1
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Hsieh CW, Chang LH, Wang YH, Li WT, Chang JK, Chen CH, Ho ML. Indoxyl Sulfate Inhibits Osteogenesis in Bone Marrow Mesenchymal Stem Cells through the AhR/Hes1 Pathway. Int J Mol Sci 2024; 25:8770. [PMID: 39201457 PMCID: PMC11354967 DOI: 10.3390/ijms25168770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/05/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
Uremic toxins cause bone disorders in patients with chronic kidney disease (CKD). These disorders are characterized by low turnover osteodystrophy and impaired bone formation in the early stages of CKD. Evidence indicates that the aryl hydrocarbon receptor (AhR) mediates signals that suppress early osteogenic differentiation in bone marrow mesenchymal stem cells (BMSCs). However, whether the AhR mediates the effects of indoxyl sulfate (IS), a uremic toxin, on BMSC osteogenesis remains unclear. We investigated whether IS affects osteogenesis through the AhR/Hes1 pathway. Expression levels of osteogenesis genes (Runx2, Bmp2, Alp, and Oc), AhR, and Hes1 were measured in mouse BMSCs (D1 cells). At concentrations of 2-50 μM, IS significantly reduced mineralization, particularly in the early stages of BMSC osteogenesis. Furthermore, IS significantly downregulated the expression of Runx2, Bmp2, Oc, and Alp. Notably, this downregulation could be prevented using an AhR antagonist and through Ahr knockdown. Mechanistically, IS induced the expression of Hes1 through AhR signaling, thereby suppressing the transcription of Runx2 and Bmp2. Our findings suggest that IS inhibits early osteogenesis of BMSCs through the AhR/Hes1 pathway, thus suppressing the transcription of Runx2 and Bmp2. Our findings may guide new therapeutic strategies against CKD-related bone disorders.
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Affiliation(s)
- Chin-Wen Hsieh
- Division of Nephrology, Department of Internal Medicine, Pingtung Christian Hospital, Pingtung 900, Taiwan;
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ling-Hua Chang
- Orthopaedic Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (L.-H.C.); (Y.-H.W.); (W.-T.L.); (J.-K.C.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yan-Hsiung Wang
- Orthopaedic Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (L.-H.C.); (Y.-H.W.); (W.-T.L.); (J.-K.C.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Wei-Ting Li
- Orthopaedic Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (L.-H.C.); (Y.-H.W.); (W.-T.L.); (J.-K.C.)
| | - Je-Ken Chang
- Orthopaedic Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (L.-H.C.); (Y.-H.W.); (W.-T.L.); (J.-K.C.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Orthopaedics, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Orthopedics, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University, Kaohsiung 801, Taiwan
| | - Chung-Hwan Chen
- Orthopaedic Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (L.-H.C.); (Y.-H.W.); (W.-T.L.); (J.-K.C.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Orthopaedics, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Orthopedics, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University, Kaohsiung 801, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Ph.D. Program in Biomedical Engineering, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Materials Engineering, College of Engineering, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
| | - Mei-Ling Ho
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Orthopaedic Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (L.-H.C.); (Y.-H.W.); (W.-T.L.); (J.-K.C.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Ph.D. Program in Biomedical Engineering, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Materials Engineering, College of Engineering, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- Department of Physiology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
- College of Professional Studies, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
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2
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Gomez Ramos B, Ohnmacht J, de Lange N, Valceschini E, Ginolhac A, Catillon M, Ferrante D, Rakovic A, Halder R, Massart F, Arena G, Antony P, Bolognin S, Klein C, Krause R, Schulz MH, Sauter T, Krüger R, Sinkkonen L. Multiomics analysis identifies novel facilitators of human dopaminergic neuron differentiation. EMBO Rep 2024; 25:254-285. [PMID: 38177910 PMCID: PMC10897179 DOI: 10.1038/s44319-023-00024-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 01/06/2024] Open
Abstract
Midbrain dopaminergic neurons (mDANs) control voluntary movement, cognition, and reward behavior under physiological conditions and are implicated in human diseases such as Parkinson's disease (PD). Many transcription factors (TFs) controlling human mDAN differentiation during development have been described, but much of the regulatory landscape remains undefined. Using a tyrosine hydroxylase (TH) human iPSC reporter line, we here generate time series transcriptomic and epigenomic profiles of purified mDANs during differentiation. Integrative analysis predicts novel regulators of mDAN differentiation and super-enhancers are used to identify key TFs. We find LBX1, NHLH1 and NR2F1/2 to promote mDAN differentiation and show that overexpression of either LBX1 or NHLH1 can also improve mDAN specification. A more detailed investigation of TF targets reveals that NHLH1 promotes the induction of neuronal miR-124, LBX1 regulates cholesterol biosynthesis, and NR2F1/2 controls neuronal activity.
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Affiliation(s)
- Borja Gomez Ramos
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Jochen Ohnmacht
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Nikola de Lange
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Elena Valceschini
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Aurélien Ginolhac
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Marie Catillon
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Daniele Ferrante
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Aleksandar Rakovic
- Institute of Neurogenetics, University of Lübeck, 23538, Lübeck, Germany
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - François Massart
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Giuseppe Arena
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Paul Antony
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Silvia Bolognin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, 23538, Lübeck, Germany
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Marcel H Schulz
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt, Germany
- German Centre for Cardiovascular Research, Partner site Rhein-Main, 60590, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University, Frankfurt am Main, Germany
| | - Thomas Sauter
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
- Centre Hospitalier de Luxembourg (CHL), L-1210, Luxembourg, Luxembourg
- Luxembourg Institute of Health (LIH), L-1445, Luxembourg, Luxembourg
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg.
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3
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Ronima K R, Dey C, Thummer RP. An Insight into the Role of GLIS1 in Embryonic Development, iPSC Generation, and Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023. [PMID: 37978100 DOI: 10.1007/5584_2023_793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The curiosity to discover transcription factors to reprogram somatic cells to induced pluripotent stem cells (iPSCs) resulted in the identification of a reprogramming factor, Gli-similar transcription factor GLIS1. This proline-rich Kruppel-like zinc finger transcription factor has a role in embryonic development, iPSC generation, and cancer. The spatial and temporal expression of GLIS1 during embryonic development implicates that it can control gene expression at specific developmental stages. Moreover, GLIS1 in combination with OCT4, SOX2, and KLF4 reprogramming factors resulted in an increase in reprogramming efficiency, giving rise to primarily bona fide iPSCs. Mutations in the GLIS1 gene are associated with several types of tumors and cancers, and it shows a tissue-specific function where it acts either as an oncogene or as a tumor suppressor gene. This review gives a comprehensive overview of GLIS1 and its important role in embryonic development, cancer, and the generation of iPSCs.
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Affiliation(s)
- Ronima K R
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Chandrima Dey
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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4
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Watson ATD, Carmona Baez A, Jima D, Reif D, Ding J, Roberts R, Kullman SW. TCDD alters essential transcriptional regulators of osteogenic differentiation in multipotent mesenchymal stem cells. Toxicol Sci 2023; 191:149-162. [PMID: 36370075 PMCID: PMC9887680 DOI: 10.1093/toxsci/kfac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Differentiation of multipotent mesenchymal stem cells (MSCs) into bone-forming osteoblasts requires strict coordination of transcriptional pathways. Aryl hydrocarbon receptor ligands, such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), have been shown to alter osteoblast differentiation in vitro and bone formation in multiple developmental in vivo models. The goal of the present study was to establish a global transcriptomic landscape during early, intermediate, and apical stages of osteogenic differentiation in vitro in response to TCDD exposure. Human bone-derived mesenchymal stem cells (hBMSCs) were cultured in growth media (GM), osteogenic differentiation media (ODM), or ODM containing 10 nM TCDD (ODM + TCDD), thus enabling a comparison of the transcriptomic profiles of undifferentiated, differentiated, and differentiated-TCDD-exposed hBMSCs, respectively. In this test system, exposure to TCDD attenuated the differentiation of hBMSCs into osteoblasts as evidenced by reduced alkaline phosphatase activity and mineralization. At various timepoints, we observed altered expression of genes that play a role in the Wnt, fibroblast growth factor, bone morphogenetic protein/transforming growth factor beta developmental pathways, as well as pathways related to extracellular matrix organization and deposition. Reconstruction of gene regulatory networks with the interactive dynamic regulatory event miner (iDREM) analysis revealed modulation of transcription factors (TFs) including POLR3G, NR4A1, RDBP, GTF2B, POU2F2, and ZEB1, which may putatively influence osteoblast differentiation and the requisite deposition and mineralization of bone extracellular matrix. We demonstrate that the combination of RNA-Seq data in conjunction with the iDREM regulatory model captures the transcriptional dynamics underlying MSC differentiation under different conditions in vitro. Model predictions are consistent with existing knowledge and provide a new tool to identify novel pathways and TFs that may facilitate a better understanding of the osteoblast differentiation process, perturbation by exogenous agents, and potential intervention strategies targeting those specific pathways.
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Affiliation(s)
- AtLee T D Watson
- Toxicology Program, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Aldo Carmona Baez
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Dereje Jima
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - David Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Jun Ding
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
| | - Reade Roberts
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Seth W Kullman
- Toxicology Program, North Carolina State University, Raleigh, North Carolina 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695, USA
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5
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Warwick T, Schulz MH, Gilsbach R, Brandes RP, Seuter S. Nuclear receptor activation shapes spatial genome organization essential for gene expression control: lessons learned from the vitamin D receptor. Nucleic Acids Res 2022; 50:3745-3763. [PMID: 35325193 PMCID: PMC9023275 DOI: 10.1093/nar/gkac178] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 12/02/2022] Open
Abstract
Spatial genome organization is tightly controlled by several regulatory mechanisms and is essential for gene expression control. Nuclear receptors are ligand-activated transcription factors that modulate physiological and pathophysiological processes and are primary pharmacological targets. DNA binding of the important loop-forming insulator protein CCCTC-binding factor (CTCF) was modulated by 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). We performed CTCF HiChIP assays to produce the first genome-wide dataset of CTCF long-range interactions in 1,25(OH)2D3-treated cells, and to determine whether dynamic changes of spatial chromatin interactions are essential for fine-tuning of nuclear receptor signaling. We detected changes in 3D chromatin organization upon vitamin D receptor (VDR) activation at 3.1% of all observed CTCF interactions. VDR binding was enriched at both differential loop anchors and within differential loops. Differential loops were observed in several putative functional roles including TAD border formation, promoter-enhancer looping, and establishment of VDR-responsive insulated neighborhoods. Vitamin D target genes were enriched in differential loops and at their anchors. Secondary vitamin D effects related to dynamic chromatin domain changes were linked to location of downstream transcription factors in differential loops. CRISPR interference and loop anchor deletion experiments confirmed the functional relevance of nuclear receptor ligand-induced adjustments of the chromatin 3D structure for gene expression regulation.
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Affiliation(s)
- Timothy Warwick
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt/Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Rhein-Main 60590, Frankfurt am Main, Germany
| | - Marcel H Schulz
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt/Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Rhein-Main 60590, Frankfurt am Main, Germany
| | - Ralf Gilsbach
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt/Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Rhein-Main 60590, Frankfurt am Main, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt/Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Rhein-Main 60590, Frankfurt am Main, Germany
| | - Sabine Seuter
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt/Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Rhein-Main 60590, Frankfurt am Main, Germany
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6
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Hu A, Zhang JW, Yang LY, Qiao PP, Lu D. AHRR contributes to inflammatory lymphangiogenesis by activating the EPAS1/VEGFD signaling axis in head and neck cancer. Am J Cancer Res 2022; 12:537-548. [PMID: 35261785 PMCID: PMC8899997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023] Open
Abstract
Lymph node metastasis (LNM) is associated with poor survival in patients with Head and Neck cancer (HNC). Aryl hydrocarbon receptor repressor (AHRR) is thought to be responsible for increased lymphangiogenesis and LNM. AHRR and endothelial PAS domain-containing protein 1 (EPAS1) are basic helix-loop-helix/per-arnt-sim family transcription factors, however, its central role in lymphangiogenesis remains to be explored. In this study, we explored that EPAS1 dimerizes with HIF-1β during lymphangiogenes and tumor growth, inducing expression of many genes, including vascular endothelial growth factor-d (VEGFD). AHRR wild-type (Ahrr +/+) transgenic carcinoma of the mice develop tumors with greater frequency than AHRR-null (Ahrr -/-) mice, even though prevalence of squamous epithelial hyperplasia is not inhibited. Hypoxia induced VEGFD protein in a genotype-dependent fashion in Ahrr +/+, Ahrr +/- and Ahrr -/- HNC. However, hypoxia induced upstream proteins in the phosphatidylinositol 3-kinase-signaling cascade to a similar extent in HNC of each Ahrr genotype, evidenced by Akt phosphorylation. These findings suggest that AHRR induces HIF-1β expression, increasing interaction with EPAS1 enhancing VEGFD production and lymphangiogenesis in HNC.
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Affiliation(s)
- An Hu
- Department of Otolaryngology-Head and Neck Surgery, Gongli Hospital, Second Military Medical UniversityPudong New Area, Shanghai 200135, China
| | - Jian-Wei Zhang
- Department of Otolaryngology-Head and Neck Surgery, Gongli Hospital, Second Military Medical UniversityPudong New Area, Shanghai 200135, China
| | - Li-Yun Yang
- Department of Otolaryngology-Head and Neck Surgery, Gongli Hospital, Second Military Medical UniversityPudong New Area, Shanghai 200135, China
| | - Pei-Pei Qiao
- Department of Otolaryngology-Head and Neck Surgery, Gongli Hospital, Second Military Medical UniversityPudong New Area, Shanghai 200135, China
- The Graduate School, Ningxia Medical UniversityYinchuan 750004, Ningxia, China
| | - Dan Lu
- Department of Otolaryngology-Head and Neck Surgery, Gongli Hospital, Second Military Medical UniversityPudong New Area, Shanghai 200135, China
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7
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Jin JY, Wu PF, Luo FM, Guo BB, Zeng L, Fan LL, Tang JY, Xiang R. GLIS Family Zinc Finger 1 was First Linked With Preaxial Polydactyly I in Humans by Stepwise Genetic Analysis. Front Cell Dev Biol 2022; 9:781388. [PMID: 35087831 PMCID: PMC8787328 DOI: 10.3389/fcell.2021.781388] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/02/2021] [Indexed: 11/27/2022] Open
Abstract
Background: Preaxial polydactyly (PPD) is one of the most common developmental malformations, with a prevalence of 0.8–1.4% in Asians. PPD is divided into four types, PPD I–IV, and PPD I is the most frequent type. Only six loci (GLI1, GLI3, STKLD1, ZRS, pre-ZRS, and a deletion located 240 kb from SHH) have been identified in non-syndromic PPD cases. However, pathogenesis of most PPD patients has never been investigated. This study aimed to understand the genetic mechanisms involved in the etiology of PPD I in a family with multiple affected members. Methods: We recruited a PPD I family (PPD001) and used stepwise genetic analysis to determine the genetic etiology. In addition, for functional validation of the identified GLIS1 variant, in vitro studies were conducted. GLIS1 variants were further screened in additional 155 PPD cases. Results: We identified a GLIS1 variant (NM_147193: c.1061G > A, p.R354H) in the PPD001 family. In vitro studies showed that this variant decreased the nuclear translocation of GLIS1 and resulted in increased cell viability and migration. RNA sequencing revealed abnormal TBX4 and SFRP2 expression in 293T cells transfected with mutant GLIS1. Additionally, we identified a GLIS1 variant (c.664G > A, p.D222N) in another PPD case. Conclusion: We identified two GLIS1 variants in PPD I patients and first linked GLIS1 with PPD I. Our findings contributed to future molecular and clinical diagnosis of PPD and deepened our knowledge of this disease.
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Affiliation(s)
- Jie-Yuan Jin
- School of Life Sciences, Central South University, Changsha, China
| | - Pan-Feng Wu
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Fang-Mei Luo
- School of Life Sciences, Central South University, Changsha, China
| | - Bing-Bing Guo
- School of Life Sciences, Central South University, Changsha, China
| | - Lei Zeng
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Liang-Liang Fan
- School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Ju-Yu Tang
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Rong Xiang
- School of Life Sciences, Central South University, Changsha, China.,Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
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8
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Del Mistro G, Riemann S, Schindler S, Beissert S, Kontermann RE, Ginolhac A, Halder R, Presta L, Sinkkonen L, Sauter T, Kulms D. Focal adhesion kinase plays a dual role in TRAIL resistance and metastatic outgrowth of malignant melanoma. Cell Death Dis 2022; 13:54. [PMID: 35022419 PMCID: PMC8755828 DOI: 10.1038/s41419-022-04502-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/26/2021] [Accepted: 12/07/2021] [Indexed: 12/19/2022]
Abstract
Despite remarkable advances in therapeutic interventions, malignant melanoma (MM) remains a life-threating disease. Following high initial response rates to targeted kinase-inhibition metastases quickly acquire resistance and present with enhanced tumor progression and invasion, demanding alternative treatment options. We show 2nd generation hexameric TRAIL-receptor-agonist IZI1551 (IZI) to effectively induce apoptosis in MM cells irrespective of the intrinsic BRAF/NRAS mutation status. Conditioning to the EC50 dose of IZI converted the phenotype of IZI-sensitive parental MM cells into a fast proliferating and invasive, IZI-resistant metastasis. Mechanistically, we identified focal adhesion kinase (FAK) to play a dual role in phenotype-switching. In the cytosol, activated FAK triggers survival pathways in a PI3K- and MAPK-dependent manner. In the nucleus, the FERM domain of FAK prevents activation of wtp53, as being expressed in the majority of MM, and consequently intrinsic apoptosis. Caspase-8-mediated cleavage of FAK as well as FAK knockdown, and pharmacological inhibition, respectively, reverted the metastatic phenotype-switch and restored IZI responsiveness. FAK inhibition also re-sensitized MM cells isolated from patient metastasis that had relapsed from targeted kinase inhibition to cell death, irrespective of the intrinsic BRAF/NRAS mutation status. Hence, FAK-inhibition alone or in combination with 2nd generation TRAIL-receptor agonists may be recommended for treatment of initially resistant and relapsed MM, respectively.
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Affiliation(s)
- Greta Del Mistro
- Experimental Dermatology, Department of Dermatology, TU-Dresden, 01307, Dresden, Germany
| | - Shamala Riemann
- Experimental Dermatology, Department of Dermatology, TU-Dresden, 01307, Dresden, Germany
| | - Sebastian Schindler
- Experimental Dermatology, Department of Dermatology, TU-Dresden, 01307, Dresden, Germany
- National Center for Tumor Diseases Dresden, TU-Dresden, 01307, Dresden, Germany
| | - Stefan Beissert
- Experimental Dermatology, Department of Dermatology, TU-Dresden, 01307, Dresden, Germany
| | - Roland E Kontermann
- Institute of Cell Biology and Immunology and Stuttgart Research Centre Systems Biology, University of Stuttgart, 70569, Stuttgart, Germany
| | - Aurelien Ginolhac
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Luana Presta
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Thomas Sauter
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Dagmar Kulms
- Experimental Dermatology, Department of Dermatology, TU-Dresden, 01307, Dresden, Germany.
- National Center for Tumor Diseases Dresden, TU-Dresden, 01307, Dresden, Germany.
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9
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Walter J, Bolognin S, Poovathingal SK, Magni S, Gérard D, Antony PMA, Nickels SL, Salamanca L, Berger E, Smits LM, Grzyb K, Perfeito R, Hoel F, Qing X, Ohnmacht J, Bertacchi M, Jarazo J, Ignac T, Monzel AS, Gonzalez-Cano L, Krüger R, Sauter T, Studer M, de Almeida LP, Tronstad KJ, Sinkkonen L, Skupin A, Schwamborn JC. The Parkinson's-disease-associated mutation LRRK2-G2019S alters dopaminergic differentiation dynamics via NR2F1. Cell Rep 2021; 37:109864. [PMID: 34686322 DOI: 10.1016/j.celrep.2021.109864] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 07/27/2021] [Accepted: 09/29/2021] [Indexed: 11/19/2022] Open
Abstract
Increasing evidence suggests that neurodevelopmental alterations might contribute to increase the susceptibility to develop neurodegenerative diseases. We investigate the occurrence of developmental abnormalities in dopaminergic neurons in a model of Parkinson's disease (PD). We monitor the differentiation of human patient-specific neuroepithelial stem cells (NESCs) into dopaminergic neurons. Using high-throughput image analyses and single-cell RNA sequencing, we observe that the PD-associated LRRK2-G2019S mutation alters the initial phase of neuronal differentiation by accelerating cell-cycle exit with a concomitant increase in cell death. We identify the NESC-specific core regulatory circuit and a molecular mechanism underlying the observed phenotypes. The expression of NR2F1, a key transcription factor involved in neurogenesis, decreases in LRRK2-G2019S NESCs, neurons, and midbrain organoids compared to controls. We also observe accelerated dopaminergic differentiation in vivo in NR2F1-deficient mouse embryos. This suggests a pathogenic mechanism involving the LRRK2-G2019S mutation, where the dynamics of dopaminergic differentiation are modified via NR2F1.
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Affiliation(s)
- Jonas Walter
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Silvia Bolognin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Suresh K Poovathingal
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Stefano Magni
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Deborah Gérard
- Department of Life Science and Medicine (DLSM), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Paul M A Antony
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Sarah L Nickels
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg; Department of Life Science and Medicine (DLSM), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Luis Salamanca
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Emanuel Berger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Lisa M Smits
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Rita Perfeito
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, Coimbra 3004-504, Portugal
| | - Fredrik Hoel
- Department of Biomedicine, University of Bergen, Jonas Lies Vei 91, 5009 Bergen, Norway
| | - Xiaobing Qing
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Jochen Ohnmacht
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg; Department of Life Science and Medicine (DLSM), University of Luxembourg, 4362 Belvaux, Luxembourg
| | | | - Javier Jarazo
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Tomasz Ignac
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Anna S Monzel
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Laura Gonzalez-Cano
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg; Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg; Centre Hospitalier de Luxembourg, Luxembourg City, Luxembourg
| | - Thomas Sauter
- Department of Life Science and Medicine (DLSM), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Michèle Studer
- Université Côte d'Azur, CNRS, Inserm, 06108 Nice, France
| | - Luis Pereira de Almeida
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, Coimbra 3004-504, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra 3000-548, Portugal
| | - Karl J Tronstad
- Department of Biomedicine, University of Bergen, Jonas Lies Vei 91, 5009 Bergen, Norway
| | - Lasse Sinkkonen
- Department of Life Science and Medicine (DLSM), University of Luxembourg, 4362 Belvaux, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg; Center for Research of Biological Systems, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jens C Schwamborn
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Belvaux, Luxembourg.
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10
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Kai Y, Li BE, Zhu M, Li GY, Chen F, Han Y, Cha HJ, Orkin SH, Cai W, Huang J, Yuan GC. Mapping the evolving landscape of super-enhancers during cell differentiation. Genome Biol 2021; 22:269. [PMID: 34526084 PMCID: PMC8442463 DOI: 10.1186/s13059-021-02485-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/02/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Super-enhancers are clusters of enhancer elements that play critical roles in the maintenance of cell identity. Current investigations on super-enhancers are centered on the established ones in static cell types. How super-enhancers are established during cell differentiation remains obscure. RESULTS Here, by developing an unbiased approach to systematically analyze the evolving landscape of super-enhancers during cell differentiation in multiple lineages, we discover a general trend where super-enhancers emerge through three distinct temporal patterns: conserved, temporally hierarchical, and de novo. The three types of super-enhancers differ further in association patterns in target gene expression, functional enrichment, and 3D chromatin organization, suggesting they may represent distinct structural and functional subtypes. Furthermore, we dissect the enhancer repertoire within temporally hierarchical super-enhancers, and find enhancers that emerge at early and late stages are enriched with distinct transcription factors, suggesting that the temporal order of establishment of elements within super-enhancers may be directed by underlying DNA sequence. CRISPR-mediated deletion of individual enhancers in differentiated cells shows that both the early- and late-emerged enhancers are indispensable for target gene expression, while in undifferentiated cells early enhancers are involved in the regulation of target genes. CONCLUSIONS In summary, our analysis highlights the heterogeneity of the super-enhancer population and provides new insights to enhancer functions within super-enhancers.
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Affiliation(s)
- Yan Kai
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02115, USA
| | - Bin E Li
- Cancer and Blood Disorders Center, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Ming Zhu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Grace Y Li
- Cancer and Blood Disorders Center, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Fei Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yingli Han
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Hye Ji Cha
- Cancer and Blood Disorders Center, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Stuart H Orkin
- Cancer and Blood Disorders Center, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Wenqing Cai
- Cancer and Blood Disorders Center, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Guo-Cheng Yuan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Genetics and Genomic Sciences, Charles Bronfman Institute for Precision Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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11
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Zablon HA, Ko CI, Puga A. Converging Roles of the Aryl Hydrocarbon Receptor in Early Embryonic Development, Maintenance of Stemness, and Tissue Repair. Toxicol Sci 2021; 182:1-9. [PMID: 34009372 PMCID: PMC8285021 DOI: 10.1093/toxsci/kfab050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor well-known for its adaptive role as a sensor of environmental toxicants and mediator of the metabolic detoxification of xenobiotic ligands. In addition, a growing body of experimental data has provided indisputable evidence that the AHR regulates critical functions of cell physiology and embryonic development. Recent studies have shown that the naïve AHR-that is, unliganded to xenobiotics but activated endogenously-has a crucial role in maintenance of embryonic stem cell pluripotency, tissue repair, and regulation of cancer stem cell stemness. Depending on the cellular context, AHR silences the expression of pluripotency genes Oct4 and Nanog and potentiates differentiation, whereas curtailing cellular plasticity and stemness. In these processes, AHR-mediated contextual responses and outcomes are dictated by changes of interacting partners in signaling pathways, gene networks, and cell-type-specific genomic structures. In this review, we focus on AHR-mediated changes of genomic architecture as an emerging mechanism for the AHR to regulate gene expression at the transcriptional level. Collective evidence places this receptor as a physiological hub connecting multiple biological processes whose disruption impacts on embryonic development, tissue repair, and maintenance or loss of stemness.
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Affiliation(s)
| | | | - Alvaro Puga
- Department of Environmental and Public Health Sciences, Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, USA
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12
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Tao S, Li H, Ma X, Ma Y, He J, Gao Y, Li J. Elevating microRNA-1-3p shuttled by cancer-associated fibroblasts-derived extracellular vesicles suppresses breast cancer progression and metastasis by inhibiting GLIS1. Cancer Gene Ther 2021; 28:634-648. [PMID: 33154575 DOI: 10.1038/s41417-020-00244-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 08/19/2020] [Accepted: 09/30/2020] [Indexed: 12/24/2022]
Abstract
Cancer-associated fibroblasts (CAFs) play supporting roles in tumor progression by releasing microvesicles that transmit oncogenic cargoes. Indeed, extracellular vesicles (EVs) have emerged as important vehicles to deliver proteins, messenger RNAs (mRNAs), and microRNAs (miRs) between cells. In this study, we aimed to outline the role and function of CAFs-derived EVs carrying miR-1-3p in breast cancer. We first experimentally determined downregulated miR-1-3p in breast cancer tissues. EVs were isolated from CAFs extracted from breast cancer tissues, which showed downregulated miR-1-3p expression relative to EVs derived from normal fibroblasts (NFs). In a co-culture system, miR-1-3p cargo was transported into breast cancer cells via CAF-derived EVs. In gain-of-function experiments, the elevation of miR-1-3p in breast cancer cells inhibited cell viability, invasion, migration, and epithelial-to-mesenchymal transition, and suppressed tumor formation and metastasis. Furthermore, EVs derived from CAFs transfected with miR-1-3p mimic were more effective in transferring miR-1-3p to suppress cancer progression and metastasis. Krüppel-like zinc-finger protein Gli-similar 1 (GLIS1) was predicted to be a putative target of miR-1-3p, which was subsequently confirmed by dual-luciferase reporter assay. We then demonstrated that overexpression of GLIS1 neutralized the effects of miR-1-3 on the development of breast cancer in vitro. These findings shed light on the underlying mechanism by which CAFs-derived EVs carrying miR-1-3p mediate the progression and metastasis of breast cancer, and highlight the potential of miR-1-3p shuttled by CAFs-derived EVs serving as a therapeutic target for breast cancer.
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Affiliation(s)
- Shuang Tao
- Department of Breast Surgery, Changzhou No. 7 People's Hospital, 213000, Changzhou, P. R. China
| | - Hong Li
- Department of Surgical Oncology, General Hospital of Ningxia Medical University, 750004, Yinchuan, P. R. China
| | - Xiuzhen Ma
- Department of Surgical Oncology, General Hospital of Ningxia Medical University, 750004, Yinchuan, P. R. China
| | - Yunfei Ma
- Ningxia Medical University, 750004, Yinchuan, P. R. China
| | - Jiale He
- Ningxia Medical University, 750004, Yinchuan, P. R. China
| | - Yali Gao
- Ningxia Medical University, 750004, Yinchuan, P. R. China
| | - Jinping Li
- Department of Surgical Oncology, General Hospital of Ningxia Medical University, 750004, Yinchuan, P. R. China.
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13
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Schmidt F, Kern F, Ebert P, Baumgarten N, Schulz MH. TEPIC 2-an extended framework for transcription factor binding prediction and integrative epigenomic analysis. Bioinformatics 2020; 35:1608-1609. [PMID: 30304373 PMCID: PMC6499243 DOI: 10.1093/bioinformatics/bty856] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/04/2018] [Accepted: 10/08/2018] [Indexed: 12/20/2022] Open
Abstract
Summary Prediction of transcription factor (TF) binding from epigenetics data and integrative analysis thereof are challenging. Here, we present TEPIC 2 a framework allowing for fast, accurate and versatile prediction, and analysis of TF binding from epigenetics data: it supports 30 species with binding motifs, computes TF gene and scores up to two orders of magnitude faster than before due to improved implementation, and offers easy-to-use machine learning pipelines for integrated analysis of TF binding predictions with gene expression data allowing the identification of important TFs. Availability and implementation TEPIC is implemented in C++, R, and Python. It is freely available at https://github.com/SchulzLab/TEPIC and can be used on Linux based systems. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Florian Schmidt
- High throughput Genomics and Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, Saarbrücken, Germany.,Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Graduate School of Computer Science, Saarland Informatics Campus, Saarbrücken, Germany
| | - Fabian Kern
- High throughput Genomics and Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, Saarbrücken, Germany.,Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Peter Ebert
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Graduate School of Computer Science, Saarland Informatics Campus, Saarbrücken, Germany
| | - Nina Baumgarten
- High throughput Genomics and Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, Saarbrücken, Germany.,Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Institute for Cardiovascular Regeneration, Goethe University, Partner site Rhein-Main, Frankfurt am Main, Germany.,German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
| | - Marcel H Schulz
- High throughput Genomics and Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, Saarbrücken, Germany.,Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Institute for Cardiovascular Regeneration, Goethe University, Partner site Rhein-Main, Frankfurt am Main, Germany.,German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
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14
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Ohnmacht J, May P, Sinkkonen L, Krüger R. Missing heritability in Parkinson's disease: the emerging role of non-coding genetic variation. J Neural Transm (Vienna) 2020; 127:729-748. [PMID: 32248367 PMCID: PMC7242266 DOI: 10.1007/s00702-020-02184-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder caused by a complex interplay of genetic and environmental factors. For the stratification of PD patients and the development of advanced clinical trials, including causative treatments, a better understanding of the underlying genetic architecture of PD is required. Despite substantial efforts, genome-wide association studies have not been able to explain most of the observed heritability. The majority of PD-associated genetic variants are located in non-coding regions of the genome. A systematic assessment of their functional role is hampered by our incomplete understanding of genotype-phenotype correlations, for example through differential regulation of gene expression. Here, the recent progress and remaining challenges for the elucidation of the role of non-coding genetic variants is reviewed with a focus on PD as a complex disease with multifactorial origins. The function of gene regulatory elements and the impact of non-coding variants on them, and the means to map these elements on a genome-wide level, will be delineated. Moreover, examples of how the integration of functional genomic annotations can serve to identify disease-associated pathways and to prioritize disease- and cell type-specific regulatory variants will be given. Finally, strategies for functional validation and considerations for suitable model systems are outlined. Together this emphasizes the contribution of rare and common genetic variants to the complex pathogenesis of PD and points to remaining challenges for the dissection of genetic complexity that may allow for better stratification, improved diagnostics and more targeted treatments for PD in the future.
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Affiliation(s)
- Jochen Ohnmacht
- LCSB, University of Luxembourg, Belvaux, Luxembourg
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Patrick May
- LCSB, University of Luxembourg, Belvaux, Luxembourg
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Rejko Krüger
- LCSB, University of Luxembourg, Belvaux, Luxembourg.
- Luxembourg Institute of Health (LIH), Transversal Translational Medicine, Strassen, Luxembourg.
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg.
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15
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Schmidt F, Kern F, Schulz MH. Integrative prediction of gene expression with chromatin accessibility and conformation data. Epigenetics Chromatin 2020; 13:4. [PMID: 32029002 PMCID: PMC7003490 DOI: 10.1186/s13072-020-0327-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 01/06/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Enhancers play a fundamental role in orchestrating cell state and development. Although several methods have been developed to identify enhancers, linking them to their target genes is still an open problem. Several theories have been proposed on the functional mechanisms of enhancers, which triggered the development of various methods to infer promoter-enhancer interactions (PEIs). The advancement of high-throughput techniques describing the three-dimensional organization of the chromatin, paved the way to pinpoint long-range PEIs. Here we investigated whether including PEIs in computational models for the prediction of gene expression improves performance and interpretability. RESULTS We have extended our [Formula: see text] framework to include DNA contacts deduced from chromatin conformation capture experiments and compared various methods to determine PEIs using predictive modelling of gene expression from chromatin accessibility data and predicted transcription factor (TF) motif data. We designed a novel machine learning approach that allows the prioritization of TFs binding to distal loop and promoter regions with respect to their importance for gene expression regulation. Our analysis revealed a set of core TFs that are part of enhancer-promoter loops involving YY1 in different cell lines. CONCLUSION We present a novel approach that can be used to prioritize TFs involved in distal and promoter-proximal regulatory events by integrating chromatin accessibility, conformation, and gene expression data. We show that the integration of chromatin conformation data can improve gene expression prediction and aids model interpretability.
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Affiliation(s)
- Florian Schmidt
- High-throughput Genomics & Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Computational Biology & Applied Algorithmics, Max-Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672 Singapore
| | - Fabian Kern
- High-throughput Genomics & Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Marcel H. Schulz
- High-throughput Genomics & Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Computational Biology & Applied Algorithmics, Max-Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Institute of Cardiovascular Regeneration, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner Site Rhein-Main, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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16
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Hamdan FH, Johnsen SA. Perturbing Enhancer Activity in Cancer Therapy. Cancers (Basel) 2019; 11:cancers11050634. [PMID: 31067678 PMCID: PMC6563029 DOI: 10.3390/cancers11050634] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/26/2019] [Accepted: 05/05/2019] [Indexed: 02/07/2023] Open
Abstract
Tight regulation of gene transcription is essential for normal development, tissue homeostasis, and disease-free survival. Enhancers are distal regulatory elements in the genome that provide specificity to gene expression programs and are frequently misregulated in cancer. Recent studies examined various enhancer-driven malignant dependencies and identified different approaches to specifically target these programs. In this review, we describe numerous features that make enhancers good transcriptional targets in cancer therapy and discuss different approaches to overcome enhancer perturbation. Interestingly, a number of approved therapeutic agents, such as cyclosporine, steroid hormones, and thiazolidinediones, actually function by affecting enhancer landscapes by directly targeting very specific transcription factor programs. More recently, a broader approach to targeting deregulated enhancer programs has been achieved via Bromodomain and Extraterminal (BET) inhibition or perturbation of transcription-related cyclin-dependent kinases (CDK). One challenge to enhancer-targeted therapy is proper patient stratification. We suggest that monitoring of enhancer RNA (eRNA) expression may serve as a unique biomarker of enhancer activity that can help to predict and monitor responsiveness to enhancer-targeted therapies. A more thorough investigation of cancer-specific enhancers and the underlying mechanisms of deregulation will pave the road for an effective utilization of enhancer modulators in a precision oncology approach to cancer treatment.
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Affiliation(s)
- Feda H Hamdan
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Steven A Johnsen
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
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