Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state

The conserved Musashi (Msi) family of RNA binding proteins are expressed in stem/progenitor and cancer cells, but generally absent from differentiated cells, consistent with a role in cell state regulation. We found that Msi genes are rarely mutated but frequently overexpressed in human cancers and are associated with an epithelial-luminal cell state. Using ribosome profiling and RNA-seq analysis, we found that Msi proteins regulate translation of genes implicated in epithelial cell biology and epithelial-to-mesenchymal transition (EMT), and promote an epithelial splicing pattern. Overexpression of Msi proteins inhibited the translation of Jagged1, a factor required for EMT, and repressed EMT in cell culture and in mammary gland in vivo. Knockdown of Msis in epithelial cancer cells promoted loss of epithelial identity. Our results show that mammalian Msi proteins contribute to an epithelial gene expression program in neural and mammary cell types. DOI: http://dx.doi.org/10.7554/eLife.03915.001

[1]  H. Okano,et al.  Musashi, a neural RNA-binding protein required for drosophila adult external sensory organ development , 1994, Neuron.

[2]  K. Mikoshiba,et al.  Mouse-Musashi-1, a neural RNA-binding protein highly enriched in the mammalian CNS stem cell. , 1996, Developmental biology.

[3]  M. Segal,et al.  Development of neuronal precursor cells and functional postmitotic neurons from embryonic stem cells in vitro , 1996, Mechanisms of Development.

[4]  K. Mikoshiba,et al.  The Neural RNA-Binding Protein Musashi1 Translationally Regulates Mammalian numb Gene Expression by Interacting with Its mRNA , 2001, Molecular and Cellular Biology.

[5]  H. Okano,et al.  Musashi: a translational regulator of cell fate. , 2002, Journal of cell science.

[6]  H. Okano,et al.  Candidate markers for stem and early progenitor cells, Musashi‐1 and Hes1, are expressed in crypt base columnar cells of mouse small intestine , 2003, FEBS letters.

[7]  R. McKay,et al.  Generating CNS neurons from embryonic, fetal, and adult stem cells. , 2003, Methods in enzymology.

[8]  Frank McCormick,et al.  Notch promotes epithelial-mesenchymal transition during cardiac development and oncogenic transformation. , 2004, Genes & development.

[9]  J. Zavadil,et al.  Integration of TGF-beta/Smad and Jagged1/Notch signalling in epithelial-to-mesenchymal transition. , 2004, The EMBO journal.

[10]  J. Zavadil,et al.  Integration of TGF‐β/Smad and Jagged1/Notch signalling in epithelial‐to‐mesenchymal transition , 2004 .

[11]  H. Okano,et al.  Function of RNA-binding protein Musashi-1 in stem cells. , 2005, Experimental cell research.

[12]  Rudolf Jaenisch,et al.  Efficient method to generate single‐copy transgenic mice by site‐specific integration in embryonic stem cells , 2006, Genesis.

[13]  Shulan Tian,et al.  Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells , 2007, Science.

[14]  A. Krainer,et al.  The gene encoding the splicing factor SF2/ASF is a proto-oncogene , 2007, Nature Structural &Molecular Biology.

[15]  M. Mattson,et al.  Involvement of Notch Signaling in Wound Healing , 2007, PloS one.

[16]  G. Lockwood,et al.  High-level JAG1 mRNA and protein predict poor outcome in breast cancer , 2007, Modern Pathology.

[17]  A. Karsan,et al.  Jagged1-mediated Notch activation induces epithelial-to-mesenchymal transition through Slug-induced repression of E-cadherin. , 2007, The Journal of experimental medicine.

[18]  R. Stewart,et al.  Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells , 2007, Science.

[19]  R. Knight,et al.  PyCogent: a toolkit for making sense from sequence , 2007, Genome Biology.

[20]  Connie J. Eaves,et al.  Jagged1-mediated Notch activation induces epithelial-to-mesenchymal transition through Slug-induced repression of E-cadherin , 2007 .

[21]  Wenjun Guo,et al.  The Epithelial-Mesenchymal Transition Generates Cells with Properties of Stem Cells , 2008, Cell.

[22]  H. Okano,et al.  Neural RNA-binding protein Musashi1 inhibits translation initiation by competing with eIF4G for PABP , 2008, The Journal of cell biology.

[23]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[24]  A. Nobel,et al.  Supervised risk predictor of breast cancer based on intrinsic subtypes. , 2009, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[25]  R. Weinberg,et al.  Transitions between epithelial and mesenchymal states: acquisition of malignant and stem cell traits , 2009, Nature Reviews Cancer.

[26]  Nicholas T. Ingolia,et al.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.

[27]  Claude C. Warzecha,et al.  ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing. , 2009, Molecular cell.

[28]  M. Colitti,et al.  Expression of a putative stem cell marker, Musashi 1, in mammary glands of ewes , 2009, Journal of Molecular Histology.

[29]  S. Gabriel,et al.  Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. , 2010, Cancer cell.

[30]  G. Berx,et al.  Key signalling nodes in mammary gland development and cancer. The Snail1-Twist1 conspiracy in malignant breast cancer progression , 2010, Breast Cancer Research.

[31]  E. Wang,et al.  Analysis and design of RNA sequencing experiments for identifying isoform regulation , 2010, Nature Methods.

[32]  Hideyuki Okano,et al.  Musashi1 regulates breast tumor cell proliferation and is a prognostic indicator of poor survival , 2010, Molecular Cancer.

[33]  Fatima Al-Shahrour,et al.  Musashi-2 regulates normal hematopoiesis and promotes aggressive myeloid leukemia , 2010, Nature Medicine.

[34]  L. Qin,et al.  Expression of a putative stem cell marker Musashi-1 in endometrium. , 2011, Histology and Histopathology.

[35]  Iannis Aifantis,et al.  Oncogenic and tumor suppressor functions of Notch in cancer: it’s NOTCH what you think , 2011, The Journal of experimental medicine.

[36]  Yibin Kang,et al.  Tumor-derived JAGGED1 promotes osteolytic bone metastasis of breast cancer by engaging notch signaling in bone cells. , 2011, Cancer cell.

[37]  Nicholas C. Flytzanis,et al.  An EMT–Driven Alternative Splicing Program Occurs in Human Breast Cancer and Modulates Cellular Phenotype , 2011, PLoS genetics.

[38]  A. MacNicol,et al.  Context-dependent regulation of Musashi-mediated mRNA translation and cell cycle regulation. , 2011, Cell cycle.

[39]  Hideyuki Okano,et al.  RNA-Binding Protein Musashi1 Modulates Glioma Cell Growth through the Post-Transcriptional Regulation of Notch and PI3 Kinase/Akt Signaling Pathways , 2012, PloS one.

[40]  Chonghui Cheng,et al.  Snail Represses the Splicing Regulator Epithelial Splicing Regulatory Protein 1 to Promote Epithelial-Mesenchymal Transition* , 2012, The Journal of Biological Chemistry.

[41]  Anke Busch,et al.  Evolution of SR protein and hnRNP splicing regulatory factors , 2012, Wiley interdisciplinary reviews. RNA.

[42]  Bruce G. Haffty,et al.  Elf5 inhibits epithelial mesenchymal transition in mammary gland development and breast cancer metastasis by transcriptionally repressing Snail2/Slug , 2012, Nature Cell Biology.

[43]  M. Surani,et al.  Dedifferentiation of Foetal CNS Stem Cells to Mesendoderm-Like Cells through an EMT Process , 2012, PloS one.

[44]  Eric T. Wang,et al.  Transcriptome-wide Regulation of Pre-mRNA Splicing and mRNA Localization by Muscleblind Proteins , 2012, Cell.

[45]  F. Rousset,et al.  RBFOX2 Is an Important Regulator of Mesenchymal Tissue-Specific Splicing in both Normal and Cancer Tissues , 2012, Molecular and Cellular Biology.

[46]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumors , 2012, Nature.

[47]  P. Osten,et al.  Molecular hierarchy of mammary differentiation yields refined markers of mammary stem cells , 2013, Proceedings of the National Academy of Sciences.

[48]  P. Das,et al.  Illuminating luminal B: QSOX1 as a subtype-specific biomarker , 2013, Breast Cancer Research.

[49]  Hiromi Hirata,et al.  Defective Escape Behavior in DEAH-Box RNA Helicase Mutants Improved by Restoring Glycine Receptor Expression , 2013, The Journal of Neuroscience.

[50]  H. Okano,et al.  Musashi-1 Post-Transcriptionally Enhances Phosphotyrosine-Binding Domain-Containing m-Numb Protein Expression in Regenerating Gastric Mucosa , 2013, PloS one.

[51]  Brendan J. Frey,et al.  A compendium of RNA-binding motifs for decoding gene regulation , 2013, Nature.

[52]  Eric T. Wang,et al.  MBNL proteins repress ES-cell-specific alternative splicing and reprogramming , 2013, Nature.

[53]  J. Inoue,et al.  NF-κB non-cell-autonomously regulates cancer stem cell populations in the basal-like breast cancer subtype , 2013, Nature Communications.

[54]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumours , 2013 .

[55]  R. Young,et al.  Transcriptional Regulation and Its Misregulation in Disease , 2013, Cell.

[56]  Xiao-Fen Chen,et al.  Transcriptional regulation and its misregulation in , 2013 .

[57]  P. Sharp,et al.  Building Robust Transcriptomes with Master Splicing Factors , 2014, Cell.

[58]  P. Sharp,et al.  RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins. , 2014, Molecular cell.

[59]  E. Sokol,et al.  Epithelial-to-mesenchymal transition activates PERK-eIF2α and sensitizes cells to endoplasmic reticulum stress. , 2014, Cancer discovery.

[60]  Michael G. Kharas,et al.  Musashi-2 controls cell fate, lineage bias, and TGF-β signaling in HSCs , 2014, The Journal of experimental medicine.