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      Intronic polyadenylation of PDGFRα in resident stem cells attenuates muscle fibrosis

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          Abstract

          The platelet-derived growth factor receptor alpha (PDGFRα) exhibits divergent effects in skeletal muscle. At physiological levels, signaling through this receptor promotes muscle development in growing embryos and proper angiogenesis in regenerating adult muscle. 1, 2 However, both increased PDGF ligand abundance and enhanced PDGFRα pathway activity cause pathological fibrosis. 3, 4 This excessive collagen deposition, which is seen in aged and diseased muscle, 57 interferes with proper muscle function and limits the effectiveness of gene- and cell-based therapies for muscle disorders. 8, 9 Although compelling evidence exists for the role of PDGFRα in fibrosis, little is known about the cells through which this pathway acts. Here we show that PDGFRα signaling regulates a population of muscle-resident fibro/adipogenic progenitors (FAPs) that play a supportive role in muscle regeneration but may also cause fibrosis when aberrantly regulated. 1013 We found that FAPs produce multiple transcriptional variants of PDGFRα with different polyadenylation sites, including an intronic variant that codes for a protein isoform containing a truncated kinase domain. This variant, upregulated during regeneration, acts as a decoy to inhibit PDGF signaling and to prevent FAP over-activation. Moreover, increasing expression of this isoform limits fibrosis in vivo, suggesting both biological relevance and therapeutic potential of modulating polyadenylation patterns in stem cell populations.

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          Most cited references18

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          PDGFRA activating mutations in gastrointestinal stromal tumors.

          Most gastrointestinal stromal tumors (GISTs) have activating mutations in the KIT receptor tyrosine kinase, and most patients with GISTs respond well to Gleevec, which inhibits KIT kinase activity. Here we show that approximately 35% (14 of 40) of GISTs lacking KIT mutations have intragenic activation mutations in the related receptor tyrosine kinase, platelet-derived growth factor receptor alpha (PDGFRA). Tumors expressing KIT or PDGFRA oncoproteins were indistinguishable with respect to activation of downstream signaling intermediates and cytogenetic changes associated with tumor progression. Thus, KIT and PDGFRA mutations appear to be alternative and mutually exclusive oncogenic mechanisms in GISTs.
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            Direct RNA sequencing.

            Our understanding of human biology and disease is ultimately dependent on a complete understanding of the genome and its functions. The recent application of microarray and sequencing technologies to transcriptomics has changed the simplistic view of transcriptomes to a more complicated view of genome-wide transcription where a large fraction of transcripts emanates from unannotated parts of genomes, and underlined our limited knowledge of the dynamic state of transcription. Most of this broad body of knowledge was obtained indirectly because current transcriptome analysis methods typically require RNA to be converted to complementary DNA (cDNA) before measurements, even though the cDNA synthesis step introduces multiple biases and artefacts that interfere with both the proper characterization and quantification of transcripts. Furthermore, cDNA synthesis is not particularly suitable for the analysis of short, degraded and/or small quantity RNA samples. Here we report direct single molecule RNA sequencing without prior conversion of RNA to cDNA. We applied this technology to sequence femtomole quantities of poly(A)(+) Saccharomyces cerevisiae RNA using a surface coated with poly(dT) oligonucleotides to capture the RNAs at their natural poly(A) tails and initiate sequencing by synthesis. We observed transcript 3' end heterogeneity and polyadenylated small nucleolar RNAs. This study provides a path to high-throughput and low-cost direct RNA sequencing and achieving the ultimate goal of a comprehensive and bias-free understanding of transcriptomes.
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              The PDGF alpha receptor is required for neural crest cell development and for normal patterning of the somites.

              Platelet-derived growth factors (PDGFs) have been implicated in the control of cell proliferation, survival and migration. Patch mutant mice harbor a deletion including the PDGF alpha receptor gene and exhibit defects of neural crest origin which affect pigmentation in heterozygotes and cranial bones in homozygotes. To verify the role of the PDGF alphaR gene during development, mice carrying a targeted null mutation were generated. No pigmentation phenotype was observed in heterozygotes. Homozygotes die during embryonic development and exhibit incomplete cephalic closure similar to that observed in a subset of Patch mutants. In addition, increased apoptosis was observed on pathways followed by migrating neural crest cells. However, alterations in mutant vertebrae, ribs and sternum were also observed, which appear to stem from a deficiency in myotome formation. These results indicate that PDGFs may exert their functions during early embryogenesis by affecting cell survival and patterning.
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                17 March 2017
                28 November 2016
                08 December 2016
                28 May 2017
                : 540
                : 7632
                : 276-279
                Affiliations
                [1 ]Paul F. Glenn Center for the Biology of Aging; Stanford University School of Medicine; Stanford, CA USA
                [2 ]Department of Neurology and Neurological Sciences; Stanford University School of Medicine; Stanford, CA USA
                [3 ]Program in Cancer Biology; Stanford University School of Medicine; Stanford, CA USA
                [6 ]Neurology Service and Rehabilitation Research and Development REAP; Veterans Affairs Palo Alto Health Care System; Palo Alto, CA USA
                Author notes
                Corresponding author: Correspondence should be addressed to T.A.R. ( rando@ 123456stanford.edu )
                [4]

                Present Address: Department of Medicine; Brigham and Women’s Hospital; Boston, MA USA.

                [5]

                Present Address: Division of Life Science; The Hong Kong University of Science and Technology; Clear Water Bay, Hong Kong, China.

                Article
                NIHMS823862
                10.1038/nature20160
                5384334
                27894125
                8c6e6576-1290-4146-96c7-cb88f0174b8d

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