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Chen S, Tang D, Deng L, Xu S. Asian-European differentiation of schizophrenia-associated genes driven by admixture and natural selection. iScience 2024; 27:109560. [PMID: 38638564 PMCID: PMC11024917 DOI: 10.1016/j.isci.2024.109560] [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: 08/22/2023] [Revised: 12/29/2023] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
The European-centered genome-wide association studies of schizophrenia (SCZ) may not be well applied to non-European populations. We analyzed 1,592 reported SCZ-associated genes using the public genome data and found an overall higher Asian-European differentiation on the SCZ-associated variants than at the genome-wide level. Notable examples included 15 missense variants, a regulatory variant SLC5A10-rs1624825, and a damaging variant TSPAN18-rs1001292. Independent local adaptations in recent 25,000 years, after the Asian-European divergence, could have contributed to such genetic differentiation, as were identified at a missense mutation LTN1-rs57646126-A in Asians, and a non-risk allele ZSWIM6-rs72761442-G in Europeans. Altai-Neanderthal-derived alleles may have opposite effects on SCZ susceptibility between ancestries. Furthermore, adaptive introgression was detected on the non-risk haplotype at 1q21.2 in Europeans, while in Asians it was observed on the SCZ risk haplotype at 3p21.31 which is also potentially ultra-violet protective. This study emphasizes the importance of including more representative Asian samples in future SCZ studies.
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Affiliation(s)
- Sihan Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Die Tang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lian Deng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
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Yugami M, Hayakawa-Yano Y, Ogasawara T, Yokoyama K, Furukawa T, Hara H, Hashikami K, Tsuji I, Takebayashi H, Araki S, Okano H, Yano M. Sbp2l contributes to oligodendrocyte maturation through translational control in Tcf7l2 signaling. iScience 2023; 26:108451. [PMID: 38213786 PMCID: PMC10783607 DOI: 10.1016/j.isci.2023.108451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/09/2023] [Accepted: 11/10/2023] [Indexed: 01/13/2024] Open
Abstract
Oligodendrocytes (OLs) are the myelin-forming cells in the CNS that support neurons through the insulating sheath of axons. This unique feature and developmental processes are achieved by extrinsic and intrinsic gene expression programs, where RNA-binding proteins can contribute to dynamic and fine-tuned post-transcriptional regulation. Here, we identified SECIS-binding protein 2-like (Sbp2l), which is specifically expressed in OLs by integrated transcriptomics. Histological analysis revealed that Sbp2l is a molecular marker of OL maturation. Sbp2l knockdown (KD) led to suppression of matured OL markers, but not a typical selenoprotein, Gpx4. Transcriptome analysis demonstrated that Sbp2l KD decreased cholesterol-biosynthesis-related genes regulated by Tcf7l2 transcription factor. Indeed, we confirmed the downregulation of Tcf7l2 protein without changing its mRNA in Sbp2l KD OPCs. Furthermore, Sbp2l KO mice showed the decrease of Tcf7l2 protein and deficiency of OL maturation. These results suggest that Sbp2l contributes to OL maturation by translational control of Tcf7l2.
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Affiliation(s)
- Masato Yugami
- Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yoshika Hayakawa-Yano
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8510, Japan
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Takahisa Ogasawara
- Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kazumasa Yokoyama
- Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takako Furukawa
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8510, Japan
| | - Hiroe Hara
- Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kentaro Hashikami
- Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Isamu Tsuji
- Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hirohide Takebayashi
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8510, Japan
| | - Shinsuke Araki
- Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masato Yano
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8510, Japan
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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Chitra U, Arnold BJ, Sarkar H, Ma C, Lopez-Darwin S, Sanno K, Raphael BJ. Mapping the topography of spatial gene expression with interpretable deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561757. [PMID: 37873258 PMCID: PMC10592770 DOI: 10.1101/2023.10.10.561757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Spatially resolved transcriptomics technologies provide high-throughput measurements of gene expression in a tissue slice, but the sparsity of this data complicates the analysis of spatial gene expression patterns such as gene expression gradients. We address these issues by deriving a topographic map of a tissue slice-analogous to a map of elevation in a landscape-using a novel quantity called the isodepth. Contours of constant isodepth enclose spatial domains with distinct cell type composition, while gradients of the isodepth indicate spatial directions of maximum change in gene expression. We develop GASTON, an unsupervised and interpretable deep learning algorithm that simultaneously learns the isodepth, spatial gene expression gradients, and piecewise linear functions of the isodepth that model both continuous gradients and discontinuous spatial variation in the expression of individual genes. We validate GASTON by showing that it accurately identifies spatial domains and marker genes across several biological systems. In SRT data from the brain, GASTON reveals gradients of neuronal differentiation and firing, and in SRT data from a tumor sample, GASTON infers gradients of metabolic activity and epithelial-mesenchymal transition (EMT)-related gene expression in the tumor microenvironment.
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Affiliation(s)
- Uthsav Chitra
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Brian J. Arnold
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
| | - Hirak Sarkar
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Ludwig Cancer Institute, Princeton Branch, Princeton University, Princeton, NJ, USA
| | - Cong Ma
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | | | - Kohei Sanno
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
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Hackler J, Demircan K, Chillon TS, Sun Q, Geisler N, Schupp M, Renko K, Schomburg L. High throughput drug screening identifies resveratrol as suppressor of hepatic SELENOP expression. Redox Biol 2022; 59:102592. [PMID: 36586222 PMCID: PMC9816962 DOI: 10.1016/j.redox.2022.102592] [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: 12/19/2022] [Accepted: 12/24/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Selenium (Se) is an essential trace element that exerts its effects mainly as the proteinogenic amino acid selenocysteine within a small set of selenoproteins. Among all family members, selenoprotein P (SELENOP) constitutes a particularly interesting protein as it serves as a biomarker and serum Se transporter from liver to privileged tissues. SELENOP expression is tightly regulated by dietary Se intake, inflammation, hypoxia and certain substances, but a systematic drug screening has hitherto not been performed. METHODS A compound library of 1861 FDA approved clinically relevant drugs was systematically screened for interfering effects on SELENOP expression in HepG2 cells using a validated ELISA method. Dilution experiments were conducted to characterize dose-responses. A most potent SELENOP inhibitor was further characterized by RNA-seq analysis to assess effect-associated biochemical pathways. RESULTS Applying a 2-fold change threshold, 236 modulators of SELENOP expression were identified. All initial hits were replicated as biological triplicates and analyzed for effects on cell viability. A set of 38 drugs suppressed SELENOP expression more than three-fold, among which were cancer drugs, immunosuppressants, anti-infectious drugs, nutritional supplements and others. Considering a 90% cell viability threshold, resveratrol, vidofludimus, and antimony potassium-tartrate were the most potent substances with suppressive effects on extracellular SELENOP concentrations. Resveratrol suppressed SELENOP levels dose-dependently in a concentration range from 0.8 μM to 50.0 μM, without affecting cell viability, along with strong effects on key genes controlling metabolic pathways and vesicle trafficking. CONCLUSION The results highlight an unexpected direct effect of the plant stilbenoid resveratrol, known for its antioxidative and health-promoting effects, on the central Se transport protein. The suppressive effects on SELENOP may increase liver Se levels and intracellular selenoprotein expression, thereby conferring additional protection to hepatocytes at the expense of systemic Se transport. Further physiological effects from this interaction require analyses in vivo and by clinical studies.
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Affiliation(s)
- Julian Hackler
- Institute for Experimental Endocrinology, Charité-Universitätsmedizin Berlin, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, 10115, Berlin, Germany
| | - Kamil Demircan
- Institute for Experimental Endocrinology, Charité-Universitätsmedizin Berlin, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, 10115, Berlin, Germany
| | - Thilo Samson Chillon
- Institute for Experimental Endocrinology, Charité-Universitätsmedizin Berlin, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, 10115, Berlin, Germany
| | - Qian Sun
- Institute for Experimental Endocrinology, Charité-Universitätsmedizin Berlin, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, 10115, Berlin, Germany
| | - Nino Geisler
- Institute for Experimental Endocrinology, Charité-Universitätsmedizin Berlin, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, 10115, Berlin, Germany
| | - Michael Schupp
- Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, 10115, Berlin, Germany
| | - Kostja Renko
- Institute for Experimental Endocrinology, Charité-Universitätsmedizin Berlin, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, 10115, Berlin, Germany,German Federal Institute for Risk Assessment, Department Experimental Toxicology and ZEBET, 12277, Berlin, Germany
| | - Lutz Schomburg
- Institute for Experimental Endocrinology, Charité-Universitätsmedizin Berlin, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, 10115, Berlin, Germany.
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Schomburg L. Selenoprotein P - Selenium transport protein, enzyme and biomarker of selenium status. Free Radic Biol Med 2022; 191:150-163. [PMID: 36067902 DOI: 10.1016/j.freeradbiomed.2022.08.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/02/2022] [Accepted: 08/15/2022] [Indexed: 11/26/2022]
Abstract
The habitual intake of selenium (Se) varies strongly around the world, and many people are at risk of inadequate supply and health risks from Se deficiency. Within the human organism, efficient transport mechanisms ensure that organs with a high demand and relevance for reproduction and survival are preferentially supplied. To this end, selenoprotein P (SELENOP) is synthesized in the liver and mediates Se transport to essential tissues such as the endocrine glands and the brain, where the "SELENOP cycle" maintains a privileged Se status. Mouse models indicate that SELENOP is not essential for life, as supplemental Se supply was capable of preventing the development of severe symptoms. However, knockout mice died under limiting supply, arguing for an essential role of SELENOP in Se deficiency. Many clinical studies support this notion, pointing to close links between health risks and low SELENOP levels. Accordingly, circulating SELENOP concentrations serve as a functional biomarker of Se supply, at least until a saturated status is achieved and SELENOP levels reach a plateau. Upon toxic intake, a further increase in SELENOP is observed, i.e., SELENOP provides information about possible selenosis. The SELENOP transcripts predict an insertion of ten selenocysteine residues. However, the decoding is imperfect, and not all these positions are ultimately occupied by selenocysteine. In addition to the selenocysteine residues near the C-terminus, one selenocysteine resides central within an enzyme-like environment. SELENOP proved capable of catalyzing peroxide degradation in vitro and protecting e.g. LDL particles from oxidation. An enzymatic activity in the intact organism is unclear, but an increasing number of clinical studies provides evidence for a direct involvement of SELENOP-dependent Se transport as an important and modifiable risk factor of disease. This interaction is particularly strong for cardiovascular and critical disease including COVID-19, cancer at various sites and autoimmune thyroiditis. This review briefly highlights the links between the growing knowledge of Se in health and disease over the last 50 years and the specific advances that have been made in our understanding of the physiological and clinical contribution of SELENOP to the current picture.
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Affiliation(s)
- Lutz Schomburg
- Charité-Universitätsmedizin Berlin, Institute for Experimental Endocrinology, Cardiovascular-Metabolic-Renal (CMR)-Research Center, Hessische Straße 3-4, 10115 Berlin, Germany.
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