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      Osteocyte Egln1/Phd2 links oxygen sensing and biomineralization via FGF23

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          Abstract

          Osteocytes act within a hypoxic environment to control key steps in bone formation. FGF23, a critical phosphate-regulating hormone, is stimulated by low oxygen/iron in acute and chronic diseases, however the molecular mechanisms directing this process remain unclear. Our goal was to identify the osteocyte factors responsible for FGF23 production driven by changes in oxygen/iron utilization. Hypoxia-inducible factor-prolyl hydroxylase inhibitors (HIF-PHI) which stabilize HIF transcription factors, increased Fgf23 in normal mice, as well as in osteocyte-like cells; in mice with conditional osteocyte Fgf23 deletion, circulating iFGF23 was suppressed. An inducible MSC cell line (‘MPC2’) underwent FG-4592 treatment and ATACseq/RNAseq, and demonstrated that differentiated osteocytes significantly increased HIF genomic accessibility versus progenitor cells. Integrative genomics also revealed increased prolyl hydroxylase Egln1 (Phd2) chromatin accessibility and expression, which was positively associated with osteocyte differentiation. In mice with chronic kidney disease (CKD), Phd1-3 enzymes were suppressed, consistent with FGF23 upregulation in this model. Conditional loss of Phd2 from osteocytes in vivo resulted in upregulated Fgf23, in line with our findings that the MPC2 cell line lacking Phd2 (CRISPR Phd2-KO cells) constitutively activated Fgf23 that was abolished by HIF1α blockade. In vitro, Phd2-KO cells lost iron-mediated suppression of Fgf23 and this activity was not compensated for by Phd1 or −3. In sum, osteocytes become adapted to oxygen/iron sensing during differentiation and are directly sensitive to bioavailable iron. Further, Phd2 is a critical mediator of osteocyte FGF23 production, thus our collective studies may provide new therapeutic targets for skeletal diseases involving disturbed oxygen/iron sensing.

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            Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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                Author and article information

                Contributors
                kenewhit@iu.edu
                Journal
                Bone Res
                Bone Res
                Bone Research
                Nature Publishing Group UK (London )
                2095-4700
                2095-6231
                18 January 2023
                18 January 2023
                2023
                : 11
                : 7
                Affiliations
                [1 ]GRID grid.257413.6, ISNI 0000 0001 2287 3919, Department of Medical and Molecular Genetics, , Indiana University School of Medicine, ; Indianapolis, IN 46202 USA
                [2 ]GRID grid.5596.f, ISNI 0000 0001 0668 7884, Laboratory of Clinical and Experimental Endocrinology, , Department of Chronic Diseases and Metabolism, KU Leuven, ; 3000 Leuven, Belgium
                [3 ]GRID grid.257413.6, ISNI 0000 0001 2287 3919, Department of Physical Therapy, , Indiana University School of Medicine, ; Indianapolis, IN 46202 USA
                [4 ]GRID grid.257413.6, ISNI 0000 0001 2287 3919, Department of Anatomy, Cell Biology, and Physiology, , Indiana University School of Medicine, ; Indianapolis, IN 46202 USA
                [5 ]GRID grid.257413.6, ISNI 0000 0001 2287 3919, Center for Computational Biology and Bioinformatics, , Indiana University School of Medicine, ; Indianapolis, IN 46202 USA
                [6 ]GRID grid.257413.6, ISNI 0000 0001 2287 3919, Departments of Medicine/Division of Nephrology, , Indiana University School of Medicine, ; Indianapolis, IN 46202 USA
                Author information
                http://orcid.org/0000-0002-1763-1867
                http://orcid.org/0000-0002-4143-2024
                http://orcid.org/0000-0002-9233-052X
                http://orcid.org/0000-0002-4471-6401
                http://orcid.org/0000-0001-8324-4462
                http://orcid.org/0000-0002-7022-585X
                Article
                241
                10.1038/s41413-022-00241-w
                9845350
                36650133
                37d614a6-453d-4f31-a391-af37ee6ebfb2
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 7 April 2022
                : 29 September 2022
                : 3 November 2022
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000062, U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases);
                Award ID: R01DK112958
                Award ID: F31-DK122679
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000050, U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI);
                Award ID: R01HL145528
                Award ID: T32-HL007910
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000069, U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS);
                Award ID: R21AR059278
                Award ID: R01-AR074473
                Award Recipient :
                Funded by: U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
                Funded by: U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
                Funded by: FundRef https://doi.org/10.13039/501100003130, Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders);
                Award ID: FWO/12H5917N
                Award Recipient :
                Funded by: U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
                Categories
                Article
                Custom metadata
                © The Author(s) 2023

                bone,metabolic bone disease
                bone, metabolic bone disease

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