1
|
Ru Y, Ma M, Zhou X, Kriti D, Cohen N, D’Souza S, Schaniel C, Motch Perrine SM, Kuo S, Pinto D, Housman G, Wu M, Holmes G, Schadt E, van Bakel H, Zhang B, Jabs EW. Transcriptomic landscape of human induced pluripotent stem cell-derived osteogenic differentiation identifies a regulatory role of KLF16. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.11.579844. [PMID: 38405902 PMCID: PMC10888757 DOI: 10.1101/2024.02.11.579844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Osteogenic differentiation is essential for bone development and metabolism, but the underlying gene regulatory networks have not been well investigated. We differentiated mesenchymal stem cells, derived from 20 human induced pluripotent stem cell lines, into preosteoblasts and osteoblasts, and performed systematic RNA-seq analyses of 60 samples for differential gene expression. We noted a highly significant correlation in expression patterns and genomic proximity among transcription factor (TF) and long noncoding RNA (lncRNA) genes. We identified TF-TF regulatory networks, regulatory roles of lncRNAs on their neighboring coding genes for TFs and splicing factors, and differential splicing of TF, lncRNA, and splicing factor genes. TF-TF regulatory and gene co-expression network analyses suggested an inhibitory role of TF KLF16 in osteogenic differentiation. We demonstrate that in vitro overexpression of human KLF16 inhibits osteogenic differentiation and mineralization, and in vivo Klf16+/- mice exhibit increased bone mineral density, trabecular number, and cortical bone area. Thus, our model system highlights the regulatory complexity of osteogenic differentiation and identifies novel osteogenic genes.
Collapse
Affiliation(s)
- Ying Ru
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Meng Ma
- Mount Sinai Genomics, Sema4, Stamford, CT, 06902, USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Divya Kriti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ninette Cohen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Present address: Division of Cytogenetics and Molecular Pathology, Zucker School of Medicine at Hofstra/Northwell, Northwell Health Laboratories, Lake Success, NY, 11030, USA
| | - Sunita D’Souza
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Present address: St Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Christoph Schaniel
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Susan M. Motch Perrine
- Department of Anthropology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Sharon Kuo
- Department of Anthropology, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Dalila Pinto
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Genevieve Housman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Meng Wu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, 55905
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905
| | - Greg Holmes
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, 55905
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905
| |
Collapse
|
2
|
Abera B, Dinka H. MAGE genes encoding for embryonic development in cattle is mainly regulated by zinc finger transcription factor family and slightly by CpG Islands. BMC Genom Data 2022; 23:19. [PMID: 35303799 PMCID: PMC8932067 DOI: 10.1186/s12863-022-01034-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/01/2022] [Indexed: 11/20/2022] Open
Abstract
Background Melanoma Antigen Genes (MAGEs) are a family of genes that have piqued the interest of scientists for their unique expression pattern. The MAGE genes can be classified into type I MAGEs that expressed in testis and other reproductive tissues while type II MAGEs that have broad expression in many tissues. Several MAGE gene families are expressed in embryonic tissues in almost all eukaryotes, which is essential for embryo development mainly during germ cell differentiation. The aim of this study was to analyze the promoter regions and regulatory elements (transcription factors and CpG islands) of MAGE genes encoding for embryonic development in cattle. Results The in silico analysis revealed the highest promoter prediction scores (1.0) for TSS were obtained for two gene sequences (MAGE B4-like and MAGE-L2) while the lowest promoter prediction scores (0.8) was obtained for MAGE B17-like. It also revealed that the best common motif, motif IV, bear a resemblance with three TF families including Zinc-finger family, SMAD family and E2A related factors. From thirteen identified TFs candidates, majority of them (11/13) were clustered to Zinc-finger family serving as transcriptionally activator role whereas three (SP1, SP3 and Znf423) of them as activator or repressor in response to physiological and pathological stimuli. On the other hand we revealed slightly rich CpG islands in the gene body and promoter regions of MAGE genes encoding for embryonic development in cattle. Conclusion This in silico analysis of gene promoter regions and regulatory elements in MAGE genes could be useful for understanding regulatory networks and gene expression patterns during embryo development in bovine.
Collapse
Affiliation(s)
- Bosenu Abera
- Department of Applied Biology, School of Applied Natural Sciences, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia.,Department of Animal Science, College of Agriculture and Natural Resources, Salale University, P.O. Box 245, Salale, Ethiopia
| | - Hunduma Dinka
- Department of Applied Biology, School of Applied Natural Sciences, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia.
| |
Collapse
|
3
|
Yang L, Shi YL, Ma Y, Ren WW, Pang GM, Liu J. Silencing KLF16 inhibits oral squamous cell carcinoma cell proliferation by arresting the cell cycle and inducing apoptosis. APMIS 2021; 130:43-52. [PMID: 34779529 DOI: 10.1111/apm.13194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 11/11/2021] [Indexed: 11/29/2022]
Abstract
Krüppel-like factor 16 (KLF16), a member of the Krüppel-like factor (KLF) family, has been extensively investigated in multiple cancer types. However, the role of KLF16 in oral squamous cell carcinoma (OSCC) remains unknown. Thus, we conducted this study to investigate its related mechanism. KLF16 expression in OSCC cell lines was quantified by western blotting. Then, OECM1 and OC3 cells were divided into Blank, siCtrl, siKLF16#1 and siKLF16#2 groups. Subsequently, cell proliferation was detected using 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assays, cell migration and invasion were detected with wound healing and Transwell assays, and cell cycle distribution and cell apoptosis were detected via flow cytometry. KLF16, p21, CDK4, Cyclin D1 and p-Rb expression was detected by western blotting. Finally, xenograft models were established in nude mice to observe the in vivo effects of KLF16 on OSCC. KLF16 protein expression was upregulated in OSCC cells. Compared to the cells in the Blank group, the OECM1 and OC3 cells in the siKLF16#1 group and siKLF16#2 group exhibited a sharp decrease in proliferation but a remarkable increase in apoptosis. Moreover, the proportion of cells in the G0/G1 phase notably increased and that in the S phase decreased, with evident decreases in cell invasion and migration. Moreover, KLF16, cyclin-dependent kinase 4 (CDK4), Cyclin D1 and p-Rb protein expression was upregulated, but p21 expression was downregulated. The mice in the siKLF16#1 and siKLF16#2 xenograft model groups exhibited slower tumour growth and smaller tumours with evident downregulation of Ki67 expression compared to the mice in the Blank group. KLF16 expression was upregulated in OSCC cells, and interfering with KLF16 led to cell cycle arrest, inhibited OSCC cell growth and promoted cell apoptosis.
Collapse
Affiliation(s)
- Lei Yang
- Department of Orthodontics, Dongfeng Stomatological Hospital, Hubei University of Medicine, Shiyan, Hubei Province, China
| | - You-Ling Shi
- Department of Orthodontics, Dongfeng Stomatological Hospital, Hubei University of Medicine, Shiyan, Hubei Province, China
| | - Yan Ma
- Department of Orthodontics, Dongfeng Stomatological Hospital, Hubei University of Medicine, Shiyan, Hubei Province, China
| | - Wei-Wei Ren
- Department of Pediatric Stomatology, Dongfeng Stomatological Hospital, Hubei University of Medicine, Shiyan, Hubei Province, China
| | - Guang-Ming Pang
- Department of Orthodontics, Dongfeng Stomatological Hospital, Hubei University of Medicine, Shiyan, Hubei Province, China
| | - Jiao Liu
- Department of Pediatric Stomatology, Dongfeng Stomatological Hospital, Hubei University of Medicine, Shiyan, Hubei Province, China
| |
Collapse
|
4
|
Investigation of Key Signaling Pathways Associating miR-204 and Common Retinopathies. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5568113. [PMID: 34646884 PMCID: PMC8505061 DOI: 10.1155/2021/5568113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/15/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
MicroRNAs are a large group of small noncoding RNAs that work in multiple cellular pathways. miR-204, as one of the key axes in the development, maintenance, and pathogenesis of the retina, plays several roles by modulating its target genes. This study was aimed at evaluating the target genes of miR-204 involved in the development and progression of common retinopathies such as glaucoma, retinoblastoma, and age-related macular degeneration. In this study, three datasets related to retinopathies (GSE50195, GSE27276, and GSE97508) were selected from Gene Expression Omnibus. miR-204 target genes were isolated from TargeScan. The shares between retinopathy and miR-204 target genes were then categorized. Using Enrichr and STRING, we highlighted the signaling pathways and the relationships between the proteins. SHC1 events in ERBB2, adherent junction's interactions, NGF signaling via TRKA from the plasma membrane, IRF3-mediated activation of type 1 IFN, pathways in upregulated genes and G0 and early G1, RORA-activated gene expression, PERK-regulated gene expression, adherent junction's interactions, and CREB phosphorylation pathways in downregulated genes were identified in glaucoma, retinoblastoma, and age-related macular degeneration. WEE1, SMC2, HMGB1, RRM2, and POLA1 proteins were also observed to be involved in the progression and invasion of retinoblastoma; SLC24A2 and DTX4 in age-related macular degeneration; and EPHB6, EFNB3, and SHC1 in glaucoma. Continuous bioinformatics analysis has shown that miR-204 has a significant presence and expression in retinal tissue, and approximately 293 genes are controlled and regulated by miR-204 in this tissue; also, target genes of miR-204 have the potential to develop various retinopathies; thus, a study of related target genes can provide appropriate treatment strategies in the future.
Collapse
|
5
|
Ávila-Mendoza J, Subramani A, Denver RJ. Krüppel-Like Factors 9 and 13 Block Axon Growth by Transcriptional Repression of Key Components of the cAMP Signaling Pathway. Front Mol Neurosci 2020; 13:602638. [PMID: 33281552 PMCID: PMC7689098 DOI: 10.3389/fnmol.2020.602638] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/21/2020] [Indexed: 01/11/2023] Open
Abstract
Krüppel-like factors (KLFs) are zinc finger transcription factors implicated in diverse biological processes, including differentiation of neural cells. The ability of mammalian neurons to elongate axons decreases during postnatal development in parallel with a decrease in cAMP, and increase in expression of several Klf genes. The paralogous KLFs 9 and 13 inhibit neurite outgrowth, and we hypothesized that their actions are mediated through repression of cAMP signaling. To test this we used the adult mouse hippocampus-derived cell line HT22 engineered to control expression of Klf9 or Klf13 with doxycycline, or made deficient for these Klfs by CRISPR/Cas9 genome editing. We also used primary hippocampal cells isolated from wild type, Klf9–/– and Klf13–/– mice. Forced expression of Klf9 or Klf13 in HT22 changed the mRNA levels of several genes involved with cAMP signaling; the predominant action was gene repression, and KLF13 influenced ∼4 times more genes than KLF9. KLF9 and KLF13 repressed promoter activity of the protein kinase a catalytic subunit alpha gene in transfection-reporter assays; KLF13, but not KLF9 repressed the calmodulin 3 promoter. Forskolin activation of a cAMP-dependent promoter was reduced after forced expression of Klf9 or Klf13, but was enhanced in Klf gene knockout cells. Forced expression of Klf9 or Klf13 blocked cAMP-dependent neurite outgrowth in HT22 cells, and axon growth in primary hippocampal neurons, while Klf gene knockout enhanced the effect of elevated cAMP. Taken together, our findings show that KLF9 and KLF13 inhibit neurite/axon growth in hippocampal neurons, in part, by inhibiting the cAMP signaling pathway.
Collapse
Affiliation(s)
- José Ávila-Mendoza
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
| | - Arasakumar Subramani
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
| | - Robert J Denver
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
| |
Collapse
|
6
|
Jiang Z, Xu Z, Hu T, Song B, Li F, Wang K. Expression of Krüppel-like factor 9 in breast cancer patients and its effect on prognosis. Oncol Lett 2020; 20:1311-1317. [PMID: 32724373 PMCID: PMC7377114 DOI: 10.3892/ol.2020.11689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
Expression of Krüppel-like factor 9 (KLF9) in breast cancer tissue and its influence on prognosis was investigated. Sixty-eight patients with breast cancer admitted in Ningde Hospital Affiliated to Fujian Medical University from February 2014 to August 2015 were collected, and the expression level of KLF9 in cancerous tissue (n=68) and normal tissue (n=68) of the patients was measured by quantitative real-time PCR (RT-qPCR). The relationship between the expression and clinical pathological features and prognosis of patients was analyzed. The expression level of KLF9 in cancerous tissue was significantly lower than that in normal tissue (P<0.05). The expression in breast cancer tissue was not significantly correlated with age, height, menstrual status, lymph node metastasis or pathological differentiation (P>0.05), but was significantly correlated with tumor size and clinical stage (P<0.05). The 1-, 2-, and 3-year survival rates in the high expression group were significantly higher than those in the low expression group (P<0.001). Univariate Cox regression analysis was carried out according to the 3-year survival of the patients, and the results showed that tumor size (P=0.009), lymph node metastasis (P=0.002), pathological differentiation (P=0.015), clinical stage (P=0.013), and KLF9 (P=0.018) were factors affecting the survival of breast cancer patients. Subsequently, multivariate Cox regression analysis of the indicators with differences showed that those indicators were independent predictors of survival of breast cancer patients. In conclusion, KLF9 expression is low in breast cancer tissue, and its expression level is related to tumor size and clinical stage. Moreover, tumor size >5 cm, lymph node metastasis, low pathological differentiation, high clinical stage and low expression of KLF9 are all important factors that cause death of patients.
Collapse
Affiliation(s)
- Zirong Jiang
- Department of Surgical Oncology, Ningde Hospital Affiliated to Fujian Medical University, Ningde, Fujian 352100, P.R. China
| | - Zhiping Xu
- Department of Surgical Oncology, Ningde Hospital Affiliated to Fujian Medical University, Ningde, Fujian 352100, P.R. China
| | - Tinghui Hu
- Department of Surgical Oncology, Ningde Hospital Affiliated to Fujian Medical University, Ningde, Fujian 352100, P.R. China
| | - Bin Song
- Department of Surgical Oncology, Ningde Hospital Affiliated to Fujian Medical University, Ningde, Fujian 352100, P.R. China
| | - Feng Li
- Department of Surgical Oncology, Ningde Hospital Affiliated to Fujian Medical University, Ningde, Fujian 352100, P.R. China
| | - Kaiyin Wang
- Department of Surgical Oncology, Ningde Hospital Affiliated to Fujian Medical University, Ningde, Fujian 352100, P.R. China
| |
Collapse
|
7
|
Hollern DP, Swiatnicki MR, Rennhack JP, Misek SA, Matson BC, McAuliff A, Gallo KA, Caron KM, Andrechek ER. E2F1 Drives Breast Cancer Metastasis by Regulating the Target Gene FGF13 and Altering Cell Migration. Sci Rep 2019; 9:10718. [PMID: 31341204 PMCID: PMC6656723 DOI: 10.1038/s41598-019-47218-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 07/12/2019] [Indexed: 12/27/2022] Open
Abstract
In prior work we demonstrated that loss of E2F transcription factors inhibits metastasis. Here we address the mechanisms for this phenotype and identify the E2F regulated genes that coordinate tumor cell metastasis. Transcriptomic profiling of E2F1 knockout tumors identified a role for E2F1 as a master regulator of a suite of pro-metastatic genes, but also uncovered E2F1 target genes with an unknown role in pulmonary metastasis. High expression of one of these genes, Fgf13, is associated with early human breast cancer metastasis in a clinical dataset. Together these data led to the hypothesis that Fgf13 is critical for breast cancer metastasis, and that upregulation of Fgf13 may partially explain how E2F1 promotes breast cancer metastasis. To test this hypothesis we ablated Fgf13 via CRISPR. Deletion of Fgf13 in a MMTV-PyMT breast cancer cell line reduces colonization of the lungs in a tail vein injection. In addition, loss of Fgf13 reduced in vitro cell migration, suggesting that Fgf13 may be critical for tumor cells to escape the primary tumor and to colonize the distal sites. The significance of this work is twofold: we have both uncovered genomic features by which E2F1 regulates metastasis and we have identified new pro-metastatic functions for the E2F1 target gene Fgf13.
Collapse
Affiliation(s)
- Daniel P Hollern
- Lineberger Comprehensive Cancer Center University of North Carolina, Chapel Hill, United States
| | - Matthew R Swiatnicki
- Department of Physiology, Michigan State University, East Lansing, United States
| | - Jonathan P Rennhack
- Department of Physiology, Michigan State University, East Lansing, United States
| | - Sean A Misek
- Department of Physiology, Michigan State University, East Lansing, United States
| | - Brooke C Matson
- University of North Carolina Department of Cell Biology, Chapel Hill, United States
| | - Andrew McAuliff
- Department of Physiology, Michigan State University, East Lansing, United States
| | - Kathleen A Gallo
- Department of Physiology, Michigan State University, East Lansing, United States
| | - Kathleen M Caron
- Lineberger Comprehensive Cancer Center University of North Carolina, Chapel Hill, United States
| | - Eran R Andrechek
- Department of Physiology, Michigan State University, East Lansing, United States.
| |
Collapse
|
8
|
Ma KH, Duong P, Moran JJ, Junaidi N, Svaren J. Polycomb repression regulates Schwann cell proliferation and axon regeneration after nerve injury. Glia 2018; 66:2487-2502. [PMID: 30306639 PMCID: PMC6289291 DOI: 10.1002/glia.23500] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 01/01/2023]
Abstract
The transition of differentiated Schwann cells to support of nerve repair after injury is accompanied by remodeling of the Schwann cell epigenome. The EED-containing polycomb repressive complex 2 (PRC2) catalyzes histone H3K27 methylation and represses key nerve repair genes such as Shh, Gdnf, and Bdnf, and their activation is accompanied by loss of H3K27 methylation. Analysis of nerve injury in mice with a Schwann cell-specific loss of EED showed the reversal of polycomb repression is required and a rate limiting step in the increased transcription of Neuregulin 1 (type I), which is required for efficient remyelination. However, mouse nerves with EED-deficient Schwann cells display slow axonal regeneration with significantly low expression of axon guidance genes, including Sema4f and Cntf. Finally, EED loss causes impaired Schwann cell proliferation after injury with significant induction of the Cdkn2a cell cycle inhibitor gene. Interestingly, PRC2 subunits and CDKN2A are commonly co-mutated in the transition from benign neurofibromas to malignant peripheral nerve sheath tumors (MPNST's). RNA-seq analysis of EED-deficient mice identified PRC2-regulated molecular pathways that may contribute to the transition to malignancy in neurofibromatosis.
Collapse
Affiliation(s)
- Ki H. Ma
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Phu Duong
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - John J. Moran
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Nabil Junaidi
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - John Svaren
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53705, USA
| |
Collapse
|
9
|
Sugiaman-Trapman D, Vitezic M, Jouhilahti EM, Mathelier A, Lauter G, Misra S, Daub CO, Kere J, Swoboda P. Characterization of the human RFX transcription factor family by regulatory and target gene analysis. BMC Genomics 2018; 19:181. [PMID: 29510665 PMCID: PMC5838959 DOI: 10.1186/s12864-018-4564-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Evolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. Here, we provide a comprehensive analysis of all the eight human RFX genes (RFX1-8), their spatial and temporal expression profiles, potential upstream regulators and target genes. RESULTS We extracted all known human RFX1-8 gene expression profiles from the FANTOM5 database derived from transcription start site (TSS) activity as captured by Cap Analysis of Gene Expression (CAGE) technology. RFX genes are broadly (RFX1-3, RFX5, RFX7) and specifically (RFX4, RFX6) expressed in different cell types, with high expression in four organ systems: immune system, gastrointestinal tract, reproductive system and nervous system. Tissue type specific expression profiles link defined RFX family members with the target gene batteries they regulate. We experimentally confirmed novel TSS locations and characterized the previously undescribed RFX8 to be lowly expressed. RFX tissue and cell type specificity arises mainly from differences in TSS architecture. RFX transcript isoforms lacking a DNA binding domain (DBD) open up new possibilities for combinatorial target gene regulation. Our results favor a new grouping of the RFX family based on protein domain composition. We uncovered and experimentally confirmed the TFs SP2 and ESR1 as upstream regulators of specific RFX genes. Using TF binding profiles from the JASPAR database, we determined relevant patterns of X-box motif positioning with respect to gene TSS locations of human RFX target genes. CONCLUSIONS The wealth of data we provide will serve as the basis for precisely determining the roles RFX TFs play in human development and disease.
Collapse
Affiliation(s)
| | - Morana Vitezic
- Department of Biology, Bioinformatics Centre, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark
| | - Eeva-Mari Jouhilahti
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, University of Oslo, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Sougat Misra
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- School of Basic and Medical Biosciences, King's College London, London, UK
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
| |
Collapse
|
10
|
Chen X, Li S, Ke Y, Wu S, Huang T, Hu W, Fu H, Guo X. KLF16 suppresses human glioma cell proliferation and tumourigenicity by targeting TFAM. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2018; 46:608-615. [PMID: 29374989 DOI: 10.1080/21691401.2018.1431654] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xiangrong Chen
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, PR China
| | - Shun Li
- Department of Neurosurgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, PR China
| | - Yumin Ke
- Department of Obstetrics and Gynaecology, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, PR China
| | - Shukai Wu
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, PR China
| | - Tianzao Huang
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, PR China
| | - Weipeng Hu
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, PR China
| | - Huangde Fu
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, PR China
| | - Xieli Guo
- Department of Neurosurgery, The Jinjiang Municipal Hospital, Quanzhou, PR China
| |
Collapse
|
11
|
He ML, Lv ZY, Shi X, Yang T, Zhang Y, Li TY, Chen J. Interleukin-10 release from astrocytes suppresses neuronal apoptosis via the TLR2/NFκB pathway in a neonatal rat model of hypoxic-ischemic brain damage. J Neurochem 2017; 142:920-933. [PMID: 28700093 DOI: 10.1111/jnc.14126] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 12/16/2022]
Abstract
The biological function of interleukin-10 (IL-10) and the relationship between IL-10 secretion and the Toll-like receptor 2 (TLR2) expression levels in the central nervous system following hypoxic-ischemic brain damage (HIBD) are poorly understood. Here, we intend to elucidate the biological function and mechanism of IL-10 secretion following HIBD. In this study, we used a neonatal rat model of HIBD and found that rats injected with adeno-associated virus-IL-10-shRNA (short hairpin RNA) exhibited partially impaired learning and memory function compared to rats administered adeno-associated virus-control-shRNA. In vitro oxygen-glucose deprivation (OGD) induced IL-10 release from astrocytes but not from neurons. Pretreatment with exogenous recombinant IL-10 alleviated OGD-mediated apoptosis of neurons but not astrocytes. In addition, we also observed that hypoxic injury induced a marked increase in IL-10 expression in astrocytes as a result of activation of the TLR2/phosphorylated nuclear factor kappa B (p-NFκB) p65 signaling cascade; furthermore, this effect disappeared upon small interfering RNA targeting rat TLR2 gene (siTLR2) treatment. Pyrrolidinedithiocarbamate, an inhibitor of NFκB activation, reduced the IL-10 expression levels in both OGD-injured astrocytes in vitro and the hippocampi of HIBD rats in vivo but did not significantly affect TLR2 expression. Furthermore, a luciferase assay revealed that p-NFκB p65 could bind the -1700/-1000 bp proximal region of the IL-10 gene promoter to regulate IL-10 secretion from astrocytes and that this interaction could be controlled by OGD treatment. These data suggest that HIBD induces IL-10 secretion from astrocytes to exert a paracrine-induced anti-apoptotic effect on injured neurons via the TLR2/NFκB signaling pathway, which may improve learning and memory dysfunction after ischemic injury.
Collapse
Affiliation(s)
- Mu Lan He
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Stem Cell Therapy Engineering Technical Center, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Ze Yu Lv
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Stem Cell Therapy Engineering Technical Center, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xia Shi
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Stem Cell Therapy Engineering Technical Center, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Ting Yang
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Stem Cell Therapy Engineering Technical Center, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yun Zhang
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Stem Cell Therapy Engineering Technical Center, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Ting-Yu Li
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Chongqing, China
| | - Jie Chen
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Stem Cell Therapy Engineering Technical Center, Children's Hospital of Chongqing Medical University, Chongqing, China
| |
Collapse
|
12
|
Ribas VT, Costa MR. Gene Manipulation Strategies to Identify Molecular Regulators of Axon Regeneration in the Central Nervous System. Front Cell Neurosci 2017; 11:231. [PMID: 28824380 PMCID: PMC5545589 DOI: 10.3389/fncel.2017.00231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/24/2017] [Indexed: 01/08/2023] Open
Abstract
Limited axon regeneration in the injured adult mammalian central nervous system (CNS) usually results in irreversible functional deficits. Both the presence of extrinsic inhibitory molecules at the injury site and the intrinsically low capacity of adult neurons to grow axons are responsible for the diminished capacity of regeneration in the adult CNS. Conversely, in the embryonic CNS, neurons show a high regenerative capacity, mostly due to the expression of genes that positively control axon growth and downregulation of genes that inhibit axon growth. A better understanding of the role of these key genes controlling pro-regenerative mechanisms is pivotal to develop strategies to promote robust axon regeneration following adult CNS injury. Genetic manipulation techniques have been widely used to investigate the role of specific genes or a combination of different genes in axon regrowth. This review summarizes a myriad of studies that used genetic manipulations to promote axon growth in the injured CNS. We also review the roles of some of these genes during CNS development and suggest possible approaches to identify new candidate genes. Finally, we critically address the main advantages and pitfalls of gene-manipulation techniques, and discuss new strategies to promote robust axon regeneration in the mature CNS.
Collapse
Affiliation(s)
- Vinicius T Ribas
- Laboratory of Neurobiology, Department of Morphology, Institute of Biological Sciences, Federal University of Minas GeraisBelo Horizonte, Brazil
| | - Marcos R Costa
- Brain Institute, Federal University of Rio Grande do NorteNatal, Brazil
| |
Collapse
|
13
|
Abstract
Although much is known about the regenerative capacity of retinal ganglion cells, very significant barriers remain in our ability to restore visual function following traumatic injury or disease-induced degeneration. Here we summarize our current understanding of the factors regulating axon guidance and target engagement in regenerating axons, and review the state of the field of neural regeneration, focusing on the visual system and highlighting studies using other model systems that can inform analysis of visual system regeneration. This overview is motivated by a Society for Neuroscience Satellite meeting, "Reconnecting Neurons in the Visual System," held in October 2015 sponsored by the National Eye Institute as part of their "Audacious Goals Initiative" and co-organized by Carol Mason (Columbia University) and Michael Crair (Yale University). The collective wisdom of the conference participants pointed to important gaps in our knowledge and barriers to progress in promoting the restoration of visual system function. This article is thus a summary of our existing understanding of visual system regeneration and provides a blueprint for future progress in the field.
Collapse
|
14
|
Ma P, Sun CQ, Wang YF, Pan YT, Chen QN, Liu WT, Liu J, Zhao CH, Shu YQ, Li W. KLF16 promotes proliferation in gastric cancer cells via regulating p21 and CDK4. Am J Transl Res 2017; 9:3027-3036. [PMID: 28670390 PMCID: PMC5489902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/09/2017] [Indexed: 06/07/2023]
Abstract
Krüppel-like factors (KLFs), such as KLF4, KLF2, KLF5 and KLF15, have been extensively investigated in multi-cancers. However, KLF16, a member of KLFs, hasn't been well identified in cancer, especially in gastric cancer (GC). Here, we investigated the roles of KLF16 in GC. In present study, we found that KLF16 expression levels were significantly up-regulated in GC tissues compared to adjacent normal tissues both in protein and mRNA levels by using immunohistochemistry assays (IHC) and real-time quantitative PCR (qPCR). And KLF16 expression levels were positively correlated to tumor size, invasion depth, lymphatic metastasis and TNM stage. Furthermore, KLF16 expression also could predict prognosis in patients with GC. Moreover, the knock-down of KLF16 could significantly suppress proliferation via increasing p21 expression and decreasing CDK4 expression in GC cell lines. In summary, these findings demonstrate that KLF16 plays a significant role in GC progression and could be a new therapeutic target for GC patients.
Collapse
Affiliation(s)
- Pei Ma
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Chong-Qi Sun
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Yan-Fen Wang
- Department of Pathology, Yangzhou No.1 People’s HospitalYangzhou, People’s Republic of China
| | - Yu-Tian Pan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Qin-Nan Chen
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Wei-Tao Liu
- Department of Pathology, Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Jie Liu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Chen-Hui Zhao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Yong-Qian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
- Department of Medical Oncology, Affiliated Sir Run Run Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
- Department of Medical Oncology, Affiliated Sir Run Run Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
| |
Collapse
|
15
|
Sun C, Ma P, Wang Y, Liu W, Chen Q, Pan Y, Zhao C, Qian Y, Liu J, Li W, Shu Y. KLF15 Inhibits Cell Proliferation in Gastric Cancer Cells via Up-Regulating CDKN1A/p21 and CDKN1C/p57 Expression. Dig Dis Sci 2017; 62:1518-1526. [PMID: 28421457 DOI: 10.1007/s10620-017-4558-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/28/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Krüppel-like factors (KLFs) have been identified in multi-cancers and act as oncogenes or tumor suppressors. The function of KLF15, one member of KLFs, has not been well elucidated, especially in gastric cancer (GC). AIMS This study was designed to investigate the prognostic value and biological functions of KLF15 in GC. METHODS KLF15 protein expression in GC patients was evaluated by immunohistochemistry assays in 50 paired GC tissues and adjacent normal tissues, and correlations between KLF15 expression and clinicopathological characteristics and prognosis were analyzed. Then, we investigated the over-expression of KLF15 on cell proliferation and its mechanism in GC cells. RESULTS KLF15 expression levels were significantly down-regulated in GC tissues compared to adjacent normal tissues. And KLF15 expression was negatively correlated with clinical stage, lymphatic metastasis, and distant metastasis. Furthermore, KLF15 expression could predict prognosis in patients with GC. Moreover, over-expression of KLF15 could inhibit cell proliferation partly via regulating CDKN1A/p21 and CDKN1C/p57. CONCLUSION These findings demonstrate that KLF15 plays a significant role in GC progression and could be a therapeutic target for GC.
Collapse
Affiliation(s)
- Chongqi Sun
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, People's Republic of China
| | - Pei Ma
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, People's Republic of China
| | - Yanfen Wang
- Department of Pathology, Yangzhou No.1 People's Hospital, Yangzhou, People's Republic of China
| | - Weitao Liu
- Department of Pathology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Qinnan Chen
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Yutian Pan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, People's Republic of China
| | - Chenhui Zhao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, People's Republic of China
| | - Yingchen Qian
- Department of Pathology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Jie Liu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, People's Republic of China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, People's Republic of China. .,Department of Medical Oncology, Affiliated Sir Run Run Hospital of Nanjing Medical University, Nanjing, People's Republic of China.
| | - Yongqian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, People's Republic of China. .,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, People's Republic of China. .,Department of Medical Oncology, Affiliated Sir Run Run Hospital of Nanjing Medical University, Nanjing, People's Republic of China.
| |
Collapse
|
16
|
KLF15 protects against isoproterenol-induced cardiac hypertrophy via regulation of cell death and inhibition of Akt/mTOR signaling. Biochem Biophys Res Commun 2017; 487:22-27. [PMID: 28336438 DOI: 10.1016/j.bbrc.2017.03.087] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 03/17/2017] [Indexed: 01/28/2023]
Abstract
Increasing evidence indicate that the Krüppel-like factor KLF15, a member of Cys2/His2 zinc-finger DNA-binding proteins, attenuates cardiac hypertrophy. However, the role of KLF15 in cardiovascular system is largely unknown and the exact molecular mechanism of its protective function is not fully elucidated. In the present study, we established a mouse model of cardiac hypertrophy and found that KLF15 expression was down-regulated in hypertrophic hearts. To evaluate the roles of KLF15 in cardiac hypertrophy, we generated transgenic mice overexpressing KLF15 of KLF15 knockdown mice and subsequently induced cardiac hypertrophy. The results indicated that KLF15 overexpression protects mice from ISO-induced cardiac hypertrophy, with reduced ratios of heart weight (HW)/body weight (BW) and cross-sectional area. We also observed that KLF15 overexpression attenuated cardiac fibrosis, inhibited apoptosis and induced autophagy in cardiomyocytes compared with KLF15 knockdown mice. More importantly, we found that the KLF15 overexpression inhibited the Akt/mTOR signaling pathway. Taken together, our findings imply that KLF15 possesses potential anti-hypertrophic and anti-fibrotic functions, possibly via regulation of cell death pathways and the inhibition of Akt/mTOR axis. KLF15 may constitute an efficient candidate drug for the treatment of heart failure and other cardiovascular diseases.
Collapse
|