
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Tanaka Y, Hysolli E, Su J, Xiang Y, Kim KY, Zhong M, Li Y, Heydari K, Euskirchen G, Snyder MP, Pan X, Weissman SM, Park IH. Transcriptome Signature and Regulation in Human Somatic Cell Reprogramming. Stem Cell Reports 2015; 4:1125-39. [PMID: 26004630 PMCID: PMC4471828 DOI: 10.1016/j.stemcr.2015.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 12/12/2022] Open
Abstract
Reprogramming of somatic cells produces induced pluripotent stem cells (iPSCs) that are invaluable resources for biomedical research. Here, we extended the previous transcriptome studies by performing RNA-seq on cells defined by a combination of multiple cellular surface markers. We found that transcriptome changes during early reprogramming occur independently from the opening of closed chromatin by OCT4, SOX2, KLF4, and MYC (OSKM). Furthermore, our data identify multiple spliced forms of genes uniquely expressed at each progressive stage of reprogramming. In particular, we found a pluripotency-specific spliced form of CCNE1 that is specific to human and significantly enhances reprogramming. In addition, single nucleotide polymorphism (SNP) expression analysis reveals that monoallelic gene expression is induced in the intermediate stages of reprogramming, while biallelic expression is recovered upon completion of reprogramming. Our transcriptome data provide unique opportunities in understanding human iPSC reprogramming. Initial transcriptional change relies on histone modifications in fibroblast Allele-specific gene expression is manifested during reprogramming A large number of spliced forms of genes are identified during reprogramming Pluripotent-specific splicing of CCNE1 (pCCNE1) enhances reprogramming
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Affiliation(s)
- Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Eriona Hysolli
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Juan Su
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA; Department of Cell Biology, Second Military Medical University, Shanghai 200433, China
| | - Yangfei Xiang
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mei Zhong
- Department of Cell Biology, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yumei Li
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA; Department of Dermatology, Jiangsu University Affiliated Hospital, Zhenjiang 212000, PRC
| | - Kartoosh Heydari
- Cancer Research Laboratory, LKS Flow Cytometry Facility, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ghia Euskirchen
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Xinghua Pan
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Sherman Morton Weissman
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA.
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118
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Kim D, Park S, Jung YG, Roh S. In vitro culture of stem-like cells derived from somatic cell nuclear transfer bovine embryos of the Korean beef cattle species, HanWoo. Reprod Fertil Dev 2015; 28:RD14071. [PMID: 25966803 DOI: 10.1071/rd14071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 04/12/2015] [Indexed: 12/27/2022] Open
Abstract
We established and maintained somatic cell nuclear transfer embryo-derived stem-like cells (SCNT-eSLCs) from the traditional Korean beef cattle species, HanWoo (Bos taurus coreanae). Each SCNT blastocyst was placed individually on a feeder layer with culture medium containing three inhibitors of differentiation (3i). Primary colonies formed after 2-3 days of culture and the intact colonies were passaged every 5-6 days. The cells in each colony showed embryonic stem cell-like morphologies with a distinct boundary and were positive to alkaline phosphatase staining. Immunofluorescence and reverse transcription-polymerase chain reaction analyses also confirmed that these colonies expressed pluripotent markers. The colonies were maintained over 50 passages for more than 270 days. The cells showed normal karyotypes consisting of 60 chromosomes at Passage 50. Embryoid bodies were formed by suspension culture to analyse in vitro differentiation capability. Marker genes representing the differentiation into three germ layers were expressed. Typical embryonal carcinoma was generated after injecting cells under the testis capsule of nude mice, suggesting that the cultured cells may also have the potential of in vivo differentiation. In conclusion, we generated eSLCs from SCNT bovine embryos, using a 3i system that sustained stemness, normal karyotype and pluripotency, which was confirmed by in vitro and in vivo differentiation.
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119
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Fbxl10 overexpression in murine hematopoietic stem cells induces leukemia involving metabolic activation and upregulation of Nsg2. Blood 2015; 125:3437-46. [PMID: 25872778 DOI: 10.1182/blood-2014-03-562694] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 03/31/2015] [Indexed: 12/21/2022] Open
Abstract
We previously reported that deficiency for Samd9L, which was cloned as a candidate gene for -7/7q- syndrome, accelerated leukemia cooperatively with enhanced expression of a histone demethylase: F-box and leucine-rich repeat protein 10 (Fbxl10, also known as Jhdm1b, Kdm2b, and Ndy1). To further investigate the role of Fbxl10 in leukemogenesis, we generated transgenic (Tg) mice that overexpress Fbxl10 in hematopoietic stem cells (HSCs). Interestingly, Fbxl10 Tg mice developed myeloid or B-lymphoid leukemia with complete penetrance. HSCs from the Tg mice exhibited an accelerated G0/G1-to-S transition with a normal G0 to G1 entry, resulting in pleiotropic progenitor cell expansion. Fbxl10 Tg HSCs displayed enhanced expression of neuron-specific gene family member 2 (Nsg2), and forced expression of Nsg2 in primary bone marrow cells resulted in expansion of immature cells. In addition, the genes involved in mitochondrial oxidative phosphorylation were markedly enriched in Fbxl10 Tg HSCs, coupled with increased cellular adenosine 5'-triphosphate levels. Moreover, chromatin immunoprecipitation followed by sequencing analysis demonstrated that Fbxl10 directly binds to the regulatory regions of Nsg2 and oxidative phosphorylation genes. These findings define Fbxl10 as a bona fide oncogene, whose deregulated expression contributes to the development of leukemia involving metabolic proliferative advantage and Nsg2-mediated impaired differentiation.
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120
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Holmgren G, Ghosheh N, Zeng X, Bogestål Y, Sartipy P, Synnergren J. Identification of stable reference genes in differentiating human pluripotent stem cells. Physiol Genomics 2015; 47:232-9. [PMID: 25852171 DOI: 10.1152/physiolgenomics.00130.2014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/31/2015] [Indexed: 01/01/2023] Open
Abstract
Reference genes, often referred to as housekeeping genes (HKGs), are frequently used to normalize gene expression data based on the assumption that they are expressed at a constant level in the cells. However, several studies have shown that there may be a large variability in the gene expression levels of HKGs in various cell types. In a previous study, employing human embryonic stem cells (hESCs) subjected to spontaneous differentiation, we observed that the expression of commonly used HKG varied to a degree that rendered them inappropriate to use as reference genes under those experimental settings. Here we present a substantially extended study of the HKG signature in human pluripotent stem cells (hPSC), including nine global gene expression datasets from both hESC and human induced pluripotent stem cells, obtained during directed differentiation toward endoderm-, mesoderm-, and ectoderm derivatives. Sets of stably expressed genes were compiled, and a handful of genes (e.g., EID2, ZNF324B, CAPN10, and RABEP2) were identified as generally applicable reference genes in hPSCs across all cell lines and experimental conditions. The stability in gene expression profiles was confirmed by reverse transcription quantitative PCR analysis. Taken together, the current results suggest that differentiating hPSCs have a distinct HKG signature, which in some aspects is different from somatic cell types, and underscore the necessity to validate the stability of reference genes under the actual experimental setup used. In addition, the novel putative HKGs identified in this study can preferentially be used for normalization of gene expression data obtained from differentiating hPSCs.
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Affiliation(s)
- Gustav Holmgren
- Systems Biology Research Center, University of Skövde, Skövde, Sweden; Department of Clinical Chemistry/Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Nidal Ghosheh
- Systems Biology Research Center, University of Skövde, Skövde, Sweden; Department of Clinical Chemistry/Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Xianmin Zeng
- Buck Institute for Research on Aging, Buck Institute, Novato, California; and
| | - Yalda Bogestål
- Systems Biology Research Center, University of Skövde, Skövde, Sweden
| | - Peter Sartipy
- Systems Biology Research Center, University of Skövde, Skövde, Sweden; AstraZeneca Research and Development, Global Medicines Development, Cardiovascular and Metabolic Diseases Global Medicines Development Unit, Mölndal, Sweden
| | - Jane Synnergren
- Systems Biology Research Center, University of Skövde, Skövde, Sweden;
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Lo NW, Intawicha P, Chiu YT, Lee KH, Lu HC, Chen CH, Chang YH, Chen CD, Ju JC. Leukemia Inhibitory Factor and Fibroblast Growth Factor 2 Critically and Mutually Sustain Pluripotency of Rabbit Embryonic Stem Cells. Cell Transplant 2015; 24:319-38. [DOI: 10.3727/096368915x686832] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Effects of leukemia inhibitory factor (LIF) and fibroblast growth factor 2 (FGF2) on establishment and maintenance of rabbit embryonic stem cell (rESC) lines were assessed. When grown on MEF feeders, rESC lines derived from fertilized embryos were established and maintained in medium containing paracrine factors LIF (via STAT3) and/or FGF2 (via MEK-ERK1/2 and PI3K-AKT). However, high levels of ERK1/2 and AKT activities in rESCs were crucial for maintaining their undifferentiated proliferation. Although rESCs under the influence of either LIF (500, 1,000, and 2,000 U/ml) or FGF2 (5, 10, and 20 ng/ml) alone had enhanced expression of pluripotency markers, peak expression occurred when both LIF (1,000 U/ml) and FGF2 (10 ng/ml) were applied. Induced dephosphorylation of STAT3, ERK1/2, and AKT by specific inhibitors limited growth of rESCs and caused remarkable losses of self-renewal capacity; therefore, we inferred that STAT3, ERK, and AKT had essential roles in maintaining rESC proliferation and self-renewal. We concluded that LIF and FGF2 jointly maintained the undifferentiated state and self-renewal of rESCs through an integrative signaling module.
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Affiliation(s)
- Neng-Wen Lo
- Department of Animal Science and Biotechnology, Tunghai University, Taichung, Taiwan
| | - Payungsuk Intawicha
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
- School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | | | - Kun-Hsiung Lee
- Division of Animal Technology, Animal Technology Laboratories, Agriculture Technology Research Institute, Hsinchu, Taiwan
| | - Hsi-Chi Lu
- Department of Food Science, Tunghai University, Taichung, Taiwan
| | - Chien-Hong Chen
- Division of Animal Technology, Animal Technology Laboratories, Agriculture Technology Research Institute, Hsinchu, Taiwan
| | - Yong-Hsuan Chang
- Department of Animal Science and Biotechnology, Tunghai University, Taichung, Taiwan
| | - Chun-Da Chen
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Jyh-Cherng Ju
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan
- Agricultural Biotechnology Center and Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Medical Research Department, China Medical University Hospital, Taichung, Taiwan
- Department of Biomedical Informatics, College of Computer Science, Asia University, Taichung, Taiwan
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122
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Doh MS, Han DMR, Oh DH, Kim SH, Choi MR, Chai YG. Profiling of Proteins Regulated by Venlafaxine during Neural Differentiation of Human Cells. Psychiatry Investig 2015; 12:81-91. [PMID: 25670950 PMCID: PMC4310925 DOI: 10.4306/pi.2015.12.1.81] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 03/07/2014] [Accepted: 03/25/2014] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE Antidepressants are known to positively influence several factors in patients with depressive disorders, resulting in increased neurogenesis and subsequent relief of depressive disorders. To study the effects of venlafaxine during neural differentiation at the cellular level, we looked at its effect on protein expression and regulation mechanisms during neural differentiation. METHODS After exposing NCCIT cell-derived EBs to venlafaxine during differentiation (1 day and 7 days), changes in protein expression were analyzed by 2-DE and MALDI-TOF MS analysis. Gene levels of proteins regulated by venlafaxine were analyzed by real-time RT-PCR. RESULTS Treatment with venlafaxine decreased expression of prolyl 4-hydroxylase (P4HB), ubiquitin-conjugating enzyme E2K (HIP2) and plastin 3 (T-plastin), and up-regulated expression of growth factor beta-3 (TGF-β3), dihydropyrimidinase-like 3 (DPYSL3), and pyruvate kinase (PKM) after differentiation for 1 and 7 days. In cells exposed to venlafaxine, the mRNA expression patterns of HIP2 and PKM, which function as negative and positive regulators of differentiation and neuronal survival, respectively, were consistent with the observed changes in protein expression. CONCLUSION Our findings may contribute to improve understanding of molecular mechanism of venlafaxine.
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Affiliation(s)
- Mi Sook Doh
- Department of Molecular and Life Sciences, Hanyang University, Ansan, Republic of Korea
| | - Dal Mu Ri Han
- Department of Molecular and Life Sciences, Hanyang University, Ansan, Republic of Korea
| | - Dong Hoon Oh
- Department of Neuropsychiatry, College of Medicine and Institute of Mental Health, Hanyang University, Seoul, Republic of Korea
| | - Seok Hyeon Kim
- Department of Neuropsychiatry, College of Medicine and Institute of Mental Health, Hanyang University, Seoul, Republic of Korea
| | - Mi Ran Choi
- Department of Molecular and Life Sciences, Hanyang University, Ansan, Republic of Korea
| | - Young Gyu Chai
- Department of Molecular and Life Sciences, Hanyang University, Ansan, Republic of Korea
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Sokolov MV, Neumann RD. Changes in human pluripotent stem cell gene expression after genotoxic stress exposures. World J Stem Cells 2014; 6:598-605. [PMID: 25426256 PMCID: PMC4178259 DOI: 10.4252/wjsc.v6.i5.598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/12/2014] [Accepted: 09/17/2014] [Indexed: 02/06/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) represent heterogeneous populations, including induced pluripotent stem cells (iPSCs), endogenous plastic somatic cells, and embryonic stem cells (ESCs). Human ESCs are derived from the inner cell mass of the blastocyst, and they are characterized by the abilities to self-renew indefinitely, and to give rise to all cell types of embryonic lineage (pluripotency) under the guidance of the appropriate chemical, mechanical and environmental cues. The combination of these critical features is unique to hESCs, and set them apart from other human cells. The expectations are high to utilize hESCs for treating injuries and degenerative diseases; for modeling of complex illnesses and development; for screening and testing of pharmacological products; and for examining toxicity, mutagenicity, teratogenicity, and potential carcinogenic effects of a variety of environmental factors, including ionizing radiation (IR). Exposures to genotoxic stresses, such as background IR, are unavoidable; moreover, IR is widely used in diagnostic and therapeutic procedures in medicine on a routine basis. One of the key outcomes of cell exposures to IR is the change in gene expression, which may underlie the ultimate hESCs fate after such a stress. However, gaps in our knowledge about basic biology of hESCs impose a serious limitation to fully realize the potential of hESCs in practice. The purpose of this review is to examine the available evidence of alterations in gene expression in human pluripotent stem cells after genotoxic stress, and to discuss strategies for future research in this important area.
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Tiedemann RL, Putiri EL, Lee JH, Hlady RA, Kashiwagi K, Ordog T, Zhang Z, Liu C, Choi JH, Robertson KD. Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome. Cell Rep 2014; 9:1554-66. [PMID: 25453758 PMCID: PMC4254561 DOI: 10.1016/j.celrep.2014.10.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 08/26/2014] [Accepted: 10/03/2014] [Indexed: 12/18/2022] Open
Abstract
Global patterns of DNA methylation, mediated by the DNA methyltransferases (DNMTs), are disrupted in all cancers by mechanisms that remain largely unknown, hampering their development as therapeutic targets. Combinatorial acute depletion of all DNMTs in a pluripotent human tumor cell line, followed by epigenome and transcriptome analysis, revealed DNMT functions in fine detail. DNMT3B occupancy regulates methylation during differentiation, whereas an unexpected interplay was discovered in which DNMT1 and DNMT3B antithetically regulate methylation and hydroxymethylation in gene bodies, a finding confirmed in other cell types. DNMT3B mediated non-CpG methylation, whereas DNMT3L influenced the activity of DNMT3B toward non-CpG versus CpG site methylation. Altogether, these data reveal functional targets of each DNMT, suggesting that isoform selective inhibition would be therapeutically advantageous.
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Affiliation(s)
- Rochelle L Tiedemann
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA; Cancer Center, Georgia Regents University, 1411 Laney Walker Boulevard, Augusta, GA 30912, USA
| | - Emily L Putiri
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Department of Biochemistry and Molecular Biology, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA; Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - Katsunobu Kashiwagi
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - Tamas Ordog
- Department of Physiology and Biomedical Engineering, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA; Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - Zhiguo Zhang
- Department of Biochemistry and Molecular Biology, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA; Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - Chen Liu
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, P.O. Box 100275, Gainesville, FL 32610, USA
| | - Jeong-Hyeon Choi
- Cancer Center, Georgia Regents University, 1411 Laney Walker Boulevard, Augusta, GA 30912, USA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA; Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA.
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Shahryari A, Rafiee MR, Fouani Y, Oliae NA, Samaei NM, Shafiee M, Semnani S, Vasei M, Mowla SJ. Two novel splice variants of SOX2OT, SOX2OT-S1, and SOX2OT-S2 are coupregulated with SOX2 and OCT4 in esophageal squamous cell carcinoma. Stem Cells 2014; 32:126-34. [PMID: 24105929 DOI: 10.1002/stem.1542] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 08/12/2013] [Indexed: 01/18/2023]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as new regulators of stem cell pluripotency and tumorigenesis. The SOX2 gene, a master regulator of pluripotency, is embedded within the third intron of a lncRNA known as SOX2 overlapping transcript (SOX2OT). SOX2OT has been suspected to participate in regulation of SOX2 expression and/or other related processes; nevertheless, its potential involvement in tumor initiation and/or progression is unclear. Here, we have evaluated a possible correlation between expression patterns of SOX2OT and those of master regulators of pluripotency, SOX2 and OCT4, in esophageal squamous cell carcinoma (ESCC) tissue samples. We have also examined its potential function in the human embryonic carcinoma stem cell line, NTERA2 (NT2), which highly expresses SOX2OT, SOX2, and OCT4. Our data revealed a significant coupregulation of SOX2OT along with SOX2 and OCT4 in tumor samples, compared to the non-tumor tissues obtained from the margin of same tumors. We also identified two novel splice variants of SOX2OT (SOX2OT-S1 and SOX2OT-S2) which coupregulated with SOX2 and OCT4 in ESCCs. Suppressing SOX2OT variants caused a profound alteration in cell cycle distribution, including a 5.9 and 6.9 time increase in sub-G1 phase of cell cycle for SOX2OT-S1 and SOX2OT-S2, respectively. The expression of all variants was significantly diminished, upon the induction of neural differentiation in NT2 cells, suggesting their potential functional links to the undifferentiated state of the cells. Our data suggest a part for SOX2OT spliced variants in tumor initiation and/or progression as well as regulating pluripotent state of stem cells.
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Affiliation(s)
- Alireza Shahryari
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Alberti L, Renaud S, Losi L, Leyvraz S, Benhattar J. High expression of hTERT and stemness genes in BORIS/CTCFL positive cells isolated from embryonic cancer cells. PLoS One 2014; 9:e109921. [PMID: 25279549 PMCID: PMC4184884 DOI: 10.1371/journal.pone.0109921] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/12/2014] [Indexed: 01/08/2023] Open
Abstract
BORIS/CTCFL is a member of cancer testis antigen family normally expressed in germ cells. In tumors, it is aberrantly expressed although its functions are not completely well-defined. To better understand the functions of BORIS in cancer, we selected the embryonic cancer cells as a model. Using a molecular beacon, which specifically targets BORIS mRNA, we demonstrated that BORIS positive cells are a small subpopulation of tumor cells (3–5% of total). The BORIS-positive cells isolated using BORIS-molecular beacon, expressed higher telomerase hTERT, stem cell (NANOG, OCT4, SOX2) and cancer stem cell marker genes (CD44 and ALDH1) compared to the BORIS-negative tumor cells. In order to define the functional role of BORIS, stable BORIS-depleted embryonic cancer cells were generated. BORIS silencing strongly down-regulated the expression of hTERT, stem cell and cancer stem cell marker genes. Moreover, the BORIS knockdown increased cellular senescence in embryonic cancer cells, revealing a putative role of BORIS in the senescence biological program. Our data indicate an association of BORIS expressing cells subpopulation with the expression of stemness genes, highlighting the critical role played by BORIS in embryonic neoplastic disease.
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Affiliation(s)
- Loredana Alberti
- Institute of Pathology, Lausanne University Hospital, Lausanne, Switzerland
| | - Stéphanie Renaud
- Institute of Biotechnology, University of Lausanne, Lausanne, Switzerland
| | - Lorena Losi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Serge Leyvraz
- Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Jean Benhattar
- Institute of Pathology, Lausanne University Hospital, Lausanne, Switzerland
- Biopath Lab, Lausanne, Switzerland
- * E-mail:
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Tooley JG, Schaner Tooley CE. New roles for old modifications: emerging roles of N-terminal post-translational modifications in development and disease. Protein Sci 2014; 23:1641-9. [PMID: 25209108 DOI: 10.1002/pro.2547] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 09/08/2014] [Indexed: 01/07/2023]
Abstract
The importance of internal post-translational modification (PTM) in protein signaling and function has long been known and appreciated. However, the significance of the same PTMs on the alpha amino group of N-terminal amino acids has been comparatively understudied. Historically considered static regulators of protein stability, additional functional roles for N-terminal PTMs are now beginning to be elucidated. New findings show that N-terminal methylation, along with N-terminal acetylation, is an important regulatory modification with significant roles in development and disease progression. There are also emerging studies on the enzymology and functional roles of N-terminal ubiquitylation and N-terminal propionylation. Here, will discuss the recent advances in the functional studies of N-terminal PTMs, recount the new N-terminal PTMs being identified, and briefly examine the possibility of dynamic N-terminal PTM exchange.
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Affiliation(s)
- John G Tooley
- Department of Biochemistry and Molecular Biology, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, Kentucky
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Tung PY, Varlakhanova NV, Knoepfler PS. Identification of DPPA4 and DPPA2 as a novel family of pluripotency-related oncogenes. Stem Cells 2014; 31:2330-42. [PMID: 23963736 DOI: 10.1002/stem.1526] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 07/07/2013] [Accepted: 07/07/2013] [Indexed: 11/07/2022]
Abstract
In order to identify novel pluripotency-related oncogenes, an expression screen for oncogenic foci-inducing genes within a retroviral human embryonic stem cell cDNA library was conducted. From this screen, we identified not only known oncogenes but also intriguingly the key pluripotency factor, DPPA4 (developmental pluripotency-associated four) that encodes a DNA binding SAP domain-containing protein. DPPA4 has not been previously identified as an oncogene but is highly expressed in embryonal carcinomas, pluripotent germ cell tumors, and other cancers. DPPA4 is also mutated in some cancers. In direct transformation assays, we validated that DPPA4 is an oncogene in both mouse 3T3 cells and immortalized human dermal fibroblasts. Overexpression of DPPA4 generates oncogenic foci (sarcoma cells) and causes anchorage-independent growth. The in vitro transformed cells also give rise to tumors in immunodeficient mice. Furthermore, functional analyses indicate that both the DNA-binding SAP domain and the histone-binding C-terminal domain are critical for the oncogenic transformation activity of DPPA4. Downregulation of DPPA4 in E14 mouse embryonic stem cells and P19 mouse embryonic carcinoma cells causes decreased cell proliferation in each case. In addition, DPPA4 overexpression induces cell proliferation through genes related to regulation of G1/S transition. Interestingly, we observed similar findings for family member DPPA2. Thus, we have identified a new family of pluripotency-related oncogenes consisting of DPPA2 and DPPA4. Our findings have important implications for stem cell biology and tumorigenesis.
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Affiliation(s)
- Po-Yuan Tung
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, California, USA; University of California Davis Genome Center, University of California Davis, Davis, California, USA; UC Davis Comprehensive Cancer Center, Shriners Hospital For Children Northern California, Sacramento, California, USA; Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, California, USA
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130
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Aneuploidy induces profound changes in gene expression, proliferation and tumorigenicity of human pluripotent stem cells. Nat Commun 2014; 5:4825. [PMID: 25198699 DOI: 10.1038/ncomms5825] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 07/25/2014] [Indexed: 12/24/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) tend to acquire genomic aberrations in culture, the most common of which is trisomy of chromosome 12. Here we dissect the cellular and molecular implications of this trisomy in hPSCs. Global gene expression analyses reveal that trisomy 12 profoundly affects the gene expression profile of hPSCs, inducing a transcriptional programme similar to that of germ cell tumours. Comparison of proliferation, differentiation and apoptosis between diploid and aneuploid hPSCs shows that trisomy 12 significantly increases the proliferation rate of hPSCs, mainly as a consequence of increased replication. Furthermore, trisomy 12 increases the tumorigenicity of hPSCs in vivo, inducing transcriptionally distinct teratomas from which pluripotent cells can be recovered. Last, a chemical screen of 89 anticancer drugs discovers that trisomy 12 raises the sensitivity of hPSCs to several replication inhibitors. Together, these findings demonstrate the extensive effect of trisomy 12 and highlight its perils for successful hPSC applications.
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131
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Vencken SF, Sethupathy P, Blackshields G, Spillane C, Elbaruni S, Sheils O, Gallagher MF, O'Leary JJ. An integrated analysis of the SOX2 microRNA response program in human pluripotent and nullipotent stem cell lines. BMC Genomics 2014; 15:711. [PMID: 25156079 PMCID: PMC4162954 DOI: 10.1186/1471-2164-15-711] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 07/15/2014] [Indexed: 12/13/2022] Open
Abstract
Background SOX2 is a core component of the transcriptional network responsible for maintaining embryonal carcinoma cells (ECCs) in a pluripotent, undifferentiated state of self-renewal. As such, SOX2 is an oncogenic transcription factor and crucial cancer stem cell (CSC) biomarker in embryonal carcinoma and, as more recently found, in the stem-like cancer cell component of many other malignancies. SOX2 is furthermore a crucial factor in the maintenance of adult stem cell phenotypes and has additional roles in cell fate determination. The SOX2-linked microRNA (miRNA) transcriptome and regulome has not yet been fully defined in human pluripotent cells or CSCs. To improve our understanding of the SOX2-linked miRNA regulatory network as a contribution to the phenotype of these cell types, we used high-throughput differential miRNA and gene expression analysis combined with existing genome-wide SOX2 chromatin immunoprecipitation (ChIP) data to map the SOX2 miRNA transcriptome in two human embryonal carcinoma cell (hECC) lines. Results Whole-microRNAome and genome analysis of SOX2-silenced hECCs revealed many miRNAs regulated by SOX2, including several with highly characterised functions in both cancer and embryonic stem cell (ESC) biology. We subsequently performed genome-wide differential expression analysis and applied a Monte Carlo simulation algorithm and target prediction to identify a SOX2-linked miRNA regulome, which was strongly enriched with epithelial-to-mesenchymal transition (EMT) markers. Additionally, several deregulated miRNAs important to EMT processes had SOX2 binding sites in their promoter regions. Conclusion In ESC-like CSCs, SOX2 regulates a large miRNA network that regulates and interlinks the expression of crucial genes involved in EMT. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-711) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian F Vencken
- Department of Histopathology, Trinity College Dublin, Sir Patrick Dun Research Laboratory, St, James's Hospital, Dublin, Ireland.
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Ben-David U. Genomic instability, driver genes and cell selection: Projections from cancer to stem cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:427-35. [PMID: 25132386 DOI: 10.1016/j.bbagrm.2014.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/03/2014] [Accepted: 08/02/2014] [Indexed: 12/13/2022]
Abstract
Cancer cells and stem cells share many traits, including a tendency towards genomic instability. Human cancers exhibit tumor-specific genomic aberrations, which often affect their malignancy and drug response. During their culture propagation, human pluripotent stem cells (hPSCs) also acquire characteristic genomic aberrations, which may have significant impact on their molecular and cellular phenotypes. These aberrations vary in size from single nucleotide alterations to copy number alterations to whole chromosome gains. A prominent challenge in both cancer and stem cell research is to identify "driver aberrations" that confer a selection advantage, and "driver genes" that underlie the recurrence of these aberrations. Following principles that are already well-established in cancer research, candidate driver genes have also been suggested in hPSCs. Experimental validation of the functional role of such candidates can uncover whether these are bona fide driver genes. The identification of driver genes may bring us closer to a mechanistic understanding of the genomic instability of stem cells. Guided by terminologies and methodologies commonly applied in cancer research, such understanding may have important ramifications for both stem cell and cancer biology. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
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Affiliation(s)
- Uri Ben-David
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Sutiwisesak R, Kitiyanant N, Kotchabhakdi N, Felsenfeld G, Andrews PW, Wongtrakoongate P. Induced pluripotency enables differentiation of human nullipotent embryonal carcinoma cells N2102Ep. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2611-9. [PMID: 25086345 DOI: 10.1016/j.bbamcr.2014.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/18/2014] [Accepted: 07/22/2014] [Indexed: 12/21/2022]
Abstract
Embryonal carcinoma (EC) cells, which are considered to be malignant counterparts of embryonic stem cells, comprise the pluripotent stem cell component of teratocarcinomas, a form of testicular germ cell tumors (GCTs). Nevertheless, many established human EC cell lines are nullipotent with limited or no capacity to differentiate under normal circumstances. In this study, we tested whether an over-expression of Yamanaka's reprogramming factors OCT4, SOX2, c-MYC and KLF4 might enable differentiation of the human nullipotent EC cells N2102Ep. Using OCT4 knockdown differentiated N2102Ep cells, we are able to derive reprogrammed N2102Ep cell lines. The induced pluripotency of N2102Ep allows the cells to differentiate toward neural lineage by retinoic acid; the expression of SSEA3 and SSEA4 is down-regulated, whereas that of neural surface markers is up-regulated. Consistent with the up-regulation of neural surface markers, the expression of the master neuroectodermal transcription factor PAX6 is also induced in reprogrammed N2102Ep. We next investigated whether PAX6 might induce spontaneous differentiation of nullipotent stem cells N2102Ep. However, while an ectopic expression of PAX6 promotes differentiation of NTERA2, it induces cell death in N2102Ep. We nevertheless find that upon induction of retinoic acid, the reprogrammed N2102Ep cells form mature neuronal morphology similar to differentiated pluripotent stem cells NTERA2 as determined by TUJ1 expression, which is absent in N2102Ep parental cells. Altogether, we conclude that the nullipotent state of human EC cells can be reprogrammed to acquire a more relaxed state of differentiation potential by Yamanaka's factors.
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Affiliation(s)
- Rujapope Sutiwisesak
- Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhonpathom 73170, Thailand; Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Narisorn Kitiyanant
- Stem Cell Research Group, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhonpathom, 73170, Thailand
| | - Naiphinich Kotchabhakdi
- Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhonpathom 73170, Thailand
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter W Andrews
- Centre for Stem Cell Biology, University of Sheffield, S10 2TN, UK
| | - Patompon Wongtrakoongate
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Centre for Stem Cell Biology, University of Sheffield, S10 2TN, UK.
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Zhou W, Guo S, Xiong Z, Liu M. Oncogenic role and therapeutic target of transient receptor potential melastatin 7 channel in malignancy. Expert Opin Ther Targets 2014; 18:1177-96. [DOI: 10.1517/14728222.2014.940894] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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135
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The hypoxia-inducible epigenetic regulators Jmjd1a and G9a provide a mechanistic link between angiogenesis and tumor growth. Mol Cell Biol 2014; 34:3702-20. [PMID: 25071150 DOI: 10.1128/mcb.00099-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Hypoxia promotes stem cell maintenance and tumor progression, but it remains unclear how it regulates long-term adaptation toward these processes. We reveal a striking downregulation of the hypoxia-inducible histone H3 lysine 9 (H3K9) demethylase JMJD1A as a hallmark of clinical human germ cell-derived tumors, such as seminomas, yolk sac tumors, and embryonal carcinomas. Jmjd1a was not essential for stem cell self-renewal but played a crucial role as a tumor suppressor in opposition to the hypoxia-regulated oncogenic H3K9 methyltransferase G9a. Importantly, loss of Jmjd1a resulted in increased tumor growth, whereas loss of G9a produced smaller tumors. Pharmacological inhibition of G9a also resulted in attenuation of tumor growth, offering a novel therapeutic strategy for germ cell-derived tumors. Finally, Jmjd1a and G9a drive mutually opposing expression of the antiangiogenic factor genes Robo4, Igfbp4, Notch4, and Tfpi accompanied by changes in H3K9 methylation status. Thus, we demonstrate a novel mechanistic link whereby hypoxia-regulated epigenetic changes are instrumental for the control of tumor growth through coordinated dysregulation of antiangiogenic gene expression.
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136
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Gan L, Schwengberg S, Denecke B. Transcriptome analysis in cardiomyocyte-specific differentiation of murine embryonic stem cells reveals transcriptional regulation network. Gene Expr Patterns 2014; 16:8-22. [PMID: 25058891 DOI: 10.1016/j.gep.2014.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 07/14/2014] [Accepted: 07/17/2014] [Indexed: 01/28/2023]
Abstract
The differentiation to cardiomyocytes is a prerequisite and an important part of heart development. A good understanding of the complicated cardiomyocyte differentiation process benefits cardiogenesis study. Embryonic stem cells (ESCs), cell lines with infinite ability to proliferate and to be differentiated into all cell types of the adult body, are important research tools for investigation of differentiation and meanwhile good models for developmental research. In the current study, genome-wide gene expression of ESCs is profiled through high throughput platform during cardiomyocyte-specific differentiation and maturation. Gene expression patterns of undifferentiated ESCs and ESC-derived cardiomyocytes provide a global overview of genes involved in cardiomyocyte-specific differentiation, whereas marker gene expression profiles of both ESC-related genes and cardiac-specific genes presented the expression pattern shift during differentiation in a pure ESC-derived cardiomyocyte cell culture system. The differentiation and maturation process was completed at day 19 after initiation of differentiation, according to our gene expression profile results. Functional analysis of regulated genes reveals over-represented biological processes, molecular functions and pathways during the differentiation and maturation process. Finally, transcription factor regulation networks were engineered based on gene expression data. Within these networks, the number of identified important regulators (Trim28, E2f4, Foxm1, Myc, Hdac1, Rara, Mef2c, Nkx2-5, Gata4) and possible key co-regulation modules (Nkx2-5 - Gata4 - Tbx5, Myc - E2F4) could be expanded. We demonstrate that a more comprehensive picture of cardiomyocyte differentiation and its regulation can be achieved solely by studying gene expression patterns. The results from our study contribute to a better and more accurate understanding of the regulation mechanisms during cardiomyocyte differentiation.
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Affiliation(s)
- Lin Gan
- Interdisciplinary Center for Clinical Research Aachen (IZKF Aachen), RWTH Aachen University, Aachen, Germany
| | | | - Bernd Denecke
- Interdisciplinary Center for Clinical Research Aachen (IZKF Aachen), RWTH Aachen University, Aachen, Germany.
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Vinnitsky V. The development of a malignant tumor is due to a desperate asexual self-cloning process in which cancer stem cells develop the ability to mimic the genetic program of germline cells. INTRINSICALLY DISORDERED PROTEINS 2014; 2:e29997. [PMID: 28232878 PMCID: PMC5314931 DOI: 10.4161/idp.29997] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/17/2014] [Accepted: 07/17/2014] [Indexed: 02/08/2023]
Abstract
To date there is no explanation why the development of almost all types of solid tumors occurs sharing a similar scenario: (1) creation of a cancer stem cell (CSC), (2) CSC multiplication and formation of a multicellular tumor spheroid (TS), (3) vascularization of the TS and its transformation into a vascularized primary tumor, (4) metastatic spreading of CSCs, (5) formation of a metastatic TSs and its transformation into metastatic tumors, and (6) potentially endless repetition of this cycle of events. The above gaps in our knowledge are related to the biology of cancer and specifically to tumorigenesis, which covers the process from the creation of a CSC to the formation of a malignant tumor and the development of metastases. My Oncogerminative Theory of Tumorigenesis considers tumor formation as a dynamic self-organizing process that mimics a self-organizing process of early embryo development. In the initial step in that process, gene mutations combined with epigenetic dysregulation cause somatic cells to be reprogrammed into CSCs, which are immortal pseudo-germline cells. Mimicking the behavior of fertilized germline cells, the CSC achieves immortality by passing through the stages of its life-cycle and developing into a pseudo-blastula-stage embryo, which manifests in the body as a malignant tumor. In this view, the development of a malignant tumor from a CSC is a phenomenon of developmental biology, which we named a desperate asexual self-cloning event. The theory explains seven core characteristics of malignant tumors: (1) CSC immortality, (2) multistep development of a malignant tumor from a single CSC, (3) heterogeneity of malignant tumor cell populations, (4) metastatic spread of CSCs, (5) invasive growth, (6) malignant progression, and (7) selective immune tolerance toward cancer cells. The Oncogerminative Theory of Tumorigenesis suggests new avenues for discovery of revolutionary therapies to treat, prevent, and eradicate cancer.
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Affiliation(s)
- Vladimir Vinnitsky
- Department of Experimental Cancer Therapeutics; R.E. Kavetsky Institute for Experimental Pathology, Oncology, and Radiobiology; Kiev, Ukraine
- Sequent Development (CRO), LLC; Madison, VA USA
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Putiri EL, Tiedemann RL, Thompson JJ, Liu C, Ho T, Choi JH, Robertson KD. Distinct and overlapping control of 5-methylcytosine and 5-hydroxymethylcytosine by the TET proteins in human cancer cells. Genome Biol 2014; 15:R81. [PMID: 24958354 PMCID: PMC4197818 DOI: 10.1186/gb-2014-15-6-r81] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/23/2014] [Indexed: 12/31/2022] Open
Abstract
Background The TET family of dioxygenases catalyze conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), but their involvement in establishing normal 5mC patterns during mammalian development and their contributions to aberrant control of 5mC during cellular transformation remain largely unknown. We depleted TET1, TET2, and TET3 in a pluripotent embryonic carcinoma cell model and examined the impact on genome-wide 5mC, 5hmC, and transcriptional patterns. Results TET1 depletion yields widespread reduction of 5hmC, while depletion of TET2 and TET3 reduces 5hmC at a subset of TET1 targets suggesting functional co-dependence. TET2 or TET3 depletion also causes increased 5hmC, suggesting these proteins play a major role in 5hmC removal. All TETs prevent hypermethylation throughout the genome, a finding dramatically illustrated in CpG island shores, where TET depletion results in prolific hypermethylation. Surprisingly, TETs also promote methylation, as hypomethylation was associated with 5hmC reduction. TET function is highly specific to chromatin environment: 5hmC maintenance by all TETs occurs at polycomb-marked chromatin and genes expressed at moderate levels; 5hmC removal by TET2 is associated with highly transcribed genes enriched for H3K4me3 and H3K36me3. Importantly, genes prone to hypermethylation in cancer become depleted of 5hmC with TET deficiency, suggesting that TETs normally promote 5hmC at these loci. Finally, all three TETs, but especially TET2, are required for 5hmC enrichment at enhancers, a condition necessary for expression of adjacent genes. Conclusions These results provide novel insight into the division of labor among TET proteins and reveal important connections between TET activity, the chromatin landscape, and gene expression.
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Wongtrakoongate P, Li J, Andrews PW. Aza-deoxycytidine induces apoptosis or differentiation via DNMT3B and targets embryonal carcinoma cells but not their differentiated derivatives. Br J Cancer 2014; 110:2131-8. [PMID: 24603304 PMCID: PMC3992495 DOI: 10.1038/bjc.2014.128] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Teratocarcinoma is a malignant male germ cell tumour, which contains stem cells and differentiated cancer tissues. DNMT3B has been shown to be highly expressed in human teratocarcinoma stem cells, and to mediate cytotoxicity of Aza-deoxycytidine (Aza-dC) in a pluripotent stem cell line NTERA2. METHODS We have established DNMT3B or POU5F1 (hereafter referred to as OCT4) knockdown in teratocarcinoma stem cells N2102Ep and TERA1 and in the pluripotent NTERA2 by a doxycycline-inducible system, and tested the cytotoxicity induced by Aza-dC. RESULTS Silencing of DNMT3B led to apoptosis of human teratocarcinoma stem cells N2102Ep and TERA1. Further, we found that induction of apoptosis or differentiation in NTERA2 and human embryonic stem cells by Aza-dC requires DNMT3B. To test whether Aza-dC inhibits proliferation of differentiated teratocarcinoma cells, we depleted OCT4 expression in N2102Ep and TERA1 cells treated with Aza-dC. Treatment with Aza-dC reduced cell number of differentiated cells to a lesser extent than their undifferentiated parental stem cells. Moreover, in contrast to the stem cells, Aza-dC failed to induce apoptosis of differentiated cells. CONCLUSIONS Our finding suggests that DNMT3B acts as an antiapoptotic gene in teratocarcinoma stem cells, and mediates apoptosis and differentiation of human pluripotent stem cells induced by Aza-dC, and that Aza-dC specifically induces apoptosis of teratocarcinoma stem cells.
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Affiliation(s)
- P Wongtrakoongate
- Centre for Stem Cell Biology, University of Sheffield, Sheffield S10 2TN, UK
| | - J Li
- Centre for Stem Cell Biology, University of Sheffield, Sheffield S10 2TN, UK
| | - P W Andrews
- Centre for Stem Cell Biology, University of Sheffield, Sheffield S10 2TN, UK
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Kushwaha R, Thodima V, Tomishima MJ, Bosl GJ, Chaganti RSK. miR-18b and miR-518b Target FOXN1 during epithelial lineage differentiation in pluripotent cells. Stem Cells Dev 2014; 23:1149-56. [PMID: 24383669 DOI: 10.1089/scd.2013.0262] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
MicroRNAs (miRNAs) regulate myriad biological processes; however, their role in cell fate choice is relatively unexplored. Pluripotent NT2/D1 embryonal carcinoma cells differentiate into an epithelial/smooth muscle phenotype when treated with bone morphogenetic protein-2 (BMP-2). To identify miRNAs involved in epithelial cell development, we performed miRNA profiling of NT2/D1 cells treated with BMP-2 at 6, 12, and 24 h, and on days 6 and 10. Integration of the miRNA profiling data with previously obtained gene expression profiling (GEP) data of NT2/D1 cells treated with BMP-2 at the same time points identified miR-18b and miR-518b as the top two miRNAs with the highest number of up-regulated predicted targets with known functions in epithelial lineage development. Silencing of miR-18b and miR-518b in NT2/D1 cells revealed several up-regulated TFs with functions in epithelial lineage development; among these, target prediction programs identified FOXN1 as the only direct target of both miRNAs. FOXN1 has previously been shown to play an important role in keratinocyte differentiation and epithelial cell proliferation. NT2/D1 and H9 human embryonic stem cells with silenced miR-18b and miR-518b showed up-regulation of FOXN1 and the epithelial markers CDH1, EPCAM, KRT19, and KRT7. A 3'UTR luciferase assay confirmed FOXN1 to be a target of the two miRNAs, and up-regulation of FOXN1 in NT2/D1 cells led to the expression of epithelial markers. Overexpression of the two miRNAs in BMP-2-treated NT2/D1 cells led to down-regulation of FOXN1 and epithelial lineage markers. These results show that miR-18b and miR-518b are upstream controllers of FOXN1-directed epithelial lineage development.
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Affiliation(s)
- Ritu Kushwaha
- 1 Cell Biology Program, Memorial Sloan-Kettering Cancer Center , New York, New York
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Chiang JH, Cheng WS, Hood L, Tian Q. An epigenetic biomarker panel for glioblastoma multiforme personalized medicine through DNA methylation analysis of human embryonic stem cell-like signature. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:310-23. [PMID: 24601786 DOI: 10.1089/omi.2013.0084] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Alterations of DNA methylation occur during the course of both stem cell development and tumorigenesis. We present a novel strategy that can be used to stratify glioblastoma multiforme (GBM) patients through the epigenetic states of genes associated with human embryonic stem cell (hESC) identity in order to 1) assess linkages between the methylation signatures of these stem cell genes and survival of GBM patients, and 2) delineate putative mechanisms leading to poor prognosis in some patient subgroups. A DNA methylation signature was established for stratifying GBM patients into several hESC methylator subgroups. The hESC methylator-negative phenotype has demonstrated poor survival and upregulation of glioma stem cell (GSC) markers, and is enriched in one of the previously defined transcriptomic phenotypes-the mesenchymal phenotype. We further identified a refined signature of 36 genes as the gene panel, including SOX2, POU3F2, FGFR2, GAP43, NTRK2, NTRK3, and NKX2-2, which are highly enriched in the nervous system. Both signatures outperformed the O6-methylguanine-DNA methyltransferase (MGMT) methylation test in predicting patient's outcome. These findings were also validated through an independent dataset of patients. Furthermore, through statistical analyses, both signatures were examined significantly. Hypomethylation of hESC-associated genes predicted poorer clinical outcome in GBM, supporting the idea that epigenetic activation of stem cell genes contributes to GBM aggression. The gene panel presented herein may be developed into clinical assays for patient stratification and future personalized medicine interventions.
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Affiliation(s)
- Jung-Hsien Chiang
- 1 Department of Computer Science and Information Engineering, National Cheng Kung University , Tainan City, Taiwan
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Li Z, Xie J, Wu J, Li W, Nie L, Sun X, Tang A, Li X, Liu R, Mei H, Wang F, Wang Z, Gui Y, Cai Z. CMTM3 inhibits human testicular cancer cell growth through inducing cell-cycle arrest and apoptosis. PLoS One 2014; 9:e88965. [PMID: 24586462 PMCID: PMC3938458 DOI: 10.1371/journal.pone.0088965] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/16/2014] [Indexed: 01/05/2023] Open
Abstract
Human CMTM3 has been proposed as a putative tumor suppressor gene. The loss of CMTM3 has been found in several carcinomas. However, the regulation of CMTM3 expression and its function in tumor progression remain largely unknown. Here, we investigated the regulation of CMTM3 expression, function and molecular mechanism in human testicular cancer cells. CMTM3 was frequently downregulated or silenced in testicular cancer cell lines and tumor tissues but highly expressed in normal testis tissues. The re-expression of CMTM3 significantly suppressed the colony formation, proliferation, and migration capacity of testicular cancer cells by inducing a G2 cell cycle arrest and apoptosis. Moreover, the re-expression of CMTM3 activated the transcription of p53, induced p53 accumulation, up-regulated the expression of p21, and increased the cleavage of caspase 9, 8, 3, and PARP. The downregulation of CMTM3 in clinical tumor tissues was associated with the methylation of a single CpG site located within the Sp1/Sp3-responsive region of the core promoter. These results indicate that CMTM3 can function as tumor suppressor through the induction of a G2 cell cycle arrest and apoptosis. CMTM3 is thus involved in testicular cancer pathogenesis, and it is frequently at least partially silenced by the methylation of a single, specific CpG site in tumor tissues.
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Affiliation(s)
- Zesong Li
- Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- * E-mail: (ZL); (ZC)
| | - Jun Xie
- Guandong Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
- Department of Clinical Laboratory, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jianting Wu
- Guandong Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Wenjie Li
- Department of Urology, Suzhou municipal Hospital, Suzhou, Anhui, China
| | - Liping Nie
- Department of Clinical Laboratory, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xiaojuan Sun
- Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Aifa Tang
- Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Xianxin Li
- Department of Clinical Laboratory, Peking University Shenzhen Hospital, Shenzhen, China
| | - Ren Liu
- Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Hongbing Mei
- Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Feng Wang
- Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhiping Wang
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, China
| | - Yaoting Gui
- Guandong Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Zhiming Cai
- Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- * E-mail: (ZL); (ZC)
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143
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Cheng WS, Chiang JH. CGPredictor: a systematic integrated analytic tool for mining and examining genome-scale cancer independent prognostic epigenetic marker panels. BMC SYSTEMS BIOLOGY 2014; 7 Suppl 6:S10. [PMID: 24565108 PMCID: PMC4029265 DOI: 10.1186/1752-0509-7-s6-s10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background Tumor biomarkers are potentially useful in several ways such as the identification of individuals at increased risk of developing cancer, in screening for early malignancies and in aiding cancer diagnoses; tumor biomarkers may also be used for determining prognosis, predicting therapeutic response, patient tracking following curative surgery for cancer and for monitoring therapy. Epigenetic alterations, especially aberrant DNA methylation, are recognized as common molecular alterations in a variety of tumors and also occur during the development of tumors. The Cancer Grade Predictor (CGPredictor) is an extendable package with functions designed to facilitate systematic integrated and rapid analysis of high-throughput methylation through the use of most self-similarity subgroups of patients supported by various validating examinations with regarded to survival outcome to obtain the identity of the target predictor. Results We used high-grade serous ovarian cancer (HGSOC) and invasive breast carcinoma (BRCA) to demonstrate the usefulness of the CGPredictor package. The clustering results and the identity predictors worked well and efficiently in producing significant results after various tests were used to validate the usefulness of CGPredictor package. Also, some of the markers for either the HGSOC or BRCA marker panel have been previously reported to reveal significant results. Even when performed using a different platform with an independent large population BRCA dataset for validation, the identity predictor provided an accurate assessment of patient conditions and produced significant results. Conclusions CGPredictor package is not a customized analysis tool designed specifically for the identification of only one or a few specific types of cancer but can be applied more broadly; moreover, the results indicate that the extracted predictors may worthy of consideration for further clinical testing to identify their potential usefulness for clinical molecular diagnosis and targeted treatments of patients with HGSOC and BRCA. So, the use of CGPredictor is feasible for examining the statistical significance of specific markers of interest and shows great potential for use with other types of cancers for cancer biomarker mining.
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Jez M, Ambady S, Kashpur O, Grella A, Malcuit C, Vilner L, Rozman P, Dominko T. Expression and differentiation between OCT4A and its Pseudogenes in human ESCs and differentiated adult somatic cells. PLoS One 2014; 9:e89546. [PMID: 24586860 PMCID: PMC3933561 DOI: 10.1371/journal.pone.0089546] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/22/2014] [Indexed: 12/02/2022] Open
Abstract
The POU5F1 gene codes for the OCT4 transcription factor, which is one of the key regulators of pluripotency. Its transcription, alternative splicing, and alternative translation leading to the synthesis of the active, nuclear localized OCT4A has been described in detail. Much less, however, is known about actively transcribed OCT4 pseudogenes, several of which display high homology to OCT4A and can be expressed and translated into proteins. Using RT-PCR followed by pseudogene-specific restriction digestion, cloning, and sequencing we discriminate between OCT4A and transcripts for pseudogenes 1, 3 and 4. We show that expression of OCT4 and its pseudogenes follows a developmentally-regulated pattern in differentiating hESCs, indicating a tight regulatory relationship between them. We further demonstrate that differentiated human cells from a variety of tissues express exclusively pseudogenes. Expression of OCT4A can, however be triggered in adult differentiated cells by oxygen and FGF2-dependent mechanisms.
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Affiliation(s)
- Mojca Jez
- Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Sakthikumar Ambady
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Olga Kashpur
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Alexandra Grella
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Christopher Malcuit
- Bioengineering Institute, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
- CellThera, Inc., Worcester, Massachusetts, United States of America
| | - Lucy Vilner
- CellThera, Inc., Worcester, Massachusetts, United States of America
| | - Primoz Rozman
- Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Tanja Dominko
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
- Bioengineering Institute, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
- CellThera, Inc., Worcester, Massachusetts, United States of America
- * E-mail:
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145
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Wongtrakoongate P, Li J, Andrews PW. DNMT3B inhibits the re-expression of genes associated with induced pluripotency. Exp Cell Res 2014; 321:231-9. [PMID: 24333507 DOI: 10.1016/j.yexcr.2013.11.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 11/28/2013] [Accepted: 11/30/2013] [Indexed: 12/11/2022]
Abstract
DNMT3B is a de novo DNA methyltransferase that is highly expressed in mouse and human embryonic stem (ES) cells and has been shown to be essential for differentiation of mouse ES cells toward different lineages. In the present study, we found that DNMT3B is rapidly down-regulated in human ES cells during retinoic acid (RA)-induced differentiation compared with DNMT3A2, which is also highly expressed in ES cells. Silencing of DNMT3B in human ES cells by an inducible shRNAi system leads to a reduction of clonal ability of the stem cells, while expression of OCT4 and NANOG is unchanged. By contrast, the germline-specific genes VASA and SCP3 and the surface antigen BE12 are down regulated following DNMT3B knockdown. Upon retinoic acid-induced differentiation, we found that depletion of DNMT3B leads to a decrease in expression of the surface antigen A2B5 and of neural tube-associated genes PAX7 and BRN3A. Consistent with its importance in stem cell differentiation, we observed that silencing of DNMT3B facilitates the generation of cells that bear the hallmarks of pluripotency. Our findings suggest a role of DNMT3B in controlling the differentiation of human ES cells and in the generation of iPS cells.
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Affiliation(s)
- Patompon Wongtrakoongate
- Centre for Stem Cell Biology, University of Sheffield, Alfred Denny Building, Western Bank, S10 2TN, United Kingdom.
| | - Jianliang Li
- Centre for Stem Cell Biology, University of Sheffield, Alfred Denny Building, Western Bank, S10 2TN, United Kingdom
| | - Peter W Andrews
- Centre for Stem Cell Biology, University of Sheffield, Alfred Denny Building, Western Bank, S10 2TN, United Kingdom.
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147
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The WNT receptor FZD7 is required for maintenance of the pluripotent state in human embryonic stem cells. Proc Natl Acad Sci U S A 2014; 111:1409-14. [PMID: 24474766 DOI: 10.1073/pnas.1323697111] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
WNT signaling is involved in maintaining stem cells in an undifferentiated state; however, it is often unclear which WNTs and WNT receptors are mediating these activities. Here we examined the role of the WNT receptor FZD7 in maintaining human embryonic stem cells (hESCs) in an undifferentiated and pluripotent state. FZD7 expression is significantly elevated in undifferentiated cells relative to differentiated cell populations, and interfering with its expression or function, either by short hairpin RNA-mediated knockdown or with a fragment antigen binding (Fab) molecule directed against FZD7, disrupts the pluripotent state of hESCs. The FZD7-specific Fab blocks signaling by Wnt3a protein by down-regulating FZD7 protein levels, suggesting that FZD7 transduces Wnt signals to activate Wnt/β-catenin signaling. These results demonstrate that FZD7 encodes a regulator of the pluripotent state and that hESCs require endogenous WNT/β-catenin signaling through FZD7 to maintain an undifferentiated phenotype.
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148
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An expression signature at diagnosis to estimate prostate cancer patients' overall survival. Prostate Cancer Prostatic Dis 2014; 17:81-90. [PMID: 24394557 PMCID: PMC3921673 DOI: 10.1038/pcan.2013.57] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/14/2013] [Accepted: 11/11/2013] [Indexed: 11/10/2022]
Abstract
Background: This study aimed to identify biomarkers for estimating the overall and prostate cancer (PCa)-specific survival in PCa patients at diagnosis. Methods: To explore the importance of embryonic stem cell (ESC) gene signatures, we identified 641 ESC gene predictors (ESCGPs) using published microarray data sets. ESCGPs were selected in a stepwise manner, and were combined with reported genes. Selected genes were analyzed by multiplex quantitative polymerase chain reaction using prostate fine-needle aspiration samples taken at diagnosis from a Swedish cohort of 189 PCa patients diagnosed between 1986 and 2001. Of these patients, there was overall and PCa-specific survival data available for 97.9%, and 77.9% were primarily treated by hormone therapy only. Univariate and multivariate Cox proportional hazard ratios and Kaplan–Meier plots were used for the survival analysis, and a k-nearest neighbor (kNN) algorithm for estimating overall survival. Results: An expression signature of VGLL3, IGFBP3 and F3 was shown sufficient to categorize the patients into high-, intermediate- and low-risk subtypes. The median overall survival times of the subtypes were 3.23, 4.00 and 9.85 years, respectively. The difference corresponded to hazard ratios of 5.86 (95% confidence interval (CI): 2.91–11.78, P<0.001) for the high-risk subtype and 3.45 (95% CI: 1.79–6.66, P<0.001) for the intermediate-risk compared with the low-risk subtype. The kNN models that included the gene expression signature outperformed the one designed on clinical parameters alone. Conclusions: The expression signature can potentially be used to estimate overall survival time. When validated in future studies, it could be integrated in the routine clinical diagnostic and prognostic procedure of PCa for an optimal treatment decision based on the estimated survival benefit.
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Honecker F, Rohlfing T, Harder S, Braig M, Gillis AJ, Glaesener S, Barett C, Bokemeyer C, Buck F, Brümmendorf TH, Looijenga LH, Balabanov S. Proteome analysis of the effects of all-trans retinoic acid on human germ cell tumor cell lines. J Proteomics 2014; 96:300-13. [DOI: 10.1016/j.jprot.2013.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 10/29/2013] [Accepted: 11/12/2013] [Indexed: 01/16/2023]
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150
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Lee KC, Wong WK, Feng B. Decoding the Pluripotency Network: The Emergence of New Transcription Factors. Biomedicines 2013; 1:49-78. [PMID: 28548056 PMCID: PMC5423462 DOI: 10.3390/biomedicines1010049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 12/25/2022] Open
Abstract
Since the successful isolation of mouse and human embryonic stem cells (ESCs) in the past decades, massive investigations have been conducted to dissect the pluripotency network that governs the ability of these cells to differentiate into all cell types. Beside the core Oct4-Sox2-Nanog circuitry, accumulating regulators, including transcription factors, epigenetic modifiers, microRNA and signaling molecules have also been found to play important roles in preserving pluripotency. Among the various regulations that orchestrate the cellular pluripotency program, transcriptional regulation is situated in the central position and appears to be dominant over other regulatory controls. In this review, we would like to summarize the recent advancements in the accumulating findings of new transcription factors that play a critical role in controlling both pluripotency network and ESC identity.
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Affiliation(s)
- Kai Chuen Lee
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Room 105A, 1/F, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, N.T., Hong Kong, China.
| | - Wing Ki Wong
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Room 105A, 1/F, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, N.T., Hong Kong, China.
| | - Bo Feng
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Room 105A, 1/F, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, N.T., Hong Kong, China.
- SBS Core Laboratory, Shenzhen Research Institute, the Chinese University of Hong Kong, 4/F CUHK Shenzhen Research Institute Building, No.10, 2nd Yuexing Road, Nanshan District, Shenzhen 518057, China.
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