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Lanciano S, Philippe C, Sarkar A, Pratella D, Domrane C, Doucet AJ, van Essen D, Saccani S, Ferry L, Defossez PA, Cristofari G. Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites. CELL GENOMICS 2024; 4:100498. [PMID: 38309261 PMCID: PMC10879037 DOI: 10.1016/j.xgen.2024.100498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/20/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
Long interspersed element 1 (L1) retrotransposons are implicated in human disease and evolution. Their global activity is repressed by DNA methylation, but deciphering the regulation of individual copies has been challenging. Here, we combine short- and long-read sequencing to unveil L1 methylation heterogeneity across cell types, families, and individual loci and elucidate key principles involved. We find that the youngest primate L1 families are specifically hypomethylated in pluripotent stem cells and the placenta but not in most tumors. Locally, intronic L1 methylation is intimately associated with gene transcription. Conversely, the L1 methylation state can propagate to the proximal region up to 300 bp. This phenomenon is accompanied by the binding of specific transcription factors, which drive the expression of L1 and chimeric transcripts. Finally, L1 hypomethylation alone is typically insufficient to trigger L1 expression due to redundant silencing pathways. Our results illuminate the epigenetic and transcriptional interplay between retrotransposons and their host genome.
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Affiliation(s)
- Sophie Lanciano
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Claude Philippe
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Arpita Sarkar
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - David Pratella
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Cécilia Domrane
- University Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Aurélien J Doucet
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Dominic van Essen
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Simona Saccani
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Laure Ferry
- University Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | | | - Gael Cristofari
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France.
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Bialecka M, Montilla-Rojo J, Roelen BAJ, Gillis AJ, Looijenga LHJ, Salvatori DCF. Humanised Mice and Immunodeficient Mice (NSG) Are Equally Sensitive for Prediction of Stem Cell Malignancy in the Teratoma Assay. Int J Mol Sci 2022; 23:ijms23094680. [PMID: 35563071 PMCID: PMC9105268 DOI: 10.3390/ijms23094680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 11/26/2022] Open
Abstract
The use of human pluripotent stem cells (hPSCs) in regenerative medicine has great potential. However, it is important to exclude that these cells can undergo malignant transformation, which could lead to the development of malignant tumours. This property of hPSCs is currently being tested using the teratoma assay, through which cells are injected into immunodeficient mice. Transplantation of stem cells in immunocompromised recipient animals certainly has a much higher incidence of tumour formation. On the other hand, the results obtained in immunodeficient mice could indicate a risk of tumour formation that is practically not present in the human immunocompetent recipient. The presence of a humanised immune system might be more representative of the human situation; therefore, we investigated if the demonstrated malignant features of chosen and well-characterised stem cell lines could be retrieved and if new features could arise in a humanised mouse model. Hu-CD34NSGTM (HIS) mice were compared side by side with immunocompromised mice (NSG) after injection of a set of benign (LU07) and malignant (LU07+dox and 2102Ep) cell lines. Analysis of the tumour development, histological composition, pathology evaluation, and malignancy-associated miRNA expression levels, both in tumour and plasma samples, revealed no differences among mouse groups. This indicates that the HIS mouse model is comparable to, but not more sensitive than, the NSG immunodeficient model for studying the malignancy of stem cells. Since in vivo teratoma assay is cumbersome, in vitro methods for the detection of malignancy are urgently needed.
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Affiliation(s)
- Monika Bialecka
- Anatomy and Physiology, Department Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands; (M.B.); (J.M.-R.); (B.A.J.R.)
| | - Joaquin Montilla-Rojo
- Anatomy and Physiology, Department Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands; (M.B.); (J.M.-R.); (B.A.J.R.)
| | - Bernard A. J. Roelen
- Anatomy and Physiology, Department Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands; (M.B.); (J.M.-R.); (B.A.J.R.)
| | - Ad J. Gillis
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (A.J.G.); (L.H.J.L.)
| | - Leendert H. J. Looijenga
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (A.J.G.); (L.H.J.L.)
| | - Daniela. C. F. Salvatori
- Anatomy and Physiology, Department Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands; (M.B.); (J.M.-R.); (B.A.J.R.)
- Correspondence:
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3
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Proteomic profiling of cisplatin-resistant and cisplatin-sensitive germ cell tumour cell lines using quantitative mass spectrometry. World J Urol 2022; 40:373-383. [PMID: 35084545 PMCID: PMC8921118 DOI: 10.1007/s00345-022-03936-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 01/07/2022] [Indexed: 01/23/2023] Open
Abstract
Purpose Advanced testicular germ cell tumours (GCT) generally have a good prognosis owing to their unique sensitivity towards cisplatin-based chemotherapies. However, cisplatin-resistant GCT have a poor outcome. Further studies are mandatory to better understand resistance mechanisms and develop therapeutic strategies for refractory GCTs. Methods Protein levels in cisplatin-resistant GCT cell lines of NTERA-2, NCCIT and 2102EP were analyzed by quantitative proteomic mass spectrometry (MS) in combination with stable isotope labelling by amino acids in cell culture (SILAC). Differentially abundant protein markers of acquired cisplatin resistance were validated by Western blotting. Comprehensive bioinformatical annotation using gene set enrichment analyses (GSEA) and STRING interaction analysis were performed to identify commonly affected pathways in cisplatin resistance and the data were compared to the GCT cohort of the ‘The Cancer Genome Atlas’.
Results A total of 4375 proteins were quantified by MS, 144 of which were found to be differentially abundant between isogenic resistant and sensitive cell line pairs (24 proteins for NTERA-2, 60 proteins for NCCIT, 75 proteins for 2102EP). Western blotting confirmed regulation of key resistance-associated proteins (CBS, ANXA1, LDHA, CTH, FDXR). GSEA revealed a statistically significant enrichment of DNA repair-associated proteins in all three resistant cell lines and specific additional processes for individual cell lines. Conclusion High resolution MS combined with SILAC is a powerful tool and 144 significantly deregulated proteins were found in cisplatin-resistant GCT cell lines. Our study provides the largest proteomic in vitro library for cisplatin resistance in GCT, yet, enabling further studies to develop new treatment options for patients with refractory GCT. Supplementary Information The online version contains supplementary material available at 10.1007/s00345-022-03936-1.
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4
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Kusena JWT, Shariatzadeh M, Studd AJ, James JR, Thomas RJ, Wilson SL. The importance of cell culture parameter standardization: an assessment of the robustness of the 2102Ep reference cell line. Bioengineered 2021; 12:341-357. [PMID: 33380247 PMCID: PMC8806261 DOI: 10.1080/21655979.2020.1870074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 11/24/2022] Open
Abstract
Work undertaken using the embryonic carcinoma 2102Ep line, highlighted the requirement for robust, well-characterized and standardized protocols. A systematic approach utilizing 'quick hit' experiments demonstrated variability introduced into culture systems resulting from slight changes to culture conditions (route A). This formed the basis for longitudinal experiments investigating long-term effects of culture parameters including seeding density and feeding regime (route B).Results demonstrated that specific growth rates (SGR) of passage 59 (P59) cells seeded at 20,000 cells/cm2 and subjected to medium exchange after 48h prior to reseeding at 72h (route B2) on average was marginally higher than, P55 cells cultured under equivalent conditions (route A1); whereby SGR values were (0.021±0.004) and (0.019±0.004). Viability was higher in route B2 over 10 passages with average viability reported as (86.3%±8.1) compared to route A1 (83.3±8.8). The metabolite data demonstrated both culture route B1 (P57 cells seeded at 66,667 cells/cm2) and B2 had consistent-specific metabolite rates (SMR) for glucose, but SMR values of route B1 was consistently lower than route B2 (0.00001 mmol, cell-1.d-1 and 0.000025).Results revealed interactions between phenotype, SMR and feeding regime that may not be accurately reflected by growth rate or observed morphology. This implies that current schemes of protocol control do not adequately account for variability, since key cell characteristics, including phenotype and SMR, change regardless of standardized seeding densities. This highlights the need to control culture parameters through defined protocols, for processes that involve culture for therapeutic use, biologics production, and reference lines.
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Affiliation(s)
- James Willard Tonderai Kusena
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire, UK
| | - Maryam Shariatzadeh
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire, UK
| | - Adam James Studd
- Stem Cell Glycobiology Group, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Jenna Rebekah James
- Stem Cell Glycobiology Group, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Robert James Thomas
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire, UK
| | - Samantha Loiuse Wilson
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire, UK
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5
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Kusena JWT, Shariatzadeh M, Thomas RJ, Wilson SL. Understanding cell culture dynamics: a tool for defining protocol parameters for improved processes and efficient manufacturing using human embryonic stem cells. Bioengineered 2021; 12:979-996. [PMID: 33757391 PMCID: PMC8806349 DOI: 10.1080/21655979.2021.1902696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 12/16/2022] Open
Abstract
Standardization is crucial when culturing cells including human embryonic stem cells (hESCs) which are valuable for therapy development and disease modeling. Inherent issues regarding reproducibility of protocols are problematic as they hinder translation to good manufacturing practice (GMP), thus reducing clinical efficacy and uptake. Pluripotent cultures require standardization to ensure that input material is consistent prior to differentiation, as inconsistency of input cells creates end-product variation. To improve protocols, developers first must understand the cells they are working with and their related culture dynamics. This innovative work highlights key conditions required for optimized and cost-effective bioprocesses compared to generic protocols typically implemented. This entailed investigating conditions affecting growth, metabolism, and phenotype dynamics to ensure cell quality is appropriate for use. Results revealed critical process parameters (CPPs) including feeding regime and seeding density impact critical quality attributes (CQAs) including specific metabolic rate (SMR) and specific growth rate (SGR). This implied that process understanding, and control is essential to maintain key cell characteristics, reduce process variation and retain CQAs. Examination of cell dynamics and CPPs permitted the formation of a defined protocol for culturing H9 hESCs. The authors recommend that H9 seeding densities of 20,000 cells/cm2, four-day cultures or three-day cultures following a recovery passage from cryopreservation and 100% medium exchange after 48 hours are optimal. These parameters gave ~SGR of 0.018 hour-1 ± 1.5x10-3 over three days and cell viabilities ≥95%±0.4, while producing cells which highly expressed pluripotent and proliferation markers, Oct3/4 (>99% positive) and Ki-67 (>99% positive).
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Affiliation(s)
- J W T Kusena
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Epinal Way, Loughborough University, Loughborough, Leicestershire, UK
| | - M Shariatzadeh
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Epinal Way, Loughborough University, Loughborough, Leicestershire, UK
| | - R J Thomas
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Epinal Way, Loughborough University, Loughborough, Leicestershire, UK
| | - S L Wilson
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Epinal Way, Loughborough University, Loughborough, Leicestershire, UK
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Dvir S, Argoetti A, Lesnik C, Roytblat M, Shriki K, Amit M, Hashimshony T, Mandel-Gutfreund Y. Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. Cell Rep 2021; 35:109198. [PMID: 34077720 DOI: 10.1016/j.celrep.2021.109198] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
Embryonic stem cell (ESC) self-renewal and cell fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during early stem cell differentiation. Notably, many RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly targeted by this factor. Using cross-linking and immunoprecipitation (CLIP-seq), we find that the pluripotency-associated STAT3 and OCT4 transcription factors interact with RNA in hESCs and confirm the binding of STAT3 to the conserved NORAD long-noncoding RNA. Our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated.
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Affiliation(s)
- Shlomi Dvir
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Chen Lesnik
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | | | | | - Michal Amit
- Accellta LTD, Haifa 320003, Israel; Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College, Karmiel 2161002, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel; Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel.
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7
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Lobo J, Constâncio V, Guimarães-Teixeira C, Leite-Silva P, Miranda-Gonçalves V, Sequeira JP, Pistoni L, Guimarães R, Cantante M, Braga I, Maurício J, Looijenga LHJ, Henrique R, Jerónimo C. Promoter methylation of DNA homologous recombination genes is predictive of the responsiveness to PARP inhibitor treatment in testicular germ cell tumors. Mol Oncol 2021; 15:846-865. [PMID: 33513287 PMCID: PMC8024740 DOI: 10.1002/1878-0261.12909] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Testicular germ cell tumors (TGCTs) are the most common cancers in men aged 15-39 years and are divided into two major groups, seminomas and nonseminomas. Novel treatment options are required for these patients, to limit side effects of chemotherapy. We hypothesized that promoter methylation of relevant homologous recombination (HR) genes might be predictive of response to poly-ADP ribose polymerase inhibitors (PARPis) in TGCTs. We report a study pipeline combining in silico, in vitro, and clinical steps. By using several databases and in silico tools, we identified BRCA1, RAD51C, PALB2, RAD54B, and SYCP3 as the most relevant genes for further investigation and pinpointed specific CpG sites with pronounced negative correlation to gene expression. Nonseminomas displayed significantly higher methylation levels for all target genes, where increased methylation was observed in patients with more differentiated subtypes and higher disease burden. We independently performed second-line targeted validation in tissue series from TGCT patients. A moderate and/or strong anti-correlation between gene expression (assessed by RNA-sequencing) and promoter methylation (assessed by 450k array) was found, for all of the targets. As a proof of concept, we demonstrated the sensitivity of TGCT cell lines to Olaparib, which associated with differential methylation levels of a subset of targets, namely BRCA1 and RAD51C. Our findings support the use of HR genes promoter methylation as a predictor of the therapeutic response to PARPis in patients with TGCT.
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Affiliation(s)
- João Lobo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P, CCC), Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Portugal.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Vera Constâncio
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P, CCC), Portugal
| | - Catarina Guimarães-Teixeira
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P, CCC), Portugal
| | - Pedro Leite-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P, CCC), Portugal
| | - Vera Miranda-Gonçalves
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P, CCC), Portugal
| | - José Pedro Sequeira
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P, CCC), Portugal
| | - Laura Pistoni
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P, CCC), Portugal.,Department of Biology, University of Pisa, Italy
| | - Rita Guimarães
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P, CCC), Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), Portugal
| | - Mariana Cantante
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P, CCC), Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), Portugal
| | - Isaac Braga
- Department of Urology, Portuguese Oncology Institute of Porto (IPOP), Portugal
| | - Joaquina Maurício
- Department of Medical Oncology, Portuguese Oncology Institute of Porto (IPOP), Portugal
| | | | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P, CCC), Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P, CCC), Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Portugal
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Targeting Germ Cell Tumors with the Newly Synthesized Flavanone-Derived Compound MLo1302 Efficiently Reduces Tumor Cell Viability and Induces Apoptosis and Cell Cycle Arrest. Pharmaceutics 2021; 13:pharmaceutics13010073. [PMID: 33430420 PMCID: PMC7826804 DOI: 10.3390/pharmaceutics13010073] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/20/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022] Open
Abstract
Less toxic treatment strategies for testicular germ cell tumor (TGCT) patients are needed, as overtreatment is a concern due to the long-term side effects of platin-based chemotherapy. Although clinical benefit from classical hypomethylating agents has to date been limited, TGCTs show an abnormal DNA methylome indicating the potential of treating TGCTs with hypomethylating drugs. We tested, for the first time in TGCT cell lines, a new synthetic flavonoid compound (MLo1302) from the 3-nitroflavanone family of DNA methyltransferase (DNMT) inhibitors. We show that MLo1302 reduces cell viability (including of cisplatin resistant cell line NCCIT-R), with IC50s (inhibitory concentration 50) within the nanomolar range for NCCIT and NTERA-2 cells, and proved its cytotoxic effect. Exposure to MLo1302 reduced DNMT protein expression, similar to decitabine, and showed a partial effect in cell differentiation, reducing protein expression of pluripotency markers. RT2 profiler expression array indicated several dysregulated targets, related to activation of apoptosis, differentiation, and cell cycle arrest. We validated these data by showing increased apoptosis, increased protein expression of cleaved caspase 8 and activated caspase 2, and reduced proliferation (BrdU assay), with increase in CDKN1A and decrease in MIB-1 expression. Therefore, synthetic drugs designed to target DNA methylation in cells may uncover effective treatments for TGCT patients.
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9
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Abstract
Mobile genetic elements have significantly shaped our genomic landscape. LINE-1 retroelements are the only autonomously active elements left in the human genome. Since new insertions can have detrimental consequences, cells need to efficiently control LINE-1 retrotransposition. Here, we demonstrate that the intrinsic immune factor TRIM5α senses and restricts LINE-1 retroelements. Previously, rhesus TRIM5α has been shown to efficiently block HIV-1 replication, while human TRIM5α was found to be less active. Surprisingly, we found that both human and rhesus TRIM5α efficiently repress human LINE-1 retrotransposition. TRIM5α interacts with LINE-1 ribonucleoprotein complexes in the cytoplasm, which is essential for restriction. In line with its postulated role as pattern recognition receptor, we show that TRIM5α also induces innate immune signaling upon interaction with LINE-1 ribonucleoprotein complexes. The signaling events activate the transcription factors AP-1 and NF-κB, leading to the down-regulation of LINE-1 promoter activity. Together, our findings identify LINE-1 as important target of human TRIM5α, which restricts and senses LINE-1 via two distinct mechanisms. Our results corroborate TRIM5α as pattern recognition receptor and shed light on its previously undescribed activity against mobile genetic elements, such as LINE-1, to protect the integrity of our genome.
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10
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Shariatzadeh M, Chandra A, Wilson SL, McCall MJ, Morizur L, Lesueur L, Chose O, Gepp MM, Schulz A, Neubauer JC, Zimmermann H, Abranches E, Man J, O’Shea O, Stacey G, Hewitt Z, Williams DJ. Distributed automated manufacturing of pluripotent stem cell products. THE INTERNATIONAL JOURNAL, ADVANCED MANUFACTURING TECHNOLOGY 2020; 106:1085-1103. [PMID: 31983799 PMCID: PMC6954896 DOI: 10.1007/s00170-019-04516-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/27/2019] [Indexed: 05/04/2023]
Abstract
Establishing how to effectively manufacture cell therapies is an industry-level problem. Decentralised manufacturing is of increasing importance, and its challenges are recognised by healthcare regulators with deviations and comparability issues receiving specific attention from them. This paper is the first to report the deviations and other risks encountered when implementing the expansion of human pluripotent stem cells (hPSCs) in an automated three international site-decentralised manufacturing setting. An experimental demonstrator project expanded a human embryonal carcinoma cell line (2102Ep) at three development sites in France, Germany and the UK using the CompacT SelecT (Sartorius Stedim, Royston, UK) automated cell culture platform. Anticipated variations between sites spanned material input, features of the process itself and production system details including different quality management systems and personnel. Where possible, these were pre-addressed by implementing strategies including standardisation, cell bank mycoplasma testing and specific engineering and process improvements. However, despite such measures, unexpected deviations occurred between sites including software incompatibility and machine/process errors together with uncharacteristic contaminations. Many only became apparent during process proving or during the process run. Further, parameters including growth rate and viability discrepancies could only be determined post-run, preventing 'live' corrective measures. The work confirms the critical nature of approaches usually taken in Good Manufacturing Practice (GMP) manufacturing settings and especially emphasises the requirement for monitoring steps to be included within the production system. Real-time process monitoring coupled with carefully structured quality systems is essential for multiple site working including clarity of decision-making roles. Additionally, an over-reliance upon post-process visual microscopic comparisons has major limitations; it is difficult for non-experts to detect deleterious culture changes and such detection is slow.
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Affiliation(s)
- Maryam Shariatzadeh
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU UK
| | - Amit Chandra
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU UK
- Present Address: Yposkesi, 26, rue Henri Auguste-Desbruères, 91100 Corbeil-Essonnes, France
| | - Samantha L Wilson
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU UK
| | - Mark J McCall
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU UK
| | - Lise Morizur
- CECS/I-STEM, 28, rue Henri Auguste-Desbruères, 91100 Corbeil-Essonnes, France
| | - Léa Lesueur
- CECS/I-STEM, 28, rue Henri Auguste-Desbruères, 91100 Corbeil-Essonnes, France
| | - Olivier Chose
- CECS/I-STEM, 28, rue Henri Auguste-Desbruères, 91100 Corbeil-Essonnes, France
| | - Michael M. Gepp
- Fraunhofer Institute for Biomedical Engineering (IBMT), Joseph-von-Fraunhofer-Weg 1, 66280 Sulzbach, Germany
- Fraunhofer Project Center for Stem Cell Process Engineering, Neunerplatz 2, 97082 Würzburg, Germany
| | - André Schulz
- Fraunhofer Institute for Biomedical Engineering (IBMT), Joseph-von-Fraunhofer-Weg 1, 66280 Sulzbach, Germany
- Present Address: Knappschaft Eye Clinic Sulzbach, An der Klinik 10, 66280 Sulzbach, Germany
| | - Julia C. Neubauer
- Fraunhofer Institute for Biomedical Engineering (IBMT), Joseph-von-Fraunhofer-Weg 1, 66280 Sulzbach, Germany
- Fraunhofer Project Center for Stem Cell Process Engineering, Neunerplatz 2, 97082 Würzburg, Germany
| | - Heiko Zimmermann
- Fraunhofer Institute for Biomedical Engineering (IBMT), Joseph-von-Fraunhofer-Weg 1, 66280 Sulzbach, Germany
- Fraunhofer Project Center for Stem Cell Process Engineering, Neunerplatz 2, 97082 Würzburg, Germany
- Saarland University, 66123 Saarbruecken, Germany
- Universidad Católica del Norte, Coquimbo, Chile
| | - Elsa Abranches
- NISBC, Blanche Lane, South Mimms, Potters Bar, EN6 3QG UK
| | - Jennifer Man
- NISBC, Blanche Lane, South Mimms, Potters Bar, EN6 3QG UK
- Present Address: Oxfordshire, UK
| | - Orla O’Shea
- NISBC, Blanche Lane, South Mimms, Potters Bar, EN6 3QG UK
| | - Glyn Stacey
- NISBC, Blanche Lane, South Mimms, Potters Bar, EN6 3QG UK
- Present Address: Adaptimmune, 60 Jubilee Avenue, Milton Park, Abingdon, Oxfordshire OX14 4RX UK
| | - Zoe Hewitt
- Centre for Stem Cell Biology (CSCB), University of Sheffield, Western Bank, Sheffield, S10 2TN UK
| | - David J Williams
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU UK
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11
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Gordeeva O. TGFβ Family Signaling Pathways in Pluripotent and Teratocarcinoma Stem Cells' Fate Decisions: Balancing Between Self-Renewal, Differentiation, and Cancer. Cells 2019; 8:cells8121500. [PMID: 31771212 PMCID: PMC6953027 DOI: 10.3390/cells8121500] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 12/11/2022] Open
Abstract
The transforming growth factor-β (TGFβ) family factors induce pleiotropic effects and are involved in the regulation of most normal and pathological cellular processes. The activity of different branches of the TGFβ family signaling pathways and their interplay with other signaling pathways govern the fine regulation of the self-renewal, differentiation onset and specialization of pluripotent stem cells in various cell derivatives. TGFβ family signaling pathways play a pivotal role in balancing basic cellular processes in pluripotent stem cells and their derivatives, although disturbances in their genome integrity induce the rearrangements of signaling pathways and lead to functional impairments and malignant transformation into cancer stem cells. Therefore, the identification of critical nodes and targets in the regulatory cascades of TGFβ family factors and other signaling pathways, and analysis of the rearrangements of the signal regulatory network during stem cell state transitions and interconversions, are key issues for understanding the fundamental mechanisms of both stem cell biology and cancer initiation and progression, as well as for clinical applications. This review summarizes recent advances in our understanding of TGFβ family functions in naїve and primed pluripotent stem cells and discusses how these pathways are involved in perturbations in the signaling network of malignant teratocarcinoma stem cells with impaired differentiation potential.
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Affiliation(s)
- Olga Gordeeva
- Kol'tsov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov str., 119334 Moscow, Russia
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12
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Singh R, Fazal Z, Freemantle SJ, Spinella MJ. Mechanisms of cisplatin sensitivity and resistance in testicular germ cell tumors. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2019; 2:580-594. [PMID: 31538140 PMCID: PMC6752046 DOI: 10.20517/cdr.2019.19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Testicular germ cell tumors (TGCTs) are a cancer pharmacology success story with a majority of patients cured even in the highly advanced and metastatic setting. Successful treatment of TGCTs is primarily due to the exquisite responsiveness of this solid tumor to cisplatin-based therapy. However, a significant percentage of patients are, or become, refractory to cisplatin and die from progressive disease. Mechanisms for both clinical hypersensitivity and resistance have largely remained a mystery despite the promise of applying lessons to the majority of solid tumors that are not curable in the metastatic setting. Recently, this promise has been heightened by the realization that distinct (and perhaps pharmacologically replicable) epigenetic states, rather than fixed genetic alterations, may play dominant roles in not only TGCT etiology and progression but also their curability with conventional chemotherapies. In this review, it discusses potential mechanisms of TGCT cisplatin sensitivity and resistance to conventional chemotherapeutics.
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Affiliation(s)
- Ratnakar Singh
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zeeshan Fazal
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sarah J Freemantle
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Michael J Spinella
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,The Carle Illinois College of Medicine , University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,The Cancer Center of Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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13
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Das MK, Evensen HSF, Furu K, Haugen TB. miRNA-302s may act as oncogenes in human testicular germ cell tumours. Sci Rep 2019; 9:9189. [PMID: 31235829 PMCID: PMC6591358 DOI: 10.1038/s41598-019-45573-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 06/10/2019] [Indexed: 12/19/2022] Open
Abstract
Testicular germ cell tumour (TGCT) represents the most common malignancy in young men in large parts of the world, but the aetiology is yet unclear. Multiple TGCT susceptibility loci have been identified, and we have shown that one of these, SPRY4, may act as a TGCT oncogene. Furthermore, many of the loci are in non-coding regions of the genome. miRNAs, a class of non-coding RNAs may play a crucial role in cell proliferation, differentiation, and apoptosis, and alteration in their expression may lead to oncogenesis. Differential expression of miRNAs in TGCT and normal testis has been reported in previous studies. In this study, we used qPCR to analyse, in normal and malignant testis tissue, the expression of the ten miRNAs that we had previously identified by sequencing to be the most upregulated in TGCT. We found high expression of these miRNAs also by qPCR analysis. The levels of miR-302a-3p, miR-302b-3p, and miR-302c-3p were downregulated after treatment of the TGCT cell lines NT2-D1 and 833 K with the chemotherapy drug cisplatin. By using miRNA inhibitor-mediated transient transfection, we inhibited the expression of the three members of miR-302 family (miR-302s). Inhibition of miR-302s resulted in a decreased cell proliferation in NT2-D1 cells, but not in 833 K cells. In both cell lines, inhibition of miR-302s resulted in decreased expression of SPRY4, which we have previously shown to regulate MAPK/ERK and PI3K/Akt signalling pathways in these cells. Inhibition of miR-302b-3p and miR-302c-3p decreased phosphorylation of ERK1/2, whereas inhibition of miR-302a-3p and miR-302b-3p led to decreased expression of the apoptosis inhibitor, survivin. Our findings suggest that miR-302s act as TGCT oncogenes by inducing the expression of SPRY4 and activating MAPK/ERK pathway while inhibiting apoptosis via increased survivin expression.
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Affiliation(s)
- Mrinal K Das
- Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway.
| | - Herman S F Evensen
- Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Kari Furu
- Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway.,Cancer Registry, Oslo, Norway
| | - Trine B Haugen
- Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
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14
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Gomes Fernandes M, Bialecka M, Salvatori DCF, Chuva de Sousa Lopes SM. Characterization of migratory primordial germ cells in the aorta-gonad-mesonephros of a 4.5-week-old human embryo: a toolbox to evaluate in vitro early gametogenesis. Mol Hum Reprod 2019. [PMID: 29528446 PMCID: PMC6018722 DOI: 10.1093/molehr/gay011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
STUDY QUESTION Which set of antibodies can be used to identify migratory and early post-migratory human primordial germ cells (hPGCs)? STUDY FINDING We validated the specificity of 33 antibodies for 31 markers, including POU5F1, NANOG, PRDM1 and TFAP2C as specific markers of hPGCs at 4.5 weeks of development of Carnegie stage (CS12–13), whereas KIT and SOX17 also marked the intra-aortic hematopoietic stem cell cluster in the aorta-gonad-mesonephros (AGM). WHAT IS KNOWN ALREADY The dynamics of gene expression during germ cell development in mice is well characterized and this knowledge has proved crucial to allow the development of protocols for the in vitro derivation of functional gametes. Although there is a great interest in generating human gametes in vitro, it is still unclear which markers are expressed during the early stages of hPGC development and many studies use markers described in mouse to benchmark differentiation of human PGC-like cells (hPGCLCs). Early post-implantation development differs significantly between mice and humans, and so some germ cells markers, including SOX2, SOX17, IFITM3 and ITGA6 may not identify mPGCs and hPGCs equally well. STUDY DESIGN, SIZE, DURATION This immunofluorescence study investigated the expression of putative hPGC markers in the caudal part of a single human embryo at 4.5 weeks of development. PARTICIPANTS/MATERIALS, SETTING, METHODS We have investigated by immunofluorescence the expression of a set of 33 antibodies for 31 markers, including pluripotency, germ cell, adhesion, migration, surface, mesenchymal and epigenetic markers on paraffin sections of the caudal part, including the AGM region, of a single human embryo (CS12–13). The human material used was anonymously donated with informed consent from elective abortions without medical indication. MAIN RESULTS AND THE ROLE OF CHANCE We observed germ cell specific expression of NANOG, TFAP2C and PRDM1 in POU5F1+ hPGCs in the AGM. The epigenetic markers H3K27me3 and 5mC were sufficient to distinguish hPGCs from the surrounding somatic cells. Some mPGC-markers were not detected in hPGCs, but marked other tissues; whereas other markers, such as ALPL, SOX17, KIT, TUBB3, ITGA6 marked both POU5F1+ hPGCs and other cells in the AGM. We used a combination of multiple markers, immunostaining different cellular compartments when feasible, to decrease the chance of misidentifying hPGCs. LARGE SCALE DATA Non-applicable. LIMITATIONS REASONS FOR CAUTION Material to study early human development is unique and very rare thus restricting the sample size. We have used a combination of antibodies limited by the number of paraffin sections available. WIDER IMPLICATIONS OF THE FINDINGS Most of our knowledge on early gametogenesis has been obtained from model organisms such as mice and is extrapolated to humans. However, since there is a dedicated effort to produce human artificial gametes in vitro, it is of great importance to determine the expression and specificity of human-specific germ cell markers. We provide a systematic analysis of the expression of 31 different markers in paraffin sections of a CS12–13 embryo. Our results will help to set up a toolbox of markers to evaluate protocols to induce hPGCLCs in vitro. STUDY FUNDING AND COMPETING INTEREST(S) M.G.F. was funded by Fundação para a Ciência e Tecnologia (FCT) [SFRH/BD/78689/2011] and S.M.C.S.L. was funded by the Interuniversity Attraction Poles (IAP, P7/07) and the European Research Council Consolidator (ERC-CoG-725722-OVOGROWTH). The authors declare no conflict of interest.
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Affiliation(s)
- Maria Gomes Fernandes
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden 2333-ZC, The Netherlands
| | - Monika Bialecka
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden 2333-ZC, The Netherlands
| | - Daniela C F Salvatori
- Central Laboratory Animal Facility, Leiden University Medical Center, Leiden 2333-ZC, The Netherlands
| | - Susana M Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden 2333-ZC, The Netherlands.,Department for Reproductive Medicine, Ghent University Hospital, Ghent 9000, Belgium
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15
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Nettersheim D, Berger D, Jostes S, Kristiansen G, Lochnit G, Schorle H. N6-Methyladenosine detected in RNA of testicular germ cell tumors is controlled by METTL3, ALKBH5, YTHDC1/F1/F2, and HNRNPC as writers, erasers, and readers. Andrology 2019; 7:498-506. [PMID: 30903744 DOI: 10.1111/andr.12612] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/18/2019] [Accepted: 02/24/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Type II testicular germ cell tumors (GCTs) arise from a common precursor lesion (germ cell neoplasia in situ) and are stratified into seminomas and non-seminomas, which differ considerably in morphology, gene expression, and epigenetic landscape. The N6-methyladenosine (6mA) epigenetic modification is the most abundant modification in mRNA and is also detectable in eukaryotic DNA. The functional role of 6mA is not fully understood, but 6mA residues may influence transcription by affecting splicing, miRNA processing, and mRNA stability. Additionally, the methyl group of 6mA destabilizes Watson-Crick base-pairing affecting RNA structure and protein binding. OBJECTIVES Here, we analyzed the presence of the 6mA epigenetic modification in germ cells and GCT tissues and cell lines. MATERIALS AND METHODS We screened for the presence of 6mA in DNA and RNA by immunohistochemistry, mass spectrometry or ELISA-based quantification assays. Additionally, expression of 6mA writer-, eraser- and reader-factors was analyzed by microarrays, qRT-PCR, western blotting and screening of public databases. RESULTS We demonstrate that 6mA is detectable in RNA, but not DNA, of GCT cell lines and tissues, fibroblasts, and Sertoli cells as well as germ cells of different developmental stages. Based on expression analyses, our results suggest METTL3, ALKBH5, YTHDC1, YTHDF1, YTHDF2 and HNRNPC as main writers, erasers, and readers of the 6mA modification in GCTs. DISCUSSION Owing to the lack of 6mA in DNA of GCTs, a functional role in regulating DNA transcription can be excluded. Interestingly, expression levels of 6mA regulators are comparable between tumor and normal tissues/cells, suggesting a similar mechanism of 6mA regulation in RNA. Finally, we demonstrate that 6mA levels in RNA increase upon differentiation of GCT cell lines, suggesting a role of 6mA in cell fate decisions. CONCLUSION In summary, our data provide the starting point for further experiments deciphering the role of 6mA in the RNA of GCTs.
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Affiliation(s)
- D Nettersheim
- Department of Urology, Urological Research Lab, Translational Urooncology, University Medical School Düsseldorf, Düsseldorf, Germany
| | - D Berger
- Department of Developmental Pathology, Institute of Pathology, Bonn University Medical School, Bonn, Germany
| | - S Jostes
- Department of Developmental Pathology, Institute of Pathology, Bonn University Medical School, Bonn, Germany
| | - G Kristiansen
- Institute of Pathology, Bonn University Medical School, Bonn, Germany
| | - G Lochnit
- Institute of Biochemistry, Protein Analytics, Justus-Liebig University Giessen, Giessen, Germany
| | - H Schorle
- Department of Developmental Pathology, Institute of Pathology, Bonn University Medical School, Bonn, Germany
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16
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Pereira GC, Sanchez L, Schaughency PM, Rubio-Roldán A, Choi JA, Planet E, Batra R, Turelli P, Trono D, Ostrow LW, Ravits J, Kazazian HH, Wheelan SJ, Heras SR, Mayer J, García-Pérez JL, Goodier JL. Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis. Mob DNA 2018; 9:35. [PMID: 30564290 PMCID: PMC6295051 DOI: 10.1186/s13100-018-0138-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease involving loss of motor neurons and having no known cure and uncertain etiology. Several studies have drawn connections between altered retrotransposon expression and ALS. Certain features of the LINE-1 (L1) retrotransposon-encoded ORF1 protein (ORF1p) are analogous to those of neurodegeneration-associated RNA-binding proteins, including formation of cytoplasmic aggregates. In this study we explore these features and consider possible links between L1 expression and ALS. RESULTS We first considered factors that modulate aggregation and subcellular distribution of LINE-1 ORF1p, including nuclear localization. Changes to some ORF1p amino acid residues alter both retrotransposition efficiency and protein aggregation dynamics, and we found that one such polymorphism is present in endogenous L1s abundant in the human genome. We failed, however, to identify CRM1-mediated nuclear export signals in ORF1p nor strict involvement of cell cycle in endogenous ORF1p nuclear localization in human 2102Ep germline teratocarcinoma cells. Some proteins linked with ALS bind and colocalize with L1 ORF1p ribonucleoprotein particles in cytoplasmic RNA granules. Increased expression of several ALS-associated proteins, including TAR DNA Binding Protein (TDP-43), strongly limits cell culture retrotransposition, while some disease-related mutations modify these effects. Using quantitative reverse transcription PCR (RT-qPCR) of ALS tissues and reanalysis of publicly available RNA-Seq datasets, we asked if changes in expression of retrotransposons are associated with ALS. We found minimal altered expression in sporadic ALS tissues but confirmed a previous report of differential expression of many repeat subfamilies in C9orf72 gene-mutated ALS patients. CONCLUSIONS Here we extended understanding of the subcellular localization dynamics of the aggregation-prone LINE-1 ORF1p RNA-binding protein. However, we failed to find compelling evidence for misregulation of LINE-1 retrotransposons in sporadic ALS nor a clear effect of ALS-associated TDP-43 protein on L1 expression. In sum, our study reveals that the interplay of active retrotransposons and the molecular features of ALS are more complex than anticipated. Thus, the potential consequences of altered retrotransposon activity for ALS and other neurodegenerative disorders are worthy of continued investigation.
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Affiliation(s)
- Gavin C. Pereira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Paul M. Schaughency
- Oncology Center-Cancer Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Alejandro Rubio-Roldán
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Jungbin A. Choi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ranjan Batra
- Department of Neurosciences, School of Medicine, University of California at San Diego, San Diego, California USA
| | - Priscilla Turelli
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Lyle W. Ostrow
- Neuromuscular Division, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, University of California at San Diego, San Diego, California USA
| | - Haig H. Kazazian
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Sarah J. Wheelan
- Oncology Center-Cancer Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Sara R. Heras
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jens Mayer
- Department of Human Genetics, Medical Faculty, University of Saarland, Homburg/Saar, Germany
| | - Jose Luis García-Pérez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John L. Goodier
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
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17
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Salvatori DCF, Dorssers LCJ, Gillis AJM, Perretta G, van Agthoven T, Gomes Fernandes M, Stoop H, Prins JB, Oosterhuis JW, Mummery C, Looijenga LHJ. The MicroRNA-371 Family as Plasma Biomarkers for Monitoring Undifferentiated and Potentially Malignant Human Pluripotent Stem Cells in Teratoma Assays. Stem Cell Reports 2018; 11:1493-1505. [PMID: 30503260 PMCID: PMC6294243 DOI: 10.1016/j.stemcr.2018.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 01/09/2023] Open
Abstract
Predicting developmental potency and risk of posttransplantation tumor formation by human pluripotent stem cells (hPSCs) and their derivatives largely rely on classical histological analysis of teratomas. Here, we investigated whether an assay based on microRNAs (miRNA) in blood plasma is able to detect potentially malignant elements. Several hPSCs and human malignant germ cell tumor (hGCT) lines were investigated in vitro and in vivo after mouse xenografting. The multiple conventional hPSC lines generated mature teratomas, while xenografts from induced hPSCs (hiPSCs) with reactivated reprogramming transgenes and hGCT lines contained undifferentiated and potentially malignant components. The presence of these elements was reflected in the mRNA and miRNA profiles of the xenografts with OCT3/4 mRNA and the miR-371 and miR-302 families readily detectable. miR-371 family members were also identified in mouse plasma faithfully reporting undifferentiated elements in the xenografts. This study demonstrated that undifferentiated and potentially malignant cells could be detected in vivo.
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Affiliation(s)
- Daniela C F Salvatori
- Central Laboratory Animal Facility, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, the Netherlands.
| | - Lambert C J Dorssers
- Department of Pathology, Laboratory for Experimental Patho-Oncology, Erasmus MC Cancer Institute, Be-432A, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Ad J M Gillis
- Department of Pathology, Laboratory for Experimental Patho-Oncology, Erasmus MC Cancer Institute, Be-432A, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Gemma Perretta
- Fondazione Guido Bernardini, Via Manfredo Camperio, 10, 20123 Milano, Italy
| | - Ton van Agthoven
- Department of Pathology, Laboratory for Experimental Patho-Oncology, Erasmus MC Cancer Institute, Be-432A, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Maria Gomes Fernandes
- Central Laboratory Animal Facility, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, the Netherlands
| | - Hans Stoop
- Department of Pathology, Laboratory for Experimental Patho-Oncology, Erasmus MC Cancer Institute, Be-432A, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Jan-Bas Prins
- Central Laboratory Animal Facility, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, the Netherlands
| | - J Wolter Oosterhuis
- Department of Pathology, Laboratory for Experimental Patho-Oncology, Erasmus MC Cancer Institute, Be-432A, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Christine Mummery
- Department of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Leendert H J Looijenga
- Department of Pathology, Laboratory for Experimental Patho-Oncology, Erasmus MC Cancer Institute, Be-432A, PO Box 2040, 3000 CA Rotterdam, the Netherlands.
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18
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Mayer J, Harz C, Sanchez L, Pereira GC, Maldener E, Heras SR, Ostrow LW, Ravits J, Batra R, Meese E, García-Pérez JL, Goodier JL. Transcriptional profiling of HERV-K(HML-2) in amyotrophic lateral sclerosis and potential implications for expression of HML-2 proteins. Mol Neurodegener 2018; 13:39. [PMID: 30068350 PMCID: PMC6091006 DOI: 10.1186/s13024-018-0275-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder. About 90% of ALS cases are without a known genetic cause. The human endogenous retrovirus multi-copy HERV-K(HML-2) group was recently reported to potentially contribute to neurodegeneration and disease pathogenesis in ALS because of transcriptional upregulation and toxic effects of HML-2 Envelope (Env) protein. Env and other proteins are encoded by some transcriptionally active HML-2 loci. However, more detailed information is required regarding which HML-2 loci are transcribed in ALS, which of their proteins are expressed, and differences between the disease and non-disease states. METHODS For brain and spinal cord tissue samples from ALS patients and controls, we identified transcribed HML-2 loci by generating and mapping HML-2-specific cDNA sequences. We predicted expression of HML-2 env gene-derived proteins based on the observed cDNA sequences. Furthermore, we determined overall HML-2 transcript levels by RT-qPCR and investigated presence of HML-2 Env protein in ALS and control tissue samples by Western blotting. RESULTS We identified 24 different transcribed HML-2 loci. Some of those loci are transcribed at relatively high levels. However, significant differences in HML-2 loci transcriptional activities were not seen when comparing ALS and controls. Likewise, overall HML-2 transcript levels, as determined by RT-qPCR, were not significantly different between ALS and controls. Indeed, we were unable to detect full-length HML-2 Env protein in ALS and control tissue samples despite reasonable sensitivity. Rather our analyses suggest that a number of HML-2 protein variants other than full-length Env may potentially be expressed in ALS patients. CONCLUSIONS Our results expand and refine recent publications on HERV-K(HML-2) and ALS. Some of our results are in conflict with recent findings and call for further specific analyses. Our profiling of HML-2 transcription in ALS opens up the possibility that HML-2 proteins other than canonical full-length Env may have to be considered when studying the role of HML-2 in ALS disease.
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Affiliation(s)
- Jens Mayer
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Christian Harz
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Gavin C. Pereira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Esther Maldener
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Sara R. Heras
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
| | - Lyle W. Ostrow
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 28217 USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, UCSD, San Diego, CA USA
| | - Ranjan Batra
- Department of Neurosciences, School of Medicine, UCSD, San Diego, CA USA
| | - Eckart Meese
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Jose Luis García-Pérez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John L. Goodier
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
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19
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Jung J, Kim Y, Song J, Yoon YJ, Kim DE, Kim JA, Jin Y, Lee YJ, Kim S, Kwon BM, Han DC. KRIBB53 binds to OCT4 and enhances its degradation through the proteasome, causing apoptotic cell death of OCT4-positive testicular germ cell tumors. Carcinogenesis 2018; 39:838-849. [DOI: 10.1093/carcin/bgy054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/11/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Jiyae Jung
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Youngmi Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Jinhoi Song
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Yae Jin Yoon
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Da-Eun Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Joo Ae Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Yena Jin
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Yu-Jin Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Seokho Kim
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Byoung-Mog Kwon
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Dong Cho Han
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
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20
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Bouma MJ, van Iterson M, Janssen B, Mummery CL, Salvatori DCF, Freund C. Differentiation-Defective Human Induced Pluripotent Stem Cells Reveal Strengths and Limitations of the Teratoma Assay and In Vitro Pluripotency Assays. Stem Cell Reports 2018; 8:1340-1353. [PMID: 28494940 PMCID: PMC5425621 DOI: 10.1016/j.stemcr.2017.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 03/10/2017] [Accepted: 03/10/2017] [Indexed: 02/06/2023] Open
Abstract
The ability to form teratomas in vivo containing multiple somatic cell types is regarded as functional evidence of pluripotency for human pluripotent stem cells (hPSCs). Since the Teratoma assay is animal dependent, laborious, and only qualitative, the PluriTest and the hPSC ScoreCard assay have been developed as in vitro alternatives. Here we compared normal hPSCs, induced hPSCs (hiPSCs) with reactivated reprogramming transgenes, and human embryonal carcinoma cells (hECs) in these assays. While normal hPSCs gave rise to typical teratomas, the xenografts of the hECs and the hiPSCs with reactivated reprogramming transgenes were largely undifferentiated and malignant. The hPSC ScoreCard assay confirmed the line-specific differentiation propensities in vitro. However, when undifferentiated cells were analyzed by the PluriTest, only hECs were identified as abnormal whereas all other cell lines were indistinguishable and resembled normal hPSCs. Our results indicate that pluripotency assays are best selected on the basis of intended downstream applications. Side-by-side comparison of teratomas/TeratoScore, hPSC ScoreCard, and PluriTest hiPSCs with reactivated transgenes form embryonal carcinomas in vivo hiPSCs with reactivated transgenes show impaired differentiation capacity in vitro • PluriTest does not distinguish hiPSCs with reactivated transgenes from normal hPSCs
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Affiliation(s)
- Marga J Bouma
- Department of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Maarten van Iterson
- Department of Molecular Epidemiology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Bart Janssen
- GenomeScan B.V., Plesmanlaan 1D, 2333 BZ Leiden, the Netherlands
| | - Christine L Mummery
- Department of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Daniela C F Salvatori
- Central Laboratory Animal Facility, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
| | - Christian Freund
- Department of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
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21
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MyD88 is an essential component of retinoic acid-induced differentiation in human pluripotent embryonal carcinoma cells. Cell Death Differ 2017; 24:1975-1986. [PMID: 28885616 DOI: 10.1038/cdd.2017.124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/02/2017] [Accepted: 06/19/2017] [Indexed: 02/06/2023] Open
Abstract
We have previously reported that myeloid differentiation primary response gene 88 (MyD88) is downregulated during all-trans retinoic acid (RA)-induced differentiation of pluripotent NTera2 human embryonal carcinoma cells (hECCs), whereas its maintained expression is associated with RA differentiation resistance in nullipotent 2102Ep hECCs. MyD88 is the main adapter for toll-like receptor (TLR) signalling, where it determines the secretion of chemokines and cytokines in response to pathogens. In this study, we report that loss of MyD88 is essential for RA-facilitated differentiation of hECCs. Functional analysis using a specific MyD88 peptide inhibitor (PepInh) demonstrated that high MyD88 expression in the self-renewal state inhibits the expression of a specific set of HOX genes. In NTera2 cells, MyD88 is downregulated during RA-induced differentiation, a mechanism that could be broadly replicated by MyD88 PepInh treatment of 2102Ep cells. Notably, MyD88 inhibition transitioned 2102Ep cells into a stable, self-renewing state that appears to be primed for differentiation upon addition of RA. At a molecular level, MyD88 inhibition combined with RA treatment upregulated HOX, RA signalling and TLR signalling genes. These events permit differentiation through a standard downregulation of Oct4-Sox2-Nanog mechanism. In line with its role in regulating secretion of specific proteins, conditioned media experiments demonstrated that differentiated (MyD88 low) NTera2 cell media was sufficient to differentiate NTera2 cells. Protein array analysis indicated that this was owing to secretion of factors known to regulate angiogenesis, neurogenesis and all three branches of TGF-β Superfamily signalling. Collectively, these data offer new insights into RA controlled differentiation of pluripotent cells, with notable parallels to the ground state model of embryonic stem cell self-renewal. These data may provide insights to facilitate improved differentiation protocols for regenerative medicine and differentiation-therapies in cancer treatment.
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22
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Ounpuu L, Klepinin A, Pook M, Teino I, Peet N, Paju K, Tepp K, Chekulayev V, Shevchuk I, Koks S, Maimets T, Kaambre T. 2102Ep embryonal carcinoma cells have compromised respiration and shifted bioenergetic profile distinct from H9 human embryonic stem cells. Biochim Biophys Acta Gen Subj 2017; 1861:2146-2154. [PMID: 28552560 DOI: 10.1016/j.bbagen.2017.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/17/2017] [Accepted: 05/23/2017] [Indexed: 02/07/2023]
Abstract
Recent studies have shown that cellular bioenergetics may be involved in stem cell differentiation. Considering that during cancerogenesis cells acquire numerous properties of stem cells, it is possible to assume that the energy metabolism in tumorigenic cells might be differently regulated. The aim of this study was to compare the mitochondrial bioenergetic profile of normal pluripotent human embryonic stem cells (hESC) and relatively nullipotent embryonal carcinoma cells (2102Ep cell line). We examined three parameters related to cellular bioenergetics: phosphotransfer system, aerobic glycolysis, and oxygen consumption. Activities and expression levels of main enzymes that facilitate energy transfer were measured. The oxygen consumption rate studies were performed to investigate the respiratory capacity of cells. 2102Ep cells showed a shift in energy distribution towards adenylate kinase network. The total AK activity was almost 3 times higher in 2102Ep cells compared to hESCs (179.85±5.73 vs 64.39±2.55mU/mg of protein) and the expression of AK2 was significantly higher in these cells, while CK was downregulated. 2102Ep cells displayed reduced levels of oxygen consumption and increased levels of aerobic glycolysis compared to hESCs. The compromised respiration of 2102Ep cells is not the result of increased mitochondrial mass, increased proton leak, and reduced respiratory reserve capacity of the cells or impairment of respiratory chain complexes. Our data showed that the bioenergetic profile of 2102Ep cells clearly distinguishes them from normal hESCs. This should be considered when this cell line is used as a reference, and highlight the importance of further research concerning energy metabolism of stem cells.
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Affiliation(s)
- Lyudmila Ounpuu
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Aleksandr Klepinin
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Martin Pook
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Indrek Teino
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Nadezda Peet
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411 Tartu, Estonia
| | - Kalju Paju
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411 Tartu, Estonia
| | - Kersti Tepp
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Vladimir Chekulayev
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Igor Shevchuk
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Sulev Koks
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Toivo Maimets
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Tuuli Kaambre
- Tallinn University, Narva mnt 25, 10120 Tallinn, Estonia; Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia.
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23
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Fang J, Jia J, Makowski M, Xu M, Wang Z, Zhang T, Hoskins JW, Choi J, Han Y, Zhang M, Thomas J, Kovacs M, Collins I, Dzyadyk M, Thompson A, O'Neill M, Das S, Lan Q, Koster R, Stolzenberg-Solomon RS, Kraft P, Wolpin BM, Jansen PWTC, Olson S, McGlynn KA, Kanetsky PA, Chatterjee N, Barrett JH, Dunning AM, Taylor JC, Newton-Bishop JA, Bishop DT, Andresson T, Petersen GM, Amos CI, Iles MM, Nathanson KL, Landi MT, Vermeulen M, Brown KM, Amundadottir LT. Functional characterization of a multi-cancer risk locus on chr5p15.33 reveals regulation of TERT by ZNF148. Nat Commun 2017; 8:15034. [PMID: 28447668 PMCID: PMC5414179 DOI: 10.1038/ncomms15034] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/23/2017] [Indexed: 12/13/2022] Open
Abstract
Genome wide association studies (GWAS) have mapped multiple independent cancer susceptibility loci to chr5p15.33. Here, we show that fine-mapping of pancreatic and testicular cancer GWAS within one of these loci (Region 2 in CLPTM1L) focuses the signal to nine highly correlated SNPs. Of these, rs36115365-C associated with increased pancreatic and testicular but decreased lung cancer and melanoma risk, and exhibited preferred protein-binding and enhanced regulatory activity. Transcriptional gene silencing of this regulatory element repressed TERT expression in an allele-specific manner. Proteomic analysis identifies allele-preferred binding of Zinc finger protein 148 (ZNF148) to rs36115365-C, further supported by binding of purified recombinant ZNF148. Knockdown of ZNF148 results in reduced TERT expression, telomerase activity and telomere length. Our results indicate that the association with chr5p15.33-Region 2 may be explained by rs36115365, a variant influencing TERT expression via ZNF148 in a manner consistent with elevated TERT in carriers of the C allele.
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Affiliation(s)
- Jun Fang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jinping Jia
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Matthew Makowski
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen 6500 HB, The Netherlands
| | - Mai Xu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jason W. Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jiyeon Choi
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Younghun Han
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA
| | - Mingfeng Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Janelle Thomas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael Kovacs
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Irene Collins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Marta Dzyadyk
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Abbey Thompson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Maura O'Neill
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Qi Lan
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Roelof Koster
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Rachael S. Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Pascal W. T. C. Jansen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen 6500 HB, The Netherlands
| | - Sara Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York City, New York 10065, USA
| | - Katherine A. McGlynn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Peter A. Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jennifer H. Barrett
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, UK
| | - Alison M. Dunning
- Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - John C. Taylor
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, UK
| | - Julia A. Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, UK
| | - D. Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, UK
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Gloria M. Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Christopher I. Amos
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA
| | - Mark M. Iles
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, UK
| | - Katherine L. Nathanson
- Translational Medicine and Human Genetics, Department of Medicine and Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michiel Vermeulen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen 6500 HB, The Netherlands
| | - Kevin M. Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Laufey T. Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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24
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Lee CQE, Gardner L, Turco M, Zhao N, Murray MJ, Coleman N, Rossant J, Hemberger M, Moffett A. What Is Trophoblast? A Combination of Criteria Define Human First-Trimester Trophoblast. Stem Cell Reports 2016; 6:257-72. [PMID: 26862703 PMCID: PMC4750161 DOI: 10.1016/j.stemcr.2016.01.006] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 12/15/2022] Open
Abstract
Controversy surrounds reports describing the derivation of human trophoblast cells from placentas and embryonic stem cells (ESC), partly due to the difficulty in identifying markers that define cells as belonging to the trophoblast lineage. We have selected criteria that are characteristic of primary first-trimester trophoblast: a set of protein markers, HLA class I profile, methylation of ELF5, and expression of microRNAs (miRNAs) from the chromosome 19 miRNA cluster (C19MC). We tested these criteria on cells previously reported to show some phenotypic characteristics of trophoblast: bone morphogenetic protein (BMP)-treated human ESC and 2102Ep, an embryonal carcinoma cell line. Both cell types only show some, but not all, of the four trophoblast criteria. Thus, BMP-treated human ESC have not fully differentiated to trophoblast. Our study identifies a robust panel, including both protein and non-protein-coding markers that, in combination, can be used to reliably define cells as characteristic of early trophoblast.
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Affiliation(s)
- Cheryl Q E Lee
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto M5G 0A4, Canada.
| | - Lucy Gardner
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Margherita Turco
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Nancy Zhao
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Matthew J Murray
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Nicholas Coleman
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Janet Rossant
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto M5G 0A4, Canada
| | - Myriam Hemberger
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ashley Moffett
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK.
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25
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Utilizing Regulatory Networks for Pluripotency Assessment in Stem Cells. CURRENT STEM CELL REPORTS 2016. [DOI: 10.1007/s40778-016-0054-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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26
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Kushwaha R, Jagadish N, Kustagi M, Mendiratta G, Seandel M, Soni R, Korkola JE, Thodima V, Califano A, Bosl GJ, Chaganti RSK. Mechanism and Role of SOX2 Repression in Seminoma: Relevance to Human Germline Specification. Stem Cell Reports 2016; 6:772-783. [PMID: 27132888 PMCID: PMC4939754 DOI: 10.1016/j.stemcr.2016.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 01/22/2023] Open
Abstract
Human male germ cell tumors (GCTs) are derived from primordial germ cells (PGCs). The master pluripotency regulator and neuroectodermal lineage effector transcription factor SOX2 is repressed in PGCs and the seminoma (SEM) subset of GCTs. The mechanism of SOX2 repression and its significance to GC and GCT development currently are not understood. Here, we show that SOX2 repression in SEM-derived TCam-2 cells is mediated by the Polycomb repressive complex (PcG) and the repressive H3K27me3 chromatin mark that are enriched at its promoter. Furthermore, SOX2 repression in TCam-2 cells can be abrogated by recruitment of the constitutively expressed H3K27 demethylase UTX to the SOX2 promoter through retinoid signaling, leading to expression of neuronal and other lineage genes. SOX17 has been shown to initiate human PGC specification, with its target PRDM1 suppressing mesendodermal genes. Our results are consistent with a role for SOX2 repression in normal germline development by suppressing neuroectodermal genes. SOX2 is repressed in hPGC, germ cell neoplasia in situ, and seminoma SOX2 repression is mediated by PcG and H3K27me3 enrichment at its promoter Retinoid signaling recruits UTX to SOX2 promoter leading to reactivation of SOX2 These studies shed light on the role of SOX2 in germline development
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Affiliation(s)
- Ritu Kushwaha
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Nirmala Jagadish
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Manjunath Kustagi
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Geetu Mendiratta
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Marco Seandel
- Department of Surgery, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Rekha Soni
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - James E Korkola
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | | | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - George J Bosl
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - R S K Chaganti
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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27
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Philippe C, Vargas-Landin DB, Doucet AJ, van Essen D, Vera-Otarola J, Kuciak M, Corbin A, Nigumann P, Cristofari G. Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci. eLife 2016; 5. [PMID: 27016617 PMCID: PMC4866827 DOI: 10.7554/elife.13926] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/25/2016] [Indexed: 12/26/2022] Open
Abstract
LINE-1 (L1) retrotransposons represent approximately one sixth of the human genome, but only the human-specific L1HS-Ta subfamily acts as an endogenous mutagen in modern humans, reshaping both somatic and germline genomes. Due to their high levels of sequence identity and the existence of many polymorphic insertions absent from the reference genome, the transcriptional activation of individual genomic L1HS-Ta copies remains poorly understood. Here we comprehensively mapped fixed and polymorphic L1HS-Ta copies in 12 commonly-used somatic cell lines, and identified transcriptional and epigenetic signatures allowing the unambiguous identification of active L1HS-Ta copies in their genomic context. Strikingly, only a very restricted subset of L1HS-Ta loci - some being polymorphic among individuals - significantly contributes to the bulk of L1 expression, and these loci are differentially regulated among distinct cell lines. Thus, our data support a local model of L1 transcriptional activation in somatic cells, governed by individual-, locus-, and cell-type-specific determinants. DOI:http://dx.doi.org/10.7554/eLife.13926.001 Retrotransposons, also known as jumping genes, have invaded the genomes of most living organisms. These fragments of DNA have the ability to move or copy themselves from one location of a chromosome to another. Depending on where they insert themselves, retrotransposons can modify the sequence of nearby genes, which can alter or even abolish their activity. Although these genetic modifications have contributed significantly to the evolution of different species, retrotransposons can also have detrimental effects; for example, by causing new cases of genetic diseases. Adult human cells have a number of mechanisms that work to keep the activity of retrotransposons at a very low level. However, in many types of cancers retrotransposons escape these defense mechanisms and ‘jump’ actively. This is thought to contribute to the development and spread of cancerous tumors. To understand how jumping genes are mobilized, a fundamental question must be answered: is the high jumping gene activity observed in some cell types a result of activating many copies of the retrotransposons, or only a few of them? This question has been difficult to address because there are more than one hundred copies of retrotransposons that could potentially move in humans, many of which have not even been referenced in the human genome map. Furthermore, each copy is almost identical to another one, making it difficult to discriminate between them. Philippe et al. have now developed an approach that can map where individual retrotransposons are located in the genome of normal and cancerous cells and measure how active these jumping genes are. This revealed that only a very restricted number of them are active in any given cell type. Moreover, different subsets of jumping genes are active in different cell types, and their locations in the genome often do not overlap. Thus, whether jumping genes are activated depends on the cell type and their position in the genome. These results are in contrast to the prevalent view that retrotransposons are activated in a more widespread manner across the genome, at least in cancerous cells. Overall, Philippe et al.’s findings pave the way towards characterizing the chromosome regions in which retrotransposons are frequently activated and understanding how they contribute to cancer and other diseases. DOI:http://dx.doi.org/10.7554/eLife.13926.002
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Affiliation(s)
- Claude Philippe
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
| | - Dulce B Vargas-Landin
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,Ecole Normale Supérieure, Paris, France
| | - Aurélien J Doucet
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
| | - Dominic van Essen
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Jorge Vera-Otarola
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Monika Kuciak
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,Ecole Normale Supérieure de Lyon, Lyon, France
| | | | - Pilvi Nigumann
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Gaël Cristofari
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
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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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29
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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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30
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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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31
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Geng Y, Zhao Y, Schuster LC, Feng B, Lynn DA, Austin KM, Stoklosa JD, Morrison JD. A Chemical Biology Study of Human Pluripotent Stem Cells Unveils HSPA8 as a Key Regulator of Pluripotency. Stem Cell Reports 2015; 5:1143-1154. [PMID: 26549849 PMCID: PMC4682066 DOI: 10.1016/j.stemcr.2015.09.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 01/06/2023] Open
Abstract
Chemical biology methods such as high-throughput screening (HTS) and affinity-based target identification can be used to probe biological systems on a biomacromolecule level, providing valuable insights into the molecular mechanisms of those systems. Here, by establishing a human embryonal carcinoma cell-based HTS platform, we screened 171,077 small molecules for regulators of pluripotency and identified a small molecule, Displurigen, that potently disrupts hESC pluripotency by targeting heat shock 70-kDa protein 8 (HSPA8), the constitutively expressed member of the 70-kDa heat shock protein family, as elucidated using affinity-based target identification techniques and confirmed by loss-of-function and gain-of-function assays. We demonstrated that HSPA8 maintains pluripotency by binding to the master pluripotency regulator OCT4 and facilitating its DNA-binding activity.
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Affiliation(s)
- Yijie Geng
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Yongfeng Zhao
- Stem Cell Center, Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Lisa Corinna Schuster
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bradley Feng
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dana A Lynn
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Katherine M Austin
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jason Daniel Stoklosa
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Joseph D Morrison
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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32
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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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33
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Andrews PW, Baker D, Benvinisty N, Miranda B, Bruce K, Brüstle O, Choi M, Choi YM, Crook JM, de Sousa PA, Dvorak P, Freund C, Firpo M, Furue MK, Gokhale P, Ha HY, Han E, Haupt S, Healy L, Hei DJ, Hovatta O, Hunt C, Hwang SM, Inamdar MS, Isasi RM, Jaconi M, Jekerle V, Kamthorn P, Kibbey MC, Knezevic I, Knowles BB, Koo SK, Laabi Y, Leopoldo L, Liu P, Lomax GP, Loring JF, Ludwig TE, Montgomery K, Mummery C, Nagy A, Nakamura Y, Nakatsuji N, Oh S, Oh SK, Otonkoski T, Pera M, Peschanski M, Pranke P, Rajala KM, Rao M, Ruttachuk R, Reubinoff B, Ricco L, Rooke H, Sipp D, Stacey GN, Suemori H, Takahashi TA, Takada K, Talib S, Tannenbaum S, Yuan BZ, Zeng F, Zhou Q. Points to consider in the development of seed stocks of pluripotent stem cells for clinical applications: International Stem Cell Banking Initiative (ISCBI). Regen Med 2015; 10:1-44. [PMID: 25675265 DOI: 10.2217/rme.14.93] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- P W Andrews
- Department of Biomedical Science, The University of Sheffield, Sheffield, UK
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Santos MCT, Silva PBG, Rodini CO, Furukawa G, Marco Antonio DS, Zanotto-Filho A, Moreira JCF, Okamoto OK. Embryonic Stem Cell-Related Protein L1TD1 Is Required for Cell Viability, Neurosphere Formation, and Chemoresistance in Medulloblastoma. Stem Cells Dev 2015; 24:2700-8. [PMID: 26159230 DOI: 10.1089/scd.2015.0052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Misexpression of stem cell-related genes may occur in some cancer cells, influencing patient's prognosis. This is the case of medulloblastoma, a common and clinically challenging malignant tumor of the central nervous system, where expression of the pluripotency factor, OCT4, is correlated with poor survival. A downstream target of OCT4, L1TD1 (LINE-1 type transposase domain-containing protein 1 family member), encodes a novel embryonic stem cell (ESC)-related protein involved in pluripotency and self-renewal of ESCs. L1TD1 is still poorly characterized and its expression pattern and function in cancer cells are virtually unknown. Although normally restricted to non-neoplastic undifferentiated cells and germ cells, we found that high L1TD1 expression also occurs in medulloblastoma cells, reaching levels similar to those found in ESCs, and is correlated with poor prognosis. Conversely to what is reported during normal cell differentiation, when differentiated cells remain healthy, despite L1TD1 downregulation, depletion of L1TD1 protein levels by targeted gene silencing significantly reduced medulloblastoma cell viability, inhibiting cell proliferation and inducing apoptosis. More strikingly, L1TD1 depletion downregulated expression of the neural stem cell markers, CD133 and Nestin, inhibited neurosphere generation capability, and sensitized medulloblastoma cells to temozolomide and cisplatin, two chemotherapeutic agents of clinical relevance in medulloblastoma treatment. Our findings provide insights about the contribution of pluripotency-related genes to a more aggressive tumor phenotype through their involvement in the acquisition of stem-like properties by cancer cells and point out L1TD1 as a potential therapeutic target in malignant brain tumors.
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Affiliation(s)
- Márcia Cristina Teixeira Santos
- 1 Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - Patrícia Benites Gonçalves Silva
- 1 Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - Carolina Oliveira Rodini
- 1 Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - Gabriela Furukawa
- 1 Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - David Santos Marco Antonio
- 1 Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - Alfeu Zanotto-Filho
- 2 Department of Biochemistry, Oxidative Stress Research Center, Federal University of Rio Grande do Sul , Porto Alegre, Brazil
| | - José C F Moreira
- 2 Department of Biochemistry, Oxidative Stress Research Center, Federal University of Rio Grande do Sul , Porto Alegre, Brazil
| | - Oswaldo Keith Okamoto
- 1 Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
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35
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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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Yuan Z, Ding S, Yan M, Zhu X, Liu L, Tan S, Jin Y, Sun Y, Li Y, Huang T. Variability of miRNA expression during the differentiation of human embryonic stem cells into retinal pigment epithelial cells. Gene 2015; 569:239-49. [PMID: 26028588 DOI: 10.1016/j.gene.2015.05.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 05/23/2015] [Accepted: 05/25/2015] [Indexed: 01/08/2023]
Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells can be induced to differentiate into retinal pigment epithelium (RPE). MiRNAs have been characterized and found playing important roles in the differentiation process of ESCs, but their length and sequence heterogeneity (isomiRs), and their non-canonical forms of miRNAs are underestimated or ignored. In this report, we found some non-canonical miRNAs (dominant isomiRs) in all differentiation stages, and 27 statistically significant editing sites were identified in 24 different miRNAs. Moreover, we found marked major-to-minor arm-switching events in 14 pre-miRNAs during the hESC to RPE cell differentiation phases. Our study for the first time reports exploring the variability of miRNA expression during the differentiation of hESCs into RPE cells and the results show that miRNA variability is a ubiquitous phenomenon in the ESC differentiation.
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Affiliation(s)
- Zhidong Yuan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China.
| | - Suping Ding
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Mingli Yan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Xiao Zhu
- Guangdong Province Key Laboratory of Medical Molecular Diagnosis, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan 523808, China
| | - Lili Liu
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Shuhua Tan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Yuanchang Jin
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Yuandong Sun
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Yufeng Li
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Ting Huang
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
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Rijlaarsdam MA, Tax DMJ, Gillis AJM, Dorssers LCJ, Koestler DC, de Ridder J, Looijenga LHJ. Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors. PLoS One 2015; 10:e0122146. [PMID: 25859847 PMCID: PMC4479500 DOI: 10.1371/journal.pone.0122146] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 02/07/2015] [Indexed: 12/18/2022] Open
Abstract
The cell of origin of the five subtypes (I-V) of germ cell tumors (GCTs) are assumed to be germ cells from different maturation stages. This is (potentially) reflected in their methylation status as fetal maturing primordial germ cells are globally demethylated during migration from the yolk sac to the gonad. Imprinted regions are erased in the gonad and later become uniparentally imprinted according to fetal sex. Here, 91 GCTs (type I-IV) and four cell lines were profiled (Illumina’s HumanMethylation450BeadChip). Data was pre-processed controlling for cross hybridization, SNPs, detection rate, probe-type bias and batch effects. The annotation was extended, covering snRNAs/microRNAs, repeat elements and imprinted regions. A Hidden Markov Model-based genome segmentation was devised to identify differentially methylated genomic regions. Methylation profiles allowed for separation of clusters of non-seminomas (type II), seminomas/dysgerminomas (type II), spermatocytic seminomas (type III) and teratomas/dermoid cysts (type I/IV). The seminomas, dysgerminomas and spermatocytic seminomas were globally hypomethylated, in line with previous reports and their demethylated precursor. Differential methylation and imprinting status between subtypes reflected their presumed cell of origin. Ovarian type I teratomas and dermoid cysts showed (partial) sex specific uniparental maternal imprinting. The spermatocytic seminomas showed uniparental paternal imprinting while testicular teratomas exhibited partial imprinting erasure. Somatic imprinting in type II GCTs might indicate a cell of origin after global demethylation but before imprinting erasure. This is earlier than previously described, but agrees with the totipotent/embryonic stem cell like potential of type II GCTs and their rare extra-gonadal localization. The results support the common origin of the type I teratomas and show strong similarity between ovarian type I teratomas and dermoid cysts. In conclusion, we identified specific and global methylation differences between GCT subtypes, providing insight into their developmental timing and underlying developmental biology. Data and extended annotation are deposited at GEO (GSE58538 and GPL18809).
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Affiliation(s)
- Martin A. Rijlaarsdam
- Department of Pathology, Erasmus MC Cancer Institute—University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - David M. J. Tax
- Faculty of Electrical Engineering, Mathematics and Computer Science Intelligent Systems—Delft Bioinformatics Lab, Technical University of Delft, Delft, The Netherlands
| | - Ad J. M. Gillis
- Department of Pathology, Erasmus MC Cancer Institute—University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lambert C. J. Dorssers
- Department of Pathology, Erasmus MC Cancer Institute—University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Devin C. Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Jeroen de Ridder
- Faculty of Electrical Engineering, Mathematics and Computer Science Intelligent Systems—Delft Bioinformatics Lab, Technical University of Delft, Delft, The Netherlands
| | - Leendert H. J. Looijenga
- Department of Pathology, Erasmus MC Cancer Institute—University Medical Center Rotterdam, Rotterdam, The Netherlands
- * E-mail:
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French A, Bravery C, Smith J, Chandra A, Archibald P, Gold JD, Artzi N, Kim HW, Barker RW, Meissner A, Wu JC, Knowles JC, Williams D, García-Cardeña G, Sipp D, Oh S, Loring JF, Rao MS, Reeve B, Wall I, Carr AJ, Bure K, Stacey G, Karp JM, Snyder EY, Brindley DA. Enabling consistency in pluripotent stem cell-derived products for research and development and clinical applications through material standards. Stem Cells Transl Med 2015; 4:217-23. [PMID: 25650438 PMCID: PMC4339854 DOI: 10.5966/sctm.2014-0233] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 11/10/2014] [Indexed: 12/27/2022] Open
Abstract
There is a need for physical standards (reference materials) to ensure both reproducibility and consistency in the production of somatic cell types from human pluripotent stem cell (hPSC) sources. We have outlined the need for reference materials (RMs) in relation to the unique properties and concerns surrounding hPSC-derived products and suggest in-house approaches to RM generation relevant to basic research, drug screening, and therapeutic applications. hPSCs have an unparalleled potential as a source of somatic cells for drug screening, disease modeling, and therapeutic application. Undefined variation and product variability after differentiation to the lineage or cell type of interest impede efficient translation and can obscure the evaluation of clinical safety and efficacy. Moreover, in the absence of a consistent population, data generated from in vitro studies could be unreliable and irreproducible. Efforts to devise approaches and tools that facilitate improved consistency of hPSC-derived products, both as development tools and therapeutic products, will aid translation. Standards exist in both written and physical form; however, because many unknown factors persist in the field, premature written standards could inhibit rather than promote innovation and translation. We focused on the derivation of physical standard RMs. We outline the need for RMs and assess the approaches to in-house RM generation for hPSC-derived products, a critical tool for the analysis and control of product variation that can be applied by researchers and developers. We then explore potential routes for the generation of RMs, including both cellular and noncellular materials and novel methods that might provide valuable tools to measure and account for variation. Multiparametric techniques to identify "signatures" for therapeutically relevant cell types, such as neurons and cardiomyocytes that can be derived from hPSCs, would be of significant utility, although physical RMs will be required for clinical purposes.
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Affiliation(s)
- Anna French
- Oxford-UCL Centre for the Advancement of Sustainable Medical Innovation and
| | | | - James Smith
- Oxford-UCL Centre for the Advancement of Sustainable Medical Innovation and
| | - Amit Chandra
- Centre for Biological Engineering, Wolfson School of Mechanical and Manufacturing Engineering, Loughborough University, Loughborough, United Kingdom
| | - Peter Archibald
- Centre for Biological Engineering, Wolfson School of Mechanical and Manufacturing Engineering, Loughborough University, Loughborough, United Kingdom
| | | | - Natalie Artzi
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Hae-Won Kim
- Department of Dental Biomaterials, School of Dentistry
| | - Richard W Barker
- Oxford-UCL Centre for the Advancement of Sustainable Medical Innovation and
| | - Alexander Meissner
- Harvard Stem Cell Institute, Cambridge, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Department of Medicine, and Department of Radiology, Stanford University School of Medicine, Stanford, California, USA
| | - Jonathan C Knowles
- Department of Nanobiomedical Science BK21 Plus NBM Global Research Center of Regenerative Medicine, and Division of Biomaterials and Tissue Engineering, UCL Eastman Dental Institute
| | - David Williams
- Centre for Biological Engineering, Wolfson School of Mechanical and Manufacturing Engineering, Loughborough University, Loughborough, United Kingdom
| | - Guillermo García-Cardeña
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Center for Excellence in Vascular Biology, Department of Pathology, and Program in Developmental and Regenerative Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Doug Sipp
- RIKEN Center for Developmental Biology, Kobe, Japan
| | - Steve Oh
- Bioprocessing Technology Institute, A*STAR Agency for Science, Technology and Research, Singapore
| | - Jeanne F Loring
- Department of Chemical Physiology and Center for Regenerative Medicine, Scripps Research Institute, La Jolla, California, USA
| | - Mahendra S Rao
- NIH Center for Regenerative Medicine, Bethesda, Maryland, USA
| | - Brock Reeve
- Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Ivan Wall
- Oxford-UCL Centre for the Advancement of Sustainable Medical Innovation and Department of Nanobiomedical Science BK21 Plus NBM Global Research Center of Regenerative Medicine, and Department of Biochemical Engineering, and Biomaterials and Tissue Engineering Laboratory, Department of Nanobiomedical Science and WCU Research Center, Dankook University, Cheonan, Republic of Korea
| | - Andrew J Carr
- Oxford-UCL Centre for the Advancement of Sustainable Medical Innovation and Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, and
| | - Kim Bure
- TAP Biosystems, Royston, United Kingdom
| | - Glyn Stacey
- National Institute for Biological Standards and Control, a Centre of the MHRA, South Mimms, United Kingdom
| | - Jeffrey M Karp
- Harvard Stem Cell Institute, Cambridge, Massachusetts; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Center for Regenerative Therapeutics and Department of Medicine, Division of Biomedical Engineering, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Evan Y Snyder
- Sanford-Burnham Medical Research Institute, La Jolla, California, USA; Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA; Sanford Consortium for Regenerative Medicine, La Jolla, California, USA;
| | - David A Brindley
- Oxford-UCL Centre for the Advancement of Sustainable Medical Innovation and Harvard Stem Cell Institute, Cambridge, Massachusetts; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA; Saïd Business School, University of Oxford, Oxford, United Kingdom; Centre for Behavioural Medicine, UCL School of Pharmacy, University College London, London, United Kingdom; Stanford-UCSF FDA Center of Excellence in Regulatory Science and Innovation (CERSI), San Francisco, California, USA
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Ffrench B, Gasch C, O'Leary JJ, Gallagher MF. Developing ovarian cancer stem cell models: laying the pipeline from discovery to clinical intervention. Mol Cancer 2014; 13:262. [PMID: 25495823 PMCID: PMC4295405 DOI: 10.1186/1476-4598-13-262] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/27/2014] [Indexed: 01/06/2023] Open
Abstract
Despite decades of research, ovarian cancer is still associated with unacceptably high mortality rates, which must be addressed by novel therapeutic approaches. One avenue through which this may be achieved is targeting of tumor-initiating 'Cancer Stem Cells' (CSCs). CSCs are sufficient to generate primary and recurrent disease through extensive rounds of asymmetric division, which maintain the CSC pool while producing the tissues that form the bulk of the tumor. CSCs thrive in the harsh tumor niche, are generally refractory to therapeutic intervention and closely-linked to the Epithelial-Mesenchymal Transition process, which facilitates invasion and metastasis. While it is well-accepted that CSC-targeting must be assessed as a novel therapeutic avenue, few ovarian CSC models have been developed due to perceived and actual difficulties associated with the process of 'CSC Discovery'. In this article we review contemporary approaches to CSC Discovery and argue that this process should start with an understanding of the specific challenges associated with clinical intervention, laying the pipeline backwards towards CSC Discovery. Such an approach would expedite the bridging of the gap between laboratory isolation and clinical targeting of ovarian CSCs.
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Affiliation(s)
- Brendan Ffrench
- Department of Histopathology, Trinity College Dublin, Trinity Centre for Health Sciences, St James Hospital, Dublin 8, Ireland.
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40
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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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41
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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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42
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Alfonso RJ, Gorroño-Etxebarria I, Rabano M, Vivanco MDM, Kypta R. Dickkopf-3 alters the morphological response to retinoic acid during neuronal differentiation of human embryonal carcinoma cells. Dev Neurobiol 2014; 74:1243-54. [DOI: 10.1002/dneu.22201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 06/03/2014] [Indexed: 11/05/2022]
Affiliation(s)
| | | | - Miriam Rabano
- Cell Biology and Stem Cells Unit; CIC bioGUNE; Spain
| | | | - Robert Kypta
- Cell Biology and Stem Cells Unit; CIC bioGUNE; Spain
- Department of Surgery and Cancer; Imperial College London; United Kingdom
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Peterson H, Abu Dawud R, Garg A, Wang Y, Vilo J, Xenarios I, Adjaye J. Qualitative modeling identifies IL-11 as a novel regulator in maintaining self-renewal in human pluripotent stem cells. Front Physiol 2013; 4:303. [PMID: 24194720 PMCID: PMC3809568 DOI: 10.3389/fphys.2013.00303] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 10/02/2013] [Indexed: 11/13/2022] Open
Abstract
Pluripotency in human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) is regulated by three transcription factors—OCT3/4, SOX2, and NANOG. To fully exploit the therapeutic potential of these cells it is essential to have a good mechanistic understanding of the maintenance of self-renewal and pluripotency. In this study, we demonstrate a powerful systems biology approach in which we first expand literature-based network encompassing the core regulators of pluripotency by assessing the behavior of genes targeted by perturbation experiments. We focused our attention on highly regulated genes encoding cell surface and secreted proteins as these can be more easily manipulated by the use of inhibitors or recombinant proteins. Qualitative modeling based on combining boolean networks and in silico perturbation experiments were employed to identify novel pluripotency-regulating genes. We validated Interleukin-11 (IL-11) and demonstrate that this cytokine is a novel pluripotency-associated factor capable of supporting self-renewal in the absence of exogenously added bFGF in culture. To date, the various protocols for hESCs maintenance require supplementation with bFGF to activate the Activin/Nodal branch of the TGFβ signaling pathway. Additional evidence supporting our findings is that IL-11 belongs to the same protein family as LIF, which is known to be necessary for maintaining pluripotency in mouse but not in human ESCs. These cytokines operate through the same gp130 receptor which interacts with Janus kinases. Our finding might explain why mESCs are in a more naïve cell state compared to hESCs and how to convert primed hESCs back to the naïve state. Taken together, our integrative modeling approach has identified novel genes as putative candidates to be incorporated into the expansion of the current gene regulatory network responsible for inducing and maintaining pluripotency.
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Affiliation(s)
- Hedi Peterson
- Quretec Ltd. Tartu, Estonia ; Faculty of Mathematics and Computer Science, Institute of Computer Science, University of Tartu Tartu, Estonia ; Faculty of Science and Technology, Institute of Molecular and Cellular Biology, University of Tartu Tartu, Estonia
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44
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Unravelling mechanisms of cisplatin sensitivity and resistance in testicular cancer. Expert Rev Mol Med 2013; 15:e12. [PMID: 24074238 DOI: 10.1017/erm.2013.13] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Testicular cancer is the most frequent solid malignant tumour type in men 20-40 years of age. At the time of diagnosis up to 50% of the patients suffer from metastatic disease. In contrast to most other metastatic solid tumours, the majority of metastatic testicular cancer patients can be cured with highly effective cisplatin-based chemotherapy. This review aims to summarise the current knowledge on response to chemotherapy and the biological basis of cisplatin-induced apoptosis in testicular cancer. The frequent presence of wild-type TP53 and the low levels of p53 in complex with the p53 negative feed-back regulator MDM2 contribute to cisplatin sensitivity. Moreover, the high levels of the pluripotency regulator Oct4 and as a consequence of Oct4 expression high levels of miR-17/106b seed family and pro-apoptotic Noxa and the low levels of cytoplasmic p21 (WAF1/Cip1) appear to be causative for the exquisite sensitivity to cisplatin-based therapy of testicular cancer. However, resistance of testicular cancer to cisplatin-based therapy does occur and can be mediated through aberrant levels of the above mentioned key players. Drugs targeting these key players showed, at least pre-clinically, a sensitising effect to cisplatin treatment. Further clinical development of such treatment strategies will lead to new treatment options for platinum-resistant testicular cancers.
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45
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Alagaratnam S, Harrison N, Bakken AC, Hoff AM, Jones M, Sveen A, Moore HD, Andrews PW, Lothe RA, Skotheim RI. Transforming pluripotency: an exon-level study of malignancy-specific transcripts in human embryonal carcinoma and embryonic stem cells. Stem Cells Dev 2013; 22:1136-46. [PMID: 23137282 DOI: 10.1089/scd.2012.0369] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To circumvent difficulties of isolating pure populations of cancer stem cells (CSCs) for the purpose of identifying malignancy-specific gene expression, we have compared exon-resolution transcriptomic profiles of 5 embryonal carcinoma (EC) cell lines, a histological subtype of germ cell tumor (GCT), to their nonmalignant caricature, specifically 6 human embryonic stem (ES) cell lines. Both cell types are readily accessible, and were purified for undifferentiated cells only. We identified a set of 28 differentially expressed genes, many of which had cancer and stemness roles. Overexpression of the recently discovered pluripotency gene NR5A2 in malignant EC cells revealed an intriguing indication of how WNT-mediated dysregulation of pluripotency is involved with malignancy. Expression of these 28 genes was further explored within 2 publically available data sets of primary EC tumors and normal testis. At the exon-level, alternative splicing events were detected in ZNF195, DNMT3B, and PMF1, and alternative promoters were detected for ASH2L and ETV5. These events were validated by reverse transcriptase-polymerase chain reaction-based methods in EC and ES lines, where the alternative splicing event in the de novo DNA methyltransferase DNMT3B may have functional consequences. In conclusion, we have identified malignancy-specific gene expression differences within a rigorous pluripotent stem cell context. These findings are of particular interest for both GCT and ES cell biology, and, in general, to the concept of CSCs.
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Affiliation(s)
- Sharmini Alagaratnam
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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46
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Wongtrakoongate P, Jones M, Gokhale PJ, Andrews PW. STELLA facilitates differentiation of germ cell and endodermal lineages of human embryonic stem cells. PLoS One 2013; 8:e56893. [PMID: 23457636 PMCID: PMC3573007 DOI: 10.1371/journal.pone.0056893] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 01/18/2013] [Indexed: 12/13/2022] Open
Abstract
Stella is a developmentally regulated gene highly expressed in mouse embryonic stem (ES) cells and in primordial germ cells (PGCs). In human, the gene encoding the STELLA homologue lies on chromosome 12p, which is frequently amplified in long-term cultured human ES cells. However, the role played by STELLA in human ES cells has not been reported. In the present study, we show that during retinoic acid (RA)-induced differentiation of human ES cells, expression of STELLA follows that of VASA, a marker of germline differentiation. By contrast, human embryonal carcinoma cells express STELLA at a higher level compared with both karyotypically normal and abnormal human ES cell lines. We found that over-expression of STELLA does not interfere with maintenance of the stem cell state of human ES cells, but following retinoic acid induction it leads to up-regulation of germline- and endodermal-associated genes, whereas neural markers PAX6 and NEUROD1 are down-regulated. Further, STELLA over-expression facilitates the differentiation of human ES cells into BE12-positive cells, in which the expression of germline- and endodermal-associated genes is enriched, and suppresses differentiation of the neural lineage. Taken together, this finding suggests a role for STELLA in facilitating germline and endodermal differentiation of human ES cells.
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Affiliation(s)
- Patompon Wongtrakoongate
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
- * E-mail: (PW); (PWA)
| | - Mark Jones
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Paul J. Gokhale
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Peter W. Andrews
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
- * E-mail: (PW); (PWA)
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Abstract
Human pluripotent stem cells (PSCs), in particular induced PSCs, are very difficult to derive, grow, and bank. They require extensive amounts of resources and time to render them useful for basic and applied research. As the derivation methods, culture systems and tissues of origin differ, so does the quality of the PSCs themselves. Consequently, there are generally accepted molecular and cellular markers that serve as benchmarks of pluripotency. PSCs undergo rigorous qualification before they can be truly considered a stem cell or completely reprogrammed into a stem-like cell as in the case of iPSCs. Morphology is a good indicator of PSCs but the further qualification of cellular markers of pluripotency and differential potential is necessary. The standard methods enclosed in this chapter delineate the techniques necessary to qualify PSCs at the cellular level.
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Reduced proficiency in homologous recombination underlies the high sensitivity of embryonal carcinoma testicular germ cell tumors to Cisplatin and poly (adp-ribose) polymerase inhibition. PLoS One 2012; 7:e51563. [PMID: 23251575 PMCID: PMC3520950 DOI: 10.1371/journal.pone.0051563] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 11/01/2012] [Indexed: 02/02/2023] Open
Abstract
Testicular Germ Cell Tumors (TGCT) and patient-derived cell lines are extremely sensitive to cisplatin and other interstrand cross-link (ICL) inducing agents. Nevertheless, a subset of TGCTs are either innately resistant or acquire resistance to cisplatin during treatment. Understanding the mechanisms underlying TGCT sensitivity/resistance to cisplatin as well as the identification of novel strategies to target cisplatin-resistant TGCTs have major clinical implications. Herein, we have examined the proficiency of five embryonal carcinoma (EC) cell lines to repair cisplatin-induced ICLs. Using γH2AX staining as a marker of double strand break formation, we found that EC cell lines were either incapable of or had a reduced ability to repair ICL-induced damage. The defect correlated with reduced Homologous Recombination (HR) repair, as demonstrated by the reduction of RAD51 foci formation and by direct evaluation of HR efficiency using a GFP-reporter substrate. HR-defective tumors cells are known to be sensitive to the treatment with poly(ADP-ribose) polymerase (PARP) inhibitor. In line with this observation, we found that EC cell lines were also sensitive to PARP inhibitor monotherapy. The magnitude of sensitivity correlated with HR-repair reduced proficiency and with the expression levels and activity of PARP1 protein. In addition, we found that PARP inhibition strongly enhanced the response of the most resistant EC cells to cisplatin, by reducing their ability to overcome the damage. These results point to a reduced proficiency of HR repair as a source of sensitivity of ECs to ICL-inducing agents and PARP inhibitor monotherapy, and suggest that pharmacological inhibition of PARP can be exploited to target the stem cell component of the TGCTs (namely ECs) and to enhance the sensitivity of cisplatin-resistant TGCTs to standard treatments.
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Proks V, Jaroš J, Pop-Georgievski O, Kučka J, Popelka Š, Dvořák P, Hampl A, Rypáček F. “Click & Seed” Approach to the Biomimetic Modification of Material Surfaces. Macromol Biosci 2012; 12:1232-42. [DOI: 10.1002/mabi.201200095] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 05/10/2012] [Indexed: 01/17/2023]
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Abstract
SIGNIFICANCE Derived from the inner cell mass of the preimplantation embryo, embryonic stem cells are prototype pluripotent stem (PS) cells that have the ability of self-renewal and differentiation into almost all cell types. Exploration of the mechanisms governing this pluripotency is important for understanding reprogramming mechanisms and stem cell behavior of PS cells and can lead to enhancing reprogramming efficiency and other applications. RECENT ADVANCES Induced pluripotent stem cells are recently discovered PS cells that can be derived from somatic cells by overexpression of pluripotency-related transcription factors. Recent studies have shown that transcription factors and their epigenetic regulation play important roles in the generating, maintaining, and differentiating these PS cells. Recent advances in sequencing technologies allow detailed analysis of target epigenomes and microRNAs (miRs), and have revealed unique epigenetic marks and miRs for PS cells. CRITICAL ISSUES Epigenetic modifications of genes include histone modifications, DNA methylation, and chromatin remodeling. Working closely with epigenetic modifiers, miRs play an important role in inducing and maintaining pluripotency. FUTURE DIRECTIONS The dynamic changes in epigenetic marks during reprogramming and their role in cell fate changes are being uncovered. This review focuses on these new advances in the epigenetics of PS cells.
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Affiliation(s)
- Ji Woong Han
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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