1
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Incekara O, Acun T. DNAJC9 expression in basal-like and luminal A breast cancer subtypes predicts worse survival. Mol Biol Rep 2023; 50:7275-7282. [PMID: 37422538 DOI: 10.1007/s11033-023-08654-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND This study aimed to analyze the role of genetic/epigenetic alterations and the prognostic value of the DNAJC9 gene in breast cancer. MATERIALS AND METHODS RT-PCR and Q-RT-PCR methods are used to examine DNAJC9 expression in breast cell lines. Survival ratios of breast cancer patients were evaluated by using bc-GenExMiner. Combined bisulfite restriction analysis and UALCAN in-silico tool were used to assess the methylation level of the DNAJC9 promoter. Mutations were searched with the help of Sanger Cosmic database and direct sequencing. RESULTS DNAJC9 mRNA expression is significantly higher in basal-like, HER2-Enriched (HER2-E), luminal A and luminal B breast cancer subtypes compared to normal breast-like samples based on DNA microarray datasets (P < 0.001). Similar results were obtained in RNA-seq datasets, except for the luminal A breast cancer subtype (P > 0.1). We did not find any mutation at the core promoter region of DNAJC9 in breast cancer and normal cell lines. Mutations of DNAJC9 are infrequent in clinical samples (<%1). DNAJC9 promoter region is hypomethylated in tumor and normal samples. DNAJC9 expression is unfavorable for survival in basal-like and luminal A breast cancer subtypes. CONCLUSIONS Mutations or promoter hypomethylation do not appear to have a role in high DNAJC9 gene expression in breast cancer. DNAJC9 expression could be suggested as a novel biomarker in basal-like and luminal A breast cancer subtypes.
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Affiliation(s)
- Oya Incekara
- Department of Molecular Biology and Genetics, Faculty of Science, Zonguldak Bulent Ecevit University, 67100, Zonguldak, Turkey
| | - Tolga Acun
- Department of Molecular Biology and Genetics, Faculty of Science, Zonguldak Bulent Ecevit University, 67100, Zonguldak, Turkey.
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2
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Lin J, Chen Y, Zhang Y, Lin H, Ouyang Z. Deciphering the role of RNA structure in translation efficiency. BMC Bioinformatics 2022; 23:559. [PMID: 36564729 PMCID: PMC9783404 DOI: 10.1186/s12859-022-05037-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND RNA secondary structure has broad impact on the fate of RNA metabolism. The reduced stability of secondary structures near the translation initiation site/start codon of the coding region promotes the efficiency of translation in both prokaryotic and eukaryotic species. However, the inaccuracy of in silico folding and the focus on the coding region limit our understanding of the global relationship between the whole mRNA structure and translation efficiency. Leveraging high-throughput RNA structure probing data in the transcriptome, we aim to systematically investigate the role of RNA structure in regulating translation efficiency. RESULTS Here, we analyze the influences of hundreds of sequence and structural features on translation efficiency in the mouse embryonic stem cells (mESCs) and zebrafish developmental stages. Our findings reveal that overall in vivo RNA structure has a higher relative importance in predicting translation efficiency than in vitro RNA structure in both mESCs and zebrafish. Also, RNA structures in 3' untranslated region (UTR) have much stronger influence on translation efficiency compared to those in coding regions or 5' UTR. Furthermore, strong alternation between in vitro and in vivo structures in 3' UTR are detected in highly translated mRNAs in mESCs but not zebrafish. Instead, moderate alteration between in vitro and in vivo RNA structures in the 5' UTR and proximal coding regions are detected in highly translated mRNAs in zebrafish. CONCLUSIONS Our results suggest the openness of the 3' UTR promotes the translation efficiency in both mice and zebrafish, with the in vivo structure in 3' UTR more important in mice than in zebrafish. This reveals a novel role of RNA secondary structure on translational regulation.
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Affiliation(s)
- Jianan Lin
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, 01003, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Yang Chen
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, 01003, USA
| | - Yuping Zhang
- Department of Statistics, University of Connecticut, Storrs, CT, 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
- Center for Quantitative Medicine, University of Connecticut, Farmington, CT, 06030, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University, New Haven, CT, 06520, USA
| | - Zhengqing Ouyang
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, 01003, USA.
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Kim W, Park E, Yoo HS, Park J, Jung YM, Park JH. Recent Advances in Monitoring Stem Cell Status and Differentiation Using Nano-Biosensing Technologies. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12172934. [PMID: 36079970 PMCID: PMC9457759 DOI: 10.3390/nano12172934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 05/14/2023]
Abstract
In regenerative medicine, cell therapies using various stem cells have received attention as an alternative to overcome the limitations of existing therapeutic methods. Clinical applications of stem cells require the identification of characteristics at the single-cell level and continuous monitoring during expansion and differentiation. In this review, we recapitulate the application of various stem cells used in regenerative medicine and the latest technological advances in monitoring the differentiation process of stem cells. Single-cell RNA sequencing capable of profiling the expression of many genes at the single-cell level provides a new opportunity to analyze stem cell heterogeneity and to specify molecular markers related to the branching of differentiation lineages. However, this method is destructive and distorted. In addition, the differentiation process of a particular cell cannot be continuously tracked. Therefore, several spectroscopic methods have been developed to overcome these limitations. In particular, the application of Raman spectroscopy to measure the intrinsic vibration spectrum of molecules has been proposed as a powerful method that enables continuous monitoring of biochemical changes in the process of the differentiation of stem cells. This review provides a comprehensive overview of current analytical methods employed for stem cell engineering and future perspectives of nano-biosensing technologies as a platform for the in situ monitoring of stem cell status and differentiation.
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Affiliation(s)
- Wijin Kim
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon-do, Korea
| | - Eungyeong Park
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Gangwon-do, Korea
| | - Hyuk Sang Yoo
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon-do, Korea
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Gangwon-do, Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Gangwon-do, Korea
| | - Young Mee Jung
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Gangwon-do, Korea
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Gangwon-do, Korea
- Correspondence: (Y.M.J.); (J.H.P.); Tel.: +82-33-250-8495 (Y.M.J.); +82-33-250-6566 (J.H.P.)
| | - Ju Hyun Park
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon-do, Korea
- Correspondence: (Y.M.J.); (J.H.P.); Tel.: +82-33-250-8495 (Y.M.J.); +82-33-250-6566 (J.H.P.)
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4
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Wang C, Yang ZZ, Guo FH, Shi S, Han XS, Zeng A, Lin H, Jing Q. Heat shock protein DNAJA1 stabilizes PIWI proteins to support regeneration and homeostasis of planarian Schmidtea mediterranea. J Biol Chem 2019; 294:9873-9887. [PMID: 31076507 DOI: 10.1074/jbc.ra118.004445] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 04/25/2019] [Indexed: 12/16/2022] Open
Abstract
PIWI proteins are key regulators of germline and somatic stem cells throughout different evolutionary lineages. However, how PIWI proteins themselves are regulated remains largely unknown. To identify candidate proteins that interact with PIWI proteins and regulate their stability, here we established a yeast two-hybrid (Y2H) assay in the planarian species Schmidtea mediterranea We show that DNAJA1, a heat shock protein 40 family member, interacts with the PIWI protein SMEDWI-2, as validated by the Y2H screen and co-immunoprecipitation assays. We found that DNAJA1 is enriched in planarian adult stem cells, the nervous system, and intestinal tissues. DNAJA1-knockdown abolished planarian regeneration and homeostasis, compromised stem cell maintenance and PIWI-interacting RNA (piRNA) biogenesis, and deregulated SMEDWI-1/2 target genes. Mechanistically, we observed that DNAJA1 is required for the stability of SMEDWI-1 and SMEDWI-2 proteins. Furthermore, we noted that human DNAJA1 binds to Piwi-like RNA-mediated gene silencing 1 (PIWIL1) and is required for PIWIL1 stability in human gastric cancer cells. In summary, our results reveal not only an evolutionarily conserved functional link between PIWI and DNAJA1 that is essential for PIWI protein stability and piRNA biogenesis, but also an important role of DNAJA1 in the control of proteins involved in stem cell regulation.
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Affiliation(s)
- Chen Wang
- From the Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.,the CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Zhen-Zhen Yang
- From the Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Fang-Hao Guo
- the CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Shuo Shi
- From the Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Xiao-Shuai Han
- the CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China, and
| | - An Zeng
- the CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Haifan Lin
- From the Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China, .,the Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut 06511
| | - Qing Jing
- the CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China, and
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5
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Abed M, Verschueren E, Budayeva H, Liu P, Kirkpatrick DS, Reja R, Kummerfeld SK, Webster JD, Gierke S, Reichelt M, Anderson KR, Newman RJ, Roose-Girma M, Modrusan Z, Pektas H, Maltepe E, Newton K, Dixit VM. The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification. PLoS One 2019; 14:e0214110. [PMID: 30951545 PMCID: PMC6450627 DOI: 10.1371/journal.pone.0214110] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/15/2019] [Indexed: 01/03/2023] Open
Abstract
Peg10 (paternally expressed gene 10) is an imprinted gene that is essential for placental development. It is thought to derive from a Ty3-gyspy LTR (long terminal repeat) retrotransposon and retains Gag and Pol-like domains. Here we show that the Gag domain of PEG10 can promote vesicle budding similar to the HIV p24 Gag protein. Expressed in a subset of mouse endocrine organs in addition to the placenta, PEG10 was identified as a substrate of the deubiquitinating enzyme USP9X. Consistent with PEG10 having a critical role in placental development, PEG10-deficient trophoblast stem cells (TSCs) exhibited impaired differentiation into placental lineages. PEG10 expressed in wild-type, differentiating TSCs was bound to many cellular RNAs including Hbegf (Heparin-binding EGF-like growth factor), which is known to play an important role in placentation. Expression of Hbegf was reduced in PEG10-deficient TSCs suggesting that PEG10 might bind to and stabilize RNAs that are critical for normal placental development.
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Affiliation(s)
- Mona Abed
- Physiological Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Erik Verschueren
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Hanna Budayeva
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Peter Liu
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Donald S. Kirkpatrick
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Rohit Reja
- Bioinformatics and Computational Biology Department, Genentech, South San Francisco, California, United States of America
| | - Sarah K. Kummerfeld
- Bioinformatics and Computational Biology Department, Genentech, South San Francisco, California, United States of America
| | - Joshua D. Webster
- Pathology Department, Genentech, South San Francisco, California, United States of America
| | - Sarah Gierke
- Pathology Department, Genentech, South San Francisco, California, United States of America
| | - Mike Reichelt
- Pathology Department, Genentech, South San Francisco, California, United States of America
| | - Keith R. Anderson
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Robert J. Newman
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Merone Roose-Girma
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Zora Modrusan
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Hazal Pektas
- The Center for Reproductive Sciences, Division of Neonatology, University of California, San Francisco, California, United States of America
| | - Emin Maltepe
- The Center for Reproductive Sciences, Division of Neonatology, University of California, San Francisco, California, United States of America
| | - Kim Newton
- Physiological Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Vishva M. Dixit
- Physiological Chemistry Department, Genentech, South San Francisco, California, United States of America
- * E-mail:
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6
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Harkness L, Chen X, Gillard M, Gray PP, Davies AM. Media composition modulates human embryonic stem cell morphology and may influence preferential lineage differentiation potential. PLoS One 2019; 14:e0213678. [PMID: 30889226 PMCID: PMC6424453 DOI: 10.1371/journal.pone.0213678] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/26/2019] [Indexed: 12/22/2022] Open
Abstract
Undifferentiated human embryonic stem cells have a distinct morphology (hESC). Changes in cell morphology during culture can be indicative of differentiation. hESC, maintained in diverse medias, demonstrated alterations in morphological parameters and subsequent alterations in underlying transcript expression and lineage differentiation. Analysis of morphological parameters showed distinct and significant differences between the undefined, less defined and Xeno-free medias while still maintaining pluripotency markers. This suggested that the less defined media may be creating dynamic instability in the cytoskeleton, with the cytoskeleton becoming more stabilised in the Xeno-free media as demonstrated by smaller and rounder cells. Examination of early lineage markers during undirected differentiation using d5 embryoid bodies demonstrated increased mesodermal lineage preference as compared to endodermal or ectoderm in cells originally cultured in Xeno-free media. Undefined media showed preference for mesoderm and ectoderm lineages, while less defined media (BSA present) demonstrated no preference. These data reveal that culture media may produce fundamental changes in cell morphology which are reflected in early lineage differentiation choice.
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Affiliation(s)
- Linda Harkness
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
- * E-mail:
| | - Xiaoli Chen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Marianne Gillard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Peter Paul Gray
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Anthony Mitchell Davies
- Translational Cell Imaging Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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7
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Smith HL, Stevens A, Minogue B, Sneddon S, Shaw L, Wood L, Adeniyi T, Xiao H, Lio P, Kimber SJ, Brison DR. Systems based analysis of human embryos and gene networks involved in cell lineage allocation. BMC Genomics 2019; 20:171. [PMID: 30836937 PMCID: PMC6399968 DOI: 10.1186/s12864-019-5558-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Little is understood of the molecular mechanisms involved in the earliest cell fate decision in human development, leading to the establishment of the trophectoderm (TE) and inner cell mass (ICM) stem cell population. Notably, there is a lack of understanding of how transcriptional networks arise during reorganisation of the embryonic genome post-fertilisation. RESULTS We identified a hierarchical structure of preimplantation gene network modules around the time of embryonic genome activation (EGA). Using network models along with eukaryotic initiation factor (EIF) and epigenetic-associated gene expression we defined two sets of blastomeres that exhibited diverging tendencies towards ICM or TE. Analysis of the developmental networks demonstrated stage specific EIF expression and revealed that histone modifications may be an important epigenetic regulatory mechanism in preimplantation human embryos. Comparison to published RNAseq data confirmed that during EGA the individual 8-cell blastomeres are transcriptionally primed for the first lineage decision in development towards ICM or TE. CONCLUSIONS Using multiple systems biology approaches to compare developmental stages in the early human embryo with single cell transcript data from blastomeres, we have shown that blastomeres considered to be totipotent are not transcriptionally equivalent. Furthermore we have linked the developmental interactome to individual blastomeres and to later cell lineage. This has clinical implications for understanding the impact of fertility treatments and developmental programming of long term health.
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Affiliation(s)
- H. L. Smith
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - A. Stevens
- Division of Developmental Biology & Medicine, School of Medical Sciences, University of Manchester, Manchester Academic Health Sciences Centre, 5th Floor Research, Royal Manchester Children’s Hospital, Oxford Road, Manchester, M13 9WL UK
| | - B. Minogue
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - S. Sneddon
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - L. Shaw
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - L. Wood
- Department of Reproductive Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - T. Adeniyi
- Department of Reproductive Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - H. Xiao
- Computer Laboratory, William Gates Building, University of Cambridge, Cambridge, UK
| | - P. Lio
- Computer Laboratory, William Gates Building, University of Cambridge, Cambridge, UK
| | - S. J. Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - D. R. Brison
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Department of Reproductive Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
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8
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Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, Iyer G, Smith LM, Sridharan R. Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports 2019; 10:627-641. [PMID: 29358085 PMCID: PMC5830946 DOI: 10.1016/j.stemcr.2017.12.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/31/2022] Open
Abstract
The heterochromatin protein 1 (HP1) family is involved in various functions with maintenance of chromatin structure. During murine somatic cell reprogramming, we find that early depletion of HP1γ reduces the generation of induced pluripotent stem cells, while late depletion enhances the process, with a concomitant change from a centromeric to nucleoplasmic localization and elongation-associated histone H3.3 enrichment. Depletion of heterochromatin anchoring protein SENP7 increased reprogramming efficiency to a similar extent as HP1γ, indicating the importance of HP1γ release from chromatin for pluripotency acquisition. HP1γ interacted with OCT4 and DPPA4 in HP1α and HP1β knockouts and in H3K9 methylation depleted H3K9M embryonic stem cell (ESC) lines. HP1α and HP1γ complexes in ESCs differed in association with histones, the histone chaperone CAF1 complex, and specific components of chromatin-modifying complexes such as DPY30, implying distinct functional contributions. Taken together, our results reveal the complex contribution of the HP1 proteins to pluripotency. Release of HP1γ from anchoring by Senp7 increases reprogramming efficiency HP1γ switches enrichment from histone H1 to histone H3.3 in pluripotent cells HP1γ interacts with OCT4 and DPPA4 independent of HP1α, HP1β, and H3K9 methylation Proteomic characterization of HP1 protein family in pluripotent cells
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Affiliation(s)
- Nur Zafirah Zaidan
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Genetics Training Program, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Kolin J Walker
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Jaime E Brown
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Gopal Iyer
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rupa Sridharan
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53715, USA.
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9
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Promotive effects of human induced pluripotent stem cell-conditioned medium on the proliferation and migration of dermal fibroblasts. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-017-0221-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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10
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Krentz NAJ, van Hoof D, Li Z, Watanabe A, Tang M, Nian C, German MS, Lynn FC. Phosphorylation of NEUROG3 Links Endocrine Differentiation to the Cell Cycle in Pancreatic Progenitors. Dev Cell 2017; 41:129-142.e6. [PMID: 28441528 DOI: 10.1016/j.devcel.2017.02.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 10/28/2016] [Accepted: 02/09/2017] [Indexed: 02/08/2023]
Abstract
During pancreatic development, proliferating pancreatic progenitors activate the proendocrine transcription factor neurogenin 3 (NEUROG3), exit the cell cycle, and differentiate into islet cells. The mechanisms that direct robust NEUROG3 expression within a subset of progenitor cells control the size of the endocrine population. Here we demonstrate that NEUROG3 is phosphorylated within the nucleus on serine 183, which catalyzes its hyperphosphorylation and proteosomal degradation. During progression through the progenitor cell cycle, NEUROG3 phosphorylation is driven by the actions of cyclin-dependent kinases 2 and 4/6 at G1/S cell-cycle checkpoint. Using models of mouse and human pancreas development, we show that lengthening of the G1 phase of the pancreatic progenitor cell cycle is essential for proper induction of NEUROG3 and initiation of endocrine cell differentiation. In sum, these studies demonstrate that progenitor cell-cycle G1 lengthening, through its actions on stabilization of NEUROG3, is an essential variable in normal endocrine cell genesis.
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Affiliation(s)
- Nicole A J Krentz
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Departments of Surgery and Cellular and Physiological Sciences, University of British Columbia, 950 28th Avenue West, Vancouver, BC V5Z 4H4, Canada
| | - Dennis van Hoof
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research and Diabetes Center, University of California San Francisco, San Francisco, CA 94143-0669, USA
| | - Zhongmei Li
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research and Diabetes Center, University of California San Francisco, San Francisco, CA 94143-0669, USA
| | - Akie Watanabe
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Departments of Surgery and Cellular and Physiological Sciences, University of British Columbia, 950 28th Avenue West, Vancouver, BC V5Z 4H4, Canada
| | - Mei Tang
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Departments of Surgery and Cellular and Physiological Sciences, University of British Columbia, 950 28th Avenue West, Vancouver, BC V5Z 4H4, Canada
| | - Cuilan Nian
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Departments of Surgery and Cellular and Physiological Sciences, University of British Columbia, 950 28th Avenue West, Vancouver, BC V5Z 4H4, Canada
| | - Michael S German
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research and Diabetes Center, University of California San Francisco, San Francisco, CA 94143-0669, USA; Department of Medicine, University of California San Francisco, 35 Medical Center Way, RMB 1025, San Francisco, CA 94143-0669, USA.
| | - Francis C Lynn
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Departments of Surgery and Cellular and Physiological Sciences, University of British Columbia, 950 28th Avenue West, Vancouver, BC V5Z 4H4, Canada.
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Bridges CR, Tan MC, Premarathne S, Nanayakkara D, Bellette B, Zencak D, Domingo D, Gecz J, Murtaza M, Jolly LA, Wood SA. USP9X deubiquitylating enzyme maintains RAPTOR protein levels, mTORC1 signalling and proliferation in neural progenitors. Sci Rep 2017; 7:391. [PMID: 28341829 PMCID: PMC5427856 DOI: 10.1038/s41598-017-00149-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/13/2017] [Indexed: 12/27/2022] Open
Abstract
USP9X, is highly expressed in neural progenitors and, essential for neural development in mice. In humans, mutations in USP9X are associated with neurodevelopmental disorders. To understand USP9X’s role in neural progenitors, we studied the effects of altering its expression in both the human neural progenitor cell line, ReNcell VM, as well as neural stem and progenitor cells derived from Nestin-cre conditionally deleted Usp9x mice. Decreasing USP9X resulted in ReNcell VM cells arresting in G0 cell cycle phase, with a concomitant decrease in mTORC1 signalling, a major regulator of G0/G1 cell cycle progression. Decreased mTORC1 signalling was also observed in Usp9x-null neurospheres and embryonic mouse brains. Further analyses revealed, (i) the canonical mTORC1 protein, RAPTOR, physically associates with Usp9x in embryonic brains, (ii) RAPTOR protein level is directly proportional to USP9X, in both loss- and gain-of-function experiments in cultured cells and, (iii) USP9X deubiquitlyating activity opposes the proteasomal degradation of RAPTOR. EdU incorporation assays confirmed Usp9x maintains the proliferation of neural progenitors similar to Raptor-null and rapamycin-treated neurospheres. Interestingly, loss of Usp9x increased the number of sphere-forming cells consistent with enhanced neural stem cell self-renewal. To our knowledge, USP9X is the first deubiquitylating enzyme shown to stabilize RAPTOR.
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Affiliation(s)
- Caitlin R Bridges
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Men-Chee Tan
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Susitha Premarathne
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Devathri Nanayakkara
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Bernadette Bellette
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Dusan Zencak
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Deepti Domingo
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Jozef Gecz
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia.,Robinson Institute, School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia
| | - Mariyam Murtaza
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Lachlan A Jolly
- Robinson Institute, School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia.
| | - Stephen A Wood
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
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12
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Biophysical regulation of mouse embryonic stem cell fate and genomic integrity by feeder derived matrices. Biomaterials 2017; 119:9-22. [DOI: 10.1016/j.biomaterials.2016.12.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 12/07/2016] [Indexed: 01/01/2023]
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13
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Singec I, Crain AM, Hou J, Tobe BTD, Talantova M, Winquist AA, Doctor KS, Choy J, Huang X, La Monaca E, Horn DM, Wolf DA, Lipton SA, Gutierrez GJ, Brill LM, Snyder EY. Quantitative Analysis of Human Pluripotency and Neural Specification by In-Depth (Phospho)Proteomic Profiling. Stem Cell Reports 2016; 7:527-542. [PMID: 27569059 PMCID: PMC5032292 DOI: 10.1016/j.stemcr.2016.07.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 10/27/2022] Open
Abstract
Controlled differentiation of human embryonic stem cells (hESCs) can be utilized for precise analysis of cell type identities during early development. We established a highly efficient neural induction strategy and an improved analytical platform, and determined proteomic and phosphoproteomic profiles of hESCs and their specified multipotent neural stem cell derivatives (hNSCs). This quantitative dataset (nearly 13,000 proteins and 60,000 phosphorylation sites) provides unique molecular insights into pluripotency and neural lineage entry. Systems-level comparative analysis of proteins (e.g., transcription factors, epigenetic regulators, kinase families), phosphorylation sites, and numerous biological pathways allowed the identification of distinct signatures in pluripotent and multipotent cells. Furthermore, as predicted by the dataset, we functionally validated an autocrine/paracrine mechanism by demonstrating that the secreted protein midkine is a regulator of neural specification. This resource is freely available to the scientific community, including a searchable website, PluriProt.
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Affiliation(s)
- Ilyas Singec
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Andrew M Crain
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Junjie Hou
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Brian T D Tobe
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Maria Talantova
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Alicia A Winquist
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Kutbuddin S Doctor
- Informatics and Data Management, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jennifer Choy
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Xiayu Huang
- Informatics and Data Management, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Esther La Monaca
- Department of Biology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - David M Horn
- Thermo Fisher Scientific Inc., San Jose, CA 95134, USA
| | - Dieter A Wolf
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Stuart A Lipton
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Gustavo J Gutierrez
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Department of Biology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Laurence M Brill
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Evan Y Snyder
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
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14
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Sarkar P, Mischler A, Randall SM, Collier TS, Dorman KF, Boggess KA, Muddiman DC, Rao BM. Identification of Epigenetic Factor Proteins Expressed in Human Embryonic Stem Cell-Derived Trophoblasts and in Human Placental Trophoblasts. J Proteome Res 2016; 15:2433-44. [PMID: 27378238 DOI: 10.1021/acs.jproteome.5b01118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Human embryonic stem cells (hESCs) have been used to derive trophoblasts through differentiation in vitro. Intriguingly, mouse ESCs are prevented from differentiation to trophoblasts by certain epigenetic factor proteins such as Dnmt1, thus necessitating the study of epigenetic factor proteins during hESC differentiation to trophoblasts. We used stable isotope labeling by amino acids in cell culture and quantitative proteomics to study changes in the nuclear proteome during hESC differentiation to trophoblasts and identified changes in the expression of 30 epigenetic factor proteins. Importantly, the DNA methyltransferases DNMT1, DNMT3A, and DNMT3B were downregulated. Additionally, we hypothesized that nuclear proteomics of hESC-derived trophoblasts may be used for screening epigenetic factor proteins expressed by primary trophoblasts in human placental tissue. Accordingly, we conducted immunohistochemistry analysis of six epigenetic factor proteins identified from hESC-derived trophoblasts-DNMT1, DNMT3B, BAF155, BAF60A, BAF57, and ING5-in 6-9 week human placentas. Indeed, expression of these proteins was largely, though not fully, consistent with that observed in 6-9 week placental trophoblasts. Our results support the use of hESC-derived trophoblasts as a model for placental trophoblasts, which will enable further investigation of epigenetic factors involved in human trophoblast development.
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Affiliation(s)
| | | | | | | | - Karen F Dorman
- Department of Obstetrics and Gynecology, University of North Carolina-Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Kim A Boggess
- Department of Obstetrics and Gynecology, University of North Carolina-Chapel Hill , Chapel Hill, North Carolina 27599, United States
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15
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Nong W, Xie TS, Li LY, Lu AG, Mo J, Gou YF, Lan G, Jiang H, Len J, Li MM, Jiang QY, Huang B. Qualitative Analyses of Protein Phosphorylation in Bovine Pluripotent Stem Cells Generated from Embryonic Fibroblasts. Reprod Domest Anim 2015; 50:989-98. [DOI: 10.1111/rda.12619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 09/07/2015] [Indexed: 12/19/2022]
Affiliation(s)
- W Nong
- College of Animal Science and Technology; Guangxi University; Nanning China
- Guangxi University of Chinese Medicine; Nanning China
| | - TS Xie
- College of Animal Science and Technology; Guangxi University; Nanning China
- Nanning Languang Biotechnology Inc.; Nanning China
| | - LY Li
- College of Animal Science and Technology; Guangxi University; Nanning China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources; Guangxi University; Nanning China
| | - AG Lu
- College of Animal Science and Technology; Guangxi University; Nanning China
- Guangxi Analysis and Testing Center; Nanning China
| | - J Mo
- Guangxi Analysis and Testing Center; Nanning China
| | - YF Gou
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - G Lan
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - H Jiang
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - J Len
- Guangxi University of Chinese Medicine; Nanning China
| | - MM Li
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - QY Jiang
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - B Huang
- College of Animal Science and Technology; Guangxi University; Nanning China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources; Guangxi University; Nanning China
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16
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Differences in the Early Development of Human and Mouse Embryonic Stem Cells. PLoS One 2015; 10:e0140803. [PMID: 26473594 PMCID: PMC4608779 DOI: 10.1371/journal.pone.0140803] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 09/30/2015] [Indexed: 01/22/2023] Open
Abstract
We performed a systematic analysis of gene expression features in early (10–21 days) development of human vs mouse embryonic cells (hESCs vs mESCs). Many development features were found to be conserved, and a majority of differentially regulated genes have similar expression change in both organisms. The similarity is especially evident, when gene expression profiles are clustered together and properties of clustered groups of genes are compared. First 10 days of mESC development match the features of hESC development within 21 days, in accordance with the differences in population doubling time in human and mouse ESCs. At the same time, several important differences are seen. There is a clear difference in initial expression change of transcription factors and stimulus responsive genes, which may be caused by the difference in experimental procedures. However, we also found that some biological processes develop differently; this can clearly be shown, for example, for neuron and sensory organ development. Some groups of genes show peaks of the expression levels during the development and these peaks cannot be claimed to happen at the same time points in the two organisms, as well as for the same groups of (orthologous) genes. We also detected a larger number of upregulated genes during development of mESCs as compared to hESCs. The differences were quantified by comparing promoters of related genes. Most of gene groups behave similarly and have similar transcription factor (TF) binding sites on their promoters. A few groups of genes have similar promoters, but are expressed differently in two species. Interestingly, there are groups of genes expressed similarly, although they have different promoters, which can be shown by comparing their TF binding sites. Namely, a large group of similarly expressed cell cycle-related genes is found to have discrepant TF binding properties in mouse vs human.
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17
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Tan Y, AlKhamees B, Jia D, Li L, Couture JF, Figeys D, Jinushi M, Wang L. MFG-E8 Is Critical for Embryonic Stem Cell-Mediated T Cell Immunomodulation. Stem Cell Reports 2015; 5:741-752. [PMID: 26455415 PMCID: PMC4649138 DOI: 10.1016/j.stemcr.2015.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 02/03/2023] Open
Abstract
The molecules and mechanisms pertinent to the low immunogenicity of undifferentiated embryonic stem cells (ESCs) remain poorly understood. Here, we provide evidence that milk fat globule epidermal growth factor 8 (MFG-E8) is a vital mediator in this phenomenon and directly suppresses T cell immune responses. MFG-E8 is enriched in undifferentiated ESCs but diminished in differentiated ESCs. Upregulation of MFG-E8 in ESCs increases the successful engraftment of both undifferentiated and differentiated ESCs across major histocompatibility complex barriers. MFG-E8 suppresses T cell activation/proliferation and inhibits Th1, Th2, and Th17 subpopulations while increasing regulatory T cell subsets. Neutralizing MFG-E8 substantially abrogates these effects, whereas addition of recombinant MFG-E8 to differentiated ESCs restores immunosuppression. Furthermore, we provide the evidence that MFG-E8 suppresses T cell activation and regulates T cell polarization by inhibiting PKCθ phosphorylation through the α3/5βV integrin receptor. Our findings offer an approach to facilitate transplantation acceptance. MFG-E8 is enriched in undifferentiated but diminished in differentiated ESCs MFG-E8 promotes allogeneic engraftment of ESC-derived tissues across the MHC barrier ESC-produced MFG-E8 inhibits Th1/Th2/Th17 while promoting regulatory T cells MFG-E8 modulates T cell polarization via inhibiting PKCθ phosphorylation
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Affiliation(s)
- Yuan Tan
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Bodour AlKhamees
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Deyong Jia
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Li Li
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Jean-François Couture
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Masahisa Jinushi
- Institute for Advanced Medical Research, Keio University School of Medicine, 35 Shinanomachi, Shinjiku-ku, Tokyo 160-8582, Japan.
| | - Lisheng Wang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.
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18
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Shoni M, Lui KO, Vavvas DG, Muto MG, Berkowitz RS, Vlahos N, Ng SW. Protein kinases and associated pathways in pluripotent state and lineage differentiation. Curr Stem Cell Res Ther 2015; 9:366-87. [PMID: 24998240 DOI: 10.2174/1574888x09666140616130217] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 06/07/2014] [Accepted: 06/12/2014] [Indexed: 02/06/2023]
Abstract
Protein kinases (PKs) mediate the reversible conversion of substrate proteins to phosphorylated forms, a key process in controlling intracellular signaling transduction cascades. Pluripotency is, among others, characterized by specifically expressed PKs forming a highly interconnected regulatory network that culminates in a finely-balanced molecular switch. Current high-throughput phosphoproteomic approaches have shed light on the specific regulatory PKs and their function in controlling pluripotent states. Pluripotent cell-derived endothelial and hematopoietic developments represent an example of the importance of pluripotency in cancer therapeutics and organ regeneration. This review attempts to provide the hitherto known kinome profile and the individual characterization of PK-related pathways that regulate pluripotency. Elucidating the underlying intrinsic and extrinsic signals may improve our understanding of the different pluripotent states, the maintenance or induction of pluripotency, and the ability to tailor lineage differentiation, with a particular focus on endothelial cell differentiation for anti-cancer treatment, cell-based tissue engineering, and regenerative medicine strategies.
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Affiliation(s)
| | | | | | | | | | | | - Shu-Wing Ng
- 221 Longwood Avenue, BLI- 449A, Boston MA 02115, USA.
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19
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Overexpression of DNAJC12 predicts poor response to neoadjuvant concurrent chemoradiotherapy in patients with rectal cancer. Exp Mol Pathol 2015; 98:338-45. [PMID: 25805104 DOI: 10.1016/j.yexmp.2015.03.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/20/2015] [Indexed: 12/16/2022]
Abstract
Genes associated with protein folding have been found to have certain prognostic significance in a subset of cancers. The aim of this study is to evaluate the clinical impact of DNAJC12 expression in patients with rectal cancers receiving neoadjuvant concurrent chemoradiotherapy (CCRT) followed by surgery. Through data mining from a public transcriptomic dataset of rectal cancer focusing on genes associated with protein folding, we found that DNAJC12, a member of the HSP40/DNAJ family, was the most significant such gene correlated with the CCRT response. We further evaluated the expression of DNAJC12 by immunohistochemistry in the pre-treatment tumor specimens from 172 patients with rectal cancers. From this set, we statistically analyzed the association of DNAJC12 expression with various clinicopathological factors, tumor regression grade, overall survival (OS), disease-free survival (DFS) and local recurrence-free survival (LRFS). High expression of DNAJC12 was significantly associated with advanced pre- and post-treatment tumor status (P<0.001), advanced pre- and post-treatment nodal status (P<0.001), increased vascular invasion (P=0.015), increased perineural invasion (P=0.023) and lower tumor regression grade (P=0.009). More importantly, high expression of DNAJC12 was found to be correlated with poor prognosis for OS (P=0.0012), DFS (P<0.0001) and LRFS (P=0.0001). In multivariate analysis, DNAJC12 overexpression still emerged as an independent prognosticator for shorter OS (P=0.040), DFS (P<0.001) and LRFS (P=0.016). The data indicate that DNAJC12 overexpression acts as a negative predictive factor for the response to neoadjuvant CCRT and was significantly associated with shorter survival in patients with rectal cancers receiving neoadjuvant CCRT followed by surgery.
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20
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The L1TD1 protein interactome reveals the importance of post-transcriptional regulation in human pluripotency. Stem Cell Reports 2015; 4:519-28. [PMID: 25702638 PMCID: PMC4376047 DOI: 10.1016/j.stemcr.2015.01.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 01/16/2015] [Accepted: 01/16/2015] [Indexed: 11/24/2022] Open
Abstract
The RNA-binding protein L1TD1 is one of the most specific and abundant proteins in pluripotent stem cells and is essential for the maintenance of pluripotency in human cells. Here, we identify the protein interaction network of L1TD1 in human embryonic stem cells (hESCs) and provide insights into the interactome network constructed in human pluripotent cells. Our data reveal that L1TD1 has an important role in RNA splicing, translation, protein traffic, and degradation. L1TD1 interacts with multiple stem-cell-specific proteins, many of which are still uncharacterized in the context of development. Further, we show that L1TD1 is a part of the pluripotency interactome network of OCT4, SOX2, and NANOG, bridging nuclear and cytoplasmic regulation and highlighting the importance of RNA biology in pluripotency. A protein interactome is constructed in human embryonic stem cells L1TD1 interacts with U2af1 and Srsf3, which are vital for somatic cell reprogramming L1TD1 is involved in the high proteasome activity of pluripotent cells L1TD1 connects uncharacterized factors to the OCT4, SOX2, and NANOG network
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21
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Murtaza M, Jolly LA, Gecz J, Wood SA. La FAM fatale: USP9X in development and disease. Cell Mol Life Sci 2015; 72:2075-89. [PMID: 25672900 PMCID: PMC4427618 DOI: 10.1007/s00018-015-1851-0] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/02/2015] [Accepted: 02/04/2015] [Indexed: 11/12/2022]
Abstract
Deubiquitylating enzymes (DUBs), act downstream of ubiquitylation. As such, these post-post-translational modifiers function as the final arbitrators of a protein substrate’s ubiquitylation status, thus regulating its fate. In most instances, DUBs moderate the absolute level of a substrate, its locality or activity, rather than being an “all-or-none” phenomenon. Yet, disruption of this quantitative regulation can produce dramatic qualitative differences. The ubiquitin-specific protease 9X (USP9X/FAM) is a substrate-specific DUB, which displays an extraordinarily high level of sequence conservation from Drosophila to mammals. It is primarily the recent revelations of USP9X’s pivotal role in human cancers, both as oncogene or tumour suppressor, in developmental disorders including intellectual disability, epilepsy, autism and developmental delay that has led to a subsequent re-examination of its molecular and cellular functions. Results from experimental animal models have implicated USP9X in neurodegeneration, including Parkinson’s and Alzheimer’s disease, as well as autoimmune diseases. In this review, we describe the current and accumulated knowledge on the molecular, cellular and developmental aspects of USP9X function within the context of the biological consequences during normal development and disease.
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Affiliation(s)
- Mariyam Murtaza
- The Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia
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22
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Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L. The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry. Proteomics 2014; 15:554-66. [PMID: 25367160 DOI: 10.1002/pmic.201400132] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 09/22/2014] [Accepted: 10/28/2014] [Indexed: 01/06/2023]
Abstract
Human embryonic stem cells (hESCs) have received considerable attention due to their therapeutic potential and usefulness in understanding early development and cell fate commitment. In order to appreciate the unique properties of these pluripotent, self-renewing cells, we have performed an in-depth multidimensional fractionation followed by LC-MS/MS analysis of the hESCs harvested from defined media to elucidate expressed, phosphorylated, O-linked β-N-acetylglucosamine (O-GlcNAc) modified, and secreted proteins. From the triplicate analysis, we were able to assign more than 3000 proteins with less than 1% false-discovery rate. This analysis also allowed us to identify nearly 500 phosphorylation sites and 68 sites of O-GlcNAc modification with the same high confidence. Investigation of the phosphorylation sites allowed us to deduce the set of kinases that are likely active in these cells. We also identified more than 100 secreted proteins of hESCs that likely play a role in extracellular matrix formation and remodeling, as well as autocrine signaling for self-renewal and maintenance of the undifferentiated state. Finally, by performing in-depth analysis in triplicate, spectral counts were obtained for these proteins and posttranslationally modified peptides, which will allow us to perform relative quantitative analysis between these cells and any derived cell type in the future.
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Affiliation(s)
- Peng Zhao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
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23
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Ybarra N, Vincent P, Smith LC, Troncy E. Oxytocin improves the expression of cardiac specific markers in porcine bone marrow stem cells differentiation. Res Vet Sci 2014; 98:42-50. [PMID: 25541154 DOI: 10.1016/j.rvsc.2014.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 08/19/2014] [Accepted: 11/26/2014] [Indexed: 11/16/2022]
Abstract
Bone marrow stem cells (BMSCs) treated with 5-azacytidine possess myogenic differentiation potential. Oxytocin (OT) induces cardiomyogenesis in murine embryonic and cardiac stem cells. We attempted to isolate, characterize, and induce OT-mediated cardiomyogenic differentiation of porcine pBMSCs. Cells were treated as: control, OT, and 5-azacytidine groups. During early passages, transcripts of Oct4, GATA4, OT receptor, and phospholamban were expressed. RT-PCR showed upregulation of GATA4 in OT and 5-azacytidine-induced groups. Immunocytochemistry revealed higher expressions of cardiac troponin T and myosin heavy chain in OT than in 5-azacytidine-induced groups (p < 0.01). Western blot analysis showed upregulation of cardiac troponin I in OT-induced pBMSCs (p < 0.01). We infer pBMSCs should be induced during early passages, when expressing transcription factors related to pluripotency and cardiomyogenesis, as well as OT receptor. The more abundant expression of cardiac specific proteins in OT-treated pBMSCs suggests OT could be a more potent cardiomyogenic inducer of pBMSC.
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Affiliation(s)
- Norma Ybarra
- GREPAQ - Department of Veterinary Biomedicine, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
| | - Patrick Vincent
- CRRA - Department of Veterinary Biomedicine, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
| | - Lawrence C Smith
- CRRA - Department of Veterinary Biomedicine, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
| | - Eric Troncy
- GREPAQ - Department of Veterinary Biomedicine, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada.
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24
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Sun Y, Yang Y, Zeng S, Tan Y, Lu G, Lin G. Identification of proteins related to epigenetic regulation in the malignant transformation of aberrant karyotypic human embryonic stem cells by quantitative proteomics. PLoS One 2014; 9:e85823. [PMID: 24465727 PMCID: PMC3895013 DOI: 10.1371/journal.pone.0085823] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 12/02/2013] [Indexed: 11/19/2022] Open
Abstract
Previous reports have demonstrated that human embryonic stem cells (hESCs) tend to develop genomic alterations and progress to a malignant state during long-term in vitro culture. This raises concerns of the clinical safety in using cultured hESCs. However, transformed hESCs might serve as an excellent model to determine the process of embryonic stem cell transition. In this study, ITRAQ-based tandem mass spectrometry was used to quantify normal and aberrant karyotypic hESCs proteins from simple to more complex karyotypic abnormalities. We identified and quantified 2583 proteins, and found that the expression levels of 316 proteins that represented at least 23 functional molecular groups were significantly different in both normal and abnormal hESCs. Dysregulated protein expression in epigenetic regulation was further verified in six pairs of hESC lines in early and late passage. In summary, this study is the first large-scale quantitative proteomic analysis of the malignant transformation of aberrant karyotypic hESCs. The data generated should serve as a useful reference of stem cell-derived tumor progression. Increased expression of both HDAC2 and CTNNB1 are detected as early as the pre-neoplastic stage, and might serve as prognostic markers in the malignant transformation of hESCs.
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Affiliation(s)
- Yi Sun
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Key Laboratory of Stem Cells and Reproductive Engineering, Ministry of Health, Changsha, China
| | - Yixuan Yang
- Key Laboratory of Molecular Biology for Infectious Diseases of Ministry of Education of China, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Sicong Zeng
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
| | - Yueqiu Tan
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Key Laboratory of Stem Cells and Reproductive Engineering, Ministry of Health, Changsha, China
| | - Guangxiu Lu
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- * E-mail: (G. Lin); (G. Lu)
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Key Laboratory of Stem Cells and Reproductive Engineering, Ministry of Health, Changsha, China
- * E-mail: (G. Lin); (G. Lu)
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25
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Deciphering the combinatorial roles of geometric, mechanical, and adhesion cues in regulation of cell spreading. PLoS One 2013; 8:e81113. [PMID: 24282570 PMCID: PMC3839898 DOI: 10.1371/journal.pone.0081113] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 10/13/2013] [Indexed: 12/12/2022] Open
Abstract
Significant effort has gone towards parsing out the effects of surrounding microenvironment on macroscopic behavior of stem cells. Many of the microenvironmental cues, however, are intertwined, and thus, further studies are warranted to identify the intricate interplay among the conflicting downstream signaling pathways that ultimately guide a cell response. In this contribution, by patterning adhesive PEG (polyethylene glycol) hydrogels using Dip Pen Nanolithography (DPN), we demonstrate that substrate elasticity, subcellular elasticity, ligand density, and topography ultimately define mesenchymal stem cells (MSCs) spreading and shape. Physical characteristics are parsed individually with 7 kilopascal (kPa) hydrogel islands leading to smaller, spindle shaped cells and 105 kPa hydrogel islands leading to larger, polygonal cell shapes. In a parallel effort, a finite element model was constructed to characterize and confirm experimental findings and aid as a predictive tool in modeling cell microenvironments. Signaling pathway inhibition studies suggested that RhoA is a key regulator of cell response to the cooperative effect of the tunable substrate variables. These results are significant for the engineering of cell-extra cellular matrix interfaces and ultimately decoupling matrix bound cues presented to cells in a tissue microenvironment for regenerative medicine.
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26
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Cell shape and cardiosphere differentiation: a revelation by proteomic profiling. Biochem Res Int 2013; 2013:730874. [PMID: 24073335 PMCID: PMC3773893 DOI: 10.1155/2013/730874] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 07/08/2013] [Indexed: 01/16/2023] Open
Abstract
Stem cells (embryonic stem cells, somatic stem cells such as neural stem cells, and cardiac stem cells) and cancer cells are known to aggregate and form spheroid structures. This behavior is common in undifferentiated cells and may be necessary for adapting to certain conditions such as low-oxygen levels or to maintain undifferentiated status in microenvironments including stem cell niches. In order to decipher the meaning of this spheroid structure, we established a cardiosphere clone (CSC-21E) derived from the rat heart which can switch its morphology between spheroid and nonspheroid. Two forms, floating cardiospheres and dish-attached flat cells, could be switched reversibly by changing the cell culture condition. We performed differential proteome analysis studies and obtained protein profiles distinct between spherical forms and flat cells. From protein profiling analysis, we found upregulation of glycolytic enzymes in spheroids with some stress proteins switched in expression levels between these two forms. Evidence has been accumulating that certain chaperone/stress proteins are upregulated in concert with cellular changes including proliferation and differentiation. We would like to discuss the possible mechanism of how these aggregates affect cell differentiation and/or other cellular functions.
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27
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Liberski AR, Al-Noubi MN, Rahman ZH, Halabi NM, Dib SS, Al-Mismar R, Billing AM, Krishnankutty R, Ahmad FS, Raynaud CM, Rafii A, Engholm-Keller K, Graumann J. Adaptation of a commonly used, chemically defined medium for human embryonic stem cells to stable isotope labeling with amino acids in cell culture. J Proteome Res 2013; 12:3233-45. [PMID: 23734825 DOI: 10.1021/pr400099j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metabolic labeling with stable isotopes is a prominent technique for comparative quantitative proteomics, and stable isotope labeling with amino acids in cell culture (SILAC) is the most commonly used approach. SILAC is, however, traditionally limited to simple tissue culture regimens and only rarely employed in the context of complex culturing conditions as those required for human embryonic stem cells (hESCs). Classic hESC culture is based on the use of mouse embryonic fibroblasts (MEFs) as a feeder layer, and as a result, possible xenogeneic contamination, contribution of unlabeled amino acids by the feeders, interlaboratory variability of MEF preparation, and the overall complexity of the culture system are all of concern in conjunction with SILAC. We demonstrate a feeder-free SILAC culture system based on a customized version of a commonly used, chemically defined hESC medium developed by Ludwig et al. and commercially available as mTeSR1 [mTeSR1 is a trade mark of WiCell (Madison, WI) licensed to STEMCELL Technologies (Vancouver, Canada)]. This medium, together with adjustments to the culturing protocol, facilitates reproducible labeling that is easily scalable to the protein amounts required by proteomic work flows. It greatly enhances the usability of quantitative proteomics as a tool for the study of mechanisms underlying hESCs differentiation and self-renewal. Associated data have been deposited to the ProteomeXchange with the identifier PXD000151.
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28
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Maury JJP, Chan KKK, Zheng L, Bardor M, Choo ABH. Excess of O-linked N-acetylglucosamine modifies human pluripotent stem cell differentiation. Stem Cell Res 2013; 11:926-37. [PMID: 23859804 DOI: 10.1016/j.scr.2013.06.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 06/06/2013] [Accepted: 06/13/2013] [Indexed: 11/27/2022] Open
Abstract
O-linked-N-acetylglucosamine (O-GlcNAc), a post translational modification, has emerged as an important cue in controlling key cell mechanisms. Here, we investigate O-GlcNAc's role in the maintenance and differentiation of human pluripotent stem cells (hPSC). We reveal that protein expression of O-GlcNAc transferase and hydrolase both decreases during hPSC differentiation. Upregulating O-GlcNAc with O-GlcNAc hydrolase inhibitors has no significant effect on either the maintenance of pluripotency in hPSC culture, or the loss of pluripotency in differentiating hPSC. However, in spontaneously differentiating hPSC, excess O-GlcNAc alters the expression of specific lineage markers: decrease of ectoderm markers (PAX6 by 53-88%, MSX1 by 26-49%) and increase of adipose-related mesoderm markers (PPARγ by 28-100%, C/EBPα by 46-135%). All other lineage markers tested (cardiac, visceral-endoderm, trophectoderm) remain minimally affected by upregulated O-GlcNAc. Interestingly, we also show that excess O-GlcNAc triggers a feedback mechanism that increases O-GlcNAc hydrolase expression by 29-91%. To the best of our knowledge, this is the first report demonstrating that excess O-GlcNAc does not affect hPSC pluripotency in undifferentiated maintenance cultures; instead, it restricts the hPSC differentiation towards specific cell lineages. These data will be useful for developing targeted differentiation protocols and aid in understanding the effects of O-GlcNAc on hPSC differentiation.
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Affiliation(s)
- Julien Jean Pierre Maury
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore
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29
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Jafari M, Mirzaie M, Sadeghi M, Marashi SA, Rezaei-Tavirani M. Exploring biological processes involved in embryonic stem cell differentiation by analyzing proteomic data. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1063-9. [DOI: 10.1016/j.bbapap.2013.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/26/2013] [Accepted: 02/03/2013] [Indexed: 10/27/2022]
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30
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Hao J, Li W, Dan J, Ye X, Wang F, Zeng X, Wang L, Wang H, Cheng Y, Liu L, Shui W. Reprogramming- and pluripotency-associated membrane proteins in mouse stem cells revealed by label-free quantitative proteomics. J Proteomics 2013; 86:70-84. [DOI: 10.1016/j.jprot.2013.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 03/10/2013] [Accepted: 04/07/2013] [Indexed: 12/15/2022]
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31
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Diekmann U, Naujok O, Blasczyk R, Müller T. Embryonic stem cells of the non-human primate Callithrix jacchus can be differentiated into definitive endoderm by Activin-A but not IDE-1/2. J Tissue Eng Regen Med 2013; 9:473-9. [PMID: 23418163 DOI: 10.1002/term.1709] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 11/01/2012] [Accepted: 12/20/2012] [Indexed: 12/14/2022]
Abstract
Pluripotent stem cells hold great promise for regenerative medicine, due to their unlimited self-renewal potential and the ability to differentiate into all somatic cell types. Differences between the rodent disease models and the situation in humans can be narrowed down with non-human primate models. The common marmoset monkey (Callithrix jacchus) is an interesting model for biomedical research because these animals are easy to breed, get relatively old (≤ 13 years), are small in size, are relatively cost-effective and have a high genetic proximity to the human. In particular, diseases of the liver and pancreas are interesting for cell replacement therapies but the in vitro differentiation of ESCs into the definitive endoderm germ layer is still a demanding task. Membrane-permeable, chemically defined small molecules can possibly replace recombinant growth factors used in most directed differentiation protocols. However, the potent small molecules IDE-1 and IDE-2 were not able to induce definitive endoderm-like cells when ESCs from the common marmoset were treated with these compounds, whereas the recombinant growth factor Activin A could force the differentiation into this lineage. Our results indicate that ESCs from the common marmoset are less sensitive or even insensitive to these small molecules. Thus, differences between the species of human ESCs and ESCs of this non-human primate might be a useful model to further evaluate the exact mode of action of these compounds.
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Affiliation(s)
- Ulf Diekmann
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany; Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
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32
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Sojoodi M, Farrokhi A, Moradmand A, Baharvand H. Enhanced maintenance of rat islets of Langerhans on laminin-coated electrospun nanofibrillar matrix in vitro. Cell Biol Int 2013; 37:370-9. [DOI: 10.1002/cbin.10045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 01/07/2013] [Indexed: 01/06/2023]
Affiliation(s)
| | - Ali Farrokhi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center; Royan Institute for Stem Cell Biology and Technology; ACECR, P.O. Box 19395-4644, Tehran; Iran
| | - Azadeh Moradmand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center; Royan Institute for Stem Cell Biology and Technology; ACECR, P.O. Box 19395-4644, Tehran; Iran
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33
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Veraksa A. Regulation of developmental processes: insights from mass spectrometry-based proteomics. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 2:723-34. [PMID: 24014456 DOI: 10.1002/wdev.102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mass spectrometry (MS)-based proteomics has become an indispensable tool for protein identification and quantification. In this paper, common MS workflows are described, with an emphasis on applications of MS-based proteomics in developmental biology. Progress has been made in the analysis of proteome changes during tissue differentiation and in various genetic perturbations. MS-based proteomics has been particularly useful for identifying novel protein interactions by affinity purification-mass spectrometry (AP-MS), many of which have been subsequently functionally validated and led to the discovery of previously unknown modes of developmental regulation. Quantitative proteomics approaches can be used to study posttranslational modifications (PTMs) of proteins such as phosphorylation, to reveal the dynamics of intracellular signal transduction. Integrative approaches combine quantitative MS-based proteomics with other high-throughput methods, with the promise of a systems level understanding of developmental regulation.
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Affiliation(s)
- Alexey Veraksa
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.
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34
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Single Mechanosensitive and Ca2+-Sensitive Channel Currents Recorded from Mouse and Human Embryonic Stem Cells. J Membr Biol 2012. [DOI: 10.1007/s00232-012-9523-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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35
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Binato R, de Souza Fernandez T, Lazzarotto-Silva C, Du Rocher B, Mencalha A, Pizzatti L, Bouzas LF, Abdelhay E. Stability of human mesenchymal stem cells during in vitro culture: considerations for cell therapy. Cell Prolif 2012; 46:10-22. [PMID: 23163975 DOI: 10.1111/cpr.12002] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/08/2012] [Indexed: 01/30/2023] Open
Abstract
Ex vivo expansion and manipulation of human mesenchymal stem cells are important approaches to immunoregulatory and regenerative cell therapies. Although these cells show great potential for use, issues relating to their overall nature emerge as problems in the field. The need for extensive cell quantity amplification in vitro to obtain sufficient cell numbers for use, poses a risk of accumulating genetic and epigenetic abnormalities that could lead to sporadic malignant cell transformation. In this study, we have examined human mesenchymal stem cells derived from bone marrow, over extended culture time, using cytogenetic analyses, mixed lymphocyte reactions, proteomics and gene expression assays to determine whether the cultures would retain their potential for use in subsequent passages. Results indicate that in vitro cultures of these cells demonstrated chromosome variability after passage 4, but their immunomodulatory functions and differentiation capacity were maintained. At the molecular level, changes were observed from passage 5 on, indicating initiation of differentiation. Together, these results lead to the hypothesis that human mesenchymal stem cells cultures can be used successfully in cell therapy up to passage 4. However, use of cells from higher passages would have to be analysed case by case.
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Affiliation(s)
- R Binato
- Bone Marrow Transplantation Unit, National Cancer Institute (INCA), Rio de Janeiro, Brazil.
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36
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Bousette N, Gramolini AO, Kislinger T. Proteomics-based investigations of animal models of disease. Proteomics Clin Appl 2012; 2:638-53. [PMID: 21136864 DOI: 10.1002/prca.200780043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cells contain a large yet, constant genome, which contains all the coding information necessary to sustain cellular physiology. However, proteins are the end products of genes, and hence dictate the phenotype of cells and tissues. Therefore, proteomics can provide key information for the elucidation of physiological and pathophysiological mechanisms by identifying the protein profile from cells and tissues. The relatively novel techniques used for the study of proteomics thus have the potential to improve diagnostic, prognostic, as well as therapeutic avenues. In this review, we first discuss the benefits of animal models over the use of human samples for the proteomic analysis of human disease. Next, we aim to demonstrate the potential of proteomics in the elucidation of disease mechanisms that may not be possible by other conventional technologies. Following this, we describe the use of proteomics for the analysis of PTM and protein interactions in animal models and their relevance to the study of human disease. Finally, we discuss the development of clinical biomarkers for the early diagnosis of disease via proteomic analysis of animal models. We also discuss the development of standard proteomes and relate how this data will benefit future proteomic research. A comprehensive review of all animal models used in conjunction with proteomics is beyond the scope of this manuscript. Therefore, we aimed to cover a large breadth of topics, which together, demonstrate the potential of proteomics as a powerful tool in biomedical research.
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Affiliation(s)
- Nicolas Bousette
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada; Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Toronto, Ontario, Canada
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37
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Hamada M, Malureanu LA, Wijshake T, Zhou W, van Deursen JM. Reprogramming to pluripotency can conceal somatic cell chromosomal instability. PLoS Genet 2012; 8:e1002913. [PMID: 22952451 PMCID: PMC3431347 DOI: 10.1371/journal.pgen.1002913] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 07/05/2012] [Indexed: 01/12/2023] Open
Abstract
The discovery that somatic cells are reprogrammable to pluripotency by ectopic expression of a small subset of transcription factors has created great potential for the development of broadly applicable stem-cell-based therapies. One of the concerns regarding the safe use of induced pluripotent stem cells (iPSCs) in therapeutic applications is loss of genomic integrity, a hallmark of various human conditions and diseases, including cancer. Structural chromosome defects such as short telomeres and double-strand breaks are known to limit reprogramming of somatic cells into iPSCs, but whether defects that cause whole-chromosome instability (W-CIN) preclude reprogramming is unknown. Here we demonstrate, using aneuploidy-prone mouse embryonic fibroblasts (MEFs) in which chromosome missegregation is driven by BubR1 or RanBP2 insufficiency, that W-CIN is not a barrier to reprogramming. Unexpectedly, the two W-CIN defects had contrasting effects on iPSC genomic integrity, with BubR1 hypomorphic MEFs almost exclusively yielding aneuploid iPSC clones and RanBP2 hypomorphic MEFs karyotypically normal iPSC clones. Moreover, BubR1-insufficient iPSC clones were karyotypically unstable, whereas RanBP2-insufficient iPSC clones were rather stable. These findings suggest that aneuploid cells can be selected for or against during reprogramming depending on the W-CIN gene defect and present the novel concept that somatic cell W-CIN can be concealed in the pluripotent state. Thus, karyotypic analysis of somatic cells of origin in addition to iPSC lines is necessary for safe application of reprogramming technology. iPSC technology has the potential to revolutionize stem-cell based regenerative medicine and would also allow for the production of patient-specific cells for disease modeling and drug discovery. One of the primary safety concerns of iPSCs is genetic instability, which is associated with cancer and various other diseases and includes abnormalities in both chromosomal structure and number. Whereas certain structural chromosome changes have been shown to preclude somatic cell reprogramming, the effect of whole-chromosome reshuffling on this process is completely unknown. Here we show that BubR1 and RanBP2 hypomorphic MEF lines, which are highly prone to erroneous chromosome segregation due to mitotic checkpoint and DNA decatenation failure, respectively, reprogram to pluripotency with normal efficiency. However, while RanBP2 hypomorphic MEFs yielded karyotypically normal iPSC clones with generally low chromosomal instability rates, BubR1 hypomorphic MEFs almost exclusively yielded aneuploid iPSC clones with high instability rates. These data provide important new insights into the genomic integrity requirements during somatic cell reprogramming, and they establish that the safe application of iPSC technology requires screening of both iPSCs and the iPSC-founder cells for chromosome number instability.
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Affiliation(s)
- Masakazu Hamada
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Liviu A. Malureanu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Tobias Wijshake
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Wei Zhou
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jan M. van Deursen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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38
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García-López J, del Mazo J. Expression dynamics of microRNA biogenesis during preimplantation mouse development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:847-54. [DOI: 10.1016/j.bbagrm.2012.03.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 03/20/2012] [Accepted: 03/21/2012] [Indexed: 01/07/2023]
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39
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Embryonic Stem Cell Interactomics: The Beginning of a Long Road to Biological Function. Stem Cell Rev Rep 2012; 8:1138-54. [DOI: 10.1007/s12015-012-9400-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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40
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Song J, Saha S, Gokulrangan G, Tesar PJ, Ewing RM. DNA and chromatin modification networks distinguish stem cell pluripotent ground states. Mol Cell Proteomics 2012; 11:1036-47. [PMID: 22822199 DOI: 10.1074/mcp.m111.011114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pluripotent stem cells are capable of differentiating into all cell types of the body and therefore hold tremendous promise for regenerative medicine. Despite their widespread use in laboratories across the world, a detailed understanding of the molecular mechanisms that regulate the pluripotent state is currently lacking. Mouse embryonic (mESC) and epiblast (mEpiSC) stem cells are two closely related classes of pluripotent stem cells, derived from distinct embryonic tissues. Although both mESC and mEpiSC are pluripotent, these cell types show important differences in their properties suggesting distinct pluripotent ground states. To understand the molecular basis of pluripotency, we analyzed the nuclear proteomes of mESCs and mEpiSCs to identify protein networks that regulate their respective pluripotent states. Our study used label-free LC-MS/MS to identify and quantify 1597 proteins in embryonic and epiblast stem cell nuclei. Immunoblotting of a selected protein subset was used to confirm that key components of chromatin regulatory networks are differentially expressed in mESCs and mEpiSCs. Specifically, we identify differential expression of DNA methylation, ATP-dependent chromatin remodeling and nucleosome remodeling networks in mESC and mEpiSC nuclei. This study is the first comparative study of protein networks in cells representing the two distinct, pluripotent states, and points to the importance of DNA and chromatin modification processes in regulating pluripotency. In addition, by integrating our data with existing pluripotency networks, we provide detailed maps of protein networks that regulate pluripotency that will further both the fundamental understanding of pluripotency as well as efforts to reliably control the differentiation of these cells into functional cell fates.
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Affiliation(s)
- Jing Song
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
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41
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Pashai N, Hao H, All A, Gupta S, Chaerkady R, De Los Angeles A, Gearhart JD, Kerr CL. Genome-wide profiling of pluripotent cells reveals a unique molecular signature of human embryonic germ cells. PLoS One 2012; 7:e39088. [PMID: 22737227 PMCID: PMC3380858 DOI: 10.1371/journal.pone.0039088] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 05/18/2012] [Indexed: 11/18/2022] Open
Abstract
Human embryonic germ cells (EGCs) provide a powerful model for identifying molecules involved in the pluripotent state when compared to their progenitors, primordial germ cells (PGCs), and other pluripotent stem cells. Microarray and Principal Component Analysis (PCA) reveals for the first time that human EGCs possess a transcription profile distinct from PGCs and other pluripotent stem cells. Validation with qRT-PCR confirms that human EGCs and PGCs express many pluripotency-associated genes but with quantifiable differences compared to pluripotent embryonic stem cells (ESCs), induced pluripotent stem cells (IPSCs), and embryonal carcinoma cells (ECCs). Analyses also identified a number of target genes that may be potentially associated with their unique pluripotent states. These include IPO7, MED7, RBM26, HSPD1, and KRAS which were upregulated in EGCs along with other pluripotent stem cells when compared to PGCs. Other potential target genes were also found which may contribute toward a primed ESC-like state. These genes were exclusively up-regulated in ESCs, IPSCs and ECCs including PARP1, CCNE1, CDK6, AURKA, MAD2L1, CCNG1, and CCNB1 which are involved in cell cycle regulation, cellular metabolism and DNA repair and replication. Gene classification analysis also confirmed that the distinguishing feature of EGCs compared to ESCs, ECCs, and IPSCs lies primarily in their genetic contribution to cellular metabolism, cell cycle, and cell adhesion. In contrast, several genes were found upregulated in PGCs which may help distinguish their unipotent state including HBA1, DMRT1, SPANXA1, and EHD2. Together, these findings provide the first glimpse into a unique genomic signature of human germ cells and pluripotent stem cells and provide genes potentially involved in defining different states of germ-line pluripotency.
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Affiliation(s)
- Nikta Pashai
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Haiping Hao
- Deep Sequencing and Microarray Core, High Throughput Biology Center, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Angelo All
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Siddharth Gupta
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Raghothama Chaerkady
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alejandro De Los Angeles
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Children’s Hospital Boston, Massachusetts, United States of America
- Department of Biological Chemistry and Molecular Pharmacology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
| | - John D. Gearhart
- Department of Cell and Developmental Biology, Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Animal Biology, Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Candace L. Kerr
- Stem Cell Program, Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Gynecology and Obstetrics, Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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Novak A, Amit M, Ziv T, Segev H, Fishman B, Admon A, Itskovitz-Eldor J. Proteomics profiling of human embryonic stem cells in the early differentiation stage. Stem Cell Rev Rep 2012; 8:137-49. [PMID: 21732092 DOI: 10.1007/s12015-011-9286-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The regulatory pathways responsible for maintaining human embryonic stem cells (hESCs) in an undifferentiated state have yet to be elucidated. Since these pathways are thought to be governed by complex protein cues, deciphering the changes that occur in the proteomes of the ESCs during differentiation is important for understanding the expansion and differentiation processes involved. In this study, we present the first quantitative comparison of the hESC protein profile in the undifferentiated and early differentiated states. We used iTRAQ (isobaric tags for relative and absolute quantification) labeling combined with two dimensional capillary chromatography coupled with tandem mass spectrometry (μLC-MS/MS) to achieve comparative proteomics of hESCs at the undifferentiated stage, and at 6, 48, and 72 h after initiation of differentiation. In addition, two dimensional electrophoresis (2-DE) was performed on differentiating hESCs at eleven points of time during the first 72 h of differentiation. The results indicate that during the first 48 h of hESC differentiation, many processes are initiated and are later reversed, including chromatin remodeling, heterochromatin spreading, a decrease in transcription and translation, a decrease in glycolytic proteins and cytoskeleton remodeling, and a decrease in focal and cell adhesion. Only 72 h after differentiation induction did the expression of the homeobox prox1 protein increase, indicating the beginning of developmental processes.
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Affiliation(s)
- Atara Novak
- Sohnis and Forman Families Center for Stem Cell and Tissue Regeneration Research, Ruth & Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
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Haskins WE, Eedala S, Jadhav YA, Labhan MS, Pericherla VC, Perlman EJ. Insights on neoplastic stem cells from gel-based proteomics of childhood germ cell tumors. Pediatr Blood Cancer 2012; 58:722-8. [PMID: 21793190 PMCID: PMC3204330 DOI: 10.1002/pbc.23282] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 06/22/2011] [Indexed: 12/16/2022]
Abstract
BACKGROUND Childhood germ cell tumors (cGCTs), believed to arise from transformed primordial germ cells by an unknown mechanism, provide a unique model system for investigating cell signaling, pluripotency, and the microenvironment of neoplastic stem cells (NSCs) in vivo. This is the first report of proteomics of cGCTs. PROCEDURE Four dysgerminomas (DYSs) and four childhood endodermal sinus tumors (cESTs), resembling self-renewing and differentiating NSCs, respectively, were selected. Proteomic studies were performed by 2-DE, SDS-PAGE, and cLC/MS/MS with protein database searching. RESULTS 2-DE: 9 of 941 spots were differentially regulated with greater than a twofold change in spot volume for at least three of four gels in each group. Two of nine spots had P values for the t-test analysis of comparisons less than 0.001, while the remaining spots had P values from 0.013 to 0.191. Top-ranked proteins were identified in nine of nine spots with 4.0-38% sequence coverage. APOA1, CRK, and PDIA3 were up-regulated in cESTs. TFG, TYMP, VCP, RBBP, FKBP4, and BiP were up-regulated in DYSs. SDS-PAGE: Up-regulation of NF45 and FKBP4 was observed in four of four cESTs and DYSs, respectively. The fold-changes observed correspond with characteristic genetic changes. CONCLUSION Differential regulation of FKBP4 and NF45, combined with previous research on immunosuppressant binding, suggests that glucocorticoid receptor signaling merits further investigation in cGCTs and NSCs.
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Affiliation(s)
- William E. Haskins
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, Department of RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249, Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249, Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Medicine, Division of Hematology & Medical Oncology, Cancer Therapy & Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229,Correspondence: William E. Haskins, Ph.D., Dept. of Biology-BSE 3.108A, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249-0662, , Phone: (210)563-4492, Fax: (210)458-5658
| | - Sruthi Eedala
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, Department of RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249, Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249, Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - Y.L. Avinash Jadhav
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, Department of RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249, Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249, Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - Manbir S. Labhan
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, Department of RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249, Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249, Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - Vidya C. Pericherla
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, Department of RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249, Department of Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249, Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249, Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - Elizabeth J. Perlman
- Department of Pathology, Northwestern University’s Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, IL, 60614
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Agrawal P, Chen YT, Schilling B, Gibson BW, Hughes RE. Ubiquitin-specific peptidase 9, X-linked (USP9X) modulates activity of mammalian target of rapamycin (mTOR). J Biol Chem 2012; 287:21164-75. [PMID: 22544753 DOI: 10.1074/jbc.m111.328021] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The mammalian target of rapamycin (mTOR) is an atypical serine/threonine kinase that responds to extracellular environment to regulate a number of cellular processes. These include cell growth, proliferation, and differentiation. Although both kinase-dependent and -independent functions of mTOR are known to be critical modulators of muscle cell differentiation and regeneration, the signaling mechanisms regulating mTOR activity during differentiation are still unclear. In this study we identify a novel mTOR interacting protein, the ubiquitin-specific protease USP9X, which acts as a negative regulator of mTOR activity and muscle differentiation. USP9X can co-immunoprecipitate mTOR with both Raptor and Rictor, components of mTOR complexes 1 and 2 (mTORC1 and -2), respectively, suggesting that it is present in both mTOR complexes. Knockdown of USP9X leads to increased mTORC1 activity in response to growth factor stimulation. Interestingly, upon initiation of differentiation of C2C12 mouse skeletal myoblasts, knockdown of USP9X increases mTORC2 activity. This increase in mTORC2 activity is accompanied by accelerated differentiation of myoblasts into myotubes. Taken together, our data describe the identification of the deubiquitinase USP9X as a novel mTORC1 and -2 binding partner that negatively regulates mTOR activity and skeletal muscle differentiation.
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Affiliation(s)
- Pooja Agrawal
- Buck Institute for Research on Aging, Novato, California 94945, USA
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45
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van Hoof D, Krijgsveld J, Mummery C. Proteomic analysis of stem cell differentiation and early development. Cold Spring Harb Perspect Biol 2012; 4:cshperspect.a008177. [PMID: 22317846 DOI: 10.1101/cshperspect.a008177] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genomics methodologies have advanced to the extent that it is now possible to interrogate the gene expression in a single cell but proteomics has traditionally lagged behind and required much greater cellular input and was not quantitative. Coupling protein with gene expression data is essential for understanding how cell behavior is regulated. Advances primarily in mass spectrometry have, however, greatly improved the sensitivity of proteomics methods over the last decade and the outcome of proteomic analyses can now also be quantified. Nevertheless, it is still difficult to obtain sufficient tissue from staged mammalian embryos to combine proteomic and genomic analyses. Recent developments in pluripotent stem cell biology have in part addressed this issue by providing surrogate scalable cell systems in which early developmental events can be modeled. Here we present an overview of current proteomics methodologies and the kind of information this can provide on the biology of human and mouse pluripotent stem cells.
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Affiliation(s)
- Dennis van Hoof
- Department of Anatomy and Embryology, Leiden University Medical Center, ZC Leiden
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46
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Tobe BT, Hou J, Crain AM, Singec I, Snyder EY, Brill LM. Phosphoproteomic analysis: an emerging role in deciphering cellular signaling in human embryonic stem cells and their differentiated derivatives. Stem Cell Rev Rep 2012; 8:16-31. [PMID: 22009073 PMCID: PMC3839940 DOI: 10.1007/s12015-011-9317-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cellular signaling is largely controlled by protein phosphorylation. This post-translational modification (PTM) has been extensively analyzed when examining one or a few protein phosphorylation events that effect cell signaling. However, protein kinase-driven signaling networks, comprising total (phospho)proteomes, largely control cell fate. Therefore, large-scale analysis of differentially regulated protein phosphorylation is central to elucidating complex cellular events, including maintenance of pluripotency and differentiation of embryonic stem cells (ESCs). The current technology of choice for total phosphoproteome and combined total proteome plus total phosphoproteome (termed (phospho)proteome) analyses is multidimensional liquid chromatography-(MDLC) tandem mass spectrometry (MS/MS). Advances in the use of MDLC for separation of peptides comprising total (phospho)proteomes, phosphopeptide enrichment, separation of enriched fractions, and quantitative peptide identification by MS/MS have been rapid in recent years, as have improvements in the sensitivity, speed, and accuracy of mass spectrometers. Increasingly deep coverage of (phospho)proteomes is allowing an improved understanding of changes in protein phosphorylation networks as cells respond to stimuli and progress from one undifferentiated or differentiated state to another. Although MDLC-MS/MS studies are powerful, understanding the interpretation of the data is important, and targeted experimental pursuit of biological predictions provided by total (phospho)proteome analyses is needed. (Phospho)proteomic analyses of pluripotent stem cells are in their infancy at this time. However, such studies have already begun to contribute to an improved and accelerated understanding of basic pluripotent stem cell signaling and fate control, especially at the systems-biology level.
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Affiliation(s)
- Brian T.D. Tobe
- The Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Junjie Hou
- The Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Andrew M. Crain
- The Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Ilyas Singec
- The Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Evan Y. Snyder
- The Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Laurence M. Brill
- The Sanford-Burnham Medical Research Institute, La Jolla, California, USA
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Jagannathan M, Sakwe AM, Nguyen T, Frappier L. The MCM-associated protein MCM-BP is important for human nuclear morphology. J Cell Sci 2012; 125:133-43. [PMID: 22250201 DOI: 10.1242/jcs.089938] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Mini-chromosome maintenance complex-binding protein (MCM-BP) was discovered as a protein that is strongly associated with human MCM proteins, known to be crucial for DNA replication in providing DNA helicase activity. The Xenopus MCM-BP homologue appears to play a role in unloading MCM complexes from chromatin after DNA synthesis; however, the importance of MCM-BP and its functional contribution to human cells has been unclear. Here we show that depletion of MCM-BP by sustained expression of short hairpin RNA (shRNA) results in highly abnormal nuclear morphology and centrosome amplification. The abnormal nuclear morphology was not seen with depletion of other MCM proteins and was rescued with shRNA-resistant MCM-BP. MCM-BP depletion was also found to result in transient activation of the G2 checkpoint, slowed progression through G2 and increased replication protein A foci, indicative of replication stress. In addition, MCM-BP depletion led to increased cellular levels of MCM proteins throughout the cell cycle including soluble MCM pools. The results suggest that MCM-BP makes multiple contributions to human cells that are not limited to unloading of the MCM complex.
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Affiliation(s)
- Madhav Jagannathan
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
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48
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Brumbaugh J, Rose CM, Phanstiel DH, Thomson JA, Coon JJ. Proteomics and pluripotency. Crit Rev Biochem Mol Biol 2011; 46:493-506. [PMID: 21999516 DOI: 10.3109/10409238.2011.624491] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The fields of mass spectrometry (MS) and stem cell biology have expanded greatly in the past twenty years. Taken alone, these fields occupy entirely different branches of science; however, the points where they overlap provide valuable insight, both in the biological and technical arenas. From a biological perspective, MS-based proteomics offers the capacity to follow post-transcriptional regulation and signaling that are (1) fundamental to pluripotency and differentiation, (2) largely beyond the reach of genomic technologies, and (3) otherwise difficult or impossible to examine on a large scale. At the same time, addressing questions fundamental to stem cell biology has compelled proteomic researchers to pursue more sensitive and creative ways to probe the proteome, both in a targeted and high-throughput manner. Here, we highlight experiments that straddle proteomics and stem cell biology, with an emphasis on studies that apply mass spectrometry to dissect pluripotency and differentiation.
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Affiliation(s)
- Justin Brumbaugh
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, USA
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49
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Gundry RL, Burridge PW, Boheler KR. Pluripotent stem cell heterogeneity and the evolving role of proteomic technologies in stem cell biology. Proteomics 2011; 11:3947-61. [PMID: 21834136 DOI: 10.1002/pmic.201100100] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 04/29/2011] [Accepted: 06/08/2011] [Indexed: 12/13/2022]
Abstract
Stem cells represent obvious choices for regenerative medicine and are invaluable for studies of human development and drug testing. The proteomic landscape of pluripotent stem cells (PSCs), in particular, is not yet clearly defined; consequently, this field of research would greatly benefit from concerted efforts designed to better characterize these cells. In this concise review, we provide an overview of stem cell potency, highlight the types and practical implications of heterogeneity in PSCs and provide a detailed analysis of the current view of the pluripotent proteome in a unique resource for this rapidly evolving field. Our goal in this review is to provide specific insights into the current status of the known proteome of both mouse and human PSCs. This has been accomplished by integrating published data into a unified PSC proteome to facilitate the identification of proteins, which may be informative for the stem cell state as well as to reveal areas where our current view is limited. These analyses provide insight into the challenges faced in the proteomic analysis of PSCs and reveal one area--the cell surface subproteome--that would especially benefit from enhanced research efforts.
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Affiliation(s)
- Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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50
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Sterrenberg JN, Blatch GL, Edkins AL. Human DNAJ in cancer and stem cells. Cancer Lett 2011; 312:129-42. [PMID: 21925790 DOI: 10.1016/j.canlet.2011.08.019] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 07/15/2011] [Accepted: 08/17/2011] [Indexed: 12/12/2022]
Abstract
The heat shock protein 40kDa (HSP40/DNAJ) co-chaperones constitute the largest and most diverse sub-group of the heat shock protein (HSP) family. DNAJ are widely accepted as regulators of HSP70 function, but also have roles as co-chaperones for the HSP90 chaperone machine, and a growing number of biological functions that may be independent of either of these chaperones. The DNAJ proteins are differentially expressed in human tissues and demonstrate the capacity to function to both promote and suppress cancer development by acting as chaperones for tumour suppressors or oncoproteins. We review the current literature on the function and expression of DNAJ in cancer, stem cells and cancer stem cells. Combining data from gene expression, proteomics and studies in other systems, we propose that DNAJ will be key regulators of cancer, stem cell and possibly cancer stem cell function. The diversity of DNAJ and their assorted roles in a range of biological functions means that selected DNAJ, provided there is limited redundancy and that a specific link to malignancy can be established, may yet provide an attractive target for specific and selective drug design for the development of anti-cancer treatments.
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Affiliation(s)
- Jason N Sterrenberg
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, Grahamstown South Africa
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